The Genomic Epidemiology Ontology aims to provide a comprehensive controlled vocabulary for infectious disease surveillance and outbreak investigations. It is an application ontology that draws on many other ontologies including anatomy, taxonomy, disease, symptoms, environment and food types for foodborn pathogen metadata. Genomic Epidemiology Ontology GENEPIO 2024-12-18 metadata section term as in existing standard term source The user interface label is the label that should be placed on a datum when presented on a form or report Damion Dooley user interface label user interface definition A user interface help annotation is a textual phrase to display with an entity on a form or report that provides some detail about what the entity is or how it is being used. Damion Dooley obsolete: user interface help true Damion Dooley obsolete: user interface hidden true A user interface feature is a pre-set list of features and their acceptable values that a user interface rendering system should use to display an entity on a form or report Damion Dooley user interface feature This annotation can be used to select the value specification that a referenced entity or specification component has for data entry. Can be scalar value specification / categorical tree specification etc. Damion Dooley obsolete: user interface value specification true UI regex normalize Damion Dooley user interface regular epression normalize UI regex validate Damion Dooley user interface regular expression validate UI regex format Damion Dooley user interface regular expression display format editor preferred label editor preferred label editor preferred term editor preferred term editor preferred term~editor preferred label The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English) PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> editor preferred label editor preferred label editor preferred term editor preferred term editor preferred term~editor preferred label example of usage A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi&gt> example of usage has curation status PERSON:Alan Ruttenberg PERSON:Bill Bug PERSON:Melanie Courtot OBI_0000281 has curation status has curation status definition definition textual definition A property representing the English language definitions of what NCI means by the concept. They may also include information about the definition's source and attribution in a form that can easily be interpreted by software. English language definitions of what NCI means by the concept. These are limited to 1024 characters. They may also include information about the definition's source and attribution in a form that can easily be interpreted by software. The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. The official definition. 2012-04-05: Barry Smith The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. Can you fix to something like: A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. Alan Ruttenberg Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. On the specifics of the proposed definition: We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> DEFINITION Allyson Lister 8.10.2019: Although the IAO definition has been included here, we have made a curation decision to allow non-Aristotelian definitions. definition definition textual definition editor note An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology. PERSON:Daniel Schober PERSON:Daniel Schober GROUP:OBI:<http://purl.obofoundry.org/obo/obi&gt> GROUP:OBI:<http://purl.obofoundry.org/obo/obi> editor note definition editor term editor Name of editor entering the definition in the file. The definition editor is a point of contact for information regarding the term. The definition editor may be, but is not always, the author of the definition, which may have been worked upon by several people Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people 20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115. PERSON:Daniel Schober PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi&gt> GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition editor definition editor term editor term editor alternative label alternative term A label for a class or property that can be used to refer to the class or property instead of the preferred rdfs:label. Alternative labels should be used to indicate community- or context-specific labels, abbreviations, shorthand forms and the like. An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent) OBO Operations committee PERSON:Daniel Schober PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi&gt> GROUP:OBI:<http://purl.obolibrary.org/obo/obi> Consider re-defing to: An alternative name for a class or property which can mean the same thing as the preferred name (semantically equivalent, narrow, broad or related). Consider re-defing to: An alternative name for a class or property which can mean the same thing as the preferred name (semantically equivalent, narrow, broad or related). alternative label alternative term alternative term alternative_term definition source Formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007 formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007 PERSON:Daniel Schober Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition source definition source definition_source has obsolescence reason Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification. PERSON:Alan Ruttenberg PERSON:Melanie Courtot has obsolescence reason curator note An administrative note of use for a curator but of no use for a user PERSON:Alan Ruttenberg curator note term tracker item An IRI or similar locator for a request or discussion of an ontology term. Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg The 'tracker item' can associate a tracker with a specific ontology term. term tracker item imported from has ID digit count Relates an ontology used to record id policy to the number of digits in the URI. The URI is: the 'has ID prefix' annotation property value concatenated with an integer in the id range (left padded with '0's to make this many digits) Person:Alan Ruttenberg has ID digit count has ID range allocated Relates a datatype that encodes a range of integers to the name of the person or organization who can use those ids constructed in that range to define new terms Person:Alan Ruttenberg has ID range allocated has ID policy for Relating an ontology used to record id policy to the ontology namespace whose policy it manages Person:Alan Ruttenberg has ID policy for term replaced by Add as annotation triples in the granting ontology Use on obsolete terms, relating the term to another term that can be used as a substitute Person:Alan Ruttenberg Person:Alan Ruttenberg term replaced by NIAID GSCID-BRC alternative term An alternative term used by the National Institute of Allergy and Infectious Diseases (NIAID) Genomic Sequencing Centers for Infectious Diseases (GSCID) and Bioinformatics Resource Centers (BRC). PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group NIAID GSCID-BRC metadata working group NIAID GSCID-BRC alternative term temporal interpretation An assertion that holds between an OWL Object Property and a temporal interpretation that elucidates how OWL Class Axioms that use this property are to be interpreted in a temporal context. An assertion that holds between an OWL Object Property and a temporal interpretation that elucidates how OWL Class Axioms that use this property are to be interpreted in a temporal context. temporal interpretation temporal interpretation http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ https://oborel.github.io/obo-relations/temporal-semantics/ relation p is the direct form of relation q iff p is a subPropertyOf q, p does not have the Transitive characteristic, q does have the Transitive characteristic, and for all x, y: x q y -> exists z1, z2, ..., zn such that x p z1 ... z2n y relation p is the direct form of relation q iff p is a subPropertyOf q, p does not have the Transitive characteristic, q does have the Transitive characteristic, and for all x, y: x q y -> exists z1, z2, ..., zn such that x p z1 ... z2n y The general property hierarchy is: "directly P" SubPropertyOf "P" Transitive(P) Where we have an annotation assertion "directly P" "is direct form of" "P" is direct form of is direct form of http://purl.obolibrary.org/obo/ro/docs/direct-and-indirect-relations/ namespace contributor creator created_by creation_date has_alternative_id An alternative label for a class or property which has a more general meaning than the preferred name/primary label. An alternative label for a class or property which has a more general meaning than the preferred name/primary label. http://orcid.org/0000-0001-5208-3432 https://github.com/information-artifact-ontology/ontology-metadata/issues/18 has broad synonym has_broad_synonym https://github.com/information-artifact-ontology/ontology-metadata/issues/18 An annotation property that links an ontology entity or a statement to a prefixed identifier or URI. Reference database or publication source. database_cross_reference has cross-reference has database cross reference hasDbXref A property representing a fully qualified synonym, contains the string, term type, source, and an optional source code if appropriate. Each subfield is deliniated to facilitate interpretation by software. An alternative label for a class or property which has the exact same meaning than the preferred name/primary label. An alternative label for a class or property which has the exact same meaning than the preferred name/primary label. An alternative label for a given entity such as a commonly used abbreviation or synonym. http://orcid.org/0000-0001-5208-3432 https://github.com/information-artifact-ontology/ontology-metadata/issues/20 FULL_SYN Synonym with Source Data has exact synonym has exact synonym has_exact_synonym https://github.com/information-artifact-ontology/ontology-metadata/issues/20 An alternative label for a class or property which has a more specific meaning than the preferred name/primary label. An alternative label for a class or property which has a more specific meaning than the preferred name/primary label. http://orcid.org/0000-0001-5208-3432 https://github.com/information-artifact-ontology/ontology-metadata/issues/19 has narrow synonym has_narrow_synonym https://github.com/information-artifact-ontology/ontology-metadata/issues/19 An alternative label for a class or property that has been used synonymously with the primary term name, but the usage is not strictly correct. http://orcid.org/0000-0001-5208-3432 https://github.com/information-artifact-ontology/ontology-metadata/issues/21 has related synonym https://github.com/information-artifact-ontology/ontology-metadata/issues/21 has synonym In subset. in_subset Comment. comment comment is defined by label label A human readable name for this class. A human-readable name for the subject. label label see also see also backward compatible with deprecated incompatible with prior version versionInfo part of has part a core relation that holds between a whole and its part Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. has_part Damion comments: In GenEpiO, If an entity has more than one value specification (in a conjunction), then it means the entitiy is a complex entity that can have a value for each specification. Minimum data requirements can be spelled out using some, min 1, max 10 etc. restrictions. has part realized in occurs in b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t occurs_in unfolds in unfolds_in Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant occurs in site of [copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant contains process obsolete has string specification of true T1 after t2 iff:= t2 before_or_simulataneous_with t1 and not (t1 simultaeous_with t2) Damion Dooley Damion Dooley's note: Intention is to have it be the inverse of "before". This allows axioms like "B after A" to be placed in class B, rather than having to phrase them as "A before B" in class A. I believe time dependency relations (conditions) don't imply existence by themselves. If B after A, and B exists, this doesn't necessarily mean that A exists, only that if A does exist, it must be before B. To add that extra existence implication probably requires the "causally downstream of" and "immediately causally downstream of" RO relations, in a closed system where B cannot exist any other way. after obsolete: has string value specification true obsolete: has categorical specification of true obsolete: has categorical value specification true hasCountryOfOrigin has unit has measurement unit label A (currently) primitive relation that relates an information artifact to an entity. 7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of "mentions" relation. Weaken the is_about relationship to be primitive. We will try to build it back up by elaborating the various subproperties that are more precisely defined. Some currently missing phenomena that should be considered "about" are predications - "The only person who knows the answer is sitting beside me" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic. person:Alan Ruttenberg Smith, Ceusters, Ruttenberg, 2000 years of philosophy is about An information artifact IA mentions an entity E exactly when it has a component/part that denotes E 7/6/2009 Alan Ruttenberg. P4 RC1 munges our GCI so remove it for now: mentions some entity equivalentTo has_part some ('generically denotes' some entity) 7/6/2009 Alan Ruttenberg: Add this relation following conversation with Jonathan Rees that N&S GCI for is_about was too strong. Really it was simply sufficient. To effect this change we introduce this relation, which is subproperty of is_about, and have previous GCI use this relation "mentions" in it's (logical) definition PERSON: Jonathan Rees Person: Alan Ruttenberg mentions A primitive, instance-level, relation obtaining between an information content entity and some portion of reality. Denotation is what happens when someone creates an information content entity E in order to specifically refer to something. The only relation between E and the thing is that E can be used to 'pick out' the thing. This relation connects those two together. Freedictionary.com sense 3: To signify directly; refer to specifically 2009-11-10 Alan Ruttenberg. Old definition said the following to emphasize the generic nature of this relation. We no longer have 'specifically denotes', which would have been primitive, so make this relation primitive. g denotes r =def r is a portion of reality there is some c that is a concretization of g every c that is a concretization of g specifically denotes r person:Alan Ruttenberg Conversations with Barry Smith, Werner Ceusters, Bjoern Peters, Michel Dumontier, Melanie Courtot, James Malone, Bill Hogan denotes relates a time stamped measurement datum to the measurement datum that was measured Alan Ruttenberg has measurement datum has_specified_input see is_input_of example_of_usage The inverse property of is_specified_input_of 8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works. PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Larry Hunter PERSON: Melanie Coutot has_specified_input is_specified_input_of some Autologous EBV(Epstein-Barr virus)-transformed B-LCL (B lymphocyte cell line) is_input_for instance of Chromum Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of. Alan Ruttenberg PERSON:Bjoern Peters is_specified_input_of has_specified_output The inverse property of is_specified_output_of PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Larry Hunter PERSON: Melanie Courtot has_specified_output is_manufactured_by http://www.affymetrix.com/products/arrays/specific/hgu133.affx is_manufactered_by http://www.affymetrix.com/ (if we decide to use these URIs for the actual entities) c is_manufactured_by o means that there was a process p in which c was built in which a person, or set of people or machines did the work(bore the "Manufacturer Role", and those people/and or machines were members or of directed by the organization to do this. Alan Ruttenberg Liju Fan has_make has_manufacturer is_manufactured_by is_specified_output_of A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of. Alan Ruttenberg PERSON:Bjoern Peters is_specified_output_of has category label A relation between a categorical measurement data item and the categorical label that indicates the value of that data item on the categorical scale. has category label specifies specifies value of A relation between a value specification and an entity which the specification is about. specifies value of has value specification A relation between an information content entity and a value specification that specifies its value. PERSON: James A. Overton OBI has value specification inheres in this fragility is a characteristic of this vase this red color is a characteristic of this apple a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence. inheres_in Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. characteristic of inheres in has participant this blood coagulation has participant this blood clot this investigation has participant this investigator this process has participant this input material (or this output material) a relation between a process and a continuant, in which the continuant is somehow involved in the process Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. has_participant http://www.obofoundry.org/ro/#OBO_REL:has_participant has participant has participant this apple has quality this red color a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist. has_quality has quality this person has role this investigator role (more colloquially: this person has this role of investigator) a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists. has_role has role this cell derives from this parent cell (cell division) this nucleus derives from this parent nucleus (nuclear division) a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'. derives_from This relation is taken from the RO2005 version of RO. It may be obsoleted and replaced by relations with different definitions. See also the 'develops from' family of relations. derives from this parent cell derives into this cell (cell division) this parent nucleus derives into this nucleus (nuclear division) a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'. derives_into derives into is location of my head is the location of my brain this cage is the location of this rat a relation between two independent continuants, the location and the target, in which the target is entirely within the location Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ location_of location of location of located in my brain is located in my head this rat is located in this cage a relation between two independent continuants, the target and the location, in which the target is entirely within the location Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ located_in http://www.obofoundry.org/ro/#OBO_REL:located_in located in located in located_in located_in (type level) https://wiki.geneontology.org/Located_in May be obsoleted, see https://github.com/oborel/obo-relations/issues/260 aligned with David Osumi-Sutherland <= Primitive instance level timing relation between events before or simultaneous with x simultaneous with y iff ω(x) = ω(y) and ω(α ) = ω(α), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point and '=' indicates the same instance in time. David Osumi-Sutherland t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2) simultaneous with T1 before t2 iff:= t1 before_or_simulataneous_with t2 and not (t1 simultaeous_with t2) David Osumi-Sutherland t1 before t2 iff:= t1 before_or_simulataneous_with t2 and not (t1 simultaeous_with t2) before David Osumi-Sutherland starts_at_end_of X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) immediately preceded by David Osumi-Sutherland ends_at_start_of meets X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) immediately precedes David Osumi-Sutherland io X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y)) starts during David Osumi-Sutherland d during X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y)) happens during https://wiki.geneontology.org/Happens_during w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity. For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit. has component A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts. The epidermis layer of a vertebrate is adjacent to the dermis. The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies. The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used. x adjacent to y if and only if x and y share a boundary. This relation acts as a join point with BSPO adjacent to adjacent to A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts. Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. Chris Mungall started by starts with x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. Chris Mungall finished by ends with p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p. consumes has input has input https://wiki.geneontology.org/Has_input p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p. produces has output has output https://wiki.geneontology.org/Has_output An organism that is a member of a population of organisms is member of is a mereological relation between a item and a collection. is member of member part of SIO member of member of has member is a mereological relation between a collection and an item. SIO has member has member inverse of has input input of inverse of has output output of inverse of upstream of causally downstream of p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q. causally upstream of all dengue disease transmitted by some mosquito A relationship that holds between a disease and organism Add domain and range constraints transmitted by a produced_by b iff some process that occurs_in b has_output a. produced by the relationship between a fraction and the number above the line Alejandra Gonzalez-Beltran Orlaith Burke Philippe Rocca-Serra AGB has numerator the relationship between a fraction and the number below the line (or divisor) Alejandra Gonzalez-Beltran Orlaith Burke Philippe Rocca-Serra AGB has denominator link two concepts, indicating a high degree of confidence that the concepts can be used interchangeably across a wide range of information retrieval applications. skos:exactMatch is a transitive property, and is a sub-property of skos:closeMatch. exactMatch An object relation between a LinkML SlotDefinition to a LocalName. Damion Dooley obsolete: has primitive data type true has specified value A relation between a value specification and a literal. This is not an RDF/OWL object property. It is intended to link a value found in e.g. a database column of 'M' (the literal) to an instance of a value specification class, which can then be linked to indicate that this is about the biological gender of a human subject. OBI has specified value An abstract class is a high level class or slot that is typically used to group common slots together and cannot be directly instantiated. Notes and comments about an element intended for external consumption. Date/time at which the element was created. Not Applicable; Missing; Not Collected; Not Provided; Restricted Access A value (string or URI) indicating the data collection state an instance of a slot has. A description of the element's purpose and use A list of terms from different schemas or terminology systems that have identical meaning. Id of the schema that defined the element. The imports entry that this element was derived from. Empty means primary source The ncname of the source of the name. 2021-04-26T22:15:07Z local_name_source A name assigned to an element in a given ontology. For slots with ranges of type number, the value must be equal to or lowe than this For slots with ranges of type number, the value must be equal to or higher than this true means that slot can have more than one value The unique name of the element within the context of the schema. Name is combined with the default prefix to form the globally unique subject of the target class. The string value of the slot must conform to this regular expression A list of possible values for a slot range. true if this slot is not required, but is recommended. true means that the slot must be present in the loaded definition. A reference. IAO:0000122 ('ready for release') status of the element. The uri that defines the possible values for the type definition URI is typically drawn from the set of URI's defined in OWL (https://www.w3.org/TR/2012/REC-owl2-syntax-20121211/#Datatype_Maps) Description of what the value is doing. The identifier of a "value set" -- a set of identifiers that form the possible values for the range of a slot A persistent, unique identifier of a molecular sequence database entry. Damion Dooley EDAM sequence accession The name of a field in a database. database field name no definition at source animal - laboratory Animals considered to be wild or feral or not adapted for domestic use. It does not include wild animals in zoos for which ANIMALS, ZOO is available. animal - wild the relative amounts of the purines and pyrimidines in a nucleic acid. base composition base compositions base ratio base ratios gc composition gc compositions gc content gc contents gc g+c composition g+c compositions g+c content g+c contents guanine + cytosine composition guanine + cytosine content base composition Animals kept by humans for companionship and enjoyment, as opposed to DOMESTIC ANIMALS such as livestock or farm animals, which are kept for economic reasons. animal - pet Domesticated farm animals raised for home use or profit but excluding POULTRY. Typically livestock includes CATTLE; SHEEP; HORSES; SWINE; GOATS; and others. livestock A generically dependent continuant which derives its existence and its entire endowment from an intending experience of consciousness (an "act") that is laden with determinate, uniformily structured content. MB: Right now we represent 'purely intentional entities' as siblings to 'information content entities'. Given their nature I am not entirly sure that this is correct. It seems that both 'information content entity' and 'simulation' are subclass to 'purely intentional entity'. purely intentional entity A duration of the parts of an infection during which the host bears an infectious disposition in a population of hosts. Mathias Brochhausen MB: In order to get the temporal occupation relations I added properties that I renamed with BFO2 URIs. infectious period duration A duration of the time interval between the host acquiring an infection and the host bearing a contagiousness disposition during the same disease course within a population of hosts. Mathias Brochhausen MB: In order to get the temporal occupation relations I added properties that I renamed with BFO2 URIs The duration of the period between when an organism becomes infected and when it becomes infectious. latent period duration Mathias Brochhausen count of simulated exposed population Mathias Brochhausen count of simulated contagious population Mathias Brochhausen count of simulated resistant population The count of (simulated organisms) in a simulated population. Mathias Brochhausen MW: I know this causes problems with our set-theoretic definition. Unfortunately the compartmental models produce fractional counts at each of their time steps, including the final step. Any ideas? I’ve considered and rejected allowing individual organisms to be fractional. Perhaps if we just replace the term “cardinality” in the definition with ‘computed size’ count of simulated population A simulation of a population or populations of organisms of a particular biological taxon that simulates a particular type of event or types of event that occur in a specified time interval. Mathias Brochhausen simulated population A measurement datum that is the output of counting. Mathias Brochhausen count The planned process of finding the number of elements in a finite set of objects. Mathias Brochhausen http://en.wikipedia.org/wiki/Counting counting Mathias Brochhausen Motivating use case is to cover Synthia data, and possibly configuration/output of the MRSA simulator in the MIDAS community (CA-MRSA Repast). hospital patient population census A purely intentional entity that simulates an entity and its properties. simulation The count of individuals in a contagious population (empirical or virtual). count of contagious population The count of individuals in a resistant population (empirical or virtual). count of resistant population The biological process of pathogen organism(s) of a particular biological taxon entering (the tissues of the body of) a host organism of another taxon from a contagious host or a contaminated thing and reproducing using host resources Mathias Brochhausen Apollo-SV defines infection acquisition rather than infection transmission, which is the direction of movement of a pathogen in current use. The Apollo-SV conceptualization is simpler when accounting for infections acquired from contaminated things. The likelihood of acquisition is expressed by parameters such as the basic reproduction rate and transmission coefficient. An infection is acquired from an infectious organism or a contaminated thing. Cannot acquire from colonized host directly - contamination results from colonized or contaminated thing and new host picks it up from contaminated thing infection acquisition 1 1 A census that is the outcome of a population survey. Damion Dooley population census Motivating use case is Synthia synthetic population data. nursery school student population census Motivating use case is Synthia synthetic population data. primary school student population census Motivating use case is Synthia synthetic population data. secondary school student population census A data set of a specific entity in a specified region at a specified time. Mathias Brochhausen census Mathias Brochhausen Motivating use case is Synthia synthetic population data. school student population census The probability of the occurence of an infection acquisition from one infected organism to another when in contact. transmission probability asymptomatic host An organism of a particular biological taxon that is the site of reproduction of an organism of a different taxon. host organism A information content entity that specifies the date of a census. Mathias Brochhausen census reference date A measurement datum that quantifies a temporal region that is occupied by a processual entity. Mathias Brochhausen duration The duration between the appearance of symptoms of a disease and the start of a treatment. Mathias Brochhausen delay from symptoms to treatment An infection acquisition whereby a susceptible host acquires an infection from an infectious host. William R. Hogan infection acquisition from infectious host The duration from the time an organism satisfies a case definition until a process or system detects the organism as satisfying that case definition Mathias Brochhausen time delay to case detection A duration that measures the temporal interval occupied by a treatment course. Mathias Brochhausen duration of treatment course The count of the number of doses that are part of a treatment course. Mathias Brochhausen number of doses in a treatment course The duration from the time an individual receives a treatment until the time a system designed to detect that the treatment occurred detects it in a population William R. Hogan time delay of treatment detection A data item that is about a proposition and has a numeric value between 0 and 1, inclusive, that is the output of some process of inference, such that 1) logical falsehoods and logical truths are assigned a value of 0 and 1, respectively, while contingent propositions are assigned some intermediate value; and 2) the process of inference conforms with rules for the calculation of probabilities, and that any interpretation of probability must specify the extent to which probabilities might be used to constrain the degrees of belief of rational agents. Matthew Diller William R. Hogan The first criterion is derived from Kolmogorov's Probability Calculus, while the second is derived from Salmon's Admissibility and Applicability Criteria of Adequacy. Salmon's ascertainability criterion is subsumed by the definition for 'data item'. probability A count of individuals in a population who meet the criteria of some case definition during some time interval. Matthew Diller William R. Hogan count of disease cases A count of disease cases in an infected population that meet the case definition criteria within a particular epidemic interval. Matthew Diller William R. Hogan count of cases in an epidemic A population census about the organisms specific to that population that were the host in some colonization acquisition. Matthew Diller William R. Hogan population colonization census An infection acquistion from infectious host that is causally downstream of some potentially infectious sexual contacting Matthew Diller Note that infections that are acquired in this manner do not fall within the class of sexually transmitted infections (STI's), ipso facto. This type of transmission can also occur with non-STI pathogens--such as meningitis and Zika. infection acquisition through sexual activity with infectious host A count of simulated or physical individuals in a population. Matthew Diller population count Qualitative description of a microbial response to antimicrobial agents and the expected clinical outcome. Bacteria may be susceptible or resistant to a broad range of antibiotic drugs or drug classes, with several intermediate states or phases. antimicrobial phenotype intermediate Intermediate sensitivity of a bacterial strain to a given antibiotic occurs when it is inhibited by a concentration of the drug that is associated with uncertain therapeutic effect. The elimination of intermediate phenotype bacteria may depend on the site of infection and/or the concentration of the administered drug. Definition from https://clsi.org. I intermediate antimicrobial phenotype resistant A bacterial strain is said to be resistant to a given antibiotic when it is inhibited in vitro by a concentration of this drug that is associated with a high likelihood of therapeutic failure. R resistant antimicrobial phenotype susceptible A bacterial strain is said to be susceptible to a given antibiotic when it is inhibited in vitro by a concentration of a drug that is associated with a high likelihood of therapeutic success. S sensitive susceptible antimicrobial phenotype nonsusceptible A bacterial strain is said to be nonsusceptible to a given antibiotic drug if it demonstrates either an intermediate or resistant phenotype when exposed to a concentration of a drug that is associated with a high likelihood of therapeutic failure, i.e. if the bacterial strain is not susceptible to the antibiotic drug but not necessarily totally resistant under all conditions. Definition from https://clsi.org. NS nonsensitive nonsensitive antimicrobial phenotype nonsusceptible antimicrobial phenotype susceptible - dose dependent A bacterial strain is said to be susceptible-dose dependent (SDD) to a given antibiotic when growth is inhibited with a high likelihood of therapeutic success, but when multiple approved dosing options exist. When a higher or more frequent dose is used, the predicted therapeutic result is the same as for susceptible individuals. SSD SDD Sensitive dose dependent antimicrobial phenotype sensitive - dose dependent susceptible dose dependent antimicrobial phenotype Multidrug-resistant organisms are defined as bacterial strains that have become resistant to multiple classes of antibacterial drugs or other agents. The phenotype of these organisms is defined by the spectrum of antibiotic drug classes to which that organism is resistant. Often, these organisms are susceptible to a narrow range of available drugs, making treatment difficult and urgent. MDRO multidrug resistance antimicrobial phenotype Uses breakpoints to create standards for interpreting the clinical outcome of an MIC value for a particular microbial species and antimicrobial agent. antimicrobial resistance testing reference standard BSAC is a British inter-professional organisation involved in antibiotic education, research and leadership. Baquero F. found that the BSAC system recommends lower breakpoints than the consensus standard of all systems for antimicrobial susceptibility testing used in Europe (BSAC, DIN, SFM, SIR, NCCLS and WRG). BSAC British Society for Antimicrobial Chemotherapy (BSAC) The Clinical and Laboratory Standards Institute develops and implements clinical laboratory testing standards. CLSI NCCLS National Committee on Clinical Laboratory Standards (NCCLS) On January 1, 2005 the National Committee on Clinical Laboratory Standards (NCCLS) changed its name to CLSI Clinical and Laboratory Standards Institute (CLSI) DIN is recognized by the Federal Government of Germany as the competent standards organization for Germany and as the national standards body representing Germany in non-governmental international standards organizations. Baquero F. found that the DIN system recommends lower breakpoints than the consensus standard of all systems for antimicrobial susceptibility testing used in Europe (BSAC, DIN, SFM, SIR, NCCLS and WRG). DIN Deutsches Institut für Normung (DIN) EUCAST is a standing committee jointly organized by ESCMID, ECDC and European national breakpoint committees; it deals with breakpoints and technical aspects of phenotypic in-vitro antimicrobial susceptibility testing. EUCAST European Committee on Antimicrobial Susceptibility Testing (EUCAST) The French Society of Microbiology (SFM) is a non-profit association which aims to bring together microbiologists from French-speaking countries, working in the domains of bacteria, viruses, Fungi and parasites, and related medical, industrial and environmental microbiology, physiology, genetics, taxonomy, hygiene, and antimicrobial agents. Baquero F. found that the SFM system recommends higher breakpoints than the consensus standard of all systems for antimicrobial susceptibility testing used in Europe (BSAC, DIN, SFM, SIR, NCCLS and WRG). SFM Société Française de Microbiologie (SFM) The measured or quantified MIC. MIC value Unit for measurement of minimum inhibitory concentration (MIC). MIC unit An experimental test conducted outside of a living organism, usually in a tube or plate. in-vitro microbial susceptibility test System of analysis for determining antimicrobial susceptibility. antimicrobial resistance test platform Microbial species are inoculated in a growth medium onto which antimicrobial agents are transferred by diffusion. diffusion method Components of complex mixtures such as plant extracts are separated across a TLC plate and tested for anti-microbial activity. thin-layer chromatography (TLC)-bioautography Allows for time-dependent or concentration-dependent analysis of antimicrobial effects. Several tubes of broth culture medium containing a suspension of the test microbe are treated with varying concentrations of the antimicrobial agent and the percentage of dead cells determined at various time points. time kill curve time-kill test Relies on the indirect measurement of microbe populations by quantifying microbial ATP production. ATP bioluminescence assay Microbes exposed to antimicrobial agents are then stained with the intercalating agent propidium iodide. Damaged cells emit a positive signal that is detected by flow cytometry analysis. Flow cytometry can also be used to discriminate between dead, damaged and live cells. flow cytofluorometric method Test that directly detect the presence of a particular resistance mechanism. mechanism-specific test The microbial species are inoculated in liquid growth medium containing incremental dilutions (usually 2-fold) of the antimicrobial agent. broth dilution method Automated system of analysis for determining antimicrobial susceptibility. automated testing platform Non-automated system of analysis for determining antimicrobial susceptibility. noncommercial testing platform manual testing platform Specific automated system of analysis for determining antimicrobial susceptibility developed by Omron. MicroScan Specific automated system of analysis for determining antimicrobial susceptibility developed by Becton Dickinson. Phoenix Specific automated system of analysis for determining antimicrobial susceptibility developed by Trek, Thermo Fisher Scientific. Sensitire Specific automated system of analysis for determining antimicrobial susceptibility developed by bioMérieux. Vitek System Vendor of automated system of analysis for determining antimicrobial susceptibility. automated testing platform vendor Specific vendor of automated system of analysis for determining antimicrobial susceptibility headquartered in New Jersey, USA. Becton Dickinson is the developer of the Phoenix automated testing platform. Becton Dickinson Specific vendor of automated system of analysis for determining antimicrobial susceptibility headquartered in France. bioMérieux is the developer of the Vitek automated testing platform. bioMérieux Specific vendor of automated system of analysis for determining antimicrobial susceptibility headquartered in Berlin and Munich. Siemens Specific vendor of automated system of analysis for determining antimicrobial susceptibility based in Japan. Omron is the developer of the MicroScan automated testing platform. Omron Specific vendor of automated system of analysis for determining antimicrobial susceptibility that was acquired by Thermo Fisher Scientific Inc. Thermo Fisher Scienfiic Inc. is headquartered in Massachusetts, USA. Trek is the developer of the Sensitire automated testing platform. Thermo Fisher Scientific Trek Broth dilution conducted on 96-well microtiter plates (≤200 µL per well). micro broth dilution method This test is a common method of evaluating the antimicrobial activity of plants or microbial extracts. In this method, bacteria are inoculated onto agar plates and the antimicrobial agent is injected into the plate and allowed to diffuse. agar well diffusion method This method is commonly used to study the antagonism between microorganisms. The first bacterial strain is inoculated onto agar plates in tight streaks. The bacteria will secrete molecules that diffuse in the agar medium; this medium is cut and placed on another agar plate inoculated with another microorganism. agar plug diffusion method This method is commonly used to study the antagonism between microorganisms. The microbial strain of interest is seeded by a single streak in the center of the agar plate. After incubation, the plate is seeded with the second microorganism by single streak perpendicular to the central streak. cross streak method The antimicrobial agent is transferred from a chromatogram to an agar plate previously inoculated with the test microorganism. agar diffusion bioautography A developed TLC plate is dipped into or sprayed with a microbial suspension and then incubated. Live microbial cells are visualized using tetrazolium salts. direct bioautography The TLC plate is covered with a molten agar medium seeded with the test microbe and the antimicrobial compounds are allowed to diffuse onto the agar medium. Tetrazolium dye staining allows for visualization. agar overlay bioassay agar overlay bioautography Assay for beta lactamase detection. chromogenic cephalosporinase test Commercial colorimetric assay for detection of chloramphenicol modifying enzyme chloramphenicol acetyltransferase. chloramphenicol acetyltransferase assay (CAT) depth:1 The tissue type used to select breakpoints from a particular standard, for the interpretation of MIC results. antimicrobial resistance tissue specificity Qualitative description of a microbial response to antimicrobial agents as described by EUCAST using breakpoints determined through in-vitro testing. These breakpoints are determined irrespective of tissue specificity of infection. EUCAST antimicrobial phenotype A microbe whose susceptibility to antibiotics is comparable to that of a reference susceptible microbe, meaning that the microbe is sensitive to the particular antibiotic. wild-type A microbe whose susceptibility to antibiotics differs from that of a reference susceptible microbe, meaning that the microbe is resistant to the particular antibiotic. non wild-type order: ARO:3004303 # nonsensitive ARO:3004300 # intermediate ARO:3004302 # sensitive ARO:3004304 # sensitive - dose dependant ARO:3004301 # resistant Qualitative description of a microbial response to antimicrobial agents as described by CLSI using breakpoints that take into consideration tissue specificity of infection. CLSI antimicrobial phenotype A method to determine microbial susceptibility to antibiotics in which test bacteria is inoculated onto an agar plate that contains a concentration gradient of antibiotic. The minimum inhibitory concentration of antibiotic is assessed. gradient plate method The National Committee for Clinical Laboratory Standards is an American organization responsible for developing accredited consensus clinical laboratory standards. National Committee for Clinical Laboratory Standards (NCCLS) SIR is a revised system for antibiotic sensitivity testing in Sweden that was proposed in 1977. The SIR system included two main changes: three sensitivity groups instead of the previous four and new breakpoints for the sensitivity groups. Swedish Reference Group for Antibiotics (SIR) The WRG is a standardized antimicrobial susceptibility testing methodology created by the Dutch Commissie Richtlijnen Gevoeligheidsbepalingen in 1981. Commissie Richtlijnen Gevoeligheidsbepalingen (CRG) Committee Guidelines Susceptibility Testing Working Group Guidelines Susceptibility Testing Werkgroep Richtlijnen Gevoeligheidsbepalingen (WRG) Specific automated system of analysis for determining antimicrobial susceptibility developed by Giles Scientific. BIOMIC Microbiology System A Nilotic Eastern population with a population size of 0.9 millions Maasai A Nilotic Eastern population with a population size of 0.1 millions Samburu A Bantu Western population with a population size of 3.8 millions Tiv A Khoisan South population with a population size of 0.13 millions Nama A Mande Western population with a population size of 2.2 millions Susu A Bantu Eastern population with a population size of 0.026 millions Taveta A Bantu Western population with a population size of 0.8 million Bassa A Nguni population with a population size of 12 millions Zulu A Nilotic Eastern population with a population size of 5 millions Dinka A Mande Western population with a population size of 14 millions Bambara A Kalenjin population with a population size of 0.3 million Sebei Masalit Bulu A Bantu Eastern population with a population size of 0.34 millions Taita A Western African population with a population size of >34 millions Igbo A Bantu Eastern population with a population size of 5.3 millions Kikuyu Terik Anuak A Kalenjin population with a population size of 937,884 Nandi Lunda A Bantu Southern population with a population size of 6 millions Tsonga A Northern African, Central African, Western African, Eastern African population with a population size of 25 millions Fulani A Western African population with a population size of 45 millions Yoruba A Nilotic Central, Nilotic Eastern, Northern African population with a population size of 0.4 million Zaghawa A Kalenjin population with a population size of 197556 Tugen A Bantu Eastern population with a population size of 2.7 Millions Meru A Cushitic Eastern population with a population size of 40 millions Oromo A Nilotic Eastern population with a population size of 1 million Fur A Nguni population with a population size of 7.9 millions Xhosa A Senufo population with a population size of 0.74 million Minianka Herero A Western African, Eastern African population with a population size of 90 millions Hausa The Nuer are a Nilotic Eastern population with a population size of 3 million. Nuer A Bantu Eastern population with a population size of 2.488 Millions Mijikenda A Bantu Central population with a population size of 1 million Fang A Gurma population with a population size of 7.6 millions Moore Mooré More Moré Moshi Mòoré Mõõré Mossi A Bantu Southern population with a population size of 5 millions Bemba A Bantu Eastern population with a population size of 4.663 millions Kamba Rendille The Ga-Adangbe are a Western African population with a population size of 2 million. Ga-Adangbe Bulsa A Bantu Eastern population with a population size of 9 millions Chewa The Soninke are a Mande Western population with a population size of 2 million. Soninke A Bantu Southern population with a population size of 15 millions Tswana A Berber Northern, Berber Western population with a population size of 2.5 millions Tuareg A Western African population with a population size of 0.93 millions Dagomba Kusasi A Gurunsi population with a population size of 0.3 millions Frafra A Gurma population with a population size of 0.8 millions Gurunsi A Western African population with a population size of 3.3 millions Gurma The Dagaaba are a Western African population with a population size of 1 million. Dagaaba A Mande Western population with a population size of 6.8 millions Dyula A Eastern African population with a population size of 1.2 millions Bihari Mauritian Mauritian Creole A Eastern African population with a population size of 0.055 millions Tamil Nankani Seychellois A Eastern African population with a population size of 0.4 million Khoisan Eastern Semitic Eastern Semite Northern Semite Central Pygmy Eastern People living in: Burundi OR Comoros OR Djibouti OR Eritrea OR Ethiopia OR Kenya OR Madagascar OR Malawi OR Mauritius OR Mayotte OR Mozambique OR Rwanda OR Réunion OR Seychelles OR Somalia OR South Sudan OR Sudan OR Uganda OR United Republic of Tanzania OR Zimbabwe Eastern African Berber Western 'The Nubians are known as people of the Nile and are located between Egypt and northern Sudan.' taken from: Culture and Customs of Sudan. Written by De Kwame Essien, Toyin Falola Ph.D. Nubian Eastern A Nubian Northern population with a population size of 0.050 million Mattokki A Ubangi Central population with a population size of 1.5 millions Banda Mahas A Nilotic Eastern population with a population size of Nilo-Saharan, Luo, River-Lake Luo The Kalenjin are a Nilotic Eastern population with a population size of 3 million. Kalenjin Pygmy Southern The Senufo are a Western African population with a population size of 2 million. Senufo A Western African population with a population size of 20 millions Akan A Toubou population with a population size of Nilo-Saharan Daza A Western African population with a population size of 0.5 millions Jola A Nilotic Western population with a population size of 5 millions Songhai A Bantu Eastern population with a population size of 15.109 millions Banyarwanda A Eastern African population with a population size of 0.462 million Ari A Eastern African population with a population size of 4 millions Gaaliin Shaigiya Messiria Hadendoa Halfawieen 'The Nuba trace their geographical roots to the area around the Nuba mountains, the uppermost regions around the Ingessana hills and communities close to the Red Sea.' taken from: Culture and Customs of Sudan. Written by De Kwame Essien, Toyin Falola Ph.D. Nuba A Berber Northern population with a population size of 0.57 million Sahrawi A Bantu Western population with a population size of 0.250 million Jarawa A Eastern African population with a population size of 1300 persons Hadza A Western African population with a population size of 1.9 millions Serer A Western African population with a population size of 0.285 million Manjak A Western African population with a population size of 0.324 million Balanta A Berber Northern population with a population size of 0.150 million Mozabite A Bantu Eastern, Bantu Southern population with a population size of 0.758 million Ngoni Lomwe A Bantu Eastern population with a population size of > 2 millions Yao A Chewa population with a population size of 2.486 millions, known as the people of the lake Mang'anja The Sena are a Bantu Eastern population with a population size of 2 million. Sena A Sudanic population with a population size of Nilo-Saharan|Satellite-Core|Satellites|Central Sudanic|West|Bongo-Bagirmi|Bongo-Baka|Bongo|Kacipo-Balesi|Tennet|Luo|Lango-Acholi Bongo Chipeta A Bantu Eastern population with a population size of 1.050 millions Nyakyusa A Cushitic Eastern population with a population size of 0.030 million Burunge A Malagasy population with a population size of 0.05 million Antankarana The Tsimihety are a Malagasy population with a population size of 1.2 million. Tsimihety The Sakalava are a Malagasy population with a population size of 1.2 million. Sakalava A Malagasy population with a population size of 1.5 millions Betsimisaraka A Malagasy population with a population size of 0.5 million Antemoro A Malagasy population with a population size of 4.359 millions Betsileo A Betsileo population with a population size of 0.015 million Zafimaniry A Malagasy population with a population size of > 5 millions Merina A Malagasy population with a population size of 0.52 million Bara A Malagasy population with a population size of 0.0012 million Vezo A Malagasy population with a population size of 0.6 million Antandroy A Malagasy population with a population size of 0.15 million Mahafaly Cafre A Eastern African population with a population size of 0.18 million Malbar Zarabe French people who were born in Metropolitan France. Zoreille A Eastern African population with a population size of 0.025 million Sinwa !Kung Ubangi Central Nilotic Central A Ubangi Central population with a population size of 0.011 million Bangba Mayogo Cushitic Eastern Nilotic Western Sudanic Bantu Central People living in: Angola OR Cameroon OR Central African Republic OR Chad OR Congo OR Democratic Republic of the Congo OR Gabon OR Zambia Central African People living in: Algeria OR Egypt OR Libya OR Mauritania OR Morocco OR Tunisia OR Western Sahara Northern African People living in: Botswana OR Eswatini OR Lesotho OR Namibia OR South Africa Southern African People living in: Benin OR Burkina Faso OR Cabo Verde OR Cote d'Ivoire OR Equatorial Guinea OR Gambia OR Ghana OR Guinea OR Guinea-Bissau OR Liberia OR Mali OR Niger OR Nigeria OR Saint Helena OR Sao Tome and Principe OR Senegal OR Sierra Leone OR Togo Western African A Nilotic Central, Nilotic Western population with a population size of >10 millions Kanuri A Central African population with a population size of < 1 million Kotoko A Central African population with a population size of 0.45 millions Masa Pygmy Central Aka A Pygmy Central population with a population size of 0.03 milion Baka_Cameroon A Pygmy Central population with a population size of 0.01 milion Mbuti A Pygmy Central population with a population size of 0.07 million Efé Sua A Pygmy Eastern, Pygmy Southern, Banyarwanda, Pygmy Central population with a population size of 0.04 million Twa Kwatay A Kanuri population with a population size of 0.655 millions Kanembu A Bantu Western, Bantu Central population with a population size of 3.3 millions with a group of 20 sub-ethnicities Beti-Pahuin A Bantu Central population with a population size of 1.1 million Chokwe A Bantu Central population with a population size of 17 millions Kongo The Luba are a Bantu Central population with a population size of >15 million. Luba A Bantu Central population with a population size of 6.4 millions Mbundu A Bantu Central population with a population size of 0.018 million Moghamo The Mongo are a Bantu Central population with a population size of >15 million. Mongo A Bantu Central population with a population size of 25 millions Ngala A Bantu Central population with a population size of 0.08 million Ngamambo A Bantu Central population with a population size of 0.025 million Tikar A Bantu Central population with a population size of 4.6 milions Ovimbundu A Kongo population with a population size of 0.5 million Mbunda A Ubangi Central population with a population size of 1.5 million Gbaya A Ubangi Central population with a population size of 0.122 million Ngbandi A Ubangi Central, Eastern African population with a population size of 1-4 millions Zande A Semite Central, Semitic Eastern population with a population size of 6 million Baggara A Western African, Nilotic Central population with a population size of 3.5 millions Sara A Nilotic Eastern, Nilotic Western, Northern African, Nilotic Central population with a population size of 2.25 millions Tabu Tebou Tebu Tibbu Tibu Toda Todaga Todga Tubu Tuda Tudaga Umbararo Toubou A Southern African population with a population size of 2.8–3.5 million Afrikaner Bantu Southern A Southern African, Eastern African population with a population size of 2.5 millions British diaspora A Southern African population with a population size of 4.7 millions Coloured A Southern African population with a population size of 0.03 millions. People of mixed race claiming both European and African descent. Goffel French diaspora Khoekhoe A Southern African population with a population size of 0.1 million San A Khoekhoe, San population with a population size of 0.4 millions Khoisan South Taa People of the place of the buffalo Banareng The Himba are a Bantu Southern population with a population size of 0.05 million. Himba Kwangali The Lemba are a Bantu Southern population with a population size of 0.05 million Lemba A Bantu Southern population with a population size of 4.037 Millions Makua A Bantu Southern population with a population size of > 28 millions Nguni A Bantu Southern population with a population size of 1.6 million Ovambo A Bantu Southern, Bantu Eastern population with a population size of 10.6 millions Shona A Bantu Southern population with a population size of 7.130 millions Sotho A Bantu Southern, Bantu Eastern population with a population size of 2 millions Tonga A Bantu Southern population with a population size of 1 million Venda A Bantu Southern population with a population size of 0.3 million Yeyi A Sotho population with a population size of 4.7 millions Pedi A Shona population with a population size of 0.75 million Kalanga A Shona population with a population size of 0.1 million Nambya Ndebele A Nguni population with a population size of 2.3 millions Swazi A Ndebele population with a population size of 1.5 million North Ndebele A Ndebele population with a population size of 0.7 million South Ndebele Kgatla Descendants of Andalusians people Andalusian A Northern African population with a population size of 38 millions Berber Northern A Eastern African, Northern African population with a population size of 20 millions Copt A Northern African population with a population size of 1.7 million Nubian Northern Algerian Berber Lybian Berber Moroccan Berber A Berber Northern population with a population size of Afro-Asiatic|Berber|Northern|Atlas Shilha Tunisian Andalusian Tunisian Berber A Semite Northern population with a population size of 85 millions Egyptian A Semite Northern population with a population size of 2 millions Haratin A Semite Northern population with a population size of >72 millions Maghrebi A Nilotic Eastern population with a population size of 0.2 million Gumuz A Semite Northern, Semitic Eastern population with a population size of 2 millions Moor Bantu Eastern A Eastern African population with a population size of 25 millions Malagasy A Eastern African population with a population size of >22 millions Nilotic Eastern A Eastern African population with a population size of 2 millions Wolaita A Nilotic Eastern population with a population size of 0.475 millon Bari A Luo population with a population size of 2 Millions Acholi Kwama A Nilotic Eastern population with a population size of 1,016 millions Turkana A Luo population with a population size of 1.7 million Alur A Luo population with a population size of 2.2 millions Lango A Luo population with a population size of 1.5 million Shilluk 'The Birked live north and east of Dago and Bayko, between Gebel Harayz and Rizaykat and are much larger tribe then either.' from a: A History of the Arabs in the Sudan. Written by De H. A. MacMichael. Birged Dongolese A Nubian Eastern population with a population size of 0.063 million Hill Nubian A Cushitic Eastern population with a population size of 6.3 million Afar A Cushitic Eastern population with a population size of 1 million Agaw A Cushitic Eastern population with a population size of 2.8 millions Beja The Bilen are a Cushitic Eastern population with a population size of 0.2 million. Bilen The Saho are a Cushitic Eastern population with a population size of 0.2 million. Saho A Cushitic Eastern population with a population size of >3 millions Sidama A Cushitic Eastern population with a population size of >20 millions Somali A Sudanic population with a population size of 11 millions Lugbara A Semitic Eastern population with a population size of 24 millions Amhara A Semitic Eastern population with a population size of 1.9 millions. Subdivided into three groups: East, North, West. Gurage Habesha A Semitic Eastern population with a population size of 0.2 millions Rashaida A Semitic Eastern population with a population size of 28 millions Sudanese Arab A Semitic Eastern population with a population size of 10.3 millions Tigrinya A Semitic Eastern population with a population size of 1.5 millions Tigré A Pygmy Eastern population with a population size of 0.25 million Baka_South_Sudan A Khoisan Eastern population with a population size of 0.06 million Sandawe A Bantu Eastern population with a population size of 2.9 Basoga The Chaga are a Bantu Eastern population with a population size of 2 million. Chaga A Bantu Eastern population with a population size of >0.4 million Embu A Bantu Eastern population with a population size of 6.7 millions Ganda A Bantu Eastern population with a population size of 2.2 millions Kisii A Bantu Eastern population with a population size of 5.4 millions Luhya A Bantu Eastern population with a population size of 1.3 millions Makonde A Bantu Eastern population with a population size of 1.4 million Nyoro A Bantu Eastern population with a population size of >0.1 millons Swahili A Bantu Eastern population with a population size of 1.546 millions Tumbuka A Western African population with a population size of 0.05 million Adele A Western African population with a population size of 0.01 million Aku Bantu Western A Western African population with a population size of 0.04 Biafada A Western African population with a population size of 0.1 million The Bubi are an amalgamation of first nation clans with various ancient mainland origins that later integrated with Krio, Efik, Igbo, Emancipado and Fernandino settlers. Bubi A Western African population with a population size of 0.128 millions Buduma A Western African population with a population size of 1.591 millions Dogon A Western African population with a population size of 1.6 millions Edo A Western African population with a population size of 0.9 millions Efik A Western African population with a population size of 0.3 millions Ekid Eket A Western African population with a population size of 1.5 millions Esan A Western African population with a population size of 6 millions Ewe The Fon are a Western African population with a population size of 4 million. Fon A Western African population with a population size of 9.6 millions Ibibio A Western African population with a population size of >14 millions Ijaw A Western African population with a population size of >30 millions Mande Western A Gurma population with a population size of 8.6 millions Mole-Dagbani The Urhobo are a Western African population with a population size of 2 million. Urhobo The Wolof are a Western African population with a population size of 4 million. Wolof A Mande Western population with a population size of 1.7 millions Bissa A Mande Western population with a population size of 13 millions Mandinka A Mande Western population with a population size of 0.4 millions Marka The Mende are a Mande Western population with a population size of 2 million. Mende A Gurunsi population with a population size of 0.161 millions Kassena A Songhai population with a population size of >5 millions Zarma A Songhai population with a population size of 0.2 million Dendi Okiek A Banyarwanda population with a population size of 16 millions Hutu A Banyarwanda, Southern African population with a population size of 3 millions Tutsi Bamileke Isoko A Pygmy Central, Western African population with a population size of 6.8 millions Kru A Bantu Central population with a population size of 260000 Duala Duala A Bantu Central population with a population size of 74000 Eshira Eshira A Bantu Central population with a population size of 215000 Hema Hema A Bantu Central population with a population size of 81500 Kota Kota A Bantu Central population with a population size of 89500 Makaa Makaa A Bantu Central population with a population size of 117030 Myene Myene A Bantu Central population with a population size of 2.355 millions Nande Nande Ngumba Ngumba Obamba Obamba A Bantu Central population with a population size of 250000 Pende Pende A Bantu Central population with a population size of 317000 Punu Punu Teke Teke A Bantu Central population with a population size of 100000 Vili Vili A Central African population with a population size of 90500 Mandar Mandar A Central African population with a population size of 1.8 millions Mangbetu Mangbetu A Central African population with a population size of 346000 Manja Manja A Central African population with a population size of 228000 Marba Marba A Central African population with a population size of 165000 Mbum Mbum A Central African population with a population size of 347614 Nzebi Nzebi A Central African population with a population size of 65000 Podoko Podoko A Pygmy Central population with a population size of 5500 Gyele Gyele Yaka Yaka Tupuri Tupuri Wuzlam Wuzlam A Central African population with a population size of 177000 Yakoma Yakoma A Bantu Eastern population with a population size of 760000 Chopi Chopi A Embu population with a population size of 195250 Mbeere Mbeere A Bantu Eastern population with a population size of 3,420 Millions Kiga Kiga A Bantu Eastern population with a population size of 89900 Lambya Lambya A Bantu Eastern population with a population size of 2.233 millions Masaba Masaba A Mijikenda population with a population size of <25,000 Segeju Segeju A Bantu Eastern population with a population size of 4,436 Millions Nkole Nkole A Bantu Eastern population with a population size of 4 Millions Nyamwezi Nyamwezi A Bantu Eastern population with a population size of 112075 Pokomo Pokomo Ndau Ndau A Bantu Eastern population with a population size of 10 Millions Sukuma Sukuma A Bantu Eastern population with a population size of 175905 Tharaka Tharaka A Cushitic Eastern population with a population size of 20103 Aweer Aweer A Cushitic Eastern population with a population size of 1104 Elmolo Elmolo A Cushitic Eastern population with a population size of 2 million Hadiya Hadiya A Oromo population with a population size of 1025000 Borana Borana A Oromo population with a population size of 700000 Gabra Gabra A Malagasy population with a population size of 50000 Antambahoaka Antambahoaka A Malagasy population with a population size of 772000 Antanosy Antanosy A Malagasy population with a population size of 100000 Bezanozano Bezanozano A Malagasy population with a population size of 1500 Mikea Mikea A Malagasy population with a population size of 200000 Sihanaka Sihanaka A Malagasy population with a population size of 400000 Tanala Tanala A Kalenjin population with a population size of 180000 Marakwet Marakwet A Kalenjin population with a population size of 969000 Pokot Pokot A Nilotic Eastern population with a population size of 260000 Kunama Kunama A Nilotic Eastern population with a population size of 108000 Nara Nara A Nilotic Eastern population with a population size of 2,873 Millions Teso Teso Jeberti Jeberti A Bemba population with a population size of 433000 Aushi Aushi Okavango Okavango A Sotho population with a population size of 3,575 Millions Lozi Lozi A Khoisan South population with a population size of 146000 Damara Damara A Western African population with a population size of 61500 Aghem Aghem A Western African population with a population size of 810000 Aja Aja A Akan population with a population size of 2 millions Fante Fante A Western African population with a population size of 2.6 million Anaang Anaang A Akan population with a population size of 5 millions Baule Baule A Western African population with a population size of 659000 Bamum Bamum Kombe Kombe Luvale Luvale A Western African population with a population size of 2500 Bedik Bedik A Western African population with a population size of 40800 Bassari Bassari A Western African population with a population size of 150000 Diffa Arabs Diffa Arabs Ditammari Ditammari Ekoi Ekoi A Western African population with a population size of 304000 Gola Gola The Guan are a Western African population with a population size of 1 million. Guan Guan A Gurma population with a population size of 1.4 million Bariba Bariba A Gurma population with a population size of 950000 Konkomba Konkomba Lilse Lilse Lobi Lobi A Gurma population with a population size of 19700 Pana Pana A Gurma population with a population size of 30900 Samoya Samoya A Western African population with a population size of 2.7 Million Itsekiri Itsekiri A Jola population with a population size of 10125 Bandial Bandial A Mande Western population with a population size of 700000 Dan Dan A Gurma population with a population size of 1.22 millions Kabye Kabye A Western African population with a population size of 104311 Krio Krio A Kru population with a population size of 214000 Krahn Krahn A Kru population with a population size of 387000 Grebo Grebo A Western African population with a population size of 311500 Kulango Kulango A Western African population with a population size of 792190 Limba Limba A Mande Western population with a population size of 115200 Jakhanke Jakhanke A Mande Western population with a population size of 363000 Kono Kono The Kpelle are a Mande Western population with a population size of 2 million. Kpelle Kpelle A Mande Western population with a population size of > 2 millions Kuranko Kuranko A Mande Western population with a population size of 165692 Loko Loko A Mande Western population with a population size of 498000 Mano Mano A Mande Western population with a population size of 240000 Vai Vai A Mande Western population with a population size of 206000 Yalunka Yalunka A Western African population with a population size of 106900 Mankanya Mankanya A Western African population with a population size of 1.407 million Oron Oron A Western African population with a population size of 140000 Papel Papel A Western African population with a population size of 134606 Sherbro Sherbro A Western African population with a population size of 2,225 Millions Temne Temne A Wolof population with a population size of 210000 Lebu Lebu Nuna Nuna A Pygmy Central population with a population size of 12500 Kango A Beti-Pahuin population with a population size of 2500000 Ewondo A Southern African population with a population size of 35500 Birwa A Western African population with a population size of 1,224,545 Kissi A Swahili population with a population size of 416,200 Ngazidja A Swahili population with a population size of 217,400 Maore A Swahili population with a population size of 45,000 Mwali A Swahili population with a population size of 365,900 Ndzwani A Bantu Eastern population with a population size of 1 million Kuria A Jola population with a population size of 117000 Karonica An entity is anything that exists or has existed or will exist. https://www.wikidata.org/wiki/Q35120 entity An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. continuant An entity that has temporal parts and that happens, unfolds or develops through time. occurrent A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) independent continuant A process is an entity that exists in time by occurring or happening, has temporal parts and always involves and depends on some entity during the time it occurs. An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) James Malone http://www.ifomis.org/bfo/1.1/span#ProcessualEntity NCIt:C29862 SNOMEDCT:415178003 An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. process process A disposition is an entity that causes a specific process or transformation in an entity in which it inheres, under specific circumstances and in conjunction with the laws of nature. For example, the disposition of vegetables to decay when not refrigerated, the disposition of blood to coagulate, the disposition of a patient with a weakened immune system to contract disease. James Malone modified from original http://www.ifomis.org/bfo/1.1/snap#Disposition NCIt:C41205 disposition disposition realizable entity A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities. A quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. A quality is an attribute that is intrinsically associated with its bearer (or its parts), but whose presence/absence and observed/measured value may vary. https://en.wikipedia.org/wiki/Quality_(philosophy) http://purl.obolibrary.org/obo/PATO_0000001 https://www.wikidata.org/wiki/Q1207505 The etymology of "quality" is fairly well elucidated coming from Middle English, from Old French qualité, from Latin qualitatem, accusative of qualitas, from qualis (“of what kind”), from Proto-Indo-European *kʷo- (“who, how”). Cicero coined qualitas as a calque to translate the Ancient Greek word ποιότης (poiótēs, “quality”), coined by Plato from ποῖος (poîos, “of what nature, of what kind”). quality A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. An experimental factor which is a property or characteristic of some other entity. For example, the mouse has the colour white. b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n &gt; 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i &lt; j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004]) b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n &gt; 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i &lt; j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004]) b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) James Malone Sirarat Sarntivijai http://www.ifomis.org/bfo/1.1/snap#SpecificallyDependentContinuant BFO:0000020 SpecificallyDependentContinuant specifically dependent continuant characteristic material property specifically dependent continuant specifically dependent continuant A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts. A role is an entity which is borne in a material entity in some kinds of natural, social or institutional contexts, but which is not essential to the fundamental definition of that material entity (i.e. the material entity exists with or without the role). For example, the role of a person as a surgeon, the role of an artificial heart in pumping blood, the role of a chemical compound in an experiment, the role of a drug in the treatment of a disease. James Malone http://www.ifomis.org/bfo/1.1/snap#Role MeSH:D012380 NCIt:C48835 http://purl.obolibrary.org/obo/CHEBI_50906 role role fiat object fiat object part ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158. object aggregate object A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time. b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time. generically dependent continuant material entity A material entity is an entity that exists in full during the length of time of its existence, persists through this time while maintaining its identity and has no temporal parts. For example a heart, a human, a fly, a microarray. An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. James Malone http://www.ifomis.org/bfo/1.1/snap#MaterialEntity material type material entity material entity immaterial entity intestinal cell line kidney cell line adenocarcinoma cell line colonic cell line Human colon adenocarcinoma cell line, established from the primary colon tumor (adenocarcinoma) of a 72-year-old Caucasian man in 1974. CACO-2 cell carcinoma cell line lung cell line Hepatoma is a cancer originating in the liver, in liver cells. More often called hepatocarcinoma or hepatocellular carcinoma. hepatoma cell line A glioma is a type of tumor that starts in the glial cells of the brain or the spine. Gliomas comprise about 30 per cent of all brain tumors and central nervous system tumors, and 80 per cent of all malignant brain tumors. glioma cell line lung cancer cell line colonic cancer cell line The MDBK cell line was derived from a kidney of an apparently normal adult steer, February 18, 1957, by S.H. Madin and N.B. Darby. MDBK cell epithelial cell line The Vero cell line was initiated from the kidney of a normal adult African green monkey on March 27, 1962, by Y. Yasumura and Y. Kawakita at the Chiba University in Chiba, Japan. Vero cell Pig kidney cell line. Original line: PK-2a; contains type C viruses. Morphology: epithelial-like. PK-15 cell lung adenocarcinoma cell line colonic adenocarcinoma cell line Human hepatoma cell line. HuH-7 cell bronchial epithelial cell line Human glioma cell line. Morphology: glial; Species: human; Tumor: glioma. U-251MG cell A highly transformed human renal epithelial line expressing two viral oncogenes, adenovirus E1a and SV40 large T antigen. HEK-293T cell respiratory epithelium cell line Human lung adenocarcinoma cell line; established from a 25-year-old caucasian male. Calu-3 cell renal epithelium cell line Rabbit renal epithelium cell line. RK-13 cell Normal human bronchial epithelial cell line. NHBE cell This line is a clone of VERO 76. VERO C1008 cell A monocarboxylic acid comprising 1,8-naphthyridin-4-one substituted by carboxylic acid, ethyl and methyl groups at positions 3, 1, and 7, respectively. An orally administered antibacterial, it is used in the treatment of lower urinary-tract infections due to Gram-negative bacteria, including the majority of E. coli, Enterobacter, Klebsiella, and Proteus species. CHEBI:7456 nalidixic acid A quinolone that is quinolin-4(1H)-one bearing cyclopropyl, carboxylic acid, fluoro and piperazin-1-yl substituents at positions 1, 3, 6 and 7, respectively. CHEBI:102718 CHEBI:3717 CHEBI:41638 ciprofloxacin A quinolinemonocarboxylic acid with broad-spectrum antibacterial activity against most gram-negative and gram-positive bacteria. Norfloxacin is bactericidal and its mode of action depends on blocking of bacterial DNA replication by binding itself to an enzyme called DNA gyrase. CHEBI:7629 norfloxacin A sulfonamide consisting of pyrimidine with methyl substituents at the 4- and 6-positions and a 4-aminobenzenesulfonamido group at the 2-position. sulfamethazine A sulfonamide antibacterial with an oxazole substituent. It has antibiotic activity against a wide range of gram-negative and gram-positive organisms. CHEBI:9343 sulfisoxazole A fluoroquinolone antibiotic, used (generally as the hydrochloride salt) to treat bacterial infections including bronchitis and urinary tract infections. It is also used to prevent urinary tract infections prior to surgery. CHEBI:6517 lomefloxacin A semisynthetic, first-generation cephalosporin antibiotic with acetoxymethyl and (2-thienylacetyl)nitrilo moieties at positions 3 and 7, respectively, of the core structure. Administered parenterally during surgery and to treat a wide spectrum of blood infections. CHEBI:41547 CHEBI:50895 cefalotin A class of carbonyl compound encompassing dicarboxylic acids and any derivatives obtained by substitution of either one or both of the carboxy hydrogens. dicarboxylic acids and O-substituted derivatives Any aromatic amide obtained by acylation of aniline. anilide delamanid thioacetazone Trd terizidone Any main group molecular entity that is gaseous at standard temperature and pressure (STP; 0degreeC and 100 kPa). gas molecular entity An alpha-oxyketone that has a hydroxy group as the alpha-oxy moiety. alpha-hydroxy ketone An alpha-hydroxy ketone in which the carbonyl group and the hydroxy group are linked by a carbon bearing two organyl groups. tertiary alpha-hydroxy ketone A carboxamide resulting from the formal condensation of a carboxylic acid with a primary amine; formula RC(=O)NHR(1). secondary carboxamide A carboxamide resulting from the formal condensation of a carboxylic acid with a secondary amine; formula RC(=O)NHR(1)R(2). tertiary carboxamide A compound having bonds between one or more metalloid atoms and one or more carbon atoms of an organyl group. organometalloidal compound Any organic heterotricyclic compound whose core skeleton consists of a benzodioxin ring that is ortho-fused to a pyran ring. pyranobenzodioxin A large group of antibiotics isolated from various species of Streptomyces and characterised by having a substituted phenoxazine ring linked to two cyclic heterodetic peptides. CHEBI:13723 CHEBI:22220 CHEBI:2445 actinomycin CHEBI:10745 CHEBI:13416 CHEBI:23833 CHEBI:25366 CHEBI:30491 CHEBI:44742 CHEBI:7860 dioxygen A 1,8-naphthyridine derivative that is 1,4-dihydro-1,8-naphthyridine with an ethyl group at the 1 position, a carboxy group at the 3-position, an oxo sustituent at the 4-position, a fluoro substituent at the 5-position and a piperazin-1-yl group at the 7 position. An antibacterial, it is used in the treatment of urinary-tract infections and gonorrhoea. CHEBI:4796 enoxacin A primary alcohol is a compound in which a hydroxy group, -OH, is attached to a saturated carbon atom which has either three hydrogen atoms attached to it or only one other carbon atom and two hydrogen atoms attached to it. CHEBI:13676 CHEBI:14887 CHEBI:26262 CHEBI:57489 CHEBI:8406 primary alcohol A cyclic peptide antibiotic produced by the actinomycete Streptomyces puniceus, used in the treatment of tuberculosis. CHEBI:15312 CHEBI:27296 CHEBI:579539 CHEBI:9995 viomycin A peptide containing ten or more amino acid residues. CHEBI:14860 CHEBI:8314 polypeptide A nucleobase-containing molecular entity with a polymeric structure comprised of a linear sequence of 13 or more nucleotide residues. CHEBI:13672 CHEBI:14859 CHEBI:8312 polynucleotide A synthetic monocyclic beta-lactam antibiotic (monobactam), used primarily to treat infections caused by Gram-negative bacteria. It inhibits mucopeptide synthesis in the bacterial cell wall, thereby blocking peptidoglycan crosslinking. CHEBI:2960 CHEBI:41008 aztreonam A lipid containing phosphoric acid as a mono- or di-ester. The term encompasses phosphatidic acids and phosphoglycerides. CHEBI:14816 CHEBI:26063 CHEBI:8150 phospholipid The nitrogen oxoanion formed by loss of a proton from nitrous acid. CHEBI:14658 CHEBI:44396 CHEBI:7585 nitrite Compounds having the structure RSR (R =/= H). Such compounds were once called thioethers. CHEBI:13694 CHEBI:26960 CHEBI:9340 organic sulfide An aromatic ether that is phenol which is substituted at C-5 by a chloro group and at C-2 by a 2,4-dichlorophenoxy group. It is widely used as a preservative and antimicrobial agent in personal care products such as soaps, skin creams, toothpaste and deodorants as well as in household items such as plastic chopping boards, sports equipment and shoes. CHEBI:29697 CHEBI:47700 triclosan An alpha-amino acid that consists of propionic acid bearing an amino substituent at position 2. CHEBI:13748 CHEBI:22277 CHEBI:2539 alanine A naturally occurring polypeptide synthesized at the ribosome. CHEBI:8526 protein polypeptide chain Amide derived from two or more amino carboxylic acid molecules (the same or different) by formation of a covalent bond from the carbonyl carbon of one to the nitrogen atom of another with formal loss of water. The term is usually applied to structures formed from alpha-amino acids, but it includes those derived from any amino carboxylic acid. X = OH, OR, NH2, NHR, etc. CHEBI:14753 CHEBI:25906 CHEBI:7990 peptide Any oligosaccharide, polysaccharide or their derivatives consisting of monosaccharides or monosaccharide derivatives linked by glycosidic bonds. See also http://www.ontobee.org/ontology/GNO?iri=http://purl.obolibrary.org/obo/GNO_00000001. glycan CHEBI:14682 CHEBI:25659 CHEBI:7737 oleandomycin High molecular weight, linear polymers, composed of nucleotides containing deoxyribose and linked by phosphodiester bonds; DNA contain the genetic information of organisms. CHEBI:13302 CHEBI:21123 CHEBI:33698 CHEBI:4291 deoxyribonucleic acid deoxyribonucleic acid A amino cyclitol glycoside that consists of streptidine having a disaccharyl moiety attached at the 4-position. The parent of the streptomycin class STR Sm Stm CHEBI:15119 CHEBI:26784 CHEBI:45745 CHEBI:9284 streptomycin A compound in which a carbonyl group is bonded to two carbon atoms: R2C=O (neither R may be H). CHEBI:13427 CHEBI:13646 CHEBI:24974 CHEBI:6127 CHEBI:8742 ketone A pyridinecarboxamide that is pyridine in which the hydrogen at position 3 is replaced by a carboxamide group. CHEBI:14645 CHEBI:25521 CHEBI:44258 CHEBI:7556 nicotinamide Any member of the group of substituted penams containing two methyl substituents at position 2, a carboxylate substituent at position 3 and a carboxamido group at position 6. CHEBI:14742 CHEBI:25869 CHEBI:7961 penicillin A compound RC(=O)H, in which a carbonyl group is bonded to one hydrogen atom and to one R group. CHEBI:13432 CHEBI:13753 CHEBI:13805 CHEBI:13806 CHEBI:22291 CHEBI:2554 CHEBI:8750 aldehyde CHEBI:14487 CHEBI:24945 CHEBI:24947 CHEBI:43482 CHEBI:6106 kanamycin A A nitrogen oxoanion formed by loss of a proton from nitric acid. Principal species present at pH 7.3. CHEBI:14654 CHEBI:44487 CHEBI:71263 nitrate A macrolide antibiotic that is tylonolide having mono- and diglycosyl moieties attached to two of its hydroxy groups. It is found naturally as a fermentation product of Streptomyces fradiae. CHEBI:15275 CHEBI:27172 CHEBI:46150 CHEBI:9787 tylosin Any member of a group of vitamers that belong to the chemical structural class called pyridines that exhibit biological activity against vitamin B3 deficiency. Vitamin B3 deficiency causes a condition known as pellagra whose symptoms include depression, dermatitis and diarrhea. The vitamers include nicotinic acid and nicotinamide (and their ionized and salt forms). vitamin B3 An organochlorine compound that is dichloro-substituted acetamide containing a nitrobenzene ring, an amide bond and two alcohol functions. CHEBI:13965 CHEBI:23106 CHEBI:23108 CHEBI:3603 CHEBI:47327 chloramphenicol A compound containing at least one carbon-halogen bond (where X is a halogen atom). CHEBI:13444 CHEBI:36684 CHEBI:8767 organohalogen compound An aminonucleoside antibiotic, derived from the Streptomyces alboniger bacterium, that causes premature chain termination during translation taking place in the ribosome. CHEBI:14970 CHEBI:26402 CHEBI:45182 CHEBI:8641 puromycin 'Lipids' is a loosely defined term for substances of biological origin that are soluble in nonpolar solvents. They consist of saponifiable lipids, such as glycerides (fats and oils) and phospholipids, as well as nonsaponifiable lipids, principally steroids. CHEBI:14517 CHEBI:25054 CHEBI:6486 lipid RNA molecules which are essential structural and functional components of ribosomes, the subcellular units responsible for protein synthesis. CHEBI:10636 CHEBI:15010 ribosomal RNA CHEBI:14472 CHEBI:43447 CHEBI:6036 isopenicillin N CHEBI:14744 CHEBI:25867 CHEBI:7964 penicillin N A penicillin in which the substituent at position 6 of the penam ring is a phenylacetamido group. CHEBI:14743 CHEBI:25866 CHEBI:45073 CHEBI:7962 benzylpenicillin Any nucleoside where the sugar component is D-ribose. CHEBI:13014 CHEBI:13015 CHEBI:13685 CHEBI:21085 CHEBI:26560 CHEBI:4240 CHEBI:8844 ribonucleoside 11alpha-hydroxy steroid An oxazinoquinoline that is 2,3-dihydro-7H-[1,4]oxazino[2,3,4-ij]quinolin-7-one substituted by methyl, carboxy, fluoro, and 4-methylpiperazin-1-yl groups at positions 3, 6, 9, and 10, respectively. 9-fluoro-3-methyl-10-(4-methylpiperazin-1-yl)-7-oxo-2,3-dihydro-7H-[1,4]oxazino[2,3,4-ij]quinoline-6-carboxylic acid A cephalosporin compound having acetoxymethyl and [2-(2-amino-1,3-thiazol-4-yl)-2-(methoxyimino)acetyl]amino side groups. CHEBI:112504 CHEBI:3497 CHEBI:41475 cefotaxime A semisynthetic cephamycin antibiotic which, in addition to the methoxy group at the 7alpha position, has 2-thienylacetamido and carbamoyloxymethyl side-groups. It is resistant to beta-lactamase. CHEBI:3500 CHEBI:41436 CHEBI:471714 CHEBI:658070 cefoxitin A glycosyl compound arising formally from the elimination of water from a glycosidic hydroxy group and an H atom bound to a nitrogen atom, thus creating a C-N bond. N-glycosyl compound Compounds with the general formula RNHC(=O)CH3. acetamides acridines Any purine ribonucleoside that is a derivative of adenosine. adenosines Any of the naturally occurring, basic nitrogen compounds (mostly heterocyclic) occurring mostly in the plant kingdom, but also found in bacteria, fungi, and animals. By extension, certain neutral compounds biogenetically related to basic alkaloids are also classed as alkaloids. Amino acids, peptides, proteins, nucleotides, nucleic acids, amino sugars and antibiotics are not normally regarded as alkaloids. Compounds in which the nitrogen is exocyclic (dopamine, mescaline, serotonin, etc.) are usually classed as amines rather than alkaloids. alkaloid alpha-D-glucoside An alcohol containing an amino functional group in addition to the alcohol-defining hydroxy group. amino alcohol amino cyclitol glycoside aminobenzoic acid aminoglycoside antibiotic Any aromatic amine that is benzene carrying at least one amino substituent and its substituted derivatives. anilines A monoatomic or polyatomic species having one or more elementary charges of the electron. anion A class of macrocyclic lactams that consist of an aromatic (phenyl or naphthyl) or quinonoid (benzoquinone or naphthoquinone) moiety that is bridged by an aliphatic chain. ansamycin http://purl.obolibrary.org/obo/CHEBI_33281 obsolete: antibiotic true arsenic molecular entity Any benzenoid aromatic compound consisting of the benzene skeleton and its substituted derivatives. benzenes Any aromatic carboxylic acid that consists of benzene in which at least a single hydrogen has been substituted by a carboxy group. benzoic acids benzopyran A glycopeptide produced by the bacterium Streptomyces verticillus. The term, 'bleomycin' refers to a family of structurally related compounds. When used as an anti-cancer agent, the chemotherapeutical forms are primarily bleomycin A2 and B2. CHEBI:584977 bleomycin bromine molecular entity calcium molecular entity Any ester of carbamic acid or its N-substituted derivatives. carbamate ester Any carbohydrate derivative that exhibits antibiotic activity. carbohydrate-containing antibiotic A class of beta-lactam antibiotics differing from the penicillins in having a 6-membered, rather than a 5-membered, side ring. Although cephalosporins are among the most commonly used antibiotics in the treatment of routine infections, and their use is increasing over time, they can cause a range of hypersensitivity reactions, from mild, delayed-onset cutaneous reactions to life-threatening anaphylaxis in patients with immunoglobulin E (IgE)-mediated allergy. CHEBI:3538 cephalosporin chelate-forming peptide chloride salt A halogen molecular entity containing one or more atoms of chlorine. chlorine molecular entity Any organochlorine compound containing a benzene ring which is substituted by one or more chlorines. chlorobenzenes chromenes chromopeptide Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity. molecular entity coumarins CHEBI:3990 cyclic amide cyclic peptide A polyol consisting of a cycloalkane containing at least three hydroxy groups, each attached to a different ring carbon atom. cyclitol A member of the class of oxazolidines that is isoxazoldin-3-one which is substituted at position 4 by an amino group. 4-amino-1,2-oxazolidin-3-one A natural or synthetic compound having a sequence of amino and hydroxy carboxylic acid residues (usually alpha-amino and alpha-hydroxy acids), commonly but not necessarily regularly alternating. depsipeptide An azole that is either one of a pair of heterocyclic organic compounds comprising three carbon atoms and two nitrogen atoms arranged in a ring. diazole Any member of the class of chlorobenzenes carrying two chloro groups at unspecified positions. dichlorobenzene Any organic heteromonocyclic compound with a structure based on a dihydropyrrole. pyrroline quinolone A compound that contains two hydroxy groups, generally assumed to be, but not necessarily, alcoholic. Aliphatic diols are also called glycols. diol erythromycins ethanolamines fluorine molecular entity Compounds containing at least one furan ring. furans glucoside Any carbohydrate derivative that consists of glycan moieties covalently attached to the side chains of the amino acid residues that constitute the peptide. CHEBI:24395 CHEBI:5478 glycopeptide Any phospholipid that contain both phosphate and carbohydrate as integral structural components. glycophospholipid A glycosyl compound resulting from the attachment of a glycosyl group to a non-acyl group RO-, RS-, RSe-, etc. The bond between the glycosyl group and the non-acyl group is called a glycosidic bond. By extension, the terms N-glycosides and C-glycosides are used as class names for glycosylamines and for compounds having a glycosyl group attached to a hydrocarbyl group respectively. These terms are misnomers and should not be used. The preferred terms are glycosylamines and C-glycosyl compounds, respectively. glycoside A chemical entity is a physical entity of interest in chemistry including molecular entities, parts thereof, and chemical substances. chemical entity A role played by the molecular entity or part thereof within a biological context. biological role halogen molecular entity heterocyclic antibiotic A cyclic compound having as ring members atoms of carbon and at least of one other element. organic heterocyclic compound A heterodetic cyclic peptide is a peptide consisting only of amino-acid residues, but in which the linkages forming the ring are not solely peptide bonds; one or more is an isopeptide, disulfide, ester, or other bond. heterodetic cyclic peptide A homodetic cyclic peptide is a cyclic peptide in which the ring consists solely of amino-acid residues in peptide linkages. homodetic cyclic peptide An imidazolidinone with oxo groups at position 2 and 4. imidazolidine-2,4-dione A compound, RkE(=O)lNHOH, derived from an oxoacid RkE(=O)l(OH) (l =/= 0) by replacing -OH with -NHOH, and derivatives thereof. Specific examples of hydroxamic acids are preferably named as N-hydroxy amides. hydroxamic acid Hydroxides are chemical compounds containing a hydroxy group or salts containing hydroxide (OH(-)). hydroxides Any benzoic acid carrying one or more phenolic hydroxy groups on the benzene ring. CHEBI:50778 hydroxybenzoic acid A five-membered organic heterocycle containing two nitrogen atoms at positions 1 and 3, or any of its derivatives; compounds containing an imidazole skeleton. imidazoles imide A compound which contains oxygen, at least one other element, and at least one hydrogen bound to oxygen, and which produces a conjugate base by loss of positive hydrogen ion(s) (hydrons). oxoacid inorganic anion A molecular entity that contains no carbon. inorganic molecular entity A salt is an assembly of cations and anions. salt organic salt A molecular entity having a net electric charge. ion kanamycins Oximes of ketones R2C=NOH (where R =/= H). ketoxime Cyclic amides of amino carboxylic acids, having a 1-azacycloalkan-2-one structure, or analogues having unsaturation or heteroatoms replacing one or more carbon atoms of the ring. lactam Any cyclic carboxylic ester containing a 1-oxacycloalkan-2-one structure, or an analogue having unsaturation or heteroatoms replacing one or more carbon atoms of the ring. lactone leucomycin lipopeptide antibiotic A macrocyclic lactone with a ring of twelve or more members which exhibits antibiotic activity. macrolide antibiotic A macrocyclic lactone with a ring of twelve or more members derived from a polyketide. macrolide A molecule all atoms of which have the same atomic number. elemental molecule Any polyatomic entity that is an electrically neutral entity consisting of more than one atom. molecule An oxoacid containing a single carboxy group. monocarboxylic acid Any hydroxybenzoic acid having a single phenolic hydroxy substituent on the benzene ring. monohydroxybenzoic acid Any benzenoid aromatic compound having a skeleton composed of two ortho-fused benzene rings. naphthalenes A member of the class of pyridines that is a substituted pyridine in which at least one of the substituents is a carboxamide or N-substituted caraboxamide group. pyridinecarboxamide organonitrogen heterocyclic antibiotic nonmetal atom oleandomycins organic heteromonocyclic compound Any organic ion with a net negative charge. organic anion An organooxygen compound with formula ROR, where R is not hydrogen. ether organic ion organic phosphate An organophosphorus compound is formally a compound containing at least one carbon-phosphorus bond, but the term is often extended to include esters and thioesters. organophosphorus compound An oxide is a chemical compound of oxygen with other chemical elements. oxide Compounds of structure R2C=NOH derived from condensation of aldehydes or ketones with hydroxylamine. Oximes from aldehydes may be called aldoximes; those from ketones may be called ketoximes. oxime Any compound that has an aldehydic or ketonic group as well as a carboxylic acid group in the same molecule. oxo carboxylic acid oxygen molecular entity organooxygen heterocyclic antibiotic penicillanic acids A chemically diverse class of peptides that exhibit antimicrobial properties. peptide antibiotic Any organic aromatic compound with a structure based on a phenylpropane skeleton. The class includes naturally occurring phenylpropanoid esters, flavonoids, anthocyanins, coumarins and many small phenolic molecules as well as their semi-synthetic and synthetic analogues. Phenylpropanoids are also precursors of lignin. phenylpropanoid Salts and esters of phosphoric and oligophosphoric acids and their chalcogen analogues. In inorganic chemistry, the term is also used to describe anionic coordination entities with phosphorus as central atom. phosphate HP(=O)(OH)2 (phosphonic acid) and its P-substituted derivatives. phosphonic acids phosphoric acid derivative phosphorus molecular entity piperazines piperidines Natural and synthetic compounds containing alternating carbonyl and methylene groups ('beta-polyketones'), biogenetically derived from repeated condensation of acetyl coenzyme A (via malonyl coenzyme A), and usually the compounds derived from them by further condensations, etc. Considered by many to be synonymous with the less frequently used terms acetogenins and ketides. polyketide A compound that contains two or more hydroxy groups. polyol Members of the class of phenols that contain 2 or more benzene rings each of which is substituted by at least one hydroxy group. polyphenol An amino acid derivative resulting from reaction of proline at the amino group or the carboxy group, or from the replacement of any hydrogen of proline by a heteroatom. The definition normally excludes peptides containing proline residues. proline derivative An amino cyclitol glycoside that is kanamycin A acylated at the N-1 position by a 4-amino-2-hydroxybutyryl group. Am Amk amikacin purine nucleoside A ribonucleoside that has a purine moiety as the nucleobase (the R group in the illustration). purine ribonucleoside A class of imidazopyrimidines that consists of purine and its substituted derivatives. CHEBI:13678 purines puromycins pyridine alkaloid Any organonitrogen heterocyclic compound based on a pyridine skeleton and its substituted derivatives. pyridines An azole that includes only one N atom and no other heteroatom as a part of the aromatic skeleton. pyrroles A nitrogen molecular entity that is electronically neutral but which contains a quaternary nitrogen. quaternary nitrogen compound Any aromatic carboxylic acid that contains a quinoline moiety that is substituted by one carboxy substituent. quinolinemonocarboxylic acid A class of aromatic heterocyclic compounds each of which contains a benzene ring ortho fused to carbons 2 and 3 of a pyridine ring. quinolines rifamycins An amino acid derivative resulting from reaction of serine at the amino group or the carboxy group, or from the replacement of any hydrogen of serine by a heteroatom. The definition normally excludes peptides containing serine residues. serine derivative A monohydroxybenzoic acid consisting of 5-aminosalicylic acid (mesalazine) linked to 4-aminobenzoyl-beta-alanine via an azo bond. balsalazide A penicillin in which the substituent at position 6 of the penam ring is a 2-amino-2-(4-hydroxyphenyl)acetamido group. Amx CHEBI:133770 amoxicillin steroid antibiotic streptomycins Any sulfur molecular entity that involves either covalently bonded or anionic sulfur. sulfide sulfur molecular entity A tertiary alcohol is a compound in which a hydroxy group, -OH, is attached to a saturated carbon atom which has three other carbon atoms attached to it. tertiary alcohol A subclass of polyketides having an octahydrotetracene-2-carboxamide skeleton, substituted with many hydroxy and other groups. tetracyclines Any oxacycle having an oxolane (tetrahydrofuran) skeleton. oxolanes Compounds containing at least one thiophene ring. thiophenes An organic tricyclic compound in which at least one of the rings of the tricyclic skeleton contains one or more heteroatoms. organic heterotricyclic compound A chemical compound containing three hydroxy groups. triol organic heterobicyclic compound A neutral compound having formal unit electrical charges of opposite sign on non-adjacent atoms. Sometimes referred to as inner salts, dipolar ions (a misnomer). zwitterion An aminobenzoic acid that is salicylic acid substituted by an amino group at position 4. PAS CHEBI:1789 CHEBI:20320 CHEBI:41152 4-aminosalicylic acid A member of the class of tetracyclines with formula C22H23ClN2O8 isolated from Streptomyces aureofaciens. CHEBI:23164 CHEBI:3653 chlortetracycline CHEBI:22218 CHEBI:2446 actinomycin D An aminoglycoside that is 2-deoxystreptamine that is substituted on the oxygen at position 4 by an (8R)-2-amino-8-O-(4-amino-4-deoxy-alpha-D-glucopyranosyl)-2,3,7-trideoxy-7-(methylamino)-D-glycero-alpha-D-allo-octodialdo-1,5:8,4-dipyranos-1-yl) group. CHEBI:40708 apramycin An organonitrogen heterocyclic antibiotic that contains a beta-lactam ring. CHEBI:10427 CHEBI:22844 beta-lactam antibiotic A complex glycopeptide from Streptomyces orientalis. It inhibits a specific step in the synthesis of the peptidoglycan layer in the Gram-positive bacteria Staphylococcus aureus and Clostridium difficile. CHEBI:27276 CHEBI:49941 CHEBI:9931 vancomycin A member of the class of rifamycins that is a a semisynthetic antibiotic derived from Amycolatopsis rifamycinica (previously known as Amycolatopsis mediterranei and Streptomyces mediterranei). Rif CHEBI:26577 CHEBI:45308 CHEBI:8858 rifampicin The conjugate base of loracarbef. loracarbef anion A coumarin-derived antibiotic obtained from Streptomyces niveus. CHEBI:25597 CHEBI:44505 CHEBI:7644 novobiocin CHEBI:26080 CHEBI:8168 phosphorus atom A amino cyclitol glycoside that is kanamycin B lacking the 3-hydroxy substituent from the 2,6-diaminoglucose ring. CHEBI:19849 CHEBI:45933 CHEBI:9610 tobramycin A glycophospholipid antibiotic compound with the lipid portion conjugated to a pentasaccharide fraction via a phosphate linkage. CHEBI:25360 CHEBI:5075 bambermycin A phosphonic acid having an (R,S)-1,2-epoxypropyl group attached to phosphorus. CHEBI:24100 CHEBI:42503 CHEBI:8159 fosfomycin Any sugar having one or more alcoholic hydroxy groups replaced by substituted or unsubstituted amino groups. CHEBI:22481 CHEBI:22530 CHEBI:2662 amino sugar A penicillin in which the substituent at position 6 of the penam ring is a 2-amino-2-phenylacetamido group. CHEBI:22536 CHEBI:2683 CHEBI:40648 CHEBI:45042 ampicillin A third-generation cephalosporin compound having 2-(2-amino-1,3-thiazol-4-yl)-2-(methoxyimino)acetylamino and [(2-methyl-5,6-dioxo-1,2,5,6-tetrahydro-1,2,4-triazin-3-yl)sulfanyl]methyl side-groups. CHEBI:23059 CHEBI:3513 CHEBI:446214 ceftriaxone A steroid antibiotic that is isolated from the fermentation broth of Fusidium coccineum. CHEBI:24133 CHEBI:42742 CHEBI:5201 fusidic acid The conjugate base formed when the carboxy group of a carboxylic acid is deprotonated. CHEBI:13626 CHEBI:13945 CHEBI:23026 CHEBI:58657 carboxylic acid anion A carboxamide derived from a monocarboxylic acid. CHEBI:13211 CHEBI:22207 CHEBI:25383 CHEBI:6977 monocarboxylic acid amide A macrolide antibiotic useful for the treatment of bacterial infections. CHEBI:46596 azithromycin A complex glycopeptide antibiotic that is isolated from Amycolatopsis orientalis. chloroeremomycin A semisynthetic penicillin having a 6beta-{(2R)-2-[(2-oxoimidazolidine-1-carbonyl)amino]-2-phenylacetyl}amino side-group. It is an antibiotic used in treating infections caused by Pseudomonas aeruginosa, Escherichia coli and Haemophilus influenzae. CHEBI:63225 azlocillin CHEBI:42746 GE2270A A twelve-membered macrolide antibiotic that is biosynthesised by Streptomyces venezuelae. methymycin A macrolide antibiotic that is narbonolide having a 3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-hexopyranosyl residue attached at position 6. It is biosynthesised by Streptomyces venezuelae. CHEBI:44624 narbomycin A macrolide antibiotic that is biosynthesised by Streptomyces venezuelae. pikromycin Pulvomycin A member of the class of rifamycins that exhibits antibiotic and antitubercular properties. rifamycin SV CHEBI:46029 telithromycin A heterodetic cyclic peptide, in which the cyclisation step involves a formal lactonisation between the carboxy group of a quinaldic acid-based residue and a secondary alcohol. An antibiotic that inhibits bacterial protein synthesis. Also acts as an antitumor agent. thiostrepton Valnemulin A compound in which a hydroxy group, -OH, is attached to a saturated carbon atom. CHEBI:13804 CHEBI:22288 CHEBI:2553 alcohol CHEBI:165316 CHEBI:357107 CHEBI:41102 CHEBI:653800 bleomycin A2 Any organic amino compound that is a derivative of ethylenediamine. ethylenediamine derivative A macrolide antibiotic produced by certain strains of Streptomyces narbonensis var. josamyceticus. josamycin A macrolide antibiotic produced by Streptomyces kitasatoensis, showing activity against a wide spectrum of pathogens. leucomycin V A fluoroquinolone antibiotic that is 4-oxo-1,4-dihydroquinoline which is substituted at positions 1, 3, 6, 7 and 8 by 2-fluoroethyl, carboxy, fluoro, 4-methylpiperazin-1-yl and fluoro groups, respectively. It is active against many Gram-positive and Gram-negative bacteria. fleroxacin Pto CHEBI:93717 Prothionamide thiamphenicol calcium sulfate dihydrate Any cyclic ether in which the oxygen atom forms part of a 3-membered ring. CHEBI:13828 CHEBI:23930 CHEBI:4812 epoxide An amide is a derivative of an oxoacid RkE(=O)l(OH)m (l =/= 0) in which an acidic hydroxy group has been replaced by an amino or substituted amino group. CHEBI:22473 CHEBI:2633 amide oxoacid derivative An organic fundamental parent is a structure used as a basis for substitutive names in organic nomenclature, containing, in addition to one or more hydrogen atoms, a single atom of an element, a number of atoms (alike or different) linked together to form an unbranched chain, a monocyclic or polycyclic ring system, or a ring assembly or ring/chain system. organic fundamental parent A chemical entity constituting the smallest component of an element having the chemical properties of the element. CHEBI:22671 CHEBI:23907 atom A derivative of an oxoacid RkE(=O)l(OH)m (l =/= 0) in which an acidic hydroxy group has been replaced by an amino or substituted amino group. primary amide A derivative of two oxoacids RkE(=O)l(OH)m (l =/= 0) in which two acyl groups are attached to the amino or substituted amino group. secondary amide A molecular entity all atoms of which have the same atomic number. elemental molecular entity An organosulfur compound is a compound containing at least one carbon-sulfur bond. CHEBI:23010 CHEBI:25714 organosulfur compound elemental oxygen diatomic oxygen An anion consisting of more than one atom. polyatomic anion A substance that kills or slows the growth of microorganisms, including bacteria, viruses, fungi and protozoans. CHEBI:22582 antimicrobial agent A heteroorganic entity is an organic molecular entity in which carbon atoms or organic groups are bonded directly to one or more heteroatoms. heteroorganic entity food role A physiological role played by any substance of either plant, animal or artificial origin which contains essential body nutrients that can be ingested by an organism to provide energy, promote growth, and maintain the processes of life. food An alkaline earth molecular entity is a molecular entity containing one or more atoms of an alkaline earth metal. alkaline earth molecular entity Any p-block element atom that is in group 15 of the periodic table: nitrogen, phosphorus, arsenic, antimony and bismuth. pnictogen A p-block molecular entity containing any pnictogen. pnictogen molecular entity Any p-block molecular entity containing a chalcogen. chalcogen molecular entity An ester of a carboxylic acid, R(1)C(=O)OR(2), where R(1) = H or organyl and R(2) = organyl. CHEBI:13204 CHEBI:23028 CHEBI:3408 carboxylic ester An atom belonging to one of the main groups (found in the s- and p- blocks) of the periodic table. main group element atom organoarsenic compound sulfur oxoacid derivative nitrogen oxoanion pnictogen oxoanion sulfonic acid derivative Any main group element atom belonging to the p-block of the periodic table. p-block element atom Any member of class of 1,2-di-O-acylglycerols joined at oxygen 3 by a glycosidic linkage to a carbohydrate part (usually a mono-, di- or tri-saccharide). Some substances classified as bacterial glycolipids have the sugar part acylated by one or more fatty acids and the glycerol part may be absent. CHEBI:24393 CHEBI:5476 glycolipid A carbon oxoacid acid carrying at least one -C(=O)OH group and having the structure RC(=O)OH, where R is any any monovalent functional group. Carboxylic acids are the most common type of organic acid. CHEBI:13428 CHEBI:13627 CHEBI:23027 carboxylic acid A molecular entity containing one or more atoms from any of groups 1, 2, 13, 14, 15, 16, 17, and 18 of the periodic table. main group molecular entity carbon group molecular entity Any molecule that consists of a series of atoms joined together to form a ring. cyclic compound A cyclic compound having as ring members atoms of the same element only. homocyclic compound A homocyclic compound in which all of the ring members are carbon atoms. carbocyclic compound hydrogen molecular entity polycyclic compound A molecule that features two fused rings. bicyclic compound A cyclically conjugated molecular entity with a stability (due to delocalization) significantly greater than that of a hypothetical localized structure (e.g. Kekule structure) is said to possess aromatic character. aromatic compound organic aromatic compound monocyclic compound heteromonocyclic compound A polycyclic compound in which at least one of the rings contains at least one non-carbon atom. heteropolycyclic compound A bicyclic compound in which at least one of the rings contains at least one skeletal heteroatom. heterobicyclic compound An s-block molecular entity is a molecular entity containing one or more atoms of an s-block element. s-block molecular entity A main group molecular entity that contains one or more atoms of a p-block element. p-block molecular entity Hydrides are chemical compounds of hydrogen with other chemical elements. hydrides A macromolecule formed by a living organism. biomacromolecule information biomacromolecule A macromolecule made up of nucleotide units and hydrolysable into certain pyrimidine or purine bases (usually adenine, cytosine, guanine, thymine, uracil), D-ribose or 2-deoxy-D-ribose and phosphoric acid. nucleic acid High molecular weight, linear polymers, composed of nucleotides containing ribose and linked by phosphodiester bonds; RNA is central to the synthesis of proteins. ribonucleic acid An amino acid in which the amino group is located on the carbon atom at the position alpha to the carboxy group. CHEBI:10208 CHEBI:13779 CHEBI:22442 CHEBI:2642 alpha-amino acid A carboxylic acid containing one or more amino groups. CHEBI:13815 CHEBI:22477 amino acid CAP Cm capreomycin An organic compound having at least one hydroxy group attached to a carbon atom. CHEBI:64710 organic hydroxy compound Any organic molecule that consists of atoms connected in the form of a ring. organic cyclic compound A heterocyclic compound formally derived from an arene by replacement of one or more methine (-C=) and/or vinylene (-CH=CH-) groups by trivalent or divalent heteroatoms, respectively, in such a way as to maintain the continuous pi-electron system characteristic of aromatic systems and a number of out-of-plane pi-electrons corresponding to the Hueckel rule (4n+2). heteroarene benzenoid aromatic compound An N-glycosyl compound that has both a nucleobase, normally adenine, guanine, xanthine, thymine, cytosine or uracil, and either a ribose or deoxyribose as functional parents. CHEBI:13661 CHEBI:25611 CHEBI:7647 nucleoside A macromolecule is a molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. macromolecule Organic aromatic compounds having one or more hydroxy groups attached to a benzene or other arene ring. CHEBI:13664 CHEBI:13825 CHEBI:25969 CHEBI:2857 phenols An amino acid whose structure includes an aromatic ring. CHEBI:13820 CHEBI:22623 CHEBI:2835 aromatic amino acid Any carboxylic acid in which the carboxy group is directly bonded to an aromatic ring. CHEBI:13817 CHEBI:13821 CHEBI:2830 aromatic carboxylic acid An amino compound in which the amino group is linked directly to an aromatic system. CHEBI:13827 CHEBI:22622 CHEBI:22646 CHEBI:2834 CHEBI:2863 aromatic amine A penicillin antibiotic having a 6beta-2-carboxy-2-phenylacetamido side-chain. carbenicillin halide salt A cephalosporin bearing chloro and (R)-2-amino-2-phenylacetamido groups at positions 3 and 7, respectively, of the cephem skeleton. CHEBI:472656 cefaclor A cephalosporin bearing methyl and (2R)-2-amino-2-(4-hydroxyphenyl)acetamido groups at positions 3 and 7, respectively, of the cephem skeleton. cefadroxil A cephalosporin compound having (R)-mandelamido and N-methylthiotetrazole side-groups. cefamandole A cephalosporin compound having 7beta-2-(2-amino-thiazol-4-yl)-2-[(Z)-hydroxyimino]-acetylamino- and 3-vinyl side groups. CHEBI:184624 cefdinir A second-generation cephalosporin antibiotic having N(1)-methyltetrazol-5-ylthiomethyl, {[(cyanomethyl)sulfanyl]acetyl}amino and methoxy side-groups at positions 3, 7beta and 7alpha respectively of the parent cephem bicyclic structure. cefmetazole A cephalosporin bearing {[1-(sulfomethyl)-1H-tetrazol-5-yl]sulfanyl}methyl and (R)-2-hydroxy-2-phenylacetamido groups at positions 3 and 7, respectively, of the cephem skeleton. cefonicid A semi-synthetic parenteral cephalosporin with a tetrazolyl moiety that confers beta-lactamase resistance. CHEBI:258120 cefoperazone Any of the glycopeptides whose structure consists of teicoplanin A3-1 in which the hydroxy group of the di(aryloxy)-substituted phenol moiety has been converted to the corresponding 2-acylamino-2-deoxy-beta-D-glucoside. Members of the class differ only in the nature of the acyl group. teicoplanin A2 A teicoplanin A2 that has decanoyl as the variable N-acyl group. teicoplanin A2-3 A third-generation cephalosporin antibiotic with methoxymethyl and (2Z)-2-(2-amino-1,3-thiazol-4-yl)-2-(methoxyimino)acetamino substituents at positions 3 and 7, respectively, of the cephem skeleton. Given by mouth as its proxetil ester prodrug, it is used to treat acute otitis media, pharyngitis, and sinusitis. CHEBI:606443 cefpodoxime A semisynthetic, second-generation cephalosporin, with prop-1-enyl and (R)-2-amino-2-(4-hydroxyphenyl)acetamido groups at positions 3 and 7, respectively, of the cephem skeleton. It is used to treat bronchitis as well as ear, skin and other bacterial infections. cefprozil A third-generation cephalosporin antibiotic bearing pyridinium-1-ylmethyl and {[(2Z)-2-(2-amino-1,3-thiazol-4-yl)-2-{[(2-carboxypropan-2-yl)oxy]imino}acetamido groups at positions 3 and 7, respectively, of the cephem skeleton. ceftazidime A third-generation cephalosporin antibiotic with a [(2Z)-2-(2-amino-1,3-thiazol-4-yl)-4-carboxybut-2-enoyl]amino substituent at the 7 position of the cephem skeleton. An orally-administered agent, ceftibuten is used as the dihydrate to treat urinary-tract and respiratory-tract infections. CHEBI:554578 ceftibuten calcium salt A depsipeptide in which the amino and hydroxy carboxylic acid residues are connected in a ring. cyclodepsipeptide A glycosyl compound arising formally from the elimination of water from a glycosidic hydroxy group and a S atom bound to a carbon atom, thus creating a C-S bond. CHEBI:22048 CHEBI:33577 S-glycosyl compound Neutral molecules having charge-separated forms with an onium atom which bears no hydrogen atoms and that is not adjacent to the anionic atom. onium betaine iminium betaine A polyclic compound in which all of the ring members are carbon atoms. carbopolycyclic compound homopolycyclic compound hexoside A semisynthetic first-generation cephalosporin antibiotic having methyl and beta-(2R)-2-amino-2-phenylacetamido groups at the 3- and 7- of the cephem skeleton, respectively. It is effective against both Gram-negative and Gram-positive organisms, and is used for treatment of infections of the skin, respiratory tract and urinary tract. cephalexin Any of naturally occurring compounds and synthetic analogues, based on the cyclopenta[a]phenanthrene carbon skeleton, partially or completely hydrogenated; there are usually methyl groups at C-10 and C-13, and often an alkyl group at C-17. By extension, one or more bond scissions, ring expansions and/or ring contractions of the skeleton may have occurred. Natural steroids are derived biogenetically from squalene which is a triterpene. CHEBI:13687 CHEBI:26768 CHEBI:9263 steroid CHEBI:24748 CHEBI:5814 hydroxy steroid Any heteroorganic entity containing at least one carbon-nitrogen bond. organonitrogen compound An amide of a sulfonic acid RS(=O)2NR'2. sulfonamide Compounds derived from oxoacids RkE(=O)l(OH)m (l =/= 0) by replacing -OH by -NRNR2 (R groups are commonly H). (IUPAC). hydrazide A hydrazide consisting of hydrazine carrying one or more carboacyl groups. carbohydrazide An oxoanion is an anion derived from an oxoacid by loss of hydron(s) bound to oxygen. CHEBI:33274 CHEBI:33436 oxoanion Any glucoside in which the glycoside group is derived from D-glucose. CHEBI:21009 CHEBI:4173 D-glucoside A first-generation cephalosporin antibiotic with a methyl substituent at position 3, and a (2R)-2-amino-2-cyclohexa-1,4-dien-1-ylacetamido substituent at position 7, of the cephem skeleton. cephradine Any fluoroarene that is a benzene or a substituted benzene carrying at least one fluoro group. fluorobenzenes An addition compound contains two or more simpler compounds that can be packed in a definite ratio into a crystal. The term covers donor-acceptor complexes (adducts) and a variety of lattice compounds. addition compound An addition compound that contains water in weak chemical combination with another compound. hydrate natural product fundamental parent A cephalosporin with ({1-[2-(dimethylamino)ethyl]-1H-tetrazol-5-yl}sulfanyl)methyl and (2-amino-1,3-thiazol-4-yl)acetamido substituents at positions 3 and 7, respectively, of the cephem skeleton. A third generation beta-lactam cephalosporin antibiotic, it is active against a broad spectrum of both Gram positive and Gram negative bacteria. cefotiam heterocyclic organic fundamental parent Any molecular entity that consists of a ring having (formally) the maximum number of noncumulative double bonds. mancude ring mancude organic heterocyclic parent organic mancude parent carbon oxoacid Any ether in which the oxygen is attached to at least one aryl substituent. aromatic ether A lactam in which the amide bond is contained within a four-membered ring, which includes the amide nitrogen and the carbonyl carbon. CHEBI:10426 CHEBI:13203 CHEBI:22845 beta-lactam A secondary alcohol is a compound in which a hydroxy group, -OH, is attached to a saturated carbon atom which has two other carbon atoms attached to it. CHEBI:13425 CHEBI:13686 CHEBI:26617 CHEBI:58662 CHEBI:8741 CHEBI:9077 secondary alcohol An azole in which the five-membered heterocyclic aromatic skeleton contains four N atoms and one C atom. tetrazoles Any carboxylic acid containing two carboxy groups. CHEBI:23692 CHEBI:36172 CHEBI:4501 dicarboxylic acid A compound formally derived from an oxoacid RkE(=O)l(OH)m (l > 0) and an alcohol, phenol, heteroarenol, or enol by linking with formal loss of water from an acidic hydroxy group of the former and a hydroxy group of the latter. CHEBI:23960 CHEBI:4859 ester A compound having a nitro group, -NO2 (free valence on nitrogen), which may be attached to carbon, nitrogen (as in nitramines), or oxygen (as in nitrates), among other elements (in the absence of specification, C-nitro compounds are usually implied). nitro compound A nitro compound having the nitro group (-NO2) attached to a carbon atom. C-nitro compound An azole in which the five-membered heterocyclic aromatic skeleton contains three N atoms and two C atoms. triazoles liposaccharide A carboxylic acid anion formed when the carboxy group of a monocarboxylic acid is deprotonated. CHEBI:13657 CHEBI:25382 CHEBI:3407 monocarboxylic acid anion An azole based on a five-membered heterocyclic aromatic skeleton containing one N and one O atom. oxazole An organosulfur compound having the structure RS(=O)2R (R =/= H). sulfone Any monocarboxylic acid having at least one additional oxo functional group. oxo monocarboxylic acid imidazopyrimidine A steroid ester obtained by formal condensation of the carboxy group of any carboxylic acid with the 3-hydroxy group of a sterol. CHEBI:13220 CHEBI:15115 CHEBI:26770 CHEBI:26772 CHEBI:9268 CHEBI:9269 sterol ester A polycyclic compound in which two rings have two or more atoms in common. bridged compound Compound comprising a beta-lactam ring fused to a saturated 5-membered ring containing one sulfur atom. penam Natural and synthetic antibiotics containing the 4-thia-1-azabicyclo[3.2.0]heptan-7-one structure, generally assumed to have the 5R configuration unless otherwise specified. penams A biological macromolecule minimally consisting of one polypeptide chain synthesized at the ribosome. CHEBI:13677 CHEBI:14911 protein organic chloride salt Any molecular entity consisting of more than one atom. polyatomic entity An ion consisting of more than one atom. polyatomic ion phosphorus oxoacid derivative phosphorus oxoacids and derivatives alkaline earth salt mancude organic heterotricyclic parent A polycyclic heteroarene that is anthracene in which one of the central CH groups is replaced by a nitrogen atom. acridine Any compound containing the carbonyl group, C=O. The term is commonly used in the restricted sense of aldehydes and ketones, although it actually includes carboxylic acids and derivatives. carbonyl compound Organic compounds containing an oxygen atom, =O, doubly bonded to carbon or another element. organic oxo compound An organochlorine compound is a compound containing at least one carbon-chlorine bond. organochlorine compound heterotricyclic compound Any member of the class of quinolines in which the quinoline skeleton is substituted by one or more amino or substituted-amino groups. aminoquinoline A bicyclic compound in which all the ring atoms are carbon. carbobicyclic compound A salt formally resulting from the reaction of hydrochloric acid with an organic base. hydrochloride O-organyl oximes R2C=NOR' (R' =/= H). oxime O-ether Any hydroxy steroid carrying a hydroxy group at position 3. 3-hydroxy steroid A 3-hydroxy steroid in which the 3-hydroxy substituent is in the alpha-position. CHEBI:71194 3alpha-hydroxy steroid 11-hydroxy steroid inorganic ion An organochalcogen compound is a compound containing at least one carbon-chalcogen bond. organochalcogen compound An organochalcogen compound containing at least one carbon-oxygen bond. organooxygen compound A compound containing at least one carbon-bromine bond. organobromine compound An organofluorine compound is a compound containing at least one carbon-fluorine bond. organofluorine compound A member of the class of cinnolines that is 6,7-methylenedioxycinnolin-4(1H)-one bearing an ethyl group at position 1 and a carboxylic acid group at position 3. An analogue of oxolinic acid, it has similar antibacterial actions. It was formerly used for the treatment of urinary tract infections. CHEBI:314701 cinoxacin organic hydride The 6-O-methyl ether of erythromycin A, clarithromycin is a macrolide antibiotic used in the treatment of respiratory-tract, skin and soft-tissue infections. It is also used to eradicate Helicobacter pylori in the treatment of peptic ulcer disease. It prevents bacteria from growing by interfering with their protein synthesis. Clr CHEBI:41676 CHEBI:442148 CHEBI:670147 clarithromycin Any ether in which the oxygen atom forms part of a ring. CHEBI:37406 cyclic ether A carbohydrate-containing antibiotic that is the semisynthetic derivative of lincomycin, a natural antibiotic. CHEBI:47331 clindamycin 3-Isopropylimino-3,5-dihydro-phenazine in which the hydrogen at position 5 is substituted substituted by a 4-chlorophenyl group, and that at position 2 is substituted by a (4-chlorophenyl)amino group. A dark red crystalline solid, clofazimine is an antimycobacterial and is one of the main drugs used for the treatment of multi-bacillary leprosy. However, it can cause red/brown discolouration of the skin, so other treatments are often preferred in light-skinned patients. Cfz CHEBI:355347 clofazimine A molecular entity consisting of two or more chemical elements. heteroatomic molecular entity Any heteroatomic molecular entity that is a chemical compound of halogen with other chemical elements. halide An amide of a carboxylic acid, having the structure RC(=O)NR2. The term is used as a suffix in systematic name formation to denote the -C(=O)NH2 group including its carbon atom. CHEBI:35354 CHEBI:35355 carboxamide Any imide in which the acyl substituents are any two from carboacyl, sulfonyl and phosphoryl mixed diacylamine CHEBI:26019 phosphoric ester organic phosphoramidate Any coumarin carrying at least one hydroxy substituent. CHEBI:24691 CHEBI:24692 hydroxycoumarin A kanamycin that is kanamycin B bearing an N-(2S)-4-amino-2-hydroxybutyryl group on the aminocyclitol ring. arbekacin An amino cyclitol glycoside that is L-chiro-inositol in which the hydroxy groups at positions 1, 4, and 6 are replaced by aminoacetyl)methylamino, amino, and methoxy groups, respectively, and in which the hydroxy group at position 3 is converted to the corresponding 2,6-diamino-2,3,4,6,7-pentadeoxy-beta-L-lyxo-heptopyranoside. The major component of fortimicin, obtained from Micromonospora olivasterospora. It is administered (as the sulfate salt) by intramuscular injection or intravenous infusion for the treatment of severe systemic infections due to sensitive Gram-negative organisms. astromicin A kanamycin that is kanamycin B lacking the 3- and 4-hydroxy groups on the 2,6-diaminosugar ring. dibekacin A carbopolyclic compound comprising of three carbocyclic rings. carbotricyclic compound heteroarenecarboxylate ester thiadiazoles Any organonitrogen compound containing a cyclic component with nitrogen and at least one other element as ring member atoms. organonitrogen heterocyclic compound Compounds based on a triazine skeleton. triazines Any organic heterocyclic compound containing at least one ring oxygen atom. oxacycle organosulfur heterocyclic compound Cyclic hemiacetals formed by intramolecular addition of a hydroxy group to an aldehydic or ketonic carbonyl group. They are thus 1-oxacycloalkan-2-ols or unsaturated analogues. lactol organic heterotetracyclic compound CHEBI:25429 CHEBI:38075 organic heteropolycyclic compound monocyclic heteroarene polycyclic heteroarene Any of a class of heterocyclic amines having a saturated five-membered ring. CHEBI:26922 CHEBI:38191 pyrrolidines imidazolidines azabicycloalkane diazolidine cephem Any organic heterocyclic compound containing a benzene ring in which two of the C-H fragments have been replaced by isolobal nitrogens (the diazine parent structure). diazines pyrazines oxazolidines The 10-methochloride salt of 3,6-diaminoacridine. Note that a mixture of this compound with 3,6-diaminoacridine (proflavine) is known as acriflavine or neutral acriflavine. 3,6-diamino-10-methylacridinium chloride CHEBI:26949 CHEBI:38417 1,3-thiazoles 1-benzopyran chromenone Compounds having the structure R2C=NNR2, formally derived from aldehydes or ketones by replacing =O by =NNH2 (or substituted analogues). hydrazone Any member of the class of fluorobenzenes containing a mono- or poly-substituted benzene ring carrying two fluorine atoms. difluorobenzene Any organic heteropolycyclic compound based on the 1,2-diaza analogue of naphthalene and its substituted derivatives. cinnolines Any compound containing morpholine as part of its structure. morpholines A hydroxycoumarin antibiotic that is obtained from Streptomyces rishiriensis and exhibits potent antibacterial and anticancer activity. coumermycin A1 Any organonitrogen heterocyclic compound based on a phenazine skeleton and derivatives. phenazines dibenzopyridine naphthofuran Any compound with a 1,2,4-triazine skeleton, in which nitrogen atoms replace carbon at positions 1, 2 and 4 of the core benzene ring structure. 1,2,4-triazines Any compound having a pyrimidine as part of its structure. CHEBI:13681 CHEBI:26448 pyrimidines cyclic ketone A 4-amino-1,2-oxazolidin-3-one that has R configuration. It is an antibiotic produced by Streptomyces garyphalus or S. orchidaceus and is used as part of a multi-drug regimen for the treatment of tuberculosis when resistance to, or toxicity from, primary drugs has developed. An analogue of D-alanine, it interferes with bacterial cell wall synthesis in the cytoplasm by competitive inhibition of L-alanine racemase (which forms D-alanine from L-alanine) and D-alanine--D-alanine ligase (which incorporates D-alanine into the pentapeptide required for peptidoglycan formation and bacterial cell wall synthesis). CYC Cs CHEBI:4030 D-cycloserine Meropenem in which the one of the two methyl groups attached to the amide nitrogen is replaced by hydrogen while the other is replaced by a 3-carboxyphenyl group. The sodium salt is used for the treatment of moderate to severe susceptible infections including intra-abdominal and acute gynaecological infections, pneumonia, and infections of the skin and of the urinary tract. CHEBI:471574 ertapenem A macrolide that is pristinamycin IIA in which the double bond between positions 26 and 26a of the pyrroline ring has been reduced and position 26R carries a [2-(diethylamino)ethyl]sulfonyl group. It is a semi-synthetic streptogramin antibiotic and often used as a mixture with quinupristin for the treatment of vancomycin-resistant Enterococcus faecium. CHEBI:42127 dalfopristin A carbapenemcarboxylic acid in which the azetidine and pyrroline rings carry 1-hydroxymethyl and in which the azetidine and pyrroline rings carry 1-hydroxymethyl and 5-(dimethylcarbamoyl)pyrrolidin-3-ylthio substituents respectively. meropenem Propylphosphonic acid in which one of the hydrogens at position 3 is substituted by a formyl(hydroxy)amino group. An antibiotic obtained from Streptomyces lavendulae, it specifically inhibits DXP reductoisomerase (EC 1.1.1.267), a key enzyme in the non-mevalonate pathway of isoprenoid biosynthesis. CHEBI:42526 fosmidomycin Destomysin A penicillin that is 6-aminopenicillanic acid in which one of the amino hydrogens is replaced by a 3-(2,6-dichlorophenyl)-5-methyl-1,2-oxazol-4-yl]formyl group. dicloxacillin An amino cyclitol glycoside that is 4,6-diaminocyclohexane-1,2,3-triol having a 2,6-diamino-2,6-dideoxy-alpha-D-glucosyl residue attached at position 1 and a beta-D-ribosyl residue attached at position 2. It is an antibiotic produced by Streptomyces ribosidificus (formerly S. thermoflavus). ribostamycin pyrazinamide A monocarboxylic acid amide resulting from the formal condensation of the carboxy group of pyrazinoic acid (pyrazine-2-carboxylic acid) with ammonia. A prodrug for pyrazinoic acid, pyrazinecarboxamide is used as part of multidrug regimens for the treatment of tuberculosis. Pza CHEBI:45281 CHEBI:8656 pyrazinecarboxamide CHEBI:45364 CHEBI:8857 rifabutin The class of beta-lactam antibiotics that whose members have a carbapenem skeleton which is variously substituted at positions 3, 4, and 6. carbapenems carbapenemcarboxylic acid pyrrolidinecarboxamide 1,3-oxazoles N-alkylpiperazine N-iminopiperazine N-arylpiperazine A compound consisting of a peptide with attached lipid. lipopeptide N-methylpiperazine Any organic heteromonocyclic compoundthat is oxane or its substituted derivatives. oxanes oxazinane tetrahydrofuranol dihydroxytetrahydrofuran double-stranded DNA A broad-spectrum, intravenous beta-lactam antibiotic of the carbapenem subgroup. CHEBI:5879 imipenem A third-generation cephalosporin antibiotic bearing vinyl and (2Z)-2-(2-amino-1,3-thiazol-4-yl)-2-[(carboxymethoxy)imino]acetamido groups at positions 3 and 7, respectively, of the cephem skeleton. It is used in the treatment of gonorrhoea, tonsilitis, pharyngitis, bronchitis, and urinary tract infections. CHEBI:3487 cefixime The hemi-aminal resulting from the condensation of the erythromycin derivative (9S)-erythromycyclamine with 2-(2-methoxyethoxy)acetaldehyde. As the oxazine ring containing the hemi-aminal group is unstable under both acidic and alkaline conditions, dirithromycin functions as a more lipid-soluble prodrug for (9S)-erythromycyclamine. Administered as enteric coated tablets to protect it from acid catalysed hydrolysis in the stomach, it is used to treat respiratory tract, skin, and soft tissue infections caused by susceptible organisms. dirithromycin A first-generation cephalosporin compound having [(5-methyl-1,3,4-thiadiazol-2-yl)sulfanyl]methyl and (1H-tetrazol-1-ylacetyl)amino side-groups at positions 3 and 7 respectively. CHEBI:3482 cefazolin Any carboxylic ester where the carboxylic acid component is acetic acid. CHEBI:13244 CHEBI:13799 CHEBI:22189 CHEBI:2406 acetate ester aminoglycoside A cephalosporin bearing (1-methylpyrrolidinium-1-yl)methyl and (2Z)-2-(2-amino-1,3-thiazol-4-yl)-2-(methoxyimino)acetamido groups at positions 3 and 7, respectively, of the cephem skeleton. CHEBI:3486 CHEBI:473919 cefepime CHEBI:26762 steroid ester CHEBI:13600 CHEBI:1619 CHEBI:35949 3-oxo monocarboxylic acid Any steroid substituted by at least one carboxy group. steroid acid Any primary amide having its amide oxygen replaced by sulfur. thiocarboxamide An ethylenediamine derivative that is ethane-1,2-diamine in which one hydrogen attached to each of the nitrogens is sutstituted by a 1-hydroxybutan-2-yl group (S,S-configuration). It is a bacteriostatic antimycobacterial drug, effective against Mycobacterium tuberculosis and some other mycobacteria. It is used (as the dihydrochloride salt) in combination with other antituberculous drugs in the treatment of pulmonary and extrapulmonary tuberculosis; resistant strains of M. tuberculosis are readily produced if ethambutol is used alone. E ETB Emb CHEBI:133410 CHEBI:659237 CHEBI:678172 ethambutol The conjugate base of clavulanic acid. clavulanate gypsum Semisynthetic derivative of erythromycin A. roxithromycin A thiocarboxamide that is pyridine-4-carbothioamide substituted by an ethyl group at position 2. A prodrug that undergoes metabolic activation by conversion to the corresponding S-oxide. ETH Eto ethionamide An azole in which the five-membered heterocyclic aromatic skeleton contains a N atom and one S atom. thiazoles erythromycin derivative Antibiotic isolated from Streptomyces clavuligerus. It acts as a suicide inhibitor of bacterial beta-lactamase enzymes. CHEBI:3736 CHEBI:43442 clavulanic acid substituted aniline carbocyclic antibiotic A semisynthetic penicillin antibiotic carrying a 3-(2-chlorophenyl)-5-methylisoxazole-4-carboxamido group at position 6. CHEBI:3765 CHEBI:49565 cloxacillin A compound formally derived from ammonia by replacing one, two or three hydrogen atoms by organyl groups. organic amino compound A quinolone that is 4-oxo-1,4-dihydroquinoline which is substituted at positions 1, 3, 6 and 7 by ethyl, carboxy, fluorine, and 4-methylpiperazin-1-yl groups, respectively. pefloxacin Monocyclic, bacterially produced or semisynthetic beta-lactam antibiotic. It lacks the double ring construction of the traditional beta-lactam antibiotics and can be easily synthesized. monobactam Any molecular entity that contains carbon. CHEBI:25700 CHEBI:33244 organic molecular entity azaarene azabicycloalkene Compounds with structure RAs=AsR. diarsenes A penicillin compound having a 6beta-[3-(2-chloro-6-fluorophenyl)-5-methyl-1,2-oxazole-4-carboxamido] side-chain. flucloxacillin A compound formally derived from ammonia by replacing one hydrogen atom by an organyl group. primary amino compound A compound formally derived from ammonia by replacing two hydrogen atoms by organyl groups. secondary amino compound A compound formally derived from ammonia by replacing three hydrogen atoms by organyl groups. tertiary amino compound A cyclic compound containing nine or more atoms as part of the cyclic system. macrocycle organic halide salt CHEBI:25556 CHEBI:7594 nitrogen molecular entity An organic molecule that is electrically neutral carrying a positive and a negative charge in one of its major canonical descriptions. In most dipolar compounds the charges are delocalized; however the term is also applied to species where this is not the case. dipolar compound Cyclopropane and its derivatives formed by substitution. cyclopropanes An alpha,beta-unsaturated ketone of general formula R(1)R(2)C=CR(3)-C(=O)R(4) (R(4) =/= H) in which the C=O function is conjugated to a C=C double bond at the alpha,beta position. enone A ketone of general formula R(1)R(2)C=CR(3)-C(=O)R(4) (R(4) =/= H) or R(1)C#C-C(=O)R(2) (R(2) =/= H) in which the ketonic C=O function is conjugated to an unsaturated C-C bond at the alpha,beta position. alpha,beta-unsaturated ketone A carboxylic ester of general formula R(1)R(2)C=CR(3)-C(=O)OR(4) (R(4) =/= H) or R(1)C#C-C(=O)OR(2) (R(2) =/= H) in which the ester C=O function is conjugated to an unsaturated C-C bond at the alpha,beta position. alpha,beta-unsaturated carboxylic ester A monocarboxylic amide of general formula R(1)R(2)C=CR(3)-C(=O)NR(4)R(5) or R(1)C#C-C(=O)NR(2)R(3) in which the amide C=O function is conjugated to an unsaturated C-C bond at the alpha,beta position. alpha,beta-unsaturated carboxylic acid amide An alpha,beta-unsaturated carboxylic acid amide of general formula R(1)R(2)C=CR(3)-C(=O)NR(4)R(5) in which the amide C=O function is conjugated to a C=C double bond at the alpha,beta position. enamide organic heterohexacyclic compound A member of the class of oxazolidines that is 1,3-oxazolidin-2-one in which the hydrogen attached to the nitrogen is replaced by an N-{[(5-nitro-2-furyl)methylene]amino} group. It has antibacterial and antiprotozoal properties, and is used in the treatment of giardiasis and cholera. furazolidone organic polycyclic compound organic tricyclic compound physiological role A compound with the general formula R2C=O (R=/=H) where one or more of the R groups contains an oxy (-O-) group. oxyketone An oxyketone with the general formula R2C(=O) (R=/=H) where one or more of the R groups contains an oxy (-O-) group and the oxy and carbonyl groups are bonded to the same carbon atom. alpha-oxyketone propicillin A monocarboxylic acid that is 4-oxo-1,4-dihydroquinoline-3-carboxylic acid which is substituted on the nitrogen by a cyclopropyl group and at positions 6, 7, and 8 by fluoro, 3-methylpiperazin-1-yl, and methoxy groups, respectively. Gatifloxacin is an antibiotic of the fourth-generation fluoroquinolone family, that like other members of that family, inhibits the bacterial topoisomerase type-II enzymes. CHEBI:101712 gatifloxacin A cyclic macromolecule containing one or more nitrogen atoms in place of carbon either as the divalent group NH for the group CH2 or a single trivalent nitrogen atom for the group CH. azamacrocycle Any organic heterotricyclic compound based on a skeleton comprised of an oxazine ring fused onto a quinoline system. oxazinoquinoline gramicidin S A parenteral third-generation cephalosporin, bearing a 2-(2-amino-1,3-thiazol-4-yl)-2-(methoxyimino)acetyl]amino group at the 7beta-position. CHEBI:112105 CHEBI:3511 ceftizoxime An imidazolidine containing one or more oxo groups. imidazolidinone Oxazoles in which the N and O atoms are adjacent. CHEBI:46813 isoxazoles An oxazolidine containing one or more oxo groups. oxazolidinone Any member of the cephamycin sub-group of cephem antibiotics, differing from cephalosporins in possessing a methoxy group at the 7alpha-position of the cephem nucleus, and in being resistant to beta-lactamase. cephamycin Grepafloxacin A cephalosporin with acetoxymethyl and 2(pyridin-4-ylsulfanyl)acetamido substituents at positions 3 and 7, respectively, of the cephem skeleton. It is used (as its sodium salt) as an antibiotic, being effective against gram-negative and gram-positive organisms. CHEBI:3544 cephapirin Any member of a group of synthetic antibiotics, similar to cephems but with carbon substituted for the sulfur; all possessing an acylated amine functionality at C-6 and (S,R) stereochemistry at C-6 and C-7. carbacephem Any member of the oxacephem sub-group of cephem antibiotics, in which the thiaazabicyclo moiety of the cephalosporins is replaced by an oxaazabicyclo moiety, and where R3 is -H or -OCH3. oxacephem A compound having the general formula RR'C(OH)OR'' (R'' =/= H). hemiacetal A cyclic compound having as ring members atoms of at least two different elements. heterocyclic compound Imipenem-cilastatin Polymyxins are antibiotics with a general structure consisting of a cyclic peptide with a long hydrophobic tail. They disrupt the structure of the bacterial cell membrane by interacting with its phospholipids. Polymyxins are produced by the Gram-positive bacterium Bacillus polymyxa and are selectively toxic for Gram-negative bacteria. polymyxin A polymyxin having a 6-methylheptanoyl group at the amino terminus. polymyxin B2 A polymyxin having a (6R)-6-methyloctanoyl group at the amino terminus. colistin A Any substance that stimulates an immune response in the body, such as through antibody production or by presentation to a T-cell receptor after binding to a major histocompability complex (MHC). Currently "K antigen" is a CHEBI_73772 chemical entity rather than a role. antigen K antigen A broad spectrum, third-generation cephalosporin antibiotic with (Z)-2-(4-methyl-1,3-thiazol-5-yl)ethenyl and (2Z)-2-(2-amino-1,3-thiazol-4-yl)-2-(methoxyimino)acetamido groups at positions 3 and 7, respectively, of the cephem skeleton. Generally administered as its orally absorbed pivaloyloxymethyl ester prodrug, it is used for the treatment of mild to moderate infections caused by susceptible strains of microorganisms in acute bacterial exacerbation of chronic bronchitis, community-acquired pneumonia, pharyngitis/tonsillitis, and uncomplicated skin and skin-structure infections. cefditoren A polymyxin having a 6-methylheptanoyl group at the amino terminus. colistin B An organooxygen compound having the structure RR'C(OR'')(OR''') (R'', R''' =/= H). Mixed acetals have R'' and R''' groups which differ. acetal An acetal in the molecule of which the acetal carbon and one or both oxygen atoms thereon are members of a ring. cyclic acetal A hemiacetal having the structure RR(1)C(OH)OR(2) (R, R(1), R(2) =/= H), derived from a ketone by formal addition of an alcohol to the carbonyl group. hemiketal An acetal of formula R2C(OR)2 (R =/= H) derived from a ketone by replacement of the oxo group by two hydrocarbyloxy groups. The class name 'ketals', once abandoned by IUPAC, has been reinstated as a subclass of acetals. ketal A ketal in the molecule of which the ketal carbon and one or both oxygen atoms thereon are members of a ring. cyclic ketal A hemiacetal having the structure R2C(OH)OR (R =/= H), derived from a ketone by formal addition of an alcohol to the carbonyl group. The term 'cyclic hemiketals', once abandoned by IUPAC, has been reinstated as a subclass of hemiacetals. cyclic hemiketal The sulfur analogue of 'acetal'. The term includes monothioacetals having the structure R2C(OR')(SR') (subclass monothioketals, R =/= H); and dithioacetals having the structure R2C(SR')2 (subclass dithioketals, R =/= H, R' =/= H). thioacetal A thioacetal having the structure R2C(OR')(SR'). The term includes monothioketals, R =/= H, as a subclass. monothioacetal A broad-spectrum oxacephem antibiotic in which the oxazine ring is substituted with a tetrazolylthiomethyl group and the azetidinone ring carries methoxy and 2-carboxy-2-(4-hydroxyphenyl)acetamido substituents. CHEBI:214506 CHEBI:44113 CHEBI:7006 moxalactam A chemical substance is a portion of matter of constant composition, composed of molecular entities of the same type or of different types. chemical substance A mixture is a chemical substance composed of multiple molecules, at least two of which are of a different kind. mixture A polypeptide comprising N-decanoyltryptophan, asparagine, aspartic acid, threonine, glycine, ornithine, aspartic acid, D-alanine, aspartic acid, glycine, D-serine, threo-3-methylglutamic acid and 3-anthraniloylalanine (also known as kynurinine) coupled in sequence and lactonised by condensation of the carboxylic acid group of the 3-anthraniloylalanine with the alcohol group of the threonine residue. CHEBI:29570 CHEBI:321017 CHEBI:478132 CHEBI:478255 daptomycin A carbohydrazide obtained by formal condensation between pyridine-4-carboxylic acid and hydrazine. Inh isoniazid isoniazide A commercially important azabicyclic antibiotic obtained from Streptomyces sapporonensis. It inhibits the Rho protein of E. coli. CHEBI:3091 bicozamycin A racemate is an equimolar mixture of a pair of enantiomers. racemate A glucoside in which the anomeric carbon of the glycosidic bond is in an alpha configuration alpha-glucoside Kanamycin is a naturally occurring antibiotic complex from Streptomyces kanamyceticus that consists of several components: kanamycin A, the major component (also usually designated as kanamycin), and kanamycins B, C, D and X the minor components. Kan kanamycin Any compound that has a nucleobase as a part. nucleobase-containing molecular entity Any cyclitol having one or more alcoholic hydroxy groups replaced by substituted or unsubstituted amino groups. amino cyclitol Any derivative of 2-deoxystreptamine. 2-deoxystreptamine derivative An ester where the ester linkage is bonded directly to an aromatic system. aromatic ester An amide in which the amide linkage is bonded directly to an aromatic system. aromatic amide A family of nitrogen molecular entities which are highly reactive and derived from nitric oxide (.NO) and superoxide (O2.(-)) produced via the enzymatic activity of inducible nitric oxide synthase 2 (NOS2) and NADPH oxidase respectively. reactive nitrogen species A carbohydrate derivative arising formally from the elimination of water from a glycosidic hydroxy group and an H atom bound to an oxygen, carbon, nitrogen or sulfur atom of a separate entity. glycosyl compound Name for a family of macrolide antibiotics with more than twenty members produced by the rare actinomycete Micromonospora griseorubida. mycinamicin A mycinamicin composed of a 16-membered ring macrolactone core, an N,N-dimethylated deoxysugar desosamine and a 2,3-di-O-methylated 6-deoxysugar mycinose. mycinamicin IV Any organooxygen compound derived from a carbohydrate by replacement of one or more hydroxy group(s) by an amino group, a thiol group or similar heteroatomic groups. The term also includes derivatives of these compounds. carbohydrate derivative A carbohydrate derivative that is formally obtained from a disaccharide. disaccharide derivative A carbohydrate derivative that is formally obtained from a monosaccharide. monosaccharide derivative A carbohydrate derivative that is formally obtained from an oligosaccharide. oligosaccharide derivative An oligosaccharide derivative that is formally obtained from a tetrasaccharide. tetrasaccharide derivative An optically active form of ofloxacin having (S)-configuration; an inhibitor of bacterial topoisomerase IV and DNA gyrase. Lfx CHEBI:6440 levofloxacin An organofluorine compound that consists of 1,3-oxazolidin-2-one bearing an N-3-fluoro-4-(morpholin-4-yl)phenyl group as well as an acetamidomethyl group at position 5. A synthetic antibacterial agent that inhibits bacterial protein synthesis by binding to a site on 23S ribosomal RNA of the 50S subunit and prevents further formation of a functional 70S initiation complex. Lzd CHEBI:6477 linezolid A quinolone that consists of 4-oxo-1,4-dihydroquinoline-3-carboxylic acid bearing a cyclopropyl substituent at position 1, a fluoro substitiuent at position 6, a (4aS,7aS)-octahydro-6H-pyrrolo[3,4-b]pyridin-6-yl group at position 7 and a methoxy substituent at position 8. A member of the fluoroquinolone class of antibacterial agents. MXF Mfx CHEBI:7007 moxifloxacin Mfx https://www.ncbi.nlm.nih.gov/books/NBK247415/bin/part3-m17.pdf 1H-imidazole substituted at C-1 by a (2-ethylsulfonyl)ethyl group, at C-2 by a methyl group and at C-5 by a nitro group. It is used as an antiprotozoal, antibacterial agent. CHEBI:32227 tinidazole Any organic heterobicyclic compound containing ortho-fused pyrrolidine and piperidine rings. pyrrolidinopiperidine A sulfonamide that is sulfanilamide acylated on the sulfonamide nitrogen. sulfacetamide Any lactone in which the cyclic carboxylic ester group forms a part of a cyclic macromolecule. CHEBI:50333 macrocyclic lactone A fused-ring beta-lactam system where the beta-lactam ring is fused to a 1,3-oxazolidine ring. oxapenam Any organic molecular entity that is acidic and contains carbon in covalent linkage. organic acid A carbohydrate-containing antibiotic produced by the actinomyces Streptomyces lincolnensis. lincomycin A carbohydrate derivative that is any derivative of a polysaccharide. polysaccharide derivative Mafenide A penicillin that is 6-aminopenicillanic acid in which one of the amino hydrogens is replaced by a 2,6-dimethoxybenzoyl group. methicillin Any monocyclic heteroarene consisting of a five-membered ring containing nitrogen. Azoles can also contain one or more other non-carbon atoms, such as nitrogen, sulfur or oxygen. azole An 18-membered macrolide that is a fermentation product obtained from the Actinomycete Dactylosporangium aurantiacum. A narrow spectrum antibiotic used for treatment of Clostridium difficile-related infections. fidaxomicin A member of the class of imidazoles substituted at C-1, -2 and -5 with 2-hydroxyethyl, nitro and methyl groups respectively. It has activity against anaerobic bacteria and protozoa, and has a radiosensitising effect on hypoxic tumour cells. It may be given by mouth in tablets, or as the benzoate in an oral suspension. The hydrochloride salt can be used in intravenous infusions. Metronidazole is a prodrug and is selective for anaerobic bacteria due to their ability to intracellularly reduce the nitro group of metronidazole to give nitroso-containing intermediates. These can covalently bind to DNA, disrupting its helical structure, inducing DNA strand breaks and inhibiting bacterial nucleic acid synthesis, ultimately resulting in bacterial cell death. CHEBI:39845 CHEBI:63636 metronidazole A penicillin in which the substituent at position 6 of the penam ring is a (2R)-2-[3-(methanesulfonyl)-2-oxoimidazolidine-1-carboxamido]-2-phenylacetamido group. mezlocillin An alpha,beta-unsaturated ester resulting from the formal condensation of the alcoholic hydroxy group of 9-hydroxynonanoic acid with the carboxy group of (2E)-4-[(2S)-tetrahydro-2H-pyran-2-yl]-3-methylbut-2-enoic acid in which the tetrahydropyranyl ring is substituted at positions 3 and 4 by hydroxy groups and at position 5 by a {(2S,3S)-3-[(2S,3S)-3-hydroxybutan-2-yl]oxiran-2-yl}methyl group. Originally isolated from the Gram-negative bacterium Pseudomonas fluorescens, it is used as a topical antibiotic for the treatment of Gram-positive bacterial infections. CHEBI:44038 mupirocin A cephalosporin having [4-(1-methylpyridinium-4-yl)-1,3-thiazol-2-yl]sulfanyl and {(2Z)-2-(ethoxyimino)-2-[5-(phosphonoamino)-1,2,4-thiadiazol-3-yl]acetyl}amino side groups located at positions 3 and 7 respectively. The N-phospho prodrug of ceftaroline, a broad-spectrum antibiotic active against methicillin-resistant Staphylococcus aureus (MRSA). It is used for the treatment of adults with acute bacterial skin and skin structure infections. ceftaroline fosamil A glycopeptide that is vancomycin substituted at position N-3'' by a 2-(decylamino)ethyl group and at position C-29 by a (phosphonomethyl)aminomethyl group. Used as its hydrochloride salt for treatment of adults with complicated skin and skin structure infections caused by bacteria. telavancin An imidazolidine-2,4-dione that is hydantoin substituted at position 1 by a [(5-nitro-2-furyl)methylene]amino group. An antibiotic that damages bacterial DNA. CHEBI:7591 nitrofurantoin Any member of a family of aminoglycosidic antibiotics produced by the bacterium Streptomyces lividus. Note that one member of this class, lividomycin A, is also known as lividomycin. lividomycins A member of the class of lividomycins that is lividomycin B in which position 4 of the diamino-L-idopyranosyl moiety has been converted into its alpha-D-mannopyranoside. lividomycin A A member of the class of lividomycins that is paromomycin in which the 2-amino-2-deoxyglucopyranosyl moiety is lacking the hydroxy group at position 3. lividomycin B A quinoline-based antimycobacterial drug used (as its fumarate salt) for the treatment of pulmonary multi-drug resistant tuberculosis by inhibition of ATP synthase, an enzyme essential for the replication of the mycobacteria. Bdq bedaquiline Any organic molecular entity derived from a natural product by partial chemical synthesis. semisynthetic derivative Any molecule that consists of at least one carbon atom as part of the electrically neutral entity. organic molecule Any naphthyridine derivative that is a derivative of 1,8-naphthyridine. 1,8-naphthyridine derivative Any organonitrogen heterocyclic compound that is a derivative of a naphthyridine. naphthyridine derivative A carbohydrate derivative in which one or more of the oxygens or hydroxy groups of the parent carbohydrate is replaced by sulfur or -SR, where R can be hydrogen or any group. thiosugar Any capsular polysaccharide derivative which is carried on the surface of a bacterial capsule or formed on the outer portion of a cell wall and masks somatic O antigens. Damion Dooley's note: 'K antigen' can't be a subclass of antigen as chemical entity is disjoint from role. Snomed: Concept 260824002 K antigen A zwitterion resulting from the transfer of a proton from the ring nitrogen to the primary amino group of D-cycloserine. The major species at pH 7.3. D-cycloserine zwitterion A penicillin in which the substituent at position 6 of the penam ring is a (2-ethoxy-1-naphthoyl)amino group. CHEBI:44256 nafcillin A tetracyclic antibacterial agent derived from neomycin, being a glycoside ester of neamine and neobiosamine B. CHEBI:44577 framycetin A semisynthetic member of the class of rifamycins and non-systemic gastrointestinal site-specific broad spectrum antibiotic. Used in the treatment of traveller's diarrhoea, hepatic encephalopathy and irritable bowel syndrome. rifaximin A carboxamide that is a hydroxamic acid in which the hydrogen of the hydroxy group is replaced by an organyl group. hydroxamic acid ester Any member of the group of eight water-soluble vitamins originally thought to be a single compound (vitamin B) that play important roles in cell metabolism. The group comprises of vitamin B1, B2, B3, B5, B6, B7, B9, and B12 (Around 20 other compounds were once thought to be B vitamins but are no longer classified as such). B vitamin An organic anion obtained by deprotonation of the carboxy, sulfo and one of the hydroxy groups as well as protonation of the amino group of A47934; major species at pH 7.3. A47934(2-) A racemate comprising equimolar amounts of levofloxacin and dextrofloxacin. It is a synthetic fluoroquinolone antibacterial agent which inhibits the supercoiling activity of bacterial DNA gyrase, halting DNA replication. Ofx CHEBI:100146 ofloxacin Any organooxygen compound that is a polyhydroxy-aldehyde or -ketone, or a compound derived from one. Carbohydrates contain only carbon, hydrogen and oxygen and usually have an empirical formula Cm(H2O)n; carbohydrate derivatives may contain other elements by substitution or condensation. carbohydrates and carbohydrate derivatives Any organic molecular entity that contains at least one C=C bond. olefinic compound A monocarboxylic acid in which the carbon of the carboxy group is directly attached to a C=C or C#C bond. alpha,beta-unsaturated monocarboxylic acid An amino cyclitol glycoside that is the 1-O-(2-amino-2-deoxy-alpha-D-glucopyranoside) and the 3-O-(2,6-diamino-2,6-dideoxy-beta-L-idopyranosyl)-beta-D-ribofuranoside of 4,6-diamino-2,3-dihydroxycyclohexane (the 1R,2R,3S,4R,6S diastereoisomer). It is obtained from various Streptomyces species. A broad-spectrum antibiotic, it is used (generally as the sulfate salt) for the treatment of acute and chronic intestinal protozoal infections, but is not effective for extraintestinal protozoal infections. It is also used as a therapeutic against visceral leishmaniasis. CHEBI:44703 paromomycin Any inorganic anion with a valency of one. monovalent inorganic anion Chalcomycin A penicillin in which the substituent at position 6 of the penam ring is a 2-[(4-ethyl-2,3-dioxopiperazin-1-yl)carboxamido]-2-phenylacetamido group. CHEBI:472443 CHEBI:475140 CHEBI:505944 piperacillin Pleuromutilin A semisynthetic glycopeptide used (as its bisphosphate salt) for the treatment of acute bacterial skin and skin structure infections caused or suspected to be caused by susceptible isolates of designated Gram-positive microorganisms including MRSA. CHEBI:29553 oritavancin A polymyxin having a (6R)-6-methyloctanoyl group at the amino terminus. polymyxin B1 Any member of the class of chlorobenzenes containing a mono- or poly-substituted benzene ring in which only one substituent is chlorine. monochlorobenzenes A carboxamide obtained by the formal condensation of the carboxy group of any carboxylic acid with ammonia. N-acylammonia Any derivative of a proteinogenic amino acid resulting from reaction at an amino group, carboxy group, or a side-chain functional group, or from the replacement of any hydrogen by a heteroatom. proteinogenic amino acid derivative Any derivative of an amino acid resulting from reaction at an amino group, carboxy group, side-chain functional group, or from the replacement of any hydrogen by a heteroatom. The definition normally excludes peptides containing amino acid residues. CHEBI:25359 amino acid derivative Pristinamycin IB A proteinogenic amino acid derivative resulting from reaction of L-proline at the amino group or the carboxy group, or from the replacement of any hydrogen of L-proline by a heteroatom. L-proline derivative pristinamycin IC A heterodetic cyclic peptide that is produced by species of Amycolatopsis and Nocardia. ristocetin A macrolide antibiotic produced by various Streptomyces species that is used to treat toxoplasmosis and various other infections of soft tissues. CHEBI:45589 CHEBI:9236 spiramycin I An organonitrogen heterocyclic antibiotic whose structure contains a quinolone or quinolone-related skeleton. quinolone antibiotic Heteroorganic entities that are microbial metabolites (or compounds derived from them) which have significant antifungal properties. antibiotic antifungal agent Any antibiotic antifungal agent used to treat fungal infections in humans or animals. antibiotic antifungal drug Any antibiotic antifungal agent that has been used as a fungicide. antibiotic fungicide An organonitrogen heterocyclic antibiotic containing a quinolone (or quinolone-like) moiety and which have a fluorine atom attached to the central ring system. fluoroquinolone antibiotic A class of sulfonamides whose members generally have bacteriostatic antibiotic properties. sulfonamide antibiotic A member of the class of furans in which the furan ring is substituted by a nitro group and which also has significant antibiotic properties. nitrofuran antibiotic Quinupristin Quinupristin-dalfopristin Any penicillin which causes the onset of an allergic reaction. penicillin allergen Any beta-lactam antibiotic which causes the onset of an allergic reaction. beta-lactam antibiotic allergen arsphenamine A mixed diacylamine resulting from the formal condensation of the nitrogen of a carboxamide with a sulphonic acid. N-sulfonylcarboxamide sparfloxacin A pyranobenzodioxin and antibiotic that is active against gram-negative bacteria and used (as its dihydrochloride pentahydrate) to treat gonorrhea. It is produced by the bacterium Streptomyces spectabilis. CHEBI:45551 spectinomycin sulbactam A sulfonamide consisting of pyrimidine with a 4-aminobenzenesulfonamido group at the 2-position. sulfadiazine A sulfonamide consisting of pyrimidine having methoxy substituents at the 5- and 6-positions and a 4-aminobenzenesulfonamido group at the 4-position. In combination with the antiprotozoal pyrimethamine (CHEBI:8673) it is used as an antimalarial. sulfadoxine A sulfonamide consisting of a 1,3,4-thiadiazole nucleus with a methyl substituent at C-5 and a 4-aminobenzenesulfonamido group at C-2. sulfamethizole An isoxazole (1,2-oxazole) compound having a methyl substituent at the 5-position and a 4-aminobenzenesulfonamido group at the 3-position. CHEBI:102247 sulfamethoxazole A member of the class of penicillanic acids that is sulbactam in which one of the exocyclic methyl hydrogens is replaced by a 1,2,3-triazol-1-yl group; used (in the form of its sodium salt) in combination with ceftolozane sulfate for treatment of complicated intra-abdominal infections and complicated urinary tract infections. CHEBI:45973 tazobactam A penicillin compound having a 6beta-[(2R)-2-carboxy-2-thiophen-3-ylacetyl]amino side-group. ticarcillin A macrolide that is (together with pristinamycin IA) a component of pristinamycin, an oral streptogramin antibiotic produced by Streptomyces pristinaespiralis. Pristinamycin exhibits bactericidal activity against Gram positive organisms including methicillin-resistant Staphylococcus aureus. CHEBI:46395 pristinamycin IIA An independent material continuant that is self-connected and retains its identity over time. portion of material A method that results in the separation of two or more components according to some property. FIX:0000002 partition separation method A separation method where colloidal particles move at different speeds according to their electrophoretic mobilities in a separation medium, across which an electric field is applied. FIX:0000097 sep:00140 cataphoresis electrophoretic analysis electrophoresis A separation method where colloidal particles move at different speeds according to their electrophoretic mobilities in a separation medium consisting of gel, across which an electric field is applied. sep:00150 gel electrophoresis An electrophoresis method where the separation medium contains a reticulated system, for example an entangled polymer network, that further separates the analytes according to their size and shape. sieving electrophoresis A separation method where colloidal particles move at different speeds according to their electrophoretic mobilities in a separation medium, across which a pulsed electric field is applied (a field in which the voltage changes direction). pulsed-field electrophoresis A separation method where colloidal particles move at different speeds according to their electrophoretic mobilities in a separation medium consisting of gel, across which a pulsed electric field is applied (one in which the voltage direction is periodically switched among three directions; one that runs through the central axis of the gel and two that run at an angle of 120° either side). PFGE pulsed field gel electrophoresis pulsed-field gel electrophoresis specimen extraction matrix Those components of a sample that are not measured by an experiment. "This observable is important where process of capturing sample can affect dna extraction." matrix A COVID-19 nucleic acid diagnostic assay that uses RT-PCR Oliver He, Asiyah Yu Lin SARS COV-2 RT-PCR https://www.fda.gov/medical-devices/emergency-situations-medical-devices/emergency-use-authorizations#covid19ivd https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7170415/ COVID-19 RT-PCR assay A COVID-19 diagnostic process by viral genome sequencing and identification of the SARS-CoV-2 based on the genome sequence. Oliver He, Asiyah Yu Lin, Hong Yu https://www.ncbi.nlm.nih.gov/pubmed/32245835 COVID-19 diagnostic process by viral genome sequencing cell line cell A cultured cell that is part of a cell line - a stable and homogeneous population of cells with a common biological origin and propagation history in culture A cultured cell that is part of a cell line - a stable and homogeneous population of cells with a common biological origin and propagation history in culture Yongqun He, Matthew Brush, Sirarat Sarntivijai, Alexander Diehl, Jie Zheng, Yu Lin, Bjoern Peters A 'cell line cell' is a part of a cell line established through the passaging/selection of a primary cultured cells or the experimental modification of an existing cell line. New types of cell line cells are established after sufficient passaging of a primary culture to establish a stable and homogenous population that qualifies as a line (typically 1-20 passages), or following some spontaneous or experimental modification that confers novel characteristics to an existing line. A cell line cell typically has mutations of five or more genes compared to the original cell that derives the cell line cell. Some gene mutations may turn on some oncogenes. Cell line cells can be in active culture, stored in a quiescent state for future use (e.g. frozen in liquid nitrogen), or applied in experimental procedures. cell line cell immortal cell line cell A cell line cell that is expected to be capable of an unlimited number of divisions, and is thus able to support indefinite propagation in vitro as part of an immortal cell line. Yongqun He, Matthew Brush, Allen Xiang, Asiyah Yu Lin, Sirarat Sarntivijai, James Malone, Jie Zheng, Tomasz Adamusiak continuous cell line cell permanent cell line cell immortal cell line cell cell line A cultured cell population that represents a genetically stable and homogenous population of cultured cells that shares a common propagation history (i.e. has been successively passaged together in culture). A cultured cell population that represents a genetically stable and homogenous population of cultured cells that shares a common propagation history (i.e. has been successively passaged together in culture). MB, SS, JZ, MAH, BP, CS, YH The term 'line' is used when a culture has undergone an intentional experimental process to establish a more uniform and stable population of cells (see 'establishing cell line'). This will require one or more passages, but may involve additional selection processes. Through such passaging and/or selection processes, the resulting 'line' attains some level of genetic stability and compositional homogeneity which is typically absent in primary cultures. Because of their relative homogeneity, ‘lines’ are capable of being characterized and stably propagated over a period of time. A new *type* of cell line can be established not only through the passaging/selection of a primary culture, but also through experimental modifications of existing lines (e.g. immortalization, stable genetic modifications, drug selection for a resistant subset, etc.). The definition provided here establishes the 'scale' of cell populations that qualify as cell lines - specifically those with a shared propagation history in culture. In this way, the 'cell line' class demarcates populations that represent what researchers actually use in the practice of science - e.g. as inputs to culturing, experimentation, and sharing. The definition is such that cell lines will exhibit important attributes. For example, they will have a relatively homogenous cell type composition as they have experienced similar selective pressures due to their continuous co-propagation. In addition, these populations can also be characterized by a passage number, again owing to their common passaging history.  As defined here, 'cell line' can refer to a population of cells in active culture, applied experimentally, or stored in a quiescent state for future use. cell line An immortal cell line cell that derives from kidney. Yue Liu, Yongqun He immortal kidney-derived cell line cell An immortal kidney-derived cell line cell that derives from rhesus macaque. Yue Liu, Yongqun He immortal rhesus macaque kidney-derived cell line cell LLC-MK subscript(2) LLC-MK subscript(2) cell cell A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane. CALOHA:TS-2035 FMA:68646 GO:0005623 KUPO:0000002 VHOG:0001533 WBbt:0004017 XAO:0003012 The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one). cell cell type cultured cell A cell in vitro that is or has been maintained or propagated as part of a cell culture. Note that this class was re-labeled to 'cultured cell' instead of 'cell line cell', as it intent was clarified to cover any cultured cells of multicellular and unicellular organisms. This includes cells actively being cultured, or cells that have been cultured but are stored in a quiescent state for future use. In having been cultured, cells must establish homeostasis and often replicate in a foreign environment. Accomodation of this stress initiates a selection of cells fit for such challenges, wherein necessary adaptive biochemical and.or genetic changes can occur. These changes can set them apart from the in vivo cells from which they derive, and such changes will typically accumulate and change over increasing time in culture. cultured cell experimentally modified cell in vitro A cell in vitro that has undergone physical changes as a consequence of a deliberate and specific experimental procedure. This class has been re-labeled to imply reference only to in vitro experimentally modified cells, similarly, the definition has been slightly updated to reflect this. 'experimentally modified cell' refers only to cells in vitro, and not modified in vivo/in environment cells. There is currently no class representing unmodified in vitro cells (other than the parent 'cell in vitro'), or a class representing modified native cells. More granular subclassing of experimentally modified cell can be found in ReO. MHB 1.12.12 experimentally modified cell in vitro A cell that is maintained or propagated in a controlled artificial environment for use in an investigation. 'In vitro', translating literally to 'in glass', typically refers to a controlled, often sterile, laboratory setting where cells or other specimens are placed by some agent for the purpose of studying or manipulating them as part of some research investigation. 'In vitro' is intended to contrast with 'native',which refers to cells or other biological entities that are found in a natural setting. It describes unicellular organisms removed from a natural environement and multicellular organism cells removed from an organism, or cells derived in culture from such displaced cells. cell in vitro A disease existing at birth, or developping during the first month after birth. congenital disease A crustacean allergy that has_allergic_trigger shrimp. shrimp allergy A bacterial pneumonia has_material_basis_in Chlamydia pneumoniae. Chlamydia pneumonia A bacterial pneumonia has_material_basis_in Streptococcus pneumoniae. Streptococcus pneumonia A bacterial infectious disease has_material_basis_in Bacteria. bacterial sepsis A gonococcal seminal vesiculitis that is characterized by back pain, perineal pain, pain with ejaculation, hematospermia and voiding symptoms resulting from inflammation located_in the seminal vesicles caused by Neisseria gonorrhoeae infection. seminal vesicle acute gonorrhea An ehrlichiosis that results in infection located in granular leukocyte, has_material_basis_in Anaplasma phagocytophilum, which is transmitted by lone star tick (Amblyomma americanum). The infection has symptom headache, has symptom muscle aches, has symptom fatigue, has symptom fever and has symptom rash. human granulocytic anaplasmosis An ehrlichiosis that results in infection located in monocyte or located in macrophage, has_material_basis_in Ehrlichia chaffeensis, which is transmitted by black-legged tick (Ixodes scapularis), transmitted by western black-legged tick (Ixodes pacificus) or transmitted by castor bean tick (Ixodes ricinus). The infection has symptom headache, has symptom muscle aches, has symptom fatigue, has symptom fever and has symptom rash. human monocytic ehrlichiosis A spotted fever that has_material_basis_in Rickettsia africae, which is transmitted_by ticks (Amblyomma hebraeum and Amblyomma variegatum). The infection has_symptom fever, has_symptom eschar and has_symptom maculopapular rash. African tick-bite fever A spotted fever that has_material_basis_in Rickettsia conorii subsp caspia, which is transmitted_by ticks (Rhipicephalus pumilio and Rhipicephalus sanguineus). The infection has_symptom fever, has_symptom eschar (usually single), has_symptom regional adenopathy, has_symptom maculopapular rash on extremities. Astrakhan spotted fever A spotted fever that has_material_basis_in Rickettsia conorii subsp indica, which is transmitted_by ticks (Rhipicephalus sanguineus). The infection has_symptom fever, has_symptom eschar, has_symptom regional adenopathy, and has_symptom maculopapular rash on extremities. Indian tick typhus A spotted fever that has_material_basis_in Rickettsia conorii subsp israelensis, which is transmitted_by ticks (Rhipicephalus sanguineus). The infection has_symptom fever, has_symptom eschar, has_symptom regional adenopathy, and has_symptom maculopapular rash on extremities. Israeli tick typhus A spotted fever that has_material_basis_in Rickettsia heilongjiangensis, which is transmitted_by ticks (Haemaphysalis concinna). The infection has_symptom fever, has_symptom eschar, has_symptom maculopapular rash, and has_symptom regional adenopathy. Far Eastern spotted fever A spotted fever that has_material_basis_in Rickettsia honei, which is transmitted_by cayenne ticks (Amblyomma cajennense). The infection has_symptom mild spotted fever, has_symptom eschar and has_symptom adenopathy. Flinders Island spotted fever A spotted fever that has_material_basis_in Rickettsia japonica, which is transmitted_by ticks (Dermacentor taiwanensis and Haemaphysalis flava). The infection has_symptom fever, has_symptom eschars, has_symptom regional adenopathy, and has_symptom rash on extremities. Japanese spotted fever A spotted fever that has_material_basis_in Rickettsia parkeri, which is transmitted_by Gulf Coast tick (Amblyomma maculatum). The infection has_symptom fever, has_symptom headache, has_symptom eschar, and has_symptom rash. Rickettsia parkeri spotted fever A spotted fever that has_material_basis_in Rickettsia rickettsii, which is transmitted_by ticks (Dermacentor variabilis and Dermacentor andersoni). The infection has_symptom fever, has_symptom headache, has_symptom abdominal pain, and has_symptom maculopapular rash progressing into papular or petechial rash. Rocky Mountain spotted fever A gastrointestinal anthrax that results in infection located in mucosa of oropharynx, has_material_basis_in Bacillus anthracis, which is transmitted by ingestion of anthrax-infected meat. The infection has symptom lesions, has symptom vomiting of blood, has symptom severe diarrhea, has symptom loss of appetite. oropharyngeal anthrax A primary bacterial infectious disease that results_in infection located_in skin, has_material_basis_in Erysipelothrix rhusiopathiae, which is transmitted_by contact with infected animals. The infection has_symptom redness of skin, has_symptom tenderness of skin and has_symptom warmth of skin. erysipeloid A disease that is the consequence of the presence of pathogenic microbial agents, including pathogenic viruses, pathogenic bacteria, fungi, protozoa, multicellular parasites, and aberrant proteins known as prions. disease by infectious agent A botulism that involves intoxication caused by botulinum neurotoxins (BoNTA, B, E and F) in adults, has_material_basis_in Clostridium botulinum A, has_material_basis_in Clostridium botulinum B, has_material_basis_in Clostridium botulinum E and has_material_basis_in Clostridium botulinum F, which are transmitted by ingestion of bacterial spores, which then grow in the intestine and release toxins. intestinal botulism A legionellosis that involves a milder respiratory illness without pneumonia. Symptoms include fever, headache and muscle aches which last for 2 to 5 days. Pontiac fever A bacterial pneumonia which is an acute pulmonary inflammatory response that develops after the inhalation of colonized oropharyngeal material containing bacteria. It is seen in individuals with dysphagia and gastric dysmotility. The disease has_symptom tachypnea and has_symptom cough. aspiration pneumonia A nervous system disease which is located in a part of the nervous system responsible for processing sensory information that consists of sensory receptors, neural pathways, and parts of the brain involved in sensory perception. Commonly recognized sensory systems are those for vision, hearing, somatic sensation (touch), taste and olfaction (smell). sensory system disease An anthrax disease that results in infection located in lung lymph nodes brought on by breathing in the spores of the bacteria Bacillus anthracis. The first symptoms of inhalation anthrax are like cold or flu symptoms and can include a sore throat, mild fever and muscle aches. Later symptoms include cough, chest discomfort, shortness of breath, tiredness and muscle aches. inhalation anthrax A respiratory system disease which involves the lower respiratory tract. lower respiratory tract disease An urogenital tuberculosis that results_in formation of granulomas located_in fallopian tube. tuberculous salpingitis A bacterial infectious disease that results_in infection by bacteria as a result of their presence or activity within the normal, healthy host, and their intrinsic virulence is, in part, a necessary consequence of their need to reproduce and spread. primary bacterial infectious disease A bacterial infectious disease that results_in infection by bacteria which are part of the normal human flora when one or more of the defense mechanisms designed to restrict them from the usually sterile internal tissues are breached by accident, by intent (surgery), or by an underlying metabolic or an infectious disorder. commensal bacterial infectious disease A bacterial infectious disease that results_in infection by bacteria in individuals whose host defense mechanisms have been compromised. opportunistic bacterial infectious disease A botulism that involves intoxication caused by botulinum neurotoxins (BoNTA, B, E and F), which are transmitted by ingestion of food contaminated with preformed toxins, has_material_basis_in Clostridium botulinum A, has_material_basis_in Clostridium botulinum B, has_material_basis_in Clostridium botulinum E and has_material_basis_in Clostridium botulinum F. The infection has symptom blurred vision, has symptom diplopia, has symptom dysarthria, has symptom dysphonia, has symptom dysphagia and has symptom descending muscle paralysis. foodborne botulism A botulism that involves intoxication caused by botulinum neurotoxins (BoNTA, B, E and F), has_material_basis_in Clostridium botulinum A, has_material_basis_in Clostridium botulinum B, has_material_basis_in Clostridium botulinum E and has_material_basis_in Clostridium botulinum F, which are transmitted by contact of spores with the open wounds, which then reproduce in an anaerobic environment to produce toxins. wound botulism A botulism that involves intoxication caused by botulinum neurotoxins (BoNTA or B) in infants, has_material_basis_in Clostridium botulinum A or has_material_basis_in Clostridium botulinum B, which are transmitted_by ingestion of bacterial spores, which then grow in the intestine and release toxins. The infection has_symptom constipation, has_symptom lethargy, has_symptom difficulty feeding, has_symptom swallowing, has_symptom ptosis, has_symptom loss of head control, and has_symptom muscle weakness. infant botulism A tularemia that results_in swelling of regional lymph glands. glandular tularemia A tularemia that results_in bacteremia and has_symptom fever, has_symptom chills, has_symptom myalgia, has_symptom malaise, and has_symptom weight loss. typhoidal tularemia A bartonellosis that results_in infection located_in endothelial cells or located_in red blood cells, has_material_basis_in Bartonella bacilliformis, which is transmitted_by sandflies of genus Lutzomyia. The infection has acute and chronic phases. The acute phase is characterized by severe hemolytic anemia and transient immunosuppression. The chronic phase is characterized by verruga peruana lesions which may ulcerate and bleed. Carrion's disease A primary bacterial infectious disease that results_in infection located_in skin or located_in subcutaneous tissue, has_material_basis_in Mycobacterium ulcerans, which could be transmitted_by insects. The bacterium produces a toxin, named mycolactone, which causes subcutaneous fat necrosis and inhibits an immune response. The infection has_symptom nodule, which is a painless, mobile swelling in the skin. Buruli ulcer disease A typhus that has_material_basis_in Rickettsia prowazekii, which is transmitted by human body louse (Pediculus humanus corporis). The infection has_symptom high fever, has_symptom cough, has_symptom rash, has_symptom severe muscle pain, has_symptom chills, has_symptom falling blood pressure, has_symptom stupor, has_symptom sensitivity to light, and has_symptom delirium. epidemic typhus A typhus that has_material_basis_in Rickettsia typhi or has_material_basis_in Rickettsia felis, which are transmitted by fleas (Xenopsylla cheopis). The infection has symptom headache, has symptom fever, has symptom chills, has symptom myalgia, has symptom nausea, has symptom vomiting, has symptom cough and has symptom rash. endemic typhus A spotted fever that has_material_basis_in Rickettsia helvetica, which is transmitted_by ticks (Ixodes sp). The infection has_symptom fever, has_symptom headache, has_symptom myalgia. aneruptive fever A primary bacterial infectious disease that results_in infection, has_material_basis_in Neorickettsia sennetsu, which is transmitted_by ingestion of raw or under-cooked gray mullet fish infected with the trematodes. The infection has_symptom fever, has_symptom malaise, has_symptom anorexia, has_symptom lymphadenopathy, has_symptom hepatosplenomegaly, has_symptom fatigue, has_symptom chills, has_symptom headache, has_symptom backache and has_symptom myalgia. sennetsu fever A skin disease that is characterized by a rash that results from a variety of causes including bacteria, viruses, toxins, drugs and autoimmune disorders. exanthem An exanthem that is characterized by a diffuse, reddened, blanchable, finely papular, sandpaper like rash due to infection by group A streptococcus and the production of an erythrogenic toxin. bacterial exanthem A congenital syphilis that is manifested during the first 3 months of life. The infection has_symptom skin lesions, has_symptom lymphadenopathy, has_symptom hepatosplenomegaly, has_symptom failure to thrive, has_symptom blood-stained nasal discharge, has_symptom perioral fissures, has_symptom meningitis, has_symptom choroiditis, has_symptom hydrocephalus, has_symptom seizures, has_symptom intellectual disability, has_symptom osteochondritis, and has_symptom pseudoparalysis. early congenital syphilis A tertiary neurosyphilis that results when chronic meningoencephalitis causes destruction of cortical parenchyma. The infection has_symptom irritability, has_symptom difficulty concentrating, has_symptom deterioration of memory, has_symptom defective judgment, has_symptom headaches, has_symptom insomnia, has_symptom fatigue, and has_symptom lethargy. parenchymatous neurosyphilis A tertiary neurosyphilis that results in inflammation located_in arteries of the brain or located_in arteries of spinal cord. The infection has_symptom headache, has_symptom neck stiffness, has_symptom dizziness, has_symptom behavioral abnormalities, has _symptom poor concentration, has_symptom memory loss, has _symptom lassitude, has_symptom insomnia, has_symptom blurred vision, has_symptom weakness and wasting of shoulder-girdle and arm muscles, has_symptom slowly progressive leg weakness with urinary or fecal incontinence or both, and has_symptom paralysis of the legs due to thrombosis of spinal arteries. meningovascular neurosyphilis A tertiary syphilis that is characterized by granulomatous lesions, called gummas, which are characterized by a center of necrotic tissue with a rubbery texture. They form in the liver, bones, and testes but may affect any organ. gummatous syphilis An intestinal disease characterized by inflammation located in all parts of digestive tract. inflammatory bowel disease A tuberculosis that occurs at body sites other than the lung. extrapulmonary tuberculosis An extrapulmonary tuberculosis that is located_in gastrointestinal tract, located_in peritoneum, located_in omentum, located_in mesentery, located_in liver, located_in spleen or located_in pancreas. abdominal tuberculosis A cancer that is classified based on the organ it starts in. organ system cancer A heart disease and a myopathy that is characterized by deterioration of the function of the heart muscle. cardiomyopathy A heart disease that is located_in the innermost layer of tissue that lines the chambers of the heart. endocardium disease A cardiovascular system disease that is located_in the fibrous sac surrounding the heart. pericardium disease An endocarditis that is characterized by inflammation of the endocardium caused by infectious agents. infective endocarditis An autoimmune disease that is the abnormal functioning of the immune system that causes your immune system to produce antibodies or T cells against cells and/or tissues in the gastrointestinal tract. autoimmune disease of gastrointestinal tract A food allergy that develops from an immune reaction to eating gluten, a protein found in wheat, barley, rye and triticale and that is characterized by stomach cramping, diarrhea and gastrointestinal upset and is unrelated to the gluten intolerance. gluten allergy A disease of anatomical entity that is located_in the thoracic cavity. thoracic disease An inflammatory bowel disease that involves inflammation located_in colon. colitis A bartonellosis that has_material_basis_in Bartonella henselae or has_material_basis_in Bartonella quintana. The disease is characterized by the proliferation of blood vessels, resulting in them forming tumour-like masses in the skin and other organs. bacillary angiomatosis An egg allergy triggered by Gallus gallus eggs. chicken egg allergy A food allergy triggered by Crustacea or Mollusca. shellfish allergy An allergic disease that is located_in the gastrointestinal tract. gastrointestinal allergy A food allergy triggered by a plant fruit product. fruit allergy A fruit allergy triggered by Malus domestica plant fruit food product. apple allergy A fruit allergy triggered by Prunus armeniaca plant fruit food product. apricot allergy A fruit allergy triggered by Prunus avium plant fruit food product. cherry allergy A fruit allergy triggered by Ziziphus mauritiana plant fruit food product. Indian plum allergy A fruit allergy triggered by Citrus sinensis plant fruit food product. orange allergy A fruit allergy triggered by Cucumis melo plant fruit food product. melon allergy A fruit allergy triggered by Prunus persica plant fruit food product. peach allergy A fruit allergy triggered by Prunus domestica plant fruit food product. plum allergy A fruit allergy triggered by Solanum lycopersicum plant fruit food product. tomato allergy A food allergy triggered by fish. fish allergy A fish allergy triggered by Gadus morhua. Atlantic cod allergy A fish allergy triggered by Salmo salar. Atlantic salmon allergy A fish allergy triggered by Cyprinus carpio. carp allergy A fish allergy triggered by Danio rerio. zebrafish allergy A fish allergy triggered by Oncorhynchus mykiss. rainbow trout allergy A milk allergy triggered by Bos taurus milk. cow milk allergy A milk allergy triggered by Capra hircus milk. goat milk allergy A shellfish allergy triggered by Mollusca. mollusc allergy A shellfish allergy triggered by Crustacea. crustacean allergy A crustacean allergy triggered by Farfantepenaeus aztecus. brown shrimp allergy A crustacean allergy triggered by Scylla paramamosain. crab allergy A crustacean allergy triggered by Fenneropenaeus indicus. Indian prawn allergy A crustacean allergy triggered by Penaeus monodon. tiger prawn allergy A crustacean allergy triggered by Litopenaeus vannamei. white shrimp allergy A mollusc allergy triggered by snails. snail allergy A snail allergy triggered by the horned turban snail. horned turban snail allergy A bone disease that is located_in the spine. spinal disease A tuberculosis located in the heart. cardiac tuberculosis An osteomyelitis characterized by multiple foci of painful swelling of bones, mainly in the metaphyses of the long bones, in addition to the pelvis, the shoulder girdle and the spine. chronic recurrent multifocal osteomyelitis A primary bacterial infectious disease caused by the bacteria of the genus Salmonella. It has symptoms diarrhea, fever, vomiting, and abdominal cramps 12 to 72 hours after infection. In most cases, the illness lasts four to seven days, and most people recover without treatment. salmonellosis A fruit allergy triggered by Fabaceae (legume) plant fruit or seed food product. legume allergy A food allergy triggered by a vegetable food product. vegetable allergy A vegetable allergy triggered by celery (Apium graveolens). celery allergy A tuberculosis that is located_in some eye, has_material_basis_in Mycobacterium tuberculosis, and has_symptom inflamed eyes. ocular tuberculosis A primary bacterial infectious disease that has_material_basis_in Borrelia miyamotoi, which is transmitted_by the blacklegged tick (Ixodes scapularis), the western blacklegged tick (Ixodes pacificus), the taiga tick (Ixodes persulcatus), or the castor bean tick (Ixodes ricinus). The infection has_symptom fever, headache, chills, muscle pain, joint pain, asthenia, fatigue and nausea, and rarely relapses. Borrelia miyamotoi disease An opportunistic bacterial infectious disease characterized by necrotizing pneumonia, acute respiratory distress syndrome, and bacteremia that has_material_basis_in Burkholderia cepacia complex, which is transmitted_by contact transmission, droplet spread transmission, vehicle-borne fomite transmission, and vehicle-borne ingestion transmission. cepacia syndrome A musculoskeletal system disease that affects the muscles. muscular disease A connective tissue disease that affects the structure or development of bone or causes an impairment of normal bone function. bone disease A disease that has_material_basis_in a genetic abnormality, error with embryonic development, infection or compromised intrauterine environment. physical disorder A bacterial meningitis that has_material_basis_in Neisseria meningitidis infection. meningococcal meningitis A bacterial meningitis that has_material_basis_in Haemophilus influenzae infection. haemophilus meningitis A male reproductive system disease that is located_in the epididymis. epididymis disease A viral infectious disease that has_material_basis_in Coronavirus. Coronavirus infectious disease An urinary system disease that is characterized by an infection in any part of the urinary system, including the kidneys, ureters, bladder or urethra. urinary tract infection A tuberculosis that is characterized by cerebral edema sometimes with features similar to acute disseminated encephalomyelitis (ADEM) and may manifest with a variety of symptoms ranging from focal neurological deficits to convulsions and decreased conscious state. tuberculous encephalopathy A vegetable allergy triggered by parsley (Petroselinum). parsley allergy A food allergy triggered by dill (Anethum graveolens). dill allergy An anthrax disease that is characterized by infection at the injection site or deep under the skin or in the muscle where the drug was injected and is caused by heroin contaminated with anthrax spores. injection anthrax A tertiary neurosyphilis that results in slow degeneration of the nerve cells and nerve fibers that carry sensory information to the brain. The infection has symptom intense, stabbing pain in the back and legs that recurs irregularly, has symptom gait ataxia, has symptom hyperesthesia, has symptom paresthesia, has symptom loss of bladder sensation leading to urine retention, has symptom erectile dysfunction. tabes dorsalis A female reproductive system disease that is characterized by an infection of the female reproductive organs. pelvic inflammatory disease A tertiary neurosyphilis that results_in mild meningitis. asymptomatic neurosyphilis A congenital syphilis that occurs in children at or greater than two years of age who acquired the infection trans-placentally. The infection has_symptom gummatous ulcers, has_symptom periosteal lesions, has_symptom paresis, has_symptom tabes, has_symptom optic atrophy, has_symptom interstitial keratitis, has_symptom sensorineural deafness, and has_symptom dental deformities. late congenital syphilis A bacterial meningitis that is characterized by inflammation of the tissues covering the brain and spinal cord. syphilitic meningitis A bone inflammation disease that has_material_basis_in infection located_in bone or located_in bone marrow. osteomyelitis A primary bacterial infectious disease that results_in infection located_in skin, has_material_basis_in Treponema carateum, which is transmitted_by contact with skin and mucous membrane of an infected person. The infection has_symptom pruritic plaque, which slowly enlarges and becomes pigmented and hyperkeratotic. pinta disease A leprosy that results in small numerous red irregularly shaped plaques. borderline leprosy A primary bacterial infectious disease that results_in infection located_in superficial peripheral nerves, located_in skin, located_in mucous membranes of the upper respiratory tract, located_in anterior chamber of the eyes, or located_in testes, has_material_basis_in Mycobacterium leprae, which is transmitted_by aerosol spread from infected nasal secretions to exposed nasal and oral mucosa. The infection has_symptom skin lesions, has_symptom sensory loss, has_symptom motor loss and has_symptom eye damage. leprosy A primary bacterial infectious disease that results in infection located_in leukocyte, has_material_basis_in Ehrlichia chaffeensis or Anaplasma phagocytophilum, which are transmitted_by lone star tick and transmitted_by black-legged tick respectively. The infection has_symptom headache, has_symptom muscle aches, has_symptom fatigue and has_symptom rash. ehrlichiosis A leprosy that results in one erythematous large plaque with well-defined borders that are elevated and that slope down into an atrophic center. tuberculoid leprosy A endocardium disease characterized by inflammation of the endocardium of the heart chambers and valves. endocarditis A primary bacterial infectious disease that results in infection located in skin, located in joint or located in bone, has_material_basis_in Treponema pallidum subsp pertenue, which is transmitted by direct skin contact with an infected person. The infection has symptom skin lesions. yaws A plague that results_in infection located_in lung, which results from direct inhalation of the bacillus and has_symptom fever, has_symptom chills, has_symptom cough and has_symptom difficulty breathing. pneumonic plague seminal vesicle chronic gonorrhea A disease by infectious agent that results_in infection, has_material_basis_in Bacteria. bacterial infectious disease gonococcal seminal vesiculitis A legionellosis that is characterized by severe form of infection producing pneumonia. Symptoms include fever, chills, and cough. Legionnaires' disease A primary bacterial infectious disease that results_in infection located_in respiratory tract, has_material_basis_in Legionella pneumophila, which is transmitted_by inhalation of droplets containing bacteria. The symptoms include dry cough, fever, headache and diarrhea. legionellosis A yaws that appears after five years of the initial infection and is characterized by disabling consequences of the nose, bones and palmar/plantar hyperkeratosis. late yaws A yaws that results in initial papule at the site of entry of bacteria. Without treatment, this is followed by disseminated skin lesions over the body. Bone pain and bone lesions may also occur. early yaws An extrapulmonary tuberculosis that results_in lymphocyte-predominant exudative pleural effusion, located_in pleura. This results from an allergic response to tuberculoprotein causing the permeabiltity of the pleural vasculature to alter leading to a sub-pleural caseous focus rupture into the pleural sac. pleural tuberculosis A breast disease characterized by painful infection of the breast tissue. mastitis An osteomyelitis that has_material_basis_in infection located_in petrous part of temporal bone. petrositis A plague that results_in infection located_in lymph node producing a bubo, which is an inflamed, necrotic, and hemorrhagic lymphoid tissue. The infection has_symptom enlarged, tender lymph nodes, has_symptom fever, has_symptom chills and has_symptom prostration. bubonic plague A spotted fever that has_material_basis_in Rickettsia australis, which is transmitted_by ticks (Ixodes holocyclus). The infection has_symptom fever, has_symptom headache, has_symptom myalgia, has_symptom maculopapular rash, and has_symptom lymphadenopathy. Queensland tick typhus A leprosy that results in early cutaneous lesions which consist of pale macules that are small, diffuse, and symmetric. This form of leprosy is characterized by hypoesthesia over extensor surfaces of the distal extremities, alopecia affecting lateral aspects of the eyebrows, saddle-nose deformity and oral lepromas. lepromatous leprosy A spotted fever that has_material_basis_in Rickettsia sibirica, which is transmitted_by ticks (Dermacentor nuttalli, Dermacentor marginatus and Haemaphysalis concinna). The infection has_symptom fever, has_symptom eschar, has_symptom regional adenopathy, and has_symptom maculopapular rash. Siberian tick typhus A female reproductive system disease that is located_in the ovary. ovarian disease A primary bacterial infectious disease that results_in systemic infection, has_material_basis_in Pasteurella multocida, which is transmitted_by animal bite, scratch, or lick. The infection has_symptom joint pain has_symptom fever, has_symptom rigors, has_symptom pneumonia, has_symptom meningeal irritation, and has_symptom tachycardia. pasteurellosis A brucellosis that involves an infection caused by Brucella suis [NCBITaxon:29461] in swine and humans. The disease has_symptom fever, has_symptom chills, has_symptom malaise, has_symptom diaphoresis, has_symptom arthralgia, has_symptom myalgia, has_symptom headache, has_symptom anorexia, and has_symptom fatigue. Brucella suis brucellosis A primary bacterial infectious disease that is caused by the bacteria of the genus Brucella, when humans come in contact with contaminated animals or animal products or ingestion of infected food products. The disease has_symptom fever, has_symptom sweat, has_symptom headache, has_symptom back pain, has_symptom physical weakness, has_symptom joint pain and has_symptom fatigue. brucellosis A primary bacterial infectious disease that is a zoonotic infectious disease affecting multiple organs, has_material_basis_in Coxiella burnetii, which is transmitted_by inhalation of air contaminated by barnyard dust containing dried placental material, birth fluids, or excreta of infected herd animals, transmitted_by ingestion of contaminated milk, transmitted_by tick bites and transmitted_by contact with infected person. The infection has_symptom fever, has_symptom headache, has_symptom cough, has_symptom pleuritic chest pain, has_symptom myalgia and has_symptom arthralgia. Q fever A primary bacterial infectious disease that results in systemic infection, has_material_basis_in Bartonella quintana, which is transmitted by body lice (Pediculus humanus corporis). The infection has symptom relapsing fever, has symptom headache, has symptom shin pain, and has symptom soreness of the muscles of the legs and back. trench fever A primary bacterial infectious disease that is caused by the bacteria of the genus Bartonella. bartonellosis A spotted fever that has_material_basis_in Rickettsia akari, which is transmitted_by house mouse mite (Liponyssoides sanguineus) found on mice and other rodents. The infection has_symptom fever, has_symptom chills, has_symptom headache, has_symptom myalgia, and has_symptom papulovesicular rash. rickettsialpox A primary bacterial infectious disease that results in infection, located in endothelial cell of artery or located in endothelial cell of vein, has_material_basis_in Rickettsia, which is transmitted by ticks and mites. The infection has symptom fever, has symptom headache, has symptom fatigue, has symptom muscle aches, and has symptom maculopapular or petechial rash. A distinctive eschar (blackened or crusted skin) may develop at the site of a tick bite. spotted fever A commensal bacterial infectious disease that results_in inflammation located_in respiratory tract, has_material_basis_in Bordetella pertussis, or has_material_basis_in Bordetella parapertussis, which produce toxins that paralyze the cilia of the respiratory epithelial cells. The infection is characterized by a prolonged, high-pitched, deeply indrawn breath (whoop). pertussis A lung disease characterized by inadequate gas exchange by the respiratory system. respiratory failure disseminated intravascular coagulation An epidemic typhus that is a mild form of the disease, which recurs in someone after a long period of latency due to immunosuppression, malnutrition or other illnesses. Brill-Zinsser disease A primary bacterial infectious disease that refers to a group of diseases, located in endothelial cells of the small venous, arterial, and capillary vessels, has_material_basis_in Rickettsia bacteria, which are transmitted by lice, transmitted by fleas, and transmitted by mites. typhus A bartonellosis that results_in infection located_in lymph node, has_material_basis_in Bartonella henselae or has_material_basis_in Bartonella clarridgeiae, which are transmitted_by scratch or bite of a kitten, or transmitted_by contact of animal's saliva with an eye or through broken skin. The infection has_symptom regional lymphadenopathy, has_symptom headache, has_symptom chills, has_symptom backache, and has_symptom abdominal pain. cat-scratch disease A primary bacterial infectious disease that results_in systemic infection, has_material_basis_in Chlamydia psittaci, which is transmitted_by inhaling aerosolized dried droppings or transmitted_by contact with infected birds. The infection has_symptom fever, has_symptom headache, has_symptom rash, has_symptom chills, and has_symptom pneumonia. ornithosis A commensal bacterial infectious disease that is caused by Chlamydia trachomatis. chlamydia A commensal bacterial infectious disease that results_in infection located_in eye, has_material_basis_in Chlamydia trachomatis (A, B, Ba and C serovars), which is transmitted_by contact with eye discharge from the infected person and transmitted_by congenital method. The infection causes eyelid to turn inward which makes eyelashes to scratch the cornea. trachoma A primary bacterial infectious disease that involves the inflammation of mucosa lining the nasal cavity, pharynx, larynx, trachea and bronchi that is characterized by the formation of granulomas, dense induration of the tissues and nodular deformity caused by Klebsiella rhinoscleromatis. rhinoscleroma A commensal bacterial infectious disease that is characterized by systemic sepsis, ulcerative or necrotic lesions and multisystem abscesses caused by Fusobacterium necrophorum. The disease often first presents as a severe tonsillitis or pharyngitis with high-grade fever and chills together with leukocytosis, cervical pain and neck swelling. Lemierre's syndrome A primary bacterial infectious disease that results in prolonged contraction of skeletal muscle fibers, has_material_basis_in Clostridium tetani, which produces tetanospasmin, a neurotoxin, which is carried to the brain and spinal cord, where it binds irreversibly to receptors inhibiting neurotransmission. Damaged upper motor neurons cannot control reflex responses to afferent sensory stimuli. tetanus A respiratory failure that results from diffuse injury to the endothelium of the lung (as in sepsis, chest trauma, massive blood transfusion, aspiration of the gastric contents, or pneumonia) and is characterized by pulmonary edema with an abnormally high amount of protein in the edematous fluid and by difficult rapid breathing and hypoxemia. adult respiratory distress syndrome A cardiovascular system disease that involves the heart. heart disease A primary bacterial infectious disease that is characterized by sore throat, low fever, and an adherent membrane (a pseudomembrane) on the tonsils, pharynx, and/or nasal cavity. A milder form of diphtheria can be restricted to the skin. It is caused by Corynebacterium diphtheriae, an aerobic Gram-positive bacterium. Diphtheria toxin spreads through the bloodstream and can lead to potentially life-threatening complications that affect other organs of the body, such as the heart and kidneys. diphtheria A bacterial meningitis that has_material_basis_in Listeria monocytogenes infection. Listeria meningitis A primary bacterial infectious disease that results_in infection, has_material_basis_in Listeria monocytogenes, which is transmitted_by ingestion of contaminated food or raw milk or transmitted_by congenital method. Ingestion of Listeria by pregnant women has_symptom nausea, has_symptom vomiting, has_symptom diarrhea, has_symptom fever, has_symptom malaise, has_symptom back pain, and has_symptom headache. Maternal infection with Listeria can result in chorioamnionitis, premature labor, spontaneous abortion, or stillbirth. listeriosis A bacterial meningitis that has_material_basis_in streptococcal bacteria. streptococcal meningitis A primary bacterial infectious disease that results_in infection, has_material_basis_in Borrelia burgdorferi, which is transmitted_by blacklegged tick (Ixodes scapularis) or transmitted_by western blacklegged tick (Ixodes pacificus). The infection has_symptom fever, has_symptom headache, has_symptom fatigue, and has_symptom skin rash called erythema migrans. If left untreated, infection can spread to joints, the heart, and the nervous system. Lyme disease A pertussis that is a milder disease caused by the bacterium Bordetella parapertussis. The disease has_symptom coughing, has_symptom sneezing, or has_symptom runny nose. Bordetella parapertussis whooping cough A leprosy that is an early form of the disease which causes one to a few hypopigmented or erythematous macules. indeterminate leprosy esophagitis A primary bacterial infectious disease that involves intoxication caused by botulinum neurotoxins (BoNTA, B, E and F) located in neuromuscular junction resulting in descending muscle paralysis, has_material_basis_in Clostridium botulinum A, has_material_basis_in Clostridium botulinum B, has_material_basis_in Clostridium botulinum E and has_material_basis_in Clostridium botulinum F. botulism A tularemia that results_in painful regional lymphadenopathy and an ulcerated skin lesion. ulceroglandular tularemia An immune system disease that is an exaggerated immune response to allergens, such as insect venom, dust mites, pollen, pet dander, drugs or some foods. allergic disease A primary bacterial infectious disease that results_in infection, has_material_basis_in Spirillum minus, which is transmitted_by contact with urine or secretions from the mouth, eye, or nose of an infected animal or transmitted_by bite of an infected animal, especially rat. The infection has_symptom chills, has_symptom relapsing fever, has_symptom rash and has_symptom joint pain. sodoku disease A female reproductive system disease that is located_in the vagina. vaginal disease A primary bacterial infectious disease that results_in infection located_in epithelium of colon, has_material_basis_in Shigella boydii, has_material_basis_in Shigella dysenteriae, has_material_basis_in Shigella flexneri, or has_material_basis_in Shigella sonnei, which produce toxins that can attack the lining of the large intestine, causing swelling, ulcers on the intestinal wall, and bloody diarrhea. The bacteria are transmitted_by ingestion of food and water contaminated with feces. shigellosis A hematopoietic system disease that is characterized by abnormal blood clotting or bleeding. blood coagulation disease An urogenital tuberculosis that is located_in epididymis, has_symptom pain and has_symptom scrotal swelling. tuberculous epididymitis A kidney disease that is characterized by hemolytic anemia, thrombocytopenia, and renal failure caused by platelet thrombi in the microcirculation of the kidney and other organs. hemolytic-uremic syndrome parametritis A respiratory failure that is characterized by deficiency of the surfactant coating the inner surface of the lungs, by failure of the lungs to expand and contract properly during breathing with resulting collapse, and by the accumulation of a protein-containing film lining the alveoli and their ducts. newborn respiratory distress syndrome A disease of anatomical entity which occurs in the blood, heart, blood vessels or the lymphatic system that passes nutrients (such as amino acids and electrolytes), gases, hormones, blood cells or lymph to and from cells in the body to help fight diseases and help stabilize body temperature and pH to maintain homeostasis. cardiovascular system disease A primary bacterial infectious disease that results_in infection, has_material_basis_in Borrelia, which is transmitted_by tick or transmitted_by body louse. relapsing fever A relapsing fever that is characterized by relapsing or recurring episodes of fever, has_material_basis_in Borrelia recurrentis, which is transmitted_by body louse (Pediculus humanus). The infection has_symptom tachypnea, has_symptom tachycardia, has_symptom hepatosplenomegaly and has_symptom lymphadenopathy. louse-borne relapsing fever A relapsing fever that is characterized by relapsing or recurring episodes of fever, has_material_basis_in Borrelia hermsii, has_material_basis_in Borrelia parkeri or has_material_basis_in Borrelia duttoni, which are transmitted_by soft ticks (Ornithodoros parkeri and Ornithodoros hermsii). The infection has_symptom tachypnea, has_symptom tachycardia, has_symptom hepatosplenomegaly and has_symptom lymphadenopathy. tick-borne relapsing fever A cystitis characterized by a sudden onset or severe symptoms. acute cystitis A tularemia that results_in inflammation of eye and swelling of lymph glands in front of the ear. oculoglandular tularemia A primary bacterial infectious disease that results_in infection, has_material_basis_in Streptobacillus moniliformis, which is transmitted_by contact with urine or secretions from the mouth, eye, or nose of an infected animal or transmitted_by bite of an infected animal, especially rat. The infection has_symptom chills, has_symptom fever, has_symptom rash and has_symptom joint pain. Haverhill fever A primary bacterial infectious disease that is a communicable systemic illness, has_material_basis_in Salmonella enterica subsp enterica serovar Typhi, which is transmitted_by ingestion of food or water contaminated with the feces of an infected person. The infection has_symptom fever, has_symptom diarrhea, has_symptom prostration, has_symptom headache, has_symptom splenomegaly, has_symptom liver enlargement, has_symptom eruption of rose-colored spots, and has_symptom leukopenia. typhoid fever A bacterial pneumonia involving Klebsiella pneumoniae infection. Patients with Klebsiella pneumonia tend to cough up a characteristic sputum that is said to resemble red-currant jelly. Klebsiella pneumonia tends to affect people with underlying diseases, such as alcoholism, diabetes and chronic lung disease. The symptoms include high fever, rigors and pleuritic pain, and hemoptysis. Klebsiella pneumonia A bacterial pneumonia that is caused by the bacterial species Mycoplasma pneumoniae. The symptoms include chest pain, chills, dry cough which is not bloody, excessive sweating, fever, headache and sore throat. Mycoplasma pneumoniae pneumonia A gastrointestinal tuberculosis that involves diffuse mucosal fold thickening, formation of ulcers and fistulae located_in intestine. The infection has_symptom abdominal pain, has_symptom gastrointestinal bleeding, has_symptom nausea and has_symptom vomiting. intestinal tuberculosis A typhus that has_material_basis_in Orientia tsutsugamushi, which is transmitted by trombiculid mites (Leptotrombidium deliense). The infection has symptom fever, has symptom headache, has symptom muscle pain, has symptom cough, has symptom maculopapular rash, has symptom eschar, has symptom splenomegaly and has symptom lymphadenopathy. scrub typhus An anthrax disease that results in infection located in mucosa of gastrointestinal tract, has_material_basis_in Bacillus anthracis, which is transmitted by ingestion of anthrax-infected meat. The infection has symptom lesions, has symptom vomiting of blood, has symptom severe diarrhea, has symptom loss of appetite. gastrointestinal anthrax A primary bacterial infectious disease that results in infection located in mucosa of mouth, located in skin or located in bone, has_material_basis_in Treponema pallidum subsp endemicum, which is transmitted by contact or transmitted by sharing of domestic utensils. The infection has symptom moist patches in the mouth, has symptom lumps in long bones, tissues around the mouth, nose, and roof of the mouth. These lumps destroy tissue, causing bones to be deformed and disfiguring the face. bejel A primary bacterial infectious disease that results in septicemic infection, has_material_basis_in Burkholderia mallei, which is transmitted by contact with tissues or body fluids of infected animals, or through mucosal surfaces such as the eyes and nose. The infection has symptom fever, has symptom chills, has symptom sweating, has symptom muscle aches, has symptom chest pain, has symptom muscle tightness, has symptom headache, has symptom mucopurulent nasal discharge, and has symptom nodular lesions in the lungs. glanders A tetanus that occurs in newborn babies when the birth cord stump gets dirty through cutting it with an unclean blade or applying substances containing bacteria to it. The infection has symptom stiff body, has symptom muscle spasms, has symptom difficulty in breathing, and has symptom exhaustion. tetanus neonatorum A primary bacterial infectious disease that results_in infection located_in intestine, has_material_basis_in Campylobacter jejuni, which is transmitted_by ingestion of contaminated food or water or transmitted_by contact with infected people or animals. The infection has_symptom diarrhea or has_symptom dysentery, has_symptom abdominal cramps and pain, and has_symptom fever. campylobacteriosis A primary bacterial infectious disease that is a sexually transmitted infection located in skin of the genitals, has_material_basis_in Haemophilus ducreyi, which is transmitted by sexual contact. The infection has symptom painful and soft ulcers. chancroid A commensal bacterial infectious disease that results_in inflammation, located_in conjunctiva of the eye, has_material_basis_in Chlamydia trachomatis, which is transmitted_by sexual contact. The infection has_symptom swollen conjunctiva and eyelids and has_symptom discharge of pus and mucus. inclusion conjunctivitis A commensal bacterial infectious disease that results_in infection located_in lymph nodes, has_material_basis_in Chlamydia trachomatis, which is transmitted_by sexual contact, and transmitted_by fomites. The infection has_symptom inguinal lymphadenitis, has_symptom abscesses in the groin area, and has_symptom lymphangitis. lymphogranuloma venereum bacterial esophagitis A brucellosis involving an infection caused by Brucella canis [NCBITaxon:36855] in dogs and humans. The disease has_symptom fever, has_symptom sweats, has_symptom weakness, has_symptom weight loss, has_symptom headache, has_symptom lymphadenopathy and has_symptom splenomegaly. Brucella canis brucellosis A spotted fever that has_material_basis_in Rickettsia conorii subsp conorii, which is transmitted_by dog tick (Rhipicephalus sanguineus). The infection has_symptom fever, has_symptom eschar (usually single), has_symptom regional adenopathy, has_symptom maculopapular rash on extremities. boutonneuse fever A commensal bacterial infectious disease that results_in infection, has_material_basis_in Streptococcus pyogenes or has_material_basis_in Staphylococcus aureus, which produce toxins that are absorbed systemically and produce the systemic manifestations. The infection has_symptom fever, has_symptom rash, has_symptom hypotension, has_symptom multiorgan failure, has_symptom desquamation, has_symptom vomiting, has_symptom diarrhea, has_symptom headache, and has_symptom nonfocal neurologic abnormalities. toxic shock syndrome A tularemia that results in formation of ulcerative lesions located in gastrointestinal tract. The infection has symptom fever, has symptom chills, has symptom malaise, has symptom muscle aches, and has symptom vomiting. gastrointestinal tularemia A urinary system disease that is located_in the ureter. ureteral disease A brucellosis that involves an infection caused by Brucella melitensis [NCBITaxon:29459] in cattle, goats, sheep and humans. The disease has_symptom fever, has_symptom malaise, has_symptom anorexia, has_symptom limb pain and has_symptom back pain. Brucella melitensis brucellosis A brucellosis that involves an infection caused by Brucella abortus [NCBITaxon:235] in cattle and humans. The disease has_symptom fever, has_symptom chills, has_symptom sweats, has_symptom weight loss, has_symptom malaise, has_symptom headaches, has_symptom myalgia, and has_symptom arthralgia. Brucella abortus brucellosis anaerobic meningitis A disease that is characterized by abnormally rapid cell division. disease of cellular proliferation A primary bacterial infectious disease that is described as an acute, diarrheal illness caused by infection of the intestine with the bacterium Vibrio cholerae, which is characterized by profuse watery diarrhea, vomiting, leg cramps, circulatory collapse and shock. cholera A disease of anatomical entity that is located_in reproductive system organs. reproductive system disease A thoracic disease which may involve inflammation of pleura, collection of air within the pleural cavity, abnormal collection of pleural fluid, abnormal growths on the pleura (pleural tumor) and pleural plaques. The main causes of pleural diseases including pleural effusions are congestive heart failure, malignancy, parapneumonic infections and pulmonary embolism. pleural disease A disease by infectious agent that results_in infection, has_material_basis_in Fungi, which pass the resistance barriers of the human or animal body. fungal infectious disease A disease of anatomical entity that located_in the respiratory system which extends from the nasal sinuses to the diaphragm. respiratory system disease A connective tissue disease that develops from an antecedent Group A Streptococcal pharyngeal infection and has_symptom carditis, has_symptom polyarthritis, has_symptom chorea, has_symptom erythema marginatum, has_symptom subcutaneous nodules, has_symptom arthralgia, has_symptom prolonged PR interval, and/or has_symptom fever. rheumatic fever A disease of anatomical entity that is located_in the integumentary system comprising the skin and its appendages. integumentary system disease A disease of cellular proliferation that is malignant and primary, characterized by uncontrolled cellular proliferation, local cell invasion and metastasis. cancer An extrapulmonary tuberculosis that results in formation of tuberculomas located_in brain or located_in spinal cord. central nervous system tuberculosis An extrapulmonary tuberculosis that results in formation of lesions located in bone. skeletal tuberculosis A bladder disease that is characterized by inflammation of the bladder. cystitis A disease of anatomical entity that occurs in the muscular and/or skeletal system. musculoskeletal system disease A disease of anatomical entity that is located_in kidney, ureter, bladder and urethra. urinary system disease A female reproductive system disease that is located_in the fallopian tube. fallopian tube disease A tularemia that is located_in lungs. The bacteria are transmitted_by breathing dusts or aerosols containing the organisms. The infection has_symptom cough, has_symptom chest has_symptom pain, and has_symptom difficulty breathing. pneumonic tularemia A primary bacterial infectious disease that has_material_basis_in Francisella tularensis, which is transmitted by dog tick bite (Dermacentor variabilis), transmitted by deer flies (Chrysops sp) or transmitted by contact with infected animal tissues. tularemia An urogenital tuberculosis that results_in inflammtion located_in ovary. tuberculous oophoritis An extrapulmonary tuberculosis that is located_in urogenital system. urogenital tuberculosis A vaginal disease that is characterized by inflammation of the vagina. vaginitis An endocrine system disease that is located_in the gonads. gonadal disease A reproductive system disease that impairs the ability to reproduce and is located in the uterus, vagina, cervix, ovaries or fallopian tubes. female reproductive system disease A primary bacterial infectious disease that involves systemic infection, has_material_basis_in Leptospira, which is transmitted by contact with water, food, or soil containing urine from the infected animals. The infection has symptom jaundice, has symptom chills, has symptom fever, has symptom muscle pain, and has symptom hepatomegaly. leptospirosis An opportunistic bacterial infectious disease that results_in disseminated infection in immunocompromised hosts, has_material_basis_in Nocardia asteroides. The infection has_symptom pneumonia, has_symptom cellulitis, has_symptom lesions in the brain or meninges, and has_symptom ascending regional lymphadenopathy. nocardiosis A gastrointestinal system infectious disease that involves inflammation of the lining of the stomach and small and large intestines, which is caused by viruses, bacteria, or parasites. Chemicals and drugs also cause gastroenteritis. The symptoms include diarrhea, loss of appetite, nausea, vomiting, cramps, and discomfort in the abdomen. gastroenteritis A blood coagulation disease that is characterized by an increased tendency to form clots. thrombophilia splenic disease An organ system cancer located in the hematological system that is characterized by uncontrolled cellular proliferation in blood, bone marrow and lymph nodes. hematologic cancer A primary bacterial infectious disease that results_in infection, has_material_basis_in Mycobacterium avium complex (MAC), which is transmitted_by inhalation or transmitted_by ingestion of via the respiratory or gastrointestinal tract respectively. The bacteria cause disseminated infection in HIV infected people, while pulmonary disease in immunocompetent persons. Mycobacterium avium complex disease A disease of anatomical entity that is located_in endocrine glands which secretes a type of hormone directly into the bloodstream to regulate the body. endocrine system disease A disease of anatomical entity that is located_in the immune system. immune system disease A Coronavirus infectious disease that results_in infection located_in respiratory tract, has_material_basis_in SARS coronavirus (SARS-CoV), which is transmitted_by droplet spread of respiratory secretions, transmitted_by ingestion of contaminated food, or transmitted_by fomites. The infection has_symptom fever, has_symptom headache, has_symptom body aches, has_symptom dry cough, and has_symptom hypoxia. severe acute respiratory syndrome A tuberculosis that is a contagious disease located_in lungs. The infection has_symptom fever, has_symptom cough, has_symptom difficulty in breathing, has_symptom inflammatory infiltrations, has_symptom formation of tubercles, has_symptom caseation, has_symptom pleural effusion, and has_symptom fibrosis. pulmonary tuberculosis A hypersensitivity reaction type I disease that is an abnormal response to a food, triggered by the body's immune system. food allergy A primary bacterial infectious disease that results_in infection located_in intestine, has_material_basis_in Salmonella enterica subsp enterica serovar Paratyphi A, B or C, which are transmitted_by ingestion of contaminated food. The infection has_symptom fever, has_symptom headache, has_symptom abdominal pain, has_symptom malaise, has_symptom anorexia, has_symptom constipation, has_symptom rosy spots on the central body, has_symptom non productive cough (in early stage of illness), has_symptom bradycardia, and has_symptom hepatosplenomegaly. paratyphoid fever An opportunistic bacterial infectious disease that has_material_basis_in Acinetobacter. Acinetobacter infectious disease A gastrointestinal system disease that is located_in the liver and/or biliary tract. hepatobiliary disease spinal cord disease A nervous system disease that affects either the spinal cord (myelopathy) or brain (encephalopathy) of the central nervous system. central nervous system disease A bone disease that results_in inflammation of the located_in bone. bone inflammation disease A vaginitis that is characterized by a grayish vaginal discharge usually of foul odor and the presence of Gardnerella vaginalis. bacterial vaginosis A disease of anatomical entity that is located_in the breast. breast disease A plague that results_in infection located_in vasculature where bacterial endotoxins cause coagulation, which leads to formation of tiny clots throughout the body. The infection has_symptom fever, has_symptom chills, has_symptom prostration, has_symptom abdominal pain, has_symptom shock and has_symptom bleeding into skin and other organs. septicemic plague A primary bacterial infectious disease that results_in infection, located_in lymph node, located_in vasculature or located_in lungs, has_material_basis_in Yersinia pestis, which is transmitted_by oriental rat flea (Xenopsylla cheopis) infected by feeding on rodents and other mammals, transmitted_by air, transmitted_by direct contact or transmitted_by ingestion of contaminated undercooked food. plague A urinary system disease that is located_in the bladder. bladder disease A food allergy that develops_from exposure to and particularly consumption of wheat, and has_symptom that are both gastrointestinal and nongastrointestinal in nature, such as diarrhea, mouth and throat irritation, headache, hives, skin rashes, and anaphylaxis. wheat allergy An integumentary system disease that is located_in skin. skin disease A cardiomyopathy that is characterized by the pathology occurring outside of the myocardium. extrinsic cardiomyopathy A primary bacterial infectious disease that is located_in lungs, located_in lymph nodes, located_in pericardium, located_in brain, located_in pleura or located_in gastrointestinal tract, has_material_basis_in Mycobacterium tuberculosis, which is transmitted_by droplets released into the air when an infected person coughs or sneezes. tuberculosis A disease is a disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism. http://purl.obolibrary.org/obo/OGMS_0000031 disease A tuberculosis that is resistant to isoniazid and rifampicin, the two most powerful first-line anti-TB drugs. multidrug-resistant tuberculosis A gastrointestinal tuberculosis that involves formation of painful ulcerative mucosal lesions located in tongue, located in palate, located in maxilla or located in mandible. oral tuberculosis A stomach disease that is an inflammation of the lining of the stomach. gastritis A gastrointestinal system disease that is located_in the mouth. mouth disease A gastritis that involves inflammation of the stomach lining caused by bacteria. The disease has_symptom abdominal pain, has_symptom indigestion, has_symptom ulcer formation, has_symptom abdominal bloating, has_symptom nausea and has_symptom vomiting. bacterial gastritis An abdominal tuberculosis that results_in infection located_in gastrointestinal tract. The infection has_symptom abdominal pain, has_symptom weight loss, has_symptom fever, has_symptom anorexia, has_symptom constipation, has_symptom nausea, and has_symptom vomiting. gastrointestinal tuberculosis A gastrointestinal tuberculosis that involves infection located_in liver, which results in the formation of tuberculous granulomas. The infection has_symptom fever, has_symptom anorexia, has_symptom weight loss, has_symptom abdominal pain and has_symptom jaundice. hepatic tuberculosis liver disease A syphilis that is the first stage of syphilis, marked by the development of a chancre, which is characterized by mononuclear leukocytic infiltration, macrophages, and lymphocytes. primary syphilis A syphilis that is characterized as the second stage of syphilis which appears from 2 to 6 months after primary infection, and is marked by lesions especially in the skin but also in organs and tissues, and that lasts from 3 to 12 weeks. secondary syphilis A primary bacterial infectious disease that is a sexually transmitted systemic disease, has_material_basis_in Treponema pallidum subsp pallidum, which is transmitted_by sexual contact, transmitted_by blood product transfusion, transmitted_by congenital method from mother to fetus or transmitted_by contact with infectious lesions. If left untreated, produces chancres, rashes, and systemic lesions in a clinical course with three stages continued over many years. syphilis An immune system disease that is an overactive immune response of the body against substances and tissues normally present in the body resulting from an abnormal functioning of the immune system that results in the production of antibodies or T cell directed against the host tissues. autoimmune disease An eye disease affecting the conjunctiva, which is the mucous membrane surrounding the eye and interior of the eyelids. conjunctival disease A food allergy that results in adverse immune reaction to one or more of the proteins in cow's milk and/or the milk of other animals, which are normally harmless to the non-allergic individual. milk allergy A food allergy that is an allergy or hypersensitivity to dietary substances from the yolk or whites of eggs, causing an overreaction of the immune system which may lead to severe physical symptoms. egg allergy A legume allergy that is an allergy or hypersensitivity to dietary substances from peanuts causing an overreaction of the immune system which in a small percentage of people may lead to severe physical symptoms. peanut allergy A food allergy that develops_from exposure to and particularly consumption of nuts, and has_symptom asthma, skin rashes, throat and eye irritation, and anaphylaxis. nut allergy subacute bacterial endocarditis A reproductive system disease that affects male reproductive organs. male reproductive system disease An extrapulmonary tuberculosis that is located_in lymph node, and has_symptom lymphadenopathy, has_symptom fever, has_symptom weight loss, has_symptom fatigue, has_symptom night sweats and has_symptom cough. lymph node tuberculosis An extrapulmonary tuberculosis that is located_in pericardium resulting in acute pericarditis, chronic pericardial effusion, cardiac tamponade or pericardial constriction. pericardial tuberculosis A commensal bacterial infectious disease that results_in infection, has_material_basis_in Actinobacillus ureae, which is a commensal of the human respiratory tract. The pathogen causes meningitis, endocarditis, bacteremia, atrophic rhinitis, bronchitis, pneumonia, conjunctivitis, peritonitis, and otitis media. actinobacillosis A primary bacterial infectious disease that results_in infection, has_material_basis_in Burkholderia pseudomallei, which is transmitted_by contact with the contaminated water or soil. The infection has_symptom fever, has_symptom respiratory distress, has_symptom chest pain, and has_symptom stomach pain. melioidosis A gastrointestinal system disease that is located_in the intestine. intestinal disease An adnexa disease that is located_in the eyelid. eyelid disease A intestinal disease located in the colon. colonic disease A lung disease that involves lung parenchyma or alveolar inflammation and abnormal alveolar filling with fluid (consolidation and exudation). It results from a variety of causes including infection with bacteria, viruses, fungi or parasites, and chemical or physical injury to the lungs. It is accompanied by fever, chills, cough, and difficulty in breathing. pneumonia A urinary system disease that is located_in the kidney. kidney disease An eye and adnexa disease that is located_in the eye. eye disease A gastrointestinal system disease that is located_in the esophagus. esophageal disease An immune system disease that results when one or more essential parts of the immune system is missing or not working properly at birth due to a genetic mutation. primary immunodeficiency disease A conjunctival disease characterized by an inflammation of the conjunctiva, the outermost layer of the eye and the inner surface of the eyelids. conjunctivitis A musculoskeletal system disease that affects tissues such as skin, tendons, and cartilage. connective tissue disease A disease that manifests in a defined anatomical structure. disease of anatomical entity A gastrointestinal tuberculosis that involves formation of tuberculous ulcers located_in esophagus. The infection has_symptom dysphagia, has_symptom cough, has_symptom chest pain, has_symptom fever and has_symptom weight loss. esophageal tuberculosis A disease of anatomical entity that has_material_basis_in hematopoietic cells. hematopoietic system disease An anthrax disease that results_in infection located_in skin, has_material_basis_in Bacillus anthracis, which is transmitted_by contact with infected animals or animal products. The infection has_symptom skin lesion that eventually forms an ulcer with a black center. cutaneous anthrax A primary bacterial infectious disease that results_in infection located_in skin, located_in lung lymph nodes or located_in gastrointestinal tract, has_material_basis_in Bacillus anthracis, transmitted_by contact with infected animals or animal products, transmitted_by airborne spores or transmitted_by ingestion of undercooked meat from infected animals and has_symptom skin ulcer, has_symptom nausea, has_symptom poor appetite, has_symptom bloody diarrhea, has_symptom fever or has_symptom shortness of breath. anthrax disease An immune system disease that is located_in the lymphatic system. lymphatic system disease An urogenital tuberculosis that is located_in urinary bladder, which results in fibrosis of bladder wall muscles. bladder tuberculosis A primary bacterial infectious disease that is a sexually transmitted infection, located_in uterus, located_in fallopian tube, located_in urethra, located_in mouth, located_in throat, located_in eye or located_in anus, has_material_basis_in Neisseria gonorrhoeae, which is transmitted_by contact with the penis, vagina, mouth, or anus or transmitted_by congenitally from mother to baby during delivery. The infection has_symptom burning sensation during urination, has_symptom discharge from the penis, has_symptom increased vaginal discharge, or has_symptom vaginal bleeding between periods. gonorrhea A gastrointestinal system disease that is located_in the stomach. stomach disease A disease of anatomical entity that is located_in the gastrointestinal tract. gastrointestinal system disease An extrinsic cardiomyopathy that is characterized as an inflammation of the heart muscle. myocarditis A syphilis that is characterized as the third stage of syphilis that develops after the disappearance of the secondary symptoms and is marked by ulcers and gummas under the skin and commonly by involvement of the skeletal, cardiovascular, and nervous systems. tertiary syphilis An urogenital tuberculosis that is located_in ureter resulting in ureteral strictures. ureter tuberculosis A gastrointestinal system disease that involves inflammation of the peritoneum resulting from perforation of the gastrointestinal tract, which produces immediate chemical inflammation followed shortly by infection from intestinal organisms. Peritonitis can also result from appendicitis, diverticulitis, strangulating intestinal obstruction, pancreatitis, pelvic inflammatory disease, mesenteric ischemia, intraperitoneal blood, barium, or peritoneo-systemic shunts, drains, and dialysis catheters in the peritoneal cavity. The symptoms include abdominal pain and tenderness, fever, fluid in the abdomen, nausea, vomiting and low urine output. peritonitis A commensal bacterial infectious disease that results in infection, which is characterized by contiguous spread, suppurative and granulomatous inflammation, and formation of multiple abscesses and sinus tracts that may discharge sulfur granules, has_material_basis_in Actinomyces israelii, has_material_basis_in Actinomyces gerencseriae, has_material_basis_in Actinomyces naeslundii, has_material_basis_in Actinomyces odontolyticus, has_material_basis_in Actinomyces viscosus, has_material_basis_in Actinomyces meyeri, has_material_basis_in Propionibacterium propionicum, which require a break in the integrity of the mucous membranes and the presence of devitalized tissue to invade deeper body structures. actinomycosis rheumatic myocarditis A lower respiratory tract disease in which the function of the lungs is adversely affected by narrowing or blockage of the airways resulting in poor air flow, a loss of elasticity in the lungs that produces a decrease in the total volume of air that the lungs are able to hold, and clotting, scarring, or inflammation of the blood vessels that affect the ability of the lungs to take up oxygen and to release carbon dioxide. lung disease A colitis that is predominantly confined to the mucosa located_in colon and includes characteristic ulcers, or open sores. ulcerative colitis An upper respiratory tract disease described as an acute contagious disease caused by Group A bacteria of the genus Streptococcus (especially various strains of S. pyogenes) and characterized by inflammation of the nose, throat, and mouth, generalized toxemia, and a red rash. scarlet fever A disease of anatomical entity that is located_in the central nervous system or located_in the peripheral nervous system. nervous system disease An aspiration pneumonia caused by anaerobic bacteria like Bacteroides fragilis, Peptostreptococcus, anaerobic streptococci, Fusobacterium species (Fusobacterium nucleatum and Fusobacterium necrophoram). Lung abscess and empyema are diagnosed in this disease. anaerobic pneumonia A pneumonia involving inflammation of the lungs caused by bacteria. bacterial pneumonia A commensal bacterial infectious disease that is characterized by widespread erythema, peeling, and necrosis of the skin, that is caused by a toxin produced by a bacterium of the genus Staphylococcus (S. aureus). The infection has_symptom redness of skin, has_symptom fluid-filled blister formation, has_symptom fever and has_symptom irritability. Ritter's disease A primary bacterial infectious disease that results_in infection located_in skin or located_in mucosa of genital tract, has_material_basis_in Klebsiella granulomatis, transmitted by sexual contact or transmitted_by contact with the open sores. The infection has_symptom painless genital ulcers. granuloma inguinale A commensal bacterial infectious disease that results in infection, located in muscle tissue, has_material_basis_in Clostridium perfringens, which produce gas that becomes trapped in the infected tissue. Gas gangrene usually develops after injuries or surgery. The infection has symptom large blisters, has symptom pain in the infected area, has symptom myonecrosis, has symptom gas production, and has symptom sepsis. gas gangrene An abdominal tuberculosis that results_in formation of granulomas or abscesses located_in spleen. splenic tuberculosis A disease by infectious agent that results in infection, has_material_basis_in Viruses. viral infectious disease A central nervous system disease that is located_in the brain. brain disease vesiculitis A meningitis that has_material_basis_in a bacterial infection. bacterial meningitis A central nervous system disease that is characterized by an inflammation of the pia-arachnoid meninges. It can be caused by growth of bacteria, fungi, or parasites within the subarachnoid space or by the growth of bacteria or viruses within the meningeal or ependymal cells. meningitis A syphilis that is characterized as having serologic proof of infection without signs or symptoms of disease. latent syphilis A brain disease that is characterized as an acute inflammation of the brain with flu-like symptoms. encephalitis A primary bacterial infectious disease that results_in infection located_in intestine caused by eating food contaminated with enterotoxins produced by bacteria, has_material_basis_in Staphylococcus aureus. The infection has_symptom diarrhea, has_symptom vomiting, has_symptom nausea, has_symptom cramps, and has_symptom weakness. staphyloenterotoxemia A bacterial conjuctivitis that is characterized by pain and tenderness in the eyeball and conjuctival discharge. ophthalmia neonatorum bacterial conjunctivitis An urogenital tuberculosis that results_in formation of granulomas located_in kidney. renal tuberculosis A respiratory system disease which involves the upper respiratory tract. upper respiratory tract disease A gastrointestinal tuberculosis that results_in inflammation located_in peritoneum, which results in formation of tubercles. The infection has_symptom abdominal discomfort, has_symptom pain, has_symptom distention from gas or fluid, has_symptom digestive disturbances and has_symptom emaciation. tuberculous peritonitis A syphilis that results_in a multisystem infection in the fetus via the placenta. congenital syphilis An extrapulmonary tuberculosis that results in formation of tiny lesions in all the organs. miliary tuberculosis A tertiary syphilis that is manifested as aneurysm formation in the ascending aorta, caused by chronic inflammatory destruction of the vasa vasorum, insufficiency of the aortic valve, or narrowing of the coronary arteries. cardiovascular syphilis internal hordeolum An eyelid disease that is characterized by an infection of the sebaceous glands at the base of the eyelashes. Styes are generally caused by a Staphylococcus aureus bacterial infection. hordeolum lymph node disease acute female pelvic peritonitis A tertiary syphilis that results in infection located in brain or located in spinal cord. tertiary neurosyphilis A exposure event involving the interaction of an exposure receptor to environmental system. environmental system exposure exposure to environmental system A exposure event involving the interaction of an exposure receptor to construction. construction exposure exposure to construction A exposure event involving the interaction of an exposure receptor to abattoir. abattoir exposure exposure to abattoir A exposure event involving the interaction of an exposure receptor to farm. farm exposure exposure to farm A exposure event involving the interaction of an exposure receptor to hospital. hospital exposure exposure to hospital A exposure event involving the interaction of an exposure receptor to laboratory facility. laboratory facility exposure exposure to laboratory A exposure event involving the interaction of an exposure receptor to office. office exposure exposure to office A exposure event involving the interaction of an exposure receptor to restaurant. restaurant exposure exposure to restaurant A exposure event involving the interaction of an exposure receptor to shop. shop exposure exposure to retail shop A history of exposure to root. root exposure exposure to organism A history of exposure to Homo sapiens. Homo sapiens exposure exposure to humans A exposure event involving the interaction of an exposure receptor to geographic feature. geographic feature exposure exposure to geographic feature A exposure event involving the interaction of an exposure receptor to petting zoo. petting zoo exposure exposure to petting zoo A exposure event involving the interaction of an exposure receptor to campground. campground exposure exposure to campground An exposure event involving Activity Activity exposure exposure to behavior An exposure event involving Violence Violence exposure exposure to violence An exposure event involving hunting behavior hunting behavior exposure exposure to hunting An astrononmical body part which delimited by physical discontinuities with its surroundings. https://en.wikipedia.org/wiki/Geographic_feature macroscopic spatial feature envoPolar This class is being depopulated and will be filled only with inferred subclasses. Please do not use this for direct annotation, favouring instead a more descriptive subclass. geographic feature constructed feature An anthropogenic geographic feature is a geographic feature resulting from the influence of human beings on nature. FTT:78 TGN:50001 anthropogenic geographic feature FTT:1242 FTT:1252 FTT:15 FTT:16 FTT:18 FTT:19 FTT:21 FTT:22 FTT:23 FTT:24 FTT:25 FTT:26 FTT:27 FTT:28 FTT:29 FTT:37 SWEETRealm:AdministrativeRegion TGN:80001 TGN:81099 TGN:81123 https://en.wikipedia.org/wiki/Administrative_region administrative area administrative region state / province / territory / region lookup:http://purl.obolibrary.org/obo/GAZ_00000448 A primary administrative division of a country, such as a state in the United States. FTT:414 FTT:569 Geonames:A.ADM1 TGN:81100 first-order administrative region A political association with effective dominion over a geographic area. FTT:424 FTT:566 FTT:567 FTT:571 SWEETRealm:Country SWEETRealm:State TGN:80006 TGN:81010 TGN:81011 TGN:81102 https://en.wikipedia.org/wiki/Nation http://purl.obolibrary.org/obo/NCIT_C25464 nation independent nation independent political entity independent sovereign nation national geopolitical entity A construction which enables the movement of humans, their animals or their vehicles. FTT:83 transport feature An enclosure for displaying selected plant or animal life. FTT:31 FTT:743 Geonames:S.GDN TGN:53010 https://en.wikipedia.org/wiki/Garden garden A geographical feature associated with water. FTT:131 FTT:280 FTT:711 FTT:761 FTT:824 FTT:825 FTT:826 FTT:827 FTT:828 FTT:829 Geonames:H.OVF envoPolar hydrographic feature Artificial watercourse with no flow or a controlled flow used for navigation, drainage or irrigation. EcoLexicon:canal FTT:129 FTT:395 FTT:407 FTT:408 Geonames:H.CNL SWEETRealm:Canal TGN:51252 https://en.wikipedia.org/wiki/Canal This class refers to the water contained in a canal channel, and not the channel itself. canal A marine water body which is constitutes the majority of an astronomical body's hydrosphere. EcoLexicon:ocean FTT:1019 FTT:943 Geonames:H.OCN LTER:695 SWEETRealm:Ocean TGN:21102 https://en.wikipedia.org/wiki/Ocean envoMarine envoPolar ocean A large expanse of saline water usually connected with an ocean. EcoLexicon:sea FTT:233 FTT:830 Geonames:H.SEA TGN:21103 https://en.wikipedia.org/wiki/Sea channel closed sea marginal sea open sea open sound open water envoMarine envoPolar sea A body of water or other liquid of considerable size contained in a depression on a landmass. EcoLexicon:lake FTT:221 FTT:704 FTT:909 Geonames:H.LK Geonames:H.LKS LTER:278 SPIRE:Lake_or_pond SWEETRealm:Lake TGN:21114 TGN:21115 catch basin open water tarn envoPolar lake A stream which, through permanent or seasonal flow processes, moves from elevated land towards lower elevations through a definite channel and empties either into a sea, lake, or another river or ends on land as bed seepage and evapotranspiration exceed water supply. EcoLexicon:river FTT:1179 FTT:251 LTER:474 SPIRE:River SWEETRealm:River TGN:21105 rio braided river "There are no official definitions for the generic term river as applied to geographic features, although in some countries or communities a stream is defined by its size. Many names for small rivers are specific to geographic location; examples are "run" in some parts of the United States, "burn" in Scotland and northeast England, and "beck" in northern England. Sometimes a river is defined as being larger than a creek, but not always: the language is vague." river A watercourse which is linear and flows across the solid portion of a planetary surface. watercourse EcoLexicon:stream FTT:105 FTT:1221 FTT:1225 FTT:1261 FTT:303 FTT:371 FTT:593 FTT:721 Geonames:H.STM Geonames:H.STMS LTER:562 SWEETRealm:Stream TGN:21106 TGN:21107 TGN:21108 TGN:21109 https://en.wikipedia.org/wiki/Stream streams braided stream fork (hydrographic lode millstream stream bend streamlet stream An artificial body of water, often contained by a dam, constructed for the purpose of water storage. lake EcoLexicon:reservoir FTT:587 FTT:588 FTT:882 Geonames:H.RSV SWEETRealm:Reservoir TGN:51259 https://en.wikipedia.org/wiki/Reservoir covered reservoir reservoir A cylindrical hole, pit, or tunnel drilled or dug down to a depth from which water, oil, or gas can be pumped or brought to the surface. EcoLexicon:well FTT:1032 FTT:1237 FTT:833 Geonames:H.WLL Geonames:H.WLLS SWEETRealm:Well TGN:51255 https://en.wikipedia.org/wiki/Well well A surface landform which provides an egress for groundwater or steam to flow out of the ground. EcoLexicon:spring FTT:982 Geonames:H.SPNG SWEETRealm:Spring TGN:21126 Springs are typically where an aquifer surface meets the ground surface or where there is a fissure. spring A flowing body of water. EcoLexicon:brook EcoLexicon:course EcoLexicon:culvert EcoLexicon:gully EcoLexicon:ravine EcoLexicon:spillway EcoLexicon:waterway FTT:105 Geonames:H.NRWS Geonames:H.RCH Geonames:H.WTRC Geonames:S.SPLY TGN:21110 TGN:21131 TGN:21133 TGN:21137 TGN:21163 TGN:21499 https://en.wikipedia.org/wiki/Watercourse culvert dredged channel fork gulch gully gut gutter kill lode narrows overflow channel passage pup race ravine reach rill rivulet run runnel seachannel seaway spillway stream tideway wash water gap watercourse An area of water bordered by land on three sides. EcoLexicon:bay FTT:190 FTT:232 FTT:235 Geonames:H.BAY Geonames:H.BAYS Geonames:H.BGHT SWEETRealm:Bay TGN:21121 TGN:21123 TGN:21127 bay A body of water, usually of smaller size than a lake. lake EcoLexicon:pond FTT:221 FTT:902 FTT:904 FTT:905 Geonames:H.PND Geonames:H.PNDS Geonames:H.POOL LTER:975 SPIRE:Lake_or_pond SWEETRealm:Pond TGN:21104 TGN:21119 https://en.wikipedia.org/wiki/Pond Pond pool (water body) pond A small, human-made channel which has been dug for draining or irrigating the land. EcoLexicon:drain FTT:129 FTT:400 FTT:403 Geonames:DTCH SWEETRealm:Drain TGN:51256 https://en.wikipedia.org/wiki/Ditch ditch Artificial watercourse with no flow or a controlled flow used drainage. canal FTT:129 FTT:401 Geonames:H.CNLD drainage canal An vegetated area which overlaps a wetland ecosystem. wetland area Place or area with clustered or scattered buildings and a permanent human population. place FTT:1097 FTT:33 Geonames:P.PPL Geonames:P.PPLS TGN:22201 TGN:83002 https://en.wikipedia.org/wiki/Populated_place populated places settlement populated place An accumulation of water of varying size. hydrographic feature EcoLexicon:waterbody FTT:131 FTT:280 FTT:827 SWEETRealm:BodyOfWater TGN:21100 TGN:21101 https://en.wikipedia.org/wiki/Water_body aquatic feature bodies of water body of water waterbody The term body of water most often refers to large accumulations of water, such as oceans, seas, and lakes, but it includes smaller pools of water such as ponds, wetlands, or more rarely, puddles. A body of water does not have to be still or contained; Rivers, streams, canals, and other geographical features where water moves from one place to another are also considered bodies of water. water body Naturally formed, subterranean open area or chamber. FTT:1071 FTT:443 FTT:445 FTT:446 FTT:447 Geonames:S.CAVE SWEETRealm:Cave TGN:21485 TGN:21486 https://en.wikipedia.org/wiki/Cave cave An underground or underwater passage. FTT:445 FTT:448 Geonames:R.TNLN SWEETRealm:Tunnel TGN:21447 https://en.wikipedia.org/wiki/Tunnel TUNNEL tunnel A construction that has been assembled by deliberate human effort. constructed feature human construction A permanent walled and roofed construction. FTT:42 Geonames:S.BLDG LTER:76 TGN:51011 https://en.wikipedia.org/wiki/Building building A barrier constructed across a watercourse to control the flow or raise the level of water. EcoLexicon:dam FTT:599 FTT:600 Geonames:S.DAM SWEETRealm:Dam TGN:51253 https://en.wikipedia.org/wiki/Dam dam An excavation in the Earth for the purpose of extracting earth materials. EcoLexicon:mine FTT:14 FTT:968 Geonames:L.MNA Geonames:S.MN TGN:54211 TGN:54212 mine FTT:1246 FTT:1247 FTT:44 FTT:45 FTT:46 FTT:48 FTT:50 FTT:51 FTT:52 FTT:57 FTT:60 FTT:62 FTT:63 FTT:64 FTT:72 FTT:74 Geonames:L.AGRC Geonames:L.RESA Geonames:S.NSY TGN:55001 barn cattle dipping tank corral dairy feedlot grange grazing allotment irrigated field nursery pastoral site sheepfold stockyard As with other classes that are "features", the subclasses of this class are being moved to more informative locations. Their relation to agriculture will be modelled by something more akin to a quality or relation to an agricultural process. agricultural ecosystem An area of land which is used for the cultivation of crops or grazing of livestock, including any agricultural constructions therein. agricultural site FTT:45 FTT:58 FTT:59 FTT:69 Geonames:S.FRM Geonames:S.FRMS Geonames:S.RNCH TGN:54011 https://en.wikipedia.org/wiki/Farm FARM farm A range of mounts which is dominated by mountains. EcoLexicon:mountain_range FTT:548 FTT:995 FTT:997 Geonames:MTS SWEETRealm:MountainRange TGN:21431 TGN:21432 https://en.wikipedia.org/wiki/Mountain_range envoPolar mountain range A region of general uniform slope, comparatively level, and of considerable extent. EcoLexicon:plain FTT:707 FTT:874 FTT:926 Geonames:T.PLN SWEETRealm:Plain TGN:21461 https://en.wikipedia.org/wiki/Plain plain A landform consisting of loose rock particles such as sand, gravel, shingle, pebbles, cobble, or even shell fragments along the shoreline of a body of water. EcoLexicon:beach EcoLexicon:to_beach FTT:237 FTT:239 Geonames:T.BCH Geonames:T.BCHS SWEETRealm:Beach TGN:21482 https://en.wikipedia.org/wiki/Beach Beach beach berm lagoon beach beach A region rendered barren or partially barren by environmental extremes, especially by low rainfall. EcoLexicon:desert FTT:1 FTT:188 Geonames:T.DSRT LTER:147 SWEETRealm:Desert TGN:21201 https://en.wikipedia.org/wiki/Desert envoPolar desert area Area of dry or relatively dry land surrounded by water or low wetland. EcoLexicon:island FTT:147 FTT:450 FTT:886 FTT:887 FTT:888 FTT:889 Geonames:T.ISL Geonames:T.ISLS SWEETRealm:Island TGN:21468 TGN:21469 TGN:21471 TGN:21475 https://en.wikipedia.org/wiki/Island envoPolar island A hydrographic feature which is located below the surface of a marine water body. EcoLexicon:fan EcoLexicon:platform EcoLexicon:ravine FTT:1020 FTT:1137 FTT:1176 FTT:1193 FTT:1194 FTT:1195 FTT:1196 FTT:5 FTT:810 FTT:984 Geonames:FRKU Geonames:FRSU Geonames:MDVU Geonames:PLFU Geonames:RAVU Geonames:RMPU Geonames:U.BSNU Geonames:U.EDGU Geonames:U.ESCU Geonames:U.FANU Geonames:U.FLTU Geonames:U.FURU Geonames:U.GAPU Geonames:U.GLYU Geonames:U.HOLU Geonames:U.LDGU Geonames:U.LEVU Geonames:U.PLNU Geonames:U.PLTU Geonames:U.PNLU Geonames:U.PRVU Geonames:U.RDGU Geonames:U.RDSU Geonames:U.RISU Geonames:U.SDLU Geonames:U.SHVU Geonames:U.SILU Geonames:U.SPRU Geonames:U.TERU Geonames:U.VALU Geonames:U.VLSU TGN:23001 TGN:23116 TGN:23117 TGN:23118 TGN:23135 TGN:23162 TGN:23181 TGN:23182 TGN:23183 TGN:23184 TGN:23188 TGN:23192 TGN:23193 TGN:23194 TGN:23195 TGN:23196 TGN:23211 TGN:23212 TGN:23301 TGN:23411 TGN:23412 TGN:23413 TGN:23415 TGN:23421 TGN:23423 TGN:23424 TGN:23431 TGN:23453 TGN:23461 TGN:23463 TGN:23467 TGN:23550 basin escarpment fan flat fork forks furrow gap gully hole hole (seafloor) ledge levee median valley moat (seafloor) pinnacle plain plateau platform province ramp ramp (seafloor) ravine ridge ridges rise rise (seafloor) saddle shelf edge undersea bank undersea basin undersea bench undersea cliff undersea fan undersea fork undersea fracture zone undersea furrow undersea gap undersea hole undersea ledge undersea levee undersea median valley undersea moat undersea peak undersea pinnacle undersea plain undersea platform undersea ramp undersea rise undersea saddle undersea shelf undersea shelf edge undersea shelf valley undersea sill undersea slope undersea spur undersea terrace undersea tongue undersea valley undersea feature An area in which grasses (Graminae) are a significant component of the vegetation. grassland area Land having a cover of trees, shrubs, or both. FTT:1083 FTT:505 FTT:506 FTT:719 FTT:774 Geonames:V.GRVPN LTER:503 SWEETRealm:Break SWEETRealm:Scrub TGN:21631 TGN:21632 TGN:21641 https://en.wikipedia.org/wiki/Woodland brigalow pine grove woodland area An area with a high density of trees. A small forest may be called a wood. EcoLexicon:forest FTT:258 FTT:506 FTT:715 FTT:717 Geonames:V.FRST LTER:2 SWEETRealm:Forest TGN:21641 TGN:21642 TGN:21645 https://en.wikipedia.org/wiki/Forest The definitions of forest can vary greatly, and different classes will be needed to support the major categories. Tree cover alone is not enough to distinguish between forests and plantations. The international definition proposed by the 2010 FAO Forestry Resource Assessment: "land spanning more than 0.5 ha with trees higher than 5 metres and canopy cover of more than 10 percent, or trees able to reach these thresholds in situ . It does not include land that is predominantly under agricultural or urban land use." - FAO. 2010. Global forest resources assessment 2010, Main report, FAO Forestry Paper 163. Rome. forested area A vegetated area which is part of a tundra ecosystem. EcoLexicon:tundra FTT:151 FTT:152 Geonames:V.TUND LTER:605 TGN:21611 envoPolar area of tundra A field which is located on land and used for agricultural purposes, such as the grazing of livestock or the cultivation of crops. agricultural site EcoLexicon:field FTT:45 FTT:61 Geonames:L.FLD SWEETRealm:Field TGN:21456 agricultural field An intentional planting of a crop, on a large scale, usually for uses other than cereal production or pasture. The term is currently most often used for plantings of trees and shrubs. The term tends also to be used for plantings maintained on economic bases other than that of subsistence farming. FTT:45 FTT:68 TGN:54041 https://en.wikipedia.org/wiki/Plantation plantation A channel of a watercource which has been constructed by humans or their technologies. EcoLexicon:artificial_channel artificial channel A geographical region whose affairs and population are administered by an authority. FTT:1093 Geonames:A.PCL TGN:80002 political entity An arid terrain with clay-rich soil that has been extensively eroded by wind and water. barren land FTT:186 FTT:187 Geonames:T.BDLD TGN:21205 https://en.wikipedia.org/wiki/Badlands badlands badland A ridge of rocks, lying near the surface of the sea, which may be visible at low tide, but is usually covered by water. EcoLexicon:reef FTT:202 FTT:203 FTT:729 Geonames:H.RF Geonames:U.RFSU Geonames:U.RFU SPIRE:Reef TGN:21479 https://en.wikipedia.org/wiki/Reef REEF atoll reef bank reef barrier reef fringing reef shore reef submerged reef rocky reef An opening of the sea into the land. FTT:463 TGN:21128 envoPolar coastal inlet A ditch that supplies water to surrounding land. canal FTT:129 FTT:406 Geonames:H.DTCHI irrigation ditch A ditch that collects water from the surrounding land. EcoLexicon:drainage_ditch FTT:129 FTT:402 Geonames:H.DTCHD drainage ditch A part of an astronomical body which is primarily composed of solid material. EcoLexicon:landform EcoLexicon:landforms FTT:754 FTT:96 SWEETRealm:Landform TGN:21400 TGN:21401 solid astronomical body part An island that does not sit on a continental shelf, and is of volcanic origin. EcoLexicon:oceanic_island https://en.wikipedia.org/wiki/Oceanic_island oceanic island A grassland ecosystem which is used for grazing of ungulate livestock as part of a farm or ranch. FTT:45 FTT:67 Geonames:L.GRAZ pasture The separation between neighbouring drainage basins (catchments). In hilly country, the divide lies along topographical peaks and ridges, but in flat country or on a high plateau (especially where the ground is marshy) the divide may be invisible - just a more or less notional line on the ground on either side of which falling raindrops will start a journey to different rivers, and even to different sides of a country or continent. FTT:220 FTT:645 Geonames:T.DVD LTER:626 SWEETRealm:Watershed TGN:21440 https://en.wikipedia.org/wiki/Watershed divide water divide watershed A facility in which fish are raised commercially in tanks or enclosures, usually for food. FTT:123 FTT:694 https://en.wikipedia.org/wiki/Fish_farm fish farm A hatchery in which the eggs of fish are hatched under artificial conditions. FTT:695 https://en.wikipedia.org/wiki/Fish_hatchery fish hatchery A flooded parcel of arable land used for growing rice and other semiaquatic crops. https://en.wikipedia.org/wiki/Paddy_field paddy field Area covered with low-growing or stunted perennial vegetation and usually not mixed with trees. FTT:1191 FTT:262 FTT:374 FTT:473 FTT:792 FTT:991 Geonames:V.SCRB SWEETRealm:Scrub TGN:21644 TGN:21652 https://en.wikipedia.org/wiki/Scrubland scrubland scrubland area A landform sunken or depressed below the surrounding area. depression EcoLexicon:depression FTT:175 FTT:215 FTT:216 Geonames:T.DPR Geonames:T.PAN Geonames:T.PANS SWEETRealm:Depression TGN:21454 TGN:21497 TGN:21521 depressed landform A lake purposefully constructed. https://en.wikipedia.org/wiki/Artificial_lake artificial lake A depressed landform which physically confines a river, slough or ocean strait, and which consists of a bed and banks. EcoLexicon:channel EcoLexicon:sea_channel FTT:1192 FTT:233 FTT:461 FTT:462 FTT:463 FTT:464 FTT:465 FTT:466 FTT:468 FTT:469 FTT:470 Geonames:H.CHN Geonames:U.SCNU Geonames:U.SCSU SWEETRealm:Channel TGN:21137 TGN:23451 channel of a watercourse A biome is an ecosystem which is undergoing climactic ecological succession. EcoLexicon:biome LTER:809 major habitat type In this definition, there is an assumption that no major perturbations are occurring or have occurred in a time frame affects the successional dynamics of the ecosystem. A "major" perturbation is one which disrupts the community's ability to restore its (near) equilibrium. Usually, pioneer or early secondary successional processes would be in effect in such scenarios. biome A tract of land which has few or no trees and is surrounded by more heavily wooded areas. FTT:259 FTT:488 Geonames:L.CLG LTER:79 TGN:21651 CLEARING clearing forest clearing There should be a better superclass than "field" which should indicate that there are no woody plants in growth form "tree" around. woodland clearing A biome which is primarily or completely situated on a landmass. LTER:798 SPIRE:Terrestrial terrestrial biome An aquatic biome which is determined by a marine water body. SPIRE:Marine envoPolar This biome includes open-ocean and unprotected coastal ecosystems, characterized by exposure to wave action, tidal fluctuation, and ocean currents as well as systems that largely resemble these. Water in the marine biome is generally within the salinity range of seawater: 30 to 38 ppt. marine biome A reservoir constructed for the purpose of providing water for irrigation. irrigation pond irrigation reservoir A facility, permanent or temporary, on land, in air, space or water, where scientific research or measurements can be undertaken. research facility An opening of the sea into the land, or of a lake into its shore. EcoLexicon:inlet FTT:233 FTT:463 Geonames:H.GULF Geonames:H.INLT SWEETRealm:Inlet TGN:21128 envoPolar inlet A field which includes at least two mounts connected by high ground and arranged in an approximately linear fashion. FTT:996 envoPolar range of mounts A step-like feature between higher and lower ground: a relatively flat or gently inclined shelf of earth, backed and fronted by steep slopes or manmade detaining walls. EcoLexicon:terrace FTT:247 FTT:248 Geonames:T.BNCH Geonames:T.TRR TGN:21498 TGN:21513 https://en.wikipedia.org/wiki/Terrace TERRACE bench ledge rock terrace terrace terrace A terrace which is used for agricultural activities. agricultural terrace Lake sediment is sediment which covers the bottom of a lake. Lake sediments are comprised mainly of clastic material (sediment of clay, silt, and sand sizes), organic debris, chemical precipitates, or combinations of these. lake sediment A field which is composed primarily of gravel. Geonames:L.GVL TGN:21502 gravel field A bounded area of land, or water, usually in its natural or semi-natural (landscaped) state and set aside for some purpose, usually to do with recreation or conservation. park A raised walkway over water, supported by piles or pillars. EcoLexicon:pier pier A building or region where sports activities can be carried out. sports facility Incorporated populated place. urban area EcoLexicon:city FTT:430 FTT:483 FTT:484 FTT:485 SWEETRealm:City TGN:83020 TGN:83040 TGN:83043 https://en.wikipedia.org/wiki/City http://purl.obolibrary.org/obo/NCIT_C80234 city An aquatic biome which is determined by a body of freshwater. SPIRE:Freshwater envoPolar freshwater biome A rock is a naturally occurring solid aggregate of one or more minerals or mineraloids. EcoLexicon:rock FTT:1010 FTT:145 Geonames:T.RK Geonames:T.RKS SWEETRealm:Rock TGN:21444 https://en.wikipedia.org/wiki/Rock From https://en.wikipedia.org/wiki/ [A mineral] is different from a rock, which can be an aggregate of minerals or non-minerals and does not have a specific chemical composition. The exact definition of a mineral is under debate, especially with respect to the requirement a valid species be abiogenic, and to a lesser extent with regards to it having an ordered atomic structure. rock An environmental material which is primarily composed of minerals, varying proportions of sand, silt, and clay, organic material such as humus, interstitial gases, liquids, and a broad range of resident micro- and macroorganisms. regolith LTER:535 SPIRE:Soil SWEETRealm:Soil https://en.wikipedia.org/wiki/Soil 'In engineering terms, soil is referred to as regolith, or loose rock material that lies above the 'solid geology'. Soil is commonly referred to as "earth" or "dirt"; technically, the term "dirt" should be restricted to displaced soil.' https://en.wikipedia.org/wiki/Soil " The upper limit of soil is the boundary between soil and air, shallow water, live plants, or plant materials that have not begun to decompose. Areas are not considered to have soil if the surface is permanently covered by water too deep (typically more than 2.5 meters) for the growth of rooted plants. The lower boundary that separates soil from the nonsoil underneath is most difficult to define. Soil consists of horizons near the Earth's surface that, in contrast to the underlying parent material, have been altered by the interactions of climate, relief, and living organisms over time. Commonly, soil grades at its lower boundary to hard rock or to earthy materials virtually devoid of animals, roots, or other marks of biological activity. For purposes of classification, the lower boundary of soil is arbitrarily set at 200 cm." Soil taxonomy, 2nd Ed., quoted in http://www.nrcs.usda.gov/wps/portal/nrcs/detail/soils/edu/?cid=nrcs142p2_054280 soil A lentic water body which is composed primarily of marine water. body of marine water marine waterbody marine water body A solid astronomical body part which is part of the planetary surface between the peak of an elevation or the bottom of a depression and relatively flat surrounding land. EcoLexicon:slope SWEETRealm:Slope https://en.wikipedia.org/wiki/Slope slope Water that has been adversely affected in quality by anthropogenic influence. EcoLexicon:waste_water SWEETRealm:Wastewater https://en.wikipedia.org/wiki/Waste_water waste water An excreta material which is composed primarily of feces, an excreta consisting of waste products expelled from an animal's digestive tract through the anus (or cloaca) during defecation. EcoLexicon:drop SPIRE:Dung SWEETRealm:Drop faeces material feces material stool ENVO bodily fluid classes differ from UBERON's treatment of bodily fluids. UBERON refers to the substance itself ("S"). We assert that UBERON's classes are the primary compositional component of the terms in ENVO ("S material"). Use of the ENVO terms is typically recommended when you wish to indicate that there may be other materials intermixed with S. This is distinct from classes such as http://purl.obolibrary.org/obo/UBERON_0001988 in that it refers to the environmental material composed primarily of feces rather than 'just' feces. fecal material The mixture of gases (roughly (by molar content/volume: 78% nitrogen, 20.95% oxygen, 0.93% argon, 0.038% carbon dioxide, trace amounts of other gases, and a variable amount (average around 1%) of water vapor) that surrounds the planet Earth. EcoLexicon:air LTER:18 SWEETRealm:Air https://en.wikipedia.org/wiki/Air envoPolar air An environmental material primarily composed of dihydrogen oxide in its liquid form. water EcoLexicon:water LTER:617 https://en.wikipedia.org/wiki/Water liquid water Particulate environmental material which is formed as a result of the transport and deposition of particles by flowing liquid. EcoLexicon:sediment EcoLexicon:sedimentation LTER:492 LTER:493 SWEETRealm:Sediment https://en.wikipedia.org/wiki/Sediment envoPolar Sediment is typically deposited on the bed or bottom of a body of water or other liquid. sediment Particulate environmental material with diameters less than 500 micrometers. EcoLexicon:dust SWEETRealm:Dust https://en.wikipedia.org/wiki/Dust envoPolar Dust occurs in and may be deposited from the atmosphere. dust Water which has a low concentration of dissolved solutes, particularly that of sodium chloride. EcoLexicon:fresh_water LTER:216 SWEETRealm:FreshWater https://en.wikipedia.org/wiki/Fresh_water freshwater envoEmpo envoPolar The lower bound of solute concentration required for water to be considered freshwater is variable, but is always less than that of seawater, and often cited as less than 1 gram of solutes per 1 litre of water. fresh water Wastewater that is contaminated with feces or urine, SWEETRealm:Sewage https://en.wikipedia.org/wiki/Sewage sewage A biome which is determined by a water body and which has ecological climax communities adapted to life in or on water. LTER:41 aquatic biome Sediment that accumulates in the flat or very gently sloping areas of the deep ocean basin floor. The three main types of deep marine sediment, also known as pelagic sediment, are siliceous oozes, calcareous oozes, and red clays. EcoLexicon:marine_sediment EcoLexicon:marine_sedimentation SWEETRealm:MarineSediment https://en.wikipedia.org/wiki/Marine_sediment deep marine sediments envoPolar deep marine sediment Revise adjacent to. Consider sampled stream sediment. Dry stream sediment. stream sediment Manure which has been derived from the aerobically decomposed remnants of organic materials. https://en.wikipedia.org/wiki/Compost compost A hospital is a building in which health care services are provided by specialized staff and equipment. https://en.wikipedia.org/wiki/Hospital hospital EcoLexicon:water_pollution https://en.wikipedia.org/wiki/Contaminated_water polluted water contaminated water Straw or other material strewn in an animal's enclosure (e.g. a stable) for it to sleep on and to absorb its faeces and urine. straw bedding animal litter http://opendata.inra.fr/EOL/EOL_0001601#bedding A building in which a business presents a selection of goods and offers to trade or sell them to customers for money or other goods. https://en.wikipedia.org/wiki/Shopping retail shop retail store retailer shop A shop in which a business offers food products for sale or trade. Whether food is the primary product offered by the business or simply one of the products it offers is not specified in this class. food shop A soil which is composed of approximately equal proportions of sand and silt, with a smaller proportion of clay. EcoLexicon:loam SWEETRealm:Loam Some authorities consider loam to be any soil material that contains 7 to 27% clay, 28 to 50% silt, and less than 52% sand. loam Soil which is part of an ecosystem used for agricultural activities. agricultural soil A portion of soil which is found in a garden. garden soil A material which is not the desired output of a process and which is typically the input of a process which removes it from its producer (e.g. a disposal process). EcoLexicon:waste SWEETRealm:Waste https://en.wikipedia.org/wiki/Waste waste material WWTP waste treatment plant Manure which is derived from the waste products of animals. This is interesting in that the "role" aspect of "waste" is (or can be) replaced by another role "fertilizer". Thus, the positioning of "manure" under waste may not be totally correct. animal manure fresh animal manure A house used for sheltering non-human animals. While humans are animals, this class does not refer to human houses. animal house An animal house which is used to house pigs. https://en.wikipedia.org/wiki/Piggery piggery A waste treatment plant which equipped to treat sewage such that its potential for environmental contamination is reduced. sewage treatment plant sewage plant Drinking water is water which may be consumed by humans with no adverse effects on their health. EcoLexicon:drinking_water SWEETRealm:DrinkingWater https://en.wikipedia.org/wiki/Drinking_water potable water drinking water A material entity that has been processed by humans or their technology in any way, including intermediate products as well as final products. manufactured good manufactured product https://en.wikipedia.org/wiki/Tap_water tap water https://en.wikipedia.org/wiki/Horse_manure horse manure Manure which is primarily composed of pig feces. pig manure An industrial building is a building within which goods are produced and, optionally, stored or within which services are rendered. It's possible that this will become an inferred class in the future. The United Nations' International Standard Industrial Classification should be referred to when expanding this branch. ISIC can also be used to identify processes. See http://unstats.un.org/unsd/cr/registry/regcst.asp?Cl=27&Lg=1. industrial building A dairy is a building in which animal milk is harvested and, optionally, processed for human consumption. https://en.wikipedia.org/wiki/Dairy 'Terminology differs between countries. For example, in the United States, the entire dairy farm is commonly called a "dairy." The building or farm area where milk is harvested from the cow is often called a "milking parlor" or "parlor." The farm area where milk is stored in bulk tanks is known as the farm's "milk house." Milk is then hauled (usually by truck) to a "dairy plant," also referred to as a "dairy", where raw milk is further processed and prepared for commercial sale of dairy products. In New Zealand, farm areas for milk harvesting are also called "milking parlours", and are historically known as "milking sheds."' https://en.wikipedia.org/wiki/Dairy dairy A food processing building is a building in which materials that contain or consist of essential body nutrients - such as carbohydrates, fats, proteins, vitamins, or minerals - and may be ingested and assimilated by an organism to produce energy, stimulate growth, and maintain life are converted alternative forms. The semantics of food are being handled by FOODON http://purl.obolibrary.org/obo/foodon.owl food processing building A bakery is a building in which raw flour-based food is baked in an oven to produce food products such as bread, cakes, pastries, and pies. These products are often sold from the bakery itself. https://en.wikipedia.org/wiki/Bakery A bakery is a food processing building and a 'food shop' at the same time. This needs to be resolved. bakery farmyard manure A brewery is a building in which alcoholic beverages are produced by brewing, that is, steeping a starch source (commonly cereal grains) in water and fermenting the resulting sweet liquid with yeast. At times, the products are also sold from the brewery. brewery A product which is composed primarily of paper. paper product A paper product which is used as legal tender in economic or other monetary trasactions. bank note currency note stable manure An air filter is a device that removes some substance from air. https://en.wikipedia.org/wiki/Air_filter This is a general definition derived from the definitions for particulate, chemical, and other air filters. Subclasses should be created if needed. air filter A building within which logs are cut into lumber products. sawmill Soil which is derived from compost. compost soil A portion of soil which is part of a cropland or a rangeland biome. farm soil A material entity which other material entities in an environmental system are primarily or partially composed of. portion of environmental material Everything under this parent must be a mass noun (i.e. not countable). All subclasses are to be understood as being composed primarily of the named entity, rather than restricted to that entity. For example, "ENVO:water" is to be understood as "environmental material composed primarly of some CHEBI:water". Instances of this class are portions of environmental materials, such as seawater in bucket, a water parcel in the photic zone of a lake, or the concrete that composes a building part. Instances of these portions may have fiat or non-fiat boundaries. For example, a water parcel has not physical boundaries, while the seawater in a bucket is bounded by the internal surfaces of the bucket. environmental material A layer of some material entity which is adjacent to one or more of its external boundaries and directly interacts with its immediate surroundings. EcoLexicon:surface http://sweetontology.net/reprSpaceGeometry/Surface https://en.wikipedia.org/wiki/Surface This class is distinct from a geometric surface, which is two-dimensional. The idea of "uppermost" may be problematic. Further, the definition of layer (the superclass of surface in rev 133) references surface. This may be another issue. Perhaps this can be made into an inferred class using 'bounding layer of' some material entity, note that 'bounding layer' implies containment, which may not be valid here. surface layer A facility in which animals are confined within enclosures and displayed to the public, and in which they may also be bred. zoo zoological park zoological garden Anthropogenic material in or on which organisms may live. anthropogenic environmental material An environmental material which is a liquid or semi-liquid mixture of water and some combination of soil, silt, and clay particles. EcoLexicon:mud LTER:356 SWEETRealm:Mud https://en.wikipedia.org/wiki/Mud mud A well which provides access to groundwater held in an aquifer. https://en.wikipedia.org/wiki/Water_well water well Particulate environmental material which is composed primarily of particles of sand with only minor proportions of other substances. EcoLexicon:sand LTER:484 SWEETRealm:Sand https://en.wikipedia.org/wiki/Sand This definition is intentionally ambiguous to support the multiple thresholds set by different authorities. Some authorities consider as sands soil material that contains 85% or more sand; the percentage of silt plus 1.5 times the percentage of clay does not exceed 15. coarse sand (sable grossier) 25% or more very coarse and coarse sand, and less than 50% any other one grade of sand. sand An environmental material which is composed primarily of pieces of gravel. EcoLexicon:gravel SWEETRealm:Gravel As with all size-based classifications, there is considerable variation in what is considered gravel. gravel A marine biome which is determined by an ocean. envoPolar Ocean biomes are determined by major bodies of saline water, principal components of the hydrosphere. Approximately 71% of the Earth's surface is covered by ocean, a continuous body of water that is customarily divided into several principal oceans and smaller seas. More than half of this area is over 3,000 metres (9,800 ft) deep. Average oceanic salinity is around 35 parts per thousand (ppt) (3.5%), and nearly all seawater has a salinity in the range of 30 to 38 ppt. ocean biome An environmental material which is composed primarily of particles. particulate matter envoAtmo envoPolar particulate environmental material Environmental material derived from living organisms and composed primarily of one or more biomacromolecules. EcoLexicon:organic_material biomass organic material A forest ecosystem which is undergoing climactic ecological succession. LTER:212 SPIRE:Forest forest biome A woodland biome is a terrestrial biome which includes, across its entire spatial extent, woody plants spaced sufficiently far apart to allow light penetration to support communities of herbaceous plants or shrubs living closer to the woodland floor. Preliminary definition. woodland biome A shrubland biome is a terrestrial biome which includes, across its entire spatial extent, dense groups of shrubs. Preliminary definition. shrubland biome A grassland ecosystem in which dominant ecological communities have reached their climax successional state. SPIRE:Savannah_or_grassland grassland biome A desert ecosystem which is undergoing climactic ecological succession. SPIRE:Desert_or_dune wwfBiome desert biome A tundra ecosystem which is undergoing climactic ecological succession. SPIRE:Tundra envoPolar wwfBiome tundra biome A mangrove biome is a terrestrial biome which includes, across its spatial extent, mangrove plants (Rhizophoraceae). Mangrove plants are able to withstand high levels of salinity as well as regions of anoxia and frequent tidal inundation. Mangrove biomes often occur near tropical and sub-tropical estuaries and depositional marine coastal environments where fine sediments (often with high organic content) collect in areas protected from high energy wave action. LTER:322 wwfBiome Preliminary definition. Depending on whether mangrove trees or shrubs are present, this class could be a child of shrubland biome or woodland biome. Consider creating the appropriate classes. mangrove biome An anthropogenic terrestrial biome is a terrestrial biome which has community structures determined by human activity. anthrome human biome Preliminary definition. anthropogenic terrestrial biome A cropland ecosystem which is undergoing climactic ecological succession. cropland biome A village biome is an anthropogenic terrestrial biome which contains settlements such as villages, towns, and/or small cities and which is primarily used for agricultural activity. Villages are also described as agricultural settlements with greater than 100 persons per square kilometre; however, no upper limit is defined. village biome A rangeland biome is an anthropogenic terrestrial biome which is primarily used for the rearing and grazing of livestock. rangeland biome A dense settlement biome is an anthropogenic terrestrial biome which is primarily used for human habitation, recreation, and industry within built structures with little other land use. dense settlement biome A biome which is determined by a freshwater lake. freshwater lake biome A freshwater biome which is determined by a freshwater river. freshwater river biome A system which has the disposition to environ one or more material entities. EcoLexicon:environment environment In ENVO's alignment with the Basic Formal Ontology, this class is being considered as a subclass of a proposed BFO class "system". The relation "environed_by" is also under development. Roughly, a system which includes a material entity (at least partially) within its site and causally influences that entity may be considered to environ it. Following the completion of this alignment, this class' definition and the definitions of its subclasses will be revised. environmental system A material entity which 1) is spatially continuous, 2) is composed of material of comparable thickness, composition, and physical properties, and 3) is physically distinct from adjacent portions of environmental material. envoPolar layer An anthropogenic environment is an environmental system which is the product of human activity. Unsatisfactory definition here. Must consider the threshold that makes an environmental system anthropogenic. anthropogenic environment A marine environment and enviroment which is determined by a marine water body. envoPolar marine environment A planetary surface is a surface layer where the solid or liquid material of a planet comes into contact with an atmosphere or outer space. a useful class: this can be used to define sub-terrestrial and sub-marine entities planetary surface A field used for the cultivation of corn or related crop plants. Requested in Issue 112 as part of the curation of metagenome submissions in the European Nucleotide Archive. maize field An unbroken expanse (as of ice) envoPolar This class was created to accommodate "fields" from agricultural fields to marine mesoscale eddy fields. Thus, it has a very broad definition which makes it less than informative when annotating. Please consider using or requesting an appropriate subclass. field A site which has its extent determined by the presence or influence of one or more components of an environmental system or the processes occurring therein. envoPolar Formerly, this class was an experimental class and a subclass of "environmental feature". It is now aligned to BFO. The class was not obsoleted as the core semantics maintained their stability through its transition. environmental zone A house is a building that provides a dwelling-place for a living entity. The provisioning of a dwelling-place can perhaps be modelled as a role. house A human house is a house which provides a dwelling-place for humans. human house A building part is a construction which is part of a building. Not recommended for annotation. This class is likely to be made into an inferred class as its subclasses are distributed among more meaningful superclasses (i.e. ceiling is_a surface layer). See for example, "building floor". The boundaries between building parts may be bona fide or fiat. building part A bathroom is a room which contains a washbasin or other fixture, such as a shower or bath, used for bathing by humans. bathing room bathroom A building part which is separated from other building parts by one or more interior walls and, optionally, outdoor areas by one or more exterior walls. room A constructed barrier is a freestanding wall, berm, or fence built to limit movement of entities across a boundary. barrier constructed barrier Glass is an amorphous (non-crystalline) solid which is often transparent. This class refers to all forms of glass. For the familiar form present in window panes and drinking glasses, consider silica-based glass. glass Silica-based glass is a glass composed primarily of silicon dioxide, the primary constituent of sand. glass Silica-based glasses are the most common manufactured variety of glass. silica-based glass A building floor is a surface layer which is part of a building and used for walking. To be more precise, a subfloor and a floor covering may be specified. Please request these classes and propose definitions if they are needed. building floor A solid, cylindrical object or column with its length greater than its diameter. This was created in response to a user request, but it is an odd class in that it specifies a shape rather than a particular material entity. It may, therefore, be deprecated when more meaningful or sensible alternatives become apparent. pole A factory (previously manufactory) or manufacturing plant is an industrial site, usually consisting of buildings and machinery, or more commonly a complex having several buildings, where workers manufacture goods or operate machines processing one product into another. manufactory manufacturing plant factory A table is a form of furniture with a flat horizontal upper surface used to support objects, for storage, show, and/or manipulation. table A desk is a table which is intended for information-manipulation tasks, including writing and use of interactive electronics. The intentional nature of this definition is problematic, but the restricted range of activities visited upon a desk is of interest. desk A piece of furniture is a movable object intended to support various human activities such as seating (e.g., chairs, stools and sofas) and sleeping (e.g., beds). The assumption is that furniture is manufactured, which is arguable. Further, according to Black's Law Dictionary (http://thelawdictionary.org/furniture/) many classes can be subclasses of 'piece of furntiure': "This term includes that which furnishes, or with which anything is furnished or supplied; whatever must be supplied to a house, a room, or the like, to make it habitable, convenient, or agreeable; goods, vessels, utensils, and other appendages necessary or convenient for housekeeping; whatever is added to the interior of a house or apartment, for use or convenience. Bell v. Holding, 27 Ind. 173.The term “furniture” embraces everything about the house that has been usually enjoyed there, including plate, linen, china, and pictures. 1 Endicott v. Endicott, 41N. J. Eq. 96, 3 Atl. 157.The word “furniture” made use of in the disposition of the law. or in the conventions or acts of persons, comprehends only such furniture as is intended for use and ornament of apartments, but not libraries which happen to be there, nor plate. Civ.Code La. art. 477." However, this would eventually be absurd and limit other groupings. Perhaps some sort of 'furnishing' BFO:function would be a better way to handle this. piece of furniture A motor vehicle is a vehicle which is propelled by an engine or motor and that does not operate on rails. Subclasses will be added by inference. motor vehicle A truck is a motor vehicle which, as its primary funcion, transports cargo rather than human passangers. lorry truck A vehicle is a mobile machine which transports people or cargo. vehicle A lentic water body is a water body in which the accumulated water, in its totality, has very little to no directed flow. lentic water body A lotic water body is a water body in which the accumulated water, in its totality, is flowing. lotic water body A manufactured structure made of interspaced structural elements such as metal or wooden bars or wires held together such that they may be used to confine, contain, or protect something. cage manufactured cage A drylot is an enclosure of limited size usually bare of vegetation and used for fattening livestock. drylot A feedlot is a plot of land on which livestock are fattened for market feedlot A landmass which is part of a planet. land planetary landmass A settlement with a high density of buildings and inhabitants. The thresholds for what makes a settlment "dense" can be determined as needed. If there is a specific threshold that should be added to ENVO, please make a new class request. dense settlement A mass of water. water mass Hydrological precipitation is a process during which any product of the condensation of atmospheric water vapour is pulled to the planetary surface by gravity. precipitation "process" is included in the label to make it clear that we are not referring to the precipitated material (e.g. snow, rain, sleet) hydrological precipitation process An area of a planet's surface which is primarily composed of bedrock, desert pavement, scarp rock, talus, material exposed by slides, volcanic material, glacial debris, sand, material exposed during strip mining, gravel, and other accumulations of earthen material in contact with an atmospheric column extending from the planetary boundary layer to the planet's exosphere with little to no physical obstruction. Barren Land (Rock/Sand/Clay) NLCD:31 envoPolar nlcd2011 According to the NLCD 2011, areas of barren land generally have less than 15% cover of vegetation. A specific threshold is not asserted in this definition. area of barren land A temperature that inheres in some portion of air. obsolete air temperature true A village is a clustered human settlement or community, larger than a hamlet but smaller than a town, with a population ranging from a few hundred to a few thousand. Though often located in rural areas, the term urban village is also applied to certain urban neighbourhoods. Villages are normally permanent, with fixed dwellings; however, transient villages can occur. Further, the dwellings of a village are fairly close to one another, not scattered broadly over the landscape, as a dispersed settlement. village A material entity which is composed of one or more chemical entities and has neither independent shape nor volume but tends to expand indefinitely. gas gaseous environmental material A material part of an astronomical body. envoAstro envoPolar Material parts of astronomical bodies generally have boundaries formed by discontinuities in qualities, composition, or other physical characterisitcs. These boundaries are sometimes sharp, and sometimes diffuse, with different classification systems and communities declaring varying thresholds (e.g. for where a shoreline, forest, or other entity begins and ends). However, some boundaries are declared by fiat - that is, by arbitrary human convention or decree - particularly by regulatory or other authorities and communities of practice. The classes in this hierarchy attempt to offer generalisable definitions that allow multiple classfiication systems to map to and interoperate through. If desired, we can create classes that declare thresholds used by a given authority or community under the more generic ones, annotated with source information. astronomical body part An environmental material which is in a solid state. This is a defined class: its subclasses will not be asserted, but filled by inference. solid environmental material An environmental material which is in a liquid state. envoPolar This is a defined class: most of its subclasses will not be asserted, but filled by inference. liquid environmental material A precipitation process is a process in which a portion of some substance segregates from a material in which that substance or its precursors were dissolved or suspended in and settles due to a force such as gravity or centrifugal force. precipitation process An animal house which is only partially surrounded by a building envelope. open animal house An animal house which has a complete building envelope. closed animal house A manufactured cage which may be used to confine, contain, or protect an animal. cage chicken cage animal cage A petting zoo is a zoological garden which contains domesticated non-human animals and some wild non-human animals that are docile enough for humans to touch and feed. petting farm Petting zoos are often nested within a zoological garden featuring wild non-human animals, not docile enough for humans to touch. petting zoo An artificial channel which transports unwanted water or waste liquids away from their source, either to a more useful area, a receptacle, or into sewers or stormwater mains as waste discharge to be released or processed. drain drainage channel plumbing drain A facility in which non-human animals are slaughtered and processed for human consumption. slaughter plant slaughterhouse abattoir A building which is used to care for a human child during the working day by a person, outside the child's immediate family, other than that child's legal guardians. child care building daycare building This is a kind of day care facility. A facility need not be a building. day care building A building in which fish are subject to a series of operations to prepare them for human consumption. This is a kind of fish processing facility. Facilities need not be buildings, factory ships may be considered fish processing facilities. fish processing building A building in which nursing aides and skilled nurses provide care and treatment to residents who have significant difficulty coping with the required activities of daily living. intermediate care facility long-term care facility old people's home skilled nursing facility care home convalescent home rest home nursing home A human house which serves as a long-term shelter for its inhabitants and within which they store personal property. This term is not to be used for hotels, hostels, inns and the like, which provides shorter-term stays. residential building A building within which food and drink are prepared and served to customers in exchange for money or other goods and/or services. eatery restaurant A part of an ecosystem which may be or has been used for one or more overnight stays by humans sheltering in tents, camper vans, caravans, or improvised shelters. camping ground camping pitch camping site campsite campground A campground which has been modified by humans to provide and maintain facilities for camping such as fire pits, road access, latrines, and garbage bins. dedicated campground A campground which has no pre-existing facilities installed or maintained by humans, usually found outside of anthropised ecosystems. impromptu campground A manufactured product which may hold a volume of heated water suitable for one or more humans to bathe in, usually for the purposes of hydrotherapy or pleasure. spa Jacuzzi hot tub Wastewater which is produced by industrial activity and which contains chemical contaminants other than those associated with urine and fecal matter. industrial wastewater A construction which is designed to hold water in which humans may swim or perform other leisure activities. pool paddling pool swimming bath swimming pool wading pool constructed swimming pool A hydraulic-engineering installation which transports water - in specified amounts, of a specified quality, and in accordance with a water-consumption plan - from a source of supply into a conduit. Sources of water include rivers, lakes, reservoirs, and other water bodies. Conduits include canals, pipelines, and tunnels. Water intakes typically transport water for purposes of hydroelectric power engineering, water supply, or irrigation. water intake A building which provides the site for food services with little or no waiting staff furnishing table service. cafeteria A food shop which sells a selection of food products that are not typical dietary components of the human population it is co-located with. deli The food products sold in a delicatessen are often considered unusual by the majority of its customers and may come from foreign food supplies which are not widely imported into its region of operation. delicatessen A truck which is equipped to cook and sell food. Due to the facilities on board, food trucks are often larger than other trucks with comparable mechanics. food truck A restaurant which provides prepared meals or other food products that the purchaser must eat off its premises. take out restaurant take-away take-out restaurant A booth with an open window on one side. This definition of kiosk is characteristic of the Western hemisphere and used in English-speaking countries. kiosk A kiosk from which food products are sold. This definition of kiosk is characteristic of the Western hemisphere and used in English-speaking countries. food kiosk A food shop in which food products are the primary offer for sale or trade. grocery store A part of an ecosystem which has been allocated to host a gathering of people for multiple entertainment or commercial activities. Fairgrounds, or parts thereof, may be constructed (e.g. concreted over) or be natural (e.g. clearings or heaths), thus land use is the key differentia. fairground A fairground which is used to exhibit agricultural technology, livestock, and farm-related activity. agricultural fairground A part of an ecosystem where people gather for the purchase and sale of provisions, livestock, and other goods. public market bazaar marketplace mercado palengke souk tianguis As with campgrounds and fairgrounds, land use is the key differentia here. The regularity of marketplace activities may provide a differentia for further growth of this branch. market A food shop in which the food products on offer are restricted to those produced in a region and cultural setting other than that of the shop's locality. ethnic food store ethnic speciality shop ethnic speciality store ethnic food shop An exchangeable device which can be connected to a plumbing system to deliver and drain water. plumbing fixture A plumbing fixture which is bowl-shaped and used for washing hands, dishwashing, and other purposes. hand basin wash basin sink fixture A plumbing fixture which may serve as a container for water in which humans or other animals may bathe. bathtub Of course, there are other uses for bathtubs. bathtub fixture A plumbing fixture within which a human or other animal may bathe under a spray of water. Indoors, there is a drain in the floor. Most showers have temperature, spray pressure and adjustable showerhead nozzle. Showering is common in Western culture due to the efficiency of using it compared with a bathtub. Its use in hygiene is, therefore, common practice. A shower uses less water on average than a bath: 80 litres for a shower compared with 150 litres for a bath. shower fixture An environmental system which is determined by materials bearing roughly homogeneous qualities. Organisational class. Not intended for annotation. environmental system determined by a quality An environmental system which is determined by a living organism. envoEmpo envoOmics environmental system determined by an organism An environmental system determined by an animal. Animal animal environment Metazoan-associated environment envoEmpo envoMeo envoOmics animal-associated environment An environmental system determined by part of a living or dead animal, or a whole small animal. Animal corpus envoEmpo envoMeo envoOmics environment associated with an animal part or small animal An environmental system which includes both living and non-living components. LTER:173 This class will be primarily filled by inference, any environmental system which necessarily includes living parts should be autoclassified here. ecosystem An environmental zone which is bounded by material parts of a land mass or the atmosphere or space adjacent to it. terrestrial environmental zone An ecosystem in which grasses (Graminae) are the dominant form of vegetation and determine the system's structure and dynamics. EcoLexicon:grassland FTT:259 FTT:760 FTT:766 Geonames:V.GRSLD LTER:232 TGN:21604 TGN:54052 GRASSLAND grassland grassland ecosystem A building which is primarily used to facilitate the buying or selling of goods or services. "Commerce includes legal, economic, political, social, cultural and technological systems that are in operation in any country or internationally." commercial building An ecosystem which is determined by communities of plants with a tree growth form and in which members of those communities form continuous or discontinuous regions of canopy cover. The definitions of forest can vary greatly, and different classes will be needed to support the major categories. Tree cover alone is not enough to distinguish between forests and plantations. The international definition proposed by the 2010 FAO Forestry Resource Assessment: "land spanning more than 0.5 ha with trees higher than 5 metres and canopy cover of more than 10 percent, or trees able to reach these thresholds in situ . It does not include land that is predominantly under agricultural or urban land use." - FAO. 2010. Global forest resources assessment 2010, Main report, FAO Forestry Paper 163. Rome. forest ecosystem An ecosystem which 1) is determined by communities of annual crops, perennial woody crops, or by actively tilled land, 2) is primarily used for agricultural activity, and 3) contains no village or larger human settlement. cropland ecosystem A layer which is primarily composed of some solid material, allowing for non-solid parts such as interstitial pockets of gas or liquid. solid layer A vegetated area is a geographic feature which has ground cover dominated by plant communities. envoPolar vegetated area A surface layer which is composed primarily of solid environmental material. solid surface layer A body of water which is primarily composed of saline water. saline body of water This class has its subclasses populated by inference. saline water body An ecosystem which 1) typically has monthly average temperatures below 10 degrees Celsius 2) has a low evapotranspiration ratio 3) is dominated by treeless terrain, covered by communities of low-growing vegetation such as dwarf shrubs, sedges and grasses, mosses, and lichens, 4) contains areas of soil underlain by permafrost with a thin active layer and 5) occurs in both polar and alpine regions (i.e., both high latitudes and high altitudes), and 5) does not have permanent snow or ice cover. SPIRE:Tundra envoPolar Tundra ecosysems are often underlaid by permafrost, with the result that drainage is bad and the soil may be saturated for long periods. It does not have a permanent snow-ice cover. Productivity is low in this biome because of the extremes of climate. tundra ecosystem A research facility in which systems of manufactured products control internal conditions and in which scientific or technological research, experiments, and measurement may be performed. research laboratory laboratory facility A liquid astronomical body part which is continuous and is delimited by physical discontinuities or non-liquid boundaries. body of liquid A part of an astronomical body which is primarily composed of liquid material. liquid astronomical body part A part of an astronomical body which is primarily composed of fluid. fluid astronomical body part A building which is primarily used for the long-term habitation of humans. domestic building A surface layer where the solid or liquid material of an astronomical body comes into contact with an atmosphere or outer space. a useful class: this can be used to define sub-terrestrial and sub-marine entities surface of an astronomical body A layer which separates two portions of environmental material which possess 1) differing compositions, 2) a discontinuity of some property, or 3) some derivative of some property in a direction normal to the interface. interface layer An ecosystem in which the composition, structure, and function of resident ecological assemblages are primarily determined by a desert. desert ecosystem A large continuous area of land, either surrounded by sea or contiguous with another landmass. landmass A part of an astronomical body which is composed of a continuous medium bearing liquid, gaseous, and solid material in variable quantities. compound astronomical body part A surface layer of an astronomical body which is primarily composed of solid material and is not covered by oceans or other bodies of water. land aquatic ecosystem marine ecosystem freshwater ecosystem An ecosystem which primarily occurs on land. terrestrial ecosystem A material entity which has been assembled through the intentional, instinctual, or deliberately programmed efforts of an organism or machine. construction An ecosystem which is formed as a result of human activity or impact. anthropised ecosystem An anthropised ecosystem which is determined by the presence of humans and their constructions. human settlement A construction in which eggs are hatched under artificial conditions. hatchery A landform which occurs on the surface of an astronomical body. The usage of "surface" here aligns with that of planetary surface: in contact with the atmosphere or space. The extent of the "surface" can vary. For rocky planets like Earth, astrogeologists consider the crust as the surface. surface landform A solid astronomical body part which has been formed from and is composed primarily of the matter of that astronomical body. Landforms may be natural or anthropogenic. This term has often has loose usage when referencing entities which are either subterranean or submerged below water bodies. In some cases, oceans themselves are considered landforms. Here, we have provided subclasses to resolve this ambiguity, but place oceans and other water bodies elsewhere.In later revisions, this hiearchy is likely to be reordered based on the formation processes of the entities within it. landform reef A textile is a manufactured product comprised of a network of natural or artificial fibers (often referred to as thread or yarn). https://en.wikipedia.org/wiki/Textile textile An organic material which is primarily composed of some natural bodily fluid or secretion such as blood, semen, saliva, blood plasma, intracellular and interstitial fluids. https://en.wikipedia.org/wiki/Bodily_fluid ENVO bodily fluid classes differ from UBERON's treatment of bodily fluids. UBERON refers to the substance itself ("S"). We assert that UBERON's classes are the primary compositional component of the terms in ENVO ("S material"). Use of the ENVO terms is typically recommended when you wish to indicate that there may be other materials intermixed with S. bodily fluid material A bodily fluid material which is composed primarily of excreta, bodily fluids consisting of matter which contains the waste products of biological processes, including urine or feces, discharged from an organism's body. ENVO bodily fluid classes differ from UBERON's treatment of bodily fluids. UBERON refers to the substance itself ("S"). We assert that UBERON's classes are the primary compositional component of the terms in ENVO ("S material"). Use of the ENVO terms is typically recommended when you wish to indicate that there may be other materials intermixed with S. excreta material Food material which can be used to meet nutritional requirements of animals, particularly livestock such as cattle, goats, sheep, horses, chickens and pigs. https://en.wikipedia.org/wiki/Animal_feed Most animal feed is from plants but some is of animal origin. Fodder refers particularly to food given to the animals (including plants cut and carried to them), rather than that which they forage for themselves. It includes hay, straw, silage, compressed and pelleted feeds, oils and mixed rations, and also sprouted grains and legumes. animal feed Contaminated animal feed is an animal feed that has become contaminated with or come contact with microorganisms or toxic chemicals. contaminated animal feed A mixture of crushed and coarsely ground bones that is used as an organic fertilizer for plants and formerly in animal feed. https://en.wikipedia.org/wiki/Bone_meal bone meal Food material which can be used to meet nutritional requirements of plants. plant feed A textile comprised of a pliable material made usually by weaving, felting, or knitting natural or synthetic fibers and filaments. https://en.wikipedia.org/wiki/Cloth cloth An environmental material which is unable to resist shear forces and continuously deforms when subject to them. fluid fluid environmental material A process in which includes the components of an environmental system as participants. This is a convenience class for organisation and should not be used for annotation. environmental system process A process during which material is displaced from its original location and transported either to a new location or back to the original location. http://orcid.org/0000-0002-3410-4655 envoPolar Experimental class for structural purposes not recommended for annotation. material transport process Sediment which has been transported through the marine water column, settling on the seafloor. http://orcid.org/0000-0002-3410-4655 marine sediments envoPolar Particles of marine sediment are primarily generated by 1) processes in terrestrial systems and transported to the marine realm by the action of rivers or aeolian processes (amongst other routes) , 2) marine organisms, 3) chemical processes in seawater, or 4) cosmogeneous input. marine sediment A structure which traverses a mass of one or more environmental materials, and encloses a roughly tubular site. http://orcid.org/0000-0002-3410-4655 envoPolar channel A vehicle which locomotes using rails and consists of a series of connected compartments used to transport passengers or cargo. train A train which is capable of and used for passenger transport. passenger train A passenger train which runs along an undergroud rail system. subway tube train underground train London Underground SkyTrain Tube U-Bahn Underground metropolitana subway train A building part which is a narrow hall or passage in a building with rooms leading off it. hall passage hallway building corridor A building which accomodates conferences. conference center conference centre conference venue A human construction in which people are educated. educational facility An institutional building in which students are educated. school school building An institutional building which temporarily houses homeless people. homeless shelter A human construction in which healthcare is provided. health facility medical facility healthcare facility A healthcare facility which is used for short-term patient care. ACC ACF acute care center acute care facility A healthcare facility in which patients are medically assessed. CAC clinical assessment centre clinical patient assessment center clinical patient assessment centre clinical patient assessment facility A healthcare facility which 1) is located in part of a hospital and 2) is used by an organizational unit within a hospital. hospital ward hospital unit facility A room in which emergency medical care is provided. A&E room ER room EW room accident & emergency department room casualty department room emergency department room emergency room room emergency ward room emergency unit room A hospital unit facility which is used to provide intensive medical care. ICU ICW ITU critical care unit critical care ward intensive care ward intensive therapy unit intensive treatment unit intensive treatment ward intensive care unit facility A room which is used for patient care during a patient's visit or stay in a healthcare facility. patient-care room examination room patient bed room patient room A healthcare facility which is used to provide outpatient health care services. clinic ambulatory care clinic outpatient clinic medical clinic A medical clinic which is used to provide family medicine services. GP clinic GP office family care clinic family doctor clinic family doctor office family medicine clinic family medicine office general medicine clinic general practice clinic general practice office family practice clinic A residential building which is used to provides long-term care for residents. LTC center LTC centre LTC facility long-term care center long-term care centre long-term care facility A long-term care facility which is used to provide care for people with complex health needs, and which typically has at least one caregiver in attendance twenty four hours a day. residential care facility group home facility A building which is used by an organization which serves a long-established role in human society. This term needs further consideration and development as semantics of institution are ambiguous at scale - e.g. are hotels institutional buildings? institutional building A market which is used for the sale and purchase of perishable goods. wet market A human construction which is used to forcibly confine humans. correctional center correctional centre correctional facility detention center detention centre gaol jail lock-up penitentiary remand center remand centre prison facility A manufactured product consisting of a duct opening which allows air to circulate. vent air vent A poll which is attached to the head, foot, or side of a bed frame. adult portable bed rail assist bar bed handle bed rail bed side rail grab bar half rail hospital bed rail safety rail side rail bedrail A manufactured product consisting of a panel on which control or monitoring instruments are set. console control board control unit display board display panel indicator panel instrument board instrument panel panel control panel A manufactured product consisting of a handle used to open or close a door. door knob door handle A pole which provides stability or support when grasped by the hand. rail, railing hand rail handrail A switch which turns a light on or off. switch, dimmer switch lightswitch light switch A manufactured product which is a storage compartment with a lock. lockable cabinet lockable cupboard locking cabinet locking cupboard locker A switch which allows patients in health care settings to alert a nurse or other health care staff member. nurse call cord nurse call button Steel which is composed primarily of a corrosion resistant alloy of iron and chromium. inox steel stainless stainless steel A paper product which is thin translucent paper. tissue Tissue paper is often used for wrapping or for protecting delicate articles. tissue paper A plumbing fixture which is bowl-shaped, part of a toilet fixture, and capable of contain human waste until it is disposed of. lavatory bowl toilet bowl A manufactured product which is composed of one or more glass or other transparent or semi-transparent materials set inside a frame, and installed in wall, door, roof or vehicle surfaces to allow the passage of light, and sometimes air. casement casement window pane sash sash window windowpane window A manufactured product which is composed of a hinged, sliding, or revolving barrier which is installed at the entrance to a building, room, vehicle, or in the framework of a cabinet. door A paper product which is a thin sheet material made of processed cellulose fibres. paper paper sheet sheet of paper An environmental material consisting of organic matter from plants and/or animals that is used in agriculture as fertilizer. animal manure compost farm slurry green manure liquid manure Most manure consists of animal feces; other sources include compost and green manure. manure A device which can connect, disconnect, or divert current in an electrical circuit. switch A manufactured product which is an alloy of iron and which typically contains a few tenths of a percent of carbon. steel An environnmental material which 1) is composed primarily of polymers with high molecular mass and 2) once deformed does not spontaneously return to its original shape. Plastik plastica 塑膠 Kunststoff envoPlastics "High molecular mass" can be ambiguous as it does not set a threshold for what is considered "high". Here we make no commitment to a threshold. plastic A plastic which is composed primarily of polymers produced by a manufacturing process. manufactured plastic envoPlastics envoPolar synthetic plastic Transmission of a disease agent (infectious pathogen, toxic chemical, etc.) from a source that is common to those who acquire the disease. Common vehicles include air, water, food, injected substances. Legionellosis is an example of common vehicle spread in air that has passed through air conditioning equipment contaminated by the causal organism. HIV disease and hepatitis B and C can be spread among illicit drug users by the common vehicle of contaminated needles and syringes. Cholera and many other waterborne diseases are spread by the common vehicle of contaminated water. common vehicle transmission A role that inheres in a material that is input as the subject of interest in a scientific technique - either as an entity about which data is generated in an assay or study, or an entity that is transformed or modified in a material processing technique (e.g. the source from which a biological sample is taken) experimental subject role An interaction between an exposure stressor and an exposure_receptor. exposure event depth:1 The condition of an organism in all aspects (e.g., functional or metabolic efficiency). See technical discussion about logic of assigning health status: https://www.w3.org/2001/sw/BestPractices/OEP/Lists-of-values-20040625/ https://en.wikipedia.org/wiki/Medical_state cmattin condition medical condition medical state Damion Dooley note: GenEpiO includes various health status descriptors here; many are annotated as included in the American AHA HIPPA or United Kingdom NHS terminologies. The challenge is to map them or order them in such a way that merged data can be analyzed. subject health status http://semanticscience.org/resource/SIO_010057 Condition Condition The process of drawing in by breathing. http://purl.obolibrary.org/obo/ExO_0000057 inhalation Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential E' oxidation-reduction potential MIxS redox potential A symptom onset date is a date-time entity that marks the start of one or more reported symptoms pertaining to an episode of human or animal illness Damion Dooley symptom onset date A substance, usually composed primarily of carbohydrates, fats, water and/or proteins, that can be eaten or drunk by an animal or human being for nutrition or pleasure. Food material for humans and animals which is processed with the intention that it be consumable as a whole or added to other food products. Damion Dooley food product foodon product type A food product made of meat, the skeletal muscle and associated fat, and other edible tissues such as organs, livers, skin, brains, bone marrow, kidneys, or lungs, of mammals. mammalian meat food product This class includes food products which are derived from or produced by a plant. plant food product A food product made from domestic pig meat (Sus domesticus or Sus scrofa scrofa). pork meat food product A food product that is derived from some cow. cow food product A cut of meat (a meat chop) cut perpendicularly to the spine of the pig and usually containing a rib or part of a vertebra, served as an individual portion. pork chop food product A food product which is derived from or produced by an animal that has a vertibrae. vertebrate animal food product A food product made from domesticated bird meat. poultry meat food product Suidae is a family of artiodactyl mammals which are commonly called pigs, hogs or boars. In addition to numerous fossil species, 17 extant species are currently recognized (or 18 counting domestic pigs and wild boars separately), classified into between four and eight genera. The family includes the domestic pig, Sus scrofa domesticus or Sus domesticus, in addition to numerous species of wild pig, such as babirusas and warthogs. All suids, or swine, are native to the Old World, ranging from Asia to Europe and Africa. swine food product bovine meat food product A food product consisting of an edible fungi or mushroom or yeast. fungus food product A food product derived from one or more microorganisms including bacteria, mold, and yeast. microbial food product invertebrate animal food product Food product that is 1) ready or nearly ready for consumption; 2) usually a composite of several foods or ingredients that often belong to distinct product types; 3) usually formulated, mixed and partially or fully cooked. prepared food product A food product which is an output of a food cooking process. food (cooked) This food product type includes food products which are derived from a large, diverse group of photosynthetic organisms. algal food product A fish food product includes products made from any fish species (aquatic vertebrate with gills and fins). fish food product A food product that is derived from some avian animal. avian animal food product Beef that has been ground. beef (ground) A food product from a category of domestic birds kept for meat, eggs, and feathers including fowl such as chickens, turkeys, and waterfowls such as domestic ducks and geese and other meat birds such as pigeons and doves and games birds including pheasants. A food product that is derived from some poultry. poultry food product A turkey meat food product is any food product made predominantly of turkey parts. turkey meat food product A fermentation process in which either carbohydrates, proteins or fats are modified through microbial, enzymatic and/or other biological process. food fermentation A cut of meat that is initially separated from the carcass of an animal during butchering. animal primal cut A product deriving from mahi-mahi or common dolphinfish (Coryphaena hippurus) also widely called dorado and dolphin. dolphinfish food product herring food product Lamb meat food product is a meat product taken from a lamb, a sheep less than a year old. lamb meat food product food product by consumer group sheep meat food product tuna food product A food product consisting of food material derived primarily from a single organism. food product by organism Any substance that can be consumed by an organism to satisfy nutritional or other health needs, or to provide a social or organoleptic food experience food foodstuff nourishment sustenance This class is the top of FOODON's main food product hierarchy which is described in the https://www.foodon.org website, and can be searched in lookup services like https://www.ebi.ac.uk/ols/ food material Roasting is a baking process when the food being baked is meats meat roasting A food evaporation process is the process of removing water from a food. food evaporation process A process involving the physical transformation of a food source or food product into some derived organic material or food product food transformation process Invertebrates are animals that neither possess nor develop a vertebral column (commonly known as a backbone or spine), derived from the notochord. This includes all animals apart from the subphylum Vertebrata. invertebrate animal Food material which has been categorized by a characteristic such as granularity or temperature. food material by characteristic A form of frying characterized by the use of minimal cooking oil or fat (compared to shallow frying or deep frying); typically using just enough oil to lubricate the pan. A pan fry takes place at lower heat than does a sauté. shallow frying A physical object quality which describes a characteristic of some food material. food material characteristic A cut of meat from a pig, that comes from the tissue along the dorsal side of the rib cage. pork loin cut of beef, british beef rump cut (british) A butchery cut of beef that is primal, sub-primal or a retail cut. butchery cut of beef A food product organized by the process which it results from. food product by process A method of precooking food where a liquid is heated to just below the boiling point. Often used to retard the spoiling of milk. food scalding A food product that is derived from some pig. pig food product pork food product A fish fillet, from the French word filet meaning a thread or strip, is the flesh of a fish which has been cut or sliced away from the bone by cutting lengthwise along one side of the fish parallel to the backbone. fish fillet mahi mahi fillet Pet food is plant or animal material intended for consumption by pets. pet food A whole breast that is obtained from a turkey. turkey breast barramundi food product barramundi fillet A herring fillet is a fillet cut of herring herring fillet A fillet cut of a tuna fish. tuna fillet A beef cut that is derived from the 6th, 7th and 8th rib of the rib primal. beef short rib Synbiotic claim refers to food ingredients or dietary supplements combining probiotics and prebiotics in a form of synergism that beneficially affect the host. synbiotic claim A cut of beef from the primal rib, one of the nine primal cuts of beef. While the entire rib section comprises ribs six through 12, a standing rib roast may contain anywhere from two to seven ribs. beef prime rib roast A fish steak, alternatively known as a fish cutlet, is a cut of fish which is cut perpendicular to the spine and can either include the bones or be boneless. fish steak A thin slice of meat from the leg or ribs of veal, pork, chicken, or mutton. cutlet A whole animal. animal A beef meat cut that has a flat-cut appearance. beef steak A beef primal cut that comes from the area below the backbone . A portion of meat from either the short loin, the sirloin, or the tenderloin muscle area. beef loin A cut of beef corresponding to the psoas major muscle, which is very tender. beef tenderloin A boneless steak cut from the sirloin region beef top loin steak A beef steak that is prepared from the beef short loin. The maximum width of the tenderloin must be at least 1/2 inch (13mm) when measured parallel to the length of the backbone. A steak of beef cut from the front of the short loin area. beef T-bone steak A beef steak that is prepared from the beef short loin. The maximum width of the tenderloin must be atleast 1.25 inches (3.2cm) when measured parallel to the length of the backbone. A steak of beef cut from the back of the short loin area. beef porterhouse steak A steak cut of beef taken from the smaller end of the tenderloin, or psoas major of the cow carcass, usually a steer or heifer. filet mignon (North America) A butchery cut of chicken that is typically boneless. chicken fillet A fruit ripeness characteristic in which a fruit has surpassed ripeness and is undergoing decomposition. overripe A fruit ripeness characteristic in which a fruit has some ripe part(s) or is about to achieve full maturity. slightly ripe A pet food that has not been heat treated or otherwise preserved. pet food (raw) A food item intended to provide pleasure or reward to an animal, and which might not be nutritious. pet treat Food contact materials are materials that are intended to be in contact with food. These can be things that are quite obvious like a glass or a can for soft drinks as well as machinery in a food factory or a coffee machine. food contact material Cultivation of plants within a polytunnel or similar tunnel. tunnel farming The rearing of domesticated animals for food. food animal rearing An approach to animal husbandry designed to maximize production, while minimizing costs by keeping livestock such as cattle, poultry, and fish at high stocking densities, at large scale, and using automated feeding systems. industrial livestock production A technology-based approach toward food production that aims to provide optimal growing conditions throughout the development of a crop located within an enclosed growing structure such as a greenhouse or building. controlled environment agriculture (CEA) production aquaculture production Aquatic farmed food production located offshore, in coastal areas or in freshwater lakes, open-net pens, or “cages”, that allow for free exchange between the farm and the surrounding environment. aquaculture open-pen rearing aquaculture closed containment pen rearing The flesh of fish fish meat A meat made up from the beef cut is known as sirloin. Ground sirloin is ground sirloin meat. ground sirloin A Japanese cooking method in which food is broiled or grilled with a glaze of soy sauce, mirin, and sugar. teriyaki cooking method An animal meat (cut) and an output of simple random sampling. random sample animal meat cut A heating container process in which the container conducts heat by being in proximity to an open flame, a hot surface or an oven. direct heating of container A heating container process in which the temperature of contained liquid is raised to a threshold. heating liquid in container cut of beef, mexican A cut of beef and part of the sub-prime cut known as the chuck. diezmillo A Japanese term to describe a uniformly cut block of skinless and boneless seafood. saku A food product that is derived from some animal. animal food product A cut of meat which is long, narrow and boneless. meat strip A cutlet made from chicken breast. chicken breast cutlet A piece or pieces or amount of substance derived from one or more organisms. organism piece A severed part of an animal. piece of animal One or more pieces of animals. piece(s) of animal A smaller cut of meat that is obtained from the larger primal cut of an animal. animal sub-primal cut An animal meat cut that is derived from a sub-primal, individual muscle cut or minor primal cut. animal retail cut An organ that derives from an animal. animal organ A cut of beef that is initially separated from the carcass of a{n} {organism} during butchering. beef primal cut A retail cut of meat from an elk that is of a size for slicing into more than one portion and is suitable for roasting. elk roast A smaller cut of beef that is obtained from the larger primal cut of beef. beef sub-primal cut A retail cut of meat from a beef that is of a size for slicing into more than one portion and is suitable for roasting. beef roast A cut of beef that is derived from a sub-primal, individual muscle cut or minor primal cut. beef retail cut A retail cut of meat from a lamb that is of a size for slicing into more than one portion and is suitable for roasting. lamb roast A retail cut of meat from a pork that is of a size for slicing into more than one portion and is suitable for roasting. pork roast A retail cut of meat from a veal that is of a size for slicing into more than one portion and is suitable for roasting. veal roast A cut of meat that is initially separated from the carcass of a lamb during butchering. lamb primal cut A cut of meat that is initially separated from the carcass of a pork during butchering. pork primal cut A cut of meat that is initially separated from the carcass of a veal during butchering. veal primal cut A smaller cut of meat that is obtained from the larger primal cut of a lamb. lamb sub-primal cut A smaller cut of meat that is obtained from the larger primal cut of a pork. pork sub-primal cut A smaller cut of meat that is obtained from the larger primal cut of a veal. veal sub-primal cut A pork meat cut that is derived from a sub-primal, individual muscle cut or minor primal cut. pork retail cut A retail cut of meat from a lamb that is perpendicular to the spine, and usually containing a rib or riblet part of a vertebra. lamb chop A retail cut of meat from a pork that is perpendicular to the spine, and usually containing a rib or riblet part of a vertebra. pork chop A severed part of a pork. piece of pig A severed part of a beef. piece of cow One or more pieces of cows. piece(s) of cow A cut of meat that is initially separated from the carcass of a bison during butchering. bison primal cut A smaller cut of meat that is obtained from the larger primal cut of a bison. bison sub-primal cut A cut of meat that is initially separated from the carcass of a buffalo during butchering. buffalo primal cut A smaller cut of meat that is obtained from the larger primal cut of a buffalo. buffalo sub-primal cut A buffalo meat cut that is derived from a sub-primal, individual muscle cut or minor primal cut. buffalo retail cut A buffalo meat cut that has a flat-cut appearance. buffalo steak A food product containing a quantity of iron large enough to make a significant contribution to nutritional needs. iron rich label claim A food product containing a quantity of vitamin A large enough to make a significant contribution to nutritional needs. vitamin A rich label claim A beef cut that comes from the 'round', the rear leg of the beef. beef round A raw beef round cut. beef round (raw) A beef cut that comes from the outside of the rear leg. beef bottom round A raw beef bottom round cut. beef bottom round (raw) A steak cut from the beef bottom round. beef bottom round steak A raw beef bottom round steak. beef bottom round steak (raw) A boneless beef bottom round steak. beef bottom round steak (boneless) A raw and boneless beef bottom round steak. beef bottom round steak (boneless, raw) A roast cut from the beef bottom round. beef bottom round roast A raw beef bottom round roast. beef bottom round roast (raw) A boneless beef bottom round roast. beef bottom round roast (boneless) A raw and boneless beef bottom round roast. beef bottom round roast (boneless, raw) A beef cut that comes from the inside of the rear leg. beef top round A raw beef top round cut. beef top round (raw) A steak cut from the beef top round. beef top round steak A raw beef top round steak. beef top round steak (raw) A boneless beef top round steak. beef top round steak (boneless) A raw and boneless beef top round steak. beef top round steak (boneless, raw) A beef top round steak in which the top cap portion has been separated off. beef top round steak (cap off) A raw beef top round steak in which the top cap portion has been separated off. beef top round steak (cap off, raw) A raw and boneless beef top round steak in which the top cap portion has been separated off. beef top round steak (cap off, boneless, raw) A roast cut from the beef top round. beef top round roast A raw beef top round roast. beef top round roast (raw) A boneless beef top round roast. beef top round roast (boneless) A raw and boneless beef top round roast. beef top round roast (boneless, raw) A beef cut that comes from the round primal, and is found on the front end of the rear leg. beef sirloin tip A raw beef sirloin tip cut. beef sirloin tip (raw) A roast cut from the beef sirloin tip. beef sirloin tip roast A raw beef sirloin tip roast. beef sirloin tip roast (raw) A steak cut from the beef sirloin tip. beef sirloin tip steak A raw beef sirloin tip steak. beef sirloin tip steak (raw) A roast that derives from beef sirloin tip and only consists of M.vastus lateralis. beef sirloin tip side roast A raw beef sirloin tip side roast. beef sirloin tip side roast (raw) A steak cut from the beef sirloin tip side roast. beef sirloin tip side steak A raw beef sirloin tip side steak. beef sirloin tip side steak (raw) A roast that derives from beef sirloin tip and only consists of M.rectus femoris. beef sirloin tip center roast A raw beef sirloin tip center roast. beef sirloin tip center roast (raw) A steak cut from the beef sirloin tip center roast. beef sirloin tip center steak A raw beef sirloin tip center steak. beef sirloin tip center steak (raw) A beef cut that is an elongated muscle located in the center of the beef round cut, and thus is named “Eye.” beef eye of round A raw beef eye of round cut. beef eye of round (raw) A roast cut from the beef eye of round. beef eye of round roast A raw beef eye of round roast. beef eye of round roast (raw) A steak cut from the beef eye of round. beef eye of round steak A raw beef eye of round steak. beef eye of round steak (raw) A beef cut that extends from the neck to the fifth rib and includes the shoulder blade and upper arm. beef chuck A steak cut from the beef chuck tender. beef chuck tender steak A raw beef chuck tender steak. beef chuck tender steak (raw) A roast cut from the beef chuck tender. beef chuck tender roast A raw beef chuck tender roast. beef chuck tender roast (raw) A large, boneless cut that comes from between the ribs and backbone. It contains a mix of tender and somewhat tough muscles, which are fabricated into smaller cuts known as the chuck eye roll and the chuck under blade. beef chuck roll A raw beef chuck roll cut. beef chuck roll (raw) The top portion of the chuck roll that is separated from the under-blade section. beef chuck eye roll A raw beef chuck eye roll cut. beef chuck eye roll (raw) A roast cut from any portion of the chuck eye roll, typically the center. beef chuck eye roast A raw beef chuck eye roast. beef chuck eye roast (raw) A steak cut from the rib end only of the chuck eye roll. beef chuck eye steak A raw beef chuck eye steak. beef chuck eye steak (raw) A cut made by splitting a chuck eye roll in half lengthwise, resulting in two boneless, country-style ribs. beef country-style rib A raw beef country-style rib. beef country-style rib (raw) A meat cut that is the flatter portion of the Chuck Roll and is under the Chuck Eye Roll. beef under blade A thin muscle that lays in the seam between the chuck eye roll and under blade. beef sierra steak A raw beef sierra steak. beef sierra steak (raw) A beef cut from the center of the under blade. beef denver steak A raw beef denver steak. beef denver steak (raw) A roast cut in which under blade with other muscles and connective tissue are removed and either left whole or portioned. beef denver roast A beef denver roast that is raw. beef denver roast (raw) A large muscle system which lies dorsal and posterior to the elbow joint, ventral and posterior to the ridge of the scapula (blade bone) and is anterior to the 6th rib. beef shoulder clod A raw beef shoulder clod. beef shoulder clod (raw) The largest section of the shoulder clod that consist of the large muscle system of the thick end of the shoulder. beef shoulder clod arm roast A raw beef shoulder clod arm roast. beef shoulder clod arm roast (raw) A steak cut across the grain from the shoulder clod arm roast. beef shoulder steak A raw beef shoulder steak. beef shoulder steak (raw) A roast cut from the beef shoulder clod. beef shoulder roast A raw beef shoulder roast. beef shoulder roast (raw) A steak cut across the grain from the shoulder clod arm roast similar to the shoulder steak. Visible connective tissue and associated lean must be removed to qualify as a Ranch Steak. beef ranch steak A raw beef ranch steak. beef ranch steak (raw) The second most tender muscle in the animal that is derived from the shoulder clod. However, internal connective tissue should be removed to preserve that tenderness. beef top blade A raw beef top blade cut. beef top blade (raw) A beef steak cut that is end-to-end from the whole top blade. beef top blade steak A raw beef top blade steak. beef top blade steak (raw) A steak cut from the top blade, where the cutting method removes internal connective tissue from the whole Top Blade. beef flat iron steak A raw beef flat iron steak. beef flat iron steak (raw) A cut that is derived from the beef chuck and must include rib 2 through 5. beef chuck short rib A raw beef chuck short rib. beef chuck short rib (raw) A cut from beef chuck short rib that is an individual muscle and is boneless. beef chuck short rib (boneless) A raw and boneless beef chuck short rib. beef chuck short rib (boneless, raw) A beef cut that is the portion of the forequarter after removal of the rib, shortplate, foreshank and brisket. beef square cut chuck A raw beef square cut chuck. beef square cut chuck (raw) A beef steak cut that is identified by its 7-shaped bone. The 7-bone is made by cutting steaks across the scapula or blade bone. beef 7-bone chuck steak A raw beef 7-bone chuck steak. beef 7-bone chuck steak (raw) A beef roast cut that is identified by its 7-shaped bone. The 7-bone is made by cutting roasts across the scapula or blade bone. beef 7-bone chuck roast A raw beef 7-bone chuck roast. beef 7-bone chuck roast (raw) A steak cut from the flat bone portion of the blade that comes from ribs 4 through 5. beef blade chuck steak A raw beef blade chuck steak. beef blade chuck steak (raw) A roast cut from the flat bone portion of the blade that comes from ribs 4 through 5. beef blade chuck roast A raw beef blade chuck roast. beef blade chuck roast (raw) A beef roast that comes from the center portion of the Chuck Roll. beef chuck roast A raw beef chuck roast. beef chuck roast (raw) A beef steak that comes from the center portion of the Chuck Roll. beef chuck steak A raw beef chuck steak. beef chuck steak (raw) A beef cut that is adjacent to the arm and includes ribs 2 through 5. beef cross-rib roast A raw beef cross-rib roast. beef cross-rib roast (raw) A steak cut from the arm bone (humerus) of the upper forelimb. beef chuck arm steak A raw beef chuck arm steak. beef chuck arm steak (raw) A roast cut from the arm bone (humerus) of the upper forelimb. beef chuck arm roast A raw beef chuck arm roast. beef chuck arm roast (raw) A beef cut that is derived from the anterior end of the untrimmed chuck roll. beef chuck neck roast A raw beef chuck neck roast. beef chuck neck roast (raw) A roast cut is made during fabrication to square off the chuck roll. beef chuck flap/edge roast A raw beef chuck flap/edge roast. beef chuck flap/edge roast (raw) A raw beef loin cut. beef loin (raw) beef short loin A raw beef short loin cut. beef short loin (raw) A raw beef T-bone steak. beef T-bone steak (raw) A cut refers to the group of muscles that extends the length of the Top Loin adjacent to the spine bone and on top of the finger bone. beef strip loin (bone-in) A raw beef strip loin that contains bone. beef strip loin (bone-in, raw) A group of muscles that extends the length of the top loin adjacent to the spine bone and on top of the finger bone. beef strip loin (boneless) A raw and boneless beef strip loin. beef strip loin (boneless, raw) A roast cut that comes from boneless beef strip loin. beef strip roast (boneless) A raw beef strip roast. beef strip roast (boneless, raw) A cut that comes from the top loin or strip loin into uniform steak. beef strip steak (boneless) A raw and boneless beef strip steak. beef strip steak (boneless, raw) A beef strip steak that contains bone material. beef strip steak (bone-in) A raw beef strip steak that contains bone material. beef strip steak (bone-in, raw) A smaller roasting option than Strip Roast. beef strip petite roast A raw beef strip petite roast. beef strip petite roast (raw) A thick cut but smaller diameter than beef strip steak. beef strip fillet A raw beef strip fillet. beef strip fillet (raw) A meat cut that is an inside muscle of the beef loin. beef tenderloin (bone-in) A raw beef tenderloin that contains bone material. beef tenderloin (bone-in, raw) A raw beef tenderloin steak. beef tenderloin steak (bone-in) A raw beef tenderloin steak. beef tenderloin steak (bone-in, raw) A cut that is a long, narrow, and lean muscle located within the loin, and is the most tender cut of beef. beef tenderloin (boneless) A raw and boneless beef tenderloin. beef tenderloin (boneless, raw) A roast cut from the larger tenderloin. beef tenderloin roast A raw beef tenderloin roast. beef tenderloin roast (raw) A boneless steak cut from the tenderloin. beef tenderloin steak A raw beef tenderloin steak. beef tenderloin steak (raw) A beef primal cut that is contained within the larger cut 'beef loin'. It is located between the short loin and the round and includes the hip section and ends at the socket of the pelvis. beef sirloin A raw beef sirloin cut. beef sirloin (raw) A beef cut that is located behind the beef short loin on the top back end of the animal. beef top sirloin butt A raw beef top sirloin butt. beef top sirloin butt (raw) A steak cut from the beef top sirloin butt that is flavourful and juicy. beef top sirloin steak A raw beef top sirloin steak. beef top sirloin steak (raw) A roast cut from the beef top sirloin. beef top sirloin roast A raw beef top sirloin roast. beef top sirloin roast (raw) A roast cut that is a smaller version of the larger {animal top sirloin roast beef top sirloin petite roast A raw beef top sirloin petite roast. beef top sirloin petite roast (raw) A cut that is portioned from a top sirloin steak. beef top sirloin fillet A raw beef top sirloin fillet. beef top sirloin fillet (raw) A beef steak cut from the triangle-shaped muscle that caps or covers the top sirloin. beef culotte steak A raw beef culotte steak. beef culotte steak (raw) A beef roast cut from the triangle-shaped muscle that caps or covers the top sirloin. beef culotte roast A raw beef culotte roast. beef culotte roast (raw) A beef sub-primal cut that is the lower portion of the sirloin section of the loin that contains three muscles that vary in tenderness. beef bottom sirloin butt A raw beef bottom sirloin butt. beef bottom sirloin butt (raw) A beef roast cut that is triangular shaped and is located at the tip of the sirloin. beef tri-tip roast A raw beef tri-tip roast. beef tri-tip roast (raw) A steak cut from the beef tri-tip section. beef tri-tip steak A raw beef tri-tip steak. beef tri-tip steak (raw) A small-sized sirloin steak. beef petite sirloin steak A raw beef petite sirloin roast. beef petite sirloin steak (raw) A small roast section of the bottom sirloin opposite the sirloin tip in the beef round. beef petite sirloin roast A raw beef petite sirloin roast. beef petite sirloin roast (raw) A boneless cut with a hearty texture that’s a good source for fajita meat. beef sirloin bavette flap A raw beef sirloin bavette flap cut. beef sirloin bavette flap (raw) A steak cut from the beef sirloin bavette flap. beef sirloin bavette steak A raw beef sirloin bavette steak. beef sirloin bavette steak (raw) A beef cut that is located below the loin primal. beef flank A raw beef flank. beef flank (raw) A steak cut from the beef flank. beef flank steak A raw beef flank steak. beef flank steak (raw) A beef cut that is located on the underside of the animal below the rib primal. The end of the sixth through the twelfth rib is contained within the plate primal cut. beef short plate A raw beef short plate cut. beef short plate (raw) A beef steak that is a trimmed, boneless portion of the diaphragm muscle attached to the 6th through 12th rib on the underside of the short plate. beef inside skirt steak A raw beef outside skirt steak. beef inside skirt steak (raw) A beef steak that is a trimmed, boneless portion of the diaphragm muscle attached to the 6th through 12th rib on the underside of the short plate. beef outside skirt steak A raw beef outside skirt steak. beef outside skirt steak (raw) A beef steak that is a thick strip of meat located on the underside of the carcass and hangs between the last rib and the loin. beef hanger steak A raw beef hanger steak. beef hanger steak (raw) A beef cut that is usually taken from the flat end of ribs 6 through 9. beef plate short rib A raw beef plate short rib. beef plate short rib (raw) A beef cut that is located on the underside of the animal, below the chuck primal, which extends from between the forelegs to the plate. beef brisket A raw beef brisket. beef brisket (raw) A beef cut that is the leaner half of the whole brisket. beef brisket flat half A raw beef brisket flat half cut. beef brisket flat half (raw) A boneless beef brisket flat half cut. beef brisket flat half (boneless) A raw and boneless beef brisket flat half cut. beef brisket flat half (boneless, raw) A beef sub-primal cut that is the less lean half of the whole Brisket. beef brisket point half A raw beef brisket point half. beef brisket point half (raw) A portion of the beef leg, which is used extensively for movement. beef shank A raw beef shank. beef shank (raw) A cross-section of beef leg. beef shank cross-cut A raw beef shank cross-cut. beef shank cross-cut (raw) A center-cut cross-section of a beef leg beef shank center cut A raw beef shank center-cut. beef shank center cut (raw) A beef cut that is situated under the front section of the backbone and used primarily for support. beef rib A raw beef rib cut. beef rib (raw) A boneless cut from the rib primal. beef ribeye roll (lip on) A raw beef ribeye roll cut. beef ribeye roll (lip on, raw) A beef rib roast that has had the sixth through the twelfth rib bones removed leaving just the rib-eye muscle. beef ribeye roast A raw beef ribeye roast. beef ribeye roast (raw) A beef steak that is a cut from the rib-eye roast. beef ribeye steak A raw beef ribeye steak. beef ribeye steak (raw) A meat cut that is located above the short rib in the rib primal between the Chuck and Loin primal. beef ribeye roll A raw beef ribeye roll cut. beef ribeye roll (raw) A smaller alternative to the ribeye roast. beef ribeye petite roast A raw beef ribeye petite roast. beef ribeye petite roast (raw) A smaller ribeye steak beef ribeye fillet A raw beef ribeye fillet. beef ribeye fillet (raw) A steak cut that is portioned from the ribeye cap roll by slicing at a right angle to the grain or muscle fibre direction. beef ribeye cap steak A raw beef ribeye cap steak. beef ribeye cap steak (raw) A cut that is portioned by slicing at a right angle to the grain or direction of muscle fibre. beef ribeye cap roll A beef ribeye cap roll cut that is raw. beef ribeye cap roll (raw) A beef cut that is situated under the front section of the backbone. beef rib sub-primal A raw beef rib sub-primal cut. beef rib sub-primal (raw) A raw beef short rib cut. beef short rib (raw) A beef cut that is portioned by the number of rib bones. beef back rib A raw beef back rib cut. beef back rib (raw) A beef steak that is a cut from the rib roast. beef rib steak A raw beef rib steak. beef rib steak (raw) A raw beef prime rib roast. beef prime rib roast (raw) A rib roast that includes ribs 9 or 10 through 12 and is next to the loin. beef small end rib roast A raw beef small end rib roast. beef small end rib roast (raw) A rib roast that includes ribs 6 through 8 or 9 and is next to the chuck. beef large end rib roast A raw beef large end rib roast. beef large end rib roast (raw) A tender, bone-in steak with a frenched rib presentation. beef cowboy steak A raw beef cowboy steak. beef cowboy steak (raw) A tender bone-in steak from the rib with a long bone and marbling that adds flavour. beef tomahawk steak A raw beef tomahawk steak. beef tomahawk steak (raw) A thin strip of beef cut from between individual ribs in the rib primal. beef rib finger A raw beef rib finger cut. beef rib finger (raw) A lamb primal cut that is the upper foreleg extending from elbow to blade bone. lamb shoulder A raw lamb shoulder cut. lamb shoulder (raw) A whole cut from the Shoulder. The cut location is the full length of the Scapula or blade bone and includes the muscle groups above and below the Scapula. lamb shoulder blade A raw lamb shoulder blade cut. lamb shoulder blade (raw) A roast that is derived from the blade portion of the lamb shoulder primal. The cut location is from either the flat bone or the center portion of the Blade lamb shoulder blade roast A raw lamb shoulder blade roast. lamb shoulder blade roast (raw) A lamb chop that is derived from the blade portion of the lamb shoulder primal. lamb shoulder blade chop A raw lamb shoulder blade chop. lamb shoulder blade chop (raw) A whole cut from the shoulder. The shoulder arm consists of the muscle groups that extend from the elbow joint to the shoulder joint and includes the first three ribs. lamb shoulder arm A raw lamb shoulder arm cut. lamb shoulder arm (raw) A roast that is derived from the arm portion of the Shoulder primal. Arm Roasts come from the shaft of the Humerus and includes the surrounding muscles that extends from the Elbow joint to the Shoulder joint. lamb shoulder arm roast A raw lamb shoulder arm roast. lamb shoulder arm roast (raw) A lamb chop that is derived from the arm portion of the lamb shoulder primal. lamb shoulder arm chop A raw lamb shoulder arm chop. lamb shoulder arm chop (raw) A primal cut that comes from the area which extends from groin to ankle. lamb leg A raw lamb leg. lamb leg (raw) A boneless lamb leg. lamb leg (boneless) A leg half that is derived from a whole leg. The anatomical location is the “half” that comes from the shank or lower section of the Leg. The half includes the center section with muscles from the bottom, eye, tip, and top. lamb shank half A raw lamb shank half cut. lamb shank half (raw) A lamb leg half that is derived from a whole leg. The anatomical location is the “Half” that comes from the Pelvic region of the Leg known as the Sirloin. The half includes the center section with muscles from the bottom, eye, tip, and top. lamb sirloin half A raw lamb sirloin half cut. lamb sirloin half (raw) A lamb sirloin half that has bones removed except for the femur and humerus bone and the designated shank (i.e. hindshank, or foreshank) is removed. lamb sirloin half (shank off, semi-boneless) A cut from lamb sirloin half (shank off, semi-boneless) that is raw. lamb sirloin half (shank off, semi-boneless, raw) A boneless cut that comes from the outside and sirloin tip portion of any boneless leg cut. lamb leg bottom A boneless cut that comes from the inside portion of any boneless leg cut and shall consist of the semimembranosus, adductor and firmly attached muscles. The inside is separated from the bottom and knuckle portion along the natural seams. lamb leg top A lamb chop that derives from the sirloin portion of the leg. The cut location extends from the anterior end of the Pelvic bone to the hip socket. lamb sirloin chop A raw lamb sirloin chop. lamb sirloin chop (raw) A boneless lamb sirloin chop. lamb sirloin chop (boneless) A raw and boneless lamb sirloin chop. lamb sirloin chop (boneless, raw) A whole rear leg containing the eye, bottom, sirloin, sirloin tip and top. leg of lamb A raw leg of lamb. leg of lamb (raw) A leg of lamb that has the shank and sirloin removed leaving only the “center” section of the leg thus the name “center cut.” leg of lamb center cut A raw leg of lamb center cut. leg of lamb center cut (raw) A lamb primal cut that is between the shoulder and loin. lamb rib A raw lamb rib. lamb rib (raw) A lamb minor primal cut that is the lower chest cavity underneath the rack that includes ribs 5-8. lamb breast A minor lamb primal cut that is meat lower shank from front leg with no hock bones. lamb foreshank A raw lamb foreshank. lamb foreshank (raw) A lamb cut that comes from the anatomical body location on either side of the spine that is located posterior to the Rack and anterior to the Sirloin or hip. lamb loin A raw lamb loin cut. lamb loin (raw) A whole cut that is derived from the short loin or any loin item that includes the sirloin. Because of its anatomical location, the tenderloin is the least exercised muscle in the carcass thus the name “Tender” Loin. The cut location is from underneath the finger bones in the short loin and the hipbone in the sirloin. lamb tenderloin A raw lamb tenderloin cut. lamb tenderloin (raw) A boneless and fatty cut from the belly of a pig. pork belly A raw pork belly. pork belly (raw) A primal skeletal area of a pig that extends from groin to ankle. pork leg A raw pork leg. pork leg (raw) A leg half that is derived from a whole pork leg. The anatomical location is the “Half” that comes from the Rump or Pelvic region of the Leg. pork leg sirloin half A raw pork leg sirloin half cut. pork leg sirloin half (raw) A leg half that is derived from a whole pork leg. The anatomical location is the “Half” that comes from the Shank or lower section of the Leg pork leg shank half A raw pork leg shank half cut. pork leg shank half (raw) A raw pork loin cut. pork loin (raw) Pork loin chop that is derived from the blade end of the pork loin and must include the blade bone/cartilage. pork loin blade chop A raw pork loin blade chop. pork loin blade chop (raw) A roast derived from the loin blade. pork loin blade roast A raw pork loin blade roast. pork loin blade roast (raw) A pork loin chop from the center cut loin. The cut location is adjacent to but after the T-Bone chop and before the Sirloin portion on the Loin. porterhouse chop A raw porterhouse chop. porterhouse chop (raw) A pork loin chop that is derived from the center cut rib section of the loin. ribeye chop A raw ribeye chop. ribeye chop (raw) A roast that is derived from the center cut rib section of the loin. ribeye roast A raw ribeye roast. ribeye roast (raw) A pork chop that is derived from the whole loin. The Sirloin is the last 5 to 7 inches of the posterior end of the Loin. Sirloin Chop comes after but is adjacent to, the posterior end of the center-cut loin. pork sirloin chop A raw pork sirloin chop. pork sirloin chop (raw) A pork chop that is derived from boneless sirloin. pork sirloin chop (boneless) A raw and boneless pork sirloin chop. pork sirloin chop (boneless, raw) A pork roast that is derived from the whole loin. The Sirloin is the last 5 to 7 inches of the posterior end of the Loin. The Sirloin Roast comes after but is adjacent to the posterior end of the Center Cut Loin. pork sirloin roast A raw pork sirloin roast. pork sirloin roast (raw) The whole tenderloin. Because of its anatomical location, the tenderloin is the least exercised muscle in the carcass, thus the name “tender” loin. The tenderloin is located underneath the Finger bones and the Hipbone in the Loin. pork tenderloin A boneless pork chop that is derived from the center-cut top loin. New York chop (boneless) A raw and boneless New York chop. New York chop (boneless, raw) A boneless roast that is derived from the center-cut top loin. New York roast (boneless) A raw New York roast. New York roast (boneless, raw) A meat cut that is derived from the blade end of a pork loin and must include not less than three (3) or more than six (6) ribs. pork loin country-style ribs Raw pork loin country-style ribs. pork loin country-style ribs (raw) Boneless pork loin country-style ribs. pork loin country-style ribs (boneless) A meat cut that is derived from the boneless blade end of the pork loin. pork loin country-style ribs (boneless, raw) Back Ribs that are derived from the pork loin. pork loin back ribs Raw pork loin back ribs. pork loin back ribs (raw) A slice that is derived from a whole pork leg. pork leg center slice A raw pork leg center slice that is raw. pork leg center slice (raw) A raw and cured pork leg center slice. pork leg center slice (cured, raw) Ribs derived from the pork belly. Spareribs are the longer rib bones and intercostal meat located below the back ribs. They begin with the second rib and extend downward to the sternum and costal cartilage, spanning the length of the Rib cage. pork spareribs Raw pork spareribs. pork spareribs (raw) Upper foreleg of a pig that extends from elbow to blade bone. pork shoulder A boneless pork shoulder. pork shoulder (boneless) Forelimb from a shoulder. pork picnic A raw pork picnic cut. pork picnic (raw) A pork roast that is derived from the picnic sub-primal of the shoulder primal. pork arm roast A raw pork arm roast. pork arm roast (raw) The section of a pork shoulder that includes the blade and 7-bone. pork shoulder blade A raw pork shoulder blade cut. pork shoulder blade (raw) A pork steak that is derived from the Shoulder Blade. The cut location is just above the shoulder joint adjacent to the picnic. pork butt steak A raw pork butt steak. pork butt steak (raw) The sirloin tip also known as the Knuckle is the muscle group of a pig that runs parallel with the (Femur) Leg bone that extends upward from the (Patella) Kneecap to the Ball of the Femur. pork sirloin tip A raw pork sirloin tip cut. pork sirloin tip (raw) A pork roast that is derived from the leg tip.The Sirloin Tip also known as the Knuckle is the muscle group that runs parallel with the (Femur) Leg bone that extends upward from the (Patella) Kneecap to the Ball of the Femur. pork sirloin tip roast A raw pork sirloin tip roast. pork sirloin tip roast (raw) A pork steak that is derived from the Top Leg, also known as an Inside Leg; the individual muscle Gracilis. It is the cap that covers the center portion of the Top Leg. pork leg cap steak A raw pork leg cap steak. pork leg cap steak (raw) A veal cut that is the portion of hindquarter remaining after the removal of loin. veal leg A raw veal leg. veal leg (raw) A cut that comes from the inside of the rear leg of a calf. veal top round A raw veal top round cut. veal top round (raw) A meat cut from the upper part of a hind leg. veal hindshank A raw veal hindshank cut. veal hindshank (raw) A veal primal cut that comes from the area below the backbone . veal loin A raw veal loin cut. veal loin (raw) A veal primal cut that is situated under the front section of the backbone and used primarily for support. veal rib A raw veal rib. veal rib (raw) A veal roast that is derived from the rib section. veal rib roast A raw veal roast. veal rib roast (raw) A veal primal cut that consist of the plate and brisket portion of the forequarter (intact) and shall contain 11 ribs. veal breast A raw veal breast. veal breast (raw) A boneless veal breast. veal breast (boneless) A raw and boneless veal breast. veal breast (boneless, raw) A veal primal cut that is the foreleg portion from the chuck. veal foreshank A raw veal foreshank cut. veal foreshank (raw) A veal primal cut that is contained within the larger primal cut 'veal loin'. It is located between the short loin and the leg (round) and includes the hip section and ends at the socket of the pelvis. veal sirloin A raw veal sirloin. veal sirloin (raw) A veal primal cut that is the upper foreleg extending from elbow to blade bone. veal shoulder A raw veal shoulder. veal shoulder (raw) A veal meat cut in which the cut location is the full length of the Scapula or blade bone and includes the muscle groups above and below the Scapula. veal shoulder blade A raw veal shoulder arm cut. veal shoulder blade (raw) A veal meat cut in which shoulder arm consists of the muscle groups that extend from the elbow joint to the shoulder joint and includes the first three ribs. veal shoulder arm A raw veal shoulder blade cut. veal shoulder arm (raw) A cut of meat that is found between the top and bottom round roast located on both hindquarters of the elk. elk eye of round roast A raw elk eye of round roast. elk eye of round roast (raw) A raw beef porterhouse steak. beef porterhouse steak (raw) A raw beef tenderloin. beef tenderloin (raw) A piece of animal meat that is derived from cow. piece of beef A piece of boneless beef. piece of beef (boneless) One or more pieces of beef. piece(s) of beef A raw butchery cut of beef. butchery cut of beef (raw) A bison meat cut that is derived from a sub-primal, individual muscle cut or minor primal cut. bison retail cut A bison meat cut that has a flat-cut appearance. bison steak A bison primal cut that is contained within the larger cut 'bison loin'. It is located between the short loin and the round and includes the hip section and ends at the socket of the pelvis. bison sirloin A raw bison sirloin cut. bison sirloin (raw) A bison cut that is located behind the short loin on the top back end of the animal. bison top sirloin butt A raw bison top sirloin butt. bison top sirloin butt (raw) A steak cut from the bison top sirloin butt. bison top sirloin steak A raw bison top sirloin steak. bison top sirloin steak (raw) A bison cut that comes from the 'round', the rear leg of the bison. bison round A raw bison round cut. bison round (raw) A bison cut that comes from the inside of the rear leg. bison top round A raw bison top round cut. bison top round (raw) A steak cut from the bison top round. bison top round steak A raw bison top round steak. bison top round steak (raw) A bison steak that is a cut from the rib-eye roast. bison ribeye steak A raw bison ribeye steak. bison ribeye steak (raw) A bison cut that extends from the neck to the fifth rib and includes the shoulder blade and upper arm. bison chuck A raw bison chuck cut. bison chuck (raw) A large muscle system which lies dorsal and posterior to the elbow joint, ventral and posterior to the ridge of the scapula (blade bone) and is anterior to the 6th rib. bison shoulder clod A raw bison shoulder clod. bison shoulder clod (raw) A buffalo cut that comes from the 'round', the rear leg of the buffalo. buffalo round A raw buffalo round cut. buffalo round (raw) A buffalo cut that comes from the inside of the rear leg. buffalo top round A raw buffalo top round cut. buffalo top round (raw) A steak cut from the buffalo top round. buffalo top round steak A raw buffalo top round steak. buffalo top round steak (raw) A raw beef primal cut. beef primal cut (raw) A raw beef sub-primal cut. beef sub-primal cut (raw) A raw beef retail cut. beef retail cut (raw) A butchery cut of animal that is typically boneless. animal fillet A raw animal fillet cut. animal fillet (raw) A raw piece of animal. piece of animal (raw) A piece of animal that contains skin. piece of animal (with skin) A piece of animal that is skinless. piece of animal (skinless) A piece of animal that contains the skin and is raw. piece of animal (with skin, raw) A raw skinless piece of animal. piece of animal (skinless, raw) A raw animal organ that is obtained from an animal during a butchery process. animal organ (raw) A piece of an animal organ. piece of animal organ A raw piece of an animal organ. A raw piece of animal organ. piece of animal organ (raw) A piece of meat that is derived from an animal. piece of animal meat A raw piece of animal meat. piece of animal meat (raw) A piece of skinless animal meat. piece of animal meat (skinless) A raw piece of skinless animal meat. piece of animal meat (skinless, raw) A piece of animal meat that contains skin. piece of animal meat (with skin) A raw piece of animal meat that contains skin. piece of animal meat (with skin, raw) A piece of boneless animal meat. piece of animal meat (boneless) A piece of animal meat that contains bone material. piece of animal meat (with bone) A raw piece of animal meat that contains bone material. piece of animal meat (with bone, raw) A whole thigh that is obtained from an animal. animal thigh A whole breast that is obtained from an animal. animal breast A whole wing that is obtained from an animal. animal wing A whole neck that is obtained from an animal. animal neck A whole leg that is obtained from an animal. animal leg A whole raw animal breast. animal breast (raw) A whole raw animal wing. animal wing (raw) A whole raw animal neck. animal neck (raw) A whole raw animal leg. animal leg (raw) A piece of an animal breast. piece of animal breast A raw piece of an animal breast. piece of animal breast (raw) A piece of skinless animal breast. piece of animal breast (skinless) A raw piece of skinless animal breast. piece of animal breast (skinless, raw) A piece of animal breast that contains skin. piece of animal breast (with skin) A raw piece of animal breast that contains skin. piece of animal breast (with skin, raw) A piece of skinless and boneless animal breast. piece of animal breast (skinless, boneless) A raw piece of skinless and boneless animal breast. piece of animal breast (skinless, boneless, raw) A piece of light meat that comes from an animal breast or wing. piece of light animal meat A raw piece of light animal meat. piece of light animal meat (raw) A piece of light animal meat that contains skin. piece of light animal meat (with skin) A raw piece of light animal meat that contains skin. piece of light animal meat (with skin, raw) A piece of skinless light animal meat. piece of light animal meat (skinless) A raw piece of skinless light animal meat. piece of light animal meat (skinless, raw) A raw cut of animal meat. butchery cut of animal (raw) A raw animal primal cut. animal primal cut (raw) A raw animal sub-primal cut. animal sub-primal cut (raw) A raw animal retail cut. animal retail cut (raw) An animal meat cut that has a flat-cut appearance. animal steak A raw animal steak. animal steak (raw) A retail cut of meat from an animal that is of a size for slicing into more than one portion and is suitable for roasting. animal roast A raw animal roast. animal roast (raw) A boneless animal roast. animal roast (boneless) A raw and boneless animal roast. animal roast (boneless, raw) A retail cut of meat from an animal that is perpendicular to the spine, and usually containing a rib or riblet part of a vertebra. animal chop A raw animal chop. animal chop (raw) A boneless animal chop. animal chop (boneless) A raw and boneless animal chop. animal chop (boneless, raw) A raw piece of boneless animal meat. piece of animal meat (boneless, raw) A skinless animal breast. animal breast (skinless) A raw skinless animal breast. animal breast (skinless, raw) An animal breast that contains skin. animal breast (with skin) A raw animal breast that contains skin. animal breast (with skin, raw) A skinless and boneless animal breast. animal breast (skinless, boneless) A raw, skinless and boneless animal breast. animal breast (skinless, boneless, raw) A boneless, seasoned and freshly frozen animal roast. animal roast (boneless, seasoned, fresh frozen) Material that derives from some avian animal. avian animal material A severed part of an avian animal. piece of avian animal A raw piece of avian animal. piece of avian animal (raw) A piece of meat that is derived from an avian animal. piece of avian animal meat A raw piece of avian animal meat. piece of avian animal meat (raw) Material that derives from some chicken. chicken material A raw chicken fillet cut. chicken fillet (raw) A severed part of a chicken. piece of chicken A piece of chicken meat which has been cut according to butchery practice. butchery cut of chicken Material that derives from some turkey. turkey material A severed part of a turkey. piece of turkey A raw piece of turkey. piece of turkey (raw) A piece of turkey that contains skin. piece of turkey (with skin) A piece of turkey that is skinless. piece of turkey (skinless) A piece of turkey that contains the skin and is raw. piece of turkey (with skin, raw) A raw skinless piece of turkey. piece of turkey (skinless, raw) An organ that derives from a turkey. turkey organ A raw animal organ that is obtained from a turkey during a butchery process. turkey organ (raw) A piece of a turkey organ. piece of turkey organ A raw piece of a turkey organ. A raw piece of turkey organ. piece of turkey organ (raw) A piece of meat that is derived from a turkey. piece of turkey meat A raw piece of turkey meat. piece of turkey meat (raw) A piece of skinless turkey meat. piece of turkey meat (skinless) A raw piece of skinless turkey meat. piece of turkey meat (skinless, raw) A piece of turkey meat that contains skin. piece of turkey meat (with skin) A raw piece of turkey meat that contains skin. piece of turkey meat (with skin, raw) A piece of boneless turkey meat. piece of turkey meat (boneless) A piece of turkey meat that contains bone material. piece of turkey meat (with bone) A raw piece of turkey meat that contains bone material. piece of turkey meat (with bone, raw) A skinless turkey breast. turkey breast (skinless) A raw skinless turkey breast. turkey breast (skinless, raw) A turkey breast that contains skin. turkey breast (with skin) A raw turkey breast that contains skin. turkey breast (with skin, raw) A skinless and boneless turkey breast. turkey breast (skinless, boneless) A raw, skinless and boneless turkey breast. turkey breast (skinless, boneless, raw) A piece of a turkey breast. piece of turkey breast A raw piece of a turkey breast. piece of turkey breast (raw) A piece of skinless turkey breast. piece of turkey breast (skinless) A raw piece of skinless turkey breast. piece of turkey breast (skinless, raw) A piece of turkey breast that contains skin. piece of turkey breast (with skin) A raw piece of turkey breast that contains skin. piece of turkey breast (with skin, raw) A piece of skinless and boneless turkey breast. piece of turkey breast (skinless, boneless) A raw piece of skinless and boneless turkey breast. piece of turkey breast (skinless, boneless, raw) Material that derives from some poultry. poultry material A severed part of a poultry. piece of poultry A raw piece of poultry. piece of poultry (raw) A raw piece of poultry meat. piece of poultry meat (raw) A piece of boneless poultry meat. piece of poultry meat (boneless) A piece of poultry meat that contains bone material. piece of poultry meat (with bone) A raw piece of poultry meat that contains bone material. piece of poultry meat (with bone, raw) A whole raw poultry breast. poultry breast (raw) A whole raw poultry wing. poultry wing (raw) A whole raw poultry neck. poultry neck (raw) A whole raw poultry leg. poultry leg (raw) Material that derives from some bison. bison material A severed part of a bison. piece of bison A raw piece of bison. piece of bison (raw) A piece of bison meat which has been cut according to butchery practice. butchery cut of bison A raw bison primal cut. bison primal cut (raw) A raw bison sub-primal cut. bison sub-primal cut (raw) A raw bison retail cut. bison retail cut (raw) A raw bison steak. bison steak (raw) A retail cut of meat from a bison that is of a size for slicing into more than one portion and is suitable for roasting. bison roast A raw bison roast. bison roast (raw) A boneless bison roast. bison roast (boneless) A raw and boneless bison roast. bison roast (boneless, raw) A retail cut of meat from a bison that is perpendicular to the spine, and usually containing a rib or riblet part of a vertebra. bison chop A raw bison chop. bison chop (raw) Material that derives from some cow. cow material A raw piece of beef. piece of cow (raw) A raw beef roast. beef roast (raw) A boneless beef roast. beef roast (boneless) A raw and boneless beef roast. beef roast (boneless, raw) A boneless, seasoned and freshly frozen beef roast. beef roast (boneless, seasoned, fresh frozen) A retail cut of meat from a beef that is perpendicular to the spine, and usually containing a rib or riblet part of a vertebra. beef chop A raw beef chop. beef chop (raw) A boneless beef chop. beef chop (boneless) A raw and boneless beef chop. beef chop (boneless, raw) Material that derives from some buffalo. buffalo material A severed part of a buffalo. piece of buffalo A raw piece of buffalo. piece of buffalo (raw) A piece of buffalo meat which has been cut according to butchery practice. butchery cut of buffalo A raw buffalo primal cut. buffalo primal cut (raw) A raw buffalo sub-primal cut. buffalo sub-primal cut (raw) A raw buffalo retail cut. buffalo retail cut (raw) A raw buffalo steak. buffalo steak (raw) A retail cut of meat from a buffalo that is of a size for slicing into more than one portion and is suitable for roasting. buffalo roast A raw buffalo roast. buffalo roast (raw) A boneless buffalo roast. buffalo roast (boneless) A raw and boneless buffalo roast. buffalo roast (boneless, raw) A retail cut of meat from a buffalo that is perpendicular to the spine, and usually containing a rib or riblet part of a vertebra. buffalo chop A raw buffalo chop. buffalo chop (raw) A food product that is derived from some lamb. lamb food product Material that derives from some lamb. lamb material A severed part of a lamb. piece of lamb A raw piece of lamb. piece of lamb (raw) A piece of lamb meat which has been cut according to butchery practice. butchery cut of lamb A raw lamb primal cut. lamb primal cut (raw) A raw lamb sub-primal cut. lamb sub-primal cut (raw) A lamb meat cut that is derived from a sub-primal, individual muscle cut or minor primal cut. lamb retail cut A raw lamb retail cut. lamb retail cut (raw) A raw lamb roast. lamb roast (raw) A boneless lamb roast. lamb roast (boneless) A raw and boneless lamb roast. lamb roast (boneless, raw) A boneless, seasoned and freshly frozen lamb roast. lamb roast (boneless, seasoned, fresh frozen) A boneless lamb chop. lamb chop (boneless) A raw and boneless lamb chop. lamb chop (boneless, raw) Material that derives from some veal. veal material A severed part of a veal. piece of veal A raw piece of veal. piece of veal (raw) A piece of veal meat which has been cut according to butchery practice. butchery cut of veal A raw veal primal cut. veal primal cut (raw) A raw veal sub-primal cut. veal sub-primal cut (raw) A veal meat cut that is derived from a sub-primal, individual muscle cut or minor primal cut. veal retail cut A raw veal retail cut. veal retail cut (raw) A raw veal roast. veal roast (raw) A boneless veal roast. veal roast (boneless) A raw and boneless veal roast. veal roast (boneless, raw) A boneless, seasoned and freshly frozen veal roast. veal roast (boneless, seasoned, fresh frozen) Material that derives from some deer. deer material A severed part of a deer. piece of deer A raw piece of deer. piece of deer (raw) Material that derives from some elk. elk material A severed part of an elk. piece of elk A raw piece of elk. piece of elk (raw) A piece of elk meat which has been cut according to butchery practice. butchery cut of elk An elk meat cut that is derived from a sub-primal, individual muscle cut or minor primal cut. elk retail cut Material that derives from some pig. pig material A raw piece of pork. piece of pig (raw) A piece of pork meat which has been cut according to butchery practice. butchery cut of pork A raw pork primal cut. pork primal cut (raw) A raw pork sub-primal cut. pork sub-primal cut (raw) A raw pork retail cut. pork retail cut (raw) A pork meat cut that has a flat-cut appearance. pork steak A raw pork steak. pork steak (raw) A raw pork roast. pork roast (raw) A boneless pork roast. pork roast (boneless) A raw and boneless pork roast. pork roast (boneless, raw) A boneless, seasoned and freshly frozen pork roast. pork roast (boneless, seasoned, fresh frozen) A boneless pork chop. pork chop (boneless) A raw and boneless pork chop. pork chop (boneless, raw) An animal fillet that is skinless. animal fillet (skinless) A raw skinless animal fillet animal fillet (skinless, raw) An animal fillet that contains skin. animal fillet (with skin) A raw animal fillet that contains skin. animal fillet (with skin, raw) An animal breast that has the bone attached to it. animal breast (bone-in) A raw bone-in animal breast. animal breast (bone-in, raw) A raw bone-in turkey breast. turkey breast (bone-in, raw) A turkey breast that has the bone attached to it. turkey breast (bone-in) fish (whole or pieces) Fish meat that has not been cooked or preserved other than perhaps by freezing. If previously frozen, it has subsequently been thawed. fish meat (raw) meat (cooked) fish fillet (frozen) mahi mahi fillet (raw) herring fillet (pickled) fish fillet (raw) meat (raw) A whole raw turkey breast. turkey breast (raw) fish fillet (smoked) herring fillet in tomato sauce tuna fillet (light meat, raw) fish fillet (with skin, raw, breaded, frozen) fish fillet (stuffed with crabmeat and shrimp) fish (portion cut) fish steak (raw) fish fillet (breaded, precooked) fish fillet (in tomato sauce) tuna fillet (raw) fish fillet (breaded) fish fillet (whitemeat, skinless, raw) herring fillet (smoked, and vegetables) herring fillet (pickled, skinless) fish fillet (breaded, frozen) herring fillet (raw) herring fillet in lemon-flavored sauce A raw pork tenderloin cut. pork tenderloin (raw) Food product for animal covers foods intended for consumption by domesticated animals. food product for animal A beef steak product which is raw and is cut from the outer part of the round of a cow. beef round steak (raw) poultry (whole or pieces) A raw beef chuck cut. beef chuck (raw) A raw pork shoulder. pork shoulder (raw) A raw pork chop. pork chop (raw) A raw lamb chop. lamb chop (raw) A food product that is raw. food (raw) beef sirloin steak (cooked) turkey breast (roasted) A raw beef steak is a flat cut of beef, with parallel faces spaced to a thickness of 1 to 5 centimetres (1⁄2 to 2 in), usually cut perpendicular to the muscle fibers, with a raw mass in common restaurant service ranging from 120 to 600 grams (4 to 21 oz). Beef steaks are usually grilled, pan fried, or broiled. A raw beef steak. beef steak (raw) processed food product A raw piece of chicken. piece of chicken (raw) meat (prepared) A piece of meat that is derived from a poultry. Meat from a poultry bird. piece of poultry meat fish fillet (quick-frozen in blocks) fish fillets and minced fish (quick-frozen in blocks) A meat product is a product organized by the form of - or processing done to - its meat component (a skeletal meat part of an animal or crustacean). meat (whole or pieces) fish fillet (unprocessed, frozen) fish fillet (deep-frozen, unprocessed) fish fillet (deep-frozen) An agency food product type is a class of food product defined by an agency or consortium. agency food product type Any chemical or chemical mixture that exists in a food material or was added to a food material. chemical food component A member of the group of eukaryotic organisms in the kingdom Fungi that includes unicellular microorganisms such as yeasts and molds, as well as multicellular fungi that produce familiar fruiting forms known as mushrooms. fungus A vertebrate animal is any species of organism within the subphylum Vertebrata (chordates with backbones). Vertebrates represent the overwhelming majority of the phylum Chordata, with currently about 69,276 species described. vertebrate animal An informal term for a large, diverse group of photosynthetic eukaryotic organisms that are not necessarily closely related, and is thus polyphyletic. algae This is a hierarchy of organisms, grouped minimally in a combination of taxonomy and consumer-oriented food groups. organism by alternate grouping A composite organism that arises from algae or cyanobacteria living among filaments of multiple fungi species in a mutualistic relationship. lichen A chemical food component in liquid form. liquid chemical food component Anatomical or other part(s) or substances derived from plant or animal or fungal organisms. organism material Material that derives from some animal. animal material Poultry, game bird or turtle eggs. egg or egg component divided into pieces, thickness <0.3 cm. medium ground and sifted (bolted) whole and pieces whole, shape achieved by forming, thickness 1.5-7 cm. finely ground divided into segments or wedges physical state, shape or form, multiple cut into short pieces The physical state of the food product (liquid, semiliquid, semisolid, or solid). Solid food products are further subdivided by shape or form. Terms are provided for products that have both liquid and solid components or that incorporate air or other gases. [FDA CFSAN 1995] food physical quality divided into pieces, thickness 0.3-1.5 cm. divided into halves medium ground divided or disintegrated sliced, thick, between 0.5 and 1.5 cm. divided into pieces, thickness more than 1.5 cm. Refers to natural or formed shape as appropriate, regardless of size, which may vary from very large (e.g., beef carcass) to very small (e.g., poppy seed, yeast cell). whole Divided into pieces whose shape is defined in relation to the shape of the whole, i.e., halves, quarters, or segments. It is used regardless of the size of the whole. divided into halves, quarters or segments disintegrated or ground sliced whole, shape achieved by forming, thickness 0.3-1.5 cm. cut into long pieces sliced, thin, below 0.5 cm. whole, shape achieved by forming, thickness bigger than 7 cm. whole, shape achieved by forming divided into quarters whole, natural shape Divided into pieces whose shape bears little or no relation to the shape of the whole. If all dimensions are below 0.2 cm., use *DISINTEGRATED OR GROUND*. Examples are: bread slice, cubed beef, sliced carrot, cut green beans, apple ring, shredded cabbage or cheese. divided into pieces whole, shape achieved by forming, thickness <0.3 cm. not heat-treated Used to broadly characterize a food product based on the extent of heat applied. Heat treatment affects the flavor and textural characteristics of a food and thus consumer preparation time. Heat treatment causes chemical changes and/or reduction of enzyme and of microbial activity and thus affects food safety and shelflife. Specifics of preparation are covered by *G. COOKING METHOD* and *H. TREATMENT APPLIED*. [FDA CFSAN 1995] extent of food heat treatment fully heat-treated partially heat-treated heat-treated heat-treated, multiple components, different degrees of treatment http://www.langual.org/langual_thesaurus.asp?termid=G0002 food cooking Cooked at moderate to high levels of heat in which no liquid is added and only small amounts of fat may be added to prevent sticking. http://www.langual.org/langual_thesaurus.asp?termid=G0004 cooking by dry heat Cooked without moisture, covered or uncovered, in an oven. http://www.langual.org/langual_thesaurus.asp?termid=G0005 food baking Cooked without moisture under or over intense direct heat. http://www.langual.org/langual_thesaurus.asp?termid=G0006 broiling or grilling Cooked without moisture over direct heat from a charcoal fire. http://www.langual.org/langual_thesaurus.asp?termid=G0007 charcoal broiling Cooking on a flat surface at medium heat with only a sufficient amount of fat used to prevent sticking. http://www.langual.org/langual_thesaurus.asp?termid=G0008 griddle cooking Cooking by agitating the food over a dry, high heat source, resulting in exploding. http://www.langual.org/langual_thesaurus.asp?termid=G0009 cooked by popping Cooking with direct heat until the surface of the food is browned, usually associated with bread or sandwiches. http://www.langual.org/langual_thesaurus.asp?termid=G0010 food toasting Cooking in a microwave oven. http://www.langual.org/langual_thesaurus.asp?termid=G0011 cooking by microwave Cooking in varying amounts of water, water-based liquid or steam. http://www.langual.org/langual_thesaurus.asp?termid=G0012 cooking by moist heat A process of cooking by moist heat which is effected by hot water or water-based liquid in a container. http://www.langual.org/langual_thesaurus.asp?termid=G0013 cooking in water or water-based liquid A cooking in water or water-based liquid process in which the liquid is boiling. http://www.langual.org/langual_thesaurus.asp?termid=G0014 boiling in container Cooked in boiling water at 212 degrees F.; water that is not absorbed into the food product is discarded after cooking. http://www.langual.org/langual_thesaurus.asp?termid=G0015 boiling and then draining Cooked in boiling water at 212 degrees F. Liquid to solid ratio is greater than 2:1. http://www.langual.org/langual_thesaurus.asp?termid=G0016 boiling in large amount of liquid http://www.langual.org/langual_thesaurus.asp?termid=G0017 boiling in small amount of liquid Cooked in boiling water at 212 degrees F. The water incorporates itself into the product being cooked or is not discarded when cooking is complete. http://www.langual.org/langual_thesaurus.asp?termid=G0018 boiling without draining Browned initially in fat and then tightly covered and cooked over low heat in a small amount of water. http://www.langual.org/langual_thesaurus.asp?termid=G0019 cooking by braising Cooking in a moderate amount of liquid at just below the boiling point. http://www.langual.org/langual_thesaurus.asp?termid=G0020 cooking by simmering http://www.langual.org/langual_thesaurus.asp?termid=G0021 cooking in steam Cooked in a pressure cooker. http://www.langual.org/langual_thesaurus.asp?termid=G0022 steaming with pressure Cooked suspended above boiling water. http://www.langual.org/langual_thesaurus.asp?termid=G0023 steaming without pressure http://www.langual.org/langual_thesaurus.asp?termid=G0024 cooking with fat or oil Cooked by adding fat or oil to those foods that do not contain fat or oil that would render during the cooking process. http://www.langual.org/langual_thesaurus.asp?termid=G0025 cooking with added fat or oil Cooked with sufficient fat or oil to coat and moisten the food being prepared, but not cooked in enough fat or oil to immerse the food. http://www.langual.org/langual_thesaurus.asp?termid=G0026 cooking in small amount of fat or oil Cooking in a very small amount of very hot fat, turning and browning the food on all sides. http://www.langual.org/langual_thesaurus.asp?termid=G0027 sautéing Cooked by frying foods quickly over high heat, stirring constantly. Only enough cooking oil is used to coat the bottom of the pan. http://www.langual.org/langual_thesaurus.asp?termid=G0028 stir-frying Cooked in hot fat or oil deep enough to immerse the food entirely. http://www.langual.org/langual_thesaurus.asp?termid=G0029 deep-frying process Cooked in fat or oil rendered from the food being prepared. http://www.langual.org/langual_thesaurus.asp?termid=G0030 cooking with inherent fat or oil http://www.langual.org/langual_thesaurus.asp?termid=G0031 heating container by immersion in water or steam A food cooking method in which heat is transferred to the outside of a container. http://www.langual.org/langual_thesaurus.asp?termid=G0032 heating container Heating a container that is placed in another container filled with boiling water. http://www.langual.org/langual_thesaurus.asp?termid=G0033 heating container in double boiler Heating a container that is placed in another container filled with water kept near the boiling point. http://www.langual.org/langual_thesaurus.asp?termid=G0034 heating container by water bath A chinese cooking technique similar to sauteing in which thick slices or chunks of floured or battered ingredients are slow seared over moderate to low heat. http://www.langual.org/langual_thesaurus.asp?termid=G0035 shallow frying process Extracting flavor and other components from food sources by immersion in water, usually at near-boiling temperature. http://www.langual.org/langual_thesaurus.asp?termid=G0036 steeping A process to bring an already fully cooked product to serving temperature. http://www.langual.org/langual_thesaurus.asp?termid=G0037 food reheating http://www.langual.org/langual_thesaurus.asp?termid=G0038 food reheating by microwave http://www.langual.org/langual_thesaurus.asp?termid=G0039 food reheating by dry heat http://www.langual.org/langual_thesaurus.asp?termid=G0040 food reheating by boil-in-bag http://www.langual.org/langual_thesaurus.asp?termid=G0041 food reheating in pan or cooking utensil A Chinese cooking technique to prepare delicate food such as bird nests, shark fins, etc. The food is covered with water and put in a covered ceramic jar and the jar is then steamed for several hours. http://www.langual.org/langual_thesaurus.asp?termid=G0043 double steaming Rotisserie is a style of roasting where meat is skewered on a spit and revolves over a flame or other heat source. http://www.langual.org/langual_thesaurus.asp?termid=G0044 rotisserie roasting Searing is a technique used in grilling, roasting, braising, sautéing, etc. that cooks the surface of the food at high temperature so that a brownish crust forms by Maillard reaction and denaturation of proteins. http://www.langual.org/langual_thesaurus.asp?termid=G0045 searing http://www.langual.org/langual_thesaurus.asp?termid=G0046 blind baking http://www.langual.org/langual_thesaurus.asp?termid=G0047 pressure frying process http://www.langual.org/langual_thesaurus.asp?termid=H0101 lactic acid fermentation http://www.langual.org/langual_thesaurus.asp?termid=H0102 proteolytic fermentation http://www.langual.org/langual_thesaurus.asp?termid=H0107 lactic acid-other agent fermentation Used to specifically characterize a food product based on the treatment or processes applied to the product or any indexed ingredient. The processes include adding, substituting or removing components or modifying the food or component, e.g., through fermentation. http://www.langual.org/langual_thesaurus.asp?termid=H0111 food treatment process A food modification process by microbial or enzymatic action which results in molecular changes in any food component. http://www.langual.org/langual_thesaurus.asp?termid=H0119 microbial/enzymatic modification process http://www.langual.org/langual_thesaurus.asp?termid=H0123 alcohol-acetic acid fermentation http://www.langual.org/langual_thesaurus.asp?termid=H0127 lipolytic fermentation A food fermentation process in which significant amounts of two or more components (i.e. carbohydrate and protein, carbohydrate and fat, protein and fat, or all three) are modified through microbial processes. Enzymatic or other biological processes may also be involved. http://www.langual.org/langual_thesaurus.asp?termid=H0128 multi-component food fermentation A food modification process where physical or chemical changes are effected in any food ingredient through a physical or non-enzymatic chemical process. http://www.langual.org/langual_thesaurus.asp?termid=H0130 physical/chemical modification process http://www.langual.org/langual_thesaurus.asp?termid=H0141 food modification process A claim that sodium has been added to an edible product. sodium added claim A claim that a mineral has been added to an edible product. mineral added claim A claim that calcium has been added to an edible product. calcium added claim A claim that iron has been added to an edible product. iron added claim A claim that potassium has been added to an edible product. potassium added claim A claim that chloride has been added to an edible product. chloride added claim http://www.langual.org/langual_thesaurus.asp?termid=H0200 acidification process Treated with moist heat to soften the grain and to transfer nutrients from the bran to the endosperm. http://www.langual.org/langual_thesaurus.asp?termid=H0220 food parboiling process (grain) A claim that phosphorus has been added to an edible product. phosphorus added claim http://www.langual.org/langual_thesaurus.asp?termid=H0225 food component addition process http://www.langual.org/langual_thesaurus.asp?termid=H0230 single component food fermentation http://www.langual.org/langual_thesaurus.asp?termid=H0232 alcohol fermentation A component separation process at the very least removes one component from an initial entity. The removed component may be captured as a process output for reuse if not destroyed in the process of removal. http://www.langual.org/langual_thesaurus.asp?termid=H0238 food component separation process Modified through complex enzymatic or microbial processes resulting in physicochemical changes in particular with respect to texture, flavor, color or shelf life of the food product. Such changes may be induced by the introduction of certain chemicals, such as sodium sulfite, salt, sugar, or other substances, such as phenolics, in dry or liquid form and often aided by smoke. Cheese should always be indexed by the appropriate narrower term under *LACTIC ACID-OTHER AGENT FERMENTED*. http://www.langual.org/langual_thesaurus.asp?termid=H0253 curing or aging http://www.langual.org/langual_thesaurus.asp?termid=H0256 carbohydrate fermentation A claim that a zinc has been added to an edible product. zinc added claim http://www.langual.org/langual_thesaurus.asp?termid=H0288 curing or aging < 2 weeks http://www.langual.org/langual_thesaurus.asp?termid=H0289 curing or aging 2 weeks to 1 month http://www.langual.org/langual_thesaurus.asp?termid=H0290 curing or aging 1 to 2 months http://www.langual.org/langual_thesaurus.asp?termid=H0291 curing or aging 2 to 4 months http://www.langual.org/langual_thesaurus.asp?termid=H0292 curing or aging 4 to 6 months http://www.langual.org/langual_thesaurus.asp?termid=H0293 curing or aging 6 to 12 months http://www.langual.org/langual_thesaurus.asp?termid=H0294 curing or aging 12 months or over http://www.langual.org/langual_thesaurus.asp?termid=H0300 acetic acid fermentation http://www.langual.org/langual_thesaurus.asp?termid=H0326 bacterial food-curing process http://www.langual.org/langual_thesaurus.asp?termid=H0327 food surface bacterial curing http://www.langual.org/langual_thesaurus.asp?termid=H0328 food interior bacterial curing http://www.langual.org/langual_thesaurus.asp?termid=H0329 mold food-curing process http://www.langual.org/langual_thesaurus.asp?termid=H0330 food surface mold curing http://www.langual.org/langual_thesaurus.asp?termid=H0331 food interior mold curing http://www.langual.org/langual_thesaurus.asp?termid=H0391 seed roasting http://www.langual.org/langual_thesaurus.asp?termid=H0396 marinading A claim that magnesium has been added to an edible product. magnesium added claim A claim that copper has been added to an edible product.. copper added claim A claim that manganese has been added to an edible product. manganese added claim A claim that selenium has been added to an edible product. selenium added claim A claim that chromium has been added to an edible product. chromium added claim A claim that molybdenum has been added to an edible product. molybdenum added claim A claim that fluoride has been added to an edible product. fluoride added claim Preservation by adding chemical preservatives (e.g., sorbic acid, sodium benzoate, BHT, calcium proprionate) to suppress or inhibit undesirable microorganisms or enzyme activity. http://www.langual.org/langual_thesaurus.asp?termid=J0100 preservation by adding chemicals http://www.langual.org/langual_thesaurus.asp?termid=J0102 food sterilization before filling http://www.langual.org/langual_thesaurus.asp?termid=J0103 food salting Smoking is the process of flavoring, browning, cooking, or preserving food by exposing it to smoke from burning or smoldering material, most often wood. http://www.langual.org/langual_thesaurus.asp?termid=J0106 food smoking The methods contributing to the prevention or retardation of microbial, enzymatic or oxidative spoilage and thus to the extension of shelf life. Index all methods for which information is available, even if a corresponding descriptor has already been used in *H. TREATMENT APPLIED*. Preservation descriptors refer to the finished food as a whole with these exceptions: (1) if the components of a multi-component food, such as cream pie, are preservation by different methods, index all methods; (2) if chemical preservatives are declared on the label, always index them even if it is known that the preservative was introduced through or is only present in a component or ingredient of the food; and (3) if the preservation method for an ingredient is declared on the label (such as brie cheese made from pasteurized milk) index it. Also use *INGREDIENT preservation by THERMAL PROCESSING* or *INGREDIENT preservation by IRRADIATION* when ingredients have been pasteurized, ultrapasteurized, sterilized or irradiated. http://www.langual.org/langual_thesaurus.asp?termid=J0107 food preservation process Preservation by immersing in or spraying with liquids (e.g., sulfite solutions) or surrounding with gases (e.g., ethylene oxide, propylene oxide or sulfur dioxide) to destroy undesirable microorganisms or inactivate enzymes. Diffusion and chemical reaction may create a residue in the food product that contributes to continuing preservation. http://www.langual.org/langual_thesaurus.asp?termid=J0108 preservation by treatment with chemicals Preservation by use of chemical to destroy, suppress or inhibit undesirable microorganisms or enzyme activity. http://www.langual.org/langual_thesaurus.asp?termid=J0109 chemical food preservation process http://www.langual.org/langual_thesaurus.asp?termid=J0110 food sterilization after filling Preservation by storage in an atmosphere in which the concentrations of oxygen and carbon dioxide are different from those in air. This reduces microbial and enzymatic activity; often used commercially in conjunction with refrigeration (e.g., refrigerated rail cars) for fresh meat and produce. http://www.langual.org/langual_thesaurus.asp?termid=J0111 preservation by storage in modified atmosphere http://www.langual.org/langual_thesaurus.asp?termid=J0112 drying under reduced pressure http://www.langual.org/langual_thesaurus.asp?termid=J0113 sterilization by irradiation http://www.langual.org/langual_thesaurus.asp?termid=J0114 food sterilization by hot filling and cooling http://www.langual.org/langual_thesaurus.asp?termid=J0115 surface pasteurization or disinfection by ultraviolet irradiation http://www.langual.org/langual_thesaurus.asp?termid=J0116 dehydration or drying Drying by heat. http://www.langual.org/langual_thesaurus.asp?termid=J0117 heat drying process http://www.langual.org/langual_thesaurus.asp?termid=J0119 pasteurization by irradiation Preservation by the use of high temperature for a time sufficient to reduce or destroy undesirable microorganisms and enzyme activity. [FDA CFSAN 1995] http://www.langual.org/langual_thesaurus.asp?termid=J0120 heat treatment food preservation Preservation by filtering out yeasts and molds, generally followed by aseptic packaging. FDA CFSAN 1995 http://www.langual.org/langual_thesaurus.asp?termid=J0121 food filtration Preservation by irradiation, primarily by gamma radiation. http://www.langual.org/langual_thesaurus.asp?termid=J0122 preservation by ionizing radiation http://www.langual.org/langual_thesaurus.asp?termid=J0123 food sterilization by heating Reduction of water in the product by osmosis. http://www.langual.org/langual_thesaurus.asp?termid=J0124 osmotic dehydration http://www.langual.org/langual_thesaurus.asp?termid=J0126 aseptic filling and sealing of food http://www.langual.org/langual_thesaurus.asp?termid=J0128 food slow freezing http://www.langual.org/langual_thesaurus.asp?termid=J0129 food sterilization by hot filling, held hot and cooling Dehydration by sublimation under reduced pressure while frozen. Usually the product is not stored frozen. http://www.langual.org/langual_thesaurus.asp?termid=J0130 freeze-drying Cooling and keeping at a temperature between 30°F and 45°F (-1°C and 7°C). Regarding food preservation regulations, the temperature range depends on national legislation. http://www.langual.org/langual_thesaurus.asp?termid=J0131 food chilling http://www.langual.org/langual_thesaurus.asp?termid=J0132 food quick freezing http://www.langual.org/langual_thesaurus.asp?termid=J0133 spray-drying http://www.langual.org/langual_thesaurus.asp?termid=J0134 shelf-drying under normal pressure http://www.langual.org/langual_thesaurus.asp?termid=J0135 pasteurization by heating Preservation by freezing a food product and keeping it at a temperature below the freezing point (20-30 degrees F) without regard to the product's physical state. http://www.langual.org/langual_thesaurus.asp?termid=J0136 food freezing Immersed in a salt brine strong enough to suppress enzyme activity and growth of undesirable organisms. http://www.langual.org/langual_thesaurus.asp?termid=J0137 food brining Preservation by the use of radiation to destroy or suppress undesirable microorganisms or enzyme activity. http://www.langual.org/langual_thesaurus.asp?termid=J0138 preservation by irradiation Packed in dry salt in sufficient quantity to suppress enzyme activity or growth of undesirable organisms. http://www.langual.org/langual_thesaurus.asp?termid=J0139 food dry salting http://www.langual.org/langual_thesaurus.asp?termid=J0140 drum-drying Dried by natural heat, usually through exposure to the sun. Includes field-dried products such as grains and dry beans. These products are included also if they have been artificially dried to return them to normal dry state, e.g. grain that has been artificially dried after harvest. http://www.langual.org/langual_thesaurus.asp?termid=J0141 natural heat drying Preservation by cooling and storage at low temperature (chilling at around 0-5°C (32 to 41°F), freezing at -18°C (0°F)) to prevent or retard microbial or enzymatic spoilage. http://www.langual.org/langual_thesaurus.asp?termid=J0142 chilling or freezing http://www.langual.org/langual_thesaurus.asp?termid=J0143 drying under normal pressure Drying by the application of artificial heat. http://www.langual.org/langual_thesaurus.asp?termid=J0144 artificial heat drying Preservation method that lowers the water activity (relative humidity) of a food product. This is accomplished by using mechanical dehydration equipment, by natural drying, by adding salt, sugar or other agents to the food or by surface drying during a refrigeration or freezing operation. This method of preservation may be used in conjunction with other preservation methods such as preservation by thermal processing. http://www.langual.org/langual_thesaurus.asp?termid=J0145 preservation by reducing water activity Preservation by adding sugar, sugar syrup or by partial inversion of disaccharides until the sugar concentration is high enough to prevent growth of microorganisms. http://www.langual.org/langual_thesaurus.asp?termid=J0146 preservation by adding sugar http://www.langual.org/langual_thesaurus.asp?termid=J0147 food sterilization at ultra high temperature (UHT) When used to describe a dairy product, means that such product shall have been thermally processed at or above 138° C (280° C) for at least 2 seconds, either before or after packaging so as to produce a product that has extended shelf life under refrigerated conditions (21 CFR 131.3 (c)). Used to describe liquid egg products that also have been thermally processed, but at a different temperature than for milk products. The egg product will have an extended shelf life under refrigerated conditions. http://www.langual.org/langual_thesaurus.asp?termid=J0148 ultra pasteurization (UP) by heat http://www.langual.org/langual_thesaurus.asp?termid=J0149 preservation by adding acid Sous-vide, French for "under vacuum", is a method of cooking that is intended to maintain the integrity of ingredients by heating them for an extended period of time in vacuum sealed plastic pouches at relatively low temperatures. Food is cooked for a long time, sometimes well over 24 hours. Unlike cooking in a slow cooker, sous-vide cooking uses airtight plastic bags placed in hot water well below boiling point (usually around 60°C or 140°F). http://www.langual.org/langual_thesaurus.asp?termid=J0150 sous vide cooking http://www.langual.org/langual_thesaurus.asp?termid=J0151 preservation of food component by heat treatment http://www.langual.org/langual_thesaurus.asp?termid=J0152 ingredient preservation by irradiation Preservation by adding spices or extracts (e.g. garlic, onion, horseradish, paprika) to suppress or inhibit undesirable micro-organisms, enzyme activity, or oxidative changes. http://www.langual.org/langual_thesaurus.asp?termid=J0153 preservation by adding spices or extracts Preservation by adding inorganic acids or salts (e.g. SO2, H2SO4, KNO4, NaNO3) to suppress or inhibit undesirable micro-organisms or enzyme activity. http://www.langual.org/langual_thesaurus.asp?termid=J0154 preservation by adding inorganic acids or salts Preservation by adding organic acids or salts (e.g. lactic acid, acetic acid, salicylic acid) to suppress or inhibit undesirable micro organisms or enzyme activity. http://www.langual.org/langual_thesaurus.asp?termid=J0155 preservation by adding organic acids or salts Preservation by adding antibiotics (e.g. nisin, tylosine, subtlin, bacitracin, chlorotetracyclin, oxytetracyclin) to kill micro organisms or stop their growth. http://www.langual.org/langual_thesaurus.asp?termid=J0156 preservation by adding antibiotics Separation of colloidal or very fine solid materials by filtration through microporous or semipermeable mediums. Membranes have pores in the range 2-20 nm diameter. http://www.langual.org/langual_thesaurus.asp?termid=J0157 food ultra-filtration http://www.langual.org/langual_thesaurus.asp?termid=J0158 pasteurization by heat after filling http://www.langual.org/langual_thesaurus.asp?termid=J0159 pasteurization by heat before filling The process of holding food at a high pressure, normally greater than 1000 bar, which leads to sterilization. Example: Fruit juice, jam. http://www.langual.org/langual_thesaurus.asp?termid=J0160 ultra high pressure sterilization Treated by electron accelerator radiation, for example to kill insects in cereals. http://www.langual.org/langual_thesaurus.asp?termid=J0161 preservation by electron accelerator radiation http://www.langual.org/langual_thesaurus.asp?termid=J0162 disinfection by irradiation http://www.langual.org/langual_thesaurus.asp?termid=J0163 drying by radiation http://www.langual.org/langual_thesaurus.asp?termid=J0165 drying by microwave radiation http://www.langual.org/langual_thesaurus.asp?termid=J0166 drying by infrared heat radiation http://www.langual.org/langual_thesaurus.asp?termid=J0168 drying under increased pressure http://www.langual.org/langual_thesaurus.asp?termid=J0169 concentration by reverse osmosis Drying by exposure to the sun. Example: cereals, spices, vegetables. http://www.langual.org/langual_thesaurus.asp?termid=J0170 sun drying Frozen very rapidly by means of refrigerating agents such as liquid nitrogen or carbon dioxide. Example: lobster frozen in liquid nitrogen. http://www.langual.org/langual_thesaurus.asp?termid=J0171 food cryogenic freezing The process of food storage involving an accompanying refrigerating agent. http://www.langual.org/langual_thesaurus.asp?termid=J0172 food storage with refrigerating agent process Preservation by storage in inert gases (e.g. nitrogen) to suppress or inhibit undesirable micro-organism growth, oxidation activity, etc. http://www.langual.org/langual_thesaurus.asp?termid=J0173 inert atmosphere storage process Storing under reduced pressure (e.g. 1.3-2 kPa) in order to suppress or inhibit undesirable micro organism growth, oxidation activity, etc. http://www.langual.org/langual_thesaurus.asp?termid=J0174 vaccume storage process Blanching is a cooking process wherein a food, usually a vegetable or fruit, is scalded in boiling water, removed after a brief, timed interval, and finally plunged into iced water or placed under cold running water (shocking or refreshing) to halt the cooking process. Blanching foods helps reduce quality loss over time. People often use blanching as a pre-treatment prior to freezing, drying, or canning—heating vegetables or fruits to inactivate enzymes, modify texture, remove the peel, and wilt tissue. Blanching is also utilized to preserve color, flavor, and nutritional value. The process has three stages: preheating, blanching, and cooling. The most common blanching methods for vegetables/fruits are hot water and steam, while cooling is either done using cold water or cool air. http://www.langual.org/langual_thesaurus.asp?termid=J0175 food blanching Storage of fruits and vegetables in an atmosphere in which the concentrations of oxygen, carbon dioxide (and often nitrogen) are different from those in air and at a low temperature. All three (four) factors are controlled at the desired levels in order to suppress the fruits' and vegetables' natural respiration. http://www.langual.org/langual_thesaurus.asp?termid=J0176 controlled atmosphere storage process Microfiltration is used to remove undesirable micro-organisms and molecules. The membranes have pore diameters from 10 to 10000 nm. Micro-filtration is often used instead of pateurisation, e.g. in the brewing industry. http://www.langual.org/langual_thesaurus.asp?termid=J0177 food micro-filtration High Temperature Short Time (HTST) pasteurization is one of the most common methods of pasteurization , which uses metal plates and hot water to raise milk temperatures to at least 72° C (161° F) for not less than 15 seconds, followed by rapid cooling. http://www.langual.org/langual_thesaurus.asp?termid=J0178 high temperature short time (HTST) pasteurization Higher Heat Shorter Time (HHST) is a process similar to HTST pasteurization, but it uses slightly different equipment and higher temperatures (83 - 127° C) for a shorter time. http://www.langual.org/langual_thesaurus.asp?termid=J0179 higher heat shorter time (HHST) pasteurization Typically involves heating milk or cream to 135° to 150° C (275° to 302° F) for 1 or 2 seconds. The milk is then packaged in sterile, hermetically-sealed (airtight) containers (aspetic filling) and can be stored without refrigeration for up to 90 days. After opening, spoilage times for UHT products are similar to those of conventionally pasteurized products. http://www.langual.org/langual_thesaurus.asp?termid=J0180 ultra high temperature (UHT) pasteurization http://www.langual.org/langual_thesaurus.asp?termid=J0181 filling conditions for pasteurization A pasteurization by heating process which uses low heat for a longer time to kill pathogenic bacteria. http://www.langual.org/langual_thesaurus.asp?termid=J0182 low-temperature-long-time (LTLT) pasteurization In the U.S., grain strength is calculated as 10 times the acid content expressed as acetic acid. For example, 40 grain vinegar = 4% acetic acid; 120 grain vinegar = 12% acetic acid. [Technically Speaking about Vinegar - A food technologist's guide to vinegar, The Vinegar Institute, 5775 Peachtree-Dunwoody Road, Atlanta, Georgia 30342, USA]. packed in vinegar with sugar Packed in a medium that is also a food product. Ingredients that are introduced through the packing medium are indexed as appropriate under *INGREDIENT OR FOOD ADDED* found in *H. TREATMENT APPLIED*. packed in edible medium packed in heavily sweetened liquid packed in lightly sweetened water or juice Packed in a modified atmosphere that contributes to preservation (e.g., applesauce packed with nitrogen in the head space or tuna salad sandwich packed in nitrogen-containing polyethylene wrapper). Also applicable to large-scale applications in shipping or storage (e.g., meat under carbon dioxide in a rail car). packed in gas other than air Packed with a gas that is liquified under pressure and that upon release of the pressure propels and aerates the food product. See 21 CFR 173.345 and 173.360 for substances used. packed with aerosol propellant packed in vegetable juice packed in water packed in salt brine packed in sweetened brine food packing medium The medium in which the food is packed for preservation and handling or the medium surrounding homemade foods, e.g., peaches cooked in sugar syrup. The packing medium may provide a controlled environment for the food. It may also serve to improve palatability and consumer appeal. food packing medium packed in vegetable oil packed in acidified salt brine Packed in sweetened water or in sweetened and/or concentrated fruit juice. For single-strength unsweetened fruit juice, use *PACKED IN FRUIT JUICE*. When the specific terms under *PACKED IN SWEETENED LIQUID* are used, the statement seen on the product label should be used for indexing. For additional information, see 21 CFR 145. packed in sweetened liquid packed in extra heavily sweetened liquid packed in fat or oil Packed in a container under high vacuum (26-29 in.). vacuum-packed packed in carbon dioxide In the U.S., grain strength is calculated as 10 times the acid content expressed as acetic acid. For example, 40 grain vinegar = 4% acetic acid; 120 grain vinegar = 12% acetic acid. [Technically Speaking about Vinegar - A food technologist's guide to vinegar, The Vinegar Institute, 5775 Peachtree-Dunwoody Road, Atlanta, Georgia 30342, USA]. packed in vinegar packed in slightly sweetened water or juice packed in nitrogen packed in gas mixture packed in gravy or sauce, dairy or egg component packed in gravy or sauce packed in gelatin packed in gravy or sauce, meat packed in gravy or sauce, vegetable packed in olive oil Packed in unsweetened single strength juice or juice prepared from concentrated fruit juice and water; if sweetener is added to the fruit juice, use the appropriate term under *PACKED IN SWEETENED LIQUID*. packed in fruit juice packed in vinegar and oil Packed in broth; includes meat, poultry or seafood packed in its' own juice. packed in broth packed in cream or milk Packed in squid or octopus ink. packed in ink packed in gravy or sauce, fruit packed in animal fat or oil In the U.S., grain strength is calculated as 10 times the acid content expressed as acetic acid. For example, 40 grain vinegar = 4% acetic acid; 120 grain vinegar = 12% acetic acid. [Technically Speaking about Vinegar - A food technologist's guide to vinegar, The Vinegar Institute, 5775 Peachtree-Dunwoody Road, Atlanta, Georgia 30342, USA]. packed in vinegar with sugar and salt A food contact material which encloses the food and can be in the type of a container, packaging or wrapping. food packaging plastic squeeze bottle or tube, top lined with foil plastic squeeze bottle or tube plastic squeeze bottle or tube, top lined with laminate plastic squeeze bottle or tube, unlined top plastic squeeze bottle or tube, top lined with cork glass container, tinless steel lid bimetal container glass container, plastic lid, paper lining laminate tube, ends lined with laminate laminate tube, ends lined with foil laminate tube, ends lined with cork paperboard tube with lid or ends textile or fabric stocking or casing ceramic or earthenware bottle ceramic or earthenware crock or jar ceramic or earthenware container paper bag, sack or pouch, plastic liner paper bag, sack or pouch, foil liner paper bag, sack or pouch, laminate liner A soft-sided paper container that is used as a bag. paper bag, sack or pouch glass container, cork stopper plastic tray or pan, laminate cover or wrapping plastic tray or pan, aluminum foil cover or wrapping plastic tray or pan, plastic cover or wrapping plastic tray or pan, paper wrapping A flat plastic container with raised edges that is used to carry things. plastic tray or pan laminate tube, unlined aluminum ends plastic wrapper paperboard tray with wrapper glass container plastic tray or pan, cardboard cover glass container, aluminum lid glass container, plastic lid, laminate lining glass container, plastic lid or stopper glass container, aluminum lid, plastic lining glass container, plastic lid, plastic lining A thin, transparent plastic film that adheres to the surface and itself, and is used to wrap objects and materials in an air-tight manner. plastic shrink-pack laminate tube, unlined plastic ends aluminum tube, unlined plastic top glass container, plastic lid, aluminum foil lining paper bag, sack or pouch, paper liner paperboard container with laminate liner glass container, tin-plated steel lid laminate bag or pouch plastic boil-in-bag paperboard container with plastic liner paperboard container with aluminum foil liner paperboard container with paper liner tinless steel plate container paperboard molded pack metal container paperboard container, waxed paperboard container, plastic coated paperboard container with window paperboard container with liner paperboard container textile or fabric container textile or fabric bag paperboard or paper container aluminum tray or pan, plastic cover or wrapping aluminum tray or pan, cardboard cover aluminum tray or pan, laminate cover or wrapping aluminum tray or pan, aluminum foil cover or wrapping aluminum tray or pan, paper wrapping aluminum tray or pan plastic bag or pouch laminate tube aluminum tube aluminum tube, top lined with laminate aluminum tube, top lined with foil aluminum tube, top lined with cork Corresponds to FSTA Thesaurus Packaging 2.2.1 Plastic container. plastic container paper wrapper wood container aluminum can, drum or barrel tin plate container wood box wood drum wood barrel, cask or wheel plastic container, molded or bubble pack laminate container aluminum container plastic container, rigid or semirigid, tin-plated steel lid plastic container, rigid or semirigid plastic container, rigid or semirigid, tinless steel lid plastic container, flexible or film plastic container, rigid or semirigid, plastic lid plastic container, rigid or semirigid, aluminum lid steel plate container aluminum foil wrapper paperboard container with foil or liner overwrap plastic container, blow-molded can, bottle or jar Classification corresponding to FSTA Thesaurus Packaging 3.1 Package Types container or wrapping by form ampul According to FSTA Thesaurus Packaging 3.1 package types, includes boil-in bag, carrier bag, flat bag, inner bag, retort pouch, shipping bag, valve bag, and valve sack bag, sack or pouch drum (container) A flexible container of distinctive construction and closure features used in the dispensing of tablet or powdered prescription medication; it is typically constructed of film or paper that may be coated or laminated to protect the contents [CFSAN Thesaurus]. envelope tube vial Classification corresponding to FSTA Thesaurus Packaging 2.1.2 Material container or wrapping by material A container which is a bottle or a jar. bottle or jar A container which is made of a thin metal and and is used for the distribution or storage of goods. can (container) leaf wrapper husk wrapper capsule multicontainer package wax container glass container, metal lid wrapper, material unspecified edible container box A narrow-necked container typically made of glass or plastic that is used to store and transport liquids. bottle jar drawn can three-part can jug or demijohn pail Classification corresponding to FSTA Thesaurus Packaging 3.2.4 Sealing/closing means sealing/closing element adhesive multicomponent adhesive multicomponent adhesive, no solvent multicomponent adhesive, organic solvent multicomponent adhesive, water soluble one component adhesive one component adhesive, organic solvent one component adhesive, water soluble thermoplastic adhesive glass stopper plastic stopper polyethylene plug polypropylene plug polyvinyl chloride plug plastic screw cap or lid plastic screw cap/pilfer proof crown cap metal screw cap or lid metal screw cap/pilfer proof wooden cork seal/gasket cork wood gasket metal gasket plastic gasket rubber gasket steel solder tin solder ceramic or earthenware bottle, coloured ceramic or earthenware bottle, uncoloured ceramic or earthenware jar, coloured ceramic or earthenware jar, uncoloured glass container, uncoloured glass container, uncoloured, light weight glass container, uncoloured, normal weight glass container, uncoloured, strengthened glass container, uncoloured, covered/protected glass container, coloured glass container, coloured, light weight glass container, coloured, normal weight glass container, coloured, strengthened glass container, coloured, covered/protected aluminum box aluminium box, plastic-coated aluminium box, varnished aluminium can, drum or barrel, plastic coated aluminium can, drum or barrel, varnished aluminium foil wrapper, coated for heat sealing aluminium foil-paper wrapper aluminum coextruded with paper aluminum combined with paper and plastic aluminum combined with regenerated cellulose laminated aluminum combination with paper stainless steel container steel plate container tinned one side steel plate container tinned both sides varnished tin-plate container natural polymer container casein resin cellulose film acetate cellulose film butyrate cellulose film propyonate cellulose film regenerated cellulose film regenerated cellulose film, coated regenerated cellulose film, coloured rubber container A paper container that has been treated with an antimicrobial agent or preservative chemical. paper container, treated lacquered paper container saturated (immersed) paper container waxed paper container A paper container that has not been treated with any agents. paper container, untreated bleached paper container kraft or brown paper container grease proof paper container imitation grease proof paper container Porous, wet-strength paper, e.g. tea bag. tissue paper container paperboard container, untreated paperboard container, surface treated paperboard container, surface treated both sides paperboard container, surface treated inside paperboard container, surface treated outside paper combined material impregnated/micro waxed paper metalized paper wrapper metalized paper coextruded with plastic metalized paper laminated with plastic metalized paper laminated with treated paper paper-aluminium foil-plastic wrapper coextruded paper-aluminium-plastic wrapper laminated paper-aluminium-plastic wrapper paper-paper combination paper-plastic combination laminate paper coextruded with plastic Corresponds to FSTA Thesaurus Packaging 2.2.1 'Type of plastic' plastic container, according to type of plastic thermoplastic sheet or container polyamide container acryl-nitrile container nylon 11 container nylon 6,6 container polycarbonate container polyester container polyester container, glass fibre strengthened linear polyester container polyethylene container high density polyethylene container low density polyethylene container linear low density polyethylene container low density polyethylene container, treated polymethylmethacrylate container polypropylene container biaxial oriented polypropylene container oriented polypropylene container polystyrene container polyvinyl chloride container unplasticized polyvinyl chloride container plasticized polyvinyl chloride container polyvinylidene chloride container thermosetting polymer container alkyd resin container amin resin container aniline-formaldehyde container carbamide-formaldehyde container diciandiamide-formaldehyde container epoxy resin container phenonile resin container polyester resin container plastic container, combined material metallized polymer container metallized polyamide container metallized polyester container polyethylene (high density) - polyamide container polyethylene (high density) - nylon 11 container polyethylene (high density) - polyester container polyethylene (high density) - polypropylene container polyethylene (low density) - polyamide container polyethylene (low density) - nylon 11 container polyethylene (low density) - polyester container polyethylene (low density) - polyethylene (high density) container polyethylene (low density) - polyethylene (low density) container polyethylene (low density) - polypropylene container polyethylene - regenerated cellulose container polyethylene - vinyl copolymer container polyvinyl chloride - polyvinylidene chloride container natural textile container animal hair container bass fibre container asbestos container cotton container leaf fibre container polymer base textile container polyamide textile container polyester textile container polyolefin textile container boil-in bag inner bag closing cap or lid closing capsule screw cap or lid peel-off lid stopper Example: egg box. recycled paperboard container polyethylene terephthalate (pet) container polyolefin container The specific container or coating materials in direct contact with the food. [FDA CFSAN 1995] food product contact surface beverage can enamel surface noncarbonated beverage can enamel surface carbonated beverage can enamel surface beer beverage can enamel surface Wax may be applied directly as a coating to the food product or may be used as a container material. Examples include wax-coated cheese, wax-coated cucumber, waxed fiberboard container, etc. food-grade wax surface enamel surface for fruit (f-enamel) PE polyethylene surface enamel surface for citrus fruit milk enamel surface for milk enamel surface for meat polypropylene surface polystyrene surface enamel surface for seafood A surface consisting of a coating that contains a specially prepared vehicle, instead of raw oil. Sometimes referred to as varnish or lacquer. food-grade enamel-coated surface Trade name of polyvinylidene chloride copolymer film. Chief packaging uses are in film and in coatings for other flexible substrates such as cellophane and paper. saran surface Trade name of polyester used in the usa. mylar surface A generic term for a class of polyamides containing repeating amide groups connected by methylene units. The most common types used in food industry are ny-lon-66 and nylon-11. nylon surface A surface of a Cryovac bag, a shrinkable version of pvdc used for vacuum packaging, e.g. of red meat. Cryovac bag plastic surface Polyvinylidene chloride surface enamel surface for corn (c-enamel) Cellophane is a thin, transparent sheet made of regenerated cellulose. cellophane A rubber hydrochloride, first introduced as a packaging film in 1936 in the U.S.A. pliofilm surface polyester surface CA: thermoplastic material made by the esterification of cellulose with acetic anhydride and acetic acid. cellulose acetate surface A surface made out of food-grade wood. food-grade wood surface food-grade plastic surface PVC polyvinyl chloride surface food-grade ceramic surface food-grade paper product surface A surface made of food-grade glass. food-grade glass surface A surface made of food-grade metal food-grade metal surface A surface made out of aluminum metal aluminum surface A surface made out of food-grade tin metal. food-grade tin surface A surface made of food-grade steel. food-grade steel surface A surface of a food-grade textile food-grade textile surface food-grade cork surface Ash which is incorporated into the surface of a food such as cheese. food-grade ash A plant leaf used as a food contact surface. leaf food contact surface A plant husk used as a food contact surface. husk food contact surface food contact surface from natural material food contact surface from human-made material latex surface A surface of Teflon, a trade name for a polymer used to provide better protection and longer life to porous metals (nickel alloys) in coextruded sheets and films. teflon surface A very thin edible covering, either natural or some form of a synthetic, that is used to enclose ground meat and other ingredients. edible casing A surface made of polymer extracted from nature. food-grade natural-based polymer surface laboratory animal as food consumer food fish as consumer pet fish as consumer non-food animal as food consumer sheep or goat as consumer food animal as consumer All narrower term definitions extracted from 58 Federal Register 2302, January 6, 1993, part 101.62(b). fat special claim poultry as consumer cattle as consumer Food produced and marketed to supply the particular dietary needs of normal infants (21 CFR 105.65) or normal toddlers (age 1 to 2 years). Junior foods are included with the strained foods for infants up to one year. Foods fall in this category only if the label bears a statement such as 'baby food', 'strained food', 'junior food' or 'toddler food'. infant or toddler as food consumer animal as food consumer Renamed from *FOOD FOR SPECIAL DIETARY USE* [LanguaL 2008]. These descriptors are used either for foods intended for special dietary use as defined in 21 CFR 105 or for foods that have special characteristics indicated in the name or labeling. Such claims would include 'low calorie', 'low cholesterol', 'diet' or 'dietetic', etc. Prior to february 1992, this category of descriptors was limited solely to food for adult humans. The category is now used in conjunction with any appropriate *CONSUMER GROUP* descriptor(s), for example, 'low sugar baby food' would be indexed by *INFANT OR TODDLER FOOD* as well as by *LOW SUGARS FOOD*. dietary claim horse as consumer Food produced and marketed for human use. human as food consumer pig as consumer pet cat as consumer Pet animals as a consumer group; products are labeled accordingly. pet animal as consumer pet bird as consumer pet dog as consumer A claim that a food is low in energy, and any claim likely to have the same meaning for the consumer, may only be made where the product does not contain more than 40 kcal (170 kJ)/100 g for solids or more than 20 kcal (80 kJ)/100 ml for liquids. For table-top sweeteners the limit of 4 kcal (17 kJ)/portion, with equivalent sweetening properties to 6 g of sucrose (approximately 1 teaspoon of sucrose), applies [REGULATION (EC) No 1924/2006 Corrigendum 2007-01-18]. Food having 40 calories or less per amount customarily consumed (and per 50 grams of food if the amount customarily consumed is small). Meals and main dishes contain 120 calories or less per 100 grams of food [US FDA] low energy food claim A claim that a food is energy-reduced, and any claim likely to have the same meaning for the consumer, may only be made where the energy value is reduced by at least 30 %, with an indication of the characteristic(s) which make(s) the food reduced in its total energy value [REGULATION (EC) No 1924/2006 Corrigendum 2007-01-18]. Food having at least 25% fewer calories per amount customarily consumed from the calories of a comparable food product. The complarable food may not be 'low calorie' [US FDA]. reduced energy food claim A claim that a food is sodium-free or salt-free, and any claim likely to have the same meaning for the consumer, may only be made where the product contains no more than 0,005 g of sodium, or the equivalent value for salt, per 100 g. [REGULATION (EC) No 1924/2006 Corrigendum 2007-01-18]. Food having less than 5 milligrams of salt or sodium per amount customarily consumed (or for meals and main dishes, less than 5 miligrams of salt or sodium per labeled serving). Such foods must not contain an ingredient that is salt or sodium or generally understood to comtain salt or sodium except where the ingredient listed is footnoted '*adds a trivial amount of {salt or sodium}' [US FDA] salt or sodium free claim A claim that a food is very low in sodium/salt, and any claim likely to have the same meaning for the consumer, may only be made where the product contains no more than 0,04 g of sodium, or the equivalent value for salt, per 100 g or per 100 ml. This claim shall not be used for natural mineral waters and other waters [REGULATION (EC) No 1924/2006 Corrigendum 2007-01-18]. Food having 35 milligrams or less salt or sodium per amount customarily consumed (and per 50 grams if the amount customarily consumed is small). Meals and main dishes contain 35 milligrams or less salt or sodium per 100 grams of food [US FDA] very low salt or sodium claim reduced salt or sodium claim A claim that a food is low in sodium/salt, and any claim likely to have the same meaning for the consumer, may only be made where the product contains no more than 0,12 g of sodium, or the equivalent value for salt, per 100 g or per 100 ml. For waters, other than natural mineral waters falling within the scope of Directive 80/777/EEC, this value should not exceed 2 mg of sodium per 100 ml [REGULATION (EC) No 1924/2006 Corrigendum 2007-01-18]. Food having 140 milligrams or less salt or sodium per amount customarily consumed. Meals and main dishes have 140 milligrams or less salt or sodium per 100 grams food [US FDA] low salt or sodium claim A claim that a food is low in fat, and any claim likely to have the same meaning for the consumer, may only be made where the product contains no more than 3 g of fat per 100 g for solids or 1,5 g of fat per 100 ml for liquids (1,8 g of fat per 100 ml for semi-skimmed milk). [REGULATION (EC) No 1924/2006 Corrigendum 2007-01-18]. Food having 3 grams of fat or less per amount customarily consumed (and per 50 grams of food if the amount customarily consumed is small). Meals and main dishes contain 3 grams or less fat per 100 grams of food and not more than 30% of calories from fat [US FDA]. low fat food Food containing at least 25% less fat per amount customarily consumed from the fat content of a comparable food product. The comparable food may not be 'low fat'. reduced fat food All narrower term definitions extracted from 58 Federal Register 2302, January 6, 1993, part 101.62(d). cholesterol special claim Food having less than 2 milligrams cholesterol per amount customarily consumed (or for meals and main dishes, less than 2 milligrams cholesterol per labeled serving). Such food must contain no ingredient that contains cholesterol except where the ingredient listed has been footnoted '*adds a trivial amount of cholesterol'. If the food contains less than 2 milligrams cholesterol per amount customarily consumed by special processing and the total fat exceeds 13 grams cholesterol per amount or labeled serving, the amount of cholesterol must be 'Substantially less' (25%) than in a comparable food with significant market share (5% of market). cholesterol free claim Food having 20 miligrams or less cholesterol per amount customarily consumed (and per 50 grams of food if the amount customarily consumed is small). Meals and main dishes contain 20 milligrams or less cholesterol per 100 grams of food. If the food qualifies by special processing and total fat exceeds 13 grams per amount and labeled serving, the amount of cholesterol must be 'substantially less' (25%) than in a comparable food with significant market share (5% of market). low in cholesterol claim Food having at least 25% less cholesterol per amount customarily consumed from the cholesterol content of a comparable food product. The comparable food may not be 'low cholesterol'. reduced cholesterol claim All narrower term definitions are extracted from 58 Federal Register 2302, January 6, 1993, part 101.60(b) and from Corrigendum to Regulation (EC) No 1924/2006 of the European Parliament and of the Council of 20 December 2006 on nutrition and health claims made on foods. energy special claim All narrower term definitions extracted from 58 Federal Register 2032, January 6, 1993, part 101.61. salt or sodium special claim A claim that a food is high in fibre, and any claim likely to have the same meaning for the consumer, may only be made where the product contains at least 6 g of fibre per 100 g or at least 3 g of fibre per 100 kcal [REGULATION (EC) No 1924/2006 Corrigendum 2007-01-18]. Food that is promoted as a source of or as high in dietary fiber (often called simply 'fiber'). high fiber food Food that is promoted as being either high or low in dietary fiber (often called simply 'fiber'). If the food is not low in total fat, total fat must be stated in conjunction with claim such as 'more fiber'. fiber special claim A claim that a food is fat-free, and any claim likely to have the same meaning for the consumer, may only be made where the product contains no more than 0,5 g of fat per 100 g or 100 ml. However, claims expressed as "X % fat-free" shall be prohibited [REGULATION (EC) No 1924/2006 Corrigendum]. Food having less than 0.5 grams fat per amount customarily consumed. Meals and main dishes have less than 0.5 grams fat per labeled serving. Such foods must contain no ingredient that is fat or understood to contain fat except when the ingredient listed has been footnoted '*adds a trivial amount of fat'. fat free food A claim that a food is energy-free, and any claim likely to have the same meaning for the consumer, may only be made where the product does not contain more than 4 kcal (17 kJ)/100 ml. For table-top sweeteners the limit of 0.4 kcal (1.7 kJ)/portion, with equivalent sweetening properties to 6 g of sucrose (approximately 1 teaspoon of sucrose), applies [REGULATION (EC) No 1924/2006 Corrigendum 2007-01-18]. Food having less than 5 calories per amount customarily consumed. Calorie amount is not defined for meals or main dishes [US FDA] energy free food claim A claim that a food is sugars-free, and any claim likely to have the same meaning for the consumer, may only be made where the product contains no more than 0,5 g of sugars per 100 g or 100 ml [REGULATION (EC) No 1924/2006 Corrigendum 2007-01-18]. Food having less than 0.5 grams sugars per amount customarily consumed (or for meals and main dishes, less than 0.5 grams sugars per labeled serving). Such foods nust contain no ingredient that is a sugar or generally understood to contain sugars except where the ingredient listed is footnoted '*adds a trivial amount of sugars' [US FDA] sugars free food A claim that a food is low in saturated fat, and any claim likely to have the same meaning for the consumer, may only be made if the sum of saturated fatty acids and trans-fatty acids in the product does not exceed 1.5 g per 100 g for solids or 0.75 g/100 ml for liquids and in either case the sum of saturated fatty acids and trans-fatty acids must not provide more than 10 % of energy. [REGULATION (EC) No 1924/2006 Corrigendum 2007-01-18]. Food having one gram or less saturated fat per amount customarily consumed and 15% or less of calories from saturated fat. Meals and main dishes contain one gram or less saturated fat per 100 grams food and less than 10% of calories from saturated fat. low in saturated fat food general label claim [REGULATION (EC) No 1924/2006 Corrigendum 2007-01-18] high energy food claim All narrower term definitions extracted from 58 Federal Register 2302, January 6, 1993, part 101.60(c). sugars special claim A claim that a food is low in sugars, and any claim likely to have the same meaning for the consumer, may only be made where the product contains no more than 5 g of sugars per 100 g for solids or 2,5 g of sugars per 100 ml for liquids [REGULATION (EC) No 1924/2006 Corrigendum 2007-01-18]. Not defined in U.S. Federal Register; no basis for a recommended intake. low sugars food low fiber food As defined in Corrigendum to Regulation (EC) No 1924/2006 of the European Parliament and of the Council of 20 December 2006 on nutrition and health claims made on foods, "claim" means any message or representation, which is not mandatory under Community or national legislation, including pictorial, graphic or symbolic representation, in any form, which states, suggests or implies that a food has particular characteristics; specificly, "nutrition claim" means any claim which states, suggests or implies that a food has particular beneficial nutritional properties due to: (a) the energy (calorific value) it (i) provides; (ii) provides at a reduced or increased rate; or (iii) does not provide; and/or (b) the nutrients or other substances it (i) contains; (ii) contains in reduced or increased proportions; or (iii) does not contain. nutrition-related claim no or reduced energy claim no or reduced fat claim no fat added claim All narrower term definitions extracted from 58 Federal Register 2302, January 6, 1993, part 101.62(c). saturated fat-related claim no animal fat added claim no tropical oils added claim no palm oil added claim rich in fiber claim naturally rich in fiber claim no or reduced salt or sodium claim no salt added claim Food having less than 5 milligrams salt per amount customarily consumed (or for meals and main dishes less than 5 milligrams salt per labeled serving). Such food must contain no ingredient that is salt or generally understood to contain salt except where the ingredient listed is footnoted '*adds a trivial amount of salt'. salt free claim low salt claim Food having less than 35 milligrams of salt per serving and per 100 grams of food. (U.S. proposed) very low salt claim reduced salt claim naturally sodium-free food no or reduced sugar claim A claim stating that sugars have not been added to a food, and any claim likely to have the same meaning for the consumer, may only be made where the product does not contain any added mono- or disaccharides or any other food used for its sweetening properties. If sugars are naturally present in the food, the following indication should also appear on the label: "CONTAINS NATURALLY OCCURRING SUGARS" [REGULATION (EC) No 1924/2006 Corrigendum]. No added sugars and 'without added sugars' are allowed if no sugar or sugar containing ingredient is added during processing. (28 Federal Register 2302, January 6, 1993) no sugars added claim starch-related claim no modified food starch added claim no starch added claim A claim about a vitamin or mineral with respect to an edible product. vitamin- or mineral-related claim color-related claim no artificial colors claim no color added claim flavor- or taste-related claim no artificial flavors claim no flavor added claim sweetener-related claim no artificial sweeteners claim unsweetened claim artificial ingredient-related claim no artificial ingredients claim no artificial additives claim preservative-related claim no nitrite/nitrate added claim no sulfite added claim no artificial preservatives claim no preservatives claim other ingredient- or constituent-related claim no msg added claim caffeine free claim naturally caffeine free claim processing-related claim A raw food that has not been frozen, heat processed or otherwise preserved. "fresh" label claim not pasteurized claim unpurified or unrefined claim unbleached claim Health claim means any claim made on the label or in labeling of a food, including a dietary supplement, that expressly or by implication, including "third party" references, written statements (e.g., a brand name including a term such as "heart"), symbols (e.g., a heart symbol), or vignettes, characterizes the relationship of any substance to a disease or health-related condition. See also 21 CFR 101.14 [http://www.accessdata.fda.gov/scripts/cdrh/cfdocs/cfcfr/CFRSearch.cfm?fr=101.14]. A claim is a health claim if in the naming of the substance or category of substances, there is a description or indication of a functionality or an implied effect on health; examples: "contains antioxidants" (the function is an antioxidant effect); "containsprobiotics/prebiotics" (the reference to probiotic/prebiotic implies a health benefit). Equally, claims which refer to an indication of a functionality in the description of a nutrient or a substance (for instance as an adjective to the substance) should also beclassified as a health claim; examples: "with prebiotic fibres" or "contains prebiotic fibres". In Europe, a health claim is any statement about a relationship between food and health [http://ec.europa.eu/food/food/labellingnutrition/claims/health_claims_en.htm], and only authorized health claims are legal [see http://ec.europa.eu/food/food/labellingnutrition/claims/community_register/health_claims_en.htm]. COMMISSION REGULATION (EU) No 432/2012 of 16 May 2012 establishes a list of permitted health claims made on foods, other than those referring to the reduction of disease risk and to children"s development and health [http://eur-lex.europa.eu/LexUriServ/LexUriServ.do?uri=OJ:L:2012:136:0001:0040:en:PDF] health-related claim tooth decay-related claim religion- or customs-related claim kosher claim USA: The 1990 Farm Act specifies that a food labeled 'organic' must meet four requirements: 1) the food must be raised by specified methods to replenish and maintain the fertility of the soil; 2) the food must be certified as having been produced with a nationally approved list of materials and practices; 3) to be eligible for certification at least three years must have elapsed between the first organic harvest and first use of nationally approved materials on land and crops;and 4) organic foods must meet all local, state and federal regulations governing the quality and safety of the food supply. Europe: Foods produced in accordance with Council Regulation (EC) No 834/2007 of 28 June 2007 on organic production and labelling of organic products and repealing Regulation (EEC) No 2092/91. [http://eur-lex.europa.eu/LexUriServ/LexUriServ.do?uri=OJ:L:2007:189:0001:0023:EN:PDF] organic food claim Considerations include amounts that are 'nutritionally trivial' and amounts that can be declared as zero on the nutrition label. An additional criterion based on amount per weight (e.g., per 100 grams) is not considered necessary because the amount of nutrient in a 'free' food is so low that even frequent and repeated consumption is unlikely to have physiological consequences. (U.S. proposed) "free" label claim An amount customarily consumed contains 20% or more of the daily nutritional value to describe protein, vitamins, minerals, dietary fiber, or potassium. May be used on meals or main dishes to indicate that product contains a food that meets the definition. "high" label claim "less" label claim A claim stating that a product is "light" or "lite", and any claim likely to have the same meaning for the consumer, shall follow the same conditions as those set for the term "reduced", see *REDUCED {NAME OF NUTRIENT} NUTRITION CLAIM [P0132]*; the claim shall also be accompanied by an indication of the characteristic(s) which make(s) the food "light" or "lite" [REGULATION (EC) No 1924/2006 Corrigendum 2007-01-18]. Used for foods that have 33.3% fewer calories than a comparable product and a minimum reduction of more than 40 calories per serving. Any other use of 'light' must specify whether it refers to the look, taste or smell; for example, 'light in color'. (U.S. FDA proposed) "light" label claim "more" label claim "source of" label claim kosher for passover claim A food consumer group is a class of organism based on their heterotrophic requirements or preferences. food consumer group no or reduced cholesterol claim (percent) fat free claim Food having less than 5 miligrams sodium per amount customarily consumed (or for meals and main dishes, less than 5 milligrams sodium per labeled serving). Such food must contain no ingredient that is sodium chloride or generally understood to contain sodium except where the ingredient listed is footnoted '*adds a trivial amount of sodium'. sodium free claim Food having 35 milligrams or less sodium per amount customarily consumed (and per 50 grams of food if the amount customarily consumed is small). Meals and main dishes contain 35 milligrams or less sodium per 100 grams food. very low sodium claim Food containing at least 25% less sodium per amount customarily consumed than the sodium content of a comparable food product. The comparable food may not be 'low sodium'. reduced sodium claim Foods having 140 milligrams or less sodium per amount customarily consumed (and per 50 grams of food if the amount customarily consumed is small). Meals and main dishes have 140 milligrams sodium per 100 grams of food. low sodium claim game as consumer rabbit as consumer other special claim label claim in food name label claim separate from food name no water added claim pareve claim noncarbonated claim lactose reduced food lactose free food unenriched claim no vitamin or mineral added claim gluten free claim egg free claim alcohol free claim kosher milchlig claim The food was quickly frozen while still fresh. "fresh frozen" label claim A claim that a food does not contain saturated fat, and any claim likely to have the same meaning for the consumer, may only be made where the sum of saturated fat and trans-fatty acids does not exceed 0,1 g of saturated fat per 100 g or 100 ml [REGULATION (EC) No 1924/2006 Corrigendum 2007-01-18]. Food having less than 0.5 grams saturated fat per amount customarily consumed (or for meals and main dishes, less than 0.5 grams saturated fat per labeled serving). Trans fatty acids are not more than 1% of total fat. Such foods contain no ingredient that is understood to contain saturated fat except where the ingredient listed has been footnoted '*adds a trivial amount of saturated fat' [US FDA]. saturated fat free food Food containing at least 25% less saturated fat per amount customarily consumed than the saturated fat content of a comparable food product. The comparable food product may not be 'low saturated fat'. reduced saturated fat food Food having at least 25% less sugars per amount customarily consumed than the sugars content of a comparable food product. reduced sugars food Wild or semiwild foods consumed only during periods of famine when no other food is available. aliment de disette A food is 'enriched' when nutrients are added to it to replace those that are lost in processing. enriched food claim A food is 'fortified' when nutrients that were never present are added to it. fortified food claim A claim that iodine has been added to an edible product. iodized claim unfortified claim Characterized by adherence to the dietary practices required by Islamic law (Webster's). halal claim adult human as food consumer infant as food consumer, 0 - 3 months infant as food consumer, 3 - 6 months infant as food consumer, 6 - 12 months toddler as food consumer, 12 months and onwards low alcohol claim probiotic claim full fat claim trans fat claim Food Quality/Food Assurance Claim indicates, with reference to the product branding, labelling or packaging, whether the product is stamped with a quality mark, as approved by the governing authority, such as USDA for USA products [Source: GS1]. food quality claim It should be noted that such claims are illegal in some countries, e.g. Denmark, and that other countries, e.g. United Kingdom, are calling for an end to the use of terms such as 'diabetic' or 'suitable for diabetics' on food labels. The European Commission is considering how foods intended specifically for people with diabetes can be controlled. diabetic or suitable for diabetics claim vegan/vegetarian or suitability for vegan/vegetarian claim no pork added claim no beef added claim Food that is promoted as being either high or low in protein. protein special claim A claim that a food is high in protein, and any claim likely to have the same meaning for the consumer, may only be made where at least 20 % of the energy value of the food is provided by protein [REGULATION (EC) No 1924/2006 Corrigendum 2007-01-18]. high protein food natural source of vitamins and or minerals claim A claim that a food is a source of fibre, and any claim likely to have the same meaning for the consumer, may only be made where the product contains at least 3 g of fibre per 100 g or at least 1,5 g of fibre per 100 kcal [REGULATION (EC) No 1924/2006 Corrigendum 2007-01-18]. source of fibre A claim that a food is a source of protein, and any claim likely to have the same meaning for the consumer, may only be made where at least 12 % of the energy value of the food is provided by protein. [REGULATION (EC) No 1924/2006 Corrigendum]. source of protein A claim that a food contains a nutrient or another substance, for which specific conditions are not laid down in this Regulation, or any claim likely to have the same meaning for the consumer, may only be made where the product complies with all the applicable provisions of this Regulation, and in particular Article 5. For vitamins and minerals the conditions of the claim "source of" shall apply. [REGULATION (EC) No 1924/2006 Corrigendum 2007-01-18]. contains {name of the nutrient or other substance} nutrition claim A claim stating that the content in one or more nutrients, other than vitamins and minerals, has been increased, and any claim likely to have the same meaning for the consumer, may only be made where the product meets the conditions for the claim "source of" and the increase in content is at least 30 % compared to a similar product. [Forordning (EF) nr. 1924/2006 Berigtigelse 2007-01-18]. increased {name of nutrient} nutrition claim Where a food naturally meets the condition(s) laid down in this Annex for the use of a nutritional claim, the term "naturally/natural" may be used as a prefix to the claim [REGULATION (EC) No 1924/2006 Corrigendum2007-01-18]. "naturally/natural" label claim A claim that a food is a source of vitamins and/or minerals, and any claim likely to have the same meaning for the consumer, may only be made where the product contains at least a significant amount as defined in the Annex to Directive 90/496/EEC or an amount provided for by derogations granted according to Article 6 of Regulation (EC) No 1925/2006 of the European Parliament and of the Council of 20 December 2006 on the addition of vitamins and minerals and of certain other substances to foods [REGULATION (EC) No 1924/2006 Corrigendum2007-01-18]. source of {name of vitamin/s} and/or {name of mineral/s} nutrition claim A claim that a food is high in vitamins and/or minerals, and any claim likely to have the same meaning for the consumer, may only be made where the product contains at least twice the value of "source of [NAME OF VITAMIN/S] and/or [NAME OF MINERAL/S]" [REGULATION (EC) No 1924/2006 Corrigendum 2007-01-18]. high {name of vitamin/s} and/or {name of mineral/s} nutrition claim A claim stating that the content in one or more nutrients has been reduced, and any claim likely to have the same meaning for the consumer, may only be made where the reduction in content is at least 30 % compared to a similar product, except for micronutrients, where a 10 % difference in the reference values as set in Directive 90/496/EEC shall be acceptable, and for sodium, or the equivalent value for salt, where a 25 % difference shall be acceptable. [REGULATION (EC) No 1924/2006 Corrigendum 2007-01-18]. reduced {name of nutrient} nutrition claim food allergen labelling Regulated by Directive 2003/89/EC of the European Parliament and of the Council of 10 November 2003 amending Directive 2000/13/EC as regards indication of the ingredients present in foodstuffs. food allergen labelling about cereals containing gluten and products thereof Regulated by Directive 2003/89/EC of the European Parliament and of the Council of 10 November 2003 amending Directive 2000/13/EC as regards indication of the ingredients present in foodstuffs. food allergen labelling about crustaceans and products thereof Regulated by Directive 2003/89/EC of the European Parliament and of the Council of 10 November 2003 amending Directive 2000/13/EC as regards indication of the ingredients present in foodstuffs. food allergen labelling about eggs and products thereof Regulated by Directive 2003/89/EC of the European Parliament and of the Council of 10 November 2003 amending Directive 2000/13/EC as regards indication of the ingredients present in foodstuffs. food allergen labelling about fish and products thereof Regulated by Directive 2003/89/EC of the European Parliament and of the Council of 10 November 2003 amending Directive 2000/13/EC as regards indication of the ingredients present in foodstuffs. food allergen labelling about peanuts and products thereof Regulated by Directive 2003/89/EC of the European Parliament and of the Council of 10 November 2003 amending Directive 2000/13/EC as regards indication of the ingredients present in foodstuffs. food allergen labelling about soybeans and products thereof Regulated by Directive 2003/89/EC of the European Parliament and of the Council of 10 November 2003 amending Directive 2000/13/EC as regards indication of the ingredients present in foodstuffs. food allergen labelling about milk and products thereof, including lactose Regulated by Directive 2003/89/EC of the European Parliament and of the Council of 10 November 2003 amending Directive 2000/13/EC as regards indication of the ingredients present in foodstuffs. food allergen labelling about nuts and products thereof Regulated by Directive 2003/89/EC of the European Parliament and of the Council of 10 November 2003 amending Directive 2000/13/EC as regards indication of the ingredients present in foodstuffs. food allergen labelling about celery and products thereof Regulated by Directive 2003/89/EC of the European Parliament and of the Council of 10 November 2003 amending Directive 2000/13/EC as regards indication of the ingredients present in foodstuffs. food allergen labelling about mustard and products thereof Regulated by Directive 2003/89/EC of the European Parliament and of the Council of 10 November 2003 amending Directive 2000/13/EC as regards indication of the ingredients present in foodstuffs. food allergen labelling about sesame seeds and products thereof Sulphur dioxide and sulphites are included in the EU list of allergens because they can cause adverse reactions in some people. Regulated by Directive 2003/89/EC of the European Parliament and of the Council of 10 November 2003 amending Directive 2000/13/EC as regards indication of the ingredients present in foodstuffs. food allergen labelling about sulphur dioxide and sulphites Contained in GS1 Allergen Code List. food allergen labelling about cocoa and products thereof Contained in GS1 Code List. food allergen labelling about coriander and products thereof Contained in GS1 Code List. food allergen labelling about lupine and products thereof Contained in GS1 Code List. food allergen labelling about corn and products thereof Contained in GS1 Code List. food allergen labelling about pod fruits and products thereof Contained in GS1 Code List. food allergen labelling about carrot and products thereof Contained in GS1 Code List. food allergen labelling about molluscs and products thereof "no trans fat" claim 'Traditional" means proven usage on the Community market for a time period showing transmission between generations; this time period should be the one generally ascribed to one human generation, at least 25 years [COUNCIL REGULATION (EC) No 509/2006 of 20 March 2006 on agricultural products and foodstuffs as traditional specialities guaranteed]. A traditional food product is a product frequently consumed or associated to specific celebrations and/or seasons, normally transmitted from one generation to another, made with care in a specific way according to the gastronomic heritage, with little or no processing/manipulation, that is distinguished and known because of its sensory properties and associated to a certain local area, region or country. [http://www.truefood.eu/] Traditional means conforming to established practice or specifications prior to the Second World War. Traditional food is a food of a specific feature or features, which distinguish it clearly from other similar products of the same category in terms of the use of traditional ingredients (raw materials or primary products), traditional composition or traditional type of production and/or processing method. [Traditional Foods in Europe, EuroFIR Synthesis report No 6, 2009] traditional food claim Ethnic food is food from countries other than the home market contributing to a different food culture than the traditional cuisine of the host country. [Ethnic Groups and Foods in Europe, EuroFIR Synthesis report No 3, 2005] "Ethnic food" has been used colloquially for a wide variety of foodstuffs, virtually any that can be identified in the public mind with a foreign source or an ethnic minority group. In the narrower ethnographic meaning, it pertains only to food prepared or consumed by members of an ethnic group as a manifestation of its ethnicity. In the end ethnic food is food that members of an ethnic group consider their own and that others attribute to them. [http://www.answers.com/topic/ethnic-cuisines] ethnic food claim Raw material (species and/or varieties) or primary product either alone or as an ingredient that has been used in identifiable geographical areas and remains in use today (taking into account cases where use was abandoned for a time and then reinstated) and its characteristics are in accordance with current specifications of national and EU legislation. [Traditional Foods in Europe, EuroFIR Synthesis report No 6, 2009] traditional ingredient claim The uniquely identifiable composition (in terms of ingredients) that was first established prior to the Second World War and passed down through generations by oral or other means (taking into account cases where composition was abandoned for a time and then reinstated) and when necessary is differentiated from the composition defined by the generally recognized characteristics of the wider food group to which the product belongs. [Traditional Foods in Europe, EuroFIR Synthesis report No 6, 2009] traditional composition claim The production and/or processing of a food that has been transmitted from generation to generation through oral tradition or other means and has been applied prior to the Second World War and remains in use (taking into account cases where composition was abandoned for a time and then reinstated) despite its adjustment to binding rules from national or EU food hygiene regulations or the incorporation of technological progress, under the condition that production and/or processing remains in line with methods used originally and that the food"s intrinsic features such as its physical, chemical, microbiological or organoleptic features are maintained. [Traditional Foods in Europe, EuroFIR Synthesis report No 6, 2009] traditional type of production and/or processing claim Authentic ethnic food is food from countries other than the home market contributing to a different food culture than the traditional cuisine of the host country. Food may be adapted by combining local and imported ingredients. [Ethnic Groups and Foods in Europe, EuroFIR Synthesis report No 3, 2005] authentic ethnic food claim Modified ethnic food: a commercially-available version of a food that has been modified to suit the taste and preference of the host country. [Ethnic Groups and Foods in Europe, EuroFIR Synthesis report No 3, 2005] modified ethnic food claim COMMISSION REGULATION (EU) No 116/2010 of 9 February 2010 amending Regulation (EC) No 1924/2006 of the European Parliament and of the Council with regard to the list of nutrition claims. monounsaturated fat claim COMMISSION REGULATION (EU) No 116/2010 of 9 February 2010 amending Regulation (EC) No 1924/2006 of the European Parliament and of the Council with regard to the list of nutrition claims polyunsaturated fat claim A claim that a food is high in monounsaturated fat, and any claim likely to have the same meaning for the consumer, may only be made where at least 45 % of the fatty acids present in the product derive from monounsaturated fat under the condition that monounsaturated fat provides more than 20 % of energy of the product [COMMISSION REGULATION (EU) No 116/2010 of 9 February 2010 amending Regulation (EC) No 1924/2006 of the European Parliament and of the Council with regard to the list of nutrition claims]. high monounsaturated fat omega-3 fatty acids claim A claim that a food is high in omega-3 fatty acids, and any claim likely to have the same meaning for the consumer, may only be made where the product contains at least 0,6 g alpha-linolenic acid per 100 g and per 100 kcal, or at least 80 mg of the sum of eicosapentaenoic acid and docosahexaenoic acid per 100 g and per 100 kcal [COMMISSION REGULATION (EU) No 116/2010 of 9 February 2010 amending Regulation (EC) No 1924/2006 of the European Parliament and of the Council with regard to the list of nutrition claims]. high omega-3 fatty acids A claim that a food is high in polyunsaturated fat, and any claim likely to have the same meaning for the consumer, may only be made where at least 45 % of the fatty acids present in the product derive from polyunsaturated fat under the condition that polyunsaturated fat provides more than 20 % of energy of the product [COMMISSION REGULATION (EU) No 116/2010 of 9 February 2010 amending Regulation (EC) No 1924/2006 of the European Parliament and of the Council with regard to the list of nutrition claims]. high polyunsaturated fat unsaturated fat claim A claim that a food is high in unsaturated fat, and any claim likely to have the same meaning for the consumer may only be made where at least 70 % of the fatty acids present in the product derive from unsaturated fat under the condition that unsaturated fat provides more than 20 % of energy of the product [COMMISSION REGULATION (EU) No 116/2010 of 9 February 2010 amending Regulation (EC) No 1924/2006 of the European Parliament and of the Council with regard to the list of nutrition claims].. high unsaturated fat A claim that a food is a source of omega-3 fatty acids, and any claim likely to have the same meaning for the consumer, may only be made where the product contains at least 0,3 g alpha-linolenic acid per 100 g and per 100 kcal, or at least 40 mg of the sum of eicosapentaenoic acid and docosahexaenoic acid per 100 g and per 100 kcal [COMMISSION REGULATION (EU) No 116/2010 of 9 February 2010 amending Regulation (EC) No 1924/2006 of the European Parliament and of the Council with regard to the list of nutrition claims]. source of omega-3 fatty acids US FDA Approved user group. human as food consumer, four years and above man as food consumer woman as food consumer pregnant or lactating woman as food consumer senior as food consumer teenager as food consumer child as food consumer, less than four years US FDA approved language lacking for the moment. calcium and osteoporosis related claim athlete as food consumer bodybuilder as food consumer menopaused woman as food consumer weight-reducer as food consumer infant as food consumer, 0 - 6 months In the United States, these claims, usually referred to as "qualified health claims", are regulated by the Food and Drug Administration in the public interest, see 21 Code of Federal Regulations § 101.14 [http://www.accessdata.fda.gov/scripts/cdrh/cfdocs/cfcfr/CFRSearch.cfm?fr=101.14] qualified health claim Structure/function claims describe the role of a nutrient or dietary ingredient intended to affect normal structure or function in humans, for example, "calcium builds strong bones". In addition, they may characterize the means by which a nutrient or dietary ingredient acts to maintain such structure or function, for example, "fiber maintains bowel regularity," or "antioxidants maintain cell integrity," or they may describe general well-being from consumption of a nutrient or dietary ingredient. [http://www.fda.gov/Food/LabelingNutrition/LabelClaims/StructureFunctionClaims/default.htm] structure/function claim The term infant is typically applied to young children between the ages of 1 month and 12 months. [http://en.wikipedia.org/wiki/Infant] infant as food consumer Native American food claim Alaskan Native food claim Apache food claim Navajo food claim Shoshone Bannock food claim Pacific food claim Northern Plains food claim Southwest Plains food claim Hopi food claim phytosterol claim A data item consisting of a claim or record of a food product's origin or processing history or suitability for some purpose. food datum cut of meat, u.s. A cut of meat from the breast or lower chest of beef or veal. brisket chuck flank rib (meat cut) round or leg (meat cut) fore shank short loin sirloin short plate loin fat back jowl, trimmed foot (meat cut) Meat cut from the area where the clod meets the edge of the pectoral muscle in an animal. shoulder (meat cut) breast (meat cut) side (meat cut) cut of meat, composite A food plant physical characteristic about the ripening stage of development of a fruit. fruit ripeness A fruit ripeness characteristic in which a fruit has not achieved full maturity and is not slightly ripe. unripe A fruit ripeness characteristic in which a fruit has achieved full maturity and is ready for utilization. ripe Boneless skeletal meat from the lower sides of meat animals; usually belly meat is smoked and cured to produce bacon. belly meat The process of producing and/or retailing post-harvest food in a consumer or industrial context. food facility preparation process The process of preparing food at a human residence. home food preparation process The process of preparing and serving food in a restaurant. restaurant food preparation process The process of preparing and serving food in a fast food outlet. fast food outlet preparation process The process of preparing food in an industrial facility. food industry preparation process The process of preparing food in a commissary. commissary food preparation process The process of preparing and serving food in a restaurant or fast food outlet. restaurant or fast food preparation process The process of sourcing and selling food at a street vending establishment. street vendor food retail process cut of meat, french quartier avant caparacon bavette flanchet hampe plat-de-cote poitrine collier basses-cotes raquette gite avant jumeau marcreuse quartier arriere cuisse gite arriere semelle tranche (meat cut) tranche grasse aloyau entre-cote faux-filet A boneless cut or slice of meat or fish. filet rumsteck A piece of animal meat which has been cut according to butchery practice. butchery cut of animal A food production process involving the rearing of an organism. agricultural food production The hunting or foraging for wild food resources. gathered wild wild food harvesting An agricultural production process involving a domesticated organism. domestic or cultivated food production tail cut of poultry meat A whole wing that is obtained from a poultry. The wing of a poultry bird. poultry wing A whole breast that is obtained from a poultry. poultry breast A whole leg that is obtained from a poultry. poultry leg A whole thigh that is obtained from a poultry. The thigh cut of a poultry bird. poultry thigh An agricultural production process involving wild plants, insects or other organisms that are tended and protected. semidomestic or semiwild food production A planned process involving the rearing, manufacture or distribution of food material. food production The cultivation of plants for food. food plant cultivation outdoor/open-air plant cultivation Open-air plant cultivation using non-organic fertilizer, pest and weed control treatments. conventional outdoor/open-air cultivation The organic cultivation of plants in an unsheltered area. outdoor/open-air organic plant cultivation under glass/protected plant cultivation conventional under glass/protected cultivation The organic cultivation of plants in a sheltered area. under glass/protected organic plant cultivation A method of growing plants, usually crops, without soil, by using mineral nutrient solutions in an aqueous solvent. hydroponic cultivation tenderloin Plant cultivation according to organic food production methods including the use of fertilizers of organic origin such as compost manure, green manure, and bone meal and places emphasis on techniques such as crop rotation and companion planting, biological pest control and the fostering of insect predators. organic plant cultivation food plant physical quality An agricultural production process that aims to produce food using natural substances and processes that have a limited negative environmental and human health impact as they encourage the responsible use of energy and natural resources like water, the maintenance of biodiversity, the preservation of regional ecological balances, enhancement of soil fertility, and animal welfare. organic food production A method of farming husbandry where the animals, for at least part of the day, can roam freely outdoors, rather than being confined in an enclosure for 24 hours each day. This term can be applied to egg, dairy, poultry, and meat production. free-range food animal rearing A meat shank or shin is the portion of meat around the tibia of the animal, the leg bone beneath the knee. [http://en.wikipedia.org/wiki/Shank_(meat)] shank (meat) A whole neck that is obtained from a poultry. The neck cut of a poultry bird. poultry neck A food packaging type which is intended for the consumer to remove or open to access food material. consumer-ready food packaging A food packaging type which is used in bulk food packaging and is removed prior to retail distribution. wholesale food bulk packaging A saku which is derived from tuna fish. tuna saku A label claim that no natural or synthetic hormones were added during the production of a food product. hormone-free food product claim A label claim that no natural or synthetic antibiotics were added during the production of a food product. antibiotic-free food product claim A label claim that the animals which the food product derives from, were not raised in caged housing systems. cage-free animal claim A label claim that the animals which the food product derives from, were raised for some portion of their lives on or with access to a pasture. pasture-raised food product claim A label claim that the animals which the food product derives from, were fed a grass or forage-based diet. grass-fed food product claim A domestic or cultivated food production in which plant or animal from which the food product derives was raised on a farm. farm-raised food product claim label claim GSCID-BRC standard The GSCID-BRC Project and Sample Application Standard captures standardized human pathogen and vector sequencing metadata to support epidemiologic and genotype-phenotype association studies for human infectious diseases. The NIAID page for specifications has a broken link for Core Project. This is the existing page: https://www.niaid.nih.gov/research/dmid-metadata-standards-core-project Link page is: https://www.niaid.nih.gov/research/human-pathogen-and-vector-sequencing-metadata-standards Damion Dooley This standard was developed by representatives of the Genome Sequencing Centers for Infectious Diseases (GSCIDs), the Bioinformatics Resource Centers (BRCs), and NIAID and informed by discussions and input with numerous collaborating scientists. GSCID-BRC Project and Sample Application Standard MIxS standard MixS is a unified standard for describing sequence data provided by the Genomic Standards Consortium (GSC) Damion Dooley Minimum Information about any (x) Sequence (MIxS) MIMARKS standard The "minimum information about a marker gene sequence" (MIMARKS) is a standard developed by the Genomic Standards Consortium (GSC) for reporting marker gene sequences. http://www.nature.com/nbt/journal/v29/n5/full/nbt.1823.html Minimum information about a marker gene sequence A data item that indicates for the given categorical variable, a respondent has chosen an other or additional response not listed. This class cannot be referred to directly as a subclass of more than one class without involving inference from the respective classes. Instances of it may exist as a kind of metadata. Usually a reference to a parent categorical class, but not a subordinate, carries the same information. Damion Dooley other (metadata value) other relevance other Other: specify the sample scope that was used. Damion Dooley https://www.ncbi.nlm.nih.gov/books/NBK54364/ other specimen scope other material Other: specify the material that was used. Damion Dooley https://www.ncbi.nlm.nih.gov/books/NBK54364/ other material derived from specimen A data item that is a free text description provided to indicate a target capture specification not covered by the other types. Damion Dooley https://www.ncbi.nlm.nih.gov/books/NBK54364/ other capture type Specify the project method Damion Dooley https://www.ncbi.nlm.nih.gov/books/NBK54364/ other project method This is an organizational category for grouping parameters relevant to a biomedical sample. Damion Dooley obsolete: draft GenEpiO BioSample standard true An NCBI antibiogram data item is an antimicrobial susceptibility and resistance datum related to drug resistant pathogens. This information is provided within an antibiogram table on BioSample records. Damion Dooley obsolete: NCBI antibiogram data item true HIPPA PHI guideline The American HIPPA Protected Health Information (PHI) guidelines cover information, including demographic information, which relates to: - the individual’s past, present, or future physical or mental health or condition, - the provision of health care to the individual, or - the past, present, or future payment for the provision of health care to the individual, and that identifies the individual or for which there is a reasonable basis to believe can be used to identify the individual. Protected health information includes many common identifiers (e.g., name, address, birth date, Social Security Number) when they can be associated with the health information listed above." https://en.wikipedia.org/wiki/Health_Insurance_Portability_and_Accountability_Act American HIPPA Protected Health Information (PHI) guidelines The natural (as opposed to laboratory) full scientific taxonomic name of a subject related to a given investigation, study and/or specimen. Damion Dooley http://purl.obolibrary.org/obo/GENEPIO_0001567 obsolete: subject species true http://purl.obolibrary.org/obo/NCIT_C45908 NCBI BioSample: intersex obsolete: intersex true Isolation date inferred from BCCDC interviews date the strain was isolated Damion Dooley http://purl.obolibrary.org/obo/GENEPIO_0000021 obsolete: isolation date true Collection Culture isolation date suggested in metadata feedback year/month/day A culture isolation date is a date-time entity marking the end of a process in which a sample is isolated as a single colony or non-mixture culture Damion Dooley GROUP: IRIDA Ontology (Morag) culture isolation date Collection Frozen date NML Labware LIMS year/month/day A culture frozen date is a date-time entity marking the beginning of a process in which a sample culture is frozen for preservation. Damion Dooley GROUP: IRIDA Ontology (Emma) culture frozen date Collection Received date NML Labware LIMS year/month/day A date which describes when a laboratory received an isolate. NML LIMS isolate received date Collection Upload date NML Labware LIMS month/day/year A date which describes when the isolate was entered into the database. NML LIMS PulseNet: UploadDate isolate upload date Pathogen Isolate inferred from BCCDC interviews gut, spine, tongue, lung Name of body site where the specimen was obtained from, such as a specific organ or tissue. Damion Dooley's note: Although term mentions "site" in label, this cannot be placed under "site" as it is intended to refer to organism material, and leads to unsatisfiable terms otherwise. GROUP: MIxS subject anatomical site http://gensc.org/ns/mixs/host_body_site depth:1 order: NCIT:C115935 # healthy NCIT:C25610 # pathologic NCIT:C28554 # deceased diseased Health or disease status of a given subject at time of specimen collection. Currently this does not differ from the 'subject health status (GSCID-BRC)' item. It may be revised to have more options in the future. Damion Dooley subject health status at time of specimen collection 1 1 Environmental Isolate sediment, chicken feces, cheese Describes the physical, environmental and/or local geographical source of the biological sample from which the sample was derived. Damion Dooley NCBI Biosample specimen source context Pathogen Isolate feces, cerebral spinal fluid (CSF) Substance produced by the body, e.g. stool, mucus, where the specimen was obtained from. Damion Dooley subject body product Environmental Isolate Geographic location depth GROUP: MIxS value (5m) Please refer to the definitions of depth in the environmental packages GROUP: MIxS collection depth datum The environmental material level refers to the material that was displaced by the sample, or material in which a sample was embedded, prior to the sampling event. Environmental material terms are generally mass nouns. Examples include: air, soil, or water. EnvO (v 2013-06-14) terms can be found via the link: www.environmentontology.org/Browse-EnvO http://purl.obolibrary.org/obo/ENVO_00010483 obsolete: specimen source environmental material true A subject sex is the phenotypic sex of given subject (human or animal) related to a given investigation, study, and/or specimen. Damion Dooley Gender is not used because it is a term referencing human social and cultural convention. subject sex specification Environmental Isolate Land use where sample was taken Environment Canada Metadata descriptive; type of human use (park, farm, urban) Human use of land involving the management and modification of natural environment or wilderness into built environment. URI: http://en.wikipedia.org/wiki/Land_use specimen collection site land use Environmental Isolate Fecal Indicator Bacteria Number Environment Canada Metadata 12,456 cfu Number of indicator micro-organisms (colony forming units) present in a sample that have been used to suggest the presence of pathogens. URI: http://www.who.int/water_sanitation_health/dwq/iwachap13.pdf fecal indicator bacteria count Environmental Isolate Conductivity GROUP: MIxS milliSiemens per centimeter An environmental datum which describes the electrical conductivity of water. GROUP: MIxS enviro package conductivity measurement datum Environmental Isolate Dissolved oxygen GROUP: MIxS micromole per kilogram An environmental datum which describes the concentration of dissolved oxygen in a sample. GROUP: MIxS enviro package dissolved oxygen concentration GMI MDM standard The Global Microbial Identifier "Minimum data for Matching" (MDM) standard is a standard that defines essential contextual data fields to be included in genomic sequence repository records. Damion Dooley the Global Microbial Identifier Minimum Data for Matching (MDM) Standard http://www.globalmicrobialidentifier.org/-/media/Sites/gmi/News-and-events/2013/6th-meeting-2013-report.ashx?la=da Environmental Isolate Soluble inorganic material GROUP: MIxS soluble organic material name;measurement value A test specification which describes the concentration of substances such as ammonia, road-salt, sea-salt, cyanide, hydrogen sulfide, thiocyanates and thiosulfate in a sample. GROUP: MIxS enviro package soluble inorganic material Environmental Isolate Soluble inorganic material GROUP: MIxS soluble inorganic material concentration Environmental Isolate Nitrite GROUP: MIxS micromole per liter An environmental datum which describes the concentration of nitrite of a sample. GROUP: MIxS enviro package nitrite concentration Environmental Isolate Nitrate GROUP: MIxS micromole per liter An environmental datum which describes the concentration of nitrate of a sample. GROUP: MIxS enviro package nitrate concentration Environmental Isolate Total phosphorous GROUP: MIxS micromole per liter An environmental datum which describes the total phosphorus concentration in a sample. GROUP: MIxS enviro package Total phosphorus concentration, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus. Can also be measured without filtering, reported as phosphorus. total phosphorous concentration 12 Environmental Isolate Stream order Environment Canada Metadata value, 1-12 Stream order is a measure of the relative size of streams (The smallest tributaries are referred to as first-order streams, while the largest river in the world, the Amazon, is a twelfth-order waterway). GROUP: Environment Canada Metadata stream order categorical measurement datum Environmental Isolate Density of bacteria in sample Environment Canada Metadata OD reading or cfu's or cells per millilitre An environmental datum which describes the number of bacteria in a sample. GROUP: Environment Canada Metadata bacteria density Lab Analytic Host Primary Enzyme PulseNet Data Capture pick list (XbaI, BlnI) Restriction enzyme for first characterization GROUP: IRIDA Ontology (Emma) primary enzyme (LMAAI) 1 1 PFGE test specification Lab Analytic Host Primary PFGE Pattern NML LIMS First PFGE pattern from given diagnostic restriction enzyme GROUP: IRIDA Ontology (Emma) PFGE primary test Lab Analytic Host Secondary Enzyme PulseNet Data Capture pick list (XbaI, BlnI) Restriction enzyme for second characterization GROUP: IRIDA Ontology (Emma) secondary enzyme (LMACI) Lab Analytic Host Secondary PFGE Pattern NML LIMS Second PFGE pattern from given diagnostic restriction enzyme GROUP: IRIDA Ontology (Emma) PFGE secondary test Lab Analytic MLST Clonal Complex inferred from BCCDC interviews and Bionumerics pick list? Multilocus sequence typing (MLST) is a technique in molecular biology for the typing of multiple loci. The procedure characterizes isolates of microbial species using the DNA sequences of internal fragments of multiple housekeeping genes. Sequence types are grouped into clonal complexes by their similarity to a central allelic profile (genotype). As such, clonal complexes represent sequence types that share a number of identical alleles e.g. 5/7 URI: http://en.wikipedia.org/wiki/Multilocus_sequence_typing ; http://eburst.mlst.net/3.asp MLST clonal complex Lab Analytic MLST Sequence Type inferred from BCCDC interviews and Bionumerics pick list? Multilocus sequence typing (MLST) is a technique in molecular biology for the typing of multiple loci. The procedure characterizes isolates of microbial species using the DNA sequences of internal fragments of multiple housekeeping genes. For each housekeeping gene, the different sequences present within a bacterial species are assigned as distinct alleles and, for each isolate, the alleles at each of the loci define the allelic profile or sequence type (ST). MLST sequence typing The process of fingerprinting the core genome of a bacteria. Add under upcomming OBI "DNA fingerprinting assay". Damion Dooley Some bacteria like E coli have a highly variable genome, and so to type them methods must focus on typing the core genome that is common to all strains. core genome fingerprinting assay Lab Analytic CGF type inferred from BCCDC interviews pick list Output of CGF. GROUP: IRIDA Ontology (Emma) CGF type Lab Analytic 16S rRNA sequencing inferred from BCCDC interviews 16S ribosomal RNA sequencing is a sequencing method used to identify and compare bacteria present within a given sample. 16S rRNA gene sequencing is a well-established method for studying phylogeny and taxonomy of samples from complex microbiomes or environments that are difficult or impossible to study. URI: http://www.illumina.com/applications/microbiology/microbial-sequencing-methods/16S-rrna-sequencing.html 16S rRNA sequencing Lab Analytic Stx toxin type metadata feedback Stx1 or Stx2 A pathogenic shiga toxin produced by STEC E. coli. GROUP: IRIDA Ontology (Emma) Stx toxin type datum Lab Analytic Stx toxin subtype metadata feedback stx1a, stx1c A shiga toxin variant. GROUP: IRIDA Ontology (Emma) Stx toxin subtype datum Lab Analytic Stx1 Toxin PCR result NML Labware LIMS CT value? A qPCR measurement result of Stx1 gene amplification. GROUP: IRIDA Ontology (Emma) Stx1 Toxin PCR result Lab Analytic Stx1 Cell Culture NML Labware LIMS A measurement datum which describes the level of Stx1 toxin derived tissue culture toxicity. GROUP: IRIDA Ontology (Emma) Stx1 cell culture level Lab Analytic Stx2 Toxin PCR result NML Labware LIMS CT value? A qPCR measurement result of Stx2 gene amplification. GROUP: IRIDA Ontology (Emma) Stx2 Toxin PCR result Lab Analytic Stx2 Cell Culture NML Labware LIMS value? A measurement datum which describes the level of Stx2 toxin derived tissue culture toxicity. GROUP: IRIDA Ontology (Emma) Stx2 cell culture level An AccuProbe assay that uses a luminometer and DNA probe designed to identify a specific bacteria or fungus species within a culture. Damion Dooley Nucleic acid hybridization tests are based on the ability of complementary nucleic acid strands to specifically align and associate to form stable double-stranded complexes (6). The ACCUPROBE method uses a single-stranded DNA probe with a chemiluminescent label that is complementary to the ribosomal RNA of the target organism. After the ribosomal RNA is released from the target organism, the labeled DNA probe combines with the target organism’s ribosomal RNA to form a stable DNA:RNA hybrid. The Selection Reagent allows for the differentiation of non-hybridized and hybridized probes.The light signal emitted by the DNA:RNA hybrids is measured by a GEN-PROBE luminometer. A positive result is a luminometer reading equal to or greater than the cut-off. A value below this cut-off is the negative result. AccuProbe culture identification assay An AccuProbe reagent kit for identifying Listeria monocytogenes. Damion Dooley URI: http://www.hologic.com/sites/default/files/package%20inserts/103051F-EN-RevC.pdf AccuProbe Listeria monocytogenes culture identification reagent kit Lab Analytic NML Labware LIMS positive, negative, not done A categorical diagnostic result of an AccuProbe test. NML LIMS AccuProbe test result Ribotyping involves the fingerprinting of genomic DNA restriction fragments that contain all or part of the genes coding for the 16S and 23S rRNA. By digesting the genes with a specific restriction enzyme, fragments of different lengths are generated. By performing a Gel electrophoresis with the digested samples, the fragments can be visualised as lines on the gel, where larger fragments are close to the start of the gel, and smaller fragments further down. After blotting onto a matrix and probing, these lines form a unique pattern for each species and can be used to identify the origin of the DNA, almost like a barcode can identify a product. ribotyping This method is based on restriction endonuclease digestion of bacterial chromosomal DNA, followed by Southern hybridization to probes for sequences in the regions of bacterial DNA coding for the 5S-16S-23S (the Escherichia coli rrnB rRNA operon) rRNA operon. The probes have been developed that are directed to highly conserved regions of the rRNA operon present in all eubacteria and can therefore be used for ribotyping most bacteria riboprinting A device that generates an automated genetic fingerprint of a bacterium from a bacterial suspension. an automated system that takes a purified bacterial suspension, lyses the cells, extracts the DNA, restriction endonuclease digests the DNA, separates the digest on a gel, transfers the DNA bands to a membrane, probes the bands with non-radioisotope-labeled, 5S-16S-23S rRNA-specific probes (Southern hybridization), photographs the membrane, and finally compares the bar code-like pattern to databases in order to identify the genus and species. Qualicon (DuPont) RiboPrinter Microbial Characterization System A dataset which is a library of RiboPrinter recognised patterns. DuPont identification pattern library Lab Analytic Riboprinter DUP Number NML Labware LIMS DUP-PST1-1211 DuPont identification number from the DuPont identification library NML LIMS RiboPrinter DUP Number Lab Analytic Riboprinter DUP similarity NML Labware LIMS The identification of an isolate was determined when the corresponding patterns matched one of the patterns of the DuPont Identification library of the RiboPrinter1 with a similarity of >0.85. The similarity threshold for an isolate joining a ribogroup is an adaptive value between 0.90 and 0.96, depending on the size of the ribogroup. Similarity of pattern to one of the patterns of the DuPont Identification library of the RiboPrinter RiboPrinter DUP similarity Sequencing Sequencing Run Date NML NGS Archive yyyy/mm/dd Date the sequencing run was performed GROUP: IRIDA Ontology (Emma) sequencing run date Sequencing Sequencing Location inferred from BCCDC interviews A laboratory sequencing datum which describes the location the sequencing run was performed. GROUP: IRIDA Ontology (Emma) sequencing location Sequencing Platform https://www.ncbi.nlm.nih.gov/books/NBK54984/table/SRA_Glossary_BK.T._platform_descriptor_t/ Illumina (MiSeq, HiSeq), PacBio, Ion Torrent, (Roche 454), SOLiD ABI A sequencing plaform (brand) is a name of a company that produces sequencer equipment. GROUP: IRIDA Ontology (Emma) sequencing platform (brand) Sequencing Workflow Derived from Sample Sheet Resequencing, FastQ only A lab sequencing datum which describes a pre-defined sequence of steps to run the automated sequencing pipeline. GROUP: IRIDA Ontology (Emma) sequencing workflow Sequencing Application Derived from Illumina Sample Sheet amplicon sequencing, WGS A lab sequencing datum which describes a pre-defined sequence of steps to run the automated sequencing pipeline. GROUP: IRIDA Ontology (Emma) sequencing application Derived from Illumina Sample Sheet the sequencing conditions and the analyte being measured GROUP: IRIDA Ontology (Emma) obsolete: sequencing assay true Sequencing Chemistry Derived from Illumina Sample Sheet amplicon, resequencing (WGS) A laboratory sequencing datum which describes the method and chemistry used to determine the order of nucleotides in a DNA molecule. GROUP: IRIDA Ontology (Emma) sequencing chemistry Sequencing Read Length Derived from Illumina Sample Sheet 151, 251 A datum of the number of base pairs per read. GROUP: IRIDA Ontology (Emma) read length A GSCID/BRC data item is a field in one of the GSCID/BRC Project and Sample Application Standard subsets. Damion Dooley obsolete: GSCID-BRC data item true Sequencing Multiplex identifiers Derived from Illumina Sample Sheet S017 Molecular barcodes, called Multiplex Identifiers (MIDs), that are used to specifically tag unique samples in a sequencing run. Sequence should be reported in uppercase letters GROUP: MIxS sequencing run multiplex identifiers Sequencing Sample Name Derived from Illumina Sample Sheet specification: http://support.illumina.com/content/dam/illumina-support/documents/documentation/system_documentation/miseq/miseq-sample-sheet-quick-ref-guide-15028392-j.pdf 1,2,3, AX234, etc. Control1, Tank1, Froglet1 A sequencing run sample identifier is an alphanumeric identifier for a sample. In bioinformatics processing this identifier is assigned to a sample in order to track it through the process of sequencing and analysis. GROUP: IRIDA Ontology (Emma) Illumina SampleSheet: Sample_ID PulseNet: SubmittedNumber sample name sample title sequencing run sample identifier Sequencing Number of cycles Derived from Illumina Sample Sheet 500 Number of sequencing chemistry cycles GROUP: IRIDA Ontology (Emma) sequencing count of chemistry cycles Sequencing Sequencing Kit Derived from Illumina Sample Sheet MiSeq reagent kit Pre-filled, ready-to-use reagent cartridges. Used to produce improved chemistry, cluster density and read length as well as improve quality (Q) scores. Reagent components are encoded to interact with the sequencing system to validate compatibility with user-defined applications. GROUP: IRIDA Ontology (Emma) sequencing kit Sequencing Sequencing Kit version Derived from Illumina Sample Sheet v2, v3 A string datum which is the version/configuration of the reagent cartidge. GROUP: IRIDA Ontology (Emma) sequencing kit version Sequencing Adapters Derived from Illumina Sample Sheet adapter A and B sequence Adapters provide priming sequences for both amplification and sequencing of the sample-library fragments. Both adapters should be reported; in uppercase letters GROUP: MIxS adapter sequence Sequencing Adapter Trimming Derived from Illumina Sample Sheet The removal of adapter sequences from demultiplexed data reads GROUP: IRIDA Ontology (Emma) read adapter trimming Sequencing inferred from BCCDC interviews Illumina metagenomic protocol (part 15044223), with Nextera Packaged kits (containing adapters, indexes, enzymes, buffers etc), tailored for specific sequencing workflows, which allow the simplified preparation of sequencing-ready libraries for small genomes, amplicons, and plasmids. GROUP: IRIDA Ontology (Emma) and http://applications.illumina.com/applications/sequencing/ngs-library-prep.html library preparation kit Sequencing Number of base pairs inferred from BCCDC interviews 300 000 The estimated size of the genome prior to sequencing. Of particular importance in the sequencing of (eukaryotic) genome which could remain in draft form for a long or unspecified period. GROUP: MIxS number of expected base pairs per genome Run QC Number of Reads Passing Filter Output from MiSeq 0.92 Raw data are filtered to remove any reads that do not meet the overall quality as measured by a chastity filter. The chastity of a base call is calculated as the ratio of the brightest intensity divided by the sum of the brightest and second brightest intensities. Clusters passing filter are represented by PF in analysis reports. Clusters pass filter if no more than one base call in the first 25 cycles has a chastity of < 0.6. URI: http://support.illumina.com/sequencing/sequencing_instruments/miseq/questions.html number of reads passing filter Run QC Cluster density Output from MiSeq 800 k/mm^2 Cluster Generation is a process by which libraries amplified into clonal clusters on a flow cell. The density of those clusters in the lane, is the cluster density. URI: https://www.broadinstitute.org/files/shared/illuminavids/clusterGenSlides.pdf sequencer flow cell cluster density Run QC above 30 Qscore Output from MiSeq >75% An assembly quality control datum that describes the quality of the identification of nucleobases generated in sequencing, where the score is logarithimically related to the probability of an error in base calling. URI: http://en.wikipedia.org/wiki/Phred_quality_score phred quality score Assembly QC Assembly Standard Term the GROUP: MIxS term encompasses assembly method; estimated error rate; method of calculation Assembly method refers to how the reads were assembled into contigs for which either a de novo or mapping (reference based) strategy is used. GROUP: MIxS assembly method Assembly QC Assembly status from within "Finishing strategy" in GROUP: MIxS standard draft or finished An assembly quality control datum that describes the status of the assembly which is categorised from draft to finished. Damion Dooley CITATION: Chain, P.S., Grafham, D.V., Fulton, R.S., Fitzgerald, M.G., Hostetler, J., Muzny, D., Ali, J., Birren, B., Bruce, D.C., Buhay, C., et al. (2009). Genomics. Genome project standards in a new era of sequencing. Science 326, 236-237. "Attempting to convey the relative integrity and reliability of the data, six levels or terms have been proposed and applied to describe genome sequences." See subclass choices. assembly status Assembly QC Coverage from within "Finishing strategy" in GROUP: MIxS 30 Coverage (read depth or depth) is the average number of reads representing a given nucleotide in the reconstructed sequence. URI: http://en.wikipedia.org/wiki/Shotgun_sequencing Damion Dooley's note: Wikipedia defines calculation with: "the length of the original genome (G), the number of reads(N), and the average read length(L) as N * L/G" read coverage Assembly QC Number of Contigs 20 http://purl.obolibrary.org/obo/IAO_0000428 A contig count is the count of contigs that belong to a sequence assembly. Damion Dooley contig count Assembly QC Assembly name Standard Term name and version of assemby Name/version of the assembly provided by the submitter that is used in the genome browsers and in the community GROUP: MIxS assembly name (identifier) Assembly QC Annotation Algorithm Standard Term Prokka Program used for annotation GROUP: IRIDA Ontology (Emma) genome annotation algorithm Assembly QC Annotation Source Standard Term annotation source description For cases where annotation was provided by a community jamboree or model organism database rather than by a specific submitter GROUP: MIxS genome annotation source Damion Dooley obsolete: NCBI BioSample data item true CDC ID Damion Dooley ID Tracker IRIDA ID ontology group An IRIDA case ID is a tracking identifier for a case used in the IRIDA.ca software system. It is used to cross-reference anonymized IDs. Damion Dooley GROUP: IRIDA Ontology (Emma) IRIDA case ID An NCBI BioProject data item is a datum within the NCBI BioProject standard collection Damion Dooley obsolete: NCBI BioProject data item true The INDISC consortium "Minimum data for Matching" standard aims to define a format to capture reads and minimum metadata. It is developed by the "Repository and storage of sequence and meta-data" workgroup 2. It is used in the Global Microbial Identifier platform. Damion Dooley http://purl.obolibrary.org/obo/GENEPIO_0000036 obsolete: INSDC MDM standard true A MixS data item is a term or field defined in the Genomic Standards Consortium MIxS standard. Damion Dooley obsolete: MIxS data item true The 'draft data standard' class contains draft representations of formal or defacto third party standards and related components. These representations may have been crafted without any involvement of related standards issuers and so no guarantee can be provided about their currency, accuracy or veracity. Damion Dooley draft data standard obsolete: HIPPA PHI data item true obsolete: PulseNet data item true The I2B2 Workbench Data Protection role standard is a standard which names and lists data protection roles between a user and a given dataset that define the level of detail a user has access to. Damion Dooley Derived from the Data Protection Track of the I2B2 Workbench software specification: https://www.i2b2.org/software/files/PDF/current/IM_Architecture.pdf I2B2 Data Protection role standard depth:1 order: NCIT:C115935 # healthy NCIT:C25610 # pathologic / diseased NCIT:C28554 # deceased A description of whether a given subject organism appeared healthy, sick or deceased at the time of specimen extraction. If sick or deceased, additional details should be provided in project-specific fields. Damion Dooley CS8 subject health status (GSCID-BRC) The GSCID-BRC Core Sample Standard is an extension of the GMI MDM data standard Damion Dooley https://www.niaid.nih.gov/research/dmid-metadata-standards-core-sample GSCID-BRC Core Sample standard A Core Project item is a field in the GSCID/BRC Project and Sample Application Core Project Standard. Damion Dooley https://www.niaid.nih.gov/research/dmid-metadata-standards-core-project GSCID-BRC Core Project standard Specimen category is a categorical variable that broadly indicates the source of a specimen in order for data processing systems like NCBI's biosample submission portal to anticipate other fields related to the source. Currently this distinguishes between "clinical or host associated" specimens and "environmental/food or other pathogen" specimens. Damion Dooley specimen category day, week, month, year Age unit of the age measurement of a subject (individual organism). Damion Dooley Feb 20, 2017: GSCID-BRC calls for an explicit field here whereas NCBI Biosample and MIxS don't. Damion Dooley NIAID GSCID-BRC metadata working group subject age - unit The National Center for Biotechnology Information offers standards for submitting genomic project data to their BioProject and BioSample databases. Damion Dooley National Center for Biotechnology Information standard NCBI standard A datum containing the city or region or more precise geographical location identifier for the site of a specimen collection event. Damion Dooley Adapted from NIAID GSCID-BRC metadata working group Note that this is expressed in a particular format in some standards. specimen collection location - city or region lookup The country of the site of a given specimen collection event. Damion Dooley NIAID GSCID-BRC metadata working group specimen collection location - country The Darwin Core is body of standards. It includes a glossary of terms (in other contexts these might be called properties, elements, fields, columns, attributes, or concepts) intended to facilitate the sharing of information about biological diversity by providing reference definitions, examples, and commentaries. Damion Dooley http://tdwg.github.io/dwc/terms/index.htm Darwin Core Terms A datetime measurement related to a person's travel with respect to potential epidemilogical implications. Damion Dooley travel history item The date of a person's departure from their primary residence (at that time) on a journey to one or more other locations. Damion Dooley travel start date The date of a person's return to some residence from a journey originating at that residence. Damion Dooley travel end date Infection aquired during travel is a boolean datum indicating a diagnosis of a traveller's infection during a given trip. Damion Dooley infection aquired during travel This is a model of the datums involved in an epidemiology investigation. Damion Dooley draft pathogenic epidemiology case investigation record The draft epi case exposure model describes datums related to the possible transmission of a pathogen between a case person and other people, places, animals etc. Damion Dooley draft pathogenic epi case exposure record A description of a food item that a case patient has come in contact with. Damion Dooley draft pathogenic epi case food record food brought back from travel An epidemiology contact network model is a definition of the information necessary to connect pathogen transmission patterns between individuals or animals in connection with an outbreak investigation. Damion Dooley epidemiology contact network model An epi contact network - human is contact information about a person who may be involved in transmitting a pathogen. Damion Dooley epi contact network model - human This is a model that provides location and transportation information about an animal that may be involved in transmitting a pathogen to a human or other animal. Damion Dooley epi contact network model - animal A note is text that provides human-readable information on one or more subjects. Damion Dooley note An epi case general info model contains datum specifications about an epidemiology investigation case including the person involved, contact information and their demographics. Damion Dooley draft pathogenic epi case general information record A record of the details around how, when, and from what an isolate was extracted. Damion Dooley draft pathogenic epi case isolate detail record A specimen source substance is an organism substance or food product or environmental substance from which the specimen was extracted. Damion Dooley specimen source substance An isolate sequence filename is the file name (http://edamontology.org/data_1050) of the contig assembly file created by a bioinformatics assembly process. Damion Dooley isolate sequence filename A cluster identifier is an identifier that locates a genomic variant of an organism within a community of past or present genetically related organisms. Damion Dooley cluster identifier A laboratory test performed on a specimen from a patient with regard to potential pathogenic disease. Damion Dooley draft pathogenic epi case test record A lab test requestor is the individual or agency requesting that one or more tests be performed on a specimen. Damion Dooley contact specification - lab test requester A food cultural origin datum indicates the cultural origin of a food product. Damion Dooley food cultural origin A record of a patient's recent travel - departure and return, mode of travel and locations visited - as it may pertain to an outbreak pathogen transmission event. Damion Dooley draft pathogenic epi case travel record Region (England) (entry subject to GAZ replacement) An epi network contact is a person who may have recieved or transmitted an infectious disease related to an outbreak investigation. Damion Dooley contact specification - epi network contact This model contains data type specifications for whole genome sequencing and epidemiology investigation contextual data. Damion Dooley public health lab epidemiology contextual data standard This is a set of datums involved in laboratory processing of whole-genome-sequenced isolates. Damion Dooley draft whole genome sequencing lab test record A data specification which records the bioinformatics process of a draft whole genome sequencing product. Damion Dooley draft WGS lab bioinformatics process record A data specification which records the sequencing datum of a draft whole genome sequencing product. Damion Dooley draft WGS lab sequencing record An NCBI SRA meta information item is a field specification for a NCBI Sequence Read Archive record. Damion Dooley NCBI SRA meta information standard https://www.ncbi.nlm.nih.gov/books/NBK47529/#_SRA_Quick_Sub_BK_Experiment_ An isolate raw read filename is the file name (http://edamontology.org/data_1050) of the raw read file created by a genomic sequencing assay. isolate raw read filename Sequencing The version identifier of a packaged kit tailored for specific sequencing workflows. Damion Dooley library preparation kit version The name and version of software used in a bioinformatics workflow to improve the quality of sequencing reads. Damion Dooley read trimming and filtering software A laboratory sequencing datum which describes the name of the bioinformatics pipeline used. Damion Dooley bioinformatics pipeline name A laboratory sequencing datum which describes the version of the bioinformatics pipeline used. Damion Dooley bioinformatics pipeline version A laboratory sequencing datum which describes the protocol for the bioinformatics pipeline. Damion Dooley bioinformatics pipeline protocol A data specification which records the sequencing quality datum of a draft whole genome sequencing product. Damion Dooley draft WGS lab sequencing quality metrics record A data specification which records the assembly quality datum of a draft whole genome sequencing product. Damion Dooley draft WGS lab assembly quality metrics record A general label indicating the primary study goal. These are only relevant for Primary submission projects (not Umbrella projects). Damion Dooley Damion Dooley's note: According to http://trace.ddbj.nig.ac.jp/news/2014-11-12_e.html, "A BioProject record can have multiple project data types" project data type Genome assembly project utilizing already existing sequence data including data that was submitted by a different group Damion Dooley https://www.ncbi.nlm.nih.gov/books/NBK54364/ assembly project A sequencing project involving clone-ends Damion Dooley https://www.ncbi.nlm.nih.gov/books/NBK54364/ clone ends project A sequencing project involving DNA methylation, histone modification, and/or chromatin accessibility datasets Damion Dooley https://www.ncbi.nlm.nih.gov/books/NBK54364/ epigenomics project Exome resequencing project Damion Dooley https://www.ncbi.nlm.nih.gov/books/NBK54364/ exome resequencing project A whole, or partial, genome sequencing project (with or without a genome assembly) Damion Dooley https://www.ncbi.nlm.nih.gov/books/NBK54364/ genome sequencing project The Relational Sequencing TB Data Platform (ReSeqTB) catalogs a vast amount of genotypic, phenotypic and related metadata from Mycobacterium tuberculosis (Mtb) strains to enable the development of clinically useful, WHO-endorsed in vitro diagnostic assays for rapid drug susceptibility testing of Mtb. Damion Dooley https://platform.reseqtb.org/ draft ReSeq Tuberculosis data platform standard In expressions like: "<= 8mg/L" The measurement comparator is a sign indicating that a measurement is above, equal to, or below a given threshold. Damion Dooley test threshold measurement comparator < The "less than" comparator indicates that a given substance was present at less than a given quantity or concentration. Damion Dooley < less than <= The "less than or equal to" comparator indicates that a given substance was present at less than or equal to a given quantity or concentration. Damion Dooley <= less than or equal to == The "equal to" comparator indicates that a given substance was present at the given quantity or concentration. Damion Dooley == equal to >= The "greater than or equal to" comparator indicates that a given substance was present at greater than or equal to a given quantity or concentration. Damion Dooley >= greater than or equal to > The "greater than" comparator indicates that a given substance was present at greater than a given quantity or concentration. Damion Dooley > greater than order: OBI:0001616 # specimen identifier OBI:0001614 # GenBank ID GENEPIO:0001100 # antibiogram drug test model GENEPIO:0002062 # amr testing reference standard GENEPIO:0002045 # amr resistance testing method GENEPIO:0002047 # ... version or reagent GENEPIO:0002049 # amr testing platform GENEPIO:0002056 # ... vendor The NCBI antibiogram standard details the reporting specifications for antimicrobial susceptibility and resistance data derived from drug resistant pathogens. This information is submitted as an antibiogram table on BioSample records. Damion Dooley NCBI Antibiogram standard https://www.ncbi.nlm.nih.gov/biosample/docs/antibiogram/ http://purl.obolibrary.org/obo/GENEPIO_0001007 obsolete: NCBI isolate AMR testing model true A restaurant or an eatery, is a business which prepares and serves food and drinks to customers in exchange for money. Damion Dooley https://en.wikipedia.org/wiki/Restaurant http://purl.obolibrary.org/obo/ENVO_01000934 obsolete: restaurant true iPHIS standard The Canadian Integrated Public Health Information System (iPHIS) System provides a standard for holding reportable disease cases from participating jurisdictions. Damion Dooley Canadian Integrated Public Health Information System (iPHIS) Standard 254532233433235152213423 The MIRU24 - international standard is a mycobacterial interspersed repetitive units (MIRU) typing method that classifies Mycobacterium tuberculosis complex (MBTC) bacteria according to a multiple locus VNTR [variable number of tandem repeats] analysis (MLVA) typing scheme of counts of repeats at 24 sequence loci. The ordering of loci is as follows: MIRU 04, MIRU 26, MIRU 40, MIRU 10, MIRU 16, MIRU 31, 424 577, 2165, 401, 3690, 4156, 2163, 1955, 4052, MIRU 02, MIRU 23, MIRU 39, MIRU 20, MIRU 24, MIRU 27, 2347, 2461, 3171 MIRU24 - international standard The MIRU24 - Canadian standard is a Mycobacterium tuberculosis typing method exactly like MIRU24 - international standard except that the report of the ordering of the matching loci is different. Damion Dooley The ordering of loci is as follows: MIRU 02, MIRU 04, MIRU 10, MIRU 16, MIRU 20, MIRU 23, MIRU 24, MIRU 26, MIRU 27, MIRU 31, MIRU 39, MIRU 40, 424, 577, 1955, 2163, 2165, 2347, 2401, 2461, 3171, 3690, 4052, 4156 MIRU24 - Canadian standard spray-wading water pool water obsolete: hot tub true A cafeteria is a type of food service location in which there is little or no waiting staff table service, whether a restaurant or within an institution such as a large office building or school. Damion Dooley https://en.wikipedia.org/wiki/Cafeteria http://purl.obolibrary.org/obo/ENVO_01000969 obsolete: cafeteria true http://purl.obolibrary.org/obo/ENVO_00003864 obsolete: bakery true A delicatessen or deli is a retail establishment that sells a selection of unusual or foreign prepared foods. Damion Dooley https://en.wikipedia.org/wiki/Delicatessen http://purl.obolibrary.org/obo/ENVO_01000970 obsolete: delicatessen true A food kiosk is a kiosk (a booth with an open window on one side) that sells food. Damion Dooley http://purl.obolibrary.org/obo/ENVO_01000974 obsolete: food kiosk true A grocery store is a retail store that primarily sells food. Damion Dooley http://purl.obolibrary.org/obo/ENVO_01000984 obsolete: grocery store true A specialty/ethnic food store is a store specializing in a particular variety of food or food of cultural / regional origin. Damion Dooley http://purl.obolibrary.org/obo/ENVO_01000988 obsolete: specialty/ethnic store true A market, or marketplace, is a location where people regularly gather for the purchase and sale of provisions, livestock, and other goods Damion Dooley http://purl.obolibrary.org/obo/ENVO_01000987 obsolete: market true A time measurement datum that pertains to a patient's medical treatment. Damion Dooley treatment history datum A restaurant providing prepared meals or other food items that the purchaser intends to eat elsewhere Damion Dooley https://en.wikipedia.org/wiki/Take-out http://purl.obolibrary.org/obo/ENVO_01000972 obsolete: take out restaurant true A treatment start date is a date/time datum which indicates the start of a particular medical treatment for a patient. Damion Dooley treatment start date canoeing / kayaking / boating hiking camping Damion Dooley http://purl.obolibrary.org/obo/PCO_0000033 obsolete: social gathering true http://purl.obolibrary.org/obo/PCO_0000035 obsolete: party true http://purl.obolibrary.org/obo/PCO_0000038 obsolete: wedding true http://purl.obolibrary.org/obo/PCO_0000039 obsolete: baby shower true http://purl.obolibrary.org/obo/PCO_0000037 obsolete: potluck true http://purl.obolibrary.org/obo/PCO_0000034 obsolete: community event true A long term care facility provides a type of residential care. It is a place of residence for people who require continual nursing care and have significant difficulty coping with the required activities of daily living. Damion Dooley https://en.wikipedia.org/wiki/Nursing_home_care http://purl.obolibrary.org/obo/ENVO_01000932 obsolete: long term care facility true A treatment end date is a date/time datum which indicates the end of a particular medical treatment for a patient. Damion Dooley treatment end date Damion Dooley food related exposure event Some bacteria are associated with particular foods. Need relationship Damion Dooley infection-specific food detail A tuberculosis treatment antibiotic is an antibiotic used in the treatment of tuberculosis. Damion Dooley tuberculosis treatment drug “Treatment of Tuberculosis Guidelines”, WHO, Geneva, 2010, 30 www.who.int/tb/ - See more at: http://www.tbfacts.org/tb-drugs/#sthash.nibuzCLV.dpuf vegetarian A time measurement datum that pertains to an organism's physical location. Damion Dooley organism location history datum This will take on a sub-herarchy of food types. food avoidance special diet water related exposure event municipal water A time measurement datum indicating the year a person immigrated to a given country. Damion Dooley immigration year of arrival bottled water An event where one or more hosts are exposed to an infectious pathogen Damion Dooley infectious disease exposure event Damion Dooley human related exposure event Damion Dooley animal related exposure event Identification or description of the specific individual from which this sample was obtained Damion Dooley https://www.ncbi.nlm.nih.gov/biosample/docs/attributes/ NCBI BioSample isolate (human name or description) Damion Dooley http://purl.obolibrary.org/obo/ENVO_01000923 obsolete: petting zoo true Damion Dooley agricultural fair An isolate passage history is a record of the cyclic growth process that led to it, including number of times its was put through the process, and the method used. Damion Dooley http://purl.obolibrary.org/obo/GENEPIO_0001835 isolate passage history datum For Eschericia coli: STEC, UPEC A pathotype is a common name for a group of organisms (of the same species) that have the same pathogenicity on a specified host https://en.wiktionary.org/wiki/pathotype NCBI pathotype Damion Dooley Duplicate term, replaced by more appropriate FOODON term FOODON:00003357 'pet treat'. obsolete: pet treat true Damion Dooley Duplicate term, replaced by more appropriate FOODON term, FOODON:00003356 obsolete: pet food (raw) true An epidemiology travel datum is a datum regarding a particular human's travel trip destination, mode, and motivation, with respect to an epidemiology investigation. Damion Dooley human exposure event - travel datum boat / cruise travel train travel bus travel car travel airline travel A travel mode is a type of transportation which a given human has used while travelling on a particular trip. Damion Dooley travel mode A travel reason is a motivation for traveling on a particular trip expressed by the traveller. Damion Dooley travel reason travel for pleasure business activity religious missionairy activity rural backpacking activity visiting relative/friends travel tour unsure of travel reason The tuberculosis draft standard is a GenEpiO set of draft genomic and clinical data items related to Mycobacterium tuberculosis that various agencies are using in their own reporting. draft tuberculosis - specimen contextual data standard Damion Dooley behavioural risk factor http://purl.obolibrary.org/obo/GENEPIO_0001686 obsolete: E. coli serotype part true Snomed: Concept 260827009 O antigen Snomed: Concept 260823008 H antigen Damion Dooley homeless status A serotype or serovar is a distinct variation within a species of bacteria or virus or among immune cells of different individuals. These microorganisms, viruses, or cells are classified together based on their cell surface antigens, allowing the epidemiologic classification of organisms to the sub-species level Damion Dooley https://en.wikipedia.org/wiki/Serotype serovar/serotype common name Salmonella serovar Salmonella serovar name Salmonella antigenic formula Damion Dooley drug use status Damion Dooley incarceration status Damion Dooley HIV status Damion Dooley HIV risk status Damion Dooley A.I.D.S status Damion Dooley drug abuse status Damion Dooley injection drug use status Damion Dooley recreational drug use status Damion Dooley methadone use status Damion Dooley substantial alcohol use/abuse status Damion Dooley smoking status A country of birth is the country that a given person (or animal) was born in. Damion Dooley country of birth Tb_1 (with respect to an Illumina SampleSheet.csv spreadsheet) 13 (with respect to a ReSeqTB SNP pipeline sample report) A sequence number is a numeric identifier of a sequence with respect to a particular data table or dataset. sequence number Damion Dooley The 'date last seen alive' is the date that a subject (patient) was last known (seen, heard, messaged) to be alive. date last seen alive second line or reserve tuberculosis drug tuberculosis infection anatomical site http://purl.obolibrary.org/obo/GENEPIO_0001007 obsolete: NCBI Antibiogram model true order: GENEPIO:0001187 # antimicrobial resistance test drug GENEPIO:0002112 # drug MIC GENEPIO:0002080 # drug minimum inhibitory concentration unit GENEPIO:0001001 # measurement comparator NCIT:C85539 # antimicrobial resistance phenotype GENEPIO:0002181 # antimicrobial resistance phenotype - ECOFF This is the minimal set of parameters for drug test results for a particular antimicrobial agent. Damion Dooley draft antibiogram drug test model http://the-vet.net/DVMWiz/Vetlibrary/Lab-%20Microbiology%20Guide%20to%20Interpreting%20MIC.htm https://www.ncbi.nlm.nih.gov/biosample/docs/antibiogram/ A date-time datum that marks the predicted start of possible human or animal exposure to a pathogen agent, directly or indirectly, based on a suspected pathogen and first symptom date-time. Damion Dooley predicted exposure start A date-time datum that marks the predicted end of possible human or animal exposure to a pathogen agent, directly or indirectly, based on a suspected pathogen and first symptom date-time. Damion Dooley predicted exposure end Map: - project that results in non-sequence map data such as genetic map, radiation hybrid map, cytogenetic map, optical map, and etc. Damion Dooley https://www.ncbi.nlm.nih.gov/books/NBK54364/ map project Metagenome: sequence analysis of environmental samples Damion Dooley https://www.ncbi.nlm.nih.gov/books/NBK54364/ metagenome project Metagenome assembly: a genome assembly generated from sequenced environmental samples Damion Dooley https://www.ncbi.nlm.nih.gov/books/NBK54364/ metagenome assembly project Other: a free text description is provided to indicate Other data type Damion Dooley https://www.ncbi.nlm.nih.gov/books/NBK54364/ other project data type Phenotype or Genotype: project correlating phenotype and genotype Damion Dooley https://www.ncbi.nlm.nih.gov/books/NBK54364/ phenotype or genotype project Proteome: large scale proteomics experiment including mass spec. analysis Damion Dooley https://www.ncbi.nlm.nih.gov/books/NBK54364/ proteome project Random Survey: sequence generated from a random sampling of the collected sample; not intended to be comprehensive sampling of the material. Damion Dooley https://www.ncbi.nlm.nih.gov/books/NBK54364/ random survey project Targeted locus (loci): project to sequence specific loci, such as a 16S rRNA sequencing Damion Dooley https://www.ncbi.nlm.nih.gov/books/NBK54364/ targeted locus (loci) project Transcriptome or Gene expression: large scale RNA sequencing or expression analysis. Includes cDNA, EST, RNA_seq, and microarray. Damion Dooley https://www.ncbi.nlm.nih.gov/books/NBK54364/ transcriptome or gene expression A sequencing project with a primary goal of identifying large or small sequence variation across populations. Damion Dooley https://www.ncbi.nlm.nih.gov/books/NBK54364/ variation project (Afghanistan|Albania|Algeria|American Samoa|Andorra|Angola|Anguilla|Antarctica|Antigua and Barbuda|Arctic Ocean|Argentina|Armenia|Aruba|Ashmore and Cartier Islands|Atlantic Ocean|Australia|Austria|Azerbaijan|Bahamas|Bahrain|Baltic Sea|Baker Island|Bangladesh|Barbados|Bassas da India|Belarus|Belgium|Belize|Benin|Bermuda|Bhutan|Bolivia|Borneo|Bosnia and Herzegovina|Botswana|Bouvet Island|Brazil|British Virgin Islands|Brunei|Bulgaria|Burkina Faso|Burundi|Cambodia|Cameroon|Canada|Cape Verde|Cayman Islands|Central African Republic|Chad|Chile|China|Christmas Island|Clipperton Island|Cocos Islands|Colombia|Comoros|Cook Islands|Coral Sea Islands|Costa Rica|Cote d'Ivoire|Croatia|Cuba|Curacao|Cyprus|Czech Republic|Democratic Republic of the Congo|Denmark|Djibouti|Dominica|Dominican Republic|East Timor|Ecuador|Egypt|El Salvador|Equatorial Guinea|Eritrea|Estonia|Ethiopia|Europa Island|Falkland Islands (Islas Malvinas)|Faroe Islands|Fiji|Finland|France|French Guiana|French Polynesia|French Southern and Antarctic Lands|Gabon|Gambia|Gaza Strip|Georgia|Germany|Ghana|Gibraltar|Glorioso Islands|Greece|Greenland|Grenada|Guadeloupe|Guam|Guatemala|Guernsey|Guinea|Guinea-Bissau|Guyana|Haiti|Heard Island and McDonald Islands|Honduras|Hong Kong|Howland Island|Hungary|Iceland|India|Indian Ocean|Indonesia|Iran|Iraq|Ireland|Isle of Man|Israel|Italy|Jamaica|Jan Mayen|Japan|Jarvis Island|Jersey|Johnston Atoll|Jordan|Juan de Nova Island|Kazakhstan|Kenya|Kerguelen Archipelago|Kingman Reef|Kiribati|Kosovo|Kuwait|Kyrgyzstan|Laos|Latvia|Lebanon|Lesotho|Liberia|Libya|Liechtenstein|Line Islands|Lithuania|Luxembourg|Macau|Macedonia|Madagascar|Malawi|Malaysia|Maldives|Mali|Malta|Marshall Islands|Martinique|Mauritania|Mauritius|Mayotte|Mediterranean Sea|Mexico|Micronesia|Midway Islands|Moldova|Monaco|Mongolia|Montenegro|Montserrat|Morocco|Mozambique|Myanmar|Namibia|Nauru|Navassa Island|Nepal|Netherlands|New Caledonia|New Zealand|Nicaragua|Niger|Nigeria|Niue|Norfolk Island|North Korea|North Sea|Northern Mariana Islands|Norway|Oman|Pacific Ocean|Pakistan|Palau|Palmyra Atoll|Panama|Papua New Guinea|Paracel Islands|Paraguay|Peru|Philippines|Pitcairn Islands|Poland|Portugal|Puerto Rico|Qatar|Republic of the Congo|Reunion|Romania|Ross Sea|Russia|Rwanda|Saint Helena|Saint Kitts and Nevis|Saint Lucia|Saint Pierre and Miquelon|Saint Vincent and the Grenadines|Samoa|San Marino|Sao Tome and Principe|Saudi Arabia|Senegal|Serbia|Seychelles|Sierra Leone|Singapore|Sint Maarten|Slovakia|Slovenia|Solomon Islands|Somalia|South Africa|South Georgia and the South Sandwich Islands|South Korea|South Sudan|Southern Ocean|Spain|Spratly Islands|Sri Lanka|State of Palestine|Sudan|Suriname|Svalbard|Swaziland|Sweden|Switzerland|Syria|Taiwan|Tajikistan|Tanzania|Tasman Sea|Thailand|Togo|Tokelau|Tonga|Trinidad and Tobago|Tromelin Island|Tunisia|Turkey|Turkmenistan|Turks and Caicos Islands|Tuvalu|USA|Uganda|Ukraine|United Arab Emirates|United Kingdom|Uruguay|Uzbekistan|Vanuatu|Venezuela|Viet Nam|Virgin Islands|Wake Island|Wallis and Futuna|West Bank|Western Sahara|Yemen|Zambia|Zimbabwe|Historical Country Names|Belgian Congo|British Guiana|Burma|Czechoslovakia|Former Yugoslav Republic of Macedonia|Korea|Netherlands Antilles|Serbia and Montenegro|Siam|USSR|Yugoslavia|Zaire)(:[a-zA-Z0-9 ]+)? help: Consult the http://www.insdc.org/country.html country list for valid options. The INSDC country qualifier is a textual controlled vocabulary used to indicate the country of origin of a DNA sample. It can also have the following format: country:sub_region, such as: "Canada:Vancouver". Damion Dooley INSDC country qualifier phenotype Phenotype: phenotypic measurements for submission to dbGaP Damion Dooley https://www.ncbi.nlm.nih.gov/books/NBK54364/ phenotype project objective genome material Damion Dooley https://www.ncbi.nlm.nih.gov/books/NBK54364/ genome material from specimen TB lineage 7 - Ethiopia An object aggregate which has as members whole organs or parts of organs, possibly from different organisms. 2021-04-19T23:36:25Z organs or organ parts A travel destination which a given human has travelled to on a particular trip and is outside Canada. 2021-05-27T04:35:17Z travel outside Canada A travel destination which a given human has travelled to on a particular trip and is outside a given province/territory of interest. 2021-05-27T04:36:13Z travel outside province/territory requires discussion A data specification established for use by The Canadian COVID-19 Genomics Network (CanCOGeN) project for SARS-CoV-2 contextual data (metadata) harmonization and curation across data providers. https://orcid.org/0000-0002-9578-0788 2021-04-24T00:18:57Z The Canadian COVID-19 Genomics Network SARS-CoV-2 specification The Canadian COVID-19 Genomics Network severe acute respiratory syndrome coronavirus 2 specification The Canadian coronavirus 2019 Genomics Network severe acute respiratory syndrome coronavirus 2 specification CanCOGeN SARS-CoV-2 specification https://github.com/cidgoh/pathogen-genomics-package An instance of a "data field category" that contains the "bioproject accession field", "biosample accession field", and "GISAID accession field". A data field category which receives a range of one or more data fields. 2022-11-23T00:33:27.896Z data field category An instance of the "database identifiers field category" that contains the "bioproject accession field". ready for release A data field category which refers to database identifier fields. database identifiers https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z database identifiers slot category database identifiers field category prov_rona_99 requires discussion An identifier data field which describes the user-defined name for the sample. sample collector sample identifier sample_collector_sample_ID specimen collector sample ID https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z sample collector sample identifier field sample collector sample identifier slot specimen collector sample ID slot Example Guidance: Every Sample ID from a single submitter must be unique. It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible. specimen collector sample ID field A livespan history item is a date-associated event pertaining to the life of a subject. Damion Dooley lifespan history item SR20-12345 requires discussion A data field which describes the primary identifer of a related specimen previously submitted to the repository. related specimen primary ID related specimen primary identifier https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z related specimen primary ID slot related specimen primary identifier field related specimen primary identifier slot Example Guidance: Store the primary ID of the related specimen previously submitted to the National Microbiology Laboratory so that the samples can be linked and tracked through the system. related specimen primary ID field prov_rona_99 requires discussion A data field which describes the identifer assigned to a sequenced isolate in Integrated Rapid Infectious Disease Analysis (IRIDA) bioinformatics platform. IRIDA sample identifier IRIDA sample name https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z IRIDA sample ID slot IRIDA sample identifier slot IRIDA sample name slot Integrated Rapid Infectious Disease Analysis sample ID field Integrated Rapid Infectious Disease Analysis sample ID slot Integrated Rapid Infectious Disease Analysis sample identifier field Integrated Rapid Infectious Disease Analysis sample identifier slot Integrated Rapid Infectious Disease Analysis sample name field Integrated Rapid Infectious Disease Analysis sample name slot Example Guidance: Store the IRIDA sample name. The IRIDA sample name will be created by the individual entering data into the IRIDA platform. IRIDA samples may be linked to metadata and sequence data, or just metadata alone. It is recommended that the IRIDA sample name be the same as, or contain, the specimen collector sample ID for better traceability. It is also recommended that the IRIDA sample name mirror the GISAID accession. IRIDA sample names cannot contain slashes. Slashes should be replaced by underscores. See IRIDA documentation for more information regarding special characters (https://irida.corefacility.ca/documentation/user/user/samples/#adding-a-new-sample). IRIDA sample name field PRJNA623807 requires discussion An identifier data field which describes the International Nucleotide Sequence Database Collaboration (INSDC) umbrella accession number of the BioProject to which the BioSample belongs. umbrella bioproject accession https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z umbrella bioproject accession slot Example Guidance: Required if submission is linked to an umbrella BioProject. An umbrella BioProject links together related BioProjects. A valid BioProject umbrella accession has prefix PRJN, PRJE or PRJD. Your laboratory can have one or many BioProjects. umbrella bioproject accession field PRJNA12345 requires discussion An identifier data field which describes the International Nucleotide Sequence Database Collaboration (INSDC) accession number of the BioProject(s) to which the BioSample belongs. bioproject accession bioproject_accession https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z bioproject accession slot Example Guidance: Required if submission is linked to a BioProject. BioProjects are an organizing tool that links together raw sequence data, assemblies, and their associated metadata. A valid BioProject accession has prefix PRJN, PRJE or PRJD, e.g., PRJNA12345 and is created once at the beginning of a new sequencing project. Your laboratory can have one or many BioProjects. bioproject accession field SAMN14180202 requires discussion A data field which describes the identifier assigned to a BioSample in International Nucleotide Sequence Database Collaboration (INSDC) archives. biosample accession biosample_accession https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z biosample accession slot Example Guidance: Store the accession returned from the BioSample submission. NCBI BioSamples will have the prefix SAMN, while ENA BioSamples will have the prefix SAMEA. biosample accession field SRR11177792 requires discussion A data field which describes the Sequence Read Archive (SRA), European Nucleotide Archive (ENA) or DDBJ Sequence Read Archive (DRA) identifier linking raw read data, methodological metadata and quality control metrics submitted to the International Nucleotide Sequence Database Collaboration (INSDC). SRA accession SRA_accession https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z SRA accession slot Sequence Read Archive accession field Sequence Read Archive accession slot DDBJ = DNA DataBank of Japan Example Guidance: Store the accession assigned to the submitted .run.. NCBI-SRA accessions start with SRR, EBI-ENA runs start with ERR and DRA accessions start with DRR. SRA accession field MN908947.3 requires discussion A data field which describes the GenBank/ENA/DDBJ identifier assigned to the sequence in the International Nucleotide Sequence Database Collaboration (INSDC) archives. GenBank accession GenBank/ENA/DDBJ accession GenBank_accession https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z GenBank accession slot GenBank/ENA/DDBJ accession field GenBank/ENA/DDBJ accession slot National Genetic Sequence Data Base accession field National Genetic Sequence Data Base accession slot GenBank = National Genetic Sequence Data Base; ENA = European Nucleotide Archive; DDBJ = DNA DataBank of Japan Example Guidance: Store the accession returned from a GenBank/ENA/DDBJ submission (viral genome assembly). GenBank accession field EPI_ISL_123456 requires discussion An identifier data field which describes the Global Initiative on Sharing Avian Influenza Data (GISAID) accession number assigned to the sequence. GISAID accession https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z GISAID accession slot Global Initiative on Sharing Avian Influenza Data accession field Global Initiative on Sharing Avian Influenza Data accession slot Example Guidance: Store the accession returned from the GISAID submission. GISAID accession field SHK123456 requires discussion A data field which describes the identifier assigned to a sample by a third party service provider. third party lab sample ID third party lab sample identifier https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z third party lab sample ID slot third party lab sample identifier field third party lab sample identifier slot Example Guidance: Store the sample identifier supplied by the third party services provider. third party lab sample ID field An instance of the "sample collection and processing field category" that contains the "sample collection date field". ready for release A data field category which refers to sample collection and processing information fields. sample collection and processing https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z sample collection and processing slot category sample collection and processing field category untreated water Public Health Agency of Canada requires discussion A data field which describes the name of the organization with which the sample collector is affiliated. sample collected by sample_collected_by https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z sample collected by slot Example Guidance: The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions. sample collected by field treated water - ambient temperature johnnyblogs@lab.ca requires discussion A data field which describes the email address of the contact responsible for follow-up regarding the sample. sample collector contact email sample_collector_contact_email https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z sample collector contact email slot Example Guidance: The email address can represent a specific individual or laboratory. sample collector contact email field 655 Lab St, Vancouver, British Columbia, V5N 2A2, Canada requires discussion A data field which describes the mailing address of the agency submitting the sample. sample collector contact address https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z sample collector contact address slot Example Guidance: The mailing address should be in the format: Street number and name, City, State/Province/Region, Country, Postal Code/Zip Code sample collector contact address field Centers for Disease Control and Prevention requires discussion A data field which describes the name of the agency that submitted the sequence to a database. Not to be confused with 'sequenced by' http://purl.obolibrary.org/obo/GENEPIO_0100416 sequence submitted by sequence_submitted_by https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z sequence submitted by slot Example Guidance: The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions. sequence submitted by field epidemiology investigation data item Unclear semantics and origin obsolete distribution event true obsolete supply point / event true RespLab@lab.ca requires discussion A data field which describes the email address of the agency responsible for submission of the sequence. Not to be confused with 'sequenced by contact email' http://purl.obolibrary.org/obo/GENEPIO_0100422 sequence submitter contact email https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z sequence submitter contact email slot Example Guidance: The email address can represent a specific individual or laboratory. sequence submitter contact email field 123 Sunnybrooke St, Toronto, Ontario, M4P 1L6, Canada requires discussion A data field which describes the mailing address of the agency responsible for submission of the sequence. Not to be confused with 'sequenced by contact address' http://purl.obolibrary.org/obo/GENEPIO_0100423 sequence submitter contact address https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z sequence submitter contact address slot Example Guidance: The mailing address should be in the format: Street number and name, City, State/Province/Region, Country, Postal Code/Zip Code sequence submitter contact address field well water - treated Well water - untreated organism datum http://purl.obolibrary.org/obo/GENEPIO_0001171 http://purl.obolibrary.org/obo/OBI_0100026 http://purl.obolibrary.org/obo/PATO_0000047 A role which inheres in an organism and is realized by the process of being alive. organism role isolate organism role 2020-03-19 requires discussion A data field which describes the date on which the sample was collected. sample collection date sample_collection_date https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z sample collection date slot Example Guidance: Record the collection date accurately in the template. Required granularity includes year, month and day. Before sharing this data, ensure this date is not considered identifiable information. If this date is considered identifiable, it is acceptable to add .jitter. to the collection date by adding or subtracting calendar days. Do not change the collection date in your original records. Alternatively, ”received date” may be used as a substitute in the data you share. The date should be provided in ISO 8601 standard format .YYYY-MM-DD.. sample collection date field animal role year requires discussion A data field which describes the precision to which the "sample collection date" was provided. sample collection date precision https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z sample collection date precision slot Used to further describe the .sample collection date field. [GENEPIO:0001174]. Example Guidance: Provide the precision of granularity to the .day., .month., or .year. for the date provided in the .sample collection date. field. The .sample collection date. will be truncated to the precision specified upon export; .day. for .YYYY-MM-DD., .month. for .YYYY-MM., or .year. for .YYYY.. sample collection date precision field 2020-03-20 requires discussion A data field which describes the date on which the sample was received. sample received date sample_received_date https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z sample received date slot Example Guidance: The date the sample was received by a lab that was not the point of collection. ISO 8601 standard .YYYY-MM-DD.. sample received date field South Africa [GAZ:00001094] requires discussion A data field which describes the country of origin of the sample. geo_loc name (country) geographical location country name https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z geo_loc name (country) slot geographical location country name field geographical location country name slot Example Guidance: Provide the country name from the pick list in the template geo_loc name (country) field plant role Damion Dooley taxonomic datum Western Cape requires discussion A data field which describes the state, province, or territory of origin of the sample. geo_loc name (state/province/territory) geographical location state or province or territory name https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z geo_loc name (state/province/territory) slot geographical location state or province or territory name field geographical location state or province or territory name slot Example Guidance: Provide the state/province/territory name from the GAZ geography ontology. Search for geography terms here: https://www.ebi.ac.uk/ols/ontologies/gaz geo_loc name (state/province/territory) field A course of treatment designed to resolve an infectious disease Damion Dooley infectious disease treatment This is a collection of drugs used to test antimicrobial resistance. This is a class of chemicals by use. They are organized more indirectly in CHEBI via 'has role' some 'antimicrobial agent'. Note: NCBI provides special requirements for antibiotic test-selection for BETA-LACTAMASE, see https://www.ncbi.nlm.nih.gov/biosample/docs/beta-lactamase/ Damion Dooley note: Used http://cts.fiehnlab.ucdavis.edu/conversion/batchConvert to convert antibiotic name to CHEBI entries. 60% match, some matches off, had to curate hits manually. Note that this is a longer list of antibiotics that we will need to incorporate, perhaps through ARO: https://www.ncbi.nlm.nih.gov/biosample/docs/antibiogram/?format=txt Damion Dooley antimicrobial resistance test drug Vancouver requires discussion A data field which describes the city of origin of the sample. geo_loc name (city) geographical location city name https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z geo_loc name (city) slot geographical location city name field geographical location city name slot Example Guidance: Provide the city name from the GAZ geography ontology. Search for geography terms here: https://www.ebi.ac.uk/ols/ontologies/gaz geo_loc name (city) field Severe acute respiratory syndrome coronavirus 2 [NCBITaxon:2697049] requires discussion A data field which describes the taxonomic name of the organism. organism https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z organism slot Example Guidance: Put the genus and species (and subspecies if applicable) of the bacteria, if known. The standardized term can be sourced from this look-up service: https://www.ebi.ac.uk/ols/ontologies/ncbitaxon. organism field Damion Dooley Judgements here are marked down after an agent's (doctor/veterenary) analysis of symptoms. analytic datum Damion Dooley http://purl.obolibrary.org/obo/DOID_4 obsolete: type of illness true A specimen which has been confirmed by laboratory test(s) to contain a disease-causing agent such as a pathogen Damion Dooley specimen with confirmed presence of disease agent Diagnostic testing [GENEPIO:0100002] requires discussion A data field which describes the reason that the sample was collected. purpose of sampling purpose_of_sampling https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z purpose of sampling slot Example Guidance: Select a value from the pick list in the template. purpose of sampling field Screening of bat specimens in museum collections. requires discussion A data field which describes additional information pertaining to the reason the sample was collected. purpose of sampling details https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z purpose of sampling details slot Example Guidance: Provide a free text description of the sampling strategy or samples collected. purpose of sampling details field Switch Health requires discussion A data field which describes the name of the third party company or laboratory that provided services. third party lab service provider name https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z third party lab service provider name slot Example Guidance: Provide the full, unabbreviated name of the company or laboratory. third party lab service provider name field swab requires discussion A data field which describes the type of specimen submitted to the National Microbiology Laboratory (NML) for testing. NML submitted specimen type National Microbiology Laboratory submitted specimen type https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z NML submitted specimen type slot National Microbiology Laboratory submitted specimen type field National Microbiology Laboratory submitted specimen type slot Example Guidance: This information is required for upload through the CNPHI LaSER system. Select the specimen type from the pick list provided. If sequence data is being submitted rather than a specimen for testing, select “Not Applicable”. NML submitted specimen type field dietary restriction A person which has a patient care role. Damion Dooley patient type obsolete: mother true Specimen sampling methods testing requires discussion A data field which describes the relationship of the current specimen to the specimen/sample previously submitted to the repository. Related specimen relationship type https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z Related specimen relationship type slot Example Guidance: Provide the tag that describes how the previous sample is related to the current sample being submitted from the pick list provided, so that the samples can be linked and tracked in the system. Related specimen relationship type field Blood [UBERON:0000178] requires discussion A data field which describes the substance obtained from an anatomical part of an organism. anatomical material anatomical_material https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z anatomical material slot Example Guidance: Provide a descriptor if an anatomical material was sampled. Use the pick list provided in the template. If a desired term is missing from the pick list, use this look-up service to identify a standardized term: https://www.ebi.ac.uk/ols/ontologies/uberon. If not applicable, leave blank. anatomical material field NCBI BioSample depth:1 lookup A subject disease outcome is an assessment of the persistence of a given disease course in a subject (patient) Damion Dooley Note that this is closely related to OGMS_0000063 "disease course" that lists chronic, progressive, transient and accute processes. subject disease outcome Nasopharynx (NP) [UBERON:0001728] requires discussion A data field which describes the anatomical part of an organism. anatomical part anatomical_part https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z anatomical part slot Example Guidance: Provide a descriptor if an anatomical part was sampled. Use the pick list provided in the template. If a desired term is missing from the pick list, use this look-up service to identify a standardized term: https://www.ebi.ac.uk/ols/ontologies/uberon. If not applicable, leave blank. anatomical part field Feces [UBERON:0001988] requires discussion A data field which describes the substance excreted/secreted from an organism. body product body_product https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z body product slot Example Guidance: Provide a descriptor if a body product was sampled. Use the pick list provided in the template. If a desired term is missing from the pick list, use this look-up service to identify a standardized term: https://www.ebi.ac.uk/ols/ontologies/uberon. If not applicable, leave blank. body product field treated water - warm/hot jacuzzi water spa water whirlpool water A host datum is a datum that pertains to infection-related information about an organism (animal or human) who is likely bearing a pathogen Damion Dooley patient as host datum Soil, water, sewage, door handle, bed handrail, face mask, etc. Example input: Face mask [OBI:0002787] requires discussion A data field which describes the substance obtained from the natural or man-made environment. environmental material environmental_material https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z environmental material slot Example Guidance: Provide a descriptor if an environmental material was sampled. Use the pick list provided in the template. If a desired term is missing from the pick list, use this look-up service to identify a standardized term: https://www.ebi.ac.uk/ols/ontologies/envo. If not applicable, leave blank. environmental material field pregnancy history item date of conception Damion Dooley lifespan history record http://purl.obolibrary.org/obo/FOODON_03450002 obsolete: food cooking method true http://purl.obolibrary.org/obo/FOODON_03470107 obsolete: food preservation method true infectious disease case datum laboratory data Hospital, wet market, bat cave, etc. Example input: Hospital [ENVO:00002173] requires discussion A data field which describes an environmental location as a site in the natural or built environment. environmental site environmental_site https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z environmental site slot Example Guidance: Provide a descriptor if an environmental site was sampled. Use the pick list provided in the template. If a desired term is missing from the pick list, use this look-up service to identify a standardized term: https://www.ebi.ac.uk/ols/ontologies/envo. If not applicable, leave blank. environmental site field Swab [GENEPIO:0100027] requires discussion A data field which describes the instrument or container used to collect the sample. collection device collection_device https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z collection device slot Example Guidance: Provide a descriptor if a collection device was used for sampling. Use the pick list provided in the template. If a desired term is missing from the pick list, use this look-up service to identify a standardized term: https://www.ebi.ac.uk/ols/ontologies/obi. If not applicable, leave blank. collection device field Damion Dooley specimen record The type of material from which the specimen was obtained. Specimens are usually categorized as food, body products or tissues, or environmental material. Damion Dooley specimen type (host or environmental context) specimen source material category Organism has a symbiotic relationship with host symbiotic role http://purl.obolibrary.org/obo/GENEPIO_0000113 obsolete: NCBI BioSample attribute package true Damion Dooley http://purl.obolibrary.org/obo/GENEPIO_0000025 http://purl.obolibrary.org/obo/GENEPIO_0000028 obsolete: host sample material true Bronchoalveolar lavage (BAL) [GENEPIO:0100032] requires discussion A data field which describes the process used to collect the sample. collection method collection_method https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z collection method slot Example Guidance: Provide a descriptor if a collection method was used for sampling. Use the pick list provided in the template. If a desired term is missing from the pick list, use this look-up service to identify a standardized term: https://www.ebi.ac.uk/ols/ontologies/obi. If not applicable, leave blank. collection method field SC2SamplingProtocol 1.2 requires discussion A data field which describes the name and version of a particular protocol used for sampling. collection protocol https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z collection protocol slot Example Guidance: Provide the name and version of the protocol used to collect the samples. collection protocol field Damion Dooley food specimen detail patient specimen environmental NCBI Biosample: environmental (swab or sampling) environmental specimen A specimen extracted from an animal Damion Dooley animal specimen built environment specimen food specimen natural environment specimen The type of person a patient had epidemiological (i.e. close proximity) contact with. Damion Dooley exposure event person Virus passage [GENEPIO:0100039] requires discussion A data field which describes any processing applied to the sample during or after receiving the sample. specimen processing https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z specimen processing slot Example Guidance: Critical for interpreting data. Select all the applicable processes from the pick list. If virus was passaged, include information in .lab host., .passage number., and .passage method. fields. If none of the processes in the pick list apply, put .not applicable.. specimen processing field Vero E6 cell line [BTO:0004755] requires discussion A data field which describes the name and description of the laboratory host used to propagate the source organism or material from which the sample was obtained. lab host https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z lab host slot Example Guidance: Type of cell line used for propagation. Select a value form the pick list. If not passaged, put .not applicable.. lab host field Damion Dooley An exposure group statistics record is a sumary of disease outbreak statistics on a certain date of a group of humans or animals potentially exposed to a pathogen. exposure group statistics record symptom history item Damion Dooley health state record http://purl.obolibrary.org/obo/NCIT_C17627 obsolete: swab true 3 requires discussion A data field which describes the number of passages. passage number https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z passage number slot Example Guidance: Provide number of known passages. If not passaged, put .not applicable. passage number field [WHICH DEFINITION?] See http://medical-dictionary.thefreedictionary.com/aspirate Damion Dooley obsolete: fluid - aspirate true AVL buffer+30%EtOH lysate received from Respiratory Lab. P3 passage in Vero-1 via bioreactor large-scale batch passage. P3 batch derived from the SP-2/reference lab strain. requires discussion A data field which describes how the organism was passaged. passage method https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z passage method slot Example Guidance: Free text. Provide a short description. If not passaged, put .not applicable.. passage method field RNA (Total) [OBI:0000895] requires discussion A data field which describes the biomaterial extracted from samples for the purpose of sequencing. biomaterial extracted https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z biomaterial extracted slot Example Guidance: Provide the biomaterial extracted from the pick list in the template. biomaterial extracted field Plant rinse is a rinse derived from plant material from one or more plants. Damion Dooley plant rinse An instance of the "host information field category" that contains the "host (scientific name) field". ready for release A data field category which refers to host information fields. host information https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z host information slot category host information field category Damion Dooley outbreak animal exposure event location Damion Dooley animal exposure process Damion Dooley animal exposure event by material Damion Dooley exposure by human contact Damion Dooley unnecessary distinction obsolete: human exposure activity type true Damion Dooley outbreak human exposure event location A process in which one or more humans may be exposed to one or more contagious human infectious disease carriers. Damion Dooley human to human exposure process water exposure by source human water activity This list would be customized to include organizations local to an application's software installation. It is an example of a set of ontology terms that would best be organized by a central authority if federated installations need to share investigator contact info for example. health authority order: HP:0000118 # symptom FLU:0000976 # onset GENEPIO:0001789 # cessation GENEPIO:0001784 # duration Damion Dooley symptom record A visual pattern caused by DNA fragments concentrated in stratefied bands in a Pulsed-field gel electrophoresis (PFGE) gel plate. PFGE pattern phage type salmonella (DT) phage type e-coli 0157 (PT) Damion Dooley sequence record A type of built structure that is suspected to be related to an outbreak investigation. Damion Dooley outbreak exposure event location http://purl.obolibrary.org/obo/ENVO_00000070 Damion Dooley lab test history record obsolete: earth surface true A data specification is a specification of a data structure that can hold a categorical, textual or numeric variable, or that has such variables or other data structures as component parts. A data standard, may be defined as a data specification, but a data specification isn't necessarily a formal or de-facto data standard - it would have to be sanctioned by a community of users and developers to take on that status. Damion Dooley data specification A specimen history item is a time-related datum about a particular specimen Damion Dooley specimen history item Human [NCBITaxon:9606] requires discussion A host field which describes the commonly used name of the host. host (common name) https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z host (common name) slot Example Guidance: Common name or scientific name are required if there was a host. Common name examples e.g. human, bat. Select a value from the pick list. If the sample was environmental, put .not applicable.. host (common name) field Homo sapiens [NCBITaxon:9606] requires discussion A host field which describes the taxonomic or scientific name of the host. host (scientific name) https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z host (scientific name) slot Example Guidance: Common name or scientific name are required if there was a host. Scientific name examples e.g. Homo sapiens. Select a value from the pick list. If the sample was environmental, put .not applicable.. host (scientific name) field Asymptomatic [NCIT:C3833] requires discussion A host field which describes the health status of the host at the time of sample collection. host health state https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z host health state slot Example Guidance: If known, select a value from the pick list. host health state field Hospitalized (ICU) [GENEPIO:0100046] requires discussion A host data field which describes additional information pertaining to the health or disease status of the host at time of collection. host health status details https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z host health status details slot Example Guidance: If known, select a value from the pick list. host health status details field Recovered [NCIT:C49498] requires discussion A host data field which describes the disease outcome in the host. host health outcome https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z host health outcome slot Example Guidance: If known, select a value from the pick list. host health outcome field COVID-19 [MONDO:0100096] requires discussion A host data field which describes the name of the disease experienced by the host. host disease host_disease https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z host disease slot Example Guidance: This field is only required if there was a host. If the host was a human select COVID-19 from the pick list. If the host was asymptomatic, this can be recorded under “host health state details”. .COVID-19. should still be provided if patient is asymptomatic. If the host is not human, and the disease state is not known or the host appears healthy, put “not applicable”. host disease field 79 requires discussion A host data field which describes the age of the host at the time of sampling. host age https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z host age slot Example Guidance: If known, provide age. Age-binning is also acceptable. host age field year [UO:0000036] requires discussion A host data field which describes the units used to measure the host's age. host age unit https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z host age unit slot Example Guidance: If known, provide the age units used to measure the host's age from the pick list. host age unit field 50 - 59 [GENEPIO:0100054] requires discussion A host data field which describes the age category of the host at the time of sampling. host age bin https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z host age bin slot Example Guidance: Age bins in 10 year intervals have been provided. If a host's age cannot be specified due to provacy concerns, an age bin can be used as an alternative. host age bin field Male [NCIT:C46109] requires discussion A host data field which describes the gender of the host at the time of sample collection. host gender https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z host gender slot Example Guidance: If known, select a value from the pick list. host gender field South Africa [GAZ:00001094] requires discussion A host geographical location field which describes the country where the host resides. host residence geo_loc name (country) https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z host residence geo_loc name (country) slot host residence geographical location country name field host residence geographical location country name slot Example Guidance: If known, select a value from the pick list. host residence geo_loc name (country) field Quebec requires discussion A host geographical location field which describes the state or province or territory of residence of the host. host residence geo_loc name (state/province/territory) https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z host residence geo_loc name (state/province/territory) slot host residence geographical location state or province or territory name field host residence geographical location state or province or territory name slot Example Guidance: Select the province/territory name from pick list provided in the template. host residence geo_loc name (state/province/territory) field BCxy123 requires discussion A host data field which describes the unique identifier by which each host can be referred to. host subject ID host subject identifier https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z host subject ID slot host subject identifier field host subject identifier slot Example Guidance: Should be a unique, user-defined identifier. This ID can help link laboratory data with epidemiological data, however, is likely sensitive information. Consult the data steward. host subject ID field 2020-03-16 requires discussion A data field which describes the date on which the symptoms began or were first noted. symptom onset date https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z symptom onset date slot Example Guidance: If known, provide the symptom onset date in ISO 8601 standard format .YYYY-MM-DD.. symptom onset date field Cough [HP:0012735], Fever [HP:0001945], Rigors (fever shakes) [HP:0025145] requires discussion A data field which describes the perceived change in function or sensation (loss, disturbance or appearance) indicative of a disease, reported by a patient. Generally, "symptoms" are subjective and reported by the patient, while "signs" are observed and reported by a clinician. However, data collected using case report forms are usually relayed by the patient and thus both are deamed "reported by a patient" in this definition. signs and symptoms https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z signs and symptoms slot Example Guidance: Select all of the symptoms experienced by the host from the pick list. signs and symptoms field Asthma [HP:0002099] requires discussion A data field which describes a medical condition that existed prior to the current infection (pre-existing condition) or a variable associated with an increased risk of disease or infection (risk factor). pre-existing conditions and risk factors https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z pre-existing conditions and risk factors slot Example Guidance: Select all of the pre-existing conditions and risk factors experienced by the host from the pick list. If the desired term is missing, contact the curation team. pre-existing conditions and risk factors field Acute respiratory failure [MONDO:0001208] requires discussion A data field which describes medical complications that are believed to have occurred as a result of host disease. complications https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z complications slot Example Guidance: Select all of the complications experienced by the host from the pick list. complications field An instance of the "host vaccination information field category" that contains the "host vaccination status field". ready for release A data field category which refers to host vaccination information fields. host vaccination information https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z host vaccination information slot category host vaccination information field category Fully Vaccinated [GENEPIO:0100100] requires discussion A data field which describes the vaccination status of the host. host vaccination status https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z host vaccination status slot Statuses associated with this field: fully vaccinated, partially vaccinated, or not vaccinated. Example Guidance: Select the vaccination status of the host from the pick list. host vaccination status field 2 requires discussion A data field which describes the number of doses of the vaccine received by the host. number of vaccine doses received https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z number of vaccine doses received slot Example Guidance: Record how many doses of the vaccine the host has received. number of vaccine doses received field An instance of the "host exposure information field category" that contains the "exposure event field". ready for release A data field category which refers to host exposure information fields. host exposure information https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z host exposure information slot category host exposure information field category South Africa [GAZ:00001094] requires discussion A geographical data field which describes the country where the host was likely exposed to the causative agent of the illness. location of exposure geo_loc name (country) https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z location of exposure geo_loc name (country) slot location of exposure geographical location country name field location of exposure geographical location country name slot Example Guidance: This location pertains to the country the host was believed to be exposed, and may not be the same as the host's country of residence. If known, provide the country name from the pick list. location of exposure geo_loc name (country) field New York City requires discussion A geographical data field which describes the name of the city that was the destination of most recent travel. destination of most recent travel (city) https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z destination city of most recent travel field destination city of most recent travel slot destination of most recent travel (city) slot Example Guidance: Provide the name of the city that the host travelled to. Use this look-up service to identify the standardized term: https://www.ebi.ac.uk/ols/ontologies/gaz destination of most recent travel (city) field California requires discussion A geographical data field which describes the name of the province that was the destination of most recent travel. destination of most recent travel (state/province/territory) https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z destination of most recent travel (state/province/territory) slot destination state or province or territory of most recent travel field destination state or province or territory of most recent travel slot Example Guidance: Provide the name of the state/province/territory that the host travelled to. Use this look-up service to identify the standardized term: https://www.ebi.ac.uk/ols/ontologies/gaz destination of most recent travel (state/province/territory) field United Kingdom [GAZ:00002637] requires discussion A geographical data field which describes the name of the country that was the destination of most recent travel. destination of most recent travel (country) https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z destination of most recent travel (country) slot Example Guidance: Provide the name of the country that the host travelled to. Use this look-up service to identify the standardized term: https://www.ebi.ac.uk/ols/ontologies/gaz destination of most recent travel (country) field 2020-03-16 requires discussion A date field which describes the date of an individual's most recent departure from their primary residence (at time of data collection) on a journey to one or more other locations. most recent travel departure date https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z most recent travel departure date slot Example Guidance: Provide the travel departure date in ISO 8601 standard format .YYYY-MM-DD.. most recent travel departure date field 2020-04-26 requires discussion A date field which describes the date of an individual's most recent return to some residence from a journey originating at that residence. most recent travel return date https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z most recent travel return date slot Example Guidance: Provide the travel return date in ISO 8601 standard format .YYYY-MM-DD.. most recent travel return date field Canada, Vancouver; USA, Seattle; Italy, Milan requires discussion A data field which describes an individuals travel history in last six months. travel history https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z travel history slot Example Guidance: Specify the countries (and more granular locations if known) travelled in the last six months; can include multiple travels. Separate multiple travel events with a semicolon. Provide as free text. travel history field Mass Gathering [GENEPIO:0100237] requires discussion A data field which describes an event leading to exposure. exposure event https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z exposure event slot Example Guidance: If known, select the exposure event from the pick list. exposure event field Direct (human-to-human contact) [TRANS:0000001] requires discussion A data field which describes the exposure transmission contact type. exposure contact level https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z exposure contact level slot Example Guidance: Select direct or indirect exposure from the pick list. exposure contact level field Patient [OMRSE:00000030] requires discussion A data field which describes the role of the host in relation to the exposure setting. host role https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z host role slot Example Guidance: Select the host's personal role(s) from the pick list provided in the template. If the desired term is missing, contact the curation team. host role field Damion Dooley diagnostic test Damion Dooley obsolete: sample datum true A laboratory sequencing datum is a datum related to the sequencing assay process applied to an isolate. Damion Dooley http://purl.obolibrary.org/obo/GENEPIO_0001681 obsolete: laboratory sequencing datum true genomic sequencing annotation datum Damion Dooley ISSUE: lab test results are appropriate to lab test types. Logic around that? lab test record sequencing assembly datum A container id is an identifier that refers to a container object about a patient specimen. Container ids are referenced in clinical patient records reported to be suspect, or lab test results. Damion Dooley container record Damion Dooley identifier of a person with the context of a health care system health care personal identifier Healthcare Setting [GENEPIO:0100201] requires discussion A data field which describes the setting leading to exposure. exposure setting https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z exposure setting slot Example Guidance: Select the host exposure setting(s) from the pick list provided in the template. If a desired term is missing, contact the curation team. exposure setting field A strain identifier is the unique microbial or eukaryotic strain name from a reference database that a sample has been matched to. Damion Dooley strain identifier A line list is a collection of suspected or known disease outbreak cases. It may also include details about healthy patients associated with an exposure event (picnic, concert etc.) who have been interviewed in order to compare food intake, assess risk factors, etc. Note that the health status of people associated with an exposure event can change from healthy or unknown status, to ill patient. Damion Dooley line list object Host role - Other: Bus Driver requires discussion A data field which describes additional host exposure information. exposure details https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z exposure details slot Example Guidance: Free text description of the exposure. exposure details field This class is a temporary holding bin for items that need a class hierarchy home, definition, and/or subclass items. Some classes have subclasses that are currently disjoint in other ontologies like ENVO, so awaiting resolution on such issues. Damion Dooley awaiting ontology review The IRIDA user ID is a user account identifier provided by the IRIDA.ca system. Damion Dooley An instance of the "host reinfection information field category" that contains the "prior infection isolate field". ready for release A data field category which refers to host reinfection information fields. host reinfection information https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z host reinfection information slot category host reinfection information field category Prior infection [GENEPIO:0100234] requires discussion A data field which describes whether there was prior Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. prior SARS-CoV-2 infection https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z prior SARS-CoV-2 infection slot Example Guidance: If known, provide infromation about whether the individual had a previous SARS-CoV-2 infection. Select a value from the pick list. prior SARS-CoV-2 infection field SARS-CoV-2/human/USA/CA-CDPH-001/2020 requires discussion A data field which describes the identifier of the isolate found in the prior Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. prior SARS-CoV-2 infection isolate https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z prior SARS-CoV-2 infection isolate ID slot prior SARS-CoV-2 infection isolate identifier field prior SARS-CoV-2 infection isolate identifier slot Example Guidance: Provide the isolate name of the most recent prior infection. Structure the .isolate. name to be ICTV/INSDC compliant in the following format: .SARS-CoV-2/host/country/sampleID/date.. prior SARS-CoV-2 infection isolate ID field 2021-01-23 requires discussion A data field which describes the date of diagnosis of the prior Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. prior SARS-CoV-2 infection date https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z prior SARS-CoV-2 infection date slot Example Guidance: Provide the date that the most recent prior infection was diagnosed. Provide the prior SARS-CoV-2 infection date in ISO 8601 standard format .YYYY-MM-DD.. prior SARS-CoV-2 infection date field Prior antiviral treatment [GENEPIO:0100037] requires discussion A data field which describes whether there was prior Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) treatment with an antiviral agent. prior SARS-CoV-2 antiviral treatment https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z prior SARS-CoV-2 antiviral treatment slot Example Guidance: If known, provide infromation about whether the individual had a previous SARS-CoV-2 antiviral treatment. Select a value from the pick list. prior SARS-CoV-2 antiviral treatment field Remdesivir requires discussion A data field which describes the name of the antiviral treatment agent administered during the prior Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. prior SARS-CoV-2 antiviral treatment agent https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z prior SARS-CoV-2 antiviral treatment agent slot Example Guidance: Provide the name of the antiviral treatment agent administered during the most recent prior infection. If no treatment was administered, put .No treatment.. If multiple antiviral agents were administered, list them all separated by commas. prior SARS-CoV-2 antiviral treatment agent field 2021-01-28 requires discussion A data field which describeds the date treatment was first administered during the prior Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. prior SARS-CoV-2 antiviral treatment date https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z prior SARS-CoV-2 antiviral treatment date slot Example Guidance: Provide the date that the antiviral treatment agent was first administered during the most recenrt prior infection. Provide the prior SARS-CoV-2 treatment date in ISO 8601 standard format .YYYY-MM-DD.. prior SARS-CoV-2 antiviral treatment date field An instance of the "sequencing field category" that contains the "sequencing date field". ready for release A data field category which refers to sequencing information fields. sequencing, sequencing information https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z sequencing information slot category sequencing slot category sequencing field category The count of healthy individuals or animals on a certain date/time from a group that was likely exposed to a pathogen Damion Dooley exposure group healthy count The count of ill individuals or animals on a certain date/time from a group that was likely exposed to a pathogen Damion Dooley exposure group ill count human general activity Baseline surveillance (random sampling) [GENEPIO:0100005] requires discussion A data field which describes the reason that the sample was sequenced. purpose of sequencing purpose_of_sequencing https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z purpose of sequencing slot Example Guidance: The reason why a sample was originally collected may differ from the reason why it was selected for sequencing. The reason a sample was sequenced may provide information about potential biases in sequencing strategy. Provide the purpose of sequencing from the picklist in the template. The reason for sample collection should be indicated in the .purpose of sampling. field. purpose of sequencing field Screened for S gene target failure (S dropout) requires discussion A data field which describes the description of why the sample was sequenced providing specific details. purpose of sequencing details https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z purpose of sequencing details slot Example Guidance: Provide an expanded description of why the sample was sequenced using pick list. The description may include the importance of the sequences for a particular public health investigation/surveillance activity/research question. Suggested standardized descriptions include: Screened for S gene target failure (S dropout), Screened for mink variants, Screened for B.1.1.7 variant, Screened for B.1.135 variant, Screened for P.1 variant, Screened due to travel history, Screened due to close contact with infected individual, Assessing public health control measures, Determining early introductions and spread, Investigating airline-related exposures, Investigating temporary foreign worker, Investigating remote regions, Investigating health care workers, Investigating schools/universities, Investigating reinfection. purpose of sequencing details field 2021-04-26 requires discussion A date field which describes the date the sample was sequenced. sequencing date https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z sequencing date slot Example Guidance: Provide the sequencing date in ISO 8601 standard format .YYYY-MM-DD.. sequencing date field XYZ_123345 requires discussion A data field which describes user-specified identifier for the library prepared for sequencing. library ID library identifier library_ID https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z library ID slot library identifier field library identifier slot Example Guidance: The library name should be unique, and can be an autogenerated ID from your LIMS, or modification of the isolate ID. library ID field 300bp requires discussion A data field which describes the length of the amplicon generated by polymerase chain reaction (PCR) amplification. amplicon size https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z amplicon size slot Example Guidance: Provide the amplicon size, including the units. amplicon size field Nextera XT requires discussion A data field which describes the name of the library preparation kit used to generate the library being sequenced. Some specification definitions may be more specific on the type of library preparation kit used (e.g. DNA). library preparation kit library_preparation_kit https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z library preparation kit slot Example Guidance: Provide the name of the library preparation kit used. library preparation kit field FAB06069 requires discussion A data field which describes the barcode of the flow cell used for sequencing. flow cell barcode https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z flow cell barcode slot Example Guidance: Provide the barcode of the flow cell used for sequencing the sample. flow cell barcode field Oxford Nanopore MinION [GENEPIO:0100142] requires discussion A data field which describes the model of the sequencing instrument used. sequencing instrument sequencing_instrument https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z sequencing instrument slot Example Guidance: Select the sequencing instrument from the pick list. sequencing instrument field 1D_DNA_MinION, ARTIC Network Protocol V3 requires discussion A data field which describes the name and version number of the sequencing protocol used. sequencing protocol name https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z sequencing protocol name slot Example Guidance: Provide the name and version of the sequencing protocol. sequencing protocol name field Genomes were generated through amplicon sequencing of 1200 bp amplicons with Freed schema primers. Libraries were created using Illumina DNA Prep kits, and sequence data was produced using Miseq Micro v2 (500 cycles) sequencing kits. requires discussion A data field which describes the protocol used to generate the sequence. sequencing protocol sequencing_protocol https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z sequencing protocol slot Example Guidance: Provide a free text description of the methods and materials used to generate the sequence. Suggested text, fill in information where indicated.: .Viral sequencing was performed following a tiling amplicon strategy using the <fill in> primer scheme. Sequencing was performed using a <fill in> sequencing instrument. Libraries were prepared using <fill in> library kit. . sequencing protocol field AB456XYZ789 requires discussion A data field which describes the manufacturer's kit number. sequencing kit number https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z sequencing kit number slot Example Guidance: Alphanumeric value. sequencing kit number field https://github.com/joshquick/artic-ncov2019/blob/master/primer_schemes/nCoV-2019/V3/nCoV-2019.tsv requires discussion A data field which describes the specifications of the primers (primer sequences, binding positions, fragment size generated, etc.) used to generate the amplicons to be sequenced. amplicon pcr primer scheme https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z amplicon pcr primer scheme slot amplicon polymerase chain reaction primer scheme field amplicon polymerase chain reaction primer scheme slot Example Guidance: Provide the name and version of the primer scheme used to generate the amplicons for sequencing. amplicon pcr primer scheme field An instance of the "bioinformatics and QC metrics field category" that contains the "dehosting method field". ready for release A data field category which refers to bioinformatics and quality control (QC) metrics fields. bioinformatics and QC metrics https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z bioinformatics and QC metrics slot category bioinformatics and Quality Control metrics field category bioinformatics and Quality Control metrics slot category bioinformatics and QC metrics field category Porechop 0.2.3 requires discussion A data field which describes the method used for raw data processing such as removing barcodes, adapter trimming, filtering etc. raw sequence data processing method https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z raw sequence data processing method slot Example Guidance: Provide the name and version numbers of the software used to process the raw data. raw sequence data processing method field Nanostripper 1.2.3 requires discussion A data field which describes the method used to remove host reads from the pathogen sequence. dehosting method https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z dehosting method slot Example Guidance: Provide the name and version number of the software used to remove host reads. dehosting method field ncov123assembly3 requires discussion A data field which describes the name of the consensus sequence. consensus sequence name https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z consensus sequence name slot Example Guidance: Provide the name and version number of the consensus sequence. consensus sequence name field pathogenassembly123.fasta requires discussion A data field which describes the user-defined filename of the FASTA file. assembly filename consensus sequence filename https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z consensus sequence filename slot Example Guidance: Provide the name and version number of the consensus sequence FASTA file. consensus sequence filename field /User/Documents/RespLab/Data/ncov123assembly.fasta requires discussion A data field which describes the filepath of the consensus sequence file. consensus sequence filepath https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z consensus sequence filepath slot Example Guidance: Provide the filepath of the consensus sequence FASTA file. consensus sequence filepath field Ivar requires discussion A data field which describes the name of the software used to generate the consensus sequence. consensus sequence software name https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z consensus sequence software name slot Example Guidance: Provide the name of the software used to generate the consensus sequence. consensus sequence software name field Damion Dooley An exposure can be narrowed down to a single date, or can be reasoned to exist with a lower and/or upper bound date. A single date exposure has lower and upper bound dates set as the same value. exposure history record Damion Dooley isolate history record Damion Dooley An outbreak date may have an official start, but because it might be ongoing, it may not have an end (yet). outbreak history record Damion Dooley Needs to cover the various pregnancy events pregnancy history record Damion Dooley Issue: a diagnosis is a set of diseases, each of which can be marked primary or secondary "Illness causality" with respect to a particular case? Requires a relation annotation. diagnosis record 1.3 requires discussion A data field which describes the version of the software used to generate the consensus sequence. consensus sequence software version https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z consensus sequence software version slot Example Guidance: Provide the version of the software used to generate the consensus sequence. consensus sequence software version field Damion Dooley exposure event record Damion Dooley hospitalization event record 95% requires discussion A data field which describes the percentage of the reference genome covered by the sequenced data, to a prescribed depth. breadth of coverage value https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z breadth of coverage value slot Example Guidance: Provide value as a percent. breadth of coverage value field An exposure can be narrowed down to a single date, or can be reasoned to exist with a lower and/or upper bound date. A single date exposure has lower and upper bound dates set as the same value. exposure history item 400x requires discussion A data field which describes the average number of reads representing a given nucleotide in the reconstructed sequence. depth of coverage value https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z depth of coverage value slot Example Guidance: Provide value as a fold of coverage. depth of coverage value field 100x requires discussion A data field which describes the threshold used as a cut-off for the depth of coverage. depth of coverage threshold https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z depth of coverage threshold slot Example Guidance: Provide the threshold fold coverage. depth of coverage threshold field ABC123_S1_L001_R1_001.fastq.gz requires discussion A data field which describes the user-specified filename of the read 1 (r1) FASTQ file. r1 fastq filename r1_fastq_filename https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z r1 fastq filename slot Example Guidance: Provide the r1 FASTQ filename. r1 fastq filename field ABC123_S1_L001_R2_001.fastq.gz requires discussion A data field which describes the user-specified filename of the read 2 (r2) FASTQ file. r2 fastq filename r2_fastq_filename https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z r2 fastq filename slot Example Guidance: Provide the r2 FASTQ filename. r2 fastq filename field /User/Documents/RespLab/Data/ABC123_S1_L001_R1_001.fastq.gz requires discussion A data field which describes the filepath of the read 1 (r1) FASTQ file. r1 fastq filepath https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z r1 fastq filepath slot Example Guidance: Provide the filepath of the r1 FASTQ file. r1 fastq filepath field /User/Documents/RespLab/Data/ABC123_S1_L001_R2_001.fastq.gz requires discussion A data field which describes the filepath of the read 2 (r2) FASTQ file. r2 fastq filepath https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z r2 fastq filepath slot Example Guidance: Provide the filepath of the r2 FASTQ file. r2 fastq filepath field batch1a_sequences.fast5 requires discussion A data field which describes the user-specified filename of the FAST5 file. fast5 filename fast5_filename https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z fast5 filename slot Example Guidance: Provide the FAST5 filename. fast5 filename field /User/Documents/RespLab/Data/batch1a_sequences.fast5 requires discussion A data field which describes the filepath of the FAST5 file. fast5 filepath https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z fast5 filepath slot Example Guidance: Provide the filepath of the FAST5 file. fast5 filepath field 387566 requires discussion A data field which describes the number of total base pairs generated by the sequencing process. number of base pairs sequenced https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z number of base pairs sequenced slot Example Guidance: Provide a numerical value (no need to include units). number of base pairs sequenced field 38677 requires discussion A data field which describes the file size of the assembled genome described as the number of base pairs. consensus genome length https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z consensus genome length slot Example Guidance: Provide a numerical value (no need to include units). consensus genome length field 300 requires discussion A data field which describes the number of N (unidentified nucleotide) symbols present in the consensus fasta sequence, per 100kbp of sequence. Ns per 100 kbp Ns per 100 kilobase pairs https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z Ns per 100 kbp slot Ns per 100 kilobase pairs field Ns per 100 kilobase pairs slot unidentified nucleotides per 100 kbp field unidentified nucleotides per 100 kbp slot Example Guidance: Provide a numerical value (no need to include units). Ns per 100 kbp field NC_045512.2 requires discussion A data field which describes the persistent, unique identifier of a genome database entry. reference genome accession https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z reference genome accession slot Example Guidance: Provide the accession number of the reference genome. reference genome accession field hospital admission date A date-time datum that marks the end of possible human or animal exposure to a pathogen agent, directly or indirectly. Damion Dooley exposure event end A date-time datum that marks the start of a human or animal exposure event to a suspected pathogen agent, directly or indirectly. Damion Dooley This datum is NOT predicted as a function of pathogen and first symptom date. exposure event start https://www.protocols.io/groups/cphln-sarscov2-sequencing-consortium/members requires discussion A data field which describes the name and version number of the bioinformatics protocol used. bioinformatics protocol https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z bioinformatics protocol slot Example Guidance: Further details regarding the methods used to process raw data, and/or generate assemblies, and/or generate consensus sequences can be provided in an SOP or protocol. Provide the name and version number of the protocol, or a link if deposited in a protocol repository. bioinformatics protocol field hospitalization history item isolate history item An outbreak date may have an official start, but because it might be ongoing, it may not have an end (yet). outbreak history item hospital discharge date A notification date is the date that an outbreak is suspected by a laboratory or other agency and is reported per outbreak detection guidelines. Damion Dooley notification date An outbreak date is on which disease onset appears to have occured Damion Dooley outbreak date An outbreak over date is the date on which a disease outbreak appears to have abated Damion Dooley outbreak over test history item An instance of the "lineage and variant information field category" that contains the "lineage/clade name field". ready for release A data field category which refers to lineage and variant information fields. lineage and variant information https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z lineage and variant information slot category lineage and variant information field category lab test result date B.1.1.7 requires discussion A data field which describes the name of the lineage or clade. lineage/clade name https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z lineage or clade name field lineage or clade name slot lineage/clade name slot Example Guidance: Provide the Pangolin or Nextstrain lineage/clade name. lineage/clade name field Pangolin requires discussion A data field which describe the name of the software used to determine the lineage/clade. lineage/clade analysis software name https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z lineage or clade analysis software name field lineage or clade analysis software name slot lineage/clade analysis software name slot Example Guidance: Provide the name of the software used to determine the lineage/clade. lineage/clade analysis software name field 2.1.10 requires discussion A data field which describes the version of the software used to determine the lineage/clade. lineage/clade analysis software version https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z lineage or clade analysis software version field lineage or clade analysis software version slot lineage/clade analysis software version slot Example Guidance: Provide the version of the software used ot determine the lineage/clade. lineage/clade analysis software version field Variant of Concern (VOC) [GENEPIO:0100083] requires discussion A data field which describes the variant classification of the lineage/clade. variant designation https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z variant designation slot Example Guidance: If the lineage/clade is considered a Variant of Concern, select Variant of Concern from the pick list. If the lineage/clade contains mutations of concern (mutations that increase transmission, clincal severity, or other epidemiological fa ctors) but it not a global Variant of Concern, select Variant. If the lineage/clade does not contain mutations of concern, leave blank. variant designation field RT-qPCR RT-qPCR TaqPath assay: S gene target failure requires discussion A data field which describes the evidence used to make the variant determination. variant evidence variant evidence details https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z variant evidence details slot variant evidence slot Example Guidance: List the set of lineage-defining mutations used to make the variant determination. If there are mutations of interest/concern observed in addition to lineage-defining mutations, describe those here. Example Guidance: Select whether the sample was screened using RT-qPCR or by sequencing from the pick list. variant evidence details field variant evidence field An instance of the "pathogen diagnostic testing field category" that contains the "diagnostic pcr protocol field". ready for release A data field category which refers to pathogen diagnostic testing information fields. pathogen diagnostic testing https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z pathogen diagnostic testing slot category pathogen diagnostic testing field category An instance of the "contributor acknowledgement field category" that contains the "authors field". ready for release A data field category which refers to contributor acknowledgement information fields. contributor acknowledgement https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z contributor acknowledgement slot category contributor acknowledgement field category Tejinder Singh, Fei Hu, Johnny Blogs requires discussion A data field which describes the names of individuals contributing to the processes of sample collection, sequence generation, analysis, and data submission. authors https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-12-22T00:55:53.808Z data authors slot data contributors fields data contributors slot Example Guidance: Include the first and last names of all individuals that should be attributed, separated by a comma. data authors field DataHarmonizer v1.4.3, PHA4GE v1.0.0 requires discussion A data field which describes the DataHarmonizer software and template version provenance. DataHarmonizer provenance https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-12-22T00:55:53.808Z DataHarmonizer provenance slot Example Guidance: The current software and template version information will be automatically generated in this field after the user utilizes the .validate. function. This information will be generated regardless as to whether the row is valid of not. DataHarmonizer provenance field A data item that is a set of entities, referenced by mention, that don't necessarily have something in common. 0000-0002-8844-9165 0000-0002-9578-0788 2022-01-31T03:45:04Z While "enumeration" is a "data item" not everything referenced within an enumeration qualifies as a "data item". Not to be confused with "data set" which describes "data item"s of the same type that have something in common. data enumeration An analytic datum which describes the observed or detectable signs, and experienced symptomps of an illness, injury, or condition. 0000-0002-9578-0788 https://en.wikipedia.org/wiki/Signs_and_symptoms 2022-01-31T23:08:50Z signs & symptoms signs and symptoms A particular attribute (feature, quality or process history) of a food sample. Damion Dooley The underlying facets will be supplied from the FoodOn food ontology. food specimen datum order: FOODON:03411564 # food source FOODON:00002381 # food product by organism FOODON:03311737 # processed food product NCIT:C71898 # brand name A food specimen type is a categorization of a food specimen, by the organism it is or came from, or by a class of food products. Damion Dooley food specimen specification An agency that has reported a disease cluster. Damion Dooley disease cluster notification agency This is a subset of OBI investigation identifier. It pertains only to NCBI Biosample projects Damion Dooley http://purl.obolibrary.org/obo/OBI_0001628 obsolete: NCBI BioProject ID true The count of individuals or animals for which no health status is available on a certain date/time from a group that was likely exposed to a pathogen. Damion Dooley exposure group unknown health status count A role which inheres in a person and is realized by the process of being in the context of civilization Damion Dooley person role An exposed person role is the role a person takes on who has been exposed to a pathogen. In serious situations this may call for special treatment, e.g. quarantine. Damion Dooley exposed person role Redundant with "term replaced by" entity. obsolete: parent-guardian role parent-guardian role true Damion Dooley illness causality pre-existing condition To restore to the normal state after some pathologic process. Damion Dooley Dorland's Illustrated Medical Dictionary, 30th ed. improving recovering resolving health trend Damion Dooley close interpersonal relationship exposure Damion Dooley Found to be redudant with another term, deprecrated in favor of said term. obsolete: household exposure true Damion Dooley exposure to individual with diarrhea Damion Dooley other human exposure Damion Dooley sexual contact exposure Damion Dooley exposure via diaper changing (human fecal) container identifier PulseNet: Outbreak outbreak identifier reference genome size The assembly genome size is the sum of all lengths of a sequence assembly's contigs. Damion Dooley As noted in Quast documentation: " The total assembly size may increase (and in some cases exceeds the genome size) due to contaminants (see Chitsaz et al. (2011)), misassembled contigs, repeats, and hubs that contribute to multiple contigs. " assembly genome size Identifier for a reference genome (used to build or compare an assembly) that is used in the genome browsers and in the community Damion Dooley reference genome identifier Assembly QC The 'genome size delta ratio' is a ratio of the difference between a sample's genome assembly size and the size of a given reference genome, over the reference genome size. The formula: | (reference_genome_size - assembly_genome_size) | / reference_genome_size This yeilds a decimal / percentage ranging from 0 = exact length, to say .1 which is equivalent to a 10% variance. If the ratio is too far from a quality control ratio that depends on the species in question, this indicates a bad assembly or a mis-identified sample. Damion Dooley genome size delta ratio Assembly QC This is the upper acceptable limit of the 'genome size delta ratio' with respect to a particular species. For Salmonella a 0.10 variance in length between an assembly size and a reference genome size may be acceptable. For E-coli a more generous 0.30 or .40 variance should be allowed, given the pathogenic subspecies’ highly dynamic genome. genome size delta ratio QC threshold Assembly QC http://purl.obolibrary.org/obo/IAO_0000428 The contig N50 length QC threshold is a minimum length threshold that a contig N50 length datum should be above for good QC. A lower length is indicative of assembly problems (insufficient read depth) or a mismatched reference genome. Damion Dooley contig N50 length QC threshold Assembly QC 2000 The contig N99 length QC threshold is the minimum length that a contig N99 or NG99 length datum can be for satisfactory QC. This threshold avoids having too many gene coding regions prematurely clipped inside short contigs. An assembly having 1% or more of its content in less than 2Kbp chunks is cause for concern. Bacterial genes are generally about 1Kbp in length. Damion Dooley contig N99 length QC threshold lookup Homo sapiens The species of the host organism from which a specimen (pathogen) organism was obtained. Use the full taxonomic name, eg, "Homo sapiens". Damion Dooley subject organism (host) taxonomic species lookup Assembly QC A single datum having to do with a metric for genomic sequence assembly quality control. A "quality control measurement" can be defined as a measurement that has some norm within a definable context, e.g. for a certain subspecies. It may be a calculated quantity. A "quality control metric" is an upper or lower bound threshold that a measurement is compared to. Surpassing the threshold may indicate an error situation. A "measure" can indicate an amount of activity, consumption, transformation, etc. but doesn't itself convey an over-stepping of bounds in the way that a metric does. Damion Dooley assembly quality control datum Damion Dooley GSCID-BRC:Clinical/host-associated pathogen NCBI:Pathogen.cl clinical or host-associated pathogen Clinical/host-associated pathogen Pathogen.cl Assembly QC http://purl.obolibrary.org/obo/IAO_0000428 The N99 length definition is identical to the N50 definition except that the threshold for determining the contigs is 1% of the nucleotides. This contig basepair length can be compared to a minimum threshold to determine if gene annotation (where contigs greater than say 2000bp are necessary) would generally succeed. Damion Dooley contig N99 Assembly QC http://purl.obolibrary.org/obo/IAO_0000428 The upper threshold of contig counts that are acceptable in a genome assembly. This may vary based on the overall genome length and depth of coverage. A large contig count may indicate insufficient read coverage. Damion Dooley contig count QC threshold Indicates how the knowledge derived from the project can be applied, and to what field(s). Damion Dooley's note: NAIAD GRCID-BRC has Project Relevance map to OBO Foundry Study Design (http://purl.obolibrary.org/obo/OBI_0500000) but this is a bit of a stretch. Damion Dooley https://www.niaid.nih.gov/research/dmid-metadata-standards-core-project project relevance agricultural project relevance medical knowledge relevance industrial processing relevance evolution modelling relevance environmental project relevance model organism relevance The NCBI BioProject model includes all datums associated with the current NCBI BioProject specification. Damion Dooley obsolete: NCBI BioProject model true http://purl.obolibrary.org/obo/GENEPIO_0000147 obsolete: NCBI SRA model true http://www.ncbi.nlm.nih.gov/biosample/docs/attributes/ http://www.ncbi.nlm.nih.gov/biosample/docs/packages/Pathogen.cl.1.0/ Damion Dooley notes: NCBI doesn't quite make the distinction but it may be helpful to distinguish sample submission facilitator vs submitter/repository organization contact? So should we have a BioSample_submission_facilitator field and a BioSample_contact_information field? Damion Dooley Damion's note: There are a few different kinds of biosample, and required fields depend on the type selected. draft NCBI BioSample model - mixed clinical and environmental/food/other monoisolate A monoisolate sample scope involves specimens from a single animal, cultured cell-line, inbred population, or possibly a heterogeneous population when a single genome assembly is generated from a pooled sample because multiple individuals are needed to collect enough material and an inbred line is not available; however, this situation is not preferred. Damion Dooley https://www.ncbi.nlm.nih.gov/books/NBK54364/ monoisolate monoisolate sample scope multiisolate A multiisolate sample scope contains multiple individuals that represent distinct specimen collections, a population (representative of a species). Damion Dooley https://www.ncbi.nlm.nih.gov/books/NBK54364/ This is often used for variation or phenotype and genotype studies. This should not be used when multiple genomes will be annotated. Eventually, multiple locus_tag prefixes will be able to be assigned to a single multiisolate genome sequencing project, but currently only a single prefix can be registered per project. Therefore, individual monoisolate projects need to be registered when more than one genome will be annotated. multiisolate sample scope multispecies A multi-species sample scope involves a sample representing multiple species. Damion Dooley https://www.ncbi.nlm.nih.gov/books/NBK54364/ multispecies sample scope environment An environment sample scope indicates that the species content of the sample is not known. Generally, nucleic acid is directly isolated from an environmental sample for analysis. This is used for metagenome studies. Damion Dooley https://www.ncbi.nlm.nih.gov/books/NBK54364/ environment sample scope A synthetic sample scope involves a sample synthesized in a laboratory. Damion Dooley https://www.ncbi.nlm.nih.gov/books/NBK54364/ synthetic sample scope Damion Dooley single cell other Other project objective: specify an objective not listed above Damion Dooley https://www.ncbi.nlm.nih.gov/books/NBK54364/ other project objective Damion Dooley GSCID-BRC:environmental/food/other NCBI:Pathogen.env environmental, food or other pathogen environmental/food/other Pathogen.env whole Whole: the project makes use of the whole sample material (most common case). Use this for whole genome sequencing studies, transcriptome studies that are not targeting specific loci, epigenetic studies of a genome, and metagenomes or unbiased transcriptome studies of metagenomes. Damion Dooley https://www.ncbi.nlm.nih.gov/books/NBK54364/ whole genomic data capture raw sequence reads A raw sequence reads project objective has the goal of submission of raw reads to SRA or Trace repositories Damion Dooley https://www.ncbi.nlm.nih.gov/books/NBK54364/ raw sequence read objective sequence A sequence project objective has a goal of submission of sequence data to standard archival sequence databases (yielding accession.version identifiers; e.g., whole genome shotgun, cDNA sequences, transcript shotgun assemblies) Damion Dooley https://www.ncbi.nlm.nih.gov/books/NBK54364/ sequence project objective analysis An "analysis project objective" indicates there was an other analysis not otherwise indicated, includes submission of BAM files. This defn. could be a negation of the "not otherwise indicated". Damion Dooley https://www.ncbi.nlm.nih.gov/books/NBK54364/ analysis objective assembly Submission of genome assembly (AGP data) Damion Dooley https://www.ncbi.nlm.nih.gov/books/NBK54364/ assembly objective annotation Sequence annotation data Damion Dooley https://www.ncbi.nlm.nih.gov/books/NBK54364/ sequence annotation objective sequence variation Variation: identification of sequence variation data for submission to dbSNP or dbVAR Damion Dooley https://www.ncbi.nlm.nih.gov/books/NBK54364/ sequence variation project objective epigenetic markers DNA methylation, histone modification, chromatin accessibility datasets Damion Dooley https://www.ncbi.nlm.nih.gov/books/NBK54364/ epigenetic markers objective expression Expression: assays of transcript or protein existence or abundance Damion Dooley https://www.ncbi.nlm.nih.gov/books/NBK54364/ transcript or protein expression objective maps Maps: non-sequence based map data; e.g., genetic, radiation hybrid, cytogenetic, etc. Damion Dooley https://www.ncbi.nlm.nih.gov/books/NBK54364/ mapping objective Phenotypic descriptive data. Damion Dooley https://www.ncbi.nlm.nih.gov/books/NBK54364/ phenotypic observation data from specimen select sequence if any sequence data is generated from this project. sequencing Damion Dooley https://www.ncbi.nlm.nih.gov/books/NBK54364/ sequencing project method array Select Array if that is the primary method and no sequence data is submitted Damion Dooley https://www.ncbi.nlm.nih.gov/books/NBK54364/ array project method mass spectrometry Select Mass Spectrometry if that is the primary method Damion Dooley https://www.ncbi.nlm.nih.gov/books/NBK54364/ mass spectrometry project method order: NCIT:C40974 # first name NCIT:C40975 # last name NCIT:C42775 # email address GENEPIO:0001756 # phone contact specification - person A categorical investigation datum is a datum pertaining to some entity examined for scientific research or diagnostic purposes and which has a scope that is broader than one of the clinical, environmental or epidemiological domains. Damion Dooley investigation datum An organism and its host share physical space but no evidence exists to determine if one benefits from this arrangement. commensal role draft isolate details model An age measurement datum which is the age since birth of a given organism that is involved in an investigation or study at a given time. Damion Dooley subject age draft NCBI component model draft IRIDA BioSample model draft GenEpiO epidemiology case record A subject description is a field containing additional information about an organism (related to an investigation, study and/or specimen) that is not included in other defined vocabulary fields. Damion Dooley http://purl.obolibrary.org/obo/GENEPIO_0001835 subject description host description NCBI BioSample The host profile or identifiers text is the "identification or description of the specific individual from which this sample was obtained". Damion Dooley NCBI BioSample: isolate host profile or identifers A subject identifier is an identifier of a subject organism within the context of a particular investigation, study, or specimen extraction event. Damion Dooley This varies in its type (numeric or string) and its central repository depending on its context (use in a particular application/instance). Note: GSCID-BRC specification states " 'Host' is not the preferred term since some specimens may lack any detectable pathogen". In other words, a person would technically (logically) only have a host identifier AFTER they have been diagnosed as having a pathogen. A health care personal identifier, or a case identifier would be better than a more ephemeral "host id" subject identifier A name of disease in a subject that is related to a given investigation, study and/or specimen. Damion Dooley NIAID GSCID-BRC metadata working group Controlled vocabulary. Human specimen source: https://bioportal.bioontology.org/ontologies/DOID or https://www.ncbi.nlm.nih.gov/mesh/1000067 subject disease INSDC term (top level) A categorical choice recorded when a measurement value was known to be recorded in the past but the observed value cannot be located or retrieved for some reason. NCBI Biosample: missing missing INSDC term (top level) 'not applicable' is an appropriate value for the measure of femur length for a patient with a missing limb A categorical choice recorded when a measurable datum does not apply to a given context. Damion Dooley not applicable INSDC term (lower level) A categorical choice recorded when a datum was not measured with respect to some entity during some process. NCBI Biosample: not collected not collected draft isolate identifier model draft GenEpiO isolate testing model draft NCBI isolate source location model draft GenEpiO isolate environment model A subject disease stage is a measure of the acuteness of a subject organism's diagnosed disease, if any, at a given time in an investigation, study or specimen extraction event. Damion Dooley http://purl.obolibrary.org/obo/GENEPIO_0001835 subject disease stage environmental datum temperature of sample de-novo assembly http://purl.obolibrary.org/obo/GENEPIO_0000025 obsolete: sample body source true contig pre-analysis minimum length QC threshold A 'contig length QC threshold' is an integer setting which can be applied by an algorithm to an array of assembly and annotation contig lengths to remove (filter out) all items less than the threshold value. The reduced array is used for calculation of statistics. Damion Dooley http://quast.bioinf.spbau.ru/manual.html QUAST specifies which of its report stats are affected by the "--min-contig" minimum contig length parameter. contig length QC threshold The NG50 length is the same as the N50 length except that the length of the reference genome is used in the calculation rather than the assembly genome size. Damion Dooley "Note that N50 is calculated in the context of the assembly size rather than the genome size. Therefore, comparisons of N50 values derived from assemblies of significantly different lengths are usually not informative, even if for the same genome. To address this, the authors of the Assemblathon competition derived a new measure called NG50. The NG50 statistic is the same as N50 except that it is 50% of the known or estimated genome size that must be of the NG50 length or longer. This allows for meaningful comparisons between different assemblies. In the typical case that the assembly size is not more than the genome size, the NG50 statistic will not be more than the N50 statistic." - wikipedia contig NG50 A contig length is the count of base pairs in a given sequence assembly contig. Damion Dooley contig length Assembly QC http://purl.obolibrary.org/obo/IAO_0000428 An assembly quality control datum which is defined as number of contigs equal to or longer than the contig N50, when the assembly itself is factored into the calculation. Damion Dooley QUAST manual contig L50 Assembly QC http://purl.obolibrary.org/obo/IAO_0000428 The LG99 count is like the L99 count except that the length of the reference genome is used in the calculation rather than the sum of assembly contig lengths. Damion Dooley contig LG99 An organism isolate datum is any datum pertaining to an isolate organism Damion Dooley obsolete: specimen from subject datum true A product of an animal, as in blood, feces, sputum, etc. that has no particular anatomical site Damion Dooley animal body product This is the scientific role or category that the subject organism or material has with respect to an investigation. Damion Dooley http://purl.obolibrary.org/obo/GENEPIO_0001237 obsolete: specimen source material category true draft GenEpiO general information record An antigenic formula is a string composed of codes representing categorized results of tests performed on various viral, bacterial or immune cell surface antigens. Damion Dooley antigenic formula http://medical-dictionary.thefreedictionary.com/antigen lookup This is the taxonomic species descriptor of a specimen isolate (an organism found within a specimen.) Damion Dooley specimen organism taxonomy (species) An identifier moe3l indicates an identifier, the organization it has been issued by, and the status of the identifier - whether it is a primary one, active or archaic. Damion Dooley identifier model help:This should be populated with a selection from INSDC.org controlled vocabulary for providers: ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/coll_dump.txt The curator organization name is the name of an organization that manages a given repository of entities (samples, isolates, sequences ...) Damion Dooley curator organization name INSDC:institution_code:BRS IRIDA:ACK Agriculture and Agri-Food Canada An isolate identifier is an identifier assigned to a given isolate by a particular agency that is handling or storing it. Damion Dooley isolate identifier An identifier status describes the principle role of an identifier assigned to an entity by its curator or handler. An entity may have a number of identifiers assigned to it over time. An identifier may be phased-out as can happen when its content is transferred to another curator. Damion Dooley identifier status A data protection role is a role (or user permission) that a user has with respect to particular data. A data server may be able to provide a protected(modified) dataset with metadata indicating what parts have a protection role with respect to the user requesting this information. A data protection role would be inherited from a user's relation to an entitiy to the entity's components or subclasses. Damion Dooley data protection role An identifier used in the initial submission of content to a repository. original submission This was created to help define a contributing organization to a repository. However this still needs organizing. The "collected_by" field is free text but contact name AND organization could be associated with this in controlled vocabulary. NCBI Contributing organization / project food - liquid draft NCBI BioSample identifier model An INSDC institution code is an identifier of an organization from a list of sequence repository organizations managed by INSDC. Damion Dooley http://www.insdc.org/controlled-vocabulary-culturecollection-qualifier INSDC institution code draft IRIDA epidemiological case model An identifier that had been used previously but is no longer promoted. Damion Dooley previous (archaic) identifier A geographical location datum is a datum that refers to a real, hypothesized or fanciful spatial location Damion Dooley geographic location datum A categorical tree specification datum is a categorical value specification which takes its value from the ontology URI identifier of any one of its subclass items; these may be organized in a hierarchy. Damion Dooley http://purl.obolibrary.org/obo/OBI_0001930 A categorical tree specification datum may have its own URI identifier as its value. This could be interpreted to mean that the datum was recorded but that no particular categorical subclass distinction was observed. This in effect makes the datum act as a boolean variable. obsolete: categorical tree specification true Damion Dooley A geographic coordinate entity composed of both latitude and longitude components. latitude and longitude coordinate (ISO 6709) order: NCIT:C25464 # country ENVO:00000005 # state / province etc. Geographical origin of the sample; use the appropriate name from this list http://www.insdc.org/documents/country-qualifier-vocabulary. Use a colon to separate the country or ocean from more detailed information about the location, eg "Canada: Vancouver" or "Germany: halfway down Zugspitze, Alps" Damion Dooley draft NCBI BioSample geo_loc_name model draft GenEpiO isolate sequencing model A case ID is a unique identifier associated with a particular episode of care for an individual or animal. Damion Dooley case identifier An animal that has had a substantial part of its reproductive organs removed surgically. Damion Dooley NCBI BioSample: neuter Not a PATO phenotypic sex catigorical value. neuter NCBI BioSample A phenotypic sex quality 'pooled male and female' is a categorical value used when the male and female categories or levels of a factor are combined. If used to describe a single organism, then the organism will be one or the other. Not a PATO phenotypic sex catigorical value. Damion Dooley NCBI BioSample: 'pooled male and female' pooled male and female A categorical choice recorded while the data for a given measurable datum has not finished being collected, is awaiting a conclusion, or has not yet been communicated. Damion Dooley undetermined in process swimming / wading Damion Dooley NECESSARY? : What details are categorical and what are freehand? This item was originally too broad; moved sub-items to Treatment. infection detail datum This is problematic - its not clear if this is reporting that antibiotics were administered, or whether they are recommended as a result of diagnosis. Damion Dooley antibiotics required The International Nucleotide Sequence Database Collaboration (INSDC) is a long-standing foundational initiative that operates between DDBJ, EMBL-EBI and NCBI. INSDC covers the spectrum of data raw reads, though alignments and assemblies to functional annotation, enriched with contextual information relating to samples and experimental configurations. Damion Dooley International Nucleotide Database Collaboration standard INSDC INSDC standard Damion Dooley outcome of pregnancy associated with illness INSDC term (lower level) A categorical choice indicating that information of an expected format was not given a value may be given at the later stage. not provided Damion Dooley stable health status http://purl.obolibrary.org/obo/GENEPIO_0002026 induced abortion live birth Damion Dooley http://purl.obolibrary.org/obo/VT_0002292 obsolete: gestation duration (weeks) true date of pregnancy outcome contact specification - physician obsolete: matrix - solid true contact specification - parent/guardian contact specification - patient draft GenEpiO case epidemiology record order: NCIT:C25464 # Country ENVO:00000005 # major administrative subdivision aka state/province/territory/region (via GenEpiO -> GAZ ) NCIT:C80234 # Municipality (via GenEpiO -> GAZ cities) NCIT:C25690 # Street Address NCIT:C25621 # postal code The address component of a contact specification. contact specification - address GENEPIO_0001829 obsolete: draft IRIDA model true A datum related to the sequencing assay process applied to an isolate. Damion Dooley laboratory sequencing datum http://purl.obolibrary.org/obo/OBI_0001901 http://purl.obolibrary.org/obo/OBI_0400103 Damion Dooley host illness associated with draft subject demographic specification K(1|2a|2ac|3|4|5|6|7|8|9|10|11|12|13|14|15|16|18a|18ab|19|20|22|23|24|26|27|28|29|30|31|34|37|39|40|41|42|43|44|45|46|47|49|50|51|52|53|54|56|96|55|74|82|84|85ab|85ac|87|92|93|95|97|98|100|101|102|103|X104|X105|X106) E. coli K antigen specification 1 6 other antigen specification E. coli serotype specification Damion's note: This will be converted to a categorical tree specification list of serovars by name or id asap. Salmonella serovar specification A lab test specification indicates the inputs and outputs (results / conclusions) of a test. Damion Dooley test specification (1/2|1/2a|1/2b|1/2c|3a|3b|3c|4a|4ab|4b|4c|4d|4e|1|7) listeria antigen obsolete: matrix - fluid true listeria serotype 1/2a listeria serotype 1/2b listeria serotype 1/2c listeria serotype 1/2 listeria serotype 3a listeria serotype 3b listeria serotype 4a listeria serotype 4b listeria serotype 4c listeria serotype 4d listeria serotype 4e non-monocytogenes listeria antigen listeria serotype 3c textual test result This is an organizational category for grouping parameters relevant to biomedical research projects. Damion Dooley obsolete: draft GenEpiO BioProject standard true Damion Dooley NCBI BioSample: collection_code NCBI BioSample collection code draft NCBI BioSample host model food - solid lab test datum Xbal Ascl Smal Blnl Apal Kpnl Taxonomy below subspecies; sometimes used in viruses to denote subgroups taken from a single isolate. Damion Dooley NCBI Biosample subgroup help:This is an optional additional subtype classification as per organism convention A viral subtype is a classification name for a virus according to some protocol. Damion Dooley NCBI BioSample viral subtype 1 1 serotype specification IRIDA An integer and character referring to a pattern of opaque or confluent lysis caused by a panel of bacteriophage infections e.g. 14a. Damion Dooley SNOMED: http://www.snomedbrowser.com/Codes/Details/272405002 phage type specification obsolete: swab - food contact surface true ATCC:26370 An NCBI culture collection is a composite identifier containing “institution code:collection code”. Annotation with a culture_collection qualifier implies that the sequence was obtained from a sample retrieved (by the submitter or a collaborator) from the indicated culture collection, or that the sequence was obtained from a sample that was deposited (by the submitter or a collaborator) in the indicated culture collection. See the description for the proper format and list of allowed institutes, http://www.insdc.org/controlled-vocabulary-culturecollection-qualifier. NCBI culture collection UAM:Mamm:52179 The NCBI specimen voucher is an identifier composed of “institution code:collection code:specimen id” parts. In addition to a specimen identifier, it includes an institution-code (and optional collection-code) taken from a controlled vocabulary maintained by the INSDC that denotes the museum or herbarium collection where the specimen resides. INSDC:specimen_voucher NCBI specimen voucher http://www.insdc.org/controlled-vocabulary-specimenvoucher-qualifier. culture identifier human; dog; horse The natural language (non-taxonomic) name of the type of organism (human or animal) that is the subject of a given investigation, study and/or specimen. Damion Dooley's note: as of 2017 this is a problematic field for NCBI Biosample because it is slotted into "host" field, yet field is listed as "host common name" which does not fit with requirement that scientific name be provided. Person: Damion Dooley subject organism common name temperature of air - average daily obsolete: swab - inanimate object surface true obsolete: swab - meat true obsolete: swab - rectal swab true obsolete: swab - tissue true unknown source patient sample human clinical specimen "environment (swab or sampling)" is a specific response for NCBI BioSample that could be mapped or unified with "environment sample" used elsewhere in GenEpiO Damion Dooley http://purl.obolibrary.org/obo/GENEPIO_0001246 obsolete: environmental (swab or sampling) true avian - wild avian - domesticated human clinical specimen - invasive In chemistry, pH is a numeric scale used to specify the acidity or basicity(alkalinity) of an aqueous solution Damion Dooley Wikipedia Normally falls within the bounds of 0 - 14 pH measurement precipitation The assembly and annotation objective is the set of objectives that assembly and annotation techniques (including instruments and software platforms) applied to a sample are meant to satisfy. This impacts on the quality control thresholds applied to the sequencing project. Damion Dooley assembly and annotation project objective Damion Dooley line list row record This class contains components under development for fulfilling GenEpiO and other standard data specifications. Components are relevant to epidemiological, laboratory, clinical or environmental pathogen sample data collection and analysis. Damion Dooley draft GenEpiO component record region lookup:http://purl.obolibrary.org/obo/GAZ_00000448 A subnational region is a type of subnational entity similar to a nation's state, province, or territory. Damion Dooley subnational region A data standard related to public health research and service delivery. Damion Dooley public health data standard Damion Dooley 0D space Reagent: material studied was obtained by chemical reaction, precipitation. Damion Dooley https://www.ncbi.nlm.nih.gov/books/NBK54364/ reagent derived material from specimen transcriptome Transcriptome: transcript and/or expression data. Damion Dooley https://www.ncbi.nlm.nih.gov/books/NBK54364/ transcriptome data from specimen proteome Proteome material is protein or peptide sequences. Damion Dooley https://www.ncbi.nlm.nih.gov/books/NBK54364/ proteome data derived from specimen purified chromosome Purified chromosome: one or more chromosomes or replicons were experimentally purified. Damion Dooley https://www.ncbi.nlm.nih.gov/books/NBK54364/ purified chromosome from specimen targeted locus/loci TargetedLocusLoci: capturing specific loci (gene, genomic region, bar code standard). Damion Dooley https://www.ncbi.nlm.nih.gov/books/NBK54364/ Targeted Locus Loci data capture clone ends CloneEnds: capturing clone end data. Damion Dooley https://www.ncbi.nlm.nih.gov/books/NBK54364/ clone end data capture exome Exome: capturing exon-specific data. Damion Dooley NCBI BioSample https://www.ncbi.nlm.nih.gov/books/NBK54364/ exome specific data capture random survey Sequences generated from a random sampling of the collected sample; not intended to be comprehensive sampling of the material Is this with respect to an isolate or a specimen derived culture? Damion Dooley https://www.ncbi.nlm.nih.gov/books/NBK54364/ random survey data capture This is a collection of various human (and animal contact location) contact information specifications used in data standards. Damion Dooley contact specification order: NCIT:C40978 # phone GENEPIO:0001896 # phone type contact specification - phone Damion Dooley millimetres per day obsolete: millisiemens true Damion Dooley millisiemens per centimetre Damion Dooley cubic metre per second umol/kg Damion Dooley micromole per kilogram Damion Dooley micromole per litre Damion Dooley quality control record Standard draft: describing the minimum information needed for submission to a public database. Damion Dooley 1 - standard draft High quality draft: describing sequences with little to no manual review. Damion Dooley 2 - high quality draft Improved high quality draft: in which data is either reviewed by people or machines to some extent to indicate that most of the genetic data is assembled correctly, but some errors may still be present. Damion Dooley 3 - improved high quality draft Annotation-directed improvement: in which genetic information in various gene regions is represented as accurately as possible. Damion Dooley 4 - annotation-directed improvement Non-contiguous finished: which includes sequences that have been reviewed by both people and machines and would be considered complete except for “recalcitrant regions” that are proving problematic for genome closure. Damion Dooley 5 - non-contiguous finished Finished: which describes un-gapped complete sequences that have minimal errors, if any. The biology of the microbe will determine whether this finished genome consists of more than one chromosome. Damion Dooley 6 - finished Assembly QC http://purl.obolibrary.org/obo/IAO_0000428 The NG99 length is the same as the N99 length except that the length of the reference genome is used in the calculation rather than the sum of assembly contig lengths. Damion Dooley contig NG99 Assembly QC http://purl.obolibrary.org/obo/IAO_0000428 An assembly quality control datum which is defined as number of contigs equal to or longer than the contig N50, when the genome size is factored into the calculation. Damion Dooley contig LG50 Assembly QC http://purl.obolibrary.org/obo/IAO_0000428 Contig L99 is the number of contigs equal to or longer than contig N99. The length of the assembly itself is used in the calculation. Damion Dooley contig L99 A subject age at time of specimen extraction is the age (since birth) of the organism at the time a given specimen was extracted. Damion Dooley subject age at time of specimen collection A public health related data standard involving a particular species of pathogen. Damion Dooley pathogen specific data standard The draft tuberculosis contextual data standard is a data standard for the collection of contextual information of a given tuberculosis case that pertain to typing, clinical treatment, and potential research questions. Damion Dooley draft tuberculosis contextual data standard 1 PulseNet:Outbreak The PulseNet Canada Salmonella submission standard details the fields required in a PuseNet Canada pathogen submission report for Salmonella in spreadsheet format Damion Dooley draft PulseNet Canada Salmonella submission standard http://www.pulsenetinternational.org/assets/PulseNet/uploads/wgs/PND18-NCBI-Biosample-Submission.pdf A PFGE pattern resulting from DNA fragmentation induced by the Xbal enzyme. PFGE Xbal pattern A PFGE pattern resulting from DNA fragmentation induced by the Blnl enzyme. PFGE Blnl pattern NLEP ID An NLEP ID is a unique identifier code for a sample registered with the Canadian "National Laboratory for Enteric Pathogens" (NLEP) Damion Dooley Pulsenet Canada spreadsheet. National Laboratory for Enteric Pathogens Identifier PulseNet spreadsheet Date an uploaded sample was re-uploaded or had its metadata modified. Damion Dooley PulseNet: UploadModifiedDate upload modified date A travel destination is a destination city (or populated place of some scale) which a given human has travelled to on a particular trip. Damion Dooley travel destination A symptom duration is a date-time entity which is the duration (in hours or days or weeks etc.) that one or more symptoms persist for in a particular human or animal Damion Dooley This may be a calculated field if symptoms are reported to cease on a particular date. Often however symptom duration is reported more generally as a date or time range since cesation date is less certain. symptom duration The city where a specimen was collected (taken) from a subject or environment Damion Dooley specimen collection location - city lookup Damion Dooley obsolete: sample city true This is the genus-level taxonomic name of an organism playing a pathogen role Damion Dooley genus of pathogen This is the species-level taxonomic name of an organism playing a pathogen role Damion Dooley species of pathogen A symptom cessation date is a date-time entity that marks the end of one or more reported symptoms pertaining to an episode of human or animal illness Damion Dooley symptom cessation date This is a catch-all category for listing specimen related terms Damion Dooley specimen datum http://purl.obolibrary.org/obo/GENEPIO_0002105 http://purl.obolibrary.org/obo/OBI_0001616 isolate identifier specification The 'data obfuscated' role between a user and given data entails that the user is authorized to see particular fields that have been transformed consistently such that statistics performed on those fields would yeild the same results as statistics applied to the un-obfuscated data. The purpose of obfuscation is to prevent related individuals or organizations from being identified. Damion Dooley data obfuscated https://www.hhs.gov/hipaa/for-professionals/privacy/special-topics/de-identification/ The 'data aggregated' role between a user and given data entails that the user is authorized to see aggregated results (like the patient count) via preset reports, queries or views. The results are not obfuscated. Damion Dooley data aggregated A 'limited data set' role between a user and given data entails that a user is authorized to see some of the fields but the remainder are withheld (or encrypted). Damion Dooley limited data set help:In this dataset, selected data have been de-identified (anonymized) for access by dataset users. A 'de-identified data' role between a user and given data entails that the user is authorized to see only those fields (including those that are encrypted) which do not contain information that could be use to identify particular individuals (whether patients or medical practitioners) or potentially organizations in the case where an investigation may implicate them. Damion Dooley's note: There is a case in the "draft tuberculosis contextual data standard" that has this be a boolean selection. If a categorical field is linked directly, and it has no underlings, this indicates that it is being treated as a boolean feature. Damion Dooley Generally de-identified data should include HIPAA patient privacy fields as indicated in https://www.hipaa.com/hipaa-protected-health-information-what-does-phi-include/ de-identified data A 'data protected' role between a user and given data entails that a user must be authorized in order to view that data. Damion Dooley data protected 1 1 A datum containing the name of persons or institute who collected a given specimen. Damion Dooley https://www.ncbi.nlm.nih.gov/biosample/docs/attributes/ specimen collector Damion Dooley NCBI BioSample culture identifier A user identifier is an identifier provided as part of an authentication process of a client (user) to a service (server). User identifiers normally persist over time, in contrast to session identifiers which are temporary. Damion Dooley user identifier sequence identifier metagenomic species identification Note: REPLACE WITH Citation: SIO_000174 ???? document citation identifier organization identifier collection identifier variant calling / pathogen identification and clustering isolate (pathogen) identification http://purl.obolibrary.org/obo/OBI_0001616 obsolete: NCBI BioSample ID - true 1) Escherichia coli O104:H4 str. C227-11 clinical isolate 2010_333_NC-6 2) CD8+ T cells from female TSG6-knockout BALB/c mouse 3) Human metagenome isolated from urine of healthy female A specimen (or sample) title should be short and informative. Each specimen title must be unique in a submission. NCBI BioSample record documentation refers to a "BioSample title", stating that it is "auto-generated if one is not supplied by the submitter." This is distinct from any assigned BioSession accession, or other "external sample identifier" that may have been issued by the source database or repository. Damion Dooley specimen title draft GenEpiO isolate source context INSDC term (lower level) A categorical choice recorded when the data for a given measurable datum is available but not shared publicly because of information privacy concerns. restricted access State (United States of America) A health status trend is a short-term prognosis about whether health is improving, worsening or unchanging Damion Dooley health status trend datum http://www.itis.gov The Integrated Taxonomic Information System (ITIS) contains authoritative taxonomic information on plants, animals, fungi, and microbes of North America and the world. Damion Dooley Integrated Taxonomic Information System ITIS ITIS https://www.nlm.nih.gov/mesh/meshhome.html MeSH is the National Library of Medicine's controlled vocabulary thesaurus. It consists of sets of terms naming descriptors in a hierarchical structure that permits searching at various levels of specificity. Damion Dooley Medical Subject Headings MSH MESH https://ncit.nci.nih.gov/ncitbrowser/ The National Cancer Institute Thesaurus (NCIt) provides reference terminology for many NCI and other systems. It covers vocabulary for clinical care, translational and basic research, and public information and administrative activities. Damion Dooley National Cancer Institude Thesaurus NCI_Thesaurus NCIt NCIT The NIFSTD ontology of the Neuroscience Information Framework is composed of a collection of OWL modules with separate modules covering major domains of neuroscience: anatomy, cell, subcellular, molecule, organism, function and dysfunction. Damion Dooley https://wiki.nci.nih.gov/display/VKC/NIFSTD+Ontology NIFSTD SNOMED CT is a large clinical health terminology product owned and distributed by SNOMED International. Damion Dooley http://www.snomed.org/snomed-ct SNOMEDCT SNOMEDCT http://www.fao.org/fishery/collection/asfis/en ASFIS is a database curated by the United Nations Food And Agriculture Organization (FAO) Fisheries and Aquaculture Statistics and Information Branch (FIPS). It contains over 12,700 species items selected according to their interest or relation to fisheries and aquaculture. Damion Dooley UN FAO Fisheries and Aquaculture Statistics and Information Branch database FAO ASFIS ASFIS FTT TGN Wikipedia is a free online encyclopedia that aims to allow anyone to edit articles. Damion Dooley https://en.wikipedia.org/wiki/Wikipedia Wikipedia SWEETRealm The GeoNames geographical database covers all countries and contains over eleven million placenames that are available for download free of charge. Damion Dooley http://www.geonames.org/ Geonames http://ecolexicon.ugr.es/en/index.htm EcoLexicon is a terminological resource developed by the LexiCon Research Group at the University of Granada. Damion Dooley EcoLexicon A standard established for use by the Integrated Rapid Infectious Disease Analysis (IRIDA) project, which is a Canadian-led initiative to build an open source, end-to-end platform for infectious disease genomic epidemiology. Damion Dooley http://www.irida.ca/ draft IRIDA standard ISO 3166-1 is part of the ISO 3166 standard published by the International Organization for Standardization (ISO), and defines codes for the names of countries, dependent territories, and special areas of geographical interest. Damion Dooley https://en.wikipedia.org/wiki/ISO_3166-2 ISO3166-1 ISO 3166-2 is part of the ISO 3166 standard published by the International Organization for Standardization (ISO), and defines codes for identifying the principal subdivisions (e.g., provinces or states) of all countries coded in ISO 3166-1. Damion Dooley https://en.wikipedia.org/wiki/ISO_3166-1 ISO3166-2 Information Technology – Codes For The Identification Of The States And Equivalent Areas Within The United States, Puerto Rico, And The Insular Areas Damion Dooley American National Standards Institute ANSI INCITS 38 Damion Dooley The Geographic Names Information System (GNIS), developed by the U.S. Geological Survey in cooperation with the U.S. Board on Geographic Names, contains information about physical and cultural geographic features in the United States and associated areas, both current and historical. https://nhd.usgs.gov/gnis.html GNISID LTER order: OBI:0001628 # investigation identifier OBI:0001616 # specimen identifier GENEPIO:0001808 # specimen title GENEPIO:0000113 # specimen category sep:00196 # specimen description OBI:0001479 # specimen from organism GENEPIO:0001640 # specimen organism taxonomy (species) GENEPIO:0000027 # specimen source context GENEPIO:0001722 # NCBI specimen voucher GENEPIO:0001429 # strain identifier GENEPIO:0001798 # NCBI BioSample culture identifier GENEPIO:0001717 # viral subtype OMP:0000207 # serotype phenotype SO:0001027 # genotype GENEPIO:0001079 # serovar GENEPIO:0001716 # subgroup GENEPIO:0001055 # NCBI pathotype GENEPIO:0001054 # isolate passage history GENEPIO:0001656 # latitude and longitude coordinate GENEPIO:0001657 # NCBI BioSample geo_loc_name model GENEPIO:0001051 # NCBI BioSample isolate (human name or description) GENEPIO:0001648 # NCBI Contributing organization / project GENEPIO:0001797 # specimen collector OBI:0001619 # specimen collection date OBI:0001888 # sequencing facility contact person GENEPIO:0001651 # INSDC institution code GENEPIO:0001721 # NCBI culture collection GENEPIO:0001567 # subject (host) taxonomic species GENEPIO:0001724 # subject organism common name GENEPIO:0001775 # subject age at time of specimen collection GENEPIO:0000026 # subject health status at time of specimen extraction GENEPIO:0000031 # subject sex GENEPIO:0001614 # subject description GENEPIO:0001617 # subject disease GENEPIO:0001625 # subject disease stage GENEPIO:0001212 # subject disease outcome A National Center for Biotechnology Information BioSample specification defines fields and terms that provide "descriptions of biological source materials used in experimental assays". Damion Dooley http://www.ncbi.nlm.nih.gov/biosample/ NCBI BioSample Pathogen.cl standard https://www.ncbi.nlm.nih.gov/biosample/docs/packages/Pathogen.cl.1.0/ 1 1 The National Center for Biotechnology Information BioProject standard is a collection of datums that describe biological data related to a single initiative, originating from a single organization or from a consortium. A BioProject record provides users a single place to find links to the diverse data types generated for that project. Damion Dooley http://www.ncbi.nlm.nih.gov/bioproject/ NCBI lists project data type and other controlled vocabulary fields at : https://www.ncbi.nlm.nih.gov/books/NBK54364/ NCBI BioProject standard 1 1 1 Objective The format of the BioProject Accession is five alpha-letters followed by one to six numbers. For example PRJNA43021 Project Accession Methodology http://www.aha.org/content/00-10/overview0302.pdf http://www.webcitation.org/5VBWPbFgY The American Hospital Association has issued HIPAA Updated Guidelines for Releasing Information on the Condition of Patients Damion Dooley American Hospital Association HIPAA Standard AHA HIPPA AHA HIPPA standard http://www.ncbi.nlm.nih.gov/pubmed/ PubMed comprises more than 26 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites. NCBI PubMed PMID PubMed PulseNet, a national and international surveillance system used to identify and respond to foodborne disease outbreaks, has a standardized laboratory method and data submission standard for pathogen isolate typing test results and related isolate contextual data. From this information clusters of disease can be identified that might represent unrecognized outbreaks. Pulse Net International BioSample Metadata PulseNet PulseNet submission standard AHA HIPPA: http://www.aha.org/content/00-10/overview0302.pdf Good - Vital signs are stable and within normal limits. Patient is conscious and comfortable. Indicators are excellent. Damion Dooley AHA Hippa: Good good health status Good satisfactory Fair - Vital signs are stable and within normal limits. Patient is conscious, but may be uncomfortable. Indicators are favorable. Damion Dooley fair health status fair Stable Serious - Vital signs may be unstable and not within normal limits. Patient is acutely ill. Indicators are questionable. Damion Dooley serious health status Serious A health status history datum is a record of the longer-term pattern or presence of a given patient's health status. Damion Dooley health status history datum (0,0) is the origin of the cartesian coordinate system. A point in zero-dimensional (0D) space in which the origin is a fixed point of reference for the geometry of the surrounding space. Damion Dooley https://en.wikipedia.org/wiki/Origin_(mathematics) "In mathematics, the origin of a Euclidean space is a special point, usually denoted by the letter O, used as a fixed point of reference for the geometry of the surrounding space. In physical problems, the choice of origin is often arbitrary, meaning any choice of origin will ultimately give the same answer. This allows one to pick an origin point that makes the mathematics as simple as possible, often by taking advantage of some kind of geometric symmetry." origin https://en.wikipedia.org/wiki/Medical_state United Kingdom National Health Service trusts, boards, etc. have some terminology in common for public disclosure of patient health conditions. Damion Dooley National Health Service terminology NHS standard Damion Dooley Damion Dooley's note: This is a contentious term. AHA calls for it never to be used, since the common phrase "critical but stable" is misleading by the very nature of "critical". The NHS however has it as one of its central terms. The use of "stable" also points to a health trend, rather than a state. A separate "health status trend datum" has been set up to capture this. critical but stable health status critical but stable NHS Terms: https://en.wikipedia.org/wiki/Medical_state Damion Dooley comfortable health status Comfortable Damion Dooley progressing well health status progressing well Damion Dooley Damion Dooley note: This term (weakly) implies that the patient is recovered enough to be released from hospital. Technically this isn't a health status though, it is a patient medical service state. discharged from hospital discharged A data item which is about the collection state of a datum at some point in time. Damion Dooley note: We'll need to incorporate NIAID GSCID-BRC Sample data standards mention: Unknown/Not Applicable/Censored Allowed Unknown/not applicable/not available/ available upon request Damion Dooley A given datum's datum status value is metadata, i.e. a statement about a particular datum, often when no actual data entry or categorical choice for that datum has been made. datum status INSDC missing value reporting terms: http://www.ebi.ac.uk/ena/about/missing-values-reporting A categorical choice indicating that a datum is available for retrieval. Damion Dooley In theory any datum that has a recorded value has 'recorded' for its datum status. recorded Patient is awaiting physician and/or assessment. Very similar to 'datum status' 'in process' status. Damion Dooley undetermined health status - awaiting assessment Damion Dooley deteriorating worsening health trend Damion Dooley An N-dimensional space consists of n dimensions, each with an origin. It can be translated via various coordinate systems, and can be populated with N and lesser dimensional vectors. n-dimensional space Damion Dooley A distance metric exists between any two members of a one-dimensional set. Should have vector as subclass? 1D space This data type is for an item that can map to a point, line, set or area on a surface (2 dimensional space) or to the surface itself. It can be a slice of a higher dimensional space. It can be defined by a cartesian or radial coordinate system. Damion Dooley 2D space Damion Dooley 3D space Damion Dooley n-dimensional coordinate This covers the description of data and abstract structure in n-dimensional space. Within space there are coordinate systems, coordinates, and entities made up of coordinates. Damion Dooley n-dimensional concept 1 1 Damion Dooley This should cover all interval data 1D coordinate 2 Damion Dooley 2D coordinate -90.0 90.0 /^[N+](:<lat>\d(\.\d+)?)$/, $lat /^S(:<lat>\d(\.\d+)?)$/, '-' + $lat /^(:<lat>[-S+N])?(:<degree>[1-8]?[0-9](:<decimal>\.\d{1,6})?)$/, $lat$degree.$decimal /^(:<lat>[-S+N])?(:<degree>90(:<decimal>\.0{1,6})?))$/, $lat$degree.$decimal /^(\d(\.\d+)?)$/, '+\1' A decimal latitude measurement in degrees in conformance with the ISO 6709 standard. This is failing Hermit reasoner since it rejects totalDigits, and fractionDigits: 'has primitive data type' exactly 1 xsd:decimal[>= -90.0 , <= 90.0 , totalDigits 8 , fractionDigits 6]' Damion Dooley latitude specification (ISO 6709) -180.0 180.0 /^(:<long>[-W+E])?(:<degree>(1[0-7]|[1-9])?[0-9])(:<decimal>\.\d{1,6})?)$/, $long$degree.$decimal /^(:<long>[-W+E])?(:<degree>180(:<decimal>\.0{1,6})?)$,$long$degree.$decimal A decimal longitude measurement in degrees in conformance with the ISO 6709 standard. Damion Dooley longitude specification (ISO 6709) 1 Damion Dooley 1D coordinate system 2 A 2D coordinate system is a coordinate system in 2 dimensional space. Each coordinate is composed of an offset from the origin of each dimension Damion Dooley 2D coordinate system 3 Damion Dooley 3D coordinate system 1 1 Damion Dooley A coordinate system composed of a radius from the origin of one dimension combined with angular offsets from the origins of the remaining dimensions. radial coordinate system 1 Damion Dooley's note: IAO lat/long can't be made a subclass of "angular coordinate" or disjoint contradiction arises with "immaterial entity" Damion Dooley angular coordinate 1 Damion Dooley A coordinate composed of a given dimension and the offset from the origin of the dimension to some point linear coordinate 1 An area calculation datum is a functional mapping of a two dimensional surface area (can be anything from an abstract polygon, to a postal code or country) to a 1 dimensional scalar. The original surface area may be curved, e.g. spheroid. The surface area can also be described using only one input - for example the radius scalar of a polar coordinate plane described by pi*r^2. Damion Dooley area calculation 1 1 1 Damion Dooley geographic coordinate Damion Dooley removed date A datetime range intermediate datum is a datetime item grouped under a process, and occuring after some process start and before some process end. Damion Dooley datetime range intermediate Damion Dooley updated date This seems to be covered by 'datetime range intermediate' Damion Dooley datetime range member - UNUSED? Damion Dooley datetime range item The ending date of a process datetime range end Damion Dooley The starting date of a process datetime range start Wikipedia: "The significant figures of a number are digits that carry meaning contributing to its measurement resolution." Damion Dooley significant digits 1 As mentioned here: http://www.datypic.com/sc/xsd11/t-xsd_dateTimeStamp.html , we could change this to dateTimeStamp if we need to enforce a time zone? Damion Dooley Some dates don't belong to a range other than the overall timeline. Other dates associated with a process fall within a range that has a start and end bound. datetime linear coordinate $year/$month/$day /^(:<year>(19|20)\d\d)([- /.])(:<month>0[1-9]|1[012])\2(:<day>0[1-9]|[12][0-9]|3[01])$/ /^(:<month>0[1-9]|1[012])([- /.])(:<day>0[1-9]|[12][0-9]|3[01])\2(:<year>(19|20)\d\d)$/ /^(:<day>0[1-9]|[12][0-9]|3[01])([- /.])(:<month>0[1-9]|1[012])\2(:<year>(19|20)\d\d)$/ $year/$month/$day A datetime set item is a datetime that has been grouped semantically under a given type of process Damion Dooley The instant is subject to the level of granularity of the observed time. Year / Month / Day / Hour / Minute / Second datetime set item Damion Dooley created date Damion Dooley entity history item Damion Dooley n-dimensional entity 1 Damion Dooley Generic term allowing for different geometries. Can encompass the infinite surface area of a plane, or some portion bounded by a circumference or polygon for example. surface area A designated area on earth is one or more areas defined by one or more boundaries. A boundary can be defined by a polygon perimeter, a lat/long and radius, or a fiat-boundary geographic featureset like a named river channel or mountain ridge; it may have one or more names associated with it. Note that areas associated with a name may change their boundary definitions over time. Damion Dooley designated area on Earth Damion Dooley landmark /^((:<FSA>[ABCEGHJKLMNPRSTVXY][0-9][ABCEGHJKLMNPRSTVWXYZ])) ?(:<LDU>[0-9][ABCEGHJKLMNPRSTVWXYZ][0-9])$/i, $FSA $LDU A Canadian postal code is a postal code that pertains to a geographic region of Canada. Note that a Canadian postal code can cover multiple communities. Secondly, postal codes can be retired, and then reintroduced elsewhere. Historical data associations may need to take the date of postal code mapping into account. Canada postal code /^((:<FSA>[ABCEGHJKLMNPRSTVXY][0-9][ABCEGHJKLMNPRSTVWXYZ]))$/i, $FSA The "Canadia postal code FSA" is the leading FSA (Forward Sortation Area) 3 character portion of a full 6 character Canadian postal code. It can be used to reduce the geographic granularity of a postal code for data generalization or obfuscation. Damion Dooley Canada postal code FSA A "USA zip code" is a five digit (Zone Improvement Plan) or 9 digit postal code pertaining to a region of the United States of America. The optional trailing 4 digits of a 9 digit zip code provide greater granularity of delivery target. Damion Dooley http://purl.obolibrary.org/obo/NCIT_C25720 obsolete: US postal code true /^([a-zAA-Z0-9 _-')*$/ alphanumeric phrase Damion Dooley entity history record Damion Dooley generic range history record Damion Dooley lingual set Damion Dooley non-lingual set phone type mobile phone type - mobile work phone type - work Damion Dooley A set does not have a direct distance metric between its members. set Damion Dooley This data type is for items that have a unique order or rank with respect to each other in a set BUT NO meaningful DISTANCE metric exists between items aside from their position in the full set. "Favorite soft drinks" or "Favorite colours" or "Closest friends" are examples. Letters of the alphabet cannot be interpreted as ordinal with respect to their use in words, since no uniform rules exist about their placement in words. But they can be ordinal insofar as they are stated in a particular order in listing off the alphabet. A distance metric becomes possible if the items have units, e.g. 5cm or 10degrees celcius. The set's elements can then be mapped to one dimension. ordered set An unordered set is a set of elements which have no intrinsic (semantic) order with respect to each other. The set of all living people is not intrinsically ordered; an ordering can only be provided by looking at some partiular feature of the given set elements. Damion Dooley The set can have a very large or infinite (open-ended) number of values. Because the elements are essentially open-ended, we can only offer a lookup-as-you-type function for selecting past-used items. Use "Categorical" for unordered sets where items are finite, pre-defined and not too numerous. Strings are only indirectly ordered insofar as strings can be sorted by character - but this requires picking apar the name strings, an examination which has no inherent semantic relation to the things being named. That one email address or name comes before another is arbitrary. Only numbers are directly ordered. unordered set Damion Dooley Subclasses here are types of string that have a particular syntactic structure or constraint to them that should be expressable using regular expressions. set of unordered strings /^(:<area>(\([0-9]{3})\)|[0-9]{3})(:<sep>[- ])?(:<central>\d{3})\2(:<station>\d{4})$/, $area $central $station ($area) $central-$station Damion Dooley phone number (North America) 1 A set of points that exist in a 2-dimensional plane. (This plane may be a cross-section of points defined in n > 2 dimensions). Damion Dooley points in 2 dimensions In Euclidean space, quadrics have dimension D = 2, and are known as quadric surfaces. Damion Dooley https://en.wikipedia.org/wiki/Quadric quadratic surface A spheroid, or ellipsoid of revolution, is a quadric surface obtained by rotating an ellipse about one of its principal axes; in other words, an ellipsoid with two equal semi-diameters. Damion Dooley https://en.wikipedia.org/wiki/Spheroid spheroid In mathematics, a plane is a flat, two-dimensional surface. A plane is the two-dimensional analogue of a point (zero dimensions), a line (one dimension) and three-dimensional space. Planes can arise as subspaces of some higher-dimensional space, as with the walls of a room, or they may enjoy an independent existence in their own right, as in the setting of Euclidean geometry." "When working exclusively in two-dimensional Euclidean space, the definite article is used, so, the plane refers to the whole space. Damion Dooley https://en.wikipedia.org/wiki/Plane_(geometry) plane Issue: this implicitly affects 'significant digits' datum. quantity unit ^([+-]?[1-9]\d*|0)(\.\d+)?$ Damion Dooley decimal ^([-+]?[1-9]\d*|0)$ Damion Dooley integer ones tens hundreds thousands tenths hundredths millions Damion Dooley Number types can have min / max limits for validation. Regular expressions would be used mostly for data entry transformation and display. number A product name and model number of a manufacturer's genomic (dna) sequencer. Damion Dooley sequencing instrument model 1 1 A circle is a simple closed shape in Euclidean geometry. It is the set of all points in a plane that are at a given distance from a given point, the centre; equivalently it is the curve traced out by a point that moves so that its distance from a given point is constant. Damion Dooley https://en.wikipedia.org/wiki/Circle circle NCBI SRA: ILLUMINA Illumina platform NCBI SRA: COMPLETE_GENOMICS Damion Dooley's note: This platform is in-house and not a product per se. Complete Genomics states: "Complete Genomics’ sequencing platform employs high-density DNA nanoarrays that are populated with DNA nanoballs (DNBs™). Base identification is performed using an unchained ligation-based read technology known as combinatorial probe-anchor ligation (cPAL™). The sequencing instrumentation is custom-developed to support this process. Details are described in our Science publication (Drmanac et al., 2010)." Complete Genomics platform 0 1 Damion Dooley earth area boundary census NCBI SRA: LS454 Roche LS454 platform NCBI SRA: PACBIO_SMRT PacBio platform NCBI SRA: AB SOLiD 4hq SOLiD 4hq System NCBI SRA: AB SOLiD 5500 SOLiD 5500 NCBI SRA: AB SOLiD 5500xl SOLiD 5500xl NCBI SRA: AB SOLiD PI System SOLiD PI System NCBI SRA: AB SOLiD System 2.0 SOLiD System 2.0 NCBI SRA: AB SOLiD System 3.0 SOLiD System 3.0 A two dimensional entity is an entity composed of one or more points on a two dimensional surface. Damion Dooley 2D entity Redundant with "term replaced by" entity. NCBI SRA: Ion Torrent PGM obsolete: Ion Torrent PGM true NCBI SRA: 454 GS FLX Titanium 454 Genome Sequencer FLX Titanium NCBI SRA: 454 GS 454 Genome Sequencer NCBI SRA: 454 GS Junior 454 Genome Sequencer Junior Redundant with "term replaced by" entity. obsolete: Illumina HiSeq Sequencer true https://www.ncbi.nlm.nih.gov/books/NBK54984/table/SRA_Glossary_BK.T._library_descriptor_te/?report=objectonly Whether any method was used to select for or against, enrich, or screen the material being sequenced. Damion Dooley NCBI SRA: LIBRARY_SELECTION library selection Selection of methylated DNA fragments using an antibody raised against 5-methylcytosine or 5-methylcytidine (m5C). NCBI SRA: 5-methylcytidine antibody 5-methylcytidine antibody method Cap-analysis gene expression. NCBI SRA: CAGE CAGE method Cot-filtered highly repetitive genomic DNA NCBI SRA: CF-H CF-H method Cot-filtered moderately repetitive genomic DNA NCBI SRA: CF-M CF-M method Cot-filtered single/low-copy genomic DNA NCBI SRA: CF-S CF-S method Cot-filtered theoretical single-copy genomic DNA NCBI SRA: CF-T CF-T method Chromatin immunoprecipitation NCBI SRA: ChIP ChIP method Deoxyribonuclease (MNase) digestion NCBI SRA: DNAse DNAse method Hypo-methylated partial restriction digest NCBI SRA: HMPR HMPR method Selection by hybridization in array or solution. NCBI SRA: Hybrid Selection Hybrid Selection method Enrichment by methyl-CpG binding domain. NCBI SRA: MBD2 protein methyl-CpG binding domain MBD2 protein methyl-CpG binding domain method Methyl Filtrated NCBI SRA: MF MF method Micrococcal Nuclease (MNase) digestion NCBI SRA: MNase MNase method Methylation Spanning Linking Library NCBI SRA: MSLL MSLL method Source material was selected by designed primers. NCBI SRA: PCR PCR method Rapid Amplification of cDNA Ends. NCBI SRA: RACE RACE method Source material was selected by randomly generated primers. NCBI SRA: RANDOM PCR RANDOM PCR method Random selection by shearing or other method. NCBI SRA: RANDOM RANDOM method Source material was selected by reverse transcription PCR NCBI SRA: RT-PCR RT-PCR method Reproducible genomic subsets, often generated by restriction fragment size selection, containing a manageable number of loci to facilitate re-sampling. NCBI SRA: Reduced Representation Reduced Representation method DNA fractionation using restriction enzymes. NCBI SRA: Restriction Digest Restriction Digest method PolyA selection or enrichment for messenger RNA (mRNA). complementary DNA. NCBI SRA: cDNA cDNA method Physical selection of size appropriate targets. NCBI SRA: size fractionation size fractionation method Other library enrichment, screening, or selection process. NCBI SRA: other other library method https://www.ncbi.nlm.nih.gov/books/NBK54984/table/SRA_Glossary_BK.T._library_descriptor_te/?report=objectonly The library source specifies the type of source material that is being sequenced. Damion Dooley library source Genomic DNA (includes PCR products from genomic DNA). Damion Dooley NCBI SRA: GENOMIC genomic source Mixed material from metagenome. Damion Dooley NCBI SRA: METAGENOMIC metagenomic source Transcription products from community targets Damion Dooley NCBI SRA: METATRANSCRIPTOMIC metatranscriptomic source Other, unspecified, or unknown library source material. Damion Dooley NCBI SRA: OTHER other library source Synthetic DNA. Damion Dooley NCBI SRA: SYNTHETIC synthetic source Transcription products or non genomic DNA (EST, cDNA, RT-PCR, screened libraries). Damion Dooley NCBI SRA: TRANSCRIPTOMIC transcriptomic source Viral RNA. Damion Dooley NCBI SRA: VIRAL RNA viral RNA source Sequencing technique intended for this library. Damion Dooley https://www.ncbi.nlm.nih.gov/books/NBK54984/table/SRA_Glossary_BK.T._library_descriptor_te/?report=objectonly library strategy Sequencing of overlapping or distinct PCR or RT-PCR products. For example, metagenomic community profiling using SSU rRNA NCBI SRA: AMPLICON amplicon strategy MethylC-seq. Sequencing following treatment of DNA with bisulfite to convert cytosine residues to uracil depending on methylation status. NCBI SRA: Bisulfite-Seq Bisulfite-Seq strategy Clone end (5', 3', or both) sequencing. NCBI SRA: CLONEEND clone end strategy Genomic clone based (hierarchical) sequencing. NCBI SRA: CLONE clone strategy Concatenated Tag Sequencing NCBI SRA: CTS CTS strategy Direct sequencing of chromatin immunoprecipitates. NCBI SRA: ChIP-Seq ChIP-Seq strategy Sequencing of hypersensitive sites, or segments of open chromatin that are more readily cleaved by DNaseI. NCBI SRA: DNase-Hypersensitivity DNase-Hypersensitivity strategy Single pass sequencing of cDNA templates NCBI SRA: EST EST strategy Sequencing intended to finish (close) gaps in existing coverage. NCBI SRA: FINISHING finishing strategy Full-length sequencing of cDNA templates NCBI SRA: FL-cDNA FL-cDNA strategy Direct sequencing of methylated fractions sequencing strategy. NCBI SRA: MBD-Seq MBD-Seq strategy Direct sequencing following MNase digestion. NCBI SRA: MNase-Seq MNase-Seq strategy Methylation-Sensitive Restriction Enzyme Sequencing strategy. NCBI SRA: MRE-Seq MRE-Seq strategy Methylated DNA Immunoprecipitation Sequencing strategy. NCBI SRA: MeDIP-Seq MeDIP-Seq strategy Library strategy not listed. NCBI SRA: OTHER other library strategy Shotgun of pooled clones (usually BACs and Fosmids). NCBI SRA: POOLCLONE pool clone strategy Random sequencing of whole transcriptome. NCBI SRA: RNA-Seq RNA-Seq strategy Random sequencing of a whole chromosome or other replicon isolated from a genome. NCBI SRA: WCS WCS strategy Random sequencing of the whole genome. NCBI SRA: WGS WGS strategy Random sequencing of exonic regions selected from the genome. NCBI SRA: WXS WXS strategy Free form text describing the protocol by which the sequencing library was constructed. Damion Dooley https://www.ncbi.nlm.nih.gov/books/NBK54984/table/SRA_Glossary_BK.T._library_descriptor_te/?report=objectonly library construction protocol The submitter's name for this library. Damion Dooley https://www.ncbi.nlm.nih.gov/books/NBK54984/table/SRA_Glossary_BK.T._library_descriptor_te/?report=objectonly NCBI SRA: LIBRARY_NAME library name A two dimensional boundary is a continuous path (loop) defined on a two dimensional surface. Damion Dooley 2D boundary cfu/100mL A colony forming unit count which is a count of viable bacterial numbers in 100 milliliters of liquid. Should this be deprecated? Need to find working examples that actually use / 100mL. Damion Dooley colony forming unit per 100 milliliter A multiplier in the decimal number system that has been applied to an accompanying number or set of numbers often to simplfy their appearance. Numbers described by multipliers may have lost significant digits through rounding or trimming. Damion Dooley decimal quantity unit draft tuberculosis - dataset features and provenance draft tuberculosis - case specimen characteristics draft tuberculosis - case subject characteristics draft tuberculosis - case risk factors draft tuberculosis - case clinical presentation draft tuberculosis - case laboratory testing draft tuberculosis - case medication draft isolate whole genome sequencing model draft tuberculosis - case model A Mycobacterium tuberculosis lineage is a named family of strains of tuberculosis, named usually with reference to their shared geographic origin. Damion Dooley Mycobacterium tuberculosis lineage A TB-Lineage identification tool using spoligotypes and MIRU data: http://tbinsight.cs.rpi.edu/run_tb_lineage.html Out-of-Africa migration and Neolithic coexpansion of Mycobacterium tuberculosis with modern humans http://www.nature.com/ng/journal/v45/n10/full/ng.2744.html TB lineage 2 - East-Asian, includes Bejing TB lineage 3 - East-African Indian, includes CAS/Delhi TB lineage 4 - Euro-American, includes Haarlem, LAM3, X, T, F11, H37Rv TB lineage 1 - Indo-Oceanic TB lineage 5 - West African 1 TB lineage 6 - West African 2 Damion Dooley An isolate preparation facility is a type of organization that provides the service of isolating organisms of interest from provided specimens. isolate preparation facility plant product geospatial name A personal health datum is a datum that pertains to the health situation or history of an individual. Personal health datum covers the following information 'has member' some 'analytic datum' 'has member' some 'behavioural risk factor' 'has member' some 'country of birth' 'has member' some 'dietary restrictions' 'has member' some 'Disease Attributes' 'has member' some 'health status history datum' 'has member' some 'health status trend datum' 'has member' some 'host hospital service status' 'has member' some 'subject disease stage' 'has member' some 'subject health status' 'has member' some 'subject health status (AHA)' 'has member' some 'subject health status (GSCID-BRC)' 'has member' some 'subject health status (NCIT)' 'has member' some 'subject health status (UK NHS)' 'has member' some 'subject health status at time of specimen extraction' 'has member' some 'tuberculosis disease anatomical site' 'has member' some comorbidity 'has member' some disease 'has member' some symptom Damion Dooley personal health datum A host hospital service status indicates the state of a host's interaction with hospital medical services. Damion Dooley host hospital service status Damion Dooley admitted to hospital Received treatment but not admitted. treated and released (not admitted to hospital) Treated and Released Received treatment. Transferred to a different facility. treated and transferred Treated and Transferred Damion Dooley satisfactory health status satisfactory depth:1 subject health status (UK NHS) depth:1 subject health status (AHA) http://purl.obolibrary.org/obo/GENEPIO_0002019 stable health trend http://purl.obolibrary.org/obo/GENEPIO_0001669 An ordinal variable is a categorical variable whose values have sequential order, but no distance metric between them. Damion Dooley http://purl.obolibrary.org/obo/STATO_0000228 obsolete: ordinal variable true mapping (reference based) data protection item subject provided consent Damion Dooley An ordinal tree specification is a value specification entity whose subclasses each represent a possible value selection, and which have a linear order with respect to their siblings. ordinal value specification consent datum agency provided consent 2019-11-17T00:43:00Z draft ISO sequence repository field Centre of circle, ellipse or parabola; centre of mass. A centre point is a point used in the description of an n-dimentional entity from which other (given) aspects of the entity are most efficienty described. A point of symmetry. The entity must have only one such point. Probably a better formal math defn? Damion Dooley centre point This covers the following entities: 'has member' some 'antimicrobial phenotype' 'has member' some 'antimicrobial resistance test drug' 'has member' some 'antimicrobial resistance test platform' 'has member' some 'antimicrobial resistance testing method' 'has member' some 'antimicrobial resistance testing method version or reagent' 'has member' some 'antimicrobial resistance testing reference standard' 'has member' some 'antimicrobial resistance testing reference standard version' 'has member' some 'antimicrobial resistance tissue specificity' 'has member' some 'antimicrobial resistant plasmid type' 'has member' some 'automated testing platform vendor' 'has member' some 'draft antibiogram drug test model' 'has member' some 'in-vitro microbial susceptibility test' 'has member' some 'measurement comparator' 'has member' some 'MIC unit' 'has member' some 'MIC value' 'has member' some 'Minimum Inhibitory Concentration Test' 'has member' some 'test drug maximum concentration' 'has member' some 'test drug minimum concentration' 'has member' some 'tuberculosis treatment drug' Damion Dooley This is a collection of antibiotic resistance process parameters and outputs phenotypic antimicrobial drug susceptibility test datum The resistance phenotype of an isolate represents the interpretation of an MIC value with regard to some breakpoint threshold e.g. resistant (R), sensitive (S), intermediate (I), wild type (WT), or non-wild type (NWT) Damion Dooley http://purl.obolibrary.org/obo/NCIT_C85539 obsolete: antimicrobial resistance phenotype true Intermediate resistance indicates that an isolate is observed to offer an intermediate level of resistance to a given antibiotic. Damion Dooley http://purl.obolibrary.org/obo/NCIT_C85560 obsolete: antibiotic intermediate resistance (I) true Non-susceptible indicates that an isolate is observed to offer complete resistance to a given antibiotic. Damion Dooley http://purl.obolibrary.org/obo/NCIT_C85561 obsolete: antibiotic nonsensitive (high resistance) true A not defined resistance indicates that an isolate was not tested against a given antibiotic, or the result of the test was inconclusive. Damion Dooley note: Is this the same as "indeterminate"? Damion Dooley N ND antibiotic resistance not defined Resistant indicates that an isolate is observed to offer a greater than intermediate level of resistance to a given antibiotic. Damion Dooley http://purl.obolibrary.org/obo/NCIT_C85562 obsolete: antibiotic resistant (R) true Susceptible indicates that an isolate is observed to offer a detectable but less than intermediate level of resistance to a given antibiotic. Damion Dooley http://purl.obolibrary.org/obo/NCIT_C85563 obsolete: antibiotic sensitive (S) true Susceptible - dose dependent indicates that an isolate is observed to offer resistance to a given antibiotic when a sufficient dose is given. Damion Dooley http://purl.obolibrary.org/obo/NCIT_C85559 obsolete: sensitive - dose dependent true A MIC test measurement resulting from a laboratory dilution method. Damion Dooley's note: is this still useful? Currently "MIC dilution measurement specification' refers directly via 'is about' to "broth dilution method" but that may be too specific. Damion Dooley MIC dilution measurement datum The type of assay used to determine the minimum inhibitory concentration. Damion Dooley http://purl.obolibrary.org/obo/NCIT_C85540 obsolete: antimicrobial resistance testing method true http://purl.obolibrary.org/obo/NCIT_C85555 obsolete: agar dilution evidence true The commercial kit or product used to determine the MIC e.g. E-Test. If a commercial product was not used, include the type of media used. Damion Dooley antimicrobial resistance testing method device or reagent antimicrobial resistant plasmid type The instrumentation used to determine minimum inhibitory concentration values. Damion Dooley http://purl.obolibrary.org/obo/ARO_3004390 obsolete: antimicrobial resistance testing platform true http://purl.obolibrary.org/obo/ARO_3004400 obsolete: Microscan true http://purl.obolibrary.org/obo/ARO_3004401 obsolete: Phoenix true http://purl.obolibrary.org/obo/ARO_3004402 obsolete: Sensititre true http://purl.obolibrary.org/obo/ARO_3004403 obsolete: Vitek true http://purl.obolibrary.org/obo/ARO_3004409 obsolete: Trek true obsolete: manual - noncommercial true The manufacturer of an antibiotic resistance lab typing platform Damion Dooley http://purl.obolibrary.org/obo/ARO_3004404 obsolete: antimicrobial resistance testing platform vendor true http://purl.obolibrary.org/obo/ARO_3004407 obsolete: Siemens true http://purl.obolibrary.org/obo/ARO_3004406 obsolete: Biomérieux true http://purl.obolibrary.org/obo/ARO_3004405 obsolete: Becton Dickinson true A manual in vitro diagnostic device used by laboratories to determine the MIC (Minimum Inhibitory Concentration) and whether or not a specific strain of bacterium or fungus is susceptible to the action of a specific antimicrobial. Damion Dooley E-Test Epsilometer test Etest (device) GM-NEG The clinical and laboratory guidelines or standards that prescribe the threshold values for determining resistance phenotypes. Damion Dooley http://purl.obolibrary.org/obo/ARO_3004360 obsolete: antimicrobial resistance testing reference standard true BSAC is a British inter-professional organisation involved in antibiotic education, research and leadership Damion Dooley BSAC obsolete: British Society for Antimicrobial Chemotherapy (BSAC) true The Clinical and Laboratory Standards Institute develops and implements clinical laboratory testing standards Damion Dooley NCCLS http://clsi.org CLSI On January 1, 2005 the National Committee on Clinical Laboratory Standards (NCCLS) changed its name to CLSI obsolete: Clinical and Laboratory Standards Institute (CLSI) true DIN is recognized by the Federal Government of Germany as the competent standards organization for Germany and as the national standards body representing Germany in non-governmental international standards organizations. Damion Dooley http://www.din.de/en/din-and-our-partners/din-e-v DIN obsolete: Deutsches Institut für Normung obsolete: German Institute for Standardization (DIN) true EUCAST is a standing committee jointly organized by ESCMID, ECDC and European national breakpoint committees; it deals with breakpoints and technical aspects of phenotypic in vitro antimicrobial susceptibility testing. Damion Dooley http://www.eucast.org/ EUCAST obsolete: European Committe on Antimicrobial Susceptibility Testing (EUCAST) true Damion Dooley NCCLS obsolete: National Committee on Clinical Laboratory Standards (NCCLS) true La SFM a vocation à rassembler les microbiologistes de France et des pays francophones, travaillant dans les différents domaines de la microbiologie médicale, industrielle, et environnementale, en physiologie, génétique, taxonomie, hygiène, agents antimicrobiens, ...concernant les bactéries, virus, champignons et parasites. The French Society of Microbiology (SFM) is a non-profit association which aims to bring together microbiologists from French-speaking countries, working in the domains of bacteria, viruses, Fungi and parasites, and related medical, industrial and environmental microbiology, physiology, genetics, taxonomy, hygiene, and antimicrobial agents. This isn't at moment considered a valid EBI antibiogram choice? Damion Dooley http://www.sfm-microbiologie.org/ SFM obsolete: Société Française de Microbiologie (SFM) true Replaced by domain appropriate term created in the Comprehensive Antibiotic Resistance Database (CARD). obsolete: SIR true Replaced by domain appropriate term created in the Comprehensive Antibiotic Resistance Database (CARD). obsolete: WRG true first line tuberculosis drug last resort antibiotic NIAID standard NIAID provides The GSCID/BRC Project and Sample Application Standard. It is designed to capture standardized human pathogen and vector sequencing metadata to support epidemiologic and genotype-phenotype association studies for human infectious diseases. Damion Dooley https://www.niaid.nih.gov/research/human-pathogen-and-vector-sequencing-metadata-standards National Institute of Allergy and Infectious Disease standard A RefSeq accession identifier is an accession identifier for selected NCBI-curated genomic, transcript and protein sequences. These identifiers are distinct from DDBJ/EMBL/GenBank identifiers. Damion Dooley RefSeq accession identifier http://www.ncbi.nlm.nih.gov/refseq/about/ A Genomic Standards Consortium standard is an international, community-driven standard to facilitate genomic data integration, discovery and comparison. Damion Dooley Genomic Standards Consortium (GSC) standard http://gensc.org/ A landform, biome or built environment at site that a given specimen was collected from. Damion Dooley specimen collection site - geographic feature A particular human patient, or a given animal or plant. An investigative subject which is an organism. Damion Dooley subject organism help=The number of passages should be expressed as a numerical value. The number of serial iterations that an isolate is grown in one environment. Damion Dooley number of passages help:The passage protocol should include, when applicable, inoculum size, media type, temperature and duration of incubation. A passage protocol should detail the number of serial iterations that an isolate is grown in one environment, and the conditions of that environment. Damion Dooley passage protocol The unit provided for an antibiotic drug test dosage. Damion Dooley http://purl.obolibrary.org/obo/ARO_3004372 obsolete: drug minimum inhibitory concentration unit true order: GENEPIO:0001237 # specimen type (host or environmental context) OBI:0001619 # specimen collection date OBI:0000659 # specimen collection process GENEPIO:0002094 # specimen collection device GENEPIO:00001600 # draft sequence repository data - geographic location ENVO:00010483 # environmental material ENVO:00002297 # environmental feature GENEPIO:0001567 # subject (host) taxonomic species GENEPIO:0000110 # subject health status GENEPIO:0001617 # subject disease GENEPIO:0000028 # subject body product GENEPIO:0000025 # specimen source anatomical site FOODON:03411564 # draft sequence repository data - food processing draft sequence repository data - specimen collection order: GENEPIO:0002105 # Specimen processing organization role NCIT:C93874 # organization name NCIT:C40974 # first name NCIT:C40975 # last name NCIT:C93582 # job title NCIT:C42775 # email address GENEPIO:0001756 # phone NCIT:C25464 # Country ENVO:00000005 # major administrative subdivision -> GAZ state/province/territory/region) NCIT:C80234 # Municipality” (via GenEpiO -> GAZ cities) NCIT:C25690 # Street Address Contact information for an organization related to specimen collection, processing or storage. Damion Dooley contact specification - specimen related organization dateFormat:ISO 8601 order: GENEPIO:0002082 # specimen related organization GENEPIO:0002081 # specimen collection GENEPIO:0002086 # geographic location GENEPIO:0002084 # isolate GENEPIO:0002087 # isolate history GENEPIO:0002106 # food specimen GENEPIO:0002088 # antibiogram GENEPIO:0002085 # sequencing GENEPIO:0002090 # sequencing QC GENEPIO:0002089 # virulence GENEPIO:0002092 # submission to EBI GENEPIO:0002091 # submission to NCBI/DDBJ This draft specification provides a collection of fields related to the contextual data of a specimen, its genomic sequencing, and its pathogenic epidemiology. Damion Dooley draft sequence repository contextual data standard order: GENEPIO:0001640 # specimen taxonomy GENEPIO:0001429 # strain identifier GENEPIO:0001644 # isolate identifier OBI:0000079 # culture medium GENEPIO:0002107 # isolation medium draft sequence repository data - isolate order: GENEPIO:0000069 # sequencing date OBI:0000079 # culture medium” (via MicrO, yields a list of formulas). GENEPIO:0002093 # sequencing dna extraction method EFO:0000683 # replicate GENEPIO:0000085 # library preparation kit GENEPIO:0000149 # library preparation kit version GENEPIO:0000075 # sequencing chemistry GENEPIO:0001921 # sequencing instrument model GENEPIO:0000150 # read trimming and filtering software GENEPIO:0000084 # read adapter trimming software GENEPIO:0002095 # read paired-end merging software GENEPIO:0000090 # assembly method GENEPIO:0000151 # bioinformatics pipeline name GENEPIO:0000153 # bioinformatics pipeline protocol GENEPIO:0000152 # bioinformatics pipeline version GENEPIO:0000095 # genome annotation algorithm draft sequence repository data - sequencing order: GENEPIO_0001656 # latitude and longitude ISO 6709 GENEPIO:0000118 # specimen collection country GENEPIO:0002097 # specimen collection state/prov/ter/region GENEPIO:0001785 # specimen collection city The geographical origin of the sample by city, region, country or latitude and logitude. Damion Dooley draft sequence repository data - geographic location order: GENEPIO:0002078 # number of passages GENEPIO:0002079 # passage protocol draft sequence repository data - isolate passage history order: GENEPIO:0001100 # antimicrobial drug tests GENEPIO:0002101 # test drug minimum concentration GENEPIO:0002100 # test drug maximum concentration GENEPIO:0002045 # antimicrobial resistance testing method GENEPIO:0002047 # antimicrobial testing method version or reagent GENEPIO:0002062 # antimicrobial resistance testing reference standard GENEPIO:0002049 # antimicrobial resistance testing platform A dataset of the minimal inhibitory concentrations (value, unit, sign (<,>, =)) and resistance phenotypes (resistant, sensitive or undetermined) of the sequenced isolate against different antibiotics tested. Damion Dooley draft sequence repository data - antibiogram order: GENEPIO:0002130 # Virulence factor name GENEPIO:0002131 # Virulence testing protocol GENEPIO:0002132 # detection limit The virulence factors determined to be present in the sequenced isolate by phenotypic or target amplification methods e.g. Shiga toxins, hemolysins. Damion Dooley draft sequence repository data - virulence order: OBI:0001941 # N50 GENEPIO_0000092 # sequencing depth / read coverage Measurements or calculated quantities used to assess the extent and success of the sequence assembly process. Metric thresholds are species-specific. Damion Dooley draft sequence repository data - sequencing quality control order: OBI:0001616 # specimen identifier GENEPIO:0001644 # isolate identifier GENEPIO:0001429 # strain identifier GENEPIO:0001640 # specimen organism taxonomy GENEPIO:0000113 # specimen category OBI:0001619 # specimen collection date GENEPIO:0001797 # specimen collector GENEPIO:0001657 # geo_loc_name GENEPIO:0001656 # latitude and longitude coord GENEPIO:0000027 # specimen source context GENEPIO:0001567 # subject organism taxonomy GENEPIO:0001724 # subject organism common name GENEPIO:0001617 # subject disease Damion Dooley draft sequence repository data - submission to NCBI/DDBJ order: GENEPIO:0001644 # isolate identifier GENEPIO:0001429 # strain identifier GENEPIO:0001640 # specimen organism taxonomy GENEPIO:0001079 # serovar GENEPIO:0002135 # EBI environmental feature GENEPIO:0000113 # specimen category OBI:0001619 # specimen collection date GENEPIO:0001797 # specimen collector GENEPIO:0002086 # geographic location GENEPIO:0000027 # specimen source context GENEPIO:0002076 # geographic feature GENEPIO:0001567 # subject taxonomy GENEPIO:0000110 # subject health status Damion Dooley draft sequence repository data - submission to EBI https://www.ebi.ac.uk/ena/submit/pathogen-data The procedure used to obtain genomic DNA from a sample through chemical, physical or mechanical means. Damion Dooley sequencing dna extraction method datum Moved term to OBI, deprecated in favour of the OBI version. obsolete: specimen collection device true The name and version of the software used to merge paired-end reads before assembly. read paired-end merging software Sequencing The name and version of the software product used for removal of adapter sequences from demultiplexed data reads GROUP: IRIDA Ontology (Emma) read adapter trimming software An ontology identifier or textual name of the most precise geographical location available for the site of a specimen collection event. Damion Dooley Adapted from NIAID GSCID-BRC metadata working group Note that this is expressed in a particular format in some standards. specimen collection location - state/province/territory/region lookup A wild type (WT) resistance phenotype indicates a bacterial pathogen belongs to a "Naïve", susceptible wild-type population with respect to a given antimicrobial. No acquired or mutational resistance mechanisms are present to the antimicrobial in question. Damion Dooley https://sisu.ut.ee/sites/default/files/amr/files/pab_new_legislation_on_amr.pdf http://purl.obolibrary.org/obo/ARO_3004432 obsolete: wild type (WT) true A non-wild type (WT) resistance phenotype indicates a bacterial pathogen has an acquired or mutational resistance mechanism present with respect to the antimicrobial in question. The bacteria has a reduced susceptibility to this agent. Damion Dooley https://sisu.ut.ee/sites/default/files/amr/files/pab_new_legislation_on_amr.pdf http://purl.obolibrary.org/obo/ARO_3004433 obsolete: non-wild type (NWT) true This is the maximum concentration of a drug applied during an an assay. Damion Dooley test drug maximum concentration A data item which describes the minimum concentration of a drug applied during an an assay Damion Dooley test drug minimum concentration The tissue type used to select breakpoints from a particular standard, for the interpretation of MIC results. Damion Dooley http://purl.obolibrary.org/obo/ARO_3004430 obsolete: antimicrobial resistance tissue specificity true depth:1 order: NCIT:C115935 # healthy NCIT:C126054 # non-pathalogical NCIT:C25610 # pathologic NCIT:C82508 # life threatening NCIT:C28554 # deceased subject health status (NCIT) order: NCIT:C40974 # first name NCIT:C40975 # last name NCIT:C93582 # job title NCIT:C42775 # email address GENEPIO:0001756 # phone contact specification - professional role An organization related to the collection, isolate production, sequencing or storage of specimen material or data. Damion Dooley specimen processing organization type order: GENEPIO:0001533 # food specimen type FOODON:03450002 # food cooking method FOODON:03440011 # extent of heat treatment FOODON:03430113 # physical state, shape or form FOODON:03470107 # food preservation method FOODON:03490100 # container or wrapping FOODON:03480020 # food packing medium FOODON:03500010 # food contact surface GENEPIO:0000139 # food cultural origin FOODON:03460111 # treatment applied to food This specification offers food source, product type, packaging and processing attributes relevant to describing a food specimen. draft sequence repository data - food specimen An isolation medium is a culture medium which has the disposition to encourage growth of particular bacteria to the exclusion of others in the same growth environment. Chris has proposed this term for OBI as "enrichment culture medium" Damion Dooley isolation medium order: GENEPIO:0000121 # start date GENEPIO:0000122 # end date GENEPIO:0001783 # travel destination GENEPIO:0001064 # travel mode GENEPIO:0001065 # travel reason This record details a person's travel movement and duration for epidemiological analysis. Damion Dooley draft travel log specification order: OBI:0001616 # BioSample_ID GENEPIO:0001640 # Species GENEPIO:0001187 # Antibiotic_Name GENEPIO:0002062 # AST_Standard GENEPIO:0002111 # Breakpoint_version NCIT:C85540 # Laboratory_typing_method GENEPIO:0002112 # Measurement GENEPIO:0002080 # Measurement_units GENEPIO:0001001 # Measurement_sign NCIT:C85539 # Resistance_phenotype GENEPIO:0002181 # Resistance_phenotype - ECOFF GENEPIO:0002049 # Platform A standard for European Bioinformatics Institute (EBI) antibiogram data submission Damion Dooley draft EBI antimicrobial susceptibility test V. 2017-08-30 https://github.com/EBI-COMMUNITY/compare-amr/blob/master/Antimicrobial-susceptibility-testing-data-submission_V_2017-08-30.pdf A MIC test measurement resulting from a laboratory diffusion method. Damion Dooley's note: is this still useful? Currently "MIC diffusion measurement specification' refers directly via 'is about' to "Disk Diffusion Method". Damion Dooley MIC diffusion measurement datum The version of the antimicrobial reistance testing reference standard protocol used in assessing an isolate. Damion Dooley antimicrobial resistance testing reference standard version This is a component of an antibiogram that enables a choice of MIC measurements based on either the diffusion or dilution method. These methods call for different numeric input ranges and units. draft sequence repository data - antibiogram MIC measurement 1 time value specification The process of collecting a portion of feces from an organism. Emma Griffiths stool collection feces collection The process of collecting a portion of urine from an organism. Emma Griffiths sputum collection The process of removal and collection of specimen material from the surface of an entity by washing, or a similar application of fluids. Emma Griffiths rinsing for specimen collection The process of collecting specimen material using a swab collection device. Emma Griffiths swabbing for specimen collection The process of collecting bodily fluids that have been discharged from blood vessels usually arising from inflammation or injury. Emma Griffiths exudate collection The removal or collection of specimen material through the use of suction. Emma Griffiths vacuuming for specimen collection A tube that contains media or preservative Emma Griffiths NOTE: there are different types of tubes with coloured caps indicating different preservatives etc. tube containing media or preservative A tube that contains antimicrobials Emma Griffiths NOTE: there are different types of tubes with coloured caps indicating different preservatives etc. tube containing antimicrobial A sterilized sampling bag that is puncture proof tabs for protection from damage due to wire-end protrusion and leak-proof closures. Emma Griffiths Whirlpak sampling bag Emma Griffiths spoon Emma Griffiths fork A shovel-like utensil that has a deep curved dish and a short handle and is used for digging into a soft substance for lifting out a portion. Emma Griffiths 2023-06-21T13:54:32Z hand scoop Emma Griffiths trier A device which generates a vacuum to provide suction of material. Emma Griffiths vaccum device investigation identifier specification order: GENEPIO:0001640 # taxonomy GENEPIO:0002086 # geographic location GENEPIO:0002076 # geographic feature GENEPIO:0002106 # food FOODON:03510136 # food consumer GENEPIO:0002094 # specimen collection device GENEPIO:0000025 # anatomical site GENEPIO:0000028 # body product GENEPIO:0001724 # host organism common name GENEPIO:0001567 # host taxonomy UBERON:0000105 # life cycle GENEPIO:0001639 # antigenic formula GENEPIO:0001718 # serotype specification GENEPIO:0000045 # PFGE test specification This is a draft (under development) collection of fields for capturing the contextual data for Enterobase (https://enterobase.warwick.ac.uk/) records. Damion Dooley draft Enterobase contextual data standard The name of the virulence factor molecule produced by a pathogen that specifically causes disease, or that influences the host's function to allow the pathogen to thrive. Emma Griffiths virulence factor name help:The protocol for determining virulence should include, when applicable, inoculum preparation, platforms and instrumentation, conditions, cell lines and animal models. The laboratory protocol used to determine virulence phenotypes and markers. Emma Griffiths virulence testing protocol name help:Detection limits should include the numerical cut-off (threshold) value and units for determining positive results e.g. qPCR value, CFUs. The detection limit denotes the smallest measure that can be detected with reasonable certainty for a given analytical procedure. Emma Griffiths detection limit A disease cluster is an unusually high incidence of a particular disease or disorder occurring in close proximity in terms of both time and geography. Damion Dooley https://en.wikipedia.org/wiki/Disease_cluster disease cluster A disease cluster in which two or more cases have been linked by an infectious disease transmission process. Damion Dooley infectious disease cluster help:used only with the source feature key; source feature keys containing the /environmental_sample qualifier should also contain the /isolation_source qualifier. entries including /environmental_sample must not include the /strain qualifier Identifies sequences derived by direct molecular isolation from a bulk environmental DNA sample (by PCR with or without subsequent cloning of the product, DGGE, or other anonymous methods) with no reliable identification of the source organism. Environmental samples include clinical samples, gut contents, and other sequences from anonymous organisms that may be associated with a particular host. They do not include endosymbionts that can be reliably recovered from a particular host, organisms from a readily identifiable but uncultured field sample (e.g., many cyanobacteria), or phytoplasmas that can be reliably recovered from diseased plants (even though these cannot be grown in axenic culture). ENA Webin:environmental_feature EBI ENA Webin environmental feature The European Nucleotide Archive (ENA) provides a comprehensive record of the world's nucleotide sequencing information, covering raw sequencing data, sequence assembly information and functional annotation. Webin is an ENA interface and standard for sequence submissions. https://www.ebi.ac.uk/ena EBI European Nucleotide Archive Webin https://www.ebi.ac.uk/ena/WebFeat/ help:Breadth of coverage should be reported as a percentage value (e.g. 95%) to a fold of coverage (e.g. 10X). breadth of coverage Eighty percent of the reference genome was covered by sequence fragments with a coverage depth of 4X; therefore, the breadth of coverage was 80% (4:5). Eighty percent of the reference genome was covered by sequence fragments with a coverage depth of 4X; therefore, the breadth of coverage was 80% (4:5). A data item which is the amount of a reference sequence covered by a sequence of interest. A data item which is the amount of a reference sequence covered by a sequence of interest. https://orcid.org/0000-0002-1107-9135 Emma Griffiths https://github.com/obi-ontology/obi/issues/1579 OBI:0002879 breadth of coverage breadth of coverage The mean contig length is the count of base pairs in the average size contig of the sequence assembly. Emma Griffiths mean contig length order: GENEPIO:0000084 # read adapter trimming (y/n) GENEPIO:0002096 # read adapter trimming software GENEPIO:0002095 # read paired-end merging software GENEPIO:0000150 # read trimming and filtering software The procedures used to remove adapters from raw sequence reads, trim low quality bases and where applicable, merge paired-end reads. Emma Griffiths raw sequence data processing datum Name of strain from which sample was obtained OR name of isolate from which sample was obtained. Damion Dooley specimen strain or isolate identifier \s*(\d(.\d{1,4})?|[1-8]\d(.\d{1,4})?|90(.0{1,4})?)\s*[WEwe]\s*(\d(.\d{1,4})?|[1-9]\d(.\d{1,4})?|1[0-7]\d(.\d{1,4})?|180(.0{1,4})?)\s*[NSns]\s* The geographical coordinates of the location where the sample was collected. Specify as degrees latitude and longitude in format "d[d.dddd] N|S d[dd.dddd] W|E", eg, 38.98 N 77.11 W Damion Dooley https://www.ncbi.nlm.nih.gov/biosample/docs/attributes/ latitude and longitude coordinate (NCBI BioSample format) decimal value specification floating point value specification unsigned integer A 32 bit number having a range 0 - 4294967295. unsigned integer value specification 1 1 date value specification 1 A specification for the size of an assembled genome as measured in base pairs. This is a decimal because the megabasepair unit may involve a fractional component. assembly genome size specification sequencing facility name specification date (ISO 8601) A date should be recorded as YYYY-MM-DD according to ISO 8601. HOWEVER ... OWL 2.0 does not include xsd:date as a permitted data type, so this value specification only accepts xsd:dateTime date value specification (ISO 8601) strain identifier specification 1 5 100 A value specification for a MIC test measurement resulting from a laboratory diffusion method. Damion Dooley MIC diffusion measurement specification unsigned short A 16 bit integer ranging from 0 - 65535 unsigned short integer value specification 1 genomic sequence length specification 1 0.01 2048.0 A value specification for a MIC test measurement resulting from a laboratory dilution method. Damion Dooley MIC dilution measurement specification The date on which a specimen was collected, in ISO 8601 format. specimen collection date (ISO 8601) date of diagnosis (ISO 8601) 1 0 A value specification which describes the age since birth of a given organism that is involved in an investigation or study at a given time. Damion Dooley subject age specification subject age at time of specimen collection specification 1 boolean A boolean value specification indicates a presence (true value) or absence (false value) of a given feature. Damion Dooley boolean value specification specimen identifier specification [A-Za-z0-9]+([_.\-][A-Za-z0-9]+)*\@[A-Za-z0-9]+([.\-][A-Za-z0-9]+){1,3} email address specification region, province, state or territory specification A specification for a geographic location that a specimen was collected at. specimen collection site specification subject organism common name specification A subject identifier specification is a specification including datatype pertaining to a given standard's subject identifier field. Damion Dooley subject identifier specification A value specification which describes the name of a disease in a subject that is related to a given investigation, study and/or specimen. Damion Dooley NIAID GSCID-BRC metadata working group Controlled vocabulary. Human specimen source: https://bioportal.bioontology.org/ontologies/DOID or https://www.ncbi.nlm.nih.gov/mesh/1000067 subject disease specification unsigned long integer A 64 bit integer ranging from 0 - 18446744073709551615 unsigned long integer value specification The physical location that a specimen was collected at. The location may be described by geographic coordinates, city or other geopolitical entity, biome, etc. Damion Dooley specimen collection site The unit provided for an antibiotic drug test dosage. Damion Dooley drug MIC unit specification Damion Dooley A datum specification for the maximum concentration of a drug applied during an an assay. test drug maximum concentration specification A value specification which describes the minimum concentration of a drug applied during an an assay. Damion Dooley test drug minimum concentration specification (1/2|1/2a|1/2b|1/2c|3a|3b|3c|4a|4ab|4b|4c|4d|4e|1|7) listeria antigen specification 1 url URL specification A value specification which describes the travel destination a given human has travelled to on a particular trip. Damion Dooley travel destination specification A data specification for a specimen source substance, which is an organism substance or food product or environmental substance from which the specimen was extracted. Damion Dooley specimen source substance specification Damion Dooley note: OBI has a variety of subclasses like "blood specimen" and "colon specimen" etc. which we have not added here. The are mapped to UBERON terms indirectly through the logic "derives from some [uberon term]". GenEpiO takes a different approach in describing this class with lists for "subject anatomical site", "subject body product", and "plant anatomy". specimen from organism specification 1 0 duration specification 2019-04-17T23:04:53Z obsolete: field specification true Damion Dooley http://purl.obolibrary.org/obo/ARO_3004431 obsolete: antimicrobial resistance phenotype - epidemiological cut-off values true Damion Dooley 2019-04-17T23:41:35Z PulseNet Canada field Damion Dooley 2019-04-17T23:41:56Z PulseNet Canada Salmonella field Damion Dooley 2019-05-03T02:44:38Z specimen collection service Damion Dooley 2019-05-03T02:49:24Z bioinformatics analysis service An isolate preparation service prepares isolates for molecular sequencing. Damion Dooley 2019-05-03T02:51:51Z isolate preparation service order: GENEPIO:0002222 # specimen collection service GENEPIO:0002226 # specimen repository/biobank service GENEPIO:0002224 # isolate preparation service OBI:0001904 # sequencing service OBI:0000992 # DNA sequencing service GENEPIO:0002223 # bioinformatics analysis service Damion Dooley 2019-05-03T02:52:19Z specimen related service Damion Dooley 2019-05-03T03:24:33Z specimen repository/biobank service An organism datum about subject health status in which vital signs are unstable and not within normal limits, patient may be unconscious and indicators are unfavorable. 2019-11-19T22:17:43Z grave critical health status critical critical A datum indicating one of six defined subspecies of Salmonella. 2019-11-25T08:45:41Z Salmonella subspecies A PFGE pattern resulting from DNA fragmentation induced by the Spel enzyme. 2019-11-25T09:07:26Z PFGE Spel pattern A collection of organisms that is indicative of faecal contamination. 2020-02-08T20:15:43Z Fecal indicator organism collections include bacterial groups such as thermotolerant coliforms or E. coli. Hence, they only infer that pathogens may be present fecal indicator An isolate derived from a food sample. Damion Dooley 2019-06-28T23:41:26Z food isolate A method for typing The RNA component of the small (30S) subunit of prokaryotic ribosomes. 2020-04-24T19:06:05Z microbial 16S RNA typing h(1|2|3|4|5|6|7|8|9|10|11|12|14|15|16|17|18|19|21|23|24|26|27|28|29|30|31|32|33|34|35|36|37|38|39|40|41|42|43|44|45|46|47|48|49|51|52|53|54|55|56) E. coli H antigen specification O([1-9][0-9][0-9]) E. coli O antigen specification 1 string string value specification A sequencing platform brand provided by Helicos corporation (now defunct). 2020-04-24T22:50:49Z Helicos platform A sequencing platform provided by the Ion Torrent company. 2020-04-24T22:54:06Z Ion Torrent platform A sequencing platform provided by Life Technologies Corporation Sequencing by Oligonucleotide Ligation and Detection 2020-04-24T22:55:31Z SOLiD sequening platform obsolete: drag swab true Rinse is the liquid output of rinsing plant, animal or other material with liquid with the objective of extracting specimen material from that liquid. Damion Dooley 2019-06-28T20:07:25Z rinse Animal rinse is a rinse derived from animal material of one or more animals. Damion Dooley 2019-06-28T20:11:45Z animal rinse obsolete: surface wipe true A low flat-bottomed laboratory container for growing a layer of organisms such as bacteria, molds, and cells on a thin layer of nutrient medium. https://en.wikipedia.org/wiki/Culture_plate 2022-09-23T10:59:09Z culture plate A fluid that is obtained from rinsing meat for the purpose of collecting materials and organisms that are on its surface. 2022-09-23T11:24:53Z fluid from meat rinse A sequencing platform provided by the BGI Genomics company. https://en.wikipedia.org/wiki/BGI_Group 2022-09-23T11:41:23Z BGI Genomics platform A sequencing platform provided by the MGI company. https://en.wikipedia.org/wiki/MGI_(company) 2022-09-23T11:43:21Z MGI platform A fecal specimen collection method in which feces is obtained by inserting the collection device into the anus of the host, or the feces is captured as it is excreted. Emma J Griffiths 2022-09-23T11:47:33Z fecal grab A DNA sequencer which is manufactured by the Illumina corporation using sequence-by-synthesis chemistry that fits on a benchtop and uses P1 and P2 flow cells. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. 2023-06-21T12:33:56Z Illumina NextSeq 1000 An adapter for MinION or GridION DNA sequencers manufactured by the Oxford Nanopore corporation that enables sequencing on smaller, single-use flow cells. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://store.nanoporetech.com/flongle.html 2023-06-21T13:02:13Z Oxford Nanopore Flongle Undigested food material, microbiota, and other materials found in the stomach. 2023-11-28T14:17:24Z stomach content A mixture of feces obtained from multiple individuals. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. 2023-11-28T14:45:32Z fecal composite Feces that was recently excreted. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. 2023-11-28T14:28:34Z feces (fresh) Feces which is deposited in the environment. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. 2023-11-28T14:50:43Z feces (environmental) A specimen collection device that is used to collect soft sediments in lakes or oceans. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. 2023-11-29T14:18:43Z box corer requires discussion A severe acute respiratory syndrome-related coronavirus which is 1) bat-derived, 2) sharing 93.3% nucleotide identity with SARS-CoV-2, and 3) contains an insertion at the S1/S2 cleavage site in the spike protein. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://en.wikipedia.org/wiki/RmYN02 https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z RmYN02 requires discussion A sampling strategy in which individuals are chosen for investigation into a disease cluster or outbreak. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Cluster/Outbreak investigation https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z The terms cluster and outbreak both describe the occurrence of new disease cases within a particular location and time period. The number of cases within a cluster are not necessarily greater than what is expected, however in an outbreak the number of cases does exceed the usual norm. In an outbreak the cases are confirmed to be epidemiologically linked while in a cluster an epidemiological connection is only suspected. Not all clusters are outbreaks, however each cluster needs to be investigated. [Source: https://covid19evidencereviews.saskhealthauthority.ca/en/permalink/coviddoc153] cluster/outbreak investigation sampling requires discussion A sampling strategy in which individuals are sampled in the context of diagnostic testing. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Diagnostic testing https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z diagnostic testing sampling requires discussion A sampling strategy in which individuals are sampled in order to perform research. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Research https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z research sampling requires discussion A sampling strategy in which individuals are sampled for surveillance investigations. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Surveillance https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z surveillance sampling requires discussion A surveillance sampling strategy in which baseline is established at the beginning of a study or project by the selection of sample units via random sampling. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Baseline surveillance (random sampling) https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z random sampling Such that each possible unit has a fixed and known or equal probability of selection. [Source: "Random Sample" (p.238) in Porta, M. (2014). A Dictionary of Epidemiology (6th ed.). Oxford University Press, Incorporated.] baseline surveillance strategy requires discussion A surveillance sampling strategy in which an aspired outcome is explicity stated. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Targeted surveillance (non-random sampling) Target" (p.279) in Porta, M. (2014). A Dictionary of Epidemiology (6th ed.). Oxford University Press, Incorporated. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z non-random sampling targeted surveillance strategy requires discussion A targeted surveillance strategy which is considered important and/or urgent. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Priority surveillance project https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z priority surveillance project strategy requires discussion A targeted surveillance strategy in which the aim is early detection of variants of concern (VoC) in individuals. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Screening for Variants of Concern (VoC) https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z screening for VOC screening for VoC screening for Variants of Concern strategy requires discussion A priority surveillance strategy in which subsets of a defined population can be identified who are, have been, or in the future may be exposed or not exposed - or exposed in different degrees - to a disease of interest and are selected to under go repeat sampling over a defined period of time. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Longitudinal surveillance (repeat sampling of individuals) Cohort Study" (p.50) in Porta, M. (2014). A Dictionary of Epidemiology (6th ed.). Oxford University Press, Incorporated. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z repeat sampling of individuals longitudinal surveillance strategy requires discussion A priority surveillance strategy in which a population that previously tested positive for a disease of interest, and since confirmed to have recovered via a negative test, are monitored for positive test indication of re-infection with the disease of interest within a defined period of time. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Re-infection surveillance https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z re-infection surveillance strategy requires discussion A priority surveillance strategy in which individuals are monitored for investigation into vaccine escape, i.e., identifying variants that contain mutations that counteracted the immunity provided by vaccine(s) of interest. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Vaccine escape surveillance https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z vaccine escape surveillance strategy requires discussion A priority surveillance strategy in which individuals are selected if they have a travel history outside of the reporting region within a specified number of days before onset of symptoms. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Travel-associated surveillance https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z travel-associated surveillance strategy requires discussion A travel-associated surveillance strategy in which individuals are selected if they have an intranational travel history within a specified number of days before onset of symptoms. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Domestic travel surveillance https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z domestic travel surveillance strategy requires discussion A travel-associated surveillance strategy in which individuals are selected if they have a travel history outside of the reporting country in a specified number of days before onset of symptoms. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. International travel surveillance https://www.eurosurveillance.org/content/10.2807/1560-7917.ES.2020.25.37.2001641 https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z international travel surveillance strategy requires discussion An international travel-associated surveillance strategy in which individuals are selected if they have a travel history of crossing an international border via air travel or ground transport. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Surveillance of international border crossing by air travel or ground transport https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z surveillance of international border crossing by air travel or ground transport strategy requires discussion An international travel-associated surveillance strategy in which individuals are selected if they have a travel history of crossing an international border via air travel. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Surveillance of international border crossing by air travel https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z surveillance of international border crossing by air travel strategy requires discussion An international travel-associated surveillance strategy in which individuals are selected if they have a travel history of crossing an international border via ground transport. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Surveillance of international border crossing by ground transport https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z surveillance of international border crossing by ground transport strategy requires discussion A travel-associated surveillance strategy in which individuals are selected if they have a travel history outside of the reporting country in a specified number of days before onset of symptoms. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Surveillance from international worker testing https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z surveillance from international worker testing strategy obsolete: cluster/outbreak investigation strategy true requires discussion An outbreak investigation sampling strategy in which individuals are chosen for investigation into a disease outbreak that has connections to two or more jurisdictions. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Multi-jurisdictional outbreak investigation https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z multi-jurisdictional outbreak investigation strategy requires discussion An outbreak investigation sampling strategy in which individuals are chosen for investigation into a disease outbreak that only has connections within a single jurisdiction. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Intra-jurisdictional outbreak investigation https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z intra-jurisdictional outbreak investigation strategy obsolete: research strategy true requires discussion A research sampling strategy in which individuals are sampled in order to perform a viral passage experiment. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Viral passage experiment https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z viral passage experiment strategy requires discussion A research sampling strategy in which samples are collected in order to test a method or protocol. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Protocol testing Protocol testing experiment https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z protocol testing sampling personal protective gown A personal protective clothing item which is a gown worn in order to provide a barrier between a person and the external environment. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-9578-0788 PPE gown personal protective equipment gown protective gown Rhiannon Cameron personal protective gown requires discussion A device which is used to collect liquid samples. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z collection cup swab requires discussion A device which is a soft, absorbent material mounted on one or both ends of a stick. A device which is a soft, absorbent material mounted on one or both ends of a stick. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-8395-2570 https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z swab swab requires discussion An aspiration process which involves putting a needle through the skin just above the pubic bone into the bladder to take a urine sample. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z suprapubic aspiration requires discussion An aspiration process which collects tracheal secretions. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z tracheal aspiration requires discussion An aspiration process which uses a vacuum source to remove a sample. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z vacuum aspiration requires discussion A filtration process which removes solid particulates from the air via an air filtration device. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z air filtration requires discussion The collection of bronchoalveolar lavage fluid (BAL) from the lungs. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z BAL bronchoalveolar lavage requires discussion The administration and evacuation of small volumes of liquid through an orogastric tube to remove toxic substances within the stomach. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z gastric lavage requires discussion A collecting specimen from organism process in which a salt water solution is taken into the oral cavity, rinsed around, and gargled before being deposited into an external collection device. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z mouth rinse and gargle saline gargle requires discussion A specimen collection process in which a sample is collected by scraping a surface with a sterile sampling device. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z scraping requires discussion A collecting specimen from organism process in which a skin site free of surface arterial flow is pierced with a sterile lancet, after a capillary blood droplet is formed a sample is captured in a capillary tupe. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z finger prick Antiviral treatment administered prior to the current regimen or test. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z prior antiviral treatment requires discussion A collecting specimen from organism process in which fluid is added to the eye prior to sample collection, effectively "washing out" ocular surface molecules. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z washout tear collection requires discussion The process of growing a virus in serial iterations. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z virus passage requires discussion A secondary RNA extraction after performing reverse transcription polymerase chain reaction (RT-PCR). The desired output is RNA. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z RNA re-extraction (post reverse transcription-polymerase chain reaction) RNA re-extraction (post RT-PCR) requires discussion 293 cells stably expressing the SARS-CoV receptor protein, angiotensin-converting enzyme 2 (ACE2). Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z 293/hACE2 cell line 293/ACE2 cell line requires discussion Eptesicus fucus (big brown bat) kidney 3B cells. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z Efk-3B clone 3B cell Efk3B cell Eptesicus fucus kidney 3B cell EFK3B cell line requires discussion Normal human primary renal cortical epithelial cells. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z human renal cortical epithelial cell line HRCE cell line requires discussion VeroE6 cells expressing the transmembrane serine protease TMPRSS2. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://cellbank.nibiohn.go.jp/~cellbank/en/search_res_det.cgi?ID=8668 https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z Vero E6/TMPRSS2 cell Vero-E6/TMPRSS2 cell VeroE6/TMPRSS2 cell line requires discussion The condition of being treated as a patient in a hospital without admission to an intensive care unit (ICU). Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Hospitalized (Non-ICU) https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z Hospitalized (non-intensive care units) hospitalized (non-ICU) datum requires discussion The condition of being treated as a patient in a hospital intensive care unit (ICU). Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Hospitalized (ICU) https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z Hospitalized (intensive care units) hospitalized (ICU) datum requires discussion Separation of people with a contagious disease from population to reduce the spread of the disease. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Mechanical Ventilation https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7338113/ https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z medically isolated datum requires discussion Medical isolation in a negative pressure environment: 6 to 12 air exchanges per hour, and direct exhaust to the outside or through a high efficiency particulate air filter. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Medically Isolated https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z medically isolated (negative pressure) datum ready for release An age group that stratifies the age of a case to be between 0 to 9 years old (inclusive). 0 - 9 https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z subject age at time of specimen collection bin (0 - 9) ready for release An age group that stratifies the age of a case to be between 10 to 19 years old (inclusive). 10 - 19 https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z subject age at time of specimen collection bin (10 - 19) ready for release An age group that stratifies the age of a case to be between 20 to 29 years old (inclusive). 20 - 29 https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z subject age at time of specimen collection bin (20 - 29) ready for release An age group that stratifies the age of a case to be between 30 to 39 years old (inclusive). 30 - 39 https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z subject age at time of specimen collection bin (30 - 39) ready for release An age group that stratifies the age of a case to be between 40 to 49 years old (inclusive). 40 - 49 https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z subject age at time of specimen collection bin (40 - 49) ready for release An age group that stratifies the age of a case to be between 50 to 59 years old (inclusive). 50 - 59 https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z subject age at time of specimen collection bin (50 - 59) ready for release An age group that stratifies the age of a case to be between 60 to 69 years old (inclusive). 60 - 69 https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z subject age at time of specimen collection bin (60 - 69) ready for release An age group that stratifies the age of a case to be between 70 to 79 years old (inclusive). 70 - 79 https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z subject age at time of specimen collection bin (70 - 79) ready for release An age group that stratifies the age of a case to be between 80 to 89 years old (inclusive). 80 - 89 https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z subject age at time of specimen collection bin (80 - 89) ready for release An age group that stratifies the age of a case to be between 90 to 99 years old (inclusive). 90 - 99 https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z subject age at time of specimen collection bin (90 - 99) ready for release An age group that stratifies the age of a case to be greater than or equal to 100 years old. 100+ https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z subject age at time of specimen collection bin (100+) ready for release Age of host at the time of sampling, expressed as an age group in years. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z subject age at time of specimen collection bin requires discussion Inability to arouse in response to one or more external stimuli. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Inability to arouse (inability to stay awake) https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z inability to stay awake inability to arouse requires discussion Persistent blue discoloration of the lips. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Cyanotic face (bluish face) https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z bluish face cyanotic face requires discussion Generalized bluish discoloration of the body and the visible mucous membranes, which occurs due to inadequate oxygenation secondary to conditions that lead to an increase in deoxygenated hemoglobin or presence of abnormal hemoglobin. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z central cyanosis requires discussion Persistent blue discoloration of the lips. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Cyanotic lips (bluish lips) https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z bluish lips cyanotic lips requires discussion Bluish discoloration of the distal extremities (hands, fingertips, toes), and can sometimes involve circumoral and periorbital areas. Mucous membranes are generally not involved. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z peripheral cyanosis requires discussion Fever that exceeds 38 degrees centigrade. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z fever (>=100.4°F) fever (>=38°C) requires discussion Focal or diffuse areas of ill-defined, hazy, increased lung attenuation, which cause pulmonary vascular indistinctness, yet through which vessels can still be identified via high-resolution computed tomography or the conventional radiograph. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Ground Glass Opacities (GGO) PMID: 12465687 https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z GGO ground glass opacities requires discussion Abnormally low blood oxygen level without the presence of dyspnea/dyspnoea. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Silent hypoxemia https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7397783/ https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z silent hypoxemia requires discussion Inflammation of infection of the ear. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Otitis https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z otitis requires discussion Fluid exuded from the pharynx posterior wall. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Pharyngeal exudate https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z pharyngeal exudate Replaced with entity from an appropriate domain ontology. obsolete: prostration true requires discussion Inflammatory chilblain-like nodules on the hands and/or fingers. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Pseudo-chilblains on fingers (covid fingers) https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z covid fingers pseudo-chilblains on fingers requires discussion Inflammatory chilblain-like nodules on the feet and/or toes. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Pseudo-chilblains on toes (covid toes) https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z covid toes pseudo-chilblains on toes requires discussion Trauma to the cardiac muscle or valves. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://www.ebi.ac.uk/ols/ontologies/ncit/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FNCIT_C45430 https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z cardiac injury requires discussion A reflex action of the respiratory tract that is used to clear the upper airways, lasting for more than 8 weeks Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z chronic cough requires discussion A persistent disease that affects the gastrointestinal tract. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z chronic gastrointestinal disease requires discussion The period of time less than or equal to six weeks after labor and delivery. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z postpartum (≤6 weeks) requires discussion The use of a drug for a reason other than which it was intended or in a manner or in quantities other than directed. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z drug abuse requires discussion The use of an injection drug for a reason other than which it was intended or in a manner or in quantities other than directed. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z injection drug abuse requires discussion An individual who is receiving or has received a transplant of a heart. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z cardiac transplant requires discussion An individual who is receiving or has received a transplant of a liver. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z liver transplant requires discussion A variant designation which is 1) a variant of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), 2) believed to have genetic mutations that increase binding affinity to human cells, 3) linked to rapid spread in human populations, and 4) is being monitored. Variant of Concern (VOC) https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z VOC VoC PHA4GE Definition: A category used for indicating that a variant of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) containing genetic mutations believed to increase binding affinity to human cells and linked to rapid spread in human populations is being monitored. variant of concern (SARS-CoV-2) requires discussion A variant designation which is 1) a variant of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), 2) demonstrated to have genetic mutations that increase binding affinity to human cells, 3) linked to rapid spread in human populations, and 4) is under surveillance. Variant of Interest (VOI) https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z VOI PHA4GE Definition: A category used for indicating that a variant of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) containing genetic mutations demonstrated to increase binding affinity to human cells and linked to rapid spread in human populations is under surveillance. variant of interest (SARS-CoV-2) requires discussion A disorder characterized by an arrhythmia with an above normal rate. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=21.09d&ns=ncit&code=C110938&key=n2078840696&b=1&n=null https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z tachyarrhythmia requires discussion A disease process that results in acute hypoxia secondary to a rapid deterioration in respiratory status.Increased capillary permeability and changes in pressure gradients within the pulmonary capillaries and vasculature are mechanisms for which noncardiogenic pulmonary edema occurs. To differentiate from cardiogenic pulmonary edema, pulmonary capillary wedge pressure is not elevated and remains less than 18 mmHg. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z noncardiogenic pulmonary edema requires discussion A clinical syndrome characterized by the acute onset of pulmonary edema following a significant central nervous system (CNS) insult. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z NPE neurogenic pulmonary edema Redundant with "term replaced by" entity. obsolete: cardiac injury true requires discussion An acute form of myocarditis, whose main characteristic is a rapidly progressive clinical course with the need for hemodynamic support. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z fulminant myocarditis requires discussion A diagnosis of Kawasaki disease (KD) based on the fulfillment of a set of clinical signs including fever of five or more days' duration with at least four of the following five signs: (i) bilateral conjunctival injection, (ii) cervical lymphadenopathy, (iii) polymorphous skin rash, (iv) changes in the lips or oral mucosa, and (v) changes of the distal extremities.Usual laboratory findings in KD patients include elevated erythrocyte sedimentation rate and C-reactive protein, hypoalbuminemeia, elevated serum hepatic transaminases and leukocytosis with thrombocytosis noted later in the course of the illness. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z complete Kawasaki syndrome complete Kawasaki disease requires discussion A diagnosis of Kawasaki disease (KD) when patients fail to meet “classic” clinical features but have laboratory findings usually associated with KD and no reasonable alternate diagnosis, they are said to have incomplete or atypical KD. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z incomplete Kawasaki syndrome incomplete Kawasaki disease requires discussion A condition of liver damage that is characterized by coagulopathy with no signs of encephalopathy. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://doi.org/10.1016/j.aohep.2018.11.009 https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z acute liver injury requires discussion A lung injury that results from mechanical stress and strain that occur during tidal ventilation in the susceptible lung. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z VILI ventilation induced lung injury requires discussion An injury in muscle tissue caused by bruising, spraining or laceration. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z muscle injury requires discussion An organ dysfunction to such a degree that normal homeostasis cannot be maintained without external clinical intervention. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://en.wikipedia.org/wiki/Organ_dysfunction https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z organ failure requires discussion A infection caused by staphylococcus bacteria, bearing the secondary infection role Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z If a secondary staphylococcus infection was identified during or after treatment of the primary infection. secondary staph infection requires discussion A infection caused by streptococcal bacteria, bearing the secondary infection role Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z If a secondary streptococcal infection was identified during or after treatment of the primary infection. secondary strep infection requires discussion A systemtic inflammatory response to infectious and/or non-fectious etiologies, resulting in life-threatening, generalized form of acute circulatory failure associated with inadequate oxygen utilization by the cells. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z Descriptive of both infectious and non-infectious etiologies. hyperinflammatory shock requires discussion A persistent form of cardiogenic shock that presents as persistent tissue hyoperfusion despite administration of adequote doses of vasoactive medications and treatmenft of the underlying aetiology. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z refractory cardiogenic shock requires discussion A persistent form of cardiogenic shock that presents simultaneously with vasoplegic shock. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z refractory cardiogenic plus vasoplegic shock requires discussion A vaccination status in which an individual has completed a full series of an authorized vaccine according to the regional health institutional guidance. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z PHA4GE Definition: A category used for indicating that a variant of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) containing genetic mutations demonstrated to increase binding affinity to human cells and linked to rapid spread in human populations is under surveillance. fully vaccinated requires discussion A vaccination status in which an individual has started but not yet fully completed a vaccine series authorized and administered according to the regional health institutional guidance. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z In general, people are considered partially vaccinated 2 weeks after their first dose in a single-dose or multi-dose vaccine series. partially vaccinated requires discussion A vaccination status in which an individual has not completed or initiated a vaccine series authorized and administered according to the regional health institutional guidance. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z unvaccinated In general, people are considered not vaccinated if they have not received a single dose or have not yet completed the 2 weeks after their first dose in a single-dose or multi-dose vaccine series. not vaccinated requires discussion A manufactured product which separates solids from fluids by adding a medium through which only a fluid can pass. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. http://purl.obolibrary.org/obo/NCIT_C41199 https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z filter requires discussion An extract which is the output of an extraction process in which messenger RNA molecules are isolated from a specimen. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. mRNA (messenger RNA) https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z messenger RNA extract mRNA extract requires discussion A DNA sequencer manufactured by the Illumina corporation. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z Illumina sequencing instrument model requires discussion A DNA sequencer manufactured by Solexa as one of its first sequencer lines, launched in 2006, and capable of sequencing 1 gigabase (Gb) of data in a single run. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z Illumina Genome Analyzer Rehomed in OBI obsolete: Illumina Genome Analyzer II true Rehomed in OBI obsolete: Illumina Genome Analyzer IIx true requires discussion A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry, and contains a HiScan Reader for sequencing and microarray-based analyses as well as an "SQ Module" to support microfluidics. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z Illumina HiScanSQ requires discussion A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry, enabling deep sequencing and high yield. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z Illumina HiSeq requires discussion A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry that oenabled sufficent depth and coverage to produce the first 30x human genome for $1000. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z Illumina HiSeq X requires discussion A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry that consists of a set of 5 HiSeq X Sequencing Systems. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z Illumina HiSeq X 5 Illumina HiSeq X Five requires discussion A DNA sequencer that consists of a set of 10 HiSeq X Sequencing Systems. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z Illumina HiSeq X 10 Illumina HiSeq X Ten Rehomed in OBI obsolete: Illumina HiSeq 1000 true requires discussion A DNA sequencer which is manufactured by the Illumina corporation, with a single flow cell and a throughput of up to 35-50 Gb per day. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z Illumina HiSeq 1500 Rehomed in OBI obsolete: Illumina HiSeq 2000 true Rehomed in OBI obsolete: Illumina HiSeq 2500 true Rehomed in OBI obsolete: Illumina HiSeq 3000 true Rehomed in OBI obsolete: Illumina HiSeq 4000 true requires discussion A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry that is lightweight. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z Illumina iSeq requires discussion A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry that is lightweight and has an output capacity between 144MB-1.2GB. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z Illumina iSeq 100 requires discussion A DNA sequencer manufactured by the Illunina corporation using sequence-by-synthesis chemistry that has an output capacirty of 6 Tb and 20 billion reads in dual flow cell mode. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z Illumina NovaSeq requires discussion A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and an output of up to 6000 Gb (32-40 B reads per run). The sequencer utilizes synthesis technology and patterned flow cells to optimize throughput and even spacing of sequencing clusters. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z Illumina NovaSeq 6000 requires discussion A DNA sequencer which is manufactured by the Illumina corporation using sequence-by-synthesis chemistry that fits on a benchtop and has an output capacity of 1.65-7.5 Gb. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z Illumina MiniSeq Rehomed in OBI obsolete: Illumina MiSeq true requires discussion A DNA sequencer which is manufactured by the Illumina corporation using sequence-by-synthesis chemistry that fits on a benchtop and has an output capacity of 1.65-7.5 Gb. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z Illumina NextSeq Rehomed in OBI obsolete: Illumina NextSeq 500 true requires discussion A DNA sequencer which is a desktop sequencer ideal for smaller-scale studies manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. The 550 is an upgrade on the 500 model. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z Illumina NextSeq 550 requires discussion A DNA sequencer which is manufactured by the Illumina corporation using sequence-by-synthesis chemistry that fits on a benchtop and has an output capacity of 30-360 Gb. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z Illumina NextSeq 2000 requires discussion A DNA sequencer manufactured by the Pacific Biosciences corporation. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z Pacific Biosciences sequencing instrument model requires discussion A DNA sequencer manufactured by the Pacific Biosciences corporation which utilizes “SMRT Cells” for single-molecule real-time sequencing. The RS was the first model made by the company. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z PacBio RS Rehomed in OBI obsolete: PacBio RS II true requires discussion A DNA sequencer built upon single molecule real-time sequencing technology, optimized for generation with long reads and high consensus accuracy, and manufactured by the Pacific Biosciences corporation Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z PacBio Sequel requires discussion A DNA sequencer built upon single molecule real-time sequencing technology, optimized for generation of highly accurate ("HiFi") long reads, and which is manufactured by the Pacific Biosciences corporation. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z PacBio Sequel II requires discussion A DNA sequencer manufactured by the Ion Torrent corporation. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z Ion Torrent sequencing instrument model requires discussion A DNA sequencer manufactured by the Ion Torrent corporation which utilizes Ion semiconductor sequencing and has an output capacity of 300 MB - 1GB. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z Ion Torrent PGM requires discussion A DNA sequencer manufactured by the Ion Torrent corporation which utilizes Ion semiconductor sequencing and has an output capacity of up to 15 Gb. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z Ion Torrent Proton requires discussion A DNA sequencer manufactured by the Ion Torrent corporation which utilizes Ion semiconductor sequencing and requires only a small amount of input material while producing data faster than the S5 model. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z Ion Torrent S5 XL requires discussion A DNA sequencer manufactured by the Ion Torrent corporation which utilizes Ion semiconductor sequencing and requires only a small amount of input material. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z Ion Torrent S5 requires discussion A DNA sequencer manufactured by the Oxford Nanopore corporation. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z Oxford Nanopore sequencing instrument model requires discussion A DNA sequencer that is manufactured by the Oxford Nanopore Technologies corporation, that can run and analyze up to five individual flow cells producing up to 150 Gb of data per run. The sequencer produces real-time results and utilizes nanopore technology with the option of running the flow cells concurrently or individual Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z Oxford Nanopore GridION requires discussion A portable DNA sequencer which is manufactured by the Oxford Nanopore Technologies corporation, that uses consumable flow cells producing up to 30 Gb of DNA sequence data per flow cell. The sequencer produces real-time results and utilizes nanopore technology with up to 512 nanopore channels in the sensor array. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z Oxford Nanopore MinION requires discussion A DNA sequencer that is manufactured by the Oxford Nanopore Technologies corporation, capable of running up to 48 flow cells and producing up to 7.6 Tb of data per run. The sequencer produces real-time results and utilizes Nanopore technology, with each flow cell allowing up to 3,000 nanopores to be sequencing simultaneously. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z Oxford Nanopore PromethION requires discussion A DNA sequencer manufactured by the BGI Genomics corporation. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z BGI Genomics sequencing instrument model requires discussion A DNA sequencer manufactured by the BGI Genomics corporation that utilizes Probe-Anchor Synthesis (cPAS) chemistry and "DNA Nanoballs". Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z BGI Genomics BGISEQ-500 requires discussion A DNA sequencer manufactured by the MGI corporation. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z MGI sequencing instrument model requires discussion A high throughput DNA sequencer manufactured by the MGI corporation with an output capacity of 1~6TB of data per day. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z MGI DNBSEQ-T7 requires discussion A DNA sequencer manufactured by the MGI corporation with an output capacity of 55GB~1440GB per run. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z MGI DNBSEQ-G400 requires discussion A DNA sequencer manufactured by the MGI corporation with an outout capacity of 55GB~330GB per run, which enables faster sequencing than the DNBSEQ-G400. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z MGI DNBSEQ-G400RS FAST requires discussion A DNA sequencer manufactured by the MGI corporation with an output capacity of 10～150 GB per run and enables different read lengths. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z MGI DNBSEQ-G50 requires discussion A gene encoding the envelope protein of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z orf4 gene (SARS-CoV-2) E gene (SARS-CoV-2) requires discussion A gene encoding the membrane glycoprotrein M protein of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z orf5 gene (SARS-CoV-2) M gene (SARS-CoV-2) requires discussion A gene encoding the nucleocapsid phosphoprotein of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z orf9 gene (SARS-CoV-2) N gene (SARS-CoV-2) requires discussion A gene encoding the Spike protein of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z orf2 gene (SARS-CoV-2) Spike gene (SARS-CoV-2) requires discussion A gene encoding the replicase polyprotein 1ab of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z rep gene (SARS-CoV-2) orf1ab gene (SARS-CoV-2) requires discussion A gene encoding the polyprotein 1a of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z pp1a gene (SARS-CoV-2) orf1a gene (SARS-CoV-2) requires discussion A gene encoding the nonstructural protein 11 of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z nsp11 gene (SARS-CoV-2) requires discussion A gene encoding the nonstructural protein 1 of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z nsp1 gene (SARS-CoV-2) requires discussion A gene encoding the nonstructural protein 2 of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z nsp2 gene (SARS-CoV-2) requires discussion A gene encoding the nonstructural protein 3 of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z nsp3 gene (SARS-CoV-2) requires discussion A gene encoding the nonstructural protein 4 of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z nsp4 gene (SARS-CoV-2) requires discussion A gene encoding the nonstructural protein 5 of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z nsp5 gene (SARS-CoV-2) requires discussion A gene encoding the nonstructural protein 6 of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z nsp6 gene (SARS-CoV-2) requires discussion A gene encoding the nonstructural protein 7 of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z nsp7 gene (SARS-CoV-2) requires discussion A gene encoding the nonstructural protein 8 of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z nsp8 gene (SARS-CoV-2) requires discussion A gene encoding the nonstructural protein 9 of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z nsp9 gene (SARS-CoV-2) requires discussion A gene encoding the nonstructural protein 10 of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z nsp10 gene (SARS-CoV-2) requires discussion A gene encoding the RNA-dependent RNA polymerase (RdRp) of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z nsp12 gene (SARS-CoV-2) RdRp gene (SARS-CoV-2) requires discussion A gene encoding the helicase (hel) of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z nsp13 gene (SARS-CoV-2) hel gene (SARS-CoV-2) requires discussion A gene encoding the nonstructural protein 14 of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z nsp14 gene (SARS-CoV-2) exoN gene (SARS-CoV-2) requires discussion A gene encoding the nonstructural protein 15 of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z nsp15 gene (SARS-CoV-2) requires discussion A gene encoding the nonstructural protein 16 of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z nsp16 gene (SARS-CoV-2) requires discussion A gene encoding the viroporin ORF3a of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z orf3a gene (SARS-CoV-2) requires discussion A gene encoding the polyprotein ORF3b of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z orf3b gene (SARS-CoV-2) requires discussion A gene encoding the nonstructural protein 6 of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z ns6 gene (SARS-CoV-2) orf6 gene (SARS-CoV-2) requires discussion A gene encoding a transmembrane protein of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z orf7a gene (SARS-CoV-2) requires discussion A gene encoding the polyprotein ORF7b of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z ns7b gene (SARS-CoV-2) orf7b gene (SARS-CoV-2) requires discussion A gene encoding the nonstructural protein 8 of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z ns8 gene (SARS-CoV-2) orf8 gene (SARS-CoV-2) requires discussion A gene encoding the viral accessory protein ORF9b of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z orf9b gene (SARS-CoV-2) requires discussion A gene encoding the membrane-associated protein ORF9c of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z orf9c gene (SARS-CoV-2) requires discussion A gene encoding the polyprotein ORF10 of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z orf10 gene (SARS-CoV-2) requires discussion A gene encoding the uncharacterized protein ORF14 of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z orf14 gene (SARS-CoV-2) requires discussion A genomic region that is untranslated at the 5' end of the genome of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. SARS-COV-2 5' UTR https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z SARS-CoV-2 5' untranslated region SARS-CoV-2 5'-UTR 5' UTR (SARS-CoV-2) requires discussion A process occuring within or in the vicinity of a human with a confirmed case of COVID-19 that exposes the recipient organism to SARS-CoV-2. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Contact with Known COVID-19 Case https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z contact with known COVID19 case contact with known COVID-19 case exposure process requires discussion A process occuring within or in the vicinity of a human patient that exposes the recipient organism to a material entity. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Contact with Patient https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z contact with patient exposure process requires discussion A process occuring within or in the vicinity of a human with a probable case of COVID-19 that exposes the recipient organism to SARS-CoV-2. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Contact with Probable COVID-19 Case https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z contact with probable COVID19 case contact with probable COVID-19 case exposure process requires discussion A process occuring within or in the vicinity of a human with acute respiratory illness that exposes the recipient organism to said acute respiratory illness. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Contact with Person with Acute Respiratory Illness https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z contact with person with acute respiratory illness exposure process requires discussion A process occuring within or in the vicinity of a human with a fever and/or cough that exposes the recipient organism to the causative agent. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Contact with Person with Fever and/or Cough https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z contact with person with fever and/or cough exposure process requires discussion A process occuring within or in the vicinity of a human, who recently travelled, that exposes the recipient organism to a material entity. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Contact with Person who Recently Travelled https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z contact with person who recently travelled exposure process requires discussion A process occuring within or in the vicinity of a human residential environment that exposes the recipient organism to a material entity. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Occupational, Residency or Patronage Exposure https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z occupational, residency or patronage exposure process requires discussion A process occuring within or in the vicinity of an animal rescue facility that exposes the recipient organism to a material entity. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Animal Rescue https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z animal rescue exposure process requires discussion A process occuring within or in the vicinity of a human childcare environment that exposes the recipient organism to a material entity. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Childcare https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z childcare exposure process requires discussion A process occuring within or in the vicinity of a human daycare environment that exposes the recipient organism to a material entity. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Daycare https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z daycare exposure process requires discussion A process occuring within or in the vicinity of a human nursery that exposes the recipient organism to a material entity. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Nursery https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z nursery exposure process requires discussion A process occuring within or in the vicinity of a community service centre that exposes the recipient organism to a material entity. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Community Service Centre https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z community service centre exposure process requires discussion A process occuring within or in the vicinity of a correctional facility that exposes the recipient organism to a material entity. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Correctional Facility https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z correctional facility exposure process requires discussion A process occuring within or in the vicinity of a dormitory that exposes the recipient organism to a material entity. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Dormitory https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z dormitory exposure process requires discussion A process occuring within or in the vicinity of a first nations reserve that exposes the recipient organism to a material entity. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. First Nations Reserve https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z first nations reserve exposure process requires discussion A process occuring within or in the vicinity of a fgroup home that exposes the recipient organism to a material entity. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Funeral Home https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z funeral home exposure process requires discussion A process occuring within or in the vicinity of a group home that exposes the recipient organism to a material entity. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Group Home https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z group home exposure process requires discussion A process occuring within or in the vicinity of a healthcare environment that exposes the recipient organism to a material entity. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Healthcare Setting https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z healthcare setting exposure process requires discussion A process occuring within or in the vicinity of an ambulance that exposes the recipient organism to a material entity. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Ambulance https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z ambulance exposure process requires discussion A process occuring within or in the vicinity of an acute care facility that exposes the recipient organism to a material entity. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Acute Care Facility https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z acute care facility exposure process requires discussion A process occuring within or in the vicinity of a medical clinic that exposes the recipient organism to a material entity. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Clinic https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z clinic exposure process requires discussion A process occuring within or in the vicinity of a community health centre that exposes the recipient organism to a material entity. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Community Health Centre https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z community health centre exposure process requires discussion A process occuring within or in the vicinity of an emergency department that exposes the recipient organism to a material entity. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Emergency Department https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z emergency department exposure process requires discussion A process occuring within or in the vicinity of an ICU that exposes the recipient organism to a material entity. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. ICU https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z ICU intensive care unit exposure process requires discussion A process occuring within or in the vicinity of a hospital ward that exposes the recipient organism to a material entity. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Ward https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z ward exposure process requires discussion A process occuring within or in the vicinity of a long-term care facility that exposes the recipient organism to a material entity. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Long-Term Care Facility https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z LTC facility long-term care facility exposure process requires discussion A process occuring within or in the vicinity of a pharmacy that exposes the recipient organism to a material entity. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Pharmacy https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z pharmacy exposure process requires discussion A process occuring within or in the vicinity of a physician's office that exposes the recipient organism to a material entity. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Physician's Office https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z physician's Office exposure process requires discussion A process occuring within or in the vicinity of a household that exposes the recipient organism to a material entity. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Household https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z household exposure process requires discussion A process occuring that exposes the recipient organism to a material entity as a consequence of said organism having insecure housing. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Insecure Housing (Homeless) https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z homeless insecure housing exposure process requires discussion A process occuring within or in the vicinity of a human occupational environment that exposes the recipient organism to a material entity. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Occupational Exposure https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z occupational exposure process requires discussion A process occuring within or in the vicinity of an office that exposes the recipient organism to a material entity. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Worksite https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z worksite exposure process requires discussion A process occuring outdoors that exposes the recipient organism to a material entity. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Outdoors https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z outdoors exposure process requires discussion A process that exposes the recipient organism to a material entity as a consequence of hiking. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Hiking Trail https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z hiking trail exposure process requires discussion A process occuring within or in the vicinity of a ski resort that exposes the recipient organism to a material entity. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Ski Resort https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z ski resort exposure process requires discussion A directive information entity which realizes sample strategy specifications. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z sampling strategy specification requires discussion A process occuring within or in the vicinity of a place of worship that exposes the recipient organism to a material entity. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Place of Worship https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z place of worship exposure process requires discussion A process occuring within or in the vicinity of a church that exposes the recipient organism to a material entity. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Church https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z church exposure process requires discussion A process occuring within or in the vicinity of a mosque that exposes the recipient organism to a material entity. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Mosque https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z mosque exposure process requires discussion A process occuring within or in the vicinity of a temple that exposes the recipient organism to a material entity. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Temple https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z temple exposure process requires discussion A process occuring within or in the vicinity of a school that exposes the recipient organism to a material entity. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. School https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z school exposure process requires discussion A process occuring within or in the vicinity of a temporary residence that exposes the recipient organism to a material entity. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Temporary Residence https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z temporary residence exposure process requires discussion A process occuring within or in the vicinity of a homeless shelter that exposes the recipient organism to a material entity. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Homeless Shelter https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z homeless shelter exposure process requires discussion A process occuring within or in the vicinity of a hotel exposure that exposes the recipient organism to a material entity. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Hotel https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z hotel exposure process requires discussion A process occuring within or in the vicinity of a veterinary facility that exposes the recipient organism to a material entity. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Veterinary Care Clinic https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z veterinary care clinic exposure process requires discussion A process occuring as a result of travel that exposes the recipient organism to a material entity. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Travel Exposure https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z travel exposure process requires discussion A process occuring within or in the vicinity of a cruise ship that exposes the recipient organism to a material entity. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Travelled on a Cruise Ship https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z travelled on a cruise ship exposure process requires discussion A process occuring within or in the vicinity of an airplane that exposes the recipient organism to a material entity. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Travelled on a Plane https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z travelled on a plane exposure process requires discussion A process occuring within or in the vicinity of ground transport that exposes the recipient organism to a material entity. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Travelled on Ground Transport https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z travelled on ground transport exposure process An absence of antiviral treatment administered prior to the current regimen or test. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z no prior antiviral treatment An infection that occurred within a host prior to the current infection. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z prior infection requires discussion A process occuring that exposes the recipient organism to a material entity. Other Exposure Setting https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z other exposure setting exposure process An absence of infection that occurred within a host prior to the current infection. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z no prior infection requires discussion A type of social behavior in which a sufficent number of humans gather together such that there is potential strain on community resources. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Mass Gathering https://en.wikipedia.org/wiki/Mass_gathering https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z mass gathering exposure datum requires discussion A human mass gathering in which humans meet at an arranged place and time in order to discuss or engage in some common interest. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Convention https://en.wikipedia.org/wiki/Convention_(meeting) https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z convention exposure datum requires discussion A human social gathering in which a group of humans formally assemble for a specific purpose. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Convocation https://en.wikipedia.org/wiki/Convocation https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z convocation exposure datum requires discussion A human social gathering at which humans gather for a planned or social occasion to carry out activities relevant to agriculture. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Agricultural Event https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z agricultural event exposure datum requires discussion A type of social behavior in which a collection of humans intentionally gathers together on a temporary basis to engage in a religious activity. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Religious Gathering https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z religious gathering exposure datum requires discussion A human eucharistic liturgical gathering in which humans perform public worship. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Mass https://en.wikipedia.org/wiki/Mass_(liturgy) https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z mass exposure datum requires discussion A human social event in which human family members congregate. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Family Gathering https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z family gathering exposure datum requires discussion A human social event in which many human members of an extended family congregate. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Family Reunion https://en.wikipedia.org/wiki/Family_reunion https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z family reunion exposure datum requires discussion A human social event in which humans gather for a ceremony connected with the final disposition of a corpse, such as a burial or cremation. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Funeral https://en.wikipedia.org/wiki/Funeral https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z funeral exposure datum Contact via airborne transmission or contact with contaminated surfaces. requires discussion A type of contact in which an individual does not come in direct contact with a source of infection. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z indirect contact requires discussion A type of indirect contact where an individual sustains unprotected exposure by being within 6 feet of an infected individual over a sustained period of time. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z face-to-face contact close indirect contact requires discussion A type of indirect contact where an individual may at the same location at the same time as a positive case; however, they may have been there only briefly, or it may have been a location that carries a lower risk of transmission. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z casual indirect contact requires discussion A role inhering in a person that is realized when the bearer is present on a given occasion or at a given place. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Attendee https://www.merriam-webster.com/dictionary/attendee https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z attendee role requires discussion A role inhering in a person that is realized when the bearer travels in a vehicle but bears little to no responsibility for vehicle operation nor arrival at its destination. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Passenger https://en.wikipedia.org/wiki/Passenger https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z passenger role requires discussion A role inhering in a person that is realized when the bearer maintains residency in a given place. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Resident https://en.wikipedia.org/wiki/Resident https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z resident role requires discussion A role inhering in a person that is realized when the bearer pays a visit to a specific place or event. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Visitor https://en.wikipedia.org/wiki/Resident https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z visitor role requires discussion A role inhering in a person that is realized when the bearer enters into any service of their own free will. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Volunteer https://en.wiktionary.org/wiki/visitor https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z volunteer role requires discussion A role inhering in a person that is realized when the bearer performs labor for a living. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Work https://en.wiktionary.org/wiki/volunteer https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z work role requires discussion A role inhering in a person that is realized when the bearer is engaged in administration or administrative work. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Administrator https://en.wiktionary.org/wiki/worker https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z administrator role requires discussion A role inhering in a person that is realized when the bearer is among the first to arrive at the scene of an emergency and has specialized training to provide assistance. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. First Responder https://en.wikipedia.org/wiki/First_responder https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z first responder role requires discussion A role inhering in a person that is realized when the bearer is a rescuer extensively trained in firefighting. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Firefighter https://en.wikipedia.org/wiki/Firefighter https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z firefighter role requires discussion A role inhering in a person that is realized when the bearer is a healthcare professional who responds to emergency calls for medical help outside of a hospital. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Paramedic https://en.wikipedia.org/wiki/Paramedic https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z paramedic role requires discussion A role inhering in a person that is realized when the bearer is a warranted law employee of a police force. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Police Officer https://en.wikipedia.org/wiki/Police_officer https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z police officer role requires discussion A role inhering in a person that is realized when the bearer is an individual who performs cleaning duties and/or is responsible for the supervision of cleaning staff. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Housekeeper https://en.wikipedia.org/wiki/Housekeeper_(domestic_worker) https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z housekeeper role requires discussion A role inhering in a person that is realized when the bearer is an employee that performs labor in a kitchen. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Kitchen Worker https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z kitchen worker role requires discussion A role inhering in a person that is realized when the bearer is an employee that performs labor in a laboratory. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Laboratory Worker https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z laboratory worker role requires discussion A role inhering in a person that is realized when the bearer works to help another person complete their daily activities. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Personal Care Aid https://www.careerexplorer.com/careers/personal-care-aide/#:~:text=A%20personal%20care%20aide%20is,as%20in%2Dhome%20caretakers). https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z personal care aide role personal care aid role requires discussion A role inhering in a person that is realized when the bearer is a health professional who specializes in dispensing prescription drugs at a healthcare facility. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Pharmacist https://en.wiktionary.org/wiki/pharmacist https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z pharmacist role requires discussion A role inhering in a person that is realized when the bearer is a professional who practices veterinary medicine. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Veterinarian https://en.wikipedia.org/wiki/Veterinarian https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z veterinarian role requires discussion A role inhering in a person that is realized when the bearer is in a state of being acquainted with a person. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Acquaintance of case https://en.wiktionary.org/wiki/acquaintance https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z acquaintance role requires discussion A role inhering in a person that is realized when the bearer is a relative of the case. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Relative of case https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z relative role requires discussion A role inhering in a person that is realized when the bearer is a person younger than the age of majority. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Child of case https://en.wikipedia.org/wiki/Child https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z child role requires discussion A role inhering in a person that is realized when the bearer is a caregiver of the offspring of their own species. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Parent of case https://en.wikipedia.org/wiki/Parent https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z guardian of case role parent of caserole parent-guardian role requires discussion A role inhering in a person that is realized when the bearer is the male parent of a child. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Father of case https://en.wikipedia.org/wiki/Father https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z father role requires discussion A role inhering in a person that is realized when the bearer is the female parent of a child. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Mother of case https://en.wikipedia.org/wiki/Mother https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z mother role requires discussion A role inhering in a person that is realized when the bearer is a significant other in a marriage, civil union, or common-law marriage. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Spouse of case https://en.wikipedia.org/wiki/Spouse https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z spouse role requires discussion A variant surveillance strategy in which a sample is sequenced because the individual from which the sample is derived has a known epidemiological link to a variant case. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Sample has epidemiological link to Variant of Concern (VoC) https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z sample has epidemiological link to VoC sample has epidemiological link to Variant of Concern strategy requires discussion A variant surveillance strategy in which a sample is sequenced because the individual from which the sample is derived has a known epidemiological link to an Omicron variant case. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Sample has epidemiological link to Omicron Variant https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z sample has epidemiological link to Omicron variant strategy requires discussion A domestic travel-associated surveillance strategy in which individuals are selected if their travel occurred within a state/province within a nation. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Interstate/ interprovincial travel surveillance https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z interstate/ interprovincial travel surveillance strategy requires discussion A domestic travel-associated surveillance strategy in which individuals are selected if their travel occurred between states/provinces within a nation. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Intra-state/ intra-provincial travel surveillance https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z intra-state/ intra-provincial travel surveillance strategy Yes [NCIT:C49488] requires discussion A data field which describes whether the sample was collected from an individual in quarantine. sample collected in quarantine https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z sample collected in quarantine slot Example Guidance: Whether a sample was collected under quarantine conditions (e.g. self-quarantining, medically isolated, staying at a quarantine hotel) can inform public health measure assessments. Use the picklist provided in the template. sample collected in quarantine field Jitter added to publicly shared collection dates to prevent re-identifiability. requires discussion A data field which describes how any data elements were altered to preserve patient privacy. data abstraction details https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z data abstraction details slot Example Guidance: If applicable, provide a description of how each data element was abstracted. data abstraction details field requires discussion A variant designation which is 1) a variant of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), 2) containing genetic mutates that may increase binding affinity to human cells, 3) linked to rapid spread in human populations, 4) is being monitored, and 5) denoted as a lower risk than a Variant of Interest (VOI). Variant Under Monitoring (VUM) https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z VBM VUM Variant Being Monitored PHA4GE Definition: A category used for indicating that a variant of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) containing genetic mutations that may increase binding affinity to human cells and linked to rapid spread in human populations is being monitored. This category denotes less risk than a Variant of Interest (VOI). variant under monitoring (SARS-CoV-2) Derbyshire requires discussion A data field which describes the county or region of origin of the sample. geo_loc name (county/region) geographical location county or region name https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z geo_loc name (county/region) slot geographical location county or region name field geographical location county or region name slot Example Guidance: Provide the county/region name from the GAZ geography ontology. Search for geography terms here: https://www.ebi.ac.uk/ols/ontologies/gaz geo_loc name (county/region) field ABCD1234 requires discussion A data field which describes the identifier used to specify an epidemiologically detected case of disease. case ID case identifier https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z case ID slot case identifier field case identifier slot Example Guidance: Provide the case identifer. The case ID greatly facilitates linkage between laboratory and epidemiological data. The case ID may be considered identifiable information. Consult the data steward before sharing. epidemiology case ID field hCoV-19/Canada/prov_rona_99/2020 requires discussion An identifier data field which describes the user-defined Global Initiative on Sharing Avian Influenza Data (GISAID) virus name assigned to the sequence. GISAID virus name https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z GISAID virus name slot Global Initiative on Sharing Avian Influenza Data virus name field Global Initiative on Sharing Avian Influenza Data virus name slot Example Guidance: GISAID virus names should be in the format .hCoV-19/Country/Identifier/year.. GISAID virus name field URI example: http://portal.vertnet.org/o/fmnh/mammals?id=33e55cfe-330b-40d9-aaae-8d042cba7542, INSDC triplet example: UAM:Mamm:52179 requires discussion A data field which describes the identifier for the physical specimen. host specimen voucher https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z host specimen voucher ID slot host specimen voucher identifier field host specimen voucher identifier slothost specimen voucher ID field host specimen voucher slot Example Guidance: Include a URI (Uniform Resource Identifier) in the form of a URL providing a direct link to the physical host specimen. If the specimen was destroyed in the process of analysis, electronic images (e-vouchers) are an adequate substitute for a physical host voucher specimen. If a URI is not available, a museum-provided globally unique identifier (GUID) can be used. If no persistent unique identifier is available, follow the INSDC guidance for populating the voucher_specimen attribute using standard triplets for institution codes (i.e., /specimen_voucher=.[<institution-code>:[<collection-code>:]]<specimen_id>.): http://www.insdc.org/controlled-vocabulary-specimenvoucher-qualifier host specimen voucher field /culture_collection="ATCC:26370 requires discussion A data field which describes the name of the source collection and unique culture identifier. culture collection https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z culture collection slot Example Guidance: Format: .<institution-code>:[<collection-code>:]<culture_id>.. For more information, see http://www.insdc.org/controlled-vocabulary-culturecollection-qualifier. culture collection ID field CanCOGeN Sampling Strategy 1.0 requires discussion A data field which describes the name of the sample plan implemented for sample collection. sample plan name https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z sample plan name slot Example Guidance: Provide the name and version of the sample plan outlining the sample strategy. sample plan name field requires discussion A specimen datum which describes the collection, isolate production, sequencing, or storage of specimen material or data. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z specimen processing An organism datum which contains additional contextual details regarding the health or disease status of a host at the time of sample collection. 2022-01-19T18:23:15.862Z host health status details at time of specimen collection A personal health datum which specifies host health complications at time of specimen collection. 0000-0002-9578-0788 2022-01-31T23:52:14Z host health complications at time of specimen collection A personal health datum which specifies host pre-existing conditions and risk factors at time of specimen collection. 0000-0002-9578-0788 2022-01-31T23:52:41Z pre-existing conditions and risk factors at time of specimen collection A personal health datum which specifies host signs and symptoms at time of specimen collection. 0000-0002-9578-0788 2022-01-31T23:53:13Z signs and symptoms at time of specimen collection requires discussion An infection detail datum which is used for classifying a variant of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), determined by the risk it poses based on available scientific evidence. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z variant designation (SARS-CoV-2) requires discussion A material entity encoding a genomic region of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z SARS-CoV-2 genomic region requires discussion A data item that describes an event in which exposure to a stressor may have occurred. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z exposure datum requires discussion A process in which a recipient organism is exposed to a material entity. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z exposure process Replaced with entity from an appropriate domain ontology. obsolete: cell line cell true requires discussion A patient as host datum which indicates the vaccination status of the patient. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z vaccination status requires discussion A genomic region encoding a gene of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z SARS-CoV-2 gene requires discussion A data enumeration which references a set of named signs and symptoms entities. signs and symptoms https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z health signs and symptoms enumeration requires discussion A data enumeration which references a set of named pre-existing conditions and risk factors entities. pre-existing conditions and risk factors https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z pre-existing conditions and risk factors enumeration requires discussion A data enumeration which references a set of named complications entities. complications https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z health complications enumeration requires discussion A data enumeration which references a set of named person role entities. host role https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 person role enumeration 38.98 N requires discussion A data field which describes the latitude coordinates of the geographical location of sample collection. geo_loc latitude geographical location latitude https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z geo_loc latitude slot geographical location latitude field geographical location latitude slot Example Guidance: Provide latitude coordinates if available. Do not use the centre of the city/region/province/state/country or the location of your agency as a proxy, as this implicates a real location and is misleading. Specify as degrees latitude in format .d[d.dddd] N|S.. geo_loc latitude field 77.11 W requires discussion A data field which describes the longitude coordinates of the geographical location of sample collection. geo_loc longitude geographical location longitude https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z geo_loc longitude slot geographical location longitude field geographical location longitude slot Example Guidance: Provide longitude coordinates if available. Do not use the centre of the city/region/province/state/country or the location of your agency as a proxy, as this implicates a real location and is misleading. Specify as degrees longitude in format .d[dd.dddd] W|E.. geo_loc longitude field 25 swabs were pooled and further prepared as a single sample during library prep. requires discussion A data field which describes detailed information regarding the processing applied to a sample during or after receiving the sample. specimen processing details https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z specimen processing details slot Example Guidance: Provide a free text description of any processing details applied to a sample. specimen processing details field Indigenous, European requires discussion A host data field which describes the self-identified ethnicity(ies) of the host. host ethnicity https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z host ethnicity slot Example Guidance: If known, provide the self-identified ethnicity or ethnicities of the host as a free text description. This is highly sensitive information which must be treated respectfully and carefully when sharing. The information may have implications for equitable access and benefit sharing. Consult your privacy officer, data steward and/or cultural services representative. host ethnicity field Pfizer-BioNTech (Comirnaty) requires discussion A data field which describes the name of the vaccine administered as the first dose of a vaccine regimen. vaccination dose 1 vaccine name vaccination dose one vaccine name https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z vaccination dose 1 vaccine name slot vaccination dose one vaccine name field vaccination dose one vaccine name slot Example Guidance: Provide the name and the corresponding manufacturer of the COVID-19 vaccine administered as the first dose by selecting a value from the pick list vaccination dose 1 vaccine name field 2021-03-01 requires discussion A host data field which describes the date the first dose of a vaccine was administered. vaccination dose 1 vaccination date vaccination dose one vaccination date https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z vaccination dose 1 vaccination date slot vaccination dose one vaccination date field vaccination dose one vaccination date slot Example Guidance: Provide the date the first dose of COVID-19 vaccine was administered. The date should be provided in ISO 8601 standard format .YYYY-MM-DD.. vaccination dose 1 vaccination date field Pfizer-BioNTech (Comirnaty) requires discussion A data field which describes the name of the vaccine administered as the second dose of a vaccine regimen. vaccination dose 2 vaccine name vaccination dose two vaccine name https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z vaccination dose 2 vaccine name slot vaccination dose two vaccine name field vaccination dose two vaccine name slot Example Guidance: Provide the name and the corresponding manufacturer of the COVID-19 vaccine administered as the second dose by selecting a value from the pick list vaccination dose 2 vaccine name field 2021-09-01 requires discussion A host data field which describes the date the second dose of a vaccine was administered. vaccination dose 2 vaccination date vaccination dose two vaccination date https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z vaccination dose 2 vaccination date slot vaccination dose two vaccination date field vaccination dose two vaccination date slot Example Guidance: Provide the date the second dose of COVID-19 vaccine was administered. The date should be provided in ISO 8601 standard format .YYYY-MM-DD.. vaccination dose 2 vaccination date field Pfizer-BioNTech (Comirnaty) requires discussion A data field which describes the name of the vaccine administered as the third dose of a vaccine regimen. vaccination dose 3 vaccine name vaccination dose three vaccine name https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z vaccination dose 3 vaccine name slot vaccination dose three vaccine name field vaccination dose three vaccine name slot Example Guidance: Provide the name and the corresponding manufacturer of the COVID-19 vaccine administered as the third dose by selecting a value from the pick list vaccination dose 3 vaccine name field 2021-12-30 requires discussion A host data field which describes the date the third dose of a vaccine was administered. vaccination dose 3 vaccination date vaccination dose three vaccination date https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z vaccination dose 3 vaccination date slot vaccination dose three vaccination date field vaccination dose three vaccination date slot Example Guidance: Provide the date the third dose of COVID-19 vaccine was administered. The date should be provided in ISO 8601 standard format .YYYY-MM-DD.. vaccination dose 3 vaccination date field Pfizer-BioNTech (Comirnaty) requires discussion A data field which describes the name of the vaccine administered as the fourth dose of a vaccine regimen. vaccination dose 4 vaccine name vaccination dose four vaccine name https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z vaccination dose 4 vaccine name slot vaccination dose four vaccine name field vaccination dose four vaccine name slot Example Guidance: Provide the name and the corresponding manufacturer of the COVID-19 vaccine administered as the fourth dose by selecting a value from the pick list vaccination dose 4 vaccine name field 2022-01-15 requires discussion A host data field which describes the date the fourth dose of a vaccine was administered. vaccination dose 4 vaccination date vaccination dose four vaccination date https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z vaccination dose 4 vaccination date slot vaccination dose four vaccination date field vaccination dose four vaccination date slot Example Guidance: Provide the date the fourth dose of COVID-19 vaccine was administered. The date should be provided in ISO 8601 standard format .YYYY-MM-DD.. vaccination dose 4 vaccination date field Pfizer-BioNTech (Comirnaty); 2021-03-01; Pfizer-BioNTech (Comirnaty); 2022-01-15 requires discussion A host data field which describes the description of the vaccines received and the administration dates of a series of vaccinations against a specific disease or a set of diseases. vaccination history https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z vaccination history slot Example Guidance: Free text description of the dates and vaccines administered against a particular disease/set of diseases. It is also acceptable to concatenate the individual dose information (vaccine name, vaccination date) separated by semicolons. vaccination history field requires discussion A role inhering in a person that is realized when the bearer is an employee that performs labor in a healthcare setting. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Healthcare Worker https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z healthcare worker role requires discussion A role inhering in a person that is realized when the bearer is an employee that performs labor which rotates according to a schedule. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Rotational Worker https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z rotational worker role requires discussion A role inhering in a person that is realized when the bearer is an employee that performs labor according to a seasonal schedule. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Seasonal Worker https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z seasonal worker role requires discussion A sampling strategy in which stored samples from past events are sequenced. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Retrospective sequencing https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-02-25T05:13:49.123Z retrospective sequencing strategy A type of contact in which an individual comes in contact with an infected person, either directly or indirectly. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-02-28T05:08:07.274Z contact with infected individual Air requires discussion A data field which describes the type of entry point a traveler arrives through. travel point of entry type https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z travel point of entry type slot Example Guidance: Select the point of entry type. travel point of entry type field day 1 requires discussion A data field which describes the day a traveller was tested on or after arrival at their point of entry. border testing test day type https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z border testing test day type slot Example Guidance: Select the test day. border testing test day type field requires discussion A process occuring within or in the vicinty of a the individual home where the patient or client is living and health care or supportive care is being being delivered, as opposed to care provided in group accommodations like clinics or nursing home. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Community Healthcare (At-Home) Setting https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2023-01-23T00:42:19.315Z at-home community healthcare exposure process Public Health Ontario (PHO) requires discussion A data field which describes the name of the agency, organization or institution responsible for sequencing the isolate's genome. Not to be confused with 'sequence_submitted_by' http://purl.obolibrary.org/obo/GENEPIO_0001159. sequenced by sequenced_by https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z sequenced by slot Example Guidance: The name of the agency should be written out in full, (with minor exceptions) and be consistent across multiple submissions. If submitting specimens rather than sequencing data, please put the .National Microbiology Laboratory (NML).. sequenced by field requires discussion A mass gathering event where the primary emphasis is on recreation. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Recreational Event https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2023-01-23T00:42:19.315Z recreational event datum requires discussion A recreational event where the primary emphasis is on a concert performance. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Concert https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2023-01-23T00:42:19.315Z concert event datum requires discussion A recreational event where the primary emphasis is a sporting deemonstration or athletic competition. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Sporting Event https://www.lawinsider.com/dictionary/sporting-and-recreational-event#:~:text=Related%20Definitions&text=Sporting%20and%20Recreational%20Event%20means,yoga%2C%20and%20other%20exercise%20gatherings. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2023-01-23T00:42:19.315Z sporting event datum requires discussion A role inhering in a person that is realized when the bearer a professional caregiver that provides health care or supportive care in the individual home where the patient or client is living, as opposed to care provided in group accommodations like clinics or nursing home. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Community Healthcare Worker https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-01-19T18:23:15.862Z community healthcare worker RespLab@lab.ca requires discussion A data field which describes the email address of the contact responsible for follow-up regarding the sequence. Not to be confused with 'sequence submitter contact email' http://purl.obolibrary.org/obo/GENEPIO_0001165 sequenced by contact email sequenced_by_contact_email https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z sequenced by contact email slot Example Guidance: The email address can represent a specific individual or lab e.g. johnnyblogs@lab.ca, or RespLab@lab.ca sequenced by contact email field 123 Sunnybrooke St, Toronto, Ontario, M4P 1L6, Canada requires discussion A data field which describes the mailing address of the agency submitting the sequence. Not to be confused with 'sequence submitter contact address' http://purl.obolibrary.org/obo/GENEPIO_0001167 sequenced by contact address https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z sequenced by contact address slot Example Guidance: The mailing address should be in the format: Street number and name, City, Province/Territory, Postal Code, Country sequenced by contact address field bvn5567, RA1-HH789 requires discussion A data field which describes an alternative sample identifier assigned to the sample by another organization. alternative sample ID alternative sample identifier alternative_sample_ID https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z alternative sample ID slot alternative sample identifier field alternative sample identifier slot Example Guidance: Provide any alternative identifiers for the sample here, separated by commas. Alternative identifiers assigned to the sample should be tracked along with original IDs to establish chain of custody. If the information is unknown or cannot be provided, leave blank or provide a null value. alternative sample ID field Topp Lab requires discussion A data field which describes the specific laboratory affiliation of the sample collector. sample collected by laboratory name sample_collected_by_laboratory_name https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z sample collected by laboratory name slot Example Guidance: Provide the name of the specific laboratory that collected the sample (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. sample collected by laboratory name field Watershed Project (HA-120) requires discussion A data field which describes the project/initiative/program for which the sample was collected. sample collection project name sample_collection_project_name https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z sample collection project name slot Example Guidance: Provide the name of the project and/or the project ID here. If the information is unknown or cannot be provided, leave blank or provide a null value. sample collection project name field National Microbiological Baseline Study in Broiler Chicken requires discussion A data field which describes the name of the study design for a surveillance project. sample plan name sample_plan_name https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z sample plan name slot Example Guidance: Provide the name of the sample plan used for sample collection. If the information is unknown or cannot be provided, leave blank or provide a null value. sample plan name field 2001_M205 requires discussion A data field which describes the identifier of the study design for a surveillance project. sample plan ID sample plan identifier sample_plan_ID https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z sample plan ID slot sample plan identifier field sample plan identifier slot Example Guidance: Provide the identifier of the sample plan used for sample collection. If the information is unknown or cannot be provided, leave blank or provide a null value. sample plan ID field Enterics Lab Manager requires discussion A data field which describes the name or job title of the contact responsible for follow-up regarding the sample. sample collector contact name sample_collector_contact_name https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z sample collector contact name slot Example Guidance: Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is more preferable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. sample collector contact name field Antimicrobial pre-treatment [GENEPIO:0100537] requires discussion A data field which describes the activities or variables introduced upstream of sample collection that may affect the sample collected. presampling activity presampling_activity https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z presampling activity slot Example Guidance: If there was presampling activity that would affect the sample prior to collection (this is different than sample processing which happens after the sample is collected), provide the experimental activities by selecting one or more values from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. presampling activity field Chicken feed containing X amount of novobiocin was fed to chickens for 72 hours prior to collection of litter. requires discussion A data field which describes the details of the activities or variables introduced upstream of sample collection that may affect the sample collected. presampling activity details presampling_activity_details https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z presampling activity details slot Example Guidance: Briefly describe the presampling activity details using free text. presampling activity details field Samples pooled [OBI:0600016] requires discussion A data field which describes the processing applied to samples post-collection, prior to further testing, characterization, or isolation procedures. specimen processing specimen_processing https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z specimen processing slot Example Guidance: Provide the sample processing information by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. specimen processing field Credit River" as opposed to "river requires discussion A data field which describes the name of a specific geographical location (i.e. toponym). geo_loc name (site) geographical location site name https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z geo_loc name (site) slot geographical location site name field geographical location site name slot Example Guidance: Provide the name of the specific geographical site using a specific noun (a word that names a certain place, thing). geo_loc name (site) field United States of America [GAZ:00002459] requires discussion A data field which describes the country of origin of a food product. food product origin geo loc name (country) food product origin geographical location country name food_product_origin geo_loc_name (country) https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z food product origin geo loc name (country) slot food product origin geographical location country name field food product origin geographical location country name slot Example Guidance: If a food product was sampled and the food product was manufactured outside of Canada, provide the name of the country where the food product originated by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. food product origin geo loc name (country) field South Africa [GAZ:00001094] requires discussion A host geographical location field which describes the country of origin of the host. host origin geo loc name (country) host origin geographical location name host_origin geo_loc_name (country) https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z host origin geo loc name (country) slot host origin geographical location name field host origin geographical location name slot Example Guidance: If a sample is from a human or animal host that originated from outside of Canada, provide the the name of the country where the host originated by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. host origin geo loc name (country) field RTE Prosciutto from deli requires discussion A data field which describes the original sample description provided by the sample collector. original sample description original_sample_description https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z original sample description slot Example Guidance: Provide the sample description provided by the original sample collector. The original description is useful as it may provide further details, or can be used to clarify higher level classifications. original sample description field 5m requires discussion A data field which describes the depth of some water. water depth water_depth https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z water depth slot Example Guidance: Provide the depth of water with a value and unit. water depth field 25C requires discussion A data field which describes the temperature of some air. air temperature air_temperature https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z air temperature slot Example Guidance: Provide the temperature of the air with a value and unit. Do not provide a symbol for degree e.g. oC air temperature field Rain [ENVO:01001564] requires discussion A data field which describes the state of the atmosphere at a place and time. Regarding heat, dryness, sunshine, wind, rain, etc. weather type weather_type https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z weather type slot Example Guidance: Provide the weather conditions at the time of sample collection. weather type field Turkey [NCBITaxon:9103] requires discussion A data field which describes the type of animal or plant population inhabiting an area. animal or plant population animal_or_plant_population https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z animal or plant population slot Example Guidance: This field should be used when a sample is taken from an environmental location inhabited by many individuals of a specific type, rather than describing a sample taken from one particular host. If applicable, provide the standardized term and ontology ID for the animal or plant population name. The standardized term can be sourced from this look-up service: https://www.ebi.ac.uk/ols/ontologies/genepio. If not applicable, leave blank. animal or plant population field Feather meal [FOODON:00003927]; Bone meal [ENVO:02000054]; Chicken breast [FOODON:00002703] requires discussion A data field which describes material consumed and digested for nutritional value or enjoyment. food product food_product https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z food product slot Example Guidance: This field includes animal feed. If applicable, provide the standardized term and ontology ID for the anatomical material. The standardized term can be sourced from this look-up service: https://www.ebi.ac.uk/ols/ontologies/foodon. If not applicable, leave blank. food product field Food (chopped) [FOODON:00002777]; Ready-to-eat (RTE) [FOODON:03316636] requires discussion A data field which describes any characteristic of the food product pertaining to its state, processing, a label claim, or implications for consumers. food product properties food_product_properties https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z food product properties slot Example Guidance: Provide any characteristics of the food product including whether it has been cooked, processed, preserved, any known information about its state (e.g. raw, ready-to-eat), any known information about its containment (e.g. canned), and any information about a label claim (e.g. organic, fat-free). food product properties field Chicken [NCBITaxon:9031] requires discussion A data field which describes the animal from which the food product was derived. animal source of food animal_source_of_food https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z animal source of food slot Example Guidance: Provide the common name of the animal. If not applicable, leave blank. Multiple entries can be provided, separated by a comma. animal source of food field Plastic tray or pan [FOODON:03490126] requires discussion A data field which describes the type of packaging used to contain a food product. food packaging food_packaging https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z food packaging slot Example Guidance: If known, provide information regarding how the food product was packaged. food packaging field Frozen at -20C requires discussion A data field which describes the way that a specimen is or was stored. sample storage method sample_storage_method https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z sample storage method slot Example Guidance: Provide a description of how the same was stored. sample storage method field PBS + 20% glycerol requires discussion A data field which describes the material or matrix in which a sample is stored. sample storage medium sample_storage_medium https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z sample storage medium slot Example Guidance: Provide a description of the material or matrix used to store the sample. sample storage medium field Sea ecotype requires discussion A host field which describes the biotype resulting from selection in a particular habitat. host (ecotype) https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z host (ecotype) slot Example Guidance: Provide the name of the ecotype of the host organism. host (ecotype) field Holstein requires discussion A host field which describes a specific group of domestic animals or plants having homogeneous appearance, homogeneous behavior, and other characteristics that distinguish it from other animals or plants of the same species and that were arrived at through selective breeding. host (breed) https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z host (breed) slot Example Guidance: Provide the name of the breed of the host organism. host (breed) field Calf [FOODON:03411349] requires discussion A host field which describes the name of the host at a certain stage of food production, which may depend on its age or stage of sexual maturity. host (food production name) https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z host (food production name) slot Example Guidance: Select the host's food production name from the pick list. host (food production name) field An instance of the "strain and isolation information field category" that contains the "isolate received date field". An instance of the "strain and isolation information field category" that contains the "microbiological method field". ready for release requires discussion A data field category which refers to strain and isolation information fields. strain and isolation information https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z 2022-06-25T03:32:51.876Z strain and isolation information slot category strain and isolation information field category MFHPB-30 requires discussion A data field which describes the laboratory method used to grow, prepare, and/or isolate the microbial isolate. microbiological method https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z microbiological method slot Example Guidance: Provide the name and version number of the microbiological method. The ID of the method is also acceptable if the ID can be linked to the laboratory that created the procedure. microbiological method field K12 requires discussion A data field which describes the strain identifier. strain https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z strain slot Example Guidance: A population or type of organisms that is genetically different from others of the same species and possessing a set of defined characteristics. If the isolate represents or is derived from, a lab reference strain or strain from a type culture collection, provide the strain identifier. strain field SARS-CoV-2/human/USA/CA-CDPH-001/2020 requires discussion A data field which describes the identifier of the specific isolate. isolate isolate ID isolate identifier https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z isolate ID slot isolate field isolate identifier field isolate identifier slot isolate slot Example Guidance: This identifier should be an unique, indexed, alpha-numeric ID within your laboratory. If submitted to the INSDC, the .isolate. name is propagated throughtout different databases. As such, structure the .isolate. name to be ICTV/INSDC compliant in the following format: .SARS-CoV-2/host/country/sampleID/date.. isolate ID field PHAC_45678 requires discussion A data field which describes an isolate identifier assigned to the isolate by another organization. alternative isolate ID alternative isolate identifier alternative_isolate_ID https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z alternative isolate ID slot alternative isolate identifier field alternative isolate identifier slot Example Guidance: If one or more alternative isolate_IDs are available, record them all here, separated by a comma. alternative isolate ID field SUB_ON_1526 requires discussion A data field which describes the identifier assigned to a progenitor isolate derived from an isolate that was directly obtained from a sample. progeny isolate ID progeny isolate identifier progeny_isolate_ID https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z progeny isolate ID slot progeny isolate identifier field progeny isolate identifier slot Example Guidance: If your sequence data pertains to progeny of an original isolate, provide the progeny_isolate_ID. progeny isolate ID field GRDI_LL_12345 requires discussion A data field which describes the identifier of the isolate in the Integrated Rapid Infectious Disease Analysis (IRIDA) platform. IRIDA isolate ID IRIDA isolate identifier IRIDA_isolate_ID https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z IRIDA isolate ID slot IRIDA isolate identifier field IRIDA isolate identifier slot Integrated Rapid Infectious Disease Analysis isolate ID field Integrated Rapid Infectious Disease Analysis isolate ID slot Integrated Rapid Infectious Disease Analysis isolate identifier field Integrated Rapid Infectious Disease Analysis isolate identifier slot Example Guidance: Provide the .sample ID. used to track information linked to the isolate in IRIDA. IRIDA sample IDs should be unqiue to avoid ID clash. This is very important in large Projects, especially when samples are shared from different organizations. Download the IRIDA sample ID and add it to the sample data in your spreadsheet as part of good data management practices. IRIDA isolate ID field 666 requires discussion A data field which describes the identifier of the project in the Integrated Rapid Infectious Disease Analysis (IRIDA) platform. IRIDA project ID IRIDA project identifier https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z IRIDA project ID slot IRIDA project identifier field IRIDA project identifier slot Integrated Rapid Infectious Disease Analysis project ID field Integrated Rapid Infectious Disease Analysis project ID slot Integrated Rapid Infectious Disease Analysis project identifier field Integrated Rapid Infectious Disease Analysis project identifier slot Example Guidance: Provide the IRIDA .project ID.. IRIDA project ID field Public Health Agency of Canada (PHAC) [GENEPIO:0100551] requires discussion A data field which describes the name of the agency, organization or institution with which the individual who performed the isolation procedure is affiliated. isolated by isolated_by https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z isolated by slot Example Guidance: Provide the name of the agency, organization or institution that isolated the original isolate in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. isolated by field Topp Lab requires discussion A data field which describes the specific laboratory affiliation of the individual who performed the isolation procedure. isolated by laboratory name isolated_by_laboratory_name https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z isolated by laboratory name slot Example Guidance: Provide the name of the specific laboratory that that isolated the original isolate (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. isolated by laboratory name field Enterics Lab Manager requires discussion A data field which describes the name or title of the contact responsible for follow-up regarding the isolate. isolated by contact name isolated_by_contact_name https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z isolated by contact name slot Example Guidance: Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is prefereable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. isolated by contact name field enterics@lab.ca requires discussion A data field which describes the email address of the contact responsible for follow-up regarding the isolate. isolated by contact email isolated_by_contact_email https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z isolated by contact email slot Example Guidance: Provide the email associated with the listed contact. As personnel turnover may render an individual's email obsolete, it is more prefereable to provide an address for a position or lab, to ensure accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. isolated by contact email field 2020-10-30 requires discussion A date field which describes the date on which the isolate was isolated from a sample. isolate collection date isolation date isolation_date https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z isolate collection date field isolate collection date slot isolation date slot Example Guidance: Provide the date according to the ISO 8601 standard .YYYY-MM-DD., .YYYY-MM. or .YYYY.. isolation date field 2020-11-15 requires discussion A date field which describes the date on which the isolate was received by the laboratory. isolate received date isolate_received_date https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z isolate received date slot Example Guidance: Provide the date according to the ISO 8601 standard .YYYY-MM-DD., .YYYY-MM. or .YYYY.. isolate received date field Heidelberg requires discussion A data field which describes the serovar of the organism. serovar https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z serotype field serotype slot serovar slot Example Guidance: Only include this information if it has been determined by traditional serological methods or a validated in silico prediction tool e.g. SISTR. serovar field SISTR 1.0.1 requires discussion A data field which describes the method used to determine the serovar. serotyping method serotyping_method https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z serotyping method slot Example Guidance: If the serovar was determined via traditional serotyping methods, put “Traditional serotyping”. If the serovar was determined via in silico methods, provide the name and version number of the software. serotyping method field 47 requires discussion A data field which describes the phagetype of the organism. phagetype https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z phagetype slot Example Guidance: Provide if known. If unknown, put “missing”. phagetype field Topp Lab requires discussion A data field which describes the specific laboratory affiliation of those responsible for sequencing the isolate's genome. sequenced by laboratory name https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z sequenced by laboratory name slot Example Guidance: Provide the name of the specific laboratory that that performed the sequencing in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. sequenced by laboratory name field Enterics Lab Manager requires discussion A data field which describes the name or title of the contact responsible for follow-up regarding the sequence. Not to be confused with 'sequence submitted by contact name' http://purl.obolibrary.org/obo/GENEPIO_0100474 sequenced by contact name sequenced_by_contact_name https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z sequenced by contact name slot Example Guidance: Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is more prefereable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. sequenced by contact name field AMR-GRDI (PA-1356) requires discussion A data field which describes the name of the project/initiative/program for which sequencing was performed. sequencing project name sequencing_project_name https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z sequencing project name slot Example Guidance: Provide the name of the project and/or the project ID here. If the information is unknown or cannot be provided, leave blank or provide a null value. sequencing project name field Illumina [GENEPIO:0001923] requires discussion A data field which describes the platform technology used to perform the sequencing. sequencing platform sequencing_platform https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z sequencing platform slot Example Guidance: Provide the name of the company that created the sequencing instrument by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. sequencing platform field Enterics Lab Manager requires discussion A data field which describes the name or title of the contact responsible for follow-up regarding the submission of the sequence to a repository or database. Not to be confused with 'sequenced by contact name' http://purl.obolibrary.org/obo/GENEPIO_0100471 sequence submitted by contact name sequence_submitted_by_contact_name https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-12-22T00:55:53.808Z sequence submitted by contact name slot Example Guidance: Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is prefereable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. sequence submitted by contact name field PMID: 33205991 requires discussion A data field which describes the identifier for a publication. publication ID publication identifier publication_ID https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-12-22T00:55:53.808Z publication ID slot publication identifier field publication identifier slot Example Guidance: If the isolate is associated with a published work which can provide additional information, provide the PubMed identifier of the publication. Other types of identifiers (e.g. DOI) are also acceptable. publication ID field Pathogen.env requires discussion A data field which describes the attribute package used to structure metadata in an International Nucleotide Sequence Database Collaboration (INSDC) BioSample. attribute package attribute_package https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-12-22T00:55:53.808Z attribute package slot Example Guidance: If the sample is from a specific human or animal, put “Pathogen.cl”. If the sample is from an environmental sample including food, feed, production facility, farm, water source, manure etc, put “Pathogen.env”. attribute package field An instance of the "public repository information field category" that contains the "publication ID field". requires discussion A data field category which refers to public repository information fields. public repository information https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-06-25T03:32:51.876Z public repository information slot category public repository information field category An instance of the "risk assessment information field category" that contains the "prevalence metrics field". requires discussion A data field category which refers to risk assessment information fields. risk assessment information https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-06-25T03:32:51.876Z risk assessment information slot category risk assessment information field category An instance of the "antimicrobial resistance field category" that contains the "AMR* laboratory typing method field". *AMR = antimicrobial resistance requires discussion A data field category which refers to antimicrobial resistance fields. antimicrobial resistance https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-06-25T03:32:51.876Z antimicrobial resistance slot category antimicrobial resistance field category Number of total samples collected, Number of positive samples requires discussion A data field which describes metrics regarding the prevalence of the pathogen of interest obtained from a surveillance project. prevalence metrics prevalence_metrics https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-12-22T00:55:53.808Z prevalence metrics slot Example Guidance: Risk assessment requires detailed information regarding the quantities of a pathogen in a specified location, commodity, or environment. As such, it is useful for risk assessors to know what types of information are available through documented methods and results. Provide the metric types that are available in the surveillance project sample plan by selecting them from the pick list. The metrics of interest are . Number of total samples collected., .Number of positive samples., .Average count of hazard organism., .Average count of indicator organism.. You do not need to provide the actual values, just indicate that the information is available. prevalence metrics field Hazard organism counts (i.e. Salmonella) do not distinguish between serovars. requires discussion A data field which describes the details pertaining to the prevalence metrics from a surveillance project. prevalence metrics details prevalence_metrics_details https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-12-22T00:55:53.808Z prevalence metrics details slot Example Guidance: If there are details pertaining to samples or organism counts in the sample plan that might be informative, provide details using free text. prevalence metrics details field Abattoir [ENVO:01000925] requires discussion A data field which describes the stage of food production. stage of production stage_of_production https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-12-22T00:55:53.808Z stage of production slot Example Guidance: Provide the stage of food production from which the sample was taken. Select a value form the pick list provided. stage of production field Vaccination [NCIT:C15346] requires discussion A data field which describes the category of the experimental intervention applied in the food production system. experimental intervention experimental_intervention https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-12-22T00:55:53.808Z experimental intervention slot Example Guidance: In some surveys, a particular intervention in the food supply chain in studied. If there was an intervention specified in the sample plan, select the intervention category from the pick list provided. experimental intervention field 2% cranberry solution mixed in feed requires discussion a data field which describes the details of the experimental intervention applied in the food production system. experiment intervention details experiment_intervention_details https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-12-22T00:55:53.808Z experiment intervention details slot Example Guidance: If an experimental intervention was applied in the survey, provide details in this field as free text. experiment intervention details field requires discussion A role inhering in a person that is realized when the bearer is engaged in child care or education work. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Child Care/Education Worker https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2023-01-23T00:42:19.315Z child care or education worker requires discussion A role inhering in a person that is realized when the bearer is engaged in operations and services that are essential to ensure the continuity of critical infrastructure operations. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Essential Worker http://purl.obolibrary.org/obo/NCIT_C179411 https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2023-01-23T00:42:19.315Z essential worker requires discussion A role inhering in a person that is realized when the bearer is an employee that performs labor internationally. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. International worker https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2023-01-23T00:42:19.315Z international worker requires discussion A role inhering in a person that is realized when the bearer is engaged in transportation. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Transport Worker https://www.lawinsider.com/dictionary/transportation-worker https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2023-01-23T00:42:19.315Z transport worker requires discussion A transport worker role inhering in a person that is realized when the bearer is the driver of a transport truck. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Transport Truck Driver https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2023-01-23T00:42:19.315Z transport truck driver requires discussion A role inhering in a person that is realized when the bearer is a sexual partner of the case. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Sexual partner of case https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2023-01-23T00:42:19.315Z sexual partner role requires discussion A process occuring within or in the vicinity of a human with a confirmed case of COVID-19 that exposes the recipient organism to Monkeypox. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Contact with Known Monkeypox Case https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2023-01-23T00:42:19.315Z contact with known Monkeypox case contact with known Monkeypox case exposure process requires discussion A process occuring within or in the vicinity of a human with a probable case of COVID-19 that exposes the recipient organism to Monkeypox. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. Contact with Probable Monkeypox Case https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2023-01-23T00:42:19.315Z contact with probable Monkeypox case contact with probable Monkeypox case exposure process Canadian Food Inspection Agency (CFIA) [GENEPIO:0100552] requires discussion A data field which describes the name of the organization that performed the antimicrobial resistance (AMR) testing. AMR testing by AMR_testing_by antimicrobial resistance testing by https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-12-22T00:55:53.808Z AMR testing by slot antimicrobial resistance testing by field antimicrobial resistance testing by slot Example Guidance: Provide the name of the agency, organization or institution that performed the AMR testing, in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. AMR testing by field Topp Lab requires discussion A data field which describes the name of the lab within the organization that performed the antimicrobial resistance (AMR) testing. AMR testing by laboratory name AMR_testing_by_laboratory_name antimicrobial resistance testing by laboratory name https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-12-22T00:55:53.808Z AMR testing by laboratory name slot antimicrobial resistance testing by laboratory name field antimicrobial resistance testing by laboratory name slot Example Guidance: Provide the name of the specific laboratory that performed the AMR testing (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. AMR testing by laboratory name field Enterics Lab Manager requires discussion A data field which describes the name of the individual or the individual's role in the organization that performed the antimicrobial resistance (AMR) testing. AMR testing by contact name AMR_testing_by_contact_name antimicrobial resistance testing by contact name https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-12-22T00:55:53.808Z AMR testing by contact name slot antimicrobial resistance testing by contact name field antimicrobial resistance testing by contact name slot Example Guidance: Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is more preferable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. AMR testing by contact name field johnnyblogs@lab.ca requires discussion A data field which describes the email of the individual or the individual's role in the organization that performed the antimicrobial resistance (AMR) testing. AMR testing by contact email AMR_testing_by_contact_email antimicrobial resistance testing by contact email https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-12-22T00:55:53.808Z AMR testing by contact email slot antimicrobial resistance testing by contact email field antimicrobial resistance testing by contact email slot Example Guidance: Provide the email associated with the listed contact. As personnel turnover may render an individual's email obsolete, it is more preferable to provide an address for a position or lab, to ensure accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. AMR testing by contact email field 2022-04-03 requires discussion A data field which describes the date the antimicrobial resistance (AMR) testing was performed. AMR testing date AMR_testing_date antimicrobial resistance testing date https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-12-22T00:55:53.808Z AMR testing date slot antimicrobial resistance testing date field antimicrobial resistance testing date slot Example Guidance: Provide the date according to the ISO 8601 standard .YYYY-MM-DD., .YYYY-MM. or .YYYY.. AMR testing date field 8 requires discussion An antimicrobial resistance (AMR) field which describes the maximum measurement for a sample to be considered “sensitive” to this antibiotic. Dependent on the units specified in the 'AMR measurement units field' [GENEPIO:0100523]. AMR testing susceptible breakpoint AMR_testing_susceptible_breakpoint antimicrobial resistance testing susceptible breakpoint https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-12-22T00:55:53.808Z AMR testing susceptible breakpoint slot antimicrobial resistance testing susceptible breakpoint field antimicrobial resistance testing susceptible breakpoint slot Example Guidance: This field should only contain a number (either an integer or a number with decimals), since the “<=” qualifier is implied. AMR testing susceptible breakpoint field 16 requires discussion An antimicrobial resistance (AMR) field which describes intermediate measurement(s) where a sample would be considered to have an “intermediate” phenotype for this antibiotic. Dependent on the units specified in the 'AMR measurement units field' [GENEPIO:0100523]. AMR testing intermediate breakpoint AMR_testing_intermediate_breakpoint antimicrobial resistance testing intermediate breakpoint https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-12-22T00:55:53.808Z AMR testing intermediate breakpoint slot antimicrobial resistance testing intermediate breakpoint field antimicrobial resistance testing intermediate breakpoint slot Example Guidance: This field should only contain a number (either an integer or a number with decimals), since the qualifier is implied. AMR testing intermediate breakpoint field 32 requires discussion An antimicrobial resistance (AMR) field which describes minimum measurement for a sample to be considered “resistant” to this antibiotic. Dependent on the units specified in the 'AMR measurement units field' [GENEPIO:0100523]. AMR testing resistant breakpoint AMR_testing_resistant_breakpoint antimicrobial resistance testing resistant breakpoint https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-12-22T00:55:53.808Z AMR testing resistant breakpoint slot antimicrobial resistance testing resistant breakpoint field antimicrobial resistance testing resistant breakpoint slot Example Guidance: This field should only contain a number (either an integer or a number with decimals), since the “>=” qualifier is implied. AMR testing resistant breakpoint field 27th ed. Wayne, PA: Clinical and Laboratory Standards Institute; 2017. requires discussion An antimicrobial resistance (AMR) field which describes additional details associated with the testing standard used for determination of resistance phenotype. AMR testing standard details AMR_testing_standard_details antimicrobial resistance testing standard details https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-12-22T00:55:53.808Z AMR testing standard details slot antimicrobial resistance testing standard details field antimicrobial resistance testing standard details slot Example Guidance: This information may include the year or location where the testing standard was published. If not applicable, leave blank. AMR testing standard details field Amoxicillin-clavulanic [ARO:3003997] requires discussion A data field which describes the name of the agent that kills or slows the growth of microorganisms, including bacteria, viruses, fungi and protozoans. antimicrobial agent name antimicrobial_agent_name https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z antimicrobial agent name slot Example Guidance: The names of the drug have already been matched with measurement, breakpoint, and phenotype fields in the template. No need to add these unless the drug of interest is not present. Use the Term Request System to request the addition of other agents. antimicrobial agent name field 4 requires discussion A data field which describes the measured value of antimicrobial resistance (AMR). Dependent on the value specified in the 'antimicrobial agent name field' [GENEPIO:0100521] AMR measurement AMR_measurement antimicrobial resistance measurement https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-12-22T00:55:53.808Z AMR measurement slot antimicrobial resistance measurement field antimicrobial resistance measurement slot Example Guidance: This field should only contain a number (either an integer or a number with decimals). AMR measurement field mg/L requires discussion A data field which describes the units of the antimicrobial resistance (AMR) measurement. Dependent on the numerical value specified in the 'AMR measurement field' [GENEPIO:0100522] AMR measurement units AMR_measurement_units antimicrobial resistance measurement units https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-12-22T00:55:53.808Z AMR measurement units slot antimicrobial resistance measurement units field antimicrobial resistance measurement units slot Example Guidance: Select the units from the pick list provided. Use the Term Request System to request the addition of other units if necessary. AMR measurement units field == requires discussion A data field which describes the qualifier associated with the antibiotic resistance (AMR) measurement. Dependent on the units specified in the 'AMR measurement units field' [GENEPIO:0100523]. AMR measurement sign AMR_measurement_sign antimicrobial resistance measurement sign https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-12-22T00:55:53.808Z AMR measurement sign slot antimicrobial resistance measurement sign field antimicrobial resistance measurement sign slot Example Guidance: Select the comparator sign from the pick list provided. Use the Term Request System to request the addition of other signs if necessary. AMR measurement sign field Susceptible antimicrobial phenotype [ARO:3004302] requires discussion A data field which describes an antimicrobial resistance (AMR) phenotype, as determined by the antibiotic susceptibility measurement and testing standard for the antibiotic specified. Dependent on the value specified in the 'antimicrobial agent name field' [GENEPIO:0100521] AMR phenotype AMR_phenotype antimicrobial resistance phenotype https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-12-22T00:55:53.808Z AMR phenotype slot antimicrobial resistance phenotype field antimicrobial resistance phenotype slot Example Guidance: Select a phenotype from the pick list provided. AMR phenotype field Broth dilution [ARO:3004397] requires discussion An antimicrobial resistance (AMR) field which describes the general method used for antibiotic susceptibility testing. AMR laboratory typing method AMR_laboratory_typing_method antimicrobial resistance laboratory typing method https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-12-22T00:55:53.808Z AMR laboratory typing method slot antimicrobial resistance laboratory typing method field antimicrobial resistance laboratory typing method slot Example Guidance: Select a typing method from the pick list provided. Use the Term Request System to request the addition of other methods if necessary. AMR laboratory typing method field Sensitire [ARO:3004402] requires discussion An antimicrobial resistance (AMR) field which describes the brand/platform used for antibiotic susceptibility testing. AMR laboratory typing platform AMR_laboratory_typing_platform antimicrobial resistance laboratory typing platform https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-12-22T00:55:53.808Z AMR laboratory typing platform slot antimicrobial resistance laboratory typing platform field antimicrobial resistance laboratory typing platform slot Example Guidance: Select a typing platform from the pick list provided. Use the Term Request System to request the addition of other platforms if necessary. AMR laboratory typing platform field CMV3AGNF requires discussion An antimicrobial resistance (AMR) field which describes the specific name and version of the plate, panel, or other platform used for antibiotic susceptibility testing. AMR laboratory typing platform version AMR_laboratory_typing_platform_version antimicrobial resistance laboratory typing platform version https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-12-22T00:55:53.808Z AMR laboratory typing platform version slot antimicrobial resistance laboratory typing platform version field antimicrobial resistance laboratory typing platform version slot Example Guidance: Include any additional information about the antimicrobial susceptibility test such as the drug panel details. AMR laboratory typing platform version field Sensititre requires discussion An antimicrobial resistance (AMR) field which describes the name of the vendor of the testing platform used. AMR vendor name AMR_vendor_name antimicrobial resistance vendor name https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-12-22T00:55:53.808Z AMR vendor name slot antimicrobial resistance vendor name field antimicrobial resistance vendor name slot Example Guidance: Provide the full name of the company (avoid abbreviations). AMR vendor name field Clinical Laboratory and Standards Institute (CLSI) [ARO:3004366] requires discussion An antimicrobial resistance (AMR) field which describes testing standard used for determination of resistance phenotype. AMR testing standard AMR_testing_standard antimicrobial resistance testing standard https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-12-22T00:55:53.808Z AMR testing standard slot antimicrobial resistance testing standard antimicrobial resistance testing standard field antimicrobial resistance testing standard slot Example Guidance: Select a testing standard from the pick list provided. AMR testing standard field M100 requires discussion An antimicrobial resistance (AMR) field which describes version number associated with the testing standard used for determination of resistance phenotype. If applicable, include a version number for the testing standard used. AMR testing standard version AMR_testing_standard_version antimicrobial resistance testing standard version https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2022-12-22T00:55:53.808Z AMR testing standard version slot antimicrobial resistance testing standard version field antimicrobial resistance testing standard version slot Example Guidance: If applicable, include a version number for the testing standard used. AMR testing standard version field Prior infection requires discussion A data field which describes the absence or presence of a prior Monkeypox infection. prior Monkeypox infection https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z prior Monkeypox infection slot Example Guidance: If known, provide information about whether the individual had a previous Monkeypox infection. Select a value from the pick list. prior Monkeypox infection field 2022-06-20 requires discussion A data field which describes the date of diagnosis of the prior Monkeypox infection. prior Monkeypox infection date https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z prior Monkeypox infection date slot Example Guidance: Provide the date that the most recent prior infection was diagnosed. Provide the prior Monkeypox infection date in ISO 8601 standard format .YYYY-MM-DD.. prior Monkeypox infection date field Prior antiviral treatment requires discussion A data field which describes the absence or presence of antiviral treatment for a prior Monkeypox infection. prior Monkeypox antiviral treatment https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z prior Monkeypox antiviral treatment slot Example Guidance: If known, provide information about whether the individual had a previous Monkeypox antiviral treatment. Select a value from the pick list. prior Monkeypox antiviral treatment field AZT was administered for HIV infection during the prior Monkeypox infection. requires discussion A data field which describes the antiviral treatment for any infection during the prior Moneypox infection period. prior antiviral treatment during prior Monkeypox infection https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z prior antiviral treatment during prior Monkeypox infection slot Example Guidance: Provide a description of any antiviral treatment administered for viral infections (not including Monkeypox treatment) during the prior Monkeypox infection period. This field is meant to capture concurrent treatment information. prior antiviral treatment during prior Monkeypox infection field A sampling strategy in which environments are sampled in the context of testing for the presence of, or change in the levels of, chemicals, pathogens or other phenomena. Environmental testing 2023-01-23T00:42:19.315Z environmental testing sampling A sampling strategy in which individuals are sampled in the context of experiments or observations performed as part of clinical research. Clinical trial 2022-09-23T11:08:21Z 2023-01-23T00:42:19.315Z clinical trial sampling clinical trial sampling strategy A sampling strategy in which samples are taken during real-life experiments which test directly whether proposed interventions actually work. Field experiment https://en.wikipedia.org/wiki/Field_experiment 2022-09-23T11:12:34Z 2023-01-23T00:42:19.315Z field experiment sampling ncov-tools ready-for-release A data field which describes the name of the method used to assess whether a sequence passed a predetermined quality control threshold. quality control method name https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-9578-0788 2023-01-23T00:42:19.315Z qc method name field qc method name slot quality control method name field quality control method name slot quality control method name field 1.2.3 ready-for-release A data field which describes the version number of the method used to assess whether a sequence passed a predetermined quality control threshold. quality control method version https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-9578-0788 2023-01-23T00:42:19.315Z qc method version field qc method version slot quality control method version field quality control method version slot quality control method version field sequence failed quality control [GENEPIO:0100564] ready-for-release A data field which describes the determination of a quality control assessment. quality control determination https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-9578-0788 2023-01-23T00:42:19.315Z qc determination field qc determination slot quality control determination field quality control determination slot quality control determination field low average genome coverage [GENEPIO:0100570] ready-for-release A data field which describes the reason contributing to, or causing, a low quality determination in a quality control assessment. quality control issues https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-9578-0788 2023-01-23T00:42:19.315Z qc issues field qc issues slot quality control issues field quality control issues slot quality control issues field CT value of 39. Low viral load. Low DNA concentration after amplification. ready-for-release A data field which describes the details surrounding a low quality determination in a quality control assessment. quality control details https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-9578-0788 2023-01-23T00:42:19.315Z qc details field qc details slot quality control details field quality control details slot quality control details field ready-for-release A data item which is a statement confirming that quality control processes were carried out and no quality issues were detected. no quality control issues identified https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-9578-0788 2023-01-23T00:42:19.315Z Example: This statement may be used in conjunction with the quality control determination statement "sequence passed quality control" to confirm that no issues were identified. It is possible that a sequence may pass QC but still have some issues worthy of noting e.g. novel indel detected. Note: quality control here refers to quality of the raw reads, consensus sequence or assembly, not the qaulity of analytical results e.g. lineage assignment. no quality control issues identified datum ready-for-release A data item which is a statement confirming that quality control processes were carried out and that the sequence met the assessment criteria. sequence passed quality control https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-9578-0788 2023-01-23T00:42:19.315Z Example: Use this statement to indicate that quality control processes were carried out and that the sequence met the assessment criteria. Note: quality control here refers to quality of the raw reads, consensus sequence or assembly, not the qaulity of analytical results e.g. lineage assignment. sequence passed quality control datum ready-for-release A data item which is a statement confirming that quality control processes were carried out and that the sequence did not meet the assessment criteria. sequence failed quality control https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-9578-0788 2023-01-23T00:42:19.315Z Example: Use this statement to indicate that quality control processes were carried out and that the sequence failed to meet the assessment criteria. Note: quality control here refers to quality of the raw reads, consensus sequence or assembly, not the qaulity of analytical results e.g. lineage assignment. sequence failed quality control datum ready-for-release A data item which is a statement confirming that quality control processes were carried out and that the sequence did not meet the assessment criteria, however the issues detected were minor. minor quality control issues identified https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-9578-0788 2023-01-23T00:42:19.315Z Example: This statement may be used in conjunction with the quality control determination statement "sequence failed quality control" to communicate that the reasons why the sequence did not meet the assessment criteria. Minor issues may include phenomena that the analyst should review e.g. amplicons detected in the negative control sequence or more mutations than expected based on the reference sequence. The details of the issues can be described in the "quality control details" field. Note: quality control here refers to quality of the raw reads, consensus sequence or assembly, not the qaulity of analytical results e.g. lineage assignment. minor quality control issues identified datum ready-for-release A data item which is a statement confirming that quality control processes were carried out however it is unclear whether the sequence meets the assessment criteria and the assessment requires review. sequence flagged for potential quality control issues https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-9578-0788 2023-01-23T00:42:19.315Z Example: This statement may be used in conjunction with other quality control determination statements to indicate potential sequence quality issues. Note: quality control here refers to quality of the raw reads, consensus sequence or assembly, not the qaulity of analytical results e.g. lineage assignment. sequence flagged for potential quality control issues datum ready-for-release A data item which is a statement confirming that quality control processes have not been carried out. quality control not performed https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-9578-0788 2023-01-23T00:42:19.315Z Example: Use this statement to indicate that quality control processes have not been performed. Note: quality control here refers to quality of the raw reads, consensus sequence or assembly, not the qaulity of analytical results e.g. lineage assignment. quality control not performed datum ready-for-release A data item that describes sequence data that does not meet quality control thresholds. low quality sequence https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-9578-0788 2023-01-23T00:42:19.315Z low quality sequence datum ready-for-release A data item that describes sequence data that contains reads from unintended targets (e.g. other organisms, other samples) due to contamination so that it does not faithfully represent the genetic information from the biological source. sequence contaminated https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-9578-0788 2023-01-23T00:42:19.315Z sequence contaminated datum ready-for-release A data item that describes sequence data in which the entire length of the genome is not sufficiently sequenced (low breadth of coverage), or particular positions of the genome are not sequenced a prescribed number of times (low depth of coverage). low average genome coverage https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-9578-0788 2023-01-23T00:42:19.315Z low average genome coverage datum ready-for-release A data item that describes sequence data in which the entire length of the genome is not sufficiently sequenced (low breadth of coverage). low percent genome captured https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-9578-0788 2023-01-23T00:42:19.315Z low percent genome captured datum ready-for-release A data item that describes average sequence read lengths that are below the expected size range given a particular sequencing instrument, reagents and conditions. read lengths shorter than expected https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-9578-0788 2023-01-23T00:42:19.315Z read lengths shorter than expected datum ready-for-release A data item that describes sequence data containing errors generated during the polymerase chain reaction (PCR) amplification process during library generation (e.g. mutations, altered read distribution, amplicon dropouts). sequence amplification artifacts https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-9578-0788 2023-01-23T00:42:19.315Z sequence amplification artifacts datum ready-for-release A data item that describes sequence data containing more errors or undetermined bases (noise) than sequence representing the biological source (signal). low signal to noise ratio https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-9578-0788 2023-01-23T00:42:19.315Z low signal to noise ratio datum ready-for-release A data item that describes sequence data that contains a lower than expected number of mutations that are usually observed in the reference sequence. low coverage of characteristic mutations https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-9578-0788 2023-01-23T00:42:19.315Z low coverage of characteristic mutations datum Tecovirimat used to treat current Monkeypox infection; AZT administered for concurrent HIV infection requires discussion A data field which describes treatment of viral infections with agents that prevent viral replication in infected cells without impairing the host cell function. antiviral therapy https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z antiviral therapy slot Example Guidance: Provide details of all current antiviral treatment during the current Monkeypox infection period. Consult with the data steward prior to sharing this information. antiviral therapy field A collection of contextual data attributes pertaining to a pathogen in an environmental sample, as specified by the International Nucleotide Sequence Database Collaboration (INSDC). 2022-09-23T10:54:21Z Environmental Pathogen Attribute Package (Pathogen.env) A sampling strategy in which individuals and/or materials are sampled for surveillance performed for research purposes. Survey study 2022-09-23T11:04:13Z 2023-01-23T00:42:19.315Z survey study sampling survey study sampling strategy PCR assay [OBI:0002740] requires discussion A data field which describes the type of planned process by which an organismal entity is associated with a taxon or taxa. taxonomic identification process taxonomic_identification_process https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z taxonomic identification process slot Example Guidance: Provide the type of method used to determine the taxonomic identity of the organism by selecting a value from the pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. taxonomic identification process field Biolog instrument requires discussion A data field which describes the details of the process used to determine the taxonomic identification of an organism. taxonomic identification process details taxonomic_identification_process_details https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z taxonomic identification process details slot Example Guidance: Briefly describe the taxonomic identififcation method details using free text. taxonomic identification process details field The "specimen collector sample ID" is where one can store sample identifiers given by the specimen collector. A data item which is a location for a predetermined type of data. https://analystanswers.com/what-is-a-data-field-definition-types-examples/ 2022-11-23T00:33:27.896Z data slot data field requires discussion A data specification established for use by The Public Health Alliance for Genomic Epidemiology (PHA4GE) project for SARS-CoV-2 contextual data (metadata) harmonization and curation across data providers. PHA4GE SARS-CoV-2 contextual data specification https://orcid.org/0000-0002-9578-0788 2022-12-09T20:18:38.910Z Public Health Alliance for Genomic Epidemiology SARS-CoV-2 specification Public Health Alliance for Genomic Epidemiology severe acute respiratory syndrome coronavirus 2 specification PHA4GE SARS-CoV-2 specification Manuscript: https://doi.org/10.1093/gigascience/giac003 GitHub: https://github.com/pha4ge/SARS-CoV-2-Contextual-Data-Specification requires discussion A data specification established for pathogen genomics contextual data (metadata) harmonization and curation across Canadian data providers. https://orcid.org/0000-0002-9578-0788 2022-12-09T20:18:38.910Z Canadian pathogen genomics specification https://github.com/cidgoh/pathogen-genomics-package requires discussion A data specification established for use by The Canadian Genomics Research & Development Initiative (GRDI) Antimicrobial Resistance (AMR) project for contextual data (metadata) harmonization and curation across data providers. https://orcid.org/0000-0002-9578-0788 2022-12-09T20:18:38.910Z Genomics Research & Development Initiative Antimicrobial Resistance One Health specification GRDI AMR One Health specification https://github.com/cidgoh/GRDI_AMR_One_Health requires discussion A data specification established for Monkeypox pathogen genomics contextual data (metadata) harmonization and curation across Canadian data providers. https://orcid.org/0000-0002-9578-0788 2022-12-09T20:18:38.910Z Canadian Monkeypox specification https://github.com/cidgoh/pathogen-genomics-package requires discussion A data specification established for Monkeypox pathogen genomics contextual data (metadata) harmonization and curation across international data providers. https://orcid.org/0000-0002-9578-0788 2022-12-09T20:18:38.910Z International Monkeypox specification https://github.com/cidgoh/pathogen-genomics-package specimen storage duration A data item which is a duration for which a specimen is stored before analysis. https://orcid.org/0000-0002-8844-9165 sample storage duration http://gensc.org/ns/mixs/samp_store_dur Rehomed in OBIB https://github.com/obi-ontology/obi/issues/1577 obsolete: specimen storage duration specimen storage duration true specimen storage temperature The refrigerator provided a sample storage temperature of -80 degree Celsius A data item which is a temperature at which a specimen is stored. https://orcid.org/0000-0002-8844-9165 sample storage temperature http://gensc.org/ns/mixs/samp_store_temp Domain appropriate replacement identified in OBIB https://github.com/obi-ontology/obi/issues/1577 obsolete: specimen storage temperature specimen storage temperature true specimen storage location molecular lab was recorded as the sample storage location. A data item which indicates the location where a specimen is stored, usually of a room or freezer. https://orcid.org/0000-0002-8844-9165 sample storage location http://gensc.org/ns/mixs/samp_store_loc Rehomed in OBIB https://github.com/obi-ontology/obi/issues/1577 obsolete: specimen storage location specimen storage location true sequence file name The sequence data for "Zika virus envelope protein (E) gene, partial cds" is stored in a file named "AF372422-1.fasta". A sequence data item which is the name of a file containing molecular sequence data. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-9578-0788 input file name Emma Griffiths https://github.com/obi-ontology/obi/issues/1579 sequence file name contig number identifier When a new genome is sequenced, it is constructed from a series of overlapping sequences known as contigs. Each contig receives an identifier code that contains a unique numerical identifier, in addition to project and assembly information, to differentiate an individual contig from others within a squence collection. A sequence data which specifies a particular contig in a sequence collection. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-9578-0788 contig identifier contig ID Emma Griffiths https://github.com/obi-ontology/obi/issues/1579 contig number identifier genomic orientation The "123" gene ORF is oriented in the 5' -> 3' direction on the DNA sense (coding) strand. A sequence data which is the orientation of a genomic element on a double stranded molecule. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-9578-0788 strand orientation strand http://purl.obolibrary.org/obo/NCIT_C48673 https://github.com/obi-ontology/obi/issues/1579 genomic orientation gene symbol gyrA A sequence data which is the short name of a gene typically derived from the gene name. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-9578-0788 http://edamontology.org/data_1026 https://github.com/obi-ontology/obi/issues/1579 gene symbol gene name Gyrase A A sequence data which is the name of a gene (typically) assigned by a person and/or according to a naming scheme. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-9578-0788 http://edamontology.org/data_2299 https://github.com/obi-ontology/obi/issues/1579 gene name breadth of coverage percentage The breadth of coverage of the sequence of interest to the reference sequence was 75%. A data item which is breadth of coverage datum as a percentage. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-9578-0788 % coverage (breadth) breadth of coverage % coverage (breadth) Emma Griffiths https://github.com/obi-ontology/obi/issues/1579 breadth of coverage percentage breadth of coverage ratio The breadth of coverage of the sequence of interest to the reference sequence was 3:4. A data item which is breadth of coverage datum as a ratio. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-9578-0788 Emma Griffiths https://github.com/obi-ontology/obi/issues/1579 breadth of coverage ratio sequence identity percentage The BLAST results for two sequences of interest resulted in a sequence identity of 50%; i.e. only 50% of the sequences matched in both nucleotide content and corresponding positions when performing a theoretically optimal local alignment. A data item which is the number of matches (identical characters) in positions from an alignment of two molecular sequences as a percentage. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-9578-0788 http://edamontology.org/data_1412 https://github.com/obi-ontology/obi/issues/1579 sequence identity percentage reference database name I used the NCBI reference sequence "RefSeq" database as a reference database for the identification and characterization of novel prokaryote sequences. A data item which is an identifier of a reference bioinformatics database. See editor note of http://purl.obolibrary.org/obo/IAO_0000650 https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-9578-0788 http://edamontology.org/data_1048 https://github.com/obi-ontology/obi/issues/1579 reference database name reference sequence The reference SARS-CoV-2 genome provided a basis for the design of PCR primers and probes to be utilized in SARS-CoV-2 detection. A sequence data which is any sequence that is used as a basis for comparison against another sequence. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-9578-0788 Emma Griffiths https://github.com/obi-ontology/obi/issues/1579 reference sequence accession number A sequence Accession number without a version suffix always refers to the latest version of the sequence. A unique identifier given to a sequence record to allow for tracking of different versions of that sequence record and the associated sequence over time in a single data repository. https://orcid.org/0000-0002-1107-9135 accession identifier https://en.wikipedia.org/wiki/Accession_number_(bioinformatics) https://github.com/obi-ontology/obi/issues/1579 accession number reference sequence accession number The "Homo sapiens DRD2 mRNA" sequence has the NCBI reference sequence identifier NM_000795. A centrally registered identifier symbol that specifies an individual sequence record in a public sequence repository and used as a basis for comparison against another sequence. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-9578-0788 reference sequence accession identifier reference accession Emma Griffiths https://github.com/obi-ontology/obi/issues/1579 reference sequence accession number sequence length measurement datum The sequence length measurement datum for the Zika virus E protein gene (AF372422.1) is 830 bp. A length measurement datum which is the number of base pairs in a sequence. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-9578-0788 Emma Griffiths https://github.com/obi-ontology/obi/issues/1579 sequence length measurement datum reference sequence length measurement datum The sequence length measurment datum for the SARS-CoV-2 reference sequence (NC_045512.2) is 29903 bp. A sequence length measurement datum which describes the number of base pairs of a reference sequence. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-9578-0788 Emma Griffiths https://github.com/obi-ontology/obi/issues/1579 reference sequence length measurement datum reference gene sequence length datum The sequence length measurment datum for the SARS-CoV-2 reference sequence (NC_045512.2) ORF1ab gene (43740578) is 21289 bp. A reference sequence length measurement datum which describes the number of base pairs of a gene retrieved from a reference sequence. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-9578-0788 reference gene length Emma Griffiths https://github.com/obi-ontology/obi/issues/1579 reference gene sequence length datum reference protein sequence length datum The sequence length measurment datum for the SARS-CoV-2 reference sequence (NC_045512.2) nps13_ZBD protein (YP_009725308.1) is 1802 bp. A reference sequence length measurement datum which describes the number of positions of a reference protein. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-9578-0788 reference protein length Emma Griffiths https://github.com/obi-ontology/obi/issues/1579 reference protein sequence length datum input sequence length measurement datum 701bp A sequence length measurement datum about a input sequence being analyzed. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-9578-0788 Emma Griffiths https://github.com/obi-ontology/obi/issues/1579 input sequence length measurement datum input gene sequence length measurement datum 1802bp A sequence length measurement datum which describes the number of base pairs of a gene of interest undergoing analysis. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-9578-0788 input gene length Emma Griffiths https://github.com/obi-ontology/obi/issues/1579 input gene sequence length measurement datum input protein sequence length measurement datum 638bp A sequence length measurement datum which describes the number of positions of a protein undergoing analysis. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-9578-0788 input protein length Emma Griffiths https://github.com/obi-ontology/obi/issues/1579 input protein sequence length measurement datum virus transport medium A processed material which is a medium designed to promote longevity of a viral sample. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-8844-9165 https://github.com/obi-ontology/obi/issues/1194 virus transport medium 2020-05-25 requires discussion A data field which describes the date recommended for the use of a product while at peak quality, this date is not a reflection of safety unless used on infant formula. food quality date food_quality_date https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z food quality date slot Example Guidance: This date is typically labeled on a food product as .best if used by., best by., .use by., or .freeze by. e.g. 5/24/2020. If the date is known, leave blank or provide a null value. food quality date field 2020-05-25 requires discussion A data field which descibes the food product's packaging date as marked by a food manufacturer or retailer. food packaging date food_packaging_date https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z food packaging date slot Example Guidance: The packaging date should not be confused with, nor replaced by a Best Before date or other food quality date. If the date is known, leave blank or provide a null value. food packaging date field requires discussion A data item which describes an organism bearing a host role. https://orcid.org/0000-0002-9578-0788 2022-12-22T00:55:53.808Z host column host slot; host organism field; host organism slot host field requires discussion A data field which describes a geographical location. geo_loc field geo_loc slot https://orcid.org/0000-0002-9578-0788 2022-12-22T00:55:53.808Z geographical location column geographical location slot geographical location field A field that describes the host country of reisdence. requires discussion A data field which describes the geographical location of a host organism. host geo_loc https://orcid.org/0000-0002-9578-0788 2022-12-22T00:55:53.808Z host geographical location column host geographical location slot host geographical location field third party lab sample ID field requires discussion A data field which describes a symbol that is part of a centrally registered identifier database (CRID) and that is sufficient to look up a record from the CRID's registry. http://purl.obolibrary.org/obo/IAO_0000577 https://orcid.org/0000-0002-9578-0788 2022-12-22T00:55:53.808Z ID column identifier column ID field ID slot identifier slot identifier field requires discussion A data field which describes the particular day, month and/or year an event has happened or will happen. https://orcid.org/0000-0002-9578-0788 2022-12-22T00:55:53.808Z date column date slot date field requires discussion A data field which describes the vaccination information of a host organism. https://orcid.org/0000-0002-9578-0788 2022-12-22T00:55:53.808Z host vaccination column host vaccination slot host vaccination field This "or" class is just to represent an equivalency with a commonly used classification, it should not have subclasses under it. (2022-12-22) 2022-12-22T22:56:03.687Z State or Province or Territory requies discussion A data field which describes antimicrobial information. https://orcid.org/0000-0002-9578-0788 2022-12-22T00:55:53.808Z antimicrobial column antimicrobial slot antimicrobial field requies discussion A data field which describes antimicrobial resistance information. https://orcid.org/0000-0002-9578-0788 2022-12-22T00:55:53.808Z AMR column antimicrobial resistance column AMR field AMR slot antimicrobial resistance slot antibiotic field antimicrobial resistance field requires discussion A data field which describes the exposure information of a host organism. https://orcid.org/0000-0002-9578-0788 2023-01-01T03:32:48.197Z exposure column exposure slot exposure field requires discussion A data field which describes prior infection information of a host organism. https://orcid.org/0000-0002-9578-0788 2023-01-01T03:32:48.197Z prior infection column prior infection slot prior infection field E gene (orf4) [GENEPIO:0100151] requires discussion A data field which describes the name of the gene used in the diagnostic reverse transcription polymerase chain reaction (RT-PCR) test. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z gene name slot gene name field PCREGene 2.0 requires discussion A data field which describes the name and version number of the reverse transcription polymerase chain reaction (RT-PCR) protocol used for diagnostic marker amplification. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z diagnostic pcr protocol slot diagnostic polymerase chain reaction protocol field diagnostic polymerase chain reaction protocol slot diagnostic pcr protocol field 21 requires discussion A data field which describes the cycle threshold (Ct) value result from a diagnostic reverse transcription polymerase chain reaction (RT-PCR) test. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z diagnostic pcr Ct value slot diagnostic polymerase chain reaction cycle threshold field diagnostic polymerase chain reaction cycle threshold slot diagnostic pcr Ct value field wet wipe A small moistened piece of plastic or cloth fabric. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-8395-2570 https://en.wikipedia.org/wiki/Wet_wipe wet wipe requires discussion A data specification established by the Public Health Alliance for Genomic Epidemiology (PHA4GE) for genomics contextual data (metadata) harmonization and curation. https://orcid.org/0000-0002-9578-0788 2023-01-22T23:12:40.795Z Public Health Alliance for Genomic Epidemiology specification PHA4GE genomics specification GitHub: https://github.com/pha4ge requires discussion A data specification established by the Public Health Alliance for Genomic Epidemiology (PHA4GE) for genomics contextual data (metadata) harmonization and curation. PHA4GE QC contextual data tags specification PHA4GE QC tags specification PHA4GE quality control contextual data tags specification https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-9578-0788 2023-01-22T23:12:40.795Z PHA4GE QC specification Public Health Alliance for Genomic Epidemiology quality control specification PHA4GE quality control specification GitHub: https://github.com/pha4ge/contextual_data_QC_tags requires discussion A data field which describes quality control information. https://orcid.org/0000-0002-9578-0788 2023-01-23T00:42:19.315Z qc column quality control column qc field qc slot quality control slot quality control field requires discussion https://orcid.org/0000-0002-9578-0788 2023-01-23T00:42:19.315Z quality control datum requires discussion A data enumeration which references a set of named quality control determination entities. quality control determination https://orcid.org/0000-0002-9578-0788 2023-01-23T00:42:19.315Z quality control determination enumeration requires discussion A data enumeration which references a set of named quality control issues entities. quality control issues https://orcid.org/0000-0002-9578-0788 2023-01-23T00:42:19.315Z quality control issues enumeration requires discussion A role inhering in a person that is realized when the bearer is engaged in child care work. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-9578-0788 2023-01-23T00:42:19.315Z childcare worker role requires discussion A role inhering in a person that is realized when the bearer is engaged in education work. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. https://orcid.org/0000-0002-9578-0788 2023-01-23T00:42:19.315Z education worker role Total coliform count data requires discussion A data field which describes the type of data that is available. The data may or may not require permission to access. available data types available_data_types https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-9578-0788 2023-05-18T05:09:29.167Z available data types slot Example Guidance: This field provides information about additional data types that are available that may provide context for interpretation of the sequence data. Provide a term from the picklist for additional data types that are available. Additional data types may require special permission to access. Contact the data provider for more information. available data types field 2m requires discussion A data field which describes the depth of some sediment. sediment depth sediment_depth https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-9578-0788 2023-05-18T05:09:29.167Z sediment depth slot Example Guidance: Provide the depth of sediment with a value and unit. sediment depth field 4C requires discussion A data field which describes the temperature of some water. water temperature water_temperature https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-9578-0788 2023-05-18T05:09:29.167Z water temperature slot Example Guidance: Provide the temperature of the water with a value and unit. Do not provide a symbol for degree e.g. oC water temperature field Beef cow production stream requires discussion A data field which describes a production pathway incorporating the processes, material entities, and conditions that participate in the generation of a particular commodity. Material entities examples: equipment, animals, locations production stream production_stream https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-9578-0788 2023-05-18T05:09:29.167Z production stream slot Example Guidance: Provide the name of the agricultural production stream from the picklist. production stream field Dorso-lateral region [BSPO:0000080] requires discussion A data field which describes a 3D anatomical region in space without well-defined compartmental boundaries. anatomical region anatomical_region https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-9578-0788 2023-05-18T05:09:29.167Z anatomical region slot Example Guidance: This field captures more granular spatial information on a host anatomical part e.g. dorso-lateral region vs back. Select a term from the picklist. anatomical region field A dataset may be annotated with the "mollusc shell length tag" to indicate the presence mollusc shell length data attributes such as a "mollusc shell length" field and "mollusc shell length unit" field. requires discussion A data item which indicates the presence of specific data attributes within a dataset. https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2023-05-18T19:08:34.869Z dataset component tag dataset data type dataset tag dataset attribute bundle requires discussion A dataset attribute bundle which indicates the presence of documentation data. https://en.wikipedia.org/wiki/Documentation used as a partial source for the "Example Guidance". documentation https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2023-05-18T19:08:34.869Z documentation attribute bundle documentation data type Example Guidance: Use this tag to indicate additional data is available that provides information that is used to describe, explain or instruct regarding some attributes of an object, system or procedure. documentation data tag requires discussion A documentation data tag which indicates the presence of data that describes experimental parameters. experimental parameters documentation https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2023-05-18T19:08:34.869Z experimental parameters documentation data type Example Guidance: Use this tag to indicate additional data is available that provides documentation describing parameters of the experiment. experimental parameters documentation tag requires discussion A documentation data tag which indicates the presence of data that describes feed history. http://purl.obolibrary.org/obo/ENVO_02000047 used as a partial source for the "Example Guidance". feed history https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2023-05-18T19:08:34.869Z feed history data type Example Guidance: Use this tag to indicate additional data is available that provides a history of food material given to meet nutritional requirements. feed history documentation tag requires discussion A documentation data tag which indicates the presence of data that describes land use information. https://www.epa.gov/report-environment/land-use used as a partial source for the "Example Guidance". land use information https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2023-05-18T19:08:34.869Z land use information data type Example Guidance: Use this tag to indicate additional data is available that provides information describing human use of the land. land use information documentation tag requires discussion A documentation data tag which indicates the presence of data that describes a history of therapeutic administration. therapeutic administration history https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2023-05-18T19:08:34.869Z therapeutic administration history documentation data type Example Guidance: Use this tag to indicate additional data is available that provides a history of therapeutics admnistered to a subject. therapeutic administration history documentation tag requires discussion A dataset attribute bundle which indicates the presence of chemical characterization data. chemical characterization https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2023-05-18T19:08:34.869Z chemical characterization attribute bundle chemical characterization data type Example Guidance: Use this tag to indicate additional data is available that provides characterization information from chemical properties. chemical characterization data tag requires discussion A chemical characterization data tag which indicates the presence of data that describes a measurement of pH. http://purl.obolibrary.org/obo/GENEPIO_0001736 used as a partial source for the "Example Guidance". pH measurement https://orcid.org/0000-0001-5275-8866 https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2023-05-18T19:08:34.869Z pH measurement characterization data tag Example Guidance: Use this tag to indicate additional data is available that provides characterization information from the measurement of pH, where pH is a numeric scale used to specify the acidity or basicity (alkalinity) of an aqueous solution. pH measurement characterization tag requires discussion A chemical characterization data tag which indicates the presence of data that describes a measurement of dissolved oxygen. https://www.epa.gov/national-aquatic-resource-surveys/indicators-dissolved-oxygen used as a partial source for the "Example Guidance". dissolved oxygen measurement https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2023-05-18T19:08:34.869Z dissolved oxygen measurement characterization data tag Example Guidance: Use this tag to indicate additional data is available that provides characterization information from the amount of oxygen that is present in water. dissolved oxygen measurement characterization tag requires discussion A chemical characterization data tag which indicates the presence of data that descibes a measurement of nitrate. http://purl.obolibrary.org/obo/NCIT:C161352 used as a partial source for the "Example Guidance". nitrate measurement https://orcid.org/0000-0001-5275-8866 https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2023-05-18T19:08:34.869Z nitrate measurement characterization data tag Example Guidance: Use this tag to indicate additional data is available that provides characterization information from the determination of the amount of nitrate present in a sample. nitrate measurement characterization tag requires discussion A chemical characterization data tag which indicates the presence of data that descibes a measurement of nitrite. http://purl.obolibrary.org/obo/NCIT:C64810 used as a partial source for the "Example Guidance". nitrite measurement https://orcid.org/0000-0001-5275-8866 https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2023-05-18T19:08:34.869Z nitrite measurement characterization data tag Example Guidance: Use this tag to indicate additional data is available that provides characterization information from the quantitative measurement of the amount of nitrite present in a sample. nitrite measurement characterization tag requires discussion A chemical characterization data tag which indicates the presence of data that describes a measurement of phosphorus. phosphorous measurement https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2023-05-18T19:08:34.869Z phosphorous measurement characterization data tag Example Guidance: Use this tag to indicate additional data is available that provides characterization information from the quantitative measurement of the amount of phosphorus present in a sample. phosphorous measurement characterization tag requires discussion A chemical characterization data tag which indicates the presence of data that describes a measurement of salinity. salinity measurement https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2023-05-18T19:08:34.869Z salinity measurement characterization data tag Example Guidance: Use this tag to indicate additional data is available that provides characterization information from the quantitative measurement of the amount of salt dissolved in a body of water. salinity measurement characterization tag requires discussion A dataset attribute bundle which indicates the presence of microbiological characterization data. microbiological characterization https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2023-05-18T19:08:34.869Z microbiological characterization attribute bundle microbiological characterization data type Example Guidance: Use this tag to indicate additional data is available that provides characterization information based on microbiological properties. microbiological characterization data tag requires discussion A microbiological characterization data tag which indicates the presence of microbiological identification data. microbiological identification https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2023-05-18T19:08:34.869Z microbiological characterization attribute bundle microbiological identification data type Example Guidance: Use this tag to indicate additional data is available that provides identification information from microbiological properties. microbiological identification data tag requires discussion A microbiological characterization data tag which indicates the presence of microbiological identification data derived using the Beckson Dickson BBL Crystal identification system. microbiological identification (Beckson Dickson BBL Crystal) https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2023-05-18T19:08:34.869Z microbiological identification data type (Beckson Dickson BBL Crystal) Example Guidance: Use this tag to indicate additional data is available that provides identification information from microbiology properties generated using Beckson Dickson BBL Crystal. microbiological identification tag (Beckson Dickson BBL Crystal) requires discussion A microbiological characterization data tag which indicates the presence of microbiological identification data dervied using the bioMérieux API identification system. microbiological identification (bioMérieux API) https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2023-05-18T19:08:34.869Z microbiological identification data type (bioMérieux API) Example Guidance: Use this tag to indicate additional data is available that provides identification information from microbiology properties generated using bioMérieux API. microbiological identification tag (bioMérieux API) requires discussion A microbiological characterization data tag which indicates the presence of microbiological identification data derived using the Biolog identification system. microbiological identification (Biolog) https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2023-05-18T19:08:34.869Z microbiological identification data type (Biolog) Example Guidance: Use this tag to indicate additional data is available that provides identification information from microbiology properties generated using Biolog. microbiological identification tag (Biolog) requires discussion A microbiological characterization data tag which indicates the presence of microbiological identification data derived using the Fatty acid methyl esters (FAME) identification system. microbiological identification (FAME) https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2023-05-18T19:08:34.869Z microbiological identification data type (Fatty acid methyl esters) Example Guidance: Use this tag to indicate additional data is available that provides identification information from microbiology properties generated using FAME. microbiological identification tag (Fatty acid methyl esters (FAME)) requires discussion A microbiological characterization data tag which indicates the presence of microbiological identification data derived using the Sensititre identification system. microbiological identification (Sensititre) https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2023-05-18T19:08:34.869Z microbiological identification data type (Sensititre) Example Guidance: Use this tag to indicate additional data is available that provides identification information from microbiology properties generated using Sensititre. microbiological identification tag (Sensititre) requires discussion A microbiological characterization data tag which indicates the presence of microbiological identification data derived using the ViTek identification system. microbiological identification (ViTek) https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2023-05-18T19:08:34.869Z microbiological identification data type (ViTek) Example Guidance: Use this tag to indicate additional data is available that provides identification information from microbiology properties generated using ViTek. microbiological identification tag (ViTek) requires discussion A microbiological characterization data tag which indicates the presence of microbiological identification data derived using phage type identification. phage type https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2023-05-18T19:08:34.869Z phage type data type Example Guidance: Use this tag to indicate additional data is available that provides identification information from phage typing. phage type identification tag requires discussion A microbiological characterization data tag which indicates the presence of microbiological identification data derived using serotype identification. https://www.cdc.gov/salmonella/reportspubs/salmonella-atlas/serotyping-importance.html used as a partial source for the "Example Guidance". serotype https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2023-05-18T19:08:34.869Z serotype data type Example Guidance: Use this tag to indicate additional data is available that provides identification information from serotyping, a subtyping test based on differences in microbial surfaces. serotype identification tag requires discussion A microbiological characterization data tag which indicates the presence of phenotypic microbiological characterization data. https://www.merriam-webster.com/dictionary/phenotyping used as a partial source for the "Example Guidance". phenotypic microbiological characterization https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2023-05-18T19:08:34.869Z phenotypic microbiological characterization attribute bundle phenotypic microbiological characterization data type Example Guidance: Use this tag to indicate additional data is available that provides characterization information from determining, analyzing, or predicting all or part of a microorganism's phenotype. phenotypic microbiological characterization data tag requires discussion A phenotypic microbiological characterization data tag which indicates the presence of antimicrobial resistance (AMR) phenotypic testing characterization data. AMR phenotypic testing https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2023-05-18T19:08:34.869Z AMR phenotypic testing data type AMR phenotypic testing tag antimicrobial resistance phenotypic testing data type Example Guidance: Use this tag to indicate additional data is available that provides phenotypic characterization using AMR testing. antimicrobial resistance (AMR) phenotypic testing characterization tag requires discussion A phenotypic microbiological characterization data tag which indicates the presence of biolog phenotype microarray characterization data. biolog phenotype microarray https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2023-05-18T19:08:34.869Z biolog phenotype microarray data type Example Guidance: Use this tag to indicate additional data is available that provides phenotypic characterization using biolog microarray technology. biolog phenotype microarray characterization tag requires discussion A dataset attribute bundle which indicates the presence of microbiological quantification data. microbiological quantification https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2023-05-18T19:08:34.869Z microbiological quantification attribute bundle microbiological quantification data type Example Guidance: Use this tag to indicate additional data is available that provides quantification information from microbiological properties. microbiological quantification data tag requires discussion A microbiological quantification data tag which indicates the presence of colony count data. colony count https://orcid.org/0000-0001-5275-8866 https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2023-05-18T19:08:34.869Z colony count data type Example Guidance: Use this tag to indicate additional data is available that provides quantification information from microbial colony counts. colony count microbiological quantification tag requires discussion A colony count microbiological quantification data tag which indicates the presence of data that describes total colony count of coliforms. total coliform count https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2023-05-18T19:08:34.869Z total coliform count data type Example Guidance: Use this tag to indicate additional data is available that provides quantification information from microbial total coliform counts. total coliform count microbiological quantification tag requires discussion A colony count microbiological quantification data tag that indicates the presence of data which describes total colony count of fecal coliforms. total fecal coliform count https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2023-05-18T19:08:34.869Z total fecal coliform count data type Example Guidance: Use this tag to indicate additional data is available that provides quantification information from microbial total colony count of coliforms that generally originate in the intestines of warm-blooded animals. total fecal coliform count microbiological quantification tag requires discussion A microbiological quantification data tag which indicates the presence of infectivity assay data. infectivity assay https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2023-05-18T19:08:34.869Z infectivity assay data type Example Guidance: Use this tag to indicate additional data is available that provides quantification information from infectivity assay(s). infectivity assay tag requires discussion A microbiological quantification data tag which indicates the presence of data which describes enzyme-linked immunosorbent assay (ELISA) toxin binding. ELISA toxin binding https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2023-05-18T19:08:34.869Z ELISA toxin binding data type enzyme-linked immunosorbent assay (ELISA) toxin binding data type Example Guidance: Use this tag to indicate additional data is available that provides quantification data from ELISA toxin binding assay(s). enzyme-linked immunosorbent assay (ELISA) toxin binding tag requires discussion A dataset attribute bundle which indicates the presence of molecular characterization data. Molecular characterization https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2023-05-18T19:08:34.869Z microbiological quantification attribute bundle molecular characterization data type Example Guidance: Use this tag to indicate additional data is available that provides characterization information from molecular properties. molecular characterization data tag requires discussion A molecular characterization data tag which indicates the presence of 16S rRNA Sanger sequencing characterization data. 16S rRNA Sanger sequencing https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2023-05-18T19:08:34.869Z 16S rRNA Sanger sequencing data type Example Guidance: Use this tag to indicate additional data is available that provides characterization information from 16S rRNA Sanger sequencing. 16S rRNA Sanger sequencing characterization tag requires discussion A molecular characterization data tag which indicates the presence of polymerase chain reaction (PCR) marker detection characterization data. PCR marker detection https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2023-05-18T19:08:34.869Z PCR marker detection data type Polymerase chain reaction (PCR) marker detection data type Example Guidance: Use this tag to indicate additional data is available that provides characterization information from PCR marker detection. polymerase chain reaction (PCR) marker detection characterization tag requires discussion A PCR marker detection characterization data tag which indicates the presence of BOX-A1R-based repetitive extragenic palindromic (BOX) PCR fingerprint data. BOX PCR fingerprint https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2023-05-18T19:08:34.869Z BOX PCR fingerprint tag BOX-A1R-based repetitive extragenic palindromic (BOX) PCR fingerprint data type Example Guidance: Use this tag to indicate additional data is available that provides characterization information from BOX PCR fingerprint assay(s). BOX-A1R-based repetitive extragenic palindromic (BOX) PCR fingerprint tag requires discussion A PCR marker detection characterization data tag which indicates the presence of enterobacterial repetitive intergenic consensus (ERIC) PCR fingerprint data. ERIC PCR fingerprint https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2023-05-18T19:08:34.869Z ERIC PCR fingerprint data type ERIC PCR fingerprint tag enterobacterial repetitive intergenic consensus polymerase chain reaction fingerprint data type Example Guidance: Use this tag to indicate additional data is available that provides characterization information from ERCI PCR fingerprint assay(s). enterobacterial repetitive intergenic consensus (ERIC) PCR fingerprint tag requires discussion A molecular characterization data tag which indicates the presence of plasmid type characterization data. plasmid type https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2023-05-18T19:08:34.869Z plasmid type data type Example Guidance: Use this tag to indicate additional data is available that provides characterization information from typing plasmids. plasmid type characterization data tag requires discussion A molecular characterization data tag which indicates the presence of ribotype characterization data. http://purl.obolibrary.org/obo/GENEPIO_0000063 used as a partial source for the "Example Guidance". ribotype https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2023-05-18T19:08:34.869Z ribotype data type Example Guidance: Use this tag to indicate additional data is available that provides characterization information from ribotyping, which involves the fingerprinting of genomic DNA restriction fragments that contain all or part of the genes coding for the 16S and 23S rRNA. ribotype characterization data tag requires discussion A dataset attribute bundle which indicates the presence of molecular quantification data. molecular quantification https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2023-05-18T19:08:34.869Z molecular quantification attribute bundle molecular quantification data type Example Guidance: Use this tag to indicate additional data is available that provides quantification information from molecular properties. molecular quantification data tag requires discussion A molecular quantification data tag which indicates the presence of quantitative polymerase chain reaction (qPCR) marker organism quantification data. qPCR marker organism quantification https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2023-05-18T19:08:34.869Z qPCR marker organism quantification data type qPCR marker organism quantification tag quantitative polymerase chain reaction (qPCR) marker organism quantification data type Example Guidance: Use this tag to indicate additional data is available that provides quantification information from qPCR marker organism assay(s). quantitative polymerase chain reaction (qPCR) marker organism quantification tag requires discussion A dataset attribute bundle which indicates the presence of physical characterization data. physical characterization https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2023-05-18T19:08:34.869Z physical characterization attribute bundle physical characterization data type Example Guidance: Use this tag to indicate additional data is available that provides characterization information from physical properties. physical characterization data tag requires discussion A physical characterization data tag which indicates the presence of data that describes conductivity measurement characterization. conductivity measurement https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2023-05-18T19:08:34.869Z conductivity measurement data type Example Guidance: Use this tag to indicate additional data is available that provides physical characterization via measurement of conductivity, including the units of measurement. conductivity measurement characterization tag requires discussion A physical characterization data tag which indicates the presence of data that describes a measurement of a mollusc shell. mollusc shell measurement https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2023-05-18T19:08:34.869Z mollusc shell measurement data type Example Guidance: Use this tag to indicate additional data is available that provides a measurement of the mollusc shell, including the units of measurement. mollusc shell measurement characterization tag requires discussion A physical characterization data tag which indicates the presence of data that describes the length of a mollusc shell. mollusc shell length https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2023-05-18T19:08:34.869Z mollusc shell length data type Example Guidance: Use this tag to indicate additional data is available that provides the length of the mollusc shell, including the units of measurement. mollusc shell length tag requires discussion A physical characterization data tag which indicates the presence of matter compostion characterization data. matter compostion https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2023-05-18T19:08:34.869Z matter compostion data type Example Guidance: Use this tag to indicate additional data is available that provides the composition of the mass of something. matter compostion characterization tag requires discussion A matter composition characterization data tag which indicates the presence of data that describes dry matter composition. dry matter composition https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2023-05-18T19:08:34.869Z dry matter composition data type Example Guidance: Use this tag to indicate additional data is available that provides the composition of the mass of something when water is completely removed. dry matter composition tag requires discussion A matter composition characterization data tag which indicates the presence of data that describes organic matter composition. organic matter composition https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2023-05-18T19:08:34.869Z organic matter composition data type Example Guidance: Use this tag to indicate additional data is available that provides the composition of the mass of something comprised of organic compounds. organic matter composition tag requires discussion A physical characterization data tag which indicates the presence of data that describes turbidity measurement. http://purl.obolibrary.org/obo/NCIT_C74723 used as a partial source for the "Example Guidance". turbidity measurement https://orcid.org/0000-0001-5275-8866 https://orcid.org/0000-0002-1107-9135 https://orcid.org/0000-0002-8844-9165 https://orcid.org/0000-0002-9578-0788 2023-05-18T19:08:34.869Z turbidity measurement data type Example Guidance: Use this tag to indicate additional data is available that provides the determination of the sample opacity, including the units of measurement. turbidity measurement tag available data types enumeration Undigested food material, microbiota, and other materials found in the digestive tract. 2023-11-28T14:09:34Z digestive tract substance Undigested food material, microbiota, and other materials found in the cecum https://www.britannica.com/science/cecum 2023-11-28T13:29:31Z caecal content Undigested food material, microbiota, and other materials found in the intestine. 2023-11-28T13:54:45Z intestinal content A specimen collection device that is designed to collect sediment samples from the hard bottoms of a body of water i.e. sand, gravel, consolidated marl or clay. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. 2023-11-29T14:21:43Z PONAR grab sampler A specimen collection device designed to penetrate soil with a hollow tube to collect soil sample cores. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. 2023-11-29T12:15:31Z soil sample probe A specimen collection process that is used to dig out an amount of sample using a scoop. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. 2023-11-29T11:21:54Z specimen collection by scooping A specimen collection process that is used to collect a sediment sample. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. 2023-11-29T11:40:32Z sediment sampling A specimen collection process that is used to collect soil sample cores. Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” id of the other term. 2023-11-29T11:47:51Z soil coring 1 A coordinate system, and a set of reference points, used to locate places on the Earth (or similar objects). Josh Hanna William R. Hogan Damion Dooley's note: This coordinate system must reference the particulars of a spheroid - its "radius = fn(lat,long)" formula - in order to yeild any distance metrics. Alternate definition: A geographic coordinate system is a 2 dimensional coordinate system superimposed onto the surface of a spheroid. geodetic datum The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or a transporter complex, a pore or a motor protein. GO:0015457 GO:0015460 GO:0044765 Note that this term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term, for e.g. to transmembrane transport, to microtubule-based transport or to vesicle-mediated transport. transport The internally coordinated responses (actions or inactions) of animals (individuals or groups) to internal or external stimuli, via a mechanism that involves nervous system activity. GO:0023032 GO:0044708 GO:0044709 GO:0007610 MeSH:D001519 NCIt:C16326 Wikipedia:Behavior behavioral response to stimulus behaviour behavioural response to stimulus 1. Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation reviews. 2. While a broader definition of behavior encompassing plants and single cell organisms would be justified on the basis of some usage (see PMID:20160973 for discussion), GO uses a tight definition that limits behavior to animals and to responses involving the nervous system, excluding plant responses that GO classifies under development, and responses of unicellular organisms that has general classifications for covering the responses of cells in multicellular organisms (e.g. cell chemotaxis). behavior A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. A process that emerges from two or more causally-connected macromolecular activities and has evolved to achieve a biological objective. Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end. GO:0000004 GO:0007582 GO:0044699 GO:0008150 MeSH:D055705 NCIt:C17828 Wikipedia:Biological_process biological process physiological process A biological process is an evolved process Note that, in addition to forming the root of the biological process ontology, this term is recommended for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. biological process biological_process A biological process that directly contributes to the process of producing new individuals by one or two organisms. The new individuals inherit some proportion of their genetic material from the parent or parents. GO:0044702 Wikipedia:Reproduction reproductive process Any biological process, occurring at the level of a multicellular organism, pertinent to its function. GO:0044707 GO:0050874 organismal physiological process Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. multicellular organismal process Behavior directed towards society, or taking place between members of the same species. Occurs predominantly, or only, in individuals that are part of a group. Wikipedia:Social_behavior social behaviour Behavior such as predation which involves members of different species is not social. Communication between members of different species is also not social behavior. social behavior Formation of hardened covering (a scab) at a wound site. The scab has multiple functions including limiting blood loss, providing structural stability to the wound and guarding against infection. scab formation A process carried out by gene products in an organism that enable the organism to engage in a symbiotic relationship, a more or less intimate association, with another organism. The various forms of symbiosis include parasitism, in which the association is disadvantageous or destructive to one of the organisms; mutualism, in which the association is advantageous, or often necessary to one or both and not harmful to either; and commensalism, in which one member of the association benefits while the other is not affected. However, mutualism, parasitism, and commensalism are often not discrete categories of interactions and should rather be perceived as a continuum of interaction ranging from parasitism to mutualism. In fact, the direction of a symbiotic interaction can change during the lifetime of the symbionts due to developmental changes as well as changes in the biotic/abiotic environment in which the interaction occurs. Microscopic symbionts are often referred to as endosymbionts. GO:0043298 GO:0044404 GO:0072519 GO:0085031 commensalism host-pathogen interaction parasitism biological process involved in symbiotic interaction Entry of a symbiont into the body, tissues, or cells of a host organism as part of the symbiont life cycle. The host is defined as the larger of the organisms involved in a symbiotic interaction. Penetration by an organism into the body, tissues, or cells of the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction. GO:0030260 GO:0044411 GO:0051806 GO:0051828 GO:0051830 GO:0075052 GO:0085027 GO:0085028 entry into host host invasion host penetration invasion into host invasion of host penetration into host entry into cell of other organism during symbiotic interaction entry into host cell via penetration peg entry into host via a specialized structure during symbiotic interaction entry into host via enzymatic degradation of host anatomical structure entry into host via enzymatic degradation of host cuticle penetration into host via a specialized structure penetration into host via a specialized structure during symbiotic interaction entry into host symbiont entry into host Any process evolved to enable an interaction with an organism of a different species. interaction with another species interspecies interaction interspecies interaction between organisms interspecies interaction with other organisms biological process involved in interspecies interaction between organisms The controlled release of a substance by a cell or a tissue. secretion Any process in which a cell, a substance, or a cellular entity, such as a protein complex or organelle, is transported, tethered to or otherwise maintained in a specific location. In the case of substances, localization may also be achieved via selective degradation. GO:1902578 establishment and maintenance of localization establishment and maintenance of position localisation establishment and maintenance of cellular component location establishment and maintenance of substance location establishment and maintenance of substrate location localization Any process that localizes a substance or cellular component. This may occur via movement, tethering or selective degradation. establishment of localisation establishment of localization An interaction between two organisms living together in more or less intimate association. The term host is used for the larger (macro) of the two members of a symbiosis; the various forms of symbiosis include parasitism, commensalism and mutualism. GO:0044112 GO:0044116 GO:0044117 GO:0044119 GO:0044121 GO:0044123 GO:0044125 interaction with host growth of symbiont in host growth of symbiont in host cell growth of symbiont in host organelle growth of symbiont in host vacuole biological process involved in interaction with host Any process in which an organism has an effect on an organism of the same species. intraspecies interaction between organisms intraspecies interaction with other organisms biological process involved in intraspecies interaction between organisms A biological process which involves another organism of the same or different species. multi-organism process An umbrella term often used in medical literature to include transgender persons and gender nonconforming people who may or may not be transgender. transgender and gender nonconforming An umbrella term often used in research to covered genderqueer and gender nonbinary identities, as well as gender nonconforming persons. genderqueer, gender non-conforming, and gender nonbinary genderqueer, gender nonconforming and gender nonbinary genderqueer, gender nonconforming, and gender nonbinary Either, a specific gender identity which is not male or female; or, more broadly, an umbrella term for gender identities not considered male or female. https://en.wikipedia.org/wiki/Category:Non-binary_gender gender non-binary "Non-binary" (with the hyphen) is more common in the United Kingdom, whereas "nonbinary" (as one word) is more common in the United States. Note that "nonbinary" as itself is preferable if the context in relationship to gender is known. Most therefore "nonbinary persons" not "gender nonbinary persons" can be used. gender nonbinary Equitable representation of persons of different genders. https://en.wikipedia.org/wiki/Gender_diversity https://www.wikidata.org/wiki/Q1501335 diversité de genre gender diversity gender diversity Having a feminine gender (identity) which is different from the sex one was assigned at birth. https://en.wikipedia.org/wiki/Transfeminine https://mogai-genders.fandom.com/wiki/Transfeminine https://www.wikidata.org/wiki/Q27679684 trans feminine transfemenino transfeminin transfeminine Having a masculine gender (identity) which is different from the sex one was assigned at birth. https://mogai-genders.fandom.com/wiki/Transmasculine https://www.wikidata.org/wiki/Q27679766 trans masculine transmasculine transmasculino transmaskulin https://lgbta.fandom.com/wiki/Cisn%27t noncisgender gender modality non-cisgender gender modality Population category defined using ancestry informative markers (AIMs) based on genetic/genomic data ancestral group ancestry category Includes individuals who either self-report or have been described by authors as European, Caucasian, White or one of the sub-populations from this region (e.g Dutch). This category also includes individuals who genetically cluster with reference populations from this region, for example 1000 Genomes and/or HapMap CEU, FIN, GBR, IBS and TSI populations. Caucasian white European Includes individuals who either self-report or have been described by authors as South Asian or one of the sub-populations from this region (e.g Asian Indian). This category also includes individuals who genetically cluster with reference populations from this region, for example 1000 Genomes and/or HapMap BEB, GIH, ITU, PJL and STU populations. South Asian Includes individuals who either self-report or have been described by authors as South East Asian or one of the sub-populations from this region (e.g Vietnamese). This category also includes includes individuals who genetically cluster with reference populations from this region, for example 1000 Genomes KHV population. We note that East Asian and South East Asian populations are often conflated. However, recent studies indicate a unique genetic background for South East Asian populations. South East Asian Includes individuals that either self-report or have been described as Asian but there was not sufficient information to allow classification as East Asian, Central Asian, South Asian or South-East Asian. Asian unspecified Asian Includes individuals who either self-report or have been described by authors as East Asian or one of the sub-populations from this region (e.g Chinese). This category also includes individuals who genetically cluster with reference populations from this region, for example 1000 Genomes and/or HapMap CDX, CHB, CHS and JPT populations. East Asian Includes individuals that either self-report or have been described as African, but there was not sufficient information to allow classification as African American, AfroCaribbean or Sub-Saharan African. African unspecified African Includes individuals who either self-report or have been described by authors as SubSaharan African or one of the subpopulations from this region (e.g. Yoruban). This category also includes individuals who genetically cluster with reference populations from this region for example 1000 Genomes and/or HapMap ESN, LWK, GWD, MSL, MKK and YRI populations. Sub-Saharan African Includes indigenous individuals of North, Central and South America, descended from the original human migration into the Americas from Siberia. We note that there does not appear to be a suitable reference population for this category and efforts are required to fill this gap. Class previously labelled as "Native American". Use of this term, alongside other terms such as "First Nations", should be discontinued in favour of the more appropriate "Indigenous American", which includes indigenous communities across the Americas while the former serve as political designations in the USA and Canada, respectively. Indigenous American Includes individuals who either self-report or are described by authors as Hispanic, Latino, Latin American or one of the sub-populations from this region. This category includes individuals with known admixture of primarily European, African and Native American ancestries, though some may have also a degree of Asian (e.g. Peru). We also note that the levels of admixture vary depending on the country, with Caribbean countries carrying higher levels of African admixture when compared to South American countries, for example. This category also includes individuals who genetically cluster with reference populations from this region, for example 1000 Genomes and/or HapMap CLM, MXL, PEL and PUR populations Jackie MacArthur Joannella Morales Latin or Admixed American Includes individuals who self-report or were described by authors as Middle Eastern, North African, Persian or one of the subpopulations from this region (e.g. Saudi Arabian). We note there is heterogeneity in this category with different degrees of admixture as well as levels of genetic isolation. We note that there does not appear to be a suitable reference population for this category and efforts are required to fill this gap. Middle Eastern/North African Greater Middle Eastern (Middle Eastern or North African or Persian) Includes individuals who either self-report or have been described by authors as African American or Afro-Caribbean. This category also includes individuals who genetically cluster with reference populations from this region, for example 1000 Genomes and/or HapMap ACB or ASW populations. We note that there is likely to be significant admixture with European ancestry populations. African American or Afro-Caribbean Includes individuals that either self-report or have been described by authors as Oceanian or one of the sub-populations from this region (e.g. Native Hawaiian). We note that there does not appear to be a suitable reference population for this category and efforts are required to fill this gap. Oceanian A population for which specific ancestry information is known but that does not fall into any of the defined ancestry categories uncategorised population Japanese non-aboriginal Taiwanese Taiwanese Chinese Korean Mongolian Macanese Singaporean Chinese Hong Kong Chinese Han Chinese Includes individuals who either self-report or have been described by authors as Central Asian. We note that there does not appear to be a suitable reference population for this population and efforts are required to fill this gap. Central Asian A population with increased genetic homogeneity and reduced genetic variation due to cultural or geographic isolation founder population population isolate genetically isolated population Italian Sardinian Val Borbera Friuli Venezia Giulia Carlantino Old Order Amish Sorb Hutterite Amish Erasmus Rucphen Orcadian Korčulan Dutch Finnish Finnish founder Dutch founder Ashkenazi Jew Sudanese Anguillan Antiguan or Barbudan Barbadian Haitian Jamaican Tajik Tajikistani Turkmen Uzbekistani Afghan Kazakhstani Kyrgyzstani Albanian Andorran Australian Austrian Belarusian Belgian Bermudian Bosnian or Herzegovinian Brazilian Bulgarian Canadian Channel Islander Chilean Croatian Czech Danish Estonian Faroese Falkland Islander French German Gibraltarian Greek Greenlander Hungarian Icelandic Manx Latvian Liechtensteiner Lithuanian Luxembourgish Maltese Monegasque Montenegrin New Zealander Norfolk Islander Norwegian Polish Portugese Irish Moldovan Romanian Russian Saint-Pierrais or Miquelonnais Sammarinese Serb Slovak Slovene Spanish Swedish Swiss Macedonian Ukrainian Argentine Bahamian Belizean Bolivian British Virgin Islander Caymanian Colombian Costa Rican Cuban Dominican Ecuadorian Salvadoran French Guianese Grenadian Guatemalan Guyanese Honduran Martinican Mexican Montserratian Nicaraguan Panamanian Paraguayan Peruvian Puerto Rican Kittitian or Nevisian Saint Lucian Saint Vincentian Surinamer Surinamese Trinidadian or Tobagonian Turks and Caicos Islander Virgin Islander Uruguayan Venezuelan Algerian Armenian Azerbaijani Bahraini Cypriote Georgian Iranian Iraqi Israeli Jordanian Kuwaiti Lebanese Libyan Moroccan Palestinian Omani Qatari Saudi Arab Saudi Tunisian Turkish Emirati Yemeni Aruban Christmas Islander Cocos Islander Curacaoan Kosovar Northern Mariana Islander South Sudanese Syrian British American American Samoan Cook Islander Fijian French Polynesian Guamanian I-Kiribati Marshallese Micronesian Nauruan New Caledonian Niuean Palauan Papuan Papua New Guinean Pitcairn Islander Samoan Solomon Islander Tokelauan Tongan Tuvaluan Ni-Vanuato Wallis and Futuna Islander Bangladeshi Bhutanese Asian Indian Indian Asian Indian Maldivian Nepalese Pakistani Sri Lankan Bruneian Cambodian Indonesian Lao Malaysian Burmese Filipino Thai Timorese Vietnamese Cameroonian Cape Verdean Chadian Ethiopian Kenyan Liberian Mauritanian Mauritian Mahoran Namibian Sao Tomean Senegalese Sierra Leonean South African St. Helenian Ugandan Angolan Beninese Motswana Burkinabe Burundian Comoran Congolese Ivoirian Djiboutian Equatorial Guinean Eritrean Gabonese Gambian Ghanaian Guinean Bissau-Guinean Mosotho Malawian Malian Mozambican Nigerien Nigerian Rwandan Togolese Tanzanian Zambian Zimbabweian Irish founder genetically homogenous Irish Includes individuals who either self-report or have been described by authors as Australian Aboriginal. These are expected to be descendents of early human migration into Australia from Eastern Asia and can be distinguished from other Asian populations by mtDNA and Y chromosome variation. Aboriginal Australian Silk Road founder Israeli Arab Arab Israeli founder Cilento Individuals who have at least six great-grandparents born in the Central Valley of Costa Rica, to ensure descent from the founder population, composed primarily of Europeans and Native Americans PMID:25584925 Costa Rican founder French Canadian founder Italian founder Northern Finnish founder Romanian founder South Tyrolean Vis founder Split founder Population for which insufficient information is available to allocate it to a specific ancestral group or which contain individuals from a range of known ancestry categories, eg American undefined ancestry population African Caribbean Afro-Caribbean African American Talana Individuals who self-identify or are reported by authors as belonging to a group of indigenous Americans living in an area consisting of what is now central and southern Arizona, as well as northwestern Mexico in the states of Sonora and Chihuahua. The majority population of the two current bands of the Akimel O'odham in the United States are based in two reservations: the Keli Akimel Oʼodham on the Gila River Indian Community (GRIC) and the On'k Akimel O'odham on the Salt River Pima-Maricopa Indian Community (SRPMIC). Akimel O'otham Pima Pima Indian Akimel O'odham Individuals who self-identify or are reported by authors as belonging to the indigenous peoples who have historically lived on the Interior Plains (the Great Plains and Canadian Prairies) of North America Plains American Indian Plains Indians Kosraean Native Hawaiian Pacific Islander Dai Chinese Dai Hui Chinese Hui Jingpo Chinese Malaysian Chinese Uygur Chinese Uigur Uygur Tibetan Han Taiwanese Taiwanese Han Sri Lankan Sinhalese Tatar Bashkir Includes individuals who either self-report or have been described by authors as Aboriginal Australian of Martu ancestry. The Martu Australian Aboriginal people are from the Western Desert region located across the Pilbara in Western Australia Mardu Aboriginal Australian Mardu Australian Aboriginal Martu Aboriginal Australian PMID:27070114 Martu Australian Aboriginal Jewish Israeli Punjabi Sikh American of European ancestry European American Native people residing in the Arctic of Alaska, northern Canada, Greenland, or eastern Siberia PMID:25884279 PMID:29220501 Class previously labelled as "Eskimo", which is outdated and culturally inappropriate. Outdated label may be added as an appropriately flagged synonym at a later stage. Inuit Includes individuals with ethnic origins in the Semitic people populating the Arabian Peninsula and other countries in the Middle East and Northern Africa PMID:27393651 PMID:28106113 Arab Includes individuals who either self-report or have been described by authors as Singaporean Malay. PMID:19700652 PMID:31626772 Singaporean Malay Includes individuals who either self-report or have been described by authors as Singaporean Indian. PMID:19700652 PMID:31626772 Singaporean Indian Includes indigenous individuals of North and Central America, descended from the original human migration into the Americas from Siberia. American Indian Indigenous in North America Includes indigenous individuals of Central and South America, descended from the original human migration into the Americas from Siberia. Indigenous in South America Individuals who self-identify or are reported by authors as belonging to a group of indigenous people of Mexico inhabiting the central Mexican Plateau (Altiplano) region. Otomi Individuals who self-identify or are reported by authors as belonging to the Mayan ethnolinguistic group of indigenous peoples of Mesoamerica. Maya Individuals who self-identify or are reported by authors as belonging to the Zapotec ethnolinguistic group of indigenous people of Mexico. The Zapotec population is concentrated in the southern state of Oaxaca, but Zapotec communities also exist in neighboring states Zapoteco Individuals who self-identify or are reported by authors as belonging to the Mazatecan ethnolinguistic group of indigenous peoples in the area known as the Sierra Mazateca, which is in the northern part of the state of Oaxaca in southern Mexico, as well as in adjacent areas of the states of Puebla and Veracruz Mazateco Individuals who self-identify or are reported by authors as belonging to a group of indigenous people of the Americas living in the state of Chihuahua in Mexico Tarahumara Rarámuri Individuals who self-identify or are reported by authors as belonging to a group of the indigenous people of Mexico, El Salvador, Guatemala, Honduras, and Nicaragua Nahua Individuals who self-identify or are reported by authors as belonging to indigenous Mesoamerican peoples of Mexico inhabiting the region known as La Mixteca of Oaxaca and Puebla as well as La Montaña Region and Costa Chica Regions of the state of Guerrero Mixtec Mixteco Individuals who self-identify or are reported by authors as belonging to the Wayúu indigenous people of the Guajira Peninsula in northernmost part of Colombia and northwest Venezuela. Guajiro Wahiro Wayu Wayuu Wayúu Individuals who self-identify or are reported by authors as belonging to an Arawakan ethnolinguistic group in Colombia and Venezuela Piapoco Individuals who self-identify or are reported by authors as belonging to a group of indigenous people native to the Nariño region of southern Colombia and neighbouring Equador Pastos Individuals who self-identify or are reported by authors as belonging to a group of indigenous people of South America who speak the Quechua languages. Although most Quechua speakers are native to Peru, there are some significant populations in Ecuador, Bolivia, Chile, Colombia, and Argentina Quichua Quechua Individuals who self-identify or are reported by authors as belonging to a group of indigenous people in the Andes and Altiplano regions of South America; about 2.3 million live in northwest Argentina, Bolivia, Chile and Peru. Aimara Aymara Individuals who self-identify or are reported by authors as belonging to a group of South American indigenous people native to the Chilean Norte Chico and the Argentine Northwest. Diaguita Individuals who self-identify or are reported by authors as belonging to a group of indigenous people of present-day south-central Chile and southwestern Argentina, including parts of present-day Patagonia Mapuche Individuals who self-identify or are reported by authors as belonging to a group of culturally-related indigenous peoples of South America, living primarily in present-day Paraguay between the Paraná River and lower Paraguay River, the Misiones Province of Argentina, southern Brazil as far east as Rio de Janeiro, and parts of Uruguay and Bolivia. Guaraní-Mbyá Guaraní Individuals who self-identify or are reported by authors as belonging to an indigenous people of Brazil, who now live in three indigenous territories (Terras Indígenas in Portuguese), Caieiras Velhas, Pau-Brasil and Comboiosare, located near the cities of Santa Cruz and Vila do Riacho in the municipality of Aracruz in northern Espírito Santo state, southeastern Brazil. Topinaquis Tupinanquins Tupinaquis Tupiniquins Tupinã-ki Tupiniquim Individuals who self-identify or are reported by authors as belonging to an Chibchan-speaking indigenous people of Colombia, descended from the Tairona culture, concentrated in northern Colombia in the Sierra Nevada de Santa Marta. Ica Ika Arhuaco Individuals who self-identify or are reported by authors as belonging to an indigenous people living in the rainforests of Peru and in the State of Acre, Brazil. Their ancestral lands are in the forests of Junín, Pasco, Huánuco and part of Ucayali in Peru. Asháninca Asháninka A population made up of 10 samples from Bantu individuals recruited in Kenya as part of the Human Genome Diversity Project. The population was assigned by the collecting project to the superpopulation African. Bantu Kenya Bantu in Kenya (HGDP) A population made up of 4 samples from Bantu individuals recruited in South Africa as part of the Human Genome Diversity Project. The population was assigned by the collecting project to the superpopulation African. Bantu South Africa Bantu in South Africa (HGDP) A population made up of 24 samples from Biaka individuals recruited in Central African Republic as part of the Human Genome Diversity Project. The population was assigned by the collecting project to the superpopulation African. Biaka Biaka in Central African Republic (HGDP) A population made up of 20 samples from Mandenka individuals recruited in Senegal as part of the Human Genome Diversity Project. The population was assigned by the collecting project to the superpopulation African. Mandenka Mandenka in Senegal (HGDP) A population made up of 13 samples from Mbuti individuals recruited in Democratic Republic of Congo as part of the Human Genome Diversity Project. The population was assigned by the collecting project to the superpopulation African. Samples from this population were used in data collections for HGDP Transcriptome. Mbuti Mbuti in Democratic Republic of Congo (HGDP) A population made up of 4 samples from San individuals recruited in Namibia as part of the Human Genome Diversity Project. The population was assigned by the collecting project to the superpopulation African. San San in Namibia (HGDP) A population made up of 18 samples from Yoruba individuals recruited in Nigeria as part of the Human Genome Diversity Project. The population was assigned by the collecting project to the superpopulation African. Yoruba Yoruba in Nigeria (HGDP) A population made up of 2 samples from Bantu Herero individuals recruited in Botswana Or Namibia as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation African. Bantu Herero Bantu Herero in Botswana Or Namibia (SGDP) A population made up of 2 samples from Bantu Kenya individuals recruited in Kenya as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation African. Bantu Kenya Bantu Kenya in Kenya (SGDP) A population made up of 2 samples from Bantu Tswana individuals recruited in Botswana Or Namibia as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation African. Bantu Tswana Bantu Tswana in Botswana Or Namibia (SGDP) A population made up of 2 samples from Biaka individuals recruited in Central African Republic as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation African. Biaka Biaka in Central African Republic (SGDP) A population made up of 3 samples from Dinka individuals recruited in Sudan as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation African. Dinka Dinka in Sudan (SGDP) A population made up of 2 samples from Esan individuals recruited in Nigeria as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation African. Esan Esan in Nigeria (SGDP) A population made up of 2 samples from Gambian individuals recruited in Gambia as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation African. Gambian Gambian in Gambia (SGDP) A population made up of 4 samples from Ju|'hoan North individuals recruited in Namibia as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation African. Ju|'hoan North Ju|'hoan North in Namibia (SGDP) A population made up of 2 samples from Khomani San individuals recruited in South Africa as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation African. Khomani San Khomani San in South Africa (SGDP) A population made up of 2 samples from Luhya individuals recruited in Kenya as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation African. Luhya Luhya in Kenya (SGDP) A population made up of 2 samples from Luo individuals recruited in Kenya as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation African. Luo Luo in Kenya (SGDP) A population made up of 3 samples from Mandenka individuals recruited in Senegal as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation African. Mandenka Mandenka in Senegal (SGDP) A population made up of 3 samples from Masai individuals recruited in Kenya as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation African. MKK Masai Masai in Kenya A population made up of 4 samples from Mbuti individuals recruited in Congo as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation African. Mbuti Mbuti in Congo (SGDP) A population made up of 2 samples from Mende individuals recruited in Sierra Leone as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation African. Mende Mende in Sierra Leone (SGDP) A population made up of 2 samples from Mozabite individuals recruited in Algeria as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation African. Mozabite Mozabite in Algeria (SGDP) A population made up of 2 samples from Saharawi individuals recruited in Western Sahara (Morocco) as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation African. Saharawi Saharawi in Western Sahara (Morocco) (SGDP) A population made up of 1 samples from Somali individuals recruited in Kenya as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation African. Somali Somali in Kenya (SGDP) A population made up of 3 samples from Yoruba individuals recruited in Nigeria as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation African. Yoruba Yoruba in Nigeria (SGDP) A population made up of 113 samples from African Ancestry individuals recruited in Southwest US as part of the 1000 Genomes Project. The population was assigned by the collecting project to the superpopulation African. ASW African Ancestry SW African Ancestry in Southwest US A population made up of 123 samples from African Caribbean individuals recruited in Barbados as part of the 1000 Genomes Project. The population was assigned by the collecting project to the superpopulation African. ACB African Caribbean African Caribbean in Barbados A population made up of 173 samples from Esan individuals recruited in Nigeria as part of the 1000 Genomes Project. The population was assigned by the collecting project to the superpopulation African. ESN Esan Esan in Nigeria A population made up of 100 samples from Fula individuals recruited in Western Division, The Gambia as part of the Gambian Genome Variation Project. The population was assigned by the collecting project to the superpopulation African. GWF Gambian Fula Gambian in Western Division, The Gambia - Fula A population made up of 100 samples from Jola individuals recruited in Western Division, The Gambia as part of the Gambian Genome Variation Project. The population was assigned by the collecting project to the superpopulation African. GWJ Gambian Jola Gambian in Western Division, The Gambia - Jola A population made up of 280 samples from Mandinka individuals recruited in Western Division, The Gambia as part of the 1000 Genomes Project. The population was assigned by the collecting project to the superpopulation African. GWD Gambian Mandinka Gambian in Western Division, The Gambia - Mandinka A population made up of 100 samples from Wolof individuals recruited in Western Division, The Gambia as part of the Gambian Genome Variation Project. The population was assigned by the collecting project to the superpopulation African. GWW Gambian Wolof Gambian in Western Division, The Gambia - Wolof A population made up of 117 samples from Luhya individuals recruited in Webuye, Kenya as part of the 1000 Genomes Project. The population was assigned by the collecting project to the superpopulation African. LWK Luhya Luhya in Webuye, Kenya A population made up of 129 samples from Mende individuals recruited in Sierra Leone as part of the 1000 Genomes Project. The population was assigned by the collecting project to the superpopulation African. MSL Mende Mende in Sierra Leone A population made up of 187 samples from Yoruba individuals recruited in Ibadan, Nigeria as part of the 1000 Genomes Project. The population was assigned by the collecting project to the superpopulation African. YRI Yoruba Yoruba in Ibadan, Nigeria A population made up of 5 samples from Colombian individuals recruited in Colombia as part of the Human Genome Diversity Project. The population was assigned by the collecting project to the superpopulation Latin or Admixed American. Colombian Colombian in Colombia (HGDP) A population made up of 9 samples from Karitiana individuals recruited in Brazil as part of the Human Genome Diversity Project. The population was assigned by the collecting project to the superpopulation Latin or Admixed American. Karitiana Karitiana in Brazil (HGDP) A population made up of 21 samples from Maya individuals recruited in Mexico as part of the Human Genome Diversity Project. The population was assigned by the collecting project to the superpopulation Latin or Admixed American. Maya Maya in Mexico (HGDP) A population made up of 12 samples from Pima individuals recruited in Mexico as part of the Human Genome Diversity Project. The population was assigned by the collecting project to the superpopulation Latin or Admixed American. Pima Pima in Mexico (HGDP) A population made up of 6 samples from Surui individuals recruited in Brazil as part of the Human Genome Diversity Project. The population was assigned by the collecting project to the superpopulation Latin or Admixed American. Surui Surui in Brazil (HGDP) A population made up of 1 samples from Chane individuals recruited in Argentina as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation Latin or Admixed American. Chane Chane in Argentina (SGDP) A population made up of 3 samples from Karitiana individuals recruited in Brazil as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation Latin or Admixed American. Karitiana Karitiana in Brazil (SGDP) A population made up of 2 samples from Mayan individuals recruited in Mexico as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation Latin or Admixed American. Mayan Mayan in Mexico (SGDP) A population made up of 3 samples from Mixe individuals recruited in Mexico as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation Latin or Admixed American. Mixe Mixe in Mexico (SGDP) A population made up of 2 samples from Mixtec individuals recruited in Mexico as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation Latin or Admixed American. Mixtec Mixtec in Mexico (SGDP) A population made up of 2 samples from Piapoco individuals recruited in Colombia as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation Latin or Admixed American. Piapoco Piapoco in Colombia (SGDP) A population made up of 2 samples from Pima individuals recruited in Mexico as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation Latin or Admixed American. Pima Pima in Mexico (SGDP) A population made up of 3 samples from Quechua individuals recruited in Peru as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation Latin or Admixed American. Quechua Quechua in Peru (SGDP) A population made up of 2 samples from Surui individuals recruited in Brazil as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation Latin or Admixed American. Surui Surui in Brazil (SGDP) A population made up of 2 samples from Zapotec individuals recruited in Mexico as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation Latin or Admixed American. Zapotec Zapotec in Mexico (SGDP) A population made up of 148 samples from Colombian individuals recruited in Medellin, Colombia as part of the 1000 Genomes Project. The population was assigned by the collecting project to the superpopulation Latin or Admixed American. CLM Colombian Colombian in Medellin, Colombia A population made up of 107 samples from Mexican Ancestry individuals recruited in Los Angeles, California as part of the 1000 Genomes Project. The population was assigned by the collecting project to the superpopulation Latin or Admixed American. MXL Mexican Ancestry Mexican Ancestry in Los Angeles, California A population made up of 130 samples from Peruvian individuals recruited in Lima, Peru as part of the 1000 Genomes Project. The population was assigned by the collecting project to the superpopulation Latin or Admixed American. PEL Peruvian Peruvian in Lima, Peru A population made up of 150 samples from Puerto Rican individuals recruited in Puerto Rico as part of the 1000 Genomes Project. The population was assigned by the collecting project to the superpopulation Latin or Admixed American. PUR Puerto Rican Puerto Rican in Puerto Rico A population made up of 2 samples from Aleut individuals recruited in Russia as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation Central Asian and Siberian. Aleut Aleut in Russia (SGDP) A population made up of 1 samples from Altaian individuals recruited in Russia as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation Central Asian and Siberian. Altaian Altaian in Russia (SGDP) A population made up of 1 samples from Chukchi individuals recruited in Russia as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation Central Asian and Siberian. Chukchi Chukchi in Russia (SGDP) A population made up of 1 samples from Eskimo Chaplin individuals recruited in Russia as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation Central Asian and Siberian. Eskimo Chaplin Eskimo Chaplin in Russia (SGDP) A population made up of 2 samples from Eskimo Naukan individuals recruited in Russia as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation Central Asian and Siberian. Eskimo Naukan Eskimo Naukan in Russia (SGDP) A population made up of 2 samples from Eskimo Sireniki individuals recruited in Russia as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation Central Asian and Siberian. Eskimo Sireniki Eskimo Sireniki in Russia (SGDP) A population made up of 3 samples from Even individuals recruited in Russia as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation Central Asian and Siberian. Even Even in Russia (SGDP) A population made up of 1 samples from Itelman individuals recruited in Russia as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation Central Asian and Siberian. Itelman Itelman in Russia (SGDP) A population made up of 2 samples from Kyrgyz individuals recruited in Kyrgyzystan as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation Central Asian and Siberian. Kyrgyz Kyrgyz in Kyrgyzystan (SGDP) A population made up of 2 samples from Mansi individuals recruited in Russia as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation Central Asian and Siberian. Mansi Mansi in Russia (SGDP) A population made up of 2 samples from Mongola individuals recruited in China as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation Central Asian and Siberian. Mongola Mongola in China (SGDP) A population made up of 2 samples from Tlingit individuals recruited in Russia as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation Central Asian and Siberian. Tlingit Tlingit in Russia (SGDP) A population made up of 2 samples from Tubalar individuals recruited in Russia as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation Central Asian and Siberian. Tubalar Tubalar in Russia (SGDP) A population made up of 2 samples from Ulchi individuals recruited in Russia as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation Central Asian and Siberian. Ulchi Ulchi in Russia (SGDP) A population made up of 2 samples from Yakut individuals recruited in Russia as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation Central Asian and Siberian. Yakut Yakut in Russia (SGDP) A population made up of 22 samples from Balochi individuals recruited in Pakistan as part of the Human Genome Diversity Project. The population was assigned by the collecting project to the superpopulation Central South Asian. Balochi Balochi in Pakistan (HGDP) A population made up of 23 samples from Brahui individuals recruited in Pakistan as part of the Human Genome Diversity Project. The population was assigned by the collecting project to the superpopulation Central South Asian. Brahui Brahui in Pakistan (HGDP) A population made up of 22 samples from Burusho individuals recruited in Pakistan as part of the Human Genome Diversity Project. The population was assigned by the collecting project to the superpopulation Central South Asian. Burusho Burusho in Pakistan (HGDP) A population made up of 18 samples from Hazara individuals recruited in Pakistan as part of the Human Genome Diversity Project. The population was assigned by the collecting project to the superpopulation Central South Asian. Hazara Hazara in Pakistan (HGDP) A population made up of 21 samples from Kalash individuals recruited in Pakistan as part of the Human Genome Diversity Project. The population was assigned by the collecting project to the superpopulation Central South Asian. Kalash Kalash in Pakistan (HGDP) A population made up of 23 samples from Makrani individuals recruited in Pakistan as part of the Human Genome Diversity Project. The population was assigned by the collecting project to the superpopulation Central South Asian. Makrani Makrani in Pakistan (HGDP) A population made up of 23 samples from Pathan individuals recruited in Pakistan as part of the Human Genome Diversity Project. The population was assigned by the collecting project to the superpopulation Central South Asian. Pathan Pathan in Pakistan (HGDP) A population made up of 22 samples from Sindhi individuals recruited in Pakistan as part of the Human Genome Diversity Project. The population was assigned by the collecting project to the superpopulation Central South Asian. Sindhi Sindhi in Pakistan (HGDP) A population made up of 8 samples from Uygur individuals recruited in China as part of the Human Genome Diversity Project. The population was assigned by the collecting project to the superpopulation Central South Asian. Uygur Uygur in China (HGDP) A population made up of 9 samples from Cambodian individuals recruited in Cambodia as part of the Human Genome Diversity Project. The population was assigned by the collecting project to the superpopulation East Asian. Cambodian Cambodian in Cambodia (HGDP) A population made up of 5 samples from Dai individuals recruited in China as part of the Human Genome Diversity Project. The population was assigned by the collecting project to the superpopulation East Asian. Dai Dai in China (HGDP) A population made up of 9 samples from Daur individuals recruited in China as part of the Human Genome Diversity Project. The population was assigned by the collecting project to the superpopulation East Asian. Daur Daur in China (HGDP) A population made up of 30 samples from Han individuals recruited in China as part of the Human Genome Diversity Project. The population was assigned by the collecting project to the superpopulation East Asian. Han Han in China (HGDP) A population made up of 7 samples from Hezhen individuals recruited in China as part of the Human Genome Diversity Project. The population was assigned by the collecting project to the superpopulation East Asian. Hezhen Hezhen in China (HGDP) A population made up of 27 samples from Japanese individuals recruited in Japan as part of the Human Genome Diversity Project. The population was assigned by the collecting project to the superpopulation East Asian. Japanese Japanese in Japan (HGDP) A population made up of 6 samples from Lahu individuals recruited in China as part of the Human Genome Diversity Project. The population was assigned by the collecting project to the superpopulation East Asian. Lahu Lahu in China (HGDP) A population made up of 8 samples from Miao individuals recruited in China as part of the Human Genome Diversity Project. The population was assigned by the collecting project to the superpopulation East Asian. Miao Miao in China (HGDP) A population made up of 8 samples from Mongolian individuals recruited in China as part of the Human Genome Diversity Project. The population was assigned by the collecting project to the superpopulation East Asian. Mongolian Mongolian in China (HGDP) A population made up of 6 samples from Naxi individuals recruited in China as part of the Human Genome Diversity Project. The population was assigned by the collecting project to the superpopulation East Asian. Naxi Naxi in China (HGDP) A population made up of 10 samples from Northern Han individuals recruited in China as part of the Human Genome Diversity Project. The population was assigned by the collecting project to the superpopulation East Asian. Northern Han Northern Han in China (HGDP) A population made up of 7 samples from Oroqen individuals recruited in China as part of the Human Genome Diversity Project. The population was assigned by the collecting project to the superpopulation East Asian. Oroqen Oroqen in China (HGDP) A population made up of 8 samples from She individuals recruited in China as part of the Human Genome Diversity Project. The population was assigned by the collecting project to the superpopulation East Asian. She She in China (HGDP) A population made up of 8 samples from Tu individuals recruited in China as part of the Human Genome Diversity Project. The population was assigned by the collecting project to the superpopulation East Asian. Tu Tu in China (HGDP) A population made up of 8 samples from Tujia individuals recruited in China as part of the Human Genome Diversity Project. The population was assigned by the collecting project to the superpopulation East Asian. Tujia Tujia in China (HGDP) A population made up of 7 samples from Xibo individuals recruited in China as part of the Human Genome Diversity Project. The population was assigned by the collecting project to the superpopulation East Asian. Xibo Xibo in China (HGDP) A population made up of 23 samples from Yakut individuals recruited in Siberia as part of the Human Genome Diversity Project. The population was assigned by the collecting project to the superpopulation East Asian. Yakut Yakut in Siberia (HGDP) A population made up of 8 samples from Yi individuals recruited in China as part of the Human Genome Diversity Project. The population was assigned by the collecting project to the superpopulation East Asian. Yi Yi in China (HGDP) A population made up of 2 samples from Ami individuals recruited in Taiwan as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation East Asian. Ami Ami in Taiwan (SGDP) A population made up of 1 samples from Atayal individuals recruited in Taiwan as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation East Asian. Atayal Atayal in Taiwan (SGDP) A population made up of 2 samples from Burmese individuals recruited in Myanmar as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation East Asian. Burmese Burmese in Myanmar (SGDP) A population made up of 2 samples from Cambodian individuals recruited in Cambodia as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation East Asian. Cambodian Cambodian in Cambodia (SGDP) A population made up of 4 samples from Dai individuals recruited in China as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation East Asian. Dai Dai in China (SGDP) A population made up of 1 samples from Daur individuals recruited in China as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation East Asian. Daur Daur in China (SGDP) A population made up of 3 samples from Han individuals recruited in China as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation East Asian. Han Han in China (SGDP) A population made up of 2 samples from Hezhen individuals recruited in China as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation East Asian. Hezhen Hezhen in China (SGDP) A population made up of 3 samples from Japanese individuals recruited in Japan as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation East Asian. Japanese Japanese in Japan (SGDP) A population made up of 2 samples from Kinh individuals recruited in Vietnam as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation East Asian. Kinh Kinh in Vietnam (SGDP) A population made up of 2 samples from Korean individuals recruited in Korea as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation East Asian. Korean Korean in Korea (SGDP) A population made up of 2 samples from Lahu individuals recruited in China as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation East Asian. Lahu Lahu in China (SGDP) A population made up of 2 samples from Miao individuals recruited in China as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation East Asian. Miao Miao in China (SGDP) A population made up of 3 samples from Naxi individuals recruited in China as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation East Asian. Naxi Naxi in China (SGDP) A population made up of 2 samples from Oroqen individuals recruited in China as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation East Asian. Oroqen Oroqen in China (SGDP) A population made up of 2 samples from She individuals recruited in China as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation East Asian. She She in China (SGDP) A population made up of 2 samples from Thai individuals recruited in Thailand as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation East Asian. Thai Thai in Thailand (SGDP) A population made up of 2 samples from Tu individuals recruited in China as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation East Asian. Tu Tu in China (SGDP) A population made up of 2 samples from Tujia individuals recruited in China as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation East Asian. Tujia Tujia in China (SGDP) A population made up of 2 samples from Uygur individuals recruited in China as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation East Asian. Uygur Uygur in China (SGDP) A population made up of 2 samples from Xibo individuals recruited in China as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation East Asian. Xibo Xibo in China (SGDP) A population made up of 2 samples from Yi individuals recruited in China as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation East Asian. Yi Yi in China (SGDP) A population made up of 109 samples from Chinese Dai individuals recruited in Xishuangbanna, China as part of the 1000 Genomes Project. The population was assigned by the collecting project to the superpopulation East Asian. CDX Dai Chinese Chinese Dai in Xishuangbanna, China A population made up of 112 samples from Han Chinese individuals recruited in Beijing, China as part of the 1000 Genomes Project. The population was assigned by the collecting project to the superpopulation East Asian. CHB Han Chinese Han Chinese in Beijing, China A population made up of 105 samples from Japanese individuals recruited in Tokyo, Japan as part of the 1000 Genomes Project. The population was assigned by the collecting project to the superpopulation East Asian. JPT Japanese Japanese in Tokyo, Japan A population made up of 124 samples from Kinh individuals recruited in Ho Chi Minh City, Vietnam as part of the 1000 Genomes Project. The population was assigned by the collecting project to the superpopulation East Asian. KHV Kinh Vietnamese Kinh in Ho Chi Minh City, Vietnam A population made up of 171 samples from Han Chinese South individuals recruited in China as part of the 1000 Genomes Project. The population was assigned by the collecting project to the superpopulation East Asian. CHS Southern Han Chinese Han Chinese South A population made up of 15 samples from Adygei individuals recruited in Caucasus, Russia as part of the Human Genome Diversity Project. The population was assigned by the collecting project to the superpopulation European. Adygei Adygei in Caucasus, Russia (HGDP) A population made up of 22 samples from Basque individuals recruited in France as part of the Human Genome Diversity Project. The population was assigned by the collecting project to the superpopulation European. Basque Basque in France (HGDP) A population made up of 10 samples from Bergamo Italian individuals recruited in Bergamo, Italy as part of the Human Genome Diversity Project. The population was assigned by the collecting project to the superpopulation European. Bergamo Italian Bergamo Italian in Bergamo, Italy (HGDP) A population made up of 24 samples from French individuals recruited in France as part of the Human Genome Diversity Project. The population was assigned by the collecting project to the superpopulation European. French French in France (HGDP) A population made up of 13 samples from Orcadian individuals recruited in Orkney as part of the Human Genome Diversity Project. The population was assigned by the collecting project to the superpopulation European. Orcadian Orcadian in Orkney (HGDP) A population made up of 23 samples from Russian individuals recruited in Russia as part of the Human Genome Diversity Project. The population was assigned by the collecting project to the superpopulation European. Russian Russian in Russia (HGDP) A population made up of 24 samples from Sardinian individuals recruited in Italy as part of the Human Genome Diversity Project. The population was assigned by the collecting project to the superpopulation European. Sardinian Sardinian in Italy (HGDP) A population made up of 6 samples from Tuscan individuals recruited in Italy as part of the Human Genome Diversity Project. The population was assigned by the collecting project to the superpopulation European. Tuscan Tuscan in Italy (HGDP) A population made up of 107 samples from British individuals recruited in England and Scotland as part of the 1000 Genomes Project. The population was assigned by the collecting project to the superpopulation European. British GBR British in England and Scotland A population made up of 184 samples from individuals resident in Utah (CEPH) with Northern and Western European ancestry recruited in Utah, USA as part of the 1000 Genomes Project. The population was assigned by the collecting project to the superpopulation European. CEPH CEU Utah residents (CEPH) with Northern and Western European ancestry A population made up of 105 samples from Finnish individuals recruited in Finland as part of the 1000 Genomes Project. The population was assigned by the collecting project to the superpopulation European. FIN Finnish Finnish in Finland A population made up of 162 samples from Iberian populations individuals recruited in Spain as part of the 1000 Genomes Project. The population was assigned by the collecting project to the superpopulation European. IBS Iberian Iberian populations in Spain A population made up of 112 samples from Toscani individuals recruited in Italy as part of the 1000 Genomes Project. The population was assigned by the collecting project to the superpopulation European. TSI Toscani Toscani in Italy A population made up of 44 samples from Bedouin individuals recruited in Negev, Israel as part of the Human Genome Diversity Project. The population was assigned by the collecting project to the superpopulation Greater Middle Eastern (Middle Eastern or North African or Persian). Bedouin Bedouin in Negev, Israel (HGDP) A population made up of 40 samples from Druze individuals recruited in Carmel, Israel as part of the Human Genome Diversity Project. The population was assigned by the collecting project to the superpopulation Greater Middle Eastern (Middle Eastern or North African or Persian). Druze Druze in Carmel, Israel (HGDP) A population made up of 27 samples from Mozabite individuals recruited in Mzab, Algeria as part of the Human Genome Diversity Project. The population was assigned by the collecting project to the superpopulation Greater Middle Eastern (Middle Eastern or North African or Persian). Mozabite Mozabite in Mzab, Algeria (HGDP) A population made up of 43 samples from Palestinian individuals recruited in Central, Israel as part of the Human Genome Diversity Project. The population was assigned by the collecting project to the superpopulation Greater Middle Eastern (Middle Eastern or North African or Persian). Palestinian Palestinian in Central, Israel (HGDP) A population made up of 11 samples from Bougainville individuals recruited in Bougainville as part of the Human Genome Diversity Project. The population was assigned by the collecting project to the superpopulation Oceanian. Bougainville Bougainville in Bougainville (HGDP) A population made up of 6 samples from Papuan Highlands individuals recruited in New Guinea as part of the Human Genome Diversity Project. The population was assigned by the collecting project to the superpopulation Oceanian. Papuan Highlands Papuan Highlands in New Guinea (HGDP) A population made up of 8 samples from Papuan Sepik individuals recruited in New Guinea as part of the Human Genome Diversity Project. The population was assigned by the collecting project to the superpopulation Oceanian. Papuan Sepik Papuan Sepik in New Guinea (HGDP) A population made up of 2 samples from Australian individuals recruited in Australia as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation Oceanian. Australian Australian in Australia (SGDP) A population made up of 2 samples from Bougainville individuals recruited in Papua New Guinea as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation Oceanian. Bougainville Bougainville in Papua New Guinea (SGDP) A population made up of 2 samples from Dusun individuals recruited in Brunei as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation Oceanian. Dusun Dusun in Brunei (SGDP) A population made up of 1 samples from Hawaiian individuals recruited in USA as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation Oceanian. Hawaiian Hawaiian in USA (SGDP) A population made up of 2 samples from Igorot individuals recruited in Philippines as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation Oceanian. Igorot Igorot in Philippines (SGDP) A population made up of 1 samples from Maori individuals recruited in New Zealand as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation Oceanian. Maori Maori in New Zealand (SGDP) A population made up of 15 samples from Papuan individuals recruited in Papua New Guinea as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation Oceanian. Papuan Papuan in Papua New Guinea (SGDP) A population made up of 2 samples from Balochi individuals recruited in Pakistan as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation South Asian. Balochi Balochi in Pakistan (SGDP) A population made up of 2 samples from Bengali individuals recruited in Bangladesh as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation South Asian. Bengali Bengali in Bangladesh (SGDP) A population made up of 2 samples from Brahmin individuals recruited in India as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation South Asian. Brahmin Brahmin in India (SGDP) A population made up of 2 samples from Brahui individuals recruited in Pakistan as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation South Asian. Brahui Brahui in Pakistan (SGDP) A population made up of 2 samples from Burusho individuals recruited in Pakistan as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation South Asian. Burusho Burusho in Pakistan (SGDP) A population made up of 2 samples from Hazara individuals recruited in Pakistan as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation South Asian. Hazara Hazara in Pakistan (SGDP) A population made up of 2 samples from Irula individuals recruited in India as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation South Asian. Irula Irula in India (SGDP) A population made up of 2 samples from Kalash individuals recruited in Pakistan as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation South Asian. Kalash Kalash in Pakistan (SGDP) A population made up of 2 samples from Kapu individuals recruited in India as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation South Asian. Kapu Kapu in India (SGDP) A population made up of 1 samples from Khonda Dora individuals recruited in India as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation South Asian. Khonda Dora Khonda Dora in India (SGDP) A population made up of 2 samples from Kusunda individuals recruited in Nepal as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation South Asian. Kusunda Kusunda in Nepal (SGDP) A population made up of 1 samples from Madiga individuals recruited in India as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation South Asian. Madiga Madiga in India (SGDP) A population made up of 2 samples from Makrani individuals recruited in Pakistan as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation South Asian. Makrani Makrani in Pakistan (SGDP) A population made up of 2 samples from Pathan individuals recruited in Pakistan as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation South Asian. Pathan Pathan in Pakistan (SGDP) A population made up of 4 samples from Punjabi individuals recruited in Pakistan as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation South Asian. Punjabi Punjabi in Pakistan (SGDP) A population made up of 2 samples from Relli individuals recruited in India as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation South Asian. Relli Relli in India (SGDP) A population made up of 2 samples from Sindhi individuals recruited in Pakistan as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation South Asian. Sindhi Sindhi in Pakistan (SGDP) A population made up of 2 samples from Yadava individuals recruited in India as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation South Asian. Yadava Yadava in India (SGDP) A population made up of 144 samples from Bengali individuals recruited in Bangladesh as part of the 1000 Genomes Project. The population was assigned by the collecting project to the superpopulation South Asian. BEB Bengali Bengali in Bangladesh A population made up of 113 samples from Gujarati Indians individuals recruited in Houston, TX as part of the 1000 Genomes Project. The population was assigned by the collecting project to the superpopulation South Asian. GIH Gujarati Gujarati Indians in Houston, TX A population made up of 158 samples from Punjabi individuals recruited in Lahore, Pakistan as part of the 1000 Genomes Project. The population was assigned by the collecting project to the superpopulation South Asian. PJL Punjabi Punjabi in Lahore, Pakistan A population made up of 128 samples from Sri Lankan Tamil individuals recruited in the UK as part of the 1000 Genomes Project. The population was assigned by the collecting project to the superpopulation South Asian. STU Tamil Sri Lankan Tamil in the UK A population made up of 118 samples from Indian Telugu individuals recruited in the UK as part of the 1000 Genomes Project. The population was assigned by the collecting project to the superpopulation South Asian. ITU Telugu Indian Telugu in the UK A population made up of 2 samples from Abkhasian individuals recruited in Abkhazia or Russia as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation West Eurasian. Abkhasian Abkhasian in Abkhazia or Russia (SGDP) A population made up of 2 samples from Adygei individuals recruited in Russia(Caucasus) as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation West Eurasian. Adygei Adygei in Russia(Caucasus) (SGDP) A population made up of 1 samples from Albanian individuals recruited in Albania as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation West Eurasian. Albanian Albanian in Albania (SGDP) A population made up of 2 samples from Armenian individuals recruited in Armenia as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation West Eurasian. Armenian Armenian in Armenia (SGDP) A population made up of 2 samples from Basque individuals recruited in France as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation West Eurasian. Basque Basque in France (SGDP) A population made up of 2 samples from Bedouin B individuals recruited in Israel(Negev) as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation West Eurasian. Bedouin B Bedouin B in Israel(Negev) (SGDP) A population made up of 2 samples from Bergamo individuals recruited in Italy(Bergamo) as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation West Eurasian. Bergamo Bergamo in Italy(Bergamo) (SGDP) A population made up of 2 samples from Bulgarian individuals recruited in Bulgaria as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation West Eurasian. Bulgarian Bulgarian in Bulgaria (SGDP) A population made up of 1 samples from Chechen individuals recruited in Russia as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation West Eurasian. Chechen Chechen in Russia (SGDP) A population made up of 2 samples from Crete individuals recruited in Greece as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation West Eurasian. Crete Crete in Greece (SGDP) A population made up of 1 samples from Czech individuals recruited in Czechoslovakia(pre1989) as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation West Eurasian. Czech Czech in Czechoslovakia(pre1989) (SGDP) A population made up of 2 samples from Druze individuals recruited in Israel(Carmel) as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation West Eurasian. Druze Druze in Israel(Carmel) (SGDP) A population made up of 2 samples from English individuals recruited in England as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation West Eurasian. English English in England (SGDP) A population made up of 2 samples from Estonian individuals recruited in Estonia as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation West Eurasian. Estonian Estonian in Estonia (SGDP) A population made up of 3 samples from Finnish individuals recruited in Finland as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation West Eurasian. Finnish Finnish in Finland (SGDP) A population made up of 3 samples from French individuals recruited in France as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation West Eurasian. French French in France (SGDP) A population made up of 2 samples from Georgian individuals recruited in Georgia as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation West Eurasian. Georgian Georgian in Georgia (SGDP) A population made up of 2 samples from Greek individuals recruited in Greece as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation West Eurasian. Greek Greek in Greece (SGDP) A population made up of 2 samples from Hungarian individuals recruited in Hungary as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation West Eurasian. Hungarian Hungarian in Hungary (SGDP) A population made up of 2 samples from Icelandic individuals recruited in Iceland as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation West Eurasian. Icelandic Icelandic in Iceland (SGDP) A population made up of 2 samples from Iranian individuals recruited in Iran as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation West Eurasian. Iranian Iranian in Iran (SGDP) A population made up of 2 samples from Iraqi Jew individuals recruited in Iraq as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation West Eurasian. Iraqi Jew Iraqi Jew in Iraq (SGDP) A population made up of 3 samples from Jordanian individuals recruited in Jordan as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation West Eurasian. Jordanian Jordanian in Jordan (SGDP) A population made up of 2 samples from Lezgin individuals recruited in Russia as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation West Eurasian. Lezgin Lezgin in Russia (SGDP) A population made up of 2 samples from North Ossetian individuals recruited in Russia as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation West Eurasian. North Ossetian North Ossetian in Russia (SGDP) A population made up of 1 samples from Norwegian individuals recruited in Norway as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation West Eurasian. Norwegian Norwegian in Norway (SGDP) A population made up of 2 samples from Orcadian individuals recruited in Orkney Islands as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation West Eurasian. Orcadian Orcadian in Orkney Islands (SGDP) A population made up of 3 samples from Palestinian individuals recruited in Israel(Central) as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation West Eurasian. Palestinian Palestinian in Israel(Central) (SGDP) A population made up of 1 samples from Polish individuals recruited in Poland as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation West Eurasian. Polish Polish in Poland (SGDP) A population made up of 2 samples from Russian individuals recruited in Russia as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation West Eurasian. Russian Russian in Russia (SGDP) A population made up of 2 samples from Saami individuals recruited in Finland as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation West Eurasian. Saami Saami in Finland (SGDP) A population made up of 1 samples from Samaritan individuals recruited in Israel as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation West Eurasian. Samaritan Samaritan in Israel (SGDP) A population made up of 3 samples from Sardinian individuals recruited in Italy as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation West Eurasian. Sardinian Sardinian in Italy (SGDP) A population made up of 2 samples from Spanish individuals recruited in Spain as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation West Eurasian. Spanish Spanish in Spain (SGDP) A population made up of 2 samples from Tajik individuals recruited in Tajikistan as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation West Eurasian. Tajik Tajik in Tajikistan (SGDP) A population made up of 2 samples from Turkish individuals recruited in Turkey as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation West Eurasian. Turkish Turkish in Turkey (SGDP) A population made up of 2 samples from Tuscan individuals recruited in Italy(Tuscany) as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation West Eurasian. Tuscan Tuscan in Italy(Tuscany) (SGDP) A population made up of 2 samples from Yemenite Jew individuals recruited in Yemen as part of the Simons Genome Diversity Project. The population was assigned by the collecting project to the superpopulation West Eurasian. Yemenite Jew Yemenite Jew in Yemen (SGDP) Includes individuals who either self-report or have been described by authors as Indigenous Siberan. This covers any indigenous groups from the northern part of the Asian contient that is commonly referred to as Siberia and which reaches from the Ural Mountains in the west to the Pacific Ocean in the east, and from the Arctic Ocean in the north to the northern borders of Kazakhstan, Mongolia and China in the south. We note that there does not appear to be a suitable reference population for this population and efforts are required to fill this gap, although smaller reference populations were defined by the SGDP. Principal-component analysis of samples from this population suggest a close genetic relatedness with some Indigenous North American populations, such as the Chipewyan. Indigenous peoples of Siberia Indigenous Siberian UMLS:C0444868 Root of all terms in the Human Phenotype Ontology. All The pattern in which a particular genetic trait or disorder is passed from one generation to the next. HP:0001425 HP:0001453 HP:0001461 HP:0010985 UMLS:C1708511 Inheritance While there is a close conceptual relationship between allelic requirement and inheritance, they serve different purposes; allelic requirement is necessary for variant annotation pipelines and to determine if a given variant in a specific context is relevant to the phenotype of the patient e.g. a heterozygous variant (in the absence of compound heterozygosity) is relevant for dominant but not for recessive disease; while inheritance is used for describing the mode of inheritance of a phenotype and is particularly applicable in the clinical setting for communicating recurrence risk, to guide family screening, and to guide reproductive advice. Mode of inheritance An abnormality of the kidney. SNOMEDCT_US:44513007 SNOMEDCT_US:90708001 UMLS:C0022658 UMLS:C0266292 Abnormal kidney Abnormality of the kidney Renal anomalies Renal anomaly The kidney is a paired organ whose primary function is the production of urine. Abnormality of the kidney An abnormality of the urinary system. UMLS:C4021821 Urinary tract abnormalities Urinary tract abnormality Urinary tract anomalies Abnormality of the urinary system A reduction in the level of performance of the kidneys in areas of function comprising the concentration of urine, removal of wastes, the maintenance of electrolyte balance, homeostasis of blood pressure, and calcium metabolism. HP:0000084 HP:0004723 SNOMEDCT_US:236423003 SNOMEDCT_US:42399005 UMLS:C0035078 UMLS:C1565489 UMLS:C1839604 Renal failure Renal failure in adulthood Renal insufficiency symptom A phenotypic abnormality. UMLS:C4021819 http://purl.obolibrary.org/obo/SYMP_0000462 Organ abnormality This is the root of the phenotypic abnormality subontology of the HPO. Phenotypic abnormality The presence of any abnormality of the genitourinary system. HP:0008658 HP:0008688 HP:0008704 HP:0008713 SNOMEDCT_US:287085006 SNOMEDCT_US:42030000 UMLS:C0042063 UMLS:C0080276 UMLS:C4020895 Abnormality of the GU system Genitourinary abnormality Genitourinary tract anomalies Genitourinary tract malformation Urogenital abnormalities Urogenital anomalies Abnormality of the genitourinary system An abnormality of head and neck. UMLS:C4021817 Abnormality of head or neck Head and neck abnormality Abnormality of head or neck An abnormality of the mouth. SNOMEDCT_US:128334002 UMLS:C0026633 Abnormal mouth Abnormality of the mouth Abnormality of the mouth Any abnormality of the tongue. UMLS:C0878638 Abnormal tongue Abnormality of the tongue Glossal abnormality Lingual abnormality Tongue abnormality Abnormality of the tongue Abnormality of the oral cavity, i.e., the opening or hollow part of the mouth. UMLS:C4025887 Abnormality of the oral cavity Abnormal oral cavity morphology Inflammation of the tongue. SNOMEDCT_US:45534005 UMLS:C0017675 Inflammation of the tongue Lingual inflammation Smooth swollen tongue Glossitis Dryness of the mouth due to salivary gland dysfunction. HP:0002709 HP:0100756 Decreased salivary flow SNOMEDCT_US:300268000 SNOMEDCT_US:56893005 SNOMEDCT_US:87715008 UMLS:C0043352 Dry mouth Dry mouth syndrome Reduced salivation Xerostomia UMLS:C4025879 Abnormality of taste sensation Abnormality of taste sensation A decreased ability to perceive flavor. SNOMEDCT_US:697990000 UMLS:C0151934 Decreased taste Decreased taste sensation Hypogeusia An abnormality of the head. UMLS:C4021812 Abnormal head Abnormality of the head Head abnormality Abnormality of the head An abnormality of the face. Abnormality of the countenance Abnormality of the physiognomy Abnormality of the visage Disorder of face SNOMEDCT_US:118930001 SNOMEDCT_US:32003007 SNOMEDCT_US:398206004 SNOMEDCT_US:398302004 UMLS:C0266617 UMLS:C1290857 UMLS:C4025871 Abnormal face Abnormality of the face Facial abnormality Disorder of the face Abnormality of the face HP:0000284 UMLS:C4025863 Abnormality of the eye region Abnormality of the region around the eyes Anomaly of the orbital region of the face Deformity of the orbital region of the face Malformation of the orbital region of the face Abnormality of the orbital region An abnormality of the nose. SNOMEDCT_US:128274005 SNOMEDCT_US:72089000 UMLS:C0240547 UMLS:C0265736 UMLS:C2235909 Abnormality of the nose Anomaly of the nose Nasal abnormality Nasal anomaly Deformity of the nose Malformation of the nose Nasal deformity Nasal malformation Abnormality of the nose Epistaxis, or nosebleed, refers to a hemorrhage localized in the nose. COHD:318556 EFO:0003895 ICD10:R04.0 ICD9:784.7 NCIT:C26766 SNOMEDCT_US:12441001 SNOMEDCT_US:249366005 UMLS:C0014591 Bloody nose Frequent nosebleeds Nasal haemorrhage Nasal hemorrhage Nose bleed Nose bleeding Nosebleed Epistaxis An inability to perceive odors. This is a general term describing inability to smell arising in any part of the process of smelling from absorption of odorants into the nasal mucous overlying the olfactory epithelium, diffusion to the cilia, binding to olfactory receptor sites, generation of action potentials in olfactory neurons, and perception of a smell. SNOMEDCT_US:44169009 UMLS:C0003126 Loss of smell Lost smell Anosmia An abnormality of the neck. SNOMEDCT_US:298390003 SNOMEDCT_US:40052002 UMLS:C0266623 UMLS:C0575167 UMLS:C4280628 Abnormality of the neck Anomaly of the neck Deformity of the neck Malformation of the neck Abnormality of the neck Any abnormality of the eye, including location, spacing, and intraocular abnormalities. SNOMEDCT_US:19416009 SNOMEDCT_US:371405004 SNOMEDCT_US:371409005 UMLS:C0015393 UMLS:C0015397 Abnormal eye Abnormality of the eye Abnormality of the eye An abnormality of the eyelids. HP:0000285 UMLS:C4021803 Abnormality of the eyelid Abnormality of the eyelids Abnormal eyelid morphology An abnormality of the conjunctiva. UMLS:C4025847 The conjunctiva is a thin, sparsely vascularized transparent membrane that covers and protects the sclera (the bulbar conjunctiva), and forms the inner lining of the eyelids (the tarsal conjunctiva). Abnormal conjunctiva morphology Abnormality of eyesight (visual perception). UMLS:C4025846 Abnormality of sight Abnormality of vision Vision issue Abnormality of vision The upper eyelid margin is positioned 3 mm or more lower than usual and covers the superior portion of the iris (objective); or, the upper lid margin obscures at least part of the pupil (subjective). SNOMEDCT_US:11934000 UMLS:C0005745 Blepharoptosis Drooping upper eyelid Eyelid ptosis Palpebral ptosis Ptosis Inflammation of the conjunctiva. SNOMEDCT_US:9826008 UMLS:C0009763 UMLS:C1864156 Pink eye Conjunctivitis An abnormality of the ear. SNOMEDCT_US:275259005 UMLS:C0266589 Abnormality of the ear Ear anomaly Either a morphological abnormality or hearing deficit. This should be split more cleanly in the future. Abnormality of the ear An anomaly of the pharynx, i.e., of the tubular structure extending from the base of the skull superiorly to the esophageal inlet inferiorly. UMLS:C4025838 The pharynx is tubular structure extending from base of skull superiorly to esophageal inlet inferiorly, and is composed of three distinct areas: the nasopharynx, the oropharynx, and the hypopharynx, with the pharyngeal walls being composed of the superior, middle, and inferior pharyngeal constrictor muscles. It is part of the digestive system and of the conducting zone of the respiratory system. Abnormality of the pharynx Lack of sharpness of vision resulting in the inability to see fine detail. HP:0007723 SNOMEDCT_US:111516008 SNOMEDCT_US:246636008 UMLS:C0344232 Blurred vision This is a very nonspecific term and it is preferable to describe the correlates of blurred vision with the corresponding terms if possible. Blurred vision An abnormality of the nervous system. HP:0001333 HP:0006987 Brain and/or spinal cord issue SNOMEDCT_US:88425004 UMLS:C0497552 Abnormality of the nervous system Neurologic abnormalities Neurological abnormality The nervous system comprises the neuraxis (brain, spinal cord, and ventricles), the autonomic nervous system, the enteric nervous system, and the peripheral nervous system. Abnormality of the nervous system Atypical behavior is an abnormality in a person's actions that can be controlled or modulated by the will of the individual. While abnormal behaviors can be difficult to control, they are distinct from other abnormal actions that cannot be affected by the individual's will. HP:0000715 HP:0002368 HP:0002456 SNOMEDCT_US:25786006 SNOMEDCT_US:277843001 UMLS:C0004941 UMLS:C0233514 Behavioral abnormality Behavioral changes Behavioral disorders Behavioral disturbances Behavioral problems Behavioral symptoms Behavioral/psychiatric abnormalities Behavioural abnormality Behavioural changes Behavioural disorders Behavioural disturbances Behavioural problems Behavioural symptoms Behavioural/Psychiatric abnormality Behavioural/psychiatric abnormality Psychiatric disorders Psychiatric disturbances Atypical behaviors should include or directly affect observable actions. While behavioral disorders often encompass abnormal thoughts, feelings, perceptions, or other cognitions, these alone would not be considered atypical behavioral features. Atypical behavior A proneness to anger, i.e., a tendency to become easily bothered or annoyed. UMLS:C2700617 Irritability Irritable Irritable mood Irritability The presence of blood in the urine. Hematuria may be gross hematuria (visible to the naked eye) or microscopic hematuria (detected by dipstick or microscopic examination of the urine). High urine occult blood SNOMEDCT_US:34436003 SNOMEDCT_US:53298000 UMLS:C0018965 Blood in urine Hematuria An abnormality of the endocrine system. SNOMEDCT_US:362969004 UMLS:C0014130 UMLS:C4025823 The endocrine system is composed of glands that secrete hormones directly into the bloodstream and includes the following glands: thyroid, parathyroids, adrenals, pancreas, gonads (testicles and ovaries), and pituitary. Many other organs, such as the kidney, liver, and heart, have secondary endocrine functions. Abnormality of the endocrine system A group of abnormalities characterized by hyperglycemia and glucose intolerance. HP:0004908 HP:0008217 HP:0008234 HP:0008260 SNOMEDCT_US:73211009 UMLS:C0011849 Diabetes mellitus The presence of chronic increased pressure in the systemic arterial system. HP:0004949 HP:0005126 SNOMEDCT_US:24184005 SNOMEDCT_US:38341003 UMLS:C0020538 UMLS:C0497247 Arterial hypertension Systemic hypertension Hypertension is sustained elevation of resting systolic BP (140 mm Hg or higher), diastolic BP (90 mm Hg or higher), or both. Hypertension An abnormality of the skeletal system. UMLS:C4021790 Abnormality of the skeletal system Skeletal abnormalities Skeletal anomalies Abnormality of the skeletal system An abnormality of the skin. HP:0001478 HP:0001479 HP:0005591 HP:0006736 HP:0007415 HP:0007580 SNOMEDCT_US:199879009 SNOMEDCT_US:95320005 UMLS:C0037268 UMLS:C0037274 Abnormality of the skin Dermatopathy Dermopathy Abnormality of the skin Bluish discoloration of the skin and mucosa due to poor circulation or inadequate oxygenation of arterial or capillary blood. SNOMEDCT_US:119419001 SNOMEDCT_US:3415004 UMLS:C0010520 Blue discoloration of the skin Cyanosis Eczema is a form of dermatitis that is characterized by scaly, pruritic, erythematous lesions located on flexural surfaces. HP:0000976 HP:0001481 SNOMEDCT_US:281104002 SNOMEDCT_US:43116000 UMLS:C0013595 Eczema The term eczema is broadly applied to a range of persistent skin conditions and can be related to a number of underlying conditions. Manifestations of eczema can include dryness and recurring skin rashes with redness, skin edema, itching and dryness, crusting, flaking, blistering, cracking, oozing, or bleeding. Eczema has several forms including atopic dermatitis, contact dermatitis, dyshidrotic eczema, nummular eczema, seborrheic dermatitis, and stasis dermatitis. Eczematoid dermatitis An abnormal accumulation of fluid beneath the skin, or in one or more cavities of the body. HP:0000990 Soft tissue swelling SNOMEDCT_US:20741006 SNOMEDCT_US:267038008 SNOMEDCT_US:423666004 SNOMEDCT_US:79654002 UMLS:C0013604 Dropsy Fluid retention Hydrops Oedema Water retention Edema may be related to one or more of the following factors: 1) increased capillary hydrostatic pressure, 2) decreased osmotic pressure of plasma, 3) decreased tissue tension and lymphatic drainage, 4) increased osmotic pressure of tissue fluids, and 5) increased capillary permeability. Edema A red eruption of the skin. Rash MEDDRA:10037844 SNOMEDCT_US:112625008 SNOMEDCT_US:271807003 UMLS:C0015230 Skin rash Skin rash UMLS:C4025812 Dermatological manifestations of systemic disorders Bluish discoloration of the skin of the hands or feet. SNOMEDCT_US:25003006 UMLS:C0221347 Persistent blue color of hands or feet Persistent blue colour of hands or feet Cyanosis is caused by increased levels of deoxygenated hemoglobin. Acrocyanosis Hard, pebble-like deposits that form within the gallbladder. SNOMEDCT_US:266474003 UMLS:C0008350 Gallstones Gallstones range in size from as small as a grain of sand to as large as a golf ball. Cholesterol gallstones are the most common type of gallstone. Gallstones resulting from too much bilirubin in the bile are referred to as pigment stones. Cholelithiasis An abnormality of the fetus or the birth of the fetus, excluding structural abnormalities. UMLS:C4025797 Abnormality of prenatal development or birth Because of the close link between prenatal developmental abnormalities and abnormalities of the birth process, a single term is chosen to subsume both classes of abnormality. Abnormality of prenatal development or birth A seizure is an intermittent abnormality of nervous system physiology characterized by a transient occurrence of signs and/or symptoms due to abnormal excessive or synchronous neuronal activity in the brain. HP:0001275 HP:0001303 HP:0002125 HP:0002182 HP:0002279 HP:0002306 HP:0002348 HP:0002391 HP:0002417 HP:0002430 HP:0002431 HP:0002432 HP:0002434 HP:0002437 HP:0002466 HP:0002479 HP:0002794 HP:0006997 HP:0010520 SNOMEDCT_US:128613002 SNOMEDCT_US:246545002 SNOMEDCT_US:313307000 SNOMEDCT_US:84757009 SNOMEDCT_US:91175000 UMLS:C0014544 UMLS:C0036572 Epileptic seizure Seizures A type of electrographic seizure has been proposed in neonates which does not have a clinical correlate, it is electrographic only. The term epilepsy is not used to describe recurrent febrile seizures. Epilepsy presumably reflects an abnormally reduced seizure threshold. Seizure The complete absence of wakefulness and consciousness, which is evident through a lack of response to any form of external stimuli. ICD-10:R40.2 SNOMEDCT_US:371632003 UMLS:C0009421 Coma Persistent vegetative state Stupor Unconsciousness Coma is generally a result of diffuse or extensive involvement of both hemispheres of the brain or lesions in the brainstem. Coma Inflammation of the meninges. SNOMEDCT_US:7180009 UMLS:C0025289 Meningitis Lack of clarity and coherence of thought, perception, understanding, or action. HP:0000731 SNOMEDCT_US:286933003 UMLS:C0009676 Confusion Disorientation Easily confused Mental disorientation Confusion Sudden impairment of blood flow to a part of the brain due to occlusion or rupture of an artery to the brain. HP:0002452 SNOMEDCT_US:230690007 UMLS:C0038454 Cerebral vascular events Cerebrovascular accident Stroke Stroke Encephalopathy is a term that means brain disease, damage, or malfunction. In general, encephalopathy is manifested by an altered mental state. SNOMEDCT_US:81308009 UMLS:C0085584 This term and its children are general and bundled terms that are kept for convenience. For new annotations, it is recommended that the specific phenotypic abnormalities be noted. Encephalopathy Reduced strength of muscles. HP:0002309 HP:0008979 HP:0009012 HP:0009061 SNOMEDCT_US:26544005 UMLS:C0151786 Muscle weakness Muscular weakness It is important clinical to distinguish between muscle weakness, fatigue, and asthenia. Fatigue describes the inability to continue performing a task after multiple repetitions; in contrast, a patient with primary weakness is unable to perform the first repetition of the task. Asthenia is a sense of weariness or exhaustion in the absence of muscle weakness. Conditions that result in intrinsic muscle weakness can be divided into several main categories: infectious, neurologic, endocrine, inflammatory, rheumatologic, genetic, metabolic, electrolyte-induced, or drug-induced. Muscle weakness Abnormal coordination of muscles involved in speech. SNOMEDCT_US:289195008 UMLS:C0234518 Slurred speech Slurred speech An abnormal structure or form of the joints, i.e., one or more of the articulations where two bones join. SNOMEDCT_US:399269003 UMLS:C0022408 UMLS:C0240083 Abnormal shape of joints Abnormality of the joints Anomaly of the joints Abnormal joint morphology A reduction in the freedom of movement of one or more joints. HP:0003101 UMLS:C1857108 Decreased joint mobility Decreased mobility of joints Limitation of joint mobility Limited joint mobility Limited joint motion Limitation of joint mobility SNOMEDCT_US:271771009 UMLS:C0152031 Joint swelling Joint swelling Joint stiffness is a perceived sensation of tightness in a joint or joints when attempting to move them after a period of inactivity. Joint stiffness typically subsides over time. HP:0002775 HP:0003033 SNOMEDCT_US:84445001 UMLS:C0162298 Joint stiffness Stiff joint Stiff joints Joint stiffness An abnormality of the liver. SNOMEDCT_US:235856003 UMLS:C0023895 UMLS:C4021780 Abnormal liver Abnormality of the liver Liver abnormality Abnormality of the liver Steatosis is a term used to denote lipid accumulation within hepatocytes. HP:0002252 HP:0200121 SNOMEDCT_US:197321007 SNOMEDCT_US:442191002 UMLS:C2711227 Fatty infiltration of liver Fatty liver Liver steatosis Steatosis Although steatosis is the hallmark of the fatty liver disease, it is not a specific feature because it can be seen as part of other disease processes, such as drug injury, Wilson disease, or hepatitis C virus infection (especially genotype-3). Involvement of less than 5% of the hepatocytes by steatosis is considered clinically insignificant and within reference range. Based on the morphologic appearance and the size of the lipid droplets within the cytoplasm of the hepatocytes, steatosis is characterized as macrovesicular or microvesicular. Macrovesicular steatosis is characterized by large lipid droplets occupying the cytoplasm, displacing the nucleus to the periphery (large droplet macrovesicular steatosis) or multiple small lipid droplets of variable size occupying the cytoplasm with the nucleus maintaining its central location (small droplet macrovesicular steatosis). Microvesicular steatosis is characterized by innumerable tiny, relatively uniform lipid vacuoles that result in a bubbly appearance of the hepatocytes. Hepatic steatosis Reduced ability of the liver to perform its functions. HP:0004393 HP:0005228 HP:0006570 SNOMEDCT_US:75183008 SNOMEDCT_US:77981007 UMLS:C0086565 UMLS:C0232744 UMLS:C3279149 Decreased liver function Liver dysfunction Decreased liver function HP:0008904 UMLS:C0262361 Abnormal growth Growth abnormality Growth issue Growth abnormality Accumulation of substantial excess body fat. SNOMEDCT_US:414915002 SNOMEDCT_US:414916001 UMLS:C0028754 Having too much body fat Obesity Obesity A thrusting or bulging out of the abdomen. UMLS:C1854928 Abdominal protuberance Belly sticks out Extended belly Protuberant abdomen An abnormality of the integument, which consists of the skin and the superficial fascia. UMLS:C4025761 Abnormality of skin, hair, or nails. Abnormality of the integument UMLS:C4021776 Abnormality of the voice Voice abnormality This term describes any abnormality of the voice, i.e., of the sounds produced by humans by the passage of air through the larynx and over the vocal cords, and then modified by the resonance organs, the nasopharynx, and the mouth. Abnormality of the voice SNOMEDCT_US:2120003 UMLS:C0234860 Weak cry Any abnormality of the cardiovascular system. HP:0003116 SNOMEDCT_US:49601007 UMLS:C0007222 UMLS:C0243050 Abnormality of the cardiovascular system Cardiovascular abnormality The cardiovascular system consists of the heart, vasculature, and the lymphatic system. Abnormality of the cardiovascular system Any structural anomaly of the heart. HP:3000001 SNOMEDCT_US:13213009 UMLS:C0018798 UMLS:C0152021 Abnormality of cardiac morphology Abnormality of the heart Abnormally shaped heart Cardiac abnormality Cardiac anomalies Cardiac anomaly Congenital heart defect Congenital heart defects Heart defect Abnormal heart morphology The presence of an abnormality of cardiac function that is responsible for the failure of the heart to pump blood at a rate that is commensurate with the needs of the tissues or a state in which abnormally elevated filling pressures are required for the heart to do so. Heart failure is frequently related to a defect in myocardial contraction. HP:0006686 SNOMEDCT_US:42343007 SNOMEDCT_US:84114007 UMLS:C0018801 UMLS:C0018802 CHF Cardiac failure Cardiac failures Cardiac insufficiency Chronic heart failure Heart failure Congestive heart failure A structural anomaly of the muscle layer of the heart wall. UMLS:C4025758 Abnormality of the myocardium Abnormal myocardium morphology A myocardial disorder in which the heart muscle is structurally and functionally abnormal, in the absence of coronary artery disease, hypertension, valvular disease and congenital heart disease sufficient to cause the observed myocardial abnormality. Fyler:1840 SNOMEDCT_US:57809008 SNOMEDCT_US:85898001 UMLS:C0878544 Disease of the heart muscle Cardiomyopathy A rapid heartrate that exceeds the range of the normal resting heartrate for age. HP:0001673 HP:0001720 SNOMEDCT_US:3424008 SNOMEDCT_US:86651002 UMLS:C0039231 UMLS:C4020868 Fast heart rate Heart racing Racing heart Tachycardia An abrupt loss of heart function. SNOMEDCT_US:397829000 SNOMEDCT_US:410429000 UMLS:C0018790 Heart stops beating Cardiac arrest Irreversible damage to heart tissue (myocardium) due to lack of oxygen after a heart attack (myocardial infarction). SNOMEDCT_US:251061000 UMLS:C1442837 Myocardial necrosis Reduced ability to pass air through the nasal cavity often leading to mouth breathing. SNOMEDCT_US:232209000 SNOMEDCT_US:267100006 SNOMEDCT_US:68235000 UMLS:C0027424 UMLS:C0027429 Blockage of nose Nasal blockage Nasal obstruction Obstruction of nose Stuffy nose Congestion of nose Nasal congestion An abnormality of the functioning of the vestibular apparatus. HP:0006917 HP:0007921 UMLS:C1843865 Impaired vestibular function Interictal vestibular dysfunction Vestibular function defect The vestibular apparatus is the nonauditory portion of the inner ear that mediates the subjective sensation of motion and spatial orientation of the head, adjusts muscular activity and body position to maintain posture, and stabilizes in space the fixation point of the eyes when the head moves, in order to provide a stable image upon the retina. The functioning of the vestibular system is often checked clinically by means of the caloric test, in which the head is tilted backward by about 60 degrees and either warm or cold water is introduced into the external auditory meatus on one side. The immediate results are usually vertigo, nausea, nystagmus, and twisting of the head and body. Abnormal vestibular function An abnormality of the birth process. SNOMEDCT_US:274127000 UMLS:C0549629 Abnormal delivery Delivery complication Abnormal delivery Reduction of total body weight. SNOMEDCT_US:161832001 SNOMEDCT_US:262285001 SNOMEDCT_US:89362005 UMLS:C1262477 Loss of weight Weight loss An abnormality of the hematopoietic system. HP:0003135 SNOMEDCT_US:191124002 SNOMEDCT_US:34093004 UMLS:C0018939 UMLS:C0850715 UMLS:C4020864 Abnormality of blood and blood-forming tissues Abnormality of the haematopoietic system Abnormality of the hematopoietic system Haematological abnormality Hematological abnormality The hematopoietic system comprises the organs that are involved in the production of blood, primarily the bone marrow, spleen, tonsils, and lymph nodes. Abnormality of blood and blood-forming tissues Any structural abnormality of erythrocytes (red-blood cells). HP:0010973 SNOMEDCT_US:12222001 UMLS:C0391870 UMLS:C4020862 Abnormality of erythrocytes Abnormality of red blood cells Abnormal erythrocyte morphology An abnormal susceptibility to bleeding, often referred to as a bleeding diathesis. A bleeding diathesis may be related to vascular, platelet and coagulation defects. HP:0004830 HP:0004834 HP:0004849 HP:0004862 HP:0004865 HP:0008183 SNOMEDCT_US:248250000 SNOMEDCT_US:64779008 UMLS:C1458140 Bleeding diathesis Bleeding tendency Hemorrhagic diathesis This term is kept for historical reasons. If possible, a more exact description of the phenotype (i.e., whether there is a vascular, platelet and coagulation defect) should be attempted. Abnormal bleeding A reduction in erythrocytes volume or hemoglobin concentration. HP:0001926 HP:0003136 HP:0005509 SNOMEDCT_US:165397008 SNOMEDCT_US:271737000 UMLS:C0002871 UMLS:C0162119 Anaemia Low number of red blood cells or haemoglobin Low number of red blood cells or hemoglobin Anemia is not a specific entity but can result from many underlying pathologic processes. The three main causes of anemia are blood loss, decreased or faulty red blood cell production, and increased destruction of red blood cells. Various classifications are in clinical use including a classification according to the mean corpuscular volume (MCV) of the erythrocytes: microcytic, macrocytic, or normocytic. Anemias can also be classified according to variations in cell size and shape, as reflected by the red-cell distribution width (RDW). Additionally, anemias can be classified into those of inadequate production and hemolytic anemias. Anemia Sudden loss of renal function, as manifested by decreased urine production, and a rise in serum creatinine or blood urea nitrogen concentration (azotemia). SNOMEDCT_US:14350001000004108 SNOMEDCT_US:14669001 UMLS:C0022660 UMLS:C2609414 AKI Acute kidney failure Acute renal failure Acute renal failure is usually classified into prerenal (response to severe volume depletion), intrinsic (response to acute cytotoxic, ischemic, or inflammatory insults) and postrenal (response to obstruction of the passage of urine) etiologies. Acute kidney injury HP:0002146 HP:0004355 HP:0004367 UMLS:C4021768 Laboratory abnormality Metabolism abnormality Abnormality of metabolism/homeostasis SNOMEDCT_US:34095006 UMLS:C0011175 Dehydration Exsiccosis Dehydration Body temperature elevated above the normal range. SNOMEDCT_US:386661006 SNOMEDCT_US:50177009 UMLS:C0015967 Fever Hyperthermia Pyrexia Fever has been defined as a state of elevated core temperature, which is often, but not necessarily, part of the defensive responses of multicellular organisms (host) to the invasion of live (microorganisms) or inanimate matter recognized as pathogenic or alien by the host. The febrile response (of which fever is a component) is a complex physiologic reaction to disease, involving a cytokine-mediated rise in core temperature, generation of acute phase reactants, and activation of numerous physiologic, endocrinologic, and immunologic systems. The rise in temperature during fever is to be distinguished from that occurring during episodes of hyperthermia. Unlike fever, hyperthermia involves an unregulated rise in body temperature in which pyrogenic cytokines are not directly involved and against which standard antipyretics are ineffective. It represents a failure of thermoregulatory homeostasis, in which there is uncontrolled heat production, inadequate heat dissipation, or defective hypothalamic thermoregulation. Fever Glucose intolerance (GI) can be defined as dysglycemia that comprises both prediabetes and diabetes. It includes the conditions of impaired fasting glucose (IFG) and impaired glucose tolerance (IGT) and diabetes mellitus (DM). HP:0000833 Abnormal glucose tolerance UMLS:C0235401 Glucose intolerance Glucose intolerance Venous or arterial thrombosis (formation of blood clots) of spontaneous nature and which cannot be fully explained by acquired risk (e.g. atherosclerosis). UMLS:C4025731 Abnormal blood clot Abnormal blood clotting Abnormal thrombosis A structural abnormality of the central nervous system. HP:0002405 HP:0002413 HP:0002481 HP:0007319 SNOMEDCT_US:23853001 UMLS:C0007682 UMLS:C4021765 Abnormality of the central nervous system Morphological abnormality of the CNS Morphological abnormality of the central nervous system Morphological central nervous system abnormality An abnormality of the viscera of the abdomen. UMLS:C4021764 Abnormality of the abdominal organs Gastrointestinal tract defects The abdominal organs comprise the stomach, small and large intestines, liver, pancreas, bile tract, and spleen. Abnormality of the abdominal organs Forceful ejection of the contents of the stomach through the mouth by means of a series of involuntary spasmic contractions. MEDDRA:10047700 SNOMEDCT_US:249497008 SNOMEDCT_US:300359004 SNOMEDCT_US:422400008 UMLS:C0042963 Emesis Throwing up Vomiting Vomiting Abnormally increased frequency (usually defined as three or more) loose or watery bowel movements a day. SNOMEDCT_US:267060006 SNOMEDCT_US:62315008 UMLS:C0011991 Diarrhea Diarrhoea Watery stool Diarrhea Difficulty in swallowing. HP:0002569 MEDDRA:10013950 SNOMEDCT_US:288939007 SNOMEDCT_US:40739000 UMLS:C0011168 Difficulty swallowing Poor swallowing Swallowing difficulties Swallowing difficulty Dysphagia Nausea is a commonly encountered symptom that has been defined as an unpleasant painless subjective feeling that one will imminently vomit. Vomiting has been defined as the forceful expulsion of the contents of the stomach, duodenum, or jejunum through the oral cavity. While nausea and vomiting are often thought to exist on a temporal continuum, this is not always the case. There are situations when severe nausea may be present without emesis and less frequently, when emesis may be present without preceding nausea. SNOMEDCT_US:16932000 UMLS:C0027498 Nausea and vomiting Nausea and vomiting A sensation of unease in the stomach together with an urge to vomit. MEDDRA:10028813 SNOMEDCT_US:422587007 UMLS:C0027497 Nausea Nausea Infrequent or difficult evacuation of feces. HP:0002241 HP:0003786 SNOMEDCT_US:14760008 SNOMEDCT_US:225595004 UMLS:C0009806 UMLS:C0237326 Constipation Costiveness Dyschezia Constipation An unpleasant sensation characterized by physical discomfort (such as pricking, throbbing, or aching) and perceived to originate in the abdomen. Gastro pain Gastrointestinal pain MEDDRA:10000081 SNOMEDCT_US:21522001 UMLS:C0000737 Abdominal pain Pain in stomach Stomach pain Abdominal pain can be crampy, achy, dull, intermittent or sharp. The terms stomach ache and stomach cramps are nonmedical terms often used to describe pain in the mid- or upper abdominal area, even though it is not the case that the (smooth) muscles of the stomach or the abdomen have cramps. Stomach pain is another layperson term commonly used to refer to abdominal pain. Abdominal pain The presence of chronic diarrhea, which is usually taken to mean diarrhea that has persisted for over 4 weeks. SNOMEDCT_US:236071009 UMLS:C0401151 Chronic diarrhea Chronic diarrhoea Chronic diarrhea An inadequate sucking reflex, resulting in the difficult of newborns to be breast-fed. UMLS:C1837142 Poor suck Poor sucking Sucking weakness Poor suck Inflammation, or an inflammatory state in the large intestine. SNOMEDCT_US:24526004 SNOMEDCT_US:302168000 UMLS:C0021390 UMLS:C0578878 Inflammation of the large intestine Inflammation of the large intestine UMLS:C1839531 Protein avoidance Anorexia, or the loss of appetite for food, is a medical condition. SNOMEDCT_US:79890006 UMLS:C0003123 Anorexia Deliberately not eating Obsessive dieting Refusing to eat Please note that this term does not refer to the condition of anorexia nervosa, which is a disorder characterized by an obsessive desire to lose weight by refusing to eat. Anorexia UMLS:C0743178 Intractable diarrhoea Intractable diarrhea Any structural abnormality of the telencephalon, which is also known as the cerebrum. UMLS:C4021762 Abnormality of the cerebrum Abnormality of the telencephalon Cerebral lesion Abnormal cerebral morphology Migraine is a chronic neurological disorder characterized by episodic attacks of headache and associated symptoms. HP:0007194 SNOMEDCT_US:37796009 UMLS:C0149931 UMLS:C0744641 Intermittent migraine headaches Migraine Migraine headache Migraine headaches Migraine An abnormality of the respiratory system, which include the airways, lungs, and the respiratory muscles. UMLS:C4018871 Respiratory abnormality Abnormality of the respiratory system An abnormality of the upper respiratory tract. UMLS:C4025727 Abnormality of the upper respiratory tract Upper respiratory tract issues Abnormality of the upper respiratory tract Any structural anomaly of the lung. SNOMEDCT_US:19829001 UMLS:C0024115 UMLS:C4021760 Abnormality of lung structure Abnormality of the lungs Abnormally shaped lung Unusual lung shape Abnormal lung morphology Inflammation of any part of the lung parenchyma. SNOMEDCT_US:233604007 UMLS:C0032285 Pneumonia Pneumonia HP:0004893 HP:0005937 HP:0006542 SNOMEDCT_US:409623005 UMLS:C0035229 UMLS:C4020855 Respiratory impairment Respiratory insufficiency Difficult or labored breathing. Dyspnea is a subjective feeling only the patient can rate, e.g., on a Borg scale. SNOMEDCT_US:230145002 SNOMEDCT_US:267036007 UMLS:C0013404 Abnormal breathing Breathing difficulty Difficult to breathe Difficulty breathing Dyspnoea Shortness of breath Trouble breathing Dyspnea HP:0006534 SNOMEDCT_US:87433001 UMLS:C0034067 Pulmonary emphysema Emphysema Asthma is characterized by increased responsiveness of the tracheobronchial tree to multiple stimuli, leading to narrowing of the air passages with resultant dyspnea, cough, and wheezing. HP:0002112 SNOMEDCT_US:195967001 SNOMEDCT_US:991000119106 UMLS:C0004096 UMLS:C3714497 Asthma Bronchial asthma Asthma An abnormality of the pulmonary pleura, the thin, transparent membrane which covers the lungs and lines the inside of the chest walls. UMLS:C4025726 Abnormality of the pleura Abnormal pleura morphology Coughing up (expectoration) of blood or blood-streaked sputum from the larynx, trachea, bronchi, or lungs. SNOMEDCT_US:66857006 SNOMEDCT_US:6686005 UMLS:C0019079 Coughing up blood Haemoptysis Hemoptysis Accumulation of air in the pleural cavity leading to a partially or completely collapsed lung. SNOMEDCT_US:36118008 UMLS:C0032326 Collapsed lung Pneumothorax Pneumothorax occurring without traumatic injury to the chest or lung. SNOMEDCT_US:80423007 UMLS:C0149781 Spontaneous collapsed lung Spontaneous pneumothorax Acute ischemic stroke (AIS) is defined by the sudden loss of blood flow to an area of the brain with the resulting loss of neurologic function. It is caused by thrombosis or embolism that occludes a cerebral vessel supplying a specific area of the brain. During a vessel occlusion, there is a core area where damage to the brain is irreversible and an area of penumbra where the brain has lost function owing to decreased blood flow but is not irreversibly injured. SNOMEDCT_US:422504002 UMLS:C0948008 Ischaemic stroke Ischemic stroke An abnormality in the sound (volume) or cadence (rate) of speech. UMLS:C0037822 Abnormal speech Abnormal vocalisation Abnormal vocalization Abnormality of speech or vocalization The term Abnormal speech pattern includes both psychiatric and neurological conditions that affect the rate, rhythm, and volume of expressed speech. Abnormal speech pattern The presence of an excessive amount of fluid in the pleural cavity. SNOMEDCT_US:60046008 UMLS:C0032227 Fluid around lungs Pleural effusion An embolus (that is, an abnormal particle circulating in the blood) located in the pulmonary artery and thereby blocking blood circulation to the lung. Usually the embolus is a blood clot that has developed in an extremity (for instance, a deep venous thrombosis), detached, and traveled through the circulation before becoming trapped in the pulmonary artery. SNOMEDCT_US:59282003 UMLS:C0034065 Blood clot in artery of lung Pulmonary embolism Replacement of normal lung tissues by fibroblasts and collagen. HP:0006523 SNOMEDCT_US:51615001 UMLS:C0034069 Pulmonary fibrosis leads to an irreversible impairment of alveolar oxygen transfer. Pulmonary fibrosis Hemorrhage affecting the gastrointestinal tract. SNOMEDCT_US:74474003 UMLS:C0017181 GI haemorrhage GI hemorrhage Gastrointestinal bleeding Gastrointestinal haemorrhage Gastrointestinal hemorrhage An abnormality of the intestine. The closely related term enteropathy is used to refer to any disease of the intestine. HP:0002628 SNOMEDCT_US:85919009 UMLS:C0021831 Abnormality of the intestine Enteropathy Abnormal intestine morphology The passage of blackish, tarry feces associated with gastrointestinal hemorrhage. Melena occurs if the blood remains in the colon long enough for it to be broken down by colonic bacteria. One degradation product, hematin, imbues the stool with a blackish color. Thus, melena generally occurs with bleeding from the upper gastrointestinal tract (e.g., stomach ulcers or duodenal ulcers), since the blood usually remains in the gut for a longer period of time than with lower gastrointestinal bleeding. SNOMEDCT_US:249627005 SNOMEDCT_US:267055007 SNOMEDCT_US:269899009 SNOMEDCT_US:2901004 SNOMEDCT_US:35064005 UMLS:C0025222 UMLS:C0474585 Black faeces Black feces Melena Any abnormality of the large intestine. UMLS:C4025715 Abnormality of the large intestine The large intestine comprises the cecum and colon. Abnormal large intestine morphology Repeated episodes of diarrhea separated by periods without diarrhea. UMLS:C0239181 Episodic diarrhea Episodic diarrhoea Intermittent diarrhoea Intermittent diarrhea Cephalgia, or pain sensed in various parts of the head, not confined to the area of distribution of any nerve. HP:0000266 HP:0001354 SNOMEDCT_US:25064002 UMLS:C0018681 Headache Headaches Headache is one of the most common types of recurrent pain as well as one of the most frequent symptoms in neurology. In addition to occasional headaches, there are well-defined headache disorders that vary in incidence, prevalence and duration and can be divided into two broad categories. In secondary headache disorders, headaches are attributed to another condition, such as brain tumor or head injury; for the primary disorders the headache is not due to another condition. Headache An abnormal sensation of spinning while the body is actually stationary. SNOMEDCT_US:271789005 SNOMEDCT_US:399090003 SNOMEDCT_US:399153001 SNOMEDCT_US:404640003 UMLS:C0012833 UMLS:C0042571 Dizzy spell Vertigo UMLS:C0542223 Loss of speech Loss of speech A disorder of the brain caused by an infectious agent that presents with fever, headache, and an altered level of consciousness. There may also be focal or multifocal neurologic deficits, and focal or generalized seizure activity. SNOMEDCT_US:45170000 UMLS:C0014038 Brain inflammation Infectious encephalitis Paroxysmal, recurrent episodes of vomiting. UMLS:C1838993 UMLS:C1857202 Episodic vomiting Episodic vomiting The passage of fresh (red) blood per anus, usually in or with stools. Most rectal bleeding comes from the colon, rectum, or anus. HP:0002255 HP:0002609 SNOMEDCT_US:236068001 SNOMEDCT_US:405729008 UMLS:C0018932 Rectal bleeding Bright red blood in stool, most frequentoly caused by hemorrhoids or diverticulosis. Hematochezia An intermittent form of abdominal pain. UMLS:C0262527 UMLS:C3808022 Episodic abdominal pain Colitis refers to an inflammation of the colon and is often used to describe an inflammation of the large intestine (colon, cecum and rectum). Colitides may be acute and self-limited or chronic, and broadly fit into the category of digestive diseases. SNOMEDCT_US:64226004 UMLS:C0009319 Colitis Vomiting that ejects the gastric contents with great force. SNOMEDCT_US:8579004 UMLS:C0221151 Projectile vomiting Projectile vomiting An abnormality of the vasculature. UMLS:C0241657 Abnormality of blood vessels Abnormality of the vasculature Vascular abnormalities Abnormality of the vasculature Low Blood Pressure, vascular hypotension. HP:0005127 HP:0006701 SNOMEDCT_US:45007003 UMLS:C0020649 Arterial hypotension Low blood pressure Hypotension Formation of a blot clot in a deep vein. The clot often blocks blood flow, causing swelling and pain. The deep veins of the leg are most often affected. SNOMEDCT_US:128053003 UMLS:C0149871 Blood clot in a deep vein Deep vein thrombosis Multiple deep venous thrombosis Deep venous thrombosis Inflammation of blood vessel. SNOMEDCT_US:31996006 UMLS:C0042384 Angiitis Inflammation of blood vessel Vasculitis Restriction of arterial blood supply to the brain associated with insufficient oxygenation to support the metabolic requirements of the tissue. SNOMEDCT_US:287731003 SNOMEDCT_US:389100007 UMLS:C0007786 UMLS:C0917798 Brain ischemia Cerebrovascular ischemia Disruption of blood oxygen supply to brain Cerebral ischemia An abnormality of the immune system. HP:0003257 HP:0003346 HP:0010986 UMLS:C4021753 Abnormality of the immune system Immunological abnormality The immune system is composed of organs and interdependent cell types that collectively protect the body from infections and from the growth of tumor cells. The organs of the immune system comprise the bone marrow, the spleen, the thymus,the lymph nodes, and the cell types comprise B cells, T cells, natural killer cells, granulocytes,dendritic cells, and macrophages. Abnormality of the immune system Enlargement (swelling) of a lymph node. HP:0002735 SNOMEDCT_US:30746006 UMLS:C0497156 Lymph node hyperplasia Swollen lymph nodes Lymphadenopathy A structural lymph node abnormality. HP:0008149 UMLS:C0149727 Abnormal lymph node histology Abnormality of the lymph nodes Abnormal lymph node morphology Very rapid breathing. HP:0002874 HP:0004346 SNOMEDCT_US:271823003 UMLS:C0231835 Increased respiratory rate or depth of breathing Polypnea In adults, a beathing rate of between 12-20 breaths per minute is normal and tachypnea is present with a ventilatory rate greater than 20 breaths per minute. Tachypnea An anomaly of the rhythm or depth of breathing. UMLS:C1837388 Abnormal pattern of respiration Abnormal respiratory patterns Unusual breathing patterns Abnormal pattern of respiration Abnormal function of the respiratory system. HP:0005952 Fyler:4200 UMLS:C4025677 Abnormal respiration Functional respiratory abnormality Abnormal respiratory system physiology Joint pain. SNOMEDCT_US:57676002 UMLS:C0003862 Arthralgias Joint pain Arthralgia is distinct from Arthritis, which is not a symptom but a diagnosis with articular inflammation or signs of osteoarthritis. Arthralgia A severe form of respiratory insufficiency characterized by inadequate gas exchange such that the levels of oxygen or carbon dioxide cannot be maintained within normal limits. HP:0004877 SNOMEDCT_US:409622000 UMLS:C1145670 Respiratory failure Respiratory failure is classified as type 1 with hypoxemia (arterial partial pressure of oxygen less than 60 mmHg) without hypercapnea, and type 2 with hypoxemia in the present of hypercapnea (partial pressure of carbon dioxide over 50 mmHg). Respiratory failure An abnormally decreased potassium concentration in the blood. SNOMEDCT_US:166690008 SNOMEDCT_US:43339004 UMLS:C0020621 Low blood potassium levels Hypokalemia An abnormally decreased calcium concentration in the blood. SNOMEDCT_US:5291005 UMLS:C0020598 Hypocalcaemia Low blood calcium levels Hypocalcemia An abnormally decreased magnesium concentration in the blood. HP:0003284 SNOMEDCT_US:190855004 UMLS:C0151723 Low blood Mg levels Low blood magnesium levels Hypomagnesemia Abnormality originating in one or more muscles, i.e., of the set of muscles of body. HP:0003197 HP:0003708 HP:0040290 UMLS:C4021745 Muscular abnormality Abnormality of the musculature An abnormality of the composition of urine or the levels of its components. HP:0011865 HP:0011866 UMLS:C4025655 Pee issues Urine issues Abnormality of urine homeostasis Abnormality of the homeostasis (concentration) of a monoatomic ion. HP:0003253 SNOMEDCT_US:237840007 UMLS:C1704431 UMLS:C4025654 Abnormality of ion homeostasis Electrolyte disorders Electrolyte disturbance Abnormal blood ion concentration Breakdown of muscle fibers that leads to the release of muscle fiber contents (myoglobin) into the bloodstream. SNOMEDCT_US:240131006 SNOMEDCT_US:89010004 UMLS:C0035410 Breakdown of skeletal muscle Rhabdomyolysis Distention of the abdomen. HP:0001542 HP:0003364 SNOMEDCT_US:41931001 SNOMEDCT_US:60728008 UMLS:C0000731 Abdominal bloating Abdominal distension Abdominal swelling Belly bloating Bloating Distended abdomen Abdominal distention can be a secondary feature associated with a number of conditions such as bowel obstruction. Abdominal distention Pain in muscle. HP:0003718 SNOMEDCT_US:68962001 UMLS:C0231528 Muscle ache Muscle pain Myalgia Paralysis of voluntary muscles means loss of contraction due to interruption of one or more motor pathways from the brain to the muscle fibers. Although the word paralysis is often used interchangeably to mean either complete or partial loss of muscle strength, it is preferable to use paralysis or plegia for complete or severe loss of muscle strength, and paresis for partial or slight loss. Motor paralysis results from deficits of the upper motor neurons (corticospinal, corticobulbar, or subcorticospinal). Motor paralysis is often accompanied by an impairment in the facility of movement. SNOMEDCT_US:44695005 UMLS:C0522224 Inability to move Paralysis Paralysis A phenotypic abnormality that is present at birth. HP:0003595 HP:0003601 HP:0003624 HP:0003660 HP:0003666 UMLS:C1836142 UMLS:C2752013 Onset at birth Symptoms present at birth Congenital onset literally means present at birth. Congenital abnormalities are thus generally acquired during fetal development. Congenital abnormalities are often but not always hereditary in nature. Whether a disease manifestation is diagnosed to be intrauterine or congenital may depend on the time at which diagnostic procedures are performed. Thus, most congenital abnormalities are also intrauterine. This term should be used for phenotypic abnormalities or diseases initially observed at the time of birth. For abnormalities observed prior to (e.g., by fetal ultrasound), use the term Antenatal onset (HP:0030674). Congenital onset Onset of disease manifestations in adulthood, defined here as at the age of 16 years or later. HP:0003585 HP:0003598 HP:0003627 HP:0003662 HP:0003669 UMLS:C1853562 Onset in adulthood Onset in early adulthood Symptoms begin in adulthood Adult onset Onset of signs or symptoms of disease between 28 days to one year of life. HP:0003576 HP:0003579 HP:0003591 HP:0003594 HP:0003599 HP:0003600 HP:0003629 HP:0003631 HP:0003667 HP:0003672 HP:0010573 UMLS:C1848924 Infantile onset Onset in first year of life Onset in infancy Onset of signs or symptoms of disease within the first 12 months of life. Infantile onset Onset of signs or symptoms of disease between the age of 5 and 15 years. HP:0003578 HP:0003580 HP:0003582 HP:0003583 HP:0003589 HP:0003592 HP:0003604 HP:0003619 HP:0003620 HP:0003625 HP:0003659 HP:0003661 HP:0003670 UMLS:C4025588 Signs and symptoms begin before 15 years of age Juvenile onset Onset of signs or symptoms of disease within the first 28 days of life. HP:0003622 UMLS:C1855106 Neonatal onset Onset in first weeks of life Onset in neonatal period Neonatal onset The age group in which disease manifestations appear. HP:0003588 HP:0003590 HP:0003597 HP:0003602 HP:0003603 HP:0003618 HP:0003626 HP:0003628 HP:0003630 HP:0003663 HP:0003664 HP:0003668 HP:0011007 MeSH:D017668 UMLS:C0206132 Age of onset Age symptoms begin Adolescent is defined by WHO as a person between 10-19 years of age. Onset Cases of the disease in question occur without a previous family history, i.e., as isolated cases without being transmitted from a parent and without other siblings being affected. HP:0001420 HP:0003747 HP:0003769 UMLS:C1853237 Isolated cases No previous family history Sporadic An abnormal, increased fatiguability of the musculature. SNOMEDCT_US:80449002 UMLS:C0242979 UMLS:C4025573 Increased muscle fatiguability Death of the fetus in utero after at least 22 weeks of gestation. HP:0001624 HP:0001625 SNOMEDCT_US:237364002 SNOMEDCT_US:276507005 UMLS:C0015927 UMLS:C0595939 Late fetal death Late foetal death Stillbirth Stillborn The age at which fetal demise is legally classified asa a miscarriage varies between countries with the US being 20 gestational weeks and the UK being 24 gestational weeks. The HPO chooses the average of these age ranges. Stillbirth An abnormality of the biliary system. UMLS:C0940767 Abnormality of the biliary system An abnormal increase or decrease of weight or an abnormal distribution of mass in the body. HP:0010718 UMLS:C0878621 UMLS:C4025357 Abnormality of body weight Abnormality of body weight Abnormally increased body weight. HP:0045083 SNOMEDCT_US:161831008 SNOMEDCT_US:262286000 SNOMEDCT_US:8943002 UMLS:C0043094 Increased body weight Increased body weight Abnormally low body weight. HP:0001823 HP:0001826 SNOMEDCT_US:161832001 SNOMEDCT_US:248342006 SNOMEDCT_US:262285001 SNOMEDCT_US:89362005 UMLS:C0041667 UMLS:C1262477 UMLS:C1844806 Decreased body weight Decreased weight Low body weight Low weight Weight less than 3rd percentile Decreased body weight Any deviation from the normal concentration of calcium in the blood circulation. HP:0040077 Abnormal blood calcium concentration Abnormal blood calcium levels Abnormal circulating Ca concentration Abnormal circulating Ca2+ concentration Abnormal circulating calcium concentration An abnormality of temperature homeostasis. UMLS:C0005904 UMLS:C1832160 Abnormality of temperature regulation Impaired temperature control Impaired temperature regulation Inability to control temperature Inability to regulate temperature Poor control of temperature Poor regulation of temperature Poor temperature control Poor temperature regulation Unable to control temperature Abnormality of temperature regulation Abnormally diminished level of attention, responsiveness, or wakefulness. SNOMEDCT_US:3006004 UMLS:C0234428 Disturbances of consciousness Lowered consciousness Reduced consciousness/confusion Reduced consciousness SNOMEDCT_US:236077008 UMLS:C0473133 Protracted diarrhoea Protracted diarrhea Inflammation of the alimentary part of the gastrointestinal system. UMLS:C1535950 GI inflammation Gastrointestinal inflammation Gastrointestinal inflammation A deficiency in the intake of energy and nutrients. SNOMEDCT_US:248325000 SNOMEDCT_US:2492009 SNOMEDCT_US:47563007 SNOMEDCT_US:65404009 SNOMEDCT_US:70241007 UMLS:C0162429 Malnutrition Malnutrition A reduced desire to eat. SNOMEDCT_US:64379006 UMLS:C0232462 Decreased appetite Loss of appetite Poor appetite Poor appetite An anomaly in the ability to perceive and distinguish scents (odors). HP:0004410 UMLS:C4021655 Abnormal sense of smell Abnormality of olfaction Abnormality of the sense of smell Smell defect Abnormality of the sense of smell A decreased sensitivity to odorants (that is, a decreased ability to perceive odors). SNOMEDCT_US:83156004 UMLS:C2364082 Decreased smell sensation Sense of smell impaired Hyposmia The formation of a blood clot inside an artery. SNOMEDCT_US:65198009 UMLS:C0151942 Blood clot in artery Arterial thrombosis Chronic inflammation of the bronchi. SNOMEDCT_US:63480004 UMLS:C0008677 Chronic bronchitis A tachycardia originating in the ventricles characterized by rapid heart rate (over 100 beats per minute) and broad QRS complexes (over 120 ms). Fyler:7160 SNOMEDCT_US:25569003 UMLS:C0042514 Ventricular tachycardia (VT) is a potentially life-threatening ventricular arrhythmia that presents as a wide QRS complex tachycardia, and is defined as three or more consecutive QRS complexes with a duration longer than 120 milliseconds (ms) and a rate of 100 beats per minute or more, whereby the complexes have a ventricular origin. VT can be subdivided as follows: (i) sustained VT persists for 30 seconds or more; (ii) non-sustained VT lasts less than 30 seconds; (iii) monomorphic VT displays a uniform QRS morphology; and (iv) polymorphic VT displays QRS morphologies that variy from beat to beat. VT is observed most commonly in individuals with structural heart disease or acute myocardial infarction (MI). VT may also be observed in in the setting of drug toxicity or electrolyte abnormalities or in individuals with Mendelian disease. Ventricular tachycardia A state of respiratory distress that requires a life saving intervention in the form of gaining airway access and instituting positive pressure ventilation. HP:0004883 UMLS:C4025279 Respiratory distress necessitating mechanical ventilation Respiratory distress requiring endotracheal intubation Respiratory distress requiring mechanical ventilation Respiratory failure requiring assisted ventilation An abnormality of magnesium ion homeostasis. HP:0008274 UMLS:C4020826 UMLS:C4025274 Abnormal Mg concentration Abnormality of magnesium homeostasis Abnormal magnesium concentration Formation of a blood clot (thrombus) inside a vein, causing the obstruction of blood flow. SNOMEDCT_US:111293003 UMLS:C0042487 Blood clot in vein Venous thrombosis Watery voluminous diarrhea resulting from an imbalance between ion and water secretion and absorption. SNOMEDCT_US:15699003 UMLS:C0267557 Secretory diarrhoea Secretory diarrhea An abnormality of the gallbladder. SNOMEDCT_US:253803008 SNOMEDCT_US:49714001 UMLS:C0266249 Abnormality of the gallbladder Anomaly of the gallbladder Abnormality of the gallbladder A pregnancy that ends at a stage in which the fetus is incapable of surviving on its own, defined as the spontaneous loss of a fetus before the 22th week of pregnancy. SNOMEDCT_US:17369002 UMLS:C0000786 Early fetal demise Early foetal demise Spontaneous abortion The age at which fetal demise is legally classified asa a miscarriage varies between countries with the US being 20 gestational weeks and the UK being 24 gestational weeks. The HPO chooses the average of these age ranges. Miscarriage A type of diabetes mellitus initially characterized by insulin resistance and hyperinsulinemia and subsequently by glucose interolerance and hyperglycemia. HP:0005965 HP:0100652 SNOMEDCT_US:44054006 UMLS:C0011860 Diabetes mellitus Type II Diabetes mellitus, noninsulin-dependent NIDDM NIDDM diabetes mellitus Non-insulin dependent diabetes Noninsulin dependent diabetes mellitus Noninsulin-dependent diabetes Type 2 diabetes Type II diabetes Persons with type II diabetes mellitus rarely develop ketoacidosis. Type II diabetes mellitus Limited neck mobility SNOMEDCT_US:161882006 SNOMEDCT_US:405947006 UMLS:C0151315 UMLS:C1320474 UMLS:C1847392 Limitation of neck motion Restricted neck movement Limitation of neck motion An anomaly that is characterized progressive airflow obstruction that is only partly reversible, inflammation in the airways, and systemic effects or comorbities. HP:0006541 SNOMEDCT_US:13645005 UMLS:C0024117 COPD Chronic obstructive pulmonary disease COPD is usually conceptualized as a disease entity. It is heterogeneous histologically and pathogenically, and conventionally includes emphysema and chronic bronchitis, It is included as a phenotype term as COPD is often annotated as a feature of other diseases. Chronic pulmonary obstruction According to the definitions of the American and British Thoracic Societies, including pulmonary functional tests, X-rays, and CT scans for items such as fibrosis, bronchiectasis, bullae, emphysema, nodular or lymphomatous abnormalities. SNOMEDCT_US:413839001 UMLS:C0746102 Chronic lung disease Chronic lung disease Abnormality of the lung parenchyma extending to the pulmonary interstitium and leading to diffuse pulmonary fibrosis. HP:0006513 HP:0006547 SNOMEDCT_US:233703007 UMLS:C0206062 Abnormal lung parenchyma morphology Abnormality in area between air sacs in lung Interstitial lung disease Interstitial pulmonary disease Abnormal pulmonary interstitial morphology Obstruction of conducting airways of the lung. HP:0006512 UMLS:C0600260 Obstructive lung disease Pulmonary obstruction Airway obstruction UMLS:C1837257 Lipid accumulation in hepatocytes UMLS:C4024752 Abnormality of eye blood vessels Abnormality of the vasculature of the eye Impaired feeding performance of an infant as manifested by difficulties such as weak and ineffective sucking, brief bursts of sucking, and falling asleep during sucking. There may be difficulties with chewing or maintaining attention. HP:0002016 HP:0002022 HP:0002568 UMLS:C2674608 Feeding difficulties in infancy Loss of elasticity of the upper and lower eyelids causing the skin to sag and bulge. SNOMEDCT_US:246815009 UMLS:C0423124 UMLS:C2674149 Baggy eyes Droopy eyelid skin Extra eyelid skin Eyelid dermatochalasia Redundant eyelid skin Dermatochalasis An abnormality of divalent inorganic cation homeostasis. UMLS:C4023648 Abnormality of divalent inorganic cation homeostasis Abnormal blood inorganic cation concentration An abnormality of cation homeostasis. UMLS:C4023646 Abnormality of cation homeostasis Abnormal blood cation concentration An abnormality of monovalent inorganic cation homeostasis. UMLS:C4023645 Abnormality of monovalent inorganic cation homeostasis Abnormal blood monovalent inorganic cation concentration An abnormality of the upper urinary tract. UMLS:C4023641 Abnormality of the upper urinary tract The upper urinary tract is a subdivision of urinary system which consists of the kidney and the ureters. Abnormality of the upper urinary tract A functional abnormality of the immune system. UMLS:C4023616 Abnormality of immune system physiology The speed at which disease manifestations appear and develop. UMLS:C4021204 Speed of onset Temporal pattern Sudden appearance of disease manifestations over a short period of time. SNOMEDCT_US:272118002 UMLS:C0205178 Acute onset The word acute is applied to different time scales depending on the disease or manifestation and does not have an exact definition in minutes, hours, or days. Acute Abnormality of glucose homeostasis. UMLS:C4023598 An abnormality of any process involved in the maintenance of an internal steady state of glucose within an organism or cell. Abnormal glucose homeostasis An abnormality of the gastrointestinal tract. SNOMEDCT_US:119292006 SNOMEDCT_US:25374005 SNOMEDCT_US:53619000 UMLS:C0012242 UMLS:C0017178 UMLS:C4023588 Abnormality of the GI tract Abnormality of the gastrointestinal tract Abnormality of the gastrointestinal tract Abnormal functionality of the cardiovascular system. UMLS:C4023587 Abnormality of cardiovascular system physiology Abnormal cardiovascular system physiology An abnormality of blood circulation. UMLS:C4020760 UMLS:C4023585 Abnormality of blood circulation The presence of hemorrhage within the body. UMLS:C1390214 Internal bleeding Internal haemorrhage Internal hemorrhage An abnormality of the regulation of body fluids. SNOMEDCT_US:1860003 SNOMEDCT_US:190902006 UMLS:C2364164 Abnormality of fluid regulation Fluid imbalance Abnormality of fluid regulation An abnormal concentration of potassium. UMLS:C4023575 Abnormal blood K concentration Abnormality of potassium homeostasis Abnormal blood potassium concentration A sudden flexion, extension, or mixed extension-flexion of predominantly proximal and truncal muscles that is usually more sustained than a myoclonic movement but not as sustained as a tonic seizure. Limited forms may occur: Grimacing, head nodding, or subtle eye movements. Epileptic spasms frequently occur in clusters. Infantile spasms are the best known form, but spasms can occur at all ages SNOMEDCT_US:28055006 UMLS:C0037769 UMLS:C1527366 Epileptic spasms Salaam convulsion Salaam convulsions Salaam seizure Salaam seizures The maximum age of onset is between 3 and 12 months, the peak being at 6 months. However, spasms may start from birth, or appear long after the age of 12 months, including into adulthood. Infantile spasms represent a specific type of seizure seen in an epilepsy syndrome of infancy and childhood known as West Syndrome. West Syndrome is characterized by infantile spasms, developmental regression, and hypsarrhythmia (as demonstrated by electroencephalography). Epileptic spasm Any morphological abnormality of the skin. Fyler:4133 UMLS:C4023528 Abnormal skin morphology Abnormal skin structure Abnormality of skin morphology Abnormal skin morphology Any abnormality of the physiological function of the skin. UMLS:C4023527 Abnormality of skin physiology Abnormality of skin physiology The presence of inflammation of the skin. That is, an abnormality of the skin resulting from the local accumulation of fluid, plasma proteins, and leukocytes. HP:0002727 HP:0007423 MP:0004947 SNOMEDCT_US:703938007 UMLS:C0011603 UMLS:C3875321 Abnormal tendency to infections of the skin Inflammatory abnormality of the skin Skin inflammation Inflammatory abnormality of the skin UMLS:C4023437 Abnormality of the urinary system physiology An abnormality of the skin that is not localized to any one particular region. UMLS:C4021157 Generalised abnormality of skin Generalized abnormality of skin Generalized abnormality of skin An abnormality of the function of the inner ear. UMLS:C4023382 Functional abnormality of the inner ear The inner ear comprises the cochlea, three semicircular canals and the vestibule (labyrinth), and is directly responsible for hearing. Additionally, the vestibule and semicircular canals function to maintain balance or equilibrium. Functional abnormality of the inner ear Delivery of a fetus through surgical incisions made through the abdominal wall (laparotomy) and the uterine wall (hysterotomy). SNOMEDCT_US:200144004 UMLS:C1384674 Caesarian section Caesarian section The age group when the cessation of life happens. UMLS:C1546180 Age of death An anomaly of the control or production of movement in the central nervous system. UMLS:C4023354 Abnormality of central motor function Abnormal central motor function UMLS:C4023353 Abnormality of coordination Coordination issue Abnormality of coordination Cognitive, psychiatric, or memory anomaly. UMLS:C4023352 Abnormality of higher mental function This includes abnormalities in speech, mood, emotions, behavior, and cognition. Abnormality of mental function A type of infection of the central nervous system that can be regarded as a sign of a pathological susceptibility to infection. SNOMEDCT_US:128117002 UMLS:C0007684 Central nervous system infection Unusual CNS infection A subjective manifestation of disease localized to the abdomen. UMLS:C0740651 Abdominal symptom Onset of disease at the age of between 1 and 5 years. HP:0003586 HP:0003617 UMLS:C1837352 Symptoms begin in childhood This term refers to ages up to but not including the fifth birthday (see Juvenile onset). Childhood onset Regurgitation of milk through the nose. SNOMEDCT_US:85023004 UMLS:C0232608 Nasal regurgitation Feeding problem necessitating nasogastric tube feeding. UMLS:C4023343 This is a severe form of feeding problems in infancy. Nasogastric tube feeding in infancy Feeding problem necessitating gastrostomy tube feeding. UMLS:C4020748 UMLS:C4023342 This is an extremely severe form of feeding problems in infancy. Gastrostomy tube feeding in infancy Any cardiac rhythm other than the normal sinus rhythm. Such a rhythm may be either of sinus or ectopic origin and either regular or irregular. An arrhythmia may be due to a disturbance in impulse formation or conduction or both. HP:0001656 HP:0001661 HP:0001665 HP:0001666 HP:0001675 HP:0001687 HP:0001721 HP:0004351 HP:0005158 SNOMEDCT_US:102594003 SNOMEDCT_US:44808001 SNOMEDCT_US:698247007 UMLS:C0003811 UMLS:C0264886 UMLS:C0522055 UMLS:C0855329 UMLS:C1832603 UMLS:C1842820 Abnormal heart rate Arrhythmias Cardiac arrhythmia Cardiac arrhythmias Cardiac rhythm disturbances Heart rhythm disorders Irregular heart beat Irregular heartbeat Arrhythmia An abnormality in the range and ease of motion of joints across their normal range. UMLS:C4023216 Abnormality of joint mobility A functional abnormality of a skeletal muscle. UMLS:C4023182 Abnormality of muscle physiology Issue with muscle function Abnormal muscle physiology A structural abnormality of a skeletal muscle. HP:0003735 UMLS:C4023181 Abnormal muscle morphology Abnormality of muscle morphology Abnormally shaped muscle Issue with muscle structure Abnormal skeletal muscle morphology An abnormality of the form, structure, or size of the skeletal system. UMLS:C4023165 Abnormality of skeletal morphology Abnormally shaped skeletal Abnormal skeletal morphology An abnormality of the function of the skeletal system. UMLS:C4023164 Abnormality of musculoskeletal physiology Abnormal musculoskeletal physiology A type of abdominal pain that comes and goes in waves, most often starting and ending suddenly and being of severe intensity. SNOMEDCT_US:9991008 UMLS:C0232488 Colicky abdominal pain can be caused by kidney stones and gallstones, among other etiologies. This type of pain is thought to be caused by spasm, obstruction, or distension of any of the hollow viscera of the gastrointestinal system. Abdominal colic An infection of the upper or lower respiratory tract. SNOMEDCT_US:275498002 UMLS:C0035243 Respiratory infection Respiratory tract infection Respiratory tract infection Impaired ability to eat related to problems gathering food and getting ready to suck, chew, or swallow it. SNOMEDCT_US:78164000 UMLS:C0232466 Feeding difficulties Feeding problems Poor feeding Feeding difficulties An abnormal functionality of the kidney. HP:0000082 HP:0000087 HP:0005566 HP:0008646 SNOMEDCT_US:39539005 UMLS:C0151746 Abnormal kidney function Abnormal renal function Abnormality of renal physiology Kidney function issue Renal functional abnormality Abnormal renal physiology A structural anomaly of the respiratory system. Fyler:4235 UMLS:C4022992 Abnormal respiratory system morphology An anomaly in the processes involved in the maintenance of an internal equilibrium. MP:0001764 UMLS:C4022950 Abnormal homeostasis A structural anomaly of the globe of the eye, or bulbus oculi. HP:0000489 HP:0012374 Fyler:4863 UMLS:C4022925 Abnormal eye structure Abnormality of the globe Abnormally shaped eye previously: Abnormal globe morphology Abnormal eye morphology A functional anomaly of the eye. Abnormal vision physiology UMLS:C4022924 Abnormal eye physiology Abnormal eye physiology A subjective feeling of tiredness characterized by a lack of energy and motivation. SNOMEDCT_US:248274002 SNOMEDCT_US:84229001 UMLS:C0015672 Fatigue Tired Tiredness Fatigue is distinct from muscle weakness. Fatigue A delay in the development of skills required to feed oneself in the toddler period (between one and three years of age). UMLS:C4022920 Delayed self-feeding during toddler years Inflammation of the large airways in the lung including any part of the bronchi from the primary bronchi to the tertiary bronchi. SNOMEDCT_US:32398004 UMLS:C0006277 Bronchitis An abnormality of the partial pressure of oxygen or carbon dioxide in the arterial blood. SNOMEDCT_US:312391003 UMLS:C0476337 Abnormal blood gas level Abnormal blood gas level Abnormally reduced blood carbon dioxide (CO2) level. SNOMEDCT_US:61031008 UMLS:C0085383 Hypocarbia Reduced carbon dioxide in the blood Hypocapnia An abnormally low level of blood oxygen. SNOMEDCT_US:389087006 UMLS:C0700292 Low blood oxygen level Note that hypoxemia is defined as a condition where arterial oxygen tension is below normal (80-100mmHg). Hypoxia is defined as the failure of oxygenation at the tissue level. Hypoxia is not measured directly by a standard laboratory value. Hypoxemia A structural anomaly of the gallbladder. UMLS:C4022904 Abnormal gallbladder structure Abnormal shape of gallbladder Abnormal gallbladder morphology A structural abnormality of the brain, which has as its parts the forebrain, midbrain, and hindbrain. UMLS:C4021085 Abnormal shape of brain Abnormality of brain morphology Abnormality of the brain Abnormal brain morphology Constipation for longer than three months with fewer than 3 bowel movements per week, straining, lumpy or hard stools, and a sensation of anorectal obstruction or incomplete defecation. SNOMEDCT_US:236069009 UMLS:C0401149 Chronic constipation Infrequent bowel movements Chronic constipation Constipation of sudden onset and lasting for less than three months. SNOMEDCT_US:197119006 UMLS:C0401148 Acute constipation An unpleasant sensory and emotional experience associated with actual or potential tissue damage, or described in terms of such damage. SNOMEDCT_US:22253000 UMLS:C0030193 Pain Pain An anomalous finding in the examination of the urine for cells. SNOMEDCT_US:310439007 UMLS:C0587955 Abnormal urine cytology Functional anomaly of the kidney persisting for at least three months. HP:0000106 HP:0001918 HP:0008671 SNOMEDCT_US:709044004 UMLS:C0748318 UMLS:C1561643 CKD Chronic kidney disease Chronic kidney disease A functional anomaly of the nervous system. UMLS:C4022811 Abnormality of nervous system physiology Abnormal nervous system physiology A structural anomaly of the nervous system. Fyler:4135 Fyler:4300 UMLS:C4022810 Abnormal shape of nervous system Abnormality of nervous system morphology Abnormal nervous system morphology Any anomaly of the inflammatory response, a response to injury or infection characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages. UMLS:C4022805 Abnormal inflammatory response Abnormal inflammatory response A abnormal increase in the inflammatory response to injury or infection. UMLS:C4022803 Increased inflammatory response Abnormal structure of the gastrointestinal tract. UMLS:C4021073 Abnormal shape of the digestive system Morphological abnormality of the GI tract Morphological abnormality of the gastrointestinal tract Morphological anomaly of the digestive system Abnormal gastrointestinal tract morphology Abnormal functionality of the gastrointestinal tract. UMLS:C4022755 Functional abnormality of the GI tract GI dysfunction Functional abnormality of the gastrointestinal tract A sudden, audible expulsion of air from the lungs through a partially closed glottis, preceded by inhalation. SNOMEDCT_US:263731006 SNOMEDCT_US:272039006 SNOMEDCT_US:49727002 UMLS:C0010200 Cough Coughing The European Respiratory Society Task Force recommended two possible definitions of cough: (1) A three-phase expulsive motor act characterized by an inspiratory effort (inspiratory phase) followed by a forced expiratory effort against a closed glottis (compressive phase) and then by opening of the glottis and rapid expiratory airflow (expulsive phase);and (2) A forced expiratory maneuver, usually against a closed glottis and associated with a characteristic sound. The term Cough or any of its more specific descendents can be modified by the terms Acute (HP:0011009), Subacute (HP:0011011), and Chronic (HP:0011010). In adults, an acute cough lasts less than 3 weeks, a subacute cough from 3 to 8 weeks, and a chronic cough longer than 8 weeks. In children aged less than 15 years a chronic cough is defined as a daily cough lasting for over 4 weeks. Cough This subontology is designed to provide terms to characterize and specify the phenotypic abnormalities defined in the Phenotypic abnormality subontology, with respect to severity, laterality, age of onset, and other aspects. HP:0000004 UMLS:C4021064 Phenotypic modifier Note that some of the terms, such as Intellectual disability, have children terms such as Severe intellectual disability that represent precomposed combinations of modifiers and phenotypic abnormality terms. This done where the medical community commonly uses these terms with a fixed meaning (for instance, the Intellectual disability terms are used with specific IQ ranges). For computational reasoning, the semantics are intended to be the same as if there was a combination of the phenotype term and the clinical modifier term. Clinical modifier position of phenotype abnormality A motor seizure is a type of seizure that is characterized at onset by involvement of the skeletal musculature. The motor event could consist of an increase (positive) or decrease (negative) in muscle contraction to produce a movement. This term describes the initial semiology of the seizure without specifying whether the onset is focal or generalized. Motor seizure Abnormal vascular morphology Any anomaly of the digestive system, a collection of organs that is made up of the gastrointestinal tract and the liver, pancreas, and gallbladder. The gastrointestinal tract is a series of hollow organs joined in a long, twisting tube from the mouth to the anus, including the mouth, esophagus, stomach, small intestine, large intestine and anus. Abnormality of the digestive system A functional anomaly of the digestive system. Abnormality of digestive system physiology A structural anomaly of the digestive system. Abnormality of digestive system morphology Abnormal digestive system morphology The anterior abdominal wall is sunken and presents a concave rather than a convex contour. Scaphoid abdomen can be observed in diseases such as congenital diaphragmatic hernia (since the abdominal contents can be in the thorax). Scaphoid abdomen Passage of many stools containing blood. Blood in stool Bloody stool Bloody bowel movement Bloody diarrhea Diarrhea that contains bright red or maroon-colored blood may be referred to as hematochezia, while melena is used to describe black, tarry, and smelly diarrhea. Bloody diarrhea Passage of many stools containing blood and mucus. Bloody mucoid diarrhea Bloody mucoid diarrhea Vomiting of material that is of fecal origin. Faecal vomiting Fecal vomiting Stercoraceous vomiting Vomiting faecal matter Vomiting fecal matter Feculent vomiting is usually due to mechanical intestinal obstruction but it can be due to paralytic obstruction (adynamic ileus). Feculent vomiting A sudden violent, spasmodic, audible expiration of breath through the nose and mouth. Sneeze A symptom or manifestation indicating a systemic or general effect of a disease and that may affect the general well-being or status of an individual. Note that we use the preferred term label constitutional symptom because this reflects common usage, but we do not restrict the term or its descendents to the narrow meaning of symptom, i.e., a complaint related by a patient to a physician. There is no generally accepted classification of what defines a constitutional symptom, but examples include weight loss, fatigue, general weakness, night sweats, shaking, chills, fever, and vomiting. Constitutional symptom A sudden sensation of feeling cold. Chills The word chills can also refer to an episode of shivering, accompanied by paleness and feeling cold. Chills Involuntary contraction or twitching of the muscles. Shivering Shuddering Shivering is a physiologic method of heat production in man and other mammals. Shivering is a bodily function in response to fever, early hypothermia or feeling cold. Shivering Severe chills with violent shivering. A rigor is an episode of shaking or exaggerated shivering which can occur with a high fever. Rigours A sudden attack of severe shivering accompanied by chills (a feeling of coldness) is called a rigor and may be associated with a marked rise in body temperature. Patients often describe rigors as an attack of uncontrollable shaking. Rigors are often a sign of infection, particularly bacterial infection. Rigors A functional anomaly of the hepatobiliary system Abnormality of hepatobiliary system physiology Any physiological abnormality of the esophagus. Abnormality of esophagus physiology Abnormality of oesophagus physiology Functional abnormality of the esophagus Functional abnormality of the oesophagus Abnormal esophagus physiology An anomaly of arterial function. Abnormal arterial physiology A reddish appearance over the white part (sclera) of the eye ranging from a few enlarged blood vessels appearing as wiggly lines over the sclera to a bright red color completely covering to sclera. Red eye Red eyes Red eye A state characterized by a feeling of weakness and loss of strength leading to a generalized weakness of the body. Lack of energy and strength Weakness Asthenia is to be distinguished from fatigue, because asthenia refers to a sensation of exhaustion which occurs before any effort. Asthenia is to be distinguished from myasthenia, which means a specific weakness of one or more muscles. Asthenia and fatigue can coexist. Asthenia Any anomaly of the vocalizing of an infant's crying, i.e.,the typically loud voice production that is accompanied by tears and agitation. Abnormal cry Inflammation (due to infection or irritation) of the pharynx. Pharyngitis An abscess is a localized collection of purulent material surrounded by inflammation and granulation. Abscess Any functional anomaly of the neck region. Abnormal neck physiology A necrotic lesion in the cerebrum resulting from a sudden insufficiency of arterial or venous blood supply due to emboli, thrombi or mechanical factors. Cerebral infarct An anomaly in intensity, frequency, or duration of the verbal or behavioral expression of emotions, feelings, or thoughts. Affect includes a combination of emotion in terms of feelings and its expression either in the verbal or behavioral (action) level. Normal expressions are often relatively short lived and familiar to the person while pathological expressions may be intense and extended and considered out of character for the individual. Affect encompasses: 1) emotions, 2) volition, and 3) what is termed the intellect or cognitive elements expressing (communicating) emotion and volition. Affect includes an internal feeling (emotion), an internal drive (will), and a motor component expression (typically speech, but also reflected in thoughts). Abnormal affect Abnormal cognitive process An anomaly of the amount or nature of abdominal sounds. Abdominal sounds (bowel sounds) are made by the movement of the intestines as they promote passage of abdominal contents by peristalsis. SNOMEDCT_US:60612008 UMLS:C0159060 Abnormal bowel sounds Abnormal bowel sounds Abnormally increased gurgling/rumbling sounds made by the movement of fluid and gas in the intestines. SNOMEDCT_US:18101008 UMLS:C0232694 Borborygmi Increased bowel sounds Hyperactive bowel sounds An decreased amount of bowel sounds. SNOMEDCT_US:15280003 UMLS:C0232695 Decreased bowel sounds Hypoactive bowel sounds Complete lack of abdominal sounds as assayed by examination of the abdomen with a stethoscope. UMLS:C4022606 Lack of bowel sounds This feature reflects lack of intestinal activity. Lack of bowel sounds Severely decreased cardiac output with evidence of inadequate end-organ perfusion (i.e., tissue hypoxia) in the presence of adequate intravascular volume. SNOMEDCT_US:89138009 UMLS:C0036980 Cardiovascular shock Cardiogenic shock can result from a number of different of cardiac insults, the most common of which is acute myocardial infarction. Cardiogenic shock Abnormality of vascular function. UMLS:C4022603 Abnormal vascular physiology A structural anomaly of the adjacent structures (i.e., adnexa) of the eye, defined as the lacrimal apparatus, the extraocular muscles and the eyelids, eyelashes, eyebrows and the conjunctiva. UMLS:C4073120 Abnormal ocular adnexa morphology Any structural anomaly of the heart and blood vessels. HP:0001632 HP:0002564 HP:0002565 UMLS:C4049796 Abnormality of cardiovascular system morphology Cardiovascular malformations Abnormal cardiovascular system morphology Any structural anomaly of the tongue. UMLS:C4280755 Abnormal tongue morphology Any functional anomaly of the tongue. UMLS:C4280754 Abnormal tongue physiology An anomalous (adventitious) sound produced by the breathing process. SNOMEDCT_US:301273002 UMLS:C0231856 Abnormal lung auscultation finding Abnormal breath sound A functional anomaly of that portion of the cardiosvascular system that carries deoxygenated blood from the heart to the lungs and returns oxygenated blood back to the heart. UMLS:C4280730 Abnormal pulmonary circulation Abnormality of respiratory circulation Abnormality of pulmonary circulation Feeding problem necessitating gastrojejunal tube feeding. UMLS:C4280681 Gastro-jejunal tube feeding in infancy The rationale for gastrojejunal tube feeding is that placing the tip of the tube beyond the ligament of Treitz prevented duodenogastric reflux or gastro-esophageal reflux. Gastrojejunal feeding tubes have since been used in children who are deemed too unfit for antireflux surgery or where fundoplication has failed. Gastrojejunal tube feeding in infancy Dilatation of the blood vessels of the conjunctiva leading to a red appearance of the sclera. Conjunctival hyperaemia Conjunctival injection Conjunctival vascular congestion Conjunctival hyperemia An anomaly of the electrical conduction physiology of the heart. Abnormality of cardiovascular system electrophysiology A chronic deviation from normal pressure in the systemic arterial system. Abnormal systemic BP Abnormal systemic blood pressure Hepatocytes (liver parenchymal cells) exhibit a bloated appearance because of expansion of the cytoplasm by accumulated material. Storage in hepatocytes Resistance of the extensor muscles of the neck to being bent forwards (i.e., impaired neck flexion) as a result of muscle spasm of the extensor muscles of the neck. Nuchal rigidity is not a fixed rigidity. Nuchal rigidity has been used as a bedside test for meningism, although its sensitivity for this purpose has been debated. Meningism is resistance to neck flexion due to painful spasm of extensor muscles resulting from meningeal irritation. The diagnosis of meningism is made in someone whose symptoms simulate meningitis, but in which no actual inflammation of these membranes is present. Nuchal rigidity can thus be observed in individuals with meningitis or with meningism. Nuchal rigidity A cough that produces phlegm or mucus. Cough with mucus production Wet cough Productive cough A cough that does not produce phlegm or mucus. Dry cough Dry coughing Nonproductive cough A distortion of the sense of taste, often characterized by the sensation of a metallic taste. Altered sense of taste Dysgeusia Metallic taste Metallic taste in mouth Parageusia A state of sudden and severe confusion. Altered consciousness or cognition Delirium The state in which profound and widespread reduction of effective tissue perfusion leads first to reversible, and then if prolonged, to irreversible cellular injury. Shock A circumscribed area of pus or necrotic debris in the skin. Skin abscess Cutaneous abscess An unpleasant sensation of tightness or pressure in the chest. Tightness in chest Tightness of chest Chest tightness Any deviation from the normal quantity of secretion of nasal mucus, a thick viscous liquid produced by the mucous membranes of the nose. Abnormal nasal mucus secretion Increased discharge of mucus from the nose. Nasal Discharge Runny Nose Rhinorrhea A type of ventricular tachycardia that is characterized by variable QRS complexes within each lead (i.e., QRS complexes may be different from beat to beat). Polymorphic ventricular tachycardia Any functional anomaly of the ear. Abnormal ear physiology The course a disease typically takes from its onset, progression in time, and eventual resolution or death of the affected individual. Clinical course A functional anomaly of the mouth (which is also known as the oral cavity). The physiological functions of the mouth include salivary gland secretory function, mastication (chewing) and preparation of food for swallowing. Abnormal oral physiology Any structural anomaly of the mouth, which is also known as the oral cavity. Abnormal oral morphology Abnormal appearance of material expectorated (coughed up) from the respiratory system and that is composed of mucus but may contain other substances such as pus, blood, microorganisms, and fibrin. Abnormal sputum morphology Abnormal sputum An anomaly of the adjacent structures (i.e., adnexa) of the eye, defined as the lacrimal apparatus, the extraocular muscles and the eyelids, eyelashes, eyebrows and the conjunctiva. Abnormality of the ocular adnexa A type of infection that is regarded as a sign of a pathological susceptibility to infection. There are five general subtypes. (i) Opportunistic infection, meaning infection by a pathogen that is not normally able to cause infection in a healthy host (e.g., pneumonia by Pneumocystis jirovecii or CMV); (ii) Unusual location (focus) of an infection (e.g., an aspergillus brain abscess); (iii) a protracted course or lack of adequate response to treatment (e.g., chronic rhinosinusitis); (iv) Unusual severity or intensity of an infection; and (v) unusual recurrence of infections. Unusual infection Intermittent pain, i.e., pain that occurs occasionally and at irregular intervals. Episodic pain A type of abdominal pain characterized by a feeling of contractions and typically fluctuating in intensity. Abdominal cramps An unusual infection classified by the affected body part. Unusual infection by anatomical site An abnormal level of an analyte measured in the blood. Abnormal circulating metabolite concentration Any deviation from the normal concentration of a metabolite in a tissue. Abnormal tissue metabolite concentration Abnormal immune system morphology Abnormal increase in blood pressure. An individual measurement of increased blood pressure does not necessarily imply hypertension. In practical terms, multiple measurements are recommended to diagnose the presence of hypertension. Increased BP Increased blood pressure Involuntary tightening of the abdominal musculature that occurs in response to touching the abdomen to avoid pain. Rigidity can occur in the presence of abdominal inflammation and usually involves only the inflamed area. Rigid abdomen Abdominal rigidity A voluntary contraction of the abdominal wall musculature to avoid pain. Abdominal guarding tends to be generalized over the entire abdomen. In contrast to abdominal rigidity, guarding can often be overcome by having the patient purposely relax the muscles; rigidity cannot be. Abdominal guarding Persistent blue color of the skin that surrounds the mouth. Bluish around mouth Circumoral cyanosis may be a sign of peripheral or of central cyanosis. Circumoral cyanosis A cutaneous wound is a defined as a disruption of normal anatomic structure and function of the skin that occurs owing to an injury of the skin. Wound healing is a dynamic, interactive process involving soluble mediators, blood cells, extracellularmatrix, and parenchymal cells. Wound healing has three phases: inflammation, tissue formation, and tissue remodeling, that overlap in time. Skin wound Cutaneous wound A cutaneous wound that is proceeding through an orderly and timely reparative process that results in sustained restoration of the anatomic and functional integrity of the skin. Wound healing accors in multiple overlapping stages, with re=-eipthelialization normally beginning on day one or two. In most clinical settings, closure of acute and chronic wounds is considered the wound healing end point, but wounds can continue to undergo remodeling or tissue maturation for several months or even years. Acute cutaneous wound A cutaneous wound that has failed to proceed through the orderly and timely process to produce an atomic and functional integrity, or proceeded through the repair process without establishing a sustained anatomic and functional result. Chronic nonhealing cutaneous wound Chronic cutaneous wound An anomaly of the musculoskeletal system, which consists of the bones of the skeleton, muscles, cartilage, tendons, ligaments, joints, and other connective tissue. The musculoskeletal system supports the weight of the body, maintains body position and produces movements of the body or of parts of the body. Abnormality of the musculoskeletal system A structural anomaly of the pharynx. Abnormal pharynx morphology Osmotic diarrhea results from the presence of osmotically active, poorly absorbed solutes in the bowel lumen that inhibit normal water and electrolyte absorption. Osmotic diarrhea involves an unabsorbed substance that draws water from the plasma into the intestinal lumen along osmotic gradients. Secretory diarrhea results from disordered electrolyte transport and, despite the term, is more commonly caused by decreased absorption rather than net secretion. Inflammatory diseases cause diarrhea with exudative, secretory, or osmotic components. Osmotic diarrhea Passage of an increased number of stools containing mucus, a thick fluid substance secreted by mucous membranes. Mucous diarrhea Mucous diarrhoea Mucoid diarrhea Any structural anomaly of a blood vessel (artery, arteriole, capillary, venule, or vein). Abnormal blood vessel morphology A sudden onset of abdominal pain with associated nausea or vomiting. The acute abdomen may be caused by an infection, inflammation, vascular occlusion, or obstruction. Acute abdominal pain Acute abdomen Ischemia is defined as a restriction of arterial blood supply to a tissue associated with insufficient oxygenation to support the metabolis requirements of the tissue. Depending on the involved tissues, clinical manifestations may include pain, pallor, lack of pulse, coldness, paresthesia, and paralysis. Additional associated manifestations include hemodynamic parameters (reduced blood pressure distal to the site of restricted arterial supply) and angiographic evidence of arterial occclusion. Tissue ischemia Feeding problem necessitating food and nutrient delivery via a tube. Tube feeding Passage of excessive amounts of gas and the feeling of abdominal fullness and bloating. Flatulence Intermittent abdominal pain with diarrhea and/or constipation. Bowel irritability Acute respiratory distress syndrome (ARDS) is defined as an acute disorder that starts within seven days of the inciting event and is characterized by bilateral lung infiltrates and severe progressive hypoxemia in the absence of any evidence of cardiogenic pulmonary edema. ARDS is defined by the patient's oxygen in arterial blood (PaO2) to the fraction of the oxygen in the inspired air (FiO2). These patients have a PaO2/FiO2 ratio of less than 300. ARDS Acute respiratory distress syndrome (ARDS) is a life-threatening condition of seriously ill patients, characterized by poor oxygenation, pulmonary infiltrates, and acuity of onset. On a microscopic level, the disorder is associated with capillary endothelial injury and diffuse alveolar damage. Once ARDS develops, patients usually have varying degrees of pulmonary artery vasoconstriction and may subsequently develop pulmonary hypertension. ARDS carries a high mortality, and few effective therapeutic modalities exist to combat this condition. ARDS can be observed as a complication of many diseases including pulmonary infection or aspiration, sepsis, trauma, massive transfusion, drowning, drug overdose, fat embolism, inhalation of toxic fumes, and pancreatitis. Acute respiratory distress syndrome Acral areas of erythema with vesicles or pustules. The lesions resemble chilblains and have purpuric areas, affecting hands and feet. Chilblain-like lesion This condition is termed pseudo-chilblain because of the similar appearance of these lesions to chilblains. Pseudochilblains may be observed in persons with COVID-19 without documented exposure to cold or other risk factors for chilblains. Pseudo-chilblain An increase in the amount of airway mucus. This feature may be characterized by frequent or excessive throat clearing (exhalation through tightly constricted laryngopharyngeal tissues accompanied by vibration of the palatoglossal arch and the vocal folds serving to clear mucus from the airway). Increased phlegm If excessive sputum production is manifested by frequent and often involuntary coughing, the HPO term Productive cough should be used. Increased sputum production Pleuritic chest pain is characterized by sudden and intense sharp, stabbing, or burning pain in the chest when inhaling and exhaling. Pleuritic chest pain A feeling of general discomfort, weakness, or lack of health. Malaise The condition of being unable to eat a full meal because of a feeling of fullness (satiety), or or feeling very full after eating only a small amount of food. Feeling full quickly when eating Not able to finish a normal-sized meal Early satiety Feeling excessively full after meals. Postprandial fullness Inability to ingest sufficient quantities of nutrition by mouth or by tube-feeding with the corresponding requirement for intravenous administration of nutrition. Dependency on parenteral nutrition Bluish discoloration of one or more regions of the face. Bluish face Cyanotic face Facial cyanosis Bluish discoloration of the distal extremities in the absence of cold temperature or stress. Peripheral cyanosis can involve hands, fingertips, or toes, and sometimes circumoral and periorbital areas. Mucous membranes are generally not involved. Peripheral cyanosis Death of a fetus in the uterus. Death before birth Intrauterine death Prenatal death Abnormal joint physiology Presence of any form of communication (e.g., verbal or non-verbal) that does not align with cultural expectations or developmental level. HP:5200128 Abnormal communication The concentration of a metabolite in the liver is above or below the limits of normal. Abnormal liver metabolite concentration Murphy's sign is elicited in patients with acute cholecystitis by asking the patient to take in and hold a deep breath while palpating the subcostal region. In practice, Murphy's sign is performed by palpating the subcostal region during inspiration. If pain is elicited and the patient suddenly stops their inspiratory effort, a positive Murphy's sign has been elicited. Murphy's sign Murphy's sign positive Sweeney's sign Positive Murphy sign Vomiting whereby the vomit has the color of bile, yellowish-green. Bilious emesis Obstipation is the inability to pass either stool or flatus (gas). Lack of flatulence No gas passage Obstipation can be a sign of an acute obstruction of the GI tract, either of the small or large bowel. Obstipation Vomiting following a coughing spell. Individuals with gastroesophageal reflux disease (GERD) will frequently vomit when coughing for a non-GI reason. Vomiting occurs during these coughing spells because the intrabdominal pressure is high from the coughing and the propensity to reflux results in stomach contents emerging as vomit. This is a historical question that allows a parent to impart information suggesting GERD at an age when it is difficult to obtain a reliable GERD history from the child. Posttussive emesis UMLS:C4022499 Mortality/Aging Recurrent abnormal consumption of food, liquids, or objects that could have negative consequences for the individual. UMLS:C4073150 Abnormal consumption behaviour Abnormal consumption behavior The condition of inability to eat normally treated by placement of a thin tube through the nose into the stomach that is then used to carry food. Nasogastric tube feeding A rare condition that is characterized by a complete loss of taste function of the tongue. Absent sense of taste Impaired taste sensation Lost taste Ageusia A chronic inflammatory bowel disease that includes characteristic ulcers, or open sores, in the colon. The main symptom of active disease is usually constant diarrhea mixed with blood, of gradual onset and intermittent periods of exacerbated symptoms contrasting with periods that are relatively symptom-free. In contrast to Crohn's disease this special form of colitis begins in the distal parts of the rectum, spreads continually upwards and affects only mucose and submucose tissue of the colon. SNOMEDCT_US:64766004 UMLS:C0009324 Colitis ulcerosa Ulcerative colitis A chronic granulomatous inflammatory disease of the intestines that may affect any part of the gastrointestinal tract from mouth to anus, causing a wide variety of symptoms. It primarily causes abdominal pain, diarrhea which may be bloody, vomiting, or weight loss, but may also cause complications outside of the gastrointestinal tract such as skin rashes, arthritis, inflammation of the eye, tiredness, and lack of concentration. Crohn's disease is thought to be an autoimmune disease, in which the body's immune system attacks the gastrointestinal tract, causing inflammation. SNOMEDCT_US:34000006 UMLS:C0010346 Granulomatous enteritis and colitis Morbus Crohn Crohn's disease A chronic inflammatory disease of the large intestine (colon, cecum and rectum). SNOMEDCT_US:54597004 UMLS:C0267375 Chronic colitis Immunological states where the immune system produces harmful responses upon reexposure to sensitizing antigens. UMLS:C0237653 Immunologic hypersensitivity Inflammation of the eye, parts of the eye or the periorbital region. HP:0007891 UMLS:C4020969 Inflammatory abnormality of the eye Ocular inflammation Inflammatory abnormality of the eye Abnormal cognition is characterized by deficits in thinking, reasoning, or remembering. HP:0002128 HP:0002129 HP:0002302 HP:0002337 HP:0002441 HP:0006972 HP:0006998 HP:0007211 SNOMEDCT_US:386806002 UMLS:C0338656 UMLS:C0683322 Abnormality of cognition Cognitive abnormality Cognitive defects Cognitive deficits Cognitive impairment Intellectual impairment An individual with cognitive impairment may experience difficulties in remembering, learning new things, concentrating, or making decisions. Cognitive impairment An abnormality of the forebrain, which has as its parts the telencephalon, diencephalon, lateral ventricles and third ventricle. UMLS:C4020967 Abnormal shape of forebrain Abnormality of forebrain morphology Abnormality of the forebrain Abnormal forebrain morphology Death between the age of 16 and 40 years. UMLS:C4022012 Death in early adulthood Death in early adulthood A chronic condition in which the pancreas produces little or no insulin. Type I diabetes mellitus is manifested by the sudden onset of severe hyperglycemia with rapid progression to diabetic ketoacidosis unless treated with insulin. SNOMEDCT_US:46635009 UMLS:C0011854 Diabetes mellitus Type I Juvenile diabetes mellitus Type 1 diabetes Type I diabetes The onset of type 1 diabetes is typically during adolescence, but it can develop at any age. Type I diabetes mellitus An anomaly of the cerebral blood vessels. UMLS:C4022001 Abnormality of the cerebral blood vessels Abnormality of the cerebral vasculature Abnormal cerebral vascular morphology Abnormal eating habits involve excessive or insufficient consumption of food, or any other abnormal pattern of food consumption. UMLS:C4021982 Abnormal eating behavior Abnormal eating behaviour Please note that this HPO term refers to an abnormal eating habit but does not directly refer to an eating disorder. An eating disorder is a psychological disorder characterized by one or more abnormal eating behaviors. Abnormal eating behavior An unpleasant sensation characterized by physical discomfort (such as pricking, throbbing, or aching) localized to the chest. SNOMEDCT_US:29857009 UMLS:C0008031 Chest pain Thoracic pain Chest pain UMLS:C4021978 Abnormal spit Abnormality of salivation Abnormality of salivation An anomaly of the lymphatic system, a network of lymphatic vessels that carry a clear fluid called lymph unidirectionally towards either the right lymphatic duct or the thoracic duct, which in turn drain into the right and left subclavian veins respectively. HP:0003012 SNOMEDCT_US:111590001 SNOMEDCT_US:234087005 SNOMEDCT_US:3305006 SNOMEDCT_US:362971004 UMLS:C0024228 UMLS:C4021976 Abnormality of the lymphatic system Systemic inflammatory response to infection. UMLS:C0036690 Infection in blood stream Sepsis Emotions are complex psychological states that involve three distinct components: a subjective experience, a physiological response, and a behavioral or expressive response. In an abnormal emotional state, an affected individual shows altered intensity, frequency, or duration of emotional experiences. UMLS:C4020949 Abnormal emotion processing Abnormal emotion/affect behavior Abnormal emotion/affect behaviour Abnormal mood/emotion/affect Abnormal mood/emotion/affect/thought Emotion dysregulation When one is assessing whether an individual has an Abnormal emotional state, emphasis should be placed on the observed clinical phenomena and subjective perceptions of the person, without regard to interpretation of the possibility of causality or context. Abnormal emotional state A small elevation of the skin containing cloudy or purulent material usually consisting of necrotic inflammatory cells. MEDDRA:10037578 SNOMEDCT_US:103605005 SNOMEDCT_US:271760008 SNOMEDCT_US:285305004 SNOMEDCT_US:47002008 UMLS:C0241157 UMLS:C0542346 Pimple Pustula Pustular lesion Pustules Skin pustule Skin pustules Pustule Any structural anomaly of the bile-secreting organ that is important for detoxification, for fat, carbohydrate, and protein metabolism, and for glycogen storage. Fyler:4447 Abnormal liver morphology Onset of disease manifestations before adulthood, defined here as before the age of 16 years, but excluding neonatal or congenital onset. Onset before adulthood Paediatric onset Pediatric onset A heterogeneous group of symptoms that are localized in the epigastric region. Typical dyspeptic symptoms include postprandial fullness, early satiation, epigastric pain and epigastric burning, but other upper gastrointestinal symptoms such as nausea, belching or abdominal bloating often occur. Indigestion Dyspepsia An abnormality of carbon dioxide (CO2) in the arterial blood. Abnormal CO2 levels in blood Abnormal blood carbon dioxide level Abnormal blood carbon dioxide level An abnormality of the partial pressure of oxygen in the arterial blood. Abnormal O2 blood concentration Abnormal blood O2 level Abnormal blood oxygen levels Abnormal blood oxygen level The presence of any atypical form of expressive language. Abnormal language feature A repeating behavior that is either immediately unproductive or has negative long-term consequences. This includes harmful coping mechanisms such as addictive behavior and failure to control impulses and compulsions. Recurrent maladaptive behavior Repetitive air swallowing and belching and that may result in abdominal distention. Aerophagia An increase in the gas content inside the bowel associated with distension of the abdomen and hydroaeric noises. The most common symptom of meteorism is a bloated sensation. It may be associated with abdominal discomfort. Some individuals may also complain of a distended stomach and excessive belching and/or passage of flatus. Meteorism Abnormal bowel sounds of an unually high frequency. This finding is characteristic of Ogilvie syndrome. High-pitched bowel sounds A directive information that describes how population units will be chosen for sample/data collection in a surveillance activity. https://github.com/SVA-SE/AHSURED/wiki/Description-of-surveillance-items-in-the-checklist https://www.fp7-risksur.eu/terminology/glossary Describe how units have been planned to be sampled Sampling at the primary sampling unit (PSU) level Describe the information used to calculate sample size at the PSU level, e.g. the number of PSU in the population (see section 6 also), (between−herd) design prevalence, desired confidence, desired power, sensitivity, specificity. If recommended parameters from international standards are used, indicate the source of such standards (e.g. OIE) Sampling at the secondary sampling unit (SSU) level Describe the information used to calculate sample size at the SSU level, e.g. the number of SSU in the population (see section 6 also), (within−herd) design prevalence, desired confidence, desired power, sensitivity, specificity. sampling strategy measurement unit label A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure. 2009-03-16: provenance: a term measurement unit was proposed for OBI (OBI_0000176) , edited by Chris Stoeckert and Cristian Cocos, and subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definition of this, different, term. 2009-03-16: review of this term done during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI. PERSON: Alan Ruttenberg PERSON: Melanie Courtot measurement unit label objective specification A directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved. 2009-03-16: original definition when imported from OBI read: "objective is an non realizable information entity which can serve as that proper part of a plan towards which the realization of the plan is directed." 2014-03-31: In the example of usage ("In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction") there is a protocol which is the ChIP assay protocol. In addition to being concretized on paper, the protocol can be concretized as a realizable entity, such as a plan that inheres in a person. The objective specification is the part that says that some protein and DNA interactions are identified. This is a specification of a process endpoint: the boundary in the process before which they are not identified and after which they are. During the realization of the plan, the goal is to get to the point of having the interactions, and participants in the realization of the plan try to do that. Answers the question, why did you do this experiment? PERSON: Alan Ruttenberg PERSON: Barry Smith PERSON: Bjoern Peters PERSON: Jennifer Fostel goal specification OBI Plan and Planned Process/Roles Branch OBI_0000217 objective specification A directive information entity that describes an action the bearer will take. Alan Ruttenberg OBI Plan and Planned Process branch action specification datum label A label is a symbol that is part of some other datum and is used to either partially define the denotation of that datum or to provide a means for identifying the datum as a member of the set of data with the same label http://www.golovchenko.org/cgi-bin/wnsearch?q=label#4n GROUP: IAO datum label software Software is a plan specification composed of a series of instructions that can be interpreted by or directly executed by a processing unit. see sourceforge tracker discussion at http://sourceforge.net/tracker/index.php?func=detail&aid=1958818&group_id=177891&atid=886178 PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Chris Stoeckert PERSON: Melanie Courtot GROUP: OBI software data item data item An information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements. a data item is an information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements. 2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers. 2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum. 2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym. 2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/ JAR: datum -- well, this will be very tricky to define, but maybe some information-like stuff that might be put into a computer and that is meant, by someone, to denote and/or to be interpreted by some process... I would include lists, tables, sentences... I think I might defer to Barry, or to Brian Cantwell Smith JAR: A data item is an approximately justified approximately true approximate belief PERSON: Alan Ruttenberg PERSON: Alan Ruttenberg PERSON: Chris Stoeckert PERSON: Chris Stoeckert PERSON: Jonathan Rees PERSON: Jonathan Rees data data item symbol An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity. 20091104, MC: this needs work and will most probably change 2014-03-31: We would like to have a deeper analysis of 'mark' and 'sign' in the future (see https://github.com/information-artifact-ontology/IAO/issues/154). PERSON: James A. Overton PERSON: Jonathan Rees based on Oxford English Dictionary symbol numeral A symbol that denotes a number. PERSON: Jonathan Rees numeral information content entity A generically dependent continuant that is about some thing. An information entity is an entity that represents information about some other entity. For example, a measurement, a clustered data set. an information content entity is an entity that is generically dependent on some artifact and stands in relation of aboutness to some entity 2014-03-10: The use of "thing" is intended to be general enough to include universals and configurations (see https://groups.google.com/d/msg/information-ontology/GBxvYZCk1oc/-L6B5fSBBTQJ). information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907). Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity. James Malone PERSON: Chris Stoeckert PERSON: Chris Stoeckert OBI_0000142 OBI_0000142 information content entity information information content entity information entity integer numeral A numeral that denotes an integer PERSON: Jonathan Rees integer numeral scalar measurement datum A scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label. a scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label. 2009-03-16: we decided to keep datum singular in scalar measurement datum, as in this case we explicitly refer to the singular form Would write this as: has_part some 'measurement unit label' and has_part some numeral and has_part exactly 2, except for the fact that this won't let us take advantage of OWL reasoning over the numbers. Instead use has measurment value property to represent the same. Use has measurement unit label (subproperty of has_part) so we can easily say that there is only one of them. PERSON: Alan Ruttenberg PERSON: Melanie Courtot scalar measurement datum An information content entity whose concretizations indicate to their bearer how to realize them in a process. 2009-03-16: provenance: a term realizable information entity was proposed for OBI (OBI_0000337) , edited by the PlanAndPlannedProcess branch. Original definition was "is the specification of a process that can be concretized and realized by an actor" with alternative term "instruction".It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term. 2013-05-30 Alan Ruttenberg: What differentiates a directive information entity from an information concretization is that it can have concretizations that are either qualities or realizable entities. The concretizations that are realizable entities are created when an individual chooses to take up the direction, i.e. has the intention to (try to) realize it. 8/6/2009 Alan Ruttenberg: Changed label from "information entity about a realizable" after discussions at ICBO Werner pushed back on calling it realizable information entity as it isn't realizable. However this name isn't right either. An example would be a recipe. The realizable entity would be a plan, but the information entity isn't about the plan, it, once concretized, *is* the plan. -Alan PERSON: Alan Ruttenberg PERSON: Bjoern Peters directive information entity curation status specification The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting) PERSON:Bill Bug GROUP:OBI:<http://purl.obolibrary.org/obo/obi> OBI_0000266 curation status specification data set A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets. 2009/10/23 Alan Ruttenberg. The intention is that this term represent collections of like data. So this isn't for, e.g. the whole contents of a cel file, which includes parameters, metadata etc. This is more like java arrays of a certain rather specific type 2014-05-05: Data sets are aggregates and thus must include two or more data items. We have chosen not to add logical axioms to make this restriction. person:Allyson Lister person:Chris Stoeckert OBI_0000042 group:OBI data set data about an ontology part Data about an ontology part is a data item about a part of an ontology, for example a term Person:Alan Ruttenberg data about an ontology part plan specification A directive information entity with action specifications and objective specifications as parts, and that may be concretized as a realizable entity that, if realized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified. 2009-03-16: provenance: a term a plan was proposed for OBI (OBI_0000344) , edited by the PlanAndPlannedProcess branch. Original definition was " a plan is a specification of a process that is realized by an actor to achieve the objective specified as part of the plan". It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term. 2014-03-31: A plan specification can have other parts, such as conditional specifications. 2022-01-16 Updated definition to that proposed by Clint Dowloand, IAO Issue 231. Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved Alan Ruttenberg Clint Dowland OBI Plan and Planned Process branch OBI_0000344 2/3/2009 Comment from OBI review. Action specification not well enough specified. Conditional specification not well enough specified. Question whether all plan specifications have objective specifications. Request that IAO either clarify these or change definitions not to use them plan specification measurement datum A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device. 2/2/2009 is_specified_output of some assay? person:Chris Stoeckert OBI_0000305 group:OBI http://www.ebi.ac.uk/efo/EFO_0001444 measurement datum A settings datum is a datum that denotes some configuration of an instrument. 2/3/2009 Feedback from OBI This should be a "setting specification". There is a question of whether it is information about a realizable or not. Pro other specification are about realizables. Cons sometimes specifies a quality which is not a realizable. Alan grouped these in placeholder for the moment. Name by analogy to measurement datum. setting datum textual entity A textual entity is a part of a manifestation (FRBR sense), a generically dependent continuant whose concretizations are patterns of glyphs intended to be interpreted as words, formulas, etc. AR, (IAO call 2009-09-01): a document as a whole is not typically a textual entity, because it has pictures in it - rather there are parts of it that are textual entities. Examples: The title, paragraph 2 sentence 7, etc. MC, 2009-09-14 (following IAO call 2009-09-01): textual entities live at the FRBR (http://en.wikipedia.org/wiki/Functional_Requirements_for_Bibliographic_Records) manifestation level. Everything is significant: line break, pdf and html versions of same document are different textual entities. PERSON: Lawrence Hunter text textual entity document part An information content entity that is part of a document. PERSON: Lawrence Hunter document part A scalar measurement datum that is the result of measurement of length quality Alan Ruttenberg length measurement datum A scalar measurement datum that is the result of measurement of mass quality 2009/09/28 Alan Ruttenberg. Fucoidan-use-case Person:Alan Ruttenberg mass measurement datum A scalar measurement datum that is the result of measuring a temporal interval 2009/09/28 Alan Ruttenberg. Fucoidan-use-case Person:Alan Ruttenberg Damion Dooley's note: See https://www.w3.org/TR/NOTE-datetime for ISO 8601 time standards time measurement datum email address Alan Ruttenberg 1/3/2012 - Provisional id, see issue at https://github.com/information-artifact-ontology/IAO/issues/130&thanks=130&ts=1325636583 Person:Alan Ruttenberg Person:Chris Stoeckart email address A symbol that is part of a CRID and that is sufficient to look up a record from the CRID's registry. PERSON: Alan Ruttenberg PERSON: Bill Hogan PERSON: Bjoern Peters PERSON: Melanie Courtot CRID symbol Original proposal from Bjoern, discussions at IAO calls Damion notes: Subclasses can actually have two components - the identifier, and the agency it is associated with. Under the general concept of "postal code" one can place particular national postal code systems like the US Postal code. centrally registered identifier symbol time stamped measurement datum A software application is software that can be directly executed by some processing unit. PERSON: Melanie Courtot PERSON: Michel Dumontier https://github.com/information-artifact-ontology/IAO/issues/80 software application notes section A part of a document containing typically short notes about the document itself and/or the authors. Often the notes section contains subsections related to funding, competing interests, ethical approval, etc. PERSON: Bill Baumgartner notes notes section 2020-04-24T22:38:17Z pregnant woman A pathogen host role borne by an organism in virtue of the fact that its extended organism contains an infectious agent. Albert Goldfain Alexander Diehl Lindsay Cowell By this definition, vectors and other organisms that may not be infected are bearers of the infectious agent host role. infectious agent host role A host role borne by an organism in virtue of the fact that its extended organism contains a pathogen. Albert Goldfain Alexander Diehl Lindsay Cowell Bearing the infectious agent host role implies bearing the pathogen host role, but the reverse is not true. See comment for infectious agent host role. pathogen host role An infectious agent host role borne by an organism in virtue of the fact that its extended organism contains an infectious agent, the infectious agent has the infectious disposition towards the host, and the host has no symptoms of the infectious disease caused by the infectious agent. Albert Goldfain Alexander Diehl Lindsay Cowell infectious agent carrier role A disposition that inheres in a material entity in virtue of the fact that the entity has a part (e.g. a gene product), which itself has a disposition to mitigate damage to the entity. Albert Goldfain Alexander Diehl Lindsay Cowell Examples include the following: CCR5 mutations protect T cells from HIV invasion. A tumor cell's resistance to chemotherapy protects the cell from damage by the drug (although this harms the patient). An insect's resistance to insecticide protects it from the insecticide. The disposition is realized in a process that mitigates damage to the bearer and has the part as a participant. protective resistance A protective resistance that mitigates the damaging effects of a drug. Albert Goldfain Alexander Diehl Lindsay Cowell drug resistance resistance to drug A disposition borne by an infectious agent that is the disposition to penetrate the epithelial barriers of an organism of another Species. Albert Goldfain Alexander Diehl Lindsay Cowell invasive disposition An infectious disease course that begins soon after infection is established and progresses rapidly to severe stages. Albert Goldfain Alexander Diehl Lindsay Cowell acute infectious disease course A disease course that is the realization of an infectious disease. Albert Goldfain Alexander Diehl Lindsay Cowell infectious disease course A chronic infectious disease course that does not progress to severe stages for a long period of time. Albert Goldfain Alexander Diehl Lindsay Cowell long-term non-progressing infectious disease course A process of infectious disease realizations and for which there is a statistically significant increase in the infectious disease incidence of a population. Albert Goldfain Alexander Diehl Lindsay Cowell infectious disease outbreak infectious disease epidemic An infection that is clinically abnormal. Albert Goldfain Alexander Diehl Lindsay Cowell infectious disorder An aggregate of organisms of the same Species. Albert Goldfain Alexander Diehl Lindsay Cowell The organism population may be delineated by spatio-temporal proximity or by demographic criteria such as age. organism population An organism population whose members have an infection. Albert Goldfain Alexander Diehl Lindsay Cowell infected population An organism population in whose members an infectious disease is being realized. Albert Goldfain Alexander Diehl Lindsay Cowell diseased population An organism population whose members each have an infectious disposition. Albert Goldfain Alexander Diehl Lindsay Cowell infectious agent population An organism population whose members are not infected with an infectious agent and who lack immunity to the infectious agent. Albert Goldfain Alexander Diehl Lindsay Cowell at-risk population susceptible population An organism population whose members are participating in non-parasitic symbiosis with a particular host. Albert Goldfain Alexander Diehl Lindsay Cowell normal resident microflora population normal resident microbiota population An organism bearing a host role. Albert Goldfain Alexander Diehl Lindsay Cowell host An organism bearing an infectious agent host role. Albert Goldfain Alexander Diehl Lindsay Cowell infectious agent host An organism bearing a pathogen host role. Albert Goldfain Alexander Diehl Lindsay Cowell pathogen host An organism bearing an infectious agent vector role. Albert Goldfain Alexander Diehl Lindsay Cowell infectious agent vector A material entity bearing an infectious agent vehicle role. Albert Goldfain Alexander Diehl Lindsay Cowell vehicle of infectious agent A biological macromolecule produced by a pathogen and that has a virulence factor disposition. Albert Goldfain Alexander Diehl Lindsay Cowell virulence factor An infection bearing the secondary infection role. Albert Goldfain Alexander Diehl Lindsay Cowell secondary infection An organism that is host to an infectious agent and has no symptoms of the infectious disease associated with the infectious agent. Albert Goldfain Alexander Diehl Lindsay Cowell asymptomatic host of infectious agent An organism who is host to an infectious agent and has symptoms of the infectious disease associated with the infectious agent Albert Goldfain Alexander Diehl Lindsay Cowell symptomatic host of infectious agent A resistance to drug that mitigates the damaging effects of an antibiotic. Albert Goldfain Alexander Diehl Lindsay Cowell antibiotic resistance A part of an extended organism that itself has as part a population of one or more infectious agents and that (1) exists as a result of processes initiated by members of the infectious agent population and is (2) clinically abnormal in virtue of the presence of this infectious agent population, or (3) has a disposition to bring clinical abnormality to immunocompetent organisms of the same Species as the host (the organism corresponding to the extended organism) through transmission of a member or offspring of a member of the infectious agent population. Albert Goldfain Alexander Diehl Lindsay Cowell The organism corresponding to the extended organism is host to the infectious agents. By this definition, parts of the host can be considered part of the infection. infection An infectious disease course that unfolds over a long period of time. Albert Goldfain Alexander Diehl Lindsay Cowell persistent infectious disease course chronic infectious disease course An organism population whose members have acquired immunity to an infectious agent. Albert Goldfain Alexander Diehl Lindsay Cowell immune population An organism population persisting in a site it has colonized. Albert Goldfain Alexander Diehl Lindsay Cowell colony A colony whose members are infectious agents. Albert Goldfain Alexander Diehl Lindsay Cowell infectious agent colony A role borne by an organism in virtue of the fact that it's extended organism contains a material entity other than the organism. Albert Goldfain Alexander Diehl Lindsay Cowell host role A process that is a systemic inflammatory response to infection. Albert Goldfain Alexander Diehl Lindsay Cowell sepsis An organism that is not infected with an infectious agent and lacks protective immunity to the infectious agent. Alex Diehl Lindsay Cowell susceptible organism domestic animal that bears a food production role. YL Livestock refers to one or more domesticated animals raised in an agricultural setting to produce commodities such as food, fiber and labor. The term "livestock" as used in this article does not include poultry or farmed fish; however the inclusion of these, especially poultry, within the meaning of "livestock" is common. (http://en.wikipedia.org/wiki/Livestock) livestock http://www.ontobee.org/ontology/MI data source Database that originally provided the interaction record for exchange purposes. PMID:14755292 Damion Dooley's note: GenEpiO is using members of this class for the first part of the hasDbXref relation. This is where we are keeping the mapping between a code and its source database. Depending on its context, hasDbXref annotations may point directly to metadata field names in the target database, and may be annotated with additional information that guides any additional specifications that impact on data conversion of these fields. source database The manner, procedure or technique by which a morphological or physiological state or property in a single individual or sample or a group of individuals or samples is assessed and a quantitative or qualitative value assigned. measurement method A postmortem examination of a body to determine the cause of death or the character and extent of changes produced by disease. autopsy tissue collection (necropsy) A postmortem examination of the body of an animal to determine the cause of death or the character and extent of changes produced by disease. A postmortem examination of the body of an animal to determine the cause of death or the character and extent of changes produced by disease. [database_cross_reference: Merriam-Webster:Merriam-Websters_Online_Dictionary--11th_Ed] necropsy necropsy A disease is a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism. DOID:4 ICD9:799.9 MEDGEN:4347 MESH:D004194 NCIT:C2991 OGMS:0000031 Orphanet:377788 SCTID:64572001 UMLS:C0012634 condition disease disease or disorder disease or disorder, non-neoplastic diseases diseases and disorders disorder disorders medical condition other disease disease A disease involving the lower respiratory tract. DOID:0050161 EFO:0009433 ICD9:478.1 ICD9:478.19 MEDGEN:712703 SCTID:128272009 UMLS:C1290325 disease of lower respiratory tract disease or disorder of lower respiratory tract disorder of lower respiratory tract lower respiratory tract disease lower respiratory tract disease or disorder lower respiratory tract disorder DOID:0050338 primary bacterial infectious disease A malignant neoplasm involving the respiratory system DOID:0050615 ICD9:165.8 ICD9:165.9 MEDGEN:756863 SCTID:449096009 UMLS:C3164456 cancer of respiratory system malignant neoplasm of respiratory system malignant respiratory system neoplasm respiratory system cancer respiratory system cancer A monogenic disease that is has material basis in a mutation in a single gene on one of the non-sex chromosomes. DOID:0050739 ICD9:758.5 MEDGEN:539205 SCTID:1899006 UMLS:C0265384 autosomal hereditary disorder autosomal inherited disease autosomal inherited disorder autosomal genetic disease A hypersensitivity reaction type II disease that involves the peripheral nervous system. DOID:0060033 peripheral nervous system autoimmune disease peripheral nervous system hypersensitivity reaction type II disease autoimmune disorder of peripheral nervous system Life-threatening respiratory failure that develops rapidly. Causes include injury, sepsis, drug overdose, and pancreatitis. It manifests with dyspnea and cyanosis and may lead to cardiovascular shock. ICD9:518.81 MEDGEN:75540 NCIT:C27043 SCTID:65710008 UMLS:C0264490 icd11.foundation:875272781 acute respiratory failure respiratory failure, acute acute respiratory failure A disorder characterized by behavioral and/or psychological abnormalities, often accompanied by physical symptoms. The symptoms may cause clinically significant distress or impairment in social and occupational areas of functioning. Representative examples include anxiety disorders, cognitive disorders, mood disorders and schizophrenia. DOID:150 MESH:D001523 MFOMD:0000004 NCIT:C2893 SCTID:74732009 Psychiatric disease Psychiatric disorder disease of mental health mental disorder mental dysfunction mental illness psychiatric disorder A non-neoplastic or neoplastic disorder that affects the pleura. Representative examples include pleural infection, pleural mesothelioma, and pleural solitary fibrous tumor. DOID:1532 ICD9:518.89 MEDGEN:10804 MESH:D010995 NCIT:C26859 SCTID:88075009 UMLS:C0032226 disease of pleura disease or disorder of pleura disorder of pleura pleura disease pleura disease or disorder pleural disorder pleural disorders non-neoplastic pleural disease pleural disorder The use of alcoholic beverages to excess, either on individual occasions ("binge drinking") or as a regular practice. DOID:1574 ICD9:305.0 ICD9:305.00 MEDGEN:39339 MESH:D000437 SCTID:15167005 UMLS:C0085762 alcohol abuse ethanol abuse alcohol abuse Acute or chronic inflammation of one or more lymph nodes. It is usually caused by an infectious process. DOID:1602 HP:0002840 ICD9:289.1 ICD9:683 MEDGEN:7410 MESH:D008199 NCIT:C26821 SCTID:41174002 UMLS:C0024205 icd11.foundation:1483611415 Inflammation of lymph node adenitis inflammation of lymph node lymph node inflammation lymph nodeitis lymphadenitis lymphadenitis (disease) acute adenitis acute lymphadenitis chronic adenitis chronic lymphadenitis lymphadenitis DOID:1672 ICD10CM:J93.0 ICD9:512.0 MEDGEN:510132 SCTID:196102003 UMLS:C0155907 icd11.foundation:304972724 spontaneous tension pneumothorax Abnormal presence of air in the pleural cavity. DOID:1673 HP:0002107 ICD9:512.8 MEDGEN:19365 MESH:D011030 NCIT:C38006 SCTID:36118008 UMLS:C0032326 icd11.foundation:1946559257 pneumothorax pneumothorax (disease) pneumothorax A disease involving the musculoskeletal system. DOID:17 EFO:0009676 ICD9:729.99 MEDGEN:6471 MESH:D009140 NCIT:C107377 SCTID:928000 UMLS:C0026857 disease of musculoskeletal system disease or disorder of musculoskeletal system disorder of musculoskeletal system musculoskeletal disease musculoskeletal system disease musculoskeletal system disease or disorder musculoskeletal system disorder musculoskeletal system disorder A disease involving the renal system. DOID:18 EFO:0009690 ICD9:V47.4 MEDGEN:21791 MESH:D014570 NCIT:C3430 SCTID:128606002 UMLS:C0042075 disease of renal system disease or disorder of renal system disease, urinary tract disease, urologic disease, urological diseases, urinary tract diseases, urologic diseases, urological disorder of renal system disorder of the urinary system disorder of urinary system non-neoplastic urinary tract disease renal system disease renal system disease or disorder urinary disease urinary system disease urinary system disorder urinary tract disease urinary tract diseases urinary tract disorder urologic disease urologic disorder urological disease urological diseases urological disorder urological disorders urinary system disorder A group of signs, symptoms, and clinicopathological characteristics that may or may not have a genetic basis and collectively define an abnormal condition. DOID:225 MEDGEN:11688 MESH:D013577 NCIT:C28193 OGMS:0000086 UMLS:C0039082 cluster, symptom clusters, symptom symptom cluster symptom clusters syndrome syndrome associated with disease or disorder syndromes syndromic disease syndromic disease or disorder syndromic disease The use of a drug for a reason other than which it was intended or in a manner or in quantities other than directed. DOID:302 ICD9:305.90 MEDGEN:152849 SCTID:66214007 UMLS:C0740858 substance abuse A category of psychiatric disorders which include disorders related to the taking of a drug of abuse (including alcohol, prescribed medications and recreational drugs). DOID:303 ICD10CM:F10-F19 MEDGEN:66746 MESH:D019966 NCIT:C92203 UMLS:C0236969 substance induced mood disorders substance-related disorder substance-related disorder A non-neoplastic or neoplastic disorder that affects the liver, bile ducts, and gallbladder. Representative examples of non-neoplastic disorders include hepatitis, cirrhosis, cholangitis, and cholecystitis. Representative examples of neoplastic disorders include hepatocellular adenoma, hepatocellular carcinoma, and cholangiocarcinoma. DOID:3118 EFO:0010284 MEDGEN:82758 NCIT:C3959 UMLS:C0267792 disease of hepatobiliary system disease or disorder of hepatobiliary system disorder of hepatobiliary system hepatobiliary disorder hepatobiliary system disease hepatobiliary system disease or disorder liver and biliary disease liver and biliary disorder liver and biliary system disorder liver and biliary tract disease hepatobiliary disorder A primary or metastatic malignant neoplasm involving any part of the digestive system. GI tumor GI tumour DOID:3119 ICD10CM:C15-C26 ICD9:239.0 MEDGEN:148231 NCIT:C4890 UMLS:C0751075 cancer of digestive system digestive system cancer gastrointestinal system cancer gastrointestinal tract cancer malignant digestive system neoplasm malignant gastrointestinal neoplasm malignant gastrointestinal system neoplasm malignant neoplasm of digestive system digestive system cancer A disease involving the central nervous system. DOID:331 EFO:0009386 MEDGEN:892343 MESH:D002493 NCIT:C2934 SCTID:23853001 UMLS:C4021765 CNS disorder central nervous disease central nervous system disease central nervous system disease or disorder central nervous system disorder disease of central nervous system disease of the central nervous system disease or disorder of central nervous system disorder of central nervous system central nervous system disorder A disease involving the breast. DOID:3463 EFO:0009483 ICD10CM:N60-N65 ICD9:610-612.99 ICD9:611.8 ICD9:611.9 MEDGEN:652 MESH:D001941 NCIT:C26709 SCTID:79604008 UMLS:C0006145 breast disease breast disease or disorder breast diseases breast disorder disease of breast disease or disorder of breast disorder of breast breast disorder A disorder characterized by the degeneration of the nervous system due to autoimmunity. Representative examples include multiple sclerosis, Guillain-Barre syndrome, and myasthenia gravis. DOID:438 MEDGEN:155946 MESH:D020274 NCIT:C99383 UMLS:C0751871 autoimmune disease of nervous system autoimmune disease, neurologic autoimmune diseases, nervous system autoimmune diseases, neurologic autoimmune disorders of the nervous system autoimmune disorders, nervous system autoimmune nervous system diseases autoimmune nervous system disorder disease, neurologic autoimmune diseases, neurologic autoimmune immune diseases, nervous system immune disorders, nervous system nervous system autoimmune disease nervous system autoimmune diseases nervous system hypersensitivity reaction type II disease nervous system immune diseases nervous system immune disorders neurologic autoimmune disease neurologic autoimmune diseases autoimmune disorder of the nervous system A primary or metastatic malignant neoplasm affecting the tissues of the thorax. thoracic tumor thoracic tumour thorax neoplasm tumor of thorax tumour of thorax DOID:5093 ICD9:195.1 MEDGEN:56320 NCIT:C3576 SCTID:188361007 UMLS:C0153661 cancer of thoracic segment of trunk malignant neoplasm of the thorax malignant neoplasm of thoracic segment of trunk malignant neoplasm of thorax malignant thoracic neoplasm malignant thoracic segment of trunk neoplasm malignant thoracic tumor malignant thoracic tumour malignant tumor of the thorax malignant tumor of thorax malignant tumour of the thorax malignant tumour of thorax thoracic segment of trunk cancer thorax cancer thoracic cancer Vasculitis affecting the blood vessels of the brain and/or spinal cord. DOID:525 MEDGEN:148408 MESH:D020293 NCIT:C84622 UMLS:C0751878 central nervous system vasculitis vasculitis of central nervous system central nervous system vasculitis A disease involving the peripheral nervous system. DOID:574 EFO:0009387 ICD9:350-359.99 ICD9:356.9 MEDGEN:892389 MESH:D010523 NCIT:C27580 SCTID:42658009 UMLS:C4025831 PNS (peripheral nervous system) diseases PNS disease PNS diseases disease of peripheral nervous system disease or disorder of peripheral nervous system disorder of peripheral nervous system disorder of the peripheral nervous system peripheral nervous system disease peripheral nervous system disease or disorder peripheral nervous system disorder peripheral nervous system disorders nerve disease, peripheral nerve diseases, peripheral neuropathy, peripheral peripheral Neuropathies peripheral nerve disease peripheral nerve diseases peripheral neuropathy peripheral nervous system disorder A broad classification of disorders that affect the cell-mediated aspect of the immune response. Circulating numbers of T lymphocytes are decreased or ineffective. DOID:613 MEDGEN:226894 NCIT:C27145 SCTID:402792003 UMLS:C1274233 T-cell immunodeficiency T-lymphocyte deficiency (finding) T-lymphocyte immunodeficiency T-cell immunodeficiency A disease that is caused by genetic modifications where those modifications are inherited from a parent's genome. genetic condition genetic disease genetic disorder DOID:630 EFO:0000508 ICD9:799.89 MEDGEN:5527 MESH:D030342 NCIT:C3101 SCTID:32895009 UMLS:C0019247 hereditary disease hereditary disease or disorder hereditary diseases inherited disease inherited genetic disease molecular disease Mendelian disease Usage note: this is intended only for diseases with an inherited genetic etiology. Somatic genetic mutations are excluded. Some ontologies use the term 'genetic disease' in the sense of inherited disorders only, we are here careful to distinguish. hereditary disease A disease involving the connective tissue. DOID:65 EFO:1001986 MEDGEN:1098 MESH:D003240 NANDO:2100172 NCIT:C26729 SCTID:105969002 UMLS:C0009782 connective tissue disease connective tissue disease or disorder connective tissue diseases connective tissue disorder connective tissue disorders disease of connective tissue disease or disorder of connective tissue disease, connective tissue disorder of connective tissue primary disorder of connective tissue tissue disease, connective Following clinical usage of the term 'connective tissue disorder' this grouping excludes some diseases affecting tissues classically considered to be connective tissue, such as bone. connective tissue disorder An imbalanced nutritional status resulting from excessive intake of nutrients. Generally, overnutrition generates an energy imbalance between food consumption and energy expenditure leading to disorders such as obesity. DOID:654 ICD9:278.8 MEDGEN:219760 MESH:D044343 SCTID:302872003 UMLS:C1257763 overnutrition A disease involving the muscle tissue. DOID:0080000 DOID:66 ICD10CM:M60-M63 MESH:D009135 disease of muscle organ disease of muscle tissue disease or disorder of muscle organ disease or disorder of muscle tissue disorder of muscle organ disorder of muscle tissue muscle organ disease muscle organ disease or disorder muscle tissue disease muscle tissue disease or disorder muscular disorder muscle tissue disorder A disease or disorder that involves the digestive system. DOID:77 ICD10CM:K00-K95 ICD9:520-579.99 ICD9:V47.3 MEDGEN:892790 MESH:D005767 NANDO:1100013 NCIT:C2990 SCTID:53619000 UMLS:C4023588 alimentary system disease digestive disease digestive system disease digestive system disease or disorder digestive system disorder disease of digestive system disease or disorder of digestive system disorder of digestive system gastroenterological system disease gastroenterological system disorder gastroenteropathy gastrointestinal disease gastrointestinal disorder gastrointestinal system disease gastrointestinal system disorder git disease stomach or intestinal disorder digestive system disorder An autoimmune, connective tissue chronic inflammatory disorder affecting the skin, joints, kidneys, lungs, heart, and the peripheral blood cells. It is more commonly seen in women than men. Variants include discoid and systemic lupus erythematosus. DOID:8857 ICD10CM:L93 ICD9:695.4 MEDGEN:98043 NCIT:C27153 SCTID:200936003 UMLS:C0409974 icd11.foundation:1443317238 lupus lupus erythematosus lupus erythematosus Necrosis of the myocardium, as a result of interruption of the blood supply to the area. It is characterized by a severe and rapid onset of symptoms that may include chest pain, often radiating to the left arm and left side of the neck, dyspnea, sweating, and palpitations. DOID:9408 EFO:0008583 ICD10CM:I21.9 ICD9:410 ICD9:410.80 ICD9:410.81 ICD9:410.82 ICD9:410.9 ICD9:410.90 ICD9:410.91 ICD9:410.92 MEDGEN:57611 NCIT:C35204 SCTID:57054005 UMLS:C0155626 icd11.foundation:1334938734 acute myocardial infarction (disease) myocardial infarction (disease), acute acute myocardial infarction Any disorder of the lymph nodes. DOID:9942 MEDGEN:78802 NCIT:C35346 SCTID:76616003 UMLS:C0272394 disease of lymph node disease or disorder of lymph node disorder of lymph node lymph node disease lymph node disease or disorder lymph node disorder lymph node disorder A tumor composed of atypical neoplastic, often pleomorphic cells that invade other tissues. Malignant neoplasms often metastasize to distant anatomic sites and may recur after excision. The most common malignant neoplasms are carcinomas (adenocarcinomas or squamous cell carcinomas), Hodgkin and non-Hodgkin lymphomas, leukemias, melanomas, and sarcomas. DOID:0050686 DOID:0050687 DOID:162 ICD9:195.8 ICD9:199 ICD9:199.1 ICDO:8000/3 MEDGEN:14297 NCIT:C9305 NIFSTD:birnlex_406 ONCOTREE:MT SCTID:363346000 UMLS:C0006826 CA cancer cell type cancer malignancy malignant growth malignant neoplasm malignant neoplasm (disease) malignant neoplastic disease malignant tumor malignant tumour neoplasm (disease), malignant neoplasm, malignant primary cancer cancer A disease involving the cardiovascular system. DOID:1287 EFO:0000319 ICD9:390-459.99 ICD9:420-429.99 ICD9:423 ICD9:423.8 ICD9:424 ICD9:429 ICD9:429.2 ICD9:429.7 ICD9:429.8 ICD9:429.81 ICD9:429.89 ICD9:459.89 ICD9:459.9 MEDGEN:2848 MESH:D002318 NANDO:1100005 NCIT:C2931 SCTID:49601007 UMLS:C0007222 cardiovascular disease cardiovascular disease (CVD) cardiovascular disorder cardiovascular system disease cardiovascular system disease or disorder disease of cardiovascular system disease of subdivision of hemolymphoid system disease or disorder of cardiovascular system disorder of cardiovascular system cardiovascular disorder A non-neoplastic or neoplastic disorder that affects the small or large intestine. DOID:5295 EFO:0009431 ICD9:520-579.99 ICD9:560-569.99 ICD9:564 ICD9:564.4 ICD9:569 ICD9:569.4 ICD9:569.49 ICD9:569.89 ICD9:569.9 ICD9:570-579.99 ICD9:575 MEDGEN:7130 MESH:D007410 NCIT:C26801 SCTID:85919009 UMLS:C0021831 disease of intestine disease or disorder of intestine disorder of intestine intestinal disease intestinal disorder intestine disease intestine disease or disorder intestinal disorder A brain disorder characterized by episodes of abnormally increased neuronal discharge resulting in transient episodes of sensory or motor neurological dysfunction, or psychic dysfunction. These episodes may or may not be associated with loss of consciousness or convulsions. DOID:1826 EFO:0000474 ICD10CM:G40 ICD10WHO:G40 ICD9:345 ICD9:345.8 ICD9:345.80 ICD9:345.9 ICD9:345.90 ICD9:345.91 MEDGEN:4506 MESH:D004827 NCIT:C3020 NIFSTD:birnlex_12718 SCTID:84757009 UMLS:C0014544 epilepsy seizure disorder epilepsy A disease involving the reproductive system. DOID:15 EFO:0000512 MEDGEN:61253 NCIT:C4875 SCTID:362968007 UMLS:C0178829 Wikipedia:Reproductive_system_disease disease of reproductive system disease or disorder of reproductive system disorder of reproductive system genital disorders genital system disease reproductive disease reproductive system disease reproductive system disease or disorder reproductive system disorder reproductive system disorder A disorder resulting from an abnormality in the immune system. DOID:2914 EFO:0000540 ICD9:279 ICD9:279.1 ICD9:279.10 ICD9:279.19 ICD9:279.4 ICD9:279.49 ICD9:279.8 ICD9:279.9 MEDGEN:5759 MESH:D007154 NANDO:1100004 NANDO:2100202 NCIT:C3507 SCTID:414029004 UMLS:C0021053 disease of immune system disease or disorder of immune system disorder of immune system immune disease immune disorder immune dysfunction immune system disease or disorder immune system disorder immune system disorder Gross necrosis of the myocardium, as a result of interruption of the blood supply to the area, as in coronary thrombosis. DOID:5844 EFO:0000612 HP:0001658 ICD10CM:I21 MEDGEN:10150 MESH:D009203 NANDO:2200248 NCIT:C27996 SCTID:22298006 UMLS:C0027051 MI MI, myocardial infarction heart attack infarction (MI), myocardial myocardial infarct myocardial infarction myocardial infarction (disease) myocardial infarction, (MI) myocardial infarction A benign or malignant tissue growth resulting from uncontrolled cell proliferation. Benign neoplastic cells resemble normal cells without exhibiting significant cytologic atypia, while malignant cells exhibit overt signs such as dysplastic features, atypical mitotic figures, necrosis, nuclear pleomorphism, and anaplasia. Representative examples of benign neoplasms include papillomas, cystadenomas, and lipomas; malignant neoplasms include carcinomas, sarcomas, lymphomas, and leukemias. cell process disease DOID:14566 EFO:0000616 HP:0002664 ICD10CM:C00-D49 ICD10CM:C7A-C7A ICD10CM:C7B-C7B ICD9:140-239.99 ICD9:239.8 ICD9:239.9 MEDGEN:10294 MESH:D009369 NCIT:C3262 ONCOTREE:OTHER SCTID:55342001 UMLS:C0027651 disease of cellular proliferation neoplasia neoplasm neoplasm (disease) neoplastic disease neoplastic growth tumor tumor disease tumour tumour disease other neoplasm neoplasm A non-neoplastic or neoplastic disorder that affects the brain, spinal cord, or peripheral nerves. DOID:863 EFO:0000618 ICD10CM:G00-G99 ICD9:349.89 ICD9:349.9 MEDGEN:14336 MESH:D009422 NCIT:C26835 SCTID:118940003 UMLS:C0027765 Wikipedia:Nervous_system_disease disease of nervous system disease or disorder of nervous system disorder of nervous system nervous system disease nervous system disease or disorder nervous system disorder neurologic disease neurologic disorder neurological disease neurological disorder 'psychiatric disorder' is not classified as a 'nervous system disorder' in Mondo (though it is often as such): the hallmarks of psychiatric disorders are based in behavior and emotional state, and the relation with nervous system malfunction or damage is not always clearly determined. nervous system disorder A non-neoplastic or neoplastic disorder that affects the respiratory system. Representative examples include pneumonia, chronic obstructive pulmonary disease, pulmonary failure, lung adenoma, lung carcinoma, and tracheal carcinoma. DOID:1579 EFO:0000684 ICD10CM:J00-J99 ICD9:460-519.99 ICD9:500-508.99 ICD9:503 ICD9:508 ICD9:508.1 ICD9:508.8 ICD9:508.9 ICD9:510-519.99 ICD9:516 ICD9:516.8 ICD9:516.9 ICD9:517 ICD9:517.8 ICD9:519 ICD9:519.1 ICD9:519.3 ICD9:519.8 ICD9:519.9 ICD9:V12.60 ICD9:V47.2 MEDGEN:48421 MESH:D012140 NANDO:1100010 NCIT:C26871 SCTID:50043002 UMLS:C0035204 disease of respiratory system disease or disorder of respiratory system disorder of respiratory system respiratory disease respiratory disorder respiratory system disease respiratory system disease or disorder respiratory system disorder respiratory system disorder Any disease caused by a virus. DOID:934 EFO:0000763 ICD9:060-066.99 ICD9:066.9 ICD9:078.89 ICD9:079.99 MESH:D014777 NCIT:C3439 SCTID:34014006 Viruses caused disease or disorder Viruses disease or disorder Viruses infection Viruses infectious disease infection, viral viral disease viral disorder viral infection virus infection viral infectious disease An infection caused by the human immunodeficiency virus. DOID:526 EFO:0000764 ICD10CM:B20-B20 ICD9:042 ICD9:042-042.99 MEDGEN:5583 MESH:D015658 NANDO:2200810 NCIT:C3108 SCTID:86406008 UMLS:C0019693 HIV infection Human immunodeficiency virus caused disease or disorder Human immunodeficiency virus disease or disorder Human immunodeficiency virus infectious disease HIV infectious disease An acute infectious disorder that is caused by gram positive or gram negative bacteria; representative examples include pneumococcal, streptococcal, salmonella, and meningeal infections. DOID:104 EFO:0000771 ICD9:040.89 ICD9:041.89 ICD9:041.9 MEDGEN:14012 MESH:D001424 NCIT:C2890 SCTID:87628006 UMLS:C0004623 Bacteria caused disease or disorder Bacteria disease or disorder Bacteria infectious disease bacterial disease bacterial disorder bacterial infection bacterial infectious disease infection, bacterial bacterial infectious disease Any condition related to a disturbance between proper intake and utilization of nourishment. DOID:374 EFO:0001069 ICD9:783.9 MEDGEN:811347 MESH:D009748 NCIT:C26836 SCTID:2492009 UMLS:C3714509 nutritional disorder nutritional disorder An excess of body weight, normally defined as an individual with a body mass index greater than 35 or a body weight greater than one hundred percent of ideal body weight. DOID:11981 EFO:0001074 ICD9:278.01 MEDGEN:18128 MESH:D009767 NIFSTD:nlx_dys_20090303 SCTID:83911000119104 UMLS:C0028756 severe obesity morbid obesity A disease involving the endocrine system. DOID:28 EFO:0001379 ICD9:259.8 ICD9:259.9 MEDGEN:4043 MESH:D004700 NANDO:1100009 NANDO:2100109 NCIT:C3009 SCTID:362969004 UMLS:C0014130 disease of endocrine system disease or disorder of endocrine system disorder of endocrine system endocrine disease endocrine disorder endocrine system disease endocrine system disease or disorder endocrine system disorder endocrinopathy thyroid or other glandular disorders endocrine system disorder A disease involving the liver. DOID:409 EFO:0001421 ICD10CM:K70-K77 ICD9:573.8 ICD9:573.9 MEDGEN:893061 MESH:D008107 NCIT:C3196 SCTID:235856003 UMLS:C4021780 disease of liver disease or disorder of liver disorder of liver hepatic disease hepatic disorder liver and intrahepatic bile duct disorder liver disease liver disease or disorder liver disorder liver disorder A disease involving the kidney. DOID:557 EFO:0003086 ICD9:583.81 MEDGEN:9635 MESH:D007674 NCIT:C3149 SCTID:90708001 UMLS:C0022658 disease of kidney disease or disorder of kidney disorder of kidney kidney disease kidney disease or disorder kidney disorder renal disease renal disorder kidney disorder A spectrum of small and large bowel inflammatory diseases of unknown etiology. It includes Crohn's disease, ulcerative colitis, and colitis of indeterminate type. DOID:0050589 EFO:0003767 ICD9:558.9 MEDGEN:43877 MESH:D015212 NANDO:2100259 NCIT:C3138 OMIMPS:266600 SCTID:24526004 UMLS:C0021390 IBD autoimmune bowel disorder inflammatory bowel disease inflammatory bowel disease A disease involving the heart and/or pericardium. DOID:114 EFO:0003777 ICD9:429.89 ICD9:429.9 ICD9:V47.2 MEDGEN:5458 MESH:D006331 NCIT:C3079 SCTID:56265001 UMLS:C0018799 cardiac disease disease of heart disease or disorder of heart disorder of heart disorder of heart/pericardium heart disease heart disease or disorder heart disorder heart trouble heart/pericardial disease heart/pericardial disease or disorder heart/pericardial disorder heart/pericardial trouble heart disorder A disease involving the lung. DOID:850 EFO:0003818 ICD9:518.89 MEDGEN:7399 MESH:D008171 NCIT:C3198 SCTID:19829001 UMLS:C0024115 disease of lung disease or disorder of lung disorder of lung lung disease lung disease or disorder lung disorder lung disorders pulmonary disease pulmonary diseases pulmonary disorder pulmonary disorders lung disorder A benign or malignant neoplasm that affects the colon or rectum. Representative examples of benign neoplasms include lipoma and leiomyoma. Representative examples of malignant neoplasms include carcinoma, lymphoma, and sarcoma. Colorectal adenomas always exhibit epithelial dysplasia and are considered premalignant neoplasms. MONDO:0021236 EFO:0004142 MEDGEN:3171 MESH:D015179 NCIT:C2956 UMLS:C0009404 colorectal neoplasm colorectal tumor colorectal tumour colorectum neoplasm colorectum neoplasm (disease) colorectum tumor colorectum tumour large bowel neoplasm large bowel tumor large bowel tumour large intestinal neoplasm large intestine neoplasm large intestine tumor large intestine tumour neoplasm of colorectum neoplasm of large bowel neoplasm of the large bowel tumor of colorectum tumor of large bowel tumor of the large bowel tumour of colorectum tumour of large bowel tumour of the large bowel colorectal neoplasm A general term used to describe any disease affecting blood vessels]. It includes vascular abnormalities caused by degenerative, metabolic and inflammatory conditions, embolic diseases, coagulative disorders, and functional disorders such as posteri or reversible encephalopathy syndrome. DOID:178 EFO:0004264 ICD10CM:I00-I99 ICD10CM:I70-I79 ICD9:442.9 MEDGEN:22621 MESH:D014652 NANDO:2100294 NCIT:C35117 SCTID:27550009 UMLS:C0042373 disease of vasculature disease or disorder of vasculature disorder of vasculature vascular disorder vascular tissue disease vasculature disease vasculature disease or disorder The etiology of vasculopathy is generally unknown and the condition is frequently not pathologically proven. Vasculitis, on the other hand, is a more specific term and is defined as inflammation of the wall of a blood vessel. However, the term vasculopathy is also used for “vasculitis” that has not been pathologically established. vascular disorder A medical condition characterized by long-term fatigue and other symptoms that limit a person's ability to carry out ordinary daily activities. DOID:8544 EFO:0004540 ICD9:780.71 ICD9:780.79 MEDGEN:5130 MESH:D015673 NCIT:C3037 Orphanet:1983 SCTID:51771007 UMLS:C0015674 CFS Postviral fatigue syndrome chronic fatigue immune dysfunction syndrome chronic fatigue syndrome myalgic encephalitis myalgic encephalomyelitis systemic exertion intolerance disease myalgic encephalomeyelitis/chronic fatigue syndrome A disorder directly resulting from the presence and activity of a microbial, viral, or parasitic agent in humans. It can be transmitted by direct or indirect contact. DOID:0050117 EFO:0005741 ICD10CM:A00-B99 ICD9:079.0 ICD9:136.8 ICD9:136.9 IDO:0000436 MEDGEN:1057 MESH:D003141 NCIT:C26726 SCTID:40733004 UMLS:C0009450 communicable disease infection infectious infectious disease infectious diseases and manifestations infectious disorder transmissible disease clinical infection Replaces 'infection' in disease hierarchy. OBI imported term infection is moved to pathologic process. This class is a container class for infectious diseases, not the process of infection itself. infectious disease Inflammatory and degenerative diseases of connective tissue structures, such as arthritis. DOID:1575 EFO:0005755 ICD9:729.0 MEDGEN:3157 MESH:D012216 NANDO:2100151 NANDO:2100152 NCIT:C27204 SCTID:396332003 UMLS:C0009326 Wikipedia:Rheumatism rheumatic disease rheumatologic disorder This is an umbrella term encompassing conditions causing chronic, often intermittent pain affecting the joints and/or connective tissue rheumatic disorder A disease affecting the brain or part of the brain. DOID:936 EFO:0005774 ICD9:348.3 ICD9:348.30 ICD9:348.8 ICD9:348.9 MEDGEN:14214 MESH:D001927 NCIT:C96413 SCTID:81308009 UMLS:C0006111 brain disease brain disease or disorder disease of brain disease or disorder of brain disorder of brain encephalopathy Editor note: NCIT has different classes for brain disease and encephalopathy brain disorder A disease involving the hematopoietic system. DOID:74 EFO:0005803 GTR:AN1320635 ICD10CM:D50-D89 ICD9:280-289.99 ICD9:289.8 ICD9:289.9 MEDGEN:5483 MESH:D006402 NANDO:1100006 NANDO:2100175 NCIT:C26323 Orphanet:97992 SCTID:414022008 UMLS:C0018939 blood disease blood disorder blood dyscrasia disease of haematopoietic system disease of hematopoietic system disease of the blood and blood-forming organs disease or disorder of haematopoietic system disease or disorder of hematopoietic system disorder of haematopoietic system disorder of hematopoietic system haematological disease haematological disorder haematological system disease haematopoietic disease haematopoietic system disease haematopoietic system disease or disorder hematologic and lymphocytic disorder hematologic disorder hematological disease hematological disorder hematological system disease hematopoietic disease hematopoietic system disease hematopoietic system disease or disorder rare hematologic disease placeholder for lymphoid disease hematologic disorder A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma. DOID:5672 DOID:9256 MEDGEN:83428 NCIT:C4978 OMIM:114500 Orphanet:466667 SCTID:363510005 UMLS:C0346629 cancer of colorectum cancer of large bowel cancer of large intestine cancer of the large bowel colon cancer, advanced, somatic colon cancer, somatic colorectal cancer colorectal cancer with chromosomal instability, somatic colorectal cancer, autosomal dominant, somatic mutation colorectal cancer, somatic colorectal cancer, susceptibility to, autosomal dominant, somatic mutation colorectum cancer malignant colorectal neoplasm malignant colorectal tumor malignant colorectal tumour malignant colorectum neoplasm malignant large bowel neoplasm malignant large bowel tumor malignant large bowel tumour malignant large intestine neoplasm malignant large intestine tumor malignant large intestine tumour malignant neoplasm of colorectum malignant neoplasm of large bowel malignant neoplasm of large intestine malignant neoplasm of the large bowel malignant neoplasm of the large intestine malignant tumor of large bowel malignant tumor of large intestine malignant tumor of the large bowel malignant tumor of the large intestine malignant tumour of large bowel malignant tumour of large intestine malignant tumour of the large bowel malignant tumour of the large intestine Editor note: some sources make distinct classes for colorectal vs large intestine. We follow NCIT and make these equivalent colorectal cancer Virus diseases caused by coronaviridae. EFO:0007223 MEDGEN:40491 UMLS:C0010078 Coronaviridae infectious disease A malignant neoplasm involving the intestine DOID:10155 EFO:0007330 ICD9:159.0 MEDGEN:87562 MESH:D007414 NCIT:C4572 SCTID:363508008 UMLS:C0346627 bowel cancer cancer of intestine cancer of the intestine intestinal cancer intestinal neoplasms, malignant intestinal tumors, malignant intestine cancer malignant intestinal neoplasm malignant intestinal neoplasms malignant intestinal tumor malignant intestinal tumors malignant intestinal tumour malignant intestinal tumours malignant intestine neoplasm malignant intestine tumor malignant intestine tumour malignant neoplasm of intestine malignant neoplasm of the intestine malignant tumor of intestine malignant tumor of the intestine malignant tumour of intestine malignant tumour of the intestine intestinal cancer A disease involving the lymphatic part of lymphoid system. DOID:75 EFO:0007352 MEDGEN:892707 MESH:D008206 NCIT:C50764 SCTID:362971004 UMLS:C4021976 disease of lymphatic part of lymphoid system disease or disorder of lymphatic part of lymphoid system disorder of lymph node and lymphatics disorder of lymphatic part of lymphoid system disorder of lymphatic system glands, swollen lymphatic disease lymphatic disorder lymphatic part of lymphoid system disease lymphatic part of lymphoid system disease or disorder swollen gland swollen glands lymphadenopathy lymphangiopathy Editor note: check alignment to anatomy, consider lymphoid system disease lymphatic system disorder Infections with viruses of the order nidovirales. The concept includes arterivirus infections and coronaviridae infections. MEDGEN:197455 MESH:D030341 UMLS:C0969753 Nidovirales caused disease or disorder Nidovirales disease or disorder Nidovirales infectious disease Autosomal recessive form of disease. DOID:0050737 EFO:1000017 ICD9:758.5 MEDGEN:539209 SCTID:85995004 UMLS:C0265388 autosomal recessive disease or disorder autosomal recessive hereditary disease autosomal recessive hereditary disorder autosomal recessive inherited disease autosomal recessive inherited disorder disease or disorder, autosomal recessive disease, autosomal recessive autosomal recessive disease Progressive and life-threatening pulmonary distress in the absence of an underlying pulmonary condition, usually following major trauma or surgery. Cases of neonatal respiratory distress syndrome are not included in this definition. EFO:1000637 ICD10CM:J80 MEDGEN:1812214 MedDRA:10001052 NCIT:C3353 UMLS:C2887484 icd11.foundation:1189702844 ARDS acute respiratory distress syndrome shock lung This disease can present as a mild ARDS (PaO2/FiO2 of 201–300 mmHg) moderate ARDS (PaO2/FiO2 of 101–200 mmHg) and severe ARDS (PaO2/FiO2 ≤100 mmHg). [PMID:30872586] acute respiratory distress syndrome A disorder resulting from loss of function or tissue destruction of an organ or multiple organs, arising from humoral or cellular immune responses of the individual to their own tissue constituents. It may be systemic (e.g., systemic lupus erythematosus), or organ specific, (e.g., thyroiditis). DOID:417 EFO:0005809 ICD9:279.4 ICD9:279.49 ICD9:720 MEDGEN:2135 MESH:D001327 NCIT:C2889 OBI:1110054 OMIM:109100 SCTID:85828009 UMLS:C0004364 autoimmune disease autoimmune disease or disorder autoimmune disorder disease, autoimmune Editor note: check OMIM autoimmune disease A primary or metastatic malignant neoplasm involving the breast. The vast majority of cases are carcinomas arising from the breast parenchyma or the nipple. Malignant breast neoplasms occur more frequently in females than in males. breast tumor breast tumour mammary tumor mammary tumour DOID:1612 ICD10CM:C50 ICD9:174.8 MEDGEN:651 NCIT:C9335 SCTID:254837009 UMLS:C0006142 breast cancer cancer of breast malignant breast neoplasm malignant breast tumor malignant breast tumour malignant neoplasm of breast malignant neoplasm of the breast malignant tumor of breast malignant tumor of the breast malignant tumour of breast malignant tumour of the breast mammary cancer primary breast cancer breast cancer A malignant neoplasm involving the lung. DOID:1324 ICD9:162.3 ICD9:162.4 ICD9:162.5 ICD9:162.8 ICD9:162.9 MEDGEN:66885 NCIT:C7377 OMIM:211980 SCTID:363358000 UMLS:C0242379 adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation adenocarcinoma of lung, somatic cancer of lung lung cancer lung cancer, protection against, autosomal dominant, somatic mutation lung cancer, resistance to, autosomal dominant, somatic mutation lung cancer, somatic lung cancer, susceptibility to, autosomal dominant, somatic mutation malignant lung neoplasm malignant lung tumor malignant lung tumour malignant neoplasm of lung malignant neoplasm of the lung malignant tumor of lung malignant tumor of the lung malignant tumour of lung malignant tumour of the lung nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation nonsmall cell lung cancer, somatic nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation lung cancer Cystic fibrosis (CF) is a genetic disorder characterized by the production of sweat with a high salt content and mucus secretions with an abnormal viscosity. DOID:1485 GARD:6233 ICD10CM:E84 ICD9:277.0 MEDGEN:41393 MESH:D003550 MedDRA:10011762 NANDO:1200922 NANDO:1201021 NANDO:2100035 NANDO:2200205 NCIT:C2975 NORD:1026 OMIM:219700 Orphanet:586 SCTID:190905008 UMLS:C0010674 icd11.foundation:514403112 CF cystic fibrosis cystic fibrosis lung disease, modifier of mucoviscidosis pseudomonas aeruginosa, susceptibility to chronic infection by, in cystic fibrosis cystic fibrosis Infant acute respiratory distress syndrome is a lung disorder that affects premature infants caused by developmental insufficiency of surfactant production and structural immaturity of the lungs. The symptoms usually appear shortly after birth and may include tachypnea, tachycardia, chest wall retractions (recession), expiratory grunting, nasal flaring and cyanosis during breathing efforts. RDS respiratory distress syndrome GARD:112 MEDGEN:368840 MESH:C566881 NORD:1659 OMIM:267450 Orphanet:70587 UMLS:C1968593 icd11.foundation:343716587 RDS of prematurity Respiratory Distress Syndrome, Infant respiratory distress syndrome in premature infants respiratory distress syndrome in premature infants A disorder resulting from inadequate blood flow in the vessels that supply the brain. Representative examples include cerebrovascular ischemia, cerebral embolism, and cerebral infarction. DOID:6713 EFO:0003763 ICD10CM:I60-I69 ICD9:430-438.99 ICD9:434.91 ICD9:437.8 ICD9:437.9 MEDGEN:858 MESH:D002561 NCIT:C2938 SCTID:62914000 UMLS:C0007820 cerebrovascular disease cerebrovascular disorder CVA CVA (cerebral vascular accident) cerebral infarction cerebrovascular accident stroke cerebrovascular disorder A disorder involving an excessive amount of body fat. DOID:9970 EFO:0001073 HP:0001513 ICD9:278.0 ICD9:278.00 MEDGEN:18127 NCIT:C3283 NIFSTD:nlx_dys_20090302 Orphanet:521399 SCTID:414916001 UMLS:C0028754 obesity obesity disease Obesity is a complex disease that may involve multiple environmental and genetic causes. See the subclass monogenic disease for genetic subtypes obesity disorder Sickle cell anemias are chronic hemolytic diseases that may induce three types of acute accidents: severe anemia, severe bacterial infections, and ischemic vasoocclusive accidents (VOA) caused by sickle-shaped red blood cells obstructing small blood vessels and capillaries. Many diverse complications can occur. DOID:0081445 DOID:10923 GARD:8614 ICD9:282.6 ICD9:282.60 ICD9:282.63 MEDGEN:287 MESH:D000755 MedDRA:10040641 NANDO:2200624 NCIT:C34383 NORD:1714 OMIM:603903 Orphanet:232 UMLS:C0002895 Haemoglobin S disease without crisis Hb SC disease Hb-S/Hb-C disease Hb-SS disease without crisis Hemoglobin S disease without crisis Sickle Cell Disease drepanocytosis haemoglobin SC disease hemoglobin SC disease sickle cell anemia sickle cell disease sickle-cell/Hb-C disease without crisis sickling disorder due to Haemoglobin S sickling disorder due to Hemoglobin S sickle cell anemia A syndrome resulting from the acquired deficiency of cellular immunity caused by the human immunodeficiency virus (HIV). It is characterized by the reduction of the Helper T-lymphocytes in the peripheral blood and the lymph nodes. Symptoms include generalized lymphadenopathy, fever, weight loss, and chronic diarrhea. Patients with AIDS are especially susceptible to opportunistic infections (usually pneumocystis carinii pneumonia, cytomegalovirus (CMV) infections, tuberculosis, candida infections, and cryptococcosis), and the development of malignant neoplasms (usually non-Hodgkin lymphoma and Kaposi sarcoma). The human immunodeficiency virus is transmitted through sexual contact, sharing of contaminated needles, or transfusion of contaminated blood. DOID:635 EFO:0000765 MEDGEN:99 MESH:D000163 NANDO:2100212 NANDO:2200809 NCIT:C2851 SCTID:62479008 UMLS:C0001175 AIDS AIDS, acquired immunodeficiency syndrome acquired immune deficiency acquired immunodeficiency disease acquired immunodeficiency syndrome, AIDS AIDS Kawasaki disease (KD) is a febrile, systemic, self-limiting vasculitis affecting children and characterized by inflammation in the medium sized vessels associated with coronary arterial aneurysms (CAA) that may be life threatening when untreated. KD is the most common cause of acquired heart disease in children in developed countries and is a risk factor for ischemic heart disease in adulthood. DOID:13378 EFO:0004246 GARD:6816 ICD9:446.1 MEDGEN:10118 MESH:D009080 MedDRA:10023320 NCIT:C34825 OMIM:611775 Orphanet:2331 SCTID:75053002 UMLS:C0026691 icd11.foundation:540285662 Kawasaki's disease MLNS acute febrile MCLS acute febrile mucocutaneous lymph node syndrome acute febrile mucocutaneous lymph node syndrome [MCLS] infantile polyarteritis nodosa mucocutaneous lymph node syndrome mucocutaneous lymph node syndrome Bleeding into one or both cerebral hemispheres including the basal ganglia and the cerebral cortex. It is often associated with hypertension and craniocerebral trauma. EFO:0005669 ICD9:431 MEDGEN:423648 MESH:D002543 SCTID:274100004 UMLS:C2937358 stroke, hemorrhagic intracerebral hemorrhage A condition of lung damage that is characterized by bilateral pulmonary infiltrates (pulmonary edema) rich in neutrophils, and in the absence of clinical heart failure. This can represent a spectrum of pulmonary lesions, endothelial and epithelial, due to numerous factors (physical, chemical, or biological). EFO:0004610 GARD:20146 MESH:D055371 MedDRA:10069351 NCIT:C155766 Orphanet:178320 SCTID:315345002 acute lung injury A diverse group of lung diseases that affect the lung parenchyma. They are characterized by an initial inflammation of pulmonary alveoli that extends to the interstitium and beyond leading to diffuse pulmonary fibrosis. Interstitial lung diseases are classified by their etiology (known or unknown causes), and radiological-pathological features. DOID:3082 EFO:0004244 ICD10CM:J80-J84 MEDGEN:1788738 MESH:D017563 MedDRA:10022611 NCIT:C164315 Orphanet:182095 SCTID:233703007 UMLS:C5441745 ILD interstitial lung disease interstitial lung disease A spectrum of rare post-infectious neuropathies that usually occur in otherwise healthy patients. GBS is clinically heterogeneous and encompasses acute inflammatory demyelinating polyradiculoneuropathy (AIDP), acute motor axonal neuropathy (AMAN) and acute motor-sensory axonal neuropathy (AMSAN), Miller-Fisher syndrome (MFS) and some other regional variants. DOID:12842 EFO:0007292 GARD:6554 ICD10CM:G61.0 MEDGEN:5399 MESH:D020275 MedDRA:10018767 NCIT:C116345 Orphanet:2103 SCTID:40956001 UMLS:C0018378 GBS Guillain Barre syndrome Guillain Barré syndrome Guillain-Barre-Strohl syndrome Guillain-Barré syndrome Guillain-Barré-Strohl syndrome acute postinfectious polyneuropathy post-infectious polyneuritis post-infective polyneuritis postinfectious polyneuritis Guillain-Barre syndrome A interstitial lung disease that occurs during childhood. MEDGEN:1842412 Orphanet:264656 SCTID:328661000119108 UMLS:C5679752 ILD specific to childhood chILD chILD syndrome childhood interstitial lung disease interstitial lung disease of childhood paediatric interstitial lung disease pediatric interstitial lung disease The terms chILD or chILD syndrome (not preferred) have been coined to memorize easily and to identify a phenotype that requires prompt and expert evaluation. interstitial lung disease specific to childhood GARD:10559 MEDGEN:853969 Orphanet:264665 UMLS:C3161253 icd11.foundation:1408868257 primary ILD specific to childhood primary interstitial lung disease specific to childhood primary interstitial lung disease specific to childhood A chronic, recurrent infection caused by the bacterium Mycobacterium tuberculosis. Tuberculosis (TB) may affect almost any tissue or organ of the body with the lungs being the most common site of infection. The clinical stages of TB are primary or initial infection, latent or dormant infection, and recrudescent or adult-type TB. Ninety to 95% of primary TB infections may go unrecognized. Histopathologically, tissue lesions consist of granulomas which usually undergo central caseation necrosis. Local symptoms of TB vary according to the part affected; acute symptoms include hectic fever, sweats, and emaciation; serious complications include granulomatous erosion of pulmonary bronchi associated with hemoptysis. If untreated, progressive TB may be associated with a high degree of mortality. This infection is frequently observed in immunocompromised individuals with AIDS or a history of illicit IV drug use. DOID:399 GARD:7827 ICD10CM:A15-A19 ICD9:017.90 ICD9:017.92 ICD9:017.94 ICD9:017.96 MEDGEN:22513 MESH:D014376 MedDRA:10044755 NCIT:C3423 NORD:1801 Orphanet:3389 SCTID:56717001 UMLS:C0041296 icd11.foundation:2072728114 tuberculosis disease active tuberculosis tuberculosis Vasculitis represents a clinically heterogenous group of diseases of multifactorial etiology characterized by inflammation of either large-sized vessels (large-vessel vasculitis, e.g. Giant-cell arteritis and Takayasu arteritis), medium-sized vessels (medium-vessel vasculitis e.g. polyarteritis nodosa and Kawasaki disease), or small-sized vessels (small-vessel vasculitis, e.g. granulomatosis with polyangiitis, microscopic polyangiitis, immunoglobulin A vasculitis, and cutaneous leukocytoclastic angiitis). Vasculitis occurs at any age, may be acute or chronic, and manifests with general symptoms such as fever, weight loss and fatigue, as well as more specific clinical signs depending on the type of vessels and organs affected. The degree of severity is variable, ranging from life or sight threatening disease (e.g. Behcet disease) to relatively minor skin disease. DOID:865 EFO:0006803 GARD:18844 MEDGEN:12054 MESH:D014657 MedDRA:10036023 MedDRA:10047115 NCIT:C26912 Orphanet:52759 SCTID:31996006 UMLS:C0042384 Wikipedia:Vasculitis icd11.foundation:572581721 systemic vasculitis vasculitis An inherited disorder characterized by structural alterations of a globin chain within the hemoglobin molecule. DOID:2860 GARD:18883 ICD10CM:D58.0 ICD10CM:D58.1 ICD9:282.7 MESH:D006453 MedDRA:10060892 NCIT:C3092 Orphanet:68364 SCTID:427306008 Hemoglobinopathies / iron metabolism hemoglobinopathies hereditary hemoglobinopathy inherited hemoglobinopathy Any disease that impairs the functioning of the muscles, either directly, being pathologies of the voluntary muscle, or indirectly, being pathologies of nerves or neuromuscular junctions DOID:440 EFO:1001902 ICD9:358 ICD9:358.9 MEDGEN:10323 MESH:D009468 MedDRA:10029323 NANDO:1100001 NANDO:2100214 Orphanet:68381 UMLS:C0027868 nerve and muscle disorder neuromuscular disease neuromuscular disease A infectious disease that involves the nervous system. ICD9:349.89 MEDGEN:108926 NCIT:C27590 Orphanet:98010 SCTID:128116006 UMLS:C0597039 nervous system infectious disease nervous system infectious disorder infectious disorder of the nervous system Infection due to organisms from the genus Mycobacteria. MEDGEN:6479 MESH:D009164 NCIT:C26831 SCTID:88415009 UMLS:C0026918 mycobacterial infection mycobacteriosis mycobacterium infection mycobacterial infectious disease A benign or malignant, primary or metastatic neoplasm involving the respiratory tract. EFO:0003853 ICD10CM:C30-C39 MEDGEN:11200 MESH:D012142 NCIT:C3355 SCTID:126667002 UMLS:C0035244 neoplasm of respiratory tract neoplasm of the respiratory tract neoplasm, respiratory tract neoplasms, respiratory tract respiratory system neoplasm respiratory tract neoplasm respiratory tract tumor respiratory tract tumour tract neoplasm, respiratory tract neoplasms, respiratory tumor of respiratory tract tumor of the respiratory tract tumour of respiratory tract tumour of the respiratory tract respiratory tract neoplasm Disease having a short and relatively severe course. ICD9:799.89 MEDGEN:1738 MESH:D000208 SCTID:2704003 UMLS:C0001314 acute disease acute diseases disease, acute acute disease Infectious disease causes by viruses in the subfamily Orthocoronavirinae (coronaviruses). In humans, coronaviruses cause respiratory tract infections that can be mild, such as some cases of the common cold (among other possible causes, predominantly rhinoviruses), and others that can be lethal, such as SARS, MERS, and COVID-19. DOID:0080599 coronavirus infectious disease Orthocoronavirinae infectious disease Disease in which there is a deficiency or defect in the mechanisms of immunity, either cellular or humoral. ICD9:279.3 MEDGEN:7034 NANDO:2100204 NCIT:C3131 OMIMPS:300755 SCTID:234532001 UMLS:C0021051 immuno-deficiency immunodeficiency immunodeficiency disorder immunodeficiency disease A benign or malignant neoplasm of the breast parenchyma. It can originate from the ducts, lobules or the breast adipose tissue. Breast neoplasms are much more common in females than males. EFO:0003869 ICD9:239.3 MEDGEN:264172 MESH:D001943 NCIT:C2910 ONCOTREE:BREAST SCTID:126926005 UMLS:C1458155 breast neoplasm breast neoplasm (disease) breast tumor breast tumour neoplasm of breast neoplasm of the breast neoplasm, breast tumor of breast tumor of the breast tumour of breast tumour of the breast breast neoplasm The significant impairment of gas exchange within the lungs resulting in hypoxia, hypercarbia, or both, to the extent that organ tissue perfusion is severely compromised. Causes include chronic obstructive pulmonary disease, asthma, emphysema, acute respiratory distress syndrome, pneumonia, pulmonary edema, pneumothorax, and congestive heart failure. Treatment requires intubation and mechanical ventilation until the time the lungs recover sufficient function. DOID:11162 EFO:0009686 ICD9:518.81 ICD9:518.83 MEDGEN:257837 MESH:D012131 NCIT:C26872 SCTID:39871006 UMLS:C1145670 icd11.foundation:370028006 failure, respiratory respiratory failure respiratory insufficiency/failure acute respiratory failure chronic respiratory failure respiratory failure A benign or malignant, primary or metastatic neoplasm involving the lungs. Representative examples of benign neoplasms include adenoma, papilloma, chondroma, and endobronchial lipoma. Representative examples of malignant neoplasms include carcinoma, carcinoid tumor, sarcoma, and lymphoma. MEDGEN:7400 MESH:D008175 NCIT:C3200 ONCOTREE:LUNG UMLS:C0024121 lung neoplasm lung neoplasm (disease) lung neoplasms lung tumor lung tumour neoplasm of lung neoplasm of the lung tumor of lung tumor of the lung tumour of lung tumour of the lung lung neoplasm A benign or malignant neoplasm involving the small or large intestine. DOID:4610 MEDGEN:43932 NCIT:C3141 ONCOTREE:BOWEL SCTID:126769007 UMLS:C0021841 intestinal neoplasm intestinal neoplasms intestinal tumor intestinal tumors intestinal tumour intestinal tumours intestine growth intestine neoplasm intestine neoplasm (disease) intestine tumor intestine tumour neoplasm of intestinal tract neoplasm of intestine neoplasm of intestines neoplasm of the intestines tumor of intestine tumor of intestines tumor of the intestines tumour of intestine tumour of intestines tumour of the intestines intestinal neoplasm A disease involving a pathogenic inflammatory response in the anatomical structure. ICD9:799.89 MEDGEN:452939 NCIT:C93210 SCTID:128139000 UMLS:C1290884 anatomical structure inflammation inflammation of anatomical structure inflammatory disease inflammatory disorder inflammatory disease Damage inflicted on the body as the direct or indirect result of an external force, with or without disruption of structural continuity. EFO:0000546 MESH:D014947 NCIT:C3671 injury trauma traumatic injury wound injury A neoplasm (disease) that involves the digestive system. EFO:0008549 MEDGEN:4846 MESH:D005770 NCIT:C3052 UMLS:C0017185 GI neoplasm GI system neoplasm GI system tumor GI system tumour GI tumor GI tumour digestive neoplasm digestive system neoplasm (disease) digestive system tumor digestive system tumour digestive tumor digestive tumour gastrointestinal neoplasm gastrointestinal system neoplasm gastrointestinal system tumor gastrointestinal system tumour gastrointestinal tumor gastrointestinal tumour neoplasm of GI system neoplasm of digestive system neoplasm of gastrointestinal system neoplasm of the GI system neoplasm of the digestive system neoplasm of the gastrointestinal system tumor of GI system tumor of digestive system tumor of gastrointestinal system tumor of the GI system tumor of the digestive system tumor of the gastrointestinal system tumour of GI system tumour of digestive system tumour of gastrointestinal system tumour of the GI system tumour of the digestive system tumour of the gastrointestinal system digestive system neoplasm A neoplasm (disease) that involves the thoracic segment of trunk. ICD10CM:C30-C39 ICD9:239.89 MEDGEN:11793 NCIT:C3406 SCTID:255058005 UMLS:C0039981 neoplasm of the thorax neoplasm of thoracic segment of trunk thoracic neoplasm thoracic segment of trunk neoplasm thoracic segment of trunk neoplasm (disease) thoracic segment of trunk tumor thoracic segment of trunk tumour thoracic tumor thoracic tumour tumor of the thorax tumor of thoracic segment of trunk tumor of thorax tumour of the thorax tumour of thoracic segment of trunk tumour of thorax neoplasm of thorax A disorder that follows infection but is distinct from the infection itself and its usual manifestations. ICD10CM:B90-B94 ICD9:139.8 MEDGEN:688819 SCTID:123976001 UMLS:C1264603 sequela of infectious disorder post-infectious disorder A post-infectious disorder that follows viral infection but is distinct from the viral infection itself and its usual manifestations. ICD9:139.8 MEDGEN:688821 SCTID:123948009 UMLS:C1264605 sequela of viral disease post-viral disorder A Disease due to or propagated by sexual contact. ICD10CM:A50-A64 ICD9:099.8 ICD9:099.9 MEDGEN:11402 MESH:D012749 NCIT:C3365 SCTID:8098009 UMLS:C0036916 STD VD VD, venereal disease disease (VD), venereal sexually Transmitted disorder sexually transmitted disease venereal disease (VD) sexually transmitted disease Viral diseases which are potentially transmitted or propagated by sexual conduct. MEDGEN:48646 MESH:D015229 UMLS:C0036918 viral sexually transmitted disease viral sexually transmitted disease Disorders related to or resulting from abuse or mis-use of alcohol. MEDGEN:68632 MESH:D019973 SCTID:29212009 UMLS:C0236664 alcohol-related disorders Virus diseases caused by the Lentivirus genus. They are multi-organ diseases characterized by long incubation periods and persistent infection. EFO:1001357 MEDGEN:38233 MESH:D016180 UMLS:C0079680 lentivirus infection Either an isolated neoplasm or a syndrome with neoplasm as a major feature. neoplastic disease or syndrome An infectious process that affects the brain and/or spinal cord. Representative examples include encephalitis, poliomyelitis, arachnoiditis, and meningitis. EFO:1001456 ICD9:349.89 MEDGEN:1684837 MESH:D002494 NCIT:C27582 SCTID:128117002 UMLS:C4759823 central nervous system infectious disease central nervous system infectious disorder infectious disease of central nervous system central nervous system infectious disorder A disease that involves the large intestine. MEDGEN:574315 SCTID:119523007 UMLS:C0341321 disease of large intestine disease or disorder of large intestine disorder of large intestine large intestine disease or disorder large intestine disorder A disorder that affects the muscle tissue of the heart. Representative examples include myocardial infarction, myocarditis, and cardiomyopathy. MEDGEN:469033 NCIT:C35544 SCTID:57809008 UMLS:C3241958 disease of myocardium disease or disorder of myocardium disorder of myocardium myocardial disease myocardial disorder myocardium disease myocardium disease or disorder myocardial disorder A malignant tumor that has spread from its original (primary) site of growth to another site close to or distant from the primary site. MEDGEN:422475 NCIT:C36263 UMLS:C2939419 malignant metastatic neoplasm metastatic cancer metastatic malignant neoplasm metastatic neoplasm, malignant Note that we currently treat secondary neoplasms as being neoplastic diseases that are derived from neoplasm; classes such as 'neoplasm', 'carcinoma' are implicitly primary. This may change in future. metastatic malignant neoplasm A malignant neoplasm that arises from a pre-existing lower grade lesion, or as a result of a primary lesion that has spread to secondary sites, or due to a complication of a cancer treatment. EFO:0009812 ICD9:198.89 ICD9:199.1 MEDGEN:473807 NCIT:C4968 SCTID:128462008 UMLS:C3266877 secondary cancer secondary malignancy secondary malignant neoplasm Note that we currently treat secondary neoplasms as being neoplastic diseases that are derived from neoplasm; classes such as 'neoplasm', 'carcinoma' are implicitly primary. This may change in future. secondary malignant neoplasm A neoplasm that arises from a pre-existing lower grade lesion, or as a result of a primary lesion that has spread to secondary sites, or due to a complication of a cancer treatment. MEDGEN:1851572 NCIT:C36255 UMLS:C5848363 secondary neoplasm secondary tumor secondary tumour Note that we currently treat secondary neoplasms as being neoplastic diseases that are derived from neoplasm; classes such as 'neoplasm', 'carcinoma' are implicitly primary. This may change in future. secondary neoplasm A tumor that has spread from its original (primary) site of growth to another site, close to or distant from the primary site. Metastasis is characteristic of advanced malignancies, but in rare instances can be seen in neoplasms lacking malignant morphology. EFO:0009709 ICDO:8000/6 MEDGEN:422476 NCIT:C3261 UMLS:C2939420 metastatic disease metastatic neoplasm metastatic tumor metastatic tumour Note that we currently treat secondary neoplasms as being neoplastic diseases that are derived from neoplasm; classes such as 'neoplasm', 'carcinoma' are implicitly primary. This may change in future. metastatic neoplasm GARD:22403 MEDGEN:1842571 Orphanet:598363 UMLS:C5680268 MIS-C/A multisystem inflammatory syndrome in children and adults A very serious type of heart attack during which one of the heart’s major arteries (one of the arteries that supplies oxygen and nutrient-rich blood to the heart muscle) is blocked. ST-segment elevation is an abnormality detected on the 12-lead ECG. MESH:D000072657 SCTID:401303003 ST segment elevation myocardial infarction STEMI acute-ST segment elevation myocardial infarction ST-elevation myocardial infarction A disorder of the nervous system related to a vascular etiology. MEDGEN:857738 NCIT:C117007 UMLS:C3898144 disease of nervous system vasculature nervous system disorder of vasculature neurovascular disorder vasculature nervous system disorder neurovascular disorder A disease or disorder that involves the erythrocyte. ICD9:289.9 MEDGEN:526127 SCTID:38292009 UMLS:C0221016 disease of erythrocyte disease or disorder of erythrocyte disorder of erythrocyte erythrocyte disease erythrocyte disease or disorder red blood cell disease red blood cell disorder erythrocyte disorder GARD:12455 ICD9:282.7 MEDGEN:42400 SCTID:80141007 UMLS:C0019045 hemoglobinopathy hemoglobinopathy A disease or disorder that involves the lymphoid system. MEDGEN:9829 SCTID:111590001 UMLS:C0024228 disease of lymphoid system disease or disorder of lymphoid system disorder of lymphoid system lymphoid system disease lymphoid system disease or disorder lymphoid system disorder Any disorder that features disrupted cell proliferation. Includes hyperplasia, neoplastic syndrome and isolated neoplasm diseases as well as precancerous conditions. neoplasm cancer or benign tumor A disease caused by infection with severe acute respiratory syndrome coronavirus 2. DOID:0080600 ICD10CM:U07.1 MEDGEN:1699653 MESH:C000657245 MESH:D000086382 SCTID:840539006 UMLS:C5203670 icd11.foundation:1730556128 2019 novel coronavirus infection 2019-nCoV infection coronavirus disease 2019 severe acute respiratory syndrome coronavirus 2 infectious disease COVID-19 Acute respiratory distress syndromet that occurs in pediatric patients and includes findings of new infiltrates (unilateral or bilateral) consistent with acute parenchymal disease, edema not fully explained by fluid overload or cardiac failure, and may present as new acute lung disease in setting of chronic lung disease and/or heart disease, and perinatal lung disease is excluded. PARDS pediatric acute respiratory distress syndrome A inflammatory syndrome in children infected by the SARS-CoV-2 with similarities to Kawasaki disease. Clinical manifestations range from fever and inflammation to myocardial injury, shock, and development of coronary artery aneurysms. DOID:0080711 NCIT:C172127 COVID-19 -related paediatric inflammatory multisystem syndrome COVID-19 -related pediatric inflammatory multisystem syndrome COVID-19 Kawasaki-like syndrome COVID-19 associated multisystem inflammatory syndrome in children MIS-C PIMS PIMS-TS PMIS SARS-CoV-2 Kawasaki-like syndrome multisystem inflammatory syndrome in children multisystem inflammatory syndrome in children associated with COVID-19 multisystem inflammatory syndrome in children associated with coronavirus disease 2019 paediatric inflammatory multisystem syndrome paediatric inflammatory multisystem syndrome temporally associated with SARS-CoV-2 paediatric inflammatory multisystem syndrome: temporally associated with SARS-CoV-2 paediatric multi-system inflammatory syndrome potentially associated with COVID-19 paediatric multisystem inflammatory syndrome pediatric inflammatory multisystem syndrome pediatric inflammatory multisystem syndrome temporally associated with SARS-CoV-2 pediatric inflammatory multisystem syndrome: temporally associated with SARS-CoV-2 pediatric multi-system inflammatory syndrome potentially associated with COVID-19 pediatric multisystem inflammatory syndrome The clinical presentation of MIS-C includes fever, severe illness, and the involvement of two or more organ systems, in combination with laboratory evidence of inflammation and laboratory or epidemiologic evidence of SARS-CoV-2 infection. Some features of MIS-C resemble Kawasaki Disease, toxic shock syndrome, and secondary hemophagocytic lymphohistiocytosis/macrophage activation syndrome. COVID-19–associated multisystem inflammatory syndrome in children A liver disease characterized by the liver losing or has lost all of its function. MEDGEN:88444 MESH:D017093 NCIT:C26922 UMLS:C0085605 hepatic failure liver failure A chronic disease triggered by acute COVID-19 infection that is characterized by persistent symptoms following the acute phase of the SARS-CoV-2 infection, which may include fatigue, coughing, dyspnea, clouding of mentation, sleep disturbances, exercise intolerance and autonomic symptoms including tachycardia upon mild exercise or standing, night sweats, temperature dysregulation, gastroparesis, constipation or loose stools, and peripheral vasoconstriction. DOID:0080848 MEDGEN:1735839 MESH:D000094024 MedDRA:10085503 MedDRA:10085504 NCIT:C179263 UMLS:C5433293 PASC long haul COVID-19 long-haul COVID-19 post-acute sequelae of COVID-19 post-acute sequelae of SARS-CoV-2 infection sequelae of COVID-19 long COVID-19 A inflammatory syndrome in adults infected by the SARS-CoV-2 with severe illness requiring hospitalization in a person aged ≥21 years; a positive test result for current or previous SARS-CoV-2 infection (nucleic acid, antigen, or antibody) during admission or in the previous 12 weeks; severe dysfunction of one or more extrapulmonary organ systems (e.g., hypotension or shock, cardiac dysfunction, arterial or venous thrombosis or thromboembolism, or acute liver injury); laboratory evidence of severe inflammation (e.g., elevated CRP, ferritin, D-dimer, or interleukin-6); and absence of severe respiratory illness (to exclude patients in which inflammation and organ dysfunction might be attributable simply to tissue hypoxia). MIS-A COVID-19–associated multisystem inflammatory syndrome in adults A SARS-CoV-2-related disease that is caused by infection by SARS-CoV-2, and manifests after the original primary infection. post-COVID-19 disorder The initial viral infectious disase that causes illness. primary viral infectious disease A heterogeneous group of genetic conditions with Mendelian (autosomal dominant, recessive, or X-linked) or chromosomal etiology characterized by abnormalities in the brain, spinal cord, nerves, or muscles. neurogenetic disease hereditary neurological disease A syndrome that occurs after therapeutic infusion of antibodies into the blood and is characterized by nausea, headache, tachycardia, hypotension, rash, and shortness of breath. It is caused by the release of cytokines from the cells that are targeted by the antibodies. Most patients experience a mild to moderate reaction; however, the reaction may be severe and life-threatening. MEDGEN:215297 MESH:D000080424 NCIT:C78251 UMLS:C0948245 CRS cytokine storm cytokine-associated toxicity cytokine release syndrome A condition beginning in the first day of life that results from inadequate surfactant production, causing increased work of breathing and impaired gas exchange. RDS respiratory distress syndrome DOID:12716 EFO:1000644 ICD9:769 NCIT:C27560 SCTID:46775006 HMD - hyaline membrane disease RDS Of newborns RDS, respiratory distress syndrome Of newborns hyaline membrane disease infant ARDS infant acute respiratory distress syndrome infant respiratory distress syndrome neonatal respiratory distress neonatal respiratory distress syndrome newborns (RDS), respiratory distress syndrome Of pulmonary hyaline membrane disease pulmonary hypoperfusion syndrome of newborn respiratory distress syndrome Of newborns respiratory distress syndrome Of newborns (RDS) respiratory distress syndrome in the newborn respiratory distress syndrome of newborn syndrome Of newborns (RDS), respiratory distress RDS of prematurity respiratory distress syndrome in premature infants newborn respiratory distress syndrome human disease or disorder human disease Pathological structure or process pathological entity Phenotypic observation of the presence or absence of a pathological entity. pathological phenotype observation Lesions leading to or consequent on failure of, or atypical movement of, blood throughout the body. circulatory disorder A syndrome consequent to uncontrolled activation of blood clotting factors leading to disseminated platelet lysis, and fibrin deposition, ultimately leading to bleeding and necrosis as a consequence of inhibition of fibrin polymerisation by degradation products. Diagnosed by microthrombi in many organs. disseminated intravascular coagulation Anatomically located instance of pathological response or entity. pathological anatomical entity the observable morphological, physiological, behavioral and other characteristics of mammalian organisms that are manifested through development and lifespan mammalian phenotype any anomaly in the cessation of function at the cellular level MP:0001647 abnormal cell viability abnormal cellular death abnormal cell death pathologic death of cells, usually from irreversible damage necrotic cell necrotic cells cellular necrosis deviation from the normal function of the immune system MP:0001789 GO:0006955 immune system/response abnormalities immune system: response/ function abnormalities abnormal immune system physiology aberrant reaction of the microcirculation characterized by movement of fluid and leukocytes from the blood into extravascular tissues inflammation inflammatory response abnormal inflammatory response greater than expected response to injury, infection, or insult increased inflammatory response local accumulation of fluid, plasma proteins, and leukocytes in the proximal portion of the respiratory passages nasal inflammation inflammation of the mucous membrane of the nose MP:0001113 nasal catarrh rhinitis any functional anomaly of the pulmonary system; inability or reduced ability to intake and exchange oxygen and carbon dioxide with the environment MGI:2173593 respiratory system dysfunction respiratory system physiology abnormalities respiratory system: respiratory distress/failure/functional anomalies abnormal respiratory system physiology local accumulation of fluid, plasma proteins, and leukocytes in the respiratory system respiratory system inflammation the observable morphological and physiological characteristics of the basic structural and functional unit of all mammalian organisms that are manifested through development and lifespan cell phenotype cellular phenotype the observable morphological and physiological characteristics of the mammalian system that protects the body from foreign substances, cells, and tissues by producing the immune response and that includes especially the thymus, spleen, lymphoid tissue, lymphocytes including the B cells and T cells, and antibodies that are manifested through development and lifespan immune system phenotype the observable morphological and physiological characteristics of the mammalian system responsible for the exchange of oxygen and carbon dioxide with the environment that are manifested through development and lifespan respiratory system phenotype any functional anomaly of the vital processes of the cell abnormal cell physiology necrosis or death of soft tissue due to lack of blood flow resulting from injury, infection or other conditions that affect blood circulation gangrenous necrosis gangrene a form of coagulative necrosis that develops in ischemic tissue, where the blood supply is inadequate to keep tissue viable, in the absence of superimposed microbial infection; can be due to peripheral artery disease or acute limb ischemia; the affected body part is dry, shrunken, and dark reddish-black and can fall off (autoamputate) if not removed surgically The term dry is used only when referring to a limb or to the gut; in other locations, this same type of necrosis is called an infarction, such as myocardial infarction dry gangrene "The action, reaction, or performance of an organism in response to external or internal stimuli." [GO:GO\:0007610] NBO:0000000 behavior behaviour behavior process Behavior related to the intake of substances. ingest consumption behavior Consumption behavior that involves burning a substance and inhaling the particulate and gas suspension emitted. smoking behavior