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