Barry Smith Alexander Alekseyenko Anna Maria Masci Haihe Wang Jianmin Wu Jie Zheng Jihad Obeid Kaiyong Liu Yongqun "Oliver" He (YH) Yu Hong OHMI is a biomedical ontology that represents the entities and relations in the domain of host-microbiome interactions. OWL-DL OHMI: A biomedical ontology in the domain of host-microbiome interactions. OHMI: Ontology of Host-Microbiome Interactions 2019-09-17 Relates an entity in the ontology to the name of the variable that is used to represent it in the code that generates the BFO OWL file from the lispy specification. Really of interest to developers only BFO OWL specification label Relates an entity in the ontology to the term that is used to represent it in the the CLIF specification of BFO2 Person:Alan Ruttenberg Really of interest to developers only BFO CLIF specification label 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 A phrase describing how a class name should be used. May also include other kinds of examples that facilitate immediate understanding of a class semantics, such as widely known prototypical subclasses or instances of the class. Although essential for high level terms, examples for low level terms (e.g., Affymetrix HU133 array) are not 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> example of usage has curation status PERSON:Alan Ruttenberg PERSON:Bill Bug PERSON:Melanie Courtot OBI_0000281 has curation status definition definition textual definition 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. 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 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 GROUP:OBI:<http://purl.obfoundry.org/obo/obi> IAO:0000116 uberon editor_note true editor_note editor note editor note term editor 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 http://code.google.com/p/information-artifact-ontology/issues/detail?id=115. 20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition editor definition editor term editor term editor alternative term An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent) PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> 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 PERSON:Daniel Schober Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition source definition source curator note An administrative note of use for a curator but of no use for a user PERSON:Alan Ruttenberg IAO:0000232 uberon curator_notes true curator_notes curator note curator notes term tracker item the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/ 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 For external terms/classes, the ontology from which the term was imported PERSON:Alan Ruttenberg PERSON:Melanie Courtot GROUP:OBI:<http://purl.obolibrary.org/obo/obi> imported from expand expression to OBO foundry unique label An alternative name for a class or property which is unique across the OBO Foundry. The intended usage of that property is as follow: OBO foundry unique labels are automatically generated based on regular expressions provided by each ontology, so that SO could specify unique label = 'sequence ' + [label], etc. , MA could specify 'mouse + [label]' etc. Upon importing terms, ontology developers can choose to use the 'OBO foundry unique label' for an imported term or not. The same applies to tools . PERSON:Alan Ruttenberg PERSON:Bjoern Peters PERSON:Chris Mungall PERSON:Melanie Courtot GROUP:OBO Foundry <http://obofoundry.org/> OBO foundry unique label elucidation person:Alan Ruttenberg Person:Barry Smith Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms elucidation has associated axiom(nl) Person:Alan Ruttenberg Person:Alan Ruttenberg An axiom associated with a term expressed using natural language has associated axiom(nl) has associated axiom(fol) Person:Alan Ruttenberg Person:Alan Ruttenberg An axiom expressed in first order logic using CLIF syntax has associated axiom(fol) an annotation property that lists keyword(s) useful for literature tagging and retrieval of sentences containing the type (or kind) of entity (e.g., interaction) as shown by the ontology term label and definition. Yongqun He has literature mining keywords ISA alternative term An alternative term used by the ISA tools project (http://isa-tools.org). Requested by Alejandra Gonzalez-Beltran https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891&atid=886178 Person: Alejandra Gonzalez-Beltran Person: Philippe Rocca-Serra ISA tools project (http://isa-tools.org) ISA alternative term 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 alternative term IEDB alternative term An alternative term used by the IEDB. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IEDB alternative term An annotation property that represents a publication that includes the evidence of the presence of a class type. Jie Zheng, Jihad, Anna Maria, Haihe, Oliver evidence publication 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 https://github.com/oborel/obo-relations/wiki/ROAndTime An assertion that involves at least one OWL object that is intended to be expanded into one or more logical axioms. The logical expansion can yield axioms expressed using any formal logical system, including, but not limited to OWL2-DL. logical macro assertion https://github.com/oborel/obo-relations/wiki/ShortcutRelations A logical macro assertion whose domain is an IRI for a property logical macro assertion on a property Used to annotate object properties to describe a logical meta-property or characteristic of the object property. logical macro assertion on an object property logical macro assertion on an annotation property 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" If we have the annotation P is-direct-form-of Q, and we have inverses P' and Q', then it follows that P' is-direct-form-of Q' Chris Mungall is direct form of relation p is the indirect form of relation q iff p is a subPropertyOf q, and there exists some p' such that p' is the direct form of q, p' o p' -> p, and forall x,y : x q y -> either (1) x p y or (2) x p' y Chris Mungall is indirect form of Used to annotate object properties representing a causal relationship where the value indicates a direction. Should be "+", "-" or "0" cjm 2018-03-13T23:59:29Z is directional form of cjm 2018-03-14T00:03:16Z is positive form of cjm 2018-03-14T00:03:24Z is negative form of An alternate textual definition for a class taken unmodified from an external source. This definition may have been used to derive a generalized definition for the new class. UBPROP:0000001 uberon external_definition true external_definition This annotation property may be replaced with an annotation property from an external ontology such as IAO external_definition Notes on the homology status of this class. UBPROP:0000003 uberon homology_notes true homology_notes This annotation property may be replaced with an annotation property from an external ontology such as IAO homology_notes Used to connect a class to an adjectival form of its label. For example, a class with label 'intestine' may have a relational adjective 'intestinal'. UBPROP:0000007 uberon has_relational_adjective true has_relational_adjective has_relational_adjective Notes on the how instances of this class vary across species. UBPROP:0000008 uberon taxon_notes true taxon_notes taxon_notes Notes on the ontogenic development of instances of this class. This annotation property may be replaced with an annotation property from an external ontology such as IAO UBPROP:0000011 uberon development_notes true development_notes development_notes Notes on how similar or equivalent classes are represented in other ontologies. This annotation property may be replaced with an annotation property from an external ontology such as IAO UBPROP:0000012 uberon external_ontology_notes true external_ontology_notes external_ontology_notes Examples of a Contributor include a person, an organisation, or a service. Typically, the name of a Contributor should be used to indicate the entity. An entity responsible for making contributions to the content of the resource. Contributor Contributor Examples of a Creator include a person, an organisation, or a service. Typically, the name of a Creator should be used to indicate the entity. An entity primarily responsible for making the content of the resource. Creator Creator Typically, Date will be associated with the creation or availability of the resource. Recommended best practice for encoding the date value is defined in a profile of ISO 8601 [W3CDTF] and follows the YYYY-MM-DD format. A date associated with an event in the life cycle of the resource. Date Date Description may include but is not limited to: an abstract, table of contents, reference to a graphical representation of content or a free-text account of the content. An account of the content of the resource. Description Description Typically, Format may include the media-type or dimensions of the resource. Format may be used to determine the software, hardware or other equipment needed to display or operate the resource. Examples of dimensions include size and duration. Recommended best practice is to select a value from a controlled vocabulary (for example, the list of Internet Media Types [MIME] defining computer media formats). The physical or digital manifestation of the resource. Format Format The present resource may be derived from the Source resource in whole or in part. Recommended best practice is to reference the resource by means of a string or number conforming to a formal identification system. A reference to a resource from which the present resource is derived. Source Source Typically, a Subject will be expressed as keywords, key phrases or classification codes that describe a topic of the resource. Recommended best practice is to select a value from a controlled vocabulary or formal classification scheme. The topic of the content of the resource. Subject and Keywords Subject and Keywords Mark Miller 2018-05-11T13:47:29Z created_by creation_date has_alternative_id has_broad_synonym database_cross_reference has_exact_synonym has_narrow_synonym disease_ontology has_obo_namespace has_related_synonym id in_subset shorthand is defined by label label label http://www.w3.org/2000/01/rdf-schema#seeAlso seeAlso true true seeAlso seeAlso is part of my brain is part of my body (continuant parthood, two material entities) my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity) this day is part of this year (occurrent parthood) a core relation that holds between a part and its whole Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other. 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 https://code.google.com/p/obo-relations/wiki/ROAndTime Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. part_of part of http://www.obofoundry.org/ro/#OBO_REL:part_of has part my body has part my brain (continuant parthood, two material entities) my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) this year has part this day (occurrent parthood) 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 https://code.google.com/p/obo-relations/wiki/ROAndTime 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 has part realized in this disease is realized in this disease course this fragility is realized in this shattering this investigator role is realized in this investigation is realized by realized_in [copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process realized in realizes this disease course realizes this disease this investigation realizes this investigator role this shattering realizes this fragility to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process realizes accidentally included in BFO 1.2 proposal - should have been BFO_0000062 obsolete preceded by true preceded by x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(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. An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. is preceded by preceded_by http://www.obofoundry.org/ro/#OBO_REL:preceded_by preceded by precedes x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), 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. precedes 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 has measurement unit label This document is about information artifacts and their representations is_about is 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 relates a process to a time-measurement-datum that represents the duration of the process Person:Alan Ruttenberg is duration of has_specified_input has_specified_input see is_input_of example_of_usage 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. 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 has_specified_output 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. PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Larry Hunter PERSON: Melanie Courtot has_specified_output is_specified_output_of 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 achieves_planned_objective A cell sorting process achieves the objective specification 'material separation objective' This relation obtains between a planned process and a objective specification when the criteria specified in the objective specification are met at the end of the planned process. BP, AR, PPPB branch PPPB branch derived modified according to email thread from 1/23/09 in accordince with DT and PPPB branch achieves_planned_objective has grain the relation of the cells in the finger of the skin to the finger, in which an indeterminate number of grains are parts of the whole by virtue of being grains in a collective that is part of the whole, and in which removing one granular part does not nec- essarily damage or diminish the whole. Ontological Whether there is a fixed, or nearly fixed number of parts - e.g. fingers of the hand, chambers of the heart, or wheels of a car - such that there can be a notion of a single one being missing, or whether, by contrast, the number of parts is indeterminate - e.g., cells in the skin of the hand, red cells in blood, or rubber molecules in the tread of the tire of the wheel of the car. Discussion in Karslruhe with, among others, Alan Rector, Stefan Schulz, Marijke Keet, Melanie Courtot, and Alan Ruttenberg. Definition take from the definition of granular parthood in the cited paper. Needs work to put into standard form PERSON: Alan Ruttenberg PAPER: Granularity, scale and collectivity: When size does and does not matter, Alan Rector, Jeremy Rogers, Thomas Bittner, Journal of Biomedical Informatics 39 (2006) 333-349 has grain objective_achieved_by This relation obtains between a a objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process. OBI OBI objective_achieved_by 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 An object property that represents the susceptible increase (compared to healthy control) of the population of a microbe in a host with a specific disease. This is a shortcut relation where the domain is microbe, and the range is a disease. Oliver He microbe susceptibly expanded in host with disease An object property that represents the susceptible increase (compared to healthy control) of the population of a microbe in a human with a specific disease. This is a shortcut relation where the domain is microbe, and the range is a disease. Oliver He microbe susceptibly expanded in human with disease An object property that represents the susceptible increase (compared to healthy control) of the population of a microbe in the gut of a human with a specific disease. This is a shortcut relation where the domain is microbe, and the range is a disease. Oliver He microbe susceptibly expanded in gut of human with disease has disease An object property that represents the susceptible decrease (compared to healthy control) of the population of a microbe in a host with a specific disease. The susceptibility is usually derived from peer-reviewed studies. This is a shortcut relation where the domain is microbe, and the range is a disease. Oliver He microbe susceptibly depleted in host with disease this is a shortcut object property that represents the phenotype that exists in a microbial population inside a host. Yongqun He, Haihe Wang, Jie Zheng microbial population phenotype in host An object property that represents the susceptible decrease (compared to healthy control) of the population of a microbe in a human with a specific disease. This is a shortcut relation where the domain is microbe, and the range is a disease. Oliver He microbe susceptibly depleted in human with disease has phenotype An object property that represents the susceptible decrease (compared to healthy control) of the population of a microbe in the gut of a human with a specific disease. This is a shortcut relation where the domain is microbe, and the range is a disease. Oliver He microbe susceptibly depleted in gut of human with disease An object property that represents the susceptible decrease (compared to healthy control) of the population of a microbe in a rat with a specific disease. This is a shortcut relation where the domain is microbe, and the range is a disease. Oliver He microbe susceptibly depleted in rat with disease An object property that represents the susceptible increase (compared to healthy control) of the population of a microbe in a rat with a specific disease. This is a shortcut relation where the domain is microbe, and the range is a disease. Oliver He microbe susceptibly expanded in rat with disease An object property that represents the susceptible decrease (compared to healthy control) of the population of a microbe in the gut of a rat with a specific disease. This is a shortcut relation where the domain is microbe, and the range is a disease. Oliver He microbe susceptibly depleted in gut of rat with disease An object property that represents the susceptible increase (compared to healthy control) of the population of a microbe in the gut of a rat with a specific disease. This is a shortcut relation where the domain is microbe, and the range is a disease. Oliver He microbe susceptibly expanded in gut of rat with disease An object property that represents a disease in a host where the host has susceptibly increased population of a microbe. This is a shortcut relation where the domain is disease, and the range is a microbe. Oliver He disease in host with susceptibly expanded microbe An object property that represents the susceptible change (compared to healthy control) of the population of a microbe in a host with a specific disease. This is a shortcut relation where the domain is microbe, and the range is a disease. Oliver He microbe susceptibly changed in host with disease An object property that represents a disease in a host where the host has susceptibly decreased population of a microbe. This is a shortcut relation where the domain is disease, and the range is a microbe. Oliver He disease in host with susceptibly depleted microbe An object property that represents the susceptible decrease (compared to healthy control) of the population of a microbe in the respiratory airway of a human with a specific disease. This is a shortcut relation where the domain is microbe, and the range is a disease. Oliver He microbe susceptibly depleted in respiratory airway of human with disease An object property that represents the susceptible increase (compared to healthy control) of the population of a microbe in the respiratory airway of a human with a specific disease. This is a shortcut relation where the domain is microbe, and the range is a disease. Oliver He microbe susceptibly expanded in respiratory airway of human with disease An object property that represents the susceptible increase (compared to healthy control) of the population of a microbe in the oral cavity of a human with a specific disease. This is a shortcut relation where the domain is microbe, and the range is a disease. Oliver He microbe susceptibly expanded in oral cavity of human with disease An object property that represents the susceptible decrease (compared to healthy control) of the population of a microbe in the oral cavity of a human with a specific disease. This is a shortcut relation where the domain is microbe, and the range is a disease. Oliver He microbe susceptibly depleted in oral cavity of human with disease microbe susceptibly expanded in mouse with disease microbe susceptibly expanded in gut of mouse with disease microbe susceptibly depleted in mouse with disease microbe susceptibly depleted in gut of mouse with disease an object property that represents the relation between a host-microbiome interaction and a microbe where the population of the microbe is depleted in a diseased host compared to a healthy host control. Oliver He has microbe depleted in diseased host an object property that represents the relation between a host-microbiome interaction and a microbe where the population of the microbe is expanded in a diseased host compared to a healthy host control. Oliver He has microbe expanded in diseased host microbe susceptibly depleted (compared to fibromyalgia patients) in gut of human with disease A subproperty of the 'has participant' object property that has the domain of host-microbiome interaction and range of a microbe where the population of the microbe has size altered in a disease host organism YH has microbe population size altered in diseased host Oliver He an object subproperty of 'has participant' in which the participant is a host organism. has host inheres in this fragility inheres in this vase this red color inheres in this apple a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence A dependent inheres in its bearer at all times for which the dependent exists. inheres_in inheres in bearer of this apple is bearer of this red color this vase is bearer of this fragility a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist. bearer_of is bearer of bearer of participates in this blood clot participates in this blood coagulation this input material (or this output material) participates in this process this investigator participates in this investigation a relation between a continuant and a process, in which the continuant is somehow involved in the process participates_in participates 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 A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process). A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants. is concretized as A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process). A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant. concretizes this catalysis function is a function of this enzyme a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists. function_of is function of function of this investigator role is a role of this person a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists. is role of role_of role of this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function) a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists. has_function has function 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 a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence has disposition inverse of has disposition disposition of derives from 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 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 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 https://code.google.com/p/obo-relations/wiki/ROAndTime located_in http://www.obofoundry.org/ro/#OBO_REL:located_in located in dos 2017-05-24T09:44:33Z A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. has component activity w 'has process component' p if p and w are processes, 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. dos 2017-05-24T09:49:21Z has component process A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. dos 2017-09-22T14:14:36Z This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations. has effector activity David Osumi-Sutherland <= Primitive instance level timing relation between events before or simultaneous with David Osumi-Sutherland t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2) simultaneous with David Osumi-Sutherland t1 before t2 iff:= t1 before_or_simulataneous_with t2 and not (t1 simultaeous_with t2) before David Osumi-Sutherland Previously had ID http://purl.obolibrary.org/obo/RO_0002122 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. during which ends David Osumi-Sutherland di Previously had ID http://purl.obolibrary.org/obo/RO_0002124 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. encompasses David Osumi-Sutherland X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) ends after 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 Previously had ID http://purl.obolibrary.org/obo/RO_0002123 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. during which starts David Osumi-Sutherland starts before 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 David Osumi-Sutherland o overlaps X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y). ends during x overlaps y if and only if there exists some z such that x has part z and z part of y http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y) overlaps 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 process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2. We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit Chris Mungall David Hill Tanya Berardini GO Regulation precludes parthood; the regulatory process may not be within the regulated process. regulates (processual) false regulates Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2. Chris Mungall negatively regulates (process to process) negatively regulates Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2. Chris Mungall positively regulates (process to process) positively regulates 'human p53 protein' SubClassOf some ('has prototype' some ('participates in' some 'DNA repair')) heart SubClassOf 'has prototype' some ('participates in' some 'blood circulation') x has prototype y if and only if x is an instance of C and y is a prototypical instance of C. For example, every instance of heart, both normal and abnormal is related by the has prototype relation to some instance of a "canonical" heart, which participates in blood circulation. Experimental. In future there may be a formalization in which this relation is treated as a shortcut to some modal logic axiom. We may decide to obsolete this and adopt a more specific evolutionary relationship (e.g. evolved from) This property can be used to make weaker forms of certain relations by chaining an additional property. For example, we may say: retina SubClassOf has_prototype some 'detection of light'. i.e. every retina is related to a prototypical retina instance which is detecting some light. Note that this is very similar to 'capable of', but this relation affords a wider flexibility. E.g. we can make a relation between continuants. Chris Mungall has prototype move to BFO? Chris Mungall Allen Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends. https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. temporal relation temporally related to inverse of starts with Chris Mungall Allen starts 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 inverse of ends with Chris Mungall ends 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. Chris Mungall consumes 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 at the beginning of p. Chris Mungall produces has output cjm holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y causally upstream of, positive effect cjm holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y causally upstream of, negative effect q inheres in part of w if and only if there exists some p such that q inheres in p and p part of w. Because part_of is transitive, inheres in is a sub-relation of inheres in part of Chris Mungall inheres in part of A mereological relationship or a topological relationship Chris Mungall Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships mereotopologically related to A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities. Chris Mungall This is a grouping relation that collects relations used for the purpose of connecting structure and function functionally related to inverse of regulates Chris Mungall regulated by (processual) regulated by inverse of negatively regulates Chris Mungall negatively regulated by inverse of positively regulates Chris Mungall positively regulated by has member is a mereological relation between a collection and an item. SIO has member inverse of has input Chris Mungall input of inverse of has output Chris Mungall output of 'protein catabolic process' SubClassOf has_direct_input some protein p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p. Chris Mungall directly consumes This is likely to be obsoleted. A candidate replacement would be a new relation 'has bound input' or 'has substrate' has direct input translation SubClassOf has_direct_output some protein p has direct input c iff c is a participanti n p, c is present at the end of p, and c is not present at the beginning of c. Chris Mungall directly produces obsolete has direct output true inverse of upstream of Chris Mungall causally downstream of Chris Mungall immediately causally downstream of p directly activates q if and only if p is immediately upstream of q and p is the realization of a function to increase the rate or activity of q Chris Mungall directly positively regulates directly activates (process to process) directly activates p directly activates q if and only if p is immediately upstream of q and p is the realization of a function to increase the rate or activity of q Chris Mungall indirectly positively regulates indirectly activates Chris Mungall directly negatively regulates directly inhibits (process to process) directly inhibits Chris Mungall indirectly negatively regulates indirectly inhibits This relation groups causal relations between material entities and causal relations between processes This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents. To define causal relations in an activity-flow type network, we make use of 3 primitives: * Temporal: how do the intervals of the two occurrents relate? * Is the causal relation regulatory? * Is the influence positive or negative The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified. For the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule. For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral. Each of these 3 primitives can be composed to yield a cross-product of different relation types. Chris Mungall Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causally related to p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain Chris Mungall causally upstream of p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q. Chris Mungall immediately causally upstream of p1 directly provides input for p2 iff there exists some c such that p1 has_output c and p2 has_input c This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit Chris Mungall directly provides input for (process to process) directly provides input for transitive form of directly_provides_input_for Chris Mungall This is a grouping relation that should probably not be used in annotation. Consider instead the child relation 'directly provides input for' (which may later be relabeled simply to 'provides input for') transitively provides input for (process to process) transitively provides input for p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q. We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2 Chris Mungall influences (processual) affects causally upstream of or within inverse of causally upstream of or within Chris Mungall causally downstream of or within p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q. Chris Mungall Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causal relation between processes Chris Mungall depends on Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. Chris Mungall directly regulates (processual) directly regulates Process(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2. directly positively regulates (process to process) directly positively regulates Process(P1) directly negatively regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2. directly negatively regulates (process to process) directly negatively regulates cjm 2018-03-13T23:55:05Z causally upstream of or within, negative effect cjm 2018-03-13T23:55:19Z causally upstream of or within, positive effect Relation between biological objects that resemble or are related to each other sufficiently to warrant a comparison. ECO:0000041 SO:similar_to sameness similar to correspondence resemblance in similarity relationship with has measurement value has specified numeric value A relation between a value specification and a number that quantifies it. A range of 'real' might be better than 'float'. For now we follow 'has measurement value' until we can consider technical issues with SPARQL queries and reasoning. PERSON: James A. Overton OBI has specified numeric value 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 entity Entity Julius Caesar Verdi’s Requiem the Second World War your body mass index BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81 Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) entity continuant Continuant 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. BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240 Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] continuant occurrent Occurrent An entity that has temporal parts and that happens, unfolds or develops through time. BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players. Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] occurrent ic IndependentContinuant a chair a heart a leg a molecule a spatial region an atom an orchestra. an organism the bottom right portion of a human torso the interior of your mouth 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]) For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] independent continuant spatial region process Process a process of cell-division, \ a beating of the heart a process of meiosis a process of sleeping the course of a disease the flight of a bird the life of an organism your process of aging. 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]) BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war) (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] process disposition Disposition an atom of element X has the disposition to decay to an atom of element Y certain people have a predisposition to colon cancer children are innately disposed to categorize objects in certain ways. the cell wall is disposed to filter chemicals in endocytosis and exocytosis BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type. b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002]) If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002]) (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] disposition realizable RealizableEntity the disposition of this piece of metal to conduct electricity. the disposition of your blood to coagulate the function of your reproductive organs the role of being a doctor the role of this boundary to delineate where Utah and Colorado meet A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances. To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] realizable entity quality Quality the ambient temperature of this portion of air the color of a tomato the length of the circumference of your waist the mass of this piece of gold. the shape of your nose the shape of your nostril 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. (axiom label in BFO2 Reference: [055-001]) If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] quality sdc SpecificallyDependentContinuant Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key of one-sided specifically dependent continuants: the mass of this tomato of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates. the disposition of this fish to decay the function of this heart: to pump blood the mutual dependence of proton donors and acceptors in chemical reactions [79 the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction the pink color of a medium rare piece of grilled filet mignon at its center the role of being a doctor the shape of this hole. the smell of this portion of mozzarella 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. 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. (axiom label in BFO2 Reference: [050-003]) Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. (iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004] (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] specifically dependent continuant role Role John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married. the priest role the role of a boundary to demarcate two neighboring administrative territories the role of a building in serving as a military target the role of a stone in marking a property boundary the role of subject in a clinical trial the student role 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. BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives. b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] role gdc GenericallyDependentContinuant The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity. the pdf file on your laptop, the pdf file that is a copy thereof on my laptop the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule. 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]) (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] generically dependent continuant function Function the function of a hammer to drive in nails the function of a heart pacemaker to regulate the beating of a heart through electricity the function of amylase in saliva to break down starch into sugar BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc. A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001]) (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] function p-boundary ProcessBoundary the boundary between the 2nd and 3rd year of your life. p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001]) Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002]) (forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002] (iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001] process boundary material MaterialEntity a flame a forest fire a human being a hurricane a photon a puff of smoke a sea wave a tornado an aggregate of human beings. an energy wave an epidemic the undetached arm of a human being An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60 BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity. BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here. A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] material entity immaterial entity Material anatomical entity that is a member of an individual species or is a viral or viroid particle. organism or virus Melissa Haendel 9/18/11 organism or virus or viroid peptide 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. peptide deoxyribonucleic acid High molecular weight, linear polymers, composed of nucleotides containing deoxyribose and linked by phosphodiester bonds; DNA contain the genetic information of organisms. deoxyribonucleic acid molecular entity Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity. We are assuming that every molecular entity has to be completely connected by chemical bonds. This excludes protein complexes, which are comprised of minimally two separate molecular entities. We will follow up with Chebi to ensure this is their understanding as well molecular entity atom A chemical entity constituting the smallest component of an element having the chemical properties of the element. atom nucleic acid 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 ribonucleic 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 macromolecule 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. polymer macromolecule cell cell PMID:18089833.Cancer Res. 2007 Dec 15;67(24):12018-25. "...Epithelial cells were harvested from histologically confirmed adenocarcinomas .." 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. cell cell cultured cell A cell in vitro that is or has been maintained or propagated as part of a cell 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. experimentally modified cell in vitro A quantitative or qualitative value which is the result of an act of assessing a morphological or physiological state or property in a single individual or sample or a group of individuals or samples, based on direct observation or experimental manipulation. Clinical_Measurement.ontology CMO:0000000 clinical measurement Any measurement related to immunoglobulin, any of several classes of proteins produced by plasma cells and lymphocytes which play essential roles in the immune system, for example, attaching to foreign substances in an effort to destroy them, in serum, the clear liquid that separates from blood after it has clotted completely, i.e. blood plasma from which fibrinogen has been removed. JSmith 2013-01-08T18:17:44Z Clinical_Measurement.ontology CMO:0001276 serum immunoglobulin measurement Any measurement related to immunoglobulins, any of several classes of proteins produced by plasma cells and lymphocytes which play essential roles in the immune system, for example, attaching to foreign substances in an effort to destroy them, in blood, the fluid that circulates through the heart, arteries, capillaries and veins carrying nutrients and oxygen to the body tissues and metabolites away from them. JSmith 2013-01-30T12:00:54Z Clinical_Measurement.ontology CMO:0001531 blood immunoglobulin measurement The amount in a specified sample of serum of one or more types of immunoglobulin A (IgA), one of the most prevalent of the five classes of antibodies produced by the body. IgA is found in all secretions of the body and is the major antibody in the tears, saliva, and mucous membranes lining the intestines and bronchi, constituting an important factor in mucosal immunity. JSmith 2014-01-27T12:21:14Z serum IgA level Clinical_Measurement.ontology CMO:0002095 serum immunoglobulin A level The amount in a specified sample of serum of one or more types of immunoglobulin G (IgG), the most abundant class of antibodies found in blood serum and lymph. IgG antibodies are active against bacteria, fungi, viruses, and foreign particles, and trigger action of the complement system. JSmith 2014-01-27T12:33:22Z serum IgG level Clinical_Measurement.ontology CMO:0002102 serum immunoglobulin G level The amount in a specified sample of serum of one or more types of immunoglobulin M (IgM), one of the five classes of antibodies produced by the body. IgM is found in circulating body fluids and is the first class of antibodies to appear in response to an initial exposure to an antigen. JSmith 2014-01-27T12:35:25Z serum IgM level Clinical_Measurement.ontology CMO:0002104 serum immunoglobulin M level An intestinal disease characterized by inflammation located_in all parts of digestive tract. EFO:0003767 KEGG:05321 MESH:D015212 NCI:C3138 OMIM:PS266600 SNOMEDCT_US_2018_03_01:24526004 UMLS_CUI:C0021390 disease_ontology DOID:0050589 Xref MGI. OMIM mapping confirmed by DO. [SN]. inflammatory bowel disease A cancer that is classified based on the organ it starts in. snadendla 2011-06-13T03:28:33Z MESH:D009371 disease_ontology DOID:0050686 organ system cancer An autoimmune hypersensitivity 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 musculoskeletal system. disease_ontology DOID:0060032 autoimmune disease of musculoskeletal system A gastrointestinal system cancer that is located_in the hepatobiliary system disease_ontology DOID:0080355 hepatobiliary system cancer A gastrointestinal system cancer that is located_in the intestine. ICD10CM:C26.0 ICD9CM:159.0 MESH:D007414 NCI2004_11_17:C4572 NCI:C4572 SNOMEDCT_US_2018_03_01:93838000 UMLS_CUI:C0346627 malignant intestinal tumors malignant neoplasm of intestine disease_ontology DOID:10155 intestinal cancer A gastrointestinal system cancer that is located_in the stomach. DOID:10539 DOID:10542 DOID:10543 DOID:4713 GARD:7704 ICD10CM:C16 ICD10CM:C16.2 ICD10CM:C16.5 ICD10CM:C16.6 ICD10CM:C16.9 ICD9CM:151 ICD9CM:151.4 ICD9CM:151.5 ICD9CM:151.6 ICD9CM:151.9 MESH:D013274 NCI:C3387 NCI:C9331 OMIM:137215 OMIM:613659 SNOMEDCT_US_2018_03_01:93717002 SNOMEDCT_US_2018_03_01:93818001 SNOMEDCT_US_2018_03_01:93867004 SNOMEDCT_US_2018_03_01:94074003 UMLS_CUI:C0024623 UMLS_CUI:C0038356 UMLS_CUI:C0153421 UMLS_CUI:C0153422 UMLS_CUI:C0153423 Ca body - stomach Ca lesser curvature - stomach ca greater curvature of stomach gastric cancer gastric neoplasm malignant neoplasm of body of stomach malignant neoplasm of lesser curve of stomach malignant tumor of body of stomach malignant tumor of greater curve of stomach malignant tumor of lesser curve of stomach disease_ontology DOID:10534 OMIM mapping confirmed by DO. [SN]. stomach cancer An arthritis that has_material_basis_in uric acid crystal deposits located_in joint. DOID:14144 EFO:0004274 ICD10CM:M10 ICD10CM:M10.9 ICD9CM:274 ICD9CM:274.0 ICD9CM:274.00 ICD9CM:274.9 MESH:D006073 MESH:D015210 NCI:C34650 SNOMEDCT_US_2018_03_01:48440001 SNOMEDCT_US_2018_03_01:90560007 UMLS_CUI:C0003868 UMLS_CUI:C0018099 Articular gout Gouty arthropathy gouty arthritis disease_ontology DOID:13189 gout A gastrointestinal system disease described as the condition of having frequent loose or liquid bowel movements. Acute diarrhea is a common cause of death in developing countries and the second most common cause of infant deaths worldwide. The loss of fluids through diarrhea can cause severe dehydration which is one cause of death in diarrhea sufferers. Along with water, sufferers also lose dangerous amounts of important salts, electrolytes, and other nutrients. There are at least four types of diarrhea: secretory diarrhea, osmotic diarrhea, motility-related diarrhea, and inflammatory diarrhea. DOID:0050006 ICD9CM:009.2 MESH:D003967 SNOMEDCT_US_2018_03_01:19213003 UMLS_CUI:C0013369 disease_ontology diarrhea of presumed infectious origin diarrhoea DOID:13250 diarrhea An autoimmune hypersensitivity disease that involves inflammation or pain in the muscles, joints, or fibrous tissue. disease_ontology DOID:1575 rheumatic disease A disease of cellular proliferation that is malignant and primary, characterized by uncontrolled cellular proliferation, local cell invasion and metastasis. ICD10CM:C80 ICD10CM:C80.1 ICD9CM:199 MESH:D009369 NCI:C9305 SNOMEDCT_US_2018_03_01:38807002 UMLS_CUI:C0006826 stedman:rlc malignant neoplasm malignant tumor primary cancer disease_ontology DOID:162 Updating out dated UMLS CUI. cancer A disease of anatomical entity that occurs in the muscular and/or skeletal system. MESH:D009140 NCI:C107377 SNOMEDCT_US_2018_03_01:928000 UMLS_CUI:C0026857 disease_ontology DOID:17 musculoskeletal system disease An organ system cancer located_in endocrine system that is characterized by uncontrolled cellular proliferation of the hormone producing glands of the endocrine system. DOID:10009 CSP2005:2009-5861 ICD10CM:C75.9 ICD9CM:194.9 MESH:D004701 NCI2004_11_17:C3010 NCI2004_11_17:C3575 NCI:C3010 NCI:C3575 SNOMEDCT_US_2018_03_01:93780007 UMLS_CUI:C0014132 UMLS_CUI:C0153658 Endocrine tumor endocrine neoplasm malignant Endocrine tumor malignant neoplasm of endocrine gland malignant tumour of endocrine gland neoplasm of endocrine gland neoplasm of endocrine system disease_ontology DOID:170 endocrine gland cancer An endocrine gland cancer located_in the pancreas. DOID:14356 DOID:1797 DOID:3588 DOID:9859 CSP2005:2014-4876 GARD:9364 ICD10CM:C25.0 ICD10CM:C25.1 ICD10CM:C25.2 ICD9CM:157.0 ICD9CM:157.1 ICD9CM:157.2 ICD9CM:157.8 KEGG:05212 MESH:D010190 MTH:NOCODE NCI2004_11_17:C3305 NCI:C3305 ORDO:1333 ORDO:217074 SNOMEDCT_US_2018_03_01:93715005 SNOMEDCT_US_2018_03_01:93823001 SNOMEDCT_US_2018_03_01:94082003 UMLS_CUI:C0030297 UMLS_CUI:C0153458 UMLS_CUI:C0153459 UMLS_CUI:C0153460 UMLS_CUI:C0153463 Ca body of pancreas Ca head of pancreas Ca tail of pancreas malignant neoplasm of body of pancreas malignant neoplasm of head of pancreas malignant neoplasm of tail of pancreas pancreas neoplasm pancreatic neoplasm pancreatic tumor disease_ontology DOID:1793 Xref MGI. pancreatic cancer A large intestine cancer that is located_in the colon. ICD10CM:C18 ICD10CM:C18.9 ICD9CM:153 ICD9CM:153.9 MESH:D003110 NCI:C9242 SNOMEDCT_US_2018_03_01:93761005 UMLS_CUI:C0007102 disease_ontology DOID:219 colon cancer 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. ICD10CM:E34.9 ICD9CM:259.9 MESH:D004700 NCI:C3009 SNOMEDCT_US_2018_03_01:67432001 UMLS_CUI:C0014130 disease_ontology DOID:28 endocrine system disease A disease of anatomical entity that is located_in the immune system. EFO:0000540 ICD10CM:D89.9 ICD9CM:279 ICD9CM:279.9 UMLS_CUI:C0041806 disease_ontology DOID:2914 immune system disease A cell type cancer that has_material_basis_in abnormally proliferating cells derives_from epithelial cells. DOID:2428 DOID:6570 CSP2005:2000-5801 MESH:D002277 MESH:D009375 NCI2004_11_17:C6927 NCI:C2916 NCI:C3709 SNOMEDCT_US_2018_03_01:68453008 SNOMEDCT_US_2018_03_01:71298006 UMLS_CUI:C0007097 UMLS_CUI:C0553707 UMLS_CUI:C1368683 epithelioma malignant Epithelioma disease_ontology DOID:305 carcinoma DOID:11500 DOID:6144 CSP2005:4004-0004 EFO:0000341 ICD10CM:J44.9 MESH:D029424 NCI2004_11_17:C3199 NCI:C3199 OMIM:606963 SNOMEDCT_US_2018_03_01:13645005 UMLS_CUI:C0024117 COLD COPD chronic obstructive airway disease chronic obstructive lung disease disease_ontology DOID:3083 chronic obstructive pulmonary disease A gastrointestinal system disease that is located_in the liver and/or biliary tract. NCI:C3959 UMLS_CUI:C0267792 liver and biliary tract disease disease_ontology DOID:3118 hepatobiliary disease An organ system cancer located_in gastrointestinal tract that is manifested in organs of the gastrointestinal system. DOID:4945 DOID:8377 ICD10CM:C26.9 ICD9CM:239.0 MESH:D004067 MESH:D005770 NCI2004_11_17:C3052 NCI2004_11_17:C4890 NCI:C3052 NCI:C4890 SNOMEDCT_US_2018_03_01:93811007 UMLS_CUI:C0012243 UMLS_CUI:C0017185 UMLS_CUI:C0685938 GI tumor digestive system cancer gastrointestinal tract cancer disease_ontology DOID:3119 gastrointestinal system cancer A bone disease that results_in inflammation of the located_in bone. CSP2005:2715-2703 MESH:D010000 SNOMEDCT_US_2018_03_01:44462005 UMLS_CUI:C0029400 Inflammatory disorder of bone bone inflammatory disease osteitis disease_ontology DOID:3342 bone inflammation disease A hepatobiliary system cancer that is located_in the liver. DOID:12300 DOID:269 DOID:7330 DOID:915 DOID:919 CSP2005:2003-2810 ICD10CM:C22.0 ICD10CM:C22.9 ICD9CM:155.0 ICD9CM:155.2 ICD9CM_2006:155.0 ICD9CM_2006:155.2 MESH:D008113 NCI2004_11_17:C34803 NCI2004_11_17:C7692 NCI:C34803 NCI:C7692 SNOMEDCT_US_2018_03_01:93870000 SNOMEDCT_US_2018_03_01:95214007 UMLS_CUI:C0023903 UMLS_CUI:C0024620 UMLS_CUI:C0345904 UMLS_CUI:C0854795 Ca liver - primary Resectable malignant neoplasm of Liver ca liver - primary hepatic cancer hepatic neoplasm malignant hepato-biliary neoplasm malignant neoplasm of liver malignant neoplasm of liver, not specified as primary or secondary malignant neoplasm of liver, primary malignant tumor of liver neoplasm of liver non-resectable primary hepatic malignant neoplasm primary liver cancer primary malignant neoplasm of Liver primary malignant neoplasm of liver resectable malignant neoplasm of the liver disease_ontology DOID:3571 liver cancer 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. MESH:D004194 NCI:C2991 SNOMEDCT_US_2018_03_01:64572001 UMLS_CUI:C0012634 disease_ontology DOID:4 disease DOID:2164 DOID:2165 DOID:46 ICD10CM:K70-K77 ICD10CM:K76.9 ICD9CM:573.9 MESH:D008107 NCI2004_11_17:C3196 NCI:C3196 SNOMEDCT_US_2018_03_01:62857009 UMLS_CUI:C0023895 disorder of liver hepatic disorder disease_ontology DOID:409 liver disease 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. ICD9CM:720 OMIM:109100 UMLS_CUI:C0003089 ls:IEDB autoimmune disease hypersensitivity reaction type II disease disease_ontology DOID:417 Xref MGI. autoimmune hypersensitivity disease A biliary tract cancer that is located_in the bile duct. DOID:10019 ICD10CM:C24.0 ICD9CM:156.1 MESH:D001650 NCI2004_11_17:C2898 NCI2004_11_17:C7483 NCI:C2898 NCI:C7483 SNOMEDCT_US_2018_03_01:93790004 UMLS_CUI:C0005396 UMLS_CUI:C0153453 Ca extrahepatic bile ducts bile duct tumor malignant neoplasm of the extrahepatic bile duct disease_ontology DOID:4606 bile duct cancer A gastrointestinal system cancer that is located_in the esophagus. DOID:10291 DOID:10292 DOID:10448 DOID:1102 DOID:1104 GARD:6383 ICD10CM:C15.3 ICD10CM:C15.4 ICD10CM:C15.5 ICD9CM:150.2 ICD9CM:150.3 ICD9CM:150.4 ICD9CM:150.5 ICD9CM:150.8 MESH:D004938 MTHICD9_2006:150.3 MTHICD9_2006:150.5 NCI2004_11_17:C3533 NCI2004_11_17:C3534 NCI2004_11_17:C3535 NCI2004_11_17:C4764 NCI:C3028 NCI:C3533 NCI:C3534 NCI:C3535 NCI:C4764 OMIM:133239 SNOMEDCT_US_2018_03_01:93656003 SNOMEDCT_US_2018_03_01:93877002 SNOMEDCT_US_2018_03_01:93895004 SNOMEDCT_US_2018_03_01:94119000 UMLS_CUI:C0014859 UMLS_CUI:C0153413 UMLS_CUI:C0153414 UMLS_CUI:C0153415 UMLS_CUI:C0153416 UMLS_CUI:C0496775 Ca lower third oesophagus Ca middle third oesophagus esophagus cancer malignant neoplasm of distal third of esophagus malignant neoplasm of lower third of oesophagus malignant neoplasm of middle third of oesophagus malignant neoplasm of proximal third of esophagus malignant neoplasm of upper third esophagus malignant tumor of Distal Third of esophagus malignant tumor of Proximal Third of esophagus malignant tumor of abdominal esophagus malignant tumor of the middle Third of the esophagus disease_ontology DOID:5041 esophageal cancer A gastrointestinal system disease that is located_in the intestine. DOID:10759 DOID:11222 DOID:11789 DOID:8531 DOID:8558 DOID:8591 ICD10CM:K63.9 ICD9CM:569.9 MESH:D007410 NCI:C26801 SNOMEDCT_US_2018_03_01:85919009 UMLS_CUI:C0021831 disease_ontology DOID:5295 intestinal disease A stomach cancer that is located_in the stomach. EFO:0000178 NCI2004_11_17:C4911 NCI:C4911 UMLS_CUI:C0699791 cancer of the stomach carcinoma of stomach gastric carcinoma disease_ontology DOID:5517 stomach carcinoma An intestinal cancer that effects the long, tube-like organ that is connected to the small intestine at one end and the anus at the other. DOID:1994 DOID:1997 ICD10CM:C18.9 MESH:D015179 NCI:C2955 NCI:C4978 NCI:C5105 SNOMEDCT_US_2018_03_01:93854002 UMLS_CUI:C0009402 UMLS_CUI:C0346629 UMLS_CUI:C1319315 disease_ontology DOID:5672 large intestine cancer An arthritis that is an autoimmune disease which develops due to an infection located elsewhere in the body. [database_cross_reference: url:http://emedicine.medscape.com/article/331347-overview][database_cross_reference: url:http://en.wikipedia.org/wiki/Reactive_arthritis] Fiessinger Leroy Reiter syndrome; Post-bacterial arthropathy; postdysenteric arthropathy; Reiter's disease; Reactive arthritis; Reiter disease reactive arthritis A musculoskeletal system disease that affects tissues such as skin, tendons, and cartilage. CSP2005:0729-7208 MESH:D003240 NCI:C26729 UMLS_CUI:C0009782 connective tissue disorder disorder of connective tissue disease_ontology DOID:65 connective tissue disease A rheumatoid arthritis that involves an autoimmune disease onset in children under 16 which attacks the healthy cells and tissue of located_in joint. DOID:10129 DOID:1264 DOID:675 ICD10CM:M08.4 ICD10CM:M08.40 ICD9CM:714.3 ICD9CM:714.31 ICD9CM:714.32 ICD9CM:714.33 NCI:C26979 NCI:C61279 OMIM:604302 ORDO:92 SNOMEDCT_US_2018_03_01:74391003 SNOMEDCT_US_2018_03_01:7441009 SNOMEDCT_US_2018_03_01:75822003 SNOMEDCT_US_2018_03_01:83793004 UMLS_CUI:C0157916 UMLS_CUI:C0157917 UMLS_CUI:C0157918 UMLS_CUI:C0409667 Pauciarticular onset juvenile chronic arthritis acute juvenile rheumatoid arthritis juvenile chronic polyarthritis juvenile idiopathic arthritis monarticular juvenile rheumatoid arthritis pauciarticular juvenile arthritis systemic juvenile rheumatoid arthritis disease_ontology DOID:676 Xref MGI. juvenile rheumatoid arthritis A liver carcinoma that has_material_basis_in undifferentiated hepatocytes. DOID:5005 EFO:0000182 NCI2004_11_17:C3099 NCI2004_11_17:C7956 NCI:C7956 OMIM:114550 UMLS_CUI:C0279607 HCC Hepatoma adult Hepatoma adult primary hepatocellular carcinoma disease_ontology DOID:684 OMIM mapping confirmed by DO. [SN]. hepatocellular carcinoma A liver cancer that has_material_basis_in epithelial cells. NCI2004_11_17:C7927 NCI:C7927 UMLS_CUI:C0279000 Liver and Intrahepatic bile duct carcinoma disease_ontology DOID:686 liver carcinoma A disease that manifests in a defined anatomical structure. DOID:1 DOID:2 DOID:5 DOID:71 DOID:72 DOID:8 disease_ontology DOID:7 disease of anatomical entity A bone inflammation disease that results_in inflammation in the joints of the spine and pelvis. The disease has_symptom pain, has_symptom stiffness in the spine, has_symptom stiffness in the neck, has_symptom stiffness in the hips, has_symptom stiffness in the jaw and has_symptom stiffness in the rib cage. EFO:0003898 GARD:9518 ICD10CM:M45 ICD9CM:720.0 MESH:D013167 NCI:C84564 ORDO:825 SNOMEDCT_US_2018_03_01:9631008 UMLS_CUI:C0038013 ls:IEDB Bekhterev syndrome Bekhterev's disease Marie-Strumpell disease disease_ontology DOID:7147 ankylosing spondylitis An arthritis that is an autoimmune disease which attacks healthy cells and tissue located_in joint. EFO:0000685 ICD10CM:M06.9 ICD9CM:714.0 KEGG:05323 MESH:D001172 MTHICD9_2006:714.0 NCI2004_11_17:C27206 NCI:C2884 OMIM:180300 SNOMEDCT_US_2018_03_01:69896004 UMLS_CUI:C0003873 Arthritis or polyarthritis, rheumatic atrophic Arthritis disease_ontology DOID:7148 OMIM mapping confirmed by DO. [SN]. rheumatoid arthritis A disease of anatomical entity that is located_in the gastrointestinal tract. DOID:27 DOID:944 CSP2005:1248-3545 ICD10CM:K92.9 ICD9CM:520-579.99 MESH:D004066 SNOMEDCT_US_2018_03_01:53619000 UMLS_CUI:C0012242 GIT disease Gastroenteropathy alimentary system disease digestive system disorder gastrointestinal disease gastrointestinal disorder disease_ontology DOID:77 gastrointestinal system disease A bone inflammation disease that involves a response to irritation or injury, characterized by joint pain, swelling, stiffness located_in joint and/or redness located_in skin over the joint. ICD10CM:M19.90 MESH:D001168 NCI:C2883 SNOMEDCT_US_2018_03_01:3723001 UMLS_CUI:C0003864 ls:IEDB Inflammatory disorder of joint disease_ontology DOID:848 arthritis A syndrome that occurs in humans with psoriasis who also experience symptoms similar to arthritis. EFO:0003778 ICD10CM:L40.5 ICD10CM:L40.50 ICD9CM:696.0 MESH:D015535 NCI:C61277 SNOMEDCT_US_2018_03_01:33339001 UMLS_CUI:C0003872 arthritis psoriatica arthropathic psoriasis disease_ontology psoriatic arthropathy DOID:9008 psoriatic arthritis A lupus erythematosus that is an inflammation of connective tissue marked by skin rashes, joint pain and swelling, inflammation of the kidneys and inflammation of the tissue surrounding the heart. CSP2005:0729-7721 EFO:0002690 GARD:10253 ICD10CM:M32 ICD10CM:M32.9 ICD9CM:710.0 KEGG:05322 MESH:D008180 MTH:U002054 NCI2004_11_17:C3201 NCI:C3201 OMIM:152700 OMIM:300809 OMIM:605480 OMIM:608437 OMIM:609903 OMIM:609939 OMIM:610065 OMIM:610066 OMIM:612254 OMIM:612378 OMIM:613145 OMIM:614420 ORDO:536 SNOMEDCT_US_2018_03_01:55464009 UMLS_CUI:C0024141 ls:IEDB Lupus Erythematosus, systemic SLE - Lupus Erythematosus, systemic disseminated lupus erythematosus disease_ontology DOID:9074 Xref MGI. systemic lupus erythematosus A large intestine cancer that is located_in the colon and/or located_in the rectum. KEGG:05210 MESH:D015179 OMIM:114500 OMIM:611469 OMIM:612230 OMIM:612231 OMIM:612232 OMIM:612589 OMIM:612590 OMIM:612592 UMLS_CUI:C1527249 disease_ontology DOID:9256 Xref MGI. OMIM mapping confirmed by DO. [SN]. colorectal cancer a material entity (1) containing at least one scattered molecular aggregate as part that is the bearer of an active ingredient role and (2) that is itself the bearer of a clinical drug role William Hogan William Hogan drug product A biome is an ecosystem to which resident ecological communities have evolved adaptations. EcoLexicon:biome LTER:173 major habitat type EcosytemType There has been some concern raised (see Issue #143) about the usefulness of the assertion that organisms have evolved within a given biome. They may have evolved adaptations elsewhere and demonstrating one or the other is often not feasible. Consider relabelling to "environmental system determined by an ecological community" or similar. biome environmental material A portion of environmental material is a fiat object which forms the medium or part of the medium of an environmental system. environmental material A system which has the disposition to environ one or more material entities. 2013-09-23T16:04:08Z EcoLexicon:environment environment In ENVO's alignment with the Basic Formal Ontology, this class is being considered as a subclass of a proposed BFO class "system". The relation "environed_by" is also under development. Roughly, a system which includes a material entity (at least partially) within its site and causally influences that entity may be considered to environ it. Following the completion of this alignment, this class' definition and the definitions of its subclasses will be revised. environmental system An environmental system which can sustain and allow the growth of an ecological population. EcoLexicon:habitat LTER:238 SWEETRealm:Habitat https://en.wikipedia.org/wiki/Habitat A habitat's specificity to an ecological population differentiates it from other environment classes. habitat An environmental system which includes both living and non-living components. This class will be primarily filled by inference, any environmental system which necessarily includes living parts should be autoclassified here. ecosystem biological_process A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. janelomax 2012-09-19T15:05:24Z GO:0000004 GO:0007582 GO:0044699 Wikipedia:Biological_process biological process physiological process biological_process single organism process single-organism process GO:0008150 Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code "no data" (ND), is used to indicate this. biological_process gene expression The process in which a gene's sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form. gene expression Any process in which an organism has an effect on an organism of a different species. interaction with another species interspecies interaction interspecies interaction with other organisms biological_process GO:0044419 interspecies interaction between organisms An interaction between two organisms living together in more or less intimate association. The term host is used for the larger (macro) of the two members of a symbiosis; the various forms of symbiosis include parasitism, commensalism and mutualism. biological_process GO:0051701 interaction with host A biological process which involves another organism of the same or different species. GO:0051706 interaction between organisms physiological interaction between organisms physiological interaction with other organism biological_process GO:0051704 multi-organism process A phenotypic abnormality. UMLS:C4021819 Organ abnormality human_phenotype HP:0000118 This is the root of the phenotypic abnormality subontology of the HPO. Phenotypic abnormality Accumulation of substantial excess body fat. MSH:D009765 SNOMEDCT_US:414915002 SNOMEDCT_US:414916001 UMLS:C0028754 Having too much body fat Obesity human_phenotype HP:0001513 Obesity Abnormally increased frequency of loose or watery bowel movements. MSH:D003967 SNOMEDCT_US:267060006 SNOMEDCT_US:62315008 UMLS:C0011991 Diarrhea Diarrhoea Watery stool human_phenotype HP:0002014 Diarrhea The presence of chronic diarrhea, which is usually taken to mean diarrhea that has persisted for over 4 weeks. SNOMEDCT_US:236071009 UMLS:C0401151 Chronic diarrhea human_phenotype Diarrhea, recurrent Recurrent diarrhea HP:0002028 Chronic diarrhea measurement unit label Examples of measurement unit labels are liters, inches, weight per volume. A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure. 2009-03-16: provenance: a term measurement unit was proposed for OBI (OBI_0000176) , edited by Chris Stoeckert and Cristian Cocos, and subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definition of this, different, term. 2009-03-16: review of this term done during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI. PERSON: Alan Ruttenberg PERSON: Melanie Courtot measurement unit label objective specification In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction. a directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved. 2009-03-16: original definition when imported from OBI read: "objective is an non realizable information entity which can serve as that proper part of a plan towards which the realization of the plan is directed." 2014-03-31: In the example of usage ("In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction") there is a protocol which is the ChIP assay protocol. In addition to being concretized on paper, the protocol can be concretized as a realizable entity, such as a plan that inheres in a person. The objective specification is the part that says that some protein and DNA interactions are identified. This is a specification of a process endpoint: the boundary in the process before which they are not identified and after which they are. During the realization of the plan, the goal is to get to the point of having the interactions, and participants in the realization of the plan try to do that. Answers the question, why did you do this experiment? PERSON: Alan Ruttenberg PERSON: Barry Smith PERSON: Bjoern Peters PERSON: Jennifer Fostel goal specification OBI Plan and Planned Process/Roles Branch OBI_0000217 objective specification Pour the contents of flask 1 into flask 2 a directive information entity that describes an action the bearer will take Alan Ruttenberg OBI Plan and Planned Process branch action specification datum label A label is a symbol that is part of some other datum and is used to either partially define the denotation of that datum or to provide a means for identifying the datum as a member of the set of data with the same label http://www.golovchenko.org/cgi-bin/wnsearch?q=label#4n GROUP: IAO 9/22/11 BP: changed the rdfs:label for this class from 'label' to 'datum label' to convey that this class is not intended to cover all kinds of labels (stickers, radiolabels, etc.), and not even all kind of textual labels, but rather the kind of labels occuring in a datum. datum label data item Data items include counts of things, analyte concentrations, and statistical summaries. a data item is an information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements. 2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers. 2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum. 2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym. 2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/ JAR: datum -- well, this will be very tricky to define, but maybe some information-like stuff that might be put into a computer and that is meant, by someone, to denote and/or to be interpreted by some process... I would include lists, tables, sentences... I think I might defer to Barry, or to Brian Cantwell Smith JAR: A data item is an approximately justified approximately true approximate belief PERSON: Alan Ruttenberg PERSON: Chris Stoeckert PERSON: Jonathan Rees data data item information content entity Examples of information content entites include journal articles, data, graphical layouts, and graphs. A generically dependent continuant that is about some thing. 2014-03-10: The use of "thing" is intended to be general enough to include universals and configurations (see https://groups.google.com/d/msg/information-ontology/GBxvYZCk1oc/-L6B5fSBBTQJ). information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907). Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity. PERSON: Chris Stoeckert OBI_0000142 information content entity 1 1 10 feet. 3 ml. a scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label. 2009-03-16: we decided to keep datum singular in scalar measurement datum, as in this case we explicitly refer to the singular form Would write this as: has_part some 'measurement unit label' and has_part some numeral and has_part exactly 2, except for the fact that this won't let us take advantage of OWL reasoning over the numbers. Instead use has measurment value property to represent the same. Use has measurement unit label (subproperty of has_part) so we can easily say that there is only one of them. PERSON: Alan Ruttenberg PERSON: Melanie Courtot scalar measurement datum An information content entity whose concretizations indicate to their bearer how to realize them in a process. 2009-03-16: provenance: a term realizable information entity was proposed for OBI (OBI_0000337) , edited by the PlanAndPlannedProcess branch. Original definition was "is the specification of a process that can be concretized and realized by an actor" with alternative term "instruction".It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term. 2013-05-30 Alan Ruttenberg: What differentiates a directive information entity from an information concretization is that it can have concretizations that are either qualities or realizable entities. The concretizations that are realizable entities are created when an individual chooses to take up the direction, i.e. has the intention to (try to) realize it. 8/6/2009 Alan Ruttenberg: Changed label from "information entity about a realizable" after discussions at ICBO Werner pushed back on calling it realizable information entity as it isn't realizable. However this name isn't right either. An example would be a recipe. The realizable entity would be a plan, but the information entity isn't about the plan, it, once concretized, *is* the plan. -Alan PERSON: Alan Ruttenberg PERSON: Bjoern Peters directive information entity curation status specification The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting) PERSON:Bill Bug GROUP:OBI:<http://purl.obolibrary.org/obo/obi> OBI_0000266 curation status specification data about an ontology part is a data item about a part of an ontology, for example a term Person:Alan Ruttenberg data about an ontology part plan specification PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice. A directive information entity with action specifications and objective specifications as parts that, when concretized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified. 2009-03-16: provenance: a term a plan was proposed for OBI (OBI_0000344) , edited by the PlanAndPlannedProcess branch. Original definition was " a plan is a specification of a process that is realized by an actor to achieve the objective specified as part of the plan". It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term. 2014-03-31: A plan specification can have other parts, such as conditional specifications. Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved Alan Ruttenberg OBI Plan and Planned Process branch OBI_0000344 2/3/2009 Comment from OBI review. Action specification not well enough specified. Conditional specification not well enough specified. Question whether all plan specifications have objective specifications. Request that IAO either clarify these or change definitions not to use them plan specification measurement datum Examples of measurement data are the recoding of the weight of a mouse as {40,mass,"grams"}, the recording of an observation of the behavior of the mouse {,process,"agitated"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}. A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device. 2/2/2009 is_specified_output of some assay? person:Chris Stoeckert OBI_0000305 group:OBI measurement datum A scalar measurement datum that is the result of measuring a temporal interval 2009/09/28 Alan Ruttenberg. Fucoidan-use-case Person:Alan Ruttenberg time measurement datum infection A part of an extended organism that itself has as part a population of one or more infectious agents and that (1) exists as a result of processes initiated by members of the infectious agent population and is (2) clinically abnormal in virtue of the presence of this infectious agent population, or (3) has a disposition to bring clinical abnormality to immunocompetent organisms of the same Species as the host (the organism corresponding to the extended organism) through transmission of a member or offspring of a member of the infectious agent population. infection Interaction is a processual entity that has two or more participants (i.e., interactors) that have an effect upon one another. YH, ZX interact, interacted, interacting, interaction, interaction, interactor, interactors, interacts, participates; plays a role, contribute, contributed, contributes, contributing, engagement, engagements, engages, engaging, involve, involved, involves, involving, act, acted, acting, acts interaction Enthesitis-related juvenile idiopathic arthritis is a subtype of juvenile idiopathic arthritis that is characterized by both arthritis and inflammation of an enthesitis site (the point at which a ligament, tendon, or joint capsule attaches to the bone). Signs and symptoms generally develop in late childhood or early adolescence and include pain, tenderness, and swelling in joints and at the enthesis. The knee and the back of the ankle (at the Achilles tendon) are the most commonly affected parts of the body. The underlying cause of enthesitis-related juvenile idiopathic arthritis is currently unknown (idiopathic). It is very rare for more than one member of a family to have juvenile arthritis; however, research suggests that having a family member with juvenile arthritis or any autoimmune disease may increase the risk of having juvenile arthritis, in general. Treatment usually involves different types of medications to help manage symptoms and/or physical therapy . GARD:0010969 ICD10:M08.8 NCIT:C119024 Orphanet:85438 SCTID:410801005 enthesitis-related JIA era enthesitis related arthritis, juvenile enthesitis-related arthritis juvenile enthesitis-related arthritis juvenile spondylarthropathy MONDO:0019437 enthesitis-related juvenile idiopathic arthritis https://rarediseases.info.nih.gov/diseases/10969/enthesitis-related-juvenile-idiopathic-arthritis Coprobacillus Coprobacillus Mus musculus house mouse mouse Mus musculus Rattus rat rats Rattus Rattus norvegicus Norway rat Rattus sp. strain Wistar brown rat rat rats Rattus norvegicus Capnocytophaga Capnocytophaga Capnocytophaga gingivalis Beggiatoa Beggiatoa Collinsella Collinsella Solobacterium moorei Solobacterium moorei Viruses Viruses Hepatitis B virus Hepatitis B virus Leptotrichia sp. Leptotrichia sp. Badula fragilis Badula fragilis Anaerovorax Anaerovorax Hepacivirus C Hepacivirus C Leptotrichiaceae Leptotrichiaceae Fusicatenibacter saccharivorans Fusicatenibacter saccharivorans Parasporobacterium Parasporobacterium Coprococcus catus Coprococcus catus Euteleostomi bony vertebrates Euteleostomi Cutibacterium acnes 17B Cutibacterium acnes 17B Methylobacteriaceae Methylobacteriaceae Burkholderiaceae Burkholderiaceae Ecdysozoa Ecdysozoa Solobacterium sp. S4-A19 Solobacterium sp. S4-A19 Proteobacteria purple bacteria purple bacteria and relatives purple non-sulfur bacteria purple photosynthetic bacteria purple photosynthetic bacteria and relatives Proteobacteria Solobacterium Solobacterium Gammaproteobacteria Gammaproteobacteria Firmicutes low G+C Gram-positive bacteria low GC Gram+ Firmicutes Peptostreptococcus Peptostreptococcus Peptostreptococcus anaerobius Peptostreptococcus anaerobius Ruminococcus Ruminococcus Ruminococcus albus Ruminococcus albus Micrococcaceae Micrococcaceae Micrococcus Human immunodeficiency virus Human immunodeficiency virus Erysipelotrichaceae Erysipelotrichaceae Acidovorax Acidivorax Acidovorax Streptococcaceae Streptococcaceae Streptococcus Streptococcus Streptococcus sanguinis Streptococcus thermophilus Streptococcus salivarius thermophilus Streptococcus thermophilus Streptococcus pyogenes Streptococcus pyogenes Streptococcus equinus Streptococcus equinus Enterococcus Enterococcus Enterococcus faecalis Enterococcus faecalis Escherichia coli #1/H766 Escherichia coli #1/H766 Spirochaetaceae Spirochaetaceae Atopobium Atopobium Atopobium parvulum Atopobium parvulum Lachnobacterium bovis Lachnobacterium bovis Fretibacterium Fretibacterium Mesangiospermae Mesangiospermae Pentapetalae Pentapetalae Clostridium Clostridium Clostridioides difficile [Clostridium] difficile Clostridioides difficile Clostridium perfringens Clostridium perfringens Anoxybacillus Anoxybacillus Erysipelatoclostridium Erysipelatoclostridium Lachnoclostridium Lachnoclostridium [Clostridium] clostridioforme Clostridium clostridioforme [Clostridium] clostridioforme Blautia coccoides Blautia coccoides Candida <Debaryomycetaceae> Candida Candida <Debaryomycetaceae> Fusobacterium nucleatum subsp. vincentii Fusibacterium nucleatum subsp. fusiforme Fusibacterium nucleatum subsp. vincentii Fusobacterium nucleatum subsp. vincentii Treponema Treponema Treponema Lactobacillus Lactobacillus Lactobacillus acidophilus Lactobacillus acidophilus Treponema denticola Lactobacillus casei Lactobacillus casei Fusobacterium hwasookii Fusobacterium hwasookii Megamonas hypermegale Megamonas hypermegale Lactobacillus sp. Lactobacillus sp. Lactobacillus reuteri Lactobacillus reuteri Lactobacillus fermentum Lactobacillus fermentum Lactobacillus murinus Lactobacillus murinus Lactobacillus salivarius Lactobacillus salivarius Eggerthellaceae Eggerthellaceae Prevotella copri Prevotella copri Actinomyces Actinomyces Bifidobacterium Bifidobacterium Bifidobacterium bifidum Bifidobacterium bifidum Bifidobacterium dentium Bifidobacterium dentium Bacteroidales Bacteroidales Rikenellaceae Rikenellaceae Rikenellaceae Porphyromonadaceae Porphyromonadaceae Prevotellaceae Prevotellaceae Corynebacterium diphtheriae Corynebacterium diphtheriae Rothia aeria Rothia aeria Eubacterium Propionibacterium Propionicibacterium Propionibacterium Actinobacteria <class> Actinobacteria high G+C Gram-positive bacteria Actinobacteria <class> Mycobacterium Mycobacterium Mycobacterium avium Mycobacterium avium PVC group PVC group Terrabacteria group Terrabacteria group Rhodococcus Selenomonadaceae Selenomonadaceae Pseudonocardia Clostridia Clostridia Clostridiales Clostridiales Lachnospiraceae Lachnospiraceae Peptostreptococcaceae Peptostreptococcaceae Eubacteriaceae Eubacteriaceae unclassified Clostridiales unclassified Clostridiales Bacillaceae Bacillaceae Lactobacillales Lactobacillales Atopobium sp. Atopobium sp. Subdoligranulum sp. 60_17 Subdoligranulum sp. 60_17 Lachnospiraceae bacterium Lachnospiraceae bacterium Yersiniaceae Yersiniaceae Morganellaceae Morganellaceae Neisseria sp. Neisseria sp. Campylobacter Campylobacter Campylobacter Desulfovibrionaceae Desulfovibrionaceae Campylobacter jejuni Campylobacter jejuni Pancrustacea Pancrustacea Bacteria eubacteria Bacteria Tannerellaceae Tannerellaceae Bacteroidia Bacteroidia Crenothrix Crenothrix Chloroflexi Actinobacteria <phylum> Actinobacteria Actinobacteria <phylum> Fusobacteriales Fusobacteriales Fusobacteriaceae Fusobacteriaceae Pseudonocardiaceae Pseudonocardiaceae Helicobacter Helicobacter Helicobacter pylori Helicobacter pylori Mycoplasma fermentans Mycoplasma fermentans Campylobacterales Campylobacterales Archaea Archaea Bifidobacterium longum Bifidobacterium longum Faecalibacterium Faecalibacterium Dialister invisus Dialister invisus Moniliophthora Moniliophthora Candidatus Portiera Candidatus Portiera Alistipes Alistipes Akkermansia Akkermansia Akkermansia muciniphila Akkermansia muciniphila Anaerotruncus Anaerotruncus Acetanaerobacterium Acetanaerobacterium Sulfurovum Sulfurovum Cardiobacterium Cardiobacterium Eukaryota eucaryotes eukaryotes Eukaryota Bifidobacterium animalis Bifidobacterium animalis Lachnospira pectinoschiza Lachnospira pectinoschiza Tannerella forsythia Tannerella forsythia Bacteroides ovatus Bacteroides ovatus Alistipes putredinis Alistipes putredinis Prevotella intermedia Prevotella intermedia Prevotella oris Prevotella oris Prevotella oulorum Betaproteobacteria Betaproteobacteria Odoribacter Odoribacter Pseudomonas Pseudomonas Salmonella enterica Salmonella enterica Anaerolineae Anaerolineaceae Anaerolineales Anaerolineales Subdoligranulum Subdoligranulum [Clostridium] scindens Clostridium scindens [Clostridium] scindens Veillonella Veillonella Bacteroides sp. Bacteroides sp. Epsilonproteobacteria Epsilonproteobacteria Roseburia hominis Roseburia hominis Bifidobacterium animalis subsp. lactis Bifidobacterium animalis subsp. lactis Clostridium sp. cp01.19 Clostridium sp. cp01.19 Pseudomonas sp. Bacteroides plebeius Bacteroides plebeius Euarchontoglires Euarchontoglires Streptococcus gallolyticus Streptococcus gallolyticus Propionibacteriaceae Propionicibacteriaceae Propionibacteriaceae Veillonellaceae Veillonellaceae Clostridiaceae Clostridiaceae Burkholderia Helicobacter hepaticus Helicobacter hepaticus unclassified Proteobacteria unclassified Proteobacteria Fusobacteria Fusobacteria Leptotrichia Leptotrichia Kingella Kingella Tetrapoda tetrapods Tetrapoda Amniota amniotes Amniota Bacteroides intestinalis Bacteroides intestinalis Phascolarctobacterium Phascolarctobacterium Parvimonas micra Parvimonas micra Coprococcus Coprococcus Opisthokonta Opisthokonta Bilateria Bilateria [Clostridium] asparagiforme Clostridium asparagiforme [Clostridium] asparagiforme Bacteroides finegoldii Bacteroides finegoldii Microbacterium Aureibacterium Microbacterium Lactobacillaceae Lactobacillaceae Streptobacillus Streptobacillus Peptostreptococcus stomatis Peptostreptococcus stomatis Bilophila Bilophila Bilophila wadsworthia Bilophila wadsworthia Prevotella stercorea Prevotella stercorea Streptococcus sp. 'group A' Streptococcus sp. 'group A' Arabidopsis thaliana mouse-ear cress thale cress thale-cress Arabidopsis thaliana Bacteroides xylanisolvens Bacteroides xylanisolvens Parabacteroides Parabacteroides Escherichia coli B Escherichia coli B Murinae Murinae Dorea formicigenerans Dorea formicigenerans Eubacterium ventriosum [Eubacterium] ventriosum Eubacterium ventriosum Barnesiella Barnesiella Dialister Dialister Dialister pneumosintes Dialister pneumosintes Blautia obeum Blautia obeum Sutterella wadsworthensis Sutterella wadsworthensis Mammalia mammals Mammalia Methylobacterium Prevotella pleuritidis Cronobacter Cronobacter Aggregatibacter Aggregatibacter Ruminococcus sp. Ruminococcus sp. Filifactor Filifactor Dictyostelium discoideum Dictyostelium discoideum Eleutherodactylus lentus Virgin Islands robber frog Eleutherodactylus lentus Dikarya Dikarya Oscillibacter Oscillibacter Pseudobutyrivibrio Pseudobutyrivibrio Pseudobutyrivibrio ruminis Pseudobutyrivibrio ruminis Ruminococcus lactaris Ruminococcus lactaris Acinetobacter Acinetobacter Gordonibacter pamelaeae Gordonibacter pamelaeae Natronobacillus Natronobacillus Fungi fungi Fungi Bacteroides caccae Bacteroides caccae Lactobacillus rhamnosus Lactobacillus rhamnosus Neisseriaceae Neisseriaceae Ascomycota ascomycetes sac fungi Ascomycota Saccharomycetales budding yeasts Saccharomycetales Schizosaccharomyces pombe fission yeast Schizosaccharomyces pombe Saccharomyces cerevisiae baker's yeast brewer's yeast Saccharomyces cerevisiae Treponema maltophilum Neurospora Neurospora Basidiomycota basidiomycetes Basidiomycota Eikenella Eikenella Clostridiales incertae sedis Clostridiales incertae sedis Ruminococcaceae Ruminococcaceae Enterobacteriaceae Enterobacteriaceae Parvimonas Parvimonas Clostridiales Family XIII. Incertae Sedis Clostridiales Family XIII. Incertae Sedis Citrobacter Citrobacter Candida albicans Candida albicans Klebsiella aerogenes [Enterobacter] aerogenes Klebsiella aerogenes Diutina rugosa Diutina rugosa Malassezia Malassezia Malassezia furfur Pityriasis (Tinea) versicolor infection agent Malassezia furfur Escherichia Escherichia Escherichia coli E. coli Escherichia/Shigella coli Escherichia coli Klebsiella Klebsiella Blautia Blautia Klebsiella pneumoniae Klebsiella pneumoniae Paraprevotella Paraprevotella Kluyvera Kluyvera Proteus mirabilis Proteus mirabilis Providencia Providencia Robinsoniella Robinsoniella Salmonella Salmonella Salmonella enterica subsp. enterica Salmonella enterica subsp. enterica Holdemania Holdemania Serratia Serratia Shigella Shigella Shigella dysenteriae Escherichia/Shigella dysenteriae Shigella dysenteriae Caenorhabditis elegans roundworm Caenorhabditis elegans Yersinia Yersinia enterocolitica Yersinia enterocolitica Vibrionaceae Vibrionaceae Fretibacterium fastidiosum Acidaminobacter Acidaminobacter Photobacterium Photobacterium Bacteroides xylanisolvens XB1A Bacteroides xylanisolvens str. XB1A Bacteroides xylanisolvens strain XB1A Bacteroides xylanisolvens XB1A Vibrio Vibrio Daphnia common water fleas Daphnia Citrobacter farmeri Citrobacter farmeri Citrobacter rodentium Citrobacter rodentium delta/epsilon subdivisions delta/epsilon subdivisions Fusobacterium sp. Fusobacterium sp. Escherichia coli ETEC TW03439 Escherichia coli ETEC TW03439 Catenisphaera adipataccumulans Catenisphaera adipataccumulans Pasteurellaceae Pasteurellaceae Aggregatibacter actinomycetemcomitans Aggregatibacter actinomycetemcomitans saccharomyceta saccharomyceta leotiomyceta leotiomyceta Drosophila melanogaster fruit fly Drosophila melanogaster Pseudomonadales Pseudomonadales Campylobacteraceae Campylobacteraceae Haemophilus Haemophilus Haemophilus parainfluenzae [Haemophilus] ducreyi Haemophilus ducreyi [Haemophilus] ducreyi Haemophilus sp. Verrucomicrobia Verrucomicrobia Collinsella aerofaciens Collinsella aerofaciens Escherichia coli NC101 Escherichia coli NC101 Escherichia coli EPEC 32/73 Escherichia coli str. EPEC 32/73 Escherichia coli strain EPEC 32/73 Escherichia coli EPEC 32/73 Malassezia restricta Malassezia restricta Malassezia sympodialis Malassezia sympodialis Fusobacterium nucleatum subsp. nucleatum Fusibacterium nucleatum subsp. nucleatum Fusobacterium nucleatum subsp. nucleatum Fusobacterium nucleatum subsp. polymorphum Fusibacterium nucleatum subsp. polymorphum Fusobacterium nucleatum subsp. polymorphum Fusobacterium nucleatum subsp. animalis Fusibacterium nucleatum subsp. animalis Fusobacterium nucleatum subsp. animalis Malassezia pachydermatis Malassezia pachydermatis Vertebrata <Metazoa> Vertebrata vertebrates Vertebrata <Metazoa> Danio rerio leopard danio zebra danio zebra fish zebrafish Danio rerio Burkholderiales Burkholderiales Chlamydia Chlamydia Chlamydia trachomatis Bacteroidaceae Bacteroidaceae Bacteroides Bacteroides Bacteroides fragilis Bacteroides fragilis Enterococcaceae Enterococcaceae Bacteroides uniformis Bacteroides uniformis Bacteroides vulgatus Bacteroides vulgatus Anura anurans frogs frogs and toads Anura Xenopus <genus> Xenopus Xenopus <genus> Porphyromonas Porphyromonas Porphyromonas gingivalis Porphyromonas gingivalis Prevotella Prevotella Roseburia Roseburya Roseburyella Roseburia Coriobacteriaceae Coriobacteriaceae Slackia Slackia Eggerthella Eggerthella lenta Eggerthella lenta Cryptobacterium curtum Cryptobacterium curtum Dolosicoccus paucivorans Dolosicoccus paucivorans Fusobacterium Fusibacterium Fusobacterium Fusobacterium Coriobacteriia Coriobacteriia Coriobacteriales Coriobacteriales Bifidobacteriales Bifidobacteriales Micrococcales Micrococcales Corynebacteriales Corynebacteriales Nocardiaceae Nocardiaceae Fusobacterium nucleatum Fusibacterium nucleatum Fusobacterium nucleatum Faecalibacterium prausnitzii [Fusobacterium] prausnitzii Faecalibacterium prausnitzii Mogibacterium Mogibacterium Magnolia globosa Magnolia globosa Umbilicariaceae Umbilicariaceae [Clostridium] hiranonis Clostridium hiranonis [Clostridium] hiranonis [Clostridium] hylemonae Clostridium hylemonae [Clostridium] hylemonae Gallus gallus bantam chicken chickens Gallus gallus Salmonella enterica subsp. enterica serovar Typhi Salmonella enterica subsp. enterica serovar Typhi Salmonella enterica subsp. enterica serovar Typhimurium Salmonella enterica subsp. enterica serovar Typhimurium Selenomonadales Negativicutes Negativicutes Bacilli Bacilli Enterobacterales Enterobacterales Flavonifractor Homo sapiens human man Homo sapiens Selenomonas Selenomonas Selenomonas Bacteroidetes Bacteroidetes Rodentia rodent Rodentia Porphyromonas macacae planned process planned process Injecting mice with a vaccine in order to test its efficacy A processual entity that realizes a plan which is the concretization of a plan specification. 'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.) We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some objectives is a planned process. Bjoern Peters branch derived 6/11/9: Edited at workshop. Used to include: is initiated by an agent This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call) planned process biological feature identification objective Biological_feature_identification_objective is an objective role carried out by the proposition defining the aim of a study designed to examine or characterize a particular biological feature. Jennifer Fostel biological feature identification objective processed material Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples Is a material entity that is created or changed during material processing. PERSON: Alan Ruttenberg processed material evaluant role When a specimen of blood is assayed for glucose concentration, the blood has the evaluant role. When measuring the mass of a mouse, the evaluant is the mouse. When measuring the time of DNA replication, the evaluant is the DNA. When measuring the intensity of light on a surface, the evaluant is the light source. a role that inheres in a material entity that is realized in an assay in which data is generated about the bearer of the evaluant role Role call - 17nov-08: JF and MC think an evaluant role is always specified input of a process. Even in the case where we have an assay taking blood as evaluant and outputting blood, the blood is not the specified output at the end of the assay (the concentration of glucose in the blood is) examples of features that could be described in an evaluant: quality.... e.g. "contains 10 pg/ml IL2", or "no glucose detected") GROUP: Role Branch OBI Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term. evaluant role assay Assay the wavelength of light emitted by excited Neon atoms. Count of geese flying over a house. A planned process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies. 12/3/12: BP: the reference to the 'physical examination' is included to point out that a prediction is not an assay, as that does not require physical examiniation. PlanAndPlannedProcess Branch measuring scientific observation OBI branch derived study assay any method assay sample preparation for assay A sample_preparation_for_assay is a protocol_application including material_enrollments and biomaterial_transformations. definition_source: OBI. PlanAndPlannedProcess Branch study OBI branch derived sample preparation for assay culture medium A growth medium or culture medium is a substance in which microorganisms or cells can grow. Wikipedia, growth medium, Feb 29, 2008 a processed material that provides the needed nourishment for microorganisms or cells grown in vitro. changed from a role to a processed material based on on Aug 22, 2011 dev call. Details see the tracker item: http://sourceforge.net/tracker/?func=detail&aid=3325270&group_id=177891&atid=886178 Modification made by JZ. Person: Jennifer Fostel, Jie Zheng OBI culture medium reagent role Buffer, dye, a catalyst, a solvating agent. A role inhering in a biological or chemical entity that is intended to be applied in a scientific technique to participate (or have molecular components that participate) in a chemical reaction that facilitates the generation of data about some entity distinct from the bearer, or the generation of some specified material output distinct from the bearer. PERSON:Matthew Brush reagent PERSON:Matthew Brush Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term. May 28 2013. Updated definition taken from ReO based on discussions initiated in Philly 2011 workshop. Former defnition described a narrower view of reagents in chemistry that restricts bearers of the role to be chemical entities ("a role played by a molecular entity used to produce a chemical reaction to detect, measure, or produce other substances"). Updated definition allows for broader view of reagents in the domain of biomedical research to include larger materials that have parts that participate chemically in a molecular reaction or interaction. (copied from ReO) Reagents are distinguished from instruments or devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in or have parts that participate in some chemical interaction or reaction during their intended participation in some technique. By contrast, instruments do not participate in a chemical reaction/interaction during the technique. Reagents are distinguished from study subjects/evaluants in that study subjects and evaluants are that about which conclusions are drawn and knowledge is sought in an investigation - while reagents, by definition, are not. It should be noted, however, that reagent and study subject/evaluant roles can be borne by instances of the same type of material entity - but a given instance will realize only one of these roles in the execution of a given assay or technique. For example, taq polymerase can bear a reagent role or an evaluant role. In a DNA sequencing assay aimed at generating sequence data about some plasmid, the reagent role of the taq polymerase is realized. In an assay to evaluate the quality of the taq polymerase itself, the evaluant/study subject role of the taq is realized, but not the reagent role since the taq is the subject about which data is generated. In regard to the statement that reagents are 'distinct' from the specified outputs of a technique, note that a reagent may be incorporated into a material output of a technique, as long as the IDENTITY of this output is distinct from that of the bearer of the reagent role. For example, dNTPs input into a PCR are reagents that become part of the material output of this technique, but this output has a new identity (ie that of a 'nucleic acid molecule') that is distinct from the identity of the dNTPs that comprise it. Similarly, a biotin molecule input into a cell labeling technique are reagents that become part of the specified output, but the identity of the output is that of some modified cell specimen which shares identity with the input unmodified cell specimen, and not with the biotin label. Thus, we see that an important criteria of 'reagent-ness' is that it is a facilitator, and not the primary focus of an investigation or material processing technique (ie not the specified subject/evaluant about which knowledge is sought, or the specified output material of the technique). reagent role material processing A cell lysis, production of a cloning vector, creating a buffer. A planned process which results in physical changes in a specified input material PERSON: Bjoern Peters PERSON: Frank Gibson PERSON: Jennifer Fostel PERSON: Melanie Courtot PERSON: Philippe Rocca Serra material transformation OBI branch derived material processing specimen role liver section; a portion of a culture of cells; a nemotode or other animal once no longer a subject (generally killed); portion of blood from a patient. a role borne by a material entity that is gained during a specimen collection process and that can be realized by use of the specimen in an investigation 22Jun09. The definition includes whole organisms, and can include a human. The link between specimen role and study subject role has been removed. A specimen taken as part of a case study is not considered to be a population representative, while a specimen taken as representing a population, e.g. person taken from a cohort, blood specimen taken from an animal) would be considered a population representative and would also bear material sample role. Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation. blood taken from animal: animal continues in study, whereas blood has role specimen. something taken from study subject, leaves the study and becomes the specimen. parasite example - when parasite in people we study people, people are subjects and parasites are specimen - when parasite extracted, they become subject in the following study specimen can later be subject. GROUP: Role Branch OBI specimen role molecular feature identification objective Molecular_feature_identification_objective is a biological_feature_identification_objective role describing a study designed to examine or characterize molecular features of a biological system, e.g. expression profiling, copy number of molecular components, epigenetic modifications. Jennifer Fostel molecular feature identification objective DNA extraction A DNA extraction is a nucleic acid extraction where the desired output material is DNA. PlanAndPlannedProcess Branch OBI branch derived DNA extraction analyte role Glucose in blood (measured in an assay to determine the concentration of glucose). A measurand role borne by a molecular entity or an atom and realized in an analyte assay which achieves the objective to measure the magnitude/concentration/amount of the analyte in the entity bearing evaluant role. interestingly, an analyte is still an analyte even if it is not detected. for this reason it does not bear a specified input role pH (technically the inverse log of [H+]) may be considered a quality; this remains to be tested. qualities such as weight, color are not assayed but measured, so they do not fall into this category. GROUP: Role Branch OBI Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term. analyte role extract Up-regulation of inflammatory signalings by areca nut extract and role of cyclooxygenase-2 -1195G>a polymorphism reveal risk of oral cancer. Cancer Res. 2008 Oct 15;68(20):8489-98. PMID: 18922923 an extract is a material entity which results from an extraction process PERSON: Philippe Rocca-Serra extracted material GROUP: OBI Biomatrial Branch extract transcription profiling assay Whole genome transcription profiling of Anaplasma phagocytophilum in human and tick host cells by tiling array analysis. BMC Genomics. 2008 Jul 31;9:364. PMID: 18671858 An assay that determines gene expression and transcription activity using ribonucleic acids collected from a material entity. This term should encompass transcription and post-transcription, but before translation into protein. So 'gene expression' itself is too broad, and we use 'transcription profiling identification objective' to constrain the scope of this term. Philippe Rocca-Serra gene expression profiling transcription profiling OBI transcription profiling assay assay objective the objective to determine the weight of a mouse. an objective specification to determine a specified type of information about an evaluated entity (the material entity bearing evaluant role) PPPB branch PPPB branch assay objective measure function A glucometer measures blood glucose concentration, the glucometer has a measure function. Measure function is a function that is borne by a processed material and realized in a process in which information about some entity is expressed relative to some reference. PERSON: Daniel Schober PERSON: Helen Parkinson PERSON: Melanie Courtot PERSON:Frank Gibson measure function material transformation objective The objective to create a mouse infected with LCM virus. The objective to create a defined solution of PBS. an objective specifiction that creates an specific output object from input materials. PERSON: Bjoern Peters PERSON: Frank Gibson PERSON: Jennifer Fostel PERSON: Melanie Courtot PERSON: Philippe Rocca-Serra artifact creation objective GROUP: OBI PlanAndPlannedProcess Branch material transformation objective DNA sequencing assay Illumina (Solexa) sequencing is an example of DNA sequencing A sequencing assay which determines information on the sequence of a DNA molecule. Philippe Rocca-Serra nucleotide sequencing url:https://en.wikipedia.org/wiki/DNA_sequencing DNA sequencing assay material separation objective The objective to obtain multiple aliquots of an enzyme preparation. The objective to obtain cells contained in a sample of blood. is an objective to transform a material entity into spatially separated components. PPPB branch PPPB branch material separation objective specimen collection process drawing blood from a patient for analysis, collecting a piece of a plant for depositing in a herbarium, buying meat from a butcher in order to measure its protein content in an investigation A planned process with the objective of collecting a specimen. Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation. Philly2013: A specimen collection can have as part a material entity acquisition, such as ordering from a bank. The distinction is that specimen collection necessarily involves the creation of a specimen role. However ordering cell lines cells from ATCC for use in an investigation is NOT a specimen collection, because the cell lines already have a specimen role. Philly2013: The specimen_role for the specimen is created during the specimen collection process. label changed to 'specimen collection process' on 10/27/2014, details see tracker: http://sourceforge.net/p/obi/obi-terms/716/ Bjoern Peters specimen collection 5/31/2012: This process is not necessarily an acquisition, as specimens may be collected from materials already in posession 6/9/09: used at workshop specimen collection process sample from organism a material obtained from an organism in order to be a representative of the whole 5/29: This is a helper class for now we need to work on this: Is taking a urine sample a material separation process? If not, we will need to specify what 'taking a sample from organism' entails. We can argue that the objective to obtain a urine sample from a patient is enough to call it a material separation process, but it could dilute what material separation was supposed to be about. sample from organism portioning objective The objective to obtain multiple aliquots of an enzyme preparation. A material separation objective aiming to separate material into multiple portions, each of which contains a similar composition of the input material. portioning objective separation into different composition objective The objective to obtain cells contained in a sample of blood. A material separation objective aiming to separate a material entity that has parts of different types, and end with at least one output that is a material with parts of fewer types (modulo impurities). We should be using has the grain relations or concentrations to distinguish the portioning and other sub-objectives separation into different composition objective specimen collection objective The objective to collect bits of excrement in the rainforest. The objective to obtain a blood sample from a patient. A objective specification to obtain a material entity for potential use as an input during an investigation. Bjoern Peters Bjoern Peters specimen collection objective host role In biology, a host is an organism that harbors a virus or parasite, or a mutual or commensal symbiont, typically providing nourishment and shelter. http://en.wikipedia.org/wiki/Host_(biology) 30 March 09 host role is a role played by an organism and realized by providing nourishment, shelter or a means of reproduction to another organism within the organism playing the host role 30Mar09 virus reproducing inside a cell; bacteria causing a disease, host can be harmed or not. we want to avoid a cat sitting on my lap and an animal care technician; these are not examples or hosts; dental cares = on tooth, but part of outer layer of tooth, so covered by "within" in the definition GROUP: Role Branch 30 Mar09 submitted by vaccine community OBI http://en.wikipedia.org/wiki/Host_(biology) host role material sample role a role borne by a portion of blood taken to represent all the blood in an organism; the role borne by a population of humans with HIV enrolled in a study taken to represent patients with HIV in general. A material sample role is a specimen role borne by a material entity that is the output of a material sampling process. 7/13/09: Note that this is a relational role: between the sample taken and the 'sampled' material of which the sample is thought to be representative off. material sample role material sampling process A specimen gathering process with the objective to obtain a specimen that is representative of the input material entity material sampling process material sample blood drawn from patient to measure his systemic glucose level. A population of humans with HIV enrolled in a study taken to represent patients with HIV in general. A material entity that has the material sample role OBI: workshop sample population sample material sample material maintenance objective An objective specification maintains some or all of the qualities of a material over time. PERSON: Bjoern Peters PERSON: Bjoern Peters material maintenance objective primary structure of DNA macromolecule a quality of a DNA molecule that inheres in its bearer due to the order of its DNA nucleotide residues. placeholder for SO BP et al primary structure of DNA macromolecule measurement device A ruler, a microarray scanner, a Geiger counter. A device in which a measure function inheres. GROUP:OBI Philly workshop OBI measurement device material maintenance a process with that achieves the objective to maintain some or all of the characteristics of an input material over time material maintenance RNA extract an extract which is the output of an extraction process in which RNA molecules are isolated from a specimen. PERSON: Chris Stoeckert PERSON: Jie Zheng Group: UPenn Group RNA extract processed specimen A tissue sample that has been sliced and stained for a histology study. A blood specimen that has been centrifuged to obtain the white blood cells. A specimen that has been intentionally physically modified. Bjoern Peters Bjoern Peters A tissue sample that has been sliced and stained for a histology study. processed specimen device A voltmeter is a measurement device which is intended to perform some measure function. An autoclave is a device that sterlizes instruments or contaminated waste by applying high temperature and pressure. A material entity that is designed to perform a function in a scientific investigation, but is not a reagent. 2012-12-17 JAO: In common lab usage, there is a distinction made between devices and reagents that is difficult to model. Therefore we have chosen to specifically exclude reagents from the definition of "device", and are enumerating the types of roles that a reagent can perform. 2013-6-5 MHB: The following clarifications are outcomes of the May 2013 Philly Workshop. Reagents are distinguished from devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in some chemical interaction or reaction during the realization of their experimental role. By contrast, devices do not participate in such chemical reactions/interactions. Note that there are cases where devices use reagent components during their operation, where the reagent-device distinction is less clear. For example: (1) An HPLC machine is considered a device, but has a column that holds a stationary phase resin as an operational component. This resin qualifies as a device if it participates purely in size exclusion, but bears a reagent role that is realized in the running of a column if it interacts electrostatically or chemically with the evaluant. The container the resin is in (“the column”) considered alone is a device. So the entire column as well as the entire HPLC machine are devices that have a reagent as an operating part. (2) A pH meter is a device, but its electrode component bears a reagent role in virtue of its interacting directly with the evaluant in execution of an assay. (3) A gel running box is a device that has a metallic lead as a component that participates in a chemical reaction with the running buffer when a charge is passed through it. This metallic lead is considered to have a reagent role as a component of this device realized in the running of a gel. In the examples above, a reagent is an operational component of a device, but the device itself does not realize a reagent role (as bearing a reagent role is not transitive across the part_of relation). In this way, the asserted disjointness between a reagent and device holds, as both roles are never realized in the same bearer during execution of an assay. PERSON: Helen Parkinson instrument OBI development call 2012-12-17. device sequence data example of usage: the representation of a nucleotide sequence in FASTA format used for a sequence similarity search. A measurement datum that representing the primary structure of a macromolecule(it's sequence) sometimes associated with an indicator of confidence of that measurement. Person:Chris Stoeckert GROUP: OBI sequence data nucleic acid extract An extract that is the output of an extraction process in which nucleic acid molecules are isolated from a specimen. PERSON: Jie Zheng UPenn Group nucleic acid extract DNA extract The output of an extraction process in which DNA molecules are purified in order to exclude DNA from organellas. Person: Jie Zheng Group: UPenn group DNA extract nucleic acid sequencer An device that is used to determine the order of nucleotides in nucleic acid sequences. PERSON: Erik Segerdell PERSON: Erik Segerdell nucleic acid sequencer protein sequencer An device that is used to determine the order of amino acids in protein sequences. PERSON: Erik Segerdell PERSON: Erik Segerdell protein sequencer RNA-seq assay An transcription profiling assay that determines an RNA sequence by analyzing the transcibed regions of the genome and or to quantitate transcript abundance. James Malone transcription profiling by high throughput sequencing EFO:0002770 RNA-seq assay transcription profiling identification objective A molecular feature identification objective that aims to characterize the abundance of transcripts Person: Chris Stoeckert, Jie Zheng Group: Penn Group transcription profiling identification objective specimen from organism A specimen that derives from an anatomical part or substance arising from an organism. Examples of tissue specimen include tissue, organ, physiological system, blood, or body location (arm). PERSON: Chris Stoeckert, Jie Zheng tissue specimen MO_954 organism_part specimen from organism sampling time measurement datum A time measurement datum when an observation is made or a sample is taken from a material as measured from some reference point. Person: Chris Stoeckert time point MO_738 timepoint sampling time measurement datum DNA sequence data The part of a FASTA file that contains the letters ACTGGGAA A sequence data item that is about the primary structure of DNA OBI call; Bjoern Peters OBI call; Melanie Courtout 8/29/11 call: This is added after a request from Melanie and Yu. They should review it further. This should be a child of 'sequence data', and as of the current definition will infer there. DNA sequence data specimen collection time measurement datum A time measurement datum that is the measure of the time when the specimens are collected. Person: Chris Stoeckert, Jie Zheng collection date NIAID GSCID-BRC metadata working group Specimen Collection Date NIAID GSCID-BRC specimen collection time measurement datum sample preparation for sequencing assay A sample preparation for assay that preparation of nucleic acids for a sequencing assay PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Nucleic Acid Preparation Method NIAID GSCID-BRC sample preparation for sequencing assay cell freezing medium A processed material that serves as a liquid vehicle for freezing cells for long term quiescent stroage, which contains chemicls needed to sustain cell viability across freeze-thaw cycles. PERSON: Matthew Brush cell freezing medium 1 1 scalar value specification A value specification that consists of two parts: a numeral and a unit label PERSON:Bjoern Peters scalar value specification value specification The value of 'positive' in a classification scheme of "positive or negative"; the value of '20g' on the quantitative scale of mass. An information content entity that specifies a value within a classification scheme or on a quantitative scale. This term is currently a descendant of 'information content entity', which requires that it 'is about' something. A value specification of '20g' for a measurement data item of the mass of a particular mouse 'is about' the mass of that mouse. However there are cases where a value specification is not clearly about any particular. In the future we may change 'value specification' to remove the 'is about' requirement. PERSON:Bjoern Peters value specification whole genome sequencing assay WGS permits comprehensive sequencing of introns and exons, whereas whole exome sequencing (WES) allows deeper sequencing of exonic regions at a lower cost. Due to the large number of genetic variants found in each genome, it is necessary to use filtering approaches to distinguish deleterious from benign variants. WES has been used successfully to identify novel genetic causes of primary immunodeficiency. Complex structural variations and non-Mendelian disorders remain challenges for WGS. A DNA sequencing assay that intends to provide information about the sequence of an entire genome of an organism. Genotyping assays should ideally identify which part of the genome the information is about. We do not currently have a good way to do this. That information should be added later. ImmPort WGS PMID:23095910 PMID:25827230 whole genome sequencing assay measurand role A role borne by a material entity and realized in an assay which achieves the objective to measure the magnitude/concentration/amount of the measurand in the entity bearing evaluant role. Person: Alan Ruttenberg, Jie Zheng https://en.wiktionary.org/wiki/measurand https://github.com/obi-ontology/obi/issues/778 measurand role organism animal fungus plant virus A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs. 10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms') 13-02-2009: OBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus. This issue is outside the scope of OBI. GROUP: OBI Biomaterial Branch WEB: http://en.wikipedia.org/wiki/Organism organism specimen Biobanking of blood taken and stored in a freezer for potential future investigations stores specimen. A material entity that has the specimen role. Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation. PERSON: James Malone PERSON: Philippe Rocca-Serra GROUP: OBI Biomaterial Branch specimen cultured cell population A cultured cell population applied in an experiment: "293 cells expressing TrkA were serum-starved for 18 hours and then neurotrophins were added for 10 min before cell harvest." (Lee, Ramee, et al. "Regulation of cell survival by secreted proneurotrophins." Science 294.5548 (2001): 1945-1948). A cultured cell population maintained in vitro: "Rat cortical neurons from 15 day embryos are grown in dissociated cell culture and maintained in vitro for 8–12 weeks" (Dichter, Marc A. "Rat cortical neurons in cell culture: culture methods, cell morphology, electrophysiology, and synapse formation." Brain Research 149.2 (1978): 279-293). A processed material comprised of a collection of cultured cells that has been continuously maintained together in culture and shares a common propagation history. 2013-6-5 MHB: This OBI class was formerly called 'cell culture', but label changed and definition updated following CLO alignment efforts in spring 2013, during which the intent of this class was clarified to refer to portions of a culture or line rather than a complete cell culture or line. PERSON:Matthew Brush cell culture sample PERSON:Matthew Brush The extent of a 'cultured cell population' is restricted only in that all cell members must share a propagation history (ie be derived through a common lineage of passages from an initial culture). In being defined in this way, this class can be used to refer to the populations that researchers actually use in the practice of science - ie are the inputs to culturing, experimentation, and sharing. The cells in such populations will be a relatively uniform population as they have experienced similar selective pressures due to their continuous co-propagation. And this population will also have a single passage number, again owing to their common passaging history. Cultured cell populations represent only a collection of cells (ie do not include media, culture dishes, etc), and include populations of cultured unicellular organisms or cultured multicellular organism cells. They can exist under active culture, stored in a quiescent state for future use, or applied experimentally. cultured cell population extraction nucleic acid extraction using phenol chloroform A material separation in which a desired component of an input material is separated from the remainder Current the output of material processing defined as the molecular entity, main component in the output material entity, rather than the material entity that have grain molecular entity. 'nucleic acid extract' is the output of 'nucleic acid extraction' and has grain 'nucleic acid'. However, the output of 'nucleic acid extraction' is 'nucleic acid' rather than 'nucleic acid extract'. We are aware of this issue and will work it out in the future. Person:Bjoern Peters Philippe Rocca-Serra extraction DNA sequencer ABI 377 DNA Sequencer, ABI 310 DNA Sequencer A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences. Trish Whetzel MO DNA sequencer collecting specimen from organism taking a sputum sample from a cancer patient, taking the spleen from a killed mouse, collecting a urine sample from a patient a process with the objective to obtain a material entity that was part of an organism for potential future use in an investigation PERSON:Bjoern Peters IEDB collecting specimen from organism environmental material collection Taking 1 liter of surface ocean water from the San Diego Mission Bay Jetty. Capturing mice living in rural Arkansas environmental_material_collection is an acquisition where an object is taken from an environment and put into a storage container. Roles include, environment, thing collected, container, acquirer. relabel the term and add axiom connecting to EnVO:'environmental material' discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/obi-terms/779/ Bjoern Peters, Alan Ruttenberg IEDB the researcher is very interested in the location environmental material collection process material component separation Using a cell sorter to separate a mixture of T cells into two fractions; one with surface receptor CD8 and the other lacking the receptor, or purification a material processing in which components of an input material become segregated in space Bjoern Peters IEDB material component separation maintaining cell culture When harvesting blood from a human, isolating T cells, and then limited dilution cloning of the cells, the maintaining_cell_culture step comprises all steps after the initial dilution and plating of the cells into culture, e.g. placing the culture into an incubator, changing or adding media, and splitting a cell culture a protocol application in which cells are kept alive in a defined environment outside of an organism. part of cell_culturing PlanAndPlannedProcess Branch OBI branch derived maintaining cell culture 'establishing cell culture' a process through which a new type of cell culture or cell line is created, either through the isolation and culture of one or more cells from a fresh source, or the deliberate experimental modification of an existing cell culture (e.g passaging a primary culture to become a secondary culture or line, or the immortalization or stable genetic modification of an existing culture or line). PERSON:Matthew Brush PERSON:Matthew Brush A 'cell culture' as used here referes to a new lineage of cells in culture deriving from a single biological source.. New cultures are established through the initial isolation and culturing of cells from an organismal source, or through changes in an existing cell culture or line that result in a new culture with unique characteristics. This can occur through the passaging/selection of a primary culture into a secondary culture or line, or experimental modifications of an existing cell culture or line such as an immortalization process or other stable genetic modification. This class covers establishment of cultures of either multicellular organism cells or unicellular organisms. establishing cell culture sequencing assay The use of the Sanger method of DNA sequencing to determine the order of the nucleotides in a DNA template An assay the uses chemical or biochemical means to infer the sequence of a biomaterial PlanAndPlannedProcess Branch OBI branch derived sequencing assay RNA extraction A RNA extraction is a nucleic acid extraction where the desired output material is RNA PlanAndPlannedProcess Branch OBI branch derived requested by Helen Parkinson for MO RNA extraction nucleic acid extraction Phenol / chlorophorm extraction disolvation of protein content folllowed by ethanol precipitation of the nucleic acid fraction over night in the fridge followed by centrifugation to obtain a nucleic acid pellet. a material separation to recover the nucleic acid fraction of an input material PlanAndPlannedProcess Branch OBI branch derived requested by Helen Parkinson for MO. Could be defined class nucleic acid extraction infection process the detrimental process in which an infectious agent colonizes or replicates in a host environment IEDB IEDB infection process disposition to infect an organism Is a role borne by an agent, and realized when in contact with or inside another organism in which it is capable of replicating and causing disease IEDB IEDB disposition to infect an organism pathologic process abnormal, harmful processes caused by or associated with a disease IEDB IEDB pathologic process A genome is a material entity that represents the entirety of an organism's hereditary information. The genome includes both the genes and the non-coding sequences of the DNA and RNA. Oliver He Book: Eugene Nester, Denise Anderson, C. Evans Roberts, Jr., Microbiology (Companion Site): A Human Perspective, 7th Edition. Mcgraw Hill, October 18, 2011. ISBN-13: 978-0073375311 WEB: http://en.wikipedia.org/wiki/Genome genome A gene is a material entity that represents the entire DNA sequence required for synthesis of a functional protein or RNA molecule. Oliver He WEB: http://www.ncbi.nlm.nih.gov/books/NBK21640/ gene A biological interaction between a microbiome and its host Oliver He, Jie Zheng, Jihad Obeid, Anna Maria Masci microbiome-host interaction https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1669-4 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4644880/ host-microbiome interaction A microbiome located in a human body JZ, YH https://www.ncbi.nlm.nih.gov/pubmed/3418802/ human microbiome A biome that consists of a collection of microorganisms (i.e., microbiota) and the surrounding environment where the microorganisms reside. Oliver He, Jie Zheng, Jihad Obeid, Anna Maria Masci https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4520061/ microbiome A microbiome located in a mouse body JZ, YH mouse microbiome A microbiome that includes a collective population of bacterial organisms. YH, JZ, JO, AA bacterial microbiome A microbiome that includes a collective population of fungal microorganisms. YH, JZ, JO, AA https://www.ncbi.nlm.nih.gov/pubmed/3708484/ fungal microbiome A microbiome that includes a collective population of virus viral microbiome A fungal microbiome that is located in the skin of a host organism YH, JZ, JO, AA https://www.ncbi.nlm.nih.gov/pubmed/3708484/ fungal microbiome of skin A fungal microbiome that is located in a mucosal site of a host organism (e.g., urogenital tract, oral cavity, and gastrointestinal tract) YH, JZ, JO, AA https://www.ncbi.nlm.nih.gov/pubmed/3708484/ fungal microbiome of mucosal site A fungal microbiome that is located in a lung of a host organism YH, JZ, JO, AA https://www.ncbi.nlm.nih.gov/pubmed/3708484/ fungal microbiome of lung A host-microbiome interaction where the microbiome interacts with the host immune system YH, JZ, JO, AA interaction between microbiome and host immune system A interaction between microbiome and host immune system where the immune system is the host adaptive immune system YH, JZ, JO, AA https://www.ncbi.nlm.nih.gov/pubmed/27366226 interaction between microbiome and adaptive immune system a human microbiome that is located in a human respiratory system JO, AA, YH microbiome in human lung a human microbiome that is located in a human lung JO, AA, YH microbiome in human respiratory system a human microbiome that is located in a human oral system JO, AA, YH microbiome in human oral a human microbiome that is located in a human gastrointestinal system JO, AA, YH microbiome in human gastrointestinal system a human microbiome that is located in a human cutaneous system JO, AA, YH microbiome in human cutaneous system a human microbiome that is located in a human urogenital system JO, AA, YH microbiome in human urogenital system A host-microbiome interaction where the host is human YH, HW human-microbiome interaction A microbiome located in a human gut. YH human gut microbiota A human being's gut microbiota contains tens of trillions of microorganisms, including at least 1000 different species of known bacteria with more than 3 million genes (150 times more than human genes). Microbiota can, in total, weigh up to 2 kg. One third of our gut microbiota is common to most people, while two thirds are specific to each one of us. In other words, the microbiota in your intestine is like an individual identity card. URL: http://www.gutmicrobiotaforhealth.com/en/about-gut-microbiota-info/ human gut microbiome An interaction between human and gut microbiome. YH human-gut microbiome interaction A human-gut microbiome interaction that is associated with bowel syndrome. YH https://www.ncbi.nlm.nih.gov/pubmed/25864640 human gut microbiome interaction in bowel syndrome A human-gut microbiome interaction that is associated with Crohn's disease. YH https://www.ncbi.nlm.nih.gov/pubmed/25864640 human gut microbiome interaction in Crohn's disease A human-gut microbiome interaction that is associated with colon cancer. YH https://www.ncbi.nlm.nih.gov/pubmed/25864640 colon cancer human-gut microbiome interaction A human-gut microbiome interaction that involves in Clostridium difficile YH https://www.ncbi.nlm.nih.gov/pubmed/4892173/ human gut microbiome and Clostridium difficile interaction A human-gut microbiome interaction where antibiotics have significant and long-lasting effects on the intestinal microbiota and consequently reduce colonization resistance against Clostridium difficile. YH https://www.ncbi.nlm.nih.gov/pubmed/4892173/ antibiotics reducing colonization resistance against C. difficile in human gut A human-gut microbiome interaction where a fecal microbiota transplantation is used to restore a human gut microbiome to a state resistant to Clostridium difficile infection. YH restoring human gut microbiome resistance to CDI by FMT https://www.ncbi.nlm.nih.gov/pubmed/4328137/ restoring human gut microbiome resistance to C. difficile infection by fecal microbiota transplantation An infection process that is caused by Clostridioides difficile. YH CDI Clostridioides difficile infection A human gut-microbiome interaction that is associated with rheumatoid arthritis (RA). YH https://www.ncbi.nlm.nih.gov/pubmed/4840970/ RA human-gut microbiome interaction An association of human gut microbiota with rheumatoid arthritis (RA) that shows a patient with RV exhibits decreased gut microbial diversity YH https://www.ncbi.nlm.nih.gov/pubmed/4840970/ patient with RA having decreased gut microbial diversity A quality with an increased quantity of a type of organism (e.g., bacteria inside human gut) compared with control. YH, HW, HY increased organism quantity compared with healthy control A quality with an decreased microbiome organism dirversity in a host microbiome environment (e.g., gut). YH, HW, HY descreased microbiome organism diversity a RA human-gut microbiome interaction that shows an decrease of Klebsiella pneumoniae in patients with RA compared with healthy controls. Haihe Wang, Hong Yu, Yongqun He https://www.ncbi.nlm.nih.gov/pubmed/?term=26214836 depletion of Klebsiella pneumoniae in RA human gut A quality with a depleted quantity of a type of organism (e.g., bacteria inside human gut) compared with control. YH, HW, HY decreased organism quantity compared with healthy controls An interaction between human and oral microbiome. YH WH YH human oral cavity microbiome interaction a RA human-gut microbiome interaction that shows an expansion of Gordonibacter pamelaeae in patients with RA compared with healthy controls. Haihe Wang, Hong Yu, Yongqun He https://www.ncbi.nlm.nih.gov/pubmed/26214836/ expansion of Gordonibacter pamelaeae in RA human gut a RA human-gut microbiome interaction that shows an expansion of Prevotellaceae in patients with chronic RA compared with healthy controls. Haihe Wang, Hong Yu, Yongqun He https://www.ncbi.nlm.nih.gov/pmc/articles/PMID:24192039/ expansion of Prevotellaceae in RA human gut a RA human-gut microbiome interaction that shows an decrease of Bifidobacterium bifidum in patients with RA compared with healthy controls. Haihe Wang, Hong Yu, Yongqun He https://www.ncbi.nlm.nih.gov/pubmed/?term=26214836 depletion of Bifidobacterium bifidum in RA human gut a RA human-gut microbiome interaction that shows an decrease of Veillonellain in patients with RA compared with healthy controls. Haihe Wang, Hong Yu, Yongqun He https://www.ncbi.nlm.nih.gov/pubmed/?term=26214836 depletion of Veillonella in RA human gut RA human-gut microbiome interaction that shows an decrease of Sutterella wadsworthensis in patients with RA compared with healthy controls. Haihe Wang, Hong Yu, Yongqun He https://www.ncbi.nlm.nih.gov/pubmed/?term=26214836 depletion of Sutterella wadsworthensis in RA human gut a RA human-gut microbiome interaction that shows an decrease of Megamonas hypermegale in patients with RA compared with healthy controls. Haihe Wang, Hong Yu, Yongqun He https://www.ncbi.nlm.nih.gov/pubmed/?term=26214836 depletion of Megamonas hypermegale in RA human gut a RA human-gut microbiome interaction that shows an expansion of [Clostridium] asparagiforme in patients with RA compared with healthy controls. Haihe Wang, Hong Yu, Yongqun He https://www.ncbi.nlm.nih.gov/pubmed/26214836/ expansion of [Clostridium] asparagiforme in RA human gut A colorectal cancer human-gut microbiome interaction where B. fragilis is increased. YH, HW https://www.ncbi.nlm.nih.gov/pubmed/24967088 https://www.ncbi.nlm.nih.gov/pubmed/27810411 expansion of B. fragilis in colorectal cancer human gut a RA human-gut microbiome interaction that shows an expansion of Eggerthella lenta in patients with RA compared with healthy controls. Haihe Wang, Hong Yu, Yongqun He https://www.ncbi.nlm.nih.gov/pubmed/26214836/ expansion of Eggerthella lenta in RA human gut A quality with a depleted quantity of a type of organism (e.g., bacteria inside human gut) in a patient with an acute disease compared with a patient control with the same disease but at a chronic stage. YH, HW, HY decreased organism quantity in acute disease patient compared with chronic disease control A host-microbiome interaction where the host is rattus. YH, HW rat-microbiome interaction a RA human-gut microbiome interaction that shows an expansion of Bifidobacterium dentium in patients with RA compared with healthy controls. Haihe Wang, Hong Yu, Yongqun He https://www.ncbi.nlm.nih.gov/pubmed/26214836/ expansion of Bifidobacterium dentium in RA human gut a RA human-gut microbiome interaction that shows an expansion of Lactobacillus sp in patients with RA compared with healthy controls. Haihe Wang, Hong Yu, Yongqun He https://www.ncbi.nlm.nih.gov/pubmed/26214836/ expansion of Lactobacillus sp in RA human gut a RA human-gut microbiome interaction that shows an expansion of Ruminococcus lactaris in patients with chronic RA compared with healthy controls. Haihe Wang, Hong Yu, Yongqun He https://www.ncbi.nlm.nih.gov/pubmed/26214836/ expansion of Ruminococcus lactaris in RA human gut a RA human-gut microbiome interaction that shows high Prevotella or high Bacteroides relative abundance, but rarely a high relative abundance of both. Haihe Wang, Yongqun He https://www.ncbi.nlm.nih.gov/pubmed/24192039 segregation of Prevotella or Bacteroides dominance in RA human gut A quality with a depleted quantity of a type of organism (e.g., bacteria inside human gut) compared with a patient control with the fibromyalgia (FM) disease. YH, HW, HY decreased organism quantity compared with fibromyalgia patients A human gut-microbiome interaction that is associated with systemic lupus erythematosus (SLE). Haihe Wang, Hong Yu, Yongqun He SLE human-gut microbiome interaction A human-gut microbiome interaction that is associated with colorectal cancer. YH, HW colorectal cancer human-gut microbiome interaction A colorectal cancer human-gut microbiome interaction where Fusobacterium sp. is increased. YH, HW https://www.ncbi.nlm.nih.gov/pubmed/23733170 https://www.ncbi.nlm.nih.gov/pubmed/23954159 https://www.ncbi.nlm.nih.gov/pubmed/25104642 expansion of Fusobacterium sp. in colorectal cancer human gut A colorectal cancer human-gut microbiome interaction where Citrobacter is decreased. YH, HW https://www.ncbi.nlm.nih.gov/pubmed/21647227 depletion of Citrobacter in colorectal cancer human gut a RA human-gut microbiome interaction that shows an expansion of Porphyromonas gingivalis in patients with RA compared with healthy controls. Haihe Wang, Hong Yu, Yongqun He https://www.ncbi.nlm.nih.gov/pubmed/20436074 / https://www.ncbi.nlm.nih.gov/pubmed/24873878/ expansion of Porphyromonas gingivalis in RA human gut A colorectal cancer human-gut microbiome interaction where Shigella is decreased. YH, HW https://www.ncbi.nlm.nih.gov/pubmed/21647227 depletion of Shigella in colorectal cancer human gut a RA human oral cavity microbiome interaction that shows an expansion of rare taxa,Prevotella intermedia in patients with RA compared with healthy controls. Haihe Wang, Hong Yu, Yongqun He https://www.ncbi.nlm.nih.gov/pubmed/22576262 https://www.ncbi.nlm.nih.gov/pubmed/27789760 expansion of Prevotella intermedia in RA human oral cavity a RA human oral cavity microbiome interaction that shows an expansion of Porphyromonas gingivalis in patients with RA compared with healthy controls. Haihe Wang, Hong Yu, Yongqun He https://www.ncbi.nlm.nih.gov/pubmed/19554393 https://www.ncbi.nlm.nih.gov/pubmed/23902301 https://www.ncbi.nlm.nih.gov/pubmed/27641915 https://www.ncbi.nlm.nih.gov/pubmed/27789760 expansion of Porphyromonas gingivalis in RA human oral cavity a RA human-gut microbiome interaction that shows an expansion of Proteus mirabilis in patients with RA compared with healthy controls. Haihe Wang, Hong Yu, Yongqun He https://www.ncbi.nlm.nih.gov/pubmed/19895906/ https://www.ncbi.nlm.nih.gov/pubmed/24873878/ expansion of Proteus mirabilis in RA human gut a RA human-gut microbiome interaction that shows an expansion of Collinsella aerofaciens in patients with RA compared with healthy controls. Haihe Wang, Hong Yu, Yongqun He https://www.ncbi.nlm.nih.gov/pubmed/27102666/ expansion of Collinsella aerofaciens in RA human gut A human gut-microbiome interaction that is associated with the diarrhea disease YH diarrheal patient-gut microbiome interaction a SLE human-gut microbiome interaction that shows an expansion of Klebsiella in patients with SLE compared with healthy controls. Haihe Wang, Hong Yu, Yongqun He https://www.ncbi.nlm.nih.gov/pubmed/27980687/ expansion of Klebsiella in SLE human gut a RA human oral cavity microbiome interaction that shows an expansion of Lactobacillus salivarius in patients with RA compared with healthy controls. Haihe Wang, Hong Yu, Yongqun He https://www.ncbi.nlm.nih.gov/pubmed/26214836 https://www.ncbi.nlm.nih.gov/pubmed/27789760 https://www.ncbi.nlm.nih.gov/pubmed/26214836 expansion of Lactobacillus salivarius in RA human oral cavity a RA human-gut microbiome interaction that shows an expansion of Clostridia in patients with RA compared with healthy controls. Haihe Wang, Hong Yu, Yongqun He https://www.ncbi.nlm.nih.gov/pubmed/26385261/ https://www.ncbi.nlm.nih.gov/pubmed/2889500/ expansion of Clostridia in RA human gut a RA human-gut microbiome interaction that shows an expansion of Clostridium perfringens in patients with RA compared with healthy controls. Haihe Wang, Hong Yu, Yongqun He https://www.ncbi.nlm.nih.gov/pubmed/2889500 expansion of Clostridium perfringens in RA human gut a SLE human-gut microbiome interaction that shows an expansion of Prevotella in patients with SLE compared with healthy controls. Haihe Wang, Hong Yu, Yongqun He https://www.ncbi.nlm.nih.gov/pubmed/27980687/ expansion of Prevotella in SLE human gut a SLE human-gut microbiome interaction that shows a depletion of Dialister in patients with SLE compared with healthy controls. Haihe Wang, Hong Yu, Yongqun He https://www.ncbi.nlm.nih.gov/pubmed/27980687/ depletion of Dialister in SLE human gut a RA human-gut microbiome interaction that shows an decrease of Bacteroides in patients with RA compared with healthy controls. Haihe Wang, Hong Yu, Yongqun He https://www.ncbi.nlm.nih.gov/pubmed/?term=26385261 depletion of Bacteroides in RA human gut a RA human-gut microbiome interaction that shows an decrease of Porphyromonas in patients with RA compared to fibromyalgia patients Haihe Wang, Hong Yu, Yongqun He https://www.ncbi.nlm.nih.gov/pubmed/18528968 https://www.ncbi.nlm.nih.gov/pubmed/?term=26385261 depletion of Porphyromonas in RA human gut compared to fibromyalgia patients a RA human-gut microbiome interaction that shows an decrease of Prevotella in patients with RA compared to fibromyalgia patients Haihe Wang, Hong Yu, Yongqun He https://www.ncbi.nlm.nih.gov/pubmed/?term=26385261 depletion of Prevotella in RA human gut compared to fibromyalgia patients An interaction between human and respiratory airway microbiome. Haihe Wang, Hong Yu, Yongqun He human respiratory airway microbiome interaction A human respiratory airway microbiome interaction that is associated with rheumatoid arthritis (RA). Haihe Wang, Hong Yu, Yongqun He RA human respiratory airway microbiome interaction RA human respiratory airway microbiome interaction that shows an decrease of Porphyromonas in patients with RA compared with healthy controls. Haihe Wang, Hong Yu, Yongqun He https://www.ncbi.nlm.nih.gov/pubmed/?term=27855721 depletion of Porphyromonas in RA human respiratory airway RA human respiratory airway microbiome interaction that shows an decrease of Prevotella in patients with RA compared with healthy controls. Haihe Wang, Hong Yu, Yongqun He https://www.ncbi.nlm.nih.gov/pubmed/?term=27855721 depletion of Prevotella in RA human respiratory airway a SLE human-gut microbiome interaction that shows a depletion of Pseudobutyrivibrio in patients with SLE compared with healthy controls. Haihe Wang, Hong Yu, Yongqun He https://www.ncbi.nlm.nih.gov/pubmed/27980687/ depletion of Pseudobutyrivibrio in SLE human gut A human oral cavity microbiome interaction that is associated with systemic lupus erythematosus (SLE). YH SLE human oral cavity microbiome interaction A human oral cavity microbiome interaction that is associated with rheumatoid arthritis (RA). YH RA human oral cavity microbiome interaction a RA human oral cavity microbiome interaction that shows an decrease of Haemophilus in patients with RA compared with healthy controls. Haihe Wang, Hong Yu, Yongqun He https://www.ncbi.nlm.nih.gov/pubmed/?term=26214836 depletion of Haemophilus in RA human oral cavity a RA human-gut microbiome interaction that shows an expansion of Actinobacteria<phylum> in patients with RA compared with healthy controls. Haihe Wang, Hong Yu, Yongqun He https://www.ncbi.nlm.nih.gov/pubmed/28376066/ expansion of Actinobacteria<phylum> in RA human gut a RA human oral cavity microbiome interaction that shows an decrease of Cardiobacterium in patients with RA compared with healthy controls. Haihe Wang, Hong Yu, Yongqun He https://www.ncbi.nlm.nih.gov/pubmed/?term=26214836 depletion of Cardiobacterium in RA human oral cavity a RA human oral cavity microbiome interaction that shows an decrease of Eikenella in patients with RA compared with healthy controls. Haihe Wang, Hong Yu, Yongqun He https://www.ncbi.nlm.nih.gov/pubmed/?term=26214836 depletion of Eikenella in RA human oral cavity a RA human oral cavity microbiome interaction that shows an expansion of Kingella in patients with RA compared with healthy controls. Haihe Wang, Hong Yu, Yongqun He https://www.ncbi.nlm.nih.gov/pubmed/?term=26214836 depletion of Kingella in RA human oral cavity a RA human oral cavity microbiome interaction that shows an expansion of Rothia aeria in patients with RA compared with healthy controls. Haihe Wang, Hong Yu, Yongqun He https://www.ncbi.nlm.nih.gov/pubmed/?term=26214836 depletion of Rothia aeria in RA human oral cavity a diarrheal patient-gut microbiome interaction that shows an decrease of Prevotella in patients in the gut of human diarrheal patient compared with healthy controls. YH http://microbiomedb.org/mbio/app/ depletion of Prevotella in diarrheal patient gut a RA human-gut microbiome interaction that shows an expansion of Prevotella copri in patients with RA compared with healthy controls. Haihe Wang, Hong Yu, Yongqun He https://www.ncbi.nlm.nih.gov/pubmed/27333153 expansion of Prevotella copri in RA human gut a RA human oral cavity microbiome interaction that shows an decrease of Haemophilus sp in patients with RA compared with healthy controls. Haihe Wang, Hong Yu, Yongqun He https://www.ncbi.nlm.nih.gov/pubmed/?term=26214836 depletion of Haemophilus spp. in RA human oral cavity a RA human oral cavity microbiome interaction that shows an increase of Cryptobacterium curtum in patients with RA compared with healthy controls. Haihe Wang, Hong Yu, Yongqun He https://www.ncbi.nlm.nih.gov/pubmed/?term=26214836 expansion of Cryptobacterium curtum in RA human oral cavity a RA human oral cavity microbiome interaction that shows an expansion of Veillonella in patients with RA compared with healthy controls. Haihe Wang, Hong Yu, Yongqun He https://www.ncbi.nlm.nih.gov/pubmed/?term=26214836 expansion of Veillonella in RA human oral cavity An interaction between rattus and gut microbiome. YH rat gut microbiome interaction a RA human-gut microbiome interaction that shows an expansion of Escherichia coli in patients with RA compared with healthy controls. Haihe Wang, Hong Yu, Yongqun He https://www.ncbi.nlm.nih.gov/pubmed/20360042/ expansion of Escherichia coli in RA human gut a SLE human oral cavity microbiome interaction that shows an decrease of Clostridiales in patients with SLE compared with healthy controls. Haihe Wang, Hong Yu, Yongqun He https://www.ncbi.nlm.nih.gov/pubmed/?term=28320468 depletion of Clostridiales in SLE human oral cavity a RA human-gut microbiome interaction that shows an decrease of Faecalibacterium in patients with RA compared with healthy controls. Haihe Wang, Hong Yu, Yongqun He https://www.ncbi.nlm.nih.gov/pubmed/?term=27333153 depletion of Faecalibacterium in RA human gut A human gut-microbiome interaction that is associated with ankylosing spondylitis (AS). Haihe Wang, Hong Yu, Yongqun He AS human-gut microbiome interaction an AS human-gut microbiome interaction that shows an expansion of Ruminococcaceae in patients with AS compared with healthy controls. Haihe Wang, Hong Yu, Yongqun He https://www.ncbi.nlm.nih.gov/pubmed/25417597/ https://www.ncbi.nlm.nih.gov/pubmed/26362739/ expansion of Ruminococcaceae in AS human gut an AS human-gut microbiome interaction that shows an expansion of Lachnospiraceae in patients with AS compared with healthy controls. Haihe Wang, Hong Yu, Yongqun He https://www.ncbi.nlm.nih.gov/pubmed/25417597/ https://www.ncbi.nlm.nih.gov/pubmed/25434931/ https://www.ncbi.nlm.nih.gov/pubmed/26331579/ expansion of Lachnospiraceae in AS human gut an AS human-gut microbiome interaction that shows an expansion of Bacteroidaceae in patients with AS compared with healthy controls. Haihe Wang, Hong Yu, Yongqun He https://www.ncbi.nlm.nih.gov/pubmed/25417597/ expansion of Bacteroidaceae in AS human gut