Converting UO terms from classes to individuals (offline, in a triplestore): (Most recently did mmHg with Ontofox, then converted in text editor... may not survive next merge.) PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX : <http://purl.obolibrary.org/obo/uo.owl#> insert { graph :individualized { ?s a ?super } } where { values ?super { <http://purl.obolibrary.org/obo/UO_0000001> <http://purl.obolibrary.org/obo/UO_0000002> } ?s rdfs:subClassOf ?super ; rdfs:label ?sublab . ?super rdfs:label ?superlab . } --- PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX : <http://purl.obolibrary.org/obo/uo.owl#> insert { graph :individualized { ?s a <http://purl.obolibrary.org/obo/UO_0000051> } } where { values ?super { <http://purl.obolibrary.org/obo/UO_0000052> } ?s rdfs:subClassOf ?super ; rdfs:label ?sublab . ?super rdfs:label ?superlab . } --- PREFIX : <http://purl.obolibrary.org/obo/uo.owl#> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX owl: <http://www.w3.org/2002/07/owl#> construct { ?s ?p ?o . ?s a owl:NamedIndividual . } where { graph :individualized { ?s a ?t } ?s ?p ?o . filter(?o != owl:Class) filter(?p != rdfs:subClassOf) } --- save results of construct statement to uo_individualized.ttl and import into TURBO Used a similar strategy for Gleason terms from NCIT: asserted (though inserts into a new named graph) that the subclasses of http://purl.obolibrary.org/obo/NCIT_C28107 and http://purl.obolibrary.org/obo/NCIT_C28084 are instances of NCIT_C28107 and NCIT_C28084. Then constructed those assertions, along with all annotations on the terms except for subClassOf, into a turtle file. Other NCIT terms were imported earlier on just by cutting and pasting between RDF files. That's the case for any term that isn't native to TURBO or didn't come from OntoFox or OntoDog (including parent terms imported to satisfy MIREOT)
OBO foundry ontologies, especially the ontology for biobanking, OBIB.
Basic approach: used ontodog to extract a base ontology view from OBIB Then used ontofox to get additional classes and properties from other OBO foundry ontologies After merging and tidying up, save as turbo_merged.owl (AND turbo_merged.rdf or turbo_merged.ttl for TopBraid Composer) ---- some manual tidying that might be required: Make [molecular entity](http://purl.obolibrary.org/obo/CHEBI_23367) a direct subclass of [material entity](http://purl.obolibrary.org/obo/BFO_0000040) and remove [chemical entity](http://purl.obolibrary.org/obo/CHEBI_24431) from [material entity](http://purl.obolibrary.org/obo/BFO_0000040). [specifically dependent continuant](http://purl.obolibrary.org/obo/BFO_0000020) isn't a direct sbclasses of [entity](http://purl.obolibrary.org/obo/BFO_0000001), only [continuant](http://purl.obolibrary.org/obo/BFO_0000002) Haven't been using [Anatomical location](http://purl.obolibrary.org/obo/FMA_50707) ... hasn't appeared at all in recent ontoanimal exports GO cellular_component appearing as direct subclass of Thing... dragged into material entity a la OBI ... hasn't appeared at all in recent ontoanimal exports ---- April 2019 manual changes (attributed to OntoFox extract, possibly from hypertension related terms?) - BFO_0000051 was erroneously labeled "part of" in addition to the correct label "has part" - [sign](http://purl.obolibrary.org/obo/OGMS_0000024) was moved out of [quality](http://purl.obolibrary.org/obo/BFO_0000019) and into [entity](http://purl.obolibrary.org/obo/BFO_0000001) ---- removed [physical object quality](http://purl.obolibrary.org/obo/PATO_0001241) from [Phenotypic abnormality](http://purl.obolibrary.org/obo/HP_0000118) removed [blood pressure](http://purl.obolibrary.org/obo/VSO_0000004) from [vital sign](http://purl.obolibrary.org/obo/OGMS_0000029)
This ontology is intended to support a semantic linked data reimplementation of biobanking and related data, typically originating in a relational format. The first implementation will be at the Penn Medicine Biobank.
todo: make a better log of terms pasted into turbo.owl with text editor or merged through any route other than ontodog or ontofox. may include BMI, DOB, mmHg, systolic blood pressure measurement datum. ICD-9 and ICD-10 as individuals. ---- https://github.com/PennTURBO/Turbo-Ontology/issues/2 Foreign terms that have asserted super-classes in turbo.owl proper, as opposed to an import file: - **Present in OBI** - Note two different styles for NCIT terms - Note inconsistency re UO terms as instances vs classes ---- - http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C49474 - http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C53489 - http://purl.obolibrary.org/obo/CL_0001061 - http://purl.obolibrary.org/obo/HTN_00000000 - http://purl.obolibrary.org/obo/HTN_00000001 - http://purl.obolibrary.org/obo/MONDO_0004992 - http://purl.obolibrary.org/obo/MONDO_0045024 - http://purl.obolibrary.org/obo/NCIT_C28084 - http://purl.obolibrary.org/obo/NCIT_C28107 - http://purl.obolibrary.org/obo/OGMS_0000031 - http://purl.obolibrary.org/obo/OGMS_0000078 - http://purl.obolibrary.org/obo/OGMS_0000096 - http://purl.obolibrary.org/obo/UO_0000009 - http://purl.obolibrary.org/obo/UO_0000015 - http://purl.obolibrary.org/obo/VSO_0000005 - http://purl.obolibrary.org/obo/VSO_0000006 - http://www.ebi.ac.uk/efo/EFO_0004340 ---- Moved to ontofox import: - **http://purl.obolibrary.org/obo/GO_0005575** - **http://purl.obolibrary.org/obo/IAO_0000010** - **http://purl.obolibrary.org/obo/IAO_0000594** - **http://purl.obolibrary.org/obo/UBERON_0001013**
BFO OWL specification label
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 CLIF specification label
Relates an entity in the ontology to the term that is used to represent it in the the CLIF specification of BFO2
editor preferred label
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
example
example of usage
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.
has curation status
PERSON:Alan Ruttenberg
PERSON:Bill Bug
PERSON:Melanie Courtot
definition
English language definitions of what NCI means by the concept. These are limited to 1024 characters. They may also include information about the definition's source and attribution in a form that can easily be interpreted by software.
The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
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.
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.
definition editor
term editor
Name of editor entering the definition in the file. The definition editor is a point of contact for information regarding the term. The definition editor may be, but is not always, the author of the definition, which may have been worked upon by several people
Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people
20110707, MC: label update to term editor and definition modified accordingly. See 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.
alternative term
An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent)
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
Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w
has obsolescence reason
Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification.
curator note
An administrative note of use for a curator but of no use for a user
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
The 'tracker item' can associate a tracker with a specific ontology term.
term tracker item
The name of the person, project, or organization that motivated inclusion of an ontology term by requesting its addition.
The 'term requester' can credit the person, organization or project who request the ontology term.
ontology term requester
imported from
For external terms/classes, the ontology from which the term was imported
expand expression to
ObjectProperty: RO_0002104 Label: has plasma membrane part Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)"
A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones
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:Bjoern Peters
PERSON:Chris Mungall
GROUP:OBO Foundry <http://obofoundry.org/>
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
has associated axiom(nl)
Person:Alan Ruttenberg
An axiom associated with a term expressed using natural language
has associated axiom(fol)
An axiom expressed in first order logic using CLIF syntax
is allocated id range
Add as annotation triples in the granting ontology
Relates an ontology IRI to an (inclusive) range of IRIs in an OBO name space. The range is give as, e.g. "IAO_0020000-IAO_0020999"
term replaced by
Use on obsolete terms, relating the term to another term that can be used as a substitute
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
ISA tools project (http://isa-tools.org)
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
the symbol assigned by the nomenclature authority
symbol from nomenclature authority
the full name assigned by the nomenclature authority
full name from nomenclature authority
NCBI GeneID
NCBI LocusTag
gene map location
modification date
The NCBITaxon ontology ID of an organism.
organism NCBITaxon ID
A chromosome ID where a gene is located.
chromosome ID of gene
an annotation property that specifies the type of a gene
type of gene
an annotation property that specifies a nomenclature status
nomenclature status
an annotation property that shows the GO information associated with a specific gene.
YH: use the convention: GO_ID (EC: xx; Qualifier: xx; PMID: xxxxx;) where GO_ID is a GO ID, EC is the Evidence Code, Qualifier is a specific association type, and PMID is a PubMed ID of a paper that supports the gene-GO association.
has GO association
An annotation property that represents a gene's association with PubMed publication(s).
YH: use the format: PMID: pmid1, pmid2, ... where pmid1 and pmid2 are specfic PubMed IDs (PMIDs).
has PubMed association
temporal interpretation
An assertion that holds between an OWL Object Property and a temporal interpretation that elucidates how OWL Class Axioms that use this property are to be interpreted in a temporal context.
An assertion that 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
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
part-of is homeomorphic for independent continuants.
R is homemorphic for C iff (1) there exists some x,y such that x R y, and x and y instantiate C and (2) for all x, if x is an instance of C, and there exists some y some such that x R y, then it follows that y is an instance of C.
R homeomorphic-for C expands to: C SubClassOf R only C. Additionally, for any class D that is disjoint with C, we can also expand to C DisjointWith R some D, D DisjointWith R some C.
Notes on the how instances of this class vary across species.
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
A metadata relation between a class and its taxonomic rank (eg species, family)
A person how is responsible for translating the entity annotations from English to another language.
PERSON:Fernanda Farinelli
translated by
A person how is responsible for translating the entity annotations from English to Portuguese.
translated to Portuguese by
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
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
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
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
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
Recommended best practice is to identify the resource by means of a string or number conforming to a formal identification system. Example formal identification systems include the Uniform Resource Identifier (URI) (including the Uniform Resource Locator (URL)), the Digital Object Identifier (DOI) and the International Standard Book Number (ISBN).
An unambiguous reference to the resource within a given context.
Resource Identifier
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
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
For example, both a 'shortcut health care encounter to diagnosis code symbol' and a 'shortcut health care encounter to diagnosis code registry URI string'might be required to create a fully-formed CRID for a diagnosis code
X 'interdependent with shortcut' Y means it would not make sense, or might not even be possible, to expand shortcut X in the absence of shortcut Y.
In general, if a shortcut triple appears in the absence of its interdependencies, the turbo expansion method should throw an exception. how to assert that both the domain and range are <http://transformunify.org/ontologies/TURBO_0000670> instantiation hybrid shortcut?
Links a 'retired placeholder' to to the corresponding class that is subject to 'referent tracking' X retires Y means that an instance of class Y will appear as an instance of class X after 'referent tracking'
replaced with IUI
the subject of this property has been demoted in the course of referent tracking, and the corresponding entity in reality is now better known by the following IUI:
referent tracked?
A boolean property that is asserted true for individuals that have been referent tracked.
this property should only be true for individuals whose URI (in RDF/OWL perspective) is a IUI, containing a UUID (according to TURBO rules)
this data item is the output of a turbo conclusionation process
:Consenter1 and :ConsenterID1 were instantiated (by Karma?) because there was a column with the semantic type 'biobank consenter symbol', with a value of '1' on some row. (Assuming other interdependent shortcut requirements are met.) If :Consenter1 and :ConsenterID1 end up in a triplestore containing other biobank consenters with 'biobank consenter symbol' values of '1' ( :Consenter2 and :ConsenterID2) and referent trcking is performed, it may be concluded that :Consenter1 and :Consenter2 are the same individual in reality. I that case, :Consenter1 and :Consenter2 would be replaced with two 'retired placeholder for biobank consenter's and one new IUI/UUID-identified referent tracked 'biobank consenter'. To document these results of referent tracking, triples would be inserted saying :ConsenterRT 'previous URI text' "Consenter1" . :ConsenterRT 'previous URI text' "Consenter2" .
'previous URI text' has subproperties that are applicable to the URIs that are inputs into and outputs from shortcut expansion and referent tracking. The shortcut expansion case follows a similar pattern to the referent tracking case. X 'previous URI text' Y means that X is some referent tracked individual, and that before referent tracking was performed, there was an individual identified by a URI with string value Y that is now identified singularly and uniquely by X. One X can have anywhere from one to an infinite number of Y X 'previous URI text's
A ‘previous URI text’ property asserted as a result of shortcut expansion
A ‘previous URI text’ property asserted as a result of referent tracking
has OMOP concept ID
A maps to B means that URI-identified class A has some relationship between URI-identified class B, outside of rdfs:subClassOf or owl:equivalentClass. Classes A and B will generally be defined and or asserted in different upstream ontologies (or other RDF artifacts) Similar in some ways to 'relatedMatch' from https://en.wikipedia.org/wiki/Simple_Knowledge_Organization_System, although SKOS defines that term an an object property.
maps to
A 'maps to' relationship in whose subject is a code (from a system like ICD or SNOMED) and the object is a disease (preferable form MonDO) This property does not imply any certainty or causality, only that some path can be drawn from the code to the disease. This path justifying each 'evidence code for disease' should be exposed in an RDF graph, possibly by grouping all assertions from one path into the same named graph, which would be annotated with a definition etc. If you have a need to find people in an EHR who 'have' a disease, looking for the mapped code is a reasonable but noisy start.
evidence code for disease
A 'maps to' relationship in which the subject is an RDF model of a R_MEDICATION row from the 'master data management' schema in the Penn Data Store relational database used by the University of Pennsylvania Healthcare System. The object would be the term for a drug (ingredient, generic product or branded product) from RxNorm, DrOn, ChEBI, etc.
PDS R_MEDICATION suggests drug term
these properties can be used to temporarily link data values to a non-data-model class. they can be used for retaining data from a "data model with shortcut properties" when the expansion needs to be processed in two or more steps, due to a limitation of federated SAPRQL queries in some triple stores: it's hard to build a link between two service blocks with a data literal appearing in both blocks.
data retained between expansion steps
previous visit id from omop visit
patient id from omop visit
this could be different from the symbol part of the denoter. in the case of instantiating data in from an OMOP schema, the symbol might come from the source identifier and this annotation might come from the OMOP primary key
visit id from omop visit
this could be used to determine a more specific type (inpatient, outpatient, ER) for a healthcare encounter instance
visit concept from omop visit
commented SPARQL query for expansion
race concept from omop person
ethnicity concept from omop person
gender concept from omop person
person id from omop person
A definition citation is a document, ontology class, person or organization from which the definition of the class is derived. It is used in the same sense as a citation in literature, in that the definition may have been derived from these sources or that this definition is related to these source.
has_alternative_id
database_cross_reference
has_dbxref
An alternative label for a given entity such as a commonly used abbreviation or synonym.
Fully qualified synonym, contains the string, term type, source, and an optional source code if appropriate. Each subfield is deliniated to facilitate interpretation by software.
has_exact_synonym
has_narrow_synonym
has_obo_namespace
has_related_synonym
has_URI
in_subset
The TURBO ontology is moving away from human-readable URIs towards the OBO Foundry practice of NAMESPACE_XXXXXXX identifiers, where the X's are numerical digits. Our software developers would like to continue using mnemonics to refer to ontology terms. Presumably this will be implemented with sameAs or equivalentClass/equivalentProperty relationships. This has_mnemonic datatype property has been created to facilitate and maintain these relationships, most likely with some SPARQL construct statements.
label
is part of
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
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.
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
b inheres_in c at t =Def. b is a dependent continuant & c is an independent continuant that is not a spatial region & b s-depends_on c at t. (axiom label in BFO2 Reference: [051-002])
Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'inheres in at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'inheres in@en(x,y,t)'.
BFO 2 Reference: Inherence is a subrelation of s-depends_on which holds between a dependent continuant and an independent continuant that is not a spatial region. Since dependent continuants cannot migrate from one independent continuant bearer to another, it follows that if b s-depends_on independent continuant c at some time, then b s-depends_on c at all times at which a exists. Inherence is in this sense redundantly time-indexed.For example, consider the particular instance of openness inhering in my mouth at t as I prepare to take a bite out of a donut, followed by a closedness at t+1 when I bite the donut and start chewing. The openness instance is then shortlived, and to say that it s-depends_on my mouth at all times at which this openness exists, means: at all times during this short life. Every time you make a fist, you make a new (instance of the universal) fist. (Every time your hand has the fist-shaped quality, there is created a new instance of the universal fist-shaped quality.)
BFO2 Reference: independent continuant that is not a spatial region
BFO2 Reference: specifically dependent continuant
(iff (inheresInAt a b t) (and (DependentContinuant a) (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))) // axiom label in BFO2 CLIF: [051-002]
inheres in at all times
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
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
[copied from inverse property 'concretizes at some time'] You may concretize a piece of software by installing it in your computer
[copied from inverse property 'concretizes at some time'] You may concretize a recipe that you find in a cookbook by turning it into a plan which exists as a realizable dependent continuant in your head.
[copied from inverse property 'concretizes at some time'] you may concretize a poem as a pattern of memory traces in your head
[copied from inverse property 'concretizes at some time'] Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'concretizes at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'concretizes@en'(x,y,t)
[copied from inverse property 'concretizes at some time'] b concretizes c at t means: b is a specifically dependent continuant & c is a generically dependent continuant & for some independent continuant that is not a spatial region d, b s-depends_on d at t & c g-depends on d at t & if c migrates from bearer d to another bearer e than a copy of b will be created in e. (axiom label in BFO2 Reference: [075-002])
concretized by at some time
You may concretize a piece of software by installing it in your computer
You may concretize a recipe that you find in a cookbook by turning it into a plan which exists as a realizable dependent continuant in your head.
you may concretize a poem as a pattern of memory traces in your head
Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'concretizes at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'concretizes@en'(x,y,t)
b concretizes c at t means: b is a specifically dependent continuant & c is a generically dependent continuant & for some independent continuant that is not a spatial region d, b s-depends_on d at t & c g-depends on d at t & if c migrates from bearer d to another bearer e than a copy of b will be created in e. (axiom label in BFO2 Reference: [075-002])
if b g-depends on c at some time t, then there is some d, such that d concretizes b at t and d s-depends_on c at t. (axiom label in BFO2 Reference: [076-001])
(forall (x y t) (if (concretizesAt x y t) (and (SpecificallyDependentContinuant x) (GenericallyDependentContinuant y) (exists (z) (and (IndependentContinuant z) (specificallyDependsOnAt x z t) (genericallyDependsOnAt y z t)))))) // axiom label in BFO2 CLIF: [075-002]
(forall (x y t) (if (genericallyDependsOnAt x y t) (exists (z) (and (concretizesAt z x t) (specificallyDependsOnAt z y t))))) // axiom label in BFO2 CLIF: [076-001]
concretizes at some time
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
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.
A pain s-depends_on the organism that is experiencing the pain
a gait s-depends_on the walking object. (All at some specific time.)
a shape s-depends_on the shaped object
one-sided s-dependence of a dependent continuant on an independent continuant: an instance of headache s-depends_on some head
one-sided s-dependence of a dependent continuant on an independent continuant: an instance of temperature s-depends_on some organism
one-sided s-dependence of a process on something: a process of cell death s-depends_on a cell
one-sided s-dependence of a process on something: an instance of seeing (a relational process) s-depends_on some organism and on some seen entity, which may be an occurrent or a continuant
one-sided s-dependence of one occurrent on another: a process of answering a question is dependent on a prior process of asking a question
one-sided s-dependence of one occurrent on another: a process of obeying a command is dependent on a prior process of issuing a command
one-sided s-dependence of one occurrent on multiple independent continuants: a relational process of hitting a ball with a cricket bat
one-sided s-dependence of one occurrent on multiple independent continuants: a relational process of paying cash to a merchant in exchange for a bag of figs
reciprocal s-dependence between occurrents: a process of buying and the associated process of selling
reciprocal s-dependence between occurrents: a process of increasing the volume of a portion of gas while temperature remains constant and the associated process of decreasing the pressure exerted by the gas
reciprocal s-dependence between occurrents: in a game of chess the process of playing with the white pieces is mutually dependent on the process of playing with the black pieces
the one-sided dependence of an occurrent on an independent continuant: football match on the players, the ground, the ball
the one-sided dependence of an occurrent on an independent continuant: handwave on a hand
the three-sided reciprocal s-dependence of the hue, saturation and brightness of a color [45
the three-sided reciprocal s-dependence of the pitch, timbre and volume of a tone [45
the two-sided reciprocal s-dependence of the roles of husband and wife [20
Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'specifically depends on at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'specifically depends on@en(x,y,t)'.
BFO 2 Reference: An entity – for example an act of communication or a game of football – can s-depends_on more than one entity. Complex phenomena for example in the psychological and social realms (such as inferring, commanding and requesting) or in the realm of multi-organismal biological processes (such as infection and resistance), will involve multiple families of dependence relations, involving both continuants and occurrents [1, 4, 28
BFO 2 Reference: S-dependence is just one type of dependence among many; it is what, in the literature, is referred to as ‘existential dependence’ [87, 46, 65, 20
BFO 2 Reference: the relation of s-depends_on does not in every case require simultaneous existence of its relata. Note the difference between such cases and the cases of continuant universals defined historically: the act of answering depends existentially on the prior act of questioning; the human being who was baptized or who answered a question does not himself depend existentially on the prior act of baptism or answering. He would still exist even if these acts had never taken place.
BFO2 Reference: specifically dependent continuant\; process; process boundary
To say that b s-depends_on a at t is to say that b and c do not share common parts & b is of its nature such that it cannot exist unless c exists & b is not a boundary of c and b is not a site of which c is the host [64
If b is s-depends_on something at some time, then b is not a material entity. (axiom label in BFO2 Reference: [052-001])
If b s-depends_on something at t, then there is some c, which is an independent continuant and not a spatial region, such that b s-depends_on c at t. (axiom label in BFO2 Reference: [136-001])
If occurrent b s-depends_on some independent continuant c at t, then b s-depends_on c at every time at which b exists. (axiom label in BFO2 Reference: [015-002])
an entity does not s-depend_on any of its (continuant or occurrent) parts or on anything it is part of. (axiom label in BFO2 Reference: [013-002])
if b s-depends_on c at t & c s-depends_on d at t then b s-depends_on d at t. (axiom label in BFO2 Reference: [054-002])
(forall (x y t) (if (and (Entity x) (or (continuantPartOfAt y x t) (continuantPartOfAt x y t) (occurrentPartOf x y) (occurrentPartOf y x))) (not (specificallyDependsOnAt x y t)))) // axiom label in BFO2 CLIF: [013-002]
(forall (x y t) (if (and (Occurrent x) (IndependentContinuant y) (specificallyDependsOnAt x y t)) (forall (t_1) (if (existsAt x t_1) (specificallyDependsOnAt x y t_1))))) // axiom label in BFO2 CLIF: [015-002]
(forall (x y t) (if (specificallyDependsOnAt x y t) (exists (z) (and (IndependentContinuant z) (not (SpatialRegion z)) (specificallyDependsOnAt x z t))))) // axiom label in BFO2 CLIF: [136-001]
(forall (x y z t) (if (and (specificallyDependsOnAt x y t) (specificallyDependsOnAt y z t)) (specificallyDependsOnAt x z t))) // axiom label in BFO2 CLIF: [054-002]
(forall (x) (if (exists (y t) (specificallyDependsOnAt x y t)) (not (MaterialEntity x)))) // axiom label in BFO2 CLIF: [052-001]
specifically depends on at all times
Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'occupies spatial region at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'occupies spatial region@en'(x,y,t)
b occupies_spatial_region r at t means that r is a spatial region in which independent continuant b is exactly located (axiom label in BFO2 Reference: [041-002])
every region r is occupies_spatial_region r at all times. (axiom label in BFO2 Reference: [042-002])
if b occupies_spatial_region r at t & b continuant_part_of b at t, then there is some r which is continuant_part_of r at t such that b occupies_spatial_region r at t. (axiom label in BFO2 Reference: [043-001])
(forall (r t) (if (Region r) (occupiesSpatialRegionAt r r t))) // axiom label in BFO2 CLIF: [042-002]
(forall (x r t) (if (occupiesSpatialRegionAt x r t) (and (SpatialRegion r) (IndependentContinuant x)))) // axiom label in BFO2 CLIF: [041-002]
(forall (x y r_1 t) (if (and (occupiesSpatialRegionAt x r_1 t) (continuantPartOfAt y x t)) (exists (r_2) (and (continuantPartOfAt r_2 r_1 t) (occupiesSpatialRegionAt y r_2 t))))) // axiom label in BFO2 CLIF: [043-001]
occupies spatial region at some time
b exists_at t means: b is an entity which exists at some temporal region t. (axiom label in BFO2 Reference: [118-002])
exists at
[copied from inverse property 'part of occurrent'] Mary’s 5th birthday occurrent_part_of Mary’s life
[copied from inverse property 'part of occurrent'] The process of a footballer’s heart beating once is an occurrent part but not a temporal_part of a game of football.
[copied from inverse property 'part of occurrent'] the first set of the tennis match occurrent_part_of the tennis match.
b has_occurrent_part c = Def. c occurrent_part_of b. (axiom label in BFO2 Reference: [007-001])
[copied from inverse property 'part of occurrent'] BFO 2 Reference: a (continuant or occurrent) part of itself. We appreciate that this is counterintuitive for some users, since it implies for example that President Obama is a part of himself. However it brings benefits in simplifying the logical formalism, and it captures an important feature of identity, namely that it is the limit case of mereological inclusion.
[copied from inverse property 'part of occurrent'] BFO2 Reference: occurrent
[copied from inverse property 'part of occurrent'] b occurrent_part_of c =Def. b is a part of c & b and c are occurrents. (axiom label in BFO2 Reference: [003-002])
(iff (hasOccurrentPart a b) (occurrentPartOf b a)) // axiom label in BFO2 CLIF: [007-001]
has occurrent part
[copied from inverse property 'proper part of occurrent'] b proper_occurrent_part_of c =Def. b occurrent_part_of c & b and c are not identical. (axiom label in BFO2 Reference: [005-001])
b has_proper_occurrent_part c = Def. c proper_occurrent_part_of b. [XXX-001
has proper occurrent part
[copied from inverse property 'occupies spatial region at some time'] Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'occupies spatial region at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'occupies spatial region@en'(x,y,t)
[copied from inverse property 'occupies spatial region at some time'] BFO2 Reference: independent continuant
[copied from inverse property 'occupies spatial region at some time'] BFO2 Reference: spatial region
[copied from inverse property 'occupies spatial region at some time'] b occupies_spatial_region r at t means that r is a spatial region in which independent continuant b is exactly located (axiom label in BFO2 Reference: [041-002])
has spatial occupant at some time
[copied from inverse property 'specifically depends on at some time'] A pain s-depends_on the organism that is experiencing the pain
[copied from inverse property 'specifically depends on at some time'] a gait s-depends_on the walking object. (All at some specific time.)
[copied from inverse property 'specifically depends on at some time'] a shape s-depends_on the shaped object
[copied from inverse property 'specifically depends on at some time'] one-sided s-dependence of a dependent continuant on an independent continuant: an instance of headache s-depends_on some head
[copied from inverse property 'specifically depends on at some time'] one-sided s-dependence of a dependent continuant on an independent continuant: an instance of temperature s-depends_on some organism
[copied from inverse property 'specifically depends on at some time'] one-sided s-dependence of a process on something: a process of cell death s-depends_on a cell
[copied from inverse property 'specifically depends on at some time'] one-sided s-dependence of a process on something: an instance of seeing (a relational process) s-depends_on some organism and on some seen entity, which may be an occurrent or a continuant
[copied from inverse property 'specifically depends on at some time'] one-sided s-dependence of one occurrent on another: a process of answering a question is dependent on a prior process of asking a question
[copied from inverse property 'specifically depends on at some time'] one-sided s-dependence of one occurrent on another: a process of obeying a command is dependent on a prior process of issuing a command
[copied from inverse property 'specifically depends on at some time'] one-sided s-dependence of one occurrent on multiple independent continuants: a relational process of hitting a ball with a cricket bat
[copied from inverse property 'specifically depends on at some time'] one-sided s-dependence of one occurrent on multiple independent continuants: a relational process of paying cash to a merchant in exchange for a bag of figs
[copied from inverse property 'specifically depends on at some time'] reciprocal s-dependence between occurrents: a process of buying and the associated process of selling
[copied from inverse property 'specifically depends on at some time'] reciprocal s-dependence between occurrents: a process of increasing the volume of a portion of gas while temperature remains constant and the associated process of decreasing the pressure exerted by the gas
[copied from inverse property 'specifically depends on at some time'] reciprocal s-dependence between occurrents: in a game of chess the process of playing with the white pieces is mutually dependent on the process of playing with the black pieces
[copied from inverse property 'specifically depends on at some time'] the one-sided dependence of an occurrent on an independent continuant: football match on the players, the ground, the ball
[copied from inverse property 'specifically depends on at some time'] the one-sided dependence of an occurrent on an independent continuant: handwave on a hand
[copied from inverse property 'specifically depends on at some time'] the three-sided reciprocal s-dependence of the hue, saturation and brightness of a color [45
[copied from inverse property 'specifically depends on at some time'] the three-sided reciprocal s-dependence of the pitch, timbre and volume of a tone [45
[copied from inverse property 'specifically depends on at some time'] the two-sided reciprocal s-dependence of the roles of husband and wife [20
[copied from inverse property 'specifically depends on at some time'] Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'specifically depends on at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'specifically depends on@en'(x,y,t)
[copied from inverse property 'specifically depends on at some time'] BFO 2 Reference: An entity – for example an act of communication or a game of football – can s-depends_on more than one entity. Complex phenomena for example in the psychological and social realms (such as inferring, commanding and requesting) or in the realm of multi-organismal biological processes (such as infection and resistance), will involve multiple families of dependence relations, involving both continuants and occurrents [1, 4, 28
[copied from inverse property 'specifically depends on at some time'] BFO 2 Reference: S-dependence is just one type of dependence among many; it is what, in the literature, is referred to as ‘existential dependence’ [87, 46, 65, 20
[copied from inverse property 'specifically depends on at some time'] BFO 2 Reference: the relation of s-depends_on does not in every case require simultaneous existence of its relata. Note the difference between such cases and the cases of continuant universals defined historically: the act of answering depends existentially on the prior act of questioning; the human being who was baptized or who answered a question does not himself depend existentially on the prior act of baptism or answering. He would still exist even if these acts had never taken place.
[copied from inverse property 'specifically depends on at some time'] BFO2 Reference: specifically dependent continuant\; process; process boundary
[copied from inverse property 'specifically depends on at some time'] To say that b s-depends_on a at t is to say that b and c do not share common parts & b is of its nature such that it cannot exist unless c exists & b is not a boundary of c and b is not a site of which c is the host [64
has specific dependent at some time
[copied from inverse property 'occupies spatiotemporal region'] BFO 2 Reference: The occupies_spatiotemporal_region and occupies_temporal_region relations are the counterpart, on the occurrent side, of the relation occupies_spatial_region.
[copied from inverse property 'occupies spatiotemporal region'] p occupies_spatiotemporal_region s. This is a primitive relation between an occurrent p and the spatiotemporal region s which is its spatiotemporal extent. (axiom label in BFO2 Reference: [082-003])
has spatiotemporal occupant
BFO 2 Reference: The occupies_spatiotemporal_region and occupies_temporal_region relations are the counterpart, on the occurrent side, of the relation occupies_spatial_region.
p occupies_spatiotemporal_region s. This is a primitive relation between an occurrent p and the spatiotemporal region s which is its spatiotemporal extent. (axiom label in BFO2 Reference: [082-003])
occupies spatiotemporal region
Mary’s 5th birthday occurrent_part_of Mary’s life
The process of a footballer’s heart beating once is an occurrent part but not a temporal_part of a game of football.
the first set of the tennis match occurrent_part_of the tennis match.
[copied from inverse property 'has occurrent part'] b has_occurrent_part c = Def. c occurrent_part_of b. (axiom label in BFO2 Reference: [007-001])
BFO 2 Reference: a (continuant or occurrent) part of itself. We appreciate that this is counterintuitive for some users, since it implies for example that President Obama is a part of himself. However it brings benefits in simplifying the logical formalism, and it captures an important feature of identity, namely that it is the limit case of mereological inclusion.
b occurrent_part_of c =Def. b is a part of c & b and c are occurrents. (axiom label in BFO2 Reference: [003-002])
occurrent_part_of is antisymmetric. (axiom label in BFO2 Reference: [123-001])
occurrent_part_of is reflexive (every occurrent entity is an occurrent_part_of itself). (axiom label in BFO2 Reference: [113-002])
occurrent_part_of is transitive. (axiom label in BFO2 Reference: [112-001])
occurrent_part_of satisfies unique product. (axiom label in BFO2 Reference: [125-001])
occurrent_part_of satisfies weak supplementation. (axiom label in BFO2 Reference: [124-001])
(forall (x y t) (if (and (occurrentPartOf x y t) (not (= x y))) (exists (z) (and (occurrentPartOf z y t) (not (exists (w) (and (occurrentPartOf w x t) (occurrentPartOf w z t)))))))) // axiom label in BFO2 CLIF: [124-001]
(forall (x y t) (if (and (occurrentPartOf x y t) (occurrentPartOf y x t)) (= x y))) // axiom label in BFO2 CLIF: [123-001]
(forall (x y t) (if (exists (v) (and (occurrentPartOf v x t) (occurrentPartOf v y t))) (exists (z) (forall (u w) (iff (iff (occurrentPartOf w u t) (and (occurrentPartOf w x t) (occurrentPartOf w y t))) (= z u)))))) // axiom label in BFO2 CLIF: [125-001]
(forall (x y z) (if (and (occurrentPartOf x y) (occurrentPartOf y z)) (occurrentPartOf x z))) // axiom label in BFO2 CLIF: [112-001]
(forall (x) (if (Occurrent x) (occurrentPartOf x x))) // axiom label in BFO2 CLIF: [113-002]
part of occurrent
[copied from inverse property 'has proper occurrent part'] b has_proper_occurrent_part c = Def. c proper_occurrent_part_of b. [XXX-001
b proper_occurrent_part_of c =Def. b occurrent_part_of c & b and c are not identical. (axiom label in BFO2 Reference: [005-001])
(iff (properOccurrentPartOf a b) (and (occurrentPartOf a b) (not (= a b)))) // axiom label in BFO2 CLIF: [005-001]
proper part of occurrent
the 4th year of your life is a temporal part of your life\. The first quarter of a game of football is a temporal part of the whole game\. The process of your heart beating from 4pm to 5pm today is a temporal part of the entire process of your heart beating.\ The 4th year of your life is a temporal part of your life
the process boundary which separates the 3rd and 4th years of your life.
your heart beating from 4pm to 5pm today is a temporal part of the process of your heart beating
b proper_temporal_part_of c =Def. b temporal_part_of c & not (b = c). (axiom label in BFO2 Reference: [116-001])
b temporal_part_of c =Def.b occurrent_part_of c & & for some temporal region t, b occupies_temporal_region t & for all occurrents d, t (if d occupies_temporal_region t & t? occurrent_part_of t then (d occurrent_part_of a iff d occurrent_part_of b)). (axiom label in BFO2 Reference: [078-003])
if b proper_temporal_part_of c, then there is some d which is a proper_temporal_part_of c and which shares no parts with b. (axiom label in BFO2 Reference: [117-002])
(forall (x y) (if (properTemporalPartOf x y) (exists (z) (and (properTemporalPartOf z y) (not (exists (w) (and (temporalPartOf w x) (temporalPartOf w z)))))))) // axiom label in BFO2 CLIF: [117-002]
(iff (properTemporalPartOf a b) (and (temporalPartOf a b) (not (= a b)))) // axiom label in BFO2 CLIF: [116-001]
(iff (temporalPartOf a b) (and (occurrentPartOf a b) (exists (t) (and (TemporalRegion t) (occupiesSpatioTemporalRegion a t))) (forall (c t_1) (if (and (Occurrent c) (occupiesSpatioTemporalRegion c t_1) (occurrentPartOf t_1 r)) (iff (occurrentPartOf c a) (occurrentPartOf c b)))))) // axiom label in BFO2 CLIF: [078-003]
temporal part of
projects onto spatial region at some time
spatial projection of spatiotemporal at some time
projects onto temporal region
temporal projection of spatiotemporal
p occupies_temporal_region t. This is a primitive relation between an occurrent p and the temporal region t upon which the spatiotemporal region p occupies_spatiotemporal_region projects. (axiom label in BFO2 Reference: [132-001])
occupies temporal region
[copied from inverse property 'occupies temporal region'] p occupies_temporal_region t. This is a primitive relation between an occurrent p and the temporal region t upon which the spatiotemporal region p occupies_spatiotemporal_region projects. (axiom label in BFO2 Reference: [132-001])
has temporal occupant
[copied from inverse property 'exists at'] BFO2 Reference: entity
[copied from inverse property 'exists at'] BFO2 Reference: temporal region
[copied from inverse property 'exists at'] b exists_at t means: b is an entity which exists at some temporal region t. (axiom label in BFO2 Reference: [118-002])
during which exists
b bearer_of c at t =Def. c s-depends_on b at t & b is an independent continuant that is not a spatial region. (axiom label in BFO2 Reference: [053-004])
Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'bearer of at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'bearer of@en(x,y,t)'.
(iff (bearerOfAt a b t) (and (specificallyDependsOnAt b a t) (IndependentContinuant a) (not (SpatialRegion a)) (existsAt b t))) // axiom label in BFO2 CLIF: [053-004]
bearer of at all times
a has_disposition b at t =Def. b disposition_of a at t. (axiom label in BFO2 Reference: [069-001])
Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'has disposition at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'has disposition@en(x,y,t)'.
(iff (hasDispositionAt a b t) (dispositionOf b a t)) // axiom label in BFO2 CLIF: [069-001]
has disposition at all times
has specific dependent at all times
Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'specifically depends on at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'specifically depends on@en'(x,y,t)
specifically depends on at some time
Mary’s arm continuant_part_of Mary in the time of her life prior to her operation
the Northern hemisphere of the planet Earth is a part of the planet Earth at all times at which the planet Earth exists.
[copied from inverse property 'has continuant part at some time'] b has_continuant_part c at t = Def. c continuant_part_of b at t. (axiom label in BFO2 Reference: [006-001])
Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'part of continuant at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'part of continuant@en'(x,y,t)
BFO 2 Reference: Immaterial entities are in some cases continuant parts of their material hosts. Thus the hold of a ship, for example, is a part of the ship; it may itself have parts, which may have names (used for example by ship stow planners, customs inspectors, and the like). Immaterial entities under both 1. and 2. can be of zero, one, two or three dimensions. We define:a(immaterial entity)[Definition: a is an immaterial entity = Def. a is an independent continuant that has no material entities as parts. (axiom label in BFO2 Reference: [028-001])
BFO2 Reference: continuantThe range for ‘t’ (as in all cases throughout this document unless otherwise specified) is: temporal region.
[copied from inverse property 'has continuant part at some time'] Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'has continuant part at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'has continuant part@en'(x,y,t)
b continuant_part_of c at t =Def. b is a part of c at t & t is a time & b and c are continuants. (axiom label in BFO2 Reference: [002-001])
continuant_part_of is antisymmetric. (axiom label in BFO2 Reference: [120-001])
continuant_part_of is reflexive (every continuant entity is a continuant_part_of itself). (axiom label in BFO2 Reference: [111-002])
continuant_part_of is transitive. (axiom label in BFO2 Reference: [110-001])
continuant_part_of satisfies unique product. (axiom label in BFO2 Reference: [122-001])
continuant_part_of satisfies weak supplementation. (axiom label in BFO2 Reference: [121-001])
if b continuant_part_of c at t and b is an independent continuant, then b is located_in c at t. (axiom label in BFO2 Reference: [047-002])
(forall (x t) (if (Continuant x) (continuantPartOfAt x x t))) // axiom label in BFO2 CLIF: [111-002]
(forall (x y t) (if (and (continuantPartOfAt x y t) (IndependentContinuant x)) (locatedInAt x y t))) // axiom label in BFO2 CLIF: [047-002]
(forall (x y t) (if (and (continuantPartOfAt x y t) (continuantPartOfAt y x t)) (= x y))) // axiom label in BFO2 CLIF: [120-001]
(forall (x y t) (if (and (continuantPartOfAt x y t) (not (= x y))) (exists (z) (and (continuantPartOfAt z y t) (not (exists (w) (and (continuantPartOfAt w x t) (continuantPartOfAt w z t)))))))) // axiom label in BFO2 CLIF: [121-001]
(forall (x y t) (if (exists (v) (and (continuantPartOfAt v x t) (continuantPartOfAt v y t))) (exists (z) (forall (u w) (iff (iff (continuantPartOfAt w u t) (and (continuantPartOfAt w x t) (continuantPartOfAt w y t))) (= z u)))))) // axiom label in BFO2 CLIF: [122-001]
(forall (x y z t) (if (and (continuantPartOfAt x y t) (continuantPartOfAt y z t)) (continuantPartOfAt x z t))) // axiom label in BFO2 CLIF: [110-001]
(iff (ImmaterialEntity a) (and (IndependentContinuant a) (not (exists (b t) (and (MaterialEntity b) (continuantPartOfAt b a t)))))) // axiom label in BFO2 CLIF: [028-001]
part of continuant at some time
[copied from inverse property 'part of continuant at some time'] Mary’s arm continuant_part_of Mary in the time of her life prior to her operation
[copied from inverse property 'part of continuant at some time'] the Northern hemisphere of the planet Earth is a part of the planet Earth at all times at which the planet Earth exists.
b has_continuant_part c at t = Def. c continuant_part_of b at t. (axiom label in BFO2 Reference: [006-001])
Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'has continuant part at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'has continuant part@en'(x,y,t)
[copied from inverse property 'part of continuant at some time'] Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'part of continuant at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'part of continuant@en'(x,y,t)
[copied from inverse property 'part of continuant at some time'] BFO 2 Reference: Immaterial entities are in some cases continuant parts of their material hosts. Thus the hold of a ship, for example, is a part of the ship; it may itself have parts, which may have names (used for example by ship stow planners, customs inspectors, and the like). Immaterial entities under both 1. and 2. can be of zero, one, two or three dimensions. We define:a(immaterial entity)[Definition: a is an immaterial entity = Def. a is an independent continuant that has no material entities as parts. (axiom label in BFO2 Reference: [028-001])
[copied from inverse property 'part of continuant at some time'] BFO 2 Reference: a (continuant or occurrent) part of itself. We appreciate that this is counterintuitive for some users, since it implies for example that President Obama is a part of himself. However it brings benefits in simplifying the logical formalism, and it captures an important feature of identity, namely that it is the limit case of mereological inclusion.
[copied from inverse property 'part of continuant at some time'] BFO2 Reference: continuant
[copied from inverse property 'part of continuant at some time'] BFO2 Reference: continuantThe range for ‘t’ (as in all cases throughout this document unless otherwise specified) is: temporal region.
[copied from inverse property 'part of continuant at some time'] b continuant_part_of c at t =Def. b is a part of c at t & t is a time & b and c are continuants. (axiom label in BFO2 Reference: [002-001])
(iff (hasContinuantPartAt a b t) (continuantPartOfAt b a t)) // axiom label in BFO2 CLIF: [006-001]
has continuant part at some time
[copied from inverse property 'has continuant part at all times'] b has_continuant_part c at t = Def. c continuant_part_of b at t. (axiom label in BFO2 Reference: [006-001])
forall(t) exists_at(y,t) -> exists_at(x,t) and 'part of continuant'(x,y,t)
This is a binary version of a ternary time-indexed, instance level, relation. Unlike the rest of the temporalized relations which temporally quantify over existence of the subject of the relation, this relation temporally quantifies over the existence of the object of the relation. The relation is provided tentatively, to assess whether the GO needs such a relation. It is inverse of 'has continuant part at all times'
[copied from inverse property 'has continuant part at all times'] Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'has continuant part at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'has continuant part@en(x,y,t)'.
part of continuant at all times that whole exists
[copied from inverse property 'part of continuant at all times'] Mary’s arm continuant_part_of Mary in the time of her life prior to her operation
[copied from inverse property 'part of continuant at all times'] the Northern hemisphere of the planet Earth is a part of the planet Earth at all times at which the planet Earth exists.
forall(t) exists_at(y,t) -> exists_at(x,t) and 'has continuant part'(x,y,t)
This is a binary version of a ternary time-indexed, instance level, relation. Unlike the rest of the temporalized relations which temporally quantify over existence of the subject of the relation, this relation temporally quantifies over the existence of the object of the relation. The relation is provided tentatively, to assess whether the GO needs such a relation. It is inverse of 'part of continuant at all times'
[copied from inverse property 'part of continuant at all times'] Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'part of continuant at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'part of continuant@en(x,y,t)'.
[copied from inverse property 'part of continuant at all times'] BFO 2 Reference: Immaterial entities are in some cases continuant parts of their material hosts. Thus the hold of a ship, for example, is a part of the ship; it may itself have parts, which may have names (used for example by ship stow planners, customs inspectors, and the like). Immaterial entities under both 1. and 2. can be of zero, one, two or three dimensions. We define:a(immaterial entity)[Definition: a is an immaterial entity = Def. a is an independent continuant that has no material entities as parts. (axiom label in BFO2 Reference: [028-001])
[copied from inverse property 'part of continuant at all times'] BFO 2 Reference: a (continuant or occurrent) part of itself. We appreciate that this is counterintuitive for some users, since it implies for example that President Obama is a part of himself. However it brings benefits in simplifying the logical formalism, and it captures an important feature of identity, namely that it is the limit case of mereological inclusion.
[copied from inverse property 'part of continuant at all times'] BFO2 Reference: continuant
[copied from inverse property 'part of continuant at all times'] BFO2 Reference: continuantThe range for ‘t’ (as in all cases throughout this document unless otherwise specified) is: temporal region.
[copied from inverse property 'part of continuant at all times'] b continuant_part_of c at t =Def. b is a part of c at t & t is a time & b and c are continuants. (axiom label in BFO2 Reference: [002-001])
has continuant part at all times that part exists
A relationship between an entity that carries a sequence (e.g. a sequence feature or collection), and the sequence it bears.
'Sequence' in the context of GENO is an abstract entity representing an ordered collection of monomeric units as carried in a biological macromolecule.
A relation that holds between two sequence features at a particular genomic location that vary in their sequence. These features will have the same position when mapped onto a reference sequence, but vary in their sequence (in whole or in part).
This property is most commonly used to relate two different alleles of a given gene (e.g. a wt and mutant instance of the BRCA2 gene). It is not a relation between an allele and the class-level gene it is a variant of (for this use is_allele_of)
varies_with
A relation linking a sequence feature to the location it occupies on some reference sequence.
has_location
has measurement unit label
is about
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.
Smith, Ceusters, Ruttenberg, 2000 years of philosophy
An information artifact IA mentions an entity E exactly when it has a component/part that denotes E
7/6/2009 Alan Ruttenberg. P4 RC1 munges our GCI so remove it for now: mentions some entity equivalentTo has_part some ('generically denotes' some entity)
7/6/2009 Alan Ruttenberg: Add this relation following conversation with Jonathan Rees that N&S GCI for is_about was too strong. Really it was simply sufficient. To effect this change we introduce this relation, which is subproperty of is_about, and have previous GCI use this relation "mentions" in it's (logical) definition
PERSON: Jonathan Rees
Person: Alan Ruttenberg
mentions
A person's name denotes the person. A variable name in a computer program denotes some piece of memory. Lexically equivalent strings can denote different things, for instance "Alan" can denote different people. In each case of use, there is a case of the denotation relation obtaining, between "Alan" and the person that is being named.
denotes is a primitive, instance-level, relation obtaining between an information content entity and some portion of reality. Denotation is what happens when someone creates an information content entity E in order to specifically refer to something. The only relation between E and the thing is that E can be used to 'pick out' the thing. This relation connects those two together. Freedictionary.com sense 3: To signify directly; refer to specifically
2009-11-10 Alan Ruttenberg. Old definition said the following to emphasize the generic nature of this relation. We no longer have 'specifically denotes', which would have been primitive, so make this relation primitive. g denotes r =def r is a portion of reality there is some c that is a concretization of g every c that is a concretization of g specifically denotes r
Conversations with Barry Smith, Werner Ceusters, Bjoern Peters, Michel Dumontier, Melanie Courtot, James Malone, Bill Hogan
denotes
m is a quality measurement of q at t when q is a quality there is a measurement process p that has specified output m, a measurement datum, that is about q
8/6/2009 Alan Ruttenberg: The strategy is to be rather specific with this relationship. There are other kinds of measurements that are not of qualities, such as those that measure time. We will add these as separate properties for the moment and see about generalizing later
From the second IAO workshop [Alan Ruttenberg 8/6/2009: not completely current, though bringing in comparison is probably important] This one is the one we are struggling with at the moment. The issue is what a measurement measures. On the one hand saying that it measures the quality would include it "measuring" the bearer = referring to the bearer in the measurement. However this makes comparisons of two different things not possible. On the other hand not having it inhere in the bearer, on the face of it, breaks the audit trail. Werner suggests a solution based on "Magnitudes" a proposal for which we are awaiting details. -- From the second IAO workshop, various comments, [commented on by Alan Ruttenberg 8/6/2009] unit of measure is a quality, e.g. the length of a ruler. [We decided to hedge on what units of measure are, instead talking about measurement unit labels, which are the information content entities that are about whatever measurement units are. For IAO we need that information entity in any case. See the term measurement unit label] [Some struggling with the various subflavors of is_about. We subsequently removed the relation represents, and describes until and only when we have a better theory] a represents b means either a denotes b or a describes describe: a describes b means a is about b and a allows an inference of at least one quality of b We have had a long discussion about denotes versus describes.
From the second IAO workshop: An attempt at tieing the quality to the measurement datum more carefully. a is a magnitude means a is a determinate quality particular inhering in some bearer b existing at a time t that can be represented/denoted by an information content entity e that has parts denoting a unit of measure, a number, and b. The unit of measure is an instance of the determinable quality.
From the second meeting on IAO: An attempt at defining assay using Barry's "reliability" wording assay: process and has_input some material entity and has_output some information content entity and which is such that instances of this process type reliably generate outputs that describes the input.
This one is the one we are struggling with at the moment. The issue is what a measurement measures. On the one hand saying that it measures the quality would include it "measuring" the bearer = referring to the bearer in the measurement. However this makes comparisons of two different things not possible. On the other hand not having it inhere in the bearer, on the face of it, breaks the audit trail. Werner suggests a solution based on "Magnitudes" a proposal for which we are awaiting details.
Alan Ruttenberg
is quality measurement of
relates a process to a time-measurement-datum that represents the duration of the process
is duration of
inverse of the relation of is quality measurement of
2009/10/19 Alan Ruttenberg. Named 'junk' relation useful in restrictions, but not a real instance relationship
is quality measured as
relates a time stamped measurement datum to the time measurement datum that denotes the time when the measurement was taken
IAO domain: [time stamped measurement datum](http://purl.obolibrary.org/obo/IAO_0000582) I would also like to use this with data items like prescriptions and diagnoses
has time stamp
relates a time stamped measurement datum to the measurement datum that was measured
has measurement datum
x designates y, if for any given group of language users, x is an information content entity, is about y, and represents y in a linguistic context..
designates
p1 is designated by p2, if p2 is an information content entity that represents p1 in a linguistic context.
is designated by
The relation between the conclusion "Gene tpbA is involved in EPS production" and the data items produced using two sets of organisms, one being a tpbA knockout, the other being tpbA wildtype tested in polysacharide production assays and analyzed using an ANOVA.
The relation between a data item and a conclusion where the conclusion is the output of a data interpreting process and the data item is used as an input to that process
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
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
is_specified_input_of
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.
is_specified_output_of
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.
modified according to email thread from 1/23/09 in accordince with DT and PPPB branch
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
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
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.
This relation obtains between an objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process.
Relating a legal person or organization to an organization in the case where the legal person or organization has a role as member of the organization.
2009/10/01 Alan Ruttenberg. Barry prefers generic is-member-of. Question of what the range should be. For now organization. Is organization a population? Would the same relation be used to record members of a population
JZ: Discussed on May 7, 2012 OBI dev call. Bjoern points out that we need to allow for organizations to be members of organizations. And agreed by the other OBI developers. So, human and organization were specified in 'Domains'. The textual definition was updated based on it.
2009/09/28 Alan Ruttenberg. Fucoidan-use-case
has organization member
Relating an organization to a legal person or organization.
See tracker: https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_id=177891&atid=886178
A relation between a value specification and an entity which the specification is about.
A relation between an information content entity and a value specification that specifies its value.
a 'part of continuant at some time' relation that incides a genome belongs to a organism.
is genome of organism
a relation between a gene and the organism where this gene belongs to the organism in nature. It does not include a foreign gene that is transferred to an organism by a genetic engineering method.
is gene of organism
This is a primitive relation. This relation is the foundation to the owners right to have the owned entity at his/her full disposal.
Reinach, A. Sämtliche Werke. Texkritische Ausgabe, München: Philosophia Verlag, 1989, p.189-204.
owns
a administrates b if c owns b and some rights and obligations grounded in the owning relation regarding b are transferred from c to a.
Mathias Brochhausen
A definition of "tranfers" object property can be found in d-acts: http:purl.obolibrary.org/iao/d-acts.owl
administrates
a is owned by b if b has complete power over a. All rights and obligations of ownership are grounded in this (primitive) relation. The claims and obligations of ownership can be partially transferred to a third party by the owner, b.
is owned by
BFO relation takes precedence.
We anticipate BFO 2.0 including and defining this relation. When it does, we will obsolete this property and declare it equivalent to the BFO 2.0 relation.
true
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 at all times'
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
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
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
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 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.
concretizes
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).
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.
It is recommended to not use this if possible in OMRSE. According to OntoBee this relation has been obsoleted and replaced with 'concretization of at all times'. As of Dec. 2, 2013 iao-main still uses this relation.
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 red color is a quality of this apple
a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence
A quality inheres in its bearer at all times for which the quality exists.
is quality of
quality_of
quality 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
this cell derives from this parent cell (cell division)
this nucleus derives from this parent nucleus (nuclear division)
a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity
This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'.
derives_from
This relation is taken from the RO2005 version of RO. It may be obsoleted and replaced by relations with different definitions. See also the 'develops from' family of relations.
derives from
this parent cell derives into this cell (cell division)
this parent nucleus derives into this nucleus (nuclear division)
a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity
This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'.
derives_into
derives into
is location of
my head is the location of my brain
this cage is the location of this rat
a relation between two independent continuants, the location and the target, in which the target is entirely within the location
Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime
location_of
location of
located in
my brain is located in my head
this rat is located in this cage
a relation between two independent continuants, the target and the location, in which the target is entirely within the location
Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus
located_in
X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)
immediately preceded by
X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)
immediately precedes
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
x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed.
in taxon
a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones).
a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b
connected to
c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system.
connects
Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure.
Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between a vein and an anatomical structure
drains
x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y
Chris Mungall
David Osumi-Sutherland
Terry Meehan
This is the transitive form of the develops from relation
develops from
develops into
'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.
has prototype
temporal relation
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.
A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.
temporally related to
starts
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.
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.
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.
has output
developmentally succeeded by
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
inheres in part of
A mereological relationship or a topological relationship
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 relationship that holds between entities participating in some developmental process (GO:0032502)
Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development
developmentally related to
An organism that is a member of a population of organisms
is member of is a mereological relation between a item and a collection.
member of
Example 1: a collection of sequences such as a genome being comprised of separate sequences of chromosomes Example 2: a collection of information entities such as a genotype being comprised of a background component and a variant component
has member is a mereological relation between a collection and an item.
has member
input of
output of
x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction).
has developmental potential involving
x has the potential to develop into y iff x develops into y or if x is capable of developing into y
has potential to develop into
x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y
has potential to directly develop into
q towards e2 if and only if q is a relational quality such that q inheres-in some e, and e != e2 and q is dependent on e2
This relation is provided in order to support the use of relational qualities such as 'concentration of'; for example, the concentration of C in V is a quality that inheres in V, but pertains to C.
A relation that holds between an attribute or a qualifier and another attribute.
This relation is intended to be used in combination with PATO, to be able to refine PATO quality classes using modifiers such as 'abnormal' and 'normal'. It has yet to be formally aligned into an ontological framework; it's not clear what the ontological status of the "modifiers" are.
A relationship between a disease and an anatomical entity where the disease has one or more features that are located in that entity.
TODO: complete range axiom once more of CARO has been mireoted in to this ontology
This relation is intentionally very general, and covers isolated diseases, where the disease is realized as a process occurring in the location, and syndromic diseases, where one or more of the features may be present in that location. Thus any given disease can have multiple locations in the sense defined here.
Relation between biological objects that resemble or are related to each other sufficiently to warrant a comparison.
regional_part_of
systemic_part_of
A is related to B iff there is some relation between A and B.
'is related to' is the top level relation in SIO
is related to
is comparable to is a relation between two entities that share at least one feature whose value can be compared.
is comparable to
is identical to is a relation between two objects that are conceptually the same notwithstanding provenance or other non-intrinsic attributes.
is identical to
aa object property chain: if individual I has role R which is realized in process P, then I 'participates in via role' P
In some database table about employment, my social security number appears in the same row with some employer identification number. (Alternatively, they both appear in the same XML or JSON path, etc.) Either way, a rule could be written in (or outside of) OWL interpreting that co-occurrence to mean that I am employed by the institution denoted by that employer identification number. Applications, like Drivetrain, may perform some (closed-world?) checks before instantiating the implied relationship: if there is, in reality, no institution denoted by the employer identification number, the system might refuse to instantiate any statement at all about who I work for.
A relationship between two information content entities that are connected or linked by placement in the same structural subdivision of a dataset and intended to be about entities that have some relationship in reality.
this is a non-owl shortcut, stating that two ICE were found on the same row of a data table. This may lead to a conclusion that the two ICEs are values borne by two things that have some relationship in reality. For example, if a patient identifier and an encounter identifier were found in the same row, one might infer that the denoted participant participated in the denoted encounter with a participation under investigation role.
an object property chain 'shortcut': if human H participates in a 'neonate stage' N that is started by 'start of neonate stage' S, then H 'born on' S
the TURBO team referent tracks births (for which each person only has one) rather than birth dates
Given that D is a data item bearing some textual value L, T is a class or instance term from some ontology or RDF linked data set, and H is this 'has matching CV term' property, D H T means that L was drawn from some controlled vocabulary containing term T, which has the same meaning as L. As a term, T will be represented by a URI, whereas L is a datatype literal (which was likely instantiated from a relational database or other non-semantic resource.) For example, if D is an instance of 'gene' (http://purl.obolibrary.org/obo/OGG_0000000002) with literal value "ENSG00000081237", <https://www.uniprot.org/uniprot/P08575> may be selected at T. In this case, the author of the triple is asserting that the value "ENSG00000081237" was drawn from the terms provided in Ensembl's RDF model. That namespace can be communicated with a 'has namespace' (TURBO_0000703) triple. D a <http://purl.obolibrary.org/obo/OGG_0000000002> D <http://transformunify.org/ontologies/TURBO_0006512> "ENSG00000081237" D <http://transformunify.org/ontologies/TURBO_0000304> <http://rdf.ebi.ac.uk/resource/ensembl/ENSG00000000003> D <http://transformunify.org/ontologies/TURBO_0000703> <http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C45763> This property is intended to enable rapid re-representation from literal values to URI-bearing terms, so T may come from a vocabulary with weak semantics. Statements about reality could be added in the future, like D <http://purl.obolibrary.org/obo/IAO_0000142> <http://purl.obolibrary.org/obo/HGNC_9667> Which says that allele information D mentions a particular gene modeled in the Protein Ontology. The 'mentions' property has stronger semantics than this 'has matching CV term' and the Protein Ontology has a stronger commitment to reality than the Uniprot RDF model.
a 'has matching CV term', where the matching term is drawn from any of the versions and variants of the International Classification of Diseases. The particular ICD falvor can be communicated with a 'has namespace' (TURBO_0000703) triple taking an object like <http://purl.obolibrary.org/obo/NCIT_C71890> for ICD-9 or <http://purl.obolibrary.org/obo/NCIT_C128691> for ICD-10-CM
This property can be used along with 'has matching CV term' or any of its sub-properties to indicate the controlled vocabulary form which a matching terms was selected.
shortcut person data model to patient CRID registry
shortcut person data model to gender identty datum
shortcut person data model to racial identity datum
shortcut person data model to ethnic identity datum
shortcut health care encounter data model to entity
shortcut health care encounter data model to encounter registry
shortcut health care encounter data model to patient registry
shortcut observation to patient registry
shortcut observation to encounter registry
shortcut observation to observation type registry
shortcut observation to observation type term
shortcut health care encounter data model to patient data model
shortcut biobank encounter data model to entity
shortcut biobank encounter data model to person data model
clinical datum about patient
has measured value (from James Overton's 2019-04-08 proposal)
has measurement specification
shortcut allele information data model to entity
shortcut allele information to zygosity value specification
shortcut allele information to biobank encounter data model
shortcut allele information to genotype identifier registry
shortcut allele information to biobank encounter identifier registry
if ?s1 'writes triples about' ?o1, then at least one triple will be submitted to some RDF model/triplestore in which ?o1 ?p ?o2
writes triples about
mentions in RDF
this predicate documents what named graph is the destination for the triples generated by the subject process.
inserted triples into
this predicate documents the named graph from which a process drew its input
sourced triples from
shortcut tumor data model to entity
shortcut tumor data model to patient registry
'is about' o inverse ('birth instance TPO birth day') o inverse ('SNS OTR birth instant')
DOB about SNS
DOB about day of birth
birth instant TPO birth day
SNS OTR birth instant
SNS starts neonate stage
neonate stage OTR NTR
birth instant TPO NTR
birth instant starts NTR
shortcut person CRID model to entity
shortcut person CRID model to singleton registry denoter
shortcut health care encounter data model to encounter id source
shortcut health care encounter data model to singleton health care encounter identifier source dentoer
shortcut tumor data model to singleton tumor registry denoter
shortcut tumor data model to singleton patient registry denoter
shortcut person data model to singleton patient CRID registry denoter
shortcut health care encounter data model to singleton patient registry denoter
shortcut allele information to singleton biobank encounter identifier registry denoter
shortcut allele information to singleton genotype identifier registry denoter
shortcut biobank encounter data model to singleton biobank encounter registry denoter
shortcut biobank encounter data model to singleton patient registry denoter
has specified allele information output
double check property type in NCIT download
Property linking a biological sequence to a string representing the ordered units that comprise the sequence (e.g. 'atgcagctagctaccgtcgatcg').
Describes the number of members in some set.
In GENO, this is used to describe things like the number of sequence features comprising a 'sequence feature set', the number of sequences in a 'biological sequence set', or the number of functional sequences defining a particular 'functional copy number complement'.
has_member_count
has measurement 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.
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.
shortcut biobank consenter to data shortcut
an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from a/n biobank consenter to a/n to data shortcut
shortcut biobank consenter to biological sex URI string
an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from a biobank consenter to a biological sex URI string
shortcut biobank consenter to dataset title
an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from a biobank consenter to a dataset title
shortcut biobank consenter to data set title
shortcut biobank consenter to textual date of birth text
an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from a biobank consenter to a textual date of birth text
shortcut biobank consenter to xsd-formatted date of birth
an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from a biobank consenter to a xsd-formatted date of birth
shortcut biobank consenter to gender identity datum text
an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from a biobank consenter to a gender identity datum text
shortcut biobank consenter to gender identity datum URI string
an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from a biobank consenter to a gender identity datum URI string
shortcut biobank consenter to biobank consenter CRID symbol
an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from a biobank consenter to a biobank consenter CRID symbol
shortcut biobank consenter to biobank consenter registry denoter
an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from a biobank consenter to a biobank consenter registry denoter
shortcut biobank consenter to biobank consenter identifier registry URI string
an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from a biobank consenter to a biobank consenter identifier registry URI string
shortcut biobank consenter to racial identity registry URI string
shortcut biobank consenter to racial identity registry denoter
shortcut biobank consenter to racial identity CRID symbol
shortcut biobank consenter to racial identity datum URI string
shortcut biobank consenter to racial identity datum veracity
shortcut biobank consenter to racial identity text
still working out the relationships between biobank encounters and health care encounters. use separate properties due to domain constraint? or make a parent class?
shortcut biobank encounter to data set title
an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from a biobank encounter to a data set title
shortcut biobank encounter to textual encounter date
an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from a biobank encounter to a textual encounter date
the textual representation of a date isn't technically interdependent with anything else. However, if it was present in tabular data, it should be passed on with this shortcut, to provide provenance for the xsd representation of the date
shortcut biobank encounter to xsd-formatted encounter date
an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from a biobank encounter to a xsd-formatted encounter date
shortcut biobank encounter to height in cm
an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from a biobank encounter to a height in cm
shortcut biobank encounter to weight in kg
an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from a biobank encounter to a weight in kg
shortcut biobank encounter to encounter CRID symbol
an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from a biobank encounter to a encounter CRID symbol
shortcut biobank encounter to encounter registry denoter
an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from a biobank encounter to a encounter registry denoter
shortcut biobank encounter to encounter identifier registry URI string
an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from a biobank encounter to a encounter identifier registry URI string
an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from a biobank encounter to a BMI
shortcut health care encounter data model to data
an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from a/n health care encounter to a/n to data
This property and any of its sub properties link an instance of "biobank study participant" with some literal value. See comments on parent class.
shortcut health care encounter data model to data to data set title
an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from a health care encounter to a data set title
This shortcut links a health care encounter ?e (OGMS_0000097) to a textual title for a dataset ?t (IAO_0000100). Expansion involve creating a dataset instance, which will be the input into an R2R instantiation process ?i. ?e rdf:type obo:OGMS_0000097 . ?d rdf:type obo:IAO_0000100 ; obo:BFO_0000051 ?p ; dc11:title ?dsTitle . ?i rdf:type :R2RInstantiation ; obo:OBI_0000293 ?d . Note that the encounter and the dataset are still not bound above. The expander must find paths (in either orientation) between the encounter and the data set, via some information content entities Here's an illustration of "any path" in sparql, but only going in one orientation. ?e rdf:type <http://purl.obolibrary.org/obo/OGMS_0000097> . ?e (:|!:)* ?o . ?o ?p ?v That is, ?v could be the value of an identifier ?o that denotes the encounter, or it could be the value of diagnosis code that is part of a diagnosis CRID that was the output of the encounter. --- TODO: what should the dataset contain as parts in our encounter only shortcut expansion? encounter id instance encounter date instance (is the fact that the text value and mapped xsd value are both values of the same instance enough to explain the conversion? i.e., which value is actually in the data set and which is derived? is the fact that a data owner made the conversion in Karma enough justification? as in the data owner is saying that they are identical values like 2 and two? is this another process?) diagnosis (the whole CRID? ** the code symbol and the registry denoter separately?** what about the mapped registry URI?... No, that's not an ice in a data set. But we might want to explain the conversion processes from string to URI, like I suggested for string to xsd date.) registry and date conversions could be rule sin the instantiation process?
shortcut health care encounter data model to data set title
shortcut health care encounter data model to textual encounter date
an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from a health care encounter to a textual encounter date
This shortcut links a health care encounter ?e (OGMS_0000097) to the textual representation ?tv of the date ?d (turbo:ProcStartTimeMeas) on which the encounter took place . Furthermore, date ?d is about the temporal boundary ?es (turbo:HealthcareEncStart) that starts encounter ?e. ?tv will typically part of some dataset (see ScEnc2DataSet.) ?e rdf:type obo:OGMS_0000097 . ?d rdf:type :ProcStartTimeMeas ; :hasTextualValue ?tv ; obo:IAO_0000136 ?es . ?es rdf:type :HealthcareEncStart ; obo:RO_0002223 ?e . Although not constrained at this point (?) the ?tv's type would reasonably be an xsd:string. Note that TURBO will typically expect an xsd:date literal bound to date instances like ?d. As of the end of August 2017, that means that the textual date value will need to be converted to an xsd:date within a python transformation, in Karma. --- the textual representation of a date isn't technically interdependent with anything else. However, if it was present in tabular data, it should be passed on with this shortcut, to provide provenance for the xsd representation of the date
shortcut health care encounter data model to xsd-formatted encounter date
an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from a health care encounter to a xsd-formatted encounter date
definition "This shortcut links a health care encounter ?e (OGMS_0000097) to and xsd:date literal ?xv, which is the measurement value* of date ?d (turbo:ProcStartTimeMeas) on which the encounter took place . Furthermore, date ?d is about the temporal boundary ?es (turbo:HealthcareEncStart) that starts encounter ?e ?xv will typcally part of some dataset (see ScEnc2DataSet.) In semi-turtle syntax, It means that ?d rdf:type :ProcStartTimeMeas ; obo:IAO_0000004 ?xv ; obo:IAO_0000136 ?es . ?e rdf:type obo:OGMS_0000097 . ?es rdf:type :HealthcareEncStart ; obo:RO_0002223 ?e . As of the end of August 2017, that means that a textual date value will need to be converted to an xsd:date within a python transformation, in Karma. *oops, this violates the xsd:float range expectation of has measurement value (IAO_0000004) as defined in the IAO owl file. I added xsd:date to that range definition within turbo.owl and turbo_merged.owl. Some applications seem to accept the dual range, but some (like top braid composer) only seem to consider one of the datatype ranges… first found in the file??? I have also created turbo:hasDateValue"
shortcut health care encounter data model to height in cm
an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from a health care encounter to a height in cm
shortcut health care encounter data model to weight in kg
an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from a health care encounter to a weight in kg
shortcut health care encounter data model to encounter ID symbol
an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from a health care encounter to a encounter ID symbol
this shortcut links a health care encounter ?e (OGMS_0000097) to the value ?iv of its identifier ?i. (turbo:EncounterID). ?i denotes ?e. ?e rdf:type obo:OGMS_0000097 . ?i rdf:type :EncounterID ; obo:IAO_0000219 ?e ; :thingLiteralValue ? iv.
shortcut health care encounter data model to encounter registry denoter
an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from a health care encounter to a encounter registry denoter
no example of use yet... we may end up saying that encounter identifiers don't really come from registries
shortcut health care encounter data model to encounter identifier registry URI string
an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from a health care encounter to a encounter identifier registry URI string
shortcut health care encounter data model to BMI
an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from a health care encounter to a BMI
Used when instantiating tabular/relational data about health care encounters that includes a BMI column. Upon expansion, :e a :healthCareEncounter ; :hasSpecifiedOutput ?BMI. :BMI a :bmiDataItem ; :hasLiteralValue "25"^^xsd:float upon participant-to-encounter joining: :BMI :isAbout :adipose . :adipose a :adiposeTissue ; :partOf :studyParticipant .
shortcut health care encounter data model to diagnosis code symbol
an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from a health care encounter to a diagnosis code symbol
this shortcut links a health care encounter ?e (OGMS_0000097) to the value ?dcv of a diagnosis code symbol ?dcs. (turbo:EncounterDiagCodeSymbol). ?dcs is part of a diagnosis CRID ?dcrid (turbo:DiagCodeRegitryID) and is typically part of some dataset (see ScEnc2DataSet.) ?dcrid is the output of the encounter ?e. ?e rdf:type obo:OGMS_0000097 ; obo:OBI_0000299 ?dcrid . ?dcrid rdf:type :DiagCrid ; obo:BFO_0000051 ?dcs . ?dcs rdf:type :EncounterDiagCodeSymbol ; :thingLiteralValue ?dcv .
shortcut health care encounter data model to diagnosis code registry denoter
an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from a health care encounter to a diagnosis code registry denoter
this shortcut links a health care encounter ?e (OGMS_0000097) to the value ?drnv of a diagnosis code registry denoter ?dcrn (turbo:DiagCodeRegitryID), which denotes a registry instance ?dcru like <http://purl.obolibrary.org/obo/NCIT_C71892> for ICD-10. The mapping from denoters of registries to URIs that already exist in some ontology like NCIT will be the responsibility of the data owner and will be executed with a python transformation in Karma. ?dcrn is part of a diagnosis CRID ?dcrid (turbo:DiagCrid) and ?drnv is typically part of some dataset (see ScEnc2DataSet.) ?dcrid is the output of the encounter ?e. ?e rdf:type obo:OGMS_0000097 ; obo:OBI_0000299 ?dcrid . ?dcrid rdf:type :DiagCrid ; obo:BFO_0000051 ?dcrn . ?dcrn rdf:type :DiagCodeRegitryID ; obo:IAO_0000219 ?dcru ; :hasTextualValue ?drnv . --- the textual representation of a diagnosis code registry isn't technically interdependent with anything else. However, if it was present in tabular data, it should be passed on with this shortcut as provenance for the diagnosis code registry URI, which is interdependent with the diagnosis code symbol.
shortcut health care encounter to diagnosis code registry denoter
shortcut health care encounter to diagnosis code registry URI string
an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from a health care encounter to a diagnosis code registry URI string
this shortcut links a health care encounter ?e (OGMS_0000097) to the URI of an instance of a diagnosis code registry ?dcru. the value ?drnv of a diagnosis code registry denoter ?dcrn (turbo:DiagCodeRegitryID) denotes a registry instance ?dcru like <http://purl.obolibrary.org/obo/NCIT_C71892> for ICD-10. The mapping from denoters of registries to URIs that already exist in some ontology like NCIT will be the responsibility of the data owner and will be executed with a python transformation in Karma. ?dcrn is part of a diagnosis CRID ?dcrid (turbo:DiagCrid) and ?drnv is typically part of some dataset (see ScEnc2DataSet.) ?dcrid is the output of the encounter ?e. ?e rdf:type obo:OGMS_0000097 ; obo:OBI_0000299 ?dcrid . ?dcrid rdf:type :DiagCrid ; obo:BFO_0000051 ?dcrn . ?dcrn rdf:type :DiagCodeRegitryID ; obo:IAO_0000219 ?dcru ; :hasTextualValue ?drnv . --- failed parse rules for Karma? assumes the tabular data being instantiated by Karma has a column of strings denoting diagnosis code registries. Ideally a Karma python transformation will convert the strings into URIs for diagnosis code registry instances from some ontology like NCIT
this property and any sub properties are used to simplify the experience of using Karma or related relational to RDF instantiation software. They link instances/individuals to data literals, even (or especially!) when the literal is about an instance of some other class, not the subject of the shortcut triple. It is the responsibility of TURBO’s Drivetrain application to expand shortcut triples into realism based semantic triples using BFO classes, based on the shortcut predicate and the class of the instance in the subject position
an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from a/n biobank encounter CRID to a/n to data
shortcut health care encounter CRID to data
an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from a/n health care encounter CRID to a/n to data
shortcut biobank encounter CRID to dataset title
an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from a/n biobank encounter CRID to a/n to dataset title
shortcut biobank encounter CRID to data set title
shortcut biobank encounter CRID to biobank encounter CRID symbol
an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from a/n biobank encounter CRID to a/n to biobank encounter CRID symbol
shortcut biobank encounter CRID to biobank encounter registry denoter
an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from a/n biobank encounter CRID to a/n to biobank encounter registry denoter
shortcut biobank encounter CRID to biobank encounter identifier registry URI string
an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from a/n biobank encounter CRID to a/n to biobank encounter identifier registry URI string
shortcut health care encounter to drug prescription text
an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from a/n health care encounter to a/n to drug prescription text
shortcut health care encounter to drug prescription CRID symbol
an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from a/n health care encounter to a/n to drug prescription CRID symbol
shortcut health care encounter CRID to dataset title
an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from a/n health care encounter CRID to a/n to dataset title
shortcut health care encounter CRID to data set title
shortcut health care encounter CRID to health care encounter CRID symbol
an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from a/n health care encounter CRID to a/n to health care encounter CRID symbol
shortcut health care encounter CRID to health care encounter registry denoter
an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from a/n health care encounter CRID to a/n to health care encounter registry denoter
shortcut health care encounter CRID to health care encounter identifier registry URI string
an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from a/n health care encounter CRID to a/n to health care encounter identifier registry URI string
shortcut biobank consenter CRID to dataset title
an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from a/n biobank consenter CRID to a/n to dataset title
shortcut biobank consenter CRID to data set title
shortcut biobank consenter CRID to biobank consenter CRID symbol
an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from a/n biobank consenter CRID to a/n to biobank consenter CRID symbol
shortcut biobank consenter CRID to biobank consenter registry denoter
an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from a/n biobank consenter CRID to a/n to biobank consenter registry denoter
shortcut biobank consenter CRID to biobank consenter identifier registry URI string
an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from a/n biobank consenter CRID to a/n to biobank consenter identifier registry URI string
shortcut diagnosis to diagnosis code symbol
an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from a/n diagnosis to a/n to diagnosis code symbol
shortcut diagnosis to diagnosis code registry denoter
an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from a/n diagnosis to a/n to diagnosis code registry denoter
shortcut diagnosis to diagnosis code registry
an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from a/n diagnosis to a/n to diagnosis code registry
shortcut prescription to prescription CRID symbol
an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from a/n prescription to a/n to prescription CRID symbol
shortcut prescription to prescription fullname/order_name
an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from a/n prescription to a/n to prescription fullname/order_name
shortcut prescription to drug uri string
an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from a/n prescription to a/n to drug uri string
has literal value
If X is a gender identity datum in a data set (and is therefore a from a subclass of owl:Thing), then it's literal value might be 'M' or 'male' or '0', or any other value provided by the author of the data set.
analogous to has specified value, but not limited to numerical ranges. links a datum to a literal.
the creation of this data property was motivated by the observation that there was no general-purpose data property in any OBO foundry ontology that took a string range. Previous label was 'literal value of any owl:Thing'
I have seen "has measurement value" used for dates, but it has a plain numerical range in (OBI? OBIB?) I had added date as a second range for hmv, but Top Braid Composer only seems to consider the “first” range when determining what relationships can be drawn between two instances in graph mode.
has a literal value that can be mapped to an ontology term
This predicate may be of narrow applicability to modeling loss-of-function reports created by Scott Damrauer (https://www.pennmedicine.org/providers/profile/scott-damrauer) and colleagues. It is used to link from an allele information instance to the gene identifier used in the source loss of function matrix file, such as eve.UPENN_Freeze_One.L2.M3.lofMatrix.txt These identifiers have had a format like "CAPG(ENSG00000042493)"
shortcut allele info to biobank encounter CRID symbol
an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from an allele info to a biobank encounter CRID symbol
shortcut allele info to geno_id CRID symbol
an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from an allele info to a genotype identifier CRID symbol
shortcut allele info to geno_id registry
an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from an allele info to a genotype identifier registry
shortcut allele info to geno_id CRID registry URI string
an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from a/n allele info to a/n to protein
shortcut allele info to protein term URI string
an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from an allele info to a gene identiifer and a zygosity level
Scott Damraurer's team identifies genes like this: SYMBOL(ENSGENEID) For a while, TURBO was constructing shortcuts like gene:SYMBOL(ENSGENEID);zygosity:N
shortcut allele info to gene concatenated text
shortcut allele info to zygosity value text
an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from a/n allele info to a/n to zygosity value text
shortcut allele info to zygosity value specification
an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from a/n allele info to a/n to zygosity value specification
an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from an allele info to the title of the dataset containing (at least) sample identifiers, gene identifiers, and zygosity values
shortcut allele info to LOF data set title
shortcut allele info to biobank encounter CRID registry
an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from a/n allele info to a/n to biobank encounter CRID registry
shortcut allele info to biobank encounter CRID registry URI string
an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from an allele info to a gene term
shortcut allele info to gene term URI string
shortcut racial identity datum to biobank consenter CRID symbol
shortcut racial identity datum to biobank consenter registry denoter
shortcut racial identity datum to biobank consenter identifier registry URI string
shortcut racial identity datum to racial identity CRID symbol
shortcut racial identity datum to racial identity registry denoter
shortcut racial identity datum to racial identity registry URI string
have not yet decided if this is necessary... if there is a white racial identity datum about me, is it necessary to say that that datum is true?
shortcut racial identity datum to boolean
shortcut racial identity datum to data set title
shortcut tumor grading datum to grading process end date
shortcut tumor grading datum to biobank consenter CRID symbol
shortcut tumor grading datum to patient identifier registry text
shortcut tumor grading datum to tissue text
shortcut tumor grading datum to patient identifier registry URI string
shortcut tumor grading datum to grade text
'who' is responsible for converting a grade text (like "G3") into a URI (like http://purl.obolibrary.org/obo/OBI_0002208)? Carnival should take responsibility for converting the patient registry text (like "HUP") into a URI, but some post-Drivetrain process will probably be responsible for converting tissue text into a FMA or Uberon URI.
shortcut tumor grading datum to grade URI string
shortcut health care encounter to patient identifier symbol
shortcut health care encounter to patient identifier registry denoter
shortcut health care encounter to patient identifier registry URI string
shortcut biobank encounter to patient identifier symbol
shortcut biobank encounter to patient identifier registry denoter
shortcut biobank encounter to patient identifier registry URI string
primary diagnoisis
order in diagnosis sequence
Do we need to specify authority? As in, Ensembl gets human symbols from HGNC?
shortcut PSA datum to patient CRID regisry denoter text
shortcut PSA datum to patient CRID symbol
shortcut PSA datum to patient CRID registry denoter URI as string
shortcut PSA valspec to concentration unit URI as string
shortcut Gleason datum to Gleason score textual value
shortcut Gleason datum to Gleason group/profile textual value
shortcut Gleason datum to Gleason score URI as string
shortcut Gleason datum to Gleason group/profile URI as string
shortcut Gleason datum to histology date
shortcut Gleason datum to patient CRID registry denoter text
shortcut Gleason datum to patient CRID registry denoter URI as string
shortcut Gleason datum to patient CRID symbol
add some date boundary shortcut? what date would be meaningful within summary staging shortcuts? the date of the staging process, or some upstream assay or sample collection?
shortcut summary staging datum to stage string
shortcut summary staging datum to patient CRID registry denoter text
shortcut summary staging datum to regden uri string
shortcut summary staging datum to patient CRID symbol
shortcut summary staging datum to data set title
shortcut Gleason datum to data set title
shortcut allele info to biobank encounter CRID registry text
shortcut allele info to geno_id CRID registry text
shortcut allele info to gene symbol text
shortcut allele info to Ensembl gene identifier text
an 'instantiation hybrid shortcut' that, after expansion by Drivetrain, enables a reasonable semantic path from a exome sequencing sample identifier to the identifier of the encounter in which the sample was colelcted
shortcut allele info to sample/encounter key
shortcut person data model to patient CRID symbol value
shortcut person data model to dataset title
shortcut person data model to DOB (textual)
shortcut person data model to DOB (xsd compliant)
shortcut person data model to first name
?x a 'data item' ; 'has representation' 'It was the best of times, it was the worst of times.' .
?x a 'data item'; 'has representation' '20 grams' .
Subject of active discussion by OBI, with similar proposals from Damion Dooley and others. Intended to bind literals to data items, in a way that is more general and succincter than has value specification -> has specified value. DD would give has parsed/atomic/literal value and has textual/raw value separate parents, so that classes could be cardinality constrained to take a single parsed/atomic/literal values but any number of textual/raw values. These properties can take any kind of literal as their object. (Previous discussions had considered separate data properties for different types of literals) James: broaden domain? remove costraint?
has a value asserted directly by some external authority, like a CSV files or database table.
has a value that can be parsed or transformed from an authoritatively asserted raw values. For example, the string "9/10/71" might be transformed to "1971-09-10"^^xsd:date OR "1971-10-09"^^xsd:date depending on the cultural origin of the raw data.
has parsed/transformed literal representation
shortcut person data model to gender identity datum text
shortcut person data model to ethnic identity datum text
shortcut person data model to racial identity datum text
shortcut observation to textual observation date
shortcut observation to xsd formatted observation date
shortcut observation to patient symbol value
shortcut observation to encounter symbol value
shortcut observation to observation type code
shortcut observation to observation value
shortcut observation to textual units label
has database primary key vaue
shortcut person data model to person PK value
shortcut observation to patient PK value
shortcut observation to encounter PK value
shortcut observation to units type code
shortcut health care encounter to previous PK
shortcut allele info to encounter PK value
shortcut tumor data model to data
shortcut tumor data model to patient CRID symbol value
shortcut tumor data model to tumor CRID symbol value
shortcut health care encounter data model to systolic BP in mmHg
shortcut health care encounter data model to diastolic BP in mmHg
shortcut person CRID data model to data
shortcut person CRID data model to symbol value
shortcut health care encounter data model to patient identifier PK
shortcut health care encounter data model to encounter identifier PK
shortcut health care encounter data model to omop encounter type concept code
International Classification of Diseases
A multiaxial, hierarchical classification system for diseases in man developed by the College of American Pathologists.
A multiaxial, hierarchical classification system for diseases in man developed by the College of American Pathologists. (NCI)
A structured nomenclature and classification of the terminology used in human and veterinary medicine developed by the College of Pathologists and American Veterinary Medical Association. Terms are applied to one of eleven independent systematized modules.
SNOMED (Systematized Nomenclature of Medicine)
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])
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]
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]
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
BFO 2 Reference: Spatial regions do not participate in processes.
Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional.
A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001])
All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001])
(forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001]
(forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001]
spatial region
Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional
A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001])
All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001])
Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002])
(forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002]
(forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001]
(forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001]
temporal region
the spatiotemporal region occupied by a human life
the spatiotemporal region occupied by a process of cellular meiosis.
the spatiotemporal region occupied by the development of a cancer tumor
A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001])
All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001])
Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001])
Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001])
Every spatiotemporal region occupies_spatiotemporal_region itself.
Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002])
(forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002]
(forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001]
(forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001]
(forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001]
(forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001]
spatiotemporal region
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]
PERSON: Fernanda Farinelli
process
processo
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 endocitosis and exocitosis
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 [89
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 entity
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]
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]
qualidade
quality
specifically dependent continuant
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 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 > 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i < 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]
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]
or with divisions drawn by cognitive subjects for practical reasons, such as the division of a cake (before slicing) into (what will become) slices (and thus member parts of an object aggregate). However, this does not mean that fiat object parts are dependent for their existence on divisions or delineations effected by cognitive subjects. If, for example, it is correct to conceive geological layers of the Earth as fiat object parts of the Earth, then even though these layers were first delineated in recent times, still existed long before such delineation and what holds of these layers (for example that the oldest layers are also the lowest layers) did not begin to hold because of our acts of delineation.Treatment of material entity in BFOExamples viewed by some as problematic cases for the trichotomy of fiat object part, object, and object aggregate include: a mussel on (and attached to) a rock, a slime mold, a pizza, a cloud, a galaxy, a railway train with engine and multiple carriages, a clonal stand of quaking aspen, a bacterial community (biofilm), a broken femur. Note that, as Aristotle already clearly recognized, such problematic cases – which lie at or near the penumbra of instances defined by the categories in question – need not invalidate these categories. The existence of grey objects does not prove that there are not objects which are black and objects which are white; the existence of mules does not prove that there are not objects which are donkeys and objects which are horses. It does, however, show that the examples in question need to be addressed carefully in order to show how they can be fitted into the proposed scheme, for example by recognizing additional subdivisions [29
the FMA:regional parts of an intact human body.
the Western hemisphere of the Earth
the division of the brain into regions
the division of the planet into hemispheres
the dorsal and ventral surfaces of the body
the upper and lower lobes of the left lung
BFO 2 Reference: Most examples of fiat object parts are associated with theoretically drawn divisions
b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004])
(forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004]
fiat object part
a collection of cells in a blood biobank.
a swarm of bees is an aggregate of members who are linked together through natural bonds
a symphony orchestra
an organization is an aggregate whose member parts have roles of specific types (for example in a jazz band, a chess club, a football team)
defined by fiat: the aggregate of members of an organization
defined through physical attachment: the aggregate of atoms in a lump of granite
defined through physical containment: the aggregate of molecules of carbon dioxide in a sealed container
defined via attributive delimitations such as: the patients in this hospital
the aggregate of bearings in a constant velocity axle joint
the aggregate of blood cells in your body
the nitrogen atoms in the atmosphere
the restaurants in Palo Alto
your collection of Meissen ceramic plates.
An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects
BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee).
ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158.
b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004])
(forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004]
object aggregate
a cube-shaped region of space
a sphere-shaped region of space,
A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001])
(forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001]
three-dimensional spatial region
atom
cell
cells and organisms
engineered artifacts
grain of sand
molecule
organelle
organism
planet
solid portions of matter
star
BFO 2 Reference: BFO rests on the presupposition that at multiple micro-, meso- and macroscopic scales reality exhibits certain stable, spatially separated or separable material units, combined or combinable into aggregates of various sorts (for example organisms into what are called ‘populations’). Such units play a central role in almost all domains of natural science from particle physics to cosmology. Many scientific laws govern the units in question, employing general terms (such as ‘molecule’ or ‘planet’) referring to the types and subtypes of units, and also to the types and subtypes of the processes through which such units develop and interact. The division of reality into such natural units is at the heart of biological science, as also is the fact that these units may form higher-level units (as cells form multicellular organisms) and that they may also form aggregates of units, for example as cells form portions of tissue and organs form families, herds, breeds, species, and so on. At the same time, the division of certain portions of reality into engineered units (manufactured artifacts) is the basis of modern industrial technology, which rests on the distributed mass production of engineered parts through division of labor and on their assembly into larger, compound units such as cars and laptops. The division of portions of reality into units is one starting point for the phenomenon of counting.
BFO 2 Reference: Each object is such that there are entities of which we can assert unproblematically that they lie in its interior, and other entities of which we can assert unproblematically that they lie in its exterior. This may not be so for entities lying at or near the boundary between the interior and exterior. This means that two objects – for example the two cells depicted in Figure 3 – may be such that there are material entities crossing their boundaries which belong determinately to neither cell. Something similar obtains in certain cases of conjoined twins (see below).
BFO 2 Reference: To say that b is causally unified means: b is a material entity which is such that its material parts are tied together in such a way that, in environments typical for entities of the type in question,if c, a continuant part of b that is in the interior of b at t, is larger than a certain threshold size (which will be determined differently from case to case, depending on factors such as porosity of external cover) and is moved in space to be at t at a location on the exterior of the spatial region that had been occupied by b at t, then either b’s other parts will be moved in coordinated fashion or b will be damaged (be affected, for example, by breakage or tearing) in the interval between t and t.causal changes in one part of b can have consequences for other parts of b without the mediation of any entity that lies on the exterior of b. Material entities with no proper material parts would satisfy these conditions trivially. Candidate examples of types of causal unity for material entities of more complex sorts are as follows (this is not intended to be an exhaustive list):CU1: Causal unity via physical coveringHere the parts in the interior of the unified entity are combined together causally through a common membrane or other physical covering\. The latter points outwards toward and may serve a protective function in relation to what lies on the exterior of the entity [13, 47
BFO 2 Reference: an object is a maximal causally unified material entity
BFO 2 Reference: ‘objects’ are sometimes referred to as ‘grains’ [74
b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001])
object
generically dependent continuant
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]
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
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
the temporal region during which a process occurs.
BFO 2 Reference: A temporal interval is a special kind of one-dimensional temporal region, namely one that is self-connected (is without gaps or breaks).
A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001])
(forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001]
one-dimensional temporal region
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
BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10
immaterial entity
a temporal region that is occupied by a process boundary
right now
the moment at which a child is born
the moment at which a finger is detached in an industrial accident
the moment of death.
temporal instant.
A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001])
(forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001]
zero-dimensional temporal region
anatomical entity
connected anatomical structure
material anatomical entity
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.
High molecular weight, linear polymers, composed of nucleotides containing deoxyribose and linked by phosphodiester bonds; DNA contain the genetic information of organisms.
An aldohexose used as a source of energy and metabolic intermediate.
A group of heterocyclic compounds with a core structure containing a benzene ring fused to a diazepine ring.
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
A chemical entity is a physical entity of interest in chemistry including molecular entities, parts thereof, and chemical substances.
A member of the class of triazolobenzodiazepines that is 4H-[1,2,4]triazolo[4,3-a][1,4]benzodiazepine carrying methyl, phenyl and chloro substituents at positions 1, 6 and 8 respectively. Alprazolam is only found in individuals that have taken this drug.
A member of the class of bilanes that is a colourless product formed in the intestine by the reduction of bilirubin.
Any substituent group or skeleton containing carbon.
A chemical entity constituting the smallest component of an element having the chemical properties of the element.
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.
High molecular weight, linear polymers, composed of nucleotides containing ribose and linked by phosphodiester bonds; RNA is central to the synthesis of proteins.
When two or more amino acids combine to form a peptide, the elements of water are removed, and what remains of each amino acid is called an amino-acid residue.
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
A compound formally derived from ammonia by replacing one, two or three hydrogen atoms by organyl groups.
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.
The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one).
A cell that is found in a natural setting, which includes multicellular organism cells 'in vivo' (i.e. part of an organism), and unicellular organisms 'in environment' (i.e. part of a natural environment).
To accommodate unicellular organisms better, 'cell in vivo' has been re-labeled 'native cell' to better represent its intended meaning - that is, that it is a cell in the context of a multicellular organism or in a natural environment. 'Native' is intended to contrast with 'in vitro', which refers to cells or other biological entities that have been intentionally placed in a controlled, non-natural setting for the purpose of study or manipulation. (MAH 1.12.12).
A cell in vitro that is or has been maintained or propagated as part of a cell culture.
A red blood cell. In mammals, mature erythrocytes are biconcave disks containing hemoglobin whose function is to transport oxygen.
A cell in vitro that has undergone physical changes as a consequence of a deliberate and specific experimental procedure.
Any of the immature or mature forms of a granular leukocyte that in its mature form has a nucleus with three to five lobes connected by slender threads of chromatin, and cytoplasm containing fine inconspicuous granules and stainable by neutral dyes.
A cell found in an organism or derived from an organism exhibiting a phenotype that deviates from the expected phenotype of any native cell type of that organism. Abnormal cells are typically found in disease states or disease models.
An abnormal cell exhibiting dysregulation of cell proliferation or programmed cell death and capable of forming a neoplasm, an aggregate of cells in the form of a tumor mass or an excess number of abnormal cells (liquid tumor) within an organism.
A neoplastic cell that is capable of entering a surrounding tissue
O peso corporal de um organismo.
The heaviness or degree to which an entire organism's body is drawn to the earth by gravity.
peso corporal
body weight
peso do corpo
Altura corporal de um organismo.
The vertical measurement of a body.
altura corporal
body height
A personal name composed of one given name, one family name, and sometimes of one or several middle names.
complete personal name
An ethnic group comprised of persons with African ancestral origins who self identify, or are identified, as African.
African
Anatomical structure which is the aggregate material substance of an individual member of the Homo sapiens species. Examples: There is only one human body.
TO DO
Human body
corpo humano
Body of vertebrate
Anatomical structure which is the aggregate material substance of an individual member of a species.
Body
corpo
Wall of blood vessel
parede do vaso sanguíneo
Cardinal organ part which is a fiat subdivision of an organ component. Examples: cervical part of wall of esophagus, mucosa of body of stomach.
Region of organ component
Hematopoietic system
Material anatomical entity in a gaseous, liquid, semisolid or solid state, with or without the admixture of cells and biological macromolecules; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures. Examples: saliva, semen, cerebrospinal fluid, respiratory air, urine, feces, blood, plasma, lymph.
substância corporal
Portion of body substance
porção de substância corporal
Body substance which consists of plasma and blood cells
Uma porção de substância corporal em estado líquido, produzido na medula óssea, constituído pelo plasma e alguns componentes celulares denominados de eritrócitos, leucócitos e plaquetas, que circula pelo sistema vascular, e tem como função o transporte de nutrientes, oxigênio, toxinas e gás carbônico pelo corpo.
sangue
NEW DEFINITION PROPOSAL: A portion of body substance in a liquid state, produced by the bone marrow, made up of plasma and some cellular components called erythrocytes, leukocytes, and platelets, which circulates through the vascular system, and has the function of transporting nutrients, oxygen, toxins and carbon dioxide through the body.
Portion of blood
porção de sangue
An allelic state that describes the degree of similarity of features at a particular location in the genome (i.e. whether the alleles or haplotypes are the same or different).
derived from https://en.wikipedia.org/wiki/Zygosity
A sequence feature (continuous extent of biological sequence) that is of genomic origin (i.e. carries sequence from the genome of a cell or organism)
This class was created largely as a modeling convenience to support organizing data for schema definitions. We may consider obsoleting it if it ends up causing confusion or complicating classification of terms in the ontology.
1. A feature being 'of genomic origin' here means only that its sequence has been located to the genome of some organism by alignment with some reference genome. This is because the sequence was originally identified in, or artificially created to replicate, sequence from an organism's genome. 2. The location of a genomic feature is defined by start and end coordinates based on alignment with a reference genome. Genomic features can span any size from a complete chromosome, to a chromosomal band or region, to a gene, to a single base pair or even junction between base pairs (this would be a sequence feature with an extent of zero). 3. As sequence features, instances of genomic features are identified by both their inherent *sequence* and their *position* in a genome - as determined by an alignment with some reference sequence. Accordingly, the 'ATG' start codon in the coding DNA sequence of the human AKT gene and the 'ATG' start codon in the human SHH gene represent two distinct genomic features despite having he same sequence, in virtue of their different positions in the genome.
genomic feature
An allele representing a highly common varaint (typically >99% in a population), that typically exhibits canonical function, and against which rare and/or non-functional mutant alleles are often compared.
'Wild-type' is typically contrasted with 'mutant', where 'wild-type' indicates a highly prevalent allele in a population (typically >99%), and/or some prototypical allele in a background genome that serves as a basis for some experimental alteration to generate a mutant allele, which can be selected for in establishing a mutant strain. The notion of wild-type alleles is more common in model organism databases, where specific mutations are generated against a wild-type reference feature. Wild-type alleles are typically but not always used as reference alleles in sequence comparison/analysis applications. More than one wild-type sequence can exist for a given feature, but typically only one allele is deemed wild-type iin the context of a single dataset or analysis.
One of a set of sequence features known to exist at a particular genomic location.
A landsacpe review found mostly gene-centric definitions of 'allele' that represented a particular version of a gene, or variation within a gene sequence [1][2][3][4][5][6][6a]. But we also found 'allele' used to refer to other types and extents of variation - including single nucleotide polymorphisms, repeat regions, and copy number variations [7][8][9][10][11], where such variations don't neccessarily impact a gene. To be maximally accommodating of how this term is used across research communities, GENO defines 'allele' broadly and allow alleles can span any locus or extent of sequence. While 'alleles' encountered in public datases typically overlap a gene, many do not. But GENO does define the 'gene allele' class as a subtype of 'allele' to refers more specifically to a specifc version of an entire gene. [1] https://isogg.org/wiki/Allele (retrieved 2018-03-17) [2] http://semanticscience.org/resource/allele (retrieved 2018-03-17) [3] https://en.wikipedia.org/wiki/Allele (retrieved 2018-03-17) [4] https://www.cancer.gov/publications/dictionaries/genetics-dictionary/def/allele (retrieved 2018-03-17) [5] http://purl.obolibrary.org/obo/SO_0001023 (retrieved 2018-03-17) [6] http://purl.obolibrary.org/obo/NCIT_C16277 (retrieved 2018-03-17) [6a] https://www.ncbi.nlm.nih.gov/mesh/68000483 [7] https://www.snpedia.com/index.php/Allele (retrieved 2018-03-17) [8] https://en.wikipedia.org/wiki/Single-nucleotide_polymorphism (retrieved 2018-03-17) [9] http://purl.obolibrary.org/obo/OGI_0000008 (retrieved 2018-03-17) [10] http://purl.obolibrary.org/obo/OBI_0001352 (retrieved 2018-03-17) [11] http://purl.phyloviz.net/ontology/typon#Allele (retrieved 2018-03-17)
variable feature
An allele is a seqeunce feature at a genomic location where variation occurs (i.e. where >1 different sequence is known to exist). An allele can span only the extent of sequence known to vary (e.g. a single base SNP, or short insertion), or it can span a larger extent that includes one or more variable features as proper parts (e.g. a 'gene allele' that spans the extent of an entire gene which contains several sequence alterations). Alleles can carry 'reference' or 'variant' sequence - depending on whether the its 'state' matches that considered to be the reference at that location. Alleles whose state differs from the reference are called 'variant alleles', and those that match the reference are called 'reference alleles'. What is considered the 'reference' state at a particular location may vary, depending on the context/goal of a particular analysis. A 'sequence alteration' is a 'variant allele' that varies along its entire extent (i.e every position varies from that of some defined reference sequence).
The set of both shha gene alleles in a diiploid zebrafish genome, e.g. fgf8a<ti282a/+>. The collection of the individual base-pairs present at the position 24126737 in both copies of chromosome 5 in a diploid human genome.
A set representing the complement of all sequence features occupying a particular genomic location across all homologous chromosomes in the genome of a single organism.
TO DO: show a VCF representation of this example. Consider making 'allelic complement' the primary label.
A 'complement' refers to an exhaustive collection of *all* objects that make up some well-defined set. Such a complement may contain 0, 1, or more than one members. The notion of a complement is useful for defining many biologically-relevant sets of sequence features. Here, a 'single locus complement' is the set of all alleles at a specified location in a particular genome. This complement is typically a pair of two features in a diploid genome (with two copies of each chromosome). E.g. a gene pair, a QTL pair, a nucleotide pair for a SNP, or a pair of entire chromosomes. The fact that we are counting how many copies of the same *sequence* exist in a genome, as opposed to how many of the same *feature*, is what sets feature-level concepts like 'single locus complement'. apart from sequence-level concepts like 'copy number complement'. To illustrate the difference, consider a duplication event that creates a new copy of the human APOE gene on a different chromosome. This creates an entirely new sequence feature at a distinct locus from that of the original APOE gene. The 'copy number complement' for sequence defined by the APOE gene locus would have a count of three, as this sequence is present three times in the genome. But the 'single locus complement' at the APOE gene locus would still have a count of two - because the duplicated copy is at a different location in the genome, and therefore does not represent a copy of the APOE locus.
1. The set of all alleles at a particular location in a genome (a 'single locus complement') - e.g. {APOE-epsilon2 / APOE-epsilon4} at the APOE locus 2. The set of all alleles that comprise a haplotype - e.g. the SNPs {rs7412-T, rs429358-T} in the APOEɛ2 allele. 3. The set of all chromosomes in a genome - e.g. {human Chr1, 2, 3, . . . 22, X, Y}
'Sets' are used to represent entities that are typically collections of more than one member. But we allow for sets that contain 0 members (an 'empty' set) or 1 member (a 'singleton' or 'unit' set), consistent with the concept of 'mathematical sets'. Sets may also include duplicates (i.e. contain more than one member representing the same feature). The notion of a 'complement' is a special case of a set, where the members necessarily comprise an exhaustive collection of all objects that make up some well-defined set. It is useful for defining many biologically-relevant sets of sequence features. For example, a 'haplotype' is the set of all genetically-linked alleles on a single chromosomal strand at a defined location - e.g. the SNP alleles {rs7412-C, rs429358-C} comprise the haplotype defining the APOEɛ4 gene allele [1]. And a 'single locus complement' is the set of all alleles at a specified location in a particular genome - e.g. the APOEɛ4 and APOEɛ4 gene alleles ([1], [2]) that make up the 'Gs270' APOE genotype [3]. [1] https://www.snpedia.com/index.php/APOE-%CE%B54 [2] https://www.snpedia.com/index.php/APOE-%CE%B52 [3] https://www.snpedia.com/index.php/Gs270
sequence feature set
A set of genomic features (i.e. sequence features that are of genomic origin).
In some cases there may be zero or only one member of such a complement, which is why this class is not defened to necessarily have some 'genomic feature' as a member.
A genomic feature is any located sequence feature in the genome, from a single nucleotide to a gene into an entire chromosome. 'Sets' are used to represent entities that are typically collections of more than one member - e.g. the set of chromosomes that make up the human genome. But we allow for sets that contain 0 members (an 'empty' set) or 1 member (a 'singleton' or 'unit' set), consistent with the concept of 'mathematical sets'. For example, a 'single locus complement' at an X-linked locus in a XY male will consist of only one allele, as there is only one X-chromosome in the genome. Note also that sets may contain duplicates (i.e. more than one member representing the same feature). For example, a homozygous 'single locus complement' is a set comprised of two of the same feature. The notion of a 'genomic feature set' differs from that of a 'genomic sequence set' in that we are counting how many copies of the same *sequence feature* exist in a genome, as opposed to how many of the same *sequence*. 'Genomic feature sets are useful for representing things like 'single locus complements', where members are sequence features whose identity is dependent on their location. By contrast, 'genomic sequence sets' are useful for describing things like 'copy number complements', which are concerned only with how many copies of a sequence exist in a genome, regardless of the location where these reside.
genomic feature set
A sequence feature or a set of such features.
GENO defines three levels of sequence-related artifacts, which are distinguished by their identity criteria. 1. 'Biological sequence' identity is dependent only on the ordering of units that comprise the sequence. 2. 'Sequence feature' identity is dependent on its sequence and the genomic position if the sequence (aligns with definition of 'sequence feature' in the Sequence Ontology). 3. 'Qualified sequence feature' identity is additionally dependent on some aspect of the physical context of the genetic material bearing the feature, extrinsic to its sequence and its genomic position. For example, its being targeted by gene knockdown reagents, its being transgenically expressed in a foreign cell from a recombinant expression construct, its having been epigenetically modified in a way that alters its expression level or pattern, or its being located in a specific cellular or anatomical location.
sequence feature or set
A linear ordering of units representing monomers of a biological macromolecule (e.g. nucleotides in DNA and RNA, amino acids in polypeptides).
GENO defines three levels of sequence-related artifacts, which are distinguished by their identity criteria. 1. 'Biological sequence' identity is dependent only on the ordering of units that comprise the sequence. 2. 'Sequence feature' identity is dependent on its sequence and the genomic location of the sequence (this is consistent with the definition of 'sequence feature' in the Sequence Ontology). 3. 'Qualified sequence feature' identity is additionally dependent on some aspect of the physical context of the genetic material in which the feature is concretized. This third criteria is extrinsic to its sequence and its genomic location. For example, the feature's physical concretization being targeted by a gene knockdown reagent in a cell (e.g. the zebrafish Shha gene as targeted by the morpholino 'Shha-MO1'), or its being transiently expressed from a recombinant expression construct (e.g. the human SHH gene as expressed in a mouse Shh knock-out cell line), or its having been epigenetically modified in a way that alters its expression level or pattern (e.g. the human SHH gene with a specific methylation pattern).
'Sequences' differ from 'sequence features' in that instances are distinguished only by their inherent ordering of units, and not by any positional aspect related to alignment with some reference sequence. Accordingly, the 'ATG' translational start codon of the human AKT gene is the same *sequence* as the 'ATG' start codon of the human SHH gene, but these represent two distinct *sequence features* in virtue of their different positions in the genome.
biological sequence
An attribute, quality, or state of a sequence feature or collection.
Sequence feature attributes can be 'intrinsic' - reflecting feature-level characteristics that depend only on the sequence, location, or genomic context of a feature or collection, or 'extrinsic' - reflecting characteristics of the physical molecule in which the feature is concretized (e.g. its cellular context, source of origin, physical appearance, etc.). Intrinsic attributes include things like allelic state, allelic phase. Extrinsic attributes include things like its cellular distribution and chromosomal band intensity.
The location of a sequence feature as defined by its start and end position on some reference coordinate system.
1. A sequence feature location is defined by its begin and end coordinates on a reference sequence, but it is not identified by a particular sequence that may reside there. The same location, as defined on a particular reference, may be occupied by different sequences in the genome of organism 1 vs that of organism 2 (e.g. if a SNV exists within this location in only one of the organisms). 2. The notion of a sequence feature location in the realm of biological sequences is analogous to a BFO:spatiotemporal region in the realm of physical entities. A spatiotemporal region can be 'occupied by' physical objects, while a genomic location is 'occupied by' sequence features. Just as a spatiotemporal region is distinct from an object that occupies it, so too a genomic location is distinct from a sequence feature that occupies it. As a more concrete example, consider the distinction between a street address and the building that occupies it as analogous to the relationship between a genomic locus and the sequence feature that resides there.
sequence feature location
A quality inhering in an 'allelic complement' (aka a 'single locus complement') that describes the allelic variability found at a particular locus in the genome of a single cell/organism
allelic state
The location of a sequence feature in a genome, defined by its start and end position on some reference genomic coordinate system
In GENO, the notion of a Genomic Location (aka Genomic Locus) plays the same role as that of a FALDO:Region in the design pattern for describing the location of a feature of interest. We define this specific GENO class because the ontological nature of FALDO:Region class is not clear in the context of the BFO and SO-based GENO model. We will work to resolve these questions and ideally converge these concepts in the future. We don't link a Genomic Location to a specific reference sequence because in the FALDO model (which GENO adopts with the exception of swapping GENO:Genomic Locus for FALDO:Region), allows the start and end positions of a region to be defined on separate reference sequences. So while a given Location is conceptually associated with a single reference, in practice it can be pragmatic to define start and stop on different references sequences.
In practice, GENO advocates describing biology at the level of genomic features - i.e. define specific terms for genes as genomic features, and not duplicate representation of the loci where each gene resides. So we might define a class representing the human Shh gene as a 'genomic feature', but not parallel this with a 'human Shh gene locus' class. The utility of the 'genomic locus' class in the ontology is primarily to be clear about the distinction, but we would only use it in modeling data if absolutely needed. For example, we would define an 'HLA gene block' as a subclass of 'genomic feature', and assert that HLA-A, HLA-B, and HLA-C genes are part/subsequences of this HLA gene block (as opposed to modeling this as an 'HLA locus' and asserting that the HLA-A, HLA-B, and HLA-C genes occupy this locus).
1. A genomic location (aka locus) is defined by its begin and end coordinates on a reference genome, independent of a particular sequence that may reside there. In GENO, we say that a genomic location is occupied_by a 'sequence feature' - where the identity of this feature depends on both it sequence, and its location in the genome (i.e. the locus it occupies). For example, the 'ATG' sequence beginning the ORF of the human SHH gene shares the *same sequence* as the 'ATG' beginning the ORF of the human AKT gene. But these are *distinct sequence features* because they occupy different genomic locations. 2. A given genomic location (e.g. the human SHH gene locus) may be occupied by different alleles (e.g. different alleles of the SHH gene). Within the genome of a single diploid organism, there is potential for two alleles to exist at such a locus (i.e. two different versions of the SHH gene). And across genomes of all members of a species, many more alleles of the SHH gene may exist and occupy this same locus. 3. The notion of a genomic location in the realm of biological sequences is analogous to a BFO:spatiotemporal region in the realm of physical entities. A spatiotemporal region can be occupied_by physical objects, while a genomic location is occupied_by sequence features. Just as a spatiotemporal region is distinct from an object that occupies it, so too a genomic locus is distinct from a sequence feature that occupies it. As a more concrete example, consider the distinction between a street address and the building that occupies it as analogous to the relationship between a genomic location and the feature that resides there.
genomic feature location
A biolocical sequence, or set of such sequences.
biological sequence or set
A biological sequence that is of genomic origin (i.e. carries sequence from the genome of a cell or organism).
A sequence being 'of genomic origin' here means only that it has been located to the genome of some organism by alignment with some reference genomic sequence. This is because the sequence was originally identified in, or artificially created to replicate, sequence from an organism's genome.
genomic sequence
The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope.
The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.
The flow of blood through the body of an animal, enabling the transport of nutrients to the tissues and the removal of waste products.
blood circulation
circulação sanguínea
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.
Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.
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. Note that 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 ND, no data, is used to indicate this.
biological_process
An individual organism identifier that is used to identify a beneficiary of some health insurance.
health insurance identifier
A CRID symbol that is sufficent to look up a patient file in a medical record registry.
medical record identifier
patient
A phenotypic abnormality.
PERSON: Fernanda Farinelli OntONeo development prioritizes the reuse of classes and entities from FMA ontology to deal with human anatomy approaches. Originally this class has reference to UBERON:0000468. UBERON ontology has cross-reference annotation (database_cross_reference) of UBERON: 0000468 to FMA_256135. Due this cross-reference annotation we opted to replace the UBERON:0000468 by FMA_256135.
This is the root of the phenotypic abnormality subontology of the HPO.
Phenotypic abnormality
A blood pressure measurement datum that is a quality measure of some diastolic blood pressure
diastolic blood pressure measurement datum
A blood pressure measurement datum that is a quality measure of some systolic blood pressure
cut and pasted int turbo.owl with text editor
systolic blood pressure measurement datum
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: Melanie Courtot
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: Barry Smith
PERSON: Bjoern Peters
PERSON: Jennifer Fostel
goal specification
OBI Plan and Planned Process/Roles Branch
Pour the contents of flask 1 into flask 2
a directive information entity that describes an action the bearer will take
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
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.
software
Software is a plan specification composed of a series of instructions that can be interpreted by or directly executed by a processing unit.
see sourceforge tracker discussion at http://sourceforge.net/tracker/index.php?func=detail&aid=1958818&group_id=177891&atid=886178
PERSON: Chris Stoeckert
GROUP: OBI
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
data
symbol
a serial number such as "12324X"
a stop sign
a written proper name such as "OBI"
An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity.
20091104, MC: this needs work and will most probably change
2014-03-31: We would like to have a deeper analysis of 'mark' and 'sign' in the future (see https://code.google.com/p/information-artifact-ontology/issues/detail?id=154).
2014-03-31: We would like to have a deeper analysis of 'mark' and 'sign' in the future (see https://github.com/information-artifact-ontology/IAO/issues/154).
PERSON: James A. Overton
based on Oxford English Dictionary
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.
An information content entity is an entity that is generically dependent on some artifact and stands in relation of aboutness to some entity
2014-03-10: The use of "thing" is intended to be general enough to include universals and configurations (see https://groups.google.com/d/msg/information-ontology/GBxvYZCk1oc/-L6B5fSBBTQJ).
information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907). Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity.
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.
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
directive information content entity
directive information entity
algorithm
PMID: 18378114.Genomics. 2008 Mar 28. LINKGEN: A new algorithm to process data in genetic linkage studies.
A plan specification which describes the inputs and output of mathematical functions as well as workflow of execution for achieving an predefined objective. Algorithms are realized usually by means of implementation as computer programs for execution by automata.
Philippe Rocca-Serra
PlanAndPlannedProcess Branch
adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg)
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)
data set
Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves).
A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets.
2009/10/23 Alan Ruttenberg. The intention is that this term represent collections of like data. So this isn't for, e.g. the whole contents of a cel file, which includes parameters, metadata etc. This is more like java arrays of a certain rather specific type
2014-05-05: Data sets are aggregates and thus must include two or more data items. We have chosen not to add logical axioms to make this restriction.
person:Allyson Lister
person:Chris Stoeckert
image
An image is an affine projection to a two dimensional surface, of measurements of some quality of an entity or entities repeated at regular intervals across a spatial range, where the measurements are represented as color and luminosity on the projected on surface.
data about an ontology part
data about an ontology part is a data item about a part of an ontology, for example a term
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
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
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.
Um dado de medição é uma entidade de conteúdo de informação que é uma gravação da saída de uma medida tal como produzida por um dispositivo.
2/2/2009 is_specified_output of some assay?
dado de medida
dado medido
valor medido
dado de medição
version number
A version number is an information content entity which is a sequence of characters borne by part of each of a class of manufactured products or its packaging and indicates its order within a set of other products having the same name.
Note: we feel that at the moment we are happy with a general version number, and that we will subclass as needed in the future. For example, see 7. genome sequence version
conclusion textual entity
that fucoidan has a small statistically significant effect on AT3 level but no useful clinical effect as in-vivo anticoagulant, a paraphrase of part of the last paragraph of the discussion section of the paper 'Pilot clinical study to evaluate the anticoagulant activity of fucoidan', by Lowenthal et. al.PMID:19696660
A textual entity that expresses the results of reasoning about a problem, for instance as typically found towards the end of scientific papers.
2009/10/23 Alan Ruttenberg: We need to work on the definition still
material information bearer
A page of a paperback novel with writing on it. The paper itself is a material information bearer, the pattern of ink is the information carrier.
a brain
a hard drive
A material entity in which a concretization of an information content entity inheres.
obsolescence reason specification
The reason for which a term has been deprecated. 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.
The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology.
textual entity
Words, sentences, paragraphs, and the written (non-figure) parts of publications are all textual entities
A textual entity is a part of a manifestation (FRBR sense), a generically dependent continuant whose concretizations are patterns of glyphs intended to be interpreted as words, formulas, etc.
AR, (IAO call 2009-09-01): a document as a whole is not typically a textual entity, because it has pictures in it - rather there are parts of it that are textual entities. Examples: The title, paragraph 2 sentence 7, etc.
MC, 2009-09-14 (following IAO call 2009-09-01): textual entities live at the FRBR (http://en.wikipedia.org/wiki/Functional_Requirements_for_Bibliographic_Records) manifestation level. Everything is significant: line break, pdf and html versions of same document are different textual entities.
PERSON: Lawrence Hunter
text
author identification
L. Hunter
A textual entity intended to identify a particular author
figure
Any picture, diagram or table
An information content entity consisting of a two dimensional arrangement of information content entities such that the arrangement itself is about something.
document
A journal article, patent application, laboratory notebook, or a book
A collection of information content entities intended to be understood together as a whole
document part
An abstract, introduction, method or results section.
an information content entity that is part of a document
A scalar measurement datum that is the result of measurement of length quality
length measurement datum
The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are "natural kinds" and the latter arbitrary collections of entities.
A denotator type indicates how a term should be interpreted from an ontological perspective.
A scalar measurement datum that is the result of measurement of mass quality
mass measurement datum
A scalar measurement datum that is the result of measuring a temporal interval
time measurement datum
Recording the current temperature in a laboratory notebook. Writing a journal article. Updating a patient record in a database.
a planned process in which a document is created or added to by including the specified input in it.
6/11/9: Edited at OBI workshop. We need to be able identify a child form of information artifact which corresponds to something enduring (not brain like). This used to be restricted to physical document or digital entity as the output, but that excludes e.g. an audio cassette tape
Bjoern Peters
wikipedia http://en.wikipedia.org/wiki/Documenting
documenting
The sentence "The article has Pubmed ID 12345." contains a CRID that has two parts: one part is the CRID symbol, which is '12345'; the other part denotes the CRID registry, which is Pubmed.
A symbol that is part of a CRID and that is sufficient to look up a record from the CRID's registry.
PERSON: Bill Hogan
Original proposal from Bjoern, discussions at IAO calls
centrally registered identifier symbol
Entries in a Column of which the header is "Pubmed ID"
The following URL: "http://www.ncbi.nlm.nih.gov/pubmed/19918065"
The following sentence contains a CRID: "The article with Pubmed ID: 19918065".
An information content entity that consists of a CRID symbol and additional information about the CRID registry to which it belongs.
An information content entity that consists of a CRID symbol and additional information about which CRID registry it belongs.
2014-05-05: In defining this term we take no position on what the CRID denotes. In particular do not assume it denotes a *record* in the CRID registry (since the registry might not have 'records').
Alan, IAO call 20101124: potentially the CRID denotes the instance it was associated with during creation.
Note, IAO call 20101124: URIs are not always CRID, as not centrally registered. We acknowledge that CRID is a subset of a larger identifier class, but this subset fulfills our current needs. OBI PURLs are CRID as they are registered with OCLC. UPCs (Universal Product Codes from AC Nielsen)are not CRID as they are not centrally registered.
CRID
centrally registered identifier
PubMed is a CRID registry. It has a dataset of PubMed identifiers associated with journal articles.
A CRID registry is a dataset of CRID records, each consisting of a CRID symbol and additional information which was recorded in the dataset through a assigning a centrally registered identifier process.
centrally registered identifier registry
time stamped measurement datum
written name
"Bill Clinton"
"The Eiffel Tower"
"United States of America"
A textual entity that denotes a particular in reality.
The qualifier "written" is to set it apart from spoken names. Also, note the restrictions to particulars. We are not naming universals. We could however, be naming, attributive collections which are particulars, so "All people located in the boundaries of the city of Little Rock, AR on June 18, 2011 at 9:50a CDT" would be a name.
A software application is software that can be directly executed by some processing unit.
PERSON: Michel Dumontier
software application
A proper name is an information content entity that is the outcome of a dubbing process and is used to refer to one instance of entity shared by a group of people to refer to that individual entity.
An identifier is an information content entity that is the outcome of a dubbing process and is used to refer to one instance of entity shared by a group of people to refer to that individual entity.
Uma entidade de conteúdo de informação que é o resultado de um processo de identificação e é usada para se referir a uma instância de entidade compartilhada por um grupo de pessoas para se referir a essa entidade individual.
Une entité de contenu informationnel qui est le résultat d'un processus de dénomination d'une entité et dont l'usage est partagé par un groupe d'individus qui s'en servent pour référer à cette entité.
proper name
Sep 29, 2016: The current definition has been amended from the previous version: "A proper name is an information content entity that is the outcome of a dubbing process and is used to refer to one instance of entity shared by a group of people to refer to that individual entity." to more accuratly reflect the necessary and sufficient condition on the class. (MB)
identifier
nom propre
nome próprio
A dubbing process is a planned process that provides a reference to an individual entity shared by a group of subscribers to refer to that individual entity.
dubbing process
A personal name is a proper name identifying an individual person.
Um nome próprio que identifica uma pessoa específica.
Un nom propre qui identifie une personne.
nome completo
nome da pessoa
Personal names "today usually comprises a given name bestowed at birth or at a young age plus a surname. It is nearly universal for a human to have a name; except in rare cases, for example feral children growing up in isolation, or infants orphaned by natural disaster for whom no written record survives.[citation needed] The Convention on the Rights of the Child specifies that a child has the right from birth to a name. Certain isolated tribes, such as the Machiguenga of the Amazon, also lack personal names." (http://en.wikipedia.org/wiki/Personal_name)
nom personnel
nome pessoal
personal name
A given name, in Western contexts often referred to as a first name, is a personal name that specifies and differentiates between members of a group of individuals, especially in a family, all of whose members usually share the same family name (surname). A given name is purposefully given, usually by a child's parents at or near birth, in contrast to an inherited one such as a family name
Un nom personnel qui différencie un individu au sein des membres d'un groupe qui partagent le même nom de famille. Un prénom est choisi et attribué volontairement à un individu plutôt que transmis.
first name
nome
given name
primeiro nome
prénom
A family name (in Western contexts often referred to as a surname or last name) is typically a part of a person's name which has been passed, according to law or custom, from one or both parents to their children.
Un nom de famille est typiquement une partie du nom d'une personne qui a été transmis, selon la loi ou la coutume, d'un des parents ou des deux parents à leurs enfants.
last name
sobrenome
último nome
último sobrenome
family name
nom de famille
nome de família
a document that denotes some identity and is concretized by the bearer of some credential role
identity document
a documented identity is the aggregate of all data items about an entity. Notice that a documented identity is not itself a document since a document is intended to be understood as a whole and data items about an individual are usually scattered across different documents.
is an aggregate of ICEs also an ICE? yes Is part_of the appropriate relation to use for data items and documented identities?
documented identity
I order a beer and the bartender authenticates my age by looking at my DOB on my driver's license. I sign into my email account, and the system authenticates my permission to read the email by checking the password I enter against my password listed in the database.
Authentication is the act of checking or verifying an identity claim (that is either tacit or explicit).
authentication
a role that inheres in a concretization of an identity document and is realized by an authentication process
Amanda Hicks
credential role
Colonel Klink giving Sergeant Schultz an order, Jake promising Jill to take her to the junior prom
A process that is carried out by a conscious being or an aggregate of conscious beings and is spontaneous, directed towards other conscious beings and aggregates thereof and needs to be perceived.
MB: Regarding the use of the term 'sponteneous' in the definition: The term is used in the following meaning of being self generated. It does not stand in contrast to being planned.
social act
A document that explains all relevant information to assist a human being in understanding the expectations and requirements of participation in a process, and is an instrument in obtaining consent and, after having obtained consent, is a record that such a consent has occurred.
Alla Karnovsky, Frank Manion, Yongqun He, Asiyah Yu Lin, Marcy Harris, Elizabeth Eisenhauer, Jonathan Vajda, Cooper Stansbury, J. Neil Otte
informed consent document
NCIt C16468
informed consent form
An informed consent form that has been filled with all required contents.
Yongqun He
completely filled informed consent form
A role that inheres in a patient or the legal guadian when he/she participates the consenting process.
Asiyah Yu Lin, Yongqun He
This class is under group discussion as of 03/26/2019.
consenter role
A disease is a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism.
A tumor composed of atypical neoplastic, often pleomorphic cells that invade other tissues. Malignant neoplasms often metastasize to distant anatomic sites and may recur after excision. The most common malignant neoplasms are carcinomas (adenocarcinomas or squamous cell carcinomas), Hodgkin and non-Hodgkin lymphomas, leukemias, melanomas, and sarcomas.
A benign or malignant tissue growth resulting from uncontrolled cell proliferation. Benign neoplastic cells resemble normal cells without exhibiting significant cytologic atypia, while malignant cells exhibit overt signs such as dysplastic features, atypical mitotic figures, necrosis, nuclear pleomorphism, and anaplasia. Representative examples of benign neoplasms include papillomas, cystadenomas, and lipomas; malignant neoplasms include carcinomas, sarcomas, lymphomas, and leukemias.
Either an isolated neoplasm or a syndrome with neoplasm as a major feature.
Any disorder that features disrupted cell proliferation. Includes hyperplasia, neoplastic syndrome and isolated neoplasm diseases as well as precancerous conditions.
Homo sapiens
humano, ser humano
PREFIX obo: <http://purl.obolibrary.org/obo/> PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX sm: <tag:stardog:api:mapping:> PREFIX turbo: <http://transformunify.org/ontologies/> PREFIX xsd: <http://www.w3.org/2001/XMLSchema#> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX ontologies: <http://transformunify.org/ontologies/> insert { graph turbo:expanedUnlinkedPeople { ?person a obo:NCBITaxon_9606 ; turbo:TURBO_0000303 ?sns ; ontologies:TURBO_0010390 ?race_concept_id ; ontologies:TURBO_0010391 ?ethnicity_concept_id ; ontologies:TURBO_0010392 ?gender_concept_id ; ontologies:TURBO_0010393 ?person_id . ?sns a obo:UBERON_0035946 . ?birthdate a <http://www.ebi.ac.uk/efo/EFO_0004950> ; obo:IAO_0000136 ?sns ; obo:IAO_0000004 ?birth_datetime ; obo:BFO_0000050 turbo:expanedUnlinkedEncounters . turbo:expanedUnlinkedPeople a obo:IAO_0000100 ; <http://purl.org/dc/elements/1.1/title> ?dataSetTitle . ?crid a obo:IAO_0000578 ; obo:IAO_0000219 ?person . ?cridSymb a obo:IAO_0000577 ; obo:BFO_0000050 ?crid ; turbo:TURBO_0010094 ?person_source_value ; obo:BFO_0000050 turbo:expanedUnlinkedEncounters . ?encRegDen obo:BFO_0000050 ?crid . } } where { service <http://localhost:5820/forvg/query> { graph <virtual://synthea_omop_rds> { ?subject <http://transformunify.org/ontologies/TURBO_0010086> ?birth_datetime . ?subject <http://transformunify.org/ontologies/TURBO_0010282> ?regden . ?subject <http://transformunify.org/ontologies/TURBO_0010079> ?person_source_value . ?subject rdf:type <http://transformunify.org/ontologies/TURBO_0010161> . ?subject <http://transformunify.org/ontologies/TURBO_0010100> ?race_concept_id . ?subject <http://transformunify.org/ontologies/TURBO_0010099> ?ethnicity_concept_id . ?subject <http://transformunify.org/ontologies/TURBO_0010098> ?gender_concept_id . ?subject <http://transformunify.org/ontologies/TURBO_0010170> ?person_id . bind(uuid() as ?person) bind(uuid() as ?sns) bind(uuid() as ?birthdate) # bind(sha1(concat("dataset", ?dataSetTitle, year(now()), month(now()), day(now()))) as ?dataset) bind(uuid() as ?crid) bind(uuid() as ?cridSymb) } } }
Denotes a person whose ancestry is in any of the countries of the central part of the African continent: Burundi, the Central African Republic, Chad, the Democratic Republic of the Congo, and Rwanda.
Denotes a person whose ancestry is in any of the countries of the northern part of the African continent: Algeria, Egypt, Libya, Morocco, Sudan, Tunisia, and Western Sahara.
Denotes a person whose ancestry is in the country of South Africa.
Denotes a person whose ancestry is in any of the Asian countries south of China, east of India, west of New Guinea and north of Australia.
Denotes a person whose ancestry is in any of the Asian countries between the Caspian Sea in the west, China in the east, Afghanistan in the south, and Russia in the north.
Denotes a person whose ancestry is in the country or continent of Australia.
Denotes a person whose ancestry is in the country of New Zealand.
Denotes a person whose ancestry is in the countries of Scandinavia: Denmark, Norway and Sweden. Finland and Iceland are generally included as part of the Scandinavian region.
A collection of ethnic geographical categories including Australian and New Zealander.
The score derived from universally embraced prostate cancer grading system developed by Dr. Donald F. Gleason in 1977. The system provides a reproducible description of the glandular architecture of prostate tissue to which a pathologist assigns a score depending primarily on the microscopic patterns of cancerous glands and cell morphology. The system correlates well with behavior at the extremes: Gleason 1+1 tumors are the most well differentiated, slowly growing and rarely spread; Gleason 4+5 tumors are the most poorly differentiated, often widely metastatic at the time of diagnosis. In the commoner intermediate grade tumors, however, behavior is extremely variable.
A grading system for prostatic carcinoma based on the microscopic glandular architectural patterns of the malignant epithelial cells. Nuclear atypia is not evaluated. It defines five patterns or grades which reflect decreasing differentiation.
Denotes a person whose ancestry is in the countries of the Indian sub-continent, including India, Pakistan, Bangladesh, and Sri Lanka.
Denotes the inhabitants of any of the countries of Europe, a person from there, or their descendants elsewhere.
Denotes a person having origins in any of the countries abutting the Mediterranean Sea, principally those of Europe.
Denotes a person having origins in any of the countries of Western Europe such as Spain, Portugal, or France.
Denotes a person having origins in any of the countries of Eastern Europe such as Czechoslovakia, Poland, Croatia, Hungary, Slovenia, Former Soviet Union, or Finland. It also includes persons who call themselves Gypsies from this region.
Denotes a person having origins in the region of southwest Asia, between the India subcontinent and Europe, including Kuwait, Turkey, Lebanon, Israel, Iraq, Iran, Jordan, Saudi Arabia, lands east of Pakistan or the other countries of the Arabian Peninsula. Also includes people of Jewish ethnicity including Sephardic and Ashkenazic.
A worker role of recruiting human subjects to partcipate in a clinical investigation in which data about human subject is collected.
human subject recuiter role
A questionnaire that comprises a set of questions about patient, such as height, weight, race, biological sex, clinical history, etc., which will be filled by a recruiter based on an Electronic Medical Record (EMR).
data confirm questionnaire
A document editing process in which one or more fields in a form are filled with related information, such as when answering a questionnare.
form filling
A role borne by some material entity which can be delivered/administrated into some organism and the role is realized during a clinical treatment process aiming to treat symptoms, signs or diagnosed disease.
medication role
A material entity that is bearer of a medication role.
medication material
A data item that reports the time of day when a blood specimen was collected.
Person: Chris Stoeckert, Helena Ellis, Jie Zheng
A collecting specimen from organism that results in a blood specimen.
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.
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)
processo planejado
Fact sheet - Regulating the companies The role of the regulator. Ofwat is the economic regulator of the water and sewerage industry in England and Wales. http://www.ofwat.gov.uk/aptrix/ofwat/publish.nsf/Content/roleofregulator_factsheet170805
a regulatory role involved with making and/or enforcing relevant legislation and governmental orders
Person:Jennifer Fostel
OBI
regulator role
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
regulatory role
Regulatory agency, Ethics committee, Approval letter; example: Browse these EPA Regulatory Role subtopics http://www.epa.gov/ebtpages/enviregulatoryrole.html Feb 29, 2008
a role which inheres in material entities and is realized in the processes of making, enforcing or being defined by legislation or orders issued by a governmental body.
GROUP: Role branch
OBI, CDISC
govt agents responsible for creating regulations; proxies for enforcing regulations. CDISC definition: regulatory authorities. Bodies having the power to regulate. NOTE: In the ICH GCP guideline the term includes the authorities that review submitted clinical data and those that conduct inspections. These bodies are sometimes referred to as competent
Jackson Labs is an organization which provide mice as experimental material
a role realized through the process of supplying materials such as animal subjects, reagents or other materials used in an investigation.
Supplier role is a special kind of service, e.g. biobank
PERSON:Jennifer Fostel
material supplier role
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.
investigation
Lung cancer investigation using expression profiling, a stem cell transplant investigation, biobanking is not an investigation, though it may be part of an investigation
a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s).
OBI branch derived
Could add specific objective specification
Following OBI call November 2012,26th: it was decided there was no need for adding "achieves objective of drawing conclusion" as existing relations were providing equivalent ability. this note closes the issue and validates the class definition to be part of the OBI core editor = PRS
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")
Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term.
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.
measuring
scientific observation
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
culture medium
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
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
a hospitalized person; a person with controlled diabetes; the patient's role http://www.fertilityjourney.com/testingAndDiagnosis/theRightDoctor/thePatientsRole/index.asp?C=55245395146924652778
a role which inheres in a person and is realized by the process of being under the care of a physician or health care provider
GROUP:Role Branch
CDISC definition: patient. Person under a physician's care for a particular disease or condition. NOTE: A subject in a clinical trial is not necessarily a patient, but a patient in a clinical trial is a subject. See also subject, trial subject, healthy volunteer. Often used interchangeably
patient role
A cell lysis, production of a cloning vector, creating a buffer.
A planned process which results in physical changes in a specified input material
material transformation
material processing
study subject role
Human subjects in a clinical trial, rats in a toxicogenomics study, tissue cutlures subjected to drug tests, fish observed in an ecotoxicology study. Parasite example: people are infected with a parasite which is then extracted; the particpant under investigation could be the parasite, the people, or a population of which the people are members, depending on the nature of the study. Lake example: a lake could realize this role in an investigation that assays pollution levels in samples of water taken from the lake.
A role that is realized through the execution of a study design in which the bearer of the role participates and in which data about that bearer is collected.
A participant can realize both "specimen role" and "participant under investigation role" at the same time. However "participant under investigation role" is distinct from "specimen role", since a specimen could somehow be involved in an investigation without being the thing that is under investigation.
GROUP: Role Branch
Following OBI call November 2012,26th: 1. it was decided there was no need for moving the children class and making them siblings of study subject role. 2. it also settles the disambiguation about 'study subject'. This is about the individual participating in the investigation/study, Not the 'topic' (as in 'toxicity study') of the investigation/study This note closes the issue and validates the class definition to be part of the OBI core editor = PRS
participant under investigation 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.
specimen role
sequence feature identification objective
Sequence_feature_identification_objective is a biological_feature_identification_objective role describing a study designed to examine or characterize molecular features exhibited at the level of a macromolecular sequence, e.g. nucleic acid, protein, polysaccharide.
Public sector workers in states that run their own OSHA programs are covered by those states. http://www.osha.gov/as/opa/worker/index.html
a personnel role played by a party who executes a component of the study plan; this can occur before, during, after or outside the study timeline
"executes the study plan" includes the suppliers and manufacturers of reagents and other materials used in the study
worker role
filter paper
a device manufacture with the intent to provide a porous unsized paper used for filtering.
Frank Gibson
population
PMID12564891. Environ Sci Technol. 2003 Jan 15;37(2):223-8. Effects of historic PCB exposures on the reproductive success of the Hudson River striped bass population.
a population is a collection of individuals from the same taxonomic class living, counted or sampled at a particular site or in a particular area
1/28/2013, BP, on the call it was raised that we may want to switch to an external ontology for all populatin terms: http://code.google.com/p/popcomm-ontology/
PERSON: Philippe Rocca-Serra
adapted from Oxford English Dictionnary
rem1: collection somehow always involve a selection process
An assay that produces a picture of an entity.
The person perform microarray experiments and submit microarray results (including raw data, processed data) with experiment description to ArrayExpress.
A role borne by an entity and that is realized in a process that is part of an investigation in which an objective is achieved. These processes include, among others: planning, overseeing, funding, reviewing.
Implementing a study means carrying out or performing the study and providing reagents or other materials used in the study and other tasks without which the study would not happen.
Philly2013: Historically, this role would have been borne only by humans or organizations. However, we now also want to enable representing investigations run by robot scientists such as ADAM (King et al, Science, 2009)
Philly2013: Historically, this role would have been borne only by humans or organizations. However, we now also want to enable investigations run by robot scientists such as ADAM (King et al, Science, 2009)
organization
PMID: 16353909.AAPS J. 2005 Sep 22;7(2):E274-80. Review. The joint food and agriculture organization of the United Nations/World Health Organization Expert Committee on Food Additives and its role in the evaluation of the safety of veterinary drug residues in foods.
An entity that can bear roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members.
An organization is a continuant entity which can play roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members.
BP: The definition summarizes long email discussions on the OBI developer, roles, biomaterial and denrie branches. It leaves open if an organization is a material entity or a dependent continuant, as no consensus was reached on that. The current placement as material is therefore temporary, in order to move forward with development. Here is the entire email summary, on which the definition is based: 1) there are organization_member_roles (president, treasurer, branch editor), with individual persons as bearers 2) there are organization_roles (employer, owner, vendor, patent holder) 3) an organization has a charter / rules / bylaws, which specify what roles there are, how they should be realized, and how to modify the charter/rules/bylaws themselves. It is debatable what the organization itself is (some kind of dependent continuant or an aggregate of people). This also determines who/what the bearer of organization_roles' are. My personal favorite is still to define organization as a kind of 'legal entity', but thinking it through leads to all kinds of questions that are clearly outside the scope of OBI. Interestingly enough, it does not seem to matter much where we place organization itself, as long as we can subclass it (University, Corporation, Government Agency, Hospital), instantiate it (Affymetrix, NCBI, NIH, ISO, W3C, University of Oklahoma), and have it play roles. This leads to my proposal: We define organization through the statements 1 - 3 above, but without an 'is a' statement for now. We can leave it in its current place in the is_a hierarchy (material entity) or move it up to 'continuant'. We leave further clarifications to BFO, and close this issue for now.
DNA extraction
A DNA extraction is a nucleic acid extraction where the desired output material is DNA.
plan
The plan of researcher X to perform an experiment according to a protocol.
A plan is a realizable entity that is the inheres in a bearer who is committed to realizing it as a planned process.
This class is included to make clear how the plan specification, the plan, and the planned process relate. OBI will however only subclass and work under the 'plan specification', and 'planned process' class, as we want to avoid to get deep into discussions of 'intend' etc.
AR, BP, JM, MC, PRS
branch derived
protocol
PCR protocol, has objective specification, amplify DNA fragment of interest, and has action specification describes the amounts of experimental reagents used (e..g. buffers, dNTPS, enzyme), and the temperature and cycle time settings for running the PCR.
A plan specification which has sufficient level of detail and quantitative information to communicate it between investigation agents, so that different investigation agents will reliably be able to independently reproduce the process.
OBI branch derived + wikipedia (http://en.wikipedia.org/wiki/Protocol_%28natural_sciences%29)
Injecting a drug into a mouse. Adding IL-2 to a cell culture. Adding NaCl into water.
is a process with the objective to place a material entity bearing the 'material to be added role' into a material bearing the 'target of material addition role'.
Class was renamed from 'administering substance', as this is commonly used only for additions into organisms.
adding a material entity into a target
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.
analyte role
drug added to a buffer contained in a tube; substance injected into an animal;
material to be added role is a protocol participant role realized by a material which is added into a material bearing the target of material addition role in a material addition process
9 March 09 from discussion with PA branch
material to be added role
Concluding that a gene is upregulated in a tissue sample based on the band intensity in a western blot. Concluding that a patient has a infection based on measurement of an elevated body temperature and reported headache. Concluding that there were problems in an investigation because data from PCR and microarray are conflicting. Concluding that 'defects in gene XYZ cause cancer due to improper DNA repair' based on data from experiments in that study that gene XYZ is involved in DNA repair, and the conclusion of a previous study that cancer patients have an increased number of mutations in this gene.
A planned process in which data gathered in an investigation is evaluated in the context of existing knowledge with the objective to generate more general conclusions or to conclude that the data does not allow one to draw general conclusion
drawing a conclusion based on data
The process of a scientist thinking about and deciding what reagents to use as part of a protocol for an experiment. Note that the scientist could be human or a "robot scientist" executing software.
a process of creating or modifying a plan specification
7/18/2011 BP: planning used to itself be a planned process. Barry Smith pointed out that this would lead to an infinite regression, as there would have to be a plan to conduct a planning process, which in itself would be the result of planning etc. Therefore, the restrictions on 'planning' were loosened to allow for informal processes that result in an 'ad hoc plan '. This required changing from 'has_specified_output some plan specifiction' to 'has_participant some plan specification'.
planning
histological sample preparation
histological sample preparation is the preparation of an input tissue via slicing and labeling to make tissue microstructure of interest visible in a future histology assay
contain function
A contain function is a function to constrain a material entities location in space
material separation function
A material separation function is a function that increases the resolution between two or more material entities. The to distinction between the entities is usually based on some associated physical quality.
filter function
A filter function is a function to prevent the flow of certain entities based on a quality or qualities of the entity while allowing entities which have different qualities to pass through
mechanical function
A mechanical function is a function that is realised via mechanical work (through an certain amount of energy transferred by some force).
transfer function
A transfer function is a function to displace a material from one location to another.
measuring glucose concentration in blood serum assay
Measuring glucose concentration in blood from a mouse. See Figure 2 of the 2016 OBI paper, PMID: 27128319.
An assay that determines the concentration of glucose molecules in a blood serum sample
Accuracy of oral liquid measuring devices: comparison of dosing cup and oral dosing syringe.Ann Pharmacother. 2008 Jan;42(1):46-52. Epub 2007 Dec 4. PMID: 18056832
a processed material which is used to introduce or draw fluids from a material entity. A syringe is made of a piston and body. the movement of the piston in the body determines the amount/volume of fluid to inject or draw
syringe
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
extracted material
Multiple Small-Dose Injections Can Reduce the Passage of Sclerosant Foam into Deep Veins During Foam Sclerotherapy for Varicose Veins. Eur J Vasc Endovasc Surg. 2008 Oct 13. PMID: 18922712
injection is process which aims at introducing a compound or a mixture into a material entity (either biological entity or instrument) by relying on devices such as syringe or injector connection, attached or forced into a vascular system (veins of an organism or tubes of a machine) or in a tissue.
injection
An assay with the objective to determine a sequence feature of DNA
creating a mouse infected with LCM virus
is the specification of an objective to add a material into a target material. The adding is asymmetric in the sense that the target material largely retains its identity
adding material objective
The objective to measure the concentration of glucose in a blood sample
an assay objective to determine the presence or concentration of an analyte in the evaluant
analyte measurement objective
Capturing genomic signatures of DNA sequence variation using a standard anonymous microarray platform. Nucleic Acids Res. 2006;34(18):e121. PMID: 17000641
An assay that measures changes (expansion, amplification, deletion, mutation) in the sequence of a DNA molecule.
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)
assay objective
example of usage: In lab test for blood glucose, the test is the assay, the blood bears evaluant_role and glucose bears the analyte role. The evaluant is considered an input to the assay and the information entity that records the measurement of glucose concentration the output
An assay with the objective to capture information about the presence, concentration, or amount of an analyte in an evaluant.
peritoneum of an animal receiving an interperitoneal injection; solution in a tube receiving additional material; location of absorbed material following a dermal application.
target of material addition role is a role realized by an entity into which a material is added in a material addition process
From Branch discussion with BP, AR, MC -- there is a need for the recipient to interact with the administered material. for example, a tooth receiving a filling was not considered to be a target role.
target of material addition role
The patients was weighed and mass was determined to be 47 kilograms
An assay that determines the mass of an evaluant
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.
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.
artifact creation objective
material transformation objective
Manufacturing is a process with the intent to produce a processed material which will have a function for future use. A person or organization (having manufacturer role) is a participant in this process
Manufacturing implies reproducibility and responsibility AR
This includes a single scientist making a processed material for personal use.
manufacturing
is the objective to manufacture a material of a certain function (device)
manufacturing objective
injecting a mouse with PBS solution, weighing it, and recording the weight according to a study design.
a planned process that carries out a study design
removed axiom has_part some (assay or 'data transformation') per discussion on protocol application mailing list to improve reasoner performance. The axiom is still desired.
6/11/9: edited at workshop. Used to be: study design execution is a process with the objective to generate data according to a concretized study design. The execution of a study design is part of an investigation, and minimally consists of an assay or data transformation.
With respect to The Accuri C6 Flow Cytometer System, the organization Accuri bears the role manufacturer role. With respect to a transformed line of tissue culture cells derived by a specific lab, the lab whose personnel isolated the cll line bears the role manufacturer role. With respect to a specific antibody produced by an individual scientist, the scientist who purifies, characterizes and distributes the anitbody bears the role manufacturer role.
Manufacturer role is a role which inheres in a person or organization and which is realized by a manufacturing process.
Illumina (Solexa) sequencing is an example of DNA sequencing
A sequencing assay which determines information on the sequence of a DNA molecule.
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.
Mixing two fluids. Adding salt into water. Injecting a mouse with PBS.
is a material processing with the objective to combine two or more material entities as input into a single material entity as output.
created at workshop as parent class for 'adding material into target', which is asymmetric, while combination encompasses all addition processes.
blood drawn from a human for glucose assay
a material entity derived from a portion of blood collected from an organism
Data representational model is an information content entity of the relationships between data items. A data representational model is encoded in a data format specification such as for cytoscape or biopax.
2009-02-28: work on this term has been finalized during the OBI workshop winter 2009
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.
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/
5/31/2012: This process is not necessarily an acquisition, as specimens may be collected from materials already in posession
a material obtained from an organism in order to be a representative of the whole
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.
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.
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
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.
is an objective to obtain an output material that contains several input materials.
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.
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
An objective specification maintains some or all of the qualities of a material over time.
A planned process in which a person or their legal representative is informed about key facts about potential risks and benefits of a process and makes a documented decision as to whether the person in question will participate.
09/28/2009 Alan Ruttenberg: This is made a subclass of the higher level processual entity in BFO because I don't want to take a stand on whether it is a process aggregate. Analogous to the situation with Material entity.
a quality of a DNA molecule that inheres in its bearer due to the order of its DNA nucleotide residues.
A ruler, a microarray scanner, a Geiger counter.
A device in which a measure function inheres.
a process with that achieves the objective to maintain some or all of the characteristics of an input material over time
A statement in a journal article indicating that the age of a patient at the onset of disease is not known. A statement indicating that the weight of a mouse was not measured.
a information content entity created to indicate that information about something is not available to the person recording it.
This class should probably end up in IAO. It could be further breaken down to indicate different kinds of lack of knowledge, e.g. inability to determine something vs. no attempt made to determine something vs. no informatino available if it was even attempted to determine something. The design pattern should be generalizable. 'unknown sex' is the first example, and needed immediately.
A device with a separation function realized in a planed process
is the injection of a material entity (bearing the administered substance role) into the muscle (bearing the target role) of an organism using a syringe
A measurement datum that is reported on a categorical scale
Jackson Lab provides experimental animals, EBI provides training on databases, a core facility provides access to a DNA sequencer.
is a role which inheres in a person or organization and is realized in in a planned process which provides access to training, materials or execution of protocols for an organization or person
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.
A tissue sample that has been sliced and stained for a histology study.
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.
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.
sequence data
A document with a set of printed or written questions with a choice of answers, devised for the purposes of a survey or statistical study.
JT: It plays a role in collecting data that could be fleshed out more; but I'm thinking it is, in itself, an edited document. JZ: based on textual definition of edited document, it can be defined as N&S. I prefer to leave questionnaire as a document now. We can add more restrictions in the future and use that to determine it is an edited document or not.
Need to clarify if this is a document or a directive information entity (or what their connection is))
PERSON: Jessica Turner
Merriam-Webster
An extract that is the output of an extraction process in which nucleic acid molecules are isolated from a specimen.
The output of an extraction process in which DNA molecules are purified in order to exclude DNA from organellas.
An device that is used to determine the order of nucleotides in nucleic acid sequences.
An device that is used to determine the order of amino acids in protein sequences.
individual organism identifier
a CRID symbol used to distinguish one individual organism from another.
MO_169 Individual
age measurement datum
A time measurement datum that is the result of measurement of age of an organism
note that we are currently defining subtypes of age measurement datum that specify when the age is relative to, e.g. planting, as we don't have adequate temporal predicates yet. life of bearer doesn't imply organism this assay measures time not developmental stage. we recognize that development can take different time periods under different conditions such as media / temperature age as a quality is dubious; we plan to revisit stages in development are currently handled with controlled vocabulary, such as 2-somite stage
PERSON: Alan Ruttenberg, Chris Stoeckert, Jie Zheng
In MageTab file, we use initialTimePoint (a process) + age (a number expected) + TimeUnit (definied in UO, such as year, hour, day, etc.) Now we use the term label indicating the start time point of measuring the age, (number + TimeUnit) are expected instances of the class
discussed on Nov 15, dev call All subtype will be defined by textual definition now.
age since birth measurement datum
An age measurement datum that is the result of the measurement of the age of an organism since birth, the process of emergence and separation of offspring from the mother.
genetic population background information
genotype information 'C57BL/6J Hnf1a+/-' in this case, C57BL/6J is the genetic population background information
a genetic characteristics information which is a part of genotype information that identifies the population of organisms
proposed and discussed on San Diego OBI workshop, March 2011
Group: OBI group
genotype information
Genotype information can be: Mus musculus wild type (in this case the genetic population background information is Mus musculus), C57BL/6J Hnf1a+/- (in this case, C57BL/6J is the genetic population background information and Hnf1a+/- is the allele information
a genetic characteristics information that is about the genetic material of an organism and minimally includes information about the genetic background and can in addition contain information about specific alleles, genetic modifications, etc.
discussed on San Diego OBI workshop, March 2011
allele information
genotype information 'C57BL/6J Hnf1a+/-' in this case, Hnf1a+/- is the allele information
a genetic alteration information that about one of two or more alternative forms of a gene or marker sequence and differing from other alleles at one or more mutational sites based on sequence. Polymorphisms are included in this definition.
Person: Chris Stoeckert, Jie Zheng
genetic alteration information
a genetic characteristics information that is about known changes or the lack thereof from the genetic background, including allele information, duplication, insertion, deletion, etc.
genetic characteristics information
a data item that is about genetic material including polymorphisms, disease alleles, and haplotypes.
MO_66 IndividualGeneticCharacteristics
MO definition: The genotype of the individual organism from which the biomaterial was derived. Individual genetic characteristics include polymorphisms, disease alleles, and haplotypes. examples in ArrayExpress wild_type MutaMouse (CD2F1 mice with lambda-gt10LacZ integration) AlfpCre; SNF5 flox/knockout p53 knock out C57Bl/6 gp130lox/lox MLC2vCRE/+ fer-15; fem-1 df/df pat1-114/pat1-114 ade6-M210/ade6-M216 h+/h+ (cells are diploid)
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).
tissue specimen
The part of a FASTA file that contains the letters ACTGGGAA
A sequence data item that is about the primary structure of DNA
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.
A nucleic acid macromolecule that is part of a cell or virion and is inherited from an immediate ancestor, or incorporated in a manner that it has the disposition to be replicated and inherited by descendants.
MHB 3-22-13: Discussions are ongoing about the label of this class, given consideration of a second class that covers nucleic acid parts of cells or virions that participate in gene expression processes as a template for expression or a direct effector of expression of some other genetic element (e.g. an siRNA), but are not necessarily heritable by progeny or inherited from ancestors. So things like transiently transfected plasmids and siRNAs would qualify as instances of this second class, but not of 'genetic material' as defined here. Also, OBI needs to import a class representing virions for an axiom on genetic material (part_of some (cell or virion).
OBI developer calls, March 4 2013 and March 11 2013
Naturally occurring or experimentally incorporated nucleic acids that meet these criteria can qualify as genetic/genomic material. Qualifying examples include: (1) inherited chromosomal DNA in germ cells, stem cells, fully differentiated cells, or cell line cells, or the DNA/RNA content of a virion; (2) natural replicons exchanged through horizontal gene transfer mechanisms such as bacterial conjugation, which are capable of replication and inheritance by progeny; (3) a chromosomally integrated gene targeting DNA construct transfected into a cell; or (4) a stable extra-chromosomal replicon delivered into cells, such as a plasmid in bacterial host with ori allowing indefinite propagation. Non-qualifying examples include a transiently transfected plasmid or siRNA oligo (as these are not able to be replicated and inherited by progeny cells).
The conclusion that a gene is upregulated in a tissue sample based on the band intensity in a western blot. The conclusion that a patient has a infection based on measurement of an elevated body temperature and reported headache. The conclusion that there were problems in an investigation because data from PCR and microarray are conflicting. The following are NOT conclusions based on data: data themselves; results from pure mathematics, e.g. "13 is prime".
An information content entity that is inferred from data.
In the Philly 2013 workshop, we recognized the limitations of "conclusion textual entity", and we introduced this as more general. The need for the 'textual entity' term going forward is up for future debate.
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.
cell freezing medium
A value specification that specifies the mass of some thing.
A value specification that is specifies one category out of a fixed number of nominal categories
A value specification that consists of two parts: a numeral and a unit label
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.
DNA was extracted from the Ficoll pellet of blood taken from congenital asplenia patients. Unamplified, high-molecular weight, RNase-treated genomic DNA (4_6 _g) was used for whole exome sequencing (WES) with the use of Agilent 71 Mb (V4 + UTR) singlesample capture and an Illumina HiSeq 2000. Sequencing was carried out so as to obtain 30_ coverage from 2 _ 100-bp paired-end reads. We used the Annovar tool (25) to annotate the resulting highquality (HQ) variants. In the regions targeted by WES capture (81.5% of the consensus coding genome), the mean numbers of single-nucleotide variants (SNVs) and small insertions/deletions (indels) detected per sample were 84,192 and13,325, respectively. After filtering, a mean of 74,398 (95.3%) high-quality (HQ) SNVs and 9,033 (70.6%) HQ indels were called. A mean of 105 coding HQ SNVs and 32 indels was identified.
A DNA sequencing assay that intends to provide information about the sequence of the protein coding components of a genome (exons).
A value specification that specifies the volume of some thing.
volume value specification
An assay to determine the volume of an evaluant.
cannot be assessed", "not applicable", "unknown
An information content entity that provides an explanation why a data item is not provided.
histologic grade according to AJCC 7th edition
A categorical value specification that is a histologic grade assigned to a tumor slide specimen according to the American Joint Committee on Cancer (AJCC) 7th Edition grading system.
histologic grade according to the Fuhrman Nuclear Grading System
A categorical value specification that is a histologic grade assigned to a tumor slide specimen according to the Fuhrman Nuclear Grading System.
Histologic Grade (Fuhrman Nuclear Grading System)
A categorical value specification that is a histologic grade assigned to a ovarian tumor.
histologic grade for ovarian tumor according to a two-tier grading system
A histologic grade for ovarian tumor that is from a two-tier histological classification of tumors.
histologic grade for ovarian tumor according to the World Health Organization
A histologic grade for ovarian tumor that is from a histological classification by the World Health Organization (WHO).
pathologic primary tumor stage for colon and rectum according to AJCC 7th edition
A categorical value specification that is a pathologic finding about one or more characteristics of colorectal cancer following the rules of the TNM American Joint Committee on Cancer (AJCC) version 7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery.
pT: Pathologic spread colorectal primary tumor (AJCC 7th Edition)
pathologic primary tumor stage for lung according to AJCC 7th edition
A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM American Joint Committee on Cancer (AJCC) version 7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery.
pT: Pathologic spread lung primary tumor (AJCC 7th Edition)
pathologic primary tumor stage for kidney according to AJCC 7th edition
A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery.
pT: Pathologic spread kidney primary tumor (AJCC 7th Edition)
pathologic primary tumor stage for ovary according to AJCC 7th edition
A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery.
pT: Pathologic spread ovarian primary tumor (AJCC 7th Edition)
pathologic lymph node stage for colon and rectum according to AJCC 7th edition
A categorical value specification that is a pathologic finding about one or more characteristics of colorectal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes.
pN: Pathologic spread colon lymph nodes (AJCC 7th Edition)
pathologic lymph node stage for lung according to AJCC 7th edition
A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes.
pathologic lymph node stage for kidney according to AJCC 7th edition
A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes.
pN: Pathologic spread kidney lymph nodes (AJCC 7th Edition)
pathologic lymph node stage for ovary according to AJCC 7th edition
A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes.
pN: Pathologic spread ovarian lymph nodes (AJCC 7th Edition)
pathologic distant metastases stage for colon according to AJCC 7th edition
A categorical value specification that is a pathologic finding about one or more characteristics of colon cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery.
M: colon distant metastases (AJCC 7th Edition)
pathologic distant metastases stage for lung according to AJCC 7th edition
A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery.
M: lung distant metastases (AJCC 7th Edition)
pathologic distant metastases stage for kidney according to AJCC 7th edition
A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery.
M: kidney distant Metastases (AJCC 7th Edition)
pathologic distant metastases stage for ovary according to AJCC 7th edition
A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery.
M: ovarian distant metastases (AJCC 7th Edition)
clinical tumor stage group according to AJCC 7th edition
A categorical value specification that is an assessment of the stage of a cancer according to the American Joint Committee on Cancer (AJCC) v7 staging systems.
Clinical tumor stage group (AJCC 7th Edition)
International Federation of Gynecology and Obstetrics cervical cancer stage value specification
A categorical value specification that is an assessment of the stage of a gynecologic cancer according to the International Federation of Gynecology and Obstetrics (FIGO) staging systems.
International Federation of Gynecology and Obstetrics ovarian cancer stage value specification
A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the FIGO classification system.
Pathologic Tumor Stage Grouping for ovarian cancer (FIGO)
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.
A specimen that is derived from prostate gland.
blood serum specimen
PMID: 18229666.Adv Med Sci. 2007;52 Suppl 1:204-6.Antioxidant activity of blood serum and saliva in patients with periodontal disease treated due to epilepsy.
A material entity which derives from blood and corresponds to blood plasma without fibrinogen or the other clotting factors.
PERSON: Maura Gasparetto
WEB: http://en.wikipedia.org/wiki/Blood_plasma
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.
Stub class to serve as root of hierarchy for imports from NCBI Taxonomy.
WEB: http://en.wikipedia.org/wiki/Organism
organismo
specimen
Biobanking of blood taken and stored in a freezer for potential future investigations stores specimen.
A material entity that has the specimen role.
GROUP: OBI Biomaterial Branch
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.
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.
organ section
A liver slice used in a perfusion experiment. Thyroidectomy during laryngectomy for advanced laryngeal carcinoma--whole organ section study with long-term functional evaluation. Clin Otolaryngol Allied Sci. 1995 Apr;20(2):145-9. PMID: 7634521
A processed material which derives from an organ and results from a process of dissection or histological sample preparation a portion(formerly an organ section is portion of an organ removed from the context of the organ)
PERSON: Helen Parkinson
GROUP: CEBS
data transformation
The application of a clustering protocol to microarray data or the application of a statistical testing method on a primary data set to determine a p-value.
A planned process that produces output data from input data.
Elisabetta Manduchi
Helen Parkinson
James Malone
Melanie Courtot
Richard Scheuermann
Ryan Brinkman
Tina Hernandez-Boussard
data analysis
data processing
Branch editors
differential expression analysis objective
Analyses implemented by the SAM (http://www-stat.stanford.edu/~tibs/SAM), PaGE (www.cbil.upenn.edu/PaGE) or GSEA (www.broad.mit.edu/gsea/) algorithms and software
A differential expression analysis objective is a data transformation objective whose input consists of expression levels of entities (such as transcripts or proteins), or of sets of such expression levels, under two or more conditions and whose output reflects which of these are likely to have different expression across such conditions.
PERSON: Elisabetta Manduchi
data transformation objective
normalize objective
An objective specification to transformation input data into output data
Modified definition in 2013 Philly OBI workshop
PERSON: James Malone
The OBI manuscript is (much) edited imformation
A document which is the output of a document editing process
edited document
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.
extraction
PMID: 18524968.Filtration of CSF improves isolation of Mycobacteria.J Clin Microbiol. 2008 Jun 4.
filtration is a process which separates components suspended in a fluid based on granularity properties relying on a filter device
OBI-Branch: adapted from wikipedia and wordnet
filtration
PMID: 18428461.Purification of oligodendrocytes and their progenitors using immunomagnetic separation and Percoll gradient centrifugation. Curr Protoc Neurosci. 2001 May;Chapter 3:Unit 3.12.
centrifugation is a process separating molecules by size or density using centrifugal forces generated by a spinning rotor. G-forces of several hundred thousand times gravity are generated in ultracentrifugation
adapted from http://www.fao.org/DOCREP/003/X3910E/X3910E06.htm
centrifugation
PMID: 18540298. Role of modified bleach method in staining of acid-fast bacilli in lymph node aspirates. Acta Cytol. 2008 May-Jun;52(3):325-8.
Staining is a process which results in the addition a class-specific (DNA, proteins, lipids, carbohydrates) dye to a substrate to qualify or quantify the presence of a specific compound.
adapted from Wikipedia: http://en.wikipedia.org/wiki/Staining
staining
PMID: 18550121.Total Prostate Specific Antigen Stability Confirmed After Long-Term Storage of Serum at -80C. J Urol. 2008 Jun 10.
A maintenance process by which material entities that are not actively metabolizing are placed in well identified location and possibly under controlled environment in ad-hoc devices/structures in order to preserve and protect them from decay/alteration and maintain availability
storage
Wax DB, Beilin Y, Hossain S, Lin HM, Reich DL. Manual editing of automatically recorded data in an anesthesia information management system. Anesthesiology. 2008 Nov;109(5):811-5. PMID: 18946292
is a planned process with specified input original document and specified output edited document
document editing
PMID: 16901087. Supporting the curation of biological databases with reusable text mining.Genome Inform. 2005;16(2):32-44.
Digital curation is the process of establishing and developing long term repositories of digital assets for current and future reference by researchers, scientists, and historians, and scholars generally.
digital curation
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
centrifuge
A device with a rapidly rotating container that applies centrifugal force to its contents
microtome
PMID: 9974145.Serial sectioning of thick tissue with a novel vibrating blade microtome. Brain Res Brain Res Protoc. 1999 Jan;3(3):302-7.
A microtome is a mechanical instrument used to cut biological specimens into very thin segments for further treatment (e.g. ISH) and ultimately microscopic or histologic examination. Most microtomes provide cooling facilities (cryo-microtome) and use a steel blade to cut a slice of defined thickness. Some are automatic, and some are driven by hand.
study design
a matched pairs study design describes criteria by which subjects are identified as pairs which then undergo the same protocols, and the data generated is analyzed by comparing the differences between the paired subjects, which constitute the results of the executed study design.
A plan specification comprised of protocols (which may specify how and what kinds of data will be gathered) that are executed as part of an investigation and is realized during a study design execution.
Editor note: there is at least an implicit restriction on the kind of data transformations that can be done based on the measured data available.
experimental design
rediscussed at length (MC/JF/BP). 12/9/08). The definition was clarified to differentiate it from protocol.
An assay that determines the grade (severity/stage) of a tumor sample, used in cancer biology to describe abnormalities/qualities of tumor cells or tissues. Values can be described by terms from NCI Thesaurus.
Compiled by Helen Parkinson for Transcriptomics thanks to Adam Witney
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
IEDB
administering substance in vivo
Balb/c mice received an intracameral or subconjunctival injection of trinitrophenylated spleen cells
injecting mice with 10 ug morphine intranasally, a patient taking two pills of 1 mg aspirin orally
A process by which a substance is intentionally given to an organism resulting in exposure of the organism to that substance.
2009-11-10. Tracker: https://sourceforge.net/tracker/?func=detail&aid=2893050&group_id=177891&atid=886178
Different routes and means of administration should go as children underneath this
Update the definition based on the discussion. Details see the tracker: https://sourceforge.net/p/obi/obi-terms/738/
needs roles such as perturber and perturbee (children of input role). Perturb is too strong. Host might be the name for one role. Others considered: Doner, Donated, Acceptor.
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
the counting of the number of cells with fluorescent label at their surface to determine the percentage of the population which was activated
An assay that uses visual examination of cells or tissue (or images of them) to make an assessment regarding a quality of the cells or tissue. This assay can include steps of staining, imaging, and judgement.
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
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).
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.
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
dialysis
the use of a dialysis bag of select pore size to remove salt from collagen isolated from mouse cartilage
a protocol application that uses diffusion through a semi-permeable membrane to separate an input material into two fractions of different composition
PERSON:Kevin Clancy
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
requested by Helen Parkinson for MO. Could be defined class
A role which inheres in an organism or part thereof from which any part including cell, organ or tissue is removed with the intention that the donated part will be placed into another organism and/or cultured in vitro.
Definition modified by HP to deal with the case where an organ may be removed for donation but is not transplanted as intended.
donor
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.
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.
WEB: http://www.ncbi.nlm.nih.gov/books/NBK21640/
In addition to the coding regions (exons), a gene includes transcription-control regions and sometimes introns. Although the majority of genes encode proteins, some encode tRNAs, rRNAs, and other types of RNA.
gene
a disposition that a gene can be used as a blueprint for generating a new form of product such as protein.
WEB: http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/objects/entrezgene/entrezgene.asn
YH: According to NCBI Gene project, there are two gene types: unknown (0) , tRNA (1) , rRNA (2) , snRNA (3) , scRNA (4) , snoRNA (5) , protein-coding (6) , pseudo (7) , transposon (8) , miscRNA (9) , ncRNA (10) , other (255). Therefore, we have generated corresponding gene dispositions. Note that we don't use the term "gene type" here to differentiate the meanings of "type" and "disposition".
gene disposition
a gene disposition that a gene can be used as a blueprint for generating a protein (i.e., a gene encodes for a protein).
protein-coding gene disposition
The genome of an organism of Homo sapiens
A gene of Homo sapiens that has a protein-coding gene disposition
Other designations: APO-1 cell surface antigen|CD95 antigen|Delta Fas/APO-1/CD95|FAS 827dupA|FAS receptor variant 9|FASLG receptor|Fas (TNF receptor superfamily, member 6)|Fas AMA|TNF receptor superfamily member 6|apoptosis antigen 1|apoptosis-mediating surface antigen FAS|tumor necrosis factor receptor superfamily member 6|tumor necrosis factor receptor superfamily, member 6
protein tyrosine phosphatase, receptor type, C
Other designations: CD45 antigen|T200 glycoprotein|T200 leukocyte common antigen|protein tyrosine phosphatase, receptor type, c polypeptide|receptor-type tyrosine-protein phosphatase C
A (combination of) quality(ies) of an organism determined by the interaction of its genetic make-up and environment that differentiates specific instances of a species from other instances of the same species.
A quality of a patient, a material entity that is part of a patient, or a processual entity that a patient participates in, any one of which is observed in a physical examination and is deemed by the clinician to be of clinical significance.
sinal
A physical sign in which a non-zero value is standardly considered to be an indication that the organism is alive.
SSVV
sinal vital
A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism.
A material entity which is clinically abnormal and part of an extended organism. Disorders are the physical basis of disease.
A sequence of acts of observing and measuring qualities of a patient performed by a clinician; measurements may occur with and without elicitation.
A bodily process that is clinically abnormal.
The totality of all processes through which a given disease instance is realized.
replace 'OBI:occurrence of disease', need to add logical definition The axioms of OBI occurence of disease: Equivalent classes: realizes some disease Superclasses: 'has part' some 'pathologic process' 'has participant' some (organism and ('has role' some 'host of immune response role')) biological_process realizes some 'host of immune response role'
The representation of a conclusion of a diagnostic process.
An anatomical structure (FMA) is pathological whenever (1) it has come into being as a result of changes in some pre-existing canonical anatomical structure, (2) through processes other than the expression of the normal complement of genes of an organism of the given type, and (3) is predisposed to have health-related consequences for the organism in question manifested by symptoms and signs.
A planned process whose completion is hypothesized by a health care provider to eliminate, prevent, or alleviate the signs and symptoms of a disorder or pathological process
A planned process with the objective to improve the health status of a patient that directly involves the treatment, diagnosis, or prevention of disease or injury of a patient
A social process that has at least one human participant and that includes as parts the treatment, diagnosis, or prevention of disease or injury--or the following of instructions of another human for treatment, diagnosis, or prevention--of a participant in the process
health care process
A temporally-connected health care process that has as participants an organization or person realizing the health care provider role and a person realizing the patient role. The health care provider role and patient are realized during the health care encounter
atendimento médico
PREFIX obo: <http://purl.obolibrary.org/obo/> PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX sm: <tag:stardog:api:mapping:> PREFIX turbo: <http://transformunify.org/ontologies/> PREFIX xsd: <http://www.w3.org/2001/XMLSchema#> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> #delete { # ?hce1 a obo:OGMS_0000097 ; # turbo:TURBO_0010385 ?linkingPk ; # turbo:TURBO_0010386 ?patientPk ; # turbo:TURBO_0010388 ?omopVisitConcept1 . # ?hce2 a obo:OGMS_0000097 ; # turbo:TURBO_0010387 ?linkingPk ; # turbo:TURBO_0010388 ?omopVisitConcept2 . #} insert { graph turbo:encounterTypesLinksParticipation { ?role a obo:OBI_0000093 ; obo:RO_0000052 ?person . ?hce1 a ?encType1 ; obo:BFO_0000055 ?role . ?hce2 a ?encType2 ; obo:BFO_0000055 ?role ; obo:RO_0002090 ?hce1 . } } where { graph turbo:expanedUnlinkedEncounters { ?hce1 a obo:OGMS_0000097 ; turbo:TURBO_0010385 ?linkingPk ; turbo:TURBO_0010386 ?patientPk ; turbo:TURBO_0010388 ?omopVisitConcept1 . ?hce2 a obo:OGMS_0000097 ; turbo:TURBO_0010387 ?linkingPk ; turbo:TURBO_0010388 ?omopVisitConcept2 . } graph turbo:expanedUnlinkedPeople { ?person a obo:NCBITaxon_9606 ; turbo:TURBO_0010393 ?patientPk . } graph <https://raw.githubusercontent.com/PennTURBO/Turbo-Ontology/master/ontologies/turbo_merged.owl> { ?encType1 rdfs:subClassOf obo:OGMS_0000097 ; turbo:TURBO_0010147 ?omopVisitConcept1 . ?encType2 rdfs:subClassOf obo:OGMS_0000097 ; turbo:TURBO_0010147 ?omopVisitConcept2 . } bind(uri(concat("http://transformunify.org/ontologies/", sha1(concat(str(?person), "patient role", year(now()), month(now()), day(now()))))) as ?role) }
PREFIX obo: <http://purl.obolibrary.org/obo/> PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX sm: <tag:stardog:api:mapping:> PREFIX turbo: <http://transformunify.org/ontologies/> PREFIX xsd: <http://www.w3.org/2001/XMLSchema#> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> insert { graph turbo:expanedUnlinkedEncounters { ?hce a obo:OGMS_0000097 ; turbo:TURBO_0010385 ?prevPk ; turbo:TURBO_0010387 ?encounterPk ; turbo:TURBO_0010386 ?patientPk ; turbo:TURBO_0010388 ?omopVisitConcept . ?hceStart a obo:BFO_0000035 ; obo:RO_0002223 ?hce . ?hceStartDate a obo:IAO_0000416 ; obo:IAO_0000136 ?hceStart ; obo:IAO_0000004 ?encStartDateVal ; obo:BFO_0000050 turbo:expanedUnlinkedEncounters . turbo:expanedUnlinkedEncounters a obo:IAO_0000100 ; <http://purl.org/dc/elements/1.1/title> ?dataSetTitle . ?crid a obo:IAO_0000578 ; obo:IAO_0000219 ?hce . ?cridSymb a obo:IAO_0000577 ; obo:BFO_0000050 ?crid ; turbo:TURBO_0010094 ?syntheaVisitId ; obo:BFO_0000050 turbo:expanedUnlinkedEncounters . ?encRegDen obo:BFO_0000050 ?crid . } } where { service <http://localhost:5820/forvg/query> { graph <virtual://synthea_omop_rds> { ?subject turbo:TURBO_0000643 ?dataSetTitle . ?subject turbo:TURBO_0000645 ?encStartDateVal . ?subject turbo:TURBO_0010270 ?encRegDen . ?subject turbo:TURBO_0000648 ?syntheaVisitId . ?subject rdf:type turbo:TURBO_0010158 . ?subject turbo:TURBO_0010174 ?prevPk . ?subject turbo:TURBO_0010380 ?patientPk . ?subject turbo:TURBO_0010381 ?encounterPk . ?subject turbo:TURBO_0010382 ?omopVisitConcept . bind(uuid() as ?hce) bind(uuid() as ?hceStart) bind(uuid() as ?hceStartDate) # bind(sha1(concat("dataset", ?dataSetTitle, year(now()), month(now()), day(now()))) as ?dataset) bind(uuid() as ?crid) bind(uuid() as ?cridSymb) } } }
PREFIX obo: <http://purl.obolibrary.org/obo/> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> delete { ?hce a obo:OGMS_0000097 ; ?p ?o . } where { ?hce a obo:OGMS_0000097 ; ?p ?o . ?p rdfs:subPropertyOf <http://transformunify.org/ontologies/TURBO_0010384> }
consulta médica
health care encounter
TODO
A health care process that involves the interpretation of a clinical picture from a given patient (input) and the assertion to the effect that the patient has a disease, disorder, or syndrome of a certain type, or none of these (output).
A health care process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies.
A treatment whose completion is hypothesized by a health care provider to prevent the signs and symptoms of a disorder or pathological process.
prophylactic treatment
A biobank is a collections of samples of biological substances (e.g. tissue, blood, DNA) which are linked to data about the samples and their donors. They have a dual nature as collections of samples and data.
definition derived from the definition of 'human biobank', based on http://www.ethikrat.org/files/der_opinion_human-biobanks.pdf
biobank
An identifier in natural language referring to a biobank.
Name of biobank
biobank proper name
An organization bearing legal personality that ownes or adminstrates a biobank.
biobank juristic person
biobank organization
A planned process that involves a human being and is intended to initiate a communication with another human being.
Contacting is the process of one human being starting a communication process with another human being. Contacting can be done using all modes of communication used by humans.
contacting
A role borne by a human being that is part of an group of individuals and acts as contact person for the group. This role gets realized by the bearer being a participant in a contacting process.
contact role
A human being that is member of a biobank organization and bears the organization contact role.
biobank contact person
A textual entity describing a study aim or a sample collection.
Sample collection or study description
sample collection or study aim description
A contact role borne by a member of a biobank organization and realized by serving as the contact for one of its biobanks.
A contact role borne by a member of a sample collection or study organization and realized by serving as the contact for the collection or the study.
biobank contact role
A diagnosis that is the main reason for the inducement of medical care.
Alice Nzinga
main diagnosis
Hint: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
primary diagnosis
A document that contains information representing health-relevant qualities of a patient written in a chronological manner and that is primarily used for patient care in a clinical setting.
prontuário do paciente, registro do paciente, registro médico
It is a chronological written account of examination, treatment, medical history or complaints.
It is used interchangeably with health record and medical chart. https://en.wikipedia.org/wiki/Medical_record
medical record
prontuário médico
A proper name that identifies a specimen and is usually in form of a label included in the specimen cassette.
specimen ID
sample donor
A Homo sapiens who contributes specimen.
specimen donor
A role in human social processes that is realized by health care processes such as seeking or providing treatment for disease and injury, diagnosing disease and injury, or undergoing diagnosis.
William R. Hogan
health care role
human health care role
A role borne by an organism and that is realized by presenting to a health care provider in a clinical encounter.
CAFE domain expert working group.
In order to avoid the presumption of the formal structures and institutions of Western civilization, bearing a patient role does not entail that the organism presents at an official place of business, with an organization formally and legally registered with various gov't entities, with a person endowed by the gov't with certain certifications.
papel de paciente
A human health care role inhering in an organization or human being that is realized by a process of providing health care services to an organism.
health care provider role
An object aggregate of organisms.
Any arbitrary collection of organisms. They need not be of the same taxonomic class.
collection of organisms
An object aggregate all of whose components are human beings.
collection of humans
A role inhering in an entity realized by social interactions in human society.
Previous definition: A role played by an entity in human social processes.
role in human social processes
A patient role that inheres in a human being.
human patient role
papel de paciente humano
An object aggregate that is not itself an organization and whose members are only organizations that have some feature in common
William R. Hogan Amanda Hicks
It is often convenient to group organizations together that otherwise might not even interact with one another.
aggregate of organizations
A role borne by a human individual or by a collection of humans regarded as possessing rights and duties enforeable at law.
Malcolm N. Shaw: International Law. Cambridge University Press, Cambridge, 2008.
We are aware of the fact that Wikipedia's definition differs from ours by saying that "Legal personality (...) is the characteristic of a non-living entity regarded by law to have the status of personhood" (http://en.wikipedia.org/wiki/Legal_personality) However, Shaw explicates: "In any legal system, certain entities, whether they be individuals or companies, will be regarded as possessing rights and duties enforceable at law. Thus an individual may prosecute or be prosecuted for assault and a company can sue for breach of contract. They are able to do this because the law recognises them as 'legal persons' possessing the capacity to have and to maintain certain rights, and being subject to perform specific duties. (...) In municipal law individuals, limited companies and public corporations are recognized as each possessing a distinct legal personality, the terms of which are circumscribed by the relevant legislation" (Shaw MN: International Law. Sixth Edition. Cambridge University Press, Cambridge, 2008). We hold that Shaw's position is ontological more prolific since it not only allows to explain how groups of individuals become recognized as unities at law, but also how different individuals can hold different legal personality roles (always against the context of one legal system). The latter will proof useful when dealing with the representing comatous patients or minorsat law in ontologies.
legal person role
An ethnic identity datum that is the output of an ethnic identification process that uses OMB terminology for ethnicity or terminology that is mapped the OMB ethnicity terms.
OMB ethnic identity datum
A racial identity is an information content entity that is the output of some racial identitification process and is intended to be a truthful statement about the genetic or cultural race of a person. Unlike data items they are not necessilary contributed or acquired by a reliable method.
racial identity datum
racial identification process
An ethnic identity datum is an information content entity that is the output of some ethnic identitification process and is intended to be a truthful statement about the cultural or national heritage of a person. Unlike data items they are not necessilary contributed or acquired by a reliable method.
ethnic identity datum
ethnic identification process
An OMB ethnic identity datum that indicates the person identified is of Cuban, Mexican, Puerto Rican, South or Central American, or other Spanish culture or origin regardless of race.
hispanic or latino identity datum
An OMB ethnic identity datum that indicates the person identified is not of Cuban, Mexican, Puerto Rican, South or Central American, or other Spanish culture or origin regardless of race.
not hispanic or latino identity datum
An identity datum is an information content entity that is the output of some identitification process and is intended to be a truthful statement about a person's social identity. Unlike data items they are not necessilary contributed or acquired by a reliable method.
identity datum
A gender identity is an information content entity that is the output of some gender identitification process and is intended to be a truthful statement about a person's subjective sense of their gender. Unlike data items they are not necessilary contributed or acquired by a reliable method.
gender identity datum
identification process
gender identification process
a gender identity datum resulting from a gender identification process in which ‘female’ is selected based on the participant's subjective sense of gender
female gender identity datum
a gender identity datum resulting from a gender identification process in which ‘male’ is selected based on the participant's subjective sense of gender
male gender identity datum
A racial identity that is the output of a racial identification process that uses OMB terminology for race or terminology that is mapped the OMB race terms and that indicates that the subject of the identity has origins in any of the original peoples of North and South America (including Central America), and maintains tribal affiliation or community attachment.
American Indian or Alaska Native identity datum
A racial identity that is the output of a racial identification process that uses OMB terminology for race or terminology that is mapped the OMB race terms and that indicates that the subject of the identity has origins in any of the original peoples of the Far East, Southeast Asia, or the Indian subcontinent.
Asian identity datum
A racial identity that is the output of a racial identification process that uses OMB terminology for race or terminology that is mapped the OMB race terms and that indicates that the subject of the identity has origins in any of the black racial groups of Africa.
black or African American identity datum
A racial identity that is the output of a racial identification process that uses OMB terminology for race or terminology that is mapped the OMB race terms and that indicates that the subject of the identity has origins in any of the original peoples of Hawaii, Guam, Samoa, or other Pacific Islands.
Native Hawaiian or other Pacific Islander identity datum
A racial identity that is the output of a racial identification process that uses OMB terminology for race or terminology that is mapped the OMB race terms and that indicates that the subject of the identity has origins in any of the original peoples of Europe, the Middle East, or North Africa.
white identity datum
A racial identity that is the output of a racial identification process that uses OMB terminology for race or terminology that is mapped the OMB race terms.
OMB racial identity datum
A time quality inhering in a bearer by virtue of how long the bearer has existed.
An organismal quality inhering in a bearer by virtue of the bearer's ability to undergo sexual reproduction in order to differentiate the individuals or types involved.
biological sex
A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure.
morphology
TODO: define this or obsolete it and move children somewhere else.
qualitative
A quality inhering in a bearer by virtue of the whether the bearer differs from normal or average.
deviation(from_normal)
A morphology quality inhering in a bearer by virtue of the bearer's physical magnitude.
size
A 1-D extent quality inhering in a bearer by virtue of the bearer's vertical dimension of extension.
altura
height
A 1-D extent quality which is equal to the distance between two points.
A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter.
A physical quality inhering in a bearer that has mass near a gravitational body.
peso
weight
A quality in which events occur in sequence.
A biological sex quality inhering in an individual or a population that only produces gametes that can be fertilised by male gametes.
A biological sex quality inhering in an individual or a population whose sex organs contain only male gametes.
A quality inhering in a bearer by virtue of the bearer's deviation from normal or average.
abnormal
A 3-D extent quality inhering in a bearer by virtue of the bearer's amount of 3-dimensional space it occupies.
A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities.
physical quality
A physical quality that inheres in a bearer by virtue of the bearer's amount of force per unit area it exerts.
pressure
pressão
A quality which inheres in a continuant.
multiply inhering quality of a physical entity
Relational qualities are qualities that hold between multiple entities. Normal (monadic) qualities such as the shape of a eyeball exist purely as a quality of that eyeball. A relational quality such as sensitivity to light is a quality of that eyeball (and connecting nervous system) as it relates to incoming light waves/particles.
physical object quality
A size quality inhering in an bearer by virtue of the bearer's extension in one dimension.
1-D extent
A size quality inhering in an bearer by virtue of the bearer's extension in three dimensions.
An organismal quality inhering in a bearer by virtue of the bearer's physical expression of sexual characteristics.
A quality that inheres in an entire organism or part of an organism.
organismal quality
A biological sex quality inhering in an individual based upon genotypic composition of sex chromosomes.
Note that the chromosomal constitution of genotypic sex varies in different organisms. In human, we have XY, XX, though abnormal XXY, X0, XYY, and other combinations are possible.
genotypic sex
genótipo do sexo
"For patient: Mr Smith, should exercise for at least 30 minutes, 3 times weekly. signed Dr. Ronnie Shuz. Date: 15/11/01"
A document authored by a health care provider that specifies how to realize some health care process for a particular patient.
Un document créé par un fournisseur de soin indiquant comment réaliser une partie d'un processus de santé pour un patient particulier.
health care prescription
prescription de santé
An author identification where the author is a particular health care provider and the document authored is a prescription.
Une identification d'auteur où l'auteur est un fournisseur de soins particulier et le document en question est une prescription.
identification de prescripteur
prescriber identification
A written name denoting a particular patient.
Un nom écrit faisant référence à un patient particulier.
identification d'un patient
patient identification
A textual entity that denotes the time of document creation.
Une entité textuelle indiquant l'instant de création d'un document.
the granular time at which the author considers the document whole, ie ready for interpretation
document creation time identification
identification de l'instant de création d'un document
"Prescription for John Smith : Ativan 2mg tablets, take 1 tablet twice daily by mouth as needed if anxious, dispense 60 tablets, renew 12 times. Signed by Dr Hazard. Date: 15/10/29"
A health care prescription specifying the initiation, modification or cessation of a drug administration.
Une ordonnance indiquant une initiation, modification ou arrêt de l'administration de médicaments.
There are prescription "order names" like "wheelchair" in PDS and upstream sources that clearly do not denote a drug. So it may be more appropriator for Drivetrain to instantiate PDRO_0000001, 'health care prescription'
drug prescription
prescription de médicaments
'Aspirin 81 mg tablet PO DIE 12 x 30 tablets (stroke prevention)' 'Cease metoprolol and aspirin' 'Aspirin 81 mg PO DIE 12 x 30 tablets' on a first prescription for Mr. Fiennes on 2018/01/01. 'Aspirin 81 mg per mouth once a day, 6x2 months' on a second prescription for Mr. Fiennes on 2019/01/01. 'Aspirin 325 mg PO die, 12x1 months' on a third prescription for Mr. Fiennes on 2019/03/01. 'Cease Aspirin' on a fourth prescription for Mr. Fiennes on 2019/04/01.
A directive information entity that is a part of a drug prescription and specifies some action(s) related to one or several drugs. It is intended to direct some actions to be performed by a patient and some pharmacist(s). It may also specify a healthcare objective.
drug prescription item
An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA, and any derivatives thereof.
An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA.
The definition above excludes protein complexes, which some also consider a protein. Those who wish to refer to a class representing both senses of the word are directed to CHEBI:36080. Proteins (in the sense defined here) that descended from a common ancestor can be classified into families and superfamilies composed of products of evolutionarily-related genes. The domain architecture of a protein is described by the order of its constituent domains. Proteins with the same domains in the same order are defined as homeomorphic [PRO:WCB].
A protein that is a translation product of the human PTPRC gene or a 1:1 ortholog thereof. It is composed of an extracellular domain, a single transmembrane segment and two tandem intracytoplasmic protein-tyrosine phosphatase domains. Contains 1 to 3 copies of the Fibronectin type III domain (Pfam:PF00041) followed by two copies of the Protein-tyrosine phosphatase (Pfam:PF00102) domain. Receptor-type tyrosine-protein phosphatase C (CD45) regulates signal transduction and lymphocyte activation by specific association with receptor molecules on T and B cells. Multiple isoforms of CD45 (180-235 kDa) can be generated asa result of alternative splicing of three variable exons 4(A), 5(B) and 6(C), encoding sequences at the N-terminal extracellular domain of the molecule.
receptor-type tyrosine-protein phosphatase C
A protein that is a translation product of the human FAS gene or a 1:1 ortholog thereof.
tumor necrosis factor receptor superfamily member 6
An organic amino compound that consists of amino acid residues (unmodified amino-acid residues and/or modified amino-acid residues) linked by peptide bonds or derivatives of such bonds.
A material entity consisting of multiple components that are causally integrated.
May be replaced by a BFO class, as discussed in http://www.jbiomedsem.com/content/4/1/43
A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids.
primary structure of sequence macromolecule
Any extent of continuous biological sequence.
A sequence feature is an extent of 'located' biological sequence, whose identity is determined by both its inherent sequence (ordering of monomeric units) and its position (start and end coordinates based on alignment with some reference). By contrast, 'biological sequences' are identified and distinguished only by their inehrent sequence, and not their position. Accordingly, the 'ATG' start codon in the coding DNA sequence of the human AKT gene is the same 'sequence' as the 'ATG' start codon in the human SHH gene, but these represent two distinct 'sequence features' in virtue of their different positions in the genome.
A collection of sequence features (typically a collection of chromosomes) that covers the sum genetic material within a cell or virion (where 'genetic material' refers to any nucleic acid that is part of a cell or virion and has been inherited from an ancestor cell or virion, and/or can be replicated and inherited by its progeny)
Genotype vs Genome in GENO: An (genomic) genotype is an information artifact representing a shorthand syntax for specifying what is known about variation in a genome sequence. This syntax has reference and variant components - a 'reference genome' and 'genomic variation complement' - that must be operated on to resolve a final genome sequence (i.e. substituting all sequences specified by the 'genomic variation complement' for the corresponding sequences in the 'reference genome'). So, while the total sequence content represented in a genotype may be greater than that in a genome, the intended resolution of these sequences is to arrive at a single genome sequence.
A genome is considered the complement of all heritable sequence features in a given cell or organism (chromosomal or extrachromosomal). This is typically a collection of >1 sequence molecules (e.g. chromosomes), but in some organisms (e.g. bacteria) it may be a single sequence macromolecule (e.g. a circular plasmid). For this reason 'genome' classifies under 'sequence feature complement'.
A sequence variant whereby the gene product has diminished or abolished function.
Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome.
A spatiotemporal region encompassing some part of the life cycle of an organism.
this class represents a proper part of the life cycle of an organism. The class 'life cycle' should not be placed here
the WBls class 'all stages' belongs here as it is the superclass of other WBls stages
we map the ZFS unknown stage here as it is logically equivalent to saying *some* life cycle stage
A fluid that is composed of blood plasma and erythrocytes.
The upper ventral region of the torso of an organism.
Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body.
Anatomical group that has its parts adjacent to one another.
Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation.
Portion of connective tissue composed of adipocytes enmeshed in areolar tissue
Excretion that is the output of a kidney
kidney excreta from some taxa (e.g. in aves) may not be liquid
Muscle tissue that consists primarily of skeletal muscle fibers.
The liquid component of blood, in which erythrocytes are suspended.
The portion of blood plasma that excludes clotting factors.
The prostate gland is a partly muscular, partly glandular body that is situated near the base of the mammalian male urethra and secretes an alkaline viscid fluid which is a major constituent of the ejaculatory fluid.
Of or pertaining to the period of time immediately following birth, or to the newborn.
A temporal boundary connecting two life cycle stages that follow in immediate succession. A temporal boundary is an abstract, instantaneous entity.
A life cycle temporal boundary that marks the start of the neonate stage of the organism.
A unit which is a standard measure of the distance between two points.
A unit which is a standard measure of the amount of matter/energy of a physical object.
A unit which is a standard measure of the dimension in which events occur in sequence.
A unit which is a standard measure of the average kinetic energy of the particles in a sample of matter.
A temperature unit which is equal to one kelvin degree. However, they have their zeros at different points. The centigrade scale has its zero at 273.15 K.
A unit which represents a standard measurement of how much of a given substance there is mixed with another substance.
A density unit which is a standard measure of the mass exerting an influence on a given area.
A concentration unit which is a standard measure of the number of moles of a given substance per liter of solution.
A unit which is a standard measure of the amount of space occupied by any substance, whether solid, liquid, or gas.
A volume unit which is equal to 10^[-15] L.
A unit which is a standard measure of the force applied to a given area.
A concentration unit which is a standard measure of the number of units, as an agreed arbitrary amount, of a given substance per a specific volume of solution.
A unit per milliliter unit which is equal to one unit of an agreed arbitrary amount per one liter.
A unit which is a standard measure of the influence exerted by some mass.
The pressure exerted by circulating blood on the walls of blood vessels.
Unless otherwise specified, a clinical report of a blood pressure is systolic left ventricular pressure over diastolic left ventricular pressure.
PA, pressão sanguínea
blood pressure
pressão arterial
valor da pressão arterial
blood pressure measurement datum
pressão arterial medida
this was pasted into the turbo ontology. remove, and reimplement as an ontofox import
These phases belong in some OBO foundry ontology of cardiac physiology. Should include the subprocesses of systole and diastole as illustrated here http://en.wikipedia.org/wiki/Cardiac_cycle .
cardiac cycle phase
fase do ciclo cardíaco
The phase of the cardiac cycle in which the heart fills with blood.
diastole
diástole
Pad, pressão sanguínea diastólica
diastolic blood pressure
pressão arterial diastólica
The phase of the cardiac cycle in which the heart contracts.
systole
sístole
Pas, pressão sanguínea sistólica
pressão arterial sistólica
systolic blood pressure
medical record part
seção do prontuário médico
a data item that denotes a centrally registered identifier registry
a centrally registered identifier registry that serves as a controlled vocabulary for racial identity datums
the (string value) symbol part of a racial identity CRID
a human that participates, along with a biobanking organization or one of its representatives, in a consenting process that has a (permission role? Fully signed consent document?) as its output
As of July 2018, the one thing that holds true of all people modeled in the TURBO graph is that they have participated in a consent process in which a representative of the Penn Medicine Biobank also participated This concept of a consenter is currently under discussion by ICO representatives
a centrally registered identifier that denotes a biobank consenter
the (string value) symbol part of a biobank consenter CRID
a (string) denoter that denotes a psatient identifier registry instance
a dataset of identifiers (specifically the symbol parts) that denote people with patient roles. These may be patients whose data appears in a health care system's (electronic) medical records.
a planned process that uses genetic data to determine the population or populations to which a person belongs has participant: some person has input some genomic data has output: genetic population background datum parts of the process: sample collection DNA extraction sequencing data transformation
a centrally registered identifier that denotes a health care encounter
the (string value) symbol part of a health care encounter CRID
a (string) denoter that denotes a health care encounter identifier registry instance
A process boundary that starts a health care encounter
a process start time measurement about the temporal boundary that starts a health care encounter
health care encounter identifier registry
a dataset of identifiers (specifically the symbol parts) that denote health care encounters
a data transformation in which data are consumed from tabular or relational sources and written back out in a semantic/RDF format
a planned process in which the following two kinds of people participate: a representative from a biobank and someone with a participant under investigation role or a donor role or a consenter role The output of this process could be demographic or vital statistics data items, like height or weight; case forms, consent documetns, etc.
I began collecting stamps at noon, EST on January 1st, 1980. This is the start time measurement of my stamp collecting process.
A time measurement datum that is the measure of the time when some process started
based on OBI_0001619 from Chris Stoeckert and Jie Zheng
A process boundary that starts a biobank encounter
a process start time measurement about the temporal boundary that starts a biobank encounter
a centrally registered identifier that denotes a biobank encounter
the (string value) symbol part of a biobank encounter CRID
a (string) denoter that denotes a biobank encounter identifier registry instance
a dataset of identifiers (specifically the symbol parts) that denote biobank encounters
A centrally registered identifier that is about some diagnosis, billing code, etc. Consists of two parts: a registry denoter string that points to a particular disease coding registry, and a symbol string like "J123.5" that points to a particular disease within that registry.
If the turbo shortcut expansion method comes across either an isolated diagnosis code shortcut or an isolated diagnosis code registry URI shortcut, an exception should be thrown (because incomplete diagnosis CRIDs are worse than absent diagnosis CRIDs?)
the (string value) symbol part of a diagnosis CRID
might be a billing or diagnosis code... something like an ICD9 or ICD10 code
A proper name string that denotes a diagnosis code/billing code registry such as ICD-9, having an URI like <http://purl.obolibrary.org/obo/NCIT_C71890>
a dataset of identifiers (specifically the symbol parts) that denote diagnoses or billing codes, like those from the International Classification of Diseases
a centrally registered identifier that denotes a prescription
at least for Penn Medicine Biobank data, it may be more appropriate to denote prescriptions (And possibly other classes) with a (yet-to-be modeled) prescription primary key
the (string value) symbol part of a prescription CRID
a (string) denoter that denotes a prescription registry instance
a dataset of identifiers (specifically the symbol parts) that denote prescriptions
a dataset of identifiers (specifically the symbol parts) that denote samples intended as input into a genotyping process, and or the derived genotyping data
a centrally registered identifier that denotes a sample intended as input into a genotyping process, and or the derived genotyping data
a (string) denoter that denotes a genotype identifier registry instance
the (string value) symbol part of a genotype CRID
a value specification that indicates whether a diploid individual is homozygous wild type (0) heterozygous (1) or homozygous (2) for some mutant
loss of function zygosity value specification
a zygosity value specification about the number of alleles of a gene that are believed to be non-functional (over specified… use zygosity value specification and bind the loss of function objective to the assay?)
retired placeholder for biobank consenter
A 'retired placeholder' for individual whose URI terms, before referent tracking, identified individuals of class 'biobank consenter'
retired placeholder for biobank consenter CRID
A 'retired placeholder' for individual whose URI terms, before referent tracking, identified individuals of class 'biobank consenter CRID'
retired placeholder for biobank consenter symbol
A 'retired placeholder' for individual whose URI terms, before referent tracking, identified individuals of class 'biobank consenter symbol'
retired placeholder for biobank consenter registry denoter
A 'retired placeholder' for individual whose URI terms, before referent tracking, identified individuals of class 'biobank consenter registry denoter'
retired placeholder for biobank consenter identifier registry
A 'retired placeholder' for individual whose URI terms, before referent tracking, identified individuals of class 'biobank consenter identifier registry'
retired placeholder for health care encounter
A 'retired placeholder' for individual whose URI terms, before referent tracking, identified individuals of class 'health care encounter'
retired placeholder for health care encounter CRID
A 'retired placeholder' for individual whose URI terms, before referent tracking, identified individuals of class 'health care encounter CRID'
retired placeholder for health care encounter symbol
A 'retired placeholder' for individual whose URI terms, before referent tracking, identified individuals of class 'health care encounter symbol'
retired placeholder for health care encounter registry denoter
A 'retired placeholder' for individual whose URI terms, before referent tracking, identified individuals of class 'health care encounter registry denoter'
retired placeholder for health care encounter start
A 'retired placeholder' for individual whose URI terms, before referent tracking, identified individuals of class 'health care encounter start'
retired placeholder for health care encounter start date
A 'retired placeholder' for individual whose URI terms, before referent tracking, identified individuals of class 'health care encounter start date'
retired placeholder for health care encounter identifier registry
A 'retired placeholder' for individual whose URI terms, before referent tracking, identified individuals of class 'health care encounter identifier registry'
retired placeholder for biobank encounter
A 'retired placeholder' for individual whose URI terms, before referent tracking, identified individuals of class 'biobank encounter'
retired placeholder for biobank encounter start
A 'retired placeholder' for individual whose URI terms, before referent tracking, identified individuals of class 'biobank encounter start'
retired placeholder for biobank encounter start date
A 'retired placeholder' for individual whose URI terms, before referent tracking, identified individuals of class 'biobank encounter start date'
retired placeholder for biobank encounter CRID
A 'retired placeholder' for individual whose URI terms, before referent tracking, identified individuals of class 'biobank encounter CRID'
retired placeholder for biobank encounter symbol
A 'retired placeholder' for individual whose URI terms, before referent tracking, identified individuals of class 'biobank encounter symbol'
retired placeholder for biobank encounter registry denoter
A 'retired placeholder' for individual whose URI terms, before referent tracking, identified individuals of class 'biobank encounter registry denoter'
retired placeholder for biobank encounter identifier registry
A 'retired placeholder' for individual whose URI terms, before referent tracking, identified individuals of class 'biobank encounter identifier registry'
retired placeholder for neonate life stage
A 'retired placeholder' for individual whose URI terms, before referent tracking, identified individuals of class 'neonate life stage'
a patient identifier registry in which the symbols correspond to medical record numbers
ENCOUNTER_PACK_ID biobank encounter registry
a patient identifier registry in which the symbols correspond to (biobank?) encounter packet identifiers
a centrally registered identifier that denotes a racial identity
length measurement assay
In the doctors office, the nurse used a meter stick to perform a length measurement assay on the patient. The resulting length mesurement datum, 1.5 meters, is about the patient's height.
a process to determine the length of an evaluant
based on mass measurement datum from OBI, specifically Helen Parkinson? Philippe Rocca-Serra?
A planned process that takes a datum as input and has a rdf:Statement as output
TURBO sex recoding process
I saw the gender identity datum 'M' in a data set describing Joey. I used an instance of the TURBO sex recoding process (with some plan specification) to draw the conclusion that Joey has a quality of type PATO:male.
A planned process that takes a gender identity datum as input and has a PATO:biological_sex as output
a data transformation with the objective of referring to entities in reality with a singular, unique Instance Unique Identifier (IUI) "Referent Tracking is a paradigm under which it is possible to refer explicitly to all of the concrete individual entities relevant to the accurate description of each patient's condition, therapies, and outcomes through the assignment of unique identifiers."
TURBO implements IUIs as IRIs with UUIDs on the righthand side
Clinical Data Wrangling using Ontological Realism and Referent Tracking http://www.referent-tracking.com/RTU/?page=papers.phtml http://www.referent-tracking.com/RTU/?page=reftrackparadigm.phtml
conclusionation frequency threshold value specification
a value specification that specifies the minumum frequency at which a value must appear in order for a comclusionation process to conclusde that it is the correct value
A planned process in which RDF triples are created (for example) stating that some person participated in some healthcare encounter, based on the co-occurrence of a value denoting the person and a value denoting the encoutner in the same row of a tabular/relational data source
A class of individuals whose URI indicators were made obsolete in the course of referent tracking. The individuals of this class or its subclasses correspond to individuals that were previously instances of some subclass of 'entity'. The referent tracking processes that create instances of 'retired placeholder’ also create smaller numbers of new, unique and singular instances of those same entity subclasses. Also see the 'replaced with IUI' annotation property that documents the input and output
A 'retired placeholder' for individual whose URI terms, before referent tracking, identified individuals of class 'adipose tissue'
A 'retired placeholder' for individual whose URI terms, before referent tracking, identified individuals of class 'biological sex'
A 'retired placeholder' for individual whose URI terms, before referent tracking, identified individuals of class 'BMI datum'
retired placeholder for value specification
A 'retired placeholder' for individual whose URI terms, before referent tracking, identified individuals of class 'value specification'
A 'retired placeholder' for individual whose URI terms, before referent tracking, identified individuals of class 'height quality'
retired placeholder for process boundary
A 'retired placeholder' for individual whose URI terms, before referent tracking, identified individuals of class 'process boundary'
retired placeholder for process start time measurement
A 'retired placeholder' for individual whose URI terms, before referent tracking, identified individuals of class 'process start time measurement'
A 'retired placeholder' for individual whose URI terms, before referent tracking, identified individuals of class 'weight quality'
a data item that is the ouput of a tumor grading process. may be part of a tumor grading report.
A planned process that takes one or more datums as input and has a single datum, statement, and or record of missing knowledge as output
there may be potentially conflicting information about an entity that has gone through a referent tracking process. For example, Joey's gender could be asserted as male, male, male and female. Depending on the rules, conclusionating might decide that Joey is in fact male.
a conclusionating process in which one authoritative body mass index is derived from zero or more, potentially conflicting BMIs
prostate specific antigen value specification
prostate specific antigen concentration datum
summarizing the stage of cancer progression
Towards an Ontology for Representing Malignant Neoplasms William D. Duncan Carmelo Gaudioso and Alexander D. Diehl
A primary key may or may not be a CRID. It is useful for linking rows between tables in the same database. It may only be reliable for one version, snapshot, etc.
relational primary key
length value specification
TURBO shortcut entity
shortcut allele information
blood pressure value specification
systolic blood pressure value specification
diastolic blood pressure value specification
is there any controversy about whether BMIs have units (and are therefore scalar in nature)?
BMI value specification
it is expected that this would typically be a data transforation, taking a mass (datum? value specification) and a length as inputs. could possibly be an assay?
BMI determination process
blood glucose measurement datum
Hemoglobin with A1c glycosylation percentage datum
Hemoglobin A1c glycosylation assay
Hemoglobin with A1c glycosylation percentage value specification
blood glucose concentration specification
health care encounter data model
healthcare prescription data model
diagnosis data model
person data model
data item data model
person primary key
patient primary key
encounter primary key
health care encounter primary key
biobank encounter primary key
person CRID data model
biobank encounter data model
a data transformation that reads triples about a Homo sapiens data model and writes triples about a Homo sapiens, including related classes like identity datums, date of birth, etc.
semantic expansion of person model
a data transformation that reads triples about a biobank encounter data model and writes triples about a biobank encounter, including related classes like process boundary and time mesuremnt datum
semantic expansion of biobank encounter model
a data transformation that reads triplesa bout a data model and writes triples about something in reality, like a material entity or planned process
still trying to idenitfy the domain and range
semantic expansion of data model
a data transformation that reads triples about a health care encounter data model and writes triples about a biobank encounter, including related classes like process boundary and time mesuremnt datum
semantic expansion of health care encounter model
a planned process that reads triples about an allele information data model and writes triples about an allele information instance, as well as related instances like the data transformation that outputs and the genetic matierial that 'is about'
semantic expansion of allele information model
denoter-based relationship insertion
an encounter participation inferencing process in which the some value is found to denote a biobank encounter
biobank encounter participation inferencing
an encounter participation inferencing process in which the some value is found to denote a health care encounter
health care encounter participation inferencing
Metriq/ORQID tumor CRID
tumor registry
tumor data model
day of birth
neonate temporal region
birth instant
biological sex datum
male biological sex datum
female biologcal sex datum
biological sex or gender identity data item
male data item
female data item
in the case of less-than-stable identifiers like primary keys, an identifier source is analogous to a CRID registry
identifier source
health care encounter identifier source
identifier source denoter
health care encounter identifier source denoter
primary key symbol
health care encounter primary key symbol
tumor registry denoter
specimen data model
genome data model
allele information determination process
a specimen that is suitable for genomic (DNA) sequencing. collected in the course of some process like a biobank encounter. could become the input into DNA extraction and (exome?) sequencing, followed by data transformation.
genome sequencing specimen
genome sequencing specimen CRID
genome sequencing specimen identifier source denoter
genome sequencing specimen identifier source
patient identifier source
graph manipulation
RDF graph manipulation
edge-vertex graph
the FORMAT is defined at https://en.wikipedia.org/wiki/Resource_Description_Framework
RDF graph
SPARQL update process
SPARQL language
disregarding versions... is this a named individual?
update specification portionof SPARQL language
database statement
SPARQL update statement generation
database update statement
SPARQL update statement
SPARQL update statement generation specification
Acorn SPARQL update fragment recipe
Acorn recipe-based SPARQL update statement generation specification
I wanted to say that this inheres in some SPARQL engine, but those are currently GDCs, not IDCs
SPARQL update plan
SPARQL update statement generation plan
SPARQL engine / triplestore
Acorn interpreter
I wanted to say that this inheres in some Acorn interpreter, bu that's currently a GDC not an IDC
Acorn SPARQL update statement generation plan
SPARQL update statement generation by Acorn
Acorn domain specific language
office vist
patient identifier source denoter
provenance data item
could come from a relational database table, a view or ephemeral query result, or a delimited file.
data column
value_as_number column
relational database
relational schema
data table
relational data table
delimited data file
omop measurement table
query result
omop person table
gender_concept_id column
relational key
database query process
birth_datetime column
person_id column
person_source_value column
Neo4J property graph
Carnval graph
race_concept_id column
omop visit_occurrence table
visit_concept_id column
visit_end_date column
visit_occurrence_id column
visit_source_value column
visit_start_date column
preceding_visit_occurrence_id column
omop procedure_occurrence table
procedure_occurrence_id column
procedure_source_value column
procedure_source_concept_id
procedure_date column
measurement_id column
measurement_concept_id column
measurement_datetime column
value_as_concept_id column
unit_concept_id column
measurement_source_value column
measurement_source_concept_id column
vocabulary_id column
omop condition_occurrence table
omop drug_exposure table
condition_occurrence_id column
condition_start_datetime column
condition_end_datetime column
condition_source_value column
condition_source_concept_id column
drug_exposure_id column
drug_exposure_start_datetime column
drug_exposure_end_date column
verbatim_end_date column
drug_type_concept_id column
days_supply column
drug_source_value column
drug_source_concept_id column
prescription writing process
used by Synthea, but doesn't appear to have a UCUM term
thousand unit per liter unit
prescription identifier source
prescription identifier source denoter
blood serum or plasma union class
point-in time, quantitative, mass/volume blood plasma or serum glucose concentration assay
blood serum or plasma specimen
An action specification indicating that an assay, especially the sample collection, should occur at a single point in time. "...to identify measures at a point in time. This is a synonym for 'spot' or 'random' as applied to urine measurements."
LThe orders for, or the results from, laboratory assays, when communicated according to LOINC, must indicate the nominal time span over which the sample was collected or over which the assay was performed. Urine samples, for example, are frequently collected in a cumulative fashion, over a period such as 24 hours. THAT EXAMPLE WOULD NOT BE A Pt ASSAY. The time scope for a Pt assay is nominally one point in time. Obviously it takes several seconds or more to fill a vacutainer with blood,
Point-in-time sample collection specification
24 hour sample collection specification
point-in time, quantitative, mass/volume blood glucose concentration assay
point-in time, quantitative, mass/volume blood hemoglobin concentration assay
point-in time, quantitative, mass/volume urine urobilinogen concentration assay
24 hour, quantitative, mass/volume urine urobilinogen concentration assay
point-in time, quantitative, confirmatory, mass/volume urine ALPRAZolam concentration assay
point-in time, quantitative, mass/volume blood plasma or serum benzodiazepines concentration assay
point-in time, quantitative, count/volume blood neutrophil assay
point-in time, quantitative, automated, volume/volume blood hematocrit assay
count per volume
count per volume datum
volume per volume datum
automated assay
confirmatory assay
mass/volume concentration datum
volume/volume percentage concentration datum
arbitrary units per 24 hours datum
A group of people with a common cultural heritage that sets them apart from others in a variety of social relationships. (MSH); A social group characterized by a distinctive social and cultural tradition maintained from generation to generation, a common history and origin and a sense of identification with the group; members of the group have distinctive features in their way of life, shared experiences and often a common genetic heritage; these features may be reflected in their experience of health and disease. (NCI); Ethnicity - an arbitrary classification of the social group a person belongs to, and either identifies with or is identified with by others, as a result of a complex of cultural, biological, geographical and other factors such as linguistic, dietary and religion traditions; ancestry, background, allegiance, or association; and physical characteristics traditionally associated with race. Increasingly the concept is used synonymously with race but this use trend has a pragmatic basis rather than scientific. (NCI); The concept of ethnic origin is an attempt to classify people, not according to their current ethnicity, but according to where their ancestors came from. Ethnic origin has become a popular classification in statistics, where the concept of race has been largely discarded. (from Wikipedia) (NCI); a group of people with a common cultural heritage that sets them apart from others in a variety of social relationships. (CSP)
An ethnic group is a population whose members have a common heritage that is real or presumed such as common culture, language, religion, behaviour or biological trait.
A term used in the United States to categorize a population group comprised of persons having origins in any of the black racial groups of Africa. Includes population subgroups (e.g., Kenyan, Nigerian, Haitian). The concept refers also to individuals who classify themselves as described.
Denotes a person having origins in any of the original peoples of the Far East, Southeast Asia, or the Indian subcontinent, including Cambodia, China, India, Japan, Korea, Malaysia, Mongolia, Pakistan, the Philippine Islands, Thailand, and Vietnam.
In North America the term is used to distinguish a person having origins in the original peoples of the Indian sub-continent from Native Americans.
Denotes the inhabitants of China, a person from there, or their descendants elsewhere.
Denotes the inhabitants of Japan, a person from there, or their descendants elsewhere.
A person of Mexican, Puerto Rican, Cuban, Central or South American or other Spanish culture or origin, regardless of race. An arbitrary ethnic classification.
An indicator of body density as determined by the relationship of BODY WEIGHT to BODY HEIGHT. BMI=weight (kg)/height squared (m2). BMI correlates with body fat (ADIPOSE TISSUE). Their relationship varies with age and gender. For adults, BMI falls into these categories: below 18.5 (underweight); 18.5-24.9 (normal); 25.0-29.9 (overweight); 30.0 and above (obese). (National Center for Health Statistics, Centers for Disease Control and Prevention)
The point in time at which an individual was born.
Propsed equivalency 'is duration of' some (process and ('ends with' some (one-dimensional temporal region' and ('has temporal part') some ('zero-dimensional temporal region' and ('has temporal occupant' some 'start of neonate stage')))))) MAM: occurent instead of process? ends instead of has_temporal_part?
date of birth
hard-imported from NCIT into the base turbo.owl file
International Classification of Diseases, Ninth Revision
International Classification of Diseases, Tenth Revision
example to be eventually removed
The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job
failed exploratory term
metadata complete
Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete.
organizational term
term created to ease viewing/sort terms for development purpose, and will not be included in a release
ready for release
Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release."
metadata incomplete
Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors.
uncurated
Nothing done yet beyond assigning a unique class ID and proposing a preferred term.
pending final vetting
All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor.
placeholder removed
An editor note should explain what were the merged terms and the reason for the merge.
terms merged
This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use.
term imported
This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created.
term split
This is to be used if none of the existing instances cover the reason for obsolescence. An editor note should indicate this new reason.
We expect to be able to mine these new reasons and add instances as required.
other
Hard to give a definition for. Intuitively a "natural kind" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents.
A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf
A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal
"definitions", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal.
A named class expression is a logical expression that is given a name. The name can be used in place of the expression.
named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions
to be replaced with external ontology term
Terms with this status should eventually replaced with a term from another ontology.
requires discussion
A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues.
An extension of the ICD-10 created by the U.S. National Center for Health Statistics so that the system could be used to capture more morbidity data. This extension included a section of procedure codes. [def-source: NCI]
International Classification of Diseases, Tenth Revision, Clinical Modification
Only individual discrete well-formed glands.
Predominantly well-formed glands with lesser component of poorly-formed/fused/cribriform glands.
Only poorly-formed/fused/cribriform glands or Predominantly well-formed glands and lesser component lacking glands or Predominantly lacking glands and lesser component of well-formed gland. Poorly-formed/fused/cribriform glands can be a more minor component.
Gleason Score 8: (4 plus 4) or (3 plus 5) or (5 plus 3)
Lacks gland formation (or with necrosis) with or without poorly formed/fused/cribriform glands. For cases with greater than 95% poorly formed/fused/cribriform glands or lack of glands on a core or at RP, the component of less than 5% well-formed glands is not factored into the grade.
A pattern of prostate carcinoma characterized by the presence of a well circumscribed nodule of separate glands which are closely packed. There is no infiltration of the surrounding parenchyma. The epithelial polarity of the malignant cells is preserved and luminal differentiation is present in all glands.
A pattern of prostate carcinoma characterized by the presence of glands that are more loosely arranged and less uniform compared to Gleason pattern 1. Minimal invasion of the surrounding parenchyma may be present. The epithelial polarity of the malignant cells is preserved and luminal differentiation is present in all glands.
A pattern of prostate carcinoma characterized by the presence of glands that are infiltrative and vary in size and shape. The epithelial polarity of the malignant cells is preserved and luminal differentiation is present in all glands.
A pattern of prostate carcinoma characterized by the presence of fused, cribriform, or poorly defined glands. There is partial loss of normal epithelial polarity.
A pattern of prostate carcinoma characterized by almost complete loss of epithelial polarity and luminal differentiation.
A Gleason score that indicates a low-grade prostatic adenocarcinoma. The score or sum is estimated by adding the most prevalent and the second most prevalent histopathologic pattern of the malignant infiltrate.
A Gleason score that indicates an intermediate-grade prostatic adenocarcinoma. The score or sum is estimated by adding the most prevalent and the second most prevalent histopathologic pattern of the malignant infiltrate.
A Gleason score that indicates a histologically aggressive prostatic adenocarcinoma. The score or sum is estimated by adding the most prevalent and the second most prevalent histopathologic pattern of the malignant infiltrate.
A Gleason score that indicates a high-grade prostatic adenocarcinoma. The score or sum is estimated by adding the most prevalent and the second most prevalent histopathologic pattern of the malignant infiltrate.
A Gleason score that indicates a highly aggressive prostatic adenocarcinoma. The score or sum is estimated by adding the most prevalent and the second most prevalent histopathologic pattern of the malignant infiltrate.
A low Gleason score that is exceptionally uncommon and indicates a low-grade, non-aggressive prostatic adenocarcinoma. The score or sum is estimated by adding the most prevalent and the second most prevalent histopathologic pattern of the malignant infiltrate.
A Gleason score that is exceptionally assigned and indicates a low-grade prostatic adenocarcinoma. The score or sum is estimated by adding the most prevalent and the second most prevalent histopathologic pattern of the malignant infiltrate.
A Gleason score that is relatively uncommon and indicates a low-grade prostatic adenocarcinoma. The score or sum is estimated by adding the most prevalent and the second most prevalent histopathologic pattern of the malignant infiltrate.
An exceptionally uncommon Gleason score that indicates a less aggressive prostatic adenocarcinoma. The score or sum is estimated by adding the most prevalent and the second most prevalent histopathologic pattern of the malignant infiltrate.
Ensembl is a joint project between EMBL-EBI and the Sanger Institute to develop a software system which produces and maintains automatic annotation on selected eukaryotic genomes. Ensembl is primarily funded by the Wellcome Trust. The Ensembl Genome Browser can be accessed through www.ensembl.org.
An extension of the ICD-9 created by the U.S. National Center for Health Statistics so that the system could be used to capture more morbidity data. This extension included a section of procedure codes. [def-source: NCI]
International Classification of Diseases, Ninth Revision, Clinical Modification
An organization which supplies technology, tools and protocols for use in high throughput applications
Affymetrix
The Edinburgh Handedness Inventory is a set of questions used to assess the dominance of a person's right or left hand in everyday activities.
PMID:5146491#Oldfield, R.C. (1971). The assessment and analysis of handedness: The Edinburgh inventory. Neuropsychologia, 9, 97-113
Advanced Instruments Inc. (AI Companies)
Nimblegen
An organization that focuses on manufacturing target enrichment probe pools for DNA sequencing.
Pacific Biosciences
An organization that supplies tools for studying the synthesis and regulation of DNA, RNA and protein. It developed a powerful technology platform called single molecule real-time (SMRT) technology which enables real-time analysis of biomolecules with single molecule resolution.
NanoString Technologies
An organization that supplies life science tools for translational research and molecular diagnostics based on a novel digital molecular barcoding technology. The NanoString platform can provide simple, multiplexed digital profiling of single molecules.
An organization that is an American multinational, biotechnology product development company, created in 2006 by the merger of Thermo Electron and Fisher Scientific.
Thermo Fisher Scientific
A histologic grade according to AJCC 7th edition indicating that the tumor cells and the organization of the tumor tissue appear close to normal.
A histologic grade according to AJCC 7th edition indicating that the tumor cells are moderately differentiated and reflect an intermediate grade.
A histologic grade according to AJCC 7th edition indicating that the tumor cells are poorly differentiated and do not look like normal cells and tissue.
A histologic grade according to AJCC 7th edition indicating that the tumor cells are undifferentiated and do not look like normal cells and tissue.
A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei are round, uniform, approximately 10um and that nucleoli are inconspicuous or absent.
A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei are slightly irregular, approximately 15um and nucleoli are evident.
A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei are very irregular, approximately 20um and nucleoli large and prominent.
A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei arei bizarre and multilobulated, 20um or greater and nucleoli are prominent and chromatin clumped.
A histologic grade for ovarian tumor according to a two-tier grading system indicating that the tumor is low grade.
A histologic grade for ovarian tumor according to a two-tier grading system indicating that the tumor is high grade.
A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is well differentiated.
A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is moderately differentiated.
A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is poorly differentiated.
A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is undifferentiated.
A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that there is no evidence of primary tumor.
A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating carcinoma in situ (intraepithelial or invasion of lamina propria).
A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor invades submucosa.
A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor invades muscularis propria.
A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor invades subserosa or into non-peritionealized pericolic or perirectal tissues.
A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor perforates visceral peritoneum.
A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor directly invades other organs or structures.
A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that there is no evidence of primary tumor.
A pathologic primary tumor stage for lung according to AJCC 7th edition indicating carcinoma in situ.
A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is 3 cm or less in greatest dimension, surrounded by lung or visceral pleura without bronchoscopic evidence of invasion more proximal than the lobar bronchus (i.e., not in the main bronchus).
A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is 2 cm or less in greatest dimension.
A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 2 cm but not more than 3 cm in greatest dimension.
A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 3 cm but not more than 7 cm or the tumor has any of the following features: involves main bronchus, 2 cm or more distal to the carina, invades visceral pleura, associated with atelectasis or obstructive pneumonitis that extends to the hilar region but does not involve the entire lung.
A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 3 cm but not more than 5 cm in greatest dimension.
A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 5 cm but not more than 7 cm in greatest dimension.
A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 7 cm or one that directly invades any of: parietal pleura, chest wall (including superior sulcus tumors), diaphragm, phrenic nerve, mediastinal pleura, parietal pericardiu or the tumor is in the main bronchus less than 2 cm distal to the carina but without involvement of the carina or there is associated atelectasis or obstructive pneumonitis of the entire lung or there is separate tumor nodule(s) in the same lobe as the primary.
A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor of any size that invades any of the following: mediastinum, heart, great vessels, trachea, recurrent laryngeal nerve, esophagus, vertebral body, carina or there is separate tumor nodule(s) in a different ipsilateral lobe to that of the primary.
A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that there is no evidence of primary tumor.
A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is 7 cm or less in greatest dimension and limited to the kidney.
A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is 4 cm or less.
A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 4 cm but not more than 7 cm.
A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 7 cm in greatest dimension and limited to the kidney.
A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 7 cm but not more than 10 cm.
A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 10 cm and limited to the kidney.
A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor extends into major veins or perinephric tissues but not into the ipsilateral adrenal gland and not beyond the Gerota fascia.
A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor grossly extends into the renal vein or its segmental (muscle containing) branches, or the tumor invades perirenal and/or renal sinus fat (peripelvic) fat but not beyond Gerota fascia.
A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor grossly extends into vena cava below diaphragm.
A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor grossly extends into vena cava above the diaphragm or Invades the wall of the vena cava.
A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor invades beyond Gerota fascia (including contiguous extension into the ipsilateral adrenal gland).
A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that there is no evidence of primary tumor.
A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to the ovaries (one or both).
A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to one ovary; capsule intact, no tumor on ovarian surface and no malignant cells in ascites or peritoneal washings.
A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to both ovaries; capsule intact, no tumor on ovarian surface and no malignant cells in ascites or peritoneal washings.
A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to one or both ovaries with capsule ruptured, tumor on ovarian surface, or malignant cells in ascites or peritoneal washings.
A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor involves one or both ovaries with pelvic extension.
A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has extension and/or implants on uterus and/or tube(s) and no malignant cells in ascites or peritoneal washings.
A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has extension to other pelvic tissues and no malignant cells in ascites or peritoneal washings.
A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has pelvic extension with malignant cells in ascites or peritoneal washings.
A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor involves one or both ovaries with microscopically confirmed peritoneal metastasis outside the pelvis and/or regional lymph node metastasis.
A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has microscopic peritoneal metastasis beyond pelvis.
A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has macroscopic peritoneal, metastatasis beyond pelvis, 2 cm or less in greatest dimension.
A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has peritoneal metastasis beyond pelvis, more than 2 cm in greatest dimension and/or regional lymph node metastasis.
A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating no regional lymph node metastsis.
A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 1-3 regional lymph nodes.
A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 1 regional lymph node.
A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 2-3 regional lymph nodes.
A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating tumor deposit(s), i.e., satellites in the subserosa, or in non-peritonealized pericolic or perirectal soft tissue without regional lymph node metastasis.
A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 4 or more regional lymph nodes.
A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 4 to 6 regional lymph nodes.
A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 7 or more regional lymph nodes.
A pathologic lymph node stage for lung according to AJCC 7th edition indicating no regional lymph node metastasis.
A pathologic lymph node stage for lung according to AJCC 7th edition indicating metastasis in ipsilateral peribronchial and/or ipsilateral hilar lymph nodes and intrapulmonary nodes, including involvement by direct extension.
A pathologic lymph node stage for lung according to AJCC 7th edition indicating metastasis in ipsilateral mediastinal and/or subcarinal lymph node(s).
A pathologic lymph node stage for lung according to AJCC 7th edition indicating metastasis in contralateral mediastinal, contralateral hilar, ipsilateral or contralateral scalene, or supraclavicular lymph node(s).
A pathologic lymph node stage for kidney according to AJCC 7th edition indicating that there is no regional lymph node metastasis.
A pathologic lymph node stage for kidney according to AJCC 7th edition indicating that there is regional lymph node metastasis.
A pathologic lymph node stage for ovary according to AJCC 7th edition indicating that there is no regional lymph node metastasis.
A pathologic lymph node stage for ovary according to AJCC 7th edition indicating that there is regional lymph node metastasis.
A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that there are no symptoms or signs of distant metastasis.
A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that there is clinical evidence of distant metastases by history, physical examination, imaging studies, or invasive procedures, but without microscopic evidence of the presumed distant metastases.
A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is confined to one organ based on clinical assessment.
A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is in more than one organ or the peritoneum based on clinical assessment.
A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that there is microscopic evidence confirming distant metastatic disease.
A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is confined to one organ and histologically confirmed.
A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is in more than one organ or the peritoneum and histologically confirmed.
A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is no distant metastasis.
A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there are distant metastases based on clinical assessment.
A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that metastasis is based on clinical assessment and a separate tumor nodule(s) in a contralateral lobe; tumor with pleural nodules OR malignant pleural or pericardial effusion.
A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is a distant metastases based on clinical assessment.
A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is a distant metastases that is histologically confirmed.
A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that metastasis is histologically confirmed and a separate tumor nodule(s) in a contralateral lobe; tumor with pleural nodules OR malignant pleural or pericardial effusion.
A pathologic distant metastases stage for kidney according to AJCC 7th edition indicating that there is no distant metastasis.
A pathologic distant metastases stage for kidney according to AJCC 7th edition indicating that there are distant metastases based on clinical assessment.
A pathologic distant metastases stage for kidney according to AJCC 7th edition indicating that there is a distant metastases that is histologically confirmed.
A pathologic distant metastases stage for ovary according to AJCC 7th edition indicating that there is no distant metastasis.
A pathologic distant metastases stage for ovary according to AJCC 7th edition indicating that there is distant metastasis except peritoneal metastasis based on clinical assessment.
A pathologic distant metastases stage for ovary according to AJCC 7th edition indicating that there is distant metastasis except peritoneal metastasis that is histologically confirmed.
A clinical tumor stage group according to AJCC 7th edition indicating a small carcinoma, either asymptomatic or giving rise to metastases without symptoms due to the primary carcinoma.
A clinical tumor stage group according to AJCC 7th edition indicating a carcinoma in situ (or melanoma in situ for melanoma of the skin or germ cell neoplasia in situ for testicular germ cell tumors) and generally is considered to have no metastatic potential.
A clinical tumor stage group according to AJCC 7th edition indicating cancers that are smaller or less deeply invasive without regional disease or nodes.
A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent but less than in Stage III and with differing characteristics from IIB and IIC.
A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent but less than in Stage III and with differing characteristics from IIA and IIC.
A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent but less than in Stage III and with differing characteristics from IIA and IIB.
A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent greater than in Stage II and with differing characteristics from IIIB and IIIC.
A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent greater than in Stage II and with differing characteristics from IIIA and IIIC.
A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent greater than in Stage II and with differing characteristics from IIIA and IIIB.
A clinical tumor stage group according to AJCC 7th edition indicating cancers in patients who present with distant metastases at diagnosis and with differing characteristics from IVB.
A clinical tumor stage group according to AJCC 7th edition indicating cancers in patients who present with distant metastases at diagnosis and with differing characteristics from IVA.
An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating invasive carcinoma which can be diagnosed only by microscopy, with deepest invasion <5 mm and the largest extension <7 mm.
An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating measured stromal invasion of <3.0 mm in depth and extension of <7.0 mm.
An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating measured stromal invasion of >3.0 mm and not >5.0 mm with an extension of not >7.0 mm.
An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating clinically visible lesions limited to the cervix uteri or pre-clinical cancers greater than stage IA
An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating clinically visible lesion limited to the cervix uteri or pre-clinical cancers greater than stage IA <4.0 cm in greatest dimension.
An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating clinically visible lesion limited to the cervix uteri or pre-clinical cancers greater than stage IA >4.0 cm in greatest dimension.
An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina without parametrial invasion.
An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina without parametrial invasion and clinically visible lesion <4.0 cm in greatest dimension.
An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina without parametrial invasion and clinically visible lesion >4.0 cm in greatest dimension.
An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina with obvious parametrial invasion.
An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating tumour involves lower third of the vagina, with no extension to the pelvic wall.
An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating extension to the pelvic wall and/or hydronephrosis or non-functioning kidney.
An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating spread of the growth to adjacent organs.
An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating spread to distant organs.
A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1, N0, and M0.
A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1a, N0, and M0.
A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1b, N0, and M0.
A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1c, N0, and M0.
A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2, N0, and M0.
A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2a, N0, and M0.
A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2b, N0, and M0.
A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2c, N0, and M0.
A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of (T3, N0, and M0) or (T3,3a,3b, NX, and M0).
A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T3a, N0, and M0 .
A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T3b, N0, and M0 .
A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of (T3c, N0,X and M0) or (any T, N1 and M0).
A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of any T, any N, and M1.
A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of (T0, N0, and M0) or (T1,1a-1c,2,2a-2c, NX, and M0) or (TX, N0,X, M0).
axiom holds for all times
## Elucidation This is used when the statement/axiom is assumed to hold true 'eternally' ## How to interpret (informal) First the "atemporal" FOL is derived from the OWL using the standard interpretation. This axiom is temporalized by embedding the axiom within a for-all-times quantified sentence. The t argument is added to all instantiation predicates and predicates that use this relation. ## Example Class: nucleus SubClassOf: part_of some cell forall t : forall n : instance_of(n,Nucleus,t) implies exists c : instance_of(c,Cell,t) part_of(n,c,t) ## Notes This interpretation is *not* the same as an at-all-times relation
A length unit which is equal to the length of the path traveled by light in vacuum during a time interval of 1/299 792 458 of a second.
is this the unit preferred by OMOP for height 3036277 / LOINC 8302-2
A time unit which is equal to the duration of 9 192 631 770 periods of the radiation corresponding to the transition between the two hyperfine levels of the ground state of the caesium 133 atom.
A length unit which is equal to one millionth of a meter or 10^[-6] m.
A length unit which is equal to one thousandth of one millionth of a meter or 10^[-9] m.
A length unit which is equal to 10 [-10] m.
A length unit which is equal to 10^[-12] m.
A mass unit which is equal to one thousandth of a kilogram or 10^[-3] kg.
A mass unit which is equal to one thousandth of a gram or 10^[-3] g.
A mass unit which is equal to one millionth of a gram or 10^[-6] g.
A mass unit which is equal to one thousandth of one millionth of a gram or 10^[-9] g.
A mass unit which is equal to 10^[-15] g.
A time unit which is equal to 60 seconds.
A time unit which is equal to 3600 seconds or 60 minutes.
A time unit which is approximately equal to the length of time of one of cycle of the moon's phases which in science is taken to be equal to 30 days.
A time unit which is equal to 12 months which is science is taken to be equal to 365.25 days.
A unit which is a standard measure of the mass of a homogeneous substance containing 6.02 x 1023 atoms or molecules.
A unit of concentration which expresses a concentration of 1 mole of solute per liter of solution (mol/L).
A unit of molarity which is equal to one millionth of a molar or 10^[-6] M.
A unit of molarity which is equal to one thousandth of one millionth of a molar or 10^[-9] M.
A unit of molarity which is equal to 10^[-12] M.
A mass unit density which is equal to mass of an object in kilograms divided by the volume in cubic meters.
A mass unit density which is equal to mass of an object in grams divided by the volume in cubic centimeters.
A dimensionless concentration unit which denotes the mass of a substance in a mixture as a percentage of the mass of the entire mixture.
A dimensionless concentration unit which denotes the mass of the substance in a mixture as a percentage of the volume of the entire mixture.
A dimensionless concentration unit which denotes the volume of the solute in mL per 100 mL of the resulting solution.
A mass unit density which is equal to mass of an object in grams divided by the volume in milliliter.
A mass unit density which is equal to mass of an object in kilograms divided by the volume in liters.
A mass unit density which is equal to mass of an object in grams divided by the volume in liters.
A mass unit density which is equal to mass of an object in milligrams divided by the volume in milliliters.
A volume per unit volume unit which is equal to one millionth of a liter of solute in one liter of solution.
A concentration unit which a measure of viable bacterial numbers in a given volume.
An independently to the base SI units defined mass unit which is equal to one twelfth of the mass of an unbound atom of the carbon-12 nuclide, at rest and in its ground state.
A mass unit which is equal to one thousand daltons.
A mass unit density which is equal to mass of an object in milligrams divided by the volume in liters.
A mass unit density which is equal to mass of an object in micrograms divided by the volume in millliters.
A mass unit density which is equal to mass of an object in micrograms divided by the volume in liters.
A unit used to express distances on a genetic map. In genetic mapping, distances between markers are determined by measuring the rate of meoitic recombination between them, which increases proportionately with the distance separating them. A cM is defined as the length of an interval in which there is a 1% probability of recombination. On the average, 1 cM is roughly equivalent to 1 megabase (Mb) of DNA, although this can vary widely due to hot and cold spots of recombination.
A unit of genetic map distance defined corresponding to an interval in which there is a 1% probability of X-irradiation induced breakage. To be completely specified, the unit must be qualified by the radiation in dosage in rads (e.g. cR8000), because this determines the actual breakage probability.
A mass unit which is equal to 1/12 the mass of 12C
A length unit which is equal to 0.0254 metres.
A length unit which is equal to 0.0254 millimetres.
A length unit which is equal to 0.3048 metres, or 12 inches.
A length unit which is equal to 0.9144 metres, or 3 feet.
A length unit which is equal to 20.1168 metres, 66 feet, or 22 yards.
A length unit which is equal to 20,116.8 metres, 660 feet, or 10 chains.
A length unit which is equal to 1,609.344 metres, or 8 furlongs.
A length unit which is equal to 3 miles, or 4,828.032 metres
A maritime length unit is one used primarily at sea.
An imperial mass unit which is equivalent to 64.798,91 milligrams.
An imperial mass unit which is equivalent to 1.771,845,195,3125 grams, or 1/256 of 1 pound.
An imperial mass unit which is equivalent to 28.349,523,125 grams, or 1/16 of 1 pound.
An imperial mass unit which is equivalent to 453.592,37 grams.
An imperial mass unit which is equivalent to 6,350.293,18 grams, or 14 pounds.
An imperial mass unit which is equivalent to 12.700,586,36 kilograms, or 28 pounds.
An imperial mass unit which is equivalent to 50.802,345,44 kilograms, 112 pounds, or 8 stone.
An imperial mass unit which is equivalent to 1,016.046,9088 kilograms, or 2,240 pounds.
Ontology for Biomedical Investigations
Advisors for this project come from the IFOMIS group, Saarbruecken and from the Co-ODE group in Manchester
Allyson Lister
Barry Smith
Bill Bug
Carlo Torniai
Chris Stoeckert
Chris Taylor
Christian Bolling
Cristian Cocos
Daniel Rubin
Daniel Schober
Dawn Field
Dirk Derom
Eric Deutsch
Gilberto Fragoso
Helen C. Causton
Holger Stenzhorn
James A. Overton
Jay Greenbaum
Jeffrey Grethe
Jessica Turner
Jie Zheng
Joe White
John Westbrook
Kevin Clancy
Larisa Soldatova
Lawrence Hunter
Liju Fan
Luisa Montecchi
Matthew Brush
Matthew Pocock
Melissa Haendel
Mervi Heiskanen
Monnie McGee
Norman Morrison
Philip Lord
Pierre Grenon
Richard Bruskiewich
Robert Stevens
Ryan R. Brinkman
Stefan Wiemann
Susanna-Assunta Sansone
Tanya Gray
The Ontology for Biomedical Investigations (OBI) is build in a collaborative, international effort and will serve as a resource for annotating biomedical investigations, including the study design, protocols and instrumentation used, the data generated and the types of analysis performed on the data. This ontology arose from the Functional Genomics Investigation Ontology (FuGO) and will contain both terms that are common to all biomedical investigations, including functional genomics investigations and those that are more domain specific.
OWL-DL
An ontology for the annotation of biomedical and functional genomics experiments.
Please cite the OBI consortium http://purl.obolibrary.org/obo/obi where traditional citation is called for. However it is adequate that individual terms be attributed simply by use of the identifying PURL for the term, in projects that refer to them.
A 'biobank organization' affiliated with the Institute for Translational Medicine and Therapeutics at the Perelman School of Medicine at the University of Pennsylvania and 'Penn Medicine': the University of Pennsylvania Health System
EMPI - Enterprise Master Patient Identifier - PDS generated internal patient identifier. Should be unique to a person (every person should have at most one EMPI, every EMPI belongs to only one person). This identifier is stable in that it should not change over time, however it is not complete in that not all patients are assigned an EMPI.
PDS PK_PATIENT_ID patient identifier registry
PDS generated internal patient identifier. Should be unique to a person (every PK_PATIENT_ID belongs to only one person).PK_PATIENT_ID is complete in that all patients do have PK_PATIENT_IDs, however it is not stable in that the value assigned to a person will change over time. Specifically, PK_PATIENT_IDs are regenerated over the weekend, so PK_PATIENT_IDs can be used to query PDS within the same work week to get consistent results, but particular PK_PATIENT_IDs from the previous week should not be used to requery PDS.
PDS PK_PATIENT_ID patient identifier source
the registry of MRNs from the Hospital University of Pennsylvania
the registry of MRNs from the Penn Presbyterian Medical Center
the registry of MRNs from the Pennsylvania Hospital
the registry of MRNs from the Chester County Hosptial
CGI ENCOUNTER_PACK_ID biobank encounter identifier registry
Integer. Generated when the CRFs are created. All CGI encounters must have this identifier. Used to link to both CRF data and inventory data.
PMBB ENCOUNTER_PACK_ID biobank encounter identifier registry
UUID. Generated when the CRFs are created. Used to link to CRF data. All PMBB encounters must have this identifier.
PMBB Blood ENCOUNTER_PACK_ID biobank encounter identifier registry
PMBB Tissue ENCOUNTER_PACK_ID biobank encounter identifier registry
PMBB ENCOUNTER_LAB_ID biobank encounter identifier registry
Integer. Generated when blood specimens are processed. Used to link to inventory data. Not all encounters have this identifier; if no specimens are received, this identifier is not generated.
PDS PK_Encounter_ID health care encounter identifier registry
PDS generated internal healthcare encounter identifier. Probably not stable over time.
PDS PK_Encounter_ID health care encounter identifier source
A 'genotype identifier registry' containing identifies issued by Regeneron to identify samples submitted by the 'Penn Medicine Biobank organization' and the resulting genotype data
-/- loss of function zygosity value specification
a 'loss of function zygosity value specification' instance indicating the conclusion that some diploid individual is homozygous for a mutant or minor allele at some locus
-/+ loss of function zygosity value specification
a 'loss of function zygosity value specification' instance indicating the conclusion that some diploid individual is heterozygous for loss of function alleles at some locus
+/+ loss of function zygosity value specification
a 'loss of function zygosity value specification' instance indicating the conclusion that some diploid individual is wild-type homozygous at some locus
a 'zygosity value specification' instance indicating the conclusion that some diploid individual is homozygous for a mutant or minor allele at some locus
a 'zygosity value specification' instance indicating the conclusion that some diploid individual is heterozygous for a mutant or minor allele at some locus
a 'zygosity value specification' instance indicating the conclusion that some diploid individual is wild-type homozygous at some locus
Requires more discussion... what are the racial identity authorities that offer values that are used in our inpout data?
PDS placeholder racial identity registry
Metriq/ORQID tumor registry
Patient 946
Neonate stage (process) 946
Start of neonate stage/birth 946
DOB TMD 946
Day of birth 946
Birth instant 946
Neonate stage temporal region 946
Male GID 946
(denoter of the) Synthea patient registry
(denoter of the) Synthea health care encounter registry
OMOP health care identifier source
(denoter of the) OMOP health care encounter identifier source
Metriq/ORQID tumor registry denoter
HUP MRN registry denoter
PDS PK_Encounter_ID health care encounter identifier source denoter
UPHS EMPI patient registry denoter
CGI Biobank Encounter registry denoter
PMBB Blood biobank encounter registry denoter
PMBB Tissue biobank encounter registry denoter
CCH MRN registry denoter
PAH MRN registry denoter
PMC MRN registry denoter
OMOP patient identifier source
(denoter of the) OMOP patient identifier source
OMOP measurement identifier source
(denoter of the) OMOP measurement identifier source
Synthea measurement registry
(denoter of the) Synthea measurement registry
Synthea procudure registry
(denoter of the) Synthea procedure registry
(denoter of the) OMOP procedure identifier source
OMOP procedure identifier source
value_as_number column from measurement query result
syntheaomop_post_icbo at pennturbo.org port 5432
cdm_synthea10 schema from syntheaomop_post_icbo at pennturbo.org port 5432
measurement in cdm_synthea10 schema from syntheaomop_post_icbo at pennturbo.org port 5432
PREFIX : <http://api.stardog.com/> PREFIX owl: <http://www.w3.org/2002/07/owl#> PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX stardog: <tag:stardog:api:> PREFIX xsd: <http://www.w3.org/2001/XMLSchema#> MAPPING FROM SQL { -- SELECT * -- FROM "cdm_synthea10"."measurement" select m.*, c.vocabulary_id, (case when m.unit_source_value = 'mmHg' then 8876 when m.unit_source_value = 'U/L' then 8645 else m.unit_concept_id end ) as more_units from cdm_synthea10.measurement m join cdm_synthea10.concept c on m.measurement_source_concept_id = c.concept_id -- WHERE "measurement_date" IS NOT NULL AND "measurement_time" IS NOT NULL AND "operator_concept_id" IS NOT NULL AND "value_as_number" IS NOT NULL AND "value_as_concept_id" IS NOT NULL AND "unit_concept_id" IS NOT NULL AND "range_low" IS NOT NULL AND "range_high" IS NOT NULL AND "provider_id" IS NOT NULL AND "visit_occurrence_id" IS NOT NULL AND "visit_detail_id" IS NOT NULL AND "measurement_source_value" IS NOT NULL AND "unit_source_value" IS NOT NULL AND "value_source_value" IS NOT NULL -- WHERE "visit_occurrence_id" < 100 -- WHERE "person_id" <= 500 } TO { ?subject <http://api.stardog.com/measurement#measurement_concept_id> ?measurement_concept_id . ?subject <http://api.stardog.com/measurement#measurement_date> ?measurement_date . ?subject <http://api.stardog.com/measurement#measurement_datetime> ?measurement_datetime . ?subject <http://api.stardog.com/measurement#measurement_id> ?measurement_id . ?subject <http://api.stardog.com/measurement#measurement_source_concept_id> ?measurement_source_concept_id . ?subject <http://api.stardog.com/measurement#measurement_source_value> ?measurement_source_value . ?subject <http://api.stardog.com/measurement#measurement_time> ?measurement_time . ?subject <http://api.stardog.com/measurement#measurement_type_concept_id> ?measurement_type_concept_id . ?subject <http://api.stardog.com/measurement#operator_concept_id> ?operator_concept_id . ?subject <http://api.stardog.com/measurement#person_id> ?person_id . ?subject <http://api.stardog.com/measurement#provider_id> ?provider_id . ?subject <http://api.stardog.com/measurement#range_high> ?range_high . ?subject <http://api.stardog.com/measurement#range_low> ?range_low . ?subject <http://api.stardog.com/measurement#unit_concept_id> ?unit_concept_id . ?subject <http://api.stardog.com/measurement#more_units> ?more_units . ?subject <http://api.stardog.com/measurement#unit_source_value> ?unit_source_value . ?subject <http://api.stardog.com/measurement#value_as_concept_id> ?value_as_concept_id . ?subject <http://api.stardog.com/measurement#value_as_number> ?value_as_number . ?subject <http://api.stardog.com/measurement#value_source_value> ?value_source_value . ?subject <http://api.stardog.com/measurement#visit_detail_id> ?visit_detail_id . ?subject <http://api.stardog.com/measurement#visit_occurrence_id> ?visit_occurrence_id . ?subject <http://api.stardog.com/measurement#vocabulary_id> ?vocabulary_id . ?subject rdf:type :measurement } WHERE { # BIND(template("measurement{measurement_id}_{person_id}_{measurement_concept_id}_{measurement_date}_{measurement_datetime}_{measurement_time}_{measurement_type_concept_id}_{operator_concept_id}_{value_as_number}_{value_as_concept_id}_{unit_concept_id}_{range_low}_{range_high}_{provider_id}_{visit_occurrence_id}_{visit_detail_id}_{measurement_source_value}_{measurement_source_concept_id}_{unit_source_value}_{value_source_value}") AS ?subject) BIND(template("measurement_{measurement_id}") AS ?subject) BIND(xsd:date(?measurement_date) AS ?measurement_date) BIND(xsd:dateTime(?measurement_datetime) AS ?measurement_datetime) BIND(xsd:double(?range_high) AS ?range_high) BIND(xsd:double(?range_low) AS ?range_low) BIND(xsd:double(?value_as_number) AS ?value_as_number) BIND(xsd:integer(?measurement_concept_id) AS ?measurement_concept_id) BIND(xsd:integer(?measurement_id) AS ?measurement_id) BIND(xsd:integer(?measurement_source_concept_id) AS ?measurement_source_concept_id) BIND(xsd:integer(?measurement_type_concept_id) AS ?measurement_type_concept_id) BIND(xsd:integer(?operator_concept_id) AS ?operator_concept_id) BIND(xsd:integer(?person_id) AS ?person_id) BIND(xsd:integer(?provider_id) AS ?provider_id) BIND(xsd:integer(?unit_concept_id) AS ?unit_concept_id) BIND(xsd:integer(?value_as_concept_id) AS ?value_as_concept_id) BIND(xsd:integer(?visit_detail_id) AS ?visit_detail_id) BIND(xsd:integer(?visit_occurrence_id) AS ?visit_occurrence_id) BIND(xsd:integer(?more_units) AS ?more_units) }
omop measurements query result, including vocab and manually asserted mmHg units for BP
more_units column from omop measurements query result...
enc_type_code
patient_encounter
Penn Data Store Master Data Managment schema
Penn Data Store database
person in cdm_synthea10 schema from syntheaomop_post_icbo at pennturbo.org port 5432
gender_concept_id column from person in cdm_synthea10 schema from syntheaomop_post_icbo at pennturbo.org port 5432
race_concept_id column from person in cdm_synthea10 schema from syntheaomop_post_icbo at pennturbo.org port 5432
person_id column from person in cdm_synthea10 schema from syntheaomop_post_icbo at pennturbo.org port 5432
birth_datetime column from person in cdm_synthea10 schema from syntheaomop_post_icbo at pennturbo.org port 5432
person_source_value column from person in cdm_synthea10 schema from syntheaomop_post_icbo at pennturbo.org port 5432
visit_occurrence in cdm_synthea10 schema from syntheaomop_post_icbo at pennturbo.org port 5432
person_id column from visit_occurrence in cdm_synthea10 schema from syntheaomop_post_icbo at pennturbo.org port 5432
visit_concept_id column from visit_occurrence in cdm_synthea10 schema from syntheaomop_post_icbo at pennturbo.org port 5432
visit_end_date column from visit_occurrence in cdm_synthea10 schema from syntheaomop_post_icbo at pennturbo.org port 5432
visit_occurrence_id column from visit_occurrence in cdm_synthea10 schema from syntheaomop_post_icbo at pennturbo.org port 5432
visit_source_value column from visit_occurrence in cdm_synthea10 schema from syntheaomop_post_icbo at pennturbo.org port 5432
visit_start_date column from visit_occurrence in cdm_synthea10 schema from syntheaomop_post_icbo at pennturbo.org port 5432
preceding_visit_occurrence_id column from visit_occurrence in cdm_synthea10 schema from syntheaomop_post_icbo at pennturbo.org port 5432
procedure_occurrence in cdm_synthea10 schema from syntheaomop_post_icbo at pennturbo.org port 5432
person_id column from procedure_occurrence in cdm_synthea10 schema from syntheaomop_post_icbo at pennturbo.org port 5432
procedure_occurrence_id column from procedure_occurrence in cdm_synthea10 schema from syntheaomop_post_icbo at pennturbo.org port 5432
visit_occurrence_id column from procedure_occurrence in cdm_synthea10 schema from syntheaomop_post_icbo at pennturbo.org port 5432
procedure_source_concept_id column from procedure_occurrence in cdm_synthea10 schema from syntheaomop_post_icbo at pennturbo.org port 5432
procedure_source_value column from procedure_occurrence in cdm_synthea10 schema from syntheaomop_post_icbo at pennturbo.org port 5432
procedure_date column from procedure_occurrence in cdm_synthea10 schema from syntheaomop_post_icbo at pennturbo.org port 5432
measurement_id column from measurement query result
person_id column from measurement query result
measurement_datetime column from measurement query result
unit_concept_id column from measurement query result
visit_occurrence_id column from measurement query result
measurement_source_value column from measurement query result
measurement_source_concept_id column from measurement query result
condition_occurrence in cdm_synthea10 schema from syntheaomop_post_icbo at pennturbo.org port 5432
PREFIX : <http://api.stardog.com/> PREFIX owl: <http://www.w3.org/2002/07/owl#> PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX stardog: <tag:stardog:api:> PREFIX xsd: <http://www.w3.org/2001/XMLSchema#> MAPPING FROM SQL { SELECT de.*, c.vocabulary_id FROM "cdm_synthea10"."drug_exposure" de join cdm_synthea10.concept c on de.drug_source_concept_id = c.concept_id -- WHERE "measurement_date" IS NOT NULL AND "measurement_time" IS NOT NULL AND "operator_concept_id" IS NOT NULL AND "value_as_number" IS NOT NULL AND "value_as_concept_id" IS NOT NULL AND "unit_concept_id" IS NOT NULL AND "range_low" IS NOT NULL AND "range_high" IS NOT NULL AND "provider_id" IS NOT NULL AND "visit_occurrence_id" IS NOT NULL AND "visit_detail_id" IS NOT NULL AND "measurement_source_value" IS NOT NULL AND "unit_source_value" IS NOT NULL AND "value_source_value" IS NOT NULL WHERE "visit_occurrence_id" < 30 } TO { ?subject <http://api.stardog.com/drug_exposure#days_supply> ?days_supply . ?subject <http://api.stardog.com/drug_exposure#dose_unit_source_value> ?dose_unit_source_value . ?subject <http://api.stardog.com/drug_exposure#drug_concept_id> ?drug_concept_id . ?subject <http://api.stardog.com/drug_exposure#drug_exposure_end_date> ?drug_exposure_end_date . ?subject <http://api.stardog.com/drug_exposure#drug_exposure_end_datetime> ?drug_exposure_end_datetime . ?subject <http://api.stardog.com/drug_exposure#drug_exposure_id> ?drug_exposure_id . ?subject <http://api.stardog.com/drug_exposure#drug_exposure_start_date> ?drug_exposure_start_date . ?subject <http://api.stardog.com/drug_exposure#drug_exposure_start_datetime> ?drug_exposure_start_datetime . ?subject <http://api.stardog.com/drug_exposure#drug_source_concept_id> ?drug_source_concept_id . ?subject <http://api.stardog.com/drug_exposure#drug_source_value> ?drug_source_value . ?subject <http://api.stardog.com/drug_exposure#drug_type_concept_id> ?drug_type_concept_id . ?subject <http://api.stardog.com/drug_exposure#lot_number> ?lot_number . ?subject <http://api.stardog.com/drug_exposure#person_id> ?person_id . ?subject <http://api.stardog.com/drug_exposure#provider_id> ?provider_id . ?subject <http://api.stardog.com/drug_exposure#quantity> ?quantity . ?subject <http://api.stardog.com/drug_exposure#refills> ?refills . ?subject <http://api.stardog.com/drug_exposure#route_concept_id> ?route_concept_id . ?subject <http://api.stardog.com/drug_exposure#route_source_value> ?route_source_value . ?subject <http://api.stardog.com/drug_exposure#sig> ?sig . ?subject <http://api.stardog.com/drug_exposure#stop_reason> ?stop_reason . ?subject <http://api.stardog.com/drug_exposure#verbatim_end_date> ?verbatim_end_date . ?subject <http://api.stardog.com/drug_exposure#visit_detail_id> ?visit_detail_id . ?subject <http://api.stardog.com/drug_exposure#visit_occurrence_id> ?visit_occurrence_id . ?subject <http://api.stardog.com/measurement#vocabulary_id> ?vocabulary_id . ?subject rdf:type :drug_exposure } WHERE { # BIND(template("drug_exposure{drug_exposure_id}_{person_id}_{drug_concept_id}_{drug_exposure_start_date}_{drug_exposure_start_datetime}_{drug_exposure_end_date}_{drug_exposure_end_datetime}_{verbatim_end_date}_{drug_type_concept_id}_{stop_reason}_{refills}_{quantity}_{days_supply}_{sig}_{route_concept_id}_{lot_number}_{provider_id}_{visit_occurrence_id}_{visit_detail_id}_{drug_source_value}_{drug_source_concept_id}_{route_source_value}_{dose_unit_source_value}") AS ?subject) BIND(template("drug_exposure_{drug_exposure_id}") AS ?subject) BIND(xsd:date(?drug_exposure_end_date) AS ?drug_exposure_end_date) BIND(xsd:date(?drug_exposure_start_date) AS ?drug_exposure_start_date) BIND(xsd:date(?verbatim_end_date) AS ?verbatim_end_date) BIND(xsd:dateTime(?drug_exposure_end_datetime) AS ?drug_exposure_end_datetime) BIND(xsd:dateTime(?drug_exposure_start_datetime) AS ?drug_exposure_start_datetime) BIND(xsd:double(?quantity) AS ?quantity) BIND(xsd:integer(?days_supply) AS ?days_supply) BIND(xsd:integer(?drug_concept_id) AS ?drug_concept_id) BIND(xsd:integer(?drug_exposure_id) AS ?drug_exposure_id) BIND(xsd:integer(?drug_source_concept_id) AS ?drug_source_concept_id) BIND(xsd:integer(?drug_type_concept_id) AS ?drug_type_concept_id) BIND(xsd:integer(?person_id) AS ?person_id) BIND(xsd:integer(?provider_id) AS ?provider_id) BIND(xsd:integer(?refills) AS ?refills) BIND(xsd:integer(?route_concept_id) AS ?route_concept_id) BIND(xsd:integer(?visit_detail_id) AS ?visit_detail_id) BIND(xsd:integer(?visit_occurrence_id) AS ?visit_occurrence_id) }
omop drug_exposure plus vocabulary
drug_exposure in cdm_synthea10 schema from syntheaomop_post_icbo at pennturbo.org port 5432
OMOP drug_exposure/prescription identifier source
OMOP condition_occurrence/diagnosis identifier source
(denoter of the) OMOP condition_occurrence/diagnosis source
(denoter of the) OMOP drug_exposure/prescription identifier source
condition_end_datetime column from condition_occurrence in cdm_synthea10 schema from syntheaomop_post_icbo at pennturbo.org port 5432
condition_occurrence_id column from condition_occurrence in cdm_synthea10 schema from syntheaomop_post_icbo at pennturbo.org port 5432
condition_source_concept_id column from condition_occurrence in cdm_synthea10 schema from syntheaomop_post_icbo at pennturbo.org port 5432
condition_start_datetime column from condition_occurrence in cdm_synthea10 schema from syntheaomop_post_icbo at pennturbo.org port 5432
condition_source_value column from condition_occurrence in cdm_synthea10 schema from syntheaomop_post_icbo at pennturbo.org port 5432
verbatim_end_date column from condition_occurrence in cdm_synthea10 schema from syntheaomop_post_icbo at pennturbo.org port 5432
person_id column from condition_occurrence in cdm_synthea10 schema
person_id column from drug_exposure query result
visit_occurrence_id column from drug_exposure in cdm_synthea10 schema from syntheaomop_post_icbo at pennturbo.org port 5432
visit_occurrence_id column from condition_occurrence in cdm_synthea10 schema from syntheaomop_post_icbo at pennturbo.org port 5432
drug_exposure_id column from omop drug_exposure plus vocabulary query result
drug_exposure_start_datetime column from omop drug_exposure plus vocabulary query result
drug_source_value column from omop drug_exposure plus vocabulary query result
PDS med order identfier source
denoter of the PDS med order identifier source
patient_class
The value of the sum of the primary and secondary Gleason scores (range 2-10). If three patterns are identified, it is the sum of the primary pattern score and the score of the least well-differentiated pattern.
The most prevalent Gleason pattern in a prostate biopsy or prostatectomy specimen. The Gleason score is defined by adding the most prevalent (primary) and second most prevalent (secondary) patterns.
The second most prevalent Gleason pattern in a prostate biopsy or prostatectomy specimen. The Gleason score is defined by adding the most prevalent (primary) and second most prevalent (secondary) patterns.
Prostate carcinoma patterns occupying less than 5% of the tumor.
A mass unit which is equal to the mass of the International Prototype Kilogram kept by the BIPM at Svres, France.
A length unit which is equal to one hundredth of a meter or 10^[-2] m.
A length unit which is equal to one thousandth of a meter or 10^[-3] m.
A mass unit which is equal to 10^[-12] g.
A unit of molarity which is equal to one thousandth of a molar or 10^[-3] M.
An area density unit which is equal to the mass of an object in kilograms divided by the surface area in meters squared.
A dimensionless ratio unit which denotes numbers as fractions of 100.
MAM manually copied class definition from UO, change from a class definition with a superclass to a named individual definition with a type, and pasted into TURBO ontology
A dimensionless concentration notation which denotes the acidity of a solution in terms of activity of hydrogen ions (H+).
A mass density unit which is equal to mass of an object in grams divided by the volume in deciliters.
A unit of pressure equal to the amount of fluid pressure one millimeter deep in mercury at zero degrees centigrade on Earth.
A mass unit density which is equal to mass of an object in nanograms divided by the volume in milliliters.
GENO is an OWL model of genotypes, their more fundamental sequence components, and links to related biological and experimental entities. At present many parts of the model are exploratory and set to undergo refactoring. In addition, many classes and properties have GENO URIs but are place holders for classes that will be imported from an external ontology (e.g. SO, ChEBI, OBI, etc). Furthermore, ongoing work will implement a model of genotype-to-phenotype associations. This will support description of asserted and inferred relationships between a genotypes, phenotypes, and environments, and the evidence/provenance behind these associations. Documentation is under development as well, and for now a slidedeck is available at http://www.slideshare.net/mhb120/brush-icbo-2013
The core Infectious Disease Ontology is an ontology of entities generally relevant to both the biomedical and clinical aspects of infectious diseases, including terms such as 'pathogen', 'host', 'vector', and 'vaccine'. The structure of IDO adheres to the Basic Formal Ontology. Terms in IDO that are within the scope of other OBO Foundry ontologies, such as the Gene Ontology, are derived from those ontologies. Other terms are defined as cross-products of terms from Foundry ontologies to the extent possible. For more information, see http://www.infectiousdiseaseontology.org/Home.html.
Vision Release: 1.0.59
OGG is a biological ontology in the area of genes and genomes. OGG uses the Basic Formal Ontology (BFO) as its upper level ontology. This OGG document contains the genes and genomes of a list of selected organisms, including human, two viruses (HIV and influenza virus), and bacteria (B. melitensis strain 16M, E. coli strain K-12 substrain MG1655, M. tuberculosis strain H37Rv, and P. aeruginosa strain PAO1). More OGG information for other organisms (e.g., mouse, zebrafish, fruit fly, yeast, etc.) may be found in other OGG subsets.
This ontology grew out of efforts to represent the reality underlying the demographic information required by the US federal government's "meaningful use" criteria for electronic medical records and a presentation by Dr. William Hogan at the Electronic Health Record of the Future conference in Buffalo, NY http://ontology.buffalo.edu/EHR/Demographics_Hogan_Buffalo_2010_09_22.ppt
William Hogan
Swetha Garimalla
The Ontology of Medically Related Social Entities
Shariq Tariq
An ontology of drug prescriptions
This is a merged version of the ontology.
Use reasoner in OBO Edit to see the correct hierarchy.
The PRotein Ontology is licensed under CC BY 4.0. Please see http://obofoundry.org/ontology/pr for details.
The OBO Relations Ontology (RO) is a collection of OWL relations (ObjectProperties) intended for use across a wide variety of biological ontologies.
Includes Ontology(OntologyID(Anonymous-21)) [Axioms: 32 Logical Axioms: 0]
Includes Ontology(OntologyID(Anonymous-21)) [Axioms: 26 Logical Axioms: 0]