derives_from
Derivation as a relation between instances. The temporal relation of derivation is more complex. Transformation, on the instance level, is just the relation of identity: each adult is identical to some child existing at some earlier time. Derivation on the instance-level is a relation holding between non-identicals. More precisely, it holds between distinct material continuants when one succeeds the other across a temporal divide in such a way that at least a biologically significant portion of the matter of the earlier continuant is inherited by the later. Thus we will have axioms to the effect that from c derives_from c1 we can infer that c and c1 are not identical and that there is some instant of time t such that c1 exists only prior to and c only subsequent to t. We will also be able to infer that the spatial region occupied by c as it begins to exist at t overlaps with the spatial region occupied by c1 as it ceases to exist in the same instant.
Derivation on the instance level (*derives_from*) holds between distinct material continuants when one succeeds the other across a temporal divide in such a way that at least a biologically significant portion of the matter of the earlier continuant is inherited by the later. We say that one class C derives_from class C' if instances of C are connected to instances of C' via some chain of instance-level derivation relations. Example: osteocyte derives_from osteoblast. Formally: C derives_immediately_from C' if and only if: given any c and any t, if c instantiates C at time t, then there is some c' and some t', such that c' instantiates C' at t' and t' earlier-than t and c *derives_from* c'. C derives_from C' if and only if: there is an chain of immediate derivation relations connecting C to C'.
derived_from
Description
An account of the content of the resource.
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.
term replaced by
Person:Alan Ruttenberg
Use on obsolete terms, relating the term to another term that can be used as a substitute
Contributor
An entity responsible for making contributions to the content of the resource.
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.
curator note
An administrative note of use for a curator but of no use for a user
PERSON:Alan Ruttenberg
OBO foundry unique label
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 .
An alternative name for a class or property which is unique across the OBO Foundry.
GROUP:OBO Foundry <http://obofoundry.org/>
PERSON:Bjoern Peters
PERSON:Chris Mungall
PERSON:Melanie Courtot
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.
preceded_by
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.
P preceded_by P' if and only if: given any process p that instantiates P at a time t, there is some process p' such that p' instantiates P' at time t', and t' is earlier than t.
Creator
An entity primarily responsible for making the content of the resource.
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.
Subject and Keywords
The topic of the content of the resource.
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.
agent_in
precedes
Resource Identifier
An unambiguous reference to the resource within a given context.
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).
Date
A date associated with an event in the life cycle of the resource.
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.
participates_in
Title
Typically, a Title will be a name by which the resource is formally known.
A name given to the resource.
inheres_in
This clarifies that only specifically dependent continuants inhere in (specifically) one independent continuant over all time. For GDCs, there in implicitly inherence to all the independent continuants in which the concretizations inhere. Should add a 'cardinality 1' restriction to the definition of specifically dependent continuant.
This relation belongs in BFO/RO, and will be in BFO 2
This relation links qualities, functions, dispositions and other dependent continuants to their bearers. Examples: A particular shape that inheres in a lung; The redness that ineres in a Drosophila eye; Catalytic activity function inheres_in catalytic molecule. Note that inherence is a functional relation: if x inheres_in y at t and x inheres_in z at t, then y=z. We leave open the possibility of a relation multiply_inheres_in, such as between a gene sequence and the multiple chromosomes it multiply inheres in. The super-relation of both inheres_in and multiply_inheres_in would be depends_on
has_bearer
A relation between a dependent continuant D and an entity E. D inheres_in E iff: given any d that instantiates D at t, there exists some e that instantiates E at t and d *inheres_in* e at t. Here *inheres_in* is the primitive instance level relation.
Relation
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 related resource.
transformed_into
derived_into
has_participant
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.
P has_participant C if and only if: given any process p that instantiates P there is some continuant c, and some time t, such that: c instantiates C at t and c participates in p at t
definition
PERSON:Daniel Schober
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.
expand expression to
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
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)"
has_specified_input
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.
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.
PERSON: Alan Ruttenberg
see is_input_of example_of_usage
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.
in branch
An annotation property indicating which module the terms belong to. This is currently experimental and not implemented yet.
has curation status
PERSON:Bill Bug
Language
A language of the intellectual content of the resource.
Recommended best practice is to use RFC 3066 [RFC3066], which, in conjunction with ISO 639 [ISO639], defines two- and three-letter primary language tags with optional subtags. Examples include "en" or "eng" for English, "akk" for Akkadian, and "en-GB" for English used in the United Kingdom.
definition source
Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w
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
Resource Type
The nature or genre of the content of the resource.
Type includes terms describing general categories, functions, genres, or aggregation levels for content. Recommended best practice is to select a value from a controlled vocabulary (for example, the DCMI Type Vocabulary [DCMITYPE]). To describe the physical or digital manifestation of the resource, use the Format element.
has_quality
A relation between an entity and a quality. For types: E has_quality Q iff: for any eEt, exists qQt such that q inheres_in e at t. For instances: e has_quality q at t iff q inheres_in e at t and q instance-of Quality [GOC:cjm]
antisymmetric property
Alan Ruttenberg
part_of antisymmetric property xsd:true
use boolean value xsd:true to indicate that the property is an antisymmetric property
definition 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
first order logic expression
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.
alternative term
An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent)
expand assertion to
A macro expansion tag applied to an annotation property which can be expanded into a more detailed axiom.
Chris Mungall
ObjectProperty: RO??? Label: spatially disjoint from Annotations: expand_assertion_to "DisjointClasses: (http://purl.obolibrary.org/obo/BFO_0000051 some ?X) (http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)"
transformation_of
When an embryonic oenocyte (a type of insect cell) is transformed into a larval oenocyte, one and the same continuant entity preserves its identity while instantiating distinct classes at distinct times. The class-level relation transformation_of obtains between continuant classes C and C1 wherever each instance of the class C is such as to have existed at some earlier time as an instance of the distinct class C1 (see Figure 2 in paper). This relation is illustrated first of all at the molecular level of granularity by the relation between mature RNA and the pre-RNA from which it is processed, or between (UV-induced) thymine-dimer and thymine dinucleotide. At coarser levels of granularity it is illustrated by the transformations involved in the creation of red blood cells, for example, from reticulocyte to erythrocyte, and by processes of development, for example, from larva to pupa, or from (post-gastrular) embryo to fetus or from child to adult. It is also manifest in pathological transformations, for example, of normal colon into carcinomatous colon. In each such case, one and the same continuant entity instantiates distinct classes at different times in virtue of phenotypic changes.
Relation between two classes, in which instances retain their identity yet change their classification by virtue of some kind of transformation. Formally: C transformation_of C' if and only if given any c and any t, if c instantiates C at time t, then for some t', c instantiates C' at t' and t' earlier t, and there is no t2 such that c instantiates C at t2 and c instantiates C' at t2.
location_of
Source
A reference to a resource from which the present resource is derived.
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.
editor preferred term
The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)
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
example
has_agent
As for has_participant, but with the additional condition that the component instance is causally active in the relevant process
Publisher
An entity responsible for making the resource available
Examples of a Publisher include a person, an organisation, or a service. Typically, the name of a Publisher should be used to indicate the entity.
Coverage
Coverage will typically include spatial location (a place name or geographic coordinates), temporal period (a period label, date, or date range) or jurisdiction (such as a named administrative entity). Recommended best practice is to select a value from a controlled vocabulary (for example, the Thesaurus of Geographic Names [TGN]) and that, where appropriate, named places or time periods be used in preference to numeric identifiers such as sets of coordinates or date ranges.
The extent or scope of the content of the resource.
In OWL 2 add AnnotationPropertyRange('is denotator type' 'denotator type')
relates an class defined in an ontology, to the type of it's denotator
is denotator type
imported from
For external terms/classes, the ontology from which the term was imported
bearer_of
has_inherer
has_inherent
A relation between an entity and a dependent continuant; the reciprocal relation of inheres_in
located_in
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
C located_in C' if and only if: given any c that instantiates C at a time t, there is some c' such that: c' instantiates C' at time t and c *located_in* c'. (Here *located_in* is the instance-level location relation.)
is_realized_by
Relation between a realizable and a process. Reciprocal relation of realizes [GOC:cjm]
Format
The physical or digital manifestation of the resource.
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).
Rights Management
Typically, a Rights element will contain a rights management statement for the resource, or reference a service providing such information. Rights information often encompasses Intellectual Property Rights (IPR), Copyright, and various Property Rights. If the Rights element is absent, no assumptions can be made about the status of these and other rights with respect to the resource.
Information about rights held in and over the resource.
realizes
Relation between a process and a function, where the unfolding of the process requires the execution of the function. Class level: P realizes F iff: given any p that instantiates P, there exists some f, t such that f instantiates F at t and p *realizes* f. Here, *realizes* is the primitive instance level relation [GOC:cjm]
example of usage: The process of 'histidine catabolism' (GO:0006548) realizes the function 'histidine ammonia lyase activity' (GO:0004397) (note: here 'activity' denotes a function and not a process). We leave open the possibility of defining in future the sub-relations directly_realizes (as bewteen a function and it's functioning) and indirectly_realizes.
has measurement unit label
is about
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
This document is about information artifacts and their representations
is_about is a (currently) primitive relation that relates an information artifact to an entity.
person:Alan Ruttenberg
mentions
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
An information artifact IA mentions an entity E exactly when it has a component/part that denotes E
PERSON: Jonathan Rees
Person: Alan Ruttenberg
denotes
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
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.
Conversations with Barry Smith, Werner Ceusters, Bjoern Peters, Michel Dumontier, Melanie Courtot, James Malone, Bill Hogan
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
is quality measurement of
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.
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
has coordinate unit label
relating a cartesian spatial coordinate datum to a unit label that together with the values represent a point
is duration of
relates a process to a time-measurement-datum that represents the duration of the process
is quality measured as
2009/10/19 Alan Ruttenberg. Named 'junk' relation useful in restrictions, but not a real instance relationship
inverse of the relation of is quality measurement of
is quality specification of
Person:Bjoern Peters
a relation between a data item and a quality of a material entity where the material entity is the specified output of a material transformation which achieves an objective specification that indicates the intended value of the specified quality.
quality is specified as
inverse of the relation of is quality specification of
has time stamp
relates a time stamped measurement datum to the time measurement datum that denotes the time when the measurement was taken
has measurement datum
relates a time stamped measurement datum to the measurement datum that was measured
results_in
capable_of
is_concretization_of
a relationship between a generically dependent continuant and at least one specifically dependent continuant upon which it existentially depends
is_specified_input_of
some Autologous EBV(Epstein-Barr virus)-transformed B-LCL (B lymphocyte cell line) is_input_for instance of Chromum Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay
is_concretized_as
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.
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.
definition needs clean up to indicate directionality
has_disposition
has_function
Relation between an independent continuant and a function.
has_output
Examples: secretory cells. Should this be has_function (export of ...)
C has_output C'
has_role
A relation between a continuant C and a role R. The reciprocal relation of role_of.
negatively_regulates
A regulation relation in which the unfolding of the regulating process *decreases* the frequency, rate or extent of the regulated process
positively_regulates
A regulation relation in which the unfolding of the regulating process *increases* the frequency, rate or extent of the regulated process
realized_by
NOTE: there appears to be some consistency in usage as to whether processes or continuants realize
Relation between a realizable and a process. Reciprocal relation of realizes
executed_during
has_realization
The process of 'histidine catabolism' (GO:0006548) realizes the function 'histidine ammonia lyase activity' (GO:0004397) (note: here 'activity' denotes a function and not a process). We leave open the possibility of defining in future the sub-relations directly_realizes (as bewteen a function and it's functioning) and indirectly_realizes. NOTE: there appears to be some consistency in usage as to whether processes or continuants realize
executes
Relation between a process and a function, where the unfolding of the process requires the execution of the function. Class level: P realizes F iff: given any p that instantiates P, there exists some f, t such that f instantiates F at t and p *realizes* f. Here, *realizes* is the primitive instance level relation
involves_execution_of
has_function_part
is_realization_of
regulates
A relation between a process and a process or quality. A regulates B if the unfolding of A affects the frequency, rate or extent of B. A is called the regulating process, B the regulates process
results_in_formation_of
Example: autophagic vacuole formation results_in_formation_of autophagic vacuole. macromolecular complex assembly results_in_formation_of a macromolecule. Note: essentially the same as biosynthesis, although in biosynthesis the assembly is via chemical reactions
results_in_creation_of
results_in_assembly_of
P results_in_formation_of C : any instance of P gives rise to a C from the parts of C. Formally: forall pP, exists some c such that c instantiates C at end-of p, and c has some parts c1, c2, ... such that the parts are connected at the end-of p and disconected at the start-of p
A relation between a relational quality and an independent continuant, subproperty of inheres that distinguishes the main bearers of a relational quality from additional dependents.
unfolds_in
Example: oocyte axis determination : The establishment, maintenance and elaboration of an axis in the oocyte. This process unfolds_in the oocyte
P unfolds_in C : the execution of P is spatially contained by C. forall pP, forall c' partipates_in p, c' located_in C at t, for some t in P
adjacent_to
Note that adjacent_to as thus defined is not a symmetric relation, in contrast to its instance-level counterpart. For it can be the case that Cs are in general such as to be adjacent to instances of C1 while no analogous statement holds for C1s in general in relation to instances of C. Examples are: nuclear membrane adjacent_to cytoplasm; seminal vesicle adjacent_to urinary bladder; ovary adjacent_to parietal pelvic peritoneum
C adjacent to C' if and only if: given any instance c that instantiates C at a time t, there is some c' such that: c' instantiates C' at time t and c and c' are in spatial proximity
contained_in
Containment obtains in each case between material and immaterial continuants, for instance: lung contained_in thoracic cavity; bladder contained_in pelvic cavity. Hence containment is not a transitive relation. If c part_of c1 at t then we have also, by our definition and by the axioms of mereology applied to spatial regions, c located_in c1 at t. Thus, many examples of instance-level location relations for continuants are in fact cases of instance-level parthood. For material continuants location and parthood coincide. Containment is location not involving parthood, and arises only where some immaterial continuant is involved. To understand this relation, we first define overlap for continuants as follows: c1 overlap c2 at t =def for some c, c part_of c1 at t and c part_of c2 at t. The containment relation on the instance level can then be defined (see definition):
C contained_in C' if and only if: given any instance c that instantiates C at a time t, there is some c' such that: c' instantiates C' at time t and c located_in c' at t, and it is not the case that c *overlaps* c' at t. (c' is a conduit or cavity.)
contains
has_improper_part
See reasons for obsoletion of improper_part_of
has_integral_part
has_part
has_proper_part
improper_part_of
OBSOLETE. The definition is "As for part_of, with the additional constraint that subject and object may be identical". However, part_of is already reflexive, therefore improper_part_of is identical to part_of. If read differently, as "improper_part_of is part_of but not proper_part_of",improper_part_of becomes identity. So, improper_part_of is either identical to part_of or to identity, and not an intuitive synonym for either of them. [Robert Hoehndorf]
As for part_of, with the additional constraint that subject and object may be identical
integral_part_of
C integral_part_of C' if and only if: C part_of C' AND C' has_part C
part_of
Parthood as a relation between instances: The primitive instance-level relation p part_of p1 is illustrated in assertions such as: this instance of rhodopsin mediated phototransduction part_of this instance of visual perception. This relation satisfies at least the following standard axioms of mereology: reflexivity (for all p, p part_of p); anti-symmetry (for all p, p1, if p part_of p1 and p1 part_of p then p and p1 are identical); and transitivity (for all p, p1, p2, if p part_of p1 and p1 part_of p2, then p part_of p2). Analogous axioms hold also for parthood as a relation between spatial regions. For parthood as a relation between continuants, these axioms need to be modified to take account of the incorporation of a temporal argument. Thus for example the axiom of transitivity for continuants will assert that if c part_of c1 at t and c1 part_of c2 at t, then also c part_of c2 at t. Parthood as a relation between classes: To define part_of as a relation between classes we again need to distinguish the two cases of continuants and processes, even though the explicit reference to instants of time now falls away. For continuants, we have C part_of C1 if and only if any instance of C at any time is an instance-level part of some instance of C1 at that time, as for example in: cell nucleus part_ of cell.
There is controversy about this relation intended to represent the relation between some arbitrary physical thing that is used as a represention/proxy/pointer to something else
For continuants: C part_of C' if and only if: given any c that instantiates C at a time t, there is some c' such that c' instantiates C' at time t, and c *part_of* c' at t. For processes: P part_of P' if and only if: given any p that instantiates P at a time t, there is some p' such that p' instantiates P' at time t, and p *part_of* p' at t. (Here *part_of* is the instance-level part-relation.)
proper_part_of
As for part_of, with the additional constraint that subject and object are distinct
relationship
this relation was superfluous, so it has been obsoleted
A relationship between two classes (terms). Relationships between classes are expressed in terms of relations on underlying instances.
has measurement value
has x coordinate value
has z coordinate value
has y coordinate value
amplified virus preparation
MC, 20101203: redefined as defined class after adding virus amplification process
An amplified virus preparation is an organimal group representing a large number of copies of one or more viruses.
An enriched cell fraction is a cell fraction that has an increased concentration of one or more cell fraction components.
MC, 20101203: added enrichment process and cell fraction from GO and restrictions to make this a defined class
A complementary ribonucleic acid is a biological macromolecule role played by a RNA molecule that serves as a complementary copy (positive copy for negative stranded RNA and vice versa).
A sequencing laboratory role is a laboratory role played by a population that performs the assay process of nucleotide or amino acid sequenceing analysis.
MC, 08092009: moved as subclass of new mireoted term OBI_0000202, investigation agent role, which can be borne by either individuals or insitutions
MC, 20100212: submitted tracker item to IDO at http://code.google.com/p/infectious-disease-ontology/issues/detail?id=25 to clarify definition of parent term virion
WEB: http://www.medterms.com/script/main/art.asp?articlekey=11558
A complete virus particle of influenza virus with its DNA or RNA core and protein coat as it exists outside the cell.
Influenza hemagglutinin is a type of hemagglutinin found on the surface of the influenza viruses. It is an antigenic glycoprotein. It is responsible for binding the virus to the cell that is being infected.
WEB: http://en.wikipedia.org/wiki/Hemagglutinin_%28influenza%29
MC, 20101201: added as subclass of hemagglutinin
20100203: submitted to PRO: http://sourceforge.net/tracker/?func=detail&atid=1135711&aid=2945554&group_id=266825
Neuraminidase enzymes are glycoside hydrolase enzymes (EC 3.2.1.18) that cleave the glycosidic linkages of neuraminic acids. Neuraminidase enzymes are a large family, found in a range of organisms. The most commonly known neuraminidase is the viral neuraminidase, a drug target for the prevention of influenza infection. The viral neuraminidases are frequently used as an antigenic determinants found on the surface of the Influenza virus. Some variants of the influenza neuraminidase confer more virulence to the virus than others. Neuraminidases, also called sialidases, catalyze the hydrolysis of terminal sialic acid residues from the newly formed virions and from the host cell receptors.[2] Sialidase activities include assistance in the mobility of virus particles through the respiratory tract mucus and in the elution of virion progeny from the infected cell.[3][4]
20100203: submitted to PRO: http://sourceforge.net/tracker/?func=detail&aid=2945634&group_id=266825&atid=1135711
WEB: http://en.wikipedia.org/wiki/Neuraminidase
virus isolation
PERSON: Melanie Courtot
WEB: http://virology-online.com/general/Test1.htm
a material separation to recover the virusfraction of an input material
haemadsorption
Influenza and parainfluenza viruses do not ordinarily induce CPE, however they possess haemagglutinins and thus the ability to absorb guinea pig RBCs as they bud from the cell. This phenomenon is known as haemadsorption. Commonly employed cell cultures include primary monkey kidney, LLC-MK2 and MDCK cells. The cell cultures are incubated with a suspension of guinea pig RBCs at 4oC or RT for 30 minutes. The unabsorbed RBCs are then removed and the cell sheet observed microscopically for the presence of haemadsorption.
the absorption of red blood cells by haemagglutinins
viral isolate
A data transformation event that encompasses the process of submitting new or updated sequence information or annotation to GenBank.
trypsin
Submitted to PRO, see https://sourceforge.net/tracker/?func=detail&atid=1135711&aid=3397087&group_id=266825
Trypsin (EC 3.4.21.4) is a serine protease found in the digestive system of many vertebrates, where it hydrolyses proteins. Trypsin is produced in the pancreas as the inactive proenzyme trypsinogen.
WEB: http://en.wikipedia.org/wiki/Trypsin
A disease phenotype that descrives the inherent severity of the disease independent of its management, including drug and other interventions.
MC, 20101119: moved from quality>output assessment > measure to scalar measurement datum
The quantity of virus in a specified suspension volume (e.g., 0.1 ml) that will infect 50% of a number (n) of cell culture microplate wells, or tubes
trypsin auxotrophic organism
An organism that requires tryspin to grow
A bird after completing the post-juvenal molt, but has not acquired the complete adult plumage. A life stage of any bird older than a nestling or chick that has not reached sexual maturity or its basic winter or first winter plumage.
An explosive expulsion of air from the lungs acting as a protective mechanism to clear the air passages or as a symptom of pulmonary disturbance.
A intensity of body moult is a measurement datum that describes the intensity of the periodic replacement of epidermis (skin), pelage (hair, fur, wool), or other external layer. In some species, other body parts may be shed, for example, wings in some insects. Examples include old feathers in birds, old hairs in mammals (especially dogs and other canidae), old skin in reptiles, and the entire exoskeleton in arthropods.
20110823, MC: need to check on the unit for this. If it has a unit it should be asserted under scalar measurement datum
20110823: this term initially refered only to bird in its definition. We may also need to create a moulting process.
Date that the virus passage(s) took place.
An annotation event is a data transformation event which encompasses adding biological information to genome sequence. This is a very complex task, and the process for doing this is rapidly evolving. Several groups are doing automated computational annotation of several genomes. Features that are added to the genome often include gene models, SNPs, and STSs.
GROUP: FLU
The GPS latitude coordinate where the sample was collected.
MC, 20101118: this is a placeholder meant to be removed when we will have a laboratory, which will allow us to define current subclass using the is_about relation
MC, 08092009: moved from quality to GDC. Those are information entities. Need additional clean up. There is no laboratory role.
MC, 20101118: moved under data item and renamed data about a laboratory from "quality of a laboratory" Those should be outsourced towards the organization ontology.
An assay which aims at determining the neuraminidase type of an influenza virus.
N typing
A young bird out of the nest and able to take care of itself, but which has not completed the post-juvenal molt.
MC, 20101119: moved from quality to scalar measurement datum.
Initial oxygen saturation is a scalar measurement datum that describes the initial volume of oxygen gas (STP) absorbed from humidity-saturated air at a total pressure of one atmosphere, per unit volume of the liquid at the temperature of measurement (units ml/l).
A date in the format: MON DD CCYY, where MON is the usual three-character abbreviation for month, DD is day of month (1-31), CCYY is the year, including the century. Date may also be reported as year CCYY. (DDMMYY).
specimen identification number
MC, 20101118: removed dbxref to PATO_0001226, count. Updated from "sample number" to "specimen identification number" as per Burke's use case
The unique number inhering in and identifying the specimen
Weariness or exhaustion from labor, exertion, or stress.
Pain in one or more muscles.
MC, 20101119: moved from quality of specimen to scalar measurement datum
A scalar measurement datum denoting the pathogenicity of a virus after several passages in cell culture.
MC, 20101201: updated definition and label
The name of the geographic province where the collection occurred.
A bird that was observed the summer following its year of hatch.
Date that the sequence was submitted (i.e. to GenBank).
Calendar date that the specimen was collected.
virus passage
A virus passage is a transforming material transformation that involves the incubation of a pathogen (as a virus) in a tissue culture, a developing egg, or a living organism to increase the amount of pathogen or to alter its characteristics
An organism which has been vaccinated
vaccination status is an IA about a vaccinated host
The name of the district where the sample was collected.
MC, 20101118: moved from specimen quality to scalar measurement datum
The sample amount as measured in grams, milliliters or other standard unit of measurement.
viral RNA extraction
primaries flight feather
Large outermost flight feathers on wing. Can vary from 9-11, but the number remains constant within a species.
The name of the country where the sample was collected.
The measure that describes the dosage of a drug or poison that is toxic to 50% of the organisms it is tested against.
A specimen collector role is a study personnel role that is performed by a erson who collects the specimen from the environment.
MC: 20101119: moved from strain specimen quality to label. Not sure this term is required.
The taxonomic name for a strain species, consisting of two words, the genus and species.
secondaries flight feather
Flight feathers, smaller than the primaries, occurring in series along rear edge of wing between scapulars, inward of primaries.
The subtype is a quality that describes the subtype of organism from which sequence was obtained.
20110826, MC: renamed from "rural" to "rural environment". Moved under environment.
Rural environment is an environment that is characterized by sparsely-populated non-urban areas, such as found in farming communities or the countryside.
Sequence coverage is the average number of reads representing a given nucleotide in the reconstructed sequence. It can be calculated from the length of the original genome (G), the number of reads(N), and the average read length(L) as N * L/G. For example, a hypothetical genome with 2,000 base pairs reconstructed from 8 reads with an average length of 500 nucleotides will have 2x redundancy. This parameter also enables one to estimate other quantities, such as the percentage of the genome covered by reads (sometimes also called coverage).
MC, 20101201: old definition was "A sequencing specification that describes the average number of times a nucleotide position was sequenced to obtain a consensus." Moved from sequencing specification to measurement datum
A virus passage history record is a passage history record that details the number of times a virus has been passaged in cell culture.
MC, 20111123: moved from quality of specimen to passage history record, and renamed accordingly (with addition of alt term)
has been scheduled for inclusion in OBI: nucleic acid sequence: A data item that is is a string of characters (e.g., A, G, C,T, U, N, R, Y, etc.) and represents the order of nucleotides found somewhere in nature or synthesized.
A sequence submitter role is a study personnel role that is repsponsible for sending sequence (DNA, RNA, Protein) data to a repository, usually GenBank.
The name of the sub-district where collection occurred.
MC, 20101201: updated label from sequencing specification to sequencing protocol to match position in hierarchy
A protocol which specifies conditions, parameters and instructions to be used when performing sequencing assays
The length is a quality that describes measure of the nucleotide or amino acid sequence from beginning to end.
20110826, MC: trasnformed into a defined class. Subclasses rural and urban were renamde and asserted under environment
A transmission environment is the environment in which the etiologic agent was harbored and spread from host to host.
Calendar date that the sample was extracted.
Date that the laboratory isolated the sample.
MC, 20101119: updated label from "replication titer" to "viral replication titer"
MC, 20101119: moved from quality to scalar mesurement dtum and updated defintiion accordingly
A scalar measurement datum that denotes the virus replication level.
A bird after hatch year.
MC, 20101118: moved from winged organism anatomy to length measurement datum
The measured length of the bird wing as the wing is held without being flattened.
Painful throat due to inflammation of the fauces and pharynx.
A strain specimen phenotype that describes the egg infectious dose 50 amount of a virus which is required to kill 50% of the eggs.
An accession number is a quality that describes the unique identifier assigned to the entire sequence record when the record is submitted to GenBank.
MC, 20101202: moved under site and definition updated from "An environment is a spatial region having environmental qualities which may sustain an organism or a community of organisms."
An environment is a site having environmental qualities which may sustain an organism or a community of organisms.
A nucleotide sequencer role is a study personnel role that is performed by a person who determines the genetic sequence for a biomateral.
MC, 20101118: this is a placeholder meant to be removed when we will have the collection process, which will allow us to define current subclass using the is_about relation
MC, 20101118: renamed from collection location context
organism treated with antibiotics
20110824, MC: renamed from "antibiotics administered" after adding correct restrictions. Note that even thought we say "organism treated with antibiotic" the sense of treated is not the one from OGMS:treatment - there doesn't have to be therapeutic intent.
An organism which has been treated with antibiotics
The measured length from the birds head to beak.
MC, 20101207: I am trying to say logically that the info submitted is about the RNA sequence that has been obtained by sequencing the RNA that had been extracted from the virion
A GenBank submission event in which the RNA sequence of a virion is submitted
A measure of the amount or concentration of hemagluttanin in solution.
The measured length of the birds beaks.
Excessive mucous secretion from the nose.
A rise of body temperature above the normal whether a natural response (as to infection) or artificially induced for therapeutic reasons.
A young bird confined to the nest. Nestlings are infant birds having little or no feathering. They may be pink and naked, covered with down feathers, or covered with needle-like feathers (called pin feathers).
A defined period when the sample was extracted.
The address that describes the physical (geographic) location of the laboratory facility.
The amount of RNA that has been sent to the lab for sequencing purposes
MC, 20101201: added definition for this term. Not sure how to deal with it though.
A plaque forming unit per size is a measure that is used in the assessment of the concentration of viruses in a sample.
The name of the city, town, or village where the sample was collected.
The measured length of the bird wing as the wing is held flat.
The GPS longitude coordinate where the sample was collected.
MC, 20101203: updated sample to specimen
The protocol specifying how to collect the specimen
A bird in the first year after hatching.
An assay which aims at determining the hemagglutanin subtype of an influenza virus.
HA typing
MC, 20101202: made it a defined class as there are several methods to identify the heagglutinin type as per http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T32-4C47KNC-5&_user=1022551&_coverDate=07%2F31%2F2004&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_searchStrId=1565330571&_rerunOrigin=google&_acct=C000050484&_version=1&_urlVersion=0&_userid=1022551&md5=c5d1a3bc08abe655acb70076b13e3a74&searchtype=a The haemagglutination-inhibition assay that is routinely used for subtyping and antigenic characterisation of influenza strains does not distinguish between A(H1N1) and A(H1N2) strains; therefore, alternative tests are required for typing the NA. The standard test used to determine neuraminidase type is a rather cumbersome and time-consuming procedure (approximately 18 h) which relies on inhibition, by antibody, of n-acetyl neuraminic acid release from a substrate such as fetuin (Aymard-Henry et al., 1973). Alternative methods of neuraminidase assay have been described, one for example relying on the agglutination of neuraminidase-treated erythrocytes by lectins (Fiszon and Hannoun, 1990 B Fiszon and C Hannoun, Comparison of neuraminidases of the same subtype but from different species using a new method of titration, J. Virol. Methods 27 (1990), pp. 79–90. Abstract | PDF (587 K) | View Record in Scopus | Cited By in Scopus (4)Fiszon and Hannoun, 1990)
The name of the laboratory conducting the scientific research, experiments, analysis or sequencing may be performed.
A nasal congestion is a symptom that is characterized by the blockage of the nasal passages usually due to membranes lining the nose becoming swollen from inflamed blood vessels.
stuffy nose
MC, 20101130: "Antibodies against the viral surface glycoprotein hemagglutinin (HA) provide protective immunity to influenza virus infection, and this protein is therefore the primary component of influenza vaccines. However, the antigenic structure of HA has changed significantly over time, a process known as antigenic drift (6), and in most years, the influenza vaccine has to be updated to ensure sufficient efficacy against newly emerging variants (7, 8). The World Health Organization coordinates a global influenza surveillance network, currently consisting of 112 national influenza centers and four collaborating centers for reference and research. This network routinely characterizes the antigenic properties of influenza viruses using a hemagglutination inhibition (HI) assay "
MC, 20101130: renamed antigenic data (from strain antigenic data) and moved under data item from strain specimen quality
Data reflecting the antigenic properties of influenza viruses characterized using a hemagglutination inhibition (HI) assay
WEB: http://www.sciencemag.org/content/305/5682/371.full
The sequence annotator role is a study personnel role of a scientist who assigns a set of characteristics to a sequence for the purpose of documenting relevant infromation from experimental results to aid in their interpretation.
A extractor role is a study personnel role that is performed by a person who extracts genetic material from a biomaterial.
RNA molecule constituting the genome of viruses
A person with the lead role on the project, as a scientist or engineer.
treatment event
MC, 20101207: I believe this term reflects the biochemical treatment of a sample and is therefore not equivalent to ogms: treatment which is a treatment to alleviate a disorder
The name of the place where the sample was collected.
MC, 20101119: moved from "data about a laboratory" to "specimen identification nmber". See http://groups.google.com/group/influenza-ontology/browse_thread/thread/91adb05b5e6b80aa?hl=en
A laboratory specimen tracking number is a specimen identification number assigned to a specimen by a laboratory with the objective to uniquely identify and follow the specimen.
Calendar date that antiviral treatment was administered.
Date when host first experienced clinical symptoms.
MC, 20101119: moved from quality>output assessment > measure to date
A defined period when the sample was collected.
A GI number is a quality that is an identifier assigned to all sequences at the NCBI, which points to a specific version of a sequence record. GI stands for GenInfo, a database system at NCBI that preceded the Entrez system.
A collection quantity is a generically dependant continuant that specifies the quantity of material collected.
Method by which virus is isolated.
The name of the state where the collection occurred.
Date that the laboratory received the sequence.
MC, 20101207: we can't say that the output information is about the input material
MC, 20101207: moved under DNA sequencing
MC, 20101207: I think genomic sequencing is an assay that has specified input some DNA (genome?) and has specified output some genotype or ICE about a sequence
20110826, MC: renamed from "urban" to "urban environment". Moved under environment.
Urban environment is an environment that is characterized by densely-populated areas, such as found in cities.
A human social group is a material entitiy that is a collection of humans, who share certain characteristics, interact with one another, accept expectations and obligations as members of the group, and share a common identity.
A pain in the head.
organism treated with antiviral drug
An organism which has been treated with antiviral drugs.
hospitalized host
A host hospitalized is a condition that indicates whether or not an organism has been hospitalized.
A bac_name is a quality that identifies the bacterial artifical chromosome (bac), a large insert cloning vector capable of handling large segments of cloned DNA, typically around 150 kb, which are used in the construction of genomic libraries for genome scale sequencing projects including human, mouse, Arabidopsis, and rice.
bird band identification number
A bird band identification number is a number identifies the individual (often the host) - analagous to a name in a human.
MC, 20101118: moved from quality of organism to identification number
A treatment that specifies which, if any, antiviral treatment has been administered to a host.
MC, 20101118: renamed "data about a genbank entry" from "qualities of genbank" and moved under data item. We should create a genbank record and use the is_about relation to link both
MC, 20101118: this is a placeholder meant to be removed when we will have the class "genbank entry", which will allow us to define current subclass using the is_about relation
A ligated ends molecule is a biological macromolecule with overhanging nucleotides that assist in the ligation process.
MC, 20101118: moved under processed material and updated definition
post disease onset sample collection period
The time period that comprises the sample collection period when the sample was collected following the disease onset.
A bird with definitive plumage or sexually mature. Adult birds are mature, independent birds who are fully feathered for flight and capable of surviving on their own (in regards to food, shelter, etc.
MC, 20101123: moved from quality of infectious disease to duration
The number of days the patient was ill.
A specimen barcode is a specimen identification number formatted as an optical machine-readable representation.
WEB: http://en.wikipedia.org/wiki/Barcode
MC, 20101118: moved from "quality of specimen" under specimen identification number.
A antibody titer is output of a measurement that describes the measure of antibodies in a biomaterial.
See http://groups.google.com/group/influenza-ontology/browse_thread/thread/12b3fb5ef0501b5b?hl=en
A passage history record is a data item recording in sequential order the hosts in which the strain has been previously subcultured in.
A plastic or metal ring attached usually to the ankle of the bird and bearing a band identification number
MC, 20101201: added as bearer of band identification number as per Burke's email at http://groups.google.com/group/influenza-ontology/msg/8781d389ec670463?hl=en
A disposition to initiate an hemagglutination process
WEB: http://en.wikipedia.org/wiki/Hemagglutinin
MC, 20101201: added as request to PRO tracker unanswered. See http://sourceforge.net/tracker/?func=detail&aid=2945554&group_id=266825&atid=1135711
Hemagglutinin is a substance that causes red blood cells to agglutinate (has disposition hemagglutination)
the process of increasing the concentration of a particule of interest in a sample
antiviral drug
A drug used specifically for treating viral infections.
WEB: http://en.wikipedia.org/wiki/Antiviral_drug
A material processing aiming at increasing the number of viruses in a specimen
neuraminidase inhibitor
The function of inhibiting the viral neuraminidase protein, thus preventing the virus from reproducing by budding from the host cell.
WEB: http://en.wikipedia.org/wiki/Neuraminidase_inhibitor
A type of neuraminidase found on the surface of influenza viruses that enables the virus to be released from the host cell.
MC, 20101202: When influenza virus replicates, it attaches to the cell surface using hemagglutinin, a molecule found on the surface of the virus which binds to sialic acid groups. Sialic acids are found on various glycoproteins at the host cell surface, and the virus exploits these groups to bind the host cell. In order for the virus to be released from the cell, neuraminidase must enzymatically cleave the sialic acid groups from host glycoproteins. As an integral part of influenza replication, blocking the synthesis of neuraminidase with neuraminidase inhibitors is an effective way to treat influenza.
WEB: http://en.wikipedia.org/wiki/Viral_neuraminidase
neuraminidase inhibitor drug
A drug targeted at the influenza virus, which work by blocking the function of the viral neuraminidase protein, thus preventing the virus from reproducing by budding from the host cell.
MC, 20101203: added this class to realize the concretization of the collection protocol
the process of collecting a specimen, either from an organism or from an environment
geographical location
A reference to a place on the Earth, by its name or by its geographical location.
conditional specification
OBI branch derived
PlanAndPlannedProcess Branch
a directive information entity that specifies what should happen if the trigger condition is fulfilled
measurement unit label
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.
A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure.
Examples of measurement unit labels are liters, inches, weight per volume.
objective specification
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."
Answers the question, why did you do this experiment?
OBI Plan and Planned Process/Roles Branch
PERSON: Barry Smith
PERSON: Bjoern Peters
PERSON: Jennifer Fostel
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.
purpose of a study; support of hypothesis, discovery of new information
narrative object
2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'textual entity' and 'figure'. Alan restored as there are OBI dependencies and this merits further discussion
A narrative object is an information content entity that is a set of propositions.
Examples of narrative objects are reports, journal articles, and patents submission.
agree - DENRIE. Issue(alan) do we only mean text? What about a story told by mime. Does music count? (no) what about an oral report. Regarding definition, saying it is a set of propositions means we loose the idea that wording matters. Maybe adjust saying a narrative object has some relationshop to a set of propositions
person:Chris Stoeckert
action specification
OBI Plan and Planned Process branch
Pour the contents of flask 1 into flask 2
a directive information entity that describes an action the bearer will take
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
software
GROUP: OBI
PERSON: Chris Stoeckert
Software is a plan specification which is a series of encoded instructions that can be directly executed by a processing unit or transformed in to a form that can be. For programming texts that are syntactically correct and which are in a language that can be executed by an interpreter this would correspond to the tokenized version of the text stripped of comments.
see sourceforge tracker discussion at http://sourceforge.net/tracker/index.php?func=detail&aid=1958818&group_id=177891&atid=886178
journal article
Examples are articles published in the journals, Nature and Science. The content can often be cited by reference to a paper based encoding, e.g. Authors, Title of article, Journal name, date or year of publication, volume and page number.
a report that is published in a journal
information carrier
12/15/09: There is a concern that some ways that carry information may be processes rather than qualities, such as in a 'delayed wave carrier'.
A quality of an information bearer that imparts the information content
The pattern in ink on a page of a paperback novel.
model number
A model number is an information content entity specifically borne by catalogs, design specifications, advertising materials, inventory systems and similar that is about manufactured objects of the same class. The model number is an alternative term for the class. The manufactered objects may or may not also bear the model number. Model numbers can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots.
manufactered items may have more than one model number, sometimes by rebranding, or because companies are sold and the products issued new model numbers
programming language
A language in which source code is written, intended to executed/run by a software interpreter. Programming languages are ways to write instructions that specify what to do, and sometimes, how to do it.
R, Perl, Java
data item
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.
Data items include counts of things, analyte concentrations, and statistical summaries.
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
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.
data
symbol
20091104, MC: this needs work and will most probably change
a smallish, word-like datum...
numeral
A symbol that denotes a number.
information content entity
Examples of information content entites include journal articles, data, graphical layouts, and graphs.
an information content entity is an entity that is generically dependent on some artifact and stands in relation of aboutness to some entity
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.
integer numeral
a numeral that denotes an integer
scalar measurement datum
10 feet. 3 ml.
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.
a scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label.
directive information entity
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.
8/6/2009 Alan Ruttenberg: Changed label from "information entity about a realizable" after discussions at ICBO
An information content entity whose concretizations indicate to their bearer how to realize them in a process.
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
time trigger
revisit?
dot plot
A dot plot is a report graph which is a graphical representation of data where each data point is represented by a single dot placed on coordinates corresponding to data point values in particular dimensions.
Dot plot of SSC-H and FSC-H.
person:Allyson Lister
graph
A diagram that presents one or more tuples of information by mapping those tuples in to a two dimensional space in a non arbitrary way.
PERSON: Lawrence Hunter
rule
MSI
PRS
a rule is an executable which guides, defines, restricts actions
example to be added
contour plot
Contour plot of SSC-H, FSC-H, and FL1-H.
generically_dependent_continuants
group:Flow Cytometry community
algorithm
A plan specification which describes inputs, 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.
PMID: 18378114.Genomics. 2008 Mar 28. LINKGEN: A new algorithm to process data in genetic linkage studies.
Philippe Rocca-Serra
adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg)
software interpreter
An algorithm that takes, as input, some digital entity, and takes action driven by the information content of that algorithm
Do we care? Jennifer: Yes, there was a particular version of R that had a bug and it was fixed later. That would imply that we mean specific version of an interpreter. So an instance of this would be a particular version of the interpreter
R program, Perl interpreter, Java virtual machine
curation status specification
Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)
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.
density plot
A density plot is a report graph which is a graphical representation of data where the tint of a particular pixel corresponds to some kind of function corresponding the the amount of data points relativelly with their distance from the the pixel.
Density plot of SSC-H and FSC-H.
report
2009-03-16: comment from Darren Natale: I am slightly uneasy with the sentence "Topic of the report is on something that has completed." Should it be restricted to those things that are completed? For example, a progress report is (usually) about something that definitely has *not* been completed, or may include (only) projections. I think the definition would not suffer if the whole sentence is deleted.
2009-03-16: this was report of results with definition: A report is a narrative object that is a formal statement of the results of an investigation, or of any matter on which definite information is required, made by some person or body instructed or required to do so.
2009-03-16: work has been done on this term 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.
2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'document'. Alan restored as there are OBI dependencies and this merits further discussion
Examples of reports are gene lists and investigation reports. These are not published (journal) articles but may be included in a journal article.
PERSON:Chris Stoeckert
a document assembled by an author for the purpose of providing information for the audience. A report is the output of a documenting process and has the objective to be consumed by a specific audience. Topic of the report is on something that has completed. A report is not a single figure. Examples of reports are journal article, patent application, grant progress report, case report (not patient record)
disagreement about where reports go. alan: only some gene lists are reports. Is a report all the content of some document? The example of usage suggests that a report may be part of some article. Term needs clarification
source code module
A source code module is a directive information entity that specifies, using a programming language, some algorithm.
The written source code that implements part of an algorithm. Test - if you know that it was written in a specific language, then it can be source code module. We mean here, roughly, the wording of a document such as a perl script.
data format specification
2009-03-16: provenance: term imported from OBI_0000187, which had original definition "A data format specification is a plan which organizes information. Example: The ISO document specifying what encompasses an XML document; The instructions in a XSD file"
A data format specification is the information content borne by the document published defining the specification. Example: The ISO document specifying what encompasses an XML document; The instructions in a XSD file
data set
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
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.
Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves).
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
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
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.
Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved
PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice.
a directive information entity that when concretized it is realized in a process in which the bearer tries to achieve the objectives, in part by taking the actions specified. Plan specifications includes parts such as objective specification, action specifications and conditional specifications.
measurement datum
2/2/2009 is_specified_output of some assay?
A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device.
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,}.
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
serial number
A serial number is an information content entity which is a unique sequence of characters borne by part of manufactured product or its packaging that is assigned to each individual in some class of products, and so can serve as a way to identify an individual product within the class. Serial numbers can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots.
Note: during the call there was some confusion between serial number and model number. We agreed that it would be very helpful for all those terms to have example of usages - please add if you have any :-)
lot number
A lot number is an information content entity which is an identical sequence of character borne by part of manufactured product or its packaging for each instances of a product class in a discrete batch of an item. Lot numbers are usually assigned to each separate production run of an item. Manufacturing as a lot might be due to a variety of reasons, for example, a single process during which many individuals are made from the same portion of source material. Lot numbers can be encoded in a pattern of other information objects, such as bar codes, numerals, or patterns of dots.
batch number
setting datum
2/3/2009 Feedback from OBI This should be a "setting specification". There is a question of whether it is information about a realizable or not. Pro other specification are about realizables. Cons sometimes specifies a quality which is not a realizable.
A settings datum is a datum that denotes some configuration of an instrument.
Alan grouped these in placeholder for the moment. Name by analogy to measurement datum.
conclusion textual entity
2009/09/28 Alan Ruttenberg. Fucoidan-use-case
2009/10/23 Alan Ruttenberg: We need to work on the definition still
A textual entity that expresses the results of reasoning about a problem, for instance as typically found towards the end of scientific papers.
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
material information bearer
An information bearer is a material_entity in which a concretization of an information content entity inheres.
a hard drive, a piece of paper with writing on it, a brain
histogram
A histogram is a report graph which is a statistical description of a distribution in terms of occurrence frequencies of different event classes.
PERSON:James Malone
heatmap
A heatmap is a report graph which is a graphical representation of data where the values taken by a variable(s) are shown as colors in a two-dimensional map.
Venn diagram
A Venn diagram is a report graph showing all hypothetically possible logical relations between a finite collection of sets.
WEB: http://en.wikipedia.org/wiki/Venn_diagram
dendrogram
A dendrogram is a report graph which is a tree diagram frequently used to illustrate the arrangement of the clusters produced by a clustering algorithm.
Dendrograms are often used in computational biology to illustrate the clustering of genes.
WEB: http://en.wikipedia.org/wiki/Dendrogram
scatter plot
A scatterplot is a graph which uses Cartesian coordinates to display values for two variables for a set of data. The data is displayed as a collection of points, each having the value of one variable determining the position on the horizontal axis and the value of the other variable determining the position on the vertical axis.
Comparison of gene expression values in two samples can be displayed in a scatter plot
WEB: http://en.wikipedia.org/wiki/Scatterplot
scattergraph
photograph
A photograph is created by projecting an image onto a photosensitive surface such as a chemically treated plate or film, CCD receptor, etc.
PERSON:Joanne Luciano
WEB: http://en.wiktionary.org/wiki/photograph
photographic print
A photographic print is a material entity upon which a photograph generically depends.
obsolescence reason specification
The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology.
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.
textual entity
A textual entity is a part of a manifestation (FRBR sense), a generically dependent continuant whose concretizations are patterns of glyphs intended to be interpreted as words, formulas, etc.
AR, (IAO call 2009-09-01): a document as a whole is not typically a textual entity, because it has pictures in it - rather there are parts of it that are textual entities. Examples: The title, paragraph 2 sentence 7, etc.
MC, 2009-09-14 (following IAO call 2009-09-01): textual entities live at the FRBR (http://en.wikipedia.org/wiki/Functional_Requirements_for_Bibliographic_Records) manifestation level. Everything is significant: line break, pdf and html versions of same document are different textual entities.
Words, sentences, paragraphs, and the written (non-figure) parts of publications are all textual entities
text
citation
Verspoor, K., Cohen, KB., Hunter, L. Textual characteristics of traditional and Open Access scientific journals are similar, BMC Bioinformatics 2009, 10:183.
a textual entity intended to identify a particular publication
author identification
A textual entity intended to identify a particular author
L. Hunter
institutional identification
A textual entity intended to identify a particular institution
University of Colorado Denver School of Medicine
caption
A textual entity that describes a figure
Figure 1: A system diagram describing the modules of the Hanalyzer. Reading methods (green) take external sources of knowledge (blue) and extract information from them, either by parsing structured data or biomedical language processing to extract information from unstructured data. Reading modules are responsible for tracking the provenance of all knowledge. Reasoning methods (yellow) enrich the knowledge that results from reading by, for example, noting two genes that are annotated to the same ontology term or database entry. All knowledge sources, read or reasoned, are assigned a reliability score, and all are combined using that score into a knowledge network (orange) that represents the integration of all sorts of relationship between a pair of genes and a combined reliability score. A data network (also orange) is created from experimental results to be analyzed. The reporting modules (pink) integrate the data and knowledge networks, producing visualizations that can be queried with the associated drill-down tool.
document title
A textual entity that names a document
Textual characteristics of traditional and Open Access scientific journals are similar
table
A textual entity that contains a two-dimensional arrangement of texts repeated at regular intervals across a spatial range, such that the spatial relationships among the constituent texts expresses propositions
| T F --+----- T | T F F | F F
table of abbreviations
A table where the constituent texts are abbreviations and their expansions
IAO information artifact ontology OBI ontology of biomedical investiations GO gene ontology
figure
An information content entity consisting of a two dimensional arrangement of information content entities such that the arrangement itself is about something.
Any picture, diagram or table
diagram
A figure that expresses one or more propositions
A molecular structure ribbon cartoon showing helices, turns and sheets and their relations to each other in space.
document
A collection of information content entities intended to be understood together as a whole
A journal article, patent application, laboratory notebook, or a book
publication
A document that has been accepted by a publisher
A journal article or book
publication about an investigation
A publication that is about an investigation
Most scientific journal articles
scientific publication
patent
A document that has been accepted by a patent authority
US Patent 6,449,603
document part
An abstract, introduction, method or results section.
an information content entity that is part of a document
abstract
A summary of the entire document that is substantially smaller than the document it summarizes. It is about the document it summarizes.
The profusion of high-throughput instruments and the explosion of new results in the scientific literature, particularly in molecular biomedicine, is both a blessing and a curse to the bench researcher. Even knowledgeable and experienced scientists can benefit from computational tools that help navigate this vast and rapidly evolving terrain. In this paper, we describe a novel computational approach to this challenge, a knowledge-based system that combines reading, reasoning and reporting methods to facilitate analysis of experimental data. Reading methods extract information from external resources, either by parsing structured data or biomedical language processing to extract information from unstructured data, and track knowledge provenance. Reasoning methods enrich the knowledge that results from reading by, for example, noting two genes that are annotated to the same ontology term or database entry. Reasoning is also used to combine all sources into a knowledge network that represents the integration of all sorts of relationships between a pair of genes, and to calculate a combined reliability score. Reporting methods combine the knowledge network with a congruent network constructed from experimental data and visualize the combined network in a tool that facilitates the knowledge-based analysis of that data.
introduction to a publication about an investigation
A part of a publication about an investigation that is about the objective specification (why the investigation is being done)
Section labelled 'introduction' of a typical scientific journal article
introduction
methods section
A part of a publication about an investigation that is about the study design of the investigation
The section labelled 'Methods' or 'Materials and Methods' in a typical scientific journal article.
results section
A part of a publication about an investigation that is about a study design execution
The section labelled 'results' in a typical scientific journal article
discussion section of a publication about an investigation
A part of a publication about an investigation that is about the study interpretation of the investigation
discussion section
references section
A part of a document that has citations as parts
The list of citations found at the end of a scientific publication, grant proposal or patent application, sometimes called "literature cited" or "bibliography"
author list
Lawrence Hunter and Kevin Brettonel Cohen
part of a document that enumerates the authors of the document
institution list
The University of Colorado Denver School of Medicine and the University of Colorado Boulder.
part of a document that has parts that are institution identifications associated with the authors of the document
author contributions section
A part of a publication that is about the specific contributions of each author
LH conceived of the hypothesis, designed the study and contributed to the writing of the manuscript. KBC executed the experiments, analyzed the data, and contributed to the writing of the manuscript.
acknowledgements section
Part of a publication that is about the contributions of people or institutions other than the authors.
The authors wish to thank Alan Ruttenberg for his constructive comments about an earlier draft of this manuscript
footnote
A part of a document that is about a specific other part of the document. Usually footnotes are spatially segregated from the rest of the document.
The referent in the text is usually indicated by a special typographic character such as * or a superscripted number, which is also used to indicate the footnote that refers to that text.
endnote
supplementary material to a document
appendix
part of a document that is segregated from the rest of the document due to its size
supplementary material
table of contents
A table that relates document parts to specific locations in a document (usually page numbers). This is also a document part (subsumption there should be inferred).
table of figures
A table that relates figures in a document to specific locations in that document (usually page numbers). This is also a document part (subsumption there should be inferred).
running title
A shorter version of a document title
copyright section
A document part that describes legal restrictions on making or distributing copies of the document
This work is licensed under a Creative Commons Attribution-Share Alike 3.0 United States License.
cartesian spatial coordinate datum
2009-08-18 Alan Ruttenberg - question to BFO list about whether the BFO sense of the lower dimensional regions is that they are always part of actual space (the three dimensional sort) http://groups.google.com/group/bfo-discuss/browse_thread/thread/9d04e717e39fb617
A cartesian spatial coordinate datum is a representation of a point in a spatial region, in which equal changes in the magnitude of a coordinate value denote length qualities with the same magnitude
one dimensional cartesian spatial coordinate datum
A cartesion spatial coordinate datum that uses one value to specify a position along a one dimensional spatial region
two dimensional cartesian spatial coordinate datum
A cartesion spatial coordinate datum that uses two values to specify a position within a two dimensional spatial region
three dimensional cartesian spatial coordinate datum
A cartesion spatial coordinate datum that uses three values to specify a position within a three dimensional spatial region
length measurement datum
A scalar measurement datum that is the result of measurement of length quality
A denotator type indicates how a term should be interpreted from an ontological perspective.
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.
mass measurement datum
A scalar measurement datum that is the result of measurement of mass quality
hypothesis textual entity
A textual entity that expresses an assertion that is intended to be tested.
time measurement datum
A scalar measurement datum that is the result of measuring a temporal interval
postal address
A textual entity that is used as directive to deliver something to a person, or organization
2010-05-24 Alan Ruttenberg. Use label for the string representation. See issue http://code.google.com/p/information-artifact-ontology/issues/detail?id=59
author role
A role inhering in a person or organization that is realized when the bearer participates in the work which is the basis of the document, in the writing of the document, and signs it with their name.
data item extraction from journal article
a planned process in which journal articles are read or processed and data items are extracted, typically for further analysis or indexing
documenting
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
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.
wikipedia http://en.wikipedia.org/wiki/Documenting
line graph
A line graph is a type of graph created by connecting a series of data points together with a line.
WEB: http://en.wikipedia.org/wiki/Line_chart
line chart
assigning a centrally registered identifier
A new pubmed ID being created for a journal article, and the associated pubmed record containing information to the journal article. A license plate number registered at the DMV to be belonging to a specific vehicle and owner. Placing a barcode on a product and entering information in a database that this barcode is assigned.
Person:Melanie Courtot
a planned process in which a new CRID is created, associated with an entity, and stored in the CRID registry thereby registering it as being associated with some entity
associating information with a CRID in the CRID registry
A planned process in which a CRID registry associates an information content entity with a CRID symbol
CRID symbol
A symbol that is part_of a CRID and that is sufficient to look up a record from the CRID's registry.
IAO call, 20101124: 12345 is not a CRID symbol. To be a CRID symbol you need to have some information about the registry within which the CRID is recorded.
Original proposal from Bjoern, discussions at IAO calls
PERSON: Bill Hogan
PMID:12345, 12345 in a database column which has header "pubmedID"
CRID
Alan, IAO call 20101124: potentially the CRID denotes the instance it was associated with during creation.
An information content entity that consists of a CRID symbol and additional information about which CRID registry it belongs.
Entries in a Column of which the header is "Pubmed ID"
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.
The following URL: "http://www.ncbi.nlm.nih.gov/pubmed/19918065"
The following sentence contains a CRID: "The article with Pubmed ID: 19918065".
CRID registry
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.
IAO call, 20101124: PubMed registry is an instance of CRID registry
looking up a CRID
A planned process in which a request to a CRID registry is made to return the information associated with a CRID symbol
time stamped measurement datum
time sampled measurement data set
A data set that is an aggregate of data recording some measurement at a number of time points. The time series data set is an ordered list of pairs of time measurement data and the corresponding measurement data acquired at that time.
experimental time series
pmid:20604925 - time-lapse live cell microscopy
symbiont role
A role borne by an organism in symbiosis.
mutualist role
A symbiont role borne by an organism in virtue of the fact that both symbionts derive a growth, survival, or fitness advantage from symbiosis.
The role is realized in processes that result in the growth, survival, or fitness advantage of either organism.
commensal role
The role is realized in processes that result in the commensal's growth, survival, or fitness advantage.
A symbiont role borne by an organism in virtue of the fact that it derives a growth, survival, or fitness advantage from symbiosis, but the other symbiont is neither advantaged nor disadvantaged.
parasite role
In the medical community, the term 'parasite' is used with the narrower meaning of eukaryotic pathogen.
The role is realized in processes that result in the parasite's growth, survival, or fitness advantage or in the other organism's growth, survival, or fitness reduction.
A symbiont role borne by an organism in virtue of the fact that it derives a growth, survival, or fitness advantage from symbiosis while the other symbiont's growth, survival, or fitness is reduced.
infectious agent role
A role borne by an infectious agent when contained in a host in which its infectious disposition can be realized.
pathogen role
A role borne by pathogen in virtue of the fact that it or one of its products is sufficiently close to an organism towards which it has the pathogenic disposition to allow realization of the pathogenic disposition.
Clostridium botulinum is an example of an entity with the capability to bear the pathogen role but that does not have the capability to bear the infectious agent role or the parasite role. The influenza viruses are examples of organisms that can bear both the infectious agent and pathogen roles.
opportunistic infectious disposition
An infectious disposition to become part of a disorder only in organisms whose defenses are compromised.
The disposition is realized in a process by which the bearer becomes part of a disorder in an immunocompromised host.
This includes individuals who are immunocompromised or who have damaged barriers that normally protect against infection (e.g. skin).
opportunitistic pathogenic disposition
primary infectious disposition
A quote from page 3 of Mandell's "Principles and Practice of Infectious Diseases" (Sixth edition): "It is useful to distinguish "principal" pathogens, which regularly cause disease in some proportion of susceptible individuals with apparently intact defense systems, from other potentially pathogenic microorganisms. ... even for most organisms classified as principal pathogens, for example, Staphylococcus aureus and the pneumococcus, some impairment or local breakdown in normal host defense mechanisms must occur for these bacteria to cause disease. ... Thus, it seems clear that the capacity of certain microorganisms to cause disease in seemingly uncompromised human hosts on a regular basis reflects some fundamental difference in their virulence capabilities from those of opportunists and the more numerous commensal species that rarely, if ever, cause disease."
A pathogen with a primary infectious disposition can cause disease or death in both immunocompromised and immunocompetent hosts.
An infectious disposition to become part of a disorder in organisms that have intact defenses.
symbiont host role
The role is realized in processes in which the host makes the relevant environmental resources available to its partner in symbiosis. A bearer of a symbiont host role is bearer also of a symbiont role.
A host role borne by an organism in virtue of the fact that its extended organism contains a second organism and provides an environment supportive for the survival, growth, maturation, or reproduction of that organism.
The relevant environmental resources may include nutrient resources, warmth, or moisture.
definitive host role
A symbiont host role borne by an organism in virtue of the fact that its partner in symbiosis reaches developmental maturity or reproduces sexually in the host.
The role is realized in developmental and reproduction processes of the host's partner in symbiosis.
primary host role
intermediate host role
The role is realized in developmental processes of the host's partner in symbiosis.
A symbiont host role borne by an organism in virtue of the fact that its partner in symbiosis utilizes the host to undergo a developmental stage transition, and the host is required for continuation of the partner's life cycle.
secondary host role
paratenic host role
A symbiont host role borne by an organism in virtue of the fact that its partner in symbiosis utilizes the host to undergo a developmental stage transition, but the host is not required for continuation of the partner's life cycle.
dead-end host role
A symbiont host role borne by an organism in virtue of the fact that its partner in symbiosis has the infectious disposition but cannot be transmitted from the host to the partner's definitive host.
incidental host role
parasite host role
A symbiont host role borne by an organism in virtue of the fact that its partner in symbiosis derives from the host a growth, survival, or fitness advantage while the host's growth, survival, or fitness is reduced.
The role is realized in processes that result in the parasite's growth, survival, or fitness advantage or in the host's growth, survival, or fitness reduction.
The partner in symbiosis bears the parasite role.
infectious agent host role
A pathogen host role borne by an organism in virtue of the fact that its extended organism contains an infectious agent.
By this definition, vectors and other organisms that may not be infected are bearers of the infectious agent host role.
pathogen host role
Bearing the infectious agent host role implies bearing the pathogen host role, but the reverse is not true. See comment for infectious agent host role.
A host role borne by an organism in virtue of the fact that its extended organism contains a pathogen.
infectious agent carrier role
An infectious agent host role borne by an organism in virtue of the fact that its extended organism contains an infectious agent, the infectious agent has the infectious disposition towards the host, and the host has no symptoms of the infectious disease caused by the infectious agent.
infectious agent transporter role
A role borne by a material entity in virtue of the fact that an infectious agent is located in or on the entity and the entity has the capability to transfer (either actively or passively) the infectious agent from one location to another.
The role is realized in a process that transfers an infectious organism from one location to another.
infectious agent vector role
An infectious agent transporter role that is borne by an organism active in the transfer of an infectious agent to an organism of another Species and in which the agent is infectious.
The role is realized in a transmission process. A bearer of a vector role is also a bearer of a host role.
mechanical vector of infectious agent role
An infectious agent vector role borne by an organism in virtue of the fact that the infectious agent does not multiply in or on the vector.
biological vector of infectious agent role
An infectious agent vector role borne by an organism in virtue of the fact that the infectious agent multiplies in or on the vector.
infectious agent vehicle role
Drinking water bears the infectious agent vehicle role, but does not bear either of the subtype roles.
An infectious agent transporter role borne by an entity in virtue of the fact that the entity is not a complete organism.
biological vehicle of infectious agent role
Examples include blood, serum, tissue, or fresh produce.
An infectious agent vehicle role borne by an entity in virtue of the fact that the entity is living or contains living cells other than those that have the infectious disposition.
fomite role
An infectious agent vehicle role borne by an entity in virtue of the fact that the entity is not alive.
reservoir of infectious agent role
A role borne by a material entity in virtue of the fact that it is a habitat in which infectious agents can persist and multiply and from which they can be transmitted in virtue of prevailing practices of potential hosts.
If the material entity bearing the reservoir role is an organism, then this organism also bears the host role. The organism may also bear the vector role.
The role is realized in a process that has as part life and multiplication processes of an infectious agent and a transmission process.
virulence factor disposition
A disposition borne by a biological macromolecule produced by a pathogen that is a disposition to undergo processes that increase the pathogen's virulence.
The virulence factor disposition is typically realized in processes that improve survival of the pathogen in a host, increase the likelihood of transmission to a host, or cause pathological processes in a host.
toxin disposition
A disposition to cause I) malfunction of cells, ii) damage to extracellular matrix, or iii) damage of cells to a degree that can result in cell death.
exotoxin disposition
The disposition is realized in a direct enzymatic process that damages host cells or extracellular matrix.
A toxin disposition to damage cells or extracellular matrix by a direct enzymatic process.
infectious agent portal of entry role
A role borne by an anatomical entity in virtue of the fact that it serves as the site through which an infectious agent enters a host.
The role is realized in a process by which an infectious agent enters a host.
infectious agent portal of exit role
A role borne by an anatomical entity in virtue of the fact that it serves as the site through which an infectious agent exits a host.
The role is realized in a process by which an infectious agent exists a host.
disinfectant role
The role is realized in the killing and/or growth inhibition of microorganisms on the non-living entity.
A role borne by a material entity in virtue of the fact that it has an antimicrobial disposition and is applied to a non-living entity.
antiseptic role
The role is realized in the killing and/or growth inhibition of microorganisms on the anatomical entity.
A role borne by a material entity in virtue of the fact that it has an antimicrobial disposition and is applied to an anatomical entity of a living organism.
primary infection role
The role is realized in a process by which the infectious disorder is established in the host.
A role borne by an infectious disorder in virtue of the fact that (1) the host has at least two distinct infectious disorders, where neither arose from the other through metastasis, (2) at the time the infectious disorder was established in the host, the host had no infectious disorder, and (3) the infectious disorder increases the host's susceptibility to infectious disorders.
secondary infection role
A role borne by an infectious disorder in virtue of the fact that (1) the host has at least two distinct infectious disorders, where neither arose from the other through metastasis, (2) at the time the infectious disorder was established in the host, the host had a primary infectious disorder, and (3) establishment of the infectious disorder occurs because of increased susceptibility to infectious disorders conferred by the primary infectious disorder.
infectious disease
The disposition is realized in an infectious disease course.
A disease whose physical basis is an infectious disorder.
tranmissible disease
adhesion disposition
The disposition is realized in an adherence to host process.
A disposition borne by a biological macromolecule that is the disposition to participate in adherence to host.
invasion disposition
A disposition borne by a biological macromolecule that is the disposition to facilitate breach of host epithelial barriers or entry into and survival in host cells.
A molecule with the invasion disposition is referred to as an invasion factor or invasin.
antimicrobial disposition
A disposition to kill or inhibit the development or reproduction of microorganisms.
The disposition is realized in the killing or growth inhibition of microorganisms.
Some instances might be functions, depending on whether the bearer is something that exists and is used for the purpose (alcohol) or something that was designed for the purpose (pine sol). Entities that kill microorganisms are referred to as microbicidal; entities that inhibit the growth of microorganisms are referred to as microbistatic.
antiviral disposition
A disposition to kill or inhibit the lifecycle of viruses.
antifungal disposition
A disposition to kill or inhibit the development or reproduction of fungal organisms.
antibacterial disposition
A disposition to kill or inhibit the reproduction of bacteria.
antiparasitic disposition
In the term name, we are using parasite in the medical sense of eukaryotic organisms that are parasitic in humans.
A disposition to kill or inhibit the development or reproduction of eukaryotic parasites.
protective resistance
This mitigation sometimes takes the form of protection. CCR5 mutations protect T cells from HIV invasion. If a patient's tumor is resistant to chemotherapy, then the patient is resistant to something beneficial, but the tumor is resistant to something damaging. In this case protective resistance inheres in the tumor's cells and in the tumor, but not in the patient. In some cases, the quality that confers the protective resistance will confer other dispositions that damage the entity, such as is the case with sickle cell trait.
The disposition is realized in a process that mitigates damage to the bearer and has the part as a participant.
A disposition that inheres in a material entity in virtue of the fact that the entity has a part (e.g. a gene product), which itself has a disposition to mitigate damage to the entity.
resistance to drug
A protective resistance that mitigates the damaging effects of a drug.
drug resistance
resistance to infectious agent
A protective resistance that inheres in an organism and mitigates the damaging effects on that organism of an infectious agent.
herd immunity to infectious organism
A collective resistance disposition that inheres in an organism population in virtue of the fact that the proportion of the population with immunity to an infectious agent is high resulting in a low number of transmissions from hosts in the population to susceptible individuals in the population and thereby mitigating the damaging effects of the infectious agent on the population.
immunity to infectious agent
A resistance to infectious agent that inheres in an organism in virtue of immune system components in the extended organism.
We don't specify that immunity results from prior exposure, because we want to include innate immunity. In addition, for adaptive immunity, there could be some low level immunity even in a primary immune response.
protective immunity to infectious agent
sterilizing immunity to infectious agent
An immunity to infectious agent that results in elimination of the infectious agent from the host.
Sterilizing immunity is typically conferred by neutralizing antibodies.
pathogenic disposition
The disposition is realized in processes that create a disorder.
The use of 'initiates' is intended to convey that a pathogenic disposition is realized when processes resulting in a disorder begin because of some action on the part of the bearer of the disposition. By this interpretation of 'initiates', disorder-causing entities such as glass, UV light, and toxins do not have a pathogenic disposition.
A disposition to initiate processes that result in a disorder.
pathogenicity
invasive disposition
A disposition borne by an infectious agent that is the disposition to penetrate the epithelial barriers of an organism of another Species.
infectious disposition
A pathogenic disposition that inheres in an organism and is the disposition for that organism (1) to be transmitted to a host, (2) to establish itself in the host, and (3) to become part of a disorder in the host.
The disposition is realized in a process that has as part a transmission process, an establishment in host process, and a process in which an entity becomes part of a disorder. The infectious disposition has a complementary disposition that inheres in an organism and is the capability to be host to an entity with an infectious disposition and to undergo processes intiated by that entity that result in a disorder.
zoonotic disposition
An infectious disease associated with an infectious agent that bears the zoonotic disposition is referred to as a zoonosis.
An infectious disposition that is the disposition to be transmitted from an infected, non-human host to a human host.
reverse zoonotic disposition
An infectious disease associated with an infectious agent that bears the reverse zoonotic disposition is referred to as a reverse zoonosis.
An infectious disposition that is the disposition to be transmitted from an infected, human host to a non-human host.
collective disposition
"... in virtue of the individual dispositions of the contstituents" is intended to capture the fact that the collective disposition results from the combination of the individual dispositions. It is not necessary that every constituent of the aggregate have a relevant individual disposition.
A disposition that inheres in a collection of entities in virtue of the individual dispositions of the constituents of that collection.
The disposition is realized in a process that has as part realizations of some of the individual dispositions.
immunosuppressed organism
An organism that is experiencing pregnancy-induced or pathologic immunosuppression.
immunocompetent organism
An organism that has immunocompetence.
contagiousness
Highly contagious infections, those with a relatively high likelihood of spread, are referred to as contagious and are those for which spread is likely as a result of data-to-day activities of the host.
The disposition is realized in a horizontal transmission process.
A disposition that inheres in a host of infectious agent and is a disposition to transmit infectious agents to organisms of the same Species through casual contact with a high likelihood of realization.
colonized host
An organism that contains a colony in or on its extended organism.
infected organism
An organism that has an infection in or on its extended organism.
co-infected organism
An organism that has two infections with distinct Species of infectious agents.
infectious agent transmissibility
The transmissibility quality varies with both the type of organism being transmitted and the type of organism to which transmission is happening.
A quality that inheres in an infectious agent and is the likelihood that the infectious agent will undergo a horizontal transmission process.
infectivity
This quality is measured by the proportion of exposed who become infected.
A quality that inheres in an infectious agent and is the liklihood that the infectious disposition will be realized upon exposure of a susceptible organism.
virulence
This quality is measured by the proportion of clinically apparent cases that are severe or fatal.
A quality that inheres in an infectious agent and is the degree to which realizations of the infectious disease caused by the infectious agent become severe or fatal.
susceptibility
Low susceptibility is often referred to as resistance. In this sense, resistance is a quality.
A quality that inheres in an entity and is the degree to which it can be harmed by another entity.
susceptibility to infectious agent
A susceptibility that inheres in an organism and is the degree to which it can be harmed by an infectious agent.
drug susceptibility
A susceptibility that is the degree to which an entity can be harmed or inhibited from surviving by a drug.
drug susceptibility of infectious agent
A drug susceptibility that inheres in an infectious agent and is the degree to which the infectious agent can be harmed or inhibited from surviving by a drug.
complex infection
An infection comprised of infectious organisms from different Species.
mixed infection
polymicrobial infection
extracellular infection
An infection for which the infectious agents that are part of the infection persist in the extracellular space of the host.
intracellular infection
An infection for which the infectious agents that are part of the infection persist inside host cells.
systemic infection
An infection for which the infectious agents that are part of the infection are distributed throughout the host.
local infection
An infection for which the infectious agents that are part of the infection are limited to a relatively small area of the host's body.
focal infection
A local infection for which symptoms are observed in parts of the host's extended organism that are distant from the infection.
acute infectious disease course
An infectious disease course that begins soon after infection is established and progresses rapidly to severe stages.
infectious disease incidence
A particular instance of infectious disease incidence will depend on a type of infectious disease, a population, and a period of time. Incidence is used as a measure of risk. Actual measures of incidence are based only on reported cases and usually specify a time interval and geographic location. Other constraints may include population demographics. These constraints will vary with the context of the incidence measure.
A quality that inheres in an organism population and is the number of realizations of an infectious disease for which the infectious disease course begins during a specified period of time.
infection incidence
A particular instance of infection incidence will depend on a type of infectious agent, a population, and a period of time. Incidence is used as a measure of risk. Actual measures of incidence are based only on reported cases and usually specify a time interval and geographic location. Other constraints may include population demographics. These constraints will vary with the context of the incidence measure.
A quality that inheres in an organism population and is the number of organisms in the population that become infected with an infectious agent during a specified period of time.
infectious disease incidence proportion
An instance of infectious disease incidence proportion is measured by dividing a measure of an instance of infectious disease incidence by the number of members of the population in which the infectious disease course had not begun at the beginning of the specified period of time over which the incidence was measured.
A quality that inheres in an organism population and is the proportion of members of the population not experiencing an infectious disease course at the beginning of a specified period of time in whom the infectious disease begins during the specified period of time.
cumulative incidence of infectious disease
infection incidence proportion
An instance of infection incidence proportion is measured by dividing a measure of an instance of infection incidence by the number of members of the population not infected at the beginning of the specified period of time over which the incidence was measured.
cumulative incidence of infection
infectious disease incidence rate
A quality that inheres in an organism population and is the infectious disease incidence proportion per unit time.
An instance of infectious disease incidence rate is measured by dividing a measure of an instance of the infectious disease incidence proportion by the length of the period of time over which the incidence was measured.
infection incidence rate
An instance of infection incidence rate is measured by dividing a measure of an instance of infection incidence proportion by the length of the period of time over which the incidence was measured.
A quality that inheres in an organism population and is the infection incidence proportion per unit time.
infectious disease prevalence
Prevalence is sometimes defined as a proportion with total population size in the denominator. A particular instance of infectious disease prevalence will depend on a type of infectious disease, a population, and a period of time. Actual measures of prevalence are based only on reported cases and usually specify a time interval and geographic location. Other constraints may include population demographics.
A quality that inheres in an organism population and is the number of realizations of an infectious disease in the population at a specified time.
infection prevalence
A quality that inheres in an organism population and is the number of organisms in the population infected with an infectious agent at a specified time.
Prevalence is sometimes defined as a proportion with total population size in the denominator. A particular instance of infection prevalence will depend on a type of infectious agent, a population, and a period of time. Actual measures of prevalence are based only on reported cases and usually specify a time interval and geographic location. Other constraints may include population demographics.
infectious disease lifetime prevalence
A quality that inheres in an organism population and is the number of organisms in the population who have, at any point during their lives, been bearers of an infectious disease and experienced realization of the disease.
Prevalence is sometimes defined as a proportion with total population size in the denominator. A particular instance of infectious disease lifetime prevalence will depend on a type of infectious disease and a population. Actual measures of prevalence are based only on reported cases and usually specify a geographic location. Other constraints may include population demographics.
infectious agent seroprevalence
Prevalence is sometimes defined as a proportion with total population size in the denominator. A particular instance of infectious agent seroprevalence will depend on a type of infectious agent and a population. Actual measures of seroprevalence are based only on tested individuals and usually specify a geographic location. Other constraints may include population demographics.
A quality that inheres in an organism population and is the number of organisms in the population that have antibody specific for an infectious agent in their serum at a specified time.
infectious disease mortality rate
A particular instance of infectious disease mortality rate will depend on a type of infectious disease and a population. Actual measures of mortality rate are based only on reported cases and usually specify a geographic location. Other constraints may include population demographics. Mortality rate is typically expressed in units of deaths per 1000 individuals per year.
A quality that inheres in an organism population and is the per capita number of deaths in the population resulting from an infectious disease over a specified period of time.
infectious disease endemicity
A quality that inheres in an organism population in virtue of the fact that infections of the type that causes an infectious disease are maintained in the population via intra-population transmission or by transmission from a local reservoir.
A particular instance of infectious disease endemicity will depend on a type of infectious agent and a population. The population may be specified by temporal, geographic, or demographic constraints. Infectious diseases that are typical or common to a particular population are referred to as endemic.
infectious disease endemic level
Infectious disease endemic level is relational to previous prevalences of the disease.
An infectious disease prevalence that is typical for an infectious disease in an organism population.
infectious disease endemic rate
Infectious disease endemic rate is relational to previous infectious disease incidence rates of the disease.
An infectious disease incidence rate that is typical for an infectious disease in an organism population.
infectious disease hyper-endemicity
An infectious disease endemicity that inheres in an organism population in virtue of the fact that the infectious disease endemic level for an infectious disease is persistently high in the population.
Hyper-endemic infectious diseases may have high endemic levels only in certain seasons. A hyper-endemic disease affects all age groups equally.
infectious disease sporadicity
A quality that inheres in an organism population by virtue of the fact that realizations of an infectious disease occur in the population with a fluctuating prevalence.
Sporadic quality of infectious disease is relational to previous prevalence of the disease.
infectious disease course
A disease course that is the realization of an infectious disease.
long-term non-progressing infectious disease course
A chronic infectious disease course that does not progress to severe stages for a long period of time.
immunization against infectious agent
A process by which an organism acquires immunity to an infectious agent.
active immunization against infectious agent
An immunization that begins with exposure of an organism to antigen and results in immunity against an infectious agent.
inoculation
vaccination against infectious agent
An active immunization that begins with exposure of an organism to a vaccine.
variolation
An active immunization that begins with exposure to smallpox in the form of a scab from a pustule and results in immunity against smallpox.
passive immunization against infectious agent
An immunization that begins with transfer to an organism of molecules not produced by that organism and that confer immunity against an infectious agent.
Examples include the injection of antibodies and the transfer of maternal antibodies to the fetus.
infectious disease epidemic
A process of infectious disease realizations and for which there is a statistically significant increase in the infectious disease incidence of a population.
For a particular instance of infectious disease epidemic, signficance is determined based on the infectious disease incidence that is typical for an infectious disease for the particular population and time period.
infectious disease outbreak
infectious disease pandemic
A process in which multiple infectious disease epidemics of the same type of infectious disease unfold over overlapping periods of time and affect organism populations located in different geographic regions, including different countries and continents.
infectious disorder
An infection that is clinically abnormal.
viremia
An infection that has as part virus particles located in the blood.
bacteremia
An infection that has as part bacteria located in the blood.
virion
A virus that is in its assembled state consisting of genomic material (DNA or RNA) surrounded by coating molecules.
organism population
The organism population may be delineated by spatio-temporal proximity or by demographic criteria such as age.
An aggregate of organisms of the same Species.
infected population
An organism population whose members have an infection.
diseased population
An organism population in whose members an infectious disease is being realized.
infectious agent population
An organism population whose members each have an infectious disposition.
susceptible population
An organism population whose members are not infected with an infectious agent and who lack immunity to the infectious agent.
at-risk population
normal resident microbiota population
An organism population whose members are particpating in non-parasitic symbiosis with a particular host.
normal resident microflora population
incubation period
A continuous temporal interval beginning with the extablishment of an infectious agent colony and ending with the onset of symptoms (or infectious disease course?).
communicability period
A continuous temporal interval during which contagiousness inhering in the bearer of a host role.
symbiont
An organism bearing a symbiont role.
obligatory symbiont
An organism that can only reach developmental maturity, replicate, or persist in symbiosis.
mutualist
An organism bearing a mutualist role.
commensal
An organism bearing a commensal role.
parasite
A organism bearing a parasite role.
pathogen
A material entity with a pathogenic disposition.
primary pathogen
An infectious agent with a primary infectious disposition.
host
An organism bearing a host role.
definitive host
An organism bearing a definitive host role.
primary host
intermediate host
A organism bearing an intermediate host role.
secondary host
paratenic host
An organism bearing a paratenic host role.
dead-end host
An organism bearing a dead-end host role.
incidental host
parasite host
An organism bearing a parasite host role.
infectious agent host
An organism bearing an infectious agent host role.
pathogen host
An organism bearing a pathogen host role.
infectious agent carrier
An organism bearing the infectious agent carrier role.
infectious agent vector
An organism bearing an infectious agent vector role.
mechanical vector of infectious agent
An infectious agent vector bearing a mechanical vector of infectious agent role.
biological vector of infectious agent
An infectious agent vector bearing a biological vector of infectious agent role.
vehicle of infectious agent
A material entity bearing an infectious agent vehicle role.
fomite
A material entity bearing a fomite role.
infectious agent reservoir
A material entity bearing an infectious agent reservoir role.
virulence factor
DL: Needs 'product of' relation. It is a product of this process: production and has_participant some (has_role some pathogen and has_disposition some 'virulence factor disposition')
A biological macromolecule produced by a pathogen and that has a virulence factor disposition.
invasion factor
A biological macromolecule that has an invasion disposition.
invasin
toxin
A molecular entity that has a toxin disposition.
exotoxin
A molecular entity bearing an exotoxin disposition.
enterotoxin
A molecular entity with an exotoxin disposition, the realization of which damages cells of the host intestinal mucosa.
endotoxin
A molecular entity with a toxin disposition and that is a structural component of a pathogen and is released from the pathogen only upon cytolysis.
IDO Error endotoxin role => endotoxin disposition
infectious agent portal of entry
An anatomical entity bearing an infectious agent portal of entry role.
infectious agent portal of exit
An anatomical entity bearing an infectious agent portal of exit role.
disinfectant
A material entity bearing a disinfectant role.
antiseptic
A material entity bearing an antiseptic role.
adhesion factor
A biological macromolecule that has an adhesion disposition.
adhesin
adhesion molecule
antimicrobial
A material entity with an antimicrobial disposition.
antiviral
A material entity bearing an antiviral disposition.
antifungal
A material entity bearing an antifungal disposition.
antiparasitic
A material entity bearing an antiparasitic disposition.
antibiotic
microbicide
A material entity with an antimicrobial disposition that is realized in a process of killing microorganisms.
DL needs 'process of killing microorganisms'
microbicidal [entity]
viricide
A material entity with an antiviral disposition that is realized in a process of killing viruses.
microbistatic
A material entity with an antimicrobial disposition that is realized in a process of inhibiting the growth of microorganisms.
DL needs 'process of inhibiting the growth of microorganisms'
primary infection
An infection bearing the primary infection role.
secondary infection
An infection bearing the secondary infection role.
zoonosis
An infectious disease that has as its physical basis an infectious disorder composed of infectious agents that have a zoonotic disposition.
aymptomatic host of infectious agent
An organism that is host to an infectious agent has no symptoms of the infectious disease associated with the infectious agent.
subclinical infection
An infection that is part of an asymptomatic host.
resistant entity
A material entity that has a resistance disposition.
chronic carrier of infectious agent
An organism who has been bearer of the infectious agent carrier role for an extended period of time.
symptomatic host of infectious agent
An organism who is host to an infectious agent and has symptoms of the infectious disease associated with the infectious agent
innate immunity to infectious agent
The disposition is realized in an innate immune response.
An immunity to infectious agent that inheres in an organism in virtue of germline encoded components that directly recognize components of potential pathogens.
humoral immunity to infectious agent
"Circulating body fluid" refers to blood, lymph, and hemolymph.
The disposition is realized in a humoral immune response.
An immunity to infectious agent that inheres in an organism in virtue of components of its circulating body fluid.
leukocyte-mediated immunity to infectious agent
An immunity to infectious agent that inheres in an organism in virtue of its leukocytes.
The disposition is realized in a leukocyte-mediated immune response.
cell-mediated immunity to infectious agent
passive immunity to infectious agent
An immunity to infectious agent that inheres in an organism in virtue of antibodies not produced by that organism.
Passive immunity results from a passive immunization.
The protective antibodies are typically introduced by injection, breast feeding, or by passing from the placenta to the fetus.
The disposition is realized in a neutralizing process carried out by the antibodies.
antibiotic resistance
A resistance to drug that mitigates the damaging effects of an antibiotic.
long-term non-progressor
An organism experiencing a long-term non-progressing infectious disease course.
emerging pathogen
An infectious agent whose infection incidence is increasing following its first introduction into a new host Species.
cytotoxin
A molecular entity with a toxin disposition, the realization of which damages host cells.
collective pathogenic disposition
A collective disposition to initiate processes that result in a disorder.
infection
The organism corresponding to the extended organism is host to the infectious agents. By this definition, parts of the host can be considered part of the infection.
A part of an extended organism that itself has as part a population of one or more infectious agents and that is (1) clinically abnormal in virtue of the presence of this infectious agent population, or (2) has a disposition to bring clinical abnormality to immunocompetent organisms of the same Species as the host (the organism corresponding to the extended organism) through transmission of a member or offspring of a member of the infectious agent popuation.
genetic resistance to infectious agent
The resistance of individuals to HIV invasion oonferred by particular CCR5 alleles is an example. Resistance against malaria conferred by the sickle cell gene is another.
A resistance to infectious agent that inheres in an organism in virtue of a specific allele or combination of alleles in its genome.
collective resistance disposition
A collective disposition the realization of which mitigates the damaging effects of some entity on members of the collection.
immunodeficient organism
An organism that has an immunodeficiency.
immunocompromised organism
chronic infectious disease course
An infectious disease course that unfolds over a long period of time.
persistent infectious disease course
immune population
An organism population whose members have acquired immunity to an infectious agent.
transmission period
A continuous temporal interval during which a transmission process occurs.
direct host exposure to infectious agent
A process in which a potential host of an infectious agent comes into direct physical contact with the infectious agent.
potential host of infectious agent
An organism that has the capability to bear a host of infectious agent role.
infectious agent
An organism that has an infectious disposition.
host exposure to environment containing infectious agent
A process in which a potential host of an infectious agent is exposed to an environment in which the infectious agent is present and physical contact between the two can occur, but such contact is not planned.
host living with infected household contact
A host exposure to environment with infectious agent where the environment is a household that also has an infected host
Alan Ruttenberg 2010/05/20- Tentative definition. Needs review by Bjoern
host living in endemic area
A host exposure to environment with infectious agent where the environment is an area in which an infectious agent is endemic
release of infectious human pathogen in laboratory
A host exposure to environment with infectious agent where the exposure is accidental; the environment is a laboratory, and the infectious agent is infectious in humans.
host coming into contact with vector of infectious agent
A host exposure to environment with infectious agent where the environment contains an infectious agent vector.
host exposure to substance that might have infectious agent
A host exposure to environment with infectious agent where the environment contains a material entity that has been assessed to confer a risk of infection.
process of establishing an infection
A process by which an infectious agent, established in a host, becomes part of an infection in the host.
colonization of host
An establishment in host process in which an organism establishes itself in a host.
Establishment of one organism in the extended organism of another (the host) involves at least one of (1) movement of the organism to a location within the host in which the organism can persist, or (2) adherence or attachment of the organism to part of the host.
establishment of a clinically abnormal colony
A colonization of host process that results in a clinically abnormal colony.
production
A process in which an entity comes into being as a result of the process.
replication
A production process in which a participant creates a copy of itself.
colonization of human anterior nares
A colonization of human process in which the colonized site is the anterior nares.
immunosuppression
A process that attenuates an immune response.
physiologic immunosuppression
An immunosuppression which unfolds as part of the natural self-regulation of an immune response.
pathologic immunosuppression
An immunosuppression process which arises as the result of a disorder.
Disorders that result in immunosuppression include those that result from infection, stress, malnutrition, and treatments such as chemotherapy or calcineurin inhibition.
colony
An organism population persisting in a site it has colonized.
infectious agent colony
A colony whose members are infectious agents.
immunodeficiency
A disorder of an immune system component that results in defective functioning of the immune system.
DL needs immune system component (FMA?) and defective functioning (OGMS?)
immunocompetence
The disposition inheres in a bearer in virtue of the fact that the bearer has all canonical immune system components and none are disordered. The disposition is realized in a successful immune response.
A disposition that is the ability to mount a normal immune response.
immunosuppressive disposition
A disposition whose realization negatively regulates an immune response.
acquired immunity to infectious agent
The disposition is realized in an immune response in which such antigen receptors participate.
An immunity to infectious agent that inheres in an organism in virtue of antigen receptors encoded by somatically diversified genes in the organism's genome and expressed by cells that have undergone selection during a primary immune response in that organism.
adaptive immunity to infectious agent
immune memory
disposition to form a non-parasitic colony
A disposition to colonize an organism and participate in mutualism or commensalism with that organism.
communicability
The disposition is realized in a direct, horizontal transmission process between members of the same Species.
An infectious disposition to be transmitted directly from one organism to another of the same Species by horizontal transmission.
establishment of localization in host
Requested addition of this term to the GO.
An establishment of localization process in which a material entity reaches a site in an organism in which it can survive, grow, multiply, or mature.
An organism begins bearing a particular host role as soon as the extended organism contains the relevant material entity, regardless of that entity's location in the extended organism. An establishment process is any process by which the entity reaches a location in the extended organism in which it can persist and continue its lifecycle. For example, an organism is host to a virus as soon as any part of the extended organism is occupied by virus particles. During an establishment process, virus particles enter host cells of the relevant type, and viral DNA is integrated into host DNA.
appearance of disorder
A process by which a disorder comes into existence.
acute infection
An infectious disorder that is the physical basis for an unfolding acute infectious disease course.
chronic infection
An infection that persists for an extended period of time.
persistent infection
host role
A role borne by an organism in virtue of the fact that it's extended organism contains a material entity other than the organism.
hospital-acquired infection
An infection resulting from a transmission process that unfolds in a hospital.
nosocomial infection
community-acquired infection
An infection resulting from a transmission process that did not unfold in a health care facility.
neurotoxin
A molecular entity with a toxin disposition, the realization of which damages or interferes with the function of nerve tissue.
metatstatic infection
An infection established as a result of spread from another infection in a non-adjacent location in the extended organism of the host.
DL needs 'another infection in a non-adjacent location'
source of infection role
A role borne by a material entity in virtue of the fact that it contains a site from which an infectious agent is transmitted.
The role is realized in a process that has as part a transmission process and a process by which the infectious agent or one of its offspring becomes part of a disorder in the host.
sepsis
A process that is a systemic inflammatory response to infection.
severe sepsis
A sepsis that results in organ dysfunction, hypotension, or hypofusion of at least one organ.
nursing-home acquired
An infection resulting from a transmission process that unfolds in a nursing home.
infectious human pathogen
An infectious agent with a capability to infect human hosts.
acquired immunodeficiency
Causes of acquired immunodeficiences include infection and drug treatments (e.g. chemotherapy).
An immunodeficiency that is not caused by a genetic predisposition.
simple infection
An infection comprised of infectious organisms all of the same Species.
re-emerging pathogen
An infectious agent whose infection incidence is increasing in a host population as a result of changes in the biology of the host or pathogen, or changes in their interactions.
pregnancy-induced immunosuppression
An immunosuppression induced by progesterone and other factors upregulated in pregnant women.
candidiasis
An infection that has as part organisms of the Genus Candida.
trichomoniasis
An infection that has as part organisms of the Species Trichomonas vaginalis.
leptospirosis
An infection that has as part organisms of the Genus Leptospira.
Shigellosis
An infection located in the bowel and that has as part organisms of the Genus Shigella.
amebiasis
An infection located in the colon and that has as part organisms of the Species Entamoeba histolytica
colonization of human
A colonization of host process in which the host is of Species Homo sapiens.
An immunodeficiency that exists in an organism because of a genetic predisposition.
A colonization of human process in which the colonized site is a perineum.
An infectious disease that has as its physical basis an infectious disorder composed of infectious agents that have a reverse zoonotic disposition.
An infectious agent with an opportunistic infectious disposition.
The disposition is realized in a transmission process.
A disposition to undergo a transmission process.
horizontal pathogen transmission process
A pathogen transmission process in which a pathogen is transmitted from one host to another of the same Species, and the two hosts are not in a parent-child relationship.
A process in which a potential host of an infectious agent is exposed to an infectious agent.
An organism that is not infected with an infectious agent and lacks protective immunity to the infectious agent.
A process which is necessary for the survival of an organism.
negative regulation of life-sustaining process
Any process that stops, prevents, or reduces the frequency, rate or extent of a life-sustaining process.
A material entity bearing a source of infection role.
A process by which a part of an organism or something contained in an organism becomes clinically abnormal.
planned process
A processual entity that realizes a plan which is the concretization of a plan specification.
material supplier role
a role realized through the process of supplying materials such as animal subjects, reagents or other materials used in an investigation.
processed material
Is a material entity that is created or changed during material processing.
investigation
a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s).
assay
A planned process with the objective to produce information about some evaluant
diagnosis textual entity
diagnosis is an assessment of a disease or injury, its likely prognosis and treatment.
material processing
A planned process which results in physical changes in a specified input material
specimen role
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.
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 creation process and that is realized by use of the specimen in 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.
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
Investigation agent role is a role borne by a person or organization which is realized in a process that is part of an investigation in which an objective is achieved. These processes include: planning, overseeing, funding, reviewing.
protocol
a protocol is a plan specification which has sufficient level of detail and quantitative information to communicate it between domain experts, so that different domain experts will reliably be able to independently reproduce the process.
cloning vector role
a vector role played by a small, self-replicating DNA or RNA molecule - usually a plasmid or chromosome - and realized in a process whereby foreign DNA or RNA is inserted into the vector during the process of cloning.
enzyme
MC: known issue: enzyme doesn't classify under material entity for now as it isn't stated that anything that has_part some material entity is a material entity. If we add as equivalent classes to material entity has_part some material entity and part_of some material entity (each one in his own necessary and sufficient block) Pellet in P3 doesn't classify any more.
(protein or rna) or has_part (protein or rna) and has_function some GO:0003824 (catalytic activity)
a planned process that realizes the concretization of a study design
DNA sequencing is a sequencing process which uses deoxyribonucleic acid as input and results in a the creation of DNA sequence information artifact using a DNA sequencer instrument.
is a material processing with the objective to combine two or more material entities as input into a single material entity as output.
a planned process with the objective of obtaining specimen.
A specimen creation objective is to obtain a material entity for potential use as an input during an investigation
A role played by a nucleic acid molecule that is used in a planned process for its ability to bind a nucleic acid molecules with complementary nucleotide sequence
a highly sensitive procedure for the measurement of soluble antigens in biologic specimens; the amount of hemagglutination reflects the amount of free antibody present after reaction with the specimen and thus varies inversely with amount of antigen in the specimen.
The clumping or clustering of red blood cells caused by certain viruses, antibodies, or other substances
A measurement datum that is reported on a categorical scale
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
sequence data
A measurement datum that representing the primary structure of a macromolecule(it's sequence) sometimes associated with an indicator of confidence of that measurement.
genotype 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.
organism
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.
An organism is 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.
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
cell culture
a cell culture is a material entity consisting of a population of cells that is maintained in vitro
data transformation
A data transformation is a process which produces output data from input data
extraction
A material separation in which a desired component of an input material is separated from the remainder
isolation event
study design
A study design is 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.
collecting specimen from organism
IEDB
a process with the objective to obtain a material entity that was part of an organism for potential future use in an investigation
taking a sputum sample from a cancer patient, taking the spleen from a killed mouse, collecting a urine sample from a patient
killing
A protocol application in which an organism is intentionally put to death
administering substance in vivo
A process by which a substance is intentionally given to an organism
environmental material collection
Bjoern Peters, Alan Ruttenberg
Taking 1 liter of surface ocean water from the San Diego Mission Bay Jetty. Capturing mice living in rural Arkansas
environmental_material_collection is an acquisition where an object is taken from an environment and put into a storage container. Roles include, environment, thing collected, container, acquirer.
material component separation
a material processing in which components of an input material become segregated in space
material portioning
a material processing in which the input substance is partitioned into a number of portions that are similar in composition.
establishing cell culture
establishing a cell culture is a process which results in creating an in vitro environment in which cells are sustained from input material containing cells. input: cell-containing material, output cell culture, part of cell culturing. Cells are originally plated at a certain concentration referred to as seeding density.
sequencing assay
the use of a chemical or biochemical means to infer the sequence of a biomaterial
RNA extraction
A RNA extraction is a nucleic acid extraction where the desired output material is RNA
nucleic acid extraction
a material separation to recover the nucleic acid fraction of an input material
A quality of a patient that is observed by the patient and is hypothesized by the patient to be a realization of a disease.
A quality of a patient that is observed by the patient or a processual entity experienced by the patient, either of which is hypothesized by the patient to be a realization of a disease.
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.
The totality of all processes through which a given disease instance is realized.
An object aggregate consisting of an organism and all material entities located within the organism, overlapping the organism, or occupying sites formed in part by the organism.
A processual entity whose completion is hypothesized (by a healthcare provider) to alleviate the signs and symptoms associated with a disorder
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
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
TODO
protein
anatomical entity
Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species.
peptide
Amide derived from two or more amino carboxylic acid molecules (the same or different) by formation of a covalent bond from the carbonyl carbon of one to the nitrogen atom of another with formal loss of water. The term is usually applied to structures formed from alpha-amino acids, but it includes those derived from any amino carboxylic acid.
deoxyribonucleic acids
High molecular weight, linear polymers, composed of nucleotides containing deoxyribose and linked by phosphodiester bonds; DNA contain the genetic information of organisms.
molecular entity
Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity.
nucleic acid
A macromolecule made up of nucleotide units and hydrolysable into certain pyrimidine or purine bases (usually adenine, cytosine, guanine, thymine, uracil), D-ribose or 2-deoxy-D-ribose and phosphoric acid.
ribonucleic acids
Naturally occurring polyribonucleotides.
messenger RNA
An RNA molecule that transfers the coding information for protein synthesis from the chromosomes to the ribosomes mRNA is formed from a DNA template by transcription. It may be a copy of a single gene or of several adjacent genes (polycistronic mRNA). On the ribosome, the sequence is converted into the programmed amino acid sequence through translation.
cell
Anatomical structure that has as its parts a maximally connected cell compartment surrounded by a plasma membrane.
leukocyte
An achromatic cell of the myeloid or lymphoid lineages capable of ameboid movement, found in blood or other tissue.
influenza
A viral infectious disease that results_in infection, located_in respiratory tract, has_material_basis_in Influenzavirus A, has_material_basis_in Influenzavirus B, or has_material_basis_in Influenzavirus C, which are transmitted_by droplet spread of oronasal secretions during coughing, sneezing, or talking from an infected person. It is a highly contagious disease that affects birds and mammals and has_symptom chills, has_symptom fever, has_symptom sore throat, has_symptom runny nose, has_symptom muscle pains, has_symptom severe headache, has_symptom cough, and has_symptom weakness.
biome
A major class of ecologically similar communities of plants, animals, and other organisms. Biomes are defined based on factors such as plant structures (such as trees, shrubs, and grasses), leaf types (such as broadleaf and needleleaf), plant spacing (forest, woodland, savanna), and other factors like climate. Unlike ecozones, biomes are not defined by genetic, taxonomic, or historical similarities. Biomes are often identified with particular patterns of ecological succession and climax vegetation.
habitat
A spatial region having environmental qualities which may sustain an organism or a community of organisms.
Lung
Lobular organ which has as its parts alveoli connected to the tracheobronchial tree. Examples: There are only two instances, right lung and left lung.
reproduction
The production by an organism of new individuals that contain some portion of their genetic material inherited from that organism.
cell fraction
A generic term for parts of cells prepared by disruptive biochemical techniques.
adaptive immune response
An immune response based on directed amplification of specific receptors for antigen produced through a somatic diversification process, and allowing for enhanced response to subsequent exposures to the same antigen (immunological memory).
leukocyte mediated immunity
Any process involved in the carrying out of an immune response by a leukocyte.
molecular_function
Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions.
catalytic activity
Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
RNA-directed RNA polymerase activity
Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1); uses an RNA template.
immune response
Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
humoral immune response
An immune response mediated through a body fluid.
biological_process
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.
death
A permanent cessation of all vital functions: the end of life; can be applied to a whole organism or to a part of an organism.
alpha-sialidase activity
Catalysis of the hydrolysis of alpha-glycosidic linkages in oligo- or poly(sialic) acids.
immunoglobulin complex
A protein complex that in its canonical form is composed of two identical immunoglobulin heavy chains and two identical immunoglobulin light chains, held together by disulfide bonds and sometimes complexed with additional proteins. An immunoglobulin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph.
B cell receptor complex
An immunoglobulin complex that is present in the plasma membrane of B cells and that in its canonical form is composed of two identical immunoglobulin heavy chains and two identical immunoglobulin light chains and a signaling subunit, a heterodimer of the Ig-alpha and Ig-beta proteins.
ribonucleoprotein complex
A macromolecular complex containing both protein and RNA molecules.
RNA polymerase complex
Any complex that possesses RNA polymerase activity; generally comprises a catalytic subunit and one or more additional subunits.
RNA-directed RNA polymerase complex
A protein complex that possesses RNA-directed RNA polymerase activity.
developmental process
A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition.
macromolecular complex
A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which the constituent parts function together.
RNA polymerase activity
Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1); the synthesis of RNA from ribonucleotide triphosphates in the presence of a nucleic acid template.
growth
The increase in size or mass of an entire organism, a part of an organism or a cell.
T cell receptor complex
A protein complex that contains a disulfide-linked heterodimer of T cell receptor (TCR) chains, which are members of the immunoglobulin superfamily, and mediates antigen recognition, ultimately resulting in T cell activation. The TCR heterodimer is associated with the CD3 complex, which consists of the nonpolymorphic polypeptides gamma, delta, epsilon, zeta, and, in some cases, eta (an RNA splice variant of zeta) or Fc epsilon chains.
cytokinesis by binary fission
A cytokinesis process that involves a set of conserved proteins including FtsZ, and results in the formation of two similarly sized and shaped cells; the process by which prokaryotic cells divide.
organelle
Organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton, and prokaryotic structures such as anammoxosomes and pirellulosomes. Excludes the plasma membrane.
protein complex
Any macromolecular complex composed of two or more polypeptide subunits, which may or may not be identical. Protein complexes may have other associated non-protein prosthetic groups, such as nucleotides, metal ions or other small molecules.
symbiosis, encompassing mutualism through parasitism
An interaction between two organisms living together in more or less intimate association. The term host is usually used for the larger (macro) of the two members of a symbiosis. The smaller (micro) member is called the symbiont organism. Microscopic symbionts are often referred to as endosymbionts. The various forms of symbiosis include parasitism, in which the association is disadvantageous or destructive to one of the organisms; mutualism, in which the association is advantageous, or often necessary to one or both and not harmful to either; and commensalism, in which one member of the association benefits while the other is not affected. However, mutualism, parasitism, and commensalism are often not discrete categories of interactions and should rather be perceived as a continuum of interaction ranging from parasitism to mutualism. In fact, the direction of a symbiotic interaction can change during the lifetime of the symbionts due to developmental changes as well as changes in the biotic/abiotic environment in which the interaction occurs.
adhesion to host
The attachment of an organism to its host via adhesion molecules, general stickiness etc., either directly or indirectly. The host is defined as the larger of the organisms involved in a symbiotic interaction.
entry into host
Penetration by an organism into the body, tissues, or cells of the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction.
entry into host through host barriers
Penetration by an organism into its host organism via active breaching of the physical barriers of the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction.
innate immune response
Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
negative regulation of viral reproduction
Any process that stops, prevents, or reduces the frequency, rate or extent of the viral life cycle, the set of processes by which a virus reproduces and spreads among hosts.
negative regulation of immune response
Any process that stops, prevents, or reduces the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus.
negative regulation of developmental process
Any process that stops, prevents or reduces the rate or extent of development, the biological process whose specific outcome is the progression of an organism over time from an initial condition (e.g. a zygote, or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
establishment of localization
Gene Ontology: http://purl.org/obo/owl/GO
The directed movement of a cell, substance or cellular entity, such as a protein complex or organelle, to a specific location.
multi-organism process
Any process by which an organism has an effect on another organism of the same or different species.
biological regulation
Any process that modulates the frequency, rate or extent of any biological process, quality or function.
mutualism
An interaction between two organisms living together in more or less intimate association in a relationship in which both organisms benefit from each other.
commensalism
An interaction between two organisms living together in more or less intimate association in a relationship in which one benefits and the other is unaffected.
Muridae
Mus
Mus musculus
Viruses
Orthomyxoviridae
Influenza A virus
Influenza B virus
Influenza C virus
Teleostomi
Euteleostomi
Mustelinae
Influenzavirus A
Influenzavirus B
Influenzavirus C
Bacteria
Homo/Pan/Gorilla group
Archaea
Eukaryota
Laurasiatheria
Euarchontoglires
Glires
Simiiformes
Hominoidea
Tetrapoda
Amniota
Theria
Sauria
Fungi/Metazoa group
Metazoa
Bilateria
Coelomata
Deuterostomia
Sciurognathi
Carnivora
Muroidea
ssRNA negative-strand viruses
Thogotovirus
Suina
Haplorrhini
Caniformia
Murinae
Mammalia
Dinosauria
Saurischia
Theropoda
Coelurosauria
Eumetazoa
Chordata
Vertebrata
Gnathostomata
Sarcopterygii
Sauropsida
Archosauria
Aves
Craniata
Cetartiodactyla
Eutheria
Primates
Catarrhini
Hominidae
Homo
Homo sapiens
Mustelidae
Mustela
Mustela putorius
Mustela putorius furo
Suidae
Sus
Sus scrofa
Rodentia
age
A time quality inhering in a bearer by virtue of how long the bearer has existed.
biological sex
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.
morphology
A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure.
trophic quality
An organismal quality inhering in a bearer by virtue of the bearer's disposition to synthesize a particular organic compound required for its growth.
size
A morphology quality inhering in a bearer by virtue of the bearer's physical magnitude.
length
A 1-D extent quality which is equal to the distance between two points.
mass
A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter.
weight
A physical quality inhering in a bearer that has mass near a gravitational body.
time
A quality in which events occur in sequence.
viability
An organismal quality inhering in a bearer or a population by virtue of the bearer's disposition to survive and develop normally or the number of surviving individuals in a given population.
female
A biological sex quality inhering in an individual or a population that only produces gametes that can be fertilised by male gametes.
male
A biological sex quality inhering in an individual or a population whose sex organs contain only male gametes.
auxotrophic
A nutritional quality inhering in a bearer by virtue of the bearer's inability to synthesize a particular organic compound required for its growth.
physical quality
A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities.
force
A physical quality inhering in a bearer by virtue of the bearer's rate of change of momentum.
physical object quality
A quality which inheres in a continuant.
dead
A viability quality inhering in a bearer by virtue of the cessation of the bearer's life.
1-D extent
A size quality inhering in an bearer by virtue of the bearer's extension in one dimension.
phenotypic sex
organismal quality
A quality that inheres in an entire organism or part of an organism.
Suggested label: pathogen transmission process
transmission process
Suggested definition: A process by which a pathogen passes from one host organism to a second host organism of the same Species.
A process that is the means during which the pathogen is transmitted directly or indirectly from its natural reservoir, a susceptible host or source to a new host.
Transmission Ontology: http://purl.org/obo/owl/TRANS
Suggested label: indirect pathogen transmission process
indirect
Indirect transmission is a transmission process during which the pathogen is indirectly transferred from a reservoir, source or host to another host by intermediary vehicles, vectors or as airborne dust particles.
contact
Contact transmission is a direct transmission process during which the pathogen is transmitted from a reservoir, source or host to another host by kissing, skin-to-skin contact, sexual intercourse, or by contact with soil or vegetation containing the pathogen.
droplet spread
Droplet spread transmission is a direct transmission process during which the pathogen is transmitted from a reservoir, source or host to another host by spray of aerosols over a short distance, spray from sneezing, coughing or talking.
airborne
Airborne transmission is an indirect transmission process during which the pathogen is indirectly transferred from a reservoir, source or host to another host while suspended in the air as dust.
vehicle-borne
Vehicle-borne transmission is an indirect transmission process during which the pathogen is indirectly transferred from a reservoir, source or host to another host by inanimate intermediary vehicle objects.
vehicle-borne ingestion
Vehicle-borne ingestion transmission is an indirect vehicle-borne transmission process during which the pathogen is indirectly transferred from a reservoir, source or host to another host by ingestion of fluids or foods or food products including: food, water, milk, or meat products.
blood
adipose tissue
Dense irregular connective tissue, which predominantly consists of adipocytes. Fat is stored in adipose tissue.
tarsometatarsus
The tarsometatarsus is a bone that is found in the lower leg of certain tetrapods, namely birds. It is formed from the fusion of several bones found in other types of animals, and homologous to the mammalian tarsal (ankle) and metatarsal (foot) bones. Despite this, the tarsometatarsus of birds is often referred to as just the tarsus or metatarsus.
Definition: An entity [bfo: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.
Examples: a heart, a person, the color of a tomato, the mass of a cloud, a symphony orchestra, the disposition of blood to coagulate, the lawn and atmosphere in front of our building
Definition: A continuant [snap:Continuant] that is either dependent on one or other independent continuant [snap:IndependentContinuant] bearers or inheres in or is borne by other entities.
Definition: A realizable entity [snap:RealizableEntity] that essentially causes a specific process or transformation in the object [snap:Object] in which it inheres, under specific circumstances and in conjunction with the laws of nature. A general formula for dispositions is: X (object [snap:Object] has the disposition D to (transform, initiate a process) R under conditions C.
Examples: the disposition of vegetables to decay when not refrigerated, the disposition of a vase to brake if dropped, the disposition of blood to coagulate, the disposition of a patient with a weakened immune system to contract disease, the disposition of metal to conduct electricity.
Definition: A material entity [snap:MaterialEntity] that is part of an object [snap:Object] but is not demarcated by any physical discontinuities.
Examples: upper and lower lobes of the left lung, the dorsal and ventral surfaces of the body, the east side of Saarbruecken, the lower right portion of a human torso
Definition: A realizable entity [snap:RealizableEntity] the manifestation of which is an essentially end-directed activity of a continuant [snap:Continuant] entity in virtue of that continuant [snap:Continuant] entity being a specific kind of entity in the kind or kinds of contexts that it is made for.
Examples: the function of a birth canal to enable transport, the function of the heart in the body: to pump blood, to receive de-oxygenated and oxygenated blood, etc., the function of reproduction in the transmission of genetic material, the digestive function of the stomach to nutriate the body, the function of a hammer to drive in nails, the function of a computer program to compute mathematical equations, the function of an automobile to provide transportation, the function of a judge in a court of law
Definition: A continuant [snap:Continuant] that is dependent on one or other independent continuant [snap:IndependentContinuant] bearers. For every instance of A requires some instance of (an independent continuant [snap:IndependentContinuant] type) B but which instance of B serves can change from time to time.
Examples: a certain PDF file that exists in different and in several hard drives
Definition: A continuant [snap:Continuant] that is a bearer of quality [snap:Quality] and realizable entity [snap:RealizableEntity] entities, in which other entities inhere and which itself cannot inhere in anything.
Examples: an organism, a heart, a leg, a person, a symphony orchestra, a chair, the bottom right portion of a human torso, the lawn and atmosphere in front of our building
Definition: An independent continuant [snap:IndependentContinuant] that is spatially extended whose identity is independent of that of other entities and can be maintained through time. Note: Material entity [snap:MaterialEntity] subsumes object [snap:Object], fiat object part [snap:FiatObjectPart], and object aggregate [snap:ObjectAggregate], which assume a three level theory of granularity, which is inadequate for some domains, such as biology.
Examples: collection of random bacteria, a chair, dorsal surface of the body
Definition: A material entity [snap:MaterialEntity] that is spatially extended, maximally self-connected and self-contained (the parts of a substance are not separated from each other by spatial gaps) and possesses an internal unity. The identity of substantial object [snap:Object] entities is independent of that of other entities and can be maintained through time.
Examples: an organism, a heart, a chair, a lung, an apple
Definition: A material entity [snap:MaterialEntity] that is a mereological sum of separate object [snap:Object] entities and possesses non-connected boundaries.
Examples: a heap of stones, a group of commuters on the subway, a collection of random bacteria, a flock of geese, the patients in a hospital
Comment: Boundaries are theoretically difficult entities to account for, however the intuitive notion of a physical boundary as a surface of some sort (whether inside or outside of a thing) will generally serve as a good guide for the use of this universal.
Definition: An independent continuant [snap:IndependentContinuant] that is a lower dimensional part of a spatial entity, normally a closed two-dimensional surface. Boundaries are those privileged parts of object [snap:Object] entities that exist at exactly the point where the object [snap:Object] is separated off from the rest of the existing entities in the world.
Examples: the surface of the skin, the surface of the earth, the surface of the interior of the stomach, the outer surface of a cell or cell wall
Definition: A spatial region [snap:SpatialRegion] with one dimension.
Examples: the part of space that is a line stretching from one end of absolute space to the other, an edge of a cube-shaped part of space
Definition: A specifically dependent continuant [snap:SpecificallyDependentContinuant] that is exhibited if it inheres in an entity or entities at all (a categorical property).
Examples: the color of a tomato, the ambient temperature of air, the circumference of a waist, the shape of a nose, the mass of a piece of gold, the weight of a chimpanzee
Comment: If a realizable entity [snap:RealizableEntity] inheres in a continuant [snap:Continuant], this does not imply that it is actually realized.
Definition: A specifically dependent continuant [snap:SpecificallyDependentContinuant] that inheres in continuant [snap: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.
Examples: the role of being a doctor, the function of the reproductive organs, the disposition of blood to coagulate, the disposition of metal to conduct electricity
Definition: A realizable entity [snap:RealizableEntity] the manifestation of which brings about some result or end that is not essential to a continuant [snap:Continuant] in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant [snap:Continuant] in some kinds of natural, social or institutional contexts.
Examples: the role of a person as a surgeon, the role of a chemical compound in an experiment, the role of a patient relative as defined by a hospital administrative form, the role of a woman as a legal mother in the context of system of laws, the role of a biological grandfather as legal guardian in the context of a system of laws, the role of ingested matter in digestion, the role of a student in a university
Comment: An instance of Site [snap:Site] is a mixture of independent continuant [snap:IndependentContinuant] entities which act as surrounding environments for other independent continuant [snap:IndependentContinuant] entities, most importantly for instances of object [snap:Object]. A site [snap:Site] is typically made of object [snap:Object] or fiat object part [snap:FiatObjectPart] entities and a surrounding medium in which is found an object [snap:Object] occupying the site [snap:Site]. Independent continuant [snap:IndependentContinuant] entities may be associated with others (which, then, are site [snap:Site] entities) through a relation of "occupation". That relation is connected to, but distinct from, the relation of spatial location. Site [snap:Site] entities are not to be confused with spatial region [snap:SpatialRegion] entities. In BFO, site [snap:Site] allows for a so-called relational view of space which is different from the view corresponding to the class spatial region [snap:SpatialRegion] (see the comment on this class).
Definition: An independent continuant [snap:IndependentContinuant] consisting of a characteristic spatial shape in relation to some arrangement of other continuant [snap:Continuant] entities and of the medium which is enclosed in whole or in part by this characteristic spatial shape. Site [snap:Site] entities are entities that can be occupied by other continuant [snap:Continuant] entities.
Examples: a particular room in a particular hospital, Maria's nostril or her intestines for a variety of bacteria.
Comment: All instances of continuant [snap:Continuant] are spatial entities, that is, they enter in the relation of (spatial) location with spatial region [snap:SpatialRegion] entities. As a particular case, the exact spatial location of a spatial region [snap:SpatialRegion] is this region itself.
Comment: An instance of spatial region [snap:SpatialRegion] is a part of space. All parts of space are spatial region [snap:SpatialRegion] entities and only spatial region [snap:SpatialRegion] entities are parts of space. Space is the entire extent of the spatial universe, a designated individual, which is thus itself a spatial region [snap:SpatialRegion].
Comment: Space and spatial region [snap:SpatialRegion] entities are entities in their own rights which exist independently of any entities which can be located at them. This view of space is sometimes called "absolutist" or "the container view". In BFO, the class site [snap:Site] allows for a so-called relational view of space, that is to say, a view according to which spatiality is a matter of relative location between entities and not a matter of being tied to space. The bridge between these two views is secured through the fact that while instances of site [snap:Site] are not spatial region [snap:SpatialRegion] entities, they are nevertheless spatial entities.
Definition: A continuant [snap:Continuant] that is neither bearer of quality [snap:Quality] entities nor inheres in any other entities.
Examples: the sum total of all space in the universe, parts of the sum total of all space in the universe
Definition: A continuant [snap: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.
Examples: the mass of a cloud, the smell of mozzarella, the liquidity of blood, the color of a tomato, the disposition of fish to decay, the role of being a doctor, the function of the heart in the body: to pump blood, to receive de-oxygenated and oxygenated blood, etc.
Definition: A spatial region [snap:SpatialRegion] with three dimensions.
Examples: a cube-shaped part of space, a sphere-shaped part of space
Definition: A spatial region [snap:SpatialRegion] with two dimensions.
Examples: the surface of a cube-shaped part of space, the surface of a sphere-shaped part of space, the surface of a rectilinear planar figure-shaped part of space
Definition: A spatial region [snap:SpatialRegion] with no dimensions.
Definition: A spatiotemporal region [span:SpatiotemporalRegion] that has temporal and spatial dimensions such that all points within the spatiotemporal region are mediately or immediately connected to all other points within the same spatiotemporal region [span:SpatiotemporalRegion].
Examples: the spatial and temporal location of an individual organism's life, the spatial and temporal location of the development of a fetus
Definition: A temporal region [span:TemporalRegion] every point of which is mediately or immediately connected with every other point of which.
Examples: the 1970s years, the time from the beginning to the end of a heart attack, the time taken up by cellular meiosis
Definition: A processual entity [span:ProcessualEntity] that is part of a process but that does not have bona fide beginnings and endings corresponding to real discontinuities.
Examples: chewing during a meal, the middle part of a rainstorm, the worst part of a heart-attack, the most interesting part of Van Gogh's life
Definition: An entity [bfo:Entity] that has temporal parts and that happens, unfolds or develops through time. Sometimes also called perdurants.
Examples: the life of an organism, a surgical operation as processual context for a nosocomical infection, the spatiotemporal context occupied by a process of cellular meiosis, the most interesting part of Van Gogh's life, the spatiotemporal region occupied by the development of a cancer tumor
Definition: A processual entity [span:ProcessualEntity] that is a maximally connected spatiotemporal whole and has bona fide beginnings and endings corresponding to real discontinuities.
Examples: the life of an organism, the process of sleeping, the process of cell-division
Definition: A processual entity [span:ProcessualEntity] that is a mereological sum of process [span:Process] entities and possesses non-connected boundaries.
Examples: the beating of the hearts of each of seven individuals in the room, the playing of each of the members of an orchestra, a process of digestion and a process of thinking taken together
Definition: A processual entity [span:ProcessualEntity] that is the fiat or bona fide instantaneous temporal process boundary.
Examples: birth, death, the forming of a synapse, the onset of REM sleep, the detaching of a finger in an industrial accident, the final separation of two cells at the end of cell-division, the incision at the beginning of a surgery
Comment: An instance of a processual context [span:ProcessualContext] is a mixture of processual entity [span:ProcessualEntity] which stand as surrounding environments for other processual entity [span:ProcessualEntity] entities. The class processual context [span:ProcessualContext] is the analogous among occurrent [span:Occurrent] entities to the class site [snap:Site] among continuant [snap:Continuant] entities.
Definition: An occurrent [span:Occurrent] consisting of a characteristic spatial shape inhering in some arrangement of other occurrent [span:Occurrent] entities. Processual context [span:ProcessualContext] entities are characteristically entities at or in which other occurrent [span:Occurrent] entities can be located or occur.
Examples: The processual context for a given manipulation occurring as part of an experiment is made of processual entities which occur in parallel, are not necessarily all parts of the experiment themselves and may involve continuant [snap:Continuant] entities which are in the spatial vicinity of the participants in the experiment.
Definition: An occurrent [span:Occurrent] that exists in time by occurring or happening, has temporal parts and always involves and depends on some entity.
Examples: the life of an organism, the process of meiosis, the course of a disease, the flight of a bird
Definition: A spatiotemporal region [span:SpatiotemporalRegion] that has spatial and temporal dimensions and every spatial and temporal point of which is not connected with every other spatial and temporal point of which.
Examples: the space and time occupied by the individual games of the World Cup, the space and time occupied by the individual liaisons in a romantic affair
Definition: A temporal region [span:TemporalRegion] every point of which is not mediately or immediately connected with every other point of which.
Examples: the time occupied by the individual games of the World Cup, the time occupied by the individual liaisons in a romantic affair
Definition: A connected spatiotemporal region [span:ConnectedSpatiotemporalRegion] at a specific moment.
Examples: the spatiotemporal region occupied by a single instantaneous temporal slice (part) of a process
Definition: A connected spatiotemporal region [span:ConnectedSpatiotemporalRegion] that endures for more than a single moment of time.
Examples: the spatiotemporal region occupied by a process or by a fiat processual part
Comment: All instances of occurrent [span:Occurrent] are spatiotemporal entities, that is, they enter in the relation of (spatiotemporal) location with spatiotemporal region [span:SpatiotemporalRegion] entities. As a particular case, the exact spatiotemporal location of a spatiotemporal region [span:SpatiotemporalRegion] is this region itself.
Comment: An instance of the spatiotemporal region [span:SpatiotemporalRegion] is a part of spacetime. All parts of spacetime are spatiotemporal region [span:SpatiotemporalRegion] entities and only spatiotemporal region [span:SpatiotemporalRegion] entities are parts of spacetime. In particular, neither spatial region [snap:SpatialRegion] entities nor temporal region [span:TemporalRegion] entities are in BFO parts of spacetime. Spacetime is the entire extent of the spatiotemporal universe, a designated individual, which is thus itself a spatiotemporal region [span:SpatiotemporalRegion]. Spacetime is among occurrents the analogous of space among continuant [snap:Continuant] entities.
Comment: Spacetime and spatiotemporal region [span:SpatiotemporalRegion] entities are entities in their own rights which exist independently of any entities which can be located at them. This view of spacetime can be called "absolutist" or "the container view". In BFO, the class processual context [span:ProcessualContext] allows for a so-called relational view of spacetime, that is to say, a view according to which spatiotemporality is a matter of relative location between entities and not a matter of being tied to spacetime. In BFO, the bridge between these two views is secured through the fact that instances of processual context [span:ProcessualContext] are too spatiotemporal entities.
Definition: An occurrent [span:Occurrent] at or in which processual entity [span:ProcessualEntity] entities can be located.
Examples: the spatiotemporal region occupied by a human life, the spatiotemporal region occupied by the development of a cancer tumor, the spatiotemporal context occupied by a process of cellular meiosis
Definition: A connected temporal region [span:ConnectedTemporalRegion] comprising a single moment of time.
Examples: right now, the moment at which a finger is detached in an industrial accident, the moment at which a child is born, the moment of death
Definition: A connected temporal region [span:ConnectedTemporalRegion] lasting for more than a single moment of time.
Examples: any continuous temporal duration during which a process occurs
Comment: All instances of occurrent [span:Occurrent] are temporal entities, that is, they enter in the relation of (temporal) location with temporal region [span:TemporalRegion] entities. As a particular case, the exact spatiotemporal location of a temporal region [span:TemporalRegion] is this region itself. Continuant [snap:Continuant] entities are not temporal entities in the technical sense just explained; they are related to time in a different way, not through temporal location but through a relation of existence at a time or during a period of time (see continuant [snap:Continuant].
Comment: An instance of temporal region [span:TemporalRegion] is a part of time. All parts of time are temporal region [span:TemporalRegion] entities and only temporal region [span:TemporalRegion] entities are parts of time. Time is the entire extent of the temporal universe, a designated individual, which is thus a temporal region itself.
Comment: Time and temporal region [span:TemporalRegion] entities are entities in their own rights which exist independently of any entities which can be located at them. This view of time can be called "absolutist" or "the container view" in analogy to what is traditionally the case with space (see spatial region [snap:SpatialRegion].
Definition: An occurrent [span:Occurrent] that is part of time.
Examples: the time it takes to run a marathon, the duration of a surgical procedure, the moment of death
example to be eventually removed
failed exploratory term
The term was used used in an attempt to structure part of the ontology but in retrospect failed to do a good job
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
placeholder
This isn't a class that OBI will keep - it's a placeholder for edits that are underway. The class name should start with an underscore
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 OBI 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."
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 definition editor.
core
Core is an instance of a grouping of terms from an ontology or ontologies. It is used by OBI to identify main classes.
Core is an instance of a grouping of terms from an ontology or ontologies. It is used by the ontology to identify main classes.
placeholder removed
terms merged
An editor note should explain what were the merged terms and the reason for the merge.
term imported
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 split
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.
other
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.
A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf
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.
"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 defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a 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.