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.
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.
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.
Title
Typically, a Title will be a name by which the resource is formally known.
A name given to the resource.
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
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.
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)"
definition
PERSON:Daniel Schober
The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
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
antisymmetric property
Alan Ruttenberg
part_of antisymmetric property xsd:true
use boolean value xsd:true to indicate that the property is an antisymmetric property
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.
first order logic expression
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
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.
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)"
alternative term
An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent)
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
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
obsolete_imported from
Replaced by IAO_0000412
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.
has measurement unit label
8/6/2009 Alan Ruttenberg: The suggestions is to deprecate specific and generically denotes in favor of a single denote relationship that corresponds to the generic sense
Smith, Ceusters, Ruttenberg, 2000 years of philosophy
The process of creation is, for example, writing down on paper the name of a friend by deliberately creating a certain pattern using ink. Here the ink + paper is the independent continuant and the carrier is the pattern in the ink. c = pattern in the ink b = paper + ink r = friend
c specifically denotes r =def r is a portion of reality & c is a particular quality & c depends specifically on some independent continuant b & b acquired c as the result of the achievement of an objective to enable pointing to r repeatedly. Marked means there is a changed or additional quality of the bearer - the quality is the information carrier. Case 1 Memory trace as mark created when reading some description of some friend. The trace can denote. Case 2 Pattern of ink arrayed on paper as mark when writing down a friend's name Case 3 Pattern of magnetic domains on scattered pieces of a hard disk platter as mark when saving a file.
see http://code.google.com/p/information-artifact-ontology/issues/detail?id=25&q=denote
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.
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
is_concretization_of
a relationship between a generically dependent continuant and at least one specifically dependent continuant upon which it existentially depends
is_concretized_as
is_specified_output_of
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
agent_in
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
derived_into
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
has_agent
As for has_participant, but with the additional condition that the component instance is causally active in the relevant process
has_improper_part
See reasons for obsoletion of improper_part_of
has_integral_part
has_part
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
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
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.)
location_of
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.)
participates_in
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.
precedes
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.
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.
transformed_into
has measurement value
has x coordinate value
has z coordinate value
has y coordinate value
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.
PERSON: Melanie Courtot
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
obsolete2_digital entity
3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 Superclass was 'digitial quality'
A digital entity is an information entity which is a collection of bits that can be interpreted by a computer. Two digital entities are the same if they are bitwise identical.
obsolete_digital entity
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
obsolete2_binary digital entity
3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 Superclass was 'digital entity'
A binary digital entity is a digital entity that is encoded in a way that is not easily human readable and that contains other than text characters.
MS Word document, ZIP file, DICOM file, JPEG file
binary digital entity
digital_entity
a unit of measure is the quality of some material entity compared to which another quality is some multiple of.
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?
obsolete_study interpretation
2009-03-16: definition was "A conclusion is a narrative object which can be published in a paper summerizing and interpreting a protocol application."
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.
A study interpretation is a textual entity about the implications of a study result. Examples include discussion of whether a hypothesis is false, whether the study failed to address the hypothesis, and whether the study results have led to new hypotheses
Lawrence Hunter
The obsoleting of narrative object required a modest change in the definition of this term. Circularity with "interpretation... interprets" has been removed, using "about the implications" instead.
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
obsolete2_text based digital entity
3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 superclass was 'digital document'
A text based digital entity is a digital entity that is encoded so that it only contains text characters.
XML file, C++ source code file
text based digital entity
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
obsolete2_report figure
A report figure is a report display element that has some aspect of illustration, but may be a composite of figures, images, and other elements
I prepended the 'report ' to make it clear that we mean parts of reports here. We may want a more generic version of 'figure', in which case this would become a defined class - figure and part_of some report
Replaced by defined version of figure
report figure
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.
2009-08-10 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
obsolete_report element
2009-03-16: needs some more work (clarify relations).
2009-03-16: was report display element with definition: A report display element is a narrative object that is part of a report. Report display elements are set off from the textual parts of a report and are typically given a label(e.g. Figure 2) which is used to refer to the element from the text. Typically the 2d layout is part of the identity of such elements.
A report element is a narrative object in which information is presented and consumed by a human being, and is part of a report. Examples of report elements are figure (dot plot), table, text portion (may include a movie or audio clip on a web page).
PERSON: Allyson Lister
There will be some issue here about whether these are defined classes. As intended these are meant to denote the parts of the report that are not textual but are typically boxed and set within the text, labelled with some identifier, and referred to in the text
report element
obsolete2_binary executable
Binary executable is a digital entity consisting of the binary representation of machine instructions of a specific processor or they may be binary pseudocode for a virtual machine. A non-source executable file is also called an object program. It is assumed that the binary executable file contains properly-formatted computer instructions. (derived from Wikipedia, Nov 1, 2007)
binary executable
person:Jennifer Fostel
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.
obsolete_report table
2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'textual entity table'. Alan restored as there are OBI dependencies and this merits further discussion
A report table is a report display element consisting of a matrix of cells layed out in a grid, some set of which are filled with some information content
report table
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.
obsolete2_digital document
3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 superclass was 'digial entity'
A digital document is a digital entity consisting of an electronic file which can be rendered into human-readable form by one or more computational applications. The digital document does not refer to the information content of the document but to an instance of the file.
digital document
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,}.
_identifier is a container under information content entity for collecting types of terms to indicate a specific instance or clas of what was used or participated in an investigation. Identifiers are borne by a product or its packaging, and can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots. Note: everybody agreed that identifier is probably a too general term. We however felt that it would be appropriate to group "identifiying" terms under some kind of umbrella. We therefore propose to use _identifier for that purpose. As per OBI conventions, the _ prefixing identifier indicates that this is a helper class and shouldn't be considered as final.
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.
Need to rework digital entity. Digital quality was suggested by Barry.
3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4
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
obsolete_survival curve
A survival curve is a report graph which is a graphical representation of data where the percentage of survival is plotted as a function of time.
WEB: http://www.graphpad.com/www/book/survive.htm
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
a planned process with the objective to establish a system that allows to refer to specific entities of a certain kind and store information about them, by establishing a CRID registry and plan specifications for the process of 1) assigning a CRID and 2) looking up a CRID.
MC, 20101124: deprecated following discussion at IAO call 20101124. Term was deemed not necessary - no use case for now.
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
planned process
A planned process is the realization of a plan borne by an agent that initiates this process in order to bring about the objective(s) specified as part of the plan specification.
A processual entity that realizes a plan which is the concretization of a plan specification.
investigation
a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s).
An investigation is a process with the objective to generate an information entity by planning protocol applications included in an overall study design, carrying them out and documenting the results. In addition, an investigation can include a sub process of interpreting the data to draw conclusions.
a planned process that realizes the concretization of a study design
study design
A study design is a plan comprising of protocols and/or data transformations that are executed as part of an investigation. The objective of the study design is to produce results (information). The study design specifies how the different data produced in the execution of the investigation are related, how they are interpreted, and what are the desired results.
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.
A 1-D extent quality which is equal to the distance between two points.
A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter.
A one dimensional extent is a dimensional extent in only one dimension, e.g. a length.
A chemical graph is a structural descriptor in which the connectivity and constitution of the chemical entity are described in terms of a mathematical graph, usually with atoms as vertices and bonds as edges, but other variants exist.
A parameter data item is a data item that plays the role of a parameter to a software method.
A numeric data item is a data item which has a value which is numeric.
A textual data item is a data item which has a value that has at least some non-numeric characters included in it.
A numeric data format specification is a data format specification for data items which are numeric, that is, they contain only numeric values.
A textual data format specification is a specification of the format of data items which are textual, that is, they consist of character data.
A chemical entity is any molecular entity or chemical substance.
Molar refractviity is a measure of the total polarizability of a mole of a substance and is dependent on the temperature, the index of refraction, and the pressure.
atomic polarizability sum is the sum of the atomic polarizabilities (including implicit hydrogens).
sum of surface area on positive parts of molecule
partial positive surface area * total positive charge on the molecule
A canonical SMILES descriptor is a SMILES descriptor that is produced using a canonicalization algorithm which results in one special generic SMILES among all valid possibilities.
charge weighted partial positive surface area
Atomic order is an atomic descriptor that specifies the ordinal position of an atom.
sum of surface area on negative parts of molecule
Chirality is a molecular entity quality which inheres in a molecular entity by virtue of the existence of another molecular entity which is the mirror image of the first one, yet non-superposable on it.
molecular entity information format specification
A molecular entity information format specification is an information content entity which specifies a format in which information about a molecular entity should be encoded.
partial negative surface area * total negative charge on the molecule
An energetic descriptor is a chemical descriptor which captures information about some aspect of the energetic behaviour of a chemical entity.
A SMILES descriptor is a structure descriptor that denotes a molecular structure as a graph.
A SMARTS descriptor is a molecular structure descriptor that conforms to the SMARTS specification.
The simplified molecular input line entry specification (SMILES) is a specification for unambiguously describing the structure of chemical molecules using short ASCII strings. SMILES strings can be imported by most molecule editors for conversion back into two-dimensional drawings or three-dimensional models of the molecules (source:wikipedia).
Smiles ARbitrary Target Specification (SMARTS) is a language for specifying substructural patterns in molecules. The SMARTS line notation is expressive and allows extremely precise and transparent substructural specification and atom typing (source:Wikipedia)
molecular structure encoding format specification
A molecular structure encoding format specification is a molecular entity format specification which specifies a format in which a molecular structure information entity may be encoded.
molecular stereochemistry format specification
A molecular stereochemistry format specification is a molecular structure format specification that specifies how to encode the stereochemical aspects of a molecular structure.
A physical descriptor is a chemical descriptor which describes some physical property (quality or disposition) of a chemical entity.
A stereochemical descriptor is a chemical descriptor which describes some aspect of the three dimensional structure of a chemical entity.
specification of stereochemistry by configuration
A specification of stereochemistry by configuration specifies a format in which the stereochemistry of a molecule should be encoded with reference to the configuration of attachments around the stereogenic centre.
specification of stereochemistry by optical activity
A specification of stereochemistry by optical activity specifies a format by which the stereochemistry of a molecule should be encoded by reference to the observable optical activity of a chiral molecule.
A molecular entity quality is a quality which inheres in a molecular entity.
an isomeric SMILES descriptor is a SMILES descriptor that written with isotopic and chiral specifications.
Molecular structure is a molecular entity quality that inheres in a molecule by virtue of its shape - the way in which the atoms which constitute the molecule are bonded together and the shape which they therefore form.
atomic connectivity molecular structure encoding format specification
An atomic connectivity molecular structure encoding format specification is a molecular structure encoding format specification which specifies a format in which the connectivity of atoms within a molecule may be specified.
molecular composition format specification
A molecular composition format specification is a molecular entity information format specification which specifies a format in which a molecular composition may be encoded.
The IUPAC International Chemical Identifier (InChI) is a textual identifier for chemical substances, designed to provide a standard and human-readable way to encode molecular information and to facilitate the search for such information in databases and on the web. Developed by IUPAC and NIST during 2000-2005, the format and algorithms are non-proprietary and the software is freely available under the open source LGPL license (though the term "InChI" is a trademark of IUPAC). [source: Wikipedia, http://en.wikipedia.org/wiki/International_Chemical_Identifier]
molecular entity name format specification
A molecular entity name format specification is a molecular entity information format specification which specifies a format in which a molecular entity name may be encoded.
Preferred IUPAC Name for Organic Compounds
A positional descriptor is a chemical descriptor which describes some aspect of the position, or location of a chemical entity, or of the relative parts of a chemical entity with respct to one another.
A molecular formula is a structure descriptor which identifies each constituent element by its chemical symbol and indicates the number of atoms of each element found in each discrete molecule of that compound.
An information entity about a molecular entity which serves to name that molecular entity.
A preferred name is a molecular entity name which is preferred, or recommended, for usage in textual annotations referring to that molecular entity.
Preferred IUPAC Name for Inorganic Compounds
The sum of the squared atom degrees of all heavy atoms.
Molecular composition is a molecular entity quality that inheres in a molecule by virtue of the atoms which constitute the molecule.
A chemical connectivity table is a structure descriptor which consists of a connection table representing bonds between atoms in a molecular entity.
An aromaticity descriptor is a chemical descriptor which indicates the aromaticity of a molecular entity.
A MOLfile is a file which contains a MOLfile encoding of a chemical structure representation. It is the concretization of a MOLfile descriptor.
A dimensional extent descriptor is a physical property descriptor which describes some measurable length, area or volume aspect of a chemical entity.
An identifying descriptor is a chemical descriptor which provides an identifier for the chemical entity it is about, which in most cases should aim to be unique and easy to use as an unambiguous reference for the chemical entity.
A bond order descriptor is a descriptor associated with a bond in a chemical entity which indicates the order of the bond (single, double or triple).
NOTE: QSAR descriptors are often just called 'chemical descriptor' or 'molecular descriptor' in the cheminformatics community.
A Quantitative Structure Activity Relationship (QSAR) descriptor is a chemical descriptor which gives a numeric, quantitative value which is believed to be associated with some aspect of the chemical or biological activity of the chemical entity.
a molecular entity descriptor is a chemical descriptor that provides information about a molecular entity.
An information entity which is about a polyatomic molecular entity.
cyclicity is a quality that inheres in a molecular entity by virtue of the presence of cycles in the connection of the atoms within the molecular entity.
A functional group descriptor is a structural descriptor which describes specific groups of atoms within molecules that are responsible for the characteristic chemical reactions of those molecules.
Polarity is a quality that inheres in a molecular entity by virtue of whether or not the molecular entity has a separation of electric charge which leads to the molecule having an electric dipole.
Polar polarity is a quality that inheres in a molecular entity when the molecular entity is polar, i.e. does possess an electric dipole.
Nonpolar polarity is a quality which inheres in a molecular entity when the molecular entity does not possess an electrical dipole.
Cyclic cyclicity inheres in a molecule when the atoms of the molecule do contain at least one cycle in the atom-atom connection paths (through bonds).
Acyclic cyclicity inheres in a molecule when the atoms within the molecule do not contain at least one cycle in the atom-atom connection paths (through the bonds).
Aromatic aromaticity is a quality that inheres in a molecular entity when it possesses at least one ring that is aromatic.
Non aromatic aromaticity is a quality that inheres in a molecular entity by virtue of the molecule possessing no rings that are aromatic.
The (integer) number of neutrons in the atoms nucleus.
The (integer) number of protons in the atoms nucleus.
Descriptors which show the relationship between two ligands attached to separate atoms that are connected by a double bond or are contained in a ring. The two ligands are said to be located cis to each other if they lie on the same side of a plane. If they are on opposite sides, their relative position is described as trans. The appropriate reference plane of a double bond is perpendicular to that of the relevant s-bonds and passes through the double bond.[source:IUPAC Gold Book - http://goldbook.iupac.org/C01092.html]
A structural descriptor is a chemical descriptor which is about some aspect of the molecular structure (composition) of a chemical entity.
A chemical quality is a quality that inheres in a molecular entity or aggregate molecular substance.
The ease of distortion of the electron cloud of a molecular entity by an electric field [source: IUPAC Gold Book - http://goldbook.iupac.org/P04711.html]
The integer number of non-H substituents of an atom.
The quality of an atom that reflects the combination of its atomic orbitals to create bonding orbitals.
A topological descriptor is a chemical descriptor which pertains to spatial properties of a geometric object that are preserved under continuous deformations of objects, for example, deformations that involve stretching.
A geometric descriptor is a descriptor that concerns information about size, shape, and relative position.
A hybridization descriptor is a chemical descriptor that is about the hybridization of atomic orbitals in a molecular entity.
Atomic valence is an atomic descriptor that specifies the maximum number of univalent atoms (originally hydrogen or chlorine atoms) which may combine with an atom of the element under consideration, or with a fragment, or for which an atom of this element can be substituted [source: IUPAC Gold Book - http://goldbook.iupac.org/V06588.html]
An atomic hardness descriptor is an atomic descriptor that estimates the difference between the ionization potential and the electron affinity of a given atom.
Valency is an atomic quality of the number of chemical bonds formed by the atom.
An atomic softness descriptor is an atomic descriptor which is about the charge delocalizing ability of a given atom.
The MOLfile atomic connectivity molecular structure encoding format specification may be found described at http://en.wikipedia.org/wiki/Chemical_table_file#Molfiles. It is composed primarily of a connection table (atoms and bonds); hydrogen may be implicit or explicit.
A chemical substance quality is a quality that inheres in an aggregate molecular substance, such as a portion of solid or liquid matter.
A crystal structure is a chemical substance quality which inheres in a crystalline solid or liquid crystal substance by virtue of the way the molecules are ordered within the crystal.
software module to calculate a chemical descriptor
A software module to calculate a chemical descriptor is software module that implements an algorithm which calculates a descriptor value for a chemical entity.
A molecular QSAR descriptor is a OSAR descriptor which gives a quantitative value to some aspect of a molecular entity.
The cycle basis of a molecular structure is the smallest set of cycles (closed paths) formed in the graph representation of the structure, from which all other cycles can be computed.
A systematic name is a molecular entity name which is formulated systematically from the structure of the molecular entity.
An IUPAC name is a systematic name which is formulated according to the rules and recommendations for chemical nomenclature set out by the International Union of Pure and Applied Chemistry (IUPAC).
An atomic quality is a molecular entity quality which inheres in an atom.
A trivial name is a molecular entity name that is in common public use and may not be related to the structure of the molecular entity.
The fused cycles in a molecular structure are those cycles from the cycle basis which share at least one bond.
A CML (Chemical Markup Language) file is an XML-based representation of the atomic connectivity of a molecular entity.
An atomic QSAR descriptor is a QSAR descriptor which gives a quantitative value to some aspect of an atom which is part of a molecular entity.
An InChI descriptor is a structure descriptor which conforms to the InChI format specification.
A MOLfile descriptor is a structure descriptor which conforms to the MOLfile format specification.
Aromaticity is a molecular entity quality that inheres in a conjugated ring of unsaturated bonds, lone pairs, or empty orbitals that exhibit a stabilization stronger than would be expected by the stabilization of conjugation alone.
An atomic connectivity index is an atomic descriptor that is a measure of atomic connectivity, which can take various forms (e.g. zero-order, or first-order).
Half the sum of all the distance matrix entries, topological index of atom-atom distances.
The formal charge gives the charge assigned to an atom in a molecule, assuming that electrons in a chemical bond are shared equally between atoms, regardless of relative electronegativity. The formal charge of any atom in a molecule can be calculated by the following equation: FC = number of valence electrons of the atom in isolation (atom in ground state) - number of non-bonding electrons on this atom in the molecule - half the total number of electrons shared in covalent bonds with other atoms in the molecule. [source:wikipedia]
A partial charge descriptor gives the charge with an absolute value of less than one elementary charge unit (that is, smaller than the charge of the electron). [source:wikipedia]
Charge is a quality that inheres in a molecular entity by virtue of the overall electric charge of the molecule, which is due to a comparison between the total number of electrons and the total number of protons.
Electronegativity is an atomic quality that describes its power to attract electrons to itself [source:IUPAC Gold Book - http://goldbook.iupac.org/E01990.html]
An electronegativity descriptor is a chemical descriptor that is about the electronegativity quality of an atom.
A chemical descriptor is a data item (quantity or value) about a chemical entity that conforms to a specification for how it is calculated, measured or recorded.
A 1-D extent quality inhering in a bearer by virtue of the bearer's dimension of extension to the circumference of a circle or sphere.
Atomic radius is the 1D extent of the electron cloud surrounding the atom.
Bond multiplicity is the extent to which participating electrons are localized in the bonding orbitals.
A bond multiplicity descriptor is a chemical descriptor that in primitive cases is defined as half of the difference between the number of bonding and antibonding electrons in a particular system, but may also be defined with relation to the strength of a single bond.
A charge descriptor is a chemical descriptor which indicates the charge of a chemical entity.
A bond length descriptor is a dimensional extent descriptor which gives the measured or predicted (idealised) length of an atom to atom bond within a chemical entity.
The quality of an atom in which the 2s orbital mixes with only one of the three p-orbitals resulting in two sp orbitals and two remaining unchanged p orbitals. spsp overlap between two atoms form a s bond and two additional p bonds formed by pp overlap.
Half the sum of all the distance matrix entries with a value of 3
software execution is a process in which the instruction set that comprises the software program is executed on a machine.
algorithm to calculate a chemical descriptor
generic SMILES descriptor
a generic SMILES descriptor is a SMILES descriptor that denotes only the labeled molecular graph (i.e. atoms and bonds, but no chiral or isotopic information).
topological polar surface area descriptor
charge weighted partial negative surface area
PPSA-1 * total molecular surface area / 1000
PPSA-2 * total molecular surface area /1000
PPSA-3 * total molecular surface area /1000
PNSA-1 * total molecular surface area /1000
PNSA-2 * total molecular surface area /1000
PNSA-3 * total molecular surface area /1000
most positive charge / total positive charge
most negative charge / total negative charge
sum of solvent accessible surface areas of atoms with absolute value of partial charges less than 0.2
sum of solvent accessible surface areas of atoms with absolute value of partial charges greater than or equal 0.2
molecular polarizability
Sum of the absolute value of the difference between atomic polarizabilities of all bonded atoms in the molecule (including implicit hydrogens)
fragment complexity descriptor
vertex adjacency matrix descriptor
Petitjean Topological Shape Index
A measure of the anisotropy in a molecule (as per Petitjean et al)
Petitjean Geometric Shape Index
A measure of the anisotropy in a molecule (as per Bath et al)
Petitjean number
the eccentricity of a vertex corresponds to the distance from that vertex to the most remote vertex in the graph. The distance is obtained from the distance matrix as the count of edges between the two vertices. If r i is the largest matrix entry in row i of the distance matrix D, then the radius is defined as the smallest of the r i . The graph diameter D is defined as the largest vertex eccentricity in the graph. Petitjean Number is the value of ( diameter - radius ) diameter .
Petitjean Shape Index
A measure of the anisotropy in a molecule
XLogP descriptor
A LogP descriptor based on the atom-type method described in Wang, R., Fu, Y., and Lai, L.. A New Atom-Additive Method for Calculating Partition Coefficients, Journal of Chemical Information and Computer Sciences. vol. 37. 1997, pp. 615-621.
MLogP descriptor
A LogP descriptor based on a simple equation using the number of carbons and hetero atoms.
maximal ratio of length to breadth descriptor
ratio of length to breath descriptor
minimal ratio of length to breadth descriptor
ionization potential descriptor
eccentric connectivity index descriptor
equilibrium constant
acid dissociation constant
the acid dissociation constant, Ka, is quantitative measure of the strength of an acid in solution. It is the equilibrium constant for a chemical reaction known as dissociation in the context of acid-base reactions.
pKa
the logarithmic measure of the acid dissociation constant (Ka)
A cycle is a part of a molecular entity that is cyclic, that is, consists of a chain of atoms where each is reachable by a bond connected to another atom, and the first atom is reachable from itself.
A substructure is a contiguous part of a molecule composed of at least two atoms and a bond.
molecular weight calculated by pipeline pilot
A molecular weight descriptor calculated by a relevant module of the Pipeline Pilot software tool.
absolute SMILES descriptor
An absolute SMILES descriptor is an isomeric SMILES descriptor that is produced using a canonicalization algorithm.
tautomer count
a count descriptor that denotes the number of tautomers.
stereocenter count
atom stereocenter count
defined atom stereocenter count
A formation energy descriptor is an energetic descriptor which gives the value for the energy of formation of a chemical entity.
A solvation energy descriptor is a chemical descriptor which gives the value for the energy of dissolving a particular chemical entity in a solvent.
A count descriptor is a chemical descriptor which is calculated by counting the number of features of a certain kind which are present in the chemical entity.
A dissociation energy descriptor is an energetic descriptor which gives a value for the dissociation energy for a chemical entity.
A dimensional extent quality is a quality that inheres in a molecular entity by virtue of a measurement of length, area or volume in a one, two or three dimensional extent.
undefined atom stereocenter count
bond stereocenter count
defined bond stereocenter count
undefined bond stereocenter count
molecular weight descriptor
The mass of a molecule calculated using the average mass of each element weighted for its natural isotopic abundance. E.g., Carbon has two natural isotopes 12 and 13 with relative abundances of 98.9% and 1.1% to yield an average mass of 12.011 g/mol
exact mass descriptor
an exact mass descriptor corresponds to the mass of the most intense molecule/ion peak in an MS spec, and when calculated denotes the mass of an ion or a molecule containing most likely isotopic composition for a single random molecule.
monoisotopic mass descriptor
The mass of a molecule calculated using the mass of the most abundant isotope of each element. E.g., Carbon has a monoisotopic mass of 12.000 g/mol.
complexity descriptor
A complexity descriptor denotes the how complicated a structure is, seen from both the point of view of the elements contained and its structural features .
Ghose/Crippen ALogP calculation algorithm
Fragment Method used for the calculation of ALogP as defined by Ghose and Crippen. Ghose, A.K., Viswanadhan V.N., and Wendoloski, J.J., Prediction of Hydrophobic (Lipophilic) Properties of Small Organic Molecules Using Fragment Methods: An Analysis of AlogP and CLogP Methods. J. Phys. Chem. A, 1998, 102, 3762-3772.
The integer number of atoms in a pi-orbital system.
bond dissociation Gibbs energy descriptor
Bond dissociation Gibbs energy descriptor captures the Gibbs energy associated with the process of breaking the bond in question. This could be measured or calculated in vacuo or in a specific Solvent, at a given temperature and pressure. Depends on molecular conformation.
The molecular entity solvation Gibbs energy descriptor reflects the Gibbs energy associated with the solvation of the molecular entity in question. This could be measured or calculated in vacuo or in a specific solvent, at a particular temperature and pressure. Depends on molecular conformation when computed.
A three dimensional extent is a dimensional extent in three dimensions, e.g. a volume.
The refractive index of a chemical substance is a measure of the manner in which light waves are bent when they enter the medium of the chemical substance.
A surface area descriptor is a descriptor which describes a measure or calculation of the surface area of a chemical entity.
A charge density descriptor is a chemical entity descriptor which indicates the distribution of the electric charge over the volume of the chemical entity.
A descriptor that provides the integer count of aromatic atoms in a given molecular entity.
A descriptor that specifies the integer count of bonds in a given molecular entity.
PubChem conformer identifier
The disposition to dissociate is the disposition of an ionic compound (complexes, or salts) to separate or split into smaller particles, ions, or radicals, usually in a reversible manner.
The linear, surface, or volume charge density is the amount of electric charge in a line, surface, or volume respectively. [source: Wikipedia, http://en.wikipedia.org/wiki/Charge_density]
A bond aromaticity descriptor is an aromaticity descriptor associated with a bond within a chemical entity which indicates whether that bond belongs to an aromatic system.
The meltability of a chemical substance is a quality which inheres in the chemical substance by virtue of the ease with which the substance can be changed from a solid to a liquid state especially by the application of heat.
The formation Gibbs energy descriptor captures the Gibbs energy associated with the formation of a molecular entity, relative to the standard state of constituent atoms. This can be measured, calculated in vacuo, or calculated with respect to a specific solvent, at a particular temperature and pressure. When calculated, the formation Gibbs energy value depends on the molecular conformation.
The largest aliphatic chain size descriptor is a count descriptor that gives the integer length (number of atoms) in the largest unbranched chain of atoms that does not contain aromatic atoms, within a given molecular entity.
Molecular entity formation enthaply descriptor captures the enthalpy associated with the formation of the molecular entity in question, relative to the standard state of constituent atoms. This could be measured or calculated in vacuo or in a specific Solvent, at a particular temperature and pressure. Depends on molecular conformation when computed.
A volume descriptor is a descriptor which describes a measure or calculation of the volume of a chemical entity.
A descriptor that provides the integer count of aromatic bonds in a given molecular entity.
A descriptor that reflects the integer number of hydrogen bond donors in a given molecular entity, as determined by a given method. In highly simplified terms, this is usually the count of all negatively or partially negatively charged heteroatoms (e.g. alcohol oxygen) that have covalently attached to them partially positively charged hydrogen atoms that are capable of participating in a hydrogen bond.
A descriptor that reflects the integer number of hydrogen bond acceptors in a given molecular entity, as determined by a given method. In highly simplified terms, this is usually the count of all negatively or partially negatively charged heteroatoms (e.g. alcohol oxygen) capable of accepting a hydrogen bond.
The largest chain size descriptor is a count descriptor that gives the integer length (number of atoms) in the largest chain in a molecular entity.
Relative permittivity is a chemical substance quality that reflects the ability of a medium composed of molecules of a given type to transmit an electric field.
The molecular entity solvation entropy descriptor reflects the entropy associated with the solvation of the molecular entity in question. This could be measured or calculated in vacuo or in a specific solvent, at a particular temperature and pressure. Depends on molecular conformation when computed.
The molecular entity solvation enthalpy descriptor reflects the enthalpy associated with the solvation of the molecular entity in question. This could be measured or calculated in vacuo or in a specific solvent, at a particular temperature and pressure. Depends on molecular conformation when computed.
The logarithm of octanol-water partition coefficient, which is the ratio of the molecules dissolved in octanol to those dissolved in pure un-ionized water upon mixture equilibration. This can be measured or predicted. The value is dimensionless. May depend on molecular conformation when computed.
Bond dissociation enthalpy descriptor captures the enthalpy associated with the process of breaking the bond in question. This could be measured or calculated in vacuo or in a specific Solvent, at a given temperature and pressure. Depends on molecular conformation.
Chemical substance refractive index descriptor is a unitless descriptor that specifies the ratio of the speed of light in vacuum to that in a given chemical substance. [IUPAC: http://goldbook.iupac.org/R05240.html]
a bond count that denotes the integer number of rotors in the molecule, generally single bonds torsion around which produces non-identical geometric molecular configurations.
The vaporizability of a chemical substance is a quality which inheres in the chemical substance by virtue of the ease with which the substance can be changed into a gaseous state.
Melting point descriptor specifies the temperature at which a chemical substance undergoes the transition from solid to liquid state under standard conditions.
The boiling point descriptor indicates the temperature at which a chemical substance undergoes a state transition from liquid to gas, at standard conditions.
The disposition to form is the disposition of an ionic compound (complexes, or salts) to form from the smaller particles, ions, or radicals from which it is constituted.
Molecular entity formaiton entropy descriptor captures the entropy associated with the formation of the molecular entity in question, relative to the standard state of constituent atoms. This could be measured or calculated in vacuo or in a specific Solvent, at a particular temperature and pressure. Depends on molecular conformation when computed.
The relative permittivity descriptor specifies the ratio of the electric field strength in vacuum to that in a given medium. It was formerly called the dielectric constant. [IUPAC Gold Book: http://goldbook.iupac.org/R05273.html ]
A two dimensional extent is a dimensional extent in two dimensions, e.g. an area.
A descriptor that specifies the integer count of atoms in a given molecular entity.
Bond dissociation entropy descriptor captures the entropy associated with the process of breaking the bond in question. This could be measured or calculated in vacuo or in a specific Solvent, at a given temperature and pressure. Depends on molecular conformation.
Chemical substance constitutes matter of constant composition, that may contain a collection of molecular entities. [IUPAC: http://goldbook.iupac.org/C01039.html]
effective rotor count
A count descriptor that takes into account flexibility of rings and rotatable bonds.
total formal charge descriptor
A charge descriptor that gives the total charge for a molecule
conformer volume descriptor
a count of the number of amino acid residues.
covalent unit count
The number of covalent units (molecule / ion) in a chemical structure
Highest Occupied Molecular Orbital Energy
A descriptor that the energy of the highest occupied 'molecular' orbital of the chemical entity.
Lowest Unoccupied Molecular Orbital Energy
A descriptor that the energy of the lowest unoccupied 'molecular' orbital of the chemical entity.
A descriptor that specifies the integer count of acidic groups in a given molecular entity.
A descriptor that specifies the integer count of basic groups in a given molecular entity.
ALogP descriptor
The ALogP descriptor described by Ghose and Crippen in 1986 and 1987.
hybridization descriptor (VSEPR)
inductive atomic hardness
TPSA (fragments)
VABC volume descriptor
heavy atom count
isotope atom count
The sum of all atoms enriched with respect to a particular atom isotope
PubMed Identifier
GenBank Protein Identifier
GenBank Nucleotide Identifier
Ertl polar surface area calculation algorithm
Fast calculation of molecular polar surface area as a sum of fragment based contributions and its application to the prediction of drug transport properties, Ertl, P., Rohde, B., Selzer, P., J. Med. Chem. 2000, 43, 3714-3717.
polar surface area descriptor calculated by Pipeline Pilot
hydrogen bond acceptor count calculated by pipeline pilot
hydrogen bond donor count calculated by pipeline pilot
rotatable bond count calculated by pipeline pilot
Number of properties defined in Lipinski’s Rule of 5 (RO5) that the compound fails. Conditions which violate the RO5 are: Molecular weight>=500 AlogP>=5 HBD>=5 HBA>=10
Lipinski rule of five violation calculation algorithm
Lipinski, C. A.; Lombardo, F.; Dominy, B. W.; Feeney, P. J. Experimental and Computational Approaches to Estimate Solubility and Permeability in Drug Discovery and Development Settings. Adv. Drug Deliv. Rev., 1997, 23, 3-25.
rule of five violations calculated by pipeline pilot
Rule of 3 passes. It is suggested that compounds that pass all these criteria are more likely to be hits in fragment screening. molecular weight <=300, number of hydrogen bond donors <=3, number of hydrogen bond acceptors <=3 AlogP <=3. RTB <=3 PSA<=60
rule of three passes calculation algorithm
A ‘Rule of Three’ for fragment-based lead discovery? Miles Congreve, Robin Carr, Chris Murray and Harren Jhoti. Drug Discovery Today, 2003,8(19), 876-877
rule of three passes calculated by pipeline pilot
MedChem Friendly These are functional groups that may not be desirable from a medicinal chemistry perspective. For example reactive groups will be flagged as “N” (not MedChem Friendly). Molecules which do not contain any of these groups will be flagged as “Y” (MedChem Friendly). The groups are defined by the following list of SMARTS: [N+]([O-])=O [C;!R](-[C;!R]=O)=[C;!R] C(-N)=S P O-N=C OS(=O)=O O1-CC-O-C-1 C(-N)=C [C;H2]-[C;H2]-[C;H2]-[C;H2]-[C;H2]-[C;H2]-[C;H2] OC1OCC(O)C1 C=N-C(-O) [N;H]-[C;H]-[N;H] [C;!R]=[C;!R]-N-[C;D1&H3,D2&H2,D3&H1,D4] [S;!R]-[C;!R]-[O;!R] [O;D2]-[C;!H0](([F,Br,I,Cl])([F,Br,I,Cl])([!F,!Br,!I,!Cl])) CC([O;!R])([O;!R]) C1-C-O1 C(=O)-S-C(=S) [S;H] SC#N
medchem friendly descriptor calculated by pipeline pilot
logP calculated by ACD/Labs PhysChem software
octanol-water distribution coefficient calculated at a given pH.
logD calculated at pH 7.4 by ACD/Labs PhysChem software
ACD_LogD(pH7.4) Distribution Coefficient calculated at pH7.4
most acidic pKa calculated by ACD/Labs PhysChem software library
most basic pKa calculated by ACD/Labs PhysChem software library
Molecular Species is a description of the predominant form of the molecule at pH7.4.
molecular species at pH 7.4 calculated by ACD/Labs PhysChem software
These are defined according to the definitions: Acid(A) ACD_MOST_ApKa <6.5 and ACD_MOST_BpKa<8.5 Bas (B) ACD_MOST_ApKa >6.5 and ACD_MOST_BpKa>8.5 Neutral (N) ACD_MOST_ApKa >6.5 and ACD_MOST_BpKa<8.5 Zwitterion (ZW) ACD_MOST_ApKa <6.5 and ACD_MOST_BpKa>8.5
ACD/Labs PhysChem software library version 12.01
Is this equivalent to IAO 'source code module' (IAO_0000096) on the same level as 'software'? From the textual definition in IAO it seems fairly close. (JH)
A software module is a collection of software methods.
A software method (also called subroutine, subprogram, procedure, method, function, or routine) is a programming language implementation of a plan specification which is capable of realizing some objective specification when part of a software application.
A software library is a collection of programming language mplementations (e.g. modules, methods) capable of realizing some objective specification when linked to a application software.
A software application is a programming language implementation of a plan specification capable of realizing some objective specification.
logD calculated at pH 5.5 by ACD/Labs PhysChem software library version 12.01
Octanol-water distribution coefficient calculated at pH 5.5 by ACD/Labs PhysChem software library version 12.01.
hydrogen bond acceptor count calculated by ACD/Labs PhysChem software library version 12.01
Hydrogen bond acceptor count that has been calculated by ACD/Labs PhysChem software library version 12.01.
hydrogen bond donor count calculated by ACD/Labs PhysChem software library version 12.01
Hydrogen bond donor count that has been calculated by ACD/Labs PhysChem software library version 12.01.
Boiling point at 760 mmHg pressure calculated by ACD/Labs PhysChem software library version 12.01
The boiling point of a substance at 760 mmHg pressure that has been calculated by ACD/Labs PhysChem software library version 12.01.
number of freely rotating bonds calculated by ACD/Labs PhysChem software library version 12.01
Number of freely rotating bonds that has been calculated by ACD/Labs PhysChem software library version 12.01.
polar surface area calculated by ACD/Labs PhysChem software library version 12.01
Polar surface area that has been calculated by ACD/Labs PhysChem software library version 12.01.
molecular weight of the corresponding free base
The molecular weight for the free base chemical structure matching this chemical structure.
molar refractivity calculated by ACD/Labs PhysChem software library version 12.01
Molar refractivity that has been calculated by ACD/Labs PhysChem software library version 12.01.
index of refraction calculated by ACD/Labs PhysChem software library version 12.01
Index of refraction that has been calculated by ACD/Labs PhysChem software library version 12.01.
polarizability calculated by ACD/Labs PhysChem software library version 12.01
Polarizability that has been calculated by ACD/Labs PhysChem software library version 12.01.
execution of ACD/Labs PhysChem software library version 12.01
A parameterized software execution of ACD/Labs PhysChem software library version 12.01. This refers to a particular run of the software.
A parameterized software execution of Pipeline Pilot. This refers to a particular run of the software.
A parameterized software execution of GGA Indigo. This refers to a particular run of the software.
molar volume calculated by ACD/Labs PhysChem software library version 12.01
Molar volume that has been calculated by ACD/Labs PhysChem software library version 12.01.
density calculated by ACD/Labs PhysChem software library version 12.01
Density that has been calculated by ACD/Labs PhysChem software library version 12.01.
flash point calculated by ACD/Labs PhysChem software library version 12.01
Flash point that has been calculated by ACD/Labs PhysChem software library version 12.01.
enthalpy of vaporization calculated by ACD/Labs PhysChem software library version 12.01
Enthalpy of vaporization that has been calculated by ACD/Labs PhysChem software library version 12.01.
vapour pressure calculated by ACD/Labs PhysChem software library version 12.01
Vapour pressure that has been calculated by ACD/Labs PhysChem software library version 12.01.
organic carbon adsorption coefficient at pH 5.5 calculated by ACD/Labs PhysChem software library version 12.01
Organic carbon adsorption coefficient at pH 5.5 that has been calculated by ACD/Labs PhysChem software library version 12.01.
organic carbon adsorption coefficient at pH 7.4 calculated by ACD/Labs PhysChem software library version 12.01
Organic carbon adsorption coefficient at pH 7.4 that has been calculated by ACD/Labs PhysChem software library version 12.01.
bioconcentration factor at pH 5.5 calculated by ACD/Labs PhysChem software library version 12.01
Bioconcentration factor at pH 7.4 that has been calculated by ACD/Labs PhysChem software library version 12.01.
bioconcentration factor at pH 7.4 calculated by ACD/Labs PhysChem software library version 12.01
number of rule of five violations calculated by ACD/Labs PhysChem software library version 12.01
Number of rule of five violations for a chemical structure that has been calculated by ACD/Labs PhysChem software library version 12.01.
surface tension calculated by ACD/Labs PhysChem software library version 12.01
Surface tension, in dyne per centimetre, that has been calculated by ACD/Labs PhysChem software library version 12.01.
Neutral charge is a quality which inheres in a molecular entity by virtue of the molecular entity possessing the same amount of electrons overall as protons, thus having an overall neutral charge.
Positive charge is a quality which inheres in a molecular entity by virtue of the molecular entity possessing more protons overall than electrons, thus having an overall positive charge.
Negative charge is a quality which inheres in a molecular entity by virtue of the molecular entity possessing more electrons overall than protons, thus having an overall negative charge.
A chemical disposition is a disposition which inheres in a chemical entity.
Database identifier used by Human Metabolome Database.
Identifier used by the ChEMBL database for compounds, assays, target, etc.
A descriptor of the ratio of the amount of a given chemical substance adsorbed per unit weight of organic carbon in soil or sediment to the concentration of the chemical substance in solution at equilibrium.
A descriptor of the ratio of the concentration of a chemical substance in an organism immersed in water to that in the surrounding water at equilibrium.
A descriptor of the volume occupied by one mole of the given substance at a given temperature and pressure.
A descriptor of the density of a given substance at a given temperature and pressure.
A descriptor of the flash point of a substance at a given pressure. The flash point is the minimum temperature at which a mixture of the substance with air can be ignited, within its explosive range.
A descriptor of the energy taken in by a chemical substance on vaporization at a given temperature and pressure.
A descriptor of the pressure exerted by the vapour phase of a chemical substance on its condensed phase at a given temperature and pressure.
A descriptor of the disposition of a portion of liquid to resist a force.
An algorithm that specifies how to determine whether data meets given criteria for correctness.
An algorithm that specifies how to transform data such that the resulting data meets given criteria for correctness.
A validation algorithm that specifies how to determine whether a structural descriptor meets given criteria for correctness.
A standardization algorithm that specifies how to transform a structural descriptor such that it meets given criteria for correctness.
A warning message that indicates that a structural descriptor does not meet some criterion for correctness.
An error message that indicates that a structural descriptor cannot be parsed.
An execution of code which implements a structural standardization algorithm.
An execution of code which implements a structural validation algorithm.
algorithm to calculate a molecular descriptor
software module to calculate a molecular descriptor
A software module to calculate a molecular descriptor is software module that implements an algorithm which calculates a descriptor value for a molecular entity.
A software message data item is a data item that plays the role of a message generated by a software implementation, for example, an error, warning or success message.
A ChEBI name is a preferred name annotated by the ChEBI database. The ChEBI name has the additional feature that it is unique within the ChEBI dataset.
Descriptor that calculates the sum of the absolute value of the difference between atomic polarizabilities of all bonded atoms in the molecule (including implicit hydrogens).
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
term created to ease viewing/sort terms for development purpose, and will not be included in a release
ready for release
Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release."
metadata incomplete
Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors.
uncurated
Nothing done yet beyond assigning a unique class ID and proposing a preferred term.
pending final vetting
All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the definition editor.
core
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.