obi import.owl
type: Ontology
version IRI: obi import.owl
version info: 2022-10-24

realizes
type: ObjectProperty
domain: BFO_0000015
range: BFO_0000017
IAO_0000111: realizes
IAO_0000112: this disease course realizes this disease
IAO_0000112: this investigation realizes this investigator role
IAO_0000112: this shattering realizes this fragility
IAO_0000600: to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])
source: obi.owl
comment: Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process

is member of organization
type: ObjectProperty
domain: Class
  union of: Homo sapiens
  union of: organization
range: organization
IAO_0000111: is member of organization
IAO_0000114: IAO_0000120
IAO_0000115: Relating a legal person or organization to an organization in the case where the legal person or organization has a role as member of the organization.
IAO_0000116: 2009/10/01 Alan Ruttenberg. Barry prefers generic is-member-of. Question of what the range should be. For now organization. Is organization a population? Would the same relation be used to record members of a population
IAO_0000116: JZ: Discussed on May 7, 2012 OBI dev call. Bjoern points out that we need to allow for organizations to be members of organizations. And agreed by the other OBI developers. So, human and organization were specified in 'Domains'. The textual definition was updated based on it.
IAO_0000117: Person:Alan Ruttenberg
IAO_0000117: Person:Helen Parkinson
IAO_0000119: Person:Alan Ruttenberg
IAO_0000119: Person:Helen Parkinson
IAO_0000232: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case
source: obi.owl

concretizes
type: ObjectProperty
domain: BFO_0000020
range: BFO_0000031
IAO_0000112: A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant).
IAO_0000112: An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process).
IAO_0000115: A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant.
source: obi.owl

has representation
type: DatatypeProperty
IAO_0000111: has representation
IAO_0000112: 12th arrondissement of Paris
IAO_0000112: 20g
IAO_0000112: I feel sick to my stomach every Tuesday
IAO_0000114: IAO_0000122
IAO_0000115: 'has representation' is a data property that attaches between an information content entity and a value that contains linguistically or computationally coded text.
IAO_0000116: Further processing may enable the value to be represented in a component data structure such as an OBI value specification.
IAO_0000117: Damion Dooley
IAO_0000117: Mark Miller
date: 2019-07-14T07:05:50Z
source: obi.owl

plan specification
type: Class
subclass of: IAO_0000033
IAO_0000111: plan specification
IAO_0000112: PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice.
IAO_0000114: IAO_0000122
IAO_0000115: A directive information entity with action specifications and objective specifications as parts that, when concretized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified.
IAO_0000116: 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.
IAO_0000116: 2014-03-31: A plan specification can have other parts, such as conditional specifications.
IAO_0000116: Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved
IAO_0000117: Alan Ruttenberg
IAO_0000119: OBI Plan and Planned Process branch
IAO_0000119: OBI_0000344
source: obi.owl
comment: 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

Homo sapiens
type: Class
subclass of: NCBITaxon_314146
subclass of: organism
IAO_0000111: Homo sapiens
IAO_0000118: human
IAO_0000118: human being
IAO_0000118: man
IAO_0000412: ncbitaxon.owl
source: obi.owl

planned process
type: Class
equivalent class: Restriction
  on property: realizes
  some values from: Restriction
    on property: concretizes
    some values from: plan specification
subclass of: BFO_0000015
IAO_0000111: planned process
IAO_0000112: Injecting mice with a vaccine in order to test its efficacy
IAO_0000114: IAO_0000122
IAO_0000115: A process that realizes a plan which is the concretization of a plan specification.
IAO_0000116: 'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.)
IAO_0000116: We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some objectives is a planned process.
IAO_0000117: Bjoern Peters
IAO_0000119: branch derived
IAO_0000232: 6/11/9: Edited at workshop. Used to include: is initiated by an agent
IAO_0000232: This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call)
IAO_0000412: obi.owl
source: obi.owl

organization
type: Class
subclass of: BFO_0000040
IAO_0000111: organization
IAO_0000112: PMID: 16353909.AAPS J. 2005 Sep 22;7(2):E274-80. Review. The joint food and agriculture organization of the United Nations/World Health Organization Expert Committee on Food Additives and its role in the evaluation of the safety of veterinary drug residues in foods.
IAO_0000114: IAO_0000122
IAO_0000115: An entity that can bear roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members.
IAO_0000116: BP: The definition summarizes long email discussions on the OBI developer, roles, biomaterial and denrie branches. It leaves open if an organization is a material entity or a dependent continuant, as no consensus was reached on that. The current placement as material is therefore temporary, in order to move forward with development. Here is the entire email summary, on which the definition is based: 1) there are organization_member_roles (president, treasurer, branch editor), with individual persons as bearers 2) there are organization_roles (employer, owner, vendor, patent holder) 3) an organization has a charter / rules / bylaws, which specify what roles there are, how they should be realized, and how to modify the charter/rules/bylaws themselves. It is debatable what the organization itself is (some kind of dependent continuant or an aggregate of people). This also determines who/what the bearer of organization_roles' are. My personal favorite is still to define organization as a kind of 'legal entity', but thinking it through leads to all kinds of questions that are clearly outside the scope of OBI. Interestingly enough, it does not seem to matter much where we place organization itself, as long as we can subclass it (University, Corporation, Government Agency, Hospital), instantiate it (Affymetrix, NCBI, NIH, ISO, W3C, University of Oklahoma), and have it play roles. This leads to my proposal: We define organization through the statements 1 - 3 above, but without an 'is a' statement for now. We can leave it in its current place in the is_a hierarchy (material entity) or move it up to 'continuant'. We leave further clarifications to BFO, and close this issue for now.
IAO_0000117: PERSON: Alan Ruttenberg
IAO_0000117: PERSON: Bjoern Peters
IAO_0000117: PERSON: Philippe Rocca-Serra
IAO_0000117: PERSON: Susanna Sansone
IAO_0000119: GROUP: OBI
source: obi.owl

organism
type: Class
subclass of: BFO_0000040
IAO_0000111: organism
IAO_0000112: animal
IAO_0000112: fungus
IAO_0000112: plant
IAO_0000112: virus
IAO_0000114: IAO_0000122
IAO_0000115: A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs.
IAO_0000116: 10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms')
IAO_0000116: 13-02-2009: OBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus. This issue is outside the scope of OBI.
IAO_0000117: GROUP: OBI Biomaterial Branch
IAO_0000119: WEB: http://en.wikipedia.org/wiki/Organism
source: obi.owl