iao-module.owl
type: Ontology
version IRI: iao-module.owl
comment: This file contains externally imported content from the Information Artifact Ontology (IAO) for import into the Open Energy Ontology (OEO). It is automatically extracted using ROBOT.

is about
type: ObjectProperty
domain: information content entity
IAO_0000112: This document is about information artifacts and their representations
IAO_0000114: IAO_0000125
IAO_0000115: A (currently) primitive relation that relates an information artifact to an entity.
IAO_0000116: 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.
IAO_0000117: person:Alan Ruttenberg
IAO_0000119: Smith, Ceusters, Ruttenberg, 2000 years of philosophy

software
type: Class
subclass of: plan specification
IAO_0000111: software
IAO_0000114: IAO_0000120
IAO_0000115: Software is a plan specification composed of a series of instructions that can be interpreted by or directly executed by a processing unit.
IAO_0000116: see sourceforge tracker discussion at http://sourceforge.net/tracker/index.php?func=detail&aid=1958818&group_id=177891&atid=886178
IAO_0000117: PERSON: Alan Ruttenberg
IAO_0000117: PERSON: Bjoern Peters
IAO_0000117: PERSON: Chris Stoeckert
IAO_0000117: PERSON: Melanie Courtot
IAO_0000119: GROUP: OBI

symbol
type: Class
subclass of: information content entity
IAO_0000111: symbol
IAO_0000112: a serial number such as "12324X"
IAO_0000112: a stop sign
IAO_0000112: a written proper name such as "OBI"
IAO_0000114: IAO_0000125
IAO_0000115: An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity.
IAO_0000116: 20091104, MC: this needs work and will most probably change
IAO_0000116: 2014-03-31: We would like to have a deeper analysis of 'mark' and 'sign' in the future (see https://github.com/information-artifact-ontology/IAO/issues/154).
IAO_0000117: PERSON: James A. Overton
IAO_0000117: PERSON: Jonathan Rees
IAO_0000119: based on Oxford English Dictionary

information content entity
type: Class
IAO_0000111: information content entity
IAO_0000112: Examples of information content entites include journal articles, data, graphical layouts, and graphs.
IAO_0000114: IAO_0000122
IAO_0000115: A generically dependent continuant that is about some thing.
IAO_0000116: 2014-03-10: The use of "thing" is intended to be general enough to include universals and configurations (see https://groups.google.com/d/msg/information-ontology/GBxvYZCk1oc/-L6B5fSBBTQJ).
IAO_0000116: 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.
IAO_0000117: PERSON: Chris Stoeckert
IAO_0000119: OBI_0000142

directive information entity
type: Class
subclass of: information content entity
IAO_0000114: IAO_0000122
IAO_0000115: An information content entity whose concretizations indicate to their bearer how to realize them in a process.
IAO_0000116: 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.
IAO_0000116: 2013-05-30 Alan Ruttenberg: What differentiates a directive information entity from an information concretization is that it can have concretizations that are either qualities or realizable entities. The concretizations that are realizable entities are created when an individual chooses to take up the direction, i.e. has the intention to (try to) realize it.
IAO_0000116: 8/6/2009 Alan Ruttenberg: Changed label from "information entity about a realizable" after discussions at ICBO
IAO_0000116: 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
IAO_0000117: PERSON: Alan Ruttenberg
IAO_0000117: PERSON: Bjoern Peters

report
type: Class
subclass of: document
IAO_0000111: report
IAO_0000112: Examples of reports are gene lists and investigation reports. These are not published (journal) articles but may be included in a journal article.
IAO_0000114: IAO_0000125
IAO_0000115: 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)
IAO_0000116: 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.
IAO_0000116: 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.
IAO_0000116: 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.
IAO_0000116: 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
IAO_0000116: 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
IAO_0000117: PERSON: Alan Ruttenberg
IAO_0000117: PERSON: Melanie Courtot
IAO_0000117: PERSON:Chris Stoeckert
IAO_0000119: GROUP: OBI
IAO_0000119: OBI_0000099

data set
type: Class
subclass of: IAO_0000027
IAO_0000111: data set
IAO_0000112: Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves).
IAO_0000114: IAO_0000125
IAO_0000115: 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.
IAO_0000116: 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
IAO_0000116: 2014-05-05: Data sets are aggregates and thus must include two or more data items. We have chosen not to add logical axioms to make this restriction.
IAO_0000117: person:Allyson Lister
IAO_0000117: person:Chris Stoeckert
IAO_0000119: OBI_0000042
IAO_0000119: group:OBI

plan specification
type: Class
subclass of: directive information entity
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
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

document
type: Class
subclass of: information content entity
IAO_0000111: document
IAO_0000112: A journal article, patent application, laboratory notebook, or a book
IAO_0000114: IAO_0000120
IAO_0000115: A collection of information content entities intended to be understood together as a whole
IAO_0000117: PERSON: Lawrence Hunter