Ontology for Biomedical Investigations

IRI:
http://purl.obolibrary.org/obo/obi/obi_core.owl
Version IRI:
http://purl.obolibrary.org/obo/obi/2023-09-20/obi_core.owl
Date :
31/07/2009
Current version :
2023-09-20
Authors :
Alan Ruttenberg
Allyson Lister
Barry Smith
Bill Bug
Bjoern Peters
Carlo Torniai
Chris Mungall
Chris Stoeckert
Chris Taylor
Christian Bolling
Cristian Cocos
Daniel Rubin
Daniel Schober
Dawn Field
Dirk Derom
Elisabetta Manduchi
Eric Deutsch
Frank Gibson
Gilberto Fragoso
Helen C. Causton
Helen Parkinson
Holger Stenzhorn
James A. Overton
James Malone
Jay Greenbaum
Jeffrey Grethe
Jennifer Fostel
Jessica Turner
Jie Zheng
Joe White
John Westbrook
Kevin Clancy
Larisa Soldatova
Lawrence Hunter
Liju Fan
Luisa Montecchi
Matthew Brush
Matthew Pocock
Melanie Courtot
Melissa Haendel
Mervi Heiskanen
Monnie McGee
Norman Morrison
Philippe Rocca-Serra
Phillip Lord
Pierre Grenon
Richard Bruskiewich
Richard Scheuermann
Robert Stevens
Ryan R. Brinkman
Stefan Wiemann
Susanna-Assunta Sansone
Tanya Gray
Tina Hernandez-Boussard
Trish Whetzel
Yongqun He
Contributors :
Advisors for this project come from the IFOMIS group, Saarbruecken and from the Co-ODE group in Manchester
Other visualisation :
Ontology source - WebVowl

Abstract

Please cite the OBI consortium http://purl.obolibrary.org/obo/obi where traditional citation is called for. However it is adequate that individual terms be attributed simply by use of the identifying PURL for the term, in projects that refer to them.

Table of Content

  1. Introduction
  2. Classes
  3. Object Properties
  4. Named Individuals
  5. Annotation Properties
  6. General Axioms
  7. Namespace Declarations

Introduction

An ontology for representing biomedical investigations, including study designs, the collection and preparation of the targets of investigation, assays, instrumentation and reagents used, as well as the data generated and the types of analysis performed on the data to reach conclusions, and their documentation.

Classes

acquisitionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0600008

has super-classes
selectionc
realizesop some concretizesop some selection criterionc
has_specified_outputop some material entityc or information content entityc
has sub-classes
information acquisitionc, material acquisitionc

action specificationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000007

has super-classes
directive information entityc

algorithmc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000064

has super-classes
plan specificationc

Amniotac back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCBITaxon_32524

has super-classes
Tetrapodac
has sub-classes
Mammaliac

analyte assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000443

has super-classes
assayc
has_specified_outputop some measurement datumc
achieves_planned_objectiveop some analyte measurement objectivec

analyte measurement objectivec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000437

has super-classes
assay objectivec

Archaeac back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCBITaxon_2157

has super-classes
organismc

assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000070

is equivalent to
achieves_planned_objectiveop some assay objectivec
has super-classes
planned processc
realizesop some evaluant rolec
has_specified_inputop some material entityc and (has roleop some evaluant rolec)
has_specified_outputop some data itemc and (is aboutop some material entityc and (has roleop some evaluant rolec))
has sub-classes
analyte assayc, cytometry assayc
is disjoint with
planningc, data transformationc, information acquisitionc

assay objectivec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000441

has super-classes
objective specificationc
has sub-classes
analyte measurement objectivec

Bacteriac back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCBITaxon_2

has super-classes
organismc

Bilateriac back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCBITaxon_33213

has super-classes
Metazoac
has sub-classes
Vertebrata <vertebrates>c

biological_processc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0008150

has super-classes
processc
has sub-classes
disease coursec
is disjoint with
planned processc

cellc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CL_0000000

has super-classes
material entityc
has sub-classes
experimentally modified cell in vitroc

cell line cellc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CLO_0000001

has super-classes
secondary cultured cellc
derives fromop some primary cultured cellc

cellular_componentc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0005575

has super-classes
material entityc

centrally registered identifierc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000578

has super-classes
information content entityc
has partop some centrally registered identifier symbolc
has partop some denotesop some centrally registered identifier registryc

centrally registered identifier registryc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000579

has super-classes
data setc

centrally registered identifier symbolc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000577

has super-classes
symbolc
part ofop some centrally registered identifierc

collection of specimensc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0002076

is equivalent to
material entityc and (has memberop only specimenc)
has super-classes
material entityc

conclusion based on datac back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001909

has super-classes
information content entityc
is_supported_by_dataop some data itemc
is_specified_output_ofop some drawing a conclusion based on datac
is in domain of
is_supported_by_dataop

continuantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000002

is defined by
http://purl.obolibrary.org/obo/bfo.owl
has super-classes
entityc
has sub-classes
generically dependent continuantc, independent continuantc, specifically dependent continuantc
is in domain of
participates inop
is in range of
has participantop
is disjoint with
occurrentc

cultured cellc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CL_0000010

has super-classes
experimentally modified cell in vitroc
has sub-classes
primary cultured cellc, secondary cultured cellc

curation status specificationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000078

is equivalent to
{ example to be eventually removed , metadata complete , organizational term , ready for release , metadata incomplete , uncurated , pending final vetting , to be replaced with external ontology term , requires discussion }
has super-classes
data about an ontology partc
has members
example to be eventually removedni, requires discussionni, to be replaced with external ontology termni

cytometry assayc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001977

is equivalent to
assayc and ((realizesop some evaluant rolec and (role ofop some cellc)) and (has_specified_inputop some cellc and (has roleop some evaluant rolec)))
has super-classes
assayc

data about an ontology partc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000102

has super-classes
data itemc
has sub-classes
curation status specificationc, denotator typec, obsolescence reason specificationc

data itemc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000027

has super-classes
information content entityc
has sub-classes
data about an ontology partc, data setc, measurement datumc
is in range of
is_supported_by_dataop

data setc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000100

has super-classes
data itemc
has sub-classes
centrally registered identifier registryc

data transformationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200000

is equivalent to
achieves_planned_objectiveop some data transformation objectivec
has super-classes
planned processc
realizesop some concretizesop some algorithmc and (has partop some objective specificationc)
has_specified_inputop only data itemc
is disjoint with
assayc, information acquisitionc

data transformation objectivec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0200166

has super-classes
objective specificationc

datum labelc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000009

has super-classes
information content entityc
has sub-classes
measurement unit labelc

denotator typec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000409

is equivalent to
{ universal , defined class , named class expression }
has super-classes
data about an ontology partc
has members
defined classni, named class expressionni, universalni

devicec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000968

has super-classes
processed materialc
is_specified_output_ofop some material processingc
has functionop some functionc
has sub-classes
measurement devicec

directive information entityc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000033

has super-classes
information content entityc
is aboutop some realizable entityc
has sub-classes
action specificationc, objective specificationc, plan specificationc, selection criterionc, study design controlled variablec, study design dependent variablec, study design independent variablec

diseasec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OGMS_0000031

has super-classes
dispositionc

disease coursec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OGMS_0000063

is equivalent to
realizesop some diseasec
has super-classes
biological_processc

dispositionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000016

is defined by
http://purl.obolibrary.org/obo/bfo.owl
has super-classes
realizable entityc
has sub-classes
diseasec, functionc
is disjoint with
rolec

documentc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000310

has super-classes
information content entityc

documentingc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000572

has super-classes
planned processc
has_specified_outputop some documentc
has_specified_inputop some information content entityc

drawing a conclusion based on datac back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000338

has super-classes
planned processc
has_specified_inputop some data itemc
has_specified_outputop some conclusion based on datac

eligibility criterionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0500026

has super-classes
selection criterionc

entityc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000001

is defined by
http://purl.obolibrary.org/obo/bfo.owl
has sub-classes
continuantc, occurrentc
is in domain of
denoted byop
is in range of
denotesop

environmental materialc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/ENVO_00010483

has super-classes
material entityc

Euarchontogliresc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCBITaxon_314146

has super-classes
Mammaliac
has sub-classes
Homo sapiensc

Eukaryotac back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCBITaxon_2759

has super-classes
organismc
has sub-classes
Opisthokontac

Euteleostomic back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCBITaxon_117571

has super-classes
Vertebrata <vertebrates>c
has sub-classes
Tetrapodac

evaluant rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000067

has super-classes
rolec
inheres inop some material entityc
realized inop only assayc

experimentally modified cell in vitroc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CL_0000578

has super-classes
cellc
processed materialc
is_specified_output_ofop some material processingc
has sub-classes
cultured cellc

functionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000034

is defined by
http://purl.obolibrary.org/obo/bfo.owl
has super-classes
dispositionc
has sub-classes
measure functionc
is in domain of
function ofop
is in range of
has functionop

generically dependent continuantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000031

is defined by
http://purl.obolibrary.org/obo/bfo.owl
has super-classes
continuantc
has sub-classes
information content entityc
is in domain of
is concretized asop
is in range of
concretizesop
is disjoint with
independent continuantc, specifically dependent continuantc, independent continuantc, specifically dependent continuantc

geographic locationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GAZ_00000448

has super-classes
sitec
is also defined as
named individual

Homo sapiensc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCBITaxon_9606

has super-classes
Euarchontogliresc

human subject enrollmentc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0600004

has super-classes
selectionc
has partop some informed consent processc
realizesop some concretizesop some eligibility criterionc
has_specified_inputop some populationc and (has partop some Homo sapiensc)
has_specified_outputop some (populationc and (has partop some Homo sapiensc)) and (has roleop some participant under investigation rolec)

immaterial entityc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000141

is defined by
http://purl.obolibrary.org/obo/bfo.owl
has super-classes
independent continuantc
has sub-classes
sitec
is disjoint with
material entityc

independent continuantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000004

is defined by
http://purl.obolibrary.org/obo/bfo.owl
has super-classes
continuantc
has sub-classes
immaterial entityc, material entityc
is in domain of
derives fromop, has functionop, has roleop
is in range of
derives fromop
is disjoint with
specifically dependent continuantc, generically dependent continuantc, specifically dependent continuantc, generically dependent continuantc

information acquisitionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0600013

has super-classes
acquisitionc
has_specified_outputop some information content entityc
is disjoint with
assayc, data transformationc

information carrierc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000015

is equivalent to
qualityc and (concretizesop some information content entityc)
has super-classes
qualityc

information content entityc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000030

has super-classes
generically dependent continuantc
is aboutop some entityc
has sub-classes
centrally registered identifierc, conclusion based on datac, data itemc, datum labelc, directive information entityc, documentc, symbolc, testable hypothesisc, value specificationc
is in domain of
denotesop, has value specificationop, is aboutop
is in range of
denoted byop

informed consent processc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000810

has super-classes
planned processc
has_specified_inputop some Homo sapiensc
has participantop some has roleop some investigation agent rolec

investigationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000066

has super-classes
planned processc
has partop some documentingc
has partop some drawing a conclusion based on datac
has partop some study design executionc
has partop some planningc and (has_specified_outputop some study designc)

investigation agent rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000202

Philly2013: Historically, this role would have been borne only by humans or organizations. However, we now also want to enable investigations run by robot scientists such as ADAM (King et al, Science, 2009)
is equivalent to
rolec and (inheres inop some bearer ofop some concretizesop some objective_achieved_byop some part ofop some investigationc)
has super-classes
rolec
realized inop only investigationc

Mammaliac back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCBITaxon_40674

has super-classes
Amniotac
has sub-classes
Euarchontogliresc

material acquisitionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0600010

has super-classes
acquisitionc
has_specified_outputop some material entityc
is disjoint with
material processingc

material entityc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000040

is defined by
http://purl.obolibrary.org/obo/bfo.owl
has super-classes
independent continuantc
has sub-classes
cellc, cellular_componentc, collection of specimensc, environmental materialc, material information bearerc, molecular entityc, organismc, organizationc, populationc, processed materialc, specimenc
is disjoint with
immaterial entityc

material information bearerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000178

is equivalent to
material entityc and (bearer ofop some concretizesop some information content entityc)
has super-classes
material entityc

material processingc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000094

is equivalent to
achieves_planned_objectiveop some material transformation objectivec
has super-classes
planned processc
has_specified_outputop some processed materialc
has_specified_inputop only material entityc
is disjoint with
material acquisitionc

material transformation objectivec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000456

has super-classes
objective specificationc

measure functionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000453

has super-classes
functionc
function ofop some processed materialc
realized inop only has_specified_outputop some measurement datumc

measurement datumc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000109

has super-classes
data itemc
has value specificationop some value specificationc

measurement devicec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000832

is equivalent to
devicec and (has functionop some measure functionc)
has super-classes
devicec

measurement unit labelc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000003

has super-classes
datum labelc

Metazoac back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCBITaxon_33208

has super-classes
Opisthokontac
has sub-classes
Bilateriac

molecular entityc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CHEBI_23367

has super-classes
material entityc

molecular_functionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/GO_0003674

has super-classes
processc

objective specificationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000005

has super-classes
directive information entityc
has sub-classes
assay objectivec, data transformation objectivec, material transformation objectivec, specimen collection objectivec
is in domain of
objective_achieved_byop
is in range of
achieves_planned_objectiveop

obsolescence reason specificationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000225

is equivalent to
{ failed exploratory term , placeholder removed , terms merged , term imported , term split }
has super-classes
data about an ontology partc
has members
term importedni, term splitni, terms mergedni

occurrentc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000003

is defined by
http://purl.obolibrary.org/obo/bfo.owl
has super-classes
entityc
has sub-classes
processc
is in domain of
has participantop
is in range of
participates inop
is disjoint with
continuantc

Opisthokontac back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCBITaxon_33154

has super-classes
Eukaryotac
has sub-classes
Metazoac

organismc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0100026

is equivalent to
Virusesc or Bacteriac or Archaeac or Eukaryotac
has super-classes
material entityc
has sub-classes
Archaeac, Bacteriac, Eukaryotac, Virusesc

organizationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000245

has super-classes
material entityc

participant under investigation rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000097

has super-classes
rolec
realized inop only study design executionc

plan specificationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000104

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
has super-classes
directive information entityc
has partop some objective specificationc
has partop some action specificationc
has sub-classes
algorithmc, protocolc, study designc

planned processc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000011

is equivalent to
realizesop some concretizesop some plan specificationc
has super-classes
processc
has sub-classes
assayc, data transformationc, documentingc, drawing a conclusion based on datac, informed consent processc, investigationc, material processingc, selectionc, specimen collection processc, study design executionc
is in domain of
achieves_planned_objectiveop, has_specified_inputop, has_specified_outputop
is in range of
is_specified_input_ofop, is_specified_output_ofop, objective_achieved_byop
is disjoint with
biological_processc

planningc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000339

has super-classes
processc
processc and (has participantop some plan specificationc)
is disjoint with
assayc

populationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000181

has super-classes
material entityc

primary cultured cellc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/CL_0000001

has super-classes
cultured cellc

processc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000015

is defined by
http://purl.obolibrary.org/obo/bfo.owl
has super-classes
occurrentc
has sub-classes
biological_processc, molecular_functionc, planned processc, planningc
is in domain of
realizesop
is in range of
realized inop

processed materialc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000047

is equivalent to
material entityc and (is_specified_output_ofop some material processingc)
has super-classes
material entityc
has sub-classes
devicec, experimentally modified cell in vitroc, processed specimenc, reagentc

processed specimenc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000953

A tissue sample that has been sliced and stained for a histology study.
is equivalent to
processed materialc and specimenc
has super-classes
processed materialc
specimenc

protocolc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000272

has super-classes
plan specificationc

qualityc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000019

is defined by
http://purl.obolibrary.org/obo/bfo.owl
has super-classes
specifically dependent continuantc
has sub-classes
information carrierc
is disjoint with
realizable entityc

reagentc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001879

(copied from ReO) Reagents are distinguished from devices/instruments that also serve as facilitators in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in or have parts that participate in some chemical interaction or reaction during their intended participation in some technique. By contrast, devices do not participate in a chemical reaction/interaction during the technique. Reagents are distinguished from study subjects/evaluants in that study subjects and evaluants are that about which conclusions are drawn and knowledge is sought in an investigation - while reagents, by definition, are not. It should be noted, however, that reagent and study subject/evaluant roles can be borne by instances of the same type of material entity - but a given instance can only realize one of these roles in the execution of a given assay. For example, taq polymerase can bear a reagent role or an evaluant role. In a DNA sequencing assay aimed at generating sequence data about some plasmid, the reagent role of the taq polymerase is realized. In an assay to evaluate the quality of the taq polymerase itself, the evaluant/study subject role of the taq is realized, but not the reagent role since the taq is the subject about which data is generated. In regard to the statement that reagents are 'distinct' from the specified outputs of a technique: note that a reagent may be incorporated into a material output of a technique, as long as the IDENTITY of this output is distinct from that of the bearer of the reagent role. For example, dNTPs input into a PCR are reagents that become part of the material output of this technique, but this output has a new identity (ie that of a 'nucleic acid molecule') that is distinct from the identity of the dNTPs that comprise it. Similarly, a biotin molecule input into a cell labeling technique are reagents that become part of the specified output, but the identity of the output is that of some modified cell specimen which shares identity with the input unmodified cell specimen, and not with the biotin label. Thus, we see that an important criteria of 'reagent-ness' is that it is a facilitator, and not the primary focus of an investigation or material processing technique (ie not the specified subject/evaluant about which knowledge is sought, or the specified output material of the technique).
is equivalent to
material entityc and (has roleop some reagent rolec)
has super-classes
processed materialc
is_specified_output_ofop some material processingc

reagent rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000086

(copied from ReO) Reagents are distinguished from instruments or devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in or have parts that participate in some chemical interaction or reaction during their intended participation in some technique. By contrast, instruments do not participate in a chemical reaction/interaction during the technique. Reagents are distinguished from study subjects/evaluants in that study subjects and evaluants are that about which conclusions are drawn and knowledge is sought in an investigation - while reagents, by definition, are not. It should be noted, however, that reagent and study subject/evaluant roles can be borne by instances of the same type of material entity - but a given instance will realize only one of these roles in the execution of a given assay or technique. For example, taq polymerase can bear a reagent role or an evaluant role. In a DNA sequencing assay aimed at generating sequence data about some plasmid, the reagent role of the taq polymerase is realized. In an assay to evaluate the quality of the taq polymerase itself, the evaluant/study subject role of the taq is realized, but not the reagent role since the taq is the subject about which data is generated. In regard to the statement that reagents are 'distinct' from the specified outputs of a technique, note that a reagent may be incorporated into a material output of a technique, as long as the IDENTITY of this output is distinct from that of the bearer of the reagent role. For example, dNTPs input into a PCR are reagents that become part of the material output of this technique, but this output has a new identity (ie that of a 'nucleic acid molecule') that is distinct from the identity of the dNTPs that comprise it. Similarly, a biotin molecule input into a cell labeling technique are reagents that become part of the specified output, but the identity of the output is that of some modified cell specimen which shares identity with the input unmodified cell specimen, and not with the biotin label. Thus, we see that an important criteria of 'reagent-ness' is that it is a facilitator, and not the primary focus of an investigation or material processing technique (ie not the specified subject/evaluant about which knowledge is sought, or the specified output material of the technique).
has super-classes
rolec

realizable entityc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000017

is defined by
http://purl.obolibrary.org/obo/bfo.owl
has super-classes
specifically dependent continuantc
has sub-classes
dispositionc, rolec
is in domain of
realized inop
is in range of
realizesop
is disjoint with
qualityc

rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000023

is defined by
http://purl.obolibrary.org/obo/bfo.owl
has super-classes
realizable entityc
has sub-classes
evaluant rolec, investigation agent rolec, participant under investigation rolec, reagent rolec, specimen rolec
is in range of
has roleop
is disjoint with
dispositionc

secondary cultured cellc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001866

A secondary cultured cell has been passaged in culture or is a descendant of such a cell that is derived through propagation in culture.
has super-classes
cultured cellc
derives fromop some primary cultured cellc
has sub-classes
cell line cellc

selectionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001928

is equivalent to
realizesop some concretizesop some selection criterionc
has super-classes
planned processc
has sub-classes
acquisitionc, human subject enrollmentc

selection criterionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001755

has super-classes
directive information entityc
has sub-classes
eligibility criterionc

sitec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000029

is defined by
http://purl.obolibrary.org/obo/bfo.owl
has super-classes
immaterial entityc
has sub-classes
geographic locationc

specifically dependent continuantc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000020

is defined by
http://purl.obolibrary.org/obo/bfo.owl
has super-classes
continuantc
has sub-classes
qualityc, realizable entityc
is in domain of
concretizesop
is in range of
bearer ofop, is concretized asop
is disjoint with
independent continuantc, generically dependent continuantc, independent continuantc, generically dependent continuantc

specimenc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0100051

is equivalent to
material entityc and (has roleop some specimen rolec)
has super-classes
material entityc
has sub-classes
processed specimenc

specimen collection objectivec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000684

has super-classes
objective specificationc

specimen collection processc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000659

is equivalent to
planned processc and (achieves_planned_objectiveop some specimen collection objectivec)
has super-classes
planned processc
has_specified_inputop some material entityc
has_specified_outputop some specimenc

specimen rolec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000112

has super-classes
rolec
inheres inop some material entityc and (is_specified_output_ofop some specimen collection processc)

study designc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0500000

has super-classes
plan specificationc
has partop some protocolc

study design controlled variablec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000785

has super-classes
directive information entityc
part ofop some study designc

study design dependent variablec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000751

has super-classes
directive information entityc
part ofop some study designc

study design executionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000471

is equivalent to
planned processc and (realizesop some concretizesop some study designc)
has super-classes
planned processc

study design independent variablec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000750

has super-classes
directive information entityc
part ofop some study designc

symbolc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000028

has super-classes
information content entityc
has sub-classes
centrally registered identifier symbolc

testable hypothesisc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001908

has super-classes
information content entityc

Tetrapodac back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCBITaxon_32523

has super-classes
Euteleostomic
has sub-classes
Amniotac

value specificationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001933

has super-classes
information content entityc
is in range of
has value specificationop

Vertebrata <vertebrates>c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCBITaxon_7742

has super-classes
Bilateriac
has sub-classes
Euteleostomic

Virusesc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCBITaxon_10239

has super-classes
organismc

Object Properties

achieves_planned_objectiveop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000417

bearer ofop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0000053

has sub-properties
has functionop, has roleop
has range
specifically dependent continuantc
is inverse of
inheres inop

concretizesop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0000059

denoted byop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000235

has domain
entityc
has range
information content entityc
is inverse of
denotesop

denotesop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000219

has super-properties
is aboutop
has domain
information content entityc
has range
entityc
is inverse of
denoted byop

derives fromop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0001000

derives intoop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0001001

is inverse of
derives fromop

function ofop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0000079

has super-properties
inheres inop
has domain
functionc
is inverse of
has functionop

has functionop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0000085

has super-properties
bearer ofop
has domain
independent continuantc
has range
functionc
is inverse of
function ofop

has memberop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002351

has characteristics : irreflexive

has super-properties
has partop
is inverse of
member ofop

has partop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000051

has characteristics : transitive

has sub-properties
has memberop, has value specificationop
is inverse of
part ofop

has participantop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0000057

has sub-properties
has_specified_inputop, has_specified_outputop
has domain
occurrentc
has range
continuantc
is inverse of
participates inop

has roleop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0000087

has super-properties
bearer ofop
has domain
independent continuantc
has range
rolec
is inverse of
role ofop

has value specificationop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001938

has super-properties
has partop
has domain
information content entityc
has range
value specificationc

has_specified_inputop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000293

has super-properties
has participantop
has domain
planned processc
is inverse of
is_specified_input_ofop

has_specified_outputop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000299

has super-properties
has participantop
has domain
planned processc
is inverse of
is_specified_output_ofop

inheres inop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0000052

has sub-properties
function ofop, role ofop
is inverse of
bearer ofop

is aboutop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000136

has sub-properties
denotesop
has domain
information content entityc

is concretized asop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0000058

is_specified_input_ofop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000295

has super-properties
participates inop
has range
planned processc
is inverse of
has_specified_inputop

is_specified_output_ofop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000312

has super-properties
participates inop
has range
planned processc
is inverse of
has_specified_outputop

is_supported_by_dataop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000124

member ofop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002350

has super-properties
part ofop
is inverse of
has memberop

objective_achieved_byop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/OBI_0000833

part ofop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000050

has characteristics : transitive

has sub-properties
member ofop
is inverse of
has partop

participates inop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0000056

has sub-properties
is_specified_input_ofop, is_specified_output_ofop
has domain
continuantc
has range
occurrentc
is inverse of
has participantop

realized inop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000054

is defined by
http://purl.obolibrary.org/obo/bfo.owl
Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process
has domain
realizable entityc
has range
processc
is inverse of
realizesop

realizesop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000055

is defined by
http://purl.obolibrary.org/obo/iao.owl
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
has domain
processc
has range
realizable entityc
is inverse of
realized inop

role ofop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0000081

has super-properties
inheres inop
is inverse of
has roleop

Named Individuals

defined classni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000420

belongs to
denotator typec

example to be eventually removedni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000002

belongs to
curation status specificationc

named class expressionni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000421

belongs to
denotator typec

requires discussionni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000428

belongs to
curation status specificationc

term importedni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000228

belongs to
obsolescence reason specificationc

term splitni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000229

belongs to
obsolescence reason specificationc

terms mergedni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000227

belongs to
obsolescence reason specificationc

to be replaced with external ontology termni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000423

belongs to
curation status specificationc

universalni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000410

belongs to
denotator typec

Annotation Properties

alternative termap back to ToC or Annotation Property ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000118

is defined by
http://purl.obolibrary.org/obo/iao.owl

BFO CLIF specification labelap back to ToC or Annotation Property ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000180

BFO OWL specification labelap back to ToC or Annotation Property ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000179

contributorap back to ToC or Annotation Property ToC

IRI: http://purl.org/dc/elements/1.1/contributor

creatorap back to ToC or Annotation Property ToC

IRI: http://purl.org/dc/elements/1.1/creator

curator noteap back to ToC or Annotation Property ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000232

is defined by
http://purl.obolibrary.org/obo/iao.owl

dateap back to ToC or Annotation Property ToC

IRI: http://purl.org/dc/elements/1.1/date

default languageap back to ToC or Annotation Property ToC

IRI: http://protege.stanford.edu/plugins/owl/protege#defaultLanguage

definitionap back to ToC or Annotation Property ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000115

is defined by
http://purl.obolibrary.org/obo/iao.owl

definition sourceap back to ToC or Annotation Property ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000119

is defined by
http://purl.obolibrary.org/obo/iao.owl

descriptionap back to ToC or Annotation Property ToC

IRI: http://purl.org/dc/elements/1.1/description

editor noteap back to ToC or Annotation Property ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000116

is defined by
http://purl.obolibrary.org/obo/iao.owl

editor preferred labelap back to ToC or Annotation Property ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000111

is defined by
http://purl.obolibrary.org/obo/iao.owl

elucidationap back to ToC or Annotation Property ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000600

is defined by
http://purl.obolibrary.org/obo/iao.owl

example of usageap back to ToC or Annotation Property ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000112

is defined by
http://purl.obolibrary.org/obo/iao.owl

formatap back to ToC or Annotation Property ToC

IRI: http://purl.org/dc/elements/1.1/format

has associated axiom(fol)ap back to ToC or Annotation Property ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000602

is defined by
http://purl.obolibrary.org/obo/iao.owl

has associated axiom(nl)ap back to ToC or Annotation Property ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000601

is defined by
http://purl.obolibrary.org/obo/iao.owl

has axiom labelap back to ToC or Annotation Property ToC

IRI: http://purl.obolibrary.org/obo/IAO_0010000

is defined by
http://purl.obolibrary.org/obo/iao.owl

has curation statusap back to ToC or Annotation Property ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000114

i a o 0000233ap back to ToC or Annotation Property ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000233

i a o 0000589ap back to ToC or Annotation Property ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000589

IEDB alternative termap back to ToC or Annotation Property ToC

IRI: http://purl.obolibrary.org/obo/OBI_9991118

imported fromap back to ToC or Annotation Property ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000412

is defined by
http://purl.obolibrary.org/obo/iao.owl

ISA alternative termap back to ToC or Annotation Property ToC

IRI: http://purl.obolibrary.org/obo/OBI_0001847

licenseap back to ToC or Annotation Property ToC

IRI: http://purl.org/dc/terms/license

sourceap back to ToC or Annotation Property ToC

IRI: http://purl.org/dc/elements/1.1/source

subjectap back to ToC or Annotation Property ToC

IRI: http://purl.org/dc/elements/1.1/subject

temporal interpretationap back to ToC or Annotation Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0001900

term editorap back to ToC or Annotation Property ToC

IRI: http://purl.obolibrary.org/obo/IAO_0000117

is defined by
http://purl.obolibrary.org/obo/iao.owl

titleap back to ToC or Annotation Property ToC

IRI: http://purl.org/dc/terms/title

General Axioms

All Disjoint Classes back to ToC

independent continuantc, specifically dependent continuantc, generically dependent continuantc

Namespace Declarations back to ToC

default namespace
http://purl.obolibrary.org/obo/obi/obi_core.owl#
2023-09-20
http://purl.obolibrary.org/obo/obi/2023-09-20/
axiom
http://purl.obolibrary.org/obo/bfo/axiom/
dc
http://purl.org/dc/elements/1.1/
issues
https://github.com/information-artifact-ontology/IAO/issues/
obi
http://purl.obolibrary.org/obo/obi/
obo
http://purl.obolibrary.org/obo/
owl
http://www.w3.org/2002/07/owl#
papers
http://www.referent-tracking.com/_RTU/papers/
protege
http://protege.stanford.edu/plugins/owl/protege#
rdf
http://www.w3.org/1999/02/22-rdf-syntax-ns#
rdfs
http://www.w3.org/2000/01/rdf-schema#
terms
http://purl.org/dc/terms/
xsd
http://www.w3.org/2001/XMLSchema#

This HTML document was obtained by processing the OWL ontology source code through LODE, Live OWL Documentation Environment, developed by Silvio Peroni .