bmslm
type: Ontology
version IRI: http://www.fealinx-biomedical.com/ontologies/bmslm/1.1
imports: bfo.owl
imports: iao-imports.owl
imports: obi core-imports.owl
imports: ro core-imports.owl
default language: en
contributor: Benoît Eynard benoit.eynard-at-utc.fr
contributor: Bertrand Tavitian bertrand.tavitian-at-inserm.fr
contributor: Daniel Balvay daniel.balvay-at-inserm.fr
contributor: Jacques Hilbey jacques.hilbey-at-inserm.fr
contributor: Jean Charlet jean.charlet-at-sorbonne-universite.fr
contributor: Marianne Allanic mallanic-ext-at-fealinx.com
contributor: Philippe Boutinaud pboutinaud-at-fealinx.com
contributor: Pierre-Yves Hervé pyherve-at-fealinx.com
creator: Amel Raboudi araboudi-at-fealinx.fr, this is the correspondent author
license: under CC-BY 3.0 license https://creativecommons.org/licenses/by/3.0/
comment: BMS-LM is a core ontology that reuses the BFO top ontology. It covers biomedical studies lifecycle and provenance management with a maximum reuse of existent ontologies. It reuses mainly OBI, IAO, RO from the OBO foundry consortium
comment: First reuse of the BMS-LM ontology was in the field of the Small Animal Biomedical Research in order to annotate and manage data, provenance, and lifecycle of molecular imaging, PET-CT, MRI, immunohistochemistry, and proteomics.
comment: This ontology is reused in the scope of the DRIVE project and will be reused for the PACIFIC project.
version info: Version 1.1

broadMatch
type: AnnotationProperty
comment: inspired form skos:broadMatch but not the same use formality. Here it is used as a simple informative annotation whereas skos:broadMatch is an object property that can be used between terms of Knowledge Organization Systems

narrowMatch
type: AnnotationProperty
comment: inspired form skos:narrowMatch but not the same use formality. Here it is used as a simple informative annotation whereas skos:narrowMatch is an object property that can be used between terms of Knowledge Organization Systems

exactMatch
type: AnnotationProperty
comment: inspired form skos:exactMatch but not the same use formality. Here it is used as a simple informative annotation whereas skos:exactMatch is an object property that can be used between terms of Knowledge Organization Systems

is derived from
type: ObjectProperty
equivalent property: wasDerivedFrom
sub property of: is influenced by
domain: Entity
range: Entity
IAO_0000112: a biological sample is derived from an organ or an organism
comment: this concept is equivalent to other two concepts: one is from BFO and the other from Prov-O
comment: this relation is taken from Prov-O. All Prov-O relations were renamed to use the present tense. Present is more appropriate to data in the course of a biomedical study
label: est dérivé de @fr

has member
type: ObjectProperty
equivalent property: hadMember
sub property of: is influenced by
IAO_0000112: a study subject group has member a study subject
comment: this concept is equivalent to other two concepts: one is from BFO and the other from Prov-O
comment: this relation is taken from Prov-O. All Prov-O relations were renamed to use the present tense. Present is more appropriate to data in the course of a biomedical study
label: a membre @fr

is attributed to
type: ObjectProperty
equivalent property: wasAttributedTo
sub property of: is influenced by
range: Agent
IAO_0000112: a -bmslm: examination protocol- is attributed to the person who created or tuned or executed it.
comment: this relation is taken from Prov-O. All Prov-O relations were renamed to use the present tense. Present is more appropriate to data in the course of a biomedical study
label: est attribué à @fr

is informed by
type: ObjectProperty
equivalent property: wasInformedBy
sub property of: is influenced by
domain: Activity
range: Activity
IAO_0000112: a -bmslm: data processing unit- is informed by its -bmslm: data processing- envelop when to be executed.
comment: this relation is taken from Prov-O. All Prov-O relations were renamed to use the present tense. Present is more appropriate to data in the course of a biomedical study
label: est informé par @fr

uses
type: ObjectProperty
equivalent property: used
sub property of: is influenced by
domain: Activity
range: Entity
IAO_0000112: a -bmslm:examination- uses a -bmslm:device-
comment: this relation is taken from Prov-O. All Prov-O relations were renamed to use the present tense. Present is more appropriate to data in the course of a biomedical study
label: utilise @fr

is generated by
type: ObjectProperty
equivalent property: wasGeneratedBy
sub property of: is influenced by
domain: Entity
range: Activity
IAO_0000112: a -bmslm:raw data unit- is generated by a -bmslm:data acquisition- process
comment: this relation is taken from Prov-O. All Prov-O relations were renamed to use the present tense. Present is more appropriate to data in the course of a biomedical study
label: est généré par @fr

is ended by
type: ObjectProperty
equivalent property: wasEndedBy
sub property of: is influenced by
IAO_0000112: a -bmslm: data processing- is ended by a -bmslm: operator-
comment: in the Pov-O W3C document (http://www.w3.org/TR/2013/REC-prov-o-20130430/) an activity can be ended by and agent (see 3.2 Expanded Terms: Example2). Thus, the -bmslm:is ended by- domain is extended to agents too.
comment: this relation is taken from Prov-O. All Prov-O relations were renamed to use the present tense. Present is more appropriate to data in the course of a biomedical study
label: est fini par @fr

actes on behalf of
type: ObjectProperty
equivalent property: actedOnBehalfOf
sub property of: is influenced by
domain: Agent
range: Agent
IAO_0000112: a -bmslm:operator- acts on behalf of a -bmslm: technical referent-
comment: this relation is taken from Prov-O. All Prov-O relations were renamed to use the present tense. Present is more appropriate to data in the course of a biomedical study
label: agit à la place de @fr

is influenced by
type: ObjectProperty
equivalent property: wasInfluencedBy
sub property of: topObjectProperty
comment: This is a superclass concept for all Prov-O relations. It is used when no other child can fit the situation.
comment: this relation is taken from Prov-O. All Prov-O relations were renamed to use the present tense. Present is more appropriate to data in the course of a biomedical study
label: est influencé par @fr

has for profile
type: ObjectProperty
IAO_0000115: the link between obo:process and obo:process profile
comment: This should be in the RO ontology because referenced in the definition of process profile. It was not found though, so it was added.
label: a pour profil de processus @fr

is associated with
type: ObjectProperty
equivalent property: wasAssociatedWith
sub property of: is influenced by
IAO_0000112: a -bmslm:examination- is associated with -bmslm:2 data collection- phase
IAO_0000112: a -bmslm:examination- is associated with a -bmslm:study subject-
comment: this relation is taken from Prov-O. All Prov-O relations were renamed to use the present tense. Present is more appropriate to data in the course of a biomedical study
label: est associé à @fr

is invalidated by
type: ObjectProperty
equivalent property: wasInvalidatedBy
sub property of: is influenced by
IAO_0000112: some -bmslm:derived data unit- may become invalidated after a -bmslm:data processing- it is then unusable
comment: this relation is taken from Prov-O. All Prov-O relations were renamed to use the present tense. Present is more appropriate to data in the course of a biomedical study
label: est invalidé par @fr

is started by
type: ObjectProperty
equivalent property: wasStartedBy
sub property of: is influenced by
IAO_0000112: is started by
comment: this relation is taken from Prov-O. All Prov-O relations were renamed to use the present tense. Present is more appropriate to data in the course of a biomedical study
label: est commencé par @fr

has for parameters
type: ObjectProperty
sub property of: has for profile
IAO_0000112: links a list of preconfigured and tested parameters for a Machine Learning script to the script reusing them
IAO_0000115: this is a bmslm relation that links parameter profile to their correspendant process
label: a pour paramètre @fr

has for protocol
type: ObjectProperty
sub property of: topObjectProperty
type: TransitiveProperty
property chain axiom: realizes
property chain axiom: concretizes
IAO_0000112: a bmslm:examination has for protocol a bmslm:examination protocol
IAO_0000115: links a process to the protocol that defines it. This is a composed relation of (obo:concretizes(obo:realizes))
label: a protocole @fr

has part
type: ObjectProperty
sub property of: topObjectProperty
IAO_0000112: a bmslm:examination has part a bmslm:data acquisition
comment: a reused relation from RO. See owl:EquivalentClasses for more info from RO
label: a partie @fr

has participant
type: ObjectProperty
sub property of: topObjectProperty
IAO_0000112: a bmslm:research study has participant a bmslm:study subject
comment: a reused relation from RO. See owl:EquivalentClasses for more info from RO
label: a participant @fr

has role
type: ObjectProperty
sub property of: topObjectProperty
IAO_0000112: a bmslm:studied organism has role a bmslm:study subject
comment: a reused relation from RO. See owl:EquivalentClasses for more info from RO
label: a role @fr

role of
type: ObjectProperty
sub property of: topObjectProperty
comment: a reused relation from RO. See owl:EquivalentClasses for more info from RO
comment: inverse of bmslm:has role
label: role de @fr

realized in
type: ObjectProperty
sub property of: topObjectProperty
IAO_0000112: a -bmslm:study subject role- is realized in -bmslm:biomedical research study-
comment: a reused relation from RO. See owl:EquivalentClasses for more info from RO
label: est réalisé dans @fr

realizes
type: ObjectProperty
sub property of: topObjectProperty
comment: a reused relation from RO. See owl:EquivalentClasses for more info from RO
comment: inverse of bmslm:realized in
label: réalise @fr

has specified input
type: ObjectProperty
sub property of: topObjectProperty
IAO_0000112: a bmslm:agent administration has specified input a bmslm:agent product
comment: a reused relation from RO. See owl:EquivalentClasses for more info from RO
label: a entrée spécifiée @fr

has specified output
type: ObjectProperty
sub property of: topObjectProperty
IAO_0000112: a -bmslm:data processing unit- has specified output a -bmslm:derived data unit-
comment: a reused relation from RO. See owl:EquivalentClasses for more info from RO
label: a comme produit spécifié @fr

concretizes
type: ObjectProperty
sub property of: topObjectProperty
comment: a reused relation from RO. See owl:EquivalentClasses for more info from RO
comment: this is used is a composition with bmslm:realizes
label: concrétise @fr

occurs in
type: ObjectProperty
sub property of: topObjectProperty
IAO_0000112: an obi:planned process occurs in a bmslm:study lifecycle phase
comment: a reused relation from RO. See owl:EquivalentClasses for more info from RO
label: a lieu à @fr

contains process
type: ObjectProperty
sub property of: topObjectProperty
IAO_0000112: a bmslm:study collection phase contains process bmslm: data acquisition
comment: a reused relation from RO. See owl:EquivalentClasses for more info from RO
label: contient processus @fr

denoted by
type: ObjectProperty
sub property of: topObjectProperty
IAO_0000112: an imaging examination process is denoted by a radiology scan datum
comment: a reused relation from RO. See owl:EquivalentClasses for more info from RO
comment: inverse of is about
label: est dénoté par @fr

is about
type: ObjectProperty
sub property of: topObjectProperty
IAO_0000112: a radiology scan datum is about an imaging examination process
comment: this relation is taken from OBO. It relates an obo:data item to the concept it is describing
label: est a propos de @fr

has value specification
type: ObjectProperty
sub property of: topObjectProperty
IAO_0000112: a data item (imaging modalities) has value specification a list of value specification (CT, PET-CTn PET-MRI, MSI, MRI, US, US-Doppler, )
comment: a reused relation from RO. See owl:EquivalentClasses for more info from RO
label: a spécification de valeurs @fr

has quality
type: ObjectProperty
sub property of: topObjectProperty
IAO_0000112: a continuant (a bmslm:agent product) has quality some inherent descriptors (color)
comment: a reused relation from RO. See owl:EquivalentClasses for more info from RO
label: a qualité @fr

part of
type: ObjectProperty
label: est partie de @fr

has identifier
type: DatatypeProperty
sub property of: topDataProperty
IAO_0000112: a protocol has identifier PROTOCOL662020
IAO_0000112: a study subject has identifier XX000MM
IAO_0000115: a data property to indicate any kind of identifier for all bmslm concepts

has value
type: DatatypeProperty
equivalent property: value
sub property of: topDataProperty
IAO_0000112: a number of frames of a dynamic PET image has value 180
IAO_0000115: a data property to specify the value of a data item when instanciating a class
exactMatch: http://purl.org/biotop/btl2.owl#hasValue

has key
type: DatatypeProperty

OBI_0000011
type: Class
IAO_0000111: BMSLM: plan realization process

OBI_0000272
type: Class
IAO_0000111: BMSLM: protocol

biomedical research study
type: Class
subclass of: OBI_0000011
subclass of: Restriction
  on property: uses
  some values from: OBI_0000272
subclass of: Restriction
  on property: is associated with
  some values from: study lifecycle phase
subclass of: Restriction
  on property: has part
  some values from: OBI_0000471
subclass of: Restriction
  on property: has participant
  some values from: study subject
subclass of: Restriction
  on property: has participant
  some values from: study subject group
subclass of: Restriction
  on property: has specified input
  some values from: ethical approval proof
IAO_0000111: research study
IAO_0000115: a planned process that follows several steps, from the specification of the study to the publication of its results.
IAO_0000118: STU
narrowMatch: OBI_0000066
exactMatch: ERO_0000347
label: étude de recherche biomédicale @fr
backward compatible with: GIN4_Study
backward compatible with: Study

study subject
type: Class
subclass of: BFO_0000023
subclass of: Restriction
  on property: is associated with
  some values from: biomedical intervention
subclass of: Restriction
  on property: is associated with
  some values from: examination
subclass of: Restriction
  on property: role of
  some values from: studied organism
subclass of: Restriction
  on property: realized in
  some values from: biomedical research study
IAO_0000111: study subject
IAO_0000115: a role played by a "studied organism" in a biomedical study by participating in the study or donating samples for the study
IAO_0000118: SSU
IAO_0000118: study participant
narrowMatch: NDDO_00000077
label: sujet dans l étude @fr
backward compatible with: GIN4_StudySub
backward compatible with: Study Subject

biological sample
type: Class
subclass of: BFO_0000030
subclass of: Restriction
  on property: is derived from
  some values from: studied organism
subclass of: Restriction
  on property: has role
  some values from: OBI_0000112
IAO_0000111: biological sample
IAO_0000115: an object that has been harvested from a living organism: organ, biological tissue, cells, shredded material, etc.
IAO_0000118: SAR identification
broadMatch: NMR:1000457
narrowMatch: OBI_0002076
narrowMatch: OBI_0100051
label: échantillon biologique @fr
backward compatible with: GIN4_SampleDef_ ICM030508 _ sample-identification
backward compatible with: Sample Result Identification

biomedical intervention
type: Class
subclass of: OBI_0000011
subclass of: Restriction
  on property: has for protocol
  some values from: biomedical intervention protocol
subclass of: Restriction
  on property: has part
  some values from: agent administration
subclass of: Restriction
  on property: realizes
  some values from: Restriction
    on property: concretizes
    some values from: biomedical intervention protocol
subclass of: Restriction
  on property: occurs in
  some values from: 2 study data collection
IAO_0000111: biomedical intervention
IAO_0000115: a planned process of taking an action that changes and influences a biological object in a research study
IAO_0000118: ITR
exactMatch: ERO_0000347
label: intervention biomédicale @fr
backward compatible with: GIN4_Interv
backward compatible with: Intervention Result

examination
type: Class
subclass of: OBI_0000011
subclass of: Restriction
  on property: has for protocol
  some values from: examination protocol
subclass of: Restriction
  on property: has part
  some values from: agent administration
subclass of: Restriction
  on property: realizes
  some values from: Restriction
    on property: concretizes
    some values from: examination protocol
subclass of: Restriction
  on property: occurs in
  some values from: 2 study data collection
subclass of: Restriction
  on property: uses
  min qualified cardinality: 1
  on class: device
subclass of: Restriction
  on property: has part
  min qualified cardinality: 1
  on class: data acquisition
IAO_0000111: examination
IAO_0000115: a planned process that consists of acquiring information on an object of interest via different means in order to describe and characterize it at a given moment from a biological and medical point of view.
IAO_0000118: EXA
exactMatch: examination
label: examen @fr
backward compatible with: Exam Result
backward compatible with: GIN4_ExamRes

examination protocol
type: Class
subclass of: OBI_0000272
subclass of: Restriction
  on property: has part
  some values from: agent administration protocol
subclass of: Restriction
  on property: has part
  min qualified cardinality: 1
  on class: data acquisition protocol
IAO_0000111: examination protocol
IAO_0000115: a protocol describing necessary steps to examine an object of interest from a biological or medical point of view.
IAO_0000118: EXD
label: protocole d'examen @fr
backward compatible with: Exam Definition
backward compatible with: GIN4_ExamDef

biomedical intervention protocol
type: Class
subclass of: OBI_0000272
subclass of: Restriction
  on property: has part
  some values from: agent administration protocol
IAO_0000111: biomedical intervention protocol
IAO_0000115: a protocol to describe the steps required to conduct a biomedical intervention
IAO_0000118: ITD
label: protocole d'intervention biomédicale @fr
backward compatible with: GIN4_IntervDef
backward compatible with: Intervention Definition

data acquisition protocol
type: Class
subclass of: OBI_0000272
subclass of: Restriction
  on property: has part
  some values from: agent administration protocol
subclass of: Restriction
  on property: has part
  min qualified cardinality: 1
  on class: expected data unit
IAO_0000111: data acquisition protocol
IAO_0000115: a protocol to describe the steps required for data acquisition
IAO_0000118: ACD
label: protocole d acquisition de données @fr
backward compatible with: Acquisition Definition

raw data unit
type: Class
subclass of: IAO_0000030
IAO_0000111: raw data unit
IAO_0000115: an i-c-e resulting from a raw data acquisition process of a research study
IAO_0000118: DUR
label: unité de données brutes résultant @fr
backward compatible with: Data Unit Result
backward compatible with: GIN4_DataUnit

data acquisition
type: Class
subclass of: OBI_0000011
subclass of: Restriction
  on property: has for protocol
  some values from: data acquisition protocol
subclass of: Restriction
  on property: has part
  some values from: agent administration
subclass of: Restriction
  on property: realizes
  some values from: Restriction
    on property: concretizes
    some values from: data acquisition protocol
subclass of: Restriction
  on property: uses
  min qualified cardinality: 1
  on class: software tool
subclass of: Restriction
  on property: has specified output
  min qualified cardinality: 1
  on class: raw data unit
IAO_0000111: data acquisition
IAO_0000112: acquiring images with a scanner
IAO_0000115: a planned process that consists of acquiring, in a homogeneous way and in a precise and indivisible period of time, data in the context of an examination.
IAO_0000118: ACQ
broadMatch: C43384
label: acquisition de données @fr
backward compatible with: Acquisition Result
backward compatible with: GIN4_Acquisition

data processing
type: Class
subclass of: OBI_0000011
subclass of: Restriction
  on property: has for protocol
  some values from: data processing protocol
subclass of: Restriction
  on property: realizes
  some values from: Restriction
    on property: concretizes
    some values from: data processing protocol
subclass of: Restriction
  on property: occurs in
  some values from: 3 study data analysis
subclass of: Restriction
  on property: has part
  min qualified cardinality: 1
  on class: data processing unit
IAO_0000111: data processing
IAO_0000115: a planned process that consists of processing and analyzing the data from the various examinations in order to deliver an analysis result. It is composed of one or more (data processing units)
IAO_0000118: PCR
broadMatch: C48177
label: chaine de traitement de données @fr
backward compatible with: GIN4_ProcessRes
backward compatible with: Processing Result

processing parameters profile
type: Class
subclass of: BFO_0000144
IAO_0000111: a process profile that allows to meta-describe a process by specifying the parameters necessary for its execution
IAO_0000115: parameters to reuse in a processing unit
IAO_0000118: PCP
label: paramètres de chaine de traitement @fr
backward compatible with: GIN4_ProcessPar
backward compatible with: Processing Parameters

published content
type: Class
subclass of: IAO_0000030
IAO_0000111: published content
IAO_0000112: a book, an article, a DOI, a website, an URI, an orcid, an beyond. This do not include published data
IAO_0000115: an i-c-e representing any content published and referenced, used or published as part of a research study (excluding data)
IAO_0000118: BBR
narrowMatch: IAO_0000013
comment: in its original version, this concept was just for articles but the variety of published content on the web had made it necessary to extend it
label: contenu publié @fr
backward compatible with: Bibliographical Reference
backward compatible with: GIN4_RefBib

reference data
type: Class
subclass of: published content
IAO_0000111: reference data
IAO_0000115: an i-c-e representing any data used as a reference in a study or published as a referenced data set in a study
IAO_0000118: RFD
label: données de références @fr
backward compatible with: GIN4_Template
backward compatible with: Reference Data

software tool
type: Class
subclass of: IAO_0000104
IAO_0000111: software tool
IAO_0000115: a design specification consisting of a series of instructions that can be interpreted by a processing unit or directly executed by it to analyze the study data. source : OBO
IAO_0000118: STL
exactMatch: IAO_0000010
label: outil logiciel @fr
backward compatible with: GIN4_Tool
backward compatible with: Software Tool

device
type: Class
subclass of: OBI_0000047
IAO_0000111: device
IAO_0000115: a material entity that is designed to perform a function in a scientific experiment (examination, processing, scientific calculation), but is not a reagent. source : OBO
IAO_0000118: AQD
IAO_0000118: DVC
exactMatch: OBI_0000968
comment: device has several configurations refered to as versions.
comment: first this was called Acquisition Device and Then it was extended to all devices of a study
label: appareil @fr
backward compatible with: Device
backward compatible with: GIN4_Scanner

study subject group
type: Class
subclass of: BFO_0000027
subclass of: Restriction
  on property: RO_0002351
  min qualified cardinality: 1
  on class: Class
    intersection of: studied organism
    intersection of: Restriction
      on property: RO_0000087
      qualified cardinality: 1
      on class: study subject
IAO_0000111: study subject group
IAO_0000115: an aggregation or a set of "bmslm:studied organism" having the "bmslm:study subject" role
IAO_0000118: SGP
label: groupe de sujets dans l étude @fr
backward compatible with: GIN4_SubGroup
backward compatible with: Study Subject Group

data processing unit
type: Class
subclass of: OBI_0000011
subclass of: Restriction
  on property: has for parameters
  some values from: processing parameters profile
subclass of: Restriction
  on property: has for protocol
  some values from: data processing unit protocol
subclass of: Restriction
  on property: realizes
  some values from: Restriction
    on property: concretizes
    some values from: data processing unit protocol
subclass of: Restriction
  on property: has specified output
  some values from: derived data unit
subclass of: Restriction
  on property: uses
  min qualified cardinality: 1
  on class: reference data
subclass of: Restriction
  on property: has specified input
  min qualified cardinality: 1
  on class: raw data unit
subclass of: Restriction
  on property: has specified input
  min qualified cardinality: 1
  on class: derived data unit
IAO_0000111: data processing unit
IAO_0000115: a planned process of analyzing input data to produce output results that are themselves inputs to a subsequent (data processing unit). This sequence composes a (data processing) process
IAO_0000118: PUR
label: unité de chaine de traitement de données @fr
backward compatible with: GIN4_ProcessUR
backward compatible with: Processing Unit Result

workflow input profile
type: Class
subclass of: BFO_0000144
subclass of: Restriction
  on property: has member
  some values from: raw data unit
subclass of: Restriction
  on property: has member
  some values from: reference data
subclass of: Restriction
  on property: has member
  some values from: device
subclass of: Restriction
  on property: has member
  some values from: data processing protocol
subclass of: Restriction
  on property: has member
  some values from: derived data unit
subclass of: Restriction
  on property: has member
  some values from: data processing unit protocol
IAO_0000111: workflow input profile
IAO_0000115: a process profile that allows to "meta-describe" a process by specifying all types of input required to launch it as part of a workflow
IAO_0000118: WFI
label: intrant de flux de traitement @fr
backward compatible with: GIN4_WorkflowIn
backward compatible with: Workflow Input

agent administration protocol
type: Class
subclass of: OBI_0000272
IAO_0000111: agent administration protocol
IAO_0000115: a protocol to describe the steps required to administrate an agent (product that acts)
IAO_0000118: AGD
label: protocole d'administration d'agent @fr
backward compatible with: Agent Definition
backward compatible with: GIN4_AgentDef

expected data unit
type: Class
subclass of: IAO_0000030
IAO_0000111: expected data unit
IAO_0000115: an i-c-e describing what must be obtained as result data of a process before producing the real result data of this process
IAO_0000118: DUD
label: spécification d'unité de données @fr
backward compatible with: Data Unit Definition
backward compatible with: GIN4_DataUnitDef

data processing protocol
type: Class
subclass of: OBI_0000272
subclass of: Restriction
  on property: has part
  min qualified cardinality: 1
  on class: data processing unit protocol
IAO_0000111: data processing protocol
IAO_0000115: a protocol to describe necessary steps to undertake an analysis or data processing
IAO_0000118: PCD
label: protocole de chaine de traitement de données @fr
backward compatible with: GIN4_ProcessDef
backward compatible with: Processing Definition

derived data unit
type: Class
subclass of: IAO_0000030
IAO_0000111: derived data unit
IAO_0000115: an i-c-e resulting from a research study data analysis process
IAO_0000118: PUR data
label: unité de données dérivées résultant @fr
backward compatible with: GIN4_ProcessUR _ IMAN_Reference _ dataset
backward compatible with: Processing Unit Result data

data processing unit protocol
type: Class
subclass of: OBI_0000272
subclass of: Restriction
  on property: has part
  some values from: expected data unit
IAO_0000111: data processing unit protocol
IAO_0000115: a protocol to describe steps required to run a (data processing unit)
IAO_0000118: PUD
label: protocole d'unité de traitement de données @fr
backward compatible with: GIN4_ProcessUD
backward compatible with: Processing Unit Definition

sample preparation protocol
type: Class
subclass of: OBI_0000272
subclass of: Restriction
  on property: has part
  some values from: agent administration protocol
IAO_0000111: sample preparation protocol
IAO_0000115: a protocol defining the required steps for the preparation of a biological sample.
IAO_0000118: SAD
label: protocole de préparation d'échantillon biologique @fr
backward compatible with: GIN4_SampleDef
backward compatible with: Sample Definition

biological sample preparation
type: Class
subclass of: OBI_0000011
subclass of: Restriction
  on property: has for protocol
  some values from: sample preparation protocol
subclass of: Restriction
  on property: has part
  some values from: agent administration
subclass of: Restriction
  on property: realizes
  some values from: Restriction
    on property: concretizes
    some values from: sample preparation protocol
subclass of: Restriction
  on property: has specified input
  some values from: biological sample
subclass of: Restriction
  on property: has specified input
  some values from: studied organism
subclass of: Restriction
  on property: occurs in
  some values from: 2 study data collection
subclass of: Restriction
  on property: has specified output
  min qualified cardinality: 1
  on class: biological sample
IAO_0000111: biological sample preparation
IAO_0000115: a planned process of transforming a biological object into a biological sample ready for examination
IAO_0000118: SAR preparation
narrowMatch: OBI_0000659
label: préparation d'échantillons biologiques @fr
backward compatible with: GIN4_Sample
backward compatible with: Sample Result Preparation

study lifecycle phase
type: Class
subclass of: BFO_0000038
IAO_0000111: study lifecycle phase
IAO_0000115: a temporal region encompassing a distinct step in a study
comment: this concept was added for the first time in the BMSLM core ontology v 1.0 in order to enable lifecycle management for a research study. It is an abstract class. Use children instead.
label: phase de cycle de vie d une étude @fr

1 study specification
type: Class
subclass of: study lifecycle phase
IAO_0000111: study specification
IAO_0000115: the first lifecycle phase in a study. It includes the definition of the study aim and scope, details about expected data acquisitions and processings, budget and ethical approvement of the study.
label: 1 spécification d étude @fr

2 study data collection
type: Class
subclass of: study lifecycle phase
subclass of: Restriction
  on property: contains process
  some values from: biomedical intervention
subclass of: Restriction
  on property: contains process
  some values from: examination
subclass of: Restriction
  on property: contains process
  some values from: biological sample preparation
subclass of: Restriction
  on property: contains process
  some values from: agent administration
IAO_0000111: study data collection
IAO_0000115: the second lifecycle phase in a study encompassing data collection using several devices and software
label: 2 collecte de données d étude @fr

3 study data analysis
type: Class
subclass of: study lifecycle phase
subclass of: Restriction
  on property: contains process
  some values from: data processing
IAO_0000111: study data analysis
IAO_0000115: the third lifecycle phase in a study encompassing the analysis and processing of data
label: 3 analyse de données d étude @fr

4 study results publishing
type: Class
subclass of: study lifecycle phase
IAO_0000111: study results publishing
IAO_0000115: the fourth lifecycle phase in a study encompassing results formatting in a publication compliant format and its publishing as an article, a data paper, a website, a web ressource etc.
label: 4 publication de données d étude @fr

ethical approval proof
type: Class
subclass of: IAO_0000310
IAO_0000115: a document attesting that the study is compliant to ethical requirements
label: document d'autorisation éthique @fr

agent product
type: Class
subclass of: BFO_0000030
IAO_0000111: agent product
IAO_0000112: 18-Fluorodeoxyglucose used in a PET-CT scan
IAO_0000112: Antibody used in immunohistochemistry
IAO_0000115: a pharmaceutical object that is produced to act on living organisms or biological samples
IAO_0000118: AGT identification
label: produit agent @fr
backward compatible with: Agent Result Identification
backward compatible with: GIN4_AgentDef_ICM030405_agent-identification

agent administration
type: Class
subclass of: OBI_0000011
subclass of: Restriction
  on property: has for protocol
  some values from: agent administration protocol
subclass of: Restriction
  on property: realizes
  some values from: Restriction
    on property: concretizes
    some values from: agent administration protocol
subclass of: Restriction
  on property: occurs in
  some values from: 2 study data collection
subclass of: Restriction
  on property: has specified input
  min qualified cardinality: 1
  on class: agent product
IAO_0000111: agent administration
IAO_0000115: a planned process of introducing a pharmaceutical product that acts on biological tissue into a living organism, or into a biological sample
IAO_0000118: AGT administration
label: administration d'agent pharmaceutique @fr
backward compatible with: Agent Result Administation
backward compatible with: GIN4_Agent

studied organism
type: Class
subclass of: BFO_0000040
subclass of: Restriction
  on property: has role
  some values from: study subject
IAO_0000111: studied organism
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_0000118: SSU organism
IAO_0000119: http://en.wikipedia.org/wiki/Organism
exactMatch: OBI_0100026
label: organisme étudié @fr
backward compatible with: GIN4_StudySub _ICM0403010104_Organism
backward compatible with: Study Subject Organism

principal investigator
type: Class
subclass of: BFO_0000023
IAO_0000115: a role played by the person referee for the project or the study. He/she is usually the head of the lab or a person from the institution coordinating a project
IAO_0000118: PI
label: investigateur principal @fr

operator
type: Class
subclass of: BFO_0000023
IAO_0000115: a role of a person doing experiments and operating using a device or a software in order to execute a study process
label: opérateur @fr

technical referent
type: Class
subclass of: BFO_0000023
IAO_0000115: a role played by an expert in the use of a ressource (device, software, method) in the course of a study
label: référent technique @fr