Benoît Eynard benoit.eynard-at-utc.fr
Bertrand Tavitian bertrand.tavitian-at-inserm.fr
Daniel Balvay daniel.balvay-at-inserm.fr
Jacques Hilbey jacques.hilbey-at-inserm.fr
Jean Charlet jean.charlet-at-sorbonne-universite.fr
Marianne Allanic mallanic-ext-at-fealinx.com
Philippe Boutinaud pboutinaud-at-fealinx.com
Pierre-Yves Hervé pyherve-at-fealinx.com
Amel Raboudi araboudi-at-fealinx.fr, this is the correspondent author
under CC-BY 3.0 license https://creativecommons.org/licenses/by/3.0/
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
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.
This ontology is reused in the scope of the DRIVE project and will be reused for the PACIFIC project.
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
broadMatch
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
narrowMatch
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
exactMatch
a biological sample is derived from an organ or an organism
this concept is equivalent to other two concepts: one is from BFO and the other from Prov-O
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
est dérivé de
is derived from
a study subject group has member a study subject
a membre
has member
a -bmslm: examination protocol- is attributed to the person who created or tuned or executed it.
est attribué à
is attributed to
a -bmslm: data processing unit- is informed by its -bmslm: data processing- envelop when to be executed.
est informé par
is informed by
a -bmslm:examination- uses a -bmslm:device-
uses
utilise
a -bmslm:raw data unit- is generated by a -bmslm:data acquisition- process
est généré par
is generated by
a -bmslm: data processing- is ended by a -bmslm: operator-
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.
est fini par
is ended by
a -bmslm:operator- acts on behalf of a -bmslm: technical referent-
actes on behalf of
agit à la place de
This is a superclass concept for all Prov-O relations. It is used when no other child can fit the situation.
est influencé par
is influenced by
the link between obo:process and obo:process profile
This should be in the RO ontology because referenced in the definition of process profile. It was not found though, so it was added.
a pour profil de processus
has for profile
a -bmslm:examination- is associated with -bmslm:2 data collection- phase
a -bmslm:examination- is associated with a -bmslm:study subject-
est associé à
is associated with
some -bmslm:derived data unit- may become invalidated after a -bmslm:data processing- it is then unusable
est invalidé par
is invalidated by
is started by
est commencé par
links a list of preconfigured and tested parameters for a Machine Learning script to the script reusing them
this is a bmslm relation that links parameter profile to their correspendant process
a pour paramètre
has for parameters
a bmslm:examination has for protocol a bmslm:examination protocol
links a process to the protocol that defines it. This is a composed relation of (obo:concretizes(obo:realizes))
a protocole
has for protocol
a bmslm:examination has part a bmslm:data acquisition
a reused relation from RO. See owl:EquivalentClasses for more info from RO
a partie
has part
a bmslm:research study has participant a bmslm:study subject
a participant
has participant
a bmslm:studied organism has role a bmslm:study subject
a role
has role
inverse of bmslm:has role
role de
role of
a -bmslm:study subject role- is realized in -bmslm:biomedical research study-
est réalisé dans
realized in
inverse of bmslm:realized in
realizes
réalise
a bmslm:agent administration has specified input a bmslm:agent product
a entrée spécifiée
has specified input
a -bmslm:data processing unit- has specified output a -bmslm:derived data unit-
a comme produit spécifié
has specified output
this is used is a composition with bmslm:realizes
concretizes
concrétise
an obi:planned process occurs in a bmslm:study lifecycle phase
a lieu à
occurs in
a bmslm:study collection phase contains process bmslm: data acquisition
contains process
contient processus
an imaging examination process is denoted by a radiology scan datum
inverse of is about
denoted by
est dénoté par
a radiology scan datum is about an imaging examination process
this relation is taken from OBO. It relates an obo:data item to the concept it is describing
est a propos de
is about
a data item (imaging modalities) has value specification a list of value specification (CT, PET-CTn PET-MRI, MSI, MRI, US, US-Doppler, )
a spécification de valeurs
has value specification
a continuant (a bmslm:agent product) has quality some inherent descriptors (color)
a qualité
has quality
est partie de
part of
a protocol has identifier PROTOCOL662020
a study subject has identifier XX000MM
a data property to indicate any kind of identifier for all bmslm concepts
has identifier
a number of frames of a dynamic PET image has value 180
a data property to specify the value of a data item when instanciating a class
has value
has key
research study
a planned process that follows several steps, from the specification of the study to the publication of its results.
STU
biomedical research study
étude de recherche biomédicale
GIN4_Study
Study
study subject
a role played by a "studied organism" in a biomedical study by participating in the study or donating samples for the study
SSU
study participant
sujet dans l étude
GIN4_StudySub
Study Subject
biological sample
an object that has been harvested from a living organism: organ, biological tissue, cells, shredded material, etc.
SAR identification
échantillon biologique
GIN4_SampleDef_ ICM030508 _ sample-identification
Sample Result Identification
biomedical intervention
a planned process of taking an action that changes and influences a biological object in a research study
ITR
intervention biomédicale
GIN4_Interv
Intervention Result
examination
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.
EXA
examen
Exam Result
GIN4_ExamRes
examination protocol
a protocol describing necessary steps to examine an object of interest from a biological or medical point of view.
EXD
protocole d'examen
Exam Definition
GIN4_ExamDef
biomedical intervention protocol
a protocol to describe the steps required to conduct a biomedical intervention
ITD
protocole d'intervention biomédicale
GIN4_IntervDef
Intervention Definition
data acquisition protocol
a protocol to describe the steps required for data acquisition
ACD
protocole d acquisition de données
Acquisition Definition
raw data unit
an i-c-e resulting from a raw data acquisition process of a research study
DUR
unité de données brutes résultant
Data Unit Result
GIN4_DataUnit
data acquisition
acquiring images with a scanner
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.
ACQ
acquisition de données
Acquisition Result
GIN4_Acquisition
data processing
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)
PCR
chaine de traitement de données
GIN4_ProcessRes
Processing Result
a process profile that allows to meta-describe a process by specifying the parameters necessary for its execution
parameters to reuse in a processing unit
PCP
paramètres de chaine de traitement
processing parameters profile
GIN4_ProcessPar
Processing Parameters
published content
a book, an article, a DOI, a website, an URI, an orcid, an beyond. This do not include published data
an i-c-e representing any content published and referenced, used or published as part of a research study (excluding data)
BBR
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
contenu publié
Bibliographical Reference
GIN4_RefBib
reference data
an i-c-e representing any data used as a reference in a study or published as a referenced data set in a study
RFD
données de références
GIN4_Template
Reference Data
software tool
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
STL
outil logiciel
GIN4_Tool
Software Tool
device
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
AQD
DVC
device has several configurations refered to as versions.
first this was called Acquisition Device and Then it was extended to all devices of a study
appareil
Device
GIN4_Scanner
study subject group
an aggregation or a set of "bmslm:studied organism" having the "bmslm:study subject" role
SGP
groupe de sujets dans l étude
GIN4_SubGroup
Study Subject Group
data processing unit
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
PUR
unité de chaine de traitement de données
GIN4_ProcessUR
Processing Unit Result
workflow input profile
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
WFI
intrant de flux de traitement
GIN4_WorkflowIn
Workflow Input
agent administration protocol
a protocol to describe the steps required to administrate an agent (product that acts)
AGD
protocole d'administration d'agent
Agent Definition
GIN4_AgentDef
expected data unit
an i-c-e describing what must be obtained as result data of a process before producing the real result data of this process
DUD
spécification d'unité de données
Data Unit Definition
GIN4_DataUnitDef
data processing protocol
a protocol to describe necessary steps to undertake an analysis or data processing
PCD
protocole de chaine de traitement de données
GIN4_ProcessDef
Processing Definition
derived data unit
an i-c-e resulting from a research study data analysis process
PUR data
unité de données dérivées résultant
GIN4_ProcessUR _ IMAN_Reference _ dataset
Processing Unit Result data
data processing unit protocol
a protocol to describe steps required to run a (data processing unit)
PUD
protocole d'unité de traitement de données
GIN4_ProcessUD
Processing Unit Definition
sample preparation protocol
a protocol defining the required steps for the preparation of a biological sample.
SAD
protocole de préparation d'échantillon biologique
GIN4_SampleDef
Sample Definition
biological sample preparation
a planned process of transforming a biological object into a biological sample ready for examination
SAR preparation
préparation d'échantillons biologiques
GIN4_Sample
Sample Result Preparation
study lifecycle phase
a temporal region encompassing a distinct step in a study
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.
phase de cycle de vie d une étude
study specification
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.
1 spécification d étude
1 study specification
study data collection
the second lifecycle phase in a study encompassing data collection using several devices and software
2 collecte de données d étude
2 study data collection
study data analysis
the third lifecycle phase in a study encompassing the analysis and processing of data
3 analyse de données d étude
3 study data analysis
study results publishing
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.
4 publication de données d étude
4 study results publishing
a document attesting that the study is compliant to ethical requirements
document d'autorisation éthique
ethical approval proof
agent product
18-Fluorodeoxyglucose used in a PET-CT scan
Antibody used in immunohistochemistry
a pharmaceutical object that is produced to act on living organisms or biological samples
AGT identification
produit agent
Agent Result Identification
GIN4_AgentDef_ICM030405_agent-identification
agent administration
a planned process of introducing a pharmaceutical product that acts on biological tissue into a living organism, or into a biological sample
AGT administration
administration d'agent pharmaceutique
Agent Result Administation
GIN4_Agent
studied organism
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.
SSU organism
organisme étudié
GIN4_StudySub _ICM0403010104_Organism
Study Subject Organism
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
investigateur principal
principal investigator
a role of a person doing experiments and operating using a device or a software in order to execute a study process
operator
opérateur
a role played by an expert in the use of a ressource (device, software, method) in the course of a study
référent technique
technical referent