OntoBiotope

Last uploaded: December 1, 2021

Details

Acronym	ONTOBIOTOPE
Visibility	Public
Description	OntoBiotope is an ontology of microorganism habitats, phenotypes and use. Its modeling principle and its lexicon reflect the biotope classification used by biologists to describe microorganism isolation sites, phenotypes and uses. OntoBiotope is developed and maintained by the Bibliome group of MaIAGE lab and microbiologists from INRAE (French National Research Institute for Agriculture, Food and Environment) from all fields of applied microbiology. OntoBiotope classes are used in the Bacteria Biotope reference dataset of BioNLP shared task to annotate the habitats and phenotype entities. It is also used to index the data of the Omnicrobe DataBase
Status	Production
Format	OBO
Contact	Claire Nédellec, claire.nedellec@inrae.fr
Categories	Biodiversity and Ecology, Natural Resources, Earth and Environment
Groups	GDR SemanDiv, National research institute for agriculture, food and the environment

Additional Metadata

copyright Holder	INRA (http://www.inra.fr/)
deprecated	false
designed For Ontology Task	http://omv.ontoware.org/2005/05/ontology#AnnotationTask
endorsed By	INRAE (http://www.inrae.fr/)
endpoint
example Identifier	http://purl.obolibrary.org/obo/OBT_001929
funded By	INRA (http://www.inrae.fr/)
Creators	Claire Nédellec
has Domain	http://aims.fao.org/aos/agrovoc/c_925, http://aims.fao.org/aos/agrovoc/c_5776, http://aims.fao.org/aos/agrovoc/c_3456, http://aims.fao.org/aos/agrovoc/c_4807
has Formality Level	http://w3id.org/nkos/nkostype#ontology
has License
Ontology Syntax	http://purl.obolibrary.org/obo/oboformat/spec.html
has Prior Version	http://data.agroportal.lirmm.fr/ontologies/ONTOBIOTOPE/submissions/7
identifier	http://doi.org/10.15454/1.4382640528105164E12
is Of Type	http://omv.ontoware.org/2005/05/ontology#DomainOntology
keywords	information extraction, corpus annotation, ontology building, biology, genetics, ecology, epidemiology, phenotypes, habitats, microorganisms
known Usage	Used by the BioNLP Shared task (Bacteria Biotope task) in 2011, 2013, 2016 and 2019 for the annotation of textual data. OntoBiotope is the ontology used in the Omnicrobe (previously called Florilege) to index habitats, phenotypes and uses of large collections of data about microbes.
Metadata vocabulary used	local:local
modification Date	2021-10-22T00:00:00+00:00
Natural Language
notes	OntoBiotope is developed and maintained by MaIAGE lab (INRAE) with the contribution of INRAE microbiologists.
preferred Namespace Prefix	obt
publisher	INRA (http://www.inra.fr/)
Release date	2019-03-01T00:00:00+00:00
URI Lookup Endpoint	http://data.agroportal.lirmm.fr/search?ontologies=ONTOBIOTOPE&require_exact_match=true&q=
use Imports	local:local
used Ontology Engineering Tool	http://oboedit.org/
version	Oct 2021

Version	Released	Modified	Uploaded	Downloads
Oct 2021 (Parsed, Indexed, Metrics, Annotator)	03/01/2019	10/22/2021	12/01/2021	OBO \| CSV \| RDF/XML \| DIFF
March 2021 (Archived)	03/01/2019	03/31/2021	04/16/2021	OBO \| DIFF
Fev 2021 (Archived)	03/01/2019		03/10/2021	OBO \| DIFF
BioNLP-OST-2019 (Archived)	03/19/2019		09/25/2019	OBO \| DIFF
1.2 (Archived)	07/24/2018		07/24/2018	OBO \| DIFF
1.2 (Archived)	07/23/2018		07/23/2018	OBO \| DIFF
1.2 (Archived)	06/29/2015		06/12/2016	OBO \| DIFF
BioNLP-ST 2013 version (Archived)	06/29/2015		06/29/2015	OBO
more...

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Go to the REST API JSON entry

Total score : 266.0 ( 55.0% ) details

Classes	4,219
Individuals	0
Properties	1
Maximum depth	13
Maximum number of children	121
Average number of children	3
Classes with a single child	470
Classes with more than 25 children	9
Classes with no definition	4,213

http://lovinra.inra.fr/2015/07/30/ontobiotope/VEST Registry

Agrisemantics Map of Data Standards

Bacteria Biotope shared task

Data to Knowledge in Agronomy and Biodiversity

Florilege

OntoBiotope

Vocabulaires Ouverts @INRAE