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Number of classes:	2320
Number of individuals:	0
Number of properties:	0
Maximum depth:	13
Maximum number of children:	42
Average number of children:	3
Classes with a single child:	248
Classes with more than 25 children:	3
Classes with no definition:	2320

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

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Acronym	ONTOBIOTOPE
Visibility	Public
Description	OntoBiotope is an ontology of microorganism habitats. Its modeling principle and its lexicon reflect the biotope classification used by biologists to describe microorganism isolation sites (e.g. GenBank, GOLD, ATCC). OntoBiotope is developed and maintained by the Meta-omics of Microbial Ecosystems (MEM) network in which 30 microbiologists from INRA (French National Institute for Agricultural Research) from all fields of applied microbiology participate. The relevance of OntoBiotope terms is evaluated through the PubMedBiotope semantic search engine. It identifies and categorizes microbial biotopes in all PubMed abstracts by applying the ToMap method (Text to Ontology Mapping) to the OntoBiotope ontology. It also indexes 3,35 millions relations between taxa and their habitats.
Status	Production
Format	OBO
Contact	Claire Nédellec, claire.nedellec@inra.fr
Home Page	http://lovinra.inra.fr/
Publications Page	https://doi.org/10.1186/1471-2105-16-S10-S1
Documentation Page	http://lovinra.inra.fr/
Categories	Biodiversity and Ecology, Natural Resources, Earth and Environment
Groups	GDR SemanDiv, INRA Linked Open Vocabularies

Additional Metadata

URI	http://purl.obolibrary.org/obo/TEMP
Natural Language
version	1.2
Release date	2018-07-24T18:02:31+02:00
keywords	information extraction, corpus annotation, natural language processing, ontology building, biology, genetics
known Usage	Used by the BioNLP Shared task (Bacteria Biotope task) in 2011, 2013 and 2016
notes	OntoBiotope is developed and maintained by the Meta-omics of Microbial Ecosystems (MEM) network in which 30 microbiologists from INRA (French National Institute for Agricultural Research) from all fields of applied microbiology participate.
Creators	Claire Nédellec
designed For Ontology Task	http://omv.ontoware.org/2005/05/ontology#AnnotationTask
endorsed By	INRA (http://www.inra.fr/)
funded By	INRA (http://www.inra.fr/)
has Domain	http://data.agroportal.lirmm.fr/categories/NATRES, http://data.bioontology.org/categories/BIODIV
has Formality Level	http://w3id.org/nkos/nkostype#ontology
has License
Ontology Syntax	http://purl.obolibrary.org/obo/oboformat/spec.html
is Of Type	http://omv.ontoware.org/2005/05/ontology#DomainOntology
has Prior Version	ONTOBIOTOPE/submissions/3
deprecated	false
publisher	INRA (http://www.inra.fr/)
identifier	http://doi.org/10.15454/1.4382640528105164E12
endpoint
URI Lookup Endpoint	http://data.agroportal.lirmm.fr/search?ontologies=ONTOBIOTOPE&require_exact_match=true&q=
example Identifier	http://purl.obolibrary.org/obo/OBT_001929
copyright Holder	INRA (http://www.inra.fr/)

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Submissions

Submission	Release Date	Upload Date	Downloads
1.2 (Parsed, Indexed, Metrics, Annotator, Error Diff)	07/24/2018	07/24/2018	OBO \| CSV \| RDF/XML
1.2 (Archived)	07/23/2018	07/23/2018	OBO
1.2 (Archived)	06/29/2015	06/12/2016	OBO
BioNLP-ST 2013 version (Archived)	06/29/2015	06/29/2015	OBO

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Project	Description	People	Institution
Bacteria Biotope shared task	The BB Task is an information extraction task involving entity... The BB Task is an information extraction task involving entity recognition, entity normalization and relation extraction. The BB Task consists in recognizing mentions of microorganisms and microbial biotopes and phenotypes in scientific and textbook text, normalizing these mentions according to domain knowledge resources (a taxonomy and an ontology), and extracting relations between them.	Claire Nédellec Claire Nédellec	INRA
Florilege	Florilege web application compiles the information about... Florilege web application compiles the information about microbes computed by advanced text-mining of the scientific literature and information from Biological Resource Centers. Florilege uses OntoBiotope to index textual mentions of microbes habitats and phenotypes. Information retrieval is supported by a powerful semantic search engine that enables ontology-based query.	Claire Nédellec Claire Nédellec	INRA
LOVInra : Linked Open Vocabularies	LOVInra est un service proposé par la Délégation à... LOVInra est un service proposé par la Délégation à l’Information Scientifique et Technique. Il s’adresse aux agents INRA qui souhaitent faire connaître des vocabulaires produits dans le cadre de leurs activités.	Sophie Aubin (sophie.aubin@versailles.inra.fr) Sophie Aubin (sophie.aubin@versailles.inra.fr)	INRA
OntoBiotope	L'ambition pour OntoBiotope est de normaliser la description... L'ambition pour OntoBiotope est de normaliser la description des habitats microbiens au travers d'une ontologie (également appelée OntoBiotope).	Claire Nedellec (claire.nedellec@jouy.inra.fr) Claire Nedellec (claire.nedellec@jouy.inra.fr)	INRA
VEST-AgroPortal Map of Standards	This VEST-AgroPortal provides a global map of existing... This VEST-AgroPortal provides a global map of existing vocabularies for the exchange of data in the field of food and agriculture. The directory is the result of the merging of records from two different sources: the VEST Registry (a registry of vocabularies of all types and all formats) and the AgroPortal (a repository of ontologies).	Valeria Pesce (valeria.pesce@fao.org) Valeria Pesce (valeria.pesce@fao.org)	Food & Agriculture Organization