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| Number of classes: | 3602 |
|---|---|
| Number of individuals: | 0 |
| Number of properties: | 0 |
| Maximum depth: | 13 |
| Maximum number of children: | 35 |
| Average number of children: | 3 |
| Classes with a single child: | 423 |
| Classes with more than 25 children: | 4 |
| Classes with no definition: | 3602 |
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Details
| 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. OntoBiotope is developed and maintained by the Bibliome group of MaIAGE lab and microbiologists from INRA (French National Institute for Agricultural Research) 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. |
| Status | Production |
| Format | OBO |
| Contact | Claire Nédellec, claire.nedellec@inra.fr |
| Home Page | http://lovinra.inra.fr/ |
| Publications Page | arXiv:1805.04107v2 |
| 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 | BioNLP-OST-2019 |
| Release date | 2019-03-19T00:00:00+00:00 |
| 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 |
| used Ontology Engineering Tool | http://oboedit.org/ |
| has Prior Version | ONTOBIOTOPE/submissions/4 |
| 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 |
|---|---|---|---|
| BioNLP-OST-2019 (Parsed, Indexed, Metrics, Annotator) | 03/19/2019 | 09/25/2019 | OBO | CSV | RDF/XML |
| 1.2 (Archived) | 07/24/2018 | 07/24/2018 | OBO |
| 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 |
| more... | |||
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Projects Using This Ontology Create new project
| Project | Description | People | Institution |
|---|---|---|---|
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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 |
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