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Single-Nucleotide Polymorphism (SNP) Ontology

Last uploaded: March 14, 2017
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Acronym SNPO
Visibility Public
Description SNP-Ontology is a domain ontology that provides a formal representation (OWL-DL) of genomic variations. Despite its name, SNP-Ontology, is not limited to the representation of SNPs but it encompasses genomic variations in a broader meaning. SNP-Ontology is general enough to enable the representation of variations observed in genome of various species. Latest versions of SNP-Ontology include the representation of haplotype and of CNV. The unambiguous representation of genomic variations provided by SNP-Ontology enables to integrate heterogeneous data related to genomic variations. To achieve this goal SNP-Ontology enables (1) to represent one variation in accordance with various ways that exist for describing it, (2) to represent the equivalence between two distinct descriptions of one variation, and (3) to represent correspondence between a genomic variation and its outcome at the transcriptome and proteome levels.
Status Beta
Format OWL
Contact Adrien Coulet, adrien.coulet@loria.fr
Groups Rice Data Interoperability working group
Additional Metadata
URIhttp://www.loria.fr/~coulet/ontology/snpontology/version1.6/snpontology_full.owl
deprecatedfalse
endpoint
example Identifierhttp://www.loria.fr/~coulet/ontology/snpontology/version1.6/snpontology_full.owl#haplotype
ContributorsMalika Smaïl-Tabbone, Pascale Benlian, Amedeo Napoli, Marie-Dominique Devignes
CreatorsAdrien Coulet
has Formality Levelhttp://w3id.org/nkos/nkostype#ontology
has Formathttps://members.loria.fr/ACoulet/files/ontology/snpontology/versionObo/061009_snpontology_lite.obo
Ontology Syntaxhttp://www.w3.org/ns/formats/RDF_XML
has Prior VersionSNPO/submissions/2
identifierhttp://www.loria.fr/~coulet/ontology/snpontology/version1.6/snpontology_full.owl
is Aligned Tohttp://agroportal.lirmm.fr/ontologies/SO
is Of Typehttp://omv.ontoware.org/2005/05/ontology#ApplicationOntology
Natural Language
notesConsistency checked by Pellet 2.0, version: full 1.6release: 02/03/2017, A domain representation of genomic variations.
preferred Namespace Urihttp://www.loria.fr/~coulet/ontology/snpontology/version1.6/snpontology_full.owl#
publisherLORIA (www.loria.fr/)
Release date2006-08-01T00:00:00+00:00
URI Lookup Endpointhttp://data.agroportal.lirmm.fr/search??ontologies=SNPO&require_exact_match=true&q=
use Importshttp://purl.org/obo/owl/SO, http://www.co-ode.org/ontologies/amino-acid/2005/10/11/amino-acid.owl
version1.6
Submissions
Version Released Uploaded Downloads
1.6 (Parsed, Indexed, Metrics, Annotator) 08/01/2006 03/14/2017 OWL | CSV | RDF/XML
TODO: Take into account alternative splicing. (Archived) 03/02/2017 03/02/2017 OWL
unknown (Archived) 01/15/2009 06/23/2015 OWL
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Metrics
Classes 90
Individuals 0
Properties 74
Maximum depth 3
Maximum number of children 24
Average number of children 4
Classes with a single child 3
Classes with more than 25 children 0
Classes with no definition 32
Visits
includedInDataCatalog
BioPortalVEST RegistryAberOWL
Projects using SNPO

Agrisemantics Map of Data Standards

RDA Wheat Interoperability Working Group

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