Registry Ontology for MicroRNA Target

The purpose of the OMIT ontology is to establish data exchange standards and common data elements in the microRNA (miR) domain. Biologists (cell biologists in particular) and bioinformaticians can make use of OMIT to leverage emerging semantic technologies in knowledge acquisition and discovery for more effective identification of important roles performed by miRs in humans' various diseases and biological processes (usually through miRs' respective target genes).

Prefix: omit
Preferred Prefix: OMIT
Alternative Prefixes: OMIT
Keywords: annotation biology cell gene gene prediction life science mirna molecular entity molecular interaction obo ontology prediction and recognition protein regulation of gene expression
Version: dev
License: CC-BY-3.0
Links: Homepage Repository OBO OWL
Publications: 2016 OmniSearch: a semantic search system based on the Ontology for MIcroRNA Target (OMIT) for microRNA-target gene interaction data; 2014 OMIT: dynamic, semi-automated ontology development for the microRNA domain; 2011 OMIT: a domain-specific knowledge base for microRNA target prediction

Identifier Standards

Pattern for Local Unique Identifiers: Local identifiers in Ontology for MicroRNA Target should match this regular expression:
^\d{7}$
Example Local Unique Identifier: 0000069 Resolve
Pattern for CURIES: Compact URIs (CURIEs) constructed from Ontology for MicroRNA Target should match this regular expression:
^OMIT:\d{7}$
Example CURIE: OMIT:0000069
Pattern for RDF URIs: http://purl.obolibrary.org/obo/OMIT_$1
Example RDF URI: http://purl.obolibrary.org/obo/OMIT_0000069

Contacts

Contact: Jingshan Huang 0000-0003-2408-2883 Huang-OMIT
Identifier Space Owner: European Bioinformatics Institute

Ontology

A summary of the relations in the Bioregistry schema can be found here.

Appears In (1): MCO

Mappings to External Registries

Mappings from records in Bioregistry to external registries comprises the metaregistry. This resource has 10 mappings to external registries with 3 unique external prefixes.

Registry Name	Registry Metaprefix	External Prefix
AberOWL	`aberowl`	`OMIT`
BioContext	`biocontext`	`OMIT`
BioPortal	`bioportal`	`OMIT`
FAIRSharing	`fairsharing`	`FAIRsharing.mf91p5`
Identifiers.org	`miriam`	`omit`
N2T	`n2t`	`omit`
OBO Foundry	`obofoundry`	`omit`
OLS	`ols`	`omit`
OntoBee	`ontobee`	`OMIT`
Wikidata (E)	`wikidata.entity`	`Q81661752`

Providers

Suggest

A provider turns a local unique identifiers from a resource into a URI. Many providers are also resolvable as URLs (i.e., they can be used in a web browser).

The local unique identifier 0000069 is used to demonstrate the providers available for Ontology for MicroRNA Target. Some providers may use a different example, which is displayed in the table below. A guide for curating additional providers can be found here.

Provider Name	Provider Code	URI
Ontology for MicroRNA Target	`omit`	http://purl.obolibrary.org/obo/OMIT_0000069
Ontology for MicroRNA Target (RDF)	`rdf`	http://purl.obolibrary.org/obo/OMIT_0000069
Bioregistry	`bioregistry`	https://bioregistry.io/omit:0000069
Identifiers.org	`miriam`	https://identifiers.org/omit:0000069
OBO Foundry	`obofoundry`	http://purl.obolibrary.org/obo/OMIT_0000069
EBI Ontology Lookup Service	`ols`	https://www.ebi.ac.uk/ols4/ontologies/omit/terms?iri=http://purl.obolibrary.org/obo/OMIT_0000069
Name-to-Thing	`n2t`	https://n2t.net/omit:0000069
BioPortal Prefixes	`bioportal`	https://bioportal.bioontology.org/ontologies/OMIT/?p=classes&conceptid=http://purl.obolibrary.org/obo/OMIT_0000069

Normalize prefixes. This can be any capitalization or punctuation variant of the synonyms listed below.

>>> import bioregistry as br
>>> br.normalize_prefix("OMIT")
'omit'

Get all synonyms:

>>> import bioregistry as br
>>> br.get_synonyms("omit")
{'OMIT'}

Get the version:

>>> import bioregistry as br
>>> br.get_version("omit")
'dev'

This name annotation was originally annotated in Bioregistry and is redistributed under the CC0 license.

Get the name:

>>> import bioregistry as br
>>> br.get_name("omit")
'Ontology for MicroRNA Target'

Get the license:

>>> import bioregistry as br
>>> br.get_license("omit")
'CC-BY-3.0'

Get the homepage:

>>> import bioregistry as br
>>> br.get_homepage("omit")
'http://omit.cis.usouthal.edu/'

Get the repository:

>>> import bioregistry as br
>>> br.get_repository("omit")
'https://github.com/OmniSearch/omit'

Get the OBO download link:

>>> import bioregistry as br
>>> br.get_obo_download("omit")
'https://raw.githubusercontent.com/OmniSearch/omit/master/src/ontology/omit.obo'

Get the OWL download link:

>>> import bioregistry as br
>>> br.get_owl_download("omit")
'http://purl.obolibrary.org/obo/omit.owl'

Get the contact's name:

>>> import bioregistry as br
>>> br.get_contact_name("omit")
'Jingshan Huang'

Get the contact's email:

>>> import bioregistry as br
>>> br.get_contact_email("omit")
'huang@southalabama.edu'

Get the contact's GitHub handle:

>>> import bioregistry as br
>>> br.get_contact_github("omit")
'Huang-OMIT'

Get the contact's ORCiD identifier:

>>> import bioregistry as br
>>> br.get_contact_orcid("omit")
'0000-0003-2408-2883'