Registry Rice Genome Annotation Project

The objective of this project is to provide high quality annotation for the rice genome Oryza sativa spp japonica cv Nipponbare. All genes are annotated with functional annotation including expression data, gene ontologies, and tagged lines.

Prefix: ricegap
Alternative Prefixes: rgap
Keywords: chromosome deoxyribonucleic acid dna dna sequence genome life science
Links: Homepage
Publications: 2024 The rice genome annotation project: an updated database for mining the rice genome; 2006 The TIGR Rice Genome Annotation Resource: improvements and new features

Identifier Standards

Pattern for Local Unique Identifiers: Local unique identifiers in Rice Genome Annotation Project should match this regular expression:
^LOC\_Os\d{1,2}g\d{5}$
Example Local Unique Identifier: LOC_Os02g13300 Resolve
Pattern for CURIES: Compact URIs (CURIEs) constructed from Rice Genome Annotation Project should match this regular expression:
^ricegap:LOC\_Os\d{1,2}g\d{5}$
Example CURIE: ricegap:LOC_Os02g13300

Contacts

Contact: C. Robin Buell 0000-0002-6727-4677

Mappings to External Registries

Mappings from records in Semantic Farm to external registries comprises the metaregistry. This resource has 5 mappings to external registries with 3 unique external prefixes.

Registry Name	Registry Metaprefix	External Prefix
BioContext	`biocontext`	`RICEGAP`
FAIRSharing	`fairsharing`	`FAIRsharing.qrw6b7`
Identifiers.org	`miriam`	`ricegap`
N2T	`n2t`	`ricegap`
Prefix Commons	`prefixcommons`	`rgap`

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 LOC_Os02g13300 is used to demonstrate the providers available for Rice Genome Annotation Project. 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
Rice Genome Annotation Project	`ricegap`	http://rice.plantbiology.msu.edu/cgi-bin/ORF_infopage.cgi?&orf=LOC_Os02g13300
Bioregistry	`bioregistry`	https://bioregistry.io/ricegap:LOC_Os02g13300
Identifiers.org	`miriam`	https://identifiers.org/ricegap:LOC_Os02g13300
Name-to-Thing	`n2t`	https://n2t.net/ricegap:LOC_Os02g13300

Extra Providers

Additional providers curated in the Semantic Farm are listed here. These are typically inherited from Identifiers.org or Prefix Commons, and need extra curation.

Provider Name	Provider Code	URL
Bio2RDF	`bio2rdf`	http://bio2rdf.org/rgap:LOC_Os02g13300

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

>>> import bioregistry as br
>>> br.normalize_prefix("rgap")
'ricegap'

Get all synonyms:

>>> import bioregistry as br
>>> br.get_synonyms("ricegap")
{'rgap'}

This name annotation was originally annotated in Identifiers.org and is redistributed under the CC BY 4.0 license.

Get the name:

>>> import bioregistry as br
>>> br.get_name("ricegap")
'Rice Genome Annotation Project'

Get the homepage:

>>> import bioregistry as br
>>> br.get_homepage("ricegap")
'https://rice.uga.edu'

Get the contact's name:

>>> import bioregistry as br
>>> br.get_contact_name("ricegap")
'C. Robin Buell'

Get the contact's email:

>>> import bioregistry as br
>>> br.get_contact_email("ricegap")
'Robin.Buell@uga.edu'

Get the contact's ORCiD identifier:

>>> import bioregistry as br
>>> br.get_contact_orcid("ricegap")
'0000-0002-6727-4677'