Registry Zebrafish Information Network Gene

ZFIN serves as the zebrafish model organism database. This collection references all zebrafish biological entities in ZFIN.

Prefix: zfin
Alternative Prefixes: ZFIN
Keywords: adult allele animal physiology antibody bibliography/documents bioresource cdna cdna/est developmental biology disease course embryo expressed sequence tag expression expression data fish gene genetic variation genetics genome genome/gene genomics model organisms mutation ontology ontology/terminology/nomenclature organism organism-specific databases pathology phenotype protein repository research sequence zebrafish zebrafish line
License: CC-BY-4.0
Links: Homepage OBO OWL OBO JSON
Publications: https://bioregistry.io/pubmed:9891346; https://bioregistry.io/pubmed:9441953; https://bioregistry.io/pubmed:35166825; 2019 The Zebrafish Information Network: new support for non-coding genes, richer Gene Ontology annotations and the Alliance of Genome Resources; 2012 ZFIN, the Zebrafish Model Organism Database: increased support for mutants and transgenics; 2011 Data extraction, transformation, and dissemination through ZFIN; 2010 ZFIN: enhancements and updates to the Zebrafish Model Organism Database; Exploring zebrafish genomic, functional and phenotypic data using ZFIN; 2010 Exploring zebrafish genomic, functional and phenotypic data using ZFIN; 2007 The Zebrafish Information Network: the zebrafish model organism database provides expanded support for genotypes and phenotypes; 2005 The Zebrafish Information Network: the zebrafish model organism database; 2003 The Zebrafish Information Network (ZFIN): the zebrafish model organism database; https://bioregistry.io/pubmed:11125057; 1999 Zebrafish in the Net

Identifier Standards

Pattern for Local Unique Identifiers: Local unique identifiers in Zebrafish Information Network Gene should match this regular expression:
^ZDB\-\w+\-\d+\-\d+$
Example Local Unique Identifier: ZDB-GENE-041118-11 Resolve
Pattern for CURIES: Compact URIs (CURIEs) constructed from Zebrafish Information Network Gene should match this regular expression:
^zfin:ZDB\-\w+\-\d+\-\d+$
Example CURIE: zfin:ZDB-GENE-041118-11

Contacts

Contact: Doug Howe 0000-0001-5831-7439

Ontology

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

In Collection (2): Global Biodata Coalition - Global Core Biodata Resources Synapse.org external links

Mappings to External Registries

Mappings from records in Bioregistry to external registries comprises the metaregistry. This resource has 12 mappings to external registries with 7 unique external prefixes.

Registry Name	Registry Metaprefix	External Prefix
BioContext	`biocontext`	`ZFIN`
FAIRSharing	`fairsharing`	`FAIRsharing.ybxnhg`
GO	`go`	`ZFIN`
Integbio	`integbio`	`nbdc00746`
Identifiers.org	`miriam`	`zfin`
N2T	`n2t`	`zfin`
NCBI	`ncbi`	`ZFIN`
Prefix Commons	`prefixcommons`	`zfin`
re3data	`re3data`	`r3d100010421`
RRID	`rrid`	`ZIRC`
UniProt	`uniprot`	`DB-0113`
Wikidata	`wikidata`	`P3870`

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 ZDB-GENE-041118-11 is used to demonstrate the providers available for Zebrafish Information Network Gene. 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
Zebrafish Information Network Gene	`zfin`	http://zfin.org/ZDB-GENE-041118-11
Bioregistry	`bioregistry`	https://bioregistry.io/zfin:ZDB-GENE-041118-11
Identifiers.org	`miriam`	https://identifiers.org/zfin:ZDB-GENE-041118-11
Name-to-Thing	`n2t`	https://n2t.net/zfin:ZDB-GENE-041118-11
Research Resource Identifiers	`rrid`	https://scicrunch.org/resolver/RRID:ZIRC_ZDB-GENE-041118-11

Extra Providers

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

Provider Name	Provider Code	URL
ZFIN through the Alliance of Genome Resources	`agr`	https://test.alliancegenome.org/gene/ZFIN:ZDB-GENE-041118-11
Bio2RDF	`bio2rdf`	http://bio2rdf.org/zfin:ZDB-GENE-041118-11

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

>>> import bioregistry as br
>>> br.normalize_prefix("ZFIN")
'zfin'

Get all synonyms:

>>> import bioregistry as br
>>> br.get_synonyms("zfin")
{'ZFIN'}

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("zfin")
'Zebrafish Information Network Gene'

Get the license:

>>> import bioregistry as br
>>> br.get_license("zfin")
'CC-BY-4.0'

Get the homepage:

>>> import bioregistry as br
>>> br.get_homepage("zfin")
'http://zfin.org'

Get the OBO download link:

>>> import bioregistry as br
>>> br.get_obo_download("zfin")
'https://w3id.org/biopragmatics/resources/zfin/zfin.obo'

Get the OWL download link:

>>> import bioregistry as br
>>> br.get_owl_download("zfin")
'https://w3id.org/biopragmatics/resources/zfin/zfin.owl.gz'

Get the JSON download link:

>>> import bioregistry as br
>>> br.get_json_download("zfin")
'https://w3id.org/biopragmatics/resources/zfin/zfin.json.gz'

Get the contact's name:

>>> import bioregistry as br
>>> br.get_contact_name("zfin")
'Doug Howe'

Get the contact's email:

>>> import bioregistry as br
>>> br.get_contact_email("zfin")
'dhowe@zfin.org'

Get the contact's ORCiD identifier:

>>> import bioregistry as br
>>> br.get_contact_orcid("zfin")
'0000-0001-5831-7439'