Registry Pfam protein family

The Pfam database contains information about protein domains and families. For each entry a protein sequence alignment and a Hidden Markov Model is stored.

Prefix: pfam
Alternative Prefixes: PF
Keywords: biocuration biology classification domain evolution evolutionary relationship between proteins via sequence similarity family and domain databases function analysis functional domain multiple sequence alignment ontology polypeptide region prediction and recognition protein protein binding domain protein domain proteome sequence sequence alignment sequence motif sequence similarity
License: CC0-1.0
Links: Homepage OBO OWL OBO JSON Part of pfam
Publications: 1999 Pfam 3.1: 1313 multiple alignments and profile HMMs match the majority of proteins; 1998 Pfam: multiple sequence alignments and HMM-profiles of protein domains; 1997 Pfam: a comprehensive database of protein domain families based on seed alignments; 2024 The Pfam protein families database: embracing AI/ML; 2021 Pfam: The protein families database in 2021; 2019 The Pfam protein families database in 2019; 2015 The Pfam protein families database: towards a more sustainable future; 2013 Pfam: the protein families database; 2011 The Pfam protein families database; 2009 The Pfam protein families database; 2007 The Pfam protein families database; 2006 Pfam: clans, web tools and services; 2004 The Pfam protein families database; 2002 The Pfam protein families database; 2000 The Pfam protein families database
References: Other https://twitter.com/PfamDB/status/1555149527228813314

Identifier Standards

Pattern for Local Unique Identifiers: Local unique identifiers in Pfam protein family should match this regular expression:
^PF\d{5}$
Example Local Unique Identifier: PF11779 Resolve
Pattern for CURIES: Compact URIs (CURIEs) constructed from Pfam protein family should match this regular expression:
^pfam:PF\d{5}$
Example CURIE: pfam:PF11779
Format String for RDF URIs: http://pfam.janelia.org/family/#$1
Example RDF URI: http://pfam.janelia.org/family/#PF11779

Contacts

Contact: Alex Bateman 0000-0002-6982-4660
Identifier Space Owner: European Bioinformatics Institute

Ontology

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

Provided By: pandit
In Collection (1): Synapse.org external links

Mappings to External Registries

Mappings from records in Bioregistry to external registries comprises the metaregistry. This resource has 13 mappings to external registries with 7 unique external prefixes.

Registry Name	Registry Metaprefix	External Prefix
BioContext	`biocontext`	`PFAM`
EDAM	`edam`	`1138`
FAIRSharing	`fairsharing`	`FAIRsharing.y3scf6`
GO	`go`	`Pfam`
Integbio	`integbio`	`nbdc00163`
Identifiers.org	`miriam`	`pfam`
N2T	`n2t`	`pfam`
NCBI	`ncbi`	`PFAM`
Prefix Commons	`prefixcommons`	`pfam`
re3data	`re3data`	`r3d100012850`
TogoID	`togoid`	`Pfam`
UniProt	`uniprot`	`DB-0073`
Wikidata	`wikidata`	`P3519`

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 PF11779 is used to demonstrate the providers available for Pfam protein family. 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
Pfam protein family	`pfam`	https://www.ebi.ac.uk/interpro/entry/pfam/PF11779
Pfam protein family (RDF)	`rdf`	http://pfam.janelia.org/family/#PF11779
Bioregistry	`bioregistry`	https://bioregistry.io/pfam:PF11779
Identifiers.org	`miriam`	https://identifiers.org/pfam:PF11779
Name-to-Thing	`n2t`	https://n2t.net/pfam:PF11779

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
Bio2RDF	`bio2rdf`	http://bio2rdf.org/pfam:PF11779
Sanger Pfam Mirror	`sanger`	http://pfam.sanger.ac.uk/family?entry=PF11779
Xfam	`xfam`	https://pfam.xfam.org/family?acc=PF11779

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

>>> import bioregistry as br
>>> br.normalize_prefix("PF")
'pfam'

Get all synonyms:

>>> import bioregistry as br
>>> br.get_synonyms("pfam")
{'PF'}

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("pfam")
'Pfam protein family'

Get the license:

>>> import bioregistry as br
>>> br.get_license("pfam")
'CC0-1.0'

Get the homepage:

>>> import bioregistry as br
>>> br.get_homepage("pfam")
'https://www.ebi.ac.uk/interpro/'

Get the OBO download link:

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

Get the OWL download link:

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

Get the JSON download link:

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

Get the contact's name:

>>> import bioregistry as br
>>> br.get_contact_name("pfam")
'Alex Bateman'

Get the contact's email:

>>> import bioregistry as br
>>> br.get_contact_email("pfam")
'agb@ebi.ac.uk'

Get the contact's ORCiD identifier:

>>> import bioregistry as br
>>> br.get_contact_orcid("pfam")
'0000-0002-6982-4660'