standards > model/format > bsg-s001588


ready Proteomics Standards Initiative Extended Fasta Format

Abbreviation: PEFF


General Information
The PSI Extended Fasta Format (PEFF) is a unified format for protein and nucleotide sequence databases to be used by sequence search engines and other associated tools (spectra library search tools, sequence alignment software, data repositories, etc). This format enables consistent extraction, display and processing of information such as protein/nucleotide sequence database entry identifier, description, taxonomy, etc. across software platforms. It also allows the representation of structural annotations such as post-translational modifications, mutations and other processing events. The proposed format has the form of a plain text file that extends the formalism of the individual sequence entries as presented in the FASTA format and that includes a header of meta data to describe relevant information about the database(s) from which the sequences have been obtained.

Homepage http://psidev.info/peff

Countries that developed this resource Worldwide

Created in 2019

Taxonomic range




Awaiting DOI assignment.

Publication for citation  Proteomics Standards Initiative Extended FASTA Format. Binz PA,Shofstahl J,Vizcaino JA,Barsnes H,Chalkley RJ,Menschaert G,Alpi E,Clauser K,Eng JK,Lane L,Seymour SL,Sanchez LFH,Mayer G,Eisenacher M,Perez-Riverol Y,Kapp EA,Mendoza L,Baker PR,Collins A,Van Den Bossche T,Deutsch EW; J Proteome Res ; 2019; 10.1021/acs.jproteome.9b00064;


Record added: Jan. 31, 2021, 8:37 p.m.
Record updated: Jan. 31, 2021, 8:37 p.m. by The FAIRsharing Team.





Support

General

Additional Information


Tools

Schemas

No XSD schemas defined


Access / Retrieve Data

Conditions of Use

Applies to: Data use

Data Release

Data Access




Publications

Proteomics Standards Initiative Extended FASTA Format.

Binz PA,Shofstahl J,Vizcaino JA,Barsnes H,Chalkley RJ,Menschaert G,Alpi E,Clauser K,Eng JK,Lane L,Seymour SL,Sanchez LFH,Mayer G,Eisenacher M,Perez-Riverol Y,Kapp EA,Mendoza L,Baker PR,Collins A,Van Den Bossche T,Deutsch EW
J Proteome Res 2019

View Paper (PubMed) View Publication

Related Standards

Reporting Guidelines

No guidelines defined

Terminology Artifacts

No semantic standards defined

Models and Formats

Identifier Schemas

No identifier schema standards defined

Metrics

No metrics standards defined


Related Databases (2)
neXtProt
neXtProt is a comprehensive human-centric discovery platform, offering its users a seamless integration of and navigation through protein-related data.

UniProt Knowledgebase
The UniProt Knowledgebase (UniProtKB) is the central hub for the collection of functional information on proteins, with accurate, consistent and rich annotation. In addition to capturing the core data mandatory for each UniProtKB entry (mainly, the amino acid sequence, protein name or description, taxonomic data and citation information), as much annotation information as possible is added. This includes widely accepted biological ontologies, classifications and cross-references, and clear indications of the quality of annotation in the form of evidence attribution of experimental and computational data. The UniProt Knowledgebase consists of two sections: a reviewed section containing manually-annotated records with information extracted from literature and curator-evaluated computational analysis (aka "UniProtKB/Swiss-Prot"), and an unreviewed section with computationally analyzed records that await full manual annotation (aka "UniProtKB/TrEMBL").

Implementing Policies

This record is not implemented by any policy.


Credit

Record Maintainer

  • This record is in need of a maintainer. If you login, you'll be able to claim this record.

Maintains