standards > model/format > DOI:10.25504/FAIRsharing.78Lz1O


ready ProForma


General Information
Developed by the Consortium for Top-Down Proteomics, ProForma is a standardized notation for writing fully characterized proteoforms. A proteoform is a specific set of amino acids arranged in a particular order, which may be further modified (cotranslationally, posttranslationally or chemically) at designated locations. This nomenclature is intended to be both machine and human readable, and to be sufficiently flexible to meet current and foreseeable needs.



How to cite this record FAIRsharing.org: ProForma; ProForma; DOI: https://doi.org/10.25504/FAIRsharing.78Lz1O; Last edited: Oct. 29, 2018, 1:24 p.m.; Last accessed: Nov 17 2018 9:55 p.m.


This record is maintained by richard.leduc@northwestern.edu

Record added: May 28, 2018, 4:19 p.m.
Record updated: June 4, 2018, 12:45 p.m. by The FAIRsharing Team.

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Support

General

Additional Information


Tools

    No tools defined


Schemas

No XSD schemas defined


Access / Retrieve Data

Conditions of Use





Publications

ProForma: A Standard Proteoform Notation.

LeDuc RD,Schwammle V,Shortreed MR,Cesnik AJ,Solntsev SK,Shaw JB,Martin MJ,Vizcaino JA,Alpi E,Danis P,Kelleher NL,Smith LM,Ge Y,Agar JN,Chamot-Rooke J,Loo JA,Pasa-Tolic L,Tsybin YO
J Proteome Res 2018

View Paper (PubMed) View Publication

Related Standards

Reporting Guidelines

No guidelines defined

Models and Formats

No syntax standards defined

Identifier Schemas

No identifier schema standards defined


Implementing Databases (3)
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").

RESID Database of Protein Modifications
The RESID Database of Protein Modifications is a comprehensive collection of annotations and structures for protein modifications including amino-terminal, carboxyl-terminal and peptide chain cross-link post-translational modifications.

UniCarbKB
UniCarbKB is an initiative that aims to promote the creation of an online information storage and search platform for glycomics and glycobiology research. The knowledgebase will offer a freely accessible and information-rich resource supported by querying interfaces, annotation technologies and the adoption of common standards to integrate structural, experimental and functional data.

Implementing Policies

This record is not implemented by any policy.