PRIDE XML Format

General Information

XML submission format for the PRIDE repository at the EBI.

Homepage http://www.ebi.ac.uk/pride/help/archive/submission/pridexml

Countries that developed this resource European Union , United Kingdom

Taxonomic range

All

Knowledge Domains

Subjects

How to cite this record FAIRsharing.org: PRIDE XML Format; PRIDE XML Format; DOI: https://doi.org/10.25504/FAIRsharing.975659; Last edited: Feb. 13, 2019, 11:02 a.m.; Last accessed: Oct 16 2019 1:32 p.m.

This record is maintained by javizca ORCID

Record updated: Feb. 13, 2019, 11:02 a.m. by The FAIRsharing Team.

Show edit history

Edits to 'https://fairsharing.org/FAIRsharing.975659' by 'The FAIRsharing Team' at 11:02, 13 Feb 2019 (approved):

	'related_standards' has been modified:
		Before:
			Gel electrophoresis Markup Language
			Extensible Markup Language
			Protein MODification
			Gene Ontology
			BRENDA tissue / enzyme source
		After:
			Gel electrophoresis Markup Language
			Extensible Markup Language
			Protein MODification
			Gene Ontology
			BRENDA tissue / enzyme source
			HUPO PSI Mass Spectrometry Controlled Vocabulary
		Added:
			HUPO PSI Mass Spectrometry Controlled Vocabulary
		Removed:

Edits to 'https://fairsharing.org/FAIRsharing.975659' by 'The FAIRsharing Team' at 10:37, 17 Jan 2019 (approved):

	'dataProcesses' has been modified:
		Before:
			PRIDE-Converter2
			PICR
		After:
		Added:
		Removed:
			PRIDE-Converter2
			PICR

Edits to 'https://fairsharing.org/FAIRsharing.975659' by 'The FAIRsharing Team' at 10:36, 17 Jan 2019 (approved):

	'organizations' has been modified:
		Before:
			Biotechnology and Biological Sciences Research Council (BBSRC), UK|https://bbsrc.ukri.org|Funds
			Engineering and Physical Sciences Research Council (EPSRC), UK|https://www.epsrc.ac.uk|Funds
			Swiss Institute of Bioinformatics (SIB), Switzerland|https://www.sib.swiss|Maintains
			The Wellcome Trust, UK|https://wellcome.ac.uk/|Funds
		After:
			Biotechnology and Biological Sciences Research Council (BBSRC), UK|https://bbsrc.ukri.org|Funds
			Engineering and Physical Sciences Research Council (EPSRC), UK|https://www.epsrc.ac.uk|Funds
			The Wellcome Trust, UK|https://wellcome.ac.uk/|Funds
			European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, UK|https://www.ebi.ac.uk/|Maintains
		Added:
			European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, UK|https://www.ebi.ac.uk/|Maintains
		Removed:
			Swiss Institute of Bioinformatics (SIB), Switzerland|https://www.sib.swiss|Maintains

	'related_standards' has been modified:
		Before:
			Gel electrophoresis Markup Language
			Extensible Markup Language
		After:
			Gel electrophoresis Markup Language
			Extensible Markup Language
			Mass Spectrometry Ontology
			Protein MODification
			Gene Ontology
			BRENDA tissue / enzyme source
		Added:
			Mass Spectrometry Ontology
			Protein MODification
			Gene Ontology
			BRENDA tissue / enzyme source
		Removed:

	'supportLinks' has been modified:
		Before:
			help|http://www.ebi.ac.uk/pride/help/archive/submission/pridexml
		After:
		Added:
		Removed:
			help|http://www.ebi.ac.uk/pride/help/archive/submission/pridexml

Edits to 'https://fairsharing.org/FAIRsharing.975659' by 'The FAIRsharing Team' at 10:19, 15 Mar 2018 (approved):

	'miriam_url' has been modified:
		Before: None
		After:

Edits to 'https://fairsharing.org/FAIRsharing.975659' by 'The FAIRsharing Team' at 10:40, 20 Dec 2016 (approved):

	'shortname' has been modified:
		Before: PRIDE XML Format
		After:

In Collections

bioCADDIE

Support

No support information provided.

Additional Information

Contact

Henning Hermjakob ORCID

Tools

PRIDE Inspector	https://github.com/PRIDE-Toolsuite/pride-inspector
PRIDE Converter 2	https://github.com/PRIDE-Toolsuite/pride-converter-2

Schemas

Name: PrideML
Version: 2.1

Download

Access / Retrieve Data

Conditions of Use

Publications

2016 update of the PRIDE database and its related tools.

Vizcaino JA,Csordas A,del-Toro N,Dianes JA,Griss J,Lavidas I,Mayer G,Perez-Riverol Y,Reisinger F,Ternent T,Xu QW,Wang R,Hermjakob H
Nucleic Acids Res 2015

View Paper (PubMed) View Publication

ProteomeXchange provides globally coordinated proteomics data submission and dissemination.

Vizcaino JA,Deutsch EW,Wang R,Csordas A,Reisinger F,Rios D,Dianes JA,Sun Z,Farrah T,Bandeira N,Binz PA,Xenarios I,Eisenacher M,Mayer G,Gatto L,Campos A,Chalkley RJ,Kraus HJ,Albar JP,Martinez-Bartolome S,Apweiler R,Omenn GS,Martens L,Jones AR,Hermjakob H
Nat Biotechnol 2014

View Paper (PubMed) View Publication

How to submit MS proteomics data to ProteomeXchange via the PRIDE database.

Ternent T,Csordas A,Qi D,Gomez-Baena G,Beynon RJ,Jones AR,Hermjakob H,Vizcaino JA
Proteomics 2014

View Paper (PubMed) View Publication

Related Standards

Reporting Guidelines

No guidelines defined

Terminology Artifacts

Models and Formats

Identifier Schemas

No identifier schema standards defined

Metrics

No metrics standards defined

Implementing Databases (3)

PRoteomics IDEntifications database
The PRIDE PRoteomics IDEntifications database is a centralized, standards compliant, public data repository that provides protein and peptide identifications together with supporting evidence.

ProteomeXchange
The ProteomeXchange consortium has been set up to provide a single point of submission of MS proteomics data to the main existing proteomics repositories, and to encourage the data exchange between them for optimal data dissemination.

iProX
iProX is a public platform for collecting and sharing raw data, analysis results and metadata obtained from proteomics experiments. The iProX repository employs a web-based proteome data submission process and open sharing of mass spectrometry-based proteomics datasets. iProX is a member of the ProteomeXchange (PX) consortium.

Implementing Policies

This record is not implemented by any policy.

Credit

Record Maintainer

This record is maintained by javizca ORCID

Funds

Biotechnology and Biological Sciences Research Council (BBSRC), UK (Government body)
Engineering and Physical Sciences Research Council (EPSRC), UK (Government body)
The Wellcome Trust, UK (Charitable foundation)

Maintains

European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, UK (Research institute) Lead

Grant Number(s)

BB/I00095X/1 (Biotechnology and Biological Sciences Research Council (BBSRC), UK)
BB/K01997X/1 (Biotechnology and Biological Sciences Research Council (BBSRC), UK)
BB/L024225/1 (Biotechnology and Biological Sciences Research Council (BBSRC), UK)
WT101477MA (The Wellcome Trust, UK)

PRIDE XML Format

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