MatrixDB: Extracellular Matrix Interaction Database

Abbreviation:MatrixDB

Recommended

General Information

MatrixDB stores experimental data established by full-length proteins, matricryptins, glycosaminoglycans, lipids and cations. MatrixDB reports interactions with individual polypeptide chains or with multimers (e.g. collagens, laminins, thrombospondins) when appropriate. Multimers are treated as permanent complexes, referencing EBI identifiers when possible. Human interactions were inferred from non-human homologous interactions when available.

Homepage http://matrixdb.univ-lyon1.fr

Countries that developed this resource France

Created in 2008

Taxonomic range

Homo sapiens

Knowledge Domains

Subjects

In the following recommendations:

How to cite this record FAIRsharing.org: MatrixDB; MatrixDB: Extracellular Matrix Interaction Database; DOI: https://doi.org/10.25504/FAIRsharing.91yrz6; Last edited: July 2, 2019, 1:27 p.m.; Last accessed: Oct 15 2019 2:42 a.m.

Publication for citation MatrixDB: integration of new data with a focus on glycosaminoglycan interactions. Clerc O,Deniaud M,Vallet SD,Naba A,Rivet A,Perez S,Thierry-Mieg N,Ricard-Blum S; Nucleic Acids Res ; 2018; 10.1093/nar/gky1035;

Record updated: July 2, 2019, 1:27 p.m. by The FAIRsharing Team.

Show edit history

Edits to 'https://fairsharing.org/FAIRsharing.91yrz6' by 'The FAIRsharing Team' at 13:27, 02 Jul 2019 (approved):

	'organizations' has been modified:
		Before:
			Institut de Biologie et Chimie des Proteines (IBCP), Centre National de la Recherche Scientifique, Lyon, France|http://www.ibcp.fr/,lang=fr|Maintains
			Laboratoire de Microbiologie et Genetique Moleculaires (LMGM), Toulouse, France|https://www-lmgm.biotoul.fr|Maintains
		After:
			Fondation pour la Recherche Mdicale, Paris,  France|https://www.frm.org/en|Funds
			Institut de Chimie et Biochimie Molculaires et Supramolculaires (ICBMS),  Lyon, France|http://www.icbms.fr/|Maintains
			Institut Franais de Bioinformatique (IFB, French Institute of Bioinformatics), France|https://www.france-bioinformatique.fr/|Funds
			Fondation pour la Recherche Mdicale|https://www.frm.org/en|Funds
		Added:
			Fondation pour la Recherche Mdicale, Paris,  France|https://www.frm.org/en|Funds
			Institut de Chimie et Biochimie Molculaires et Supramolculaires (ICBMS),  Lyon, France|http://www.icbms.fr/|Maintains
			Institut Franais de Bioinformatique (IFB, French Institute of Bioinformatics), France|https://www.france-bioinformatique.fr/|Funds
			Fondation pour la Recherche Mdicale|https://www.frm.org/en|Funds
		Removed:
			Institut de Biologie et Chimie des Proteines (IBCP), Centre National de la Recherche Scientifique, Lyon, France|http://www.ibcp.fr/,lang=fr|Maintains
			Laboratoire de Microbiologie et Genetique Moleculaires (LMGM), Toulouse, France|https://www-lmgm.biotoul.fr|Maintains

	'standardsImplemented' has been modified:
		Before:
			Gene Ontology
			Molecular Interaction Tabular
			Minimum Information about a Molecular Interaction Experiment
			Chemical Entities of Biological Interest
			Molecular Interaction eXtensible Markup Language
		After:
			Chemical Entities of Biological Interest
			Gene Ontology
			Molecular Interaction Tabular
			Molecular Interaction eXtensible Markup Language
			Minimum Information about a Molecular Interaction Experiment
			PSI Molecular Interaction Controlled Vocabulary
		Added:
			PSI Molecular Interaction Controlled Vocabulary
		Removed:

	'supportLinks' has been modified:
		Before:
			training|https://www.youtube.com/watch?list=PLw61Ua8TujDRLFSZMZChqmqX7yFBYLaz0&v=BCHp12lefK4
		After:
			help|http://matrixdb.univ-lyon1.fr/data/Tutorial_MatrixDB_v3.pdf
			training|https://www.youtube.com/watch?list=PLw61Ua8TujDRLFSZMZChqmqX7yFBYLaz0&v=BCHp12lefK4
		Added:
			help|http://matrixdb.univ-lyon1.fr/data/Tutorial_MatrixDB_v3.pdf
		Removed:

	'name' has been modified:
		Before: MatrixDB: Extracellular Matrix interactions database
		After: MatrixDB: Extracellular Matrix Interaction Database

	'onto_disciplines' has been modified:
		Before:
			Life Sciences
		After:
			Biology
			Life Sciences
		Added:
			Biology
		Removed:

	'grants' has been modified:
		Before:
		After:
			DBI20141231336
		Added:
			DBI20141231336
		Removed:

	'publications' has been modified:
		Before:
			MatrixDB, a database focused on extracellular protein-protein and protein-carbohydrate interactions.|Chautard E., Ballut L., Thierry-Mieg N., Ricard-Blum S., |Bioinformatics|2009
			MatrixDB, the extracellular matrix interaction database: updated content, a new navigator and expanded functionalities.|Launay G,Salza R,Multedo D,Thierry-Mieg N,Ricard-Blum S|Nucleic Acids Res|2014
			MatrixDB, the extracellular matrix interaction database.|Chautard E,Fatoux-Ardore M,Ballut L,Thierry-Mieg N,Ricard-Blum S|Nucleic Acids Res|2010
		After:
			MatrixDB, a database focused on extracellular protein-protein and protein-carbohydrate interactions.|Chautard E., Ballut L., Thierry-Mieg N., Ricard-Blum S., |Bioinformatics|2009
			MatrixDB, the extracellular matrix interaction database: updated content, a new navigator and expanded functionalities.|Launay G,Salza R,Multedo D,Thierry-Mieg N,Ricard-Blum S|Nucleic Acids Res|2014
			MatrixDB, the extracellular matrix interaction database.|Chautard E,Fatoux-Ardore M,Ballut L,Thierry-Mieg N,Ricard-Blum S|Nucleic Acids Res|2010
			MatrixDB: integration of new data with a focus on glycosaminoglycan interactions.|Clerc O,Deniaud M,Vallet SD,Naba A,Rivet A,Perez S,Thierry-Mieg N,Ricard-Blum S|Nucleic Acids Res|2018
		Added:
			MatrixDB: integration of new data with a focus on glycosaminoglycan interactions.|Clerc O,Deniaud M,Vallet SD,Naba A,Rivet A,Perez S,Thierry-Mieg N,Ricard-Blum S|Nucleic Acids Res|2018
		Removed:

	'description' has been modified:
		Before: MatrixDB is a database reporting mammalian protein-protein and protein-carbohydrate interactions involving extracellular molecules.  Interactions with lipids and cations are also reported.  Full-length molecules, fragments and multimers present in the extracellular matrix are all included in the database.
		After: MatrixDB stores experimental data established by full-length proteins, matricryptins, glycosaminoglycans, lipids and cations.
MatrixDB reports interactions with individual polypeptide chains or with multimers (e.g. collagens, laminins, thrombospondins) when appropriate. Multimers are treated as permanent complexes, referencing EBI identifiers when possible. Human interactions were inferred from non-human homologous interactions when available.

Edits to 'https://fairsharing.org/FAIRsharing.91yrz6' by 'The FAIRsharing Team' at 19:32, 11 Jan 2018 (approved):

	'domains' has been modified:
		Before:
			Life Science|domain|http://www.fairsharing.org/ontology/SRAO_0000069
			Molecular interactions|pathways and networks||http://edamontology.org/topic_0602
			Protein|None|http://purl.obolibrary.org/obo/PR_000000001
			Small molecule|material|http://purl.obolibrary.org/obo/MI_0328
		After:
			Life Science|domain|http://www.fairsharing.org/ontology/SRAO_0000069
			Protein|None|http://purl.obolibrary.org/obo/PR_000000001
			Small molecule|material|http://purl.obolibrary.org/obo/MI_0328
			Protein interactions||http://edamontology.org/topic_0128
			Carbohydrate||http://purl.obolibrary.org/obo/CHEBI_16646
			Molecular interaction|process|http://purl.obolibrary.org/obo/MI_0000
			Lipid|None|http://purl.obolibrary.org/obo/CHEBI_18059
		Added:
			Protein interactions||http://edamontology.org/topic_0128
			Carbohydrate||http://purl.obolibrary.org/obo/CHEBI_16646
			Molecular interaction|process|http://purl.obolibrary.org/obo/MI_0000
			Lipid|None|http://purl.obolibrary.org/obo/CHEBI_18059
		Removed:
			Molecular interactions|pathways and networks||http://edamontology.org/topic_0602

In Collections

International Molecular Exchange Consortium (IMEx)

Support

General

help	Tutorial
training	Help Video

Additional Information

Contact	Sylvie Ricard-Blum
Identifiers.org	MIR:00000068

Tools

No tools defined

Access / Retrieve Data

Conditions of Use

Applies to: Data use

Publicly available data

Data Access

Advanced Search

http://matrixdb.univ-lyon1.fr/queries.html

Publications

MatrixDB, a database focused on extracellular protein-protein and protein-carbohydrate interactions.

Chautard E., Ballut L., Thierry-Mieg N., Ricard-Blum S.,
Bioinformatics 2009

View Paper (PubMed) View Publication

MatrixDB, the extracellular matrix interaction database: updated content, a new navigator and expanded functionalities.

Launay G,Salza R,Multedo D,Thierry-Mieg N,Ricard-Blum S
Nucleic Acids Res 2014

View Paper (PubMed) View Publication

MatrixDB, the extracellular matrix interaction database.

Chautard E,Fatoux-Ardore M,Ballut L,Thierry-Mieg N,Ricard-Blum S
Nucleic Acids Res 2010

View Paper (PubMed) View Publication

MatrixDB: integration of new data with a focus on glycosaminoglycan interactions.

Clerc O,Deniaud M,Vallet SD,Naba A,Rivet A,Perez S,Thierry-Mieg N,Ricard-Blum S
Nucleic Acids Res 2018

View Paper (PubMed) View Publication

Related Standards

Reporting Guidelines

Minimum Information about a Molecular Interaction Experiment

Terminology Artifacts

Models and Formats

Identifier Schemas

No identifier schema standards defined

Metrics

No metrics standards defined

Related Databases

Implementing Policies

European Molecular Biology Organisation Press Recommended Databases and Data Standards

Credit

Record Maintainer

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Funds

Fondation pour la Recherche Médicale, Paris, France (Charitable foundation)
Institut Français de Bioinformatique (IFB, French Institute of Bioinformatics), France (Research institute)
Fondation pour la Recherche Médicale

Maintains

Institut de Chimie et Biochimie Moléculaires et Supramoléculaires (ICBMS), Lyon, France (Research institute) Lead

Grant Number(s)

DBI20141231336 (Fondation pour la Recherche Médicale)

MatrixDB: Extracellular Matrix Interaction Database

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