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Protocols specifications


Unique identifier OMICS_21131
Restrictions to use None
Community driven No
Data access File download, Browse, Application programming interface
User data submission Not allowed
Content license Creative Commons CC4 Attribution
Maintained Yes



  • person_outline Camille Laibe

Publication for citations


Evolution of computational models in BioModels Database and the Physiome Model Repository

BMC Syst Biol
PMCID: 5898004
PMID: 29650016
DOI: 10.1186/s12918-018-0553-2

[…] BML annotation scheme. In June 2006, the introduction of qualified references to external resources [] affected all annotated models. In August 2012, URNs in the annotations were replaced by links to, causing another major update of the database. In June 2017, the BioModels Database team revised the annotations in a majority of their models. For example, they annotated many models […]


Using the Semantic Web for Rapid Integration of WikiPathways with Other Biological Online Data Resources

PLoS Comput Biol
PMCID: 4918977
PMID: 27336457
DOI: 10.1371/journal.pcbi.1004989

[…] /DataNode>In the GPML vocabulary, used for semantic representation of pathway diagrams, the markup elements and values are described as classes and properties, each with their respective> rdf:type gpml:DataNode. rdfs:label “Glucose”@en. gpml:graphId “dba83”.


The systems biology format converter

BMC Bioinformatics
PMCID: 4820913
PMID: 27044654
DOI: 10.1186/s12859-016-1000-2
call_split See protocol

[…] ystem-dependent code. The advantage is that the specific SBFC converters directly rely on the development of the original external converters reducing code duplication.Each format is identified by an URI [] or an internet media type. If none of them exists, the developers of the format and converter classes must agree on an identifier (URI) for this format. SBFC allows multiple cla […]


The health care and life sciences community profile for dataset descriptions

PMCID: 4991880
PMID: 27602295
DOI: 10.7717/peerj.2331

[…] itory access is possible through data catalogs such as Neuroscience Information Framework (NIF) (, accessed June 2016), BioSharing (, accessed June 2016), Registry (, accessed June 2016), Integbio Database Catalog (, accessed June 2016), Force11 (, accesse […]


Bioinformatics Mining and Modeling Methods for the Identification of Disease Mechanisms in Neurodegenerative Disorders

Int J Mol Sci
PMCID: 4691095
PMID: 26690135
DOI: 10.3390/ijms161226148

[…] object. The entities themselves and their relationships are encoded using Uniform Resource Identifiers (URIs) which are provided by domain-specific ontologies. Recently established resources such as provide resolvable and persistent URIs to the community. Sharing such uniquely resolvable URIs enables different domain RDF graphs to be linked and traversed using query languages such […]


Data integration in biological research: an overview

PMCID: 4557916
PMID: 26336651
DOI: 10.1186/s40709-015-0032-5

[…] ould be a step ahead of its current state.An effort to help with the discoverability of the identifiers and assist the researcher with knowledge on how to query data across databases has be done from []. This is a registry that facilitates the discovery of resources in life sciences and allows to decouple the identification of records by the physical locations on the web where they […]


Looking to check out a full list of citations? institution(s)
European Bioinformatics Institute, Hinxton, Cambridge, UK funding source(s)
Supported by EMBL, ELIXIR (Preparatory Phase) and BBSRC (grants BB/E005748/1 and JPA 1729). reviews

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