publication . Article . Other literature type . 2018

BED: a Biological Entity Dictionary based on a graph data model

Godard, Patrice; van Eyll, Jonathan;
Open Access English
  • Published: 01 May 2018 Journal: F1000Research, volume 7 (eissn: 2046-1402, Copyright policy)
  • Publisher: (:unav)
Abstract
The understanding of molecular processes involved in a specific biological system can be significantly improved by combining and comparing different data sets and knowledge resources. However, these information sources often use different identification systems and an identifier conversion step is required before any integration effort. Mapping between identifiers is often provided by the reference information resources and several tools have been implemented to simplify their use. However, most of these tools do not combine the information provided by individual resources to increase the completeness of the mapping process. Also, deprecated identifiers from for...
Subjects
free text keywords: microarray, database, proteomics, identifiers, Software Tool Article, transcriptomics, genomics, Articles, RNA-seq
Related Organizations
37 references, page 1 of 3

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Durinck S Spellman PT Birney E: Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt.Nat Protoc.2009;4(8):1184–1191. 10.1038/nprot.2009.97 19617889 [OpenAIRE] [PubMed] [DOI]

Fabregat A Korninger F Viteri G: Reactome graph database: Efficient access to complex pathway data.PLoS Comput Biol.2018;14(1):e1005968. 10.1371/journal.pcbi.1005968 29377902 [OpenAIRE] [PubMed] [DOI]

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Godard P: patzaw/BED: Publication (V2) release (Version v1.1.0).Zenodo.2018a 10.5281/zenodo.1244150 [OpenAIRE] [DOI]

37 references, page 1 of 3
Abstract
The understanding of molecular processes involved in a specific biological system can be significantly improved by combining and comparing different data sets and knowledge resources. However, these information sources often use different identification systems and an identifier conversion step is required before any integration effort. Mapping between identifiers is often provided by the reference information resources and several tools have been implemented to simplify their use. However, most of these tools do not combine the information provided by individual resources to increase the completeness of the mapping process. Also, deprecated identifiers from for...
Subjects
free text keywords: microarray, database, proteomics, identifiers, Software Tool Article, transcriptomics, genomics, Articles, RNA-seq
Related Organizations
37 references, page 1 of 3

Allaire JJ Wickham H Ushey K: rstudioapi: Safely Access the RStudio API.2017 Reference Source

Almende BV Thieurmel B Robert T: visNetwork: Network Visualization using ’vis.js’ Library.2017 Reference Source

Chang W Cheng J Allaire JJ: shiny: Web Application Framework for R.2017 Reference Source

Cheng J: miniUI: Shiny UI Widgets for Small Screens.2016 Reference Source

Chiricozzi A Guttman-Yassky E Suárez-Fariñas M: Integrative responses to IL-17 and TNF-α in human keratinocytes account for key inflammatory pathogenic circuits in psoriasis.J Invest Dermatol.2011;131(3):677–87. 10.1038/jid.2010.340 21085185 [OpenAIRE] [PubMed] [DOI]

Clarivate Analytics: MetaCore delivers high-quality biological systems content in context.2017 Reference Source

CRAN: The Comprehensive R Archive Network. Reference Source

Crick F: Central dogma of molecular biology.Nature.1970;227(5258):561–563. 10.1038/227561a0 4913914 [PubMed] [DOI]

Dai X Li J Liu T: HRGRN: A Graph Search-Empowered Integrative Database of Arabidopsis Signaling Transduction, Metabolism and Gene Regulation Networks.Plant Cell Physiol.2016;57(1):e12. 10.1093/pcp/pcv200 26657893 [OpenAIRE] [PubMed] [DOI]

Davis S Meltzer PS: GEOquery: a bridge between the Gene Expression Omnibus (GEO) and BioConductor.Bioinformatics.2007;23(14):1846–1847. 10.1093/bioinformatics/btm254 17496320 [PubMed] [DOI]

Docker inc: Docker Community Edition.2017 Reference Source

Durinck S Spellman PT Birney E: Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt.Nat Protoc.2009;4(8):1184–1191. 10.1038/nprot.2009.97 19617889 [OpenAIRE] [PubMed] [DOI]

Fabregat A Korninger F Viteri G: Reactome graph database: Efficient access to complex pathway data.PLoS Comput Biol.2018;14(1):e1005968. 10.1371/journal.pcbi.1005968 29377902 [OpenAIRE] [PubMed] [DOI]

Gerstein MB Bruce C Rozowsky JS: What is a gene, post-ENCODE? History and updated definition.Genome Res.2007;17(6):669–81. 10.1101/gr.6339607 17567988 [PubMed] [DOI]

Godard P: patzaw/BED: Publication (V2) release (Version v1.1.0).Zenodo.2018a 10.5281/zenodo.1244150 [OpenAIRE] [DOI]

37 references, page 1 of 3
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publication . Article . Other literature type . 2018

BED: a Biological Entity Dictionary based on a graph data model

Godard, Patrice; van Eyll, Jonathan;