publication . Article . 2015

Tools and data services registry: a community effort to document bioinformatics resources

Ison, J.; Rapacki, K.; Mé nager, H.; Kalaš , M.; Rydza, E.; Chmura, P.; Anthon, C.; Beard, N.; ...
Open Access English
  • Published: 03 Nov 2015 Journal: Nucleic Acids Research, volume 44, issue D1, pages D38-D47 (issn: 0305-1048, eissn: 1362-4962, Copyright policy)
Abstract
Life sciences are yielding huge data sets that underpin scientific discoveries fundamental to improvement in human health, agriculture and the environment. In support of these discoveries, a plethora of databases and tools are deployed, in technically complex and diverse implementations, across a spectrum of scientific disciplines. The corpus of documentation of these resources is fragmented across the Web, with much redundancy, and has lacked a common standard of information. The outcome is that scientists must often struggle to find, understand, compare and use the best resources for the task at hand. Here we present a community-driven curation effort, support...
Subjects
free text keywords: Computational Biology, Data Curation, Registries, Software, :Matematikk og naturvitenskap: 400::Informasjons- og kommunikasjonsvitenskap: 420::Systemutvikling og -arbeid: 426 [VDP], :Mathematics and natural scienses: 400::Information and communication science: 420::System development and design: 426 [VDP], Bioinformatikk / Bioinformatics, molecular-biology; software-development; life sciences; web services; collection; compilation; seqanswers; framework, Settore BIO/11 - Biologia Molecolare, Settore INF/01 - Informatica, bioinformatique, gestion de données, base de données, outil informatique, Database Issue, [SDV]Life Sciences [q-bio], bioinformatics, tools, registry, elixir, /dk/atira/pure/researchoutput/pubmedpublicationtype/D016428, Journal Article, /dk/atira/pure/researchoutput/pubmedpublicationtype/D052061, Research Support, N.I.H., Extramural, /dk/atira/pure/researchoutput/pubmedpublicationtype/D013485, Research Support, Non-U.S. Gov't, Computational Biology; Data Curation; Registries; Software, /dk/atira/pure/sustainabledevelopmentgoals/good_health_and_well_being, SDG 3 - Good Health and Well-being, Biology and Life Sciences, SEQANSWERS, COMPILATION, COLLECTION, WEB SERVICES, MOLECULAR-BIOLOGY, LIFE SCIENCES, SOFTWARE-DEVELOPMENT, FRAMEWORK, Ecology and Environment, Data and Information, Settore BIO/11, Settore BIO/18 - Genetica, Software development, business.industry, business, Data as a service, Web service, computer.software_genre, computer, Bioinformatics, Data curation, Scientific disciplines, Biology, Documentation, Dissemination, Implementation, ddc:
Funded by
EC| ELIXIR-EXCELERATE
Project
ELIXIR-EXCELERATE
ELIXIR-EXCELERATE: Fast-track ELIXIR implementation and drive early user exploitation across the life-sciences.
  • Funder: European Commission (EC)
  • Project Code: 676559
  • Funding stream: H2020 | RIA
Validated by funder
,
EC| BIOMEDBRIDGES
Project
BIOMEDBRIDGES
Building data bridges between biological and medical infrastructures in Europe
  • Funder: European Commission (EC)
  • Project Code: 284209
  • Funding stream: FP7 | SP4 | INFRA
,
NIH| Gene Ontology Consortium
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5U41HG002273-14
  • Funding stream: NATIONAL HUMAN GENOME RESEARCH INSTITUTE
Communities
EGI FederationEGI Projects: BioMedBridges
Instruct-ERICInstruct-ERIC Projects: Building data bridges between biological and medical infrastructures in Europe
38 references, page 1 of 3

1. May,M. (2014) Life science technologies: Big biological impacts from big data. Science, 344, 1298-1300.

2. Parnell,L.D., Lindenbaum,P., Shameer,K., Dall'Olio,G.M., Swan,D.C., Jensen,L.J., Cockell,S.J., Pedersen,B.S., Mangan,M.E., Miller,C.A. et al. (2011) BioStar: an online question & answer resource for the bioinformatics community. PLoS Comput. Biol., 7, e1002216.

3. Logan,D.W., Sandal,M., Gardner,P.P., Manske,M. and Bateman,A. (2010) Ten simple rules for editing Wikipedia. PLoS Comput. Biol., 6, e1000941.

4. The UniProt Consortium. (2014) Activities at the Universal Protein Resource (UniProt). Nucleic Acids Res., 42, D191-D198.

5. Orchard,S., Ammari,M., Aranda,B., Breuza,L., Briganti,L., Broackes-Carter,F., Campbell,N.H., Chavali,G., Chen,C., Del-Toro,N. et al. (2013) The MIntAct project'IntAct as a common curation platform for 11 molecular interaction databases. Nucleic Acids Res., 42, D358-D363.

6. Kasprzyk,A. (2011) BioMart: driving a paradigm change in biological data management. Database, 2011, bar049. [OpenAIRE]

7. Smedley,D., Haider,S., Durinck,S., Pandini,L., Provero,P., Allen,J., Arnaiz,O., Awedh,M.H., Baldock,R., Barbiera,G. et al. (2015) The BioMart community portal: an innovative alternative to large, centralized data repositories. Nucleic Acids Res., 43, W589-W598.

8. Chervitz,S., Fuellen,G., Dagdigian,C., Brenner,S., Birney,E. and Korf,I. (1998) Bioperl: standard perl modules for bioinformatics. Bio Informatics Technology and Systems (BITS), 10, 1611-1618

9. Pocock,M., Down,T. and Hubbard,T. (2000) BioJava: open source components for bioinformatics. ACM SIGBIO Newsl., 20, 10-12.

10. Chapman,B. and Chang,J. (2000) Biopython: Python tools for computational biology. ACM SIGBIO Newsl., 20, 15-19.

11. Stajich,J.E., Block,D., Boulez,K., Brenner,S.E., Chervitz,S.A., Dagdigian,C., Fuellen,G., Gilbert,J.G., Korf,I., Lapp,H. et al. (2002) The Bioperl toolkit: Perl modules for the life sciences. Genome Res., 12, 1611-1618.

12. Cock,P.J.A., Antao,T., Chang,J.T., Chapman,B.A., Cox,C.J., Dalke,A., Friedberg,I., Hamelryck,T., Kauff,F., Wilczynski,B. et al. (2009) Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics, 25, 1422-1423. [OpenAIRE]

13. Goto,N., Prins,P., Nakao,M., Bonnal,R., Aerts,J. and Katayama,T. (2010) BioRuby: bioinformatics software for the Ruby programming language. Bioinformatics, 26, 2617-2619. [OpenAIRE]

14. Prlic´,A., Yates,A., Bliven,S.E., Rose,P.W., Jacobsen,J., Troshin,P.V., Chapman,M., Gao,J., Koh,C.H., Foisy,S. et al. (2012) BioJava: an open-source framework for bioinformatics in 2012. Bioinformatics, 28, 2693-2695. [OpenAIRE]

15. Bonnal,R.J., Aerts,J., Githinji,G., Goto,N., MacLean,D., Miller,C.A., Mishima,H., Pagani,M., Ramirez-Gonzalez,R., Smant,G. et al. (2012) Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics. Bioinformatics, 28, 1035-1037.

38 references, page 1 of 3
Abstract
Life sciences are yielding huge data sets that underpin scientific discoveries fundamental to improvement in human health, agriculture and the environment. In support of these discoveries, a plethora of databases and tools are deployed, in technically complex and diverse implementations, across a spectrum of scientific disciplines. The corpus of documentation of these resources is fragmented across the Web, with much redundancy, and has lacked a common standard of information. The outcome is that scientists must often struggle to find, understand, compare and use the best resources for the task at hand. Here we present a community-driven curation effort, support...
Subjects
free text keywords: Computational Biology, Data Curation, Registries, Software, :Matematikk og naturvitenskap: 400::Informasjons- og kommunikasjonsvitenskap: 420::Systemutvikling og -arbeid: 426 [VDP], :Mathematics and natural scienses: 400::Information and communication science: 420::System development and design: 426 [VDP], Bioinformatikk / Bioinformatics, molecular-biology; software-development; life sciences; web services; collection; compilation; seqanswers; framework, Settore BIO/11 - Biologia Molecolare, Settore INF/01 - Informatica, bioinformatique, gestion de données, base de données, outil informatique, Database Issue, [SDV]Life Sciences [q-bio], bioinformatics, tools, registry, elixir, /dk/atira/pure/researchoutput/pubmedpublicationtype/D016428, Journal Article, /dk/atira/pure/researchoutput/pubmedpublicationtype/D052061, Research Support, N.I.H., Extramural, /dk/atira/pure/researchoutput/pubmedpublicationtype/D013485, Research Support, Non-U.S. Gov't, Computational Biology; Data Curation; Registries; Software, /dk/atira/pure/sustainabledevelopmentgoals/good_health_and_well_being, SDG 3 - Good Health and Well-being, Biology and Life Sciences, SEQANSWERS, COMPILATION, COLLECTION, WEB SERVICES, MOLECULAR-BIOLOGY, LIFE SCIENCES, SOFTWARE-DEVELOPMENT, FRAMEWORK, Ecology and Environment, Data and Information, Settore BIO/11, Settore BIO/18 - Genetica, Software development, business.industry, business, Data as a service, Web service, computer.software_genre, computer, Bioinformatics, Data curation, Scientific disciplines, Biology, Documentation, Dissemination, Implementation, ddc:
Funded by
EC| ELIXIR-EXCELERATE
Project
ELIXIR-EXCELERATE
ELIXIR-EXCELERATE: Fast-track ELIXIR implementation and drive early user exploitation across the life-sciences.
  • Funder: European Commission (EC)
  • Project Code: 676559
  • Funding stream: H2020 | RIA
Validated by funder
,
EC| BIOMEDBRIDGES
Project
BIOMEDBRIDGES
Building data bridges between biological and medical infrastructures in Europe
  • Funder: European Commission (EC)
  • Project Code: 284209
  • Funding stream: FP7 | SP4 | INFRA
,
NIH| Gene Ontology Consortium
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5U41HG002273-14
  • Funding stream: NATIONAL HUMAN GENOME RESEARCH INSTITUTE
Communities
EGI FederationEGI Projects: BioMedBridges
Instruct-ERICInstruct-ERIC Projects: Building data bridges between biological and medical infrastructures in Europe
38 references, page 1 of 3

1. May,M. (2014) Life science technologies: Big biological impacts from big data. Science, 344, 1298-1300.

2. Parnell,L.D., Lindenbaum,P., Shameer,K., Dall'Olio,G.M., Swan,D.C., Jensen,L.J., Cockell,S.J., Pedersen,B.S., Mangan,M.E., Miller,C.A. et al. (2011) BioStar: an online question & answer resource for the bioinformatics community. PLoS Comput. Biol., 7, e1002216.

3. Logan,D.W., Sandal,M., Gardner,P.P., Manske,M. and Bateman,A. (2010) Ten simple rules for editing Wikipedia. PLoS Comput. Biol., 6, e1000941.

4. The UniProt Consortium. (2014) Activities at the Universal Protein Resource (UniProt). Nucleic Acids Res., 42, D191-D198.

5. Orchard,S., Ammari,M., Aranda,B., Breuza,L., Briganti,L., Broackes-Carter,F., Campbell,N.H., Chavali,G., Chen,C., Del-Toro,N. et al. (2013) The MIntAct project'IntAct as a common curation platform for 11 molecular interaction databases. Nucleic Acids Res., 42, D358-D363.

6. Kasprzyk,A. (2011) BioMart: driving a paradigm change in biological data management. Database, 2011, bar049. [OpenAIRE]

7. Smedley,D., Haider,S., Durinck,S., Pandini,L., Provero,P., Allen,J., Arnaiz,O., Awedh,M.H., Baldock,R., Barbiera,G. et al. (2015) The BioMart community portal: an innovative alternative to large, centralized data repositories. Nucleic Acids Res., 43, W589-W598.

8. Chervitz,S., Fuellen,G., Dagdigian,C., Brenner,S., Birney,E. and Korf,I. (1998) Bioperl: standard perl modules for bioinformatics. Bio Informatics Technology and Systems (BITS), 10, 1611-1618

9. Pocock,M., Down,T. and Hubbard,T. (2000) BioJava: open source components for bioinformatics. ACM SIGBIO Newsl., 20, 10-12.

10. Chapman,B. and Chang,J. (2000) Biopython: Python tools for computational biology. ACM SIGBIO Newsl., 20, 15-19.

11. Stajich,J.E., Block,D., Boulez,K., Brenner,S.E., Chervitz,S.A., Dagdigian,C., Fuellen,G., Gilbert,J.G., Korf,I., Lapp,H. et al. (2002) The Bioperl toolkit: Perl modules for the life sciences. Genome Res., 12, 1611-1618.

12. Cock,P.J.A., Antao,T., Chang,J.T., Chapman,B.A., Cox,C.J., Dalke,A., Friedberg,I., Hamelryck,T., Kauff,F., Wilczynski,B. et al. (2009) Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics, 25, 1422-1423. [OpenAIRE]

13. Goto,N., Prins,P., Nakao,M., Bonnal,R., Aerts,J. and Katayama,T. (2010) BioRuby: bioinformatics software for the Ruby programming language. Bioinformatics, 26, 2617-2619. [OpenAIRE]

14. Prlic´,A., Yates,A., Bliven,S.E., Rose,P.W., Jacobsen,J., Troshin,P.V., Chapman,M., Gao,J., Koh,C.H., Foisy,S. et al. (2012) BioJava: an open-source framework for bioinformatics in 2012. Bioinformatics, 28, 2693-2695. [OpenAIRE]

15. Bonnal,R.J., Aerts,J., Githinji,G., Goto,N., MacLean,D., Miller,C.A., Mishima,H., Pagani,M., Ramirez-Gonzalez,R., Smant,G. et al. (2012) Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics. Bioinformatics, 28, 1035-1037.

38 references, page 1 of 3
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