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

J 2016

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

ISON, Jon, Kristoffer RAPACKI, Herve MENAGER, Matus KALAS, Emil RYDZA et. al.

Basic information

Original name

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

Authors

ISON, Jon (208 Denmark), Kristoffer RAPACKI (208 Denmark), Herve MENAGER (250 France), Matus KALAS (578 Norway), Emil RYDZA (208 Denmark), Piotr CHMURA (208 Denmark), Christian ANTHON (208 Denmark), Niall BEARD (826 United Kingdom of Great Britain and Northern Ireland), Karel BERKA (203 Czech Republic), Dan BOLSER (826 United Kingdom of Great Britain and Northern Ireland), Tim BOOTH (826 United Kingdom of Great Britain and Northern Ireland), Anthony BRETAUDEAU (250 France), Jan BREZOVSKÝ (203 Czech Republic, guarantor, belonging to the institution), Rita CASADIO (380 Italy), Gianni CESARENI (380 Italy), Frederik COPPENS (56 Belgium), Michael CORNELL (826 United Kingdom of Great Britain and Northern Ireland), Gianmauro CUCCURU (380 Italy), Kristian DAVIDSEN (208 Denmark), Gianluca DELLA VEDOVA (380 Italy), Tunca DOGAN (826 United Kingdom of Great Britain and Northern Ireland), Olivia DOPPELT-AZEROUAL (250 France), Laura EMERY (826 United Kingdom of Great Britain and Northern Ireland), Elisabeth GASTEIGER (756 Switzerland), Thomas GATTER (276 Germany), Tatyana GOLDBERG (276 Germany), Marie GROSJEAN (250 France), Bjoern GRUNING (276 Germany), Manuela HELMER-CITTERICH (380 Italy), Hans IENASESCU (208 Denmark), Vassilios IOANNIDIS (756 Switzerland), Martin Closter JESPERSEN (208 Denmark), Rafael JIMENEZ (826 United Kingdom of Great Britain and Northern Ireland), Nick JUTY (826 United Kingdom of Great Britain and Northern Ireland), Peter JUVAN (705 Slovenia), Maximilian KOCH (826 United Kingdom of Great Britain and Northern Ireland), Camille LAIBE (826 United Kingdom of Great Britain and Northern Ireland), Jing-Woei LI (156 China), Luana LICATA (380 Italy), Fabien MAREUIL (250 France), Ivan MICETIC (380 Italy), Rune Mollegaard FRIBORG (208 Denmark), Sebastien MORETTI (756 Switzerland), Chris MORRIS (826 United Kingdom of Great Britain and Northern Ireland), Steffen MOLLER (276 Germany), Aleksandra NENADIC (826 United Kingdom of Great Britain and Northern Ireland), Hedi PETERSON (233 Estonia), Giuseppe PROFITI (380 Italy), Peter RICE (826 United Kingdom of Great Britain and Northern Ireland), Paolo ROMANO (380 Italy), Paola RONCAGLIA (826 United Kingdom of Great Britain and Northern Ireland), Rabie SAIDI (826 United Kingdom of Great Britain and Northern Ireland), Andrea SCHAFFERHANS (276 Germany), Veit SCHWAMMLE (208 Denmark), Callum SMITH (826 United Kingdom of Great Britain and Northern Ireland), Maria Maddalena SPEROTTO (208 Denmark), Heinz STOCKINGER (756 Switzerland), Radka SVOBODOVÁ VAŘEKOVÁ (203 Czech Republic, belonging to the institution), Silvio C. E. TOSATTO (380 Italy), Victor DE LA TORRE (724 Spain), Paolo UVA (380 Italy), Allegra VIA (380 Italy), Guy YACHDAV (276 Germany), Federico ZAMBELLI (380 Italy), Gert VRIEND (528 Netherlands), Burkhard ROST (276 Germany), Helen PARKINSON (826 United Kingdom of Great Britain and Northern Ireland), Peter LONGREEN (208 Denmark) and Soren BRUNAK (208 Denmark)

Edition

Nucleic Acids Research, Oxford, Oxford University Press, 2016, 0305-1048

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10600 1.6 Biological sciences

Country of publisher

United Kingdom of Great Britain and Northern Ireland

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

URL

Impact factor

Impact factor: 10.162

RIV identification code

RIV/00216224:14310/16:00089977

Organization unit

Faculty of Science

DOI

http://dx.doi.org/10.1093/nar/gkv1116

UT WoS

000371261700005

Keywords in English

MOLECULAR-BIOLOGY; SOFTWARE-DEVELOPMENT; LIFE SCIENCES; WEB SERVICES; COLLECTION; COMPILATION; SEQANSWERS; FRAMEWORK

Abstract

V originále

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, supported by ELIXIR-the European infrastructure for biological information-that aspires to a comprehensive and consistent registry of information about bioinformatics resources. The sustainable upkeep of this Tools and Data Services Registry is assured by a curation effort driven by and tailored to local needs, and shared amongst a network of engaged partners. As of November 2015, the registry includes 1785 resources, with depositions from 126 individual registrations including 52 institutional providers and 74 individuals. With community support, the registry can become a standard for dissemination of information about bioinformatics resources: we welcome everyone to join us in this common endeavour. The registry is freely available at https://bio.tools.

Citovat

ISON, Jon, Kristoffer RAPACKI, Herve MENAGER, Matus KALAS, Emil RYDZA, Piotr CHMURA, Christian ANTHON, Niall BEARD, Karel BERKA, Dan BOLSER, Tim BOOTH, Anthony BRETAUDEAU, Jan BREZOVSKÝ, Rita CASADIO, Gianni CESARENI, Frederik COPPENS, Michael CORNELL, Gianmauro CUCCURU, Kristian DAVIDSEN, Gianluca DELLA VEDOVA, Tunca DOGAN, Olivia DOPPELT-AZEROUAL, Laura EMERY, Elisabeth GASTEIGER, Thomas GATTER, Tatyana GOLDBERG, Marie GROSJEAN, Bjoern GRUNING, Manuela HELMER-CITTERICH, Hans IENASESCU, Vassilios IOANNIDIS, Martin Closter JESPERSEN, Rafael JIMENEZ, Nick JUTY, Peter JUVAN, Maximilian KOCH, Camille LAIBE, Jing-Woei LI, Luana LICATA, Fabien MAREUIL, Ivan MICETIC, Rune Mollegaard FRIBORG, Sebastien MORETTI, Chris MORRIS, Steffen MOLLER, Aleksandra NENADIC, Hedi PETERSON, Giuseppe PROFITI, Peter RICE, Paolo ROMANO, Paola RONCAGLIA, Rabie SAIDI, Andrea SCHAFFERHANS, Veit SCHWAMMLE, Callum SMITH, Maria Maddalena SPEROTTO, Heinz STOCKINGER, Radka SVOBODOVÁ VAŘEKOVÁ, Silvio C. E. TOSATTO, Victor DE LA TORRE, Paolo UVA, Allegra VIA, Guy YACHDAV, Federico ZAMBELLI, Gert VRIEND, Burkhard ROST, Helen PARKINSON, Peter LONGREEN and Soren BRUNAK. Tools and data services registry: a community effort to document bioinformatics resources. Nucleic Acids Research. Oxford: Oxford University Press, 2016, vol. 44, D1, p. "D38"-"D47", 10 pp. ISSN 0305-1048. Available from: https://dx.doi.org/10.1093/nar/gkv1116.

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   author = {Ison, Jon and Rapacki, Kristoffer and Menager, Herve and Kalas, Matus and Rydza, Emil and Chmura, Piotr and Anthon, Christian and Beard, Niall and Berka, Karel and Bolser, Dan and Booth, Tim and Bretaudeau, Anthony and Brezovský, Jan and Casadio, Rita and Cesareni, Gianni and Coppens, Frederik and Cornell, Michael and Cuccuru, Gianmauro and Davidsen, Kristian and Della Vedova, Gianluca and Dogan, Tunca and DoppeltandAzeroual, Olivia and Emery, Laura and Gasteiger, Elisabeth and Gatter, Thomas and Goldberg, Tatyana and Grosjean, Marie and Gruning, Bjoern and HelmerandCitterich, Manuela and Ienasescu, Hans and Ioannidis, Vassilios and Jespersen, Martin Closter and Jimenez, Rafael and Juty, Nick and Juvan, Peter and Koch, Maximilian and Laibe, Camille and Li, JingandWoei and Licata, Luana and Mareuil, Fabien and Micetic, Ivan and Friborg, Rune Mollegaard and Moretti, Sebastien and Morris, Chris and Moller, Steffen and Nenadic, Aleksandra and Peterson, Hedi and Profiti, Giuseppe and Rice, Peter and Romano, Paolo and Roncaglia, Paola and Saidi, Rabie and Schafferhans, Andrea and Schwammle, Veit and Smith, Callum and Sperotto, Maria Maddalena and Stockinger, Heinz and Svobodová Vařeková, Radka and Tosatto, Silvio C. E. and de la Torre, Victor and Uva, Paolo and Via, Allegra and Yachdav, Guy and Zambelli, Federico and Vriend, Gert and Rost, Burkhard and Parkinson, Helen and Longreen, Peter and Brunak, Soren},
   article_location = {Oxford},
   article_number = {D1},
   doi = {http://dx.doi.org/10.1093/nar/gkv1116},
   keywords = {MOLECULAR-BIOLOGY; SOFTWARE-DEVELOPMENT; LIFE SCIENCES; WEB SERVICES; COLLECTION; COMPILATION; SEQANSWERS; FRAMEWORK},
   language = {eng},
   issn = {0305-1048},
   journal = {Nucleic Acids Research},
   title = {Tools and data services registry: a community effort to document bioinformatics resources},
   url = {https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkv1116},
   volume = {44},
   year = {2016}
}

TY  - JOUR
ID  - 1345757
AU  - Ison, Jon - Rapacki, Kristoffer - Menager, Herve - Kalas, Matus - Rydza, Emil - Chmura, Piotr - Anthon, Christian - Beard, Niall - Berka, Karel - Bolser, Dan - Booth, Tim - Bretaudeau, Anthony - Brezovský, Jan - Casadio, Rita - Cesareni, Gianni - Coppens, Frederik - Cornell, Michael - Cuccuru, Gianmauro - Davidsen, Kristian - Della Vedova, Gianluca - Dogan, Tunca - Doppelt-Azeroual, Olivia - Emery, Laura - Gasteiger, Elisabeth - Gatter, Thomas - Goldberg, Tatyana - Grosjean, Marie - Gruning, Bjoern - Helmer-Citterich, Manuela - Ienasescu, Hans - Ioannidis, Vassilios - Jespersen, Martin Closter - Jimenez, Rafael - Juty, Nick - Juvan, Peter - Koch, Maximilian - Laibe, Camille - Li, Jing-Woei - Licata, Luana - Mareuil, Fabien - Micetic, Ivan - Friborg, Rune Mollegaard - Moretti, Sebastien - Morris, Chris - Moller, Steffen - Nenadic, Aleksandra - Peterson, Hedi - Profiti, Giuseppe - Rice, Peter - Romano, Paolo - Roncaglia, Paola - Saidi, Rabie - Schafferhans, Andrea - Schwammle, Veit - Smith, Callum - Sperotto, Maria Maddalena - Stockinger, Heinz - Svobodová Vařeková, Radka - Tosatto, Silvio C. E. - de la Torre, Victor - Uva, Paolo - Via, Allegra - Yachdav, Guy - Zambelli, Federico - Vriend, Gert - Rost, Burkhard - Parkinson, Helen - Longreen, Peter - Brunak, Soren
PY  - 2016
TI  - Tools and data services registry: a community effort to document bioinformatics resources
JF  - Nucleic Acids Research
VL  - 44
IS  - D1
SP  - "D38"-"D47"
EP  - "D38"-"D47"
PB  - Oxford University Press
SN  - 03051048
KW  - MOLECULAR-BIOLOGY
KW  - SOFTWARE-DEVELOPMENT
KW  - LIFE SCIENCES
KW  - WEB SERVICES
KW  - COLLECTION
KW  - COMPILATION
KW  - SEQANSWERS
KW  - FRAMEWORK
UR  - https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkv1116
L2  - https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkv1116
N2  - 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, supported by ELIXIR-the European infrastructure for biological information-that aspires to a comprehensive and consistent registry of information about bioinformatics resources. The sustainable upkeep of this Tools and Data Services Registry is assured by a curation effort driven by and tailored to local needs, and shared amongst a network of engaged partners. As of November 2015, the registry includes 1785 resources, with depositions from 126 individual registrations including 52 institutional providers and 74 individuals. With community support, the registry can become a standard for dissemination of information about bioinformatics resources: we welcome everyone to join us in this common endeavour. The registry is freely available at https://bio.tools.
ER  -

ISON, Jon, Kristoffer RAPACKI, Herve MENAGER, Matus KALAS, Emil RYDZA, Piotr CHMURA, Christian ANTHON, Niall BEARD, Karel BERKA, Dan BOLSER, Tim BOOTH, Anthony BRETAUDEAU, Jan BREZOVSKÝ, Rita CASADIO, Gianni CESARENI, Frederik COPPENS, Michael CORNELL, Gianmauro CUCCURU, Kristian DAVIDSEN, Gianluca DELLA VEDOVA, Tunca DOGAN, Olivia DOPPELT-AZEROUAL, Laura EMERY, Elisabeth GASTEIGER, Thomas GATTER, Tatyana GOLDBERG, Marie GROSJEAN, Bjoern GRUNING, Manuela HELMER-CITTERICH, Hans IENASESCU, Vassilios IOANNIDIS, Martin Closter JESPERSEN, Rafael JIMENEZ, Nick JUTY, Peter JUVAN, Maximilian KOCH, Camille LAIBE, Jing-Woei LI, Luana LICATA, Fabien MAREUIL, Ivan MICETIC, Rune Mollegaard FRIBORG, Sebastien MORETTI, Chris MORRIS, Steffen MOLLER, Aleksandra NENADIC, Hedi PETERSON, Giuseppe PROFITI, Peter RICE, Paolo ROMANO, Paola RONCAGLIA, Rabie SAIDI, Andrea SCHAFFERHANS, Veit SCHWAMMLE, Callum SMITH, Maria Maddalena SPEROTTO, Heinz STOCKINGER, Radka SVOBODOVÁ VAŘEKOVÁ, Silvio C. E. TOSATTO, Victor DE LA TORRE, Paolo UVA, Allegra VIA, Guy YACHDAV, Federico ZAMBELLI, Gert VRIEND, Burkhard ROST, Helen PARKINSON, Peter LONGREEN and Soren BRUNAK. Tools and data services registry: a community effort to document bioinformatics resources. \textit{Nucleic Acids Research}. Oxford: Oxford University Press, 2016, vol.~44, D1, p.~''D38''-''D47'', 10 pp. ISSN~0305-1048. Available from: https://dx.doi.org/10.1093/nar/gkv1116.

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