• The bio.tools registry of software tools and data resources for the life sciences 

      Ison, Jon; Ienasescu, Hans-Ioan; Chmura, Piotr; Rydza, Emil; Ménager, Hervé; Kalaš, Matúš; Schwämmle, Veit; Grüning, Björn A.; Beard, Niall; Lopez, Rodrigo; Duvaud, Severine; Stockinger, Heinz; Persson, Bengt; Svobodová Vařeková, Radka; Raček, Tomáš; Vondrášek, Jiří; Peterson, Hedi; Salumets, Ahto; Jonassen, Inge; et al., +18 authors (total 37) (Peer reviewed; Journal article, 2019-08-12)
      Bioinformaticians and biologists rely increasingly upon workflows for the flexible utilization of the many life science tools that are needed to optimally convert data into knowledge. We outline a pan-European enterprise ...
    • BioXSD: the common data-exchange format for everyday bioinformatics web services 

      Kalaš, Matúš; Puntervoll, Pål; Joseph, Alexandre; Bartaševičiūtė, Edita; Töpfer, Armin; Venkataraman, Prabakar; Pettifer, Steve; Bryne, Jan Christian; Ison, Jon; Blanchet, Christophe; Rapacki, Kristoffer; Jonassen, Inge (Peer reviewed; Journal article, 2010)
      Motivation: The world-wide community of life scientists has access to a large number of public bioinformatics databases and tools, which are developed and deployed using diverse technologies and designs. More and more of ...
    • Community curation of bioinformatics software and data resources 

      Ison, Jon; Ménager, Hervé; Brancotte, Bryan; Jaaniso, Erik; Salumets, Ahto; Raček, Tomáš; Lamprecht, Anna-Lena; Palmblad, Magnus; Kalaš, Matúš; Chmura, Piotr; Hancock, John M; Schwämmle, Veit; Ienasescu, Hans-Ioan (Peer reviewed; Journal article, 2019)
      The corpus of bioinformatics resources is huge and expanding rapidly, presenting life scientists with a growing challenge in selecting tools that fit the desired purpose. To address this, the European Infrastructure for ...
    • EDAM: an ontology of bioinformatics operations, types of data and identifiers, topics and formats 

      Ison, Jon; Kalaš, Matúš; Jonassen, Inge; Bolser, Dan; Uludag, Mahmut; McWilliam, Hamish; Malone, James; Lopez, Rodrigo; Pettifer, Steve; Rice, Peter (Peer reviewed; Journal article, 2013)
      Motivation: Advancing the search, publication and integration of bioinformatics tools and resources demands consistent machine-understandable descriptions. A comprehensive ontology allowing such descriptions is therefore ...
    • The EMBRACE web service collection 

      Pettifer, Steve; Ison, Jon; Kalaš, Matúš; Thorne, David; McDermott, Philip; Jonassen, Inge; Ali, Liaquat; Fernandez, Jose M; Rodriguez, Jose M; Pisano, David G; Blanchet, Christophe; Uludag, Mahmut; Rice, Peter; Bartaseviciute, Edita; Rapacki, Kristoffer; Hekkelman, Maarten; Sand, Olivier; Stockinger, Heinz; Clegg, Andrew B; Bongcam-Rudloff, Eric; Salzemann, Jean; Breton, Vincent; Attwood, Teresa K; Cameron, Graham; Vriend, Gert (Peer reviewed; Journal article, 2010-05-10)
      The EMBRACE (European Model for Bioinformatics Research and Community Education) web service collection is the culmination of a 5-year project that set out to investigate issues involved in developing and deploying web ...
    • Tools and data services registry: a community effort to document bioinformatics resources 

      Ison, Jon; Rapacki, Kristoffer; Ménager, Hervé; Kalaš, Matúš; et al., 69 authors (Peer reviewed; Journal article, 2015-11-03)
      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 ...
    • Using registries to integrate bioinformatics tools and services into workbench environments 

      Ménager, Hervé; Kalaš, Matúš; Rapacki, Kristoffer; Ison, Jon (Peer reviewed; Journal article, 2015)
      The diversity and complexity of bioinformatics resources presents significant challenges to their localisation, deployment and use, creating a need for reliable systems that address these issues. Meanwhile, users demand ...