• BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains 

      Katayama, Toshiaki; Wilkinson, Mark D.; Aoki-Kinoshita, Kiyoko F.; Kawashima, Shuichi; Yamamoto, Yasunori; Yamaguchi, Atsuko; Okamoto, Shinobu; Kawano, Shin; Kim, Jin-Dong; Wang, Yue; Wu, Hongyan; Kano, Yoshinobu; Ono, Hiromasa; Bono, Hidemasa; Kocbek, Simon; Aerts, Jan; Akune, Yukie; Antezana, Erick; Arakawa, Kazuharu; Aranda, Bruno; Baran, Joachim; Bolleman, Jerven; Bonnal, Raoul J. P.; Buttigieg, Pier Luigi; Campbell, Matthew P.; Chen, Yi-an; Chiba, Hirokazu; Cock, Peter J. A.; Cohen, K. Bretonnel; Constantin, Alexandru; Duck, Geraint; Dumontier, Michel; Fujisawa, Takatomo; Fujiwara, Toyofumi; Goto, Naohisa; Hoehndorf, Robert; Igarashi, Yoshinobu; Itaya, Hidetoshi; Ito, Maori; Iwasaki, Wataru; Kalaš, Matúš; Katoda, Takeo; Kim, Taehong; Kokubu, Anna; Komiyama, Yusuke; Kotera, Masaaki; Laibe, Camille; Lapp, Hilmar; Lütteke, Thomas; Marshall, M. Scott; Mori, Takaaki; Mori, Hiroshi; Morita, Mizuki; Murakami, Katsuhiko; Nakao, Mitsuteru; Narimatsu, Hisashi; Nishide, Hiroyo; Nishimura, Yosuke; Nyström-Persson, Johan; Ogishima, Soichi; Okamura, Yasunobu; Okuda, Shujiro; Oshita, Kazuki; Packer, Nicki H; Prins, Pjotr; Ranzinger, Rene; Rocca-Serra, Philippe; Sansone, Susanna; Sawaki, Hiromichi; Shin, Sung-Ho; Splendiani, Andrea; Strozzi, Francesco; Tadaka, Shu; Toukach, Philip; Uchiyama, Ikuo; Umezaki, Masahito; Vos, Rutger; Whetzel, Patricia L.; Yamada, Issaku; Yamasaki, Chisato; Yamashita, Riu; York, William S.; Zmasek, Christian M.; Kawamoto, Shoko; Takagi, Toshihisa (Peer reviewed; Journal article, 2014-02-05)
      Abstract The application of semantic technologies to the integration of biological data and the interoperability of bioinformatics analysis and visualization tools has been the common theme of a series of annual BioHackathons ...
    • EDAM-bioimaging: the ontology of bioimage informatics operations, topics, data, and formats (update 2020) 

      Kalaš, Matúš; Plantard, Laure; Lindblad, Joakim; Jones, Martin; Sladoje, Nataša; Kirschmann, Moritz A.; Chessel, Anatole; Scholz, Leandro; Rössler, Fabianne; Nicolás Sáenz, Laura; Gómez de Mariscal, Estibaliz; Bogovic, John; Dufour, Alexandre; Heiligenstein, Xavier; Waithe, Dominic; Domart, Marie-Charlotte; Karreman, Matthia; Van de Plas, Raf; Haase, Robert; Hörl, David; Paavolainen, Lassi; Vrhovac Madunić, Ivana; Karaica, Dean; Muñoz-Barrutia, Arrate; Sampaio, Paula; Sage, Daniel; Munck, Sebastian; Golani, Ofra; Moore, Josh; Levet, Florian; Ison, Jon; Gaignard, Alban; Ménager, Hervé; Zhang, Chong; Miura, Kota; Colombelli, Julien; Paul-Gilloteaux, Perrine (Others, 2020)
      EDAM is a well-established ontology of operations, topics, types of data, and data formats that are used in bioinformatics and its neighbouring fields [1,2] . EDAM-bioimaging is an extension of EDAM dedicated to bioimage ...
    • EDAM: the bioscientific data analysis ontology (update 2021) [version 1; not peer reviewed] 

      Black, Melissa; Lamothe, Lucie; Eldakroury, Hager; Kierkegaard, Mads; Priya, Ankita; Machinda, Anne; Singh Khanduja, Uttam; Patoliya, Drashti; Rathi, Rashika; Che Nico, Tawah Peggy; Umutesi, Gloria; Blankenburg, Claudia; Op, Anita; Chieke, Precious; Babatunde, Omodolapo; Laurie, Steve; Neumann, Steffen; Schwämmle, Veit; Kuzmin, Ivan; Hunter, Chris; Karr, Jonathan; Ison, Jon; Gaignard, Alban; Brancotte, Bryan; Ménager, Hervé; Kalaš, Matúš (Others, 2021)
      EDAM [1] is a domain ontology of data analysis and data management in bio- and other sciences, and science-based applications. It comprises concepts related to analysis, modelling, optimisation, and data life-cycle. ...
    • EDAM: the ontology of bioinformatics operations, topics, data, and formats (update 2020) 

      Kalaš, Matúš; Ménager, Hervé; Gaignard, Alban; Schwämmle, Veit; Ison, Jon (Others, 2020)
      Project website: http://edamontology.org Source code: https://github.com/edamontology/edamontology License: CC BY-SA 4.0 EDAM is an ontology of well-established, familiar concepts that are prevalent within bioinformatics, ...
    • Efforts towards accessible and reliable bioinformatics 

      Kalaš, Matúš (Doctoral thesis, 2015-11-19)
      The aim of the presented work was contributing to making scientific computing more accessible, reliable, and thus more efficient for researchers, primarily computational biologists and molecular biologists. Many approaches ...
    • WSDL Workshop. Semantic web application in HTML5 for the discovery, construction and analysis of workflows 

      Nozal Canadas, Rafael Adolfo (Master thesis, 2013-11-20)
      WSDL-Workshop is a HTML5 web application for the discovery and exploration of web services and for analysing the compatibility between web services. This is the result of a mathematical model developed from WSDL1.1. The ...