EDAM: the bioscientific data analysis ontology (update 2021) [version 1; not peer reviewed]
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. Targetting usability by diverse end users, the structure of EDAM is relatively simpl...
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| creator | 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 |
| description | 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. Targetting usability by diverse end users, the structure of EDAM is relatively simple, divided into 4 main sections: Topic Operation Data (incl. Identifier) Format EDAM is used in numerous resources, for example Bio.tools, Galaxy, Debian, or the ELIXIR Europe training portal TeSS. Thanks to the annotations with EDAM, computational tools, workflows, standards, data, and learning materials are easier to find, compare, choose, and integrate. EDAM contributes to open science by allowing semantic annotation of processed data, thus making the data more understandable, findable, and comparable. EDAM and its applications lower the barrier and effort for scientists and citizens alike, towards doing scientific research in a more open, reliable, and inclusive way. The main improvements in 2021 include: The addition of essential concepts of data management and open science Improved automated validation (CI) Improved contribution processes towards more inclusion and engagement with communities of scientific experts, software engineers, and volunteers Easier to contribute, and therefore new contributors and new collaborations. And welcoming more! News from the applications: Galaxy can now visualise the tools panel sorted by EDAM. The EDAM community brings together software engineers and science experts (academic, industrial, citizen), professionals and volunteers. It can be followed and contributed to via various channels. One option is GitHub, with dedicated repositories incl. edamontology and others. Other platforms for contributions to EDAM are especially the generic ontology browsers of the NCBO BioPortal (EDAM, EDAM Bioimaging [2]) and WebProtégé (EDAM, EDAM Bioimaging; free registration required also for viewing). The main communication channel is Gitter. Along with the ontology, the community has developed a number of tools that enhance user experience with EDAM: EDAM Browser [3] is a lightweight and fast web-based ontology browser that provides a number of user-oriented features such as aggregated search across various EDAM-annotated resources (e.g. Bio.tools, TeSS), and suggesting changes to EDAM. EDAMmap is a tool for text mining EDAM concepts from articles. EDAM Popovers is a web-browser add-on/extension for showing details of EDAM concepts found |
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| fullrecord | <record><control><sourceid>cristin_3HK</sourceid><recordid>TN_cdi_cristin_nora_11250_2988255</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><sourcerecordid>11250_2988255</sourcerecordid><originalsourceid>FETCH-cristin_nora_11250_29882553</originalsourceid><addsrcrecordid>eNqNyrEKwjAQgOEuDqK-w7npIDSRQtVJtOLi5lYkxPSqB-GuJLHSt9fBB3D6h-8fZ3V13F-2kJ4Id5LoCDlRSw4amyxYtn6IFEE4iZfHAItX9xUEnWu1hLrHEEkY1A5YEnSIAQL2hG9sbtNs1FofcfbrJJufquvhvHKBYiI2LMEapXSRG70pS10U63-eDz6hOP0</addsrcrecordid><sourcetype>Open Access Repository</sourcetype><iscdi>true</iscdi><recordtype>text_resource</recordtype></control><display><type>text_resource</type><title>EDAM: the bioscientific data analysis ontology (update 2021) [version 1; not peer reviewed]</title><source>NORA - Norwegian Open Research Archives</source><creator>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</creator><creatorcontrib>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</creatorcontrib><description>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. Targetting usability by diverse end users, the structure of EDAM is relatively simple, divided into 4 main sections: Topic Operation Data (incl. Identifier) Format EDAM is used in numerous resources, for example Bio.tools, Galaxy, Debian, or the ELIXIR Europe training portal TeSS. Thanks to the annotations with EDAM, computational tools, workflows, standards, data, and learning materials are easier to find, compare, choose, and integrate. EDAM contributes to open science by allowing semantic annotation of processed data, thus making the data more understandable, findable, and comparable. EDAM and its applications lower the barrier and effort for scientists and citizens alike, towards doing scientific research in a more open, reliable, and inclusive way. The main improvements in 2021 include: The addition of essential concepts of data management and open science Improved automated validation (CI) Improved contribution processes towards more inclusion and engagement with communities of scientific experts, software engineers, and volunteers Easier to contribute, and therefore new contributors and new collaborations. And welcoming more! News from the applications: Galaxy can now visualise the tools panel sorted by EDAM. The EDAM community brings together software engineers and science experts (academic, industrial, citizen), professionals and volunteers. It can be followed and contributed to via various channels. One option is GitHub, with dedicated repositories incl. edamontology and others. Other platforms for contributions to EDAM are especially the generic ontology browsers of the NCBO BioPortal (EDAM, EDAM Bioimaging [2]) and WebProtégé (EDAM, EDAM Bioimaging; free registration required also for viewing). The main communication channel is Gitter. Along with the ontology, the community has developed a number of tools that enhance user experience with EDAM: EDAM Browser [3] is a lightweight and fast web-based ontology browser that provides a number of user-oriented features such as aggregated search across various EDAM-annotated resources (e.g. Bio.tools, TeSS), and suggesting changes to EDAM. EDAMmap is a tool for text mining EDAM concepts from articles. EDAM Popovers is a web-browser add-on/extension for showing details of EDAM concepts found in a website. Great e.g. for code and textual data on GitHub References: [1] Ison, J., Kalaš, M., Jonassen, I., et al. (2013). EDAM: an ontology of bioinformatics operations, types of data and identifiers, topics and formats. Bioinformatics, 29(10): 1325-1332. DOI: 10.1093/bioinformatics/btt113 [2] Matúš Kalaš, Laure Plantard, Joakim Lindblad, Martin Jones, Nataša Sladoje, Moritz A. Kirschmann, Anatole Chessel, Leandro Scholz, Fabienne Rössler, Laura Nicolás Sáenz, Estibaliz Gómez de Mariscal, John Bogovic, Alexandre Dufour, Xavier Heiligenstein, Dominic Waithe, Marie-Charlotte Domart, Matthia Karreman, Raf Van de Plas, Robert Haase, David Hörl, Lassi Paavolainen, Ivana Vrhovac Madunić, Dean Karaica, Arrate Muñoz-Barrutia, Paula Sampaio, Daniel Sage, Sebastian Munck, Ofra Golani, Josh Moore, Florian Levet, Jon Ison, Alban Gaignard, Hervé Ménager, Chong Zhang, Kota Miura, Julien Colombelli, Perrine Paul-Gilloteaux, and welcoming new contributors! (2020). EDAM-bioimaging: the ontology of bioimage informatics operations, topics, data, and formats (update 2020) [version 1; not peer reviewed]. F1000Research, 9(ELIXIR):162 (Poster) DOI: 10.7490/f1000research.1117826.1 [3] Brancotte, B., Blanchet, C. and Ménager, H. (2018). A reusable tree-based web-visualization to browse EDAM ontology, and contribute to it. J. Open Source Softw., 3(27): 698. DOI: 10.21105/joss.00698</description><language>eng</language><publisher>F1000</publisher><subject>Håndtering av forskningsdata ; Life Science ; Livsvitenskap ; Ontologi ; Ontology ; Open Science ; Research data management</subject><creationdate>2021</creationdate><rights>info:eu-repo/semantics/openAccess</rights><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>230,780,885,26567</link.rule.ids><linktorsrc>$$Uhttp://hdl.handle.net/11250/2988255$$EView_record_in_NORA$$FView_record_in_$$GNORA$$Hfree_for_read</linktorsrc></links><search><creatorcontrib>Black, Melissa</creatorcontrib><creatorcontrib>Lamothe, Lucie</creatorcontrib><creatorcontrib>Eldakroury, Hager</creatorcontrib><creatorcontrib>Kierkegaard, Mads</creatorcontrib><creatorcontrib>Priya, Ankita</creatorcontrib><creatorcontrib>Machinda, Anne</creatorcontrib><creatorcontrib>Singh Khanduja, Uttam</creatorcontrib><creatorcontrib>Patoliya, Drashti</creatorcontrib><creatorcontrib>Rathi, Rashika</creatorcontrib><creatorcontrib>Che Nico, Tawah Peggy</creatorcontrib><creatorcontrib>Umutesi, Gloria</creatorcontrib><creatorcontrib>Blankenburg, Claudia</creatorcontrib><creatorcontrib>Op, Anita</creatorcontrib><creatorcontrib>Chieke, Precious</creatorcontrib><creatorcontrib>Babatunde, Omodolapo</creatorcontrib><creatorcontrib>Laurie, Steve</creatorcontrib><creatorcontrib>Neumann, Steffen</creatorcontrib><creatorcontrib>Schwämmle, Veit</creatorcontrib><creatorcontrib>Kuzmin, Ivan</creatorcontrib><creatorcontrib>Hunter, Chris</creatorcontrib><creatorcontrib>Karr, Jonathan</creatorcontrib><creatorcontrib>Ison, Jon</creatorcontrib><creatorcontrib>Gaignard, Alban</creatorcontrib><creatorcontrib>Brancotte, Bryan</creatorcontrib><creatorcontrib>Ménager, Hervé</creatorcontrib><creatorcontrib>Kalaš, Matúš</creatorcontrib><title>EDAM: the bioscientific data analysis ontology (update 2021) [version 1; not peer reviewed]</title><description>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. Targetting usability by diverse end users, the structure of EDAM is relatively simple, divided into 4 main sections: Topic Operation Data (incl. Identifier) Format EDAM is used in numerous resources, for example Bio.tools, Galaxy, Debian, or the ELIXIR Europe training portal TeSS. Thanks to the annotations with EDAM, computational tools, workflows, standards, data, and learning materials are easier to find, compare, choose, and integrate. EDAM contributes to open science by allowing semantic annotation of processed data, thus making the data more understandable, findable, and comparable. EDAM and its applications lower the barrier and effort for scientists and citizens alike, towards doing scientific research in a more open, reliable, and inclusive way. The main improvements in 2021 include: The addition of essential concepts of data management and open science Improved automated validation (CI) Improved contribution processes towards more inclusion and engagement with communities of scientific experts, software engineers, and volunteers Easier to contribute, and therefore new contributors and new collaborations. And welcoming more! News from the applications: Galaxy can now visualise the tools panel sorted by EDAM. The EDAM community brings together software engineers and science experts (academic, industrial, citizen), professionals and volunteers. It can be followed and contributed to via various channels. One option is GitHub, with dedicated repositories incl. edamontology and others. Other platforms for contributions to EDAM are especially the generic ontology browsers of the NCBO BioPortal (EDAM, EDAM Bioimaging [2]) and WebProtégé (EDAM, EDAM Bioimaging; free registration required also for viewing). The main communication channel is Gitter. Along with the ontology, the community has developed a number of tools that enhance user experience with EDAM: EDAM Browser [3] is a lightweight and fast web-based ontology browser that provides a number of user-oriented features such as aggregated search across various EDAM-annotated resources (e.g. Bio.tools, TeSS), and suggesting changes to EDAM. EDAMmap is a tool for text mining EDAM concepts from articles. EDAM Popovers is a web-browser add-on/extension for showing details of EDAM concepts found in a website. Great e.g. for code and textual data on GitHub References: [1] Ison, J., Kalaš, M., Jonassen, I., et al. (2013). EDAM: an ontology of bioinformatics operations, types of data and identifiers, topics and formats. Bioinformatics, 29(10): 1325-1332. DOI: 10.1093/bioinformatics/btt113 [2] Matúš Kalaš, Laure Plantard, Joakim Lindblad, Martin Jones, Nataša Sladoje, Moritz A. Kirschmann, Anatole Chessel, Leandro Scholz, Fabienne Rössler, Laura Nicolás Sáenz, Estibaliz Gómez de Mariscal, John Bogovic, Alexandre Dufour, Xavier Heiligenstein, Dominic Waithe, Marie-Charlotte Domart, Matthia Karreman, Raf Van de Plas, Robert Haase, David Hörl, Lassi Paavolainen, Ivana Vrhovac Madunić, Dean Karaica, Arrate Muñoz-Barrutia, Paula Sampaio, Daniel Sage, Sebastian Munck, Ofra Golani, Josh Moore, Florian Levet, Jon Ison, Alban Gaignard, Hervé Ménager, Chong Zhang, Kota Miura, Julien Colombelli, Perrine Paul-Gilloteaux, and welcoming new contributors! (2020). EDAM-bioimaging: the ontology of bioimage informatics operations, topics, data, and formats (update 2020) [version 1; not peer reviewed]. F1000Research, 9(ELIXIR):162 (Poster) DOI: 10.7490/f1000research.1117826.1 [3] Brancotte, B., Blanchet, C. and Ménager, H. (2018). A reusable tree-based web-visualization to browse EDAM ontology, and contribute to it. J. Open Source Softw., 3(27): 698. DOI: 10.21105/joss.00698</description><subject>Håndtering av forskningsdata</subject><subject>Life Science</subject><subject>Livsvitenskap</subject><subject>Ontologi</subject><subject>Ontology</subject><subject>Open Science</subject><subject>Research data management</subject><fulltext>true</fulltext><rsrctype>text_resource</rsrctype><creationdate>2021</creationdate><recordtype>text_resource</recordtype><sourceid>3HK</sourceid><recordid>eNqNyrEKwjAQgOEuDqK-w7npIDSRQtVJtOLi5lYkxPSqB-GuJLHSt9fBB3D6h-8fZ3V13F-2kJ4Id5LoCDlRSw4amyxYtn6IFEE4iZfHAItX9xUEnWu1hLrHEEkY1A5YEnSIAQL2hG9sbtNs1FofcfbrJJufquvhvHKBYiI2LMEapXSRG70pS10U63-eDz6hOP0</recordid><startdate>2021</startdate><enddate>2021</enddate><creator>Black, Melissa</creator><creator>Lamothe, Lucie</creator><creator>Eldakroury, Hager</creator><creator>Kierkegaard, Mads</creator><creator>Priya, Ankita</creator><creator>Machinda, Anne</creator><creator>Singh Khanduja, Uttam</creator><creator>Patoliya, Drashti</creator><creator>Rathi, Rashika</creator><creator>Che Nico, Tawah Peggy</creator><creator>Umutesi, Gloria</creator><creator>Blankenburg, Claudia</creator><creator>Op, Anita</creator><creator>Chieke, Precious</creator><creator>Babatunde, Omodolapo</creator><creator>Laurie, Steve</creator><creator>Neumann, Steffen</creator><creator>Schwämmle, Veit</creator><creator>Kuzmin, Ivan</creator><creator>Hunter, Chris</creator><creator>Karr, Jonathan</creator><creator>Ison, Jon</creator><creator>Gaignard, Alban</creator><creator>Brancotte, Bryan</creator><creator>Ménager, Hervé</creator><creator>Kalaš, Matúš</creator><general>F1000</general><scope>3HK</scope></search><sort><creationdate>2021</creationdate><title>EDAM: the bioscientific data analysis ontology (update 2021) [version 1; 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not peer reviewed]</btitle><date>2021</date><risdate>2021</risdate><abstract>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. Targetting usability by diverse end users, the structure of EDAM is relatively simple, divided into 4 main sections: Topic Operation Data (incl. Identifier) Format EDAM is used in numerous resources, for example Bio.tools, Galaxy, Debian, or the ELIXIR Europe training portal TeSS. Thanks to the annotations with EDAM, computational tools, workflows, standards, data, and learning materials are easier to find, compare, choose, and integrate. EDAM contributes to open science by allowing semantic annotation of processed data, thus making the data more understandable, findable, and comparable. EDAM and its applications lower the barrier and effort for scientists and citizens alike, towards doing scientific research in a more open, reliable, and inclusive way. The main improvements in 2021 include: The addition of essential concepts of data management and open science Improved automated validation (CI) Improved contribution processes towards more inclusion and engagement with communities of scientific experts, software engineers, and volunteers Easier to contribute, and therefore new contributors and new collaborations. And welcoming more! News from the applications: Galaxy can now visualise the tools panel sorted by EDAM. The EDAM community brings together software engineers and science experts (academic, industrial, citizen), professionals and volunteers. It can be followed and contributed to via various channels. One option is GitHub, with dedicated repositories incl. edamontology and others. Other platforms for contributions to EDAM are especially the generic ontology browsers of the NCBO BioPortal (EDAM, EDAM Bioimaging [2]) and WebProtégé (EDAM, EDAM Bioimaging; free registration required also for viewing). The main communication channel is Gitter. Along with the ontology, the community has developed a number of tools that enhance user experience with EDAM: EDAM Browser [3] is a lightweight and fast web-based ontology browser that provides a number of user-oriented features such as aggregated search across various EDAM-annotated resources (e.g. Bio.tools, TeSS), and suggesting changes to EDAM. EDAMmap is a tool for text mining EDAM concepts from articles. EDAM Popovers is a web-browser add-on/extension for showing details of EDAM concepts found in a website. Great e.g. for code and textual data on GitHub References: [1] Ison, J., Kalaš, M., Jonassen, I., et al. (2013). EDAM: an ontology of bioinformatics operations, types of data and identifiers, topics and formats. Bioinformatics, 29(10): 1325-1332. DOI: 10.1093/bioinformatics/btt113 [2] Matúš Kalaš, Laure Plantard, Joakim Lindblad, Martin Jones, Nataša Sladoje, Moritz A. 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DOI: 10.21105/joss.00698</abstract><pub>F1000</pub><oa>free_for_read</oa></addata></record> |
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| title | EDAM: the bioscientific data analysis ontology (update 2021) [version 1; not peer reviewed] |
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