{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,3]],"date-time":"2025-11-03T09:07:02Z","timestamp":1762160822627},"reference-count":8,"publisher":"Oxford University Press (OUP)","issue":"17","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2010,9,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: In recent years, the number of knowledge bases developed using Wiki technology has exploded. Unfortunately, next to their numerous advantages, classical Wikis present a critical limitation: the invaluable knowledge they gather is represented as free text, which hinders their computational exploitation. This is in sharp contrast with the current practice for biological databases where the data is made available in a structured way. Here, we present WikiOpener an extension for the classical MediaWiki engine that augments Wiki pages by allowing on-the-fly querying and formatting resources external to the Wiki. Those resources may provide data extracted from databases or DAS tracks, or even results returned by local or remote bioinformatics analysis tools. This also implies that structured data can be edited via dedicated forms. Hence, this generic resource combines the structure of biological databases with the flexibility of collaborative Wikis.<\/jats:p>\n               <jats:p>Availability: The source code and its documentation are freely available on the MediaWiki website: http:\/\/www.mediawiki.org\/wiki\/Extension:WikiOpener.<\/jats:p>\n               <jats:p>Contact: \u00a0sbrohee@esat.kuleuven.be<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btq348","type":"journal-article","created":{"date-parts":[[2010,7,1]],"date-time":"2010-07-01T02:24:28Z","timestamp":1277951068000},"page":"2210-2211","source":"Crossref","is-referenced-by-count":6,"title":["Biological knowledge bases using Wikis: combining the flexibility of Wikis with the structure of databases"],"prefix":"10.1093","volume":"26","author":[{"given":"Sylvain","family":"Broh\u00e9e","sequence":"first","affiliation":[{"name":"1 ESAT-SCD. Katholieke Universiteit Leuven, Kasteelpark Arenberg 10, B-3001 Leuven, Belgium and 2Universit\u00e9 de Toulouse, UPS, Laboratoire de Microbiologie et G\u00e9n\u00e9tique Mol\u00e9culaire, Centre National de la Recherche Scientifique, F-31000 Toulouse, France"}]},{"given":"Roland","family":"Barriot","sequence":"additional","affiliation":[{"name":"1 ESAT-SCD. Katholieke Universiteit Leuven, Kasteelpark Arenberg 10, B-3001 Leuven, Belgium and 2Universit\u00e9 de Toulouse, UPS, Laboratoire de Microbiologie et G\u00e9n\u00e9tique Mol\u00e9culaire, Centre National de la Recherche Scientifique, F-31000 Toulouse, France"},{"name":"1 ESAT-SCD. Katholieke Universiteit Leuven, Kasteelpark Arenberg 10, B-3001 Leuven, Belgium and 2Universit\u00e9 de Toulouse, UPS, Laboratoire de Microbiologie et G\u00e9n\u00e9tique Mol\u00e9culaire, Centre National de la Recherche Scientifique, F-31000 Toulouse, France"}]},{"given":"Yves","family":"Moreau","sequence":"additional","affiliation":[{"name":"1 ESAT-SCD. Katholieke Universiteit Leuven, Kasteelpark Arenberg 10, B-3001 Leuven, Belgium and 2Universit\u00e9 de Toulouse, UPS, Laboratoire de Microbiologie et G\u00e9n\u00e9tique Mol\u00e9culaire, Centre National de la Recherche Scientifique, F-31000 Toulouse, France"}]}],"member":"286","published-online":{"date-parts":[[2010,6,30]]},"reference":[{"key":"2023012508013097100_B1","doi-asserted-by":"crossref","first-page":"295","DOI":"10.1093\/bib\/bbn053","article-title":"A pitfall of wiki solution for biological databases","volume":"10","author":"Arita","year":"2009","journal-title":"Brief. Bioinform."},{"key":"2023012508013097100_B2","doi-asserted-by":"crossref","first-page":"16","DOI":"10.1186\/gm137","article-title":"Collaboratively charting the gene-to-phenotype network of human congenital heart defects","volume":"2","author":"Barriot","year":"2010","journal-title":"Genome Med."},{"key":"2023012508013097100_B3","doi-asserted-by":"crossref","first-page":"D1","DOI":"10.1093\/nar\/gkn942","article-title":"Nucleic acids research annual database issue and the nar online molecular biology database collection in 2009","volume":"37","author":"Galperin","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"2023012508013097100_B4","doi-asserted-by":"crossref","first-page":"R121","DOI":"10.1186\/gb-2008-9-8-r121","article-title":"Proteopedia - a scientific \u2018wiki\u2019 bridging the rift between three-dimensional structure and function of biomacromolecules","volume":"9","author":"Hodis","year":"2008","journal-title":"Genome Biol."},{"key":"2023012508013097100_B5","doi-asserted-by":"crossref","first-page":"1289","DOI":"10.1126\/science.320.5881.1289b","article-title":"The emerging world of wikis","volume":"320","author":"Hu","year":"2008","journal-title":"Science"},{"key":"2023012508013097100_B6","doi-asserted-by":"crossref","first-page":"R89","DOI":"10.1186\/gb-2008-9-5-r89","article-title":"Calling on a million minds for community annotation in wikiproteins","volume":"9","author":"Mons","year":"2008","journal-title":"Genome Biol."},{"key":"2023012508013097100_B7","doi-asserted-by":"crossref","first-page":"e184","DOI":"10.1371\/journal.pbio.0060184","article-title":"Wikipathways: pathway editing for the people","volume":"6","author":"Pico","year":"2008","journal-title":"PLoS Biol."},{"key":"2023012508013097100_B8","doi-asserted-by":"crossref","first-page":"389","DOI":"10.1016\/S0955-0674(00)00226-X","article-title":"A genomic view of yeast membrane transporters","volume":"13","author":"Van Belle","year":"2001","journal-title":"Curr. Opin. Cell Biol."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/26\/17\/2210\/48854444\/bioinformatics_26_17_2210.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/26\/17\/2210\/48854444\/bioinformatics_26_17_2210.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T08:01:42Z","timestamp":1674633702000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/26\/17\/2210\/198818"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2010,6,30]]},"references-count":8,"journal-issue":{"issue":"17","published-print":{"date-parts":[[2010,9,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btq348","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2010,9,1]]},"published":{"date-parts":[[2010,6,30]]}}}