WikiPathways: connecting communities
Abstract WikiPathways (https://www.wikipathways.org) is a biological pathway database known for its collaborative nature and open science approaches. With the core idea of the scientific community developing and curating biological knowledge in pathway models, WikiPathways lowers all barriers for ac...
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Veröffentlicht in: | Nucleic acids research 2021-01, Vol.49 (D1), p.D613-D621 |
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creator | Martens, Marvin Ammar, Ammar Riutta, Anders Waagmeester, Andra Slenter, Denise N Hanspers, Kristina A. Miller, Ryan Digles, Daniela Lopes, Elisson N Ehrhart, Friederike Dupuis, Lauren J Winckers, Laurent A Coort, Susan L Willighagen, Egon L Evelo, Chris T Pico, Alexander R Kutmon, Martina |
description | Abstract
WikiPathways (https://www.wikipathways.org) is a biological pathway database known for its collaborative nature and open science approaches. With the core idea of the scientific community developing and curating biological knowledge in pathway models, WikiPathways lowers all barriers for accessing and using its content. Increasingly more content creators, initiatives, projects and tools have started using WikiPathways. Central in this growth and increased use of WikiPathways are the various communities that focus on particular subsets of molecular pathways such as for rare diseases and lipid metabolism. Knowledge from published pathway figures helps prioritize pathway development, using optical character and named entity recognition. We show the growth of WikiPathways over the last three years, highlight the new communities and collaborations of pathway authors and curators, and describe various technologies to connect to external resources and initiatives. The road toward a sustainable, community-driven pathway database goes through integration with other resources such as Wikidata and allowing more use, curation and redistribution of WikiPathways content.
Graphical Abstract
Graphical Abstract
WikiPathways enables research communities to collaborate on molecular pathway curation to create reusable, machine-readable pathway models. The pathway collections are freely available and integrated with many analysis tools and resources. |
doi_str_mv | 10.1093/nar/gkaa1024 |
format | Article |
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WikiPathways (https://www.wikipathways.org) is a biological pathway database known for its collaborative nature and open science approaches. With the core idea of the scientific community developing and curating biological knowledge in pathway models, WikiPathways lowers all barriers for accessing and using its content. Increasingly more content creators, initiatives, projects and tools have started using WikiPathways. Central in this growth and increased use of WikiPathways are the various communities that focus on particular subsets of molecular pathways such as for rare diseases and lipid metabolism. Knowledge from published pathway figures helps prioritize pathway development, using optical character and named entity recognition. We show the growth of WikiPathways over the last three years, highlight the new communities and collaborations of pathway authors and curators, and describe various technologies to connect to external resources and initiatives. The road toward a sustainable, community-driven pathway database goes through integration with other resources such as Wikidata and allowing more use, curation and redistribution of WikiPathways content.
Graphical Abstract
Graphical Abstract
WikiPathways enables research communities to collaborate on molecular pathway curation to create reusable, machine-readable pathway models. The pathway collections are freely available and integrated with many analysis tools and resources.</description><identifier>ISSN: 0305-1048</identifier><identifier>EISSN: 1362-4962</identifier><identifier>DOI: 10.1093/nar/gkaa1024</identifier><identifier>PMID: 33211851</identifier><language>eng</language><publisher>England: Oxford University Press</publisher><subject>COVID-19 - pathology ; Data Curation ; Database Issue ; Databases, Factual ; Humans ; User-Computer Interface</subject><ispartof>Nucleic acids research, 2021-01, Vol.49 (D1), p.D613-D621</ispartof><rights>The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research. 2021</rights><rights>The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c510t-d1d08db98c7f3e4b823b8c9a9f491f151f708b1138fb09d3461ae35f1d9115583</citedby><cites>FETCH-LOGICAL-c510t-d1d08db98c7f3e4b823b8c9a9f491f151f708b1138fb09d3461ae35f1d9115583</cites><orcidid>0000-0001-5934-3559 ; 0000-0003-3477-7443 ; 0000-0001-5410-599X ; 0000-0001-5706-2163 ; 0000-0003-1224-9690 ; 0000-0003-2230-0840 ; 0000-0003-1661-6304 ; 0000-0002-7699-8191 ; 0000-0001-9773-4008 ; 0000-0001-8449-1318 ; 0000-0002-7770-620X ; 0000-0002-9454-4783 ; 0000-0002-4693-0591 ; 0000-0002-5301-3142 ; 0000-0002-8399-8990 ; 0000-0001-7542-0286 ; 0000-0003-2606-3045</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC7779061/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC7779061/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,864,885,1604,27924,27925,53791,53793</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/33211851$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Martens, Marvin</creatorcontrib><creatorcontrib>Ammar, Ammar</creatorcontrib><creatorcontrib>Riutta, Anders</creatorcontrib><creatorcontrib>Waagmeester, Andra</creatorcontrib><creatorcontrib>Slenter, Denise N</creatorcontrib><creatorcontrib>Hanspers, Kristina</creatorcontrib><creatorcontrib>A. Miller, Ryan</creatorcontrib><creatorcontrib>Digles, Daniela</creatorcontrib><creatorcontrib>Lopes, Elisson N</creatorcontrib><creatorcontrib>Ehrhart, Friederike</creatorcontrib><creatorcontrib>Dupuis, Lauren J</creatorcontrib><creatorcontrib>Winckers, Laurent A</creatorcontrib><creatorcontrib>Coort, Susan L</creatorcontrib><creatorcontrib>Willighagen, Egon L</creatorcontrib><creatorcontrib>Evelo, Chris T</creatorcontrib><creatorcontrib>Pico, Alexander R</creatorcontrib><creatorcontrib>Kutmon, Martina</creatorcontrib><title>WikiPathways: connecting communities</title><title>Nucleic acids research</title><addtitle>Nucleic Acids Res</addtitle><description>Abstract
WikiPathways (https://www.wikipathways.org) is a biological pathway database known for its collaborative nature and open science approaches. With the core idea of the scientific community developing and curating biological knowledge in pathway models, WikiPathways lowers all barriers for accessing and using its content. Increasingly more content creators, initiatives, projects and tools have started using WikiPathways. Central in this growth and increased use of WikiPathways are the various communities that focus on particular subsets of molecular pathways such as for rare diseases and lipid metabolism. Knowledge from published pathway figures helps prioritize pathway development, using optical character and named entity recognition. We show the growth of WikiPathways over the last three years, highlight the new communities and collaborations of pathway authors and curators, and describe various technologies to connect to external resources and initiatives. The road toward a sustainable, community-driven pathway database goes through integration with other resources such as Wikidata and allowing more use, curation and redistribution of WikiPathways content.
Graphical Abstract
Graphical Abstract
WikiPathways enables research communities to collaborate on molecular pathway curation to create reusable, machine-readable pathway models. 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WikiPathways (https://www.wikipathways.org) is a biological pathway database known for its collaborative nature and open science approaches. With the core idea of the scientific community developing and curating biological knowledge in pathway models, WikiPathways lowers all barriers for accessing and using its content. Increasingly more content creators, initiatives, projects and tools have started using WikiPathways. Central in this growth and increased use of WikiPathways are the various communities that focus on particular subsets of molecular pathways such as for rare diseases and lipid metabolism. Knowledge from published pathway figures helps prioritize pathway development, using optical character and named entity recognition. We show the growth of WikiPathways over the last three years, highlight the new communities and collaborations of pathway authors and curators, and describe various technologies to connect to external resources and initiatives. The road toward a sustainable, community-driven pathway database goes through integration with other resources such as Wikidata and allowing more use, curation and redistribution of WikiPathways content.
Graphical Abstract
Graphical Abstract
WikiPathways enables research communities to collaborate on molecular pathway curation to create reusable, machine-readable pathway models. The pathway collections are freely available and integrated with many analysis tools and resources.</abstract><cop>England</cop><pub>Oxford University Press</pub><pmid>33211851</pmid><doi>10.1093/nar/gkaa1024</doi><orcidid>https://orcid.org/0000-0001-5934-3559</orcidid><orcidid>https://orcid.org/0000-0003-3477-7443</orcidid><orcidid>https://orcid.org/0000-0001-5410-599X</orcidid><orcidid>https://orcid.org/0000-0001-5706-2163</orcidid><orcidid>https://orcid.org/0000-0003-1224-9690</orcidid><orcidid>https://orcid.org/0000-0003-2230-0840</orcidid><orcidid>https://orcid.org/0000-0003-1661-6304</orcidid><orcidid>https://orcid.org/0000-0002-7699-8191</orcidid><orcidid>https://orcid.org/0000-0001-9773-4008</orcidid><orcidid>https://orcid.org/0000-0001-8449-1318</orcidid><orcidid>https://orcid.org/0000-0002-7770-620X</orcidid><orcidid>https://orcid.org/0000-0002-9454-4783</orcidid><orcidid>https://orcid.org/0000-0002-4693-0591</orcidid><orcidid>https://orcid.org/0000-0002-5301-3142</orcidid><orcidid>https://orcid.org/0000-0002-8399-8990</orcidid><orcidid>https://orcid.org/0000-0001-7542-0286</orcidid><orcidid>https://orcid.org/0000-0003-2606-3045</orcidid><oa>free_for_read</oa></addata></record> |
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subjects | COVID-19 - pathology Data Curation Database Issue Databases, Factual Humans User-Computer Interface |
title | WikiPathways: connecting communities |
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