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WikiPathways: connecting communities

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 a...

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Autores principales: 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
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7779061/
https://www.ncbi.nlm.nih.gov/pubmed/33211851
http://dx.doi.org/10.1093/nar/gkaa1024
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author 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
author_facet 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
author_sort Martens, Marvin
collection PubMed
description 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.
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spelling pubmed-77790612021-01-07 WikiPathways: connecting communities 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 Nucleic Acids Res Database Issue 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. Oxford University Press 2020-11-19 /pmc/articles/PMC7779061/ /pubmed/33211851 http://dx.doi.org/10.1093/nar/gkaa1024 Text en © The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Database Issue
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
WikiPathways: connecting communities
title WikiPathways: connecting communities
title_full WikiPathways: connecting communities
title_fullStr WikiPathways: connecting communities
title_full_unstemmed WikiPathways: connecting communities
title_short WikiPathways: connecting communities
title_sort wikipathways: connecting communities
topic Database Issue
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7779061/
https://www.ncbi.nlm.nih.gov/pubmed/33211851
http://dx.doi.org/10.1093/nar/gkaa1024
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