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WikiPathways: Pathway Editing for the People

Alexander R Pico, Thomas Kelder, Martijn P van Iersel, Kristina Hanspers, Bruce R Conklin, Chris Evelo
2008 PLoS Biology  
Even prior to this publication introducing WikiPathways, we have seen strong signs of community participation.  ...  We envision WikiPathways being part of a broader effort to extend curation capacity to larger groups and communities.  ... 
doi:10.1371/journal.pbio.0060184 pmid:18651794 pmcid:PMC2475545 fatcat:ohczavszz5b3dpsllugdbwxcfe

WikiPathways: building research communities on biological pathways

T. Kelder, M. P. van Iersel, K. Hanspers, M. Kutmon, B. R. Conklin, C. T. Evelo, A. R. Pico
2011 Nucleic Acids Research  
New features are discussed, as well as developments in the community of contributors.  ...  WikiPathways is seeing steady growth in the number of users, page views and edits for each pathway.  ...  Therefore, we aim to make WikiPathways content more accessible and connected through semantic technologies.  ... 
doi:10.1093/nar/gkr1074 pmid:22096230 pmcid:PMC3245032 fatcat:wmolsaazdnhpbd27cydgovi2hu

Creating biological pathways for WikiPathways using PathVisio

Friederike Ehrhart, Martina Kutmon, Egon Willighagen, Kristina Hanspers, Alexander Pico, Linda Rieswijk, Penny Nymark
2017 Figshare  
What is WikiPathways WikiPathways was established to facilitate the contribution and maintenance of pathway information by the biology community.  ...  More importantly, the open, public approach of WikiPathways allows for broader participation by the entire community, ranging from students to senior experts in each field.  ...  INTRODUCTION WHAT IS WIKIPATHWAYS WikiPathways was established to facilitate the contribution and maintenance of pathway information by the biology community.  ... 
doi:10.6084/m9.figshare.4668349.v1 fatcat:v35v6n3tnzgwhalcpfcwmixnqq

Community curation on WikiPathways: How we assist knowledge collection

Chris Evelo
2009 Nature Precedings  
WikiPathwaysWikiPathways Public resource for biological pathways • Wiki: -Anyone can contribute and curate • More up-to-date representation of biological knowledge Ask for tool or pathways • We need  ...  Automatic pathway (table) generator for any GO level • Ask for tool or pathways • Go statistics in GenMAPP, Go_Elite, R (through webservice) KEGG • Automatic pathway converter • -Original -Community  ...  Connect to Genome Databases  ... 
doi:10.1038/npre.2009.3115.1 fatcat:r3f6twg7bzg5xkbbyp7db6m2em

WikiPathways: capturing the full diversity of pathway knowledge

Martina Kutmon, Anders Riutta, Nuno Nunes, Kristina Hanspers, Egon L. Willighagen, Anwesha Bohler, Jonathan Mélius, Andra Waagmeester, Sravanthi R. Sinha, Ryan Miller, Susan L. Coort, Elisa Cirillo (+3 others)
2015 Nucleic Acids Research  
We introduce the Quick Edit feature for pathway authors and curators, in addition to new means of publishing pathways and maintaining custom pathway collections to serve specific research topics and communities  ...  WikiPathways (http://www.wikipathways.org) is an open, collaborative platform for capturing and disseminating models of biological pathways for data visualization and analysis.  ...  ACKNOWLEDGEMENTS Thanks to all the people who contributed to WikiPathways content, code and discussions. We are grateful for the support of the Google Summer of Code program.  ... 
doi:10.1093/nar/gkv1024 pmid:26481357 pmcid:PMC4702772 fatcat:4xge7wkrtbajzaoudxgakyc3aa

WikiPathways: a multifaceted pathway database bridging metabolomics to other omics research

Denise N Slenter, Martina Kutmon, Kristina Hanspers, Anders Riutta, Jacob Windsor, Nuno Nunes, Jonathan Mélius, Elisa Cirillo, Susan L Coort, Daniela Digles, Friederike Ehrhart, Pieter Giesbertz (+10 others)
2017 Nucleic Acids Research  
New search options, monthly downloads, more links to metabolite databases, and new portals make pathway knowledge more effortlessly accessible to individual researchers and research communities.  ...  Due to the open and collaborative nature of the WikiPathways platform, our content keeps growing and is getting more accurate, making WikiPathways a reliable and rich pathway database.  ...  ACKNOWLEDGEMENTS Thanks to all the people who contributed to WikiPathways content, code and discussions and who used the content of WikiPathways in their projects. FUNDING  ... 
doi:10.1093/nar/gkx1064 pmid:29136241 pmcid:PMC5753270 fatcat:ecbus4xpjfdjzd3n2urxs32exy

WikiPathways App for Cytoscape: Making biological pathways amenable to network analysis and visualization

Martina Kutmon, Samad Lotia, Chris T Evelo, Alexander R Pico
2014 F1000Research  
In this paper we present the open-source WikiPathways app for Cytoscape ( ) that can be used to import http://apps.cytoscape.org/apps/wikipathways biological pathways for data visualization and network  ...  WikiPathways is an open, collaborative biological pathway database that provides fully annotated pathway diagrams for manual download or through web services.  ...  Results The WikiPathways app in Cytoscape provides convenient access to the community-curated collection of biological pathways at WikiPathways.  ... 
doi:10.12688/f1000research.4254.2 pmid:25254103 pmcid:PMC4168754 fatcat:k3xai5veqbbspf3q6tggstbl4e

WikiPathways App for Cytoscape: Making biological pathways amenable to network analysis and visualization

Martina Kutmon, Samad Lotia, Chris T Evelo, Alexander R Pico
2014 F1000Research  
In this paper we present the open-source WikiPathways app for Cytoscape ( ) that can be used to import http://apps.cytoscape.org/apps/wikipathways biological pathways for data visualization and network  ...  WikiPathways is an open, collaborative biological pathway database that provides fully annotated pathway diagrams for manual download or through web services.  ...  Results The WikiPathways app in Cytoscape provides convenient access to the community-curated collection of biological pathways at WikiPathways.  ... 
doi:10.12688/f1000research.4254.1 fatcat:ykncmkehkncnddquvqhycghuzy

Introducing WikiPathways as a Data-Source to Support Adverse Outcome Pathways for Regulatory Risk Assessment of Chemicals and Nanomaterials

Marvin Martens, Tim Verbruggen, Penny Nymark, Roland Grafström, Lyle D. Burgoon, Hristo Aladjov, Fernando Torres Andón, Chris T. Evelo, Egon L. Willighagen
2018 Frontiers in Genetics  
Automatic connection through linkage of identifiers between the databases showed that only 30% of AOP-Wiki chemicals were found on WikiPathways.  ...  A new AOP Portal on WikiPathways is presented to allow the community of AOP developers to collaborate and populate the molecular pathways that underlie the KEs of AOP-Wiki.  ...  Because the AOP-KB is driven by a scientific community to develop, share and discuss AOPs, this community can also describe the molecular processes underlying the AOPs and contribute to WikiPathways and  ... 
doi:10.3389/fgene.2018.00661 pmid:30622555 pmcid:PMC6308971 fatcat:k32w6h6zazg5xhhtj6bulgi3gu

Using the Semantic Web for Rapid Integration of WikiPathways with Other Biological Online Data Resources

Andra Waagmeester, Martina Kutmon, Anders Riutta, Ryan Miller, Egon L. Willighagen, Chris T. Evelo, Alexander R. Pico, Christos A. Ouzounis
2016 PLoS Computational Biology  
Author Summary WikiPathways is a crowd-sourced online platform for biological pathways. It is based on the same underlying platform as Wikipedia.  ...  WikiPathways, an online collaborative pathway resource, is now available in the semantic web through a SPARQL endpoint at http://sparql. wikipathways.org.  ...  This is done to be able to reflect the semantics used in the WikiPathways community.  ... 
doi:10.1371/journal.pcbi.1004989 pmid:27336457 pmcid:PMC4918977 fatcat:tkjaukwptfe4tct6kflm4ssyry

Biotransformation pathway maps in WikiPathways enable direct visualization of drug metabolism related expression changes

Danyel G.J. Jennen, Stan Gaj, Pieter J. Giesbertz, Joost H.M. van Delft, Chris T. Evelo, Jos C.S. Kleinjans
2010 Drug Discovery Today  
made available to the community at WikiPathways [20] .  ...  In addition, cross-references to other gene identifiers and protein identifiers are connected using an Ensembl-based derby database mapping in the BridgeDb framework.  ... 
doi:10.1016/j.drudis.2010.08.002 pmid:20708095 fatcat:5nb653k3mrctfmka2wkoexymgi

Interoperability starts with resources, identifiers, and linking

Egon Willighagen
2021 Zenodo  
, Micelio, the NanoSafety Cluster projects, the emerging ELIXIR Toxicology Community, the ELIXIR Metabolomics Community, ELXIR-NL, and of ELIXIR itself.  ...  Acknowledgments This presentation was not possible without the work from many members of the Dept. of Bioinformatics -BiGCaT, the WikiPathways project and collaborators from NextProt and Complex Portal  ...  The first example comes from the ELIXIR Metabolomics Community where various ELIXIR Core Data Resources (ChEMBL, ChEBI, Rhea) and the ELIXIR-NL service WikiPathways [1] are connected using metabolite  ... 
doi:10.5281/zenodo.4954810 fatcat:psp2spebszd27lgmmbgjfytz5e

Bioinformatics and systems biology in the fight against COVID-19

Lauren J. Dupuis, Martina Kutmon, Denise Slenter, Chris T. Evelo
2020 Zenodo  
The scientific research community all over the world has sprung into action to aid in the fight against COVID-19.  ...  Bioinformatics at Maastricht University (https://www.maastrichtuniversity.nl/research/bioinformatics) are at the forefront in curating computer models of COVID-19 molecular processes in the online database WikiPathways  ...  WikiPathways is built on the same premise as Wikipedia -community curation. Everybody can contribute, curate, discuss and use the entire knowledge base of biological pathways.  ... 
doi:10.5281/zenodo.3954187 fatcat:bo7m7kjhjfat3cmxqxhwlwtcve

Understanding signaling and metabolic paths using semantified and harmonized information about biological interactions [article]

Ryan Miller, Egon Willighagen, Chris Evelo, Martina Kutmon, Andra Waagmeester, Anwesha Bohler
2020 bioRxiv   pre-print
Conclusion This paper demonstrates that most of the graphical biological knowledge from WikiPathways is modelled in the semantic layer of WikiPathways with the semantic information intact and connectivity  ...  The usability of the WikiPathways pathway and connectivity information has shown to be useful and has been integrated into other platforms.  ...  Acknowledgements A thank you to the authors and curation teams at WikiPathways, they require a special acknowledgement for their maintenance of the primary resource used for analysis.  ... 
doi:10.1101/2020.07.31.230599 fatcat:yleaiblfiffnpa633sxog6sthe

The role of bioinformatics in pathway curation

A. S. Waagmeester, T. Kelder, C. T. A. Evelo
2008 Genes & Nutrition  
WikiPathways applies a similar approach to biological pathway information. Pathway diagrams on WikiPathways can be created and curated by every member of the scientific community.  ...  WikiPathways builds upon the concept of community-based curation of biological knowledge using a wiki [5, 10, 12] . A wiki is a website the content of which can be edited by users.  ... 
doi:10.1007/s12263-008-0098-x pmid:19034548 pmcid:PMC2593017 fatcat:rzbowrplindixfl3sdtbjrh5ca
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