Help:Authors

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Current revision (08:32, 21 May 2020) (view source)
(Added also a link for just the SARS-CoV-2 identifiers.)
 
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__NOTOC__ <!-- Turn off Table of Contents -->
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This page explains which tools are available for pathway building and curation. Our pathway building tool is called [https://www.pathvisio.org/ Pathvisio].
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<font size=5> Share Your Pathway Knowledge </font>
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* If you have never build a pathway model before, we would advise you to use our online learning tool [http://academy.wikipathways.org/ WikiPathways Academy].
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Over 700 researchers and pathway enthusiasts have shared their time and knowledge here at WikiPathways. We see ~100 new pathways each year along with thousands of [[WikiPathways:Statistics|edits and updates]].  
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* If you directly want to start editing, please download the [https://www.pathvisio.org/downloads/ local PathVisio installation] and the [https://www.pathvisio.org/plugin/wikipathways-plugin/ WikiPathways plugin].
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'''''Join the effort''''' to collect pathway knowledge in a format that can be broadly redistributed and made useful to [[Help:Tools_using_WikiPathways|active biomedical research]].
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Please be aware that new users (starting in 2019) need to request access to use the WikiPathways plugin; which can be done [http://plugins.pathvisio.org/wp-client/request-webservice-access/ here] or through sending a message to our team on our [https://groups.google.com/forum/#!forum/wikipathways-discuss google discussion forum].
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* More information on how to search and edit pathways through this plugin can be found [http://plugins.pathvisio.org/wp-client/tutorials/ here].
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<section begin=covid-help/>
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<div class="frontPagePanel redBg" style="width:95%;margin:1em;width=100%">
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<h2 class="frontPagePanel redFg">Call to Action: COVID-19</h2>
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We are helping to coordinate an international effort to build and curate pathway models relevant to the COVID-19 pandemic. Review the resources below to see how you can get involved.
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* '''[[Portal:Disease/COVIDPathways|Rapidly growing collection of COVID-19 pathways]]'''. If you find or add a pathway at WikiPathways that should be included in this collection, please [https://groups.google.com/forum/#!forum/wikipathways-discuss let us know].
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* '''[https://gladstone-bioinformatics.shinyapps.io/shiny-covidpathways/ Published pathway figures related to COVID-19]'''. Useful resource of previously published ''(but not modeled)'' pathways for direct translation as new pathways or to inform related pathway curation.
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* '''[https://alexanderpico.github.io/SARS-CoV-2_Alignments/ Protein sequence alignments of SARS-CoV-2]'''. Useful resource mapping SARS-CoV-2 proteins to those previously studied, including many solved structures.
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* '''[https://covid.pages.uni.lu/map_curation COVID-19 disease map initiative].''' An even broader community of pathway curators working with WikiPathways, Pathway Commons, Reactome, Cell Designer and more. Great community and set of resources, including repos, file shares, mailing list and Slack channel.
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* '''[https://egonw.github.io/SARS-CoV-2-Queries/sparql/virusProteinsAll.code.html Human Coronavirus protein identifiers] and [https://egonw.github.io/SARS-CoV-2-Queries/sparql/virusProteins.code.html SARS-CoV-2 protein identifiers]'''
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* '''[https://pubchem.ncbi.nlm.nih.gov/#query=coronavirus&tab=pathway PubChem list of the COVID-19 Portal pathways]'''
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IMPORTANT: WikiPathways is dedicated to [https://www.go-fair.org/fair-principles FAIR standards]. All content at WikiPathways is freely available for use and reuse by a [[WikiPathways:License_Terms|CC0 waiver]].
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</div>
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<section end=covid-help />
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== For Pathway Authors and Curators ==
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<font size=5> Getting Started </font>
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&nbsp;<font size=4>1.</font> If you are brand new to pathway modeling, then we recommend starting with our '''online workshop''': [https://github.com/gladstone-institutes/Bioinformatics-Workshops/wiki/Introduction-to-Pathway-Modeling Introduction to Pathway Modeling] (scroll down to the "Online Learning" section). Also check out this helpful '''tutorial and set of guidelines''' for [https://enanomapper.github.io/tutorials/Pathway/Pathway.html new pathway authors], which includes links to '''video tutorials''' as well.
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&nbsp;<font size=4>2.</font> If you want more practice with the pathway drawing tool and WikiPathways, then check out our '''online learning tool''' [http://academy.wikipathways.org/ WikiPathways Academy].
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&nbsp;<font size=4>3.</font> When you are ready to start editing at WikiPathways, be sure that you have PathVisio and the WikiPathways plugin installed (see Step 1) and '''check-in with the community''' at [https://groups.google.com/forum/#!forum/wikipathways-discuss google discussion forum] to confirm your account and ask any questions you might have.
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== Resources for Pathway Authors and Curators ==
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* [https://github.com/gladstone-institutes/Bioinformatics-Workshops/wiki/Introduction-to-Pathway-Modeling Introduction to Pathway Modeling]
* [http://academy.wikipathways.org/ WikiPathways Academy]
* [http://academy.wikipathways.org/ WikiPathways Academy]
* [https://www.wikipathways.org/img_auth.php/d/d0/Instructions_for_WikiPathways_Authors.pdf Instructions for Authors]
* [https://www.wikipathways.org/img_auth.php/d/d0/Instructions_for_WikiPathways_Authors.pdf Instructions for Authors]
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* [[:Help:New Contributor Quickstart|New Contributor Quickstart]]
 
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* [https://wikipathways.github.io/academy/qaprotocol.html Quality Assurance Protocol]
 
* [[:Help:PathwayStyling|Styling WikiPathways Models in Cytoscape]]
* [[:Help:PathwayStyling|Styling WikiPathways Models in Cytoscape]]
* [[:Help:Editing Pathways|Editing Pathways]]
* [[:Help:Editing Pathways|Editing Pathways]]
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* [[:Help:WikiPathways Portals|WikiPathways Portals]]
* [[:Help:WikiPathways Portals|WikiPathways Portals]]
* [[Template:User_ORCID|How to add your ORCID identifier]]
* [[Template:User_ORCID|How to add your ORCID identifier]]
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* [https://wikipathways.github.io/academy/qaprotocol.html Quality Assurance Protocol]

Current revision


Share Your Pathway Knowledge

Over 700 researchers and pathway enthusiasts have shared their time and knowledge here at WikiPathways. We see ~100 new pathways each year along with thousands of edits and updates.

Join the effort to collect pathway knowledge in a format that can be broadly redistributed and made useful to active biomedical research.


Call to Action: COVID-19

We are helping to coordinate an international effort to build and curate pathway models relevant to the COVID-19 pandemic. Review the resources below to see how you can get involved.

IMPORTANT: WikiPathways is dedicated to FAIR standards. All content at WikiPathways is freely available for use and reuse by a CC0 waiver.


Getting Started

 1. If you are brand new to pathway modeling, then we recommend starting with our online workshop: Introduction to Pathway Modeling (scroll down to the "Online Learning" section). Also check out this helpful tutorial and set of guidelines for new pathway authors, which includes links to video tutorials as well.

 2. If you want more practice with the pathway drawing tool and WikiPathways, then check out our online learning tool WikiPathways Academy.

 3. When you are ready to start editing at WikiPathways, be sure that you have PathVisio and the WikiPathways plugin installed (see Step 1) and check-in with the community at google discussion forum to confirm your account and ask any questions you might have.

Resources for Pathway Authors and Curators

Personal tools