Curation Jamboree Oct 2011
From WikiPathways
(Difference between revisions)
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* Support: WikiPathways admins and curators will be available in an online chat channel during the event to answer all your questions. | * Support: WikiPathways admins and curators will be available in an online chat channel during the event to answer all your questions. | ||
| - | + | == Getting started == | |
| - | + | ||
* Take a look at our [[Special:BrowsePathwaysPage|archive]] to identify pathways where you might contribute your expertise. | * Take a look at our [[Special:BrowsePathwaysPage|archive]] to identify pathways where you might contribute your expertise. | ||
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If you don't have a specific set of pathways in mind, we have prepared a list of suggested curation tasks as well as lists of pathways in need of work. | If you don't have a specific set of pathways in mind, we have prepared a list of suggested curation tasks as well as lists of pathways in need of work. | ||
| - | == Suggested tasks == | + | === Suggested tasks === |
* Add ontology tags [[Curation_Jamboree_Oct_2011#Add_ontology_tags|Details]] | * Add ontology tags [[Curation_Jamboree_Oct_2011#Add_ontology_tags|Details]] | ||
* Create and clean up groups and complexes [[Curation_Jamboree_Oct_2011#Create_groups_and_complexes|Details]] | * Create and clean up groups and complexes [[Curation_Jamboree_Oct_2011#Create_groups_and_complexes|Details]] | ||
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* Add pathway description to pathways with missing description [[Curation_Jamboree_Sep_2010#Add description|Details]] | * Add pathway description to pathways with missing description [[Curation_Jamboree_Sep_2010#Add description|Details]] | ||
| - | === Add ontology tags === | + | ==== Add ontology tags ==== |
| - | === Create groups and complexes === | + | ==== Create groups and complexes ==== |
| - | === Update datanode annotation === | + | ==== Update datanode annotation ==== |
The purpose of this task is to add annotation for datanodes that are unannotated. You can find pathways with missing datanode annotation [http://www.wikipathways.org//index.php?title=Special:SpecialCurationTags&showPathwaysFor=Curation:MissingXRef here]. | The purpose of this task is to add annotation for datanodes that are unannotated. You can find pathways with missing datanode annotation [http://www.wikipathways.org//index.php?title=Special:SpecialCurationTags&showPathwaysFor=Curation:MissingXRef here]. | ||
# Review the datanode annotations in the DataNodes list at the bottom of the pathway page to identify unannotated datanodes. Instructions for how to update datanode annotation can be found [[Help:Tutorial:Step_3|here]]. | # Review the datanode annotations in the DataNodes list at the bottom of the pathway page to identify unannotated datanodes. Instructions for how to update datanode annotation can be found [[Help:Tutorial:Step_3|here]]. | ||
# After you have updated the pathways, if all datanodes in the pathway are correctly annotated, remove the [[Template:Curation:MissingXRef|MissingXRef tag]] from the pathway. | # After you have updated the pathways, if all datanodes in the pathway are correctly annotated, remove the [[Template:Curation:MissingXRef|MissingXRef tag]] from the pathway. | ||
| - | === Connect interactions === | + | ==== Connect interactions ==== |
A pathway may be tagged with the [[Template:Curation:NoInteractions|Unconnected interactions tag]] anytime ANY lines in the pathway are not connected to another object in the pathway. This includes lines that are purely graphical and that shouldn't be connected to objects. | A pathway may be tagged with the [[Template:Curation:NoInteractions|Unconnected interactions tag]] anytime ANY lines in the pathway are not connected to another object in the pathway. This includes lines that are purely graphical and that shouldn't be connected to objects. | ||
* To find out which lines are unconnected, click the ''Edit'' button to open the pathway in the editor and click Ctrl+L to highlight all unconnected lines. | * To find out which lines are unconnected, click the ''Edit'' button to open the pathway in the editor and click Ctrl+L to highlight all unconnected lines. | ||
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* Once the pathway contains no unconnected lines, or if the remaining unconnected lines are purely graphical, remove the [[Template:Curation:NoInteractions|Unconnected lines tag]] from the pathway. | * Once the pathway contains no unconnected lines, or if the remaining unconnected lines are purely graphical, remove the [[Template:Curation:NoInteractions|Unconnected lines tag]] from the pathway. | ||
| - | === Add literature reference === | + | ==== Add literature reference ==== |
# Find pathways without literature references [http://www.wikipathways.org//index.php?title=Special:SpecialCurationTags&showPathwaysFor=Curation:NeedsReference here] | # Find pathways without literature references [http://www.wikipathways.org//index.php?title=Special:SpecialCurationTags&showPathwaysFor=Curation:NeedsReference here] | ||
# A literature reference can be from a publication or text book. For example, you may be able to find literature references for specific pathways by searching [http://www.ncbi.nlm.nih.gov/pubmed/ PubMed] or [http://en.wikipedia.org/wiki/Main_Page Wikipedia]. Instructions for how to add literature references to pathways can be found in the [[Help:Tutorial:Step_9|tutorial]]. | # A literature reference can be from a publication or text book. For example, you may be able to find literature references for specific pathways by searching [http://www.ncbi.nlm.nih.gov/pubmed/ PubMed] or [http://en.wikipedia.org/wiki/Main_Page Wikipedia]. Instructions for how to add literature references to pathways can be found in the [[Help:Tutorial:Step_9|tutorial]]. | ||
# Once you have added at least one literature reference to the pathway, remove the [[Template:Curation:NeedsReference|NeedsReference tag]] from the pathway. | # Once you have added at least one literature reference to the pathway, remove the [[Template:Curation:NeedsReference|NeedsReference tag]] from the pathway. | ||
| - | === Add description === | + | ==== Add description ==== |
# Find pathways with missing descriptions [http://www.wikipathways.org//index.php?title=Special:SpecialCurationTags showPathwaysFor=Curation:MissingDescription here] | # Find pathways with missing descriptions [http://www.wikipathways.org//index.php?title=Special:SpecialCurationTags showPathwaysFor=Curation:MissingDescription here] | ||
# A description can be from an outside source (publication, textbook, website) or it can be your own original description. Instructions for how to add descriptions to pathways can be found in the [[Help:Tutorial:Step_10|tutorial]]. | # A description can be from an outside source (publication, textbook, website) or it can be your own original description. Instructions for how to add descriptions to pathways can be found in the [[Help:Tutorial:Step_10|tutorial]]. | ||
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# Once you have added a description to the pathway, remove the [[Template:Curation:MissingDescription|MissingDescription tag]] from the pathway. | # Once you have added a description to the pathway, remove the [[Template:Curation:MissingDescription|MissingDescription tag]] from the pathway. | ||
| - | ==== Sources for descriptions ==== | + | ===== Sources for descriptions ===== |
Following are some suggested sources for pathway descriptions. | Following are some suggested sources for pathway descriptions. | ||
* [http://en.wikipedia.org/wiki/Main_Page Wikipedia] | * [http://en.wikipedia.org/wiki/Main_Page Wikipedia] | ||
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* [http://highwire.stanford.edu/ Scientific literature] | * [http://highwire.stanford.edu/ Scientific literature] | ||
| - | ==== Citing sources ==== | + | ===== Citing sources ===== |
Citing requirements varies between sources, so it is a good idea to find out the specific requirements for any particular source that you use for descriptions. In general, please cite the source for the description in the actual Descriptions section of the pathway with a direct link to the source (i.e. http://en.wikipedia.org/wiki/TGF_beta_signaling_pathway). | Citing requirements varies between sources, so it is a good idea to find out the specific requirements for any particular source that you use for descriptions. In general, please cite the source for the description in the actual Descriptions section of the pathway with a direct link to the source (i.e. http://en.wikipedia.org/wiki/TGF_beta_signaling_pathway). | ||
Below are instructions and examples for how to cite specific sources: | Below are instructions and examples for how to cite specific sources: | ||
| - | ===== Wikipedia ===== | + | ====== Wikipedia ====== |
* Cite Wikipedia in the Description section, and include a link to the relevant page at Wikipedia. | * Cite Wikipedia in the Description section, and include a link to the relevant page at Wikipedia. | ||
* [[Pathway:WP111|Wikipedia example]] | * [[Pathway:WP111|Wikipedia example]] | ||
| - | ===== PharmGKB ===== | + | ====== PharmGKB ====== |
* Cite PharmGKB in the Description section, and include a link to the relevant pathway page at PharmGKB. | * Cite PharmGKB in the Description section, and include a link to the relevant pathway page at PharmGKB. | ||
* If the pathway page at PharmGKB indicates that the pathway has been published in the Pharmacogenetics and Genomics journal, review the publication to see if the text used as a description appears in the publication. If so, add the citation to the Bibliography. | * If the pathway page at PharmGKB indicates that the pathway has been published in the Pharmacogenetics and Genomics journal, review the publication to see if the text used as a description appears in the publication. If so, add the citation to the Bibliography. | ||
* [[Pathway:WP554|PharmGKB example]] | * [[Pathway:WP554|PharmGKB example]] | ||
| - | ===== Reactome ===== | + | ====== Reactome ====== |
* Cite Reactome in the Description section, and include a link to the relevant pathway page at Reactome. | * Cite Reactome in the Description section, and include a link to the relevant pathway page at Reactome. | ||
* [[Pathway:WP466|Reactome example]] | * [[Pathway:WP466|Reactome example]] | ||
| - | ===== KEGG ===== | + | ====== KEGG ====== |
* Cite KEGG in the Description section, and include a link to the relevant pathway page at KEGG. | * Cite KEGG in the Description section, and include a link to the relevant pathway page at KEGG. | ||
* [[Pathway:WP558|KEGG example]] | * [[Pathway:WP558|KEGG example]] | ||
| - | ===== Scientific literature ===== | + | ====== Scientific literature ====== |
* Cite the original publication in the Description section, and if available include a link to open access publications. | * Cite the original publication in the Description section, and if available include a link to open access publications. | ||
* Add the citation to the Bibliography | * Add the citation to the Bibliography | ||
* [[Pathway:WP339|Literature example]] | * [[Pathway:WP339|Literature example]] | ||
Revision as of 23:21, 12 September 2011
Join us for a curation jamboree!
Have you always wanted to contribute to WikiPathways but didn't know where to start? Here's your chance! We are organizing our third curation event to improve the quality and extent of our pathways. Curation events are open to all registered WikiPathways users, no prior experience necessary!
- When: October 6-7, 2011
- Support: WikiPathways admins and curators will be available in an online chat channel during the event to answer all your questions.
Getting started
- Take a look at our archive to identify pathways where you might contribute your expertise.
- Create a pathway based on a review article in your field of study.
If you don't have a specific set of pathways in mind, we have prepared a list of suggested curation tasks as well as lists of pathways in need of work.
Suggested tasks
- Add ontology tags Details
- Create and clean up groups and complexes Details
- Update datanode annotation (xrefs) for datanodes with missing or incorrect annotation. Details
- Connect interactions Details
- Add literature references to pathways with no literature reference. Details
- Add pathway description to pathways with missing description Details
Add ontology tags
Create groups and complexes
Update datanode annotation
The purpose of this task is to add annotation for datanodes that are unannotated. You can find pathways with missing datanode annotation here.
- Review the datanode annotations in the DataNodes list at the bottom of the pathway page to identify unannotated datanodes. Instructions for how to update datanode annotation can be found here.
- After you have updated the pathways, if all datanodes in the pathway are correctly annotated, remove the MissingXRef tag from the pathway.
Connect interactions
A pathway may be tagged with the Unconnected interactions tag anytime ANY lines in the pathway are not connected to another object in the pathway. This includes lines that are purely graphical and that shouldn't be connected to objects.
- To find out which lines are unconnected, click the Edit button to open the pathway in the editor and click Ctrl+L to highlight all unconnected lines.
- For lines representing interactions between datanodes or between datanodes and other objects, connect any unconnected lines according to instructions in Help.
- Once the pathway contains no unconnected lines, or if the remaining unconnected lines are purely graphical, remove the Unconnected lines tag from the pathway.
Add literature reference
- Find pathways without literature references here
- A literature reference can be from a publication or text book. For example, you may be able to find literature references for specific pathways by searching PubMed or Wikipedia. Instructions for how to add literature references to pathways can be found in the tutorial.
- Once you have added at least one literature reference to the pathway, remove the NeedsReference tag from the pathway.
Add description
- Find pathways with missing descriptions showPathwaysFor=Curation:MissingDescription here
- A description can be from an outside source (publication, textbook, website) or it can be your own original description. Instructions for how to add descriptions to pathways can be found in the tutorial.
- If you add a description copied from an outside source, please cite the source. Some common sources for descriptions and details on how to cite them are listed below.
- If you add a description for a particular human pathway, consider also adding the description to that same pathway in other species, where appropriate. This may require some editing to change or exclude species names. Please use your own judgment to decide if the description applies to additional species.
- Once you have added a description to the pathway, remove the MissingDescription tag from the pathway.
Sources for descriptions
Following are some suggested sources for pathway descriptions.
Citing sources
Citing requirements varies between sources, so it is a good idea to find out the specific requirements for any particular source that you use for descriptions. In general, please cite the source for the description in the actual Descriptions section of the pathway with a direct link to the source (i.e. http://en.wikipedia.org/wiki/TGF_beta_signaling_pathway). Below are instructions and examples for how to cite specific sources:
Wikipedia
- Cite Wikipedia in the Description section, and include a link to the relevant page at Wikipedia.
- Wikipedia example
PharmGKB
- Cite PharmGKB in the Description section, and include a link to the relevant pathway page at PharmGKB.
- If the pathway page at PharmGKB indicates that the pathway has been published in the Pharmacogenetics and Genomics journal, review the publication to see if the text used as a description appears in the publication. If so, add the citation to the Bibliography.
- PharmGKB example
Reactome
- Cite Reactome in the Description section, and include a link to the relevant pathway page at Reactome.
- Reactome example
KEGG
- Cite KEGG in the Description section, and include a link to the relevant pathway page at KEGG.
- KEGG example
Scientific literature
- Cite the original publication in the Description section, and if available include a link to open access publications.
- Add the citation to the Bibliography
- Literature example
