Curation Jamboree Sep 2010

From WikiPathways

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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: September 23-24, 2010
• Support: WikiPathways admins and curators will be available in an online chat channel during the event to answer all your questions.

If you have a particular area of expertise, take a look at our archive to identify pathways where you might contribute your expertise, or better yet, missing pathways that you would like to contribute.

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 pathway links to pathways Details
• Add new cellular compartments Details
• Update datanode annotation (xrefs) for datanodes with missing or incorrect annotation. Details
• Add literature references to pathways with no literature reference. Details
• Add pathway description to pathways with missing description Details

Link pathways

Pathways often contain representations of links to other pathways as a link to a label with the pathway name. The purpose of this task is to replace such labels with a an actual pathway ID.

1. Find a label on a pathway that refers to another pathway. For example, on the Glycolysis pathway, there are several links to other pathways (Pentose phosphate, Glycogen metabolism etc).
2. Find the WikiPathways (WP) identifier corresponding to the pathway in the link, for example WP134 for the human pentose phosphate pathway. You can find pathways and their identifiers through Browse or through the Search interface on the main page. Please note that pathways are species-specific.
3. Remove the label representing the pathway.
4. Add a pathway node (using the pathway button on the toolbar) and double click to open the properties dialog
5. Enter the text of the original label in the 'text label' field.
6. Set 'Biological Type' to 'Pathway'.
7. Set 'Database' to 'WikiPathways'.
8. Enter the identifier found in step 2 in the 'Identifier' field.
9. Click 'Ok' to close the dialog and save the pathway.

Add cellular compartments

Many pathways contain various user-defined graphics depicting cellular compartments. The purpose of this task is to replace these non-standard graphics with the corresponding WikiPathways objects, and also to identify pathways where cellular compartment graphics are missing altogether.

1. Find a pathway to update. This can either be pathway with existing cellular compartment graphics (like the Interferon I pathway), or a pathway where cellular compartment information is missing.
2. Before deleting the existing graphic (for example an oval representing the nucleus), first create the corresponding object by selecting from the objects in the side panel. For example, choose the Nucleus (double oval) to replace an oval representing the nucleus.
3. Size and place the new object so that it fits into the pathway where the original graphic is placed, then delete the original and replace it with the new object.

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.

1. 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.
2. After you have updated the pathways, if all datanodes in the pathway are correctly annotated, remove the MissingXRef tag from the pathway.

Add literature reference

1. Find pathways without literature references here
2. 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.
3. Once you have added at least one literature reference to the pathway, remove the NeedsReference tag from the pathway.

Add description

1. Find pathways with missing descriptions showPathwaysFor=Curation:MissingDescription here
2. 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.
3. 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.
4. 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.
5. 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.

• Wikipedia
• PharmGKB
• Reactome
• KEGG
• Scientific literature

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

Participants

Mark Scott, Alexander Pico, Kristina Hanspers, Thomas Kelder, Martijn van Iersel, Allan Kuchinsky, Jildau Bouwman, JT. Saito, Ferry Jagers, Martina Kutmon