Curation Jamboree Sep 2010

From WikiPathways

Revision as of 23:48, 7 September 2010

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. Click here to go to the chat channel..

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
• Feedback on toolbar buttons and other UI
• 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 links to other pathways as a label linked to with an arrow or line. The purpose of this task is to replace such links with a link to an actual pathway ID.

1. Find a label on the 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 idnetifier found in step 2 in the 'identifier' field.
9. Click 'ok' to close the dialog and save the pathway.

Update datanode annotation

If a pathway you are working on is tagged with the MissingXRef tag:

• 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.
• If all datanodes in the pathway are correctly annotated, remove the MissingXRef 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.