Curation Jamboree 2010

From WikiPathways

Current revision

Join us for a curation jamboree!

• When: February 11-12, 2010
• Focus: To add descriptions and literature references to pathways

Specific tasks

1. Add pathway description to pathways with missing description Details
2. Add at least one literature reference to pathways with no literature reference. Details
3. Update datanode annotation (xrefs) for datanodes with missing or incorrect annotation. Details
4. Connect interactions between entities Details
5. Add/remove curation tags where appropriate Details

Guidelines for editing

Add description

• Find pathways with missing descriptions 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.

• 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

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.

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.

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.

Updating tags

The goal is to tag pathways accurately according to the tag descriptions below:

• Analysis Collection: Pathways that don't have major flaws in terms of connected datanodes and interactions, and overall completeness. Descriptions and literature references are not relevant. Pathways that are tagged as Analysis collection may also have the Featured tag. If so, the featured tag should be removed unless the pathway satisfies the below criteria for the Featured tag.
• Featured: Pathways that are considered the best of WP. These pathways should be fully connected (datanodes and interactions), have a meaningful layout and have a description.

Participants

Alexander Pico, Kristina Hanspers, Thomas Kelder, Martijn van Iersel, Caroline Miller, Matthew, Jill Dunham, Chris Evelo, Michiel Adriaens, Andra Waagmeester, Nathan Salomonis,