Curation Jamboree Oct 2011

From WikiPathways

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 next 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: Thursday and Friday, October 6-7, 2011
• Support: WikiPathways admins and curators will host local events in San Francisco (US), Cambridge (UK) and Maastricht (NL) and will also be available in an online chat channel during the event to answer all your questions.
• Local meetups:
  • San Francisco: Gladstone Institutes, Thursday Oct 6, 10am-4pm, lobby A; and Friday Oct 7, 10am-4pm, conference room 264A

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

The purpose of this task is to add relevant ontology terms to pathways, which serves as a way of organizing WikiPathways content. WikiPathways can be tagged with ontology terms from pathway, disease and cell type ontologies.

1. Review the contents of the pathway, pathway description and bibliography to get an idea of what ontology tags are relevant.
2. In the Ontology Tags section of the pathway page, find tags either by searching or by browsing the available ontologies.
3. After selecting a term, add it to the pathway by clicking the Add check mark.

Create groups and complexes

The purpose of this task is to group pathway objects together in groups and complexes where relevant, and also to review and edit existing group/complex designations to make sure that the correct version is used.

1. Find pathways in your area of expertise using the Browse feature.
2. In edit mode, create complexes and groups by first selecting a set of items, then right-clicking to select either Group or Create complex.
3. You can identify existing complexes by a beige bounding box and dashed outline. Existing groups can only be seen by hovering over the bounding box of the group, which then appears light blue with a dashed outline.
4. Update any connections involving members of the group or complex by connecting them to the group or complex instead, where appropriate. See details in Help.

In general, the complex type should be used for any grouping of objects representing a functional group. The group type should be used to represent groups of similar objects, that are not complexed into a functional unit.

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.

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. You can list pathways per curation tag here.

1. 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.
2. For lines representing interactions between datanodes or between datanodes and other objects, connect any unconnected lines according to instructions in Help.
3. 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

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 using the Show Pathways link per curation tag 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

Alexander Pico, Kristina Hanspers, Thomas Kelder, Martijn van Iersel, Nathan Salomonis, Martina Kutmon, Federica Eduati