Curation Jamboree Jul 2013

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!

>>> LIVE CHAT<<< (Available during the event)

• When: Thursday and Friday, July 11-12, 2013
• Support: WikiPathways admins and curators will host local events in San Francisco (US) and Maastricht (NL) and will also be available in an online chat channel during the event to answer all your questions.

Below a list of tasks we need your help with.

Suggested tasks

• Add ontology tags Details
• Connect interactions Details
• Fix pathway titles Details
• Update curation tags 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.

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. For purely graphical lines, replace the line with a graphical line, available in the Basic shapes drop-down menu, or in the Graphical elements section of the Objects side panel.
4. Once all interactions have been connected and graphical lines have been converted, remove the Unconnected lines tag from the pathway.

Fix titles

Browse our archive to find bad pathway titles.

Pathway titles should be descriptive. To find a reasonable title, you may need to review the biology described in the pathway, identify key players, or even review literature references indicated by the authors.

Here are some examples of pathway titles that have been improved:

CAMK => CAM Kinase pathway

Selenium => Selenium Micronutrient Network

Keap1-Nrf2 Pathway => Transcriptional activation by NRF2 [clue: see referenced figure]

Update curation tags

The goal is to make sure that Analysis and Featured collections are up-to-date. The following tasks are relevant for both collections:

Analysis collection

Featured pathways collection

• Starting with the above lists, identify pathways where the relevant tag is outdated. This will be noted with a red "no" in the column "Applies to latest revision".
• Review recent edits by reviewing the pathway history. If necessary, compare relevant revisions in the DiffViewer. If the recent edits are inaccurate or degrade quality, then revert the pathway to a revision prior to the latest set of edits.
• If recent changes are good, then apply the "Analysis" and "Featured" tags to the latest revision.

• If the pathway is already tagged with the Analysis collection and Featured pathway tags and recent edits are good, then update these tags.
• If a pathway is not already tagged as Analysis and Featured, assess if one or both tags should be added to the latest revision. Here are the requirements:
  • Analysis collection: All interactions must be complete, and most datanodes must be annotated. About 80% coverage of Gene Product datanodes is sufficient, given that some elements might not have mappings. Overall, the pathway should be useful for downstream data visualization and analysis.
  • Featured pathway: In addition to meeting Analysis collection requirements, it must have a good description and one or more ontology tags. Non-typical pathways, including gene lists and abstract networks, should be excluded. Overall, a Featured pathway should have a consistent and informative annotated layout that contributes to the understanding of the biological process.
• Remove tags that have been addressed and are now outdated. For example the Missing description tag, |Data nodes with missing database annotation tag and Incomplete interactions tag.