WormBase-Caltech Weekly Calls

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November 7, 2013

Upload Schedule

  • Citace upload deadline will be 6pm Monday, November 25th (added to WormBase calendar)

Diseases in Curation Status Form

  • Ranjana is still waiting on finalization of the Disease paper flagging pipeline
  • Once that is finalized, Chris and Juancarlos will help get Disease into the Curation Status Form as a data type

Topics Filtering in the Curation Status Form

  • Juancarlos has implemented a filtering mechanism whereby paper lists in the Curation Status Form (CSF) can be further filtered based on topic
  • Currently the Sandbox CSF reads WBPaper IDs from a flat file for the current Unfolded Protein Response topic
  • In the future, the CSF will determine which papers are affiliated with a topic via the Topic Curation OA
  • Eventually, papers that are flagged as potentially relevant to a topic (by any means) will be submitted in batch to the Topic Curation OA, which will then be read by the CSF

Adding the Textpresso paper flagging pipeline to the Curation Status Form

  • As an additional paper flagging pipeline, we will add Textpresso to the Curation Status Form
  • This pipeline will be added once other features (i.e. topic filtering) have been sorted out
  • Data types that are flagged by this pipeline include Disease and Transgenes

Topic Curation OA

  • Juancarlos will add a field to the Topic Curation OA that indicates the status of a paper/entry with respect to the topic
  • The entry for this "Topic Paper Status" field will be a drop down menu with three options: Not Checked, Relevant, or Irrelevant
  • Juancarlos will build a tool that will allow curators to enter a list of WBPaper IDs in batch to the Topic Curation OA, where each entered paper will be given a default status of "Not Checked"
  • This batch paper submission form will have it's own URL, but will also be linked to via the OA's Term Info panel
  • Papers that are flagged as "Not Checked" or "Irrelevant" will not be dumped into ACEDB, but "Relevant" papers will be
  • Papers that are flagged as "Not Checked" or "Relevant" will be recognized by the Curation Status Form when filtering for papers relevant (or potentially so) to a topic
  • When a curator clicks the "New" button in the Topic Curation OA, that new line (new PGID) will be assigned a "Relevant" status by default

Bulk Paper ID Converter

  • Juancarlos will build a stand-alone tool (CGI) to allow curators to convert paper IDs to WBPaper IDs from other paper ID formats (e.g. PMID, DOI, etc.) (Actually, it'll be a new function in the paper display CGI)
  • The tool will provide a list of WBPapers as output, with a mapping from the entered IDs to the WBPaper IDs, as well as an output notification for any paper IDs that did not successfully map to a WBPaper ID

Unfolded Protein Response (UPR): WS241 Curation Topic

  • Curators are making good progress, but may not be totally complete* by the upload date (*depending on our definition of complete)
  • We decided to have a UPR Topic 'Jamboree' on Monday, November 11 2013 at 10am Pacific Standard Time
  • In future, we may want to have this jamboree at the curation cycle midpoint (about one month after curation cycle begins); need to come up with a regular schedule scheme
  • It will be important to recognize, for a given topic, what are the core components of the topic and related pathway that we need to focus on; we should minimize emphasis on peripheral components of the topic or pathway
  • We will want to provide a public notice (likely via the WormBase blog) about what topic we have focused on for that release of the database/website (at the time the site goes live for that release)
  • The purpose of the jamboree is for people to discuss their thoughts on the topic after the initial curation period, and to help draw up a clear and concise WikiPathway diagram for the central components and interactions related to the topic