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

November 14, 2013


  1. person_lineage
  2. Feature/Interaction curation
  3. New OA Features: batch submission & adding multiple new rows
  4. Curation Status Form - Topic Filtering in place
  5. Topic Curation - Unfolded Protein Response: status and notes from jamboree
  6. SAB meeting?
  7. Wiki archive pages - cleaning up documentation
  8. WormBase Caltech Calendar

SAB Meeting

  • Separate meeting? Discussion topic - ACEDB/Database issues, smaller attendance
  • SAB not decided yet

Person Lineage

  • Lineage links usually through a PI to a lab
  • New PI took Cold Spring Harbor worm course
  • How to describe worm intellectual lineage?
  • Prioritize WBPersons as ones who publish (meeting abstracts, papers, etc.)

Meeting abstract verification

  • International meeting abstract missing from GSA submission
  • Abstract didn't meet deadline for abstract submission
  • Author(s) can submit a Worm Breeder's Gazette article if they want it recognized by WormBase

FlyBase Disease curation collaboration

  • Ranjana in communication with FlyBase curators
  • FlyBase working on concise-description-like summaries of disease models like ours
  • FlyBase cleaning up OMIM descriptions (making more generally readable) and curating relevant Fly orthologs
  • How to best update descriptions over time?

Feature Curation

  • Sequence features (?Feature objects) are now curatable as interaction entities (interactors) for physical or regulatory interactions
  • There are two new fields in the "Interaction" OA and one new field in the "Gene Regulation" OA
  • There are >300,000 feature objects that currently can be entered by an "ontology" field
  • Feature objects need to be entered by WBsf ID number currently (may add 'public name' entry later)

New OA Tools

  • Adding multiple new rows to the OA at once
    • Juancarlos added a "Number of New Rows" entry field to the left of the "New" button on the OA
    • Will be '1' by default, will pop up an entry field when clicked, and default back to '1' once multiple new rows have been added
    • Curators can add up to 100 new rows at a time in the main OA, and 1000 at a time in the 'Batch/Invisible Mode' OA
  • There is now a batch OA upload script that allows bulk upload of data to a given OA
    • The script accepts a tab-delimited file as in input
    • A Google spreadsheet has been created
    • This spreadsheet has drop down fields in the header row containing the names of Postgres tables
    • Select the Postgres tables into which you would like to batch submit data, enter the data, and download the tab-delimited file of the worksheet by selecting "Download as > Plain text" from the "File" menu
    • Documentation on the entire process will be available soon
    • An issue with batch submission is that bogus data CAN be entered if, for example, it is mis-spelled or mistyped
    • Curators need to run the script on the Sandbox first and check their data before moving to Tazendra

WormBase Wiki 'Archive' Page Proposal

  • Currently, many pages on the Wiki have current/up-to-date documentation intermixed with outdated/obsolete documentation
  • Proposal is to create an 'Archive' version of any given documentation page by creating a new version of a Wiki page that only differs in name by the addition of a '_archive' in the page title.
  • Old or outdated documentation can be moved to the '*_archive' page to clear up space on the main page
  • A link to the 'Archive' page will be made available on the main documentation page
  • Creation of an 'Archive' page will allow old documentation to remain searchable from the Wiki search tool

UPR Topic Curation

  • Had 'jamboree' on Monday
  • We still need to work out a general mechanism for efficiently creating pathway diagrams
  • The current WikiPathways interface view of browsing pathways would benefit from:
    • Clear user/browser access to detailed annotations of nodes and edges (currently seems available only through the edit mode)
    • A clear legend of icons, node shapes, and arrow types, also only clearly available through the edit mode
  • We do have ~2 months after CIT data upload to polish of the WikiPathway diagram, so we can focus on/prioritize data type curation before the data upload
  • It's clear that we may want to have multiple versions of a pathway diagram (for different contexts, for example)
    • We could generate a general/canonical pathway diagram that can serve as a template for other diagram 'versions'
    • Maybe we can create a generic pathway title like "Unfolded Protein Response" to which we add context-specific suffixes like "Embryonic development" or "Intestine specific" versions of the pathway, for example
    • Need a strategy as to how to display multiple pathway diagrams from a single 'Topic' page