Difference between revisions of "WormBase-Caltech Weekly Calls"
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== November 7, 2013 == | == November 7, 2013 == | ||
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=== Upload Schedule === | === Upload Schedule === | ||
* Citace upload deadline will be 6pm Monday, November 25th (added to WormBase calendar) | * Citace upload deadline will be 6pm Monday, November 25th (added to WormBase calendar) | ||
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=== Diseases in Curation Status Form === | === Diseases in Curation Status Form === | ||
* Ranjana is still waiting on finalization of the Disease paper flagging pipeline | * 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 | * Once that is finalized, Chris and Juancarlos will help get Disease into the Curation Status Form as a data type | ||
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=== Topics Filtering in the Curation Status Form === | === Topics Filtering in the Curation Status Form === | ||
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* In the future, the CSF will determine which papers are affiliated with a topic via the Topic Curation OA | * 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 | * 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 | ||
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=== Topic Curation OA === | === Topic Curation OA === | ||
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* 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.) | * 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.) | ||
* 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 | * 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 | ||
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=== Unfolded Protein Response (UPR): WS241 Curation Topic === | === Unfolded Protein Response (UPR): WS241 Curation Topic === | ||
Revision as of 20:01, 7 November 2013
Contents
Previous Years
2013 Meetings
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
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.)
- 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
