Fetch retracted status from Retraction Watch and display information

griffithlab / civic-v2

CIViC is an open access, open source, community-driven web resource for Clinical Interpretation of Variants in Cancer

https://civicdb.org

MIT License

19 stars 5 forks source link

Fetch retracted status from Retraction Watch and display information #1011

Closed susannasiebert closed 4 months ago

susannasiebert commented 6 months ago

This PR adds retraction information from Retraction Watch to CIViC Sources. Sources identified from the Retraction Watch CSV are marked as retracted in the database. We also save the retraction reasons, date, and nature. EIDs using these sources are flagged by CIViCbot as part of the job that pulls this information. The Retracted Nature is displayed as a tag next to the PubMed ID, with a red error tag format for Retractions and yellow warning format for all other retraction nature types (Expression of concern, Reinstatement, Correction). The retraction tag popover displays the retraction date and reasons as well as linkouts to Retraction Watch.

Sources without a retracted status are displayed as usual.

Example of Retraction status tag next to PubMed ID:

Popover for Retraction Status:

Example of Correction tag:

Example of Reinstatement tag:

susannasiebert commented 6 months ago

Some thoughts on additional improvements:

prevent retracted sources (as marked in our database) from being used for new EIDs. Q: Should this apply to all retracted sources or only the ones of the Retraction type (i.e. not Expression of concern, Reinstatement, or Correction)
format source tags differently for retracted sources. Q: Should this also include Expression of concern, Reinstatement, or Correction types? Should they be displayed a third way?
Q: How should items that change/are removed from Reaction Watch be handled?
Q: Should the EID flag contain more information than it currently does?

susannasiebert commented 6 months ago

Decisions from today's meeting:

[x] Only sources with retraction_nature "Retraction" have their EID flagged
[x] Source tags with retraction_nature "Retraction" will be displayed in grey (similar to deprecated Variants)
[x] Sources with retraction_nature "Retraction" ~will not show up in the source typeahead and~ will throw a server error if used in an EID
Source retraction info will be updated. If the retraction_nature changes from Retraction to anything else update flags as follows
- [x] If the original retraction flag is still open, close it.
- [x] If the original retraction flag is resolved and the EID is rejected: flag it again to potentially re-evaluate for acceptance.

Other changes:

[x] Update source browse table: either pull in the retractionNature for greying out of the source tag or exclude sources with retraction_nature "Retraction"