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Remove mgi xref mappings via ccds and uniprot

Marek Szuba requested to merge remove_mgi_xref_via_ccds_uniprot into feature/xref_sprint

Created by: premanand17

Requirements

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  • Review the contributing guidelines for this repository; remember in particular:
    • do not modify code without testing for regression
    • provide simple unit tests to test the changes
    • if you change the schema you must patch the test databases as well, see Updating the schema
    • the PR must not fail unit testing

Description

Removed the sections from the ini file corresponding to MGI ccds and uniprot sources. Removed the call to get the source id from 'MGI' source name and uniprot as it is not applicable anymore.

Use case

For mouse, we use MGI symbols as the official naming source. To increase the coverage, we use third-party mappings to MGI, including CCDS and UniProt mappings. As of the latest update, we have 14 MGI xrefs obtained via CCDS mappings and another 52 via UniProt. These updates will remove those additional mappings to get the mappings from a single source ie MGI.

Benefits

We get the mappings only from single source (MGI)

Possible Drawbacks

We may miss the mappings for the some minimal ids. (14-ccds, 52-uniprot)

Testing

Tested it by running the xref_parser script and checked the _xref database for row counts. modules/t/xref_parser.t also passes

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