Complete review of integration network datasets for new cell types

[dosumis]

REVIEWED: PBMC https://docs.google.com/spreadsheets/d/1zvUAhZiKiKM6NL3kZUZ0A89aic1Gbsk47NdBOc2gXTY/edit#gid=1562746368

TO CHECK: EYE https://docs.google.com/spreadsheets/d/1WTs7AFd4outzbr_w-ct6Us1F4owYUKzTG0C-nzh-0jQ/edit#gid=1347957631

TO DO: KIDNEY https://docs.google.com/spreadsheets/d/1hBIHgecAjyNhLth3eSpZVEwWObfUtROI/edit#gid=658716720 Lung https://docs.google.com/spreadsheets/d/1MAPPx8DNF7HSQlLne9X09oQKsFHOvT9jOTBZhnhQ3CA/edit#gid=506808579. - co-ord with @aleixpuigb

(Note - last spreadsheet here may have more datasets for eye & Kidney - please check

[ghost]

UPDATED LINKS

PBMC: DONE

EYE: DONE Reviewed by @bvarner-ebi, @aleixpuigb. From CAP Data Wrangler: met with two researchers from the retina bionetwork: the datasets on CellXGene are from individual publications that were uploaded by the authors. The retina bionetwork re-analyzed the the raw data from these publications using same the version of CellRanger and genome annotation. The re-analyzed datasets have been submitted to Lattice for formatting and we will have access to them once that is complete. I do not know when that is. Eye mappings - Synonyms added

KIDNEY: First pass review DONE- few studies appear on CxG

LUNG: TO DO

[dosumis]

Make sure synonyms captured in ontology when new terms added or existing terms mapped.

[ghost]

@aleixpuigb, can you confirm you are reviewing the lung datasets? If so, can you add the status of the review (TO DO, IN PROGRESS, ON HOLD, etc)?

[aleixpuigb]

@bvarner-ebi, the status is TO DO, as I haven't started it yet.

[dosumis]

Check with Mary and Evan about status of other integration efforts - in particular gut.

[ghost]

Check with Mary and Evan about status of other integration efforts - in particular gut.

Per Mary regrading gut bionetwork references: There is [no update], we have not contacted them by email and I do not have any information beyond what is the HCAIT_overview sheet

[ghost]

@aleixpuigb, checking to see if there is a status update on the lung datasets. If done, I propose this ticket can be closed. If pending or in progress, may I reassign this to you, @aleixpuigb?

The gut sheet on HCAIT_overview sheet remains unpopulated.

[aleixpuigb]

I am reassigning to myself

[github-actions[bot]]

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