Replacing outdated ontology term

[idazucchi]

Description of the task:

the ontology term for idiopathic pulmonary fibrosis is obsolete, it needs to be replaced with interstitial lung disease 2

I compiled a list of projects that need to be updated by checking which projects published in the DCP have the idiopatic fibrosis term Acceptance criteria for the task:

• [ ] check the project list - is it complete?
• [ ] update these projects
  • [x] lungFibrosisProteinSignatures
  • [x] lungPopulationsIPF
  • [ ] healthyIPFLungMesenchymalCells - in complete status, not sure how to proceed
  • [x] pulmonaryFibrosisPathobiology
  • [x] PulmonaryFibrosisGSE135893 - still in exporting, but all donor and specimen entities have been exported

[idazucchi]

• [x] healthyIPFLungMesenchymalCells - in complete status, needs to be kicked back to metadata valid @ESapenaVentura
• [x] PulmonaryFibrosisGSE135893 - still in exporting, but all donor and specimen entities have been exported - check in grafana @ESapenaVentura

[ESapenaVentura]

• For the first project, the one in complete status, I have kicked it back to metadata valid but I can't redeploy the status tracker yet, I have contacted amnon
• For the second project, I feel like this has a similar issue as to what happened with kuppe's dataset. There's something telling the exporter to expect 43 jobs but there are only 42, which causes the submission to get stuck in exporting forever. If the data is already in the staging area, feel free to create a ticket for this issue and fill out the import form :)

[idazucchi]

• [ ] healthyIPFLungMesenchymalCells - updated the ontology term but graph validation issues have appeared - will resume discussion after the release
• [x] PulmonaryFibrosisGSE135893 - I've checked the staging area for PulmonaryFibrosisGSE135893 and I found the right number of json files with the new timestamp for the donors (12) and specimens (6) I've filled out the import form

to do:

• [x] force the status to exported
• [ ] discuss graph validation issues with the UCSC team
• [ ] discuss possibility of updating the linking (expanding existing subgraphs ?) with the DCP components

[Wkt8]

Downstream components cannot cope with a linking process update which changes the linking of files to cell suspensions. Potentially https://github.com/HumanCellAtlas/dcp2/pull/60 will allow this.

[ESapenaVentura]

PulmonaryFibrosisPathobiology is not complete

A donor and a specimen have the outdated term

[idazucchi]

• [x] force PulmonaryFibrosisGSE135893's status to Exported It has already been imported but we forgot to update the submission's status in ingest

cc @amnonkhen

[amnonkhen]

status change to Exported

[ESapenaVentura]

PulmonaryFibrosisPathobiology has been corrected and exported!

[MightyAx]

Waiting on HumanCellAtlas/dcp2#60

[Wkt8]

There is an alternate method of updating linking which is in the works which will replace HumanCellAtlas/dcp2#60. Sit tight.

[idazucchi]

I've reviewed healthyIPFLungMesenchymalCells ~200 fastq files don't have a cell suspension linked, nor any other input biomaterial, and they are not in a process, not linked to any protocol they are absent from the dcp but they are in the google staging area

I'm checking if they are in any of the linking files because I'm not sure anymore of what the linking looked like originally

we can either:

• [x] discuss again how to update this now --> keep ticket
• [ ] drop the update until we need to work on the dataset again --> close ticket