Library construction ontology now exists for null ontology_ids and can be updated

[NoopDog]

For context see HumanCellAtlas/dcp2#13

See rows 2,3,4 of https://docs.google.com/spreadsheets/d/1Wk7SGxEz00AkNokYv3YlFHJVF9U6THKcrvgHARsnau8/edit#gid=0

Project Detail Page	project_id	library_preparation_protocol_id	ontology_id	ontology_label	text
https://data.humancellatlas.org/explore/projects/88ec040b-8705-4f77-8f41-f81e57632f7d	88ec040b-8705-4f77-8f41-f81e57632f7d	5bd07f13-2672-4a90-8ae4-97ca56b1ac23	null	null	sci-RNA-seq
https://data.humancellatlas.org/explore/projects/88ec040b-8705-4f77-8f41-f81e57632f7d	88ec040b-8705-4f77-8f41-f81e57632f7d	5e21e36c-f789-42f1-b81c-f8e280622d78	null	null	Seq-Well
https://data.humancellatlas.org/explore/projects/88ec040b-8705-4f77-8f41-f81e57632f7d	88ec040b-8705-4f77-8f41-f81e57632f7d	ee388b7a-9eed-40ad-be52-9626db47a204	null	null	CEL-seq2

The terms sci-RNA-seq, Seq-Well, and CEL-seq2

now exist under OBI:0000711

https://www.ebi.ac.uk/ols/ontologies/efo/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo/OBI_0000711

and the ontology IDs for these library preparation protocols can be updated.

[clairerye]

We agreed these should be updated now the terms are available and we should be able to do this is a straight forward manner using updates in the UI.

[rays22]

I tried to edit the ontology labels of the library preparation protocols for this project in Ingest, but the Protocols tab failed to load on several attempts on 2021-05-28.
The tab seemed to be stuck in a state of
Loading...
for more than an hour.
On another day I will check if this failure of loading the protocols is persistent or just a one-off.

[rays22]

The project has a status of Complete in Ingest. I need an EBI HCA dev to set it to Valid so that I can do any metadata edits in the UI.

[rays22]

• I have managed to add the missing library protocol method ontology terms in Ingest UI.

• EFO:0010550 sci-RNA-seq

    "library_construction_method" : {
      "ontology" : "EFO:0010550",
      "ontology_label" : "sci-RNA-seq",
      "text" : "sci-RNA-seq"
    },

• EFO:0008919 Seq-Well

    "library_construction_method" : {
      "ontology" : "EFO:0008919",
      "ontology_label" : "Seq-Well",
      "text" : "Seq-Well"
    },

• EFO:0010010 CEL-seq2

    "library_construction_method" : {
      "ontology" : "EFO:0010010",
      "ontology_label" : "CEL-seq2",
      "text" : "CEL-seq2"
    },

• I still need the project status to be reverted from Complete to Valid before I can export the update.

[rays22]

I am still blocked from exporting this update, because of the Complete status of the project.

[clairerye]

@yusra-haider are you able to look into this please? - sorry I am way behind. I see you have done it already

[rays22]

@yusra-haider has changed the project status to Valid, but I was told to wait with exporting the updates, because this is a DCP1 project.

[clairerye]

Thanks, it has now been clarified so we can go ahead and export. Slack conversation - https://embl-ebi-ait.slack.com/archives/C01360XN04S/p1623070775056500

[rays22]

The export of the update is blocked by unresponsive Ingest project page.

[yusra-haider]

@clairerye , @rays22

We can't export it yet, it's a dcp 1 dataset and requires that I make changes to the dcpVersion values in the database.

The referenced slack conversation was just me confirming that we can export dcp 1 metadata to the staging area for dcp 2 projects

Please wait till I fix the database values. I will export it, monitor the export and send an update

[clairerye]

ok thanks, apologies I misunderstood the slack thread

[yusra-haider]

@rays22 https://contribute.data.humancellatlas.org/submissions/detail?uuid=d1610c4a-76c6-4b69-af63-c74af869fa75&project=88ec040b-8705-4f77-8f41-f81e57632f7d has been successfully exported

[rays22]

Thank you @yusra-haider .
I have filled in an import request for this update targeting release 7.