library_preparation_protocol.library_construction_method.ontology_label differs markedly from text

[NoopDog]

We might want to check this one as the ontology_text says 10X 5' v2 sequencing but the ontology_label says 10X 3' v2 sequencing. One of them may be a typo.

Project Detail Page	project_id	library_preparation_protocol_id	ontology_id	ontology_label	text
https://data.humancellatlas.org/explore/projects/9d97f01f-9313-416e-9b07-560f048b2350	9d97f01f-9313-416e-9b07-560f048b2350	71f59197-d9fe-4ced-b2c7-43cbfecc5eb4	EFO:0009899	10X 3' v2 sequencing	10X 5' v2 sequencing

For context see
https://docs.google.com/spreadsheets/d/1Wk7SGxEz00AkNokYv3YlFHJVF9U6THKcrvgHARsnau8/edit#gid=0

and

HumanCellAtlas/dcp2#13

[clairerye]

This was wrangled by Parisa, I will ask her to clarify which is correct.

[rays22]

I can not fix this issue until Parisa confirms what the correct library preparation technology versions were used for each of the two library preparation protocols in the project.

library_preparation_protocol.uuid   library_preparation_protocol.protocol_core.protocol_id  library_preparation_protocol.protocol_core.protocol_name    library_preparation_protocol.protocol_core.protocol_description    library_preparation_protocol.library_construction_method.text   library_preparation_protocol.library_construction_method.ontology    library_preparation_protocol.library_construction_method.ontology_label library_preparation_protocol.library_construction_kit.retail_name
71f59197-d9fe-4ced-b2c7-43cbfecc5eb4    LP_a30170acbd2e4c58c9e3ce4445691dfe Genomics_prep_10x_5'_v2 The single-cell capturing and downstream library constructions were performed using the Chromium Single Cell 5′ library or 3' v2 library preparation kit according to the manufacturer’s protocol (10x Genomics).    10X  5' v2 sequencing   EFO:0009899 10X 3' v2 sequencing    Chromium Single Cell 5′ v2 library preparation kit
cded2c1e-c49b-4e2c-9b32-6c14553a5f0b    LP_a30170acbd2e4c58c9e3ce4445691dfe.1   Genomics_prep_10x_3'_v2 The single-cell capturing and downstream library constructions were performed using the Chromium Single Cell 5′ library or 3' v2 library preparation kit according to the manufacturer’s protocol (10x Genomics).    10X 3' v2 sequencing    EFO:0009900 10X 5' v2 sequencing    Chromium Single Cell 3′ v2 library preparation kit

[rays22]

I am still blocked from progressing on this update until I get the necessary information from Parisa to my query email of 28/5/2021.

[willrockout]

It is 5' and 3' it just seems that the ontologies were accidentally switched. Follow the name and other information for which is which

[rays22]

Thank you @willrockout .

• I have swapped the ontology terms and IDs so that they match the library_preparation_protocol.protocol_core.protocol_name

Genomics_prep_10x_5'_v2	-->	10x 5' v2 (EFO:0009900)
Genomics_prep_10x_3'_v2	-->	10x 3' v2 (EFO:0009899)

• I am trying to export the updated project to the DCP now.

[rays22]

• I have export the updated project,
• and filled-in the DCP import form

The update should fix the ontology issue in release 7.

[NoopDog]

Thanks, Ray! Do you know what release this will end up in? Cheers, D

…

On Fri, Jun 11, 2021 at 10:33 AM Ray Stefancsik ***@***.***> wrote: - I have export the updated project <https://contribute.data.humancellatlas.org/projects/detail?uuid=9d97f01f-9313-416e-9b07-560f048b2350> , - and filled-in the DCP import form <https://docs.google.com/forms/d/e/1FAIpQLSeokUTa-aVXGDdSNODEYetxezasFKp2oVLz65775lgk5t0D2w/viewform?gxids=7628> The update should fix the ontology issue. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#335 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAYW6ENJTLKSNOTX63JOT3LTSJCFLANCNFSM45D7KRZQ> .

-- Dave Rogers Partner, Clever Canary M: 646 286 5371 http://clevercanary.com @clevercanary @_DaveRogers https://www.linkedin.com/pub/dave-rogers/0/90/92

[rays22]

Release 7 is the target.

[NoopDog]

Thank you.

…

On Fri, Jun 11, 2021 at 10:55 AM Ray Stefancsik ***@***.***> wrote: Release 7 is the target. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#335 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAYW6EKENPCUZJLZ77U5NFDTSJEZDANCNFSM45D7KRZQ> .

-- Dave Rogers Partner, Clever Canary M: 646 286 5371 http://clevercanary.com @clevercanary @_DaveRogers https://www.linkedin.com/pub/dave-rogers/0/90/92