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HumanCellAtlas / ontology

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GSE107746 #64

Closed Asgton closed 3 years ago

Asgton commented 4 years ago

collection_protocol_4

ontology for 'hydrolisis' collection protocol

At last, we removed zona pellucida of oocytes by hydrolysis with 0.012 M hydrochloric acid to obtain naked oocyte without contamination of GCs

Asgton commented 4 years ago

organ part ontology id for preovulatory follicle

paolaroncaglia commented 4 years ago

Hi @Asgton , I'm new to this project, I'll be helping with HCA ontology requests. Do I understand correctly that you are looking for a term to represent the hydrolysis protocol above? If so I'll create one in EFO in the 'protocol' branch. Do you also need a term for preovulatory follicle? If so, would the existing Uberon term UBERON:0003982 'mature ovarian follicle' fit your need? (It has a related synonym of "preovulatory follicle".) Thanks, Paola

paolaroncaglia commented 4 years ago

Hi @pnejad and @mshadbolt ,

May I please ask for your advice on this ticket - would you agree with my proposed strategy above?

Many thanks, Paola

pnejad commented 4 years ago

@paolaroncaglia Sorry for the delayed response. Asgton is a former team member who has since moved on. Your proposed plan works great:

Could you please tag me in the EFO ticket for hydrolysis so I can follow when it is released?

paolaroncaglia commented 4 years ago

@pnejad

@paolaroncaglia Sorry for the delayed response. Asgton is a former team member who has since moved on. Your proposed plan works great:

* hydrolysis to be added to EFO's protocol step

* UBERON:0003982 to be used for preovulatory follicle

Could you please tag me in the EFO ticket for hydrolysis so I can follow when it is released?

Sure, the ticket is https://github.com/EBISPOT/efo/issues/891 and I tagged you there. Thanks.

pnejad commented 3 years ago

@paolaroncaglia Hydrolysis is not being recognized by HCAO, is this something that will be resolved after the developers release the new version of HCAO?

paolaroncaglia commented 3 years ago

Hi @pnejad ,

@paolaroncaglia Hydrolysis is not being recognized by HCAO, is this something that will be resolved after the developers release the new version of HCAO?

The term EFO_0010892 'hydrolisis collection protocol' is in the HCA OLS production instance, see here please. A typo sneaked in (hydrolisis for hydrolysis) for which I apologize; possibly that's why you couldn't find the term? I noticed the typo yesterday and it will be surely fixed in time for the next HCAO release (ticket here). Please let me know if EFO_0010892 is not available to you, that'd be a broader issue than the typo to look into.

Thanks, Paola

pnejad commented 3 years ago

Hi @paolaroncaglia, we tested the submission of our dataset with the incorrect spelling to see if there are any issues with EFO_0010892, and ingest is still giving us an error.

paolaroncaglia commented 3 years ago

Hi @pnejad ,

Hi @paolaroncaglia, we tested the submission of our dataset with the incorrect spelling to see if there are any issues with EFO_0010892, and ingest is still giving us an error.

Is the ingest still failing with the new release that @zoependlington just made today, see https://github.com/ebi-ait/hca-ebi-dev-team/issues/409? If yes, could you please provide more details, e.g. error log?

Thank you, I'm not sure what the problem is but we'll address it as promptly as we can.

Paola

paolaroncaglia commented 3 years ago

Note for self: I'm closing this ticket as it was resolved elsewhere (see https://github.com/ebi-ait/hca-ebi-dev-team/issues/409#issuecomment-827672324 and following comments in that ticket).