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[ENQ] Mouse strains and developmental stage #70

Closed paolaroncaglia closed 3 years ago

paolaroncaglia commented 3 years ago

From @pnejad (via Slack):

"One of the GEO datasets we are wrangling (GSE75659) has mouse samples with mixed strains. The paper tells us the strain for both mother and father, but I can’t find the appropriate ontology in EFO. Do you have any suggestions for what we can use for the strain ontology?

CAST/EiJ (mother) x C57BL/6J (father) C57BL/6J (mother) x CAST/EiJ (father) C57BL/6J (mother) x CAST/EiJ (father) C57BL/6J (mother) x CAST/EiJ (father) CAST/EiJ (mother) x C57BL/6J (father)

For this same dataset I need to find an EFO ontology for developmental stage = mouse adult stage. I’m unsure what to use here as well."

Note for self: GSE75659 is described in PMID:27668657. Also note for self, it's actually just 2 mixed strains: CAST/EiJ (mother) x C57BL/6J (father) C57BL/6J (mother) x CAST/EiJ (father)

paolaroncaglia commented 3 years ago

@pnejad For the mouse samples above, I will create 2 new terms in EFO, see https://github.com/EBISPOT/efo/issues/921. (Now done, will be in EFO release scheduled for Jan 18th 2021.)

paolaroncaglia commented 3 years ago

@pnejad In response to your question "For this same dataset I need to find an EFO ontology for developmental stage = mouse adult stage. I’m unsure what to use here as well." I suggest EFO:0001272 'adult' (subclass of EFO:0000399 'developmental stage'). The organism (mouse) will be captured separately by NCBITaxon I presume. I'll close this ticket unless you have any concern. Thanks.

paolaroncaglia commented 3 years ago

@pnejad But if you have any other question about that same GEO dataset, feel free to add it in this ticket!

pnejad commented 3 years ago

Thank you @paolaroncaglia

For this dataset we also need to cell type ontologies:

The specimen came from E15 mouse embryos and there was no further enrichment to tell us what type of brain or liver cell. Are there CL ontologies we could use here?

paolaroncaglia commented 3 years ago

@pnejad (tagging @dosumis for feedback) I believe there are no existing terms that you could use. We could create

CL:NEW1 'embryonic brain cell' equivalent to CL:0002321 'embryonic cell' and part of some UBERON:6001060 'embryonic brain'

and

CL:NEW2 'embryonic liver cell' equivalent to CL:0002321 'embryonic cell' and part of some UBERON:0003894 'liver primordium'

and tag them both as subsets "location_grouping" and "added_for_HCA" and possibly add an editor's note on the lines of "Specimens described in PMID:27668657 came from E15 mouse embryos. No further enrichment information was available about specific types of brain or liver cells."

@dosumis I think that the Uberon terms above are meant to be species-neutral, correct?

However, in this case I'm unsure if the CL terms would really add any information wrt curating to UBERON:6001060 'embryonic brain' and UBERON:0003894 'liver primordium'. Discuss.

dosumis commented 3 years ago

However, in this case I'm unsure if the CL terms would really add any information wrt curating to UBERON:6001060 'embryonic brain' and UBERON:0003894 'liver primordium'. Discuss.

I agree. There's no need to add completely generic cellXlocation terms to CL. Suspect this is to fill a slot in curation.

paolaroncaglia commented 3 years ago

Resolution from today's curators call: no need for new CL classes.

paolaroncaglia commented 3 years ago

@pnejad I'll close this ticket as I think we addressed all requests and questions, but if there's more, please feel free to open a new ticket. Thanks!

ANiknejad commented 3 years ago

Hello @pnejad @paolaroncaglia

I put a comment here about the question of Parisa, "For this same dataset I need to find an EFO ontology for developmental stage = mouse adult stage. I’m unsure what to use here as well."

Actually in the same way there is Hsapdv for human developmental stages, it exists also Mmusdv, the ontology for mouse developmental stages HumanCellAtlas already makes use of HsapDv, and MmusDv is fully aligned with HsapDv, allowing meaningful comparisons.

https://github.com/obophenotype/developmental-stage-ontologies/tree/master/src

I will be happy to communicate with you in more details, should you have comments about the species specific developmental stages ontologies. Best regards,

Anne Niknejad bgee.org curator

pnejad commented 3 years ago

Thank you for the clarification, Anne!

On Mon, Jun 14, 2021 at 6:03 AM Anne Niknejad @.***> wrote:

Hello @pnejad https://github.com/pnejad @paolaroncaglia https://github.com/paolaroncaglia

I put a comment here about the question of Parisa, "For this same dataset I need to find an EFO ontology for developmental stage = mouse adult stage. I’m unsure what to use here as well."

Actually in the same way there is Hsapdv for human developmental stages, it exists also Mmusdv, the ontology for mouse developmental stages HumanCellAtlas already makes use of HsapDv, and MmusDv is fully aligned with HsapDv, allowing meaningful comparisons.

https://github.com/obophenotype/developmental-stage-ontologies/tree/master/src

I will be happy to communicate with you in more details, should you have comments about the species specific developmental stages ontologies. Best regards,

Anne Niknejad bgee.org curator

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