[ITR] Microscopy ontology branch

[paolaroncaglia]

This is a placeholder, following a Slack conversation with Laura Clarke: "when we start capturing imaging data we are going to need microscopy ontologies, if the current microscopy ontologies specified by the schema are still the right ones to use is a different question". I believe that the current schema is pointing to FBbi:00000241 'microscopy', which isn't in HCAO at the moment.

• [ ] Evaluate if there's a need for HCA to import FBbi:00000241 'microscopy' into HCAO, or evaluate alternative options.

[paolaroncaglia]

Hi @pnejad and @dosumis , I'm reviewing tickets in this tracker. Just a reminder about this one; please feel free to add the topic to one of our monthly meetings' agenda if/when appropriate. Thanks. Paola

[pnejad]

@paolaroncaglia thank you for bringing this to my attention! I will talk to the wranglers to get a better understanding of ontology needs for imaging assays.

[dosumis]

@pnejad to check with @gabsie re term requirements. We can then revisit and assess whether the current ontology is sufficient.

[dosumis]

Note that specific assays (e.g. Merfish) are/should-be in EFO.

[paolaroncaglia]

Note that specific assays (e.g. Merfish) are/should-be in EFO.

FYI, to expand on some of the concepts that @dosumis mentioned, EFO already has e.g. EFO:0008992 MERFISH EFO:0010961 'Visium Spatial Gene Expression' Both are also in the EFO HCA subset.

[pnejad]

@paolaroncaglia I checked in with the wranglers and this tickets can be closed. If we need any ontologies related to microscopy in the future we can create a new ticket.

[paolaroncaglia]

@pnejad thank you for your feedback! Closing now.