Questions about spatial resolution of UBERON ontologies

[mshadbolt]

As a data wrangler for the WSSS projects I need to try to match the spatial organ terms they are using with suitable ontology organ and organ part ontologies. There are a few organs where there are gaps in specific spatial ontologies and I want to understand if these are terms that could/should be added to UBERON, or if we need to look in to using an alternate ontology, e.g. Biological Spatial Ontology to get a more specific definition of the spatial area the specimen was taken from. Some examples I have so far are:

Kidney

• Upper pole
• Lower pole

Uterus

• Lower section
• Mid section
• Upper section

Small Intestine

• Subsections of jejunum
• terminal ileum
• second part of duodenum Skeletal muscle
• Intercostal muscle between rib 2 and 3

Bone

• Head/distal end

Liver

• Surface central region
• Surface cranial region
• Deep parenchymal central region (towards hilum)

We have also had feedback from CBTM who think that they need more fine grained terms to accurately capture some of the samples they are collecting from organs.

[mshadbolt]

@zoe @simonjupp was just wondering if you have any thoughts about how to get better spatial resolution when defining where specimens are being taken from within organs.

[simonjupp]

If we can standardise to a common model on the spatial index, then we should look to add this as a new property in the metadata schema so users can provide alongside the uberon term for the primary biopsy site name.

For the specific biopsy site, many of these should already be covered by Uberon/FMA (https://www.ebi.ac.uk/ols/ontologies/fma). It would be good to get a list of the ones you've encountered that didn't map to anything.

[mshadbolt]

See the first post of the ticket for a list of organ parts that don't map to terms in the uberon ontology. We don't use the FMA ontology.

[mshadbolt]

@simonjupp do you think we should add the FMA ontology to our schema to allow a wider variety of anatomy terms to be used for organ parts?

[simonjupp]

We can import from FMA. These will end up as subclasses of uberon terms in the HCAO so it won't effect validation. Just let @zoependlington know the list of FMA terms you want.

[mshadbolt]

I made a ticket (#54) to add some terms from the FMA as children of organ terms in UBERON in our HCAO

[paolaroncaglia]

Hi @mshadbolt,

I made a ticket (#54) to add some terms from the FMA as children of organ terms in UBERON in our HCAO

Any objection if I close this ticket as a duplicate of #54? I will then look into #54 and address any missing task (I see that Zoë has already done some work).

Thanks, Paola

[mshadbolt]

ok sounds good