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dcppc / metadata-matrix

Mapping of metadata elements that are common to the TopMed, GTEx and MODs.
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MonDO-DO bridge file #3

Open nsuvarnaiari opened 6 years ago

nsuvarnaiari commented 6 years ago

@cmungall We extracted anatomy mappings from uberon-bridge-to-fma.owl file (http://uberon.github.io/downloads.html). Thanks for suggesting us to use the bridge file. Can you point me to the bridge file for MonDO-DO? I also remember you mentioning about an API for accessing the bridge files? Could you pls send that information as well?

Coming back to uberon-bridge-to-fma.owl file, I did notice that the file does not have uberon- fma mappings for the terms when the term from uberon is exactSynonym in FMA. Eg: No mapping in bridge file for UBERON_0001211(Peyer's Patch) and FMA:15054 (exactSynonym- Peyer's Patch). I think it makes more sense to add those mappings as well.

cmungall commented 6 years ago

We can make a separate bridge file for MONDO in the future, but for now these are distributed inside the main mondo.owl distribution. LMK if you want help extracting these with SPARQL.

For http://purl.obolibrary.org/obo/FMA_15054 we deliberately map this to UBERON:0003454 ! small intestine Peyer's patch

i.e.

           is_a UBERON:0001962 ! gut-associated lymphoid tissue
            is_a UBERON:0001211 ! Peyer's patch *** 
             is_a UBERON:0003453 ! large intestine Peyer's patch
             is_a UBERON:0003454 ! small intestine Peyer's patch <-- FMA:15054

This is a good example of how using OWL reasoning over lexical mapping alone can be more precise. The FMA class refers to the SI form of the tissue, the uberon class PP is more general and is applicable to SI and LI forms.