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dcppc / metadata-matrix

Mapping of metadata elements that are common to the TopMed, GTEx and MODs.
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Human Phenotype Ontology - Mammalian Phenotype Ontology mappings #4

Open nsuvarnaiari opened 5 years ago

nsuvarnaiari commented 5 years ago

Hi @cmungall ,

We are planning on expanding Metadata Matrix to include phenotype mappings from Human Phenotype Ontology (HPO) and Mammalian Phenotype Ontology (MP). I see there is a mapping file at https://github.com/obophenotype/upheno but generated in 2016. Is it possible to generate a new one that we could use? Or, is there any other place where I could get the mappings from.

Thanks for your help in advance. Suvvi

cmungall commented 5 years ago

Hi Suvvi

Yes, we probably should not have checked in the derived files into github. The underlying bridging axioms are all being actively worked on.

Before recommending the best course of action, what kind of mappings are required? Precise equivalence, or some kind of quantitative measure?

nsuvarnaiari commented 5 years ago

@cmungall , We are looking at precise equivalence (equivalence axioms) for now.

Thanks, Suvvi

cmungall commented 5 years ago

Would API access be sufficient for now?

We can also look at providing dumps/bdbags for these. If we wanted to do this in the DC context, is there a particular bucket we can use?

nsuvarnaiari commented 5 years ago

Hi @cmungall ,

I will provide you ftp transfer account details soon. Dropbox is an option too if the files are not too big. I am not very sure about the bucket option.

Thanks, Suvvi

cmungall commented 5 years ago

I would go with our own S3 buckets over FTP. My question was more if there was a preferred commons bucket to use. I'd assumed that knowledge artefacts in the commons would play by certain rules, e.g. always use bdbag. But maybe not a big deal

nsuvarnaiari commented 5 years ago

Hi @cmungall ,

I am not very sure if there is a preferred commons bucket to use. I can grab the file from wherever you prefer to place. Bdbag is fine by me.

Thanks, Suvvi

nsuvarnaiari commented 5 years ago

Hi @cmungall ,

Just checking if you had a chance to look into the options for providing the file. We will need this file for completing one of the DCPPC milestones.

Thanks, Suvvi