annotate schema with edam

[cmungall]

low priority but easy to do

annotate elements of the schema using edam:

https://www.ebi.ac.uk/ols/ontologies/edam

[dwinston]

It took me a while to find what "EDAM" means.

Its name originates from ‘EMBRACE Data And Methods’, as it was initiated by the EMBRACE project (Pettifer et al., 2010).

The EMBRACE (European Model for Bioinformatics Research and Community Education) web service collection is the culmination of a 5-year project

from https://doi.org/10.1093/bioinformatics/btt113 and then https://doi.org/10.1093/nar/gkq297

[brynnz22]

@cmungall is this issue still needed? I am happy to work on this. I have worked with the EDAM ontology quite a bit previously. If so, by "annotating" the schema do you mean adding annotations to various nmdc slots with a tag to the EDAM term?

[turbomam]

One of the SKOS-inspired mappings slots would be a better choice than annotations

https://linkml.io/linkml-model/docs/mappings/

If we are 100% sure that we are using a nmdc-schema element in a way that follows that semantics of an EDAM term, we could consider assining the EDAM CURIe as the slot_uri or class_uri

[turbomam]

Or the meaning of a permissible value in an enum

[brynnz22]

Okay sounds good. I will work on this. Thanks @turbomam

[turbomam]

see also Supplement to nmdc-schema style and collaboration guide

A (provisional) preference level of -1 doesn't mean that edam mappings shouldn't be used. It means that mappings form higher ranked namespaces should be prioritized.

[turbomam]

Note that edam CURIes will require separate prefixes for the four domains. For examples: https://bioregistry.io/registry/edam.data

[turbomam]

See also:

• https://github.com/microbiomedata/nmdc-schema/issues/514#issuecomment-1315448008