Ingest Weissman et al human microbiome taxa microbial trait data

[realmarcin]

The data is from this paper: Exploring the functional composition of the human microbiome using a hand-curated microbial trait database https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-021-04216-2

The dataset itself is Additional File 1: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-021-04216-2#MOESM1

To start we could perform NER with the same dictionaries as Madin et al - so NCBI Taxonomy, ENVO, ECOCORE, ChEBI.

There are additional numerical columns of interest here beyond what Madin et al provided:

• Temperature ranges
• pH ranges
• NaCl ranges (need to get unit from paper)
• Growth on an expanded set of subtrates
• oxygen.Preference is separate column
• Shape is encoded in two ways: as a string and as 0/1 for select shapes
• A few other traits are 0/1 and performing NER on field names would give us the entity in many cases.

[cmungall]

OK, here is the drill:

1. add step to fetch this in the Makefile
2. run through linkml-model-enrichment to get the first pass of the schema (https://github.com/linkml/linkml-model-enrichment)
3. this should also give you enums with ontology term IDs that will need manually checked, though not sure if @turbomam's code integrated yet
4. refine the schema manually, including adding mappings to biolink
5. lightweight python to make kgx

See https://docs.google.com/document/d/1iEsLp9pDvjGjgWMSLArtNf6Jwan-wjMl6_viQGyTWG8/edit# for approach