Ingest Disbiome microbiome data - Githubissues

Knowledge-Graph-Hub / kg-microbe

https://knowledge-graph-hub.github.io/kg-microbe/index.html

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Ingest Disbiome microbiome data #12

Open realmarcin opened 3 years ago

realmarcin commented 3 years ago

Disbiome database is a collection of microbiome compositional effects related to human disease

https://disbiome.ugent.be/home

Here is an example record for a disbiome entry: https://disbiome.ugent.be/experimentdetail/11342

The pertitent pieces of info for KG ingestion are:

"Disease" (MESH?)
"Organism" (taxonomic string)
"Qualititative outcome" (reduced, elevated etc)
"Sample type" (material really) eg faeces
Three level anatomical "Location" (MESH?)
possibly 'Reference classification database' (eg SILVA)
possibly cohort details? (eg age, BMI, M/F ratio)

realmarcin commented 3 years ago

DOIs available in NCBI Biosample data? Would be a possible join with Disbiome data.

OGER on "Disease" with MONDO ontology.

OGER on "Organism" with NCBI taxonomy.

OGER on "Sample type" and "Location" with UBERON ontology (but modeled as node/edge properties).