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Knowledge-Graph-Hub / kg-covid-19

An instance of KG Hub to produce a knowledge graph for COVID-19 response.
https://github.com/Knowledge-Graph-Hub/kg-covid-19/wiki
BSD 3-Clause "New" or "Revised" License
80 stars 26 forks source link

ingest PubChem COVID-19 Disease Map #317

Open realmarcin opened 4 years ago

realmarcin commented 4 years ago

Name of the dataset COVID-19 Disease Map

https://pubchem.ncbi.nlm.nih.gov/#query=COVID-19%20Disease%20Map&tab=pathway&source=COVID-19%20Disease%20Map

Mapping or relevant fields A clear and concise description of what which fields you would want to be ingested.

If possible, highlight which fields map to nodes and which fields map to edges. Refer to Data Preparation for guidelines on how the final transformed data should be represented.

Additional context Add any other context, requests, concerns.

nlharris commented 4 years ago

This is missing "A clear and concise description of what which fields you would want to be ingested. If possible, highlight which fields map to nodes and which fields map to edges." Also, needs info about how ingesting this data source would benefit kg-covid-19. (That can go under "Additional context.")

cmungall commented 3 years ago

what is the status of this ticket? is it actionable?

justaddcoffee commented 3 years ago

Looks like a valuable dataset. I think though we are missing a clear idea of what data exactly we want to ingest here, and what this buys us.

Looks like by PubChem's count there are 537 compounds, 177 genes, 179 proteins, 606 pathways, 19 bioassays, and 196 papers available for ingest. Which of these data would we like to ingest, and what might be redundant with other ingests (e.g. seems likely that genes, proteins, and literature are captured already by other ingests)?