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outbreak-info / outbreak.info-resources

A curated repository of metadata of resources on COVID-19 and SARS-CoV-2
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[DDE GUIDE ISSUE] Ontology look up failure #124

Open gtsueng opened 4 years ago

gtsueng commented 4 years ago

For infectiousAgent property, a search of SARS-CoV-2 (https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=2697049) fails. A search of SARS showed many strains of SARS coronavirus (seemingly country specific strains), but we're interested in species lvl.

Similarily, for the species property, search results seem to be missing human / Homo sapiens. Search for 'human' returned many human viruses, but not 'human' itself, search for homo sapien, homosapien, returns nothing--not being able to find something obvious like 'humans' will make the system seem less credible

Laura suspects issue may be due to something like it’s reading only the first ontology and not both, or something?

In any case, not returning an appropriate result for a straightforward search like 'human' will make the guide seem less credible, and will affect the data integrity (since people will be manually entering variations on each concept.

gtsueng commented 4 years ago

Note that this issue also exists in the NIAID guide. Another possibility is that the taxonomic search being limited to viruses as searching for human will turn up human viruses dog will turn up dog viruses, etc.