Closed mjy closed 4 years ago
Interesting! Could you share the GloBI url for the unexpected results?
@mjy I had a look at the suspicious behavior and found that the root cause is a mapping bug in v0.3.8 of GloBI taxon map at http://doi.org/10.5281/zenodo.1489121 .
curl --silent "https://zenodo.org/record/1489121/files/taxonMap.tsv.gz" | gunzip | grep "Apis mellifera scutellata"
produces (header added):
providedTaxonId | providedTaxonName | resolvedTaxonId | resolvedTaxonName |
---|---|---|---|
EOL:10455995 | EOL:10455995 | Apis mellifera scutellata | |
EOL:10455995 | INAT_TAXON:121322 | Apis mellifera scutellata | |
EOL:10455995 | NCBI:212527 | Apis mellifera scutellata | |
EOL:10455995 | OTT:85741 | Apis mellifera scutellata | |
EOL:10455995 | WD:Q2034820 | Apis mellifera scutellata | |
INAT_TAXON:121322 | Apis mellifera scutellata | GBIF:1341976 | Apis mellifera |
INAT_TAXON:121322 | Apis mellifera scutellata | INAT_TAXON:47219 | Apis mellifera |
INAT_TAXON:121322 | Apis mellifera scutellata | IRMNG:11307057 | Apis mellifera |
INAT_TAXON:121322 | Apis mellifera scutellata | ITIS:154396 | Apis mellifera |
INAT_TAXON:121322 | Apis mellifera scutellata | NBN:NHMSYS0000875423 | Apis mellifera |
INAT_TAXON:121322 | Apis mellifera scutellata | NCBI:7460 | Apis mellifera |
INAT_TAXON:121322 | Apis mellifera scutellata | OTT:461645 | Apis mellifera |
INAT_TAXON:121322 | Apis mellifera scutellata | WD:Q30034 | Apis mellifera |
which shows that subspecies Apis mellifera scutellata was mapped to its species, Apis mellifera. The underlying cause is expected to be some exception due to network / system outage or rate limit related to the API used (in this case iNaturalist) which prompted another attempt to match the name by its species, which then succeeded. Rate limits make perfect sense to protect a system, but does impose difficulties for continuous batch processes like those used in GloBI.
I am planning to re-map the said names (and similar mapping errors) and include the corrections in the next version of GloBI's taxon graph. Will keep this issue open until the changes have propagated.
Am open to suggestions on how to improve this taxon name linking business.
Thanks for reporting and your patience.
@mjy Just revisited the Apis millifera vs. Apis mellifera scutellata name mapping bug . I've narrowed the criteria for selecting matching taxa to avoid including subspecies names that were matched to species taxa. Regardless, the GloBI taxon map could use some TLC.
After applying the changes, the expected results are displayed:
so instead of
When I browse to list of interactions then I see a taxon name (Apis mellifera) when I click to expand that record then I see a different taxon name (Apis mellifera scutellata) which is a little odd then I click that I get "no interaction found" which seems odd, because where did I come from?
now:
When I browse to list of interactions then I see a taxon name (Apis mellifera) when I click to expand that record then I see a different taxon name (Apis mellifera) then I click that I get an expected non-empty list of related interactions
See attached screenshots.
Closing issue, but please do holler / comment if you believe this issue has not been resolved.