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globalbioticinteractions / globalbioticinteractions.github.io

source files for GloBI website
https://globalbioticinteractions.org
MIT License
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Bug(?) - interface pivots between names shown, and finds no interactions #66

Closed mjy closed 4 years ago

mjy commented 5 years ago 
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?
screen shot 2018-11-20 at 10 29 27 am screen shot 2018-11-20 at 10 29 43 am
jhpoelen commented 5 years ago

Interesting! Could you share the GloBI url for the unexpected results?

jhpoelen commented 5 years ago

@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.

jhpoelen commented 4 years ago

@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.

Screenshot from 2019-09-20 11-30-58 Screenshot from 2019-09-20 11-31-22 Screenshot from 2019-09-20 11-38-50

Closing issue, but please do holler / comment if you believe this issue has not been resolved.