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fathomnet / worms-server

Fast WoRMS name server
http://fathomnet.org:8888/docs/
MIT License
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Filter for Marine/Brackish Taxa Only #5

Open lauravchrobak opened 1 week ago

lauravchrobak commented 1 week ago

I am trying to use the worms module to find Marine/brackish species only and have found that my queries are not exclusive to marine taxa. For example, the following call worms.find_names_containing('Lumbricus terrestris') produces ['Lumbricus terrestris', 'Lumbricus terrestris lacteus', 'Lumbricus terrestris minor', 'Lumbricus terrestris platyurus', 'Lumbricus terrestris rubidus']. I am seeing that there is filter functionality on the WoRMS website. If you search for Lumbricus terrestris with 'Marine Brackish' only checked then earth worms are not found. Can we add functionality to filter for this to the fathomnet worms module?

lauravchrobak commented 1 week ago

I see that in the AphiaRecords Schemas of the REST API the following are fields: image

lauravchrobak commented 1 week ago

Perhaps just this line needs to be updated?

hohonuuli commented 1 week ago

I had originally tried filtering out non marine species but it broke things and I had to disable that filter. We could try to revisit it as our service doesn't care about non-marine species. See MutableWormsNode.scala#73

lauravchrobak commented 1 week ago

Ahh got it, yes I think this would be really useful functionality - would be worth checking with @kakanikatija to see if we want other subgroups like freshwater or brackish as well.

kakanikatija commented 1 week ago

for future-proofing, brackish and freshwater would be good to include.

hohonuuli commented 1 week ago

Tech note. The various flags in speciesprofile.txt appear to be applied inconsistently in the WoRMS data with values of 1, 0, and no value. have to run some testing with the no value fields and probably default a missing value to true to be safe.


taxonID isMarine    isFreshwater    isTerrestrial   isExtinct   isBrackish
urn:lsid:marinespecies.org:taxname:1            1   1   1       1
urn:lsid:marinespecies.org:taxname:2            1   1   1       1
[...]
urn:lsid:marinespecies.org:taxname:101472   1               
urn:lsid:marinespecies.org:taxname:101473   1               
urn:lsid:marinespecies.org:taxname:101474   1               
urn:lsid:marinespecies.org:taxname:101475   1               
urn:lsid:marinespecies.org:taxname:101476   1   0   0   0   0
urn:lsid:marinespecies.org:taxname:101477   1   0   0   0   0
urn:lsid:marinespecies.org:taxname:101478   1   0   0   0   0
urn:lsid:marinespecies.org:taxname:101479   1   0   0       0
urn:lsid:marinespecies.org:taxname:101480   1   1   0       1
urn:lsid:marinespecies.org:taxname:101481   1   0   0       0
urn:lsid:marinespecies.org:taxname:101482   1   0   0   0   0
urn:lsid:marinespecies.org:taxname:101483   1   0   0   0   0
urn:lsid:marinespecies.org:taxname:101484   1