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Is there a way to make the NCBI entrez or datasets API respect biomial nomenclature within requests?

TL;DR: NCBI API does not respect species name when giving the whole species name.

I am trying to go through the NCBI databases looking for genomic data on specific species. I am using NCBI entrez Direct. I am using the following one liner:

esearch -db assembly -query "{insert species name here}" | esummary | xtract -pattern DocumentSummary -element SpeciesName

An example run with an actual species name:

esearch -db assembly -query "Aristolochia cretica" | esummary | xtract -pattern DocumentSummary -element SpeciesName

Produces the output

Aristolochia contorta
Aristolochia fimbriata

This is an issue for me because I requested "Aristolochia cretica" and got "Aristolochia contorta" and "Aristolochia fimbriata".

Second example:

esearch -db assembly -query "Physaria geyeri" | esummary | xtract -pattern DocumentSummary -element SpeciesName

Output:

Physaria ovalifolia
Physaria fendleri
Physaria acutifolia

third example:

esearch -db assembly -query "Vicia serinica" | esummary | xtract -pattern DocumentSummary -element SpeciesName

Vicia sativa
Vicia sativa
Vicia faba

I want the API to be mindful of the specific name as well. I am following this official manaul and I might have missed something but I am not being able to find a way to account for this behaviour.

Is writing something myself the only solution? Or is there a flag or setting I am missing?

ncbi entrez
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updated by GenoMax GenoMax • written by rijan_dhakal • rijan_dhakal

1 answer

NCBI API does not respect species name when giving the whole species name.

Not correct.

Or is there a flag or setting I am missing?

Add [ORGN] to scientific name.

You are looking for an organism that does not seem to have any data in assembly database. So if you do

$ esearch -db assembly -query "Aristolochia cretica [ORGN]" | esummary | xtract -pattern DocumentSummary -element SpeciesName

you get nothing but doing

$ esearch -db assembly -query "Aristolochia contorta [ORGN]" | esummary | xtract -pattern DocumentSummary -element SpeciesName
Aristolochia contorta

gets the correct output.

Taxonomy database does not seem to know about

$ esearch -db taxonomy -query "Aristolochia cretica [ORGN]"  | esummary

but if you look for

$ esearch -db taxonomy -query "Aristolochia contorta [ORGN]"  | esummary | xtract -pattern DocumentSummary -element ScientificName
Aristolochia contorta

You get the correct output.

Looks like only these two species have genomes in Aristolochia genus: https://www.ncbi.nlm.nih.gov/genome/?term=Aristolochia

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written by GenoMax GenoMax

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