Batch Entrez outputs nothing

Question

[antoinefelden]

Hi,

I'm trying to use Batch Entrez (https://www.ncbi.nlm.nih.gov/sites/batchentrez) to look up the identifiers below, but although UID are recognised (and return records in the CBI database) - the output is empty.

Any idea why? Thanks! Reproducible example (to copy paste in a .txt document):

KF771749.1
KF153813.1
MG737737.1
MK091921.1
MG173246.1
JQ073586.1
HM402114.1
MG851790.1
KP317997.1
MG737738.1

[vkkodali_ncbi]

I am able to load them just fine. I am able to click on the "Retrieve records for 10 UID(s)" link and go to Nucleotide with the 10 records.

[antoinefelden]

Ok, weird, I am also able to click "Retrieve records for 10 UID(s)" link, but then the page is empty... https://ibb.co/RNRTbh7

[GenoMax]

vkkodali : I also get

Received lines: 10
Rejected lines: 0
Removed duplicates: 0
Passed to Entrez: 10
Retrieve records for 10 UID(s)

But when I click on retrieve records I get

No query #1 in history for Nucleotide

with Firefox. With Safari and Chrome I get a blank page, as in no data but the rest of the page shows up fine.

Looks like some cookie setting has to be turned on/relaxed?

[antoinefelden]

If I try with Firefox, the tab name becomes "Error - Nucleotide - NCBI", so there is something wrong going on... (see screenshot https://ibb.co/b78Yd3Y) Still under investigation!

[GenoMax]

What are you looking to get from these? An EntrezDirect solution would likely be possible.

[antoinefelden]

I'm wanting to retrieve taxonomy info from UIDs - which EntrezDirect looks like it's doing! Thanks! esearch -db "nucleotide" -query "MG737737.1" gives me the record, and I can then pipe it into efetch (using one UID as an example). The output is pretty large, any pointer about how to parse the output and only retrieve Species name and taxonomic family?

Answer 1

[GenoMax]

Using EntrezDirect:

$ esearch -db nuccore -query "MG737737" | elink -target taxonomy | esummary | xtract -pattern DocumentSummary -element TaxId | xargs -n 1 sh -c 'efetch -db taxonomy -id "$0" -format xml' | xtract -pattern Taxon -block "*/Taxon" -unless Rank -equals "no rank" -tab "\n" -element Rank,ScientificName
superkingdom    Eukaryota
clade   Opisthokonta
kingdom Metazoa
clade   Eumetazoa
clade   Bilateria
clade   Protostomia
clade   Ecdysozoa
clade   Panarthropoda
phylum  Arthropoda
clade   Mandibulata
clade   Pancrustacea
subphylum   Hexapoda
class   Insecta
clade   Dicondylia
subclass    Pterygota
infraclass  Neoptera
cohort  Paraneoptera
order   Hemiptera
suborder    Auchenorrhyncha
infraorder  Cicadomorpha
superfamily Cicadoidea
family  Cicadidae
subfamily   Cicadettinae
tribe   Cicadettini
genus   Kikihia

[antoinefelden]

Although there is a species name associated with this taxon (Kikihia muta, https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=140081 ) the command only retrieve taxonomy down to genus. Other queries do output full species names (example below). Is there a way to retrieve full species name for this one?

Working example with species name:

esearch -db nuccore -query "AB893129.1" | elink -target taxonomy | esummary | xtract -pattern DocumentSummary -element TaxId | xargs -n 1 sh -c 'efetch -db taxonomy -id "$0" -format xml' | xtract -pattern Taxon -block "*/Taxon" -unless Rank -equals "no rank" -tab "\n" -element Rank,ScientificName

[GenoMax]

Not sure I understand your question completely but if you are interested in getting species name for a specific taxID then you can simply do

$ efetch -db taxonomy -id "140081"
1. Kikihia muta
    species, bugs

Using following query it is not possible to get the species name.

$ efetch -db taxonomy -id "140081" -format native -mode xml | xtract -pattern Taxon -block "*/Taxon" -unless Rank -equals "no rank" -tab "\n" -element Rank,ScientificName
superkingdom    Eukaryota
clade   Opisthokonta
kingdom Metazoa
clade   Eumetazoa
clade   Bilateria
clade   Protostomia
clade   Ecdysozoa
clade   Panarthropoda
phylum  Arthropoda
clade   Mandibulata
clade   Pancrustacea
subphylum   Hexapoda
class   Insecta
clade   Dicondylia
subclass    Pterygota
infraclass  Neoptera
cohort  Paraneoptera
order   Hemiptera
suborder    Auchenorrhyncha
infraorder  Cicadomorpha
superfamily Cicadoidea
family  Cicadidae
subfamily   Cicadettinae
tribe   Cicadettini
genus   Kikihia