Question: Batch Entrez outputs nothing
0
gravatar for antoinefelden
29 days ago by
antoinefelden30 wrote:

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
batch entrez ncbi • 236 views
ADD COMMENTlink modified 27 days ago by genomax91k • written 29 days ago by antoinefelden30

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.

ADD REPLYlink written 29 days ago by vkkodali2.1k

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

ADD REPLYlink modified 29 days ago • written 29 days ago by antoinefelden30

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?

ADD REPLYlink modified 29 days ago • written 29 days ago by genomax91k

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!

ADD REPLYlink written 28 days ago by antoinefelden30
1

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

ADD REPLYlink written 28 days ago by genomax91k

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?

ADD REPLYlink written 27 days ago by antoinefelden30
1
gravatar for genomax
27 days ago by
genomax91k
United States
genomax91k wrote:

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
ADD COMMENTlink written 27 days ago by genomax91k
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