Hello,
I have list of app. 10000 organisms and want to gain taxonomy information for them (phylum, class, order,...) into some tabular file. I know NCBI Taxonomy browse (https://www.ncbi.nlm.nih.gov/Taxonomy/TaxIdentifier/tax_identifier.cgi), but the output is only taxonomy IDs - I need description (for example for Pinus nigra virus 1, instead this lineage: 2267679 446548 186534 2169561 10239 I need to gain this: Viruses; Ortervirales; Caulimoviridae; unclassified Caulimoviridae.
Thank you very much
Martin
you can use accession numbers or taxid to retrieve lineage of organism on command line
Batch ENTREZ
https://www.ncbi.nlm.nih.gov/sites/batchentrez
will take a list of the taxid numbers (ask to search taxonomy database with the list) and in the out put you can select full information. Then extract the LINEAGE line from each:
Scientific Name: Cacao swollen shoot virus
Taxonomy ID: 31559
Division: viruses
Rank: species
Lineage: Viruses; Ortervirales; Caulimoviridae; Badnavirus
Genetic Code: Standard (translation table 1)
I think you should also be able to search with the common names rather than taxid number, but I am not having luck with that. When I search taxonomy with Human Immunodeficiency Virus Type 1 it works, but in Batch ENTREZ it treats each word as a query and fails. When I use quotes
"Human Immunodeficiency Virus Type 1"
around each name, it says the quote character is illegal.
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