RDF Taxonomy Converter

This program processes an RDF taxonomy file and creates a tab-delimited text file with the extracted taxonomy terms

• The RDF taxonomy file can be downloaded from ftp.uniprot.org (see below)
• The RDF file is an XML representation of the taxonomy names browsable at https://www.uniprot.org/taxonomy/

Console Switches

The RDF Taxonomy Converter is a console application, and must be run from the Windows command prompt.

RDF_Taxonomy_Converter.exe
 InputFilePath [/O:OutputFilePath]
 [/IncludeRank]
 [/IncludeParents] [/IncludeGrandparents] 
 [/CommonName] [/Synonym] [/Mnemonic] [/OtherNames]
 [/Postgres]
 [/ParamFile:ParamFileName.conf] [/CreateParamFile]

InputFilePath is a path to the input file

• Optionally, instead use /I:InputFilePath to specify the file name
• The normal extension for an RDF taxonomy file is .rdf
• See below for an excerpt from an example input file

Use /O or -O to specify the output file path

Use /IncludeRank:False to disable including the classification rank (family, genus, species, etc.) in the output

Use /IncludeParents:False to disable including columns Parent_Term_Name and Parent_Term_ID in the output

Use /IncludeGrandparents:False to disable including columns Grandparent_Term_Name and Grandparent_Term_ID in the output

Use /CommonName:False to disable including the common name

Use /Synonym:False to disable including the synonym

Use /IncludeMnemonic:False to disable including the mnemonic name (a five letter abbreviation of the scientific name)

Use /OtherNames:False to disable creating a file listing other names for the taxonomy terms

Use /Postgres to use \N for null values (empty columns in the output file) and to escape backslashes

• This allows the data file to be imported using the COPY command in psql
• The file must be readable by the PostgreSQL server process, for example directory /tmp/
  • Example commands:

$ psql

\c dms

CREATE TABLE ont.t_tmp_newt (
    term_pk text,
    term_name text,
    identifier int,
    is_leaf int,
    rank text,
    parent_term_name text NULL,
    parent_term_id int NULL,
    grandparent_term_name text NULL,
    grandparent_term_id int NULL,
    common_name text NULL,
    synonym text NULL,
    mnemonic text NULL
);

COPY ont.t_tmp_newt FROM '/tmp/taxonomy_info_pg.txt' WITH (FORMAT TEXT, HEADER, DELIMITER E'\t');

The processing options can be specified in a parameter file using /ParamFile:Options.conf or /Conf:Options.conf

• Define options using the format ArgumentName=Value
• Lines starting with # or ; will be treated as comments
• Additional arguments on the command line can supplement or override the arguments in the parameter file

Use /CreateParamFile to create an example parameter file

• By default, the example parameter file content is shown at the console
• To create a file named Options.conf, use /CreateParamFile:Options.conf

Downloading and Processing UniProt Taxonomy Terms

• Use FileZilla (or WinSCP) to connect to ftp.uniprot.org
• Navigate to /pub/databases/uniprot/current_release/rdf
• Download file taxonomy.rdf.xz
• Use 7-Zip to extract the .rdf file
• Process the .rdf file using RDF_Taxonomy_Converter.exe

Example Input File Excerpt

<?xml version='1.0' encoding='UTF-8'?>
<rdf:RDF xml:base="http://purl.uniprot.org/taxonomy/" xmlns="http://purl.uniprot.org/core/" xmlns:foaf="http://xmlns.com/foaf/0.1/" xmlns:owl="http://www.w3.org/2002/07/owl#" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:skos="http://www.w3.org/2004/02/skos/core#">
<owl:Ontology rdf:about="">
<owl:imports rdf:resource="http://purl.uniprot.org/core/"/>
</owl:Ontology>
<rdf:Description rdf:about="10239">
<rdf:type rdf:resource="http://purl.uniprot.org/core/Taxon"/>
<rank rdf:resource="http://purl.uniprot.org/core/Superkingdom"/>
<mnemonic>9VIRU</mnemonic>
<scientificName>Viruses</scientificName>
<otherName>Vira</otherName>
<otherName>Viridae</otherName>
<rdfs:subClassOf rdf:resource="http://purl.uniprot.org/core/Taxon"/>
<rdf:Description rdf:about="10090">
<rdf:type rdf:resource="http://purl.uniprot.org/core/Taxon"/>
<rank rdf:resource="http://purl.uniprot.org/core/Species"/>
<replaces rdf:resource="85055"/>
<mnemonic>MOUSE</mnemonic>
<scientificName>Mus musculus</scientificName>
<commonName>Mouse</commonName>
<otherName>LK3 transgenic mice</otherName>
<otherName>Mus musculus Linnaeus, 1758</otherName>
<otherName>Mus sp. 129SV</otherName>
<otherName>house mouse</otherName>
<rdfs:subClassOf rdf:resource="862507"/>
<rdf:Description rdf:about="10090#strain-020">
<rdf:type rdf:resource="http://purl.uniprot.org/core/Strain"/>
<name>020</name>
</rdf:Description>

Contacts

Written by Matthew Monroe for PNNL (Richland, WA)
E-mail: matthew.monroe@pnnl.gov or proteomics@pnnl.gov
Website: https://github.com/PNNL-Comp-Mass-Spec/ or https://www.pnnl.gov/integrative-omics

License

The RDF Taxonomy Converter is licensed under the 2-Clause BSD License; you may not use this program except in compliance with the License. You may obtain a copy of the License at https://opensource.org/licenses/BSD-2-Clause

Copyright 2024 Battelle Memorial Institute