JGI's taxonomy server is now public-facing! It translates gi numbers, taxid numbers, organism names, and accessions to plaintext NCBI taxids, or complete JSON-formatted lineage, or semicolon-delimited lineage. The main page gives usage information. You can use it from the browser by entering something like:
or from the command line like this:
Plaintext taxid is supported by entering "pt_" in front of the query format, like this:
Semicolon-delimited output is supported by entering "sc_" in front of the query format, like this:
Comma-delimited terms may be used for batch processing, and underscores may be substituted for spaces (in names), e.g. /tax/name/homo_sapiens,mus_musculus
Simplified taxonomy (containing only subspecies, species, genus, family, order, class, phylum, kingdom, and superkingdom) is available by using "/simpletax/" instead of "/tax/", and common-ancestor lookup is possible with the "ancestor" query type:
Please let me know if you experience any problems or can think of a useful addition!
or from the command line like this:
Code:
curl "http://taxonomy.jgi-psf.org/tax/name/homo_sapiens" {"homo_sapiens": { "name": "Homo sapiens", "tax_id": "9606", "level": "species", "species": { "name": "Homo sapiens", "tax_id": "9606" }, "genus": { "name": "Homo", "tax_id": "9605" }, "subfamily": { "name": "Homininae", "tax_id": "207598" }, "family": { "name": "Hominidae", "tax_id": "9604" }, "superfamily": { "name": "Hominoidea", "tax_id": "314295" }, "parvorder": { "name": "Catarrhini", "tax_id": "9526" }, "infraorder": { "name": "Simiiformes", "tax_id": "314293" }, "suborder": { "name": "Haplorrhini", "tax_id": "376913" }, "order": { "name": "Primates", "tax_id": "9443" }, "superorder": { "name": "Euarchontoglires", "tax_id": "314146" }, "no rank": { "name": "Boreoeutheria", "tax_id": "1437010" }, "no rank 2": { "name": "Eutheria", "tax_id": "9347" }, "no rank 3": { "name": "Theria", "tax_id": "32525" }, "class": { "name": "Mammalia", "tax_id": "40674" }, "no rank 4": { "name": "Amniota", "tax_id": "32524" }, "no rank 5": { "name": "Tetrapoda", "tax_id": "32523" }, "no rank 6": { "name": "Dipnotetrapodomorpha", "tax_id": "1338369" }, "no rank 7": { "name": "Sarcopterygii", "tax_id": "8287" }, "no rank 8": { "name": "Euteleostomi", "tax_id": "117571" }, "no rank 9": { "name": "Teleostomi", "tax_id": "117570" }, "no rank 10": { "name": "Gnathostomata", "tax_id": "7776" }, "no rank 11": { "name": "Vertebrata", "tax_id": "7742" }, "subphylum": { "name": "Craniata", "tax_id": "89593" }, "phylum": { "name": "Chordata", "tax_id": "7711" }, "no rank 12": { "name": "Deuterostomia", "tax_id": "33511" }, "no rank 13": { "name": "Bilateria", "tax_id": "33213" }, "no rank 14": { "name": "Eumetazoa", "tax_id": "6072" }, "kingdom": { "name": "Metazoa", "tax_id": "33208" }, "no rank 15": { "name": "Opisthokonta", "tax_id": "33154" }, "superkingdom": { "name": "Eukaryota", "tax_id": "2759" } }}
Code:
curl http://taxonomy.jgi-psf.org/tax/pt_accession/NZ_AAAA01000057.1 97393
Code:
curl http://taxonomy.jgi-psf.org/tax/sc_accession/NZ_AAAA01000057.1 Archaea;Euryarchaeota;Thermoplasmata;Thermoplasmatales;Ferroplasmaceae;Ferroplasma;Ferroplasma acidarmanus
Simplified taxonomy (containing only subspecies, species, genus, family, order, class, phylum, kingdom, and superkingdom) is available by using "/simpletax/" instead of "/tax/", and common-ancestor lookup is possible with the "ancestor" query type:
Code:
curl http://taxonomy.jgi-psf.org/simpletax/name/ancestor/canis_lupus,mus_musculus {"canis_lupus,mus_musculus": { "name": "Mammalia", "tax_id": "40674", "level": "class", "class": { "name": "Mammalia", "tax_id": "40674" }, "phylum": { "name": "Chordata", "tax_id": "7711" }, "kingdom": { "name": "Metazoa", "tax_id": "33208" }, "superkingdom": { "name": "Eukaryota", "tax_id": "2759" } }}