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  • Introducing JGI's Taxonomy Server

    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:

    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"
       }
    }}
    Plaintext taxid is supported by entering "pt_" in front of the query format, like this:

    Code:
    curl http://taxonomy.jgi-psf.org/tax/pt_accession/NZ_AAAA01000057.1
    97393
    Semicolon-delimited output is supported by entering "sc_" in front of the query format, like this:

    Code:
    curl http://taxonomy.jgi-psf.org/tax/sc_accession/NZ_AAAA01000057.1
    Archaea;Euryarchaeota;Thermoplasmata;Thermoplasmatales;Ferroplasmaceae;Ferroplasma;Ferroplasma acidarmanus
    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:

    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"
       }
    }}
    Please let me know if you experience any problems or can think of a useful addition!

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