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Old 02-01-2017, 03:54 PM   #1
Brian Bushnell
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Location: Walnut Creek, CA

Join Date: Jan 2014
Posts: 2,707
Default 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:

http://taxonomy.jgi-psf.org/tax/gi/1234

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!
Brian Bushnell is offline   Reply With Quote