Rich dense OTU table - Example biom file from http://biom-format.org/documentation/format_versions/biom-1.0.html

rich_dense.biom

{
 "id":null,
 "format": "Biological Observation Matrix 0.9.1-dev",
 "format_url": "http://biom-format.org/documentation/format_versions/biom-1.0.html",
 "type": "OTU table",
 "generated_by": "QIIME revision 1.4.0-dev",
 "date": "2011-12-19T19:00:00",
 "rows":[
    {"id":"GG_OTU_1", "metadata":{"taxonomy":["k__Bacteria", "p__Proteobacteria", "c__Gammaproteobacteria", "o__Enterobacteriales", "f__Enterobacteriaceae", "g__Escherichia", "s__"]}},
    {"id":"GG_OTU_2", "metadata":{"taxonomy":["k__Bacteria", "p__Cyanobacteria", "c__Nostocophycideae", "o__Nostocales", "f__Nostocaceae", "g__Dolichospermum", "s__"]}},
    {"id":"GG_OTU_3", "metadata":{"taxonomy":["k__Archaea", "p__Euryarchaeota", "c__Methanomicrobia", "o__Methanosarcinales", "f__Methanosarcinaceae", "g__Methanosarcina", "s__"]}},
    {"id":"GG_OTU_4", "metadata":{"taxonomy":["k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Halanaerobiales", "f__Halanaerobiaceae", "g__Halanaerobium", "s__Halanaerobiumsaccharolyticum"]}},
    {"id":"GG_OTU_5", "metadata":{"taxonomy":["k__Bacteria", "p__Proteobacteria", "c__Gammaproteobacteria", "o__Enterobacteriales", "f__Enterobacteriaceae", "g__Escherichia", "s__"]}}
    ],
 "columns":[
    {"id":"Sample1", "metadata":{
                             "BarcodeSequence":"CGCTTATCGAGA",
                             "LinkerPrimerSequence":"CATGCTGCCTCCCGTAGGAGT",
                             "BODY_SITE":"gut",
                             "Description":"human gut"}},
    {"id":"Sample2", "metadata":{
                             "BarcodeSequence":"CATACCAGTAGC",
                             "LinkerPrimerSequence":"CATGCTGCCTCCCGTAGGAGT",
                             "BODY_SITE":"gut",
                             "Description":"human gut"}},
    {"id":"Sample3", "metadata":{
                             "BarcodeSequence":"CTCTCTACCTGT",
                             "LinkerPrimerSequence":"CATGCTGCCTCCCGTAGGAGT",
                             "BODY_SITE":"gut",
                             "Description":"human gut"}},
    {"id":"Sample4", "metadata":{
                             "BarcodeSequence":"CTCTCGGCCTGT",
                             "LinkerPrimerSequence":"CATGCTGCCTCCCGTAGGAGT",
                             "BODY_SITE":"skin",
                             "Description":"human skin"}},
    {"id":"Sample5", "metadata":{
                             "BarcodeSequence":"CTCTCTACCAAT",
                             "LinkerPrimerSequence":"CATGCTGCCTCCCGTAGGAGT",
                             "BODY_SITE":"skin",
                             "Description":"human skin"}},
    {"id":"Sample6", "metadata":{
                             "BarcodeSequence":"CTAACTACCAAT",
                             "LinkerPrimerSequence":"CATGCTGCCTCCCGTAGGAGT",
                             "BODY_SITE":"skin",
                             "Description":"human skin"}}
            ],
 "matrix_type": "dense",
 "matrix_element_type": "int",
 "shape": [5,6],
 "data":  [[0,0,1,0,0,0],
           [5,1,0,2,3,1],
           [0,0,1,4,2,0],
           [2,1,1,0,0,1],
           [0,1,1,0,0,0]]
}