API
Documentation of the API (a work in progress)
Get one barcode: api.php?barcode=<processid>
Return information for an individual barcode. Each barcode is identified by a unique processid.
Example: api.php?record=SSDA1071-07
A single barcode has a unique processid, it may also be assigned to a BIN, and
have a taxonmic identification. The lineage lists the taxonomic classifcation of
the barcode. The barcode itself is represented as a nucleotide sequence nuc and a vector (embedding)
of frequencies of the 1024 possible 5-mers for a DNA sequence (e.g., "AAAAA", "AAAAC", "AAAAG", etc.)
This vector is used to compare the similarity of barcodes. the barcode may also have information
on where it occurs, and a list of datasets that it belongs too.
{
"processid": "SSDA1071-07",
"identification": "Gonimbrasia anthina",
"lineage": [
"k__Animalia",
"p__Arthropoda",
"c__Insecta",
"o__Lepidoptera",
"f__Saturniidae",
"sf__Saturniinae",
"t__Bunaeini",
"g__Gonimbrasia",
"s__Gonimbrasia anthina"
],
"marker_code": "COI-5P",
"embedding": "[0,0,0,0,0,0,0,0,0,0,0,0,0.003773585,0,0.003773585,0.00754717,0,0,0.003773585,0,0,0,0,0,0,0,0,0,0,0.00754717,0,0.003773585,0,0,0,0,0,0.003773585,0,0,0,0,0,0,0.003773585,0,0,0.003773585,0.00754717,0.003773585,0.003773585,0.00754717,0,0,0,0,0.003773585,0,0,0,0.003773585,0.00754717,0.011320755,0.011320755,0,0,0,0,0,0,0,0,0,0.003773585,0,0,0,0,0,0,0,0,0.003773585,0,0,0.003773585,0,0,0,0,0,0,0.003773585,0,0,0,0,0,0,0,0,0,0,0.003773585,0,0,0,0,0,0,0,0,0,0,0,0.003773585,0,0.003773585,0,0.003773585,0,0,0,0,0,0.003773585,0,0,0,0,0,0.003773585,0,0,0,0,0,0,0,0,0.003773585,0,0,0,0,0.003773585,0,0,0,0,0,0.003773585,0,0,0,0,0,0.003773585,0,0.003773585,0.003773585,0,0.003773585,0.003773585,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.003773585,0,0,0,0,0,0,0,0,0.003773585,0,0,0.003773585,0.003773585,0,0.00754717,0.01509434,0,0.003773585,0,0.003773585,0.003773585,0.003773585,0,0.003773585,0.00754717,0,0,0.00754717,0.003773585,0,0,0,0,0,0,0,0,0,0,0.003773585,0,0,0,0,0,0,0,0.003773585,0,0,0,0,0,0,0,0,0,0,0,0,0.011320755,0.003773585,0.00754717,0.011320755,0,0.003773585,0.003773585,0,0.003773585,0,0.00754717,0.003773585,0.00754717,0,0.003773585,0.00754717,0,0,0,0.003773585,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.003773585,0,0,0,0,0.003773585,0,0,0,0,0,0,0,0,0,0.003773585,0,0,0,0.003773585,0,0,0,0,0,0,0,0,0,0,0.003773585,0,0,0,0,0,0,0,0,0,0.003773585,0,0,0,0,0,0,0,0,0,0,0,0.003773585,0,0,0,0,0,0,0.003773585,0,0,0,0,0,0.00754717,0.003773585,0.003773585,0.003773585,0,0,0,0,0,0,0.003773585,0.003773585,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.00754717,0,0,0,0,0,0,0.003773585,0,0,0.003773585,0,0,0,0,0,0.00754717,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.003773585,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.003773585,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.003773585,0.003773585,0,0.00754717,0,0.003773585,0,0,0,0,0,0.003773585,0,0,0,0,0,0,0,0.003773585,0,0,0,0,0,0,0,0,0.003773585,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.00754717,0,0,0,0,0.003773585,0.003773585,0,0.00754717,0,0,0,0.00754717,0,0,0,0.00754717,0,0,0,0.003773585,0.00754717,0,0,0.003773585,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.003773585,0,0,0,0.003773585,0,0,0,0,0,0,0,0,0,0,0.00754717,0.003773585,0,0,0,0,0,0,0,0.00754717,0,0,0.003773585,0,0,0,0,0,0.003773585,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.003773585,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.003773585,0,0,0,0,0,0,0,0,0,0,0.00754717,0.00754717,0.00754717,0.003773585,0,0,0,0,0,0,0.003773585,0.003773585,0,0.003773585,0,0,0.003773585,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.003773585,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.003773585,0,0,0,0,0,0,0,0,0,0,0,0,0,0.003773585,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.003773585,0,0,0,0,0,0,0,0,0,0,0,0.003773585,0,0,0,0.003773585,0.003773585,0,0,0.003773585,0,0.003773585,0,0.003773585,0.011320755,0,0,0.02264151,0,0,0,0,0,0.003773585,0,0.003773585,0,0,0,0,0.003773585,0,0,0,0.003773585,0,0,0,0,0,0,0.003773585,0.00754717,0,0,0,0,0,0,0.003773585,0.018867925,0.003773585,0.003773585,0,0,0,0.003773585,0,0,0,0,0,0.018867925,0,0.003773585,0.003773585,0.003773585,0,0,0,0,0,0.003773585,0,0,0,0,0,0.003773585,0,0,0,0,0,0,0.003773585,0,0.003773585,0,0,0,0,0,0,0,0,0.003773585,0,0.003773585,0,0,0,0,0,0,0,0,0,0,0,0.003773585,0,0,0,0,0,0,0.003773585,0,0,0,0,0,0,0,0,0,0,0,0.00754717,0,0,0,0,0,0,0,0,0,0,0,0,0,0.003773585,0,0.00754717,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.011320755,0,0.003773585,0.003773585,0,0,0,0,0.003773585,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.003773585,0,0.018867925,0,0.003773585,0,0,0,0,0.00754717,0,0.01509434,0,0,0.00754717,0,0,0,0.003773585,0.003773585,0.003773585,0,0,0.003773585,0,0,0,0.003773585,0,0,0.003773585,0,0,0,0.00754717,0,0,0,0,0.01509434,0,0,0,0,0,0,0.003773585,0.011320755,0,0,0.00754717,0.003773585,0.003773585,0,0,0.003773585,0,0.00754717,0,0.00754717,0.003773585,0.00754717,0.018867925]",
"nuc": "--------------------------------------TGGGAACTTCTATAAGCCTATTAATTCGAATAGAATTAGGAACTCCTGGATATTTAATTGGAAATGATCAAATTTATAATACTATCGTAACAGCTCACGCTTTTATTATAATTTTTTTCATAGTTATACCTATTATAATTGGAGGATTTGGAAATTGATTAATTCCATTAATATTAGGAGCACCAGATATAGCTTTCCCCCGAATAAATAATATAAGTTTTTGATTATTACCCCCTTCTTTAACTCTTTTAATTTTTGGAAGTATTGTT---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------",
"nuc_basecount": 269,
"datasets": [
"DS-GOMIM01",
"DS-BLDSAT",
"DS-ALLSAT",
"DS-SATBUN02",
"DS-SATYP1"
],
"feature": {
"type": "Feature",
"geometry": {
"type": "Point",
"coordinates": [
12.948474,
6.2941685
]
},
"properties": {
"name": "SSDA1071-07",
"identification": "Gonimbrasia anthina"
}
},
"status": 200
}
Get related sequences: api.php?barcode=<processid>&related
If you add the &related parameter the API will return most similar sequences to the barcode. By default you will get the first 100 sequences. You can set the &limit parameter to say how many sequences you want.
"Related" is measured using the similarity of the k-mer vectors for the sequences.
Example: api.php?record=SSDA1071-07&related&limit=10
Get a BIN: api.php?bin=<bin_uri>
Return a list of all the barcodes in the same BIN.
Example: api.php?bin=BOLD%3AAAC2863