Overview

DASH provides a REST-style API with support for custom filtering and ordering. Due to the very large size of the data, DASH operates somewhat differently from other REST services.

This API is currently undergoing beta testing. All endpoints are currently functional, but query input parameters, query output format, and error reporting may change slightly before full release. Upon release the API will be versioned so that updates to the API are released at new web addresses. This means that updates will not break existing tools which rely on an older version of the API.

Usage examples in more programming languages and more complete documentation of the various errors and status codes is coming soon.

Output Format

Example Query Result - Success

{"StatusCode":-1,"StatusMessage":"","MD5":"144d0495e039ed43593146f2f0d586ea","PDBID":"158L_A","Quality":0.4035559892654419,"DepositionDate":"1994-06-20T00:00:00Z","IsMD5Representative":true,"MD5Representative":"158L_A","IsClusterRepresentative":true,"ClusterRepresentative":"158L_A","Sequence":"MNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNTNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAALINMVFQMGETGVAGFTNALAMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGTWDAYKNL","Length":164}

Example Query Result - Limited

{"StatusCode":1,"StatusMessage":"Query results returned successfully, but limited to 100 results. Use `limited=0` for unlimited results (may be slow!).","MD5":"144d0495e039ed43593146f2f0d586ea","PDBID":"158L_A","Quality":0.4035559892654419,"DepositionDate":"1994-06-20T00:00:00Z","IsMD5Representative":true,"MD5Representative":"158L_A","IsClusterRepresentative":true,"ClusterRepresentative":"158L_A","Sequence":"MNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNTNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAALINMVFQMGETGVAGFTNALAMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGTWDAYKNL","Length":164}

DASH Query Basics

    ./REST1.0/domains?format=XML
    ./REST1.0/chains?format=XML

    ./REST1.0/domains?filter=length<100
    ./REST1.0/domains?filter=pdbid=5VZ0_A
    ./REST1.0/chains?filter=length<100
    ./REST1.0/chains?filter=pdbid=5VZ0_A

    ./REST1.0/domains?filter=length<100&limit=10
    ./REST1.0/chains?filter=length<100&limit=10

    ./REST1.0/domains?filter=length<20&limit=0
    ./REST1.0/chains?filter=length<20&limit=0

    ./REST1.0/domains?order=length=asc&limit=1000
    ./REST1.0/chains?order=length=asc&limit=1000

    ./REST1.0/domains?filter=depositiondate>=2017-01-01,depositiondate<=2017-12-31&columns=pdbid,length,depositiondate&order=length=desc&limit=10
    ./REST1.0/chains?filter=depositiondate>=2017-01-01,depositiondate<=2017-12-31&columns=pdbid,length,depositiondate&order=length=desc&limit=10

DASH Client for MAFFT

Python 2 Example Program

#!/usr/bin/env python
####
#NOTE:
#  This script is meant to get people started using the DASH REST API.
#  If implementing DASH as part of an automated process or in publicly-available
#    software it is also important to follow HTTP query best practices in order to
#    account for common network errors.
####
import json
import urllib2

dash_rest_url = "https://sysimm.org/dash/REST1.0"

def query_dash(url):
    print "Querying %s" % (url)
    #Download response from server
    response = urllib2.urlopen(url)
    raw_response = response.read()
    #Split response into lines
    json_object_lines = raw_response.splitlines()
    #Parse JSON objects
    json_objects = [json.loads(line) for line in json_object_lines]
    #Check JSON objects for errors
    for json_object in json_objects:
        if json_object["StatusCode"] > 0:
            code = json_object["StatusCode"]
            message = json_object["StatusMessage"]
            print "Status (%d): %s" % (code, message)
    return json_objects

#Build a query URL to search for 5 DASH representatives for a sequence
sequence = "QVQLQQSGPEDVKPGASVKISCKASGYSLSTSGMGVNWVKQSPGKGLEWLAHIYWDDDKRYNPSLKSRATLTVDKSSSTVYLELRSLTSEDSSVYYCARRGGSSHYYAMDYWGQGTTVTVSS"
search_url = "%s/domain_search_sequence?filter=sequence=%s&limit=5" % (dash_rest_url, sequence)

#Query DASH for representatives
dash_reps = query_dash(search_url)

for dash_rep in dash_reps:
    #Build a query URL to fetch top 5 alignments by score for search results
    alignment_url = "%s/domain_alignments?filter=id1=%s&order=score=desc&limit=5" % (dash_rest_url, dash_rep["ID"])
    #Query DASH for alignments
    alignments = query_dash(alignment_url)
    #Output information from alignments
    for alignment in alignments:
        print "---------"
        print "%s vs. %s - %d" % (alignment["ID1"], alignment["ID2"], alignment["SCORE"])
        print "PRIMS1: %s" % (alignment["PRIMS1"])
        print "SECOS1: %s" % (alignment["SECOS1"])
        print "PRIMS2: %s" % (alignment["PRIMS2"])
        print "SECOS2: %s" % (alignment["SECOS2"])
        print "EQUIV: %s" % (alignment["EQUIVALENCE"])

Data Type Reference

Endpoint List & Column Type Reference

GET - ./REST1.0/chains

GET - ./REST1.0/domains

GET - ./REST1.0/chain_search_sequence

GET - ./REST1.0/domain_search_sequence

POST - ./REST1.0/chain_search_sequence

POST - ./REST1.0/domain_search_sequence

GET - ./REST1.0/chain_alignments_metadata

GET - ./REST1.0/domain_alignments_metadata

GET - ./REST1.0/chain_alignments

GET - ./REST1.0/domain_alignments

POST - ./REST1.0/chain_alignments

POST - ./REST1.0/domain_alignments

GET - ./REST1.0/unsupported_chains

Bug Reporting & Feedback