IBServlets
Here are some examples about how to query the Interaction Browser servlets for data. The response to each of these queries is a JSON object that can be parsed for the information of interest.
- To find genes:
- search annotations for genes
- http://sysbio.soe.ucsc.edu/nets/data/annodb/annot?organism=9606&searchString=hypertension
- get network neighbors
- http://sysbio.soe.ucsc.edu/nets/data/trackdb/neighbors?trackList=Trus05_15902297,Tachibana05_16197558&biodeList=6712,3936,26072,51696,146988,4153
- get common network neighbors
- http://sysbio.soe.ucsc.edu/nets/data/trackdb/commonNeighbors?trackList=Sun06_16616334,Ross07_17413031,&biodeList=675,9918,6472,2146
- search for best pBLAST of genes' protein
- http://sysbio.soe.ucsc.edu/nets/data/annodb/bestPBlast?9606=7157,1234,6712,79109,3936,26072,51696,146988,57573,4153,8434,3976&10090=22059
- Corey's iterative Bayes pathway expansion
- http://sysbio.soe.ucsc.edu/nets/data/iterativeBayesPathwayExpander/expand?organism=9606&iterations=5&cutoff=0.5&queryset=1017,1019,1029,1058,1059,1063,11200,1163,1387,2033,2099,2119,2305,2353,255626,2619,2931,3175,3304,332,3910,4313,4609,4751,4775,5347,5604,5925,595,6502,6667,675,7039,7515,891,898,9133,9212,994&networks=Ma05_15994924,Rieger04_15356296,Frasor04_14973112,human_biogrid_Affinity_Capture-Western
- find the nodes in a network that constitute a shortest path between 2 nodes
- http://sysbio.soe.ucsc.edu/nets/data/trackdb/shortestPath?trackList=UCSC_Superpathway,human_biogrid&origins=114790&destinations=7157
- To find tracks:
- get available tracks for an organism
- http://sysbio.soe.ucsc.edu/nets/data/trackdb/trackList?organism=9606
- get track recommendations (be patient with this one... it should take 15 to 20 seconds to complete)
- http://sysbio.soe.ucsc.edu/nets/data/trdb/tr6?organism=9606&biodes=8776,4659,51592,22823,26100,490,3895,2186,9802
- To find edges:
- get all edges in a track that are relevant to a list of IDs
- http://sysbio.soe.ucsc.edu/nets/data/trackdb/edges?trackName=Tachibana05_16197558&biodeList=6712,79109,3936,26072,51696,146988,57573,4153,8434,3976
- get new edges in a track to append to an existing network
- http://sysbio.soe.ucsc.edu/nets/data/trackdb/newEdges?trackName=Tachibana05_16197558&biodeList1=6712,3936,26072,51696,146988,4153&biodeList2=55709,3976,64839
- To find sets of genes:
- get available set types
- http://sysbio.soe.ucsc.edu/nets/data/setsdb/setsList?organism=9606
- search for a string in a set's name
- http://sysbio.soe.ucsc.edu/nets/data/setsdb/setsName?setType=human_Go&searchString=development
- get a set's members by the set's name
- http://sysbio.soe.ucsc.edu/nets/data/setsdb/getSet?setType=human_Go&setName=kidney%20development
- To query external services for ID mappings:
- Grinder
- http://sysbio.soe.ucsc.edu/nets/data/queryExternal/grinderMapMulti?organism=9606&ids=snph,chac1,actn3,maybe_a_typo,pja1,prkdc,RAD21L1,Rorc,kcnk16
- Synergizer (currently broken, probably due to synergizer api changes)
- http://sysbio.soe.ucsc.edu/nets/data/queryExternal/synergizerMultiMap?organism=9606&ids=snph,chac1,actn3,maybe_a_typo,pja1,prkdc,RAD21L1,Rorc,kcnk16
- To query BioInt services (these services currently broken):
- get available pathways
- http://sysbio.soe.ucsc.edu/nets/data/queryBioInt/getPathways
- get pathway features
- http://sysbio.soe.ucsc.edu/nets/data/queryBioInt/getPathwayFeatures?bioInt_pathway_id=36871
- get pathway interactions
- http://sysbio.soe.ucsc.edu/nets/data/queryBioInt/getPathwayInteractions?bioInt_pathway_id=36871