UbiBrowser 2.0 has an application programming interface (API) which enables you to get the data without using the graphical user interface of the web page. The API is convenient if you need to programmatically access some information. We currently provide an implementation using HTTP, where the database information is accessed by HTTP requests. The API will allow one protein in each query.
As UbiBrowser 2.0 API works like normal HTTP request you can access it like any other webpage. Just copy/paste the following URL into your browser to get the result XML file:
Three parameters are needed for the request. "process" has two selections: "ubiquitination" or "deubiquitination", decided the prediction process is "ubiquitination" or "deubiquitination". "type" also has two selections: "enzyme" or "substrate". If you want to regard the input protein as enzyme/DUB, you should let "type=enzyme", as substrate let "type=substrate". parameter "term" need to assigned the input protein ID. Uniprot Accession number or Identifier is allowed.
Please "sleep" one second between each call, so that our server won't get overloaded!
O94782#Uniprot accession number of DUB USP1#DUB gene name A5YKK6#Uniprot accession number of substrate CNOT1#substrate gene name H.sapiens#species 0.877#prediction confidence score 91.88#prediction likelihood ratio 929#the rank of this pair 0.031671274#the p-value of predicted pair LOW#the confidence level USP#the subfamily of DUB 4.84#the likelihood ratio of evidence enriched domain pair PF00443#enzyme contained enriched domain PF00782#substrate contained enriched domain 1.76#the likelihood ratio of evidence enriched GO term pair GO:0004843#enzyme contained enriched GO term GO:0016791#substrate contained enriched GO term 17.47#the likelihood ratio of network topology 7#the number of network loops 0.057#the likelihood ratio of network topology 3.50#the likelihood ratio of evidence motif L....N.....P#the enzyme recognized motif with highest score L..L..S#other enzyme recognized motif L..L....N A.AA IL..V I...L.W O94782 USP1 A2PYH4 HFM1 0.840 45.28 141 0.004671219 MIDDLE USP 7.35 PF00443 PF00270 1.76 GO:0004175 GO:0003676 3.50 L....N.....P N.L...P L....L..N L..L....N L..N.L IL..V