A comprehensive database for proteome-wide known and predicted
ubiquitin ligase/deubiquitinase-substrate interactions in eukaryotic species

Application Programming Interface (API)


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:

http://ubibrowser.ncpsb.org.cn/v2/home/API?process=deubiquitination&type=enzyme&term=UBP1_HUMAN

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.

Attention

Please "sleep" one second between each call, so that our server won't get overloaded!

The sample result xml:


<?xml version="1.0" encoding="UTF-8" standalone="no" ?>
<result>	
	<Interaction>
		<enzyme_uniprot_AC>O94782</enzyme_uniprot_AC>			#Uniprot accession number of DUB
		<enzyme_gene_name>USP1</enzyme_gene_name>			#DUB gene name
		<substrate_uniprot_AC>A5YKK6</substrate_uniprot_AC>		#Uniprot accession number of substrate
		<substrate_gene_name>CNOT1</substrate_gene_name>		#substrate gene name
		<species>H.sapiens</species>					#species
		<confidence_score>0.877</confidence_score>			#prediction confidence score
		<likelihood_ratio>91.88</likelihood_ratio>			#prediction likelihood ratio
		<rank>929</rank>						#the rank of this pair
		<P-value>0.031671274</P-value>					#the p-value of predicted pair
		<Level>LOW</Level>						#the confidence level
		<enzyme_type>USP</enzyme_type>					#the subfamily of DUB
		<DOMAIN>
			<DOMAIN_LR>4.84</DOMAIN_LR>				#the likelihood ratio of evidence enriched domain pair
			<domain_enzyme>PF00443</domain_enzyme>			#enzyme contained enriched domain
			<domain_substrate>PF00782</domain_substrate>		#substrate contained enriched domain
		</DOMAIN>
		<GO>
			<GO_LR>1.76</GO_LR>					#the likelihood ratio of evidence enriched GO term pair
			<GO_enzyme>GO:0004843</GO_enzyme>			#enzyme contained enriched GO term
			<GO_substrate>GO:0016791</GO_substrate>			#substrate contained enriched GO term
		</GO>
		<NET>
			<NET_LR>17.47</NET_LR>					#the likelihood ratio of network topology
			<NET_number>7</NET_number>				#the number of network loops
			<NET_score>0.057</NET_score>						#the likelihood ratio of network topology

		</NET>
		<MOTIF>
			<MOTIF_LR>3.50</MOTIF_LR>				#the likelihood ratio of evidence motif
			<motif>L....N.....P</motif>				#the enzyme recognized motif with highest score
			<motif_other>L..L..S</motif_other>			#other enzyme recognized motif
			<motif_other>L..L....N</motif_other>
			<motif_other>A.AA</motif_other>
			<motif_other>IL..V</motif_other>
			<motif_other>I...L.W</motif_other>
		</MOTIF>
	</Interaction>
	<Interaction>
		<enzyme_uniprot_AC>O94782</enzyme_uniprot_AC>
		<enzyme_gene_name>USP1</enzyme_gene_name>
		<substrate_uniprot_AC>A2PYH4</substrate_uniprot_AC>
		<substrate_gene_name>HFM1</substrate_gene_name>
		<confidence_score>0.840</confidence_score>
		<likelihood_ratio>45.28</likelihood_ratio>
		<rank>141</rank>
		<P-value>0.004671219</P-value>
		<Level>MIDDLE</Level>
		<enzyme_type>USP</enzyme_type>
		<DOMAIN>
			<DOMAIN_LR>7.35</DOMAIN_LR>
			<domain_enzyme>PF00443</domain_enzyme>
			<domain_substrate>PF00270</domain_substrate>
		</DOMAIN>
		<GO>
			<GO_LR>1.76</GO_LR>
			<GO_enzyme>GO:0004175</GO_enzyme>
			<GO_substrate>GO:0003676</GO_substrate>
		</GO>
		<MOTIF>
			<MOTIF_LR>3.50</MOTIF_LR>
			<motif>L....N.....P</motif>
			<motif_other>N.L...P</motif_other>
			<motif_other>L....L..N</motif_other>
			<motif_other>L..L....N</motif_other>
			<motif_other>L..N.L</motif_other>
			<motif_other>IL..V</motif_other>
		</MOTIF>
	</Interaction>
</result>