REST @ Bioware

This page describes how to programatically access data and services from bioware.ucd.ie.

SLiMPrints3

The base url is : http://bioware.ucd.ie/rest/slimprints
The program takes the option uniprotid as a requiered parameter.

Therefore a sample query would look like http://bioware.ucd.ie/rest/slimprints?uniprotid=P04637

A text file with the SLiMPrints results will be returned.

SLiMSearch3

SLiMSearch is available to search for motifs in protein sequences.
The base url is : http://bioware.ucd.ie/rest/slimsearch

It takes the following arguments:
  • motif="RegEx" where RegEx is the regular expression representation of the motif.
  • uniprotid : one ID from a UniProt entry
  • taxonid=9606 where 9606 should be replaced with the taxon Id from NCBI of your search species.
  • orthdb=Orthdb where Orthdb can be ref, metazoa, fungi, trypanosomes, viridiplantae, apicomplexa, amoebozoa, archaea, bacteria. Default is ref, which is the uniprot reference proteomes dataset.
  • filename is the name of the results file that will be returned otherwise the default filename of slimsearchresults + motif name will be returned.
Therefore a sample query would look like http://bioware.ucd.ie/rest/slimsearch?motif="[KRHQSAP][DENQT]EL$"

motif is the only required parameter.

SLiMFinder

The base url is http://bioware.ucd.ie/rest/slimfinder

SLiMFinder takes the following arguments:
  • uniprotidlist=uniprotid*uniprotid*...*uniprotid : at least 3 IDs
  • dismask=T/F : Whether to mask ordered regions (see rje_disorder for options). Default = F
  • consmask=T/F : Mask residues based on relative conservation. Default = F
  • ftmask=T/F/[XX,XX,XX] : UniProt features to mask out. Default = [EM,DOMAIN,TRANSMEM]
Therefore a sample query would look like: http://bioware.ucd.ie/rest/slimfinder?uniprotidlist=DYIN_DROME*SWA_DROME*SWA_DROPS*DC1I1_MOUSE&consmask=F

uniprotidlist is the only required parameter.

CompariMotif

The base url is http://bioware.ucd.ie/rest/comparimotif

CompariMotif takes the following arguments:
  • motifs=RegEx_RegEx_..._RegEx, where RegEx is the regular expression representation of the motif.
  • cfmotifs=RegEx_RegEx_..._RegEx OR searchdb=elm/mnm/phm/lit/com/com_nophos/ned/all (exclusive OR)
  • cytoscape=t/f (optional, default value=f). If set to True, the xgmml is returned. If not, the tdt file is returned.
Therefore a sample query would look like http://bioware.ucd.ie/rest/comparimotif?motifs=P..P.[KR]_KK{2,3}&searchdb=ned&cytoscape=t

motifs is required parameter.

PeptideLocator

The base url is http://bioware.ucd.ie/rest/peploc

The program takes the option uniprotid as an option.

Therefore to access a particular UniProt entry you would call the following url http://bioware.ucd.ie/rest/peploc?uniprotid=P15502
A text file with the PeptideLocator bioactivity scores will be returned. It is possible to programmatically access this url however, we would ask that you wait 30 seconds between each call to the server.

SLiMPred

The base url is http://bioware.ucd.ie/rest/slimpred

The program takes the option uniprotid as an option.

Therefore to access a particular UniProt entry you would call the following url http://bioware.ucd.ie/rest/slimpred?uniprotid=P04637
A text file with the SLiMPred scores will be returned. It is possible to programmatically access this url however, we would ask that you wait 30 seconds between each call to the server.

Gopher

Gopher is accessible for downloading pre-computed alignments contrusted using Gopher.
The base url for gopher is http://bioware.ucd.ie/rest/gopher

It takes the following arguments: uniprotid(UniProt) and taxonid(NCBI) in the following format uniprotid=P04637&taxonid=9606
You can also just enter the uniprot id: http://bioware.ucd.ie/rest/gopher?uniprotid=P04637, and we will fetch the taxonid from the uniprot entry.
Scores

It is also possible to download the newick format tree for each alignment using the type=tree parameter. We also provide scores for each protein used in slimsearch and these are available using the type=scores parameter.
Future

In the future we will also be making different alignments available for particular groups of species: These will take the option orthdb=
'ref' = Uniprot Reference Proteomes
'metazoa' = Uniprot Complete Proteomes Metazoan class
'fungi' = Uniprot Complete Proteomes Fungi Class
'trypanosomes' = Trypanosomes Complete Proteomes Class
'viridiplantae' = Plants Complete Proteomes Class
'apicomplexa' = Apicomplexa Complete Proteomes
'amoebozoa' = Ameobozoa Complete Proteomes
'archaea' = Archaea Complete Proteomes
'bacteria' = Bacteria Complete Proteomes