Bioware

Edwards Lab | Shields Lab | ?

REST @ Bioware

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

    General parameters

  • For almost all these tools, three parameters can be appended to the URL in order to change the returned results type.
  • » json=t/f : If not set or set to "f", the returned result is the normal one. One text file in most of cases. If set to "t" the result is split into lines and the list of lines is put in a python dictionnary (to allow a better sustainability of the server). Then the returned result is a JSON stream with the pattern : {'lines':list_of_lines}
  • » php=t/f : If json is set to "t" we look at the php parameter. If not set or set to "f", the returned result is the normal JSON stream (Cf. previous paragraph). If set to "t", the returned result is also a JSON stream but corresponding to the Job ID. In general, the JobID is used to retrieve other results files.
  • » mail=email_adress : If this parameter is set, an email will be sent to the adress when the job finished. The mail contains the jobID if available and the results'URL.

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The Bioware's Slimfinder server is out of date. we recomment to use the REST server hosted by the EdwardsLab at UNSW http://www.slimsuite.unsw.edu.au/servers.php.

under the "Run REST server job" area enter slimfinder in the "Prog:" box and enter sequence UNIPROT accessions IDs and options in the options box

e.g.
Prog: slimfinder Options: uniprotid=Q90372,Q14108,P11344&dismask=T

Disorder masking (dismask=T) is very strongly recommended. Other options are also available and described under the SLIMBuild and SLiMChance tabs of the documentation (http://rest.slimsuite.unsw.edu.au/slimfinder)

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