FunSimMat - Functional Similarity Matrix

XML-RPC Server

FunSimMat provides an XML-RPC interface for performing automatic queries and processing of the results. The interface is available at http://funsimmat.bioinf.mpi-inf.mpg.de/xmlrpc.php. It provides the same query options as the web front end. It accepts the accession numbers of the GO terms as comma-delimited list and returns the rows of the results table in the form of an array.
The functions supported by the XML-RPC server are listed below. Examples for the use of the XML-RPC interface in different programming languages (Java, Python, PHP) are given here.
New parameters, that were introduced with FunSimMat release 3.1, are optional. This ensures that the XML-RPC server stays compatible with existing scripts. These parameters are marked red.

Semantic similarity search

A semantic all-against-all comparison of a list of GO terms can be performed with the function:

Semantic.getSemSims(list)
Parameters:
    list: String, comma-delimited list of GO term accessions, e.g. GO:0000001,GO:0000002
Return value:
    An array with the rows of the results table. Each row is an array of Strings.
    The first row contains the column headers.

Comparing one protein / protein family with a list of proteins / protein families

A functional comparison of a protein / protein family with a list of proteins / protein families is performed
with one of the following functions:

Functional.getScoresGp2List(acc1, accList, resultCount)
Parameters:
    acc1: String, protein or protein family accession, e.g. P48559, PF00255, or SM00043
    accList: String, comma-delimited list of protein / protein family accessions, e.g. Q06324,Q02486
    resultCount: String, encodes the number of top results and the ontology to sort by;
      using -1_bp will return all results, e.g. 20_cc returns the 20 results with the highest CC simrel score
Return value:
    An array with the rows of the results table. Each row is an array of Strings.
    The first row contains the column headers.

Functional.getScoresGp2Taxon(acc1, taxon, resultCount, level)
Parameters:
    acc1: String, protein or protein family accession, e.g. P48559, PF00255, or SM00043
    taxon: String, the NCBI Taxonomy accession of the taxon, e.g. 9606 for human
    resultCount: String, encodes the number of top results and the ontology to sort by;
      using -1_bp will return all results, e.g. 20_cc returns the 20 results with the highest CC simrel score
    level: String, determines the level of the comparison, either "0" for comparison to all
      annotation classes, or "-1" for comparing to superclasses only
Return value:
    An array with the rows of the results table. Each row is an array of Strings.
    The first row contains the column headers.

Functional.getScoresGp2Mim(acc1, mim, resultCount)
Parameters:
    acc1: String, protein or protein family accession, e.g. P48559, PF00255, or SM00043
    mim: String, the NCBI MIM accession of the MIM, e.g. 222100 for Diabetes mellitus type I
    resultCount: String, encodes the number of top results and the ontology to sort by;
      using -1_bp will return all results, e.g. 20_cc returns the 20 results with the highest CC simrel score
Return value:
    An array with the rows of the results table. Each row is an array of Strings.
    The first row contains the column headers.

Functional.getScoresGp2Db(acc1, resultCount, level)
Parameters:
    acc1: String, protein or protein family accession, e.g. P48559, PF00255, or SM00043
    resultCount: String, encodes the number of top results and the ontology to sort by;
      using -1_bp will return all results, e.g. 20_cc returns the 20 results with the highest CC simrel score
    level: String, determines the level of the comparison, either "0" for comparison to all
      annotation classes, or "-1" for comparing to superclasses only
Return value:
    An array with the rows of the results table. Each row is an array of Strings.
    The first row contains the column headers.

Comparing a list of GO terms with a list of proteins / protein families

There are two functions for performing comparisons between a functional profile and a list
of proteins / protein families:

Functional.getScoresBa2Taxon(type, goString, taxon, resultCount, level)
Parameters:
    type: String, Go term type: bp, mf, or cc
    goString: String, comma-delimited list of GO term accessions, e.g. GO:0000001,GO:0000002
    taxon: String, the NCBI Taxonomy accession of the taxon, e.g. 9606 for human
    resultCount: String, encodes the number of top results and the ontology to sort by;
      using -1_bp will return all results, e.g. 20_cc returns the 20 results with the highest CC simrel score
    level: String, determines the level of the comparison, either "0" for comparison to all
      annotation classes, or "-1" for comparing to superclasses only
Return value:
    An array with the rows of the results table. Each row is an array of Strings.
    The first row contains the column headers.

Functional.getScoresBa2Mim(type, goString, mim, resultCount, level)
Parameters:
    type: String, Go term type: bp, mf, or cc
    goString: String, comma-delimited list of GO term accessions, e.g. GO:0000001,GO:0000002
    mim: String, the NCBI MIM accession of the MIM, e.g. 222100 for Diabetes mellitus type I
    resultCount: String, encodes the number of top results and the ontology to sort by;
      using -1_bp will return all results, e.g. 20_cc returns the 20 results with the highest CC simrel score
    level: String, determines the level of the comparison, either "0" for comparison to all
      annotation classes, or "-1" for comparing to superclasses only
Return value:
    An array with the rows of the results table. Each row is an array of Strings.
    The first row contains the column headers.

Functional.getScoresBa2Db(type, goString, resultCount, level)
Parameters:
    type: String, Go term type: bp, mf, or cc
    goString: String, comma-delimited list of GO term accessions, e.g. GO:0000001,GO:0000002
    resultCount: String, encodes the number of top results and the ontology to sort by;
      using -1_bp will return all results, e.g. 20_cc returns the 20 results with the highest CC simrel score
    level: String, determines the level of the comparison, either "0" for comparison to all
      annotation classes, or "-1" for comparing to superclasses only
Return value:
    An array with the rows of the results table. Each row is an array of Strings.
    The first row contains the column headers.

Perform disease protein prioritization

A functional comparison of an OMIM entry with a list of human proteins is performed
with one of the following functions:

Functional.getScoresGp2List(acc1, accList, as, resultCount)
Parameters:
    acc1: String, OMIM accession, e.g. 114480
    accList: String, comma-delimited list of protein / protein family accessions, e.g. "P04439,P30455"
    as: String, the annotation strategy to be used, either as1 or as1_t2
    resultCount: String, encodes the number of top results and the ontology to sort by;
      using -1_bp will return all results, e.g. 20_cc returns the 20 results with the highest CC simrel score
Return value:
    An array with the rows of the results table. Each row is an array of Strings.
    The first row contains the column headers.

Functional.getScoresGp2Taxon(acc1, taxon, as, resultCount, level)
Parameters:
    acc1: String, OMIM accession, e.g. P48559
    taxon: String, the NCBI Taxonomy accession of the taxon, should be 9606 for human; other taxa work with as set to "as1"
    as: String, the annotation strategy to be used, either as1 or as1_t2
    resultCount: String, encodes the number of top results and the ontology to sort by;
      using -1_bp will return all results, e.g. 20_cc returns the 20 results with the highest CC simrel score
    level: String, determines the level of the comparison, either "0" for comparison to all
      annotation classes, or "-1" for comparing to superclasses only
Return value:
    An array with the rows of the results table. Each row is an array of Strings.
    The first row contains the column headers.