FunSimMat - Functional Similarity Matrix

RestLike Interface

FunSimMat provides a RestLike Interface. This allows for passing all query parameters in the URL instead of filling the
query form. An example is: http://funsimmat.bioinf.mpi-inf.mpg.de/query.php?type=gp2list&gp1=P48559&gps=O43687,Q09HT1,P04439

Semantic similarity search

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

URL Parameters:
type=semsim
gos: String, comma-delimited list of GO term accessions, e.g. GO:0000001,GO:0000002

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:

Comparison to list of accessions:
URL Parameters:
    type=gp2list
    gp1: String, protein or protein family accession, e.g. P48559, PF00255, or SM00043
    gps: String, comma-delimited list of protein / protein family accessions, e.g. Q06324,Q02486
    topCount: String, encodes the number of top results; using -1 will return all results
    topSort: String, sort with respect to this ontology; bp, cc, or mf

Comparison to taxon:
URL Parameters:
    type=gp2list
    gp1: 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
    topCount: String, encodes the number of top results; using -1 will return all results
    topSort: String, sort with respect to this ontology; bp, cc, or mf
    level: String, determines the level of the comparison, either "0" for comparison to all
      annotation classes, or "-1" for comparing to superclasses only

Comparison to MIM:
URL Parameters:
    type=gp2list
    gp1: 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
    topCount: String, encodes the number of top results; using -1 will return all results
    topSort: String, sort with respect to this ontology; bp, cc, or mf

Comparison to complete database:
URL Parameters:
    type=gp2list
    gp1: String, protein or protein family accession, e.g. P48559, PF00255, or SM00043
    topCount: String, encodes the number of top results; using -1 will return all results
    topSort: String, sort with respect to this ontology; bp, cc, or mf
    level: String, determines the level of the comparison, either "0" for comparison to all
      annotation classes, or "-1" for comparing to superclasses only

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:

Comparison to taxon:
URL Parameters:
    type=ba
    gos: String, comma-delimited list of GO term accessions, e.g. GO:0000001,GO:0000002
    goType: String, Go term type: bp, mf, or cc
    taxon: String, the NCBI Taxonomy accession of the taxon, e.g. 9606 for human
    topCount: String, encodes the number of top results; using -1 will return all results
    level: String, determines the level of the comparison, either "0" for comparison to all
      annotation classes, or "-1" for comparing to superclasses only

Comparison to MIM:
URL Parameters:
    type=ba
    gos: String, comma-delimited list of GO term accessions, e.g. GO:0000001,GO:0000002
    goType: String, Go term type: bp, mf, or cc
    mim: String, the NCBI MIM accession of the MIM, e.g. 222100 for Diabetes mellitus type I
    topCount: String, encodes the number of top results; using -1 will return all results

Comparison to complete database:
URL Parameters:
    type=ba
    gos: String, comma-delimited list of GO term accessions, e.g. GO:0000001,GO:0000002
    goType: String, Go term type: bp, mf, or cc
    topCount: String, encodes the number of top results; using -1 will return all results
    level: String, determines the level of the comparison, either "0" for comparison to all
      annotation classes, or "-1" for comparing to superclasses only

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:

Comparison to list of accessions:
URL Parameters:
    type=medsim
    gp1: String, OMIM accession, e.g. 114480
    as: String, the annotation strategy to be used, either as1 or as1_t2
    gps: String, comma-delimited list of protein / protein family accessions, e.g. Q06324,Q02486
    topCount: String, encodes the number of top results; using -1 will return all results
    topSort: String, sort with respect to this ontology; bp, cc, or mf
Comparison to all human proteins:
URL Parameters:
    type=medsim
    gp1: String, OMIM accession, e.g. 114480
    as: String, the annotation strategy to be used, either as1 or as1_t2
    topCount: String, encodes the number of top results; using -1 will return all results
    topSort: String, sort with respect to this ontology; bp, cc, or mf
    level: String, determines the level of the comparison, either "0" for comparison to all
      annotation classes, or "-1" for comparing to superclasses only