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OMA
Service Documentation :  SOAP interface for the OMA Browser at http://omabrowser.org
SOAP Method : TestOrthology
Documentation: Test the orthology relationship between two entries. Possible answers are 'not orthologous', '1:1 orthologs', '1:many orthologs' or 'many:1 orthologs'. The two parameters are preferably OMA entry identifiers (e.g. ECOLI1190). Many other IDs are also supported (e.g. Ensembl protein/gene identifiers, SwissProt IDs, etc.) whenever they were annotated in the original databases.
ServerAddress:
TestOrthology.EntryID1:
TestOrthology.EntryID2:
 
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SOAP Method : ListOrthologs
Documentation: Lists all orthologs for a given entry. To learn more about the exact relationship to the returned entries, use the TestOrthology function. To get more information, specifically the protein sequence and the organism, use the GetEntry function. The argument is preferably an OMA entry identifier (e.g. ECOLI1190). Many other IDs are also supported (e.g. Ensembl protein/gene identifiers, SwissProt IDs, etc.), whenever they were annotated in the original databases.
ServerAddress:
ListOrthologs.EntryID:
 
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SOAP Method : GetOMAGroup
Documentation: For any OMA group, this function returns a list IDs of all member proteins.
ServerAddress:
GetOMAGroup.GroupNr:
 
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SOAP Method : GetEntry
Documentation: Given an OMA entry identifier or another ID, this functions lists all possible IDs and cross-references for this entry that were found in the original database. Also returned are the protein sequence, the OMA group, the organism name and chromosome and locus.
ServerAddress:
GetEntry.EntryID:
 
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SOAP Method : IdentifySequence
Documentation: This function provides an easy way to map any sequence to the OMA entries by searching the input protein sequence in the OMA database. A list of all entries that contain this sequence is returned.
ServerAddress:
IdentifySequence.Sequence:
 
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SOAP Method : GetMatrixInfo
Documentation: This function returns the name of the current data set as well as the number of species and OMA groups in this data set.
ServerAddress:
 
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SOAP Method : ListIDTypes
Documentation: Get the list of ID types, which is of the form [[0,"OMA ID"], [1,"SwissProt ID"], ...].
ServerAddress:
 
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SOAP Method : ListSpecies
Documentation: Get the list of species covered by OMA in the form of [SpeciesCodes, TaxonId], defined by UniProt and NCBI respectively. [["HUMAN",9606],...]. This list is does not have any particular sorting.
ServerAddress:
 
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SOAP Method : ListOrthologsBetweenGenomePair
Documentation: Get the list of orthologs between two genomes. The result consists of the pair of IDs (according to requested type), the type of orthology (1:1 orthologs, ...) and the OMA group they belong, if they are members of the same group (otherwise -1 is returned).
ServerAddress:
ListOrthologsBetweenGenomePair.Genome1:
ListOrthologsBetweenGenomePair.Genome2:
ListOrthologsBetweenGenomePair.IDType1:
ListOrthologsBetweenGenomePair.IDType2:
 
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SOAP Method : ListOrthologsInGenome
Documentation: Get for a list of genes all its orthologs in a given target genomes. The query genes do not need to belong to the same species. The result consists of the pair of IDs (according to requested type), the type of orthology (1:1 orthologs, ...) and the OMA group they belong, if they are members of the same group (otherwise -1 is returned).
ServerAddress:
ListOrthologsInGenome.IDs.return[0]:
ListOrthologsInGenome.IDs.return[1]:
ListOrthologsInGenome.genome:
ListOrthologsInGenome.idtype:
 
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SOAP Method : MapIDs
Documentation: Map a list of IDs (of any type) to a IDs of a specified type. Use the ListIDType command to obtain a list of possible ID types
ServerAddress:
MapIDs.InIDs.return[0]:
MapIDs.InIDs.return[1]:
MapIDs.OutType:
 
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