| OMA |
Service Documentation :
SOAP interface for the OMA Browser at
http://omabrowser.org
| SOAP Method : TestOrthology |
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| 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.
| | | |
| | 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.
| | | |
| | SOAP Method : GetOMAGroup |
|---|
| Documentation: |
For any OMA group, this function returns a list IDs of all
member proteins.
| | | |
| | SOAP Method : GetEntry |
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| 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. | | | |
| | 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.
| | | |
| | SOAP Method : GetMatrixInfo |
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| 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.
| | | |
| | SOAP Method : ListIDTypes |
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| Documentation: |
Get the list of ID types, which is of the form
[[0,"OMA ID"], [1,"SwissProt ID"], ...].
| | | |
| | 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.
| | | |
| | SOAP Method : ListOrthologsBetweenGenomePair |
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| 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).
| | | |
| | 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).
| | | |
| | SOAP Method : MapIDs |
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| 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
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