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biodomws - WebService

This is a short description of the biodom WebService at BiBiServ.
If you're not familiar with using webservices in general you should have a closer look to our webservice related linklist.

WSDL - methods, parameters and datatypes

biodomws consists of four services (AlignmentML, SequenceML, RNAStructML and RNAStructAlignmentML) for converting native formats in xml and back. Each service has its own functions, which are desribed below. Contrary to most of the other Webservices at BiBiServ, all functions of this service return directly the result of the query.

AlignmentML
AlignmentML is a XML schema with the grammar for representing multiple sequence alignments

function input output description
fromFasta FASTA as string
Score as Integer
SequenceType as int
AlignmentML as XML converting FASTA to an AlignmentML XML Document
fromClustal clustal as string
Score as Integer
SequenceType as int
AlignmentML as XML converting clustal to an AlignmentML XML Document
toFasta AlignmentML as XML FASTA as string retrieving FASTA from an AlignmentML XML Document

SequenceML
SequenceML is a XML schema with the grammar for representing multiple sequences with some meta information (FASTA replacement)

function input output description
fromFasta FASTA as string
SequenceType as int
SequenceML as XML converting FASTA to an SequenceML XML Document
toFasta SequenceML as XML FASTA as string retrieving FASTA from an SequenceML XML Document

RNAStructML
RNAStructML is a XML schema with the grammar for representing RNA secondary structure information

function input output description
fromDotBracketFasta DotBracketFasta as String RNAStructML as XML converting DotBracketFasta to an RNAStructML XML Document
toDotBracketFasta RNAStructML as XML DotBracketFasta as string retrieving DotBracketFasta from an RNAStructML XML Document

RNAStructAlignmentML
RNAStructAlignmentML is a XML schema with the grammar for representing multiple RNA secondary structure alignments

function input output description
fromAlignedDotBracketFasta AlignedDotBracketFasta as String RNAStructAlignmentML as XML converting Aligned DotBracketFasta to an RNAStructAlignmentML XML Document
toAlignedDotBracketFasta RNAStructAlignmentML as XML AlignedDotBracketFasta as string retrieving AlignedDotBracketFasta from an RNAStructAlignmentML XML Document

Constants for SequenceType


Sequence Type Value
NucleicAcid 0
AminoAcid 1
Free Sequence 2
Empty Sequence 3
Unknown Sequence Type 4

Example Java clients

The Example Java clients are based on Apache Axis.
biodomwsCAlignmentMLtoFasta.java, alignmentml.xml
biodomwsCSequenceMLtoFasta.java, sequenceml.xml
biodomwsCAlignmentMLfromFasta.java
biodomwsCAlignmentMLfromClustal.java
biodomwsCSequenceMLfromFasta.java

Example Perl clients

The example perl clients are based on SOAP::Lite.
biodomwsCSequenceMLfromFasta.pl, fasta.fas
biodomwsCAlignmentMLfromFasta.pl, fasta.fas
biodomwsCAlignmentMLfromClustal.pl, clustal.clu
Welcome
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Wed Dec 19 13:56:33 2012