The PEDANT 3 Web Service
Attention: The Web service endpoint URL has changed to http://pedant.gsf.de/webservice
I. Introduction
The PEDANT Web Service provides programmatic access to the pre-calculated analyses of protein sequences from all PEDANT genomes.
PEDANT 3 provides flexible workflows for different analysis. These
work-flows can be easily adapted and expanded to meet special needs,
e.g. to analyse prokaryotic genomes leaving out analysis steps only
meaningful in eukaryota.
Please note, that this service provides access to pre-calculated data
and does not allow to carry out analysis steps for new genomes.
II.) The PEDANT data-scheme
The Web-Service encapsulates the underlying data scheme of the PEDANT 3 system in order to allow access in a easy and generic manner. However, some concepts are necessary to fully understand the service.
The PEDANT 3 system knows different classes of entities. Only classes corresponding to some result are reported. These are:
The organism
The PEDANT database is structured by organisms (datasets). Each
query must refer to one organism. Access to different organism can only
be done by independent service calls. It is not possible to query the
system like 'give me all EC Numbers from all bacteria'. Such a query
must be done in a consecutive manner. In consequence, each method needs
the organisms name as parameter, except the method getAvailableGenomes
The contig
Each organism provides a list of contigs. The properties of a contig include:
- the contig name
- a description
- a quality property
- start
- stop
- length
- type (an internal variable)
- the number of the genetic code
The genetic element
the genetic element type describes elements which reside on a contig. These include:
- orf
- deleted orf
- tRNA
- exon
- intermediate_orf
- deleted_orf
- miscRNA
- miscFeature
- snRNA
An orf entry consists out of following properties:
- code (this code is unique for each database. Most often, it is the gi-number of a protein/gene)
- a description
- type (here orf)
- DNA sequence
- amino-acid sequence
- length of protein
- length of DNA
- the pI Value
- start
- stop
- strand
- molecular weight
- a score
Different kinds of results: Memo, Evidence, Annotation
The way PEDANT 3 saves results of an analysis is rather generic. A method will result in a final prediction which is deduced by one or more evidences. For example, if a GO annotation is transfered by homology, the final result is the GO number newly assigned to the protein. These assignment might be supported by several close homologs in well annotated data-sets. This fact is saved within the PEDANT 3 system.(However, by standard the system will provide You with the final result). The final results are uniformly stored in Memo objects, the evidences as Evidence objects. Since the Evidence objects must hold very different kind of data, they come with an additional Parse object which activates/de-activates and names variables used in the object according to the actual method. This is transparent to the user since the Parse object is evaluated and the data is properly processed by the access layer underlying the service.
Annotation is an own generic type which does not describe an outcome of an analysis but an automatic transfered or by hand curated piece of information of a genetic element. (For example gene-names, locus tags etc. parsed out from gene-bank or by-hand assignment of literature).
III.) The Web Service
The Web Service is a SOAP based, document-style Web Service. A Java access API is available here and a jar file including all referenced libraries can be downloaded here.
You will find the WSDL file here.
Each query (except getAvailableGenomes) is restricted to a maximal
page size of 500 in order to avoid too large result-documents. The user
can iteratively query the data giving a page-number and a page-size. If
the result-set is smaller than the page-size, all data is fetched. For
details, please look into the example code.
In case of constraint violence, a PedantWSException is thrown. The FaultString value starts with "Invalid parameter: <details of the parameter constraint>".
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