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RFC 013: A Web Services Description of DAS

Author: Brian King (brian.king@animorphics.net)

Date: 12  June, 2002 

Related Documents:

This page in .doc format Genome Locations (.doc format) DAS2 Schema DAS2 Resources
  1. Introduction
  2. This document is a proposal for recasting the Distributed Annotation Service (DAS) protocol 1.5 as a Web Service. The proposed Web Service API will be known as DAS 2.0. The purpose for defining DAS as a Web Service is to improve the chances for application interoperability by more strictly defining the DAS data types and messages, and by making the DAS services available through web service registries.

  3. Architecture
    1. Service Defintions
    2. The DAS 2.0 genomic web service is defined using Web Services Description Language (WSDL) and XML Schema. The definitions of data types, operations, and bindings form a layered, modular architecture. Each layer is defined in a WSDL or Schema file where the higher level files include the definitions in the lower levels. The following table summarizes the definition files.

      Table 1 Genomic Service Definition Files

      File Name

      Format

      Purpose

      GenomicWebService.wsdl

      WSDL

      Example binding to URL

      GenomicBinding.wsdl

      WSDL

      SOAP message binding

      GenomicService.wsdl

      WSDL

      Abstract Genomic Service definition

      annotation.xsd

      XML Schema

      DAS data types definition

      lscore.xsd

      XML Schema

      I3C life science identifier definition

      lscore.xsd defines data types which may be used across life sciences. Currently it contains only the definition of the life sciences identifier. annotation.xsd defines the genomic data exchanged in DAS. GenomicService.wsdl is an abstract service definition of the operations supported by a Genomic service.

    3. Namespaces

    WSDL documents use names from several different standards including the WSDL, SOAP, and XML Schema standards. DAS specific names are also introduced in the service definition. The tables below summarize the service definition namespaces.

     

    Table 2 Web Service Definition Namespaces

    Description

    URI

    Prefix

    XML Schema Instance names

    http://www.w3.org/2001/XMLSchema-instance

    xsi

    XML Schema names

    http://www.w3.org/2001/XMLSchema

    xsd

    SOAP names

    http://schemas.xmlsoap.org/wsdl/soap/

    soap

    SOAP encoding names

    http://schemas.xmlsoap.org/soap/encoding

    soap-enc

    Web Service Definition names

    http://schemas.xmlsoap.org/wsdl/

    wsdl

     

    Table 3 I3C Core Namespace

    Description

    URI

    Prefix

    Life Sciences Core names

    http://www.i3c.org/names/core

    ls

     

    Table 4 Namespaces Introduced by DAS

    Description

    URI

    Prefix

    DAS WSDL names

    http://www.biodas.org/names/wsdl

    *

    DAS Data Types

    http://www.biodas.org/names/annotation

    das

    The DAS WSDL names URI is the value of the "targetNamespace" of the DAS WSDL definitions. This namespace is used for binding references within the DAS WSDL document. The DAS Data Types namespace is the namespace of the XML Schema used to define the DAS data types.

    *Note that the DAS WSDL documents may use the conventional prefix "tns" for "this namespace".

  4. Operations
  5. The heart of the DAS 2.0 specification is the definition of web operations for retrieving genomic annotations on sequences. These operations are briefly described in this section.

    1. getDataSources
    2. Returns the data sources that are available from this server. This operation replaces the DAS 1.0 dsn query.

    3. getAnnotatedResources
    4. Returns the identifiers of the available annotated sequences . This operation replaces the DAS 1.0 entry_points query.

    5. getAnnotationTypes
    6. Returns the list of annotation types available on the identified segment. This operation replaces the DAS 1.0 types query.

    7. getAnnotations
    8. Returns the annotations within a specified segment. This operation replaces the DAS 1.0 features query.

    9. getAnnotationsByLocation

    Returns the annotations within a specified segment and location. This operation replaces the DAS 1.0 features query used with the optional start and end parameters.

    The WSDL definition of these operations is in GenomicService.wsdl.

     

  6. Data Types
  7. The XML Schema definitions of the data types exchanged in DAS 2.0 messages are found in annotation.xsd and lscore.xsd.

     

  8. References

"Web Services Description Language (WSDL) 1.1" (http://www.w3.org/TR/wsdl)

"Namespaces in XML" (http://www.w3.org/TR/1999/REC-xml-names-19990114/)

Distributed Sequence Annotation System (http://www.biodas.org/documents/spec.html)