Diff for "BioWebServiceConnectivity"

TableOfContents([2])

Proposal

(Still under construction!) These days, there are several public biological database web wervices such as Biomart, NCBI, or KEGG. It is very useful for many users if Cytoscape have an access to those huge data resources through simple user interface. By using this function, users can access virtually all kinds of annotations for the nodes, including variety of ID's, sequences, descriptions, orthologs, pathway names which contains the nodes, etc. Also, this is a general solution for all types of node ID mapping problems Cytoscape currently have. In addition, users can access network database web services thirough the same mechanism. The goal of this project is the following:

• Implement a mechanism to manage web service clients in the Cytoscape core.
• Design an interface which wraps each web service client.
• Design mechanism how web service clients communicate with the core (Event handling).
• Implement an simple UI for importing annotations and networks from the web services.

Biological Questions / Use Cases

• User loaded network with EntrezGene ID as node identifier into Cytoscape. He/she needs to import annotation files with Gene Symbol as the key.

• I need to check the orthologs for the genes in my network.

• I want to expand existing network with known interaction data in [http://www.ebi.ac.uk/intact/site/index.jsf IntAct]

• Mapping known pathways onto network data in Cytoscape.
• Executing an analysis program running on remote server which is implemented as a web service.

General Notes

Each web service is a building block to make higher-level functions. This means plugin writers should be able to use registered web services as if they are local Java APIs. To achive this, we should be careful to separate UI from the core web service clients.

Requirements

This component consists of 5 parts:

1. Web Service Client Manager in the core
   • - Maintaining list of web service clients.

     - Each web service client implements an interface WebServiceClient

2. Attribute mapping module - Mapping fetched annotations onto CyAttributes.

3. Event Handlers - Implementing custom event and its listeners only for WebServiceClients

4. Web Service Clients - these are jar files which contains properties and classes created from WSDL. They will be loaded as normal cytoscape plugins.
5. GUI for each web services

Deferred Items

Open Issues

• Taxonomy of the services

Backward Compatibility

• Pathway Commons / cPath integration to the new Network Import UI

Expected growth and plan for growth

References

Biological Web Services

• [http://taverna.sourceforge.net/index.php?doc=services.html Biological Web Services] by myGrid/Taverna Project

• [http://www.biomart.org/martservice.html Biomart]

• [http://www.ncbi.nlm.nih.gov/entrez/query/static/esoap_help.html NCBI Entrez E-Utilities SOAP Service]

• [http://www.ebi.ac.uk/~intact/devsite/modules/ws.html IntAct Web Services]

• [http://www.ebi.ac.uk/uniprot/remotingAPI/ UniProtJAPI]

• [http://www.genome.jp/kegg/soap/ KEGG API]

• [http://www.reactome.org/cgi-bin/mart Reactome Mart Service] (Implemented with Biomart backend)

Technologies Around Web Service

• [http://ws.apache.org/axis/ Apache Axis]

• [https://metro.dev.java.net/ GlassFish Metro Project]

• [https://jax-ws.dev.java.net/ JAX-WS] (part of Metro project)

Implementation Plan

Web Service Client Manager

• attachment:wsc_design.png

Web Service Client Manager is a mechanism to manage list of clients loaded in Cytoscape. Usually, a Web Service Client (WSC) is created from a WSDL and packed as a jar file. The WSC jar file must contain classes implementing the following interfaces:

• CytoscapePlugin

• WebServiceClient

This means each of WSC is a Cytoscape plugin. Therefore, all WSC will be loaded through Plugin Manager which is already in the core. Once WSC is loaded through Plugin Manager, WSC registers itself to Web Service Client Manager. Plugin writers can access all web services by using the following method:

WebServiceClientManager.getClient(client_name);

Custom Event Model

Instead of using standard PropertyChange events, core and clients sending custom events.

CyWebServiceEvent

CyWebServiceEventListener

Individual Client Design

Shared Components

Web Service Clients use the following components in the core:

• Client Property and Tunables
• Network Import Panel
• Attribute Import Panel

ID Mapping and Attribute Import

Biomart

attachment:biomartidmapping1.png

Biomart client mainly used as ID mapping.

UniProt

Recently, UniProt released UniProt Java Remoting API (UniProtJAPI). We will wrap this API with the WebServiceClient interface in Cytoscape.

KEGG

Network Import

IntAct

NCBI

• attachment:ncbi_network1.png

NCBI Entrez database has a unified web service called [http://www.ncbi.nlm.nih.gov/entrez/query/static/esoap_java_help.html NCBI E-Utilities]. The [http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene Entrez Gene] database will be the main resource for Cytoscape. This DB can be accessed through the E-Utilities web service. Users can use both keywords and list of Entrez Gene ID as the search term. Actual network data will be extracted form Interaction section of the returned data. Since we can extract interactions of one gene at a time, we need use Java SE 5's new Concurrency Framework to run multiple threads for fetching data efficiently.

Comments

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SarahKillcoyne August 16, 2007

This RFC would seem to be very related to the [:DataIntegration: Data Integration] one. Might be useful to discuss this as part of a larger web services integration if we decide a larger, more general solution would be useful.