Workflow Navigation System

Category Cross-Omics>Workflow Knowledge Bases/Systems/Tools

Abstract The Workflow Navigation System (WNS) aims to help non- programming biologists perform analysis tasks by providing the next applicable service(s) on a Web browser according to the output of a previously selected service.

With this function, users can apply multiple services consecutively, by following links without any programming or manual copy-and-paste operations via a Web browser.

The listed services are determined automatically by the system referring to the dictionaries of service categories, the input/output types of services and HTML tags.

Although any workflow can be defined using Web Application Programming Interfaces (APIs), it is sometimes difficult for users to implement their workflows because of the burden of understanding how to utilize multiple Web APIs.

At other times, the user would like to determine the composition of workflow(s) dynamically depending on the output of a previous service instead of pre-determining it.

To support workflow execution in such cases, the manufacturers have developed the Workflow Navigation System which enables ‘dynamic workflow execution’ by listing only the next executable service(s) on a Web browser according to an output of a previously executed service.

This process eliminates the need for any programming, and thus, users only need to select a ‘service name’ that they would like to execute from a list.

The WNS system consists of three (3) components:

1) Meta information about services such as categories, Web Services Description Language (WSDL) locations and parameter names of the method;

2) Dictionaries on categories, input/output types of services and HTML tags; and

3) A Web interface generator that generates a Web page from Meta information, dictionaries, and Simple Object Access Protocol (SOAP) results.

The ‘category dictionary’ is created to display services in groups on a web-browser. The input/output type dictionary stores a list of data items for each parameter name.

For example, ‘DDBJ FlatFile’ parameter consists of seven (7) data items such as an organism, a nucleotide sequence and a product. The HTML tag dictionary stores pairs of data items and HTML tags that are used to generate the Web page components for those items.

Since there may be many executable services (e.g. 40 methods are currently possible for FlatFile, which is the output of a GetDDBJEntry method in a GetEntry service - see WABI below…), the manufacturer sets a prioritization among Web APIs in a configuration file.

Referring to this at runtime, only frequently used services are displayed in the default page.

Workflow Navigation System services --

You can use several bioinformatic services with a common web interface.

This system provides Not only the result of a service but also the next service to be executed using the result.

1) Keyword search -

Keyword search includes - database search systems - by using keywords such as gene name, organism name and accession number, etc.

The databases are the Nucleotide database of the DNA Data Bank of Japan (DDBJ) and the Amino acid sequence database such as DAD, the Universal Protein Resource (UniProt) and PRF, the protein structure databases of the Protein Data Bank (PDB), and the Unified Taxonomy database.

2) Sequence search -

Sequence search includes - database search systems - by using a nucleotide sequence or amino acid sequence. BLAST and FASTA services are also available.

3) Classify -

Classify provides the function of multiple sequence alignments by ClustalW and the database search of the Taxonomic database.

Web APIs for biology (WABI) --

The manufacturer provides an extensive set of Web APIs for biology (WABI) based on the Simple Object Access Protocol (SOAP) and the Representational State Transfer (REST) technologies.

WABI currently provides 129 Web APIs (methods) from 21 services, such as keyword search, data retrieval and homology search and DDBJ original analysis systems.

These methods can be used as building blocks for the development of customized workflows.

WABI also provides the function that enables users to asynchronously retrieve execution results of time-consuming methods.

For example, for those services that process large amounts of data such as BLAST and ClustalW, both synchronous and asynchronous versions of the method are prepared, such as searchParam and searchParamAsync, respectively.

When a user invokes a method with an asynchronous version, a requestId is assigned to the invocation and the user can receive its result at any time by invoking the getAsyncResult or getAysncResultMime method of the RequestManager service with the requestId.

Using these services, users only need to define their analysis tasks with a programming language (Perl, Java, C, Ruby or Python), and thus, can avoid manual copying-and-pasting or developing complex parser programs.

In addition, typical workflows, that is, a series of processing tasks, are provided so that frequently used analysis procedures can be carried out without any programming.

WABI currently provides eight (8) workflows such as the Blast-ClustalW workflow and the SNP workflow. These workflows are constructed by applying several Web APIs.

The semantics of each workflow is defined using the Unified Modeling Language (UML) notation so that end users can understand its function unambiguously.

A Web service can be also used to construct human interfaces for link navigation. The manufacturers have developed a Workflow Navigation System (see above...) to improve the usability of Web interfaces using Web services as the components of the system.

With this system, users can execute other non-predefined workflows by following automatically generated links on a Web browser.

WABI also provides wiki-style Web pages, called the Cookbook, to share know-how in using WABI services, such as ‘How can we retrieve entries by specifying sequence length against the DDBJ database?’ and ‘How can we obtain a BLAST result with an XML format?’

System Requirements

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Manufacturer

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Web APIs for biology (WABI) and Workflow Navigation System

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G6G Abstract Number 20528

G6G Manufacturer Number 104145