ral
ssBioMed Cent
BMC Bioinformatics
Open Acce
Research
SWS: accessing SRS sites contents through Web Services
Paolo Romano* and Domenico Marra
Address: Bioinformatics, National Cancer Research Institute (IST), Genova, I-16132, Italy
Email: Paolo Romano* - paolo.romano@istge.it; Domenico Marra - domenico.marra@istge.it
* Corresponding author
Abstract
Background: Web Services and Workflow Management Systems can support creation and
deployment of network systems, able to automate data analysis and retrieval processes in
biomedical research. Web Services have been implemented at bioinformatics centres and workflow
systems have been proposed for biological data analysis.
New databanks are often developed by taking into account these technologies, but many existing
databases do not allow a programmatic access. Only a fraction of available databanks can thus be
queried through programmatic interfaces. SRS is a well know indexing and search engine for
biomedical databanks offering public access to many databanks and analysis tools. Unfortunately,
these data are not easily and efficiently accessible through Web Services.
Results: We have developed ‘SRS by WS’ (SWS), a tool that makes information available in SRS
sites accessible through Web Services. Information on known sites is maintained in a database,
srsdb. SWS consists in a suite of WS that can query both srsdb, for information on sites and
databases, and SRS sites. SWS returns results in a text-only format and can be accessed through a
WSDL compliant client. SWS enables interoperability between workflow systems and SRS
implementations, by also managing access to alternative sites, in order to cope with network and
maintenance problems, and selecting the most up-to-date among available systems.
Conclusions: Development and implementation of Web Services, allowing to make a
programmatic access to an exhaustive set of biomedical databases can significantly improve
automation of in-silico analysis. SWS supports this activity by making biological databanks that are
managed in public SRS sites available through a programmatic interface.
Background
Technologies for the automation of biological data
analysis
ation, data integration is needed in order to achieve a bet-
ter and wider view of available information, to
automatically carry out analysis and/or searches involving
from Italian Society of Bioinformatics (BITS): Annual Meeting 2007
Naples, Italy. 26-28 April 2007
Published: 26 March 2008
BMC Bioinformatics 2008, 9(Suppl 2):S15 doi:10.1186/1471-2105-9-S2-S15
<supplement> <title> <p>Italian Society of Bioinformatics (BITS): Annual Meeting 2007</p> </title> <editor>Graziano Pesole</editor> <note>Research</note> </supplement>
This article is available from: http://www.biomedcentral.com/1471-2105/9/S2/S15
© 2008 Romano and Marra; licensee BioMed Central Ltd.
This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0),
which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.Page 1 of 7
(page number not for citation purposes)
Biological data is available in heterogeneous information
systems that are distributed over the Internet. In this situ-
more databases and software and to perform analysis
involving large data sets. In this frame, the need is felt for

BMC Bioinformatics 2008, 9(Suppl 2):S15 http://www.biomedcentral.com/1471-2105/9/S2/S15
a system that is able to improve the information accessi-
bility by raising it at an automatic level.
Among current ICT technologies, Workflow Management
Systems (WMS), in connection with Web Services (WS),
seem to be the most promising ones. A recent paper pre-
sented a methodology for the automation of in-silico data
analysis processes through workflow management sys-
tems that takes into account the synergic use of XML
schema, XML data storage, data and task ontologies, Web
Services, workflows systems and enactment portals [1].
More specifically, reasons for the setting up of WS in bio-
informatics have already been presented by many authors
[2-4]. WS have already been implemented by many Insti-
tutes and service centres in the biomedical field. Partial
lists of Web Services for bioinformatics are available at the
myGrid Wiki site [5] and in the Taverna web site [6]. Also,
Web Services can be retrieved and accessed through the
MOBY Central [7], a WS archive based on BioMOBY [8],
an open source software that implements an architecture
for the discovery and distribution of biological data
through Web Services.
Workflows are defined as “computerized facilitations or
automations of a business process, in whole or part”
(Workflow Management Coalition, WfMC) [9]. Their goal
is the implementation of data analysis processes in stand-
ardized environments and their main advantages relate to
effectiveness, reproducibility, reusability of procedures
and of intermediate results and traceability.
Some WMS have also been proposed in bioinformatics
[10-18], the Taverna Workbench [19,20] from the Euro-
pean Bioinformatics Institute (EBI, [21]) probably being
the best known among open source applications devel-
oped by public research institutes. It is able to build com-
plex analysis workflows, to access both remote and local
processors of various kinds, to launch execution of work-
flows and to display different types of results, including
text, web pages and various kinds of images and diagrams.
Processors that can be used through the Taverna Work-
bench include Web Services. One kind of Web Services
that can be accessed by using Taverna Workbench, are
those implemented by using Soaplab [22,23], a tool for
the rapid deployment of Web Services developed at EBI by
Martin Senger.
Extending available contents
New information sources are often developed by taking
into account above mentioned technologies. Otherwise,
many databases, developed during previous years, do not
offer a programmatic access to them: this reduces the
information that is available for automated analysis.
Sequence Retrieval System (SRS, [24,25]) is a well known
indexing and search engine for biomedical databanks,
developed by Thure Etzold at EBI and currently distrib-
uted by BioWisdom Ltd. SRS is able to efficiently query a
set of local databases. Among its most original and useful
features are the possibility of querying many databases
together and of integrating data retrieval and data analysis
in the same tool. SRS is usually searched through its user
interface, the CGI compliant software wgetz, that offers a
rich set of alternatives ways to interact with SRS and to
compose queries in its query language. It is possible to
interact with SRS by creating ad hoc URLs that either spec-
ify a query or request a specific output, such as the list of
available databanks and the description of fields compos-
ing a library. Examples of this are presented in table 1.
From its version 8, SRS is based on a new architecture
where software components communicate among them
by using Web Services. These do not follow agreed W3C
standards, are proprietary and are not publicly available.
For these reasons, they cannot be used in a open environ-
ment for integrating contents of SRS libraries with other
network data sources.
SRS used to be free for academic and no-profit institutes.
Through its many public sites, it offers access to more than
1,000 databanks and about 180 analysis tools. The most
important databank, like GenBank, Interpro, and Gene
Ontology, can be included in many sites. This partial
redundancy can be used to overcome possible sites'
crashes and network faults that can occur at any time.
Although some SRS libraries are subsets or subsections of
other, this does not mean that they have less relevance
and interest for researchers. For the sake of the SRS system
Table 1: Some ways to interact with SRS 7 and to compose queries in its query language.
Show list of databanks wgetz?-page+databanks
Show databank's information wgetz?-page+LibInfo+-lib+libname
Show databank field's information wgetz?-page+FieldInfo+-lib+libname+-bf+fieldname
Query databank wgetz?-e+[libname-fieldname:terms]
Query multiple databanks wgetz?-e+[{libnames}-fieldname:terms]
Query databank (return text only) wgetz?-e+[libname-fieldname:terms]+-ascii
Query databank (return some fields only) wgetz?-f+fields+[libname-fieldname:terms]+-asciiPage 2 of 7
(page number not for citation purposes)
This table shows some of the many possibilities of interacting with SRS version 7 by submitting arguments and options to wgetz through the URL
(HTML forms GET method). This kind of interaction is the basis of perl scripts that are run by SWS services.

BMC Bioinformatics 2008, 9(Suppl 2):S15 http://www.biomedcentral.com/1471-2105/9/S2/S15
they effectively are different databases, each of them hav-
ing its special interest. Advantages of considering such
libraries as real databases include, for subsets, improve-
ment of performances, and, for subsections and views,
simplified data management. The latter topic is especially
important when considering automated analysis. Unfor-
tunately, SRS libraries are not accessible through WS. So,
a tool that would allow to interact with these databanks
through Web Services would be extremely useful.
Previous work for Web Services for SRS libraries
To our knowledge, the only attempt to develop a system
that is able to interact with SRS through Web Services was
made by the group of Prof. Douglas Kell at the University
of Manchester [26]. They developed srs2acd, a set of java
classes that are able to create AJAX Command Definition
(ACD) [27] files for accessing each databank that is avail-
able in an SRS site, given its main URL. These files can
then be used for deploying Web Services by using the Soa-
plab tool. Each one of the resulting Web Services is then
specially devoted to a unique implementation, i.e. to one
database in one SRS site. Main limitations of this tool are
that each implementation has a related Web Service, thus
producing a high number of services, and that access to
alternative, but equivalent, WS is not automatically man-
aged.
The list of public SRS sites
A list of SRS public sites [28] is maintained by BioWisdom
Ltd [29]. This information is available as a simple, par-
tially structured, HTML page. The list allows to identify all
available copies of a given database and to compare them
on the basis of their number of entries. It also provides the
status of each site at a given date, although it is only
updated once per day.
As previously said, the same library can be included in
many SRS sites. This duplication and partial overlap can
support fault tolerance and help overcome sites' crashes
and network faults. An analysis of the status of sites (active
and non-active) over a period of 65 consecutive days
showed that less than the 50% of sites was always active
in that period.
Transparent access to SRS contents
A system for accessing SRS contents, without the need of
specifying which implementation should be queried,
would be useful. This ‘transparent’ access to SRS would
allow researchers using workflow management systems to
abstract their workflow from the connection details and
would offer them a way for avoiding network problems.
Such system should be able to check which sites are avail-
able at the time of execution of the workflow and select
In this paper, we present a set of Web Services that makes
information available in public SRS sites accessible as a
whole, not singularly, through a programmatic access. It
enables WMS to access all active SRS sites and to query
needed libraries. It also manages access to alternative, but
equivalent implementations, by also selecting the most
up-to-date among available systems.
Results
A suite of Web Services
We have developed SWS (SRS by WS), a suite of WS allow-
ing to query biological databases available in public SRS
sites, without specifying which one, and to return results
in a simple text-only format. It allows to check sites, to
query selected libraries and to retrieve essential informa-
tion on sites, such as lists of included databases and tools,
and on databases, such as sites where they are imple-
mented and related sizes/versions.
SWS can be invoked by specifying the name of the data-
bank to be queried and the query terms. It then automat-
ically choose the best site, performs the query and returns
complete results. Users can also specify the following
information: the SRS site to be queried, the fields where
the information must be searched, the desired output
fields.
Available Web Services
SWS currently includes five Web Services. The following
three WS allow to retrieve information on available data-
bases. getDBs retrieves acronyms of all libraries that are
available in a specified site, or in all known sites, if none
is specified. Similarly, getSites retrieves acronyms of all
SRS sites that include a specified library, or of all sites if no
library is specified. Finally, getImplementations retrieves
all implementations of a specified library. These WS are
only available for informative reasons, they do not actu-
ally query any SRS site. Instead, results can be used to
identify available libraries and to choose sites and librar-
ies to be queried in following steps.
The fourth WS, querySWS, allows to actually perform que-
ries on a specified library. The query (i.e. terms that must
be searched in the database) is a mandatory parameter.
The site, instead, can be omitted. In this case, SWS identi-
fies the best one by selecting, among those that are active,
the site where that specific library has the greatest number
of entries and, when more sites have the same number,
the most recent version of SRS (this function is currently
limited to SRS versions 6 and 7). Further parameters of
this WS allow to determine which parts (fields) of the
library must be queried, and which parts of the entries
(records) must be returned.Page 3 of 7
(page number not for citation purposes)
the ‘best’ site, i.e. the site including the most up-to-date
information, among active sites.

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Finally, the fifth WS, testSites, allows to check for the
availability of a site at a given time. Input parameters are
the acronym of the site to be checked, the number of
retries (in case of initial failure) and the time between
retries. All these parameters are optional. When no site is
specified, all sites are tested.
WS name, inputs and outputs are summarized in table 2.
Availability of the tool
SWS is available on-line [30]. Through this site, users and
software agents can retrieve WSDL descriptions of Web
Services included in SWS. Some WSDL compliant WMS,
such as Taverna Workbench, can directly interact with
SWS through this interface and execute the services.
A support site for SWS is also available on-line [31]. In this
site, a description of the software and usage information
of single WS are provided, together with contacts data. We
plan to allow, in the near future, downloading all files
needed to implement a local version of SWS, including
data structure, scripts for retrieving information on avail-
able sites, ACD definitions for a Soaplab implementation
of Web Services, scripts that actually implement the serv-
ices and installation instructions. SWS is being developed
as an open source and it is under refinement and contin-
uous development.
Discussion
We believe automation of data analysis and retrieval proc-
esses will offer bioinformatics the possibility of imple-
menting a really machine-oriented, distributed analysis
environment. For this to happen, the development and
implementation of WS that allow to make access to an
exhaustive set of biomedical databases and analysis soft-
ware is needed. Only a few of the many biological data
sources that are currently available on-line can be queried
through standard programmatic interfaces. Our tool SWS
contributes to overcoming this limitation by supporting
programmatic access to known SRS sites. Contrary to
other similar tools, SWS offers a unique point of access for
all sites because it leverages from a database of available
sites, databanks and implementations that is derived by
BioWisdom's list of public SRS sites and kept up-to-date
by using own scripts. BioWisdom's list is a useful reference
enabling SWS not to start from scratch. It is used both as
a starting list and to check for new sites. An exhaustive list
of public SRS sites is very difficult to achieve, we hope that
in the near future we can set up an alternative list and
receive information on new sites. By querying this data-
base, SWS can determine which is the best site for each
databank at any given time, and it therefore overcomes, at
least partially, possible problems arising from sites'
crashes and network faults. This is achieved b using the
number of records included in the databank since, usu-
ally, this increases each time a new version of the data-
bank is released. Information regarding databases' version
is not usually available and, thus, it can only rarely be
used. SWS also allows for the creation of workflows that
are not dependent on one single site and can, therefore,
work more consistently.
SWS currently presents some limitations that we plan to
overcome in the near future. It is currently not able to
query sites using SRS 8, due to the difficulty in building
queries through wgetz with this version. This limitation
can be considered a minor one, since the vast majority of
public SRS sites is still based on SRS 7. We plan to over-
Table 2: SWS Web Services and related inputs and output.
Web Service name and description Inputs Outputs
getDBs Retrieve data from srsdb about
libraries.
lib: the acronym of the library. Default value:
ALL
Output: list of libraries' acronyms
getSites Retrieve data from srsdb about SRS
sites.
site: the acronym of the site. Default value:
ALL
Output: list of sites and related info
getImplementations Retrieve data from
srsdb about implementations of libraries in SRS
public sites.
lib: the acronym of the library. Default value:
ALLsite: the acronym of the site. Default value:
ALL
Output: list of implementations and related
info
testSites Check actual availability of sites. site: the acronym of the site. Default value:
ALLretries: the number of retries after an
initial failure. Default value: 1time: time
between retries. Default value: 5 secs
activity: status of sites in one of the forms:
<site> is active<site> is not active
querySWS Query a specified library and
return entries related to queried terms.
lib: the acronym of the library. No default
value.site: the acronym of the site. Default
value: best sitequery: the query (terms to be
queried). No default value.in_fields: list of
library's fields to be searched. Default:
AllTextout_fields: list of library's fields to be
returned. Default: all
Entries: library's entries matching queryPage 4 of 7
(page number not for citation purposes)
This table lists SWS services by specifying their name, function, input and output.

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come this limitation by collaborating with administrators
of SRS sites with specific expertise on this version. Another
limitation of SWS is that it can presently only be effi-
ciently used when the SRS configuration of a databank is
known. In this case, both searched and retrieved fields can
be specified. This can be overcome by adding support for
the retrieval of descriptions of databanks fields. Another
limitation refers to the scarce information that SWS
reports about the databanks and sites it used for a query.
In fact, it's true that users are not informed about which
data set was used. This problem is going to be faced by
including detailed information on data provenance,
mainly comprising date, time, site, database, db version,
number of records. Finally, access to tools (analysis soft-
ware) that are available in SRS sites is not possible. We
don't see this point as a limitation, because of the availa-
bility of alternative Web Services offering access to this
software, like, e.g., EMBOSS [32] related ones.
Conclusions
Web Services are the most promising among ICT tools, in
view of the automation of network based data retrieval
and analysis in biology. We developed SWS, a suite of
Web Services that support query and retrieve of data from
databases included in public SRS sites. These Web Services
can increase the amount of data that currently is available
for the setting up of complex workflows and can in fact
improve automation of in-silico analysis by extending pos-
sible applications.
SWS is available for interested researchers through their
workflow management systems, provided they are SOAP
compliant and can use WSDL descriptions. The tool will
soon be available for downloading from the SWS support
site for local implementations.
SWS is currently being further developed in the sphere of
the Laboratory of Interdisciplinary Technologies in Bioin-
formatics – LITBIO [33].
Methods
The list of public SRS sites
The list of public SRS sites that is maintained by BioWis-
dom Ltd is divided into three sections. The first section is
made up of a list of sites. The second includes libraries
(i.e., databases) and related implementations (i.e. sites
where the library is available). The third section includes
tools (i.e., analysis software) and related implementa-
tions. BioWisdom's list is very essential, and it only
includes a few data. See table 3 for a commented list of
available data.
The list allows to identify all available copies of a given
database. Unluckily, not all SRS sites include information
on databases' version, so this data cannot be regularly
used. In order to compare databanks, the number of their
entries can be used instead. Usually, this number depends
on the version of the database and it is higher for later
releases. So, one can assume that the higher is the number
of entries of a database, the most recent is the release.
The local database srsdb
BioWisdom's reference list is checked daily and informa-
tion regarding available sites and libraries is stored into a
local database, srsdb, based on MySQL open source data-
base management system [34]. Srsdb contents are kept
up-to-date by running a perl script that checks the actual
status of the sites each hour. Srsdb includes three tables,
one for sites, one for libraries and one for implementa-
tions. While the two former tables are used for describing
the sites and the libraries as separate entities, the latter
Table 3: Information published in BioWisdom list of public SRS sites.
Information on the sites
Site's acronym Short acronym of the site, often the acronym of the institute where it resides
Site's description Long description of the site, usually the name and country of the Institute hosting the site
Site's URL The URL for the home page of the SRS site (not the institute)
No of libraries and tools at the site The number of libraries and the number of tools that are available at the site. Sites that are not currently
active are labelled here with ‘Could not access site’
SRS version of the site The number of the version of SRS that is available at the site. It ranges from 6 to 8. The most frequent version
is 7.1.x .
Information on the library
Library's acronym Short acronym of the library, usually an internationally known acronym
Information on the implementation of a library in a site
Site Acronym of site, same as above
URL The URL of the CGI program (either wgetz or srs, depending on SRS version). Specific parameters and
options are appended to this URL to compose the query.
No of entries Number of entries of the library in the current site
Information on the implementation of a tool in a site
Site Acronym of the site, same as above
URL The URL of the CGI program, same as above for librariesPage 5 of 7
(page number not for citation purposes)
This table lists and comments information that is included in the list of SRS sites that BioWisdom maintains. This information is included in a HTML
file having a regular disposition of tags, allowing to extract data by automatically scanning the file.

BMC Bioinformatics 2008, 9(Suppl 2):S15 http://www.biomedcentral.com/1471-2105/9/S2/S15
table joins them by specifying characteristics of the imple-
mentations of each library in every site. The information
included in the database essentially is the same that is
included in the list of public sites. Only a few data are
retrieved by further querying the sites. Figure 1 shows the
simple srsdb schema.
Web Services
Web Services were implemented by means of perl scripts.
These can also be run through command lines. Two types
of services were implemented, one for querying srsdb and
one for querying and checking SRS sites. Services and
command lines usage information are available in addi-
tional file 1.
The first three scripts, i.e. getDBs, getSites and getImple-
mentations, just interpret line arguments, query the srsdb
database and return results to standard output. The fourth
script, querySWS, initially queries the local database for
retrieving information on available sites and databases
that is needed to perform the remote query and then it car-
ries out the actual request by searching the chosen site.
Results are retrieved by using the GNU Wget non-interac-
tive network downloader and returned to standard out-
put, after checking for errors. The last script, testSites,
retrieves from srsdb information on sites to be checked
and then check if they are active, returning this informa-
tion to the user.
Web Services deployment
Web Services have been deployed by using Soaplab
[22,23], a SOAP-based Analysis Web Service tool provid-
ing a programmatic access to local, command-line appli-
cations and to the contents of ordinary web pages. The
only requirements of Soaplab are the Apache Tomcat serv-
let engine [35] with the Axis SOAP toolkit [36], a Java Vir-
tual Machine [37] and, optionally, perl [38] and MySQL.
Once the server has been installed, new Web Services are
deployed (added to the system) by defining simple
descriptions of related execution commands. Definitions
are written in the AJAX Command Definition (ACD) lan-
guage [27] and are then converted into XML before they
can be used by remote users.
List of abbreviations used
ACD: AJAX Command Definition
EBI: European Bioinformatics Institute
EMBOSS: European Molecular Biology Open Software
Suite
HTML: HyperText Markup Language
ICT: Information and Communication Technology
LITBIO: Laboratory of Interdisciplinary Technologies in
Bioinformatics
SOAP: Simple Object Access Protocol
SRS: Sequence Retrieval System
SQL: Structured Query Language
SWS: SRS by Web Services
URL: Uniform Resource Locator
W3C: World Wide Web Consortium
WfMC: Workflow Management Coalition
WMS: Workflow Management System
WS: Web Services
WSDL: Web Services Description Language
XML: Extensible Markup Language
Competing interests
Schema of the srsdb databaseFigure 1
Schema of the srsdb database. This figure shows the
schema of the srsdb database. Srsdb includes three tables:
one for sites, one for libraries and one for implementations.
The two former tables describes sites and libraries as sepa-
rate entities, the latter table is a join that specifies character-Page 6 of 7
(page number not for citation purposes)
The authors declare that they have no competing interests.istics of implementations of specific libraries in specific sites.

BMC Bioinformatics 2008, 9(Suppl 2):S15 http://www.biomedcentral.com/1471-2105/9/S2/S15
Authors' contributions
PR conceived the study, participated in its design, coordi-
nated and contributed to the development and imple-
mentation of software, and drafted the manuscript. DM
participated in the design of the study and contributed to
the development of software. All authors read and
approved the final manuscript.
Additional material
Acknowledgements
This work was partially supported by the Italian Ministry of Education, Uni-
versity and Research (MIUR), project “Laboratory of Interdisciplinary
Technologies in Bioinformatics - LITBIO”. Our system is partially based on
open source and is available under GNU Lesser General Public Licence
(LGPL).
This article has been published as part of BMC Bioinformatics Volume 9 Sup-
plement 2, 2008: Italian Society of Bioinformatics (BITS): Annual Meeting
2007. The full contents of the supplement are available online at http://
www.biomedcentral.com/1471-2105/9?issue=S2
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Additional file 1
SWS: usage of scriptsDescription: SWS perl scripts and their usage are
presented in the classical “usage style” where the script name is followed
by all possible parameters, values and defaults.
Click here for file
[http://www.biomedcentral.com/content/supplementary/1471-
2105-9-S2-S15-S1.pdf]Page 7 of 7
(page number not for citation purposes)
Analysis Workflows. In In Proceedings of the 1st Annual Meeting of
the Bioinformatics Italian Society (BITS2004) Padua, Italy; 2004:25. 26-27
March 2004