Web Services 4 Life Sciences: A Curated Catalogue of Life Science Web Services

Lead Research Organisation: University of Manchester
Department Name: Computer Science


WS4LS is an initiative aimed at providing easy access to a catalogue of Web Services relevant to the life science communities. Web Services are defined by the W3C as a software system designed to enable machine to machine interoperability over a network. However, the discovery of Web Services is today quite a difficult task for bench scientists whom do not have the time or means to endeavor in the informatics related to these. Web Services are poorly described. WS4LS intends to provide easy, human accessible content documenting Web Services by extensive use of service ontologies through which it will be trivial to discover a function or operation, as required by the end user. Until recently, laboratories had to invest locally in the implementation and maintenance of bioinformatic tools and databases to carry out both day to day as well as complex tasks. WS4LS addresses the 'where and how' of Web Services for scientists and exposes how to build these into local analytical pipelines. WS4LS will also provide the means for creating communities that will share knowledge and enhance scientific interactions at various levels. WS4LS e-scientists communities will complement existing efforts and generate a Google-like Coop [http://www.google.com/coop/].

Technical Summary

The Catalogue will have one common Web interface, hosting portals to advanced curation and discovery tools. The look and feel will be 'Web 2.0'; that is, of an online social community (a la FaceBook), social sharing and tagging site (a ls Flickr or Connotea) and shop (a la Amazon or Ebay), similar to Web Services List but more user friendly. For curation and acquisition, we intend to couple a traditionally 'exclusive' curated resource for high quality annotation and discovery, with a modern participatory online community approach inspired by social community sites, and shopping sites for browsing and recommendations. By these means we aim to ease improve the sustainability of the catalogue, make it more relevant, and give the community 'ownership' in the catalogue. Past evidence suggest that moderators and good citizenship practices will emerge, who can contribute to the moderation pipeline of the official curator. For discovery, we intend to couple the traditional 'form-filling' search mechanisms (like the Feta Discovery Service) with a modern facet-based 'shopping' style web interface like /facet [?] or Amazon and a social network web site with blogs, discussion forums, tags, shared bookmarks, recommendations and ratings etc; and a Google-style interface. For tool developers and service providers, we intend to serve them with quality, machine-level, annotations from the expert curators that they can use for automated service matching, for example [?]. We will provide them with APIs to incorporate the Catalogue into their tools and workbenches; a special upload annotation environment and access to services for migrating applications to be Web Services.


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Description This was an infrastructure project. We developed, and continue to support and curate, a Web Services Catalogue for the Web Services of the Life Sciences community. Thus bioinformaticians and developers of bioinformatics tools can find, annotate, monitor and advertise web services. This means that they can be reused beyond their original authors and that reinvention can be reduced.

The Catalogue is in active use and has spawned clones for the Biodiversity Community. It forms part of the Software Catalogue of the ELIXIR European Research Infrastructure and feeds the ELIXIR Tools registry http://bio.tools. tBoth catalogues are still in use although their codebases are now deprecated. New EU projects (2019) in ELIXIR and biodiversity (Synthesys+) will look to migrate these catalogues to new platforms hosted by major ESFRIs. The Catalogues have influenced these EU platforms.

An iPad/iPhone app was also developed for mobile access to the Catalogue, and it has been fully integrated into the Taverna Workflow Management System (http://www.taverna.org.uk)
Exploitation Route The BioCatalogue is already in use, and became part of the ELIXIR Tools Registry feeds (http://www.bio.tools). The resource is freely accessible.
the BioDiversityCatalogue (http://www.biodiversitycatalogue.org) is still in active use by TDWG (Biodiversity Information Standards (TDWG)

The software is open source and freely available under a BSD license.

The findings on web service management and the quality of web service publishing, has been reported in international conferences and publications.
Sectors Agriculture, Food and Drink,Chemicals,Digital/Communication/Information Technologies (including Software),Education,Environment,Pharmaceuticals and Medical Biotechnology

URL http://www.biocatalogue.org
Description The BioCatalogue (http://www.biocatalogue.org) is managed by University of Manchester and it is hosted at the EMBL-EBI. It currently has 1200+ services, 260 service providers, 878 members and 1350 archived services The prime publication Jiten Bhagat, Franck Tanoh, Eric Nzuobontane, Thomas Laurent, Jerzy Orlowski, Marco Roos, Katy Wolstencroft, Sergejs Aleksejevs, Robert Stevens, Steve Pettifer, Rodrigo Lopez, Carole A. Goble, BioCatalogue: a universal catalogue of web services for the life sciences, Nucleic Acids Research, Volume 38, Issue suppl_2, 1 July 2010, Pages W689-W694, https://doi.org/10.1093/nar/gkq394 has had over 260 citations. It forms part of the ELIXIR-UK portfolio of resources and contributes to the ELIXIR registry. The BioCatalogue spawned the BioDiversityCatalogue (www.biodiversitycatalogue.org) for BioDiversity Services which forms part of the BioDiversity Virtual eLab (http://www.biovel.eu). The spin off BioDiversityCatalogure remains in use. In the EU project Synthesys+ award (2019) the plan is to migrate the content to a new platform The content feeds the EU Research Infrastructure ELIXIR bio.tools catalogue. A generalised platform for Web Service Catalogues - the ServiceCatalographer, has been spawned as a factory for making specialist Web Service Registries (http://www.servicecatalogue.org.uk/). The platform was also adopted by PANACEA - a USA catalogue of Web services that automated the process of acquisition, production, maintenance and updating of the language resources required by machine translation. An iPad/iPhone app was also developed for mobile access to the Catalogue, and it has been fully integrated into the Taverna Workflow Management System (http://www.taverna.org.uk). The BioCatalogue as a read API for integration into third party applications. Active BioCatalogue development has ceased in favour of new systems and registries such as bio.tools. In 2017 the content was migrated to the bio.tools platform of the ELIXIR EU Research Infrastructure. The infrastructure is still functioning thans to the splendid quality of the software engineering; however, resources have not been available since 2017 to maintain it. We plan to officially retire the service in 2021
First Year Of Impact 2008
Sector Agriculture, Food and Drink,Digital/Communication/Information Technologies (including Software),Education,Environment,Pharmaceuticals and Medical Biotechnology
Impact Types Economic

Description FP7 Infrastructures BioVel: Biodiversity Virtual eLaboratory
Amount € 1,120,000 (EUR)
Funding ID 283359 
Organisation European Commission 
Department Seventh Framework Programme (FP7)
Sector Public
Country European Union (EU)
Start 08/2011 
End 12/2014
Description INFRADEV-3-2015, 676559, ELIXIR-EXCELERATE
Amount € 19,000,000 (EUR)
Funding ID INFRADEV-3-2015, 676559 
Organisation European Commission H2020 
Sector Public
Country Belgium
Start 09/2015 
End 08/2019
Title BioCatalogue 
Description The BioCatalogue is a Web-based Catalogue of Life Science Web Services. 
Type Of Technology Webtool/Application 
Year Produced 2008 
Open Source License? Yes  
Impact The BioCatalogue (http://www.biocatalogue.org) continues to be actively used. It is managed by University of Manchester and it is hosted at the EMBL-EBI. It currently has 1188 active services, 262 service providers and 789 members and 1350 archived services. It forms part of the ELIXIR-UK portfolio of resources and contributes to the ELIXIR Tools registry bio.tools. In 2017 it was decided to discontinue active development in favour of contributing to bio.tools. 
URL http://www.biocatalogue.org
Title BiodiversityCatalogue 
Description A Catalogue of Biodiversity Web Services 
Type Of Technology Webtool/Application 
Year Produced 2013 
Open Source License? Yes  
Impact Widely adopted by the EU Biodiversity community and planned to be hosted by Naturalis. in 2018: 75 services, 55 service providers and 137 members. 
URL http://www.biodiversitycatalogue.org