Sealife

Call: IST-2004-2.4.11 Integrated biomedical information for better health
Priority: Sixth Framework Programme, Priority 2, Information Society Technologies
Type: Specific targeted research project
Start date: April 2006
End date: March 2009
Total R&D costs: 2.6M EUR
EC contribution: 2.2M EUR

Sealife leaflet: pdf doc

Participants:

• 1. Michael Schroeder, Biotec, TU Dresden, Germany
• 2. Albert Burger, Dept. of Computing, Heriot-Watt University, Edinburgh, UK
• 3. Patty Kostkova, City eHealth Research Center, City University, London, UK
• 4. Robert Stevens, BioHealth Informatics Group, University of Manchester, UK
• 5. Bianca Habermann, Scionics, Dresden, Germany
• 6. Olivier Corby, Edelweiss research team, Inria Sophia-Antipolis, France

Objective:
The objective of Sealife is the conception and realisation of a semantic Grid browser for the Life Sciences, which will link the existing Web to the currently emerging eScience infrastructure. The Sealife browsers allow users to automatically link a host of Web servers and Web/Grid services to the Web content he/she is visiting. This is accomplished using eScience's growing number of Web/Grid Services and its XML-based standards and ontologies. The browsers identify terms in the pages being browsed through the background knowledge held in ontologies. Through the use of Semantic Hyperlinks, which link identified ontology terms to servers and services, the Sealife browsers offer a new dimension of context-based information integration.

The browsers have access to a comprehensive background knowledge of life science topics consisting of domain specific ontologies and dictionaries of proteins. They comprise an advanced text-mining module, which is able to automatically extract ontology terms from free text to form Semantic Hyperlinks. A service module, which enables users to link through semantically identified terms to web/grid services to facilitate actions on the data identified.

The Sealife browsers will be demonstrated within three application scenarios in evidence-based medicine, literature and patent mining, and molecular biology, all relating to the study of infectious diseases. The three applications vertically integrate the molecule/cell, the tissue/organ and the patient/population level by covering the analysis of high-throughput screening data for endocytosis (the molecular entry pathway into the cell), the expression of proteins in the spatial context of tissue and organs, and a high-level library on infectious diseases designed for clinicians and their patients.

To achieve maximum impact, Sealife has put together an advisory board with members from the World Wide Web Consortium, Pfizer, AstraZeneca, Unilever, the UK's National Health Service and the Public Health Agency of Canada. Together, Sealife members and its board will showcase the opportunities presented by building user facing generic tools over semantically rich eScience infrastructure.

Sealife is built on existing tools developed by its partners:

• Dresden: GoPubMed, an ontology-based search engine for the life sciences
• Manchester: COHSE, a Conceptual Open Hypermedia Service which provides GeneOntology annotations for free text and MyGrid for life science web services
• London: NeLI, the National electronic Library for Infection
• Edinburgh: EMAP, the Edinburgh Mouse Atlas Project (MRC Human Genetics Unit)
• Inria Sophia-Antipolis: CORESE, the COnceptual REsource Search Engine

The Sealife project aims at developing Semantic Grid browsers for the Life Sciences which link the existing Web to the currently emerging eScience infrastructure, thus creating a Semantic Web on top of the existing Web.
Ontologies and controlled vocabularies form the main source of knowledge repositories as input for Sealife browsers.
Such browsers allow users to automatically link a host of Web servers and Web/Grid services to the Web content they are visiting, allowing for further processing. This is accomplished by using eScience’s growing number of Web/Grid Services and its XML-based standards and ontologies.
The browsers identify terms in the pages being browsed through the background knowledge held in ontologies. Through the use of semantic hyperlinks, which link identified ontology terms to servers and services, the Sealife browsers offer a new dimension of context-based information integration.

The Sealife browsers and relevant work developed by all partners under the Sealife project are the following:

• Dresden:
  • GoPubMed, an ontology-based search engine for the life sciences.
  • GoWeb, an ontology-based search engine for the web.
  • GoGene, an ontology-based search engine for genes.
  • OBO-edit Ontology Generation Plugin, an OBO-edit plugin for generating ontologies.
  
  
• Manchester:
  • COHSE, a Conceptual Open Hypermedia Service which provides GeneOntology annotations for free text and MyGrid for life science web services
  • SKOSEd, a graphical editor for working with the W3C Simple Knowledge Organisation System (SKOS). The editor is built on top of the Protege 4 platform.
  • Fact++, the new generation of the well-known FaCT OWL-DL reasoner. It supports OWL DL as well as the forthcoming standard OWL 2.
  • TerMine plugin, a tool for the Protege 4 OWL ontology editor that allows developers to use entity recognition tools over a corpus of text and import extracted terms/concepts into their ontology. It currently works with the Idavoll and TerMine entity extraction tools.
  • OBO to SKOS converter: this online service converts a Open Biomedical Ontologies (OBO) formatted file into a SKOS style representation. It exports in a range of formats including RDF/XML.
  • Learning a Cell Type Ontology: accompanying material and experimental results for experiments with Ontology Learning in Biology are available here.
  
  
• London:
  • NeLI, the National electronic Library for Infection
  • Explore NeLI with COHSE (requires IE7)
  • Evaluate NeLI with COHSE (requires IE7)
  • Evaluate NeLI with CORESE (requires Firefox)
  • Evaluate GoPubMed
  • The NeLI vocabulary (beta version, under construction)
  • The NeLIVoca Web Service, a Java service used to query the NeLI vocabulary using Sparql and Jena (deployed under the JBOSS container of J2EE applications).
  
  
• Edinburgh:
  • Heriot-Watt University, Edinburgh SEALIFE Project Home Page
  • Goal Generation And Planning System
  • Argumentation System
  • Evaluation of GGAPS and Argumentation Systems
  • Task Composition Manager
  
  
• Inria Sophia-Antipolis:
  • CORESE, the COnceptual REsource Search Engine
  • Installation of the Corese-based Sealife Browser
  • Demo of MeatAnnot generating RDF annotation
  • Corese tutorial
  
  
• Scionics:
  • RiDDLE, a database containing DEQOR-optimized esiRNAs for the transcriptomes of human, mouse and rat.
  • HMMerThread, a database of remotely conserved domains in entire genomes.
  • VYPER (viral PYPer), a fully automated web-tool for phylogenetic reconstruction and therefore epidemiology of bacterial and viral strains.