SeaLife Simon Jupp

A Semantic Grid Browser for the Life Sciences Applied to the Study of Infectious Diseases

SeaLife

Simon Jupp


SeaLife

Conception and realisation of a Semantic Grid Browser, which links the current Web to the emerging eScience infrastructure

• Partners: Manchester, Dresden, Edinburgh, London, Inria Sophia-Antipolis, Scionics

• Objectives:– Many grids, few users: make Web servers and services accessible to end users– Semantic Hyperlinks: use ontologies and background knowledge to map web

contents to services– Shopping cart: Service composition and enactment module

• Application: from cells, via tissue to patients– Evidence-based medicine– Patent and literature mining– Molecular biology

• Implementations:– COHSE– GoPubMed– CORESE


Objective• We have a World Wide Web of data • We have e-science and a grid of bioinformatics services• We have text-mining tools, ontologies, web services and W3C standards

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Evidence based medicine

"Ribavirin with or without alpha interferon for chronic hepatitis C"

• Background Knowledge: MeSH, Disease Ontology, SNOMED…• UK based Resources:

– National Institute for Health and Clinical Excellence (NICE)– National Electronic Library of Infection (NeLI)– Health protection Agency (HPA)


Molecular Biology

‘’Rabaptin-5 interacts with the small GTPase Rab5 and is an essential component of the fusion machinery for targeting endocytic vesicles to early endosomes’’

• Background Knowledge: – Rabaptin-5 and Rab5 are proteins – endocytosis as GO biological process – early endosome as GO cellular component.

• Resources:

– Get sequences, execute alignment service– Add proteins to “shopping cart” Rab5– PubMed query for relevant abstracts


A Sealife browser

• Definition: A SeaLife browser is any web browser that can identify domain concepts in web documents via text-mining or use of background knowledge, and provides context based links to related services/resources on the web/grid.

• Several exists: COHSE, GoPubMed, Magpie, PiggyBank, KIM, Concept Web Linker….


Implementations

• COHSE - Conceptual Open Hypermedia Service– Dynamic linking system for WWW documents– Uses background knowledge (ontologies) to identify domain concepts– Service module for navigating to relevant documents on the Web

• GoPubMed– Ontology based search engine: Query expansion and results filtering– Supports What, Who, Where, When.


Web Navigation• The Semantic Web is still a Web to be used by humans

– A collection of linked nodes• Navigation is still an important aspect of information gathering on the Web

– Serendipitous information retrieval

• Problem– Links are typically embedded– Hard coded– Difficult to author– Ownership– Unary– Legacy resources– Offer little in the way of semantics

• Approach– Exploit Semantic Web components to add links

dynamically to documents– Exploit knowledge structure to drive Navigation


Web Navigation with COHSE

• Knowledge Service

– Text processor and background knowledge identify concepts in a page

• Resource Manager

– Finds links targets for concepts

found in the page

• DLS

– Dynamically adds the links to

the page and manages requests

to the resource manager

• Can be run as browser plugin

or through a proxy


NeLI use case

• National Electronic Library of Infection, London, UK. – Evidence based, quality tagged resource for public and clinical health records– Diverse set of users

• GPs, Clinicians, Molecular biologists, General Public– Many documents, few hyperlinks

• Can COHSE provide useful links to relevant external documents?– Evaluation is underway

• Searching for guidelines on the use of "Ribavirin with or without alpha interferon for chronic hepatitis C"

– Clinicians need up to date, authoritative information


COHSE-NeLI Demo

http://www.cs.man.ac.uk/~sjupp/downloads/COHSE-NELI-2009-demo.mov


Background knowledge

• What semantics do we need for the background knowledge to drive navigation?

• Richer and more granular knowledge is better for navigation.

• The type of background knowledge varies between types users and the task at hand.

– E.g. Nurses, doctors, public, medic etc..


Phenotype

Sequence

Proteins

Gene products Transcript

Pathways

Cell type

BRENDA tissue / enzyme source

Development

Anatomy

Phenotype

Plasmodium life cycle

-Sequence types and features-Genetic Context

- Molecule role - Molecular Function- Biological process - Cellular component

-Protein covalent bond -Protein domain -UniProt taxonomy

-Pathway ontology -Event (INOH pathway ontology) -Systems Biology -Protein-protein interaction

-Arabidopsis development -Cereal plant development -Plant growth and developmental stage -C. elegans development -Drosophila development FBdv fly development.obo OBO yes yes -Human developmental anatomy, abstract version -Human developmental anatomy, timed version

-Mosquito gross anatomy-Mouse adult gross anatomy -Mouse gross anatomy and development -C. elegans gross anatomy-Arabidopsis gross anatomy -Cereal plant gross anatomy -Drosophila gross anatomy -Dictyostelium discoideum anatomy -Fungal gross anatomy FAO -Plant structure -Maize gross anatomy -Medaka fish anatomy and development -Zebrafish anatomy and development

-NCI Thesaurus -Mouse pathology -Human disease -Cereal plant trait -PATO PATO attribute and value.obo -Mammalian phenotype -Habronattus courtship -Loggerhead nesting -Animal natural history and life history

eVOC (Expressed Sequence Annotation for Humans)


Knowledge representation

Tuberculosis

TBInfectious Disease

Bacteria

Lung

Mycobacterium bovisCoughing

Chest X-ray

BCG vaccine Isoniazid

abbreviation Is a

vaccine

Caused by

drug

Affects

Similar to

SymptomDiagnosis/detection

Can’t make these close links with strict semantics!


SKOS conversions

Tuberculosis

TBInfectious Disease

Bacteria

Lung

Mycobacterium bovisCoughing

Chest X-ray

BCG vaccine Isoniazid

skos:altLabelskos:broader

skos:narrower

skos:broader

skos:related

skos:related

skos:narrower

skos:relatedskos:narrower

• We need “something to do with” semantics for Navigation• SKOS provides standard for common representation with “enough” semantics


COHSE and e-science

• Enhancements to COHSE, working prototype available– Addition of text-mining component

• Identifies Genes, Proteins, Chemicals in text

• Query service repositories– E.g. myExperiment, BioCatalogue, Bio-moby– Execute services and workflows within the browser

• Edinburgh developed shopping cart and argumentation services– Shop online for your genes, proteins, sequences etc…– Shop online for services and workflows– All from within your web browser!– But that’s the future….


Summary

• Range of Semantic Web browsers under development

• Semi-automated addition of semantic content to existing resources is the only viable option in many cases

• What are we waiting for?– More background knowledge– Semantic web services description

Documents

SeaLife Simon Jupp