The University of Manchester
Bio-Health Informatics Group
Department of Computer Science
|Tel :||+44 (0)161 275 6817|
|E-mail :||Simon.Jupp AT manchester.ac.uk|
I am currently working with Dr Robert Stevens in the Bio-Health Informatics Group (BHIG) at the University of Manchester. I have degrees in both Biochemistry and Computer Science
and now work somewhere between both disciplines (also known as a bioinformatician). My research interests are generally related to information management, but more specifically, using computers to imporve
the way we capture, manage and share knowledge about biology. Most of my work is now focused on the use of ontologies to capture knowledge in some computationally useful form. I previously worked on the Sealife project which developed a series of Semantic Grid browser for searching and navgiating health care and life sciences data on the Web. Given that the Web is now central to the way we manage and communicate data I am naturally interested in the Semantic Web and its related technologies, such as RDF and OWL.
I have recently started work on the e-LICO project where the goal is to build a platform for data mining and data-intensive sciences. The e-LICO platform will be closely aligned to the myGRID platform which already provides tools to suppor e-Science. e-LICO will be showcased in a systems biology task: biomarker discovery and molecular pathway modelling for diseases affecting the kidney and urinary pathways, this work will involve the construction of a Kidney and Urinary Pathway (KUP) Ontology.
I am also a tutor on the popular 'Introduction to implmenting ontologies in OWL' tutorial, this is a two day hands on course that we hold at the at the University of Manchester. If you are interesting in learning about Ontologies, OWL and the Protege OWL editor then I highly recommend it! More details are available here
- Kidney and Urinary Pathway
Knowledge Base The KUPKB is a repository of multi-omics
data covering a range of experimental data relating to renal
physiology and renal disease. The data is mostly lists of
genes, proteins, miRNA and metabolites that have been
identified in a range of highthroughput experiments, such as
micro-array or mass spec. We represent all this data in RDF
and annotate the experimental data using a range of
ontologies. By using the ontologies we can integrate the
data and provide powerful query and exploration tools. The
data is also integrated with several public databases such as
Entrez Gene, Uniprot, KEGG, String, HMDB, GOA, Homologene and
MicroCOSM. Whilst the real power comes from exploring this
data using a query language like SPARQL the kupkb.org website
shows how we can present this data to biologist using a simple user
interface. The site itself is backed by a
BigOWLIM/Sesame triple store and all the data in the KUPKB is
available as Linked Data.
- OBO to SKOS Converter
- Protege 4 SKOS editor
- Java SKOS API
- TerMine plugin for Protege 4. This plugin uses the TerMine tool to extract candidate concepts from any corpus of text and an interface to bring them into a OWL ontology.
- Text to Ontology with Text2Onto