Ismael Navas-Delgado, María Jesús García-Godoy, Maria del Mar Roldán-García, José F. Aldana-Montes

{ismael, mjgarciag, mmar, jfam}@lcc.uma.es

Use of Linked Data in Life Sciences

Biopax and Semantics

Introduction

Reasoning over real complex ontologies with

large sets of data is a need. BioPax Level 3

(Level 4 under development) is an Owl ontology

(OWL Species: DL, DL Expressivity: SHIF(D),

Consistent: Yes). BioPax Level 3 has 4 officially

identified databases, and more DBs public data

as BioPax Level 3 instances. For example,

Reactome Database has a size of 1.54 GB with

around 2 980 230 triples.

Universidad de

Málaga

Biopax community is producing sets of data in RDF files, but most of them are not available through query interfaces. The

publication of SPARQL endpoints is feasible with current sets of data, but the use of reasoning in these interfaces is unfeasible in

many cases. The use of large scale reasoners is a need to take advantage of these data sets.

Research

Results

BioPax Level 3 is a complex OWL ontology (transitive,

reflexive, inverse and functional properties, restrictions in

most of the classes, 70 classes). And there are big data

sets in OWL format for this ontology (from 20MB to 45GB of

data). However, there are some known problems:

• Undetected Abox inconsistencies because of the lack of

scalable reasoners

• Lack of SPARQL endpoints to query these data

A first analysis over these data sets have provided us with

some information about the main current status of data

available as BioPax Level 3 instances. Now, we aim to

make use of a scalable reasoner to detect Abox

inconsistencies and deal with them through the BioPax

community.

2. Experiment on Reactome (P.falcifarum, 8MB)

1. General results of

DBOWL for UOB

Benchmark queries

Semantics enhancement of BioPax Level 3 is a need to take

advantage of standard reasoners. BioPax Level 4 should

address these problems to help data providers to publish

consistent data with respect to OWL.

Conclusions

Acknowledgements

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