Bio-LarK

Biomedical Large Knowledge Collider

The Bio-LarK project aims to develop and aggregate, in time, a series of platforms and tools to enable researchers and scientists to represent, acquire and process biomedical data, using Semantic Web technologies. Gradually, it will comprise ontologies focused on representing and modeling disorder - phenotype - genotype relations, text mining and concept recognition services - again focused on disorders and phenotypes, and finally, diverse knowledge discovery and exploration tools to analyze and interpret data drawn from heterogeneous information sources. Most work revolves around mining, enriching and using the Human Phenotype Ontology.

Funding acknowledgements:

  • Australian Research Council (ARC) - Linkage grant SKELETOME (LP100100156)
  • Australian Research Council (ARC) - Discovery Early Career Researcher Award (DECRA) (DE120100508)
  • RD-Connect-European Union Seventh Framework Programme (HEALTH. 2012.2. 1.1-1-C) under grant agreement number 305444: RD Connect: An integrated platform connecting databases, registries, biobanks and clinical bioinformatics for rare disease research
  • Australian National Health and Medical Research Council APP1055319 under the NHMRC–European Union Collaborative Research Grants scheme

The project received continuous support from the International Rare Disease Research Consortium (IRDiRC) and the Office of Population Health Genomics, The Western Australian Government Department of Health, as part of its commitment to the goals of the IRDiRC.

Most tools and resources are developed in collaboration with Nigel Collier from the European Bioinformatics Institute, Anika Oellrich from the Mouse Genome Informatics Group, Wellcome Trust Sanger Institute and the Computational Biology and Bioinformatics Group at the Charite Medical University Berlin.

The computing resources are support in part by the NeCTAR research cloud. NeCTAR is an Australian Government project conducted as part of the Super Science initiative and financed by the Education Investment Fund.

Currently available platforms and services include: