title: BioFed: federated query processing over life sciences linked open data.
abstract: BACKGROUND
  Biomedical data, e.g. from knowledge bases and ontologies, is increasingly made available following open linked data principles, at best as RDF triple data. This is a necessary step towards unified access to biological data sets, but this still requires solutions to query multiple endpoints for their heterogeneous data to eventually retrieve all the meaningful information. Suggested solutions are based on query federation approaches, which require the submission of SPARQL queries to endpoints. Due to the size and complexity of available data, these solutions have to be optimised for efficient retrieval times and for users in life sciences research. Last but not least, over time, the reliability of data resources in terms of access and quality have to be monitored. Our solution (BioFed) federates data over 130 SPARQL endpoints in life sciences and tailors query submission according to the provenance information. BioFed has been evaluated against the state of the art solution FedX and forms an important benchmark for the life science domain.
  
  
  METHODS
  The efficient cataloguing approach of the federated query processing system 'BioFed', the triple pattern wise source selection and the semantic source normalisation forms the core to our solution. It gathers and integrates data from newly identified public endpoints for federated access. Basic provenance information is linked to the retrieved data. Last but not least, BioFed makes use of the latest SPARQL standard (i.e., 1.1) to leverage the full benefits for query federation. The evaluation is based on 10 simple and 10 complex queries, which address data in 10 major and very popular data sources (e.g., Dugbank, Sider).
  
  
  RESULTS
  BioFed is a solution for a single-point-of-access for a large number of SPARQL endpoints providing life science data. It facilitates efficient query generation for data access and provides basic provenance information in combination with the retrieved data. BioFed fully supports SPARQL 1.1 and gives access to the endpoint's availability based on the EndpointData graph. Our evaluation of BioFed against FedX is based on 20 heterogeneous federated SPARQL queries and shows competitive execution performance in comparison to FedX, which can be attributed to the provision of provenance information for the source selection.
  
  
  CONCLUSIONS
  Developing and testing federated query engines for life sciences data is still a challenging task. According to our findings, it is advantageous to optimise the source selection. The cataloguing of SPARQL endpoints, including type and property indexing, leads to efficient querying of data resources over the Web of Data. This could even be further improved through the use of ontologies, e.g., for abstract normalisation of query terms.
authors.affiliation: Insight Centre for Data Analytics, National University of Ireland (NUIG), Galway, Ireland. ali.hasnain@insight-centre.org.
authors.forename: Ali
authors.initials: A
authors.lastname: Hasnain
authors.affiliation: Insight Centre for Data Analytics, National University of Ireland (NUIG), Galway, Ireland.
authors.forename: Qaiser
authors.initials: Q
authors.lastname: Mehmood
authors.affiliation: Insight Centre for Data Analytics, National University of Ireland (NUIG), Galway, Ireland.
authors.forename: Syeda
authors.initials: S
authors.lastname: Sana E Zainab
authors.affiliation: Universität Leipzig, IFI/AKSW, Leipzig, PO 100920, D-04009, Germany.
authors.forename: Muhammad
authors.initials: M
authors.lastname: Saleem
authors.affiliation: IBM, IDA Business Park, Galway, Ireland.
authors.forename: Claude
authors.initials: C
authors.lastname: Warren
authors.affiliation: Insight Centre for Data Analytics, National University of Ireland (NUIG), Galway, Ireland.
authors.forename: Durre
authors.initials: D
authors.lastname: Zehra
authors.affiliation: Insight Centre for Data Analytics, National University of Ireland (NUIG), Galway, Ireland.
authors.forename: Stefan
authors.initials: S
authors.lastname: Decker
authors.affiliation: Insight Centre for Data Analytics, National University of Ireland (NUIG), Galway, Ireland.
authors.forename: Dietrich
authors.initials: D
authors.lastname: Rebholz-Schuhmann
mesh_terms: D064229:Biological Ontologies; D001690:Biological Science Disciplines; D057225:Data Mining / Q000379:methods* / Q000592:standards; D020407:Internet; D012015:Reference Standards; D014584:User-Computer Interface
keywords: Life sciences dataset; Linked open data; SPARQL query federation