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BioFed: federated query processing over life sciences linked open data

Ali Hasnain, Qaiser Mehmood, Syeda Sana e Zainab, Muhammad Saleem, Claude Warren, Durre Zehra, Stefan Decker, Dietrich Rebholz-Schuhmann
2017 Journal of Biomedical Semantics  
Our solution (BioFed) federates data over 130 SPARQL endpoints in life sciences and tailors query submission according to the provenance information.  ...  Biomedical data, e.g. from knowledge bases and ontologies, is increasingly made available following open linked data principles, at best as RDF triple data.  ...  Availability of supporting data BioFed is available through an online interface to run real time federated queries http://vmurq09.deri.ie:8007/.  ... 
doi:10.1186/s13326-017-0118-0 pmid:28298238 pmcid:PMC5353896 fatcat:ie4bsrw7dnh6hpxh7vy6672uha

Federated Query Formulation and Processing through BioFed

Ali Hasnain, Syeda Sana e Zainab, Durre Zehra, Qaiser Mehmood, Muhammad Saleem, Dietrich Rebholz-Schuhmann
2017 Extended Semantic Web Conference  
This paper demonstrates BioFed, a federated SPARQL query processing system customised for LS-LOD.  ...  A single interface for accessing life sciences (LS) data is a natural need to master the data deluge in this domain.  ...  Acknowledgements The work presented in this paper has been partly funded by EU FP7 GRANA-TUM project (project number 270139) and Science Foundation Ireland under Grant No. SFI/12/RC/2289.  ... 
dblp:conf/esws/HasnainZZM0R17 fatcat:xy5gqunsgzferl4ussvzsbeytm

Enabling Semantic Queries Across Federated Bioinformatics Databases [article]

Ana Sima, Tarcisio Mendes de Farias, Erich Zbinden, Maria Anisimova, Manuel Gil, Heinz Stockinger, Kurt Stockinger, Marc Robinson-Rechavi, Christophe Dessimoz
2019 biorxiv/medrxiv   pre-print
We identified and formally described intersection points (i.e. virtual links) among the three data sources. These allow performing joint queries across the data stores.  ...  To enable federated queries across these sources, we first defined a new semantic model for gene expression called GenEx.  ...  Funding Swiss National Research Programme 75 'Big Data' (167149); Swiss National Science Foundation (150654); Swiss State Secretariat for Education, Research and Innovation (SIB Infrastructure grants)  ... 
doi:10.1101/686600 fatcat:ajkv2fmvzvbxje3kychiolirxm

Enabling semantic queries across federated bioinformatics databases

2019 Database: The Journal of Biological Databases and Curation  
Data integration promises to be one of the main catalysts in enabling new insights to be drawn from the wealth of biological data available publicly.  ...  However, the heterogeneity of the different data sources, both at the syntactic and the semantic level, still poses significant challenges for achieving interoperability among biological databases.  ...  Funding Swiss National Research Programme 75 'Big Data' (167149); Swiss National Science Foundation (150654); Swiss State Secretariat for Education, Research and Innovation (SIB Infrastructure grants)  ... 
doi:10.1093/database/baz106 pmid:31697362 pmcid:PMC6836710 fatcat:o4fk52tkvrajfmf7qcdmgcygvu

PIBAS FedSPARQL: a web-based platform for integration and exploration of bioinformatics datasets

Marija Djokic-Petrovic, Vladimir Cvjetkovic, Jeremy Yang, Marko Zivanovic, David J. Wild
2017 Journal of Biomedical Semantics  
As a query builder, our system allows researchers to intuitively construct and run Federated SPARQL queries across multiple data sources, including global initiatives, such as Bio2RDF, Chem2Bio2RDF, EMBL-EBI  ...  From the input topic, subtopic, template and keyword, a corresponding initial Federated SPARQL query is created and executed.  ...  Acknowledgements The authors are grateful to the Ministry of Education, Science and Technological Development of the Republic of Serbia for financial support (Grant Nos. III41010).  ... 
doi:10.1186/s13326-017-0151-z pmid:28931422 pmcid:PMC5607505 fatcat:5r3ddl2ornfkzg5v4tz3eiizou

Dataset Search In Biodiversity Research: Do Metadata In Data Repositories Reflect Scholarly Information Needs? [article]

Felicitas Löffler, Valentin Wesp, Birgitta König-Ries, Friederike Klan
2020 arXiv   pre-print
The increasing amount of research data provides the opportunity to link and integrate data to create novel hypotheses, to repeat experiments or to compare recent data to data collected at a different time  ...  Our findings indicate that environments, materials and chemicals, species, biological and chemical processes, locations, data parameters and data types are important search interests in biodiversity research  ...  The German Federation for Biological Data (GFBio) [Diepenbroek et al., 2014 ] is a national infrastructure for research data management in the green Life Sciences and provides a search over more than  ... 
arXiv:2002.12021v1 fatcat:rnegb77pyvawjhpkupofib3m44

In Search of Big Medical Data Integration Solutions -A Comprehensive Survey

Houssein Dhayne, Rafiqul Haque, Rima Kilany, Yehia Taher
2019 IEEE Access  
Several data integration technologies and tools have been developed over the last two decades.  ...  The data-intensive industries have been experiencing a wide variety of challenges in terms of processing, managing, and analysis of data.  ...  in the life sciences domain.  ... 
doi:10.1109/access.2019.2927491 fatcat:6ooixehrznfdnbwghzfeds3mky

Integrative annotation and knowledge discovery of kinase post-translational modifications and cancer-associated mutations through federated protein ontologies and resources

Liang-Chin Huang, Karen E. Ross, Timothy R. Baffi, Harold Drabkin, Krzysztof J. Kochut, Zheng Ruan, Peter D'Eustachio, Daniel McSkimming, Cecilia Arighi, Chuming Chen, Darren A. Natale, Cynthia Smith (+4 others)
2018 Scientific Reports  
In this study, we employ federated queries linking information from the Protein Kinase Ontology, iPTMnet, Protein Ontology, neXtProt, and the Mouse Genome Informatics to identify key knowledge gaps in  ...  There is high interest in protein Published: xx xx xxxx OPEN www.nature.com/scientificreports/  ...  Hundreds of RDF data resources, including nearly 100 in the life sciences are available within the Linked Open Data 30 (LOD) initiative.  ... 
doi:10.1038/s41598-018-24457-1 pmid:29695735 pmcid:PMC5916945 fatcat:bxzho6wisfckfhrza5vaabisya

Point-of-care biosensor system

Arvind Sai Sarathi Vasan
2013 Frontiers in bioscience (Scholar edition)  
In: Proceedings of IEEE/NLM Life Science Systems and Application 164.  ...  In: Proceedings of the International Federation for 256.  ... 
doi:10.2741/s357 pmid:23277036 fatcat:kymehvonrfg33f26vd6nwef2dy

Query Optimization Techniques For Scaling Up To Data Variety [article]

Philipp Daniel Rohde, University, My, University, My
2019
Ontario is a federated query engine capable of processing queries over heterogeneous data sources.  ...  This thesis proposes new heuristics tailored to the problem of query processing over heterogeneous data sources including heuristics specifically designed for certain data models.  ...  One of these subclouds is of the Life Science domain, referred to as Life Science Linked Open Data (LSLOD) cloud. There is an existing set of benchmarking queries for this subcloud [21] .  ... 
doi:10.15488/5130 fatcat:22hxm2nupnhbza5tomcjrnkyui

ABSTRACTS

2016 Journal of nematology  
Small tubers were dipped for 5 minutes in bacterial suspension, planted in a 5 L pot with naturally infested soil and kept in an open room under ambient environmental conditions during the summer.  ...  Lawrence. 209 Rouse Life Sciences, Auburn University, Auburn, AL 36849.  ...  , College of Life Sciences, University of Dundee, Dundee, DD1 5EH, United Kingdom.  ... 
doi:10.21307/jofnem-2017-038 fatcat:uefdcep5anenxmpagigpw6ma5e

Annals of the University of Oradea, Fascicle: Environmental Protection, Vol. XXXIII, 2019

University of Oradea, Faculty of Environment Protection
2020 Zenodo  
Bl. 1939 Biof.  ...  Some of the best techniques for extracting information from data include the use of traditional techniques for data mining that are linked to but not constrained by biophysical processes.  ...  At the end of aerial data post-processing UAV, were generated topographic models, was made data export in various formats, including Google Earth and LIDAR files (LAS), which then could be processed and  ... 
doi:10.5281/zenodo.4111072 fatcat:tejuhilpnbctdduuspyvolutgy

A Candidate Gene Analysis of Vitamin B12 Deficiency in Elderly Women and the Nursing Implications of Personalized Medicine

Emma Louise Kurnat-Thoma
2016
Availability of genetic data greatly enhances the biologic understanding of these processes.  ...  Vitamin B12 analogs bound to the transcobalamin I protein turn over extremely slowly and demonstrate a half-life of approximately 10 days (Finkler & Hall, 1967) .  ...  Currently over 1200 tests are clinically available. Genome The entirety of an individual's genetic code, approximately 6 billion nucleotides comprising 23,500 genes.  ... 
doi:10.26053/0h-de9z-4b00 fatcat:i6saduma6vghjjp2mr5nwsljwy