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An Intelligent SPARQL Query Builder for Exploration of Various Life-science Databases

Atsuko Yamaguchi, Kouji Kozaki, Kai Lenz, Hongyan Wu, Norio Kobayashi
2014 International Semantic Web Conference  
Database integration of a wide variety of life-science data is an important issue for comprehensive data analysis.  ...  To overcome this problem, we propose an intelligent SPARQL query builder that aids users with no knowledge on SPARQL in building queries.  ...  This work was supported by JSPS KAKENHI Grant Number 25280081 and the National Bioscience Database Center (NBDC) of the Japan Science and Technology Agency (JST).  ... 
dblp:conf/semweb/YamaguchiKLWK14 fatcat:glvuevxfsrgjtbni4xzpzirkgu

Semantic inference using chemogenomics data for drug discovery

Qian Zhu, Yuyin Sun, Sashikiran Challa, Ying Ding, Michael S Lajiness, David J Wild
2011 BMC Bioinformatics  
This approach allows multiple evidence paths between compounds and diseases to be identified using a rule-set and semantically annotated data, and for these evidence paths to be clustered to show overall  ...  We have previously described a tool called WENDI for aggregating information pertaining to new chemical compounds, effectively creating evidence paths relating the compounds to genes, diseases and so on  ...  We thank Bret Davidson for correcting English. We would like to thank the anonymous reviewers for their helpful comments and suggestions.  ... 
doi:10.1186/1471-2105-12-256 pmid:21699718 pmcid:PMC3225082 fatcat:udmnme6lzneytj3ruo5i7r46zy

Semantic Models in Web based Educational System Integration

Geraud Fokou Pelap, Catherine Faron Zucker, Fabien Gandon
2018 Proceedings of the 14th International Conference on Web Information Systems and Technologies  
, both in terms of functionalities and efficiency compared to existing operational solutions.  ...  In this paper we propose and evaluate a semantic Web approach to support the features and interoperability of a real industrial e-Education system in production.  ...  To represent property chains on Cocons a relational database was not efficient, obliging to perform joins between table Cocon and itself.  ... 
doi:10.5220/0006940000780089 dblp:conf/webist/PelapFG18 fatcat:3ocgd6d63zbqnlfh7dlr7xamxa

Leveraging Logical Rules for Efficacious Representation of Large Orthology Datasets

Tarcisio M. Farias, Hirokazu Chiba, Jesualdo Tomás Fernández-Breis
2017 Workshop on Semantic Web Applications and Tools for Life Sciences  
In the semantic web applied to life sciences, ontologies provide a basis to define concepts and to describe data in biological databases, thereby facilitate data interoperability across multiple resources  ...  However, ORTH ontology lacks a basis to infer pairwise relations between genes besides more specific and accurate definitions of class restrictions, property domains and property ranges -which is hampering  ...  Several classes in life sciences related ontologies are not supposed to be instantiated or they are singleton classes (i.e. the class is only instantiated once).  ... 
dblp:conf/swat4ls/FariasCF17 fatcat:wfim3kj4hzdnjk472c3yemi5rm

Chem2Bio2RDF: A Linked Open Data Portal for Systems Chemical Biology

Bin Chen, Ying Ding, Huijun Wang, David J. Wild, Xiao Dong, Yuyin Sun, Qian Zhu, Madhuvanthi Sankaranarayanan
2010 2010 IEEE/WIC/ACM International Conference on Web Intelligence and Intelligent Agent Technology  
The portal is based on D2R server and provides a SPARQL endpoint, but adds on few unique features like RDF faceted browser, user-friendly SPARQL query generator, MEDLINE/PubMed cross validation service  ...  The Chem2Bio2RDF portal is a Linked Open Data (LOD) portal for systems chemical biology aiming for facilitating drug discovery.  ...  Flexible and efficient data integration is highly desired in life sciences.  ... 
doi:10.1109/wi-iat.2010.183 dblp:conf/webi/ChenDWWDSZS10 fatcat:vkemgreejrg7davpqvsakvtm6u

RP-Filter: A Path-Based Triple Filtering Method for Efficient SPARQL Query Processing [chapter]

Kisung Kim, Bongki Moon, Hyoung-Joo Kim
2012 Lecture Notes in Computer Science  
Currently, most RDF databases store RDF data in a relational table called triple table and carry out several join operations on the triple tables for SPARQL query processing.  ...  However, the execution plans with many joins might be inefficient due to a large amount of intermediate data being passed between join operations.  ...  We used two datasets: YAGO2 [14] as a small real-life dataset and LUBM [15] as a large synthetic dataset. We generated the LUBM dataset with 10,000 universities 1 . Acknowledgements.  ... 
doi:10.1007/978-3-642-29923-0_3 fatcat:bxqyzzolyvfotpvfeerbxszkya

Semantic Integration and Enrichment of Heterogeneous Biological Databases [chapter]

Ana Claudia Sima, Kurt Stockinger, Tarcisio Mendes de Farias, Manuel Gil
2019 Msphere  
In particular, we introduce natural language search interfaces, which alleviate the need for database users to be familiar with technical query languages.  ...  We present an extensive timeline of milestones in data integration based on Semantic Web technologies in the field of life sciences.  ...  Acknowledgments We would like to thank all the members of the Bio-SODA SNF project at ZHAW Zurich University of Applied Sciences, at the University of Lausanne (UNIL) and at the SIB Swiss Institute of  ... 
doi:10.1007/978-1-4939-9074-0_22 pmid:31278681 fatcat:obis2izjszbpvjsm2kbhxjyo34

EpiK: A Knowledge Base for Epidemiological Modeling and Analytics of Infectious Diseases

S.M.Shamimul Hasan, Edward A. Fox, Keith Bisset, Madhav V. Marathe
2017 Journal of Healthcare Informatics Research  
The queries are constructed using SPARQL Protocol and RDF Query Language (SPARQL) over the EpiK.  ...  A query bank is developed-the queries capture a broad range of questions that can be posed and answered during a typical case study pertaining to disease outbreaks.  ...  They are harder to build, largely due to the expertise in computing and data science needed to build them.  ... 
doi:10.1007/s41666-017-0010-9 pmid:35415398 pmcid:PMC8982844 fatcat:m5d3lglydfh27pcdbx22icguay

Semantic integration of information about orthologs and diseases: The OGO system

Jose Antonio Miñarro-Gimenez, Mikel Egaña Aranguren, Rodrigo Martínez Béjar, Jesualdo Tomás Fernández-Breis, Marisa Madrid
2011 Journal of Biomedical Informatics  
Many of the systems that perform such task, however, only offer a SPARQL query interface, which is difficult to use for life scientists.  ...  Such interface allows the users to define SPARQL queries through a graphical process, therefore not requiring SPARQL expertise. (J.A. Miñarro-Gimenez), megana@fi. upm.es (M.  ...  path for finding the data.  ... 
doi:10.1016/j.jbi.2011.08.002 pmid:21864715 fatcat:hie3rc5u3vbovj32slomiixkgi

A Semantic Approach for Automated Rule Compliance Checking in Construction Industry

Dongming Guo, Erling Onstein, Angela Daniela La Rosa
2021 IEEE Access  
To guarantee to generate exact SPARQL query results, a generated SPARQL query with a quantitative filter about a property value of an instance should contain a class, an instance of this class, a property  ...  We discussed an approach for generating the shortest path in ref [29] , so we don't introduce it here. The structure of shortest path can be used to create a SPARQL query.  ...  ERLING ONSTEIN received his M.S. degree in 1983 in Photogrammetry and Surveying, and a PhD degree in Geographical Information Technology in 2004, from the Norwegian University of Life Sciences (NMBU).  ... 
doi:10.1109/access.2021.3108226 fatcat:5cdjckggqfcahgfqlvot4exc3u

RIKEN MetaDatabase

Norio Kobayashi, Satoshi Kume, Kai Lenz, Hiroshi Masuya
2018 International Journal on Semantic Web and Information Systems (IJSWIS)  
This paper describes the technical knowledge obtained through the development and operation of the RIKEN MetaDatabase to accelerate life science data distribution.  ...  Recently, the number and heterogeneity of life science datasets published on the Web have increased significantly.  ...  Unfortunately, current standardised SPARQL federated query search (https://www.w3.org/TR/sparql11-federated-query/) is not efficient, and queries must be limited for a quick response.  ... 
doi:10.4018/ijswis.2018010106 fatcat:o3bx674wtrgplb23tumhj3c7ia

Improving integrative searching of systems chemical biology data using semantic annotation

Bin Chen, Ying Ding, David J Wild
2012 Journal of Cheminformatics  
Through a series of scientific case studies we demonstrate how this (i) simplifies the process of building SPARQL queries, (ii) enables useful new kinds of queries on the data and (iii) makes possible  ...  nodes and edges in the RDF graph, enabling a much richer range of semantic queries to be issued.  ...  Acknowledgements We thank Shanshan Chen, Kuochung Peng, Qian Zhu, Jaehong Shin and other members of the cheminformatics group at Indiana University for discussion and comments.  ... 
doi:10.1186/1758-2946-4-6 pmid:22401035 pmcid:PMC3320537 fatcat:ytua3lgimjbqhbtlj6mwxxmrdu

The RDF-3X engine for scalable management of RDF data

Thomas Neumann, Gerhard Weikum
2009 The VLDB journal  
Although RDF-3X is optimized for queries, it also provides good support for efficient online updates by means of a staging architecture: direct updates to the main database indexes are deferred, and instead  ...  The query optimizer is able to choose optimal join orders even for complex queries, with a cost model that includes statistical synopses for entire join paths.  ...  provides RDF support for semantic data integration in life sciences and enterprises [12, 40] .  ... 
doi:10.1007/s00778-009-0165-y fatcat:2v5hunczijavfixacbudpsotfi

Bio-SODA: Enabling Natural Language Question Answering over Knowledge Graphs without Training Data [article]

Ana Claudia Sima, Tarcisio Mendes de Farias, Maria Anisimova, Christophe Dessimoz, Marc Robinson-Rechavi, Erich Zbinden, Kurt Stockinger
2021 arXiv   pre-print
Bio-SODA uses a generic graph-based approach for translating user questions to a ranked list of SPARQL candidate queries.  ...  Furthermore, Bio-SODA uses a novel ranking algorithm that includes node centrality as a measure of relevance for selecting the best SPARQL candidate query.  ...  ACKNOWLEDGMENTS We thank the Swiss National Science Foundation for funding (NRP 75, grant 407540_167149), Lukas Blunschi for the implementation of the SODA system for keyword search system over relational  ... 
arXiv:2104.13744v4 fatcat:swbggfd34ng7fgh7qaiqokvxa4

WGB: Towards a Universal Graph Benchmark [chapter]

Khaled Ammar, M. Tamer Özsu
2014 Lecture Notes in Computer Science  
WGB includes the basic graph queries which are used for building graph applications.  ...  to real-life ones.  ...  This research was partially supported by a fellowship from IBM Centre for Advanced Studies (CAS), Toronto.  ... 
doi:10.1007/978-3-319-10596-3_6 fatcat:meji5npkx5g4rpcfsrppgatzb4
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