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Prototype Implementation of SPARQL Builder for Life-science Databases by Intelligent Schema Analysis on RDF datasets

Norio Kobayashi, Kai Lenz, Hongyan Wu, Kouji Kozaki, Atsuko Yamaguchi
2014 Workshop on Semantic Web Applications and Tools for Life Sciences  
To address this problem, we propose an intelligent SPARQL query builder that enables users to build a query without knowledge of SPARQL or the data schema.  ...  Metadata publication in accordance with the semantic web as a database is a trend for providing and integrating various life-science data.  ...  We thank Dr Yasunori Yamamoto for useful comments for improvement of the SPARQL Builder metadata specification.  ... 
dblp:conf/swat4ls/KobayashiLWKY14 fatcat:7ezfgxtatnbrzc37nlmlukk6pe

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.  ...  The tool assists users in generating queries for cross-database annotations based on RDF and enhances the value of life-science data by exploring and integrating these data.  ...  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

RIKEN MetaDatabase

Norio Kobayashi, Satoshi Kume, Kai Lenz, Hiroshi Masuya
2018 International Journal on Semantic Web and Information Systems (IJSWIS)  
Recently, the number and heterogeneity of life science datasets published on the Web have increased significantly.  ...  This paper describes the technical knowledge obtained through the development and operation of the RIKEN MetaDatabase to accelerate life science data distribution.  ...  The RIKEN MetaDatabase also provides SPARQL Builder Metadata (http://sparqlbuilder.org/), which are generated and published for more intelligent SPARQL searches.  ... 
doi:10.4018/ijswis.2018010106 fatcat:o3bx674wtrgplb23tumhj3c7ia

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
available KGQA systems by an F1-score of least 20% and by an even higher factor on more complex bioinformatics datasets.  ...  In this paper, we focus on the challenges of natural language processing over knowledge graphs of scientific datasets.  ...  databases [5] , on which our prototype is based, and Katrin Affolter  ... 
arXiv:2104.13744v4 fatcat:swbggfd34ng7fgh7qaiqokvxa4

The 3rd DBCLS BioHackathon: improving life science data integration with Semantic Web technologies

Toshiaki Katayama, Mark D Wilkinson, Gos Micklem, Shuichi Kawashima, Atsuko Yamaguchi, Mitsuteru Nakao, Yasunori Yamamoto, Shinobu Okamoto, Kenta Oouchida, Hong-Woo Chun, Jan Aerts, Hammad Afzal (+54 others)
2013 Journal of Biomedical Semantics  
BioHackathon 2010 was the third in a series of meetings hosted by the Database Center for Life Sciences (DBCLS) in Tokyo, Japan.  ...  The overall goal of the BioHackathon series is to improve the quality and accessibility of life science research data on the Web by bringing together representatives from public databases, analytical tool  ...  importance for life sciences.  ... 
doi:10.1186/2041-1480-4-6 pmid:23398680 pmcid:PMC3598643 fatcat:fm5xaotu3nbafibe3pm3js4d7u

Search, access, and explore life science nanopublications on the Web

Fabio Giachelle, Dennis Dosso, Gianmaria Silvello
2021 PeerJ Computer Science  
For the time being, NanoWeb focuses on the life science domain where the vastest amount of nanopublications are available.  ...  There are millions of nanopublications currently available on the Web, especially in the life science domain.  ...  ACKNOWLEDGEMENTS The authors wish to thank Erika Fabris for the work on the citation of nanopublications and the development of some APIs used in this work.  ... 
doi:10.7717/peerj-cs.335 pmid:33816986 pmcid:PMC7959622 fatcat:cxmldprn4fcezbiryjdsrwskfy

Introduction to Linked Data and Its Lifecycle on the Web [chapter]

Axel-Cyrille Ngonga Ngomo, Sören Auer, Jens Lehmann, Amrapali Zaveri
2014 Lecture Notes in Computer Science  
The term Linked Data refers to a set of best practices for publishing and interlinking structured data on the Web.  ...  While many standards, methods and technologies developed within by the Semantic Web community are applicable for Linked Data, there are also a number of specific characteristics of Linked Data, which have  ...  This work was supported by a grant from the European Union's 7th Framework Programme provided for the projects LOD2 (GA no. 257943), GeoKnow (GA no. 318159) and the Eureka project SCMS.  ... 
doi:10.1007/978-3-319-10587-1_1 fatcat:2vba6rydjvehro3cwcakafnn5e

EMBnet.journal 19 Suppl. B

EMBnet Journal
2013 EMBnet journal  
We believe that the adoption of the technologies presented here can benefits to the whole scientific community by improving the quality of web tools while diminishing the time spent on software development  ...  Acknowledgements This work was supported by the Innovative Medicines Initiative Joint Undertaking under grant agreement n° 115191 for Open PHACTS, resources of which are composed of financial contribution  ...  RDF Schema 4 (RDFS).  ... 
doi:10.14806/ej.19.b.749 fatcat:h6kgq2g4ljbn7jrq6xpkbh2eie

State Of The Art Analysis Report

Miguel Ángel Esbrí
2014 Zenodo  
projects, as well as initia-tives and policies and data sources repositories (specially at local, national and European level) which are relevant for defining and implementing the different aspects of  ...  This document is the "State of the art analysis report" deliverable and its main objective is to collect information about standards, existing technologies, architectures and systems developed in other  ...  databases to RDF datasets.  ... 
doi:10.5281/zenodo.200497 fatcat:otpyumabc5fbpgqmixtgmt7hli

A Frame-Based Approach for Integrating Heterogeneous Knowledge Sources [article]

Jacobo Rouces Gonzalez
2016 Ph.d.-serien for Det Teknisk-Naturvidenskabelige Fakultet, Aalborg Universitet  
All FrameBase data (schema, ReDer rules, integration rules, instance data, and gold standards) is published under a Creative Commons CC-BY 4.0 International license at http://framebase.org.  ...  that allows to review and curate complex integration rules produced by state-of-the-art integration algorithms.  ...  An advantage of this approach is that it provides richer ReDer rules in FrameBase, but the disadvantage is that being driven by FrameBase, it may have poor recall for real-life datasets, both because of  ... 
doi:10.5278/vbn.phd.engsci.00102 fatcat:plxgbsgmlrclxdwkpvd6xzy5mm

Investigating Approaches of Integrating BIM, IoT, and Facility Management for Renovating Existing Buildings: A Review

Abubaker Basheer Abdalwhab Altohami, Nuzul Azam Haron, Aidi Hizami Ales@Alias, Teik Hua Law
2021 Sustainability  
The importance of building information is highly attached to the ability of conventional storing to provide professional analysis.  ...  The first step to better integrating IoT and Building Information Modeling (BIM) can be performed by implementing the Service-Oriented-Architecture (SOA) to combining software and other services by replacing  ...  The combination of IoT and the Lean and Injury-Free (LIFE) construction management may conceptualize the implementation of the topics in existing systems to designing and creating a valid prototypical  ... 
doi:10.3390/su13073930 fatcat:5con44dqrbhv3pjkwdncots2ey

Semantic Data Ingestion for Intelligent, Value-Driven Big Data Analytics

Jeremy Debattista, Judie Attard, Rob Brennan
2018 2018 4th International Conference on Big Data Innovations and Applications (Innovate-Data)  
In this position paper we describe a conceptual model for intelligent Big Data analytics based on both semantic and machine learning AI techniques (called AI ensembles).  ...  These processes are linked to business outcomes by explicitly modelling data value and using semantic technologies as the underlying mode for communication between the diverse processes and organisations  ...  valuable insights and comments on this work.  ... 
doi:10.1109/innovate-data.2018.00008 dblp:conf/obd/DebattistaAB18 fatcat:3hiyg2rd4fh2hdx37jelozkz5e

29th International Conference on Data Engineering [book of abstracts]

2013 2013 IEEE 29th International Conference on Data Engineering Workshops (ICDEW)  
We implement our solution in a prototype system built on top of Oracle with no modifications to the database internals.  ...  These regular parts, i.e. tables, are identified on ingestion by a schema discovery algorithm --as such users will gain an SQL view of the regular part of the RDF data.  ...  At the conference, volunteers may be identified by their black ICDE-13 shirts.  ... 
doi:10.1109/icdew.2013.6547409 fatcat:wadzpuh3b5htli4mgb4jreoika

PARTHENOS D3.2 Guidelines for Common Policies Implementation (Final)

Hella Hollander, Francesca Morselli, Frank Uiterwaal, Femmy Admiraal, Marnix van Berchum, Thorsten Trippel, Lene Offersgaard, Sara Di Giorgio, Paola Ronzino
2019 Zenodo  
the Humanities by the harmonization of policy definition and their implementation.  ...  The document presents the final definition of PARTHENOS high-level principles, offered as common guidelines to build bridges between different, although tightly interrelated fields and stakeholders within  ...  Provide information about best practices in data citation to research communities and make it easy for data users to cite data, e.g. by using a standardised button which says 'How to cite this dataset'  ... 
doi:10.5281/zenodo.2575435 fatcat:mt62leprp5c63ggfadprgrjn5i

PhD thesis: SQL Comprehension and Synthesis [article]

George Obaido
2022 arXiv   pre-print
We present algorithms based on: regular expressions for the recognition of simple query constructs, context-free grammars for the recognition of nested queries, and a jumping finite automaton for the synthesis  ...  One of the pivotal reasons given for these difficulties lies with the simple syntax of SQL, which is often misleading and hard to understand.  ...  into SPARQL Protocol and RDF Query Language (SPARQL) queries.  ... 
arXiv:2203.03469v1 fatcat:mutfduvr2jgezmaomd4otvcpje
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