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Emerging Practices for Mapping and Linking Life Sciences Data Using RDF - A Case Series

M. Scott Marshall, Richard Boyce, Helena Deus, Jun Zhao, Egon Willighagen, Matthias Samwald, Elgar Pichler, Janos Hajagos, Eric Pruddhommeaux, Susie Stephens
2012 Social Science Research Network  
This experience has helped the interest group define a general data workflow for mapping health care and life science (HCLS) data to RDF and linking it with other Linked Data sources.  ...  useful for identifying the tools, techniques, and practices employed by earlier developers.  ...  We thank the participants of the Linked Open Drug Data task force and the W3C Health Care and Life Science (HCLS) Interest Group.  ... 
doi:10.2139/ssrn.3198960 fatcat:tdvajggevrctlobcb456r3jzhq

Systems chemical biology and the Semantic Web: what they mean for the future of drug discovery research

David J. Wild, Ying Ding, Amit P. Sheth, Lee Harland, Eric M. Gifford, Michael S. Lajiness
2012 Drug Discovery Today  
Recent Semantic Web technologies such as RDF and SPARQL are technical enablers of systems chemical biology, facilitating the deployment of advanced algorithms for searching and mining large integrated  ...  as chemogenomics, are central to emerging new paradigms of drug discovery such as drug repurposing and personalized medicine.  ...  BOX 1 Terminology used in the Semantic Web and life sciences RDF: Originally used for describing resources on the Web, RDF is now the most fundamental way of representing data points and relationships  ... 
doi:10.1016/j.drudis.2011.12.019 pmid:22222943 fatcat:ihung2o5cnhrjbytslxfm2lxx4

Linked data and provenance in biological data webs

J. Zhao, A. Miles, G. Klyne, D. Shotton
2009 Briefings in Bioinformatics  
The Web is now being used as a platform for publishing and linking life science data. The Web's linking architecture can be exploited to join heterogeneous data from multiple sources.  ...  This article presents design patterns for representing and querying provenance information relating to mapping links between heterogeneous data from sources in the domain of functional genomics.  ...  RDF is to data what HTML is to documents, and also uses URIs for identification and linking.  ... 
doi:10.1093/bib/bbn044 pmid:19060306 fatcat:pnoz2bhujvabhds7njglexzk4u

Semantic Web meets Integrative Biology: a survey

H. Chen, T. Yu, J. Y. Chen
2012 Briefings in Bioinformatics  
In this review, we provide insight into how SW technologies can be used to build open, standardized and interoperable solutions for interdisciplinary integration on a global basis.  ...  We identify a series of bioinformatics problems posed by interdisciplinary integration: (i) data integration that interconnects structured data across related biomedical domains; (ii) ontology integration  ...  The work of the authors is funded by China National Science Foundation (NSFC61070156), and China national 863 program China Cloud Initiative.  ... 
doi:10.1093/bib/bbs014 pmid:22492191 fatcat:n5xm5kbc75ethlnfwfmgwdtnhq

A journey to Semantic Web query federation in the life sciences

Kei-Hoi Cheung, H Robert Frost, M Scott Marshall, Eric Prud'hommeaux, Matthias Samwald, Jun Zhao, Adrian Paschke
2009 BMC Bioinformatics  
As a community effort, the BioRDF task force, within the Semantic Web for Health Care and Life Sciences Interest Group, is exploring how these emerging approaches can be utilized to execute distributed  ...  Methods and results: We have created two health care and life science knowledge bases. We have explored a variety of Semantic Web approaches to describe, map, and dynamically query multiple datasets.  ...  This article has been published as part of BMC Bioinformatics Volume 10 Supplement 10, 2009: Semantic Web Applications and Tools for Life Sciences, 2008.  ... 
doi:10.1186/1471-2105-10-s10-s10 pmid:19796394 pmcid:PMC2755818 fatcat:ovbiczh3wnajbpqba5byn3f4fq

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.  ...  those data using their tools and interfaces.  ...  Among the most prominent of these early-adopters have been the life and health science communities [3] where numerous Linked Data initiatives have emerged.  ... 
doi:10.1186/2041-1480-4-6 pmid:23398680 pmcid:PMC3598643 fatcat:fm5xaotu3nbafibe3pm3js4d7u

Building performance optimisation: A hybrid architecture for the integration of contextual information and time-series data

Shushan Hu, Edward Corry, Edward Curry, William J.N. Turner, James O'Donnell
2016 Automation in Construction  
v e r s i o n o f a w o r k t h a t  ...  Publication information Automation in Construction, 70 : 51-61 Publisher Elsevier Item record/more information http://hdl.handle.net/10197/7880 Publisher's statement þÿ T h i s i s t h e a u t h o r s  ...  A mapping module that integrates contextual data and time-series data used 278 for building performance definition.  ... 
doi:10.1016/j.autcon.2016.05.018 fatcat:ja3qjpqbnfha7jelppracrk7iq

Implementation of linked data in the life sciences at BioHackathon 2011

Kiyoko F Aoki-Kinoshita, Akira R Kinjo, Mizuki Morita, Yoshinobu Igarashi, Yi-an Chen, Yasumasa Shigemoto, Takatomo Fujisawa, Yukie Akune, Takeo Katoda, Anna Kokubu, Takaaki Mori, Mitsuteru Nakao (+4 others)
2015 Journal of Biomedical Semantics  
and developed specific RDF and SPARQL use cases.  ...  Linked Data has gained some attention recently in the life sciences as an effective way to provide and share data.  ...  We note that since the writing of this original manuscript, a similar manuscript describing emerging practices for mapping and linking life sciences data has been published, which may also be a good reference  ... 
doi:10.1186/2041-1480-6-3 pmid:25973165 pmcid:PMC4429360 fatcat:hrwxw6k25jfmpkbsdr22yn4a7y

Biomedical semantics in the Semantic Web

Andrea Splendiani, Albert Burger, Adrian Paschke, Paolo Romano, M Marshall
2011 Journal of Biomedical Semantics  
The Semantic Web offers an ideal platform for representing and linking biomedical information, which is a prerequisite for the development and application of analytical tools to address problems in data-intensive  ...  We report here a few reflections on these questions, following discussions at the SWAT4LS (Semantic Web Applications and Tools for Life Sciences) workshop series, of which this Journal of Biomedical Semantics  ...  This article has been published as part of Journal of Biomedical Semantics Volume 2 Supplement 1, 2011: Semantic Web Applications and Tools for Life Sciences (SWAT4LS), 2009.  ... 
doi:10.1186/2041-1480-2-s1-s1 pmid:21388570 pmcid:PMC3105493 fatcat:iwbnqzgvqfcojdn4yubjoeskla

Semantic Web Atlas: Putting Gene Expression Data into Biological Context

Simon Jupp, Helen E. Parkinson, James Malone
2012 Workshop on Semantic Web Applications and Tools for Life Sciences  
The RDF representation provides new opportunities for data integration, querying, error detection and curation.  ...  We show how the RDF representation of the GXA adds value to the existing data through a series of novel biological questions which interrogate the different resources and which were not previously possible  ...  Acknowledgements We acknowledge funds from EMBL (JM, HP) and The National Center for Biomedical Ontology, one of the National Centers for Biomedical Computing supported by the NHGRI, the NHLBI, and the  ... 
dblp:conf/swat4ls/JuppPM12 fatcat:hcxgop27fbbnnajg7xkrdyeyjm

Using RDF to Describe and Link Social Science Data to Related Resources on the Web

Stefan Kramer, Amber Leahey, Humphrey Southall, Johanna Vompras, Joachim Wackerowz
2012 Social Science Research Network  
We briefly discuss emerging or known issues surrounding the potential use of linked data within each of the defined use cases.  ...  We provide a case for leveraging the Data Documentation Initiative (DDI) to enable semantic linking of social science data to other data and related resources on the Web.  ...  Workshop Title: Semantic Statistics for Social, Behavioural, and Economic Sciences: Leveraging the DDI Model for the Web  Attribution.  ... 
doi:10.2139/ssrn.2176657 fatcat:kssviqbttjainb5zgcnekyv6gy

Managing Big, Linked, and Open Earth-Observation Data: Using the TELEIOS\/LEO software stack

Manolis Koubarakis, Kostis Kyzirakos, Charalampos Nikolaou, George Garbis, Konstantina Bereta, Roi Dogani, Stella Giannakopoulou, Panayiotis Smeros, Dimitrianos Savva, George Stamoulis, Giannis Vlachopoulos, Stefan Manegold (+4 others)
2016 IEEE Geoscience and Remote Sensing Magazine  
We present the life cycle of big, linked, and open EO data and show how to support their various stages using the software stack developed by the European Union (EU) research projects TELEIOS and the Linked  ...  In this article, we argue that if EO data are published using the linked data paradigm, then the data discovery, data integration, and development of applications becomes easier.  ...  R2RML is a language for expressing the mappings from relational data to RDF terms, and RML is a more general language for expressing the mappings from files of different formats (e.g., CSV and XML) to  ... 
doi:10.1109/mgrs.2016.2530410 fatcat:ha4yibpkb5cdhfxrhkev4625vm

Interlinking Scientific Data on a Global Scale

Christian Bizer
2013 Data Science Journal  
For serializing RDF data, RDF/XML and RDFa syntax are widely used in the Linked Data context.  ...  Linked Data in Life Science The usage of Linked Data technologies to share life-science data on a global scale is a good example of how the technologies could also be applied in other scientific disciplines  ... 
doi:10.2481/dsj.grdi-002 fatcat:nftr4gspfrfqvatk6qbc4f23y4

Workshop summary: Workshop on Semantics and Analytics for Emergency Response (SAFE2015)

Eva Blomqvist, Vitaveska Lanfranchi, Suvodeep Mazumdar, Tomi Kauppinen, Carsten Keßler
2015 International Conference on Information Systems for Crisis Response and Management  
, Linked Data analytics for Emergency Response.  ...  This paper provides a brief summary for the first workshop in the SAFE workshop series.  ...  ACKNOWLEDGMENTS We would like to thank our contributors and also the program committee whose detailed feedback resulted in a rich collection of papers.  ... 
dblp:conf/iscram/BlomqvistLMKK15 fatcat:2ci5xiw5azayjk4gsydip4om6y

From artifacts to aggregations: Modeling scientific life cycles on the semantic Web

Alberto Pepe, Matthew Mayernik, Christine L. Borgman, Herbert Van de Sompel
2009 Journal of the American Society for Information Science and Technology  
Our analysis is framed by studies of scientific practices in a large, multi-disciplinary, multi-university science and engineering research center, the Center for Embedded Networked Sensing (CENS).  ...  We demonstrate a conceptual implementation of OAI-ORE to represent the scientific life cycles of embedded networked sensor applications in seismology and environmental sciences.  ...  Borgman is a founding Co-Principal Investigator and research lead of the Data Practices Team. The CENS Deployment Center is supported by core CENS funding.  ... 
doi:10.1002/asi.21263 fatcat:c6bk4j5sezgctfsdxdnvmnobgi
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