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Automatic Curation of Clinical Trials Data in LinkedCT [chapter]

Oktie Hassanzadeh, Renée J. Miller
2015 Lecture Notes in Computer Science  
The Linked Clinical Trials (LinkedCT) project started back in 2008 with the goal of providing a Linked Data source of clinical trials.  ...  In this paper, we present a detailed description of the system along with a brief outline of technical challenges involved in curating the raw XML data into high-quality Linked Data.  ...  Data Curation in LinkedCT In this section, we describe the end-to-end curation process we have designed to construct an up-to-date high-quality Linked Data source out of the XML data published by ClinicalTrials.gov  ... 
doi:10.1007/978-3-319-25010-6_16 fatcat:k25ynxmpqndwhonvgjzch3vrli

VizCurator

Bahar Ghadiri Bashardoost, Christina Christodoulakis, Soheil Hassas Yeganeh, Renée J. Miller, Kelly Lyons, Oktie Hassanzadeh
2015 Proceedings of the 24th International Conference on World Wide Web - WWW '15 Companion  
We will demonstrate VizCurator using LinkedCT.org, a five-star open data set mapped from the XML NIH clinical trials data (clinicaltrials.gov) that we have been maintaining and curating for several years  ...  More importantly, VizCurator provides a rich set of tools for data curation.  ...  This research was partially funded by the GRAND NCE as part of the MEOW project, and by NSERC BIN.  ... 
doi:10.1145/2740908.2742845 dblp:conf/www/BashardoostCYML15 fatcat:zfvzeolzqrh2dhpr6rhvzkeegq

Analyzing Linked Data Quality with LiQuate [chapter]

Edna Ruckhaus, Maria-Esther Vidal, Simón Castillo, Oscar Burguillos, Oriana Baldizan
2014 Lecture Notes in Computer Science  
The number of datasets in the Linking Open Data (LOD) cloud as well as LOD-based applications have exploded in the last years.  ...  We demonstrate the capabilities of LiQuate (Linked Data Quality Assessment), a tool that relies on Bayesian Networks to analyze the quality of data and links in the LOD cloud.  ...  number of clinical trials.  ... 
doi:10.1007/978-3-319-11955-7_72 fatcat:u43xtwwmxrdd3alcdr6nz3swfe

Hubble: Linked Data Hub for Clinical Decision Support [chapter]

Rinke Hoekstra, Sara Magliacane, Laurens Rietveld, Gerben de Vries, Adianto Wibisono, Stefan Schlobach
2015 Lecture Notes in Computer Science  
This paper describes the Hubble prototype system for clinical decision support that demonstrates the speed, ease and flexibility of producing and using a Linked Data version of the AERS dataset for clinical  ...  The AERS datasets is one of the few remaining, large publicly available medical data sets that until now have not been published as Linked Data.  ...  Examples are medical vocabularies such as SnomedCT, MeSH, MedDRA, and the NCI Thesaurus (all part of the Unified Medical Language System (UMLS)), 4 and datasets such as LinkedCT (clinical trials), Sider  ... 
doi:10.1007/978-3-662-46641-4_45 fatcat:r7nly2wblvds5cyou5dsnjbnyq

Dynamic enhancement of drug product labels to support drug safety, efficacy, and effectiveness

Richard D Boyce, John R Horn, Oktie Hassanzadeh, Anita de Waard, Jodi Schneider, Joanne S Luciano, Majid Rastegar-Mojarad, Maria Liakata
2013 Journal of Biomedical Semantics  
We found that approximately one in five efficacy/effectiveness claims were relevant to the Clinical Studies section of a psychotropic drug product, with most relevant claims providing new information.  ...  The resulting Linked Data set maps 409 efficacy/effectiveness study results, 784 drug-drug interactions, and 112 metabolic pathway assertions derived from three clinically-oriented drug information sources  ...  The content is solely the responsibility of the authors and does not represent the official views of AHRQ. JS's work was supported by Science Foundation Ireland under Grant No.  ... 
doi:10.1186/2041-1480-4-5 pmid:23351881 pmcid:PMC3698101 fatcat:bje6mmdsnrdohhfbwbuzdqt77u

Publishing Chinese medicine knowledge as Linked Data on the Web

Jun Zhao
2010 Chinese Medicine  
Conclusion: Publishing CM knowledge in Linked Data provides a point of departure for integration of CM databases.  ...  Methods: Linked Data approach was used in publishing CM knowledge.  ...  JZ would also like to thank Anja Jentzsch and the Linked Open Drug Data project members for helping create some of the data links between RDF-TCM and LODD and Olaf Hartig for his contribution in the SQUIN-powered  ... 
doi:10.1186/1749-8546-5-27 pmid:20663193 pmcid:PMC2936390 fatcat:52riusi4yzgtzdatsb3lueu6ni

PAnG

Philip Anderson, Andreas Thor, Joseph Benik, Louiqa Raschid, Maria Esther Vidal
2012 Proceedings of the 2012 international conference on Management of Data - SIGMOD '12  
They are common in the life sciences and health sciences, where concepts such as genes, proteins or clinical trials are annotated with controlled vocabulary terms from ontologies.  ...  We present a tool, PAnG (Patterns in Annotation Graphs), that is based on a complementary methodology of graph summarization and dense subgraphs.  ...  On the right of Figure 1 is a fragment of the relevant GO ontology. The second dataset is the NIH clinical trial data and the corresponding hyperlinked collection LinkedCT 2 [3] .  ... 
doi:10.1145/2213836.2213930 dblp:conf/sigmod/AndersonTBRV12 fatcat:67sg27qgrbcodafwnxmx2kmi6a

Biomedical Semantic Resources for Drug Discovery Platforms [chapter]

Ali Hasnain, Dietrich Rebholz-Schuhmann
2017 Lecture Notes in Computer Science  
Since the data sources are publicly available, the amount of content can be measured giving an overview on the accessible content but also on the state of the data representation in comparison to the existing  ...  The amount of data is constantly increasing as well as the complexity of data.  ...  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.  ... 
doi:10.1007/978-3-319-70407-4_34 fatcat:2bzddzat5zdcrinfwd6m4xqlai

Curadoria de dados de pesquisa em repositórios de ensaios clínicos: uma revisão de escopo | Curating research data in clinical trial repositories: a scoping review

Fabiana De Melo Amaral Gonçalves Pinto, Janaynne Carvalho Do Amaral, Melina De Brito Dos Santos
2019 Liinc em Revista  
curating research data in clinical trial repositories.  ...  As a final reflection, it highlights the challenge of discussing and implementing the practice of curating research data produced by clinical trials and highlights the vast and timely field to be explored  ...  Automatic Curation of Clinical Trials Data in LinkedCT. In: ARENAS, M. et al. (Ed.).  ... 
doi:10.18617/liinc.v15i2.4766 fatcat:eshh5xoqanbrpjaeki7noo4ajq

Ontology-based federated data access to human studies information

Ida Sim, Simona Carini, Samson W Tu, Landon T Detwiler, James Brinkley, Shamim A Mollah, Karl Burke, Harold P Lehmann, Swati Chakraborty, Knut M Wittkowski, Brad H Pollock, Thomas M Johnson (+2 others)
2012 AMIA Annual Symposium Proceedings  
Human studies are one of the most valuable sources of knowledge in biomedical research, but data about their design and results are currently widely dispersed in siloed systems.  ...  First, the Ontology of Clinical Research (OCRe) provides the reference semantics.  ...  Its contents are solely the responsibility of the authors and do not necessarily represent the official view of NCRR or NIH.  ... 
pmid:23304360 pmcid:PMC3540523 fatcat:oahd77qjjbetjajfp3rowk6ndm

BioASQ: A Challenge on Large-Scale Biomedical Semantic Indexing and Question Answering [chapter]

Georgios Balikas, Anastasia Krithara, Ioannis Partalas, George Paliouras
2015 Lecture Notes in Computer Science  
Hence, the architecture can also be seen as our view of how relevant work from fields such as information retrieval, hierarchical classification, question answering, ontologies, and linked data can be  ...  BIOASQ aims to push towards systems that will allow biomedical workers to express their information needs in natural language and that will return concise and user-understandable answers by combining information  ...  At the same time, new specialised data sources appear, which are complementary to generic ones (e.g., LinkedCT for clinical trials, and Orphanet for rare diseases 8 ) or combine several specialized resources  ... 
doi:10.1007/978-3-319-24471-6_3 fatcat:evlqerqosnbl7j7o46a7pertsu

Towards linked open gene mutations data

Achille Zappa, Andrea Splendiani, Paolo Romano
2012 BMC Bioinformatics  
In this paper, we discuss issues related to the integration of mutation data in the Linked Open Data infrastructure, part of the Semantic Web framework.  ...  Automatic mappings to RDF were first created by using D2RQ and later manually refined by introducing concepts and properties from domain vocabularies and ontologies, as well as links to Linked Open Data  ...  This article has been published as part of BMC Bioinformatics  ... 
doi:10.1186/1471-2105-13-s4-s7 pmid:22536974 pmcid:PMC3303732 fatcat:hplgsf3xgraebfc5ftzfehz56m

The Ontology of Clinical Research (OCRe): An informatics foundation for the science of clinical research

Ida Sim, Samson W. Tu, Simona Carini, Harold P. Lehmann, Brad H. Pollock, Mor Peleg, Knut M. Wittkowski
2014 Journal of Biomedical Informatics  
In this paper, we describe the key informatics use cases of each phase of a study's scientific lifecycle, present OCRe and the principles behind its modeling, and describe applications of OCRe and associated  ...  constitute the science of clinical research.  ...  To date, CRI has focused on facilitating conduct of clinical trials and management of clinical data for secondary research use.  ... 
doi:10.1016/j.jbi.2013.11.002 pmid:24239612 pmcid:PMC4019723 fatcat:dnkyifk6szgtljg4z46qasaw34

Open data integration

Renée J. Miller
2018 Proceedings of the VLDB Endowment  
Open data plays a major role in supporting both governmental and organizational transparency.  ...  We describe a research agenda and recent progress in developing scalable data-analysis or query-aware data discovery algorithms that provide high recall and accuracy over massive data repositories.  ...  NSERC funded this work along with the Northeastern College of Computer and Information Science.  ... 
doi:10.14778/3229863.3240491 fatcat:i7hcebup6bhrrjidunk4zh7shq

Consolidating drug data on a global scale using Linked Data

Milos Jovanovik, Dimitar Trajanov
2017 Journal of Biomedical Semantics  
As a consequence, the drug data available on the Web are independently curated by national institutions from each country, leaving the data in varying languages, with a varying structure, granularity level  ...  Therefore, one of the main challenges in the realm of drug data is the consolidation and integration of large amounts of heterogeneous data into a comprehensive dataspace, for the purpose of developing  ...  Cyril and Methodius" University in Skopje, as part of the "SemBigData: Using Semantic Web Technologies to Connect and Explore Big Data" research project.  ... 
doi:10.1186/s13326-016-0111-z pmid:28109310 pmcid:PMC5251285 fatcat:klrd2u7g6vd3vnxdlmx5yzpft4
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