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Harvest: an open platform for developing web-based biomedical data discovery and reporting applications

Jeffrey W Pennington, Byron Ruth, Michael J Italia, Jeffrey Miller, Stacey Wrazien, Jennifer G Loutrel, E Bryan Crenshaw, Peter S White
2014 JAMIA Journal of the American Medical Informatics Association  
Contributors JWP oversaw project operations, study design, and manuscript authoring; BR, MJI, JM, SW, and JGL contributed substantially to platform development and evaluation; EBC provided domain expertise  ...  Open Access This is an Open Access article distributed in accordance with the Creative Commons Attribution Non Commercial (CC BY-NC 3.0) license, which permits others to distribute, remix, adapt, build  ...  DISCUSSION Our results indicate that Harvest facilitates construction of accessible biomedical data discovery applications by providing informatics researchers with open, standards-based components, an  ... 
doi:10.1136/amiajnl-2013-001825 pmid:24131510 pmcid:PMC3932456 fatcat:wnvcl53uczbvzeoy373okeyd6y

Knowledge Beacons: Web services for data harvesting of distributed biomedical knowledge

Lance M. Hannestad, Vlado Dančík, Meera Godden, Imelda W. Suen, Kenneth C. Huellas-Bruskiewicz, Benjamin M. Good, Christopher J. Mungall, Richard M. Bruskiewich, Vasilis J. Promponas
2021 PLoS ONE  
science knowledge management platform, we designed a Representational State Transfer (REST) web services Application Programming Interface (API) specification, which we call a Knowledge Beacon.  ...  The continually expanding distributed global compendium of biomedical knowledge is diffuse, heterogeneous and huge, posing a serious challenge for biomedical researchers in knowledge harvesting: accessing  ...  CJM and BMG coined the name "Knowledge Beacon" to express the architectural vision of uniformly wrapped knowledge sources for distributed knowledge discovery and harvesting.  ... 
doi:10.1371/journal.pone.0231916 pmid:33755673 fatcat:djgwa5dhhncaxf7epi4zree5ka

Knowledge Beacons: Web Service Workflow for FAIR Data Harvesting of Distributed Biomedical Knowledge [article]

Lance M Hannestad, Vlado Dančík, Wun Ting Imelda Suen, Meera Godden, Kenneth Casimir Huellas-Bruskiewicz, Benjamin M Good, Christopher J Mungall, Richard Michael Bruskiewich
2020 bioRxiv   pre-print
Translational Sciences (NCATS) to develop a biomedical science knowledge management platform, we de-signed a Representational State Transfer (REST) web services Application Programming Inter-face (API  ...  The continually expanding distributed global compendium of biomedical knowledge is diffuse, heterogeneous and huge, posing a serious challenge for biomedical researchers in knowledge harvesting: accessing  ...  This work arises out of an earlier 62 effort to develop a web application called "Knowledge.Bio" [7] to provide enhanced navigation 63 through the knowledge base of PubMed cited concepts and relationships  ... 
doi:10.1101/2020.04.06.027425 fatcat:74bq6rielrfvfjziigck7rqyha

Harvesting the promise of AOPs: An assessment and recommendations

Annamaria Carusi, Mark R. Davies, Giovanni De Grandis, Beate I. Escher, Geoff Hodges, Kenneth M.Y. Leung, Maurice Whelan, Catherine Willett, Gerald T. Ankley
2018 Science of the Total Environment  
However, it is increasingly apparent that the potential stakeholder community for the AOP concept and AOP KBs is broader than scientists and regulators directly involved in chemical safety assessment.  ...  In this paper we identify and describe those stakeholders who currently-or in the futurecould benefit from the application of the AOP framework and knowledge to specific problems.  ...  LaLone and M. Hecker for their coordination, organization, and guidance of the workshop.  ... 
doi:10.1016/j.scitotenv.2018.02.015 pmid:30045572 pmcid:PMC5888775 fatcat:xhshlrta6nfu5akav6n5rkwr4q

A Survey on Energy Harvesting and Integrated Data Sharing in Wireless Body Area Networks

Xiaoling Xu, Lei Shu, Mohsen Guizani, Mei Liu, Junye Lu
2015 International Journal of Distributed Sensor Networks  
In this attempt, we focus mostly on energy acquisition, data integration and data sharing, and collaboration of WBANs, from the viewpoint of energy harvesting development, the social network and smartphone  ...  application in WBANs, and the integration of WBANs and cloud system networks computing to analyze related issues of WBANs.  ...  The method and application of piezoelectric devices topology optimization design for energy harvesting devices have been reported.  ... 
doi:10.1155/2015/438695 fatcat:rllkkr3fcbfozbd4rrznudxzye

Social networks, web-based tools and diseases: implications for biomedical research

Fabricio F. Costa
2013 Drug Discovery Today  
In this article, I will review how social networks and other web-based tools are changing the way we approach and track diseases in biomedical research.  ...  The emergence of different types of social networks has fostered connections between individuals, thus facilitating data exchange in a variety of fields.  ...  PatientsLikeMe is an example of a web-based social networking site that captures patient-reported data from people with life-changing diseases [17] .  ... 
doi:10.1016/j.drudis.2012.10.006 pmid:23103282 fatcat:citthrjhkfhvlbsn252egtaswu

The Biomedical Research Infrastructure Software as a Service Kit (BRISSKit): technical description

Oliver W. Butters, Shajid Issa, Jeff Lusted, Malcolm Newbury, Russ Parsloe, Nick Holden, Robert C. Free, Tim Beck, Rebecca C. Wilson, Paul R. Burton, Jonathan A. Tedds
2016 F1000Research  
it is possible for a biomedical research platform to be supplied as a service.  ...  We describe a technical implementation of an infrastructure to manage the full research ecosystem from participant management, to data and sample collection, and finally to data storage, interrogation  ...  web based open source applications in biomedical researchThere are various web based and open source applications being used (and developed) in biomedical research, for example: the Galaxy project (http  ... 
doi:10.12688/f1000research.8736.1 fatcat:b2pbpyhip5fiplxulm4x6e7vry

Open PHACTS: semantic interoperability for drug discovery

Antony J. Williams, Lee Harland, Paul Groth, Stephen Pettifer, Christine Chichester, Egon L. Willighagen, Chris T. Evelo, Niklas Blomberg, Gerhard Ecker, Carole Goble, Barend Mons
2012 Drug Discovery Today  
The goal of the project is to deliver and sustain an 'open pharmacological space' using and enhancing state-of-the-art semantic web standards and technologies.  ...  It is focused on practical and robust applications to solve specific questions in drug discovery research.  ...  We acknowledge all of the collaborators for their contributions to Open PHACTS.  ... 
doi:10.1016/j.drudis.2012.05.016 pmid:22683805 fatcat:qnqlnrdv3zbijesyhdat2knoeu

Challenges for Ontology Repositories and Applications to Biomedicine & Agronomy

Clément Jonquet
2017 Symposium on Information Management and Big Data  
In this position paper, we describe six high level challenges for ontology repositories: metadata & selection, multilingualism, alignment, new generic ontology-based services, annotations & linked data  ...  Ontology libraries and repositories are usually developed to address certain needs and communities.  ...  I also acknowledge the National Center for Biomedical Ontologies for their insights and thanks all my collaborators in Montpellier or Stanford interested like me on ontology repositories.  ... 
dblp:conf/simbig/Jonquet17 fatcat:v7xrirond5dkzjqy7u4nyra3yu

DataMed: Finding useful data across multiple biomedical data repositories [article]

Lucila Ohno-Machado, Susanna-Assunta Sansone, George Alter, Ian Fore, Jeffrey Grethe, Hua Xu, Alejandra Gonzalez-Beltran, Philippe Rocca-Serra, Ergin Soysal, Nansu Zong, Hyeon-eui Kim
2016 bioRxiv   pre-print
As part of the NIH Big Data to Knowledge initiative, we work with an international community of researchers, service providers and knowledge experts to develop and test a data index and search engine,  ...  The value of broadening searches for data across multiple repositories has been identified by the biomedical research community.  ...  The co-authors, which are the lead investigators and chairs/co-chairs of the core activities, thank all contributors to the bioCADDIE Consortium and list them here in alphabetical order within each activity  ... 
doi:10.1101/094888 fatcat:c6g77satwbdajoyrh7u4fptvoa

Foundry: a message-oriented, horizontally scalable ETL system for scientific data integration and enhancement

Ibrahim Burak Ozyurt, Jeffrey S Grethe
2018 Database: The Journal of Biological Databases and Curation  
Applicability of the system for scientific data is illustrated in biomedical and earth science domains.  ...  We also introduce a data transformation language for biomedical curators allowing for the transformation and combination of data/metadata from heterogeneous data sources.  ...  Acknowledgements We thank Yueling Li for her help in transformation script curation and the bioCADDIE Core Technical Team for their curation and testing efforts during the development of the system introduced  ... 
doi:10.1093/database/bay130 pmid:30576493 pmcid:PMC6301337 fatcat:heklhujo3jaehjnf6idgjggmka

ReVeaLD: A user-driven domain-specific interactive search platform for biomedical research

Maulik R. Kamdar, Dimitris Zeginis, Ali Hasnain, Stefan Decker, Helena F. Deus
2014 Journal of Biomedical Informatics  
in biomedical discovery.  ...  In this report we present ReVeaLD (a Real-time Visual Explorer and Aggregator of Linked Data), a user-centered visual analytics platform devised to increase intuitive interaction with data from distributed  ...  knowledge discovery, and Ronan Fox, whose comments and advice were extremely valuable for the development of the platform, as well as for improving the manuscript.  ... 
doi:10.1016/j.jbi.2013.10.001 pmid:24135450 fatcat:kkbnap7ocfgkhhyi64nycjlaz4

The Sixth Annual VIVO Conference

Carol Minton Morris
2015 D-Lib Magazine  
and discover" with the VIVO open source semantic web application.  ...  VIVO, an open source semantic web application.  ... 
doi:10.1045/september2015-morris fatcat:p4baznqxczahrgi4in3umlchju

The MERG Suite: Tools for discovering competencies and associated learning resources

Ravi Bhupatiraju, William R Hersh, Valerie Smothers, Michael Fordis, Peter S Greene
2008 Source Code for Biology and Medicine  
Methods: We built a tool suite for authoring and discovery of medical e-learning metadata. The end-user usability of the tool suite was evaluated through a web-based survey.  ...  This project focused on developing federated discovery services for competency-based medical e-learning content.  ...  Application Platforms We used Karrigell [14] , an open source pure Python based web server for Python based designs and used GlassFish [15] , an open source Java Application Server for the later Java  ... 
doi:10.1186/1751-0473-3-7 pmid:18479525 pmcid:PMC2416363 fatcat:iijh6zi6cramneeigkjxnmnnje

Review and evaluation of electronic health records-driven phenotype algorithm authoring tools for clinical and translational research

Jie Xu, Luke V. Rasmussen, Pamela L. Shaw, Guoqian Jiang, Richard C. Kiefer, Huan Mo, Jennifer A. Pacheco, Peter Speltz, Qian Zhu, Joshua C. Denny, Jyotishman Pathak, William K. Thompson (+1 others)
2015 JAMIA Journal of the American Medical Informatics Association  
Objective To review and evaluate available software tools for electronic health record-driven phenotype authoring in order to identify gaps and needs for future development.  ...  Materials and Methods Candidate phenotype authoring tools were identified through (1) literature search in four publication databases (PubMed, Embase, Web of Science, and Scopus) and (2) a web search.  ...  Harvest 15 Harvest is a software toolkit designed for building web-based application to perform custom query of a dataset for data discovery and reporting purpose.  ... 
doi:10.1093/jamia/ocv070 pmid:26224336 pmcid:PMC5009915 fatcat:2wov5k2znnc6jcyqs5kxrdzfxi
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