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Identifying data sharing in biomedical literature

Heather A Piwowar, Wendy W Chapman, Wendy Chapman
2008 AMIA Annual Symposium Proceedings  
Using regular expression patterns and machine learning algorithms on open access biomedical literature, our system was able to identify 61% of articles with shared datasets with 80% precision.  ...  Unfortunately, it is difficult to measure the effectiveness of these initiatives because data can be shared in such a variety of mechanisms and locations.  ...  Method We developed a pilot NLP application to identify references to data sharing in the biomedical literature and compared its predictive performance against a reference standard of bibliographic citations  ... 
pmid:18998887 pmcid:PMC2655927 fatcat:mlxar2a3c5hw7bddb5wl3536ly

Identifying Data Sharing in Biomedical Literature

Heather Piwowar, Wendy Chapman
2008 Nature Precedings  
Using regular expression patterns and machine learning algorithms on open access biomedical literature, our system was able to identify 61% of articles with shared datasets with 80% precision.  ...  Unfortunately, it is difficult to measure the effectiveness of these initiatives because data can be shared in such a variety of mechanisms and locations.  ...  Method We developed a pilot NLP application to identify references to data sharing in the biomedical literature and compared its predictive performance against a reference standard of bibliographic citations  ... 
doi:10.1038/npre.2008.1721.2 fatcat:3qhcvwk54rdffpngpif2qpj2iy

Identifying Data Sharing in Biomedical Literature

Heather Piwowar, Wendy Chapman
2008 Nature Precedings  
Using regular expression patterns and machine learning algorithms on open access biomedical literature, our system was able to identify 61% of articles with shared datasets with 80% precision.  ...  Unfortunately, it is difficult to measure the effectiveness of these initiatives because data can be shared in such a variety of mechanisms and locations.  ...  Method We developed a pilot NLP application to identify references to data sharing in the biomedical literature and compared its predictive performance against a reference standard of bibliographic citations  ... 
doi:10.1038/npre.2008.1721.1 fatcat:4gdsy4bb6zg4fexfcvjaoabvb4

Incorporating collaboratory concepts into informatics in support of translational interdisciplinary biomedical research

E LEE, D MCDONALD, N ANDERSON, P TARCZYHORNOCH
2009 International Journal of Medical Informatics  
There is, however, a growing body of literature on the study and fostering of collaboration in fields such as computer supported cooperative work (CSCW) and information science (IS).  ...  Due to its complex nature, modern biomedical research has become increasingly interdisciplinary and collaborative in nature.  ...  The goal of this review is to identify concepts in the collaboratory research literature that can inform biomedical informatics to better support interdisciplinary biomedical research.  ... 
doi:10.1016/j.ijmedinf.2008.06.011 pmid:18706852 pmcid:PMC2606933 fatcat:xvc5d2dr6rcldhj2chxygtc7ti

Equitable data sharing in epidemics and pandemics

Bridget Pratt, Susan Bull
2021 BMC Medical Ethics  
To explore these questions, we undertook a systematic scoping review of the literature on data sharing in epidemics and pandemics and thematically analyzed identified literature for its discussion of ethical  ...  We wanted to both understand how equity in data sharing is being conceptualized and draw out other important values and norms for data sharing in epidemics and pandemics.  ...  Failure to generate and share non-biomedical research data While much of the identified literature focused on generating and sharing biomedical research data during epidemics and pandemics, there is concern  ... 
doi:10.1186/s12910-021-00701-8 pmid:34615519 fatcat:3fb4ga4vefgktlps7n7rumgyo4

Repeat: a framework to assess empirical reproducibility in biomedical research

Leslie D. McIntosh, Anthony Juehne, Cynthia R. H. Vitale, Xiaoyan Liu, Rosalia Alcoser, J. Christian Lukas, Bradley Evanoff
2017 BMC Medical Research Methodology  
Methods: The aim of the proceeding work is to develop an assessment tool operationalizing key concepts of research transparency in the biomedical domain, specifically for secondary biomedical data research  ...  Results: RepeAT includes 119 unique variables grouped into five categories (research design and aim, database and data collection methods, data mining and data cleaning, data analysis, data sharing and  ...  Availability of data and materials Data and associated materials related to this work can be accessed within a designated WashingtonUniversity in St.  ... 
doi:10.1186/s12874-017-0377-6 pmid:28923006 pmcid:PMC5604503 fatcat:jxoghd7ixffmdmvfybyucwn7ve

Research data management in health and biomedical citizen science: practices and prospects

Ann Borda, Kathleen Gray, Yuqing Fu
2019 JAMIA Open  
Results Health and biomedical citizen science platforms and projects are diverse in terms of types of work with data and data management activities that in themselves may have scientific merit.  ...  Background Public engagement in health and biomedical research is being influenced by the paradigm of citizen science.  ...  The chosen platforms were based on their frequency as identified examples in the literature review results; the prevalence of health and biomedical projects supported through these platforms; and the use  ... 
doi:10.1093/jamiaopen/ooz052 pmid:32607493 pmcid:PMC7309241 fatcat:olhmvou57namzgzuxpllvzsiky

SimText: A text mining framework for interactive analysis and visualization of similarities among biomedical entities [article]

Marie Gramm, Eduardo Perez-Palma, Sarah M Schumacher-Bass, Jarrod E Dalton, Costin Leu, Daniel Blankenberg, Dennis Lal
2020 bioRxiv   pre-print
Literature exploration in PubMed on a large number of biomedical entities (e.g., genes, diseases, experiments) can be time consuming and challenging comparing many entities to one other.  ...  techniques and visualization in a Shiny web application.  ...  We collected names from 182 researchers from the Lerner Research Institute of the Cleveland Clinic as entities, the department they are working in as a grouping variable to identify shared interest of  ... 
doi:10.1101/2020.07.06.190629 fatcat:arp45s6tt5a7npgh6fbrhfzmyq

Reproducible research practices, transparency, and open access data in the biomedical literature, 2015–2017

Joshua D. Wallach, Kevin W. Boyack, John P. A. Ioannidis, Ulrich Dirnagl
2018 PLoS Biology  
According to a previous evaluation of 441 biomedical journals articles published in 2000-2014, the biomedical literature largely lacked transparency in important dimensions.  ...  practices across the biomedical literature and to make features related to reproducibility more readily visible in PubMed.  ...  biomedical literature.  ... 
doi:10.1371/journal.pbio.2006930 pmid:30457984 pmcid:PMC6245499 fatcat:eptiiv3ctrg2heo4oauyjmqyye

SimText: A text mining framework for interactive analysis and visualization of similarities among biomedical entities

Marie Macnee, Eduardo Pérez-Palma, Sarah Schumacher-Bass, Jarrod Dalton, Costin Leu, Daniel Blankenberg, Dennis Lal, Jonathan Wren
2021 Bioinformatics  
Literature exploration in PubMed on a large number of biomedical entities (e.g., genes, diseases or experiments) can be time-consuming and challenging, especially when assessing associations between entities  ...  techniques in an interactive app.  ...  A literature search shows that SimText can help to identify similar genes beyond clinical phenotype grouping as both genes share similarities in biology: KCNQ4, as well as KCNB1 encode potassium channels  ... 
doi:10.1093/bioinformatics/btab365 pmid:34037702 fatcat:h54e2umkarfx5e2f2ge74svpca

Linked Open Data in the Biomedical Information Area: A Keywords Analysis

Stefano Bonacina
2019 Studies in Health Technology and Informatics  
The objective of this paper was to determine the extent of the usage of "Linked Open Data" within biomedical literature.  ...  Applying PRISMA statement for literature reviews, forty-six papers were included in the analysis and keywords identified. Keywords have been classified according to MeSH categories, when possible.  ...  Applying the PRISMA statement for literature reviews, fortysix papers have been included in the analysis and their keywords identified.  ... 
doi:10.3233/shti190468 pmid:31438165 fatcat:orfirtiavneazphmo7cg7gru6u

DiiS: A Biomedical Data Access Framework for Aiding Data Driven Research Supporting FAIR Principles

Priya Deshpande, Alexander Rasin, Jacob Furst, Daniela Raicu, Sameer Antani
2019 Data  
Our research work describes the challenges inhibiting data producers, data stewards, and data brokers in achieving FAIR goals for sharing biomedical data.  ...  Vast amounts of clinical and biomedical research data are produced daily.  ...  To develop this architecture, we first performed an extensive literature survey that identified the need for biomedical data integration, existing systems that address integration problems, and limitations  ... 
doi:10.3390/data4020054 fatcat:qnx7ahj2yvbc5ccuu66asiko54

Towards mature use of semantic resources for biomedical analyses

D Rebholz-Schuhmann, F Rinaldi, S Pyysalo, N Collier, U Hahn
2011 Journal of Biomedical Semantics  
Combining semantic resources with biomedical data analysis is developing into a dedicated research domain and stimulates related research in biomedical research fields.  ...  BioNLP shared tasks [1] [2] [3] .  ...  Combining semantic resources with biomedical data analysis is developing into a dedicated research domain and stimulates related research in biomedical research fields.  ... 
doi:10.1186/2041-1480-2-s5-i1 pmid:22166304 pmcid:PMC3239298 fatcat:gyyjdxtguzdd5cnlzdqzu3kqii

A framework for assessing clinical trial informatics systems: case of caBIG and its clinical trial management system

Katherine Kosman, Amir Talaei Khoei, Amir Hossein Ghapanchi, Pradeep Ray
2012 International Journal of Computers in Healthcare  
Finally, this article presents 5 important gaps in the literature and calls for future research to fill those gaps.  ...  In particular, we will focus on those articles that have worked on a special type of CTIS called the Cancer Biomedical Informatics Grid (caBIG), developed by the National Cancer Institute, and its Clinical  ...  Gaps Identified in the Literature This paper conducted a systematic literature review and through analyzing the 67 extracted studies from 2001-2011, classified the literature into the 3 broad categories  ... 
doi:10.1504/ijcih.2012.046982 fatcat:c53sykpkdjg5pcqdulkpk7gp2q

Realizing the Promise of a Digital Ecosystem for Science and Scholarship

Michael Huerta, PhD
2017 Merrill Series on The Research Mission of Public Universities  
For example, in the former data are not shared, while the latter depends upon sharing data (and other DROs).  ...  and medical literature digitally, in a database system called MEDLARS.  ... 
doi:10.17161/merrill.2017.7745 fatcat:qmcktfj54jed7cxanbzd56kjbi
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