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The NCI Thesaurus quality assurance life cycle

Sherri de Coronado, Lawrence W. Wright, Gilberto Fragoso, Margaret W. Haber, Elizabeth A. Hahn-Dantona, Francis W. Hartel, Sharon L. Quan, Tracy Safran, Nicole Thomas, Lori Whiteman
2009 Journal of Biomedical Informatics  
The National Cancer Institute Enterprise Vocabulary Services (NCI EVS) uses a wide range of quality assurance (QA) techniques to maintain and extend NCI Thesaurus (NCIt).  ...  Both automated and manual QA techniques are employed throughout the editing and publication cycle, which includes inserting and editing NCIt in NCI Metathesaurus.  ...  after selecting NCI Thesaurus.  ... 
doi:10.1016/j.jbi.2009.01.003 pmid:19475726 fatcat:7c2zca6jrfby5jwsw2it3qt35u

A quality improvement model for healthcare terminologies

Tae Youn Kim, Amy Coenen, Nicholas Hardiker
2010 Journal of Biomedical Informatics  
The TQI model, adapted from Donabedian's approach, encompasses structure, process, and outcome components in relation to a terminology life cycle -change request, editing, and publication.  ...  The TQI model represented the complexity of activities involved in terminology quality management.  ...  Similarly, the National Cancer Institute (NCI) established a set of review criteria in the areas of terminology content, structure, editorial process, and documentation for NCI Thesaurus (NCIt) [20, 21  ... 
doi:10.1016/j.jbi.2010.08.006 pmid:20723616 fatcat:2hmxx4yox5eqvogzwqh2q7j3fe

National Center for Biomedical Ontology [chapter]

Mark A. Musen
2013 Encyclopedia of Systems Biology  
insights from this research to the practice of medicine.  ...  In biomedicine, one of the most fruitful approaches has been to use software tools and knowledge resources known as ontologies-machineprocessable descriptions of scientific domains-that can promote the  ...  terms in the National Cancer Institute (NCI) Thesaurus.  ... 
doi:10.1007/978-1-4419-9863-7_1515 fatcat:3fb7uzhelvgdzlcbmuaekggtyu

2022 AHA/ACC Key Data Elements and Definitions for Cardiovascular and Noncardiovascular Complications of COVID-19: A Report of the American College of Cardiology/American Heart Association Task Force on Clinical Data Standards

Biykem Bozkurt, Sandeep R. Das, Daniel Addison, Aakriti Gupta, Hani Jneid, Sadiya S. Khan, George Augustine Koromia, Prathit A. Kulkarni, Kathleen LaPoint, Eldrin F. Lewis, Erin D. Michos, Pamela N. Peterson (+3 others)
2022 Circulation. Cardiovascular Quality and Outcomes  
NCI Thesaurus Code: C62087 63 PR interval The time interval between the start of the P-wave and the beginning of the QRS complex in the cardiac cycle NCI Thesaurus Code: C83502 63 QTc interval The time  ...  NCI Thesaurus Code: C95802 63 Hypoxic ischemic encephalopathy Injury to the central nervous system that occurs when there is insufficient delivery of oxygen to all or part of the brain NCI Thesaurus Code  ...  artery • Numeric, mm Hg NCI Thesaurus Code: C129958 63 PA systolic pressure The blood pressure in the pulmonary artery during the contraction of the left ventricle of the heart • Numeric, mm Hg NCI  ... 
doi:10.1161/hcq.0000000000000111 pmid:35737748 pmcid:PMC9297692 fatcat:uywjw42zmjcqrkso3x53czgvxe

Methods in biomedical ontology

Alexander C. Yu
2006 Journal of Biomedical Informatics  
At the same time, it has become apparent that the challenges of properly constructing and maintaining ontologies have proven more difficult than many workers in the field initially expected.  ...  Research on ontologies is becoming widespread in the biomedical informatics community.  ...  Acknowledgments The author thanks James Cimino and an anonymous reviewer for their valuable feedback.  ... 
doi:10.1016/j.jbi.2005.11.006 pmid:16387553 fatcat:lejoszoldnhupo7irv6f6c2q5i

FEDRR: fast, exhaustive detection of redundant hierarchical relations for quality improvement of large biomedical ontologies

Guangming Xing, Guo-Qiang Zhang, Licong Cui
2016 BioData Mining  
Each redundant relation represents a possibly unintended defect that needs to be corrected in the ontology quality assurance process.  ...  Results: This paper introduces a novel and scalable approach, called FEDRR -Fast, Exhaustive Detection of Redundant Relations -for quality assurance work during ontological evolution.  ...  The content is solely the responsibility of the authors and does not necessarily represent the official views of the NIH.  ... 
doi:10.1186/s13040-016-0110-8 pmid:27777627 pmcid:PMC5057496 fatcat:g2hhrbmubjbvho72biedanmnle

Auditing as Part of the Terminology Design Life Cycle

H. Min, Y. Perl, Y. Chen, M. Halper, J. Geller, Y. Wang
2006 JAMIA Journal of the American Medical Informatics Association  
Results: A sample of the area taxonomy and p-area taxonomy for the Biological Process (BP) hierarchy of the National Cancer Institute Thesaurus (NCIT) was derived from the application of our methodology  ...  Techniques have been developed for finding cycles, 20 reverse hierarchical relationships, 21 concept redundancy and ambiguity, 22 and redundant categorization. 23 The UMLS Semantic Network (SN) 24 was  ...  Typically, software life cycle models list auditing as part of quality assurance, one of the support activities. 4 It is normally assumed that a software quality assurance audit is performed by a team  ... 
doi:10.1197/jamia.m2036 pmid:16929044 pmcid:PMC1656963 fatcat:rnbjumgbxzfsphfvxmtkn46qq4

AACR-FDA-NCI Cancer Biomarkers Collaborative Consensus Report: Advancing the Use of Biomarkers in Cancer Drug Development

S. N. Khleif, J. H. Doroshow, W. N. Hait
2010 Clinical Cancer Research  
biomarkers into the cancer drug development enterprise, and to set in motion the necessary action plans and collaborations to see the promise of biomarkers come to fruition, efficiently delivering quality  ...  In 2007, the AACR-FDA-NCI Cancer Biomarkers Collaborative stepped into the national effort to bring together disparate stakeholders to clearly delineate these barriers, to develop recommendations for integrating  ...  AACR-FDA-NCI Cancer Biomarkers Collaborative  ... 
doi:10.1158/1078-0432.ccr-10-0880 pmid:20501613 fatcat:fgyhoaghtbf2vi6m2cbqesezua

Using the CER Hub to ensure data quality in a multi-institution smoking cessation study

Kari L Walker, Olga Kirillova, Suzanne E Gillespie, David Hsiao, Valentyna Pishchalenko, Akshatha Kalsanka Pai, Jon E Puro, Robert Plumley, Rustam Kudyakov, Weiming Hu, Art Allisany, MaryAnn McBurnie (+2 others)
2014 JAMIA Journal of the American Medical Informatics Association  
To ensure uniformity of data derived from different EHR systems and implementations, the CER Hub informatics platform developed a quality assurance (QA) process using tools and data formats available through  ...  The tool, deployed to each study site, generated error reports indicating data problems to be fixed locally and aggregate data sharable with the central site for quality review.  ...  (1) validation of values in individual fields, (2) validation of relationships between data entities (including fields, records, datasets), (3) validation of time represented by data entities, (4) life-cycle  ... 
doi:10.1136/amiajnl-2013-002629 pmid:24993545 pmcid:PMC4215049 fatcat:hwlo5ijhzzaynpu5zdonmvbml4

The words of prevention, part I: changing the model

Marc Jamoulle, Enrique Gavilán, Raquel Vaz Cardoso, María Ana Mariño, Miguel Pizzanelli
2015 Revista Brasileira de Medicina de Família e Comunidade  
Latin-American and Caribbean Center on Health Sciences Information of the Pan American Health Organization in São Paulo, for their kind remark and help.  ...  thanks to Niels Bentzen, emeritus professor of general practice in Trondheim, Norway and Wonca International Classification Committee past chair; and to Arthur Treuherz, chief terminologist at BIREME, the  ...  (From World Organization of National Colleges, Academies and Academic Associations of General Practitioners/Family Physicians WONCA. 35 Debriefing, quality assurance, and improvement processes, which  ... 
doi:10.5712/rbmfc10(35)1062 fatcat:ldyf5a47xfdnho6jchmjyw2wo4

Complex overlapping concepts: An effective auditing methodology for families of similarly structured BioPortal ontologies

Ling Zheng, Yan Chen, Gai Elhanan, Yehoshua Perl, James Geller, Christopher Ochs
2018 Journal of Biomedical Informatics  
We demonstrate quality assurance results for both of them. Furthermore, in this paper we observe two novel, important, and useful phenomena during quality assurance of "overlapping concepts."  ...  The fifth ontology is the Neoplasm subhierarchy of the National Cancer Institute thesaurus (NCIt). The sixth ontology is the Infectious Disease subhierarchy of SNOMED CT.  ...  The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.  ... 
doi:10.1016/j.jbi.2018.05.015 pmid:29852316 pmcid:PMC6609446 fatcat:itsh3cctojhgdovevm7xtpqcie

Outlier concepts auditing methodology for a large family of biomedical ontologies

Ling Zheng, Hua Min, Yan Chen, Vipina Keloth, James Geller, Yehoshua Perl, George Hripcsak
2020 BMC Medical Informatics and Decision Making  
To improve the Quality Assurance (QA) scalability, a family-based QA framework, where one QA technique is potentially applicable to a whole family of ontologies with similar structural features, was developed  ...  Together with the four previous ontologies from the same family, we fulfilled the "six out of six" condition required to show the scalability for the whole family.  ...  Discussion Quality assurance of ontologies is an essential part of their life cycle [37] . Various techniques have been introduced to help with the auditing of ontologies.  ... 
doi:10.1186/s12911-020-01311-x pmid:33319713 pmcid:PMC7737254 fatcat:7h45cquf4ngd7fh7n7ipxrlfhy

Data Lakes, Clouds and Commons: A Review of Platforms for Analyzing and Sharing Genomic Data [article]

Robert L. Grossman
2018 arXiv   pre-print
Data lakes provide an alternative to data commons and simply provide access to data, with the data curation and analysis deferred until later and delegated to those that access the data.  ...  It can be quite labor intensive to curate, import and analyze the data in a data commons.  ...  Figure 2 . 2 Data commons support the entire life cycle of data, including defining the data model, importing data, cleaning data, exploring data, analyzing data, and then sharing new research discoveries  ... 
arXiv:1809.01699v2 fatcat:wh2jq5nlenbapppiuthdxerccm

Desiderata for domain reference ontologies in biomedicine

Anita Burgun
2006 Journal of Biomedical Informatics  
The purpose of this paper is to explore how two domain reference ontologies-the FMA and the Chemical Entities of Biological Interest (ChEBI) ontology, can be used (i) to align existing terminologies, (  ...  Domain reference ontologies represent knowledge about a particular part of the world in a way that is independent from specific objectives, through a theory of the domain.  ...  Acknowledgment The author thanks Olivier Bodenreider and Olivier Dameron for providing valuable insight.  ... 
doi:10.1016/j.jbi.2005.09.002 pmid:16266830 fatcat:rs266b2rh5bo5dvyccqzrgkcrq

Automated Tools for Clinical Research Data Quality Control using NCI Common Data Elements

Cody L Hudson, Umit Topaloglu, Jiang Bian, William Hogan, Thomas Kieber-Emmons
Poor data quality can result in the inefficient use of research data or can even require the repetition of the performed studies, a costly process.  ...  In this work, these tools are built and tested on the open-source LimeSurvey software and research data analyzed and identified to contain various data quality issues captured by the Comprehensive Research  ...  We also would like to thank University of Arkansas at Little Rock Information Quality Graduate Program for their support and guidance.  ... 
pmid:25717402 pmcid:PMC4333694 fatcat:mgs37tuk2bdbhjltnjky6bgt54
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