[ { "key": "VM4Q874R", "version": 4, "library": { "type": "group", "id": 222666, "name": "KUMC Biomedical Informatics", "links": { "alternate": { "href": "https://www.zotero.org/groups/kumc_biomedical_informatics", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/222666/items/VM4Q874R", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/kumc_biomedical_informatics/items/VM4Q874R", "type": "text/html" } }, "meta": { "createdByUser": { "id": 201035, "username": "connolly", "name": "Dan Connolly", "links": { "alternate": { "href": "https://www.zotero.org/connolly", "type": "text/html" } } }, "creatorSummary": "Stead et al.", "parsedDate": "1982-11-02", "numChildren": 2 }, "data": { "key": "VM4Q874R", "version": 4, "itemType": "journalArticle", "title": "A Chartless Record--Is It Adequate?", "creators": [ { "creatorType": "author", "firstName": "W.W.", "lastName": "Stead" }, { "creatorType": "author", "firstName": "W.E.", "lastName": "Hammond" }, { "creatorType": "author", "firstName": "M.J.", "lastName": "Straube" } ], "abstractNote": "The computerized medical record supported by The Medical Record (TMR) has been the only record of physician patient encounters on the nephrology service of the Durham Veteran's Administration Medical Center since April 1981. Physicians using the system evaluated the adequacy of the computerized record as a replacement for the paper chart. The computerized record was able to capture and display all pertinent data. Manual or computerized narratives provided a useful supplement to the core computerized record only in those rare instances that a physician needed to point out which of the data in the record were important to his decision making.", "publicationTitle": "Proceedings of the Annual Symposium on Computer Application in Medical Care", "publisher": "", "place": "", "date": "1982-11-02", "volume": "", "issue": "", "section": "", "partNumber": "", "partTitle": "", "pages": "89-94", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Proc Annu Symp Comput Appl Med Care", "DOI": "", "citationKey": "", "url": "http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2580254/", "accessDate": "2013-10-10T21:31:46Z", "PMID": "null", "PMCID": "PMC2580254", "ISSN": "0195-4210", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "PubMed Central", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [ "RXTSMPC8" ], "relations": {}, "dateAdded": "2013-10-10T21:59:42Z", "dateModified": "2013-10-10T21:59:42Z" } }, { "key": "57RUSTMA", "version": 4, "library": { "type": "group", "id": 222666, "name": "KUMC Biomedical Informatics", "links": { "alternate": { "href": "https://www.zotero.org/groups/kumc_biomedical_informatics", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/222666/items/57RUSTMA", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/kumc_biomedical_informatics/items/57RUSTMA", "type": "text/html" } }, "meta": { "createdByUser": { "id": 201035, "username": "connolly", "name": "Dan Connolly", "links": { "alternate": { "href": "https://www.zotero.org/connolly", "type": "text/html" } } }, "creatorSummary": "Dinu et al.", "parsedDate": "2006-04", "numChildren": 1 }, "data": { "key": "57RUSTMA", "version": 4, "itemType": "journalArticle", "title": "Pivoting approaches for bulk extraction of Entity-Attribute-Value data", "creators": [ { "creatorType": "author", "firstName": "Valentin", "lastName": "Dinu" }, { "creatorType": "author", "firstName": "Prakash", "lastName": "Nadkarni" }, { "creatorType": "author", "firstName": "Cynthia", "lastName": "Brandt" } ], "abstractNote": "Entity-Attribute-Value (EAV) data, as present in repositories of clinical patient data, must be transformed (pivoted) into one-column-per-parameter format before it can be used by a variety of analytical programs. Pivoting approaches have not been described in depth in the literature, and existing descriptions are dated. We describe and benchmark three alternative algorithms to perform pivoting of clinical data in the context of a clinical study data management system. We conclude that when the number of attributes to be returned is not too large, it is feasible to use static SQL as the basis for views on the data. An alternative but more complex approach that utilizes hash tables and the presence of abundant random-access-memory can achieve improved performance by reducing the load on the database server.", "publicationTitle": "Computer methods and programs in biomedicine", "publisher": "", "place": "", "date": "Apr 2006", "volume": "82", "issue": "1", "section": "", "partNumber": "", "partTitle": "", "pages": "38-43", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Comput Methods Programs Biomed", "DOI": "10.1016/j.cmpb.2006.02.001", "citationKey": "", "url": "", "accessDate": "", "PMID": "16556470", "PMCID": "", "ISSN": "0169-2607", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "eng", "libraryCatalog": "NCBI PubMed", "callNumber": "", "rights": "", "extra": "", "tags": [ { "tag": "Algorithms", "type": 1 }, { "tag": "Automatic Data Processing", "type": 1 }, { "tag": "Clinical Trials as Topic", "type": 1 }, { "tag": "Humans", "type": 1 }, { "tag": "Medical Informatics Applications", "type": 1 }, { "tag": "Medical Records", "type": 1 }, { "tag": "Software", "type": 1 }, { "tag": "United States", "type": 1 } ], "collections": [ "RXTSMPC8" ], "relations": {}, "dateAdded": "2013-10-10T21:59:42Z", "dateModified": "2013-10-10T21:59:42Z" } }, { "key": "XUCXG98E", "version": 4, "library": { "type": "group", "id": 222666, "name": "KUMC Biomedical Informatics", "links": { "alternate": { "href": "https://www.zotero.org/groups/kumc_biomedical_informatics", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/222666/items/XUCXG98E", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/kumc_biomedical_informatics/items/XUCXG98E", "type": "text/html" } }, "meta": { "createdByUser": { "id": 201035, "username": "connolly", "name": "Dan Connolly", "links": { "alternate": { "href": "https://www.zotero.org/connolly", "type": "text/html" } } }, "creatorSummary": "Waitman et al.", "parsedDate": "2011", "numChildren": 2 }, "data": { "key": "XUCXG98E", "version": 4, "itemType": "journalArticle", "title": "Expressing Observations from Electronic Medical Record Flowsheets in an i2b2 based Clinical Data Repository to Support Research and Quality Improvement", "creators": [ { "creatorType": "author", "firstName": "Lemuel R.", "lastName": "Waitman" }, { "creatorType": "author", "firstName": "Judith J.", "lastName": "Warren" }, { "creatorType": "author", "firstName": "E. LaVerne", "lastName": "Manos" }, { "creatorType": "author", "firstName": "Daniel W.", "lastName": "Connolly" } ], "abstractNote": "While nursing documentation in electronic medical record (EMR) flowsheets may represent the largest investment of clinician time with information systems, organizations lack tools to visualize and repurpose this data for research and quality improvement. Incorporating flowsheet documentation into a clinical data repository and methods to reduce the flowsheet ontology’s redundancy are described. 411 million flowsheet observations, derived from an EMR predominantly used in inpatient, outpatient oncology, and emergency room settings, were incorporated into a repository using the i2b2 framework. The local flowsheet ontology contained 720 “templates” employing 5,379 groups (2,678 distinct), 37,836 measures (13,659 distinct) containing 226,666 choices for a total size of 270,641. Aggressive pruning and clustering resulted in 150 templates, 743 groups (615 distinct), 6,950 measures (4,066 distinct) with 22,497 choices, and size of 30,371. Making nursing data accessible within i2b2 provides a new perspective for contributing clinical organizations and heightens collaboration between the academic and clinical activities.", "publicationTitle": "AMIA Annual Symposium Proceedings", "publisher": "", "place": "", "date": "2011", "volume": "2011", "issue": "", "section": "", "partNumber": "", "partTitle": "", "pages": "1454-1463", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "AMIA Annu Symp Proc", "DOI": "", "citationKey": "", "url": "http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3243191/", "accessDate": "2013-08-09T00:28:36Z", "PMID": "22195209", "PMCID": "PMC3243191", "ISSN": "1942-597X", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "PubMed Central", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [ "RXTSMPC8" ], "relations": {}, "dateAdded": "2013-10-10T21:59:42Z", "dateModified": "2013-10-10T21:59:42Z" } }, { "key": "I2A8385F", "version": 4, "library": { "type": "group", "id": 222666, "name": "KUMC Biomedical Informatics", "links": { "alternate": { "href": "https://www.zotero.org/groups/kumc_biomedical_informatics", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/222666/items/I2A8385F", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/kumc_biomedical_informatics/items/I2A8385F", "type": "text/html" } }, "meta": { "createdByUser": { "id": 201035, "username": "connolly", "name": "Dan Connolly", "links": { "alternate": { "href": "https://www.zotero.org/connolly", "type": "text/html" } } }, "creatorSummary": "Foulkes et al.", "parsedDate": "2010-11-11", "numChildren": 1 }, "data": { "key": "I2A8385F", "version": 4, "itemType": "journalArticle", "title": "Triple-negative breast cancer", "creators": [ { "creatorType": "author", "firstName": "William D", "lastName": "Foulkes" }, { "creatorType": "author", "firstName": "Ian E", "lastName": "Smith" }, { "creatorType": "author", "firstName": "Jorge S", "lastName": "Reis-Filho" } ], "abstractNote": "Triple-negative breast cancer, so called because it lacks expression of the estrogen receptor, progesterone receptor, and HER2, is often, but not always, a basal-like breast cancer. This review focuses on its origin, molecular and clinical characteristics, and treatment.", "publicationTitle": "The New England journal of medicine", "publisher": "", "place": "", "date": "Nov 11, 2010", "volume": "363", "issue": "20", "section": "", "partNumber": "", "partTitle": "", "pages": "1938-1948", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "N. Engl. J. Med.", "DOI": "10.1056/NEJMra1001389", "citationKey": "", "url": "", "accessDate": "", "PMID": "21067385", "PMCID": "", "ISSN": "1533-4406", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "eng", "libraryCatalog": "NCBI PubMed", "callNumber": "", "rights": "", "extra": "", "tags": [ { "tag": "Antineoplastic Agents", "type": 1 }, { "tag": "Breast Neoplasms", "type": 1 }, { "tag": "Female", "type": 1 }, { "tag": "Genes, BRCA1", "type": 1 }, { "tag": "Humans", "type": 1 }, { "tag": "Mutation", "type": 1 }, { "tag": "Prognosis", "type": 1 }, { "tag": "Receptor, erbB-2", "type": 1 }, { "tag": "Receptors, Estrogen", "type": 1 }, { "tag": "Receptors, Progesterone", "type": 1 }, { "tag": "Survival Rate", "type": 1 } ], "collections": [ "RXTSMPC8" ], "relations": {}, "dateAdded": "2013-10-10T21:59:42Z", "dateModified": "2013-10-10T21:59:42Z" } }, { "key": "E5GZKXZ4", "version": 4, "library": { "type": "group", "id": 222666, "name": "KUMC Biomedical Informatics", "links": { "alternate": { "href": "https://www.zotero.org/groups/kumc_biomedical_informatics", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/222666/items/E5GZKXZ4", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/kumc_biomedical_informatics/items/E5GZKXZ4", "type": "text/html" } }, "meta": { "createdByUser": { "id": 201035, "username": "connolly", "name": "Dan Connolly", "links": { "alternate": { "href": "https://www.zotero.org/connolly", "type": "text/html" } } }, "creatorSummary": "Kennedy and Craig", "parsedDate": "2004", "numChildren": 1 }, "data": { "key": "E5GZKXZ4", "version": 4, "itemType": "journalArticle", "title": "Global registries for measuring pharmacoeconomic and quality-of-life outcomes: focus on design and data collection, analysis and interpretation", "creators": [ { "creatorType": "author", "firstName": "Lisa", "lastName": "Kennedy" }, { "creatorType": "author", "firstName": "Ann-Marie", "lastName": "Craig" } ], "abstractNote": "Disease registries have traditionally been vehicles for the collection of clinical data, in most instances following a large number of patients for a long time period in an observational manner, and enhancing our understanding of disease aetiology and epidemiology. However, over recent decades, the potential for additional data collection and analyses to be conducted within the framework of a registry has been recognised and utilised. This is evident by the sheer number of registries that are now referenced in the medical literature, covering a vast array of therapeutic areas and topics much more varied than incidence, prevalence and survival. The opportunity to collect QOL and pharmacoeconomic data has been utilised within the registry framework as more and more countries have increased their demands for such information for regulatory procedures, including pricing and reimbursement decisions. This increased need for information has led to a marked increase in the number of registries undertaken that are primarily sponsored by the pharmaceutical industry. Disease registries offer tremendous opportunities to realise improvements in care. The length of data collection and the large number of patients involved offer some unusual advantages for QOL and health economic analyses; however, these advantages are not yet fully exploited.", "publicationTitle": "PharmacoEconomics", "publisher": "", "place": "", "date": "2004", "volume": "22", "issue": "9", "section": "", "partNumber": "", "partTitle": "", "pages": "551-568", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Pharmacoeconomics", "DOI": "", "citationKey": "", "url": "", "accessDate": "", "PMID": "15209525", "PMCID": "", "ISSN": "1170-7690", "archive": "", "archiveLocation": "", "shortTitle": "Global registries for measuring pharmacoeconomic and quality-of-life outcomes", "language": "eng", "libraryCatalog": "NCBI PubMed", "callNumber": "", "rights": "", "extra": "", "tags": [ { "tag": "Data Collection", "type": 1 }, { "tag": "Data Interpretation, Statistical", "type": 1 }, { "tag": "Drug Therapy", "type": 1 }, { "tag": "Humans", "type": 1 }, { "tag": "Outcome Assessment (Health Care)", "type": 1 }, { "tag": "Quality of Life", "type": 1 }, { "tag": "Registries", "type": 1 }, { "tag": "Research Design", "type": 1 }, { "tag": "World Health", "type": 1 } ], "collections": [ "RXTSMPC8" ], "relations": {}, "dateAdded": "2013-10-10T21:59:42Z", "dateModified": "2013-10-10T21:59:42Z" } }, { "key": "9S54B9RB", "version": 4, "library": { "type": "group", "id": 222666, "name": "KUMC Biomedical Informatics", "links": { "alternate": { "href": "https://www.zotero.org/groups/kumc_biomedical_informatics", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/222666/items/9S54B9RB", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/kumc_biomedical_informatics/items/9S54B9RB", "type": "text/html" } }, "meta": { "createdByUser": { "id": 201035, "username": "connolly", "name": "Dan Connolly", "links": { "alternate": { "href": "https://www.zotero.org/connolly", "type": "text/html" } } }, "creatorSummary": "Harris et al.", "parsedDate": "2009-04", "numChildren": 1 }, "data": { "key": "9S54B9RB", "version": 4, "itemType": "journalArticle", "title": "Research electronic data capture (REDCap)--a metadata-driven methodology and workflow process for providing translational research informatics support", "creators": [ { "creatorType": "author", "firstName": "Paul A", "lastName": "Harris" }, { "creatorType": "author", "firstName": "Robert", "lastName": "Taylor" }, { "creatorType": "author", "firstName": "Robert", "lastName": "Thielke" }, { "creatorType": "author", "firstName": "Jonathon", "lastName": "Payne" }, { "creatorType": "author", "firstName": "Nathaniel", "lastName": "Gonzalez" }, { "creatorType": "author", "firstName": "Jose G", "lastName": "Conde" } ], "abstractNote": "Research electronic data capture (REDCap) is a novel workflow methodology and software solution designed for rapid development and deployment of electronic data capture tools to support clinical and translational research. We present: (1) a brief description of the REDCap metadata-driven software toolset; (2) detail concerning the capture and use of study-related metadata from scientific research teams; (3) measures of impact for REDCap; (4) details concerning a consortium network of domestic and international institutions collaborating on the project; and (5) strengths and limitations of the REDCap system. REDCap is currently supporting 286 translational research projects in a growing collaborative network including 27 active partner institutions.", "publicationTitle": "Journal of biomedical informatics", "publisher": "", "place": "", "date": "Apr 2009", "volume": "42", "issue": "2", "section": "", "partNumber": "", "partTitle": "", "pages": "377-381", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "J Biomed Inform", "DOI": "10.1016/j.jbi.2008.08.010", "citationKey": "", "url": "", "accessDate": "", "PMID": "18929686", "PMCID": "", "ISSN": "1532-0480", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "eng", "libraryCatalog": "NCBI PubMed", "callNumber": "", "rights": "", "extra": "", "tags": [ { "tag": "Biomedical Research", "type": 1 }, { "tag": "Clinical Trials as Topic", "type": 1 }, { "tag": "Data Collection", "type": 1 }, { "tag": "Humans", "type": 1 }, { "tag": "Internet", "type": 1 }, { "tag": "Medical Informatics", "type": 1 }, { "tag": "Software", "type": 1 } ], "collections": [ "RXTSMPC8" ], "relations": {}, "dateAdded": "2013-10-10T21:59:42Z", "dateModified": "2013-10-10T21:59:42Z" } }, { "key": "Q5842WNM", "version": 4, "library": { "type": "group", "id": 222666, "name": "KUMC Biomedical Informatics", "links": { "alternate": { "href": "https://www.zotero.org/groups/kumc_biomedical_informatics", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/222666/items/Q5842WNM", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/kumc_biomedical_informatics/items/Q5842WNM", "type": "text/html" } }, "meta": { "createdByUser": { "id": 201035, "username": "connolly", "name": "Dan Connolly", "links": { "alternate": { "href": "https://www.zotero.org/connolly", "type": "text/html" } } }, "creatorSummary": "Murphy et al.", "parsedDate": "2010-03-01", "numChildren": 3 }, "data": { "key": "Q5842WNM", "version": 4, "itemType": "journalArticle", "title": "Serving the enterprise and beyond with informatics for integrating biology and the bedside (i2b2)", "creators": [ { "creatorType": "author", "firstName": "Shawn N.", "lastName": "Murphy" }, { "creatorType": "author", "firstName": "Griffin", "lastName": "Weber" }, { "creatorType": "author", "firstName": "Michael", "lastName": "Mendis" }, { "creatorType": "author", "firstName": "Vivian", "lastName": "Gainer" }, { "creatorType": "author", "firstName": "Henry C.", "lastName": "Chueh" }, { "creatorType": "author", "firstName": "Susanne", "lastName": "Churchill" }, { "creatorType": "author", "firstName": "Isaac", "lastName": "Kohane" } ], "abstractNote": "Informatics for Integrating Biology and the Bedside (i2b2) is one of seven projects sponsored by the NIH Roadmap National Centers for Biomedical Computing (http://www.ncbcs.org). Its mission is to provide clinical investigators with the tools necessary to integrate medical record and clinical research data in the genomics age, a software suite to construct and integrate the modern clinical research chart. i2b2 software may be used by an enterprise's research community to find sets of interesting patients from electronic patient medical record data, while preserving patient privacy through a query tool interface. Project-specific mini-databases (“data marts”) can be created from these sets to make highly detailed data available on these specific patients to the investigators on the i2b2 platform, as reviewed and restricted by the Institutional Review Board. 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