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Auditing the UMLS for redundant classifications. 审核UMLS是否存在冗余分类。
Proceedings. AMIA Symposium Pub Date : 2002-01-01
Yi Peng, Michael H Halper, Yehoshua Perl, James Geller
{"title":"Auditing the UMLS for redundant classifications.","authors":"Yi Peng,&nbsp;Michael H Halper,&nbsp;Yehoshua Perl,&nbsp;James Geller","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>The UMLS's Semantic Network (SN) serves as a valuable abstraction for the underlying concept repository called the Metathesaurus (META). Specifically, the SN forms a classification layer for the META, with each of the META's constituent concepts assigned to one or more semantic types in the SN. The rule in the design of the SN is to have concepts explicitly assigned to the lowest possible semantic types in the SN's IS-A hierarchy. Implicit assignment to higher semantic types can be inferred via the IS-A relationships. However, in subsequent versions of the UMLS, unnecessary, simultaneous assignments to descendant and ancestor semantic types have been discovered (e.g., 8,622 in the UMLS 1998 version and 12,657 in the 2001 version). The assignment of concepts to such ancestor semantic types is called redundant classification. There is a need for an automated auditing tool that can identify all these redundant classifications. In this paper, an efficient algorithm for this auditing task is introduced. Details of its application to the current (2001) version of the UMLS are presented and the results are discussed.</p>","PeriodicalId":79712,"journal":{"name":"Proceedings. AMIA Symposium","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2002-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2244162/pdf/procamiasymp00001-0653.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"22139849","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Using medication list--problem list mismatches as markers of potential error. 使用药物列表-问题列表不匹配作为潜在错误的标记。
Proceedings. AMIA Symposium Pub Date : 2002-01-01
James D Carpenter, Paul N Gorman
{"title":"Using medication list--problem list mismatches as markers of potential error.","authors":"James D Carpenter,&nbsp;Paul N Gorman","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>The goal of this project was to specify and develop an algorithm that will check for drug and problem list mismatches in an electronic medical record (EMR). The algorithm is based on the premise that a patient's problem list and medication list should agree, and a mismatch may indicate medication error. Successful development of this algorithm could mean detection of some errors, such as medication orders entered into a wrong patient record, or drug therapy omissions, that are not otherwise detected via automated means. Additionally, mismatches may identify opportunities to improve problem list integrity. To assess the concept's feasibility, this study compared medications listed in a pharmacy information system with findings in an online nursing adult admission assessment, serving as a proxy for the problem list. Where drug and problem list mismatches were discovered, examination of the patient record confirmed the mismatch, and identified any potential causes. Evaluation of the algorithm in diabetes treatment indicates that it successfully detects both potential medication error and opportunities to improve problem list completeness. This algorithm, once fully developed and deployed, could prove a valuable way to improve the patient problem list, and could decrease the risk of medication error.</p>","PeriodicalId":79712,"journal":{"name":"Proceedings. AMIA Symposium","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2002-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2244138/pdf/procamiasymp00001-0147.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"22140251","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Usability evaluation of an experimental text summarization system and three search engines: implications for the reengineering of health care interfaces. 实验文本摘要系统和三个搜索引擎的可用性评估:对医疗界面再造的启示。
Proceedings. AMIA Symposium Pub Date : 2002-01-01
Andre W Kushniruk, Min-Yem Kan, Kathleen McKeown, Judith Klavans, Desmond Jordan, Mark LaFlamme, Vimia L Patel
{"title":"Usability evaluation of an experimental text summarization system and three search engines: implications for the reengineering of health care interfaces.","authors":"Andre W Kushniruk,&nbsp;Min-Yem Kan,&nbsp;Kathleen McKeown,&nbsp;Judith Klavans,&nbsp;Desmond Jordan,&nbsp;Mark LaFlamme,&nbsp;Vimia L Patel","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>This paper describes the comparative evaluation of an experimental automated text summarization system, Centrifuser and three conventional search engines - Google, Yahoo and About.com. Centrifuser provides information to patients and families relevant to their questions about specific health conditions. It then produces a multidocument summary of articles retrieved by a standard search engine, tailored to the user's question. Subjects, consisting of friends or family of hospitalized patients, were asked to \"think aloud\" as they interacted with the four systems. The evaluation involved audio- and video recording of subject interactions with the interfaces in situ at a hospital. Results of the evaluation show that subjects found Centrifuser's summarization capability useful and easy to understand. In comparing Centrifuser to the three search engines, subjects' ratings varied; however, specific interface features were deemed useful across interfaces. We conclude with a discussion of the implications for engineering Web-based retrieval systems.</p>","PeriodicalId":79712,"journal":{"name":"Proceedings. AMIA Symposium","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2002-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2244493/pdf/procamiasymp00001-0461.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"22140257","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Improved coding of the primary reason for visit to the emergency department using SNOMED. 改进了使用SNOMED访问急诊科的主要原因的编码。
Proceedings. AMIA Symposium Pub Date : 2002-01-01
James C McClay, James Campbell
{"title":"Improved coding of the primary reason for visit to the emergency department using SNOMED.","authors":"James C McClay,&nbsp;James Campbell","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>There are over 100 million visits to emergency departments in the United States annually that could be a source of data for multiple uses including disease surveillance, health services research, quality assurance activates, and research. The patients' motivations for seeking care or the reason for visit (RFV) are recorded in every case. Efforts to utilize this rich source of data are hampered by inconsistent data entry and coding. This study analyzes ICD-9-CM, SNOMED-RT, and SNOMED-CT encoding of the RFV for accuracy. Each encoded reason for visit was compared to the text entry recorded at the time of visit to determine the closeness of fit. Each coded entry was judged to be an exact lexical match, a synonym, a broader or narrower concept or no match. SNOMED-CT was a lexical match or synonym for 93% of the text entries, while SNOMED-RT matched 87%, and ICD-9-CM matched 40%. We demonstrate that SNOMED coding of the RFV is more accurate than ICD-9-CM coding.</p>","PeriodicalId":79712,"journal":{"name":"Proceedings. AMIA Symposium","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2002-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2244135/pdf/procamiasymp00001-0540.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"22138397","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
The lexical properties of the gene ontology. 基因本体的词法特性。
Proceedings. AMIA Symposium Pub Date : 2002-01-01
Alexa T McCray, Allen C Browne, Olivier Bodenreider
{"title":"The lexical properties of the gene ontology.","authors":"Alexa T McCray,&nbsp;Allen C Browne,&nbsp;Olivier Bodenreider","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>The Gene Ontology (GO) is a construct developed for the purpose of annotating molecular information about genes and their products. The ontology is a shared resource developed by the GO Consortium, a group of scientists who work on a variety of model organisms. In this paper we investigate the nature of the strings found in the Gene Ontology and evaluate them for their usefulness in natural language processing (NLP). We extend previous work that identified a set of properties that reliably identifies natural language phrases in the Unified Medical Language System (UMLS). The results indicate that a large percentage (79%) of GO terms are potentially useful for NLP applications. Some 35% of the GO terms were found in a corpus derived from the MEDLINE bibliographic database, and 27% of the terms were found in the current edition of the UMLS.</p>","PeriodicalId":79712,"journal":{"name":"Proceedings. AMIA Symposium","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2002-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2244431/pdf/procamiasymp00001-0545.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"22138398","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Research for research: tools for knowledge discovery and visualization. 为研究而研究:知识发现和可视化的工具。
Proceedings. AMIA Symposium Pub Date : 2002-01-01
Erik M Van Mulligen, Christiaan Van Der Eijk, Jan A Kors, Bob J A Schijvenaars, Barend Mons
{"title":"Research for research: tools for knowledge discovery and visualization.","authors":"Erik M Van Mulligen,&nbsp;Christiaan Van Der Eijk,&nbsp;Jan A Kors,&nbsp;Bob J A Schijvenaars,&nbsp;Barend Mons","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>This paper describes a method to construct from a set of documents a spatial representation that can be used for information retrieval and knowledge discovery. The proposed method has been implemented in a prototype system and allows the researcher to browse interactively and in real-time a network of relationships obtained from a set of full text articles. These relationships are combined with the potential relationships between concepts as defined in the UMLS semantic network. The browser allows the user to select a seed term and find all related concepts, to find a path between concepts (hypothesis testing), and to retrieve the references to documents or database entries that support the relationship between concepts.</p>","PeriodicalId":79712,"journal":{"name":"Proceedings. AMIA Symposium","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2002-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2244229/pdf/procamiasymp00001-0876.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"22138406","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Relationships among Internet health information use, patient behavior and self efficacy in newly diagnosed cancer patients who contact the National Cancer Institute's NCI Atlantic Region Cancer Information Service (CIS). 接触美国国家癌症研究所大西洋地区癌症信息服务(CIS)的新诊断癌症患者的互联网健康信息使用、患者行为和自我效能之间的关系
Proceedings. AMIA Symposium Pub Date : 2002-01-01
Linda Fleisher, Sarah Bass, Sheryl Burt Ruzek, Nancy McKeown-Conn
{"title":"Relationships among Internet health information use, patient behavior and self efficacy in newly diagnosed cancer patients who contact the National Cancer Institute's NCI Atlantic Region Cancer Information Service (CIS).","authors":"Linda Fleisher,&nbsp;Sarah Bass,&nbsp;Sheryl Burt Ruzek,&nbsp;Nancy McKeown-Conn","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>This NCI funded study examined the relationship between the use of Internet health information by people newly diagnosed with cancer (N=500), with patient task behavior and perceived self efficacy. Study variables were compared among Direct users of Internet health information (people using the Internet themselves), Indirect users of Internet health information (people receiving Internet health information from friends or family members), and Non-users of Internet health information (people not using the Internet or receiving health information from the Internet). The subjects were recruited from persons who called the Atlantic Region of the NCI's Cancer Information Service (CIS), located at Fox Chase Cancer Center in Philadelphia, PA. Follow up phone interviews were done with participants six weeks after initial contact to assess impact of the use of the Internet on perceived patient task behavior and self efficacy. Results show significant relationships between Internet use and all study variables.</p>","PeriodicalId":79712,"journal":{"name":"Proceedings. AMIA Symposium","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2002-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2244151/pdf/procamiasymp00001-0301.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"22138809","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
PQL: a declarative query language over dynamic biological schemata. PQL:基于动态生物模式的声明性查询语言。
Proceedings. AMIA Symposium Pub Date : 2002-01-01
P Mork, R Shaker, A Halevy, P Tarczy-Hornoch
{"title":"PQL: a declarative query language over dynamic biological schemata.","authors":"P Mork,&nbsp;R Shaker,&nbsp;A Halevy,&nbsp;P Tarczy-Hornoch","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>We introduce the PQL query language (PQL) used in the GeneSeek genetic data integration project. PQL incorporates many features of query languages for semi-structured data. To this we add the ability to express metadata constraints like intended semantics and database curation approach. These constraints guide the dynamic generation of potential query plans. This allows a single query to remain relevant even in the presence of source and mediated schemas that are continually evolving, as is often the case in data integration.</p>","PeriodicalId":79712,"journal":{"name":"Proceedings. AMIA Symposium","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2002-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2244486/pdf/procamiasymp00001-0574.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"22138831","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Maximum entropy modeling for mining patient medication status from free text. 从自由文本中挖掘患者用药状态的最大熵模型。
Proceedings. AMIA Symposium Pub Date : 2002-01-01
Serguei V Pakhomov, Alexander Ruggieri, Christopher G Chute
{"title":"Maximum entropy modeling for mining patient medication status from free text.","authors":"Serguei V Pakhomov,&nbsp;Alexander Ruggieri,&nbsp;Christopher G Chute","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Using a classification scheme of patient medication status we sought to recognize and categorize medications mentioned in the unrestricted text of clinical documents generated in clinical practice. The categories refer to the patient's status with respect to the medication such as discontinuation, start or initiation, and continuation of a given medication. This categorization is performed with a machine learning technique, Maximum Entropy (ME), that is well suited to incorporating heterogeneous sources of information necessary for classifying patient's medication status. We use hand labeled training data to generate ME models and test 5 different training feature sets. Our results show that the most optimal feature set includes a combination of the following: two words preceding and following the mention of the drug, the subject of the sentence in which the drug mention occurs, the 2 words following the subject, and a binary feature vector of lexicalized semantic cues indicative of medication status or its change. The average predictive power of a model trained on these features is approximately 89%.</p>","PeriodicalId":79712,"journal":{"name":"Proceedings. AMIA Symposium","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2002-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2244576/pdf/procamiasymp00001-0628.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"22139291","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Using a neural network with flow cytometry histograms to recognize cell surface protein binding patterns. 利用流式细胞术直方图神经网络识别细胞表面蛋白结合模式。
Proceedings. AMIA Symposium Pub Date : 2002-01-01
Eun-Young Kim, Qing Zeng, James Rawn, Matthew Wand, Alan J Young, Edgar Milford, Steven J Mentzer, Robert A Greenes
{"title":"Using a neural network with flow cytometry histograms to recognize cell surface protein binding patterns.","authors":"Eun-Young Kim,&nbsp;Qing Zeng,&nbsp;James Rawn,&nbsp;Matthew Wand,&nbsp;Alan J Young,&nbsp;Edgar Milford,&nbsp;Steven J Mentzer,&nbsp;Robert A Greenes","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Flow cytometric systems are being used increasingly in all branches of biological science including medicine. To develop analytic tools for identifying unknown molecules such as the antibodies that recognize different structure in the identical antigens, we explored use of a neural network in flow cytometry data comparison. Peak locations were extracted from flow cytometry histograms and we used the Marquardt backpropagation neural networks to recognize identical or similar binding patterns between antibodies and antigens based on the peak locations. The neural network showed 93.8% to 99.6% correct classification rates for identical or similar molecules. This suggests that the neural network technique can be useful in flow cytometry histogram data analysis.</p>","PeriodicalId":79712,"journal":{"name":"Proceedings. AMIA Symposium","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2002-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2244407/pdf/procamiasymp00001-0421.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"22139717","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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