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Biomedical subjects

James J Cimino

Publications and source records attributed to James J Cimino.

At least 19 recordsLinked to original sources
PubMed2026

Implementing a Multi-Ancestry Polygenic Risk Score for Coronary Heart Disease in a Diverse Cohort.

PURPOSE: We describe a prospective cohort study (NCT05277116) conducted in phase IV of the electronic MEdical Records and GEnomics (eMERGE) Network to implement a multi-ancestry polygenic risk score for coronary heart disease (PRSCHD: PGS004696) and assess outcomes after return of results (RoR). METHODS: PRSCHD was considered alongside family history (FamHxCHD), monogenic risk from familial hypercholesterolemia (FH), and clinical risk factors, to return CHD risk as part of a Genome Informed Risk Assessment (GIRA) report. Participants with high PRSCHD (top 5th percentile) or FH received their results from study personnel, while participants with FamHxCHD were informed by mail/email. Results were placed in the electronic health record and communicated to the primary care provider. The primary outcome of initiation/intensification of lipid lowering therapy within 12 months after RoR is compared between participants with PRSCHD ≥95th percentile and those with PRSCHD 90th-94th percentile, using a regression discontinuity design. Secondary outcomes include ordering of screening tests, a new CHD diagnosis, and lifestyle changes. RESULTS: By April 2025, 20,421 adults were enrolled: mean age 50±15 years (range 18-75 years), 68% female, 50% belonging to health disparity groups, and 40% non-White by self-report. Prevalence of CHD, FamHxCHD, high PRSCHD and FH was 4.0%, 10.2%, 4.3% and 0.7%, respectively; 14.3% had at least one of the three CHD genetic risk factors and CHD risk estimates were highest in those who self-reported as Black. CONCLUSION: The prevalence of increased genetic risk for CHD was high and at least one of the three genetic risk factors for CHD was present in 14.2% of the cohort. Analyses are underway to assess outcomes after PRSCHD implementation in the context of FamHxCHD, FH, and clinical risk, across the age spectrum in a diverse cohort.

PRS↗
PubMed2007

Analysis of a study of the users, uses, and future agenda of the UMLS.

OBJECTIVES: The UMLS constitutes the largest existing collection of medical terms. However, little has been published about the users and uses of the UMLS. This study sheds light on these issues. DESIGN: We designed a questionnaire consisting of 26 questions and distributed it to the UMLS user mailing list. Participants were assured complete confidentiality of their replies. To further encourage list members to respond, we promised to provide them with early results prior to publication. Sector analysis of the responses, according to employment organizations is used to obtain insights into some responses. RESULTS: We received 70 responses. The study confirms two intended uses of the UMLS: access to source terminologies (75%), and mapping among them (44%). However, most access is just to a few sources, led by SNOMED, MeSH, and ICD. Out of 119 reported purposes of use, terminology research (37), information retrieval (19), and terminology translation (14) lead. Four important observations are that the UMLS is widely used as a terminology (77%), even though it was not designed as one; many users (73%) want the NLM to mark concepts with multiple parents in an indented hierarchy and to derive a terminology from the UMLS (73%). Finally, auditing the UMLS is a top budget priority (35%) for users. CONCLUSIONS: The study reports many uses of the UMLS in a variety of subjects from terminology research to decision support and phenotyping. The study confirms that the UMLS is used to access its source terminologies and to map among them. Two primary concerns of the existing user base are auditing the UMLS and the design of a UMLS-based derived terminology.

Consumer Behavior↗
PubMed2006

Representation of ophthalmology concepts by electronic systems: intercoder agreement among physicians using controlled terminologies.

OBJECTIVE: To assess intercoder agreement for ophthalmology concepts by 3 physician coders using 5 controlled terminologies (International Classification of Diseases 9, Clinical Modification [ICD9CM]; Current Procedural Terminology, fourth edition; Logical Observation Identifiers, Names, and Codes [LOINC]; Systematized Nomenclature of Medicine, Clinical Terms [SNOMED-CT]; and Medical Entities Dictionary). DESIGN: Noncomparative case series. PARTICIPANTS: Five complete ophthalmology case presentations selected from a publicly available journal. METHODS: Each case was parsed into discrete concepts. Electronic or paper browsers were used independently by 3 physician coders to assign a code for every concept in each terminology. A match score representing adequacy of assignment for each concept was assigned on a 3-point scale (0, no match; 1, partial match; 2, complete match). For every concept, the level of intercoder agreement was determined by 2 methods: (1) based on exact code matching with assignment of complete agreement when all coders assigned the same code, partial agreement when 2 coders assigned the same code, and no agreement when all coders assigned different codes, and (2) based on manual review for semantic equivalence of all assigned codes by an independent ophthalmologist to classify intercoder agreement for each concept as complete agreement, partial agreement, or no agreement. Subsequently, intercoder agreement was calculated in the same manner for the subset of concepts judged to have adequate coverage by each terminology, based on receiving a match score of 2 by at least 2 of the 3 coders. MAIN OUTCOME MEASURES: Intercoder agreement in each controlled terminology: complete, partial, or none. RESULTS: Cases were parsed into 242 unique concepts. When all concepts were analyzed by manual review, the proportion of complete intercoder agreement ranged from 12% (LOINC) to 44% (SNOMED-CT), and the difference in intercoder agreement between LOINC and all other terminologies was statistically significant (P<0.004). When only concepts with adequate terminology were analyzed by manual review, the proportion of complete intercoder agreement ranged from 33% (LOINC) to 64% (ICD9CM), and there were no statistically significant differences in intercoder agreement among any pairs of terminologies. CONCLUSIONS: The level of intercoder agreement for ophthalmic concepts in existing controlled medical terminologies is imperfect. Intercoder reproducibility is essential for accurate and consistent electronic representation of medical data.

Decision Support Systems, Clinical↗
PubMed2006

Terminology model discovery using natural language processing and visualization techniques.

Medical terminologies are important for unambiguous encoding and exchange of clinical information. The traditional manual method of developing terminology models is time-consuming and limited in the number of phrases that a human developer can examine. In this paper, we present an automated method for developing medical terminology models based on natural language processing (NLP) and information visualization techniques. Surgical pathology reports were selected as the testing corpus for developing a pathology procedure terminology model. The use of a general NLP processor for the medical domain, MedLEE, provides an automated method for acquiring semantic structures from a free text corpus and sheds light on a new high-throughput method of medical terminology model development. The use of an information visualization technique supports the summarization and visualization of the large quantity of semantic structures generated from medical documents. We believe that a general method based on NLP and information visualization will facilitate the modeling of medical terminologies.

Automation↗
PubMed2006

Requirements specification for automated fall and injury risk assessment.

Fall and injury prevention continues to be a challenge in the acute care environment. Identification of patients at risk can guide preventive care for these individuals. The following study employed usability engineering methods via a series of focus groups, to specify functional and design requirements for an automated Fall-Injury Risk Assessment Instrument. Focus groups were held with interdisciplinary decision makers and end-users to identify functional and design specifications for the automated instrument. The results were mapped to usability heuristics, which were used to guide design decisions. The main elements identified were data completeness, workflow processes, resource access, and cognitive burden. The main usability factors identified were efficiency of user, match with real world, error prevention, recognition not recall and minimalist design. Focus groups are a useful methodology to specify requirements for healthcare applications. Outcomes evaluation of the automated instrument is in process.

Academic Medical Centers↗
PubMed2006

An automated approach to studying health resource and infobutton use.

Many studies have found that clinicians require access to medical knowledge sources while viewing data in their patients' health records. To address this need, we have been developing links to various on-line health information resources from our Web-based clinical information system (WebCIS). Clinicians can access these resources through a "Health Resources" Web page or use context-sensitive "infobuttons" that automatically link to specific resources. To assist in understanding how clinicians interact with these two mechanisms, we have been exploring the use of an automated approach to answer questions about usage for guiding the further development of links to resources. In this paper, we discuss the use of a knowledge discovery technique (CIS Usage Mining) to obtain usage statistics from log files that record interactions with health resources and infobuttons in WebCIS, describe a Web-based interface developed to present the results, and summarize how the results could be applied. The availability of effective links to on-line medical knowledge sources from the patient health record can assist in resolving information needs, potentially improving patient care and decision-making.

Access to Information↗
PubMed2005

In defense of the Desiderata.

A 1998 paper that delineated desirable characteristics, or desiderata for controlled medical terminologies attempted to summarize emerging consensus regarding structural issues of such terminologies. Among the Desiderata was a call for terminologies to be "concept oriented." Since then, research has trended toward the extension of terminologies into ontologies. A paper by Smith, entitled "From Concepts to Clinical Reality: An Essay on the Benchmarking of Biomedical Terminologies" urges a realist approach that seeks terminologies composed of universals, rather than concepts. The current paper addresses issues raised by Smith and attempts to extend the Desiderata, not away from concepts, but towards recognition that concepts and universals must both be embraced and can coexist peaceably in controlled terminologies. To that end, additional Desiderata are defined that deal with the purpose, rather than the structure, of controlled medical terminologies.

Biology↗
PubMed2005

Heuristic evaluation of paper-based Web pages: a simplified inspection usability methodology.

Online medical information, when presented to clinicians, must be well-organized and intuitive to use, so that the clinicians can conduct their daily work efficiently and without error. It is essential to actively seek to produce good user interfaces that are acceptable to the user. This paper describes the methodology used to develop a simplified heuristic evaluation (HE) suitable for the evaluation of screen shots of Web pages, the development of an HE instrument used to conduct the evaluation, and the results of the evaluation of the aforementioned screen shots. In addition, this paper presents examples of the process of categorizing problems identified by the HE and the technological solutions identified to resolve these problems. Four usability experts reviewed 18 paper-based screen shots and made a total of 108 comments. Each expert completed the task in about an hour. We were able to implement solutions to approximately 70% of the violations. Our study found that a heuristic evaluation using paper-based screen shots of a user interface was expeditious, inexpensive, and straightforward to implement.

Computer Graphics↗
PubMed2005

Relationship structures and semantic type assignments of the UMLS Enriched Semantic Network.

OBJECTIVE: The Enriched Semantic Network (ESN) was introduced as an extension of the Unified Medical Language System (UMLS) Semantic Network (SN). Its multiple subsumption configuration and concomitant multiple inheritance make the ESN's relationship structures and semantic type assignments different from those of the SN. A technique for deriving the relationship structures of the ESN's semantic types and an automated technique for deriving the ESN's semantic type assignments from those of the SN are presented. DESIGN: The technique to derive the ESN's relationship structures finds all newly inherited relationships in the ESN. All such relationships are audited for semantic validity, and the blocking mechanism is used to block invalid relationships. The mapping technique to derive the ESN's semantic type assignments uses current SN semantic type assignments and preserves nonredundant categorizations, while preventing new redundant categorizations. RESULTS: Among the 426 newly inherited relationships, 326 are deemed valid. Seven blockings are applied to avoid inheritance of the 100 invalid relationships. Sixteen semantic types have different relationship structures in the ESN as compared to those in the SN. The mapping of semantic type assignments from the SN to the ESN avoids the generation of 26,950 redundant categorizations. The resulting ESN contains 138 semantic types, 149 IS-A links, 7,303 relationships, and 1,013,876 semantic type assignments. CONCLUSION: The ESN's multiple inheritance provides more complete relationship structures than in the SN. The ESN's semantic type assignments avoid the existing redundant categorizations appearing in the SN and prevent new ones that might arise due to multiple parents. Compared to the SN, the ESN provides a more accurate unifying semantic abstraction of the UMLS Metathesaurus.

Semantics↗
PubMed2005

Toward semantic interoperability in home health care: formally representing OASIS items for integration into a concept-oriented terminology.

OBJECTIVE: The authors aimed to (1) formally represent OASIS-B1 concepts using the Logical Observation Identifiers, Names, and Codes (LOINC) semantic structure; (2) demonstrate integration of OASIS-B1 concepts into a concept-oriented terminology, the Medical Entities Dictionary (MED); (3) examine potential hierarchical structures within LOINC among OASIS-B1 and other nursing terms; and (4) illustrate a Web-based implementation for OASIS-B1 data entry using Dialogix, a software tool with a set of functions that supports complex data entry. DESIGN AND MEASUREMENTS: Two hundred nine OASIS-B1 items were dissected into the six elements of the LOINC semantic structure and then integrated into the MED hierarchy. Each OASIS-B1 term was matched to LOINC-coded nursing terms, Home Health Care Classification, the Omaha System, and the Sign and Symptom Check-List for Persons with HIV, and the extent of the match was judged based on a scale of 0 (no match) to 4 (exact match). OASIS-B1 terms were implemented as a Web-based survey using Dialogix. RESULTS: Of 209 terms, 204 were successfully dissected into the elements of the LOINC semantics structure and integrated into the MED with minor revisions of MED semantics. One hundred fifty-one OASIS-B1 terms were mapped to one or more of the LOINC-coded nursing terms. CONCLUSION: The LOINC semantic structure offers a standard way to add home health care data to a comprehensive patient record to facilitate data sharing for monitoring outcomes across sites and to further terminology management, decision support, and accurate information retrieval for evidence-based practice. The cross-mapping results support the possibility of a hierarchical structure of the OASIS-B1 concepts within nursing terminologies in the LOINC database.

Dictionaries, Medical as Topic↗
PubMed2005

Participant perceptions of the influences of the NLM-sponsored Woods Hole medical informatics course.

This report provides an evaluation of the National Library of Medicine-sponsored Woods Hole Medical Informatics (WHMI) course and the extent to which the objectives of the program are achieved. Two studies were conducted to examine the participants' perceptions of both the short-term (spring 2002) and the long-term influences (1993 through 2002) on knowledge, skills, and behavior. Data were collected through the use of questionnaires, semistructured telephone interviews, and participant observation methods to provide both quantitative and qualitative assessment. The participants of the spring 2002 course considered the course to be an excellent opportunity to increase their knowledge and understanding of the field of medical informatics as well as to meet and interact with other professionals in the field to establish future collaborations. Past participants remained highly satisfied with their experience at Woods Hole and its influence on their professional careers and their involvement in a broad range of activities related to medical informatics. This group considered their knowledge and understanding of medical informatics to be of greater quality, had increased their networking with other professionals, and were more confident and motivated to work in the field. Many of the participants feel and show evidence of becoming effective agents of change in their institutions in the area of medical informatics, which is one of the objectives of the program.

Fellowships and Scholarships↗
PubMed2005

Representation of ophthalmology concepts by electronic systems: adequacy of controlled medical terminologies.

OBJECTIVE: To assess the adequacy of 5 controlled medical terminologies (International Classification of Diseases 9, Clinical Modification [ICD9-CM]; Current Procedural Terminology 4 [CPT-4]; Systematized Nomenclature of Medicine, Clinical Terms [SNOMED-CT]; Logical Identifiers, Names, and Codes [LOINC]; Medical Entities Dictionary [MED]) for representing concepts in ophthalmology. DESIGN: Noncomparative case series. PARTICIPANTS: Twenty complete ophthalmology case presentations were sequentially selected from a publicly available ophthalmology journal. METHODS: Each of the 20 cases was parsed into discrete concepts, and each concept was classified along 2 axes: (1) diagnosis, finding, or procedure and (2) ophthalmic or medical concept. Electronic or paper browsers were used to assign a code for every concept in each of the 5 terminologies. Adequacy of assignment for each concept was scored on a 3-point scale. Findings from all 20 case presentations were combined and compared based on a coverage score, which was the average score for all concepts in that terminology. MAIN OUTCOME MEASURES: Adequacy of assignment for concepts in each terminology, based on a 3-point Likert scale (0, no match; 1, partial match; 2, complete match). RESULTS: Cases were parsed into 1603 concepts. SNOMED-CT had the highest mean overall coverage score (1.625+/-0.667), followed by MED (0.974+/-0.764), LOINC (0.781+/-0.929), ICD9-CM (0.280+/-0.619), and CPT-4 (0.082+/-0.337). SNOMED-CT also had higher coverage scores than any of the other terminologies for concepts in the diagnosis, finding, and procedure categories. Average coverage scores for ophthalmic concepts were lower than those for medical concepts. CONCLUSIONS: Controlled terminologies are required for electronic representation of ophthalmology data. SNOMED-CT had significantly higher content coverage than any other terminology in this study.

Humans↗
PubMed2005

Using patient data to retrieve health knowledge.

BACKGROUND: We sought to study a variety of terminologic approaches to the use of clinical data for searching on-line information resources. METHODS: We used a collection of narrative text and coded data to search a variety of text-based, concept-based, and concept-indexed resources. RESULTS: Automated retrievals using original terms could be accomplished and technically produced ample results. However, quality of the results varied with the resource. Terminology translations were difficult to accomplish and produced variable results. CONCLUSIONS: Current resources support automated retrieval; however, achieving quality results varies with the terms and the resources, with term translation productive only in select situations.

Abstracting and Indexing↗
PubMed2004

An enriched unified medical language system semantic network with a multiple subsumption hierarchy.

OBJECTIVE: The Unified Medical Language System's (UMLS's) Semantic Network's (SN's) two-tree structure is restrictive because it does not allow a semantic type to be a specialization of several other semantic types. In this article, the SN is expanded into a multiple subsumption structure with a directed acyclic graph (DAG) IS-A hierarchy, allowing a semantic type to have multiple parents. New viable IS-A links are added as warranted. DESIGN: Two methodologies are presented to identify and add new viable IS-A links. The first methodology is based on imposing the characteristic of connectivity on a previously presented partition of the SN. Four transformations are provided to find viable IS-A links in the process of converting the partition's disconnected groups into connected ones. The second methodology identifies new IS-A links through a string matching process involving names and definitions of various semantic types in the SN. A domain expert is needed to review all the results to determine the validity of the new IS-A links. RESULTS: Nineteen new IS-A links are added to the SN, and four new semantic types are also created to support the multiple subsumption framework. The resulting network, called the Enriched Semantic Network (ESN), exhibits a DAG-structured hierarchy. A partition of the ESN containing 19 connected groups is also derived. CONCLUSION: The ESN is an expanded abstraction of the UMLS compared with the original SN. Its multiple subsumption hierarchy can accommodate semantic types with multiple parents. Its representation thus provides direct access to a broader range of subsumption knowledge.

Algorithms↗
PubMed2004

Approach to mobile information and communication for health care.

Evidence suggests that inadequate access to information and ineffective communication are proximal causes of errors and other adverse events in-patient care. Within the context of reducing these proximal causes of errors, we explore the use of novel information-based approaches to improve information access and communication in health care settings. This paper describes the approaches for and the design of extensions to a clinical information system used to improve information access and communication at the point of care using information-based handheld wireless applications. These extensions include clinical and information resources, event monitoring, and a virtual whiteboard (VWB).

Computers, Handheld↗
PubMed2004

Towards the development of a conceptual distance metric for the UMLS.

The objective of this work is to investigate the feasibility of conceptual similarity metrics in the framework of the Unified Medical Language System (UMLS). We have investigated an approach based on the minimum number of parent links between concepts, and evaluated its performance relative to human expert estimates on three sets of concepts for three terminologies within the UMLS (i.e., MeSH, ICD9CM, and SNOMED). The resulting quantitative metric enables computer-based applications that use decision thresholds and approximate matching criteria. The proposed conceptual matching supports problem solving and inferencing (using high-level, generic concepts) based on readily available data (typically represented as low-level, specific concepts). Through the identification of semantically similar concepts, conceptual matching also enables reasoning in the absence of exact, or even approximate, lexical matching. Finally, conceptual matching is relevant for terminology development and maintenance, machine learning research, decision support system development, and data mining research in biomedical informatics and other fields.

Algorithms↗
PubMed2004

Promoting patient safety and enabling evidence-based practice through informatics.

OBJECTIVES: The purposes of this article are to highlight the role of informatics in promoting patient safety and enabling evidence-based practice (EBP), 2 significant aspects for assuring healthcare quality; to delineate some challenges for the future; and to provide key recommendations for education, practice, policy, and research. METHODS: First, we describe the components of an informatics infrastructure for patient safety and evidence-based practice. Second, we address the role of informatics in 4 areas: 1) information access; 2) automated surveillance for real-time error detection and prevention; 3) communication among members of the healthcare team; and 4) standardization of practice patterns. Last, we delineate some future challenges for nursing and for informatics and provide key recommendations for education, practice, policy, and research. RESULTS: The components of an informatics infrastructure are available and applications that bring together these components to promote patient safety and enable EBP have demonstrated positive or promising results. CONCLUSIONS: Challenges must be addressed so that an informatics infrastructure and related applications that promote patient safety and enable EBP can be realized.

Equipment Safety↗