Quality Assurance of UMLS Semantic Type Assignments Using SNOMED CT Hierarchies.

BACKGROUND: The Unified Medical Language System (UMLS) is one of the largest biomedical terminological systems, with over 2.5 million concepts in its Metathesaurus repository. The UMLS's Semantic Network (SN) with its collection of 133 high-level semantic types serves as an abstraction layer on top of the Metathesaurus. In particular, the SN elaborates an aspect of the Metathesaurus's concepts via the assignment of one or more types to each concept. Due to the scope and complexity of the Metathesaurus, errors are all but inevitable in this semantic-type assignment process. OBJECTIVES: To develop a semi-automated methodology to help assure the quality of semantic-type assignments within the UMLS. METHODS: The methodology uses a cross-validation strategy involving SNOMED CT's hierarchies in combination with UMLS semantic types. Semantically uniform, disjoint concept groups are generated programmatically by partitioning the collection of all concepts in the same SNOMED CT hierarchy according to their respective semantic-type assignments in the UMLS. Domain experts are then called upon to review the concepts in any group having a small number of concepts. It is our hypothesis that a semantic-type assignment combination applicable only to a very small number of concepts in a SNOMED CT hierarchy is an indicator of potential problems. RESULTS: The methodology was applied to the UMLS 2013AA release along with the SNOMED CT from January 2013. An overall error rate of 33% was found for concepts proposed by the quality-assurance methodology. Supporting our hypothesis, that number was four times higher than the error rate found in control samples. CONCLUSION: The results show that the quality-assurance methodology can aid in effective and efficient identification of UMLS semantic-type assignment errors.

Partitioning an object-oriented terminology schema.

Controlled medical terminologies are increasingly becoming strategic components of various healthcare enterprises. However, the typical medical terminology can be difficult to exploit due to its extensive size and high density. The schema of a medical terminology offered by an object-oriented representation is a valuable tool in providing an abstract view of the terminology, enhancing comprehensibility and making it more usable. However, schemas themselves can be large and unwieldy. We present a methodology for partitioning a medical terminology schema into manageably sized fragments that promote increased comprehension. Our methodology has a refinement process for the subclass hierarchy of the terminology schema. The methodology is carried out by a medical domain expert in conjunction with a computer. The expert is guided by a set of three modeling rules, which guarantee that the resulting partitioned schema consists of a forest of trees. This makes it easier to understand and consequently use the medical terminology. The application of our methodology to the schema of the Medical Entities Dictionary (MED) is presented.

A metaschema of the UMLS based on a partition of its semantic network.

The Unified Medical Language System's (UMLS's) Semantic Network (SN) provides an important conceptual abstraction that helps orient users to the vast knowledge content of its Metathesaurus. However, the SN is itself large and complex, and can also benefit from an additional abstract view of its own. In this paper, we present a metaschema that serves such a purpose. This metaschema is derived from a previously developed partitioning methodology for the SN. The metaschema is formally defined, and used to provide partial compact views of the SN.

Representing the UMLS as an object-oriented database: modeling issues and advantages.

OBJECTIVE: The Unified Medical Language System (UMLS) combines many well-established authoritative medical informatics terminologies in one knowledge representation system. Such a resource is very valuable to the health care community and industry. However, the UMLS is very large and complex and poses serious comprehension problems for users and maintenance personnel. The authors present a representation to support the user's comprehension and navigation of the UMLS. DESIGN: An object-oriented database (OODB) representation is used to represent the two major components of the UMLS-the Metathesaurus and the Semantic Network-as a unified system. The semantic types of the Semantic Network are modeled as semantic type classes. Intersection classes are defined to model concepts of multiple semantic types, which are removed from the semantic type classes. RESULTS: The authors provide examples of how the intersection classes help expose omissions of concepts, highlight errors of semantic type classification, and uncover ambiguities of concepts in the UMLS. The resulting UMLS OODB schema is deeper and more refined than the Semantic Network, since intersection classes are introduced. The Metathesaurus is classified into more mutually exclusive, uniform sets of concepts. The schema improves the user's comprehension and navigation of the Metathesaurus. CONCLUSIONS: The UMLS OODB schema supports the user's comprehension and navigation of the Metathesaurus. It also helps expose and resolve modeling problems in the UMLS.

Modeling the UMLS using an OODB.

The Unified Medical Language System combines many well established authoritative medical informatics terminologies in one system. Such a resource is very valuable to the healthcare industry. However, the UMLS is very large and complex and poses serious comprehension problems for users and maintenance personnel. Furthermore, the sets of concepts of semantic types are not semantically uniform and thus are difficult to study. We describe a method to represent two components of the UMLS, the Metathesaurus (META) and the Semantic Network, as an OODB. The resulting UMLS OODB schema is deeper and more refined than the Semantic Network. It offers semantically uniform classes, which improves support for comprehension and navigation of META. The UMLS OODB also exposes problems in the semantic type classifications.

Benefits of an object-oriented database representation for controlled medical terminologies.

OBJECTIVE: Controlled medical terminologies (CMTs) have been recognized as important tools in a variety of medical informatics applications, ranging from patient-record systems to decision-support systems. Controlled medical terminologies are typically organized in semantic network structures consisting of tens to hundreds of thousands of concepts. This overwhelming size and complexity can be a serious barrier to their maintenance and widespread utilization. The authors propose the use of object-oriented databases to address the problems posed by the extensive scope and high complexity of most CMTs for maintenance personnel and general users alike. DESIGN: The authors present a methodology that allows an existing CMT, modeled as a semantic network, to be represented as an equivalent object-oriented database. Such a representation is called an object-oriented health care terminology repository (OOHTR). RESULTS: The major benefit of an OOHTR is its schema, which provides an important layer of structural abstraction. Using the high-level view of a CMT afforded by the schema, one can gain insight into the CMT's overarching organization and begin to better comprehend it. The authors' methodology is applied to the Medical Entities Dictionary (MED), a large CMT developed at Columbia-Presbyterian Medical Center. Examples of how the OOHTR schema facilitated updating, correcting, and improving the design of the MED are presented. CONCLUSION: The OOHTR schema can serve as an important abstraction mechanism for enhancing comprehension of a large CMT, and thus promotes its usability.

A methodology for partitioning a vocabulary hierarchy into trees.

Controlled medical vocabularies are useful in application areas such as medical information systems and decision-support systems. However, such vocabularies are large and complex, and working with them can be daunting. It is important to provide a means for orienting vocabulary designers and users to the vocabulary's contents. We describe a methodology for partitioning a vocabulary based on an IS-A hierarchy into small meaningful pieces. The methodology uses our disciplined modeling framework to refine the IS-A hierarchy according to prescribed rules in a process carried out by a user in conjunction with the computer. The partitioning of the hierarchy implies a partitioning of the vocabulary. We demonstrate the methodology with respect to a complex sample of the MED, an existing medical vocabulary.

Converting an integrated hospital formulary into an object-oriented database representation.

Controlled Medical Vocabularies (CMVs) have proven to be extremely useful in their support of the tasks of information sharing and integration, communication among various software applications, and decision support. Modeling a CMV as an Object-Oriented Database (OODB) provides additional benefits such as increased support for vocabulary comprehension and flexible access. In this paper, we describe the process of modeling and converting an existing integrated hospital formulary (i.e., set of pharmacological concepts) into an equivalent OODB representation, which, in general, we refer to as an Object-Oriented Healthcare Vocabulary Repository (OOHVR). The source for our example OOHVR is a formulary provided by the Connecticut Healthcare Research and Education Foundation (CHREF). Utilizing this source formulary together with the semantic hierarchy composed of major and minor drug classes defined as part of the National Drug Code (NDC) directory, we constructed a CMV that was eventually converted into its OOHVR form (the CHREF-OOHVR). The actual conversion step was carried out automatically by a program, called the OOHVR Generator, that we have developed. At present, the CHREF-OOHVR is running on top of ONTOS, a commercial OODB management system, and is accessible on the Web.

Partitioning a vocabulary's IS-A hierarchy into trees.

Controlled medical vocabularies are useful in application areas such as medical information-systems and decision-support. However, such vocabularies are large and complex, and working with them can be daunting. It is important to provide a means for orienting users to the vocabulary's contents. This paper introduces a methodology for partitioning a vocabulary into small, meaningful pieces. The partitioning is done with respect to the vocabulary's IS-A hierarchy. The methodology, based on a set of rules for refining the IS-A hierarchy, is a process carried out by a user in conjunction with the computer. The methodology is demonstrated on a complex portion of a vocabulary.

Utilizing OODB schema modeling for vocabulary management.

Comprehension of complex controlled vocabularies is often difficult. We present a method, facilitated by an object-oriented database, for depicting such a vocabulary (the Medical Entities Dictionary (MED) from the Columbia-Presbyterian Medical Center) in a schematic way which uses a sparse inheritance network of area classes. The resulting Object Oriented Health Vocabulary repository (OOHVR) allows visualization of the 43,000 MED concepts as 90 area classes. This view has provided valuable information to those responsible with maintaining the MED. As a result, the MED organization has been improved and some previously-unrecognized errors and inconsistencies have been removed. We believe that this schematic approach allows improved comprehension of the gestalt of large controlled medical vocabulary.

Long-term responses of women to indole-3-carbinol or a high fiber diet.

We test the hypothesis that the estrogen metabolite ratio 2-OH-estrone:estriol can be raised via dietary indole-3-carbinol (I3C) and that this higher ratio can be sustained over a 3-month test period. We also explore the possible role of pure fiber on estradiol metabolism. Using a randomized clinical trial with three arms, each containing 20 subjects, arm 1 received 400 mg/day of I3C daily for 3 months, arm 2 received 20 g of alpha-cellulose daily for the same time period as a source of added fiber, and arm 3 received a placebo dose. Blood levels of a variety of biochemical parameters were measured. The urinary 2-OH-estrone:estriol estrogen metabolite ratio was measured monthly at the same time of the menstrual cycle. While no changes were observed in the control and alpha-cellulose-treated arms, a substantial mean increase in the ratio was observed in the I3C-treated arm at month 1; that increase was maintained over the 3-month time period. Three of the 20 subjects in this I3C-treated group differed from the others in that no significant change in the metabolite ratio was observed at any time point. The results suggest that I3C can serve to increase the 2-OH-estrone:estriol metabolite ratio in a sustained manner without detectable side effects and that some individuals may be resistant to such change.

Psychological distress and surveillance behaviors of women with a family history of breast cancer.

Women with a family history of breast cancer are at increased risk for developing the disease. This study investigated the beliefs of women at high risk for breast cancer (one or more first-degree relatives with breast cancer) about their breast cancer risk and the impact of this information on their surveillance behaviors and psychological distress. The Health Belief Model and the Fear Arousing Communications Theory were used in this study. Two hundred and seventeen women, enrolled in a breast protection program, completed a questionnaire regarding health beliefs and behaviors, social support, and psychological distress. While 94% came in for regularly scheduled mammograms, only 69% came in for regular clinical breast examinations. A discriminant function analysis revealed that increased cancer anxiety decreased regular clinical examinations (coefficient = -.65). Only 40% performed breast self-examination monthly, 10% never performed breast self-examination, and 50% did not perform breast self-examination regularly. High breast self-examination performance prior to coming to the program was the best predictor of current breast self-examination, and high anxiety predicted poor adherence to monthly breast self-examination (multiple R = .61). More than 27% of the women at high risk were defined as having a level of psychological distress consistent with the need for counseling. Women reporting more barriers to screening, fewer social supports, and low social desirability had more psychological distress (multiple R = .75). Higher anxiety was directly related to poor attendance at a clinical breast examination and poor adherence to monthly breast self-examination.(ABSTRACT TRUNCATED AT 250 WORDS)

Modulation of the cancer susceptibility measure, adenosine diphosphate ribosyl transferase (ADPRT), by differences in low-dose n-3 and n-6 fatty acids.

Adenosine diphosphate ribosyl transferase (ADPRT) is related to oxidants, and lower values for ADPRT in white cells suggest increased cancer susceptibility. Ordinarily, oxidants are generated intracellularly via metabolism of n-6 fatty acids common in western diets. However, n-3 fatty acids in fish oils might limit oxidants via competitive inhibition of key enzymes, elevate ADPRT, and lower cancer risk. In this controlled trial, 47 women were assigned either lecithin (an n-6 fatty acid, 7.2 g daily) or eicosapentaenoic acid-docosahexaenoic acid (n-3 fatty acids, 1.5 g daily) for six weeks, and 45 women completed all four visits. After six weeks, ADPRT increased by 9.3 +/- 10.8% (SD) for the n-3 fatty acid group relative to the n-6 fatty acid group. For the subset of 39 women with good compliance, ADPRT increased by 20.9 +/- 11.1% (nonparametric p = 0.039). This increase persisted after adjustment for regression to the mean. The trial suggests a "normalizing" effect of low-dose n-3 fatty acids on the ADPRT measure.

DNA repair synthesis in individuals with and without a family history of cancer.

The influence of family history on DNA repair synthesis, unscheduled DNA synthesis (UDS), was assessed in volunteers with or without a family history of cancer. UDS, following treatment of mononuclear leukocytes with N-acetoxy-2-acetylaminofluorene, was measured as the incorporation of [3H]thymidine into DNA in the presence of hydroxyurea. The positive family history group (n = 71) had an average of 2.4 first-degree relatives with cancer, defined as any major cancer, excluding skin cancer: 31 participants reported that cancer occurred in both their parents. The "no family history' comparison group (n = 29) had no family history of cancer through the second degree. There was a significant reduction in UDS in cells from individuals with family history, compared to those with no family history (P greater than 0.002). This relationship was not explained by factors known to influence UDS, such as age, smoking or hypertension. We conclude that reduced UDS in mononuclear leukocytes is associated with a family history of any major cancer, and is not confined to a history of cancer of any single organ site. This conclusion is further supported by the observation that individuals (n = 13) with parents who had an earlier onset of cancer (less than 60 years) also had a significantly lower DNA repair synthesis than those (n = 18) whose parents had later diagnosis of cancer (greater than 60 years).