Structural Patterns under X-Rays: Is SNOMED CT Growing Straight?

This article describes the challenges of implementing SNOMED CT into electronic clinical documentation systems for discharge summaries, synoptic operative notes and ambulatory documentation. Four significant implementation challenges were identified throughout these projects, which required collaboration between specialists across several disciplines to resolve. The challenges included: designing the graphical user interface for selecting SNOMED CT values, gathering and validating template specifications that use SNOMED CT subsets, handling SNOMED CT subsets and extensions, and, creating algorithms and the technological infrastructure to generate fast, meaningful, non-redundant search results. Our experiences suggest that, while the usage of SNOMED CT in tertiary care settings is promising, collaboration between specialists from multiple disciplines is needed to utilize their unique project management, data modeling, technical, and clinical skills in overcoming implementation challenges.

The possibility of post-coordination of SNOMED CT concepts, especially by clinical users, is both an asset and a challenge for SNOMED CT implementation. To get insight in the applicability of post-coordination, we analyzed scenarios for user-directed coordination that are described in the documentation of SNOMED CT. The analyses were based on experiences from previous and ongoing research and implementation work, including national mapping projects, and investigations on collection of data for multiple uses. These scenarios show various usability and representation problems: high number of relationships for refinement and qualification, improper options for refinement, incorrect formal definitions, and lack of support for applying editorial rules. Improved user-directed coordination in SNOMED CT in real practice requires advanced sanctioning, increased consistency of definitions of concepts in SNOMED CT, and real-time analysis of the post-coordinate expression.

From lexical regularities to axiomatic patterns for the quality assurance of biomedical terminologies and ontologies

We present a scalable, SPARQL-based computational pipeline for testing the lattice-theoretic properties of partial orders represented as RDF triples. The use case for this work is quality assurance in biomedical ontologies, one desirable property of which is conformance to lattice structures. At the core of our pipeline is the algorithm called NuMi, for detecting the Number of Minimal upper bounds of any pair of elements in a given finite partial order. Our technical contribution is the coding of NuMi completely in SPARQL. To show its scalability, we applied NuMi to the entirety of SNOMED CT, the largest clinical ontology (over 300,000 conepts). Our experimental results have been groundbreaking: for the first time, all non-lattice pairs in SNOMED CT have been identified exhaustively from 34 million candidate pairs using over 2.5 billion queries issued to Virtuoso. The percentage of non-lattice pairs ranges from 0 to 1.66 among the 19 SNOMED CT hierarchies. These non-lattice pairs represent target areas for focused curation by domain experts. RDF, SPARQL and related tooling provide an e cient platform for implementing lattice algorithms on large data structures.

SNOMED CT is important for clinical applications, such as Electronic Health Record (EHR) encoding. However, inconsistency in modeling its concepts may prevent SNOMED CT from providing proper support for clinical use. This study provides an effective methodology for locating inconsistently modeled SNOMED CT concepts. One can expect lexically similar concepts to be modeled similarly. Positional similarity sets, sets of lexically similar concepts having only one different word at the same position of their names, are introduced. Concepts in such sets have a higher likelihood of being unjustifiably inconsistently modeled. A technique to incorporate three structural indicators into the selected sets is provided to further improve the likelihood of finding inconsistently modeled concepts. An analysis of a sample of 50 such sets and for each of these three indicators is performed. The sample of positional similarity sets is found to have 18.6% inconsistent concepts. The use of structural indicators is shown to further improve the likelihood of finding inconsistently modeled concepts up to 41.6% with high statistical significance when compared to the previous sample of positional similarity sets. Positional similarity sets with different structural indicators are shown to help identify inconsistencies in concept modeling with high likelihood. Furthermore, such sets enable the comparison of concept modeling in the context of other lexically similar concepts, which enhances the effectiveness of corrections by auditors. Such quality assurance methods can be used to supplement IHTSDO's own efforts in order to improve the quality of SNOMED CT.

BackgroundThe volume and complexity of patient data – especially in personalised medicine – is steadily increasing, both regarding clinical data and genomic profiles: Typically more than 1,000 items (e.g., laboratory values, vital signs, diagnostic tests etc.) are collected per patient in clinical trials. In oncology hundreds of mutations can potentially be detected for each patient by genomic profiling. Therefore data integration from multiple sources constitutes a key challenge for medical research and healthcare.MethodsSemantic annotation of data elements can facilitate to identify matching data elements in different sources and thereby supports data integration. Millions of different annotations are required due to the semantic richness of patient data. These annotations should be uniform, i.e., two matching data elements shall contain the same annotations. However, large terminologies like SNOMED CT or UMLS don’t provide uniform coding. It is proposed to develop semantic annotations of medical data elements based on a large-scale public metadata repository. To achieve uniform codes, semantic annotations shall be re-used if a matching data element is available in the metadata repository.ResultsA web-based tool called ODMedit (https://odmeditor.uni-muenster.de/) was developed to create data models with uniform semantic annotations. It contains ~800,000 terms with semantic annotations which were derived from ~5,800 models from the portal of medical data models (MDM). The tool was successfully applied to manually annotate 22 forms with 292 data items from CDISC and to update 1,495 data models of the MDM portal.ConclusionUniform manual semantic annotation of data models is feasible in principle, but requires a large-scale collaborative effort due to the semantic richness of patient data. A web-based tool for these annotations is available, which is linked to a public metadata repository.

Investigating subsumption in SNOMED CT: An exploration into large description logic-based biomedical terminologies

OBJECTIVES/SPECIFIC AIMS: Dependence and abuse of prescription opioid pain medication has substantially increased over the last decade. The consistent rise in opioid dependence contributes to the rising prescription drug overdose deaths over the last decade. The study of the distribution and determinants of opioid dependence among patients who are treated with chronic pain medications prescribed by their healthcare providers would aid in answering some key questions about potential abuse and overdose on opioids. The descriptive epidemiology of opioid dependence would help in identifying the vulnerable age group, race, ethnicity, and type of opioid pain medications that more commonly result in dependence. METHODS/STUDY POPULATION: We implemented an Observational Medical Outcomes Partnership/Observational Health Data Sciences and Informatics (OMOP/OHDSI) database, to hold structured EHR data from our Allscripts patient records. We also created a high-throughput phenotyping, natural language processing system that can parse 7,000,000 clinical notes in 1.5 hours. This runs as a web service and provides a modular component based NLP system. After the full semantic parse, we match the content against any number of ontologies. For each match we tag it as either a positive, negative, or uncertain assertion. We then perform automated compositional expressions. The codes are stored in a Berkley database (BDB) NOSQL database and the compositional expressions are stored in Neo4J (a graph database) and Graph DB (a triple store). This flexibility allows rapid retrieval of complex questions in real time. The High-Throughput Phenotyping (HTP) Natural Language Processing (NLP) Subsystem (HTP-NLP) is software that produces, given biomedical text, semantic annotations of the text. The semantic annotations identify conceptual entities—their attributes, the relations they have with other entities and the events they participate in, as expressed in the input text. The conceptual entities, relations, attributes, and events identified are specified by various knowledge representations (KRs) as documented in Coding Sources. Examples of coding sources are medical terminologies [eg, SNOMED CT, RxNorm, LOINC and open biomedical ontologies (OBO) foundry ontologies, eg, gene ontology (GO), functional model of anatomy, OBI, and others]. The annotation results may be displayed or output in formats suitable for further processing. Entity identified is assigned a truth value from 0 to 1. Values from the text are assigned to entities from ontologies such as SNOMED CT. The retrospective analysis of EHR data from local clinic patients was performed using queries on the problem list, demographic data, and medication list of all the patients in the database. The OMOP/OHDSI database was collected from Allscripts EHRs from 2010 to 2015. This common data model helps in the systematic analysis of disparate observational databases of clinic records from the primary care and family medicine clinics in Western New York region. The database contained 212,343 patient records that were parsed and deidentified. Specific research IDs were assigned to each of the patient records and stored in a secure firewall device for data analytics. The entire 212,343 records were queried for opioid dependence from the ICD-9 and 10 diagnostic codes and SNOMED CT codes mapped to both the clinical notes and the problem list for each patient based on the mapped ICD and SNOMED CT codes. In total, 1356 patients were identified as to having opioid dependence. The records were stratified into 7 age groups from age 18 to 28 and ending with age 79–89 years. RESULTS/ANTICIPATED RESULTS: Of the 212,343 patients in the database 1356 patients revealed opioid dependence on the problem list, ICD9-10 codes and prescription opioid pain medication with or without Buprenorphine and Naloxone (Suboxone) in the medication list. The prevalence of opioid dependence in the clinic population was 0.64% (95% CI: 0.61%–0.67%) over a 5-year period. The 7,000,000 patient records generated 750,000,000 SNOMED CT codes (on average 107 codes per record). The highest numbers of opioid dependence were seen in the 29 to 38 years’ age group. That comprised 39.38% (95% CI: 36.78%–41.98%) of the total opioid dependent population but accounted for only 2.03% of whole clinic population in this age group (95% CI: 1.86% to 2.2%). The subjects were then stratified by race and ethnicity. There were 1005 patients with opioid dependence, in the non-Hispanic population (total number 108,402). Among the White non-Hispanic or Latino population with opioid dependence, 41.33% (95% CI: 38.27%–44.39%) were 29–38 years old. The next common age group among the White Non-Hispanic opioid dependent subjects was 19–28 years, comprising of 22.48% (95% CI: 19.88%–25.08%) of the total number of White non-Hispanic or Latino opioid dependent population. Among the total clinic population Hispanics comprise 51.24%, but they comprise only 2.58% (95% CI: 1.74%–3.42%) of the total opioid dependent population. The non-Hispanic population comprise 51.05% of total clinic population while the percent of people who are opioid dependent is 83.26% (95% CI: 83.04%–83.48%) of the total 1356 opioid dependent population. DISCUSSION/SIGNIFICANCE OF IMPACT: The trends of opioid dependence among the clinic population in the study indicate that the prevalence is more in a certain section of the population. The predominance is among the non-Hispanic White population in the 19–38 years of age. The prevalence in younger age implies that the complications related to opioid dependence would be there for a longer duration of time. The prevalence of dependence in this clinic population would be rising if this trend continues. Interventions at curbing prescription opioid dependence is necessary for the vulnerable population. The findings suggest that a broad based approach is necessary to address this problem. The distribution of opioid dependence in this patient population indicate the need for special attention to these specific age group and race ethnicities. The young age of many of the addicted patients demonstrate the risks of legitimate opioid prescriptions in leading this age group towards addiction and implies the need for routine screening for substance abuse. The evidence of complications of opioid overdose among long-term opioid users and risk of abuse with other agents including illicit agents makes the need for an approach that uses real-time interventions in addition to effect long-term improvement in addiction rates. A potentially cost-effective approach to implement monitoring programs and clinical decision support tools would be to develop inter operable linkage from the EHRs to the state Department of Healths’ prescription monitoring programs.

BackgroundNarrative medical reports do not use standardized terminology and often bring insufficient information for statistical processing and medical decision making. Objectives of the paper are to propose a method for measuring diversity in medical reports written in any language, to compare diversities in narrative and structured medical reports and to map attributes and terms to selected classification systems.MethodsA new method based on a general concept of f-diversity is proposed for measuring diversity of medical reports in any language. The method is based on categorized attributes recorded in narrative or structured medical reports and on international classification systems. Values of categories are expressed by terms. Using SNOMED CT and ICD 10 we are mapping attributes and terms to predefined codes. We use f-diversities of Gini-Simpson and Number of Categories types to compare diversities of narrative and structured medical reports. The comparison is based on attributes selected from the Minimal Data Model for Cardiology (MDMC).ResultsWe compared diversities of 110 Czech narrative medical reports and 1119 Czech structured medical reports. Selected categorized attributes of MDMC had mostly different numbers of categories and used different terms in narrative and structured reports. We found more than 60% of MDMC attributes in SNOMED CT. We showed that attributes in narrative medical reports had greater diversity than the same attributes in structured medical reports. Further, we replaced each value of category (term) used for attributes in narrative medical reports by the closest term and the category used in MDMC for structured medical reports. We found that relative Gini-Simpson diversities in structured medical reports were significantly smaller than those in narrative medical reports except the "Allergy" attribute.ConclusionsTerminology in narrative medical reports is not standardized. Therefore it is nearly impossible to map values of attributes (terms) to codes of known classification systems. A high diversity in narrative medical reports terminology leads to more difficult computer processing than in structured medical reports and some information may be lost during this process. Setting a standardized terminology would help healthcare providers to have complete and easily accessible information about patients that would result in better healthcare.

The estimation of semantic similarity between words is an important task in many language related applications. In the past, several approaches to assess similarity by evaluating the knowledge modelled in an ontology have been proposed. However, in many domains, knowledge is dispersed through several partial and/or overlapping ontologies. Because most previous works on semantic similarity only support a unique input ontology, we propose a method to enable similarity estimation across multiple ontologies. Our method identifies different cases according to which ontology/ies input terms belong. We propose several heuristics to deal with each case, aiming to solve missing values, when partial knowledge is available, and to capture the strongest semantic evidence that results in the most accurate similarity assessment, when dealing with overlapping knowledge. We evaluate and compare our method using several general purpose and biomedical benchmarks of word pairs whose similarity has been assessed by human experts, and several general purpose (WordNet) and biomedical ontologies (SNOMED CT and MeSH). Results show that our method is able to improve the accuracy of similarity estimation in comparison to single ontology approaches and against state of the art related works in multi-ontology similarity assessment.

Sample based texture synthesis allows the generation of arbitrarily sized textures based on a small sample image. One main drawback of the technique is that a new pixel or patch is selected only considering local information in the generated texture. Thus structural error can't assure to be avoided for structural textures. To accelerate texture synthesis process and to avoid structural mismatch in the output picture, we present in this paper a structural pattern analysis (SPA) algorithm and a texture synthesis method using the algorithm. The pattern analysis tool also quantizes the texture randomness in macro scope view. It can be used in other applications such as automatic texture classification and quality evaluation of synthesized texture. We illustrate our result with some examples.

This article presents recent progresses made in using scalable cloud computing environment, Hadoop and MapReduce, to perform ontology quality assurance (OQA), and points to areas of future opportunity. The standard sequential approach used for implementing OQA methods can take weeks if not months for exhaustive analyses for large biomedical ontological systems. With OQA methods newly implemented using massively parallel algorithms in the MapReduce framework, several orders of magnitude in speed-up can be achieved (e.g., from three months to three hours). Such dramatically reduced time makes it feasible not only to perform exhaustive structural analysis of large ontological hierarchies, but also to systematically track structural changes between versions for evolutional analysis. As an exemplar, progress is reported in using MapReduce to perform evolutional analysis and visualization on the Systemized Nomenclature of Medicine—Clinical Terms (SNOMED CT), a prominent clinical terminology system. Future opportunities in three areas are described: one is to extend the scope of MapReduce-based approach to existing OQA methods, especially for automated exhaustive structural analysis. The second is to apply our proposed MapReduce Pipeline for Lattice-based Evaluation (MaPLE) approach, demonstrated as an exemplar method for SNOMED CT, to other biomedical ontologies. The third area is to develop interfaces for reviewing results obtained by OQA methods and for visualizing ontological alignment and evolution, which can also take advantage of cloud computing technology to systematically pre-compute computationally intensive jobs in order to increase performance during user interactions with the visualization interface. Advances in these directions are expected to better support the ontological engineering lifecycle.

Observational Health Data Sciences and Informatics (OHDSI) is an international research community dedicated to large-scale observational studies using real-world healthcare data. Participation in OHDSI requires mapping local terminology systems to the OHDSI Standard Vocabulary (OSV) and transforming healthcare data into the Observational Medical Outcomes Partnership Common Data Model (OMOP CDM), a standardized database schema. Adherence to the OSV and CDM enables the integration of datasets from different countries and regions, facilitating international cross-sectional analyses and supporting the discovery of large-scale evidence and new medical knowledge. Despite the globally recognized healthcare technology and systems excellence in Japan, Japanese real-world data (RWD) remain underutilized in international research. This is primarily due to reliance on domestically managed controlled terminologies in Japan that are not aligned with international controlled terminologies such as SNOMED CT, making mapping Japanese RWD to the CDM challenging. In addition, the wide variety of pharmaceutical products in Japan has hindered the establishment of mappings to RxNorm, the standardized drug terminology used in OHDSI. Previously, we used a Large Language Model (LLM) to map Japanese pharmaceutical data to RxNorm. A sampling-based evaluation confirmed that the LLM could accurately identify mapping candidates. Pharmacists and a medical informatics researcher validated these mappings, resulting in an ingredient-based mapping of Japanese pharmaceutical terms to RxNorm. Researchers interested in pharmacoepidemiology, pharmacoeconomics, and drug-related clinical decision support systems integrated with Japanese RWD can benefit significantly from this dataset. It also contains information about the target drugs, their translated names, LLM-generated suggestions, and reference data, making it suitable for developing and validating natural language processing and machine learning techniques for terminology mapping.

The purpose of this study was to determine factors perceived to influence the successful use of laptop computers by clients of the Crippled Children’s Association of South Australia. The study was conducted in two phases: (i) a consultation phase involving key stakeholders; and (ii) a survey phase in which a questionnaire was distributed. Five key themes were identified by the consultation phase which grouped together similar factors perceived to influence the successful use of laptop computers. These themes were factors related to: (i) the laptop user; (ii) the laptop user’s parents/family; (iii) attributes of the laptop; (iv) the laptop user’s school; and (v) support and assistance which the laptop user may receive. A questionnaire was developed around these themes. Participants rated the importance of factors within these themes in relation to successful laptop computer use by children with disabilities. Results identified the most important factors across the whole sample were portability and teachers ability to adapt learning tasks to suit laptop use. However, each stakeholder group rated different factors as most important. Recommendations for a collaborative approach to laptop computer prescription, ongoing follow up and quality assurance, and the provision of training and development opportunities are suggested.

PHC in Sweden has developed rather slowly during the last two decades, though there is a long tradition of “provincial medici”. Even more slowly information technology has spread in PHC, at least in Sweden. Two years ago only 1–2% of general practitioners used personal computers or minicomputers in their work, mainly for patient administrative purposes. Presently there is a growing interest in computerized medical records, the reason being a shortage of secretaries and perhaps a growing interest in quality assurance in health care.KeywordsHealth Care SectorNurse AssistantData DictionaryQuality CircleDistrict NurseThese keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.