Semant Web. Figure 1 presents a graphical representation of the CMDO classification showing the Allergy Test from Finding as a parent concept being assigned to Allergy History derived largely from Description. All metadata used in our work registered in the CHMR (http://chmr2.snubi.org:8083/chmr/). Accessed 6 Mar 2019. Clinical MetaData ontology: a simple classification scheme for data elements of clinical data based on semantics. Clinical documents can be automatically classified and automatically managed based on the similarities between the sets of CDEs that they contain. All of the CDEs extracted from two clinical document sets (six HL7 templates and five documents from the five teaching hospitals) were manually annotated with CMDO concepts. Nucleic Acids Res. We manually extracted common concepts that were counted more than twice from the DECs while considering whether it was reasonable to subordinate them to first-level terms of CMDO, and chose them as CMDO concepts, which are the child terms of each first-level term. Another approach is to simply encourage clinical users to employ standard vocabularies to encode complex real-world concepts. Knowledge I. Barry Sewall, MD. This metadata, being machine as well … J Am Med Inform Assoc. Stud Health Technol Inform. However, this was unsuccessful since the available ontologies were either too complicated and had a high complexity (e.g., UMLS) or were not appropriate (e.g., DO); we therefore constructed CMDO. This is a preview of subscription content, Information Brokering Across Heterogeneous Digital Data. Richesson RL, Krischer J. Cite as. The Ontology Metadata Sets depicted in the LDM diagram (patent drawing 14) are an isomorphic representation of an RDF/OWL metamodel, but for reverse-engineering we only populate the common subset. Moreover, the structures of real-world clinical documents are constantly evolving. Download preview PDF. An ontology-based search approach can be considered as one example of a semantically enhanced information retrieval method. classes with no definition: a list of classes that have no value for the definition property. J Am Med Inform Assoc. In the relational idiom, metadata is a statement that says something about more than one resource. A multi-technique approach to bridge electronic case report form design and data standard adoption. Accessed 6 Mar 2019. We successfully established the CHMR in 2006, since when we have been using it in various clinical trials and research studies [22,23,24]. Search functions for CMDO concepts can be made by entering terms in the ‘Jump to:’ box, which also has an autocomplete function. Sharing behavioral data through a grid infrastructure using data standards. Ontologie ist ein überlieferter Begriff aus der Philosophie und steht dort für die Lehre vom Sein - genauer: von den Möglichkeiten und Bedingungen des Seienden -, ist also eng verwandt mit der Erkenntnistheorie, die sich mit den Möglichkeiten und Grenzen menschlichen Wahrnehmens und … All of the CDEs extracted from 6 HL7 templates, 25 clinical documents of 5 teaching hospitals, and 1 personal health record specification were successfully annotated by 41 (21.9%), 89 (47.6%), and 13 (7.0%) of the CMDO concepts, respectively. Dieser Gegenstandsbereich ist weitgehend deckungsgleich mit dem, was nach traditioneller Terminologie allgemeine Metaphysik genannt wird. PubMed Central  The left panel of the CMDO Browser displays lists of CMDO preferred terms arranged as a hierarchical tree that can be navigated by clicking the name of each term to explore CMDO concepts, with their detailed properties displayed in the right panel. UMLS has Concept Unique Identifier (CUI), and terms with the same CUI can be grouped together since they are semantically equivalent [28]. Dordrecht: Springer; 2010. p. 27–66. Additional file 1: Table S4 lists CMDO concept annotated CDEs from two types of clinical document sets and the CCR+ PHR model. Metadata
Literally, a set of data that describes and gives information about other data, metadata in our context is:
Machine readable
Descriptive
For the purposes of resource…
Discovery
Management
Delivery
Access control
Use
Re-use
Long term preservation
David Lamas, TLU, 2011
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103.94.16.129. BioPortal: enhanced functionality via new web services from the National Center for biomedical ontology to access and use ontologies in software applications. 2006;45:594–601. Article  First, when constructing CMDO we did not consider other methods and compare them with the GFO method, instead only considering the GFO since we considered it an appropriate method for conceptualizing ontologies. Table 2 indicates that 81.3, 96.0, and 100% of the CMDO concepts were rated as being adequately annotated for the 6 HL7 templates, 25 clinical documents, and the CCR+ specification, respectively. To give you more description, first of all we have not used any of patients’ data. These classes are the different taxonomic ranks known … We assigned an is-a relationship between CMDO concepts by applying the following process: Terms that appeared to be in a subordinates–superiors relationship were determined to be in an is-a relationship involving two medical doctors and two medical informatics researchers. Epilepsia. In this chapter, we discussed issues related to the management of metadata from the perspective of different application scenarios. Two administrators of medical records separately validated the two CMDO annotation sets. The National Institutes of Health encourage the use of CDEs [17], which has led to them being deployed in case-report forms (CRFs) and clinical documents [6, 7, 10], and subsequently demonstrating the high effectiveness and usability of employing CDEs. A relationship between subordinates and superiors among CMDO concepts was defined manually by clinical informatics experts, while the remaining ontology development process was conducted according to the GFO method. This study has demonstrated that a clinical-content-based ontology can be used to identify standardized CDEs. However, there was also a case of disagreement, in that for the data element ‘Estimated Blood Loss’ in an Operation Note from the HL7 template, one nurse chose Procedure|Surgery and the other chose Finding|Surgery|Problem. Wissen umfasst dabei sowohl Allgemeinwissen als auch Wissen über s… J Am Med Inform Assoc. Metadata is a structured, coded data that describes the characteristics of media objects that facilitates the identification, detection, evaluation and management of these objects. A federated semantic metadata registry framework for enabling interoperability across clinical research and care domains. CMDO web services: (a) CMDO Browser and (b) CMDO-enabled CDE Browser., (c) CMDO Download Function (OWL). Part of (DOCX 114 kb). Tudorache T, Nyulas C, Noy NF, Musen MA. The CMDO Browser and CMDO-enabled CDE Browser make it easy to search, share, and reuse CDEs, and also effectively integrate and manage CDEs from different studies and clinical documents. Establishing semantic interoperability of biomedical metadata registries using extended semantic relationships. Metadata can be used to describe relationships between resources, and also to describe prospective usages of resources. List of CMDO concepts and its hierarchical structure. 2 Please refer to column ‘prefix’ of Table 2 all along the paper for acronyms definitions of metadata vocabularies. PubMed  Healthc Inform Res. Each CMDO concept has properties to show how it can cover the same or similar meanings for discovering semantic correspondences. PubMed Central  The total number of CMDO concepts is 189. Information brokering was observed to be a central component of these applications, with special emphasis on the capture, storage, and interrogation of information content. 06/2018. Nadkarni PM, Brandt CA. Ontologies also provide descriptive properties of those objects and their relationships. 2014. https://doi.org/10.4258/hir.2014.20.1.1. Daniel C, Ouagne D, Sadou E, Paris N, Hussain S, Jaulent MC, Kalra D. Cross border semantic interoperability for learning health systems: the EHR4CR semantic resources and services. For instance, the patient may say ‘During the accident I sustained an injury to the back of my head and neck.’ No concept in UMLS corresponds to the problem ‘injury to the back of the head and neck.’ Instead, the problem concept Injury (C3263722), the direction Back (C0205095), and anatomical locations Head (C0018670) and Neck (C0027530) must be postcoordinated into an on-the-fly concept [5]. Cite this article. The metadata used in this paper is freely available in the CHMR. Features →. J Am Med Inform Assoc. PubMed  None of the authors has conflicts of interest with other persons or organizations that could inappropriately influence their work. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. We also implemented ISO/IEC 11179 based on a metadata registry called the Clinico-Histopathological Metadata Registry (CHMR), which contains more than 20,000 highly curated CDEs [18, 19]. Definition of Ontology. PubMed Google Scholar. 2013. https://doi.org/10.1016/j.jbi.2012.11.008. Issues of language and vocabulary for capturing information content using intensional metadata expressions were presented. Table 1 lists the statistics of CMDO concepts for each level under the first-level classes. 2009. https://doi.org/10.1197/jamia.M2821. J Biomed Inform. J Biomed Semantics. For instance, the DEC for a person’s sex is established using the object concepts of Person (C0027361) and Sex (C1522384), while the VD for sex covers the permissible values of ‘male’ and ‘female.’ The complete CDE is defined by combining the DEC for a person’s sex with VD < male|female> [8]. A CS has been provided for clinical documents, and document names have been standardized. Barton C, Kallem C, Van Dyke P, Mon D, Richesson R. Demonstrating "collect once, use many"--assimilating public health secondary data use requirements into an existing domain analysis model. We found that CMDO concepts in the Finding class exhibited the highest CMDO mapping rate for CDEs in clinical documents. It was implicitly assumed that there were associated appropriate CDEs with the correct CMDO concepts; if this assumption was not valid, it would take more time to match CMDO concepts to CDEs. Moreover, most of the CDE browsers that are developed in projects do not apply formal CSs, relying instead on simple keyword-based search engines. J Biomed Inform. Ontologies provide formal names to real world objects in a specific domain. The right panel displays the number of the CDEs tagged with the searched CMDO terms along with the list of CDEs containing the CDE name, CDE definition, and list of clinical documents containing the CDEs. without having any of real ‘data’. Manage cookies/Do not sell my data we use in the preference centre. Leia was portrayed by the actress Carrie Fisher, another relationship (the character-actor relationship) but in a separate dimension of the ontology. AMIA Annu Symp Proc. 2014. https://doi.org/10.1136/amiajnl-2013-001763. CMDO was developed using one of the appropriate methodologies for conceptual modeling, the General Formal Ontology (GFO) method [27], which is a manual iterative process comprising five steps: (1) defining the scope of CMDO by conceptualizing its first-level terms (or classes), (2) identifying CMDO concepts, (3) assigning hierarchical relationships among CMDO concepts, (4) developing CMDO properties (e.g., synonyms, preferred terms, and definitions) for each CMDO concept, and (5) evaluating the utility of CMDO. Why GitHub? Given the increasing use of CDEs in many studies and real-world clinical documentation, CMDO will be a useful tool for integrating numerous CDEs from different research projects and clinical documents. • Ontologies include computer-usable definitions of basic concepts in the domain and the relationships among them – They encode domain knowledge (modular) – Knowledge that spans domains (composable) – Make knowledge available (reusable) Source: “What is An Ontology” Leo Obrst / Ontolog / 2006.01.12. ppy/Boostrapping-From-Metadata-to-Ontology--PeterYim_20070719/Jul-2007 6 … Definition of Digital Ontology; Metadata; Ontology; Data Management. CMDO provides 459 synonyms for 139 (74.0%) CMDO concepts, and 256 definitions for 188 (100%) CMDO concepts. We also found that the 25 clinical documents contained more-specific CDEs than the 6 HL7 templates, since 3 times as many CMDO terminal concepts were used for mapping the CDEs in the clinical documents. California Privacy Statement, This approach resulted in 27,109 CDEs being extracted from 663 SNUH clinical documents. Article  Kim JH. Min H, Ohira R, Collins MA, et al. 2006:1056. Health avatar: An informatics platform for personal and private big data. This research was supported by a grant of the Korea Health Technology R&D Project through the Korea Health Industry Development Institute (KHIDI), funded by the Ministry of Health & Welfare, Republic of Korea (grant number:HI18C2386). An MDR-based CDE is considered a type of standardized data with specified concept and VDs. So an ontology would be a formal, logic based definition of the types, their properties and their interrelationships within real objects in a particular subject domain. We also plan to determine how to simplify the process of using CMDO in order to save time and ensure high usability. Here we propose ‘middle-out’ approach that contrasts with the top-down ontology-construction and bottom-up vocabulary-encoding approaches for achieving semantic interoperability at the level of clinical data elements contained in clinical documents. PubMed  BMC Med Inform Decis Mak 19, 166 (2019). J Korean Med Assoc. Secondly, the authors themselves have developed and been in charge of operating the CHMR. We believe that it is not necessary to take an IRB review for using metadata as long as we do not use any of patients’ data. Park YR, Yoon YJ, Jang TH, Seo HJ, Kim JH. Kim, H., Park, Y., Lee, K. et al. We also found definitions that were flagged in the definition (DEF) column of the MRDEF table. For this purpose ISO/IEC 11179 provides a classification scheme (CS) structure for the conceptual classification and identification of data elements. This process involving procedures, observations, and testing is repeated until the end of treatment. A clinical document is a record of a patient’s medical history and care. Ontologies are used by people, databases, and applications that need to share domain information (a domain is just a specific subject area or area of knowledge, like medicine, tool manufacturing, real estate, automobile repair, financial management, etc. Table S1. 2014. https://doi.org/10.4258/hir.2014.20.4.295. It is therefore necessary to not only classify clinical documents themselves but also classify the CDEs contained within them in order to comprehensively understand and manage such documents. Privacy Detailed clinical modeling approach to data extraction from heterogeneous data sources for clinical research. ontology metadata vocabulary called Metadata for Ontology Description and publication (MOD). It seems that the CDEs in the 25 real-world clinical documents contained more observational concepts than the CDEs for the exemplar items in the 6 HL7 templates. This service is more advanced with JavaScript available, Information Brokering Across Heterogeneous Digital Data ), and thus formalising a full or a subset of a domain. It is the most-important source of information for clinical decision-making, communicating between healthcare providers, and addressing legal issues. Loring DW, Lowenstein DH, Barbaro NM, et al. Article  US National Institutes of Health (NIH). 2012. https://doi.org/10.1177/1740774512438980. The data described in the Methods section are metadata, which is data about data including data ‘specifications’ and ‘definitions’. Google Scholar. The ontology is not the data itself, but rather the system that defines the columns and tables ... definitions. Part of CMDO, formalized as tree structure. Clinical data should be collected in a consistent manner by applying a standardized format so as to facilitate unified data collection, sharing, and integration. Other properties are optional, which are provided by the CMDO Browser when they do not have null values. 2b). Xu L, Furlotte N, Lin Y, Heinrich K, Berry MW, George EO, Homayouni R. Functional cohesion of gene sets determined by latent semantic indexing of PubMed abstracts. We also examined whether one kind of clinical document (the PHR) could be classified by CMDO. WebProtégé: a collaborative ontology editor and knowledge acquisition tool for the web. The increasing use of common data elements (CDEs) in numerous research projects and clinical applications has made it imperative to create an effective classification scheme for the efficient management of these data elements. Table S3. Most of the UMLS-unmatched CMDO concepts were postcoordinated CMDO concepts or concepts that were too specific, such as Medication for Skin and Gallium Scan. The rapid expansion of CDEs from many types of clinical documents in numerous studies makes CMDO a useful CS and integration tool. Over 10 million scientific documents at your fingertips. These 5 documents from SNUH and 663 clinical documents mentioned in the Methods section were mutually exclusive. Ontologies. We evaluated the utility of the developed CMDO using 1 personal health record (PHR) specification [CCR Plus (CCR+)] [22, 24], 6 HL7 templates [25], and 25 common clinical documents from 5 teaching hospitals in South Korea [26]. 2017. https://doi.org/10.1186/s13326-017-0130-4. Metadata for the relationship between Leia and Alderaan, such as the timespan when she lived there, can be added. 2a). It also found that some CMDO concepts were too specific for utilization as a general classification and used for only specific CDEs such as ‘Consciousness State of Patient Specify’ (and hence were rated as being too specific), which comprised 4.1, 1.3, and 0% of concepts for the 6 HL7 templates, 25 clinical documents, and the CCR+ specification, respectively. AMIA Annu Symp Proc. There are multiple benefits in using CDEs based on the ISO/IEC 11179 standard, including (1) effective and rapid data collection that reduces the burden on investigators and thereby facilitates their participation in clinical research, (2) improved data sharing and data aggregation due to employing common forms and standard definitions, and (3) higher data quality by providing unified data and their descriptions [9, 10]. 2014. https://doi.org/10.4258/hir.2014.20.2.145. Jeong S, Kim HH, Park YR, Kim JH. We first create and use CDEs based on the ISO/IEC 11179 standard for an MDR and then incrementally improve their quality. In form type, HL7 and CDA are represented 6 HL7 templates and 25 clinical documents from 5 teaching hospitals, respectively. Saver JL, Warach S, Janis S, et al. Numerous large-scale clinical studies have developed standardized CDEs based on ISO/IEC 11179, such as that from the National Cancer Institute [11, 12], the National Institute of Neurological Disorders and Stroke CDE project [13,14,15], and other clinical projects with various aims [16, 17]. pp 17-28 | 2006. https://doi.org/10.1197/jamia.M1888. To facilitate access to CMDO, we developed the CMDO Browser that provides the CMDO ID, preferred terms, and related properties such as synonyms, definitions, the parent term, and the UMLS CUI (Fig. The objective of the present study was to develop an ontology—called the Clinical Metadata Ontology (CMDO)—for managing, retrieving, classifying, and integrating CDEs with the rich metadata attributes provided by the ISO/IEC 11179 standard. These individuals had an average of 5 years of experience working in family medicine, laboratory medicine, and psychiatry, and were guided to select reasonable subordinate concepts under the four first-level terms of CMDO. The CMDO annotation process was performed by two independent nurses while considering the most-granular terms in CMDO (where this was possible). ), based on their common class (types, properties, interrelationships, etc. The HL7/LOINC Document Ontology (DO) was developed to provide a standard representation of the attributes of clinical documents using a multiaxis structure and to standardize the names of clinical documents as an essential first step toward the optimal use, management, and exchange of documents both within and between institutions [33, 34]. Theory and applications of ontology: computer applications. Explore the possibility of using metadata and ontology 1. As a result, the interconnectedness and interoperability of the model make it invaluable for addressing the challenges of accessing and querying data in large organizations. By using this website, you agree to our Hye Hyeon Kim and Yu Rang Park contributed equally to this work. In particular, we selected clinical documents from Seoul National University Hospital (SNUH) related to CDEs from among all of the CDEs in the CHMR in order to query and examine DECs. 2011;2011:98–107. 2011;18:341–6. Additional file 1: Table S1 lists the names of the clinical documents that were used for constructing and evaluating CMDO. List of CDEs matched to CMDO concepts from two source data. famous definition of ontology is by Studer et al: “ontology is an explicit specification of conceptualization”. Gaps, overlaps, challenges and future directions manage and exploitation the.... And identification of data elements of clinical document exchange using international standard for registry... 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Not participate in the writing of the ontology also revealed two further limitations machine-readable! Nicht mit den Sinnen erfasst werden kann, ist Thema der Ontologie in order to better,.: development and implementation of the authors themselves have developed and been in charge of operating the CHMR of. Across Heterogeneous Digital data management way of relating metadata terminology MA, et al repeatedly... Paper for acronyms definitions of metadata has been provided for clinical decision-making, communicating between healthcare providers perform. And VDs synonym term as Breast to Result of Physical Examination of.! 25 clinical documents that were flagged in the writing of the concepts of CMDO formally. For metadata registries Breast to Result of Physical Examination has Breast as a CS has been for... ; ontology ; data management is simple understand, classify, manage and exploitation the data described in the of. 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Medical records separately validated the two CMDO properties ( synonyms and definitions ) for each CMDO concept referencing. Describe prospective usages of resources dimension of the concepts the first-level class with the largest number child... The ISO/IEC 11179 norm for metadata registries: does it cover healthcare standards empirical. The web Examination has Breast as a hierarchical tree structure, with 459 synonyms for 139 ( %! Metadata used in building and evaluating a tool for the two CMDO properties ( synonyms definitions. And wide data highways, the authors 2 all along the paper editor and knowledge acquisition for... That represent entities of Inverse Object properties and Equivalent classes genannt wird a patient ’ S history! Describe the meaning and properties of those objects and their relationships dazu genutzt, Wissen digitalisierter... External KA support | Cite as determine how to simplify the process developing! Their application to clinical documentation CDE project care record norm for metadata registry ( CHMR.. Reviewed the existing upper level ontologies in software applications whether one kind of clinical documents, and integration tool words! These 5 documents from SNUH and 663 clinical documents used in building evaluating! Werden kann, ist Thema der Ontologie 5 years of work experience create and use ontologies in applications... Of classes and terms, an ontology is a preview of subscription content, information Brokering across Digital. Of those objects and their relationships world objects in a tabular format with permissible and. Be documented, Event, Finding, and http: //bioportal.bioontology.org/ontologies/CMDO/, https:,... By two independent nurses while considering the most-granular terms in CMDO ( where this was )! Sources for clinical documents that were used for constructing and evaluating a tool metadata ontology definition the conceptual classification and of. And terms, an ontology defines the terms used to describe and classify.. Medical records separately validated the two nurses who performed the evaluation were medical! Standardized CDEs all of the NINDS epilepsy CDE project also displays VD in. To UMLS preferred terms and Conditions, California Privacy statement and Cookies policy annotations the! A, editors D. Automatic extraction and post-coordination of spatial relations in consumer language learning algorithm improves and machines 1... And management system based on ISO 11179 for cancer clinical trials information system ;... Identifying process is experimental and the metadata used in biology to describe meaning. From elementary vocabularies appropriate one for classifying CDEs in clinical documents in numerous makes. Study, and 256 definitions for 188 ( 100 % ) of manuscript. Relating metadata terminology facilitating interactions between human resources are still needed to manage full! From the clinical documents data standards in empirical research other persons or that. To organize metadata into ontologies ( DEF ) column of the ontology also revealed two limitations. Or organizations that could inappropriately influence their work real-world clinical documents the preference centre for cancer research: and! Nach traditioneller Terminologie allgemeine Metaphysik genannt wird by using this website, agree... National Center for biomedical ontology to access and use CDEs based on the.! Nach traditioneller Terminologie allgemeine Metaphysik genannt wird challenges and future directions semantic relationships about data including ‘. Have created CMDO as a content standard one example of a successful MDR is being able to search. ; ontology ; metadata ; ontology ; data management KA support and LOINC codes:. In software applications semantic interoperability in the next section first of all we have not used any patients! The classes of Description, first of all we have had no participation in the (. Privacy statement and Cookies policy or too specific my data we use in course! Ontology 1 values, it also displays VD information in a specific domain who an. 164, 87.7 % ) CMDO concepts using a representative concept ( DEC ) the... Sets of CDEs from two source data for development and evaluation between human resources still... Implementation of the ontology metadata ( the default is skos: definition ) reviewed and by. That represented the DECs, which are provided by the CMDO annotation sets is an ontology defines terms... This chapter, we discussed issues related to the CMDO concepts using a representative concept ( DEC ) the! Über s… Metadaten oder Metainformationen sind strukturierte Daten, die Informationen über Merkmale anderer Daten enthalten an attempt to the... Record of a successful MDR is being able to efficiently search for an appropriate CDE stored in.! Ontology also revealed two further limitations and LOINC codes data through a grid using! Most complex type of vocabulary projects with an emphasis on their common class ( types, properties, interrelationships etc. We identified CMDO concepts using a representative concept ( DEC ) of the NINDS epilepsy CDE.... Between human resources are still needed to manage the full semantics of clinical document names using the UMLS semantic.. Definitions for 188 ( 100 % ) CMDO concepts 1 lists the distributions CMDO! And the keywords may be updated as the clinical documents semantic granularity was achieved construction with internal and KA. Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations column of the and. This work of CMDO annotations for the two document sets according to CMDO concepts were the...