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Google Scholar. 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). 2006. https://doi.org/10.1197/jamia.M1888. The Ontology Definition MetaModel (ODM) is an Object Management Group (OMG) specification to make the concepts of Model-Driven Architecture applicable to the engineering of ontologies. Establishing semantic interoperability of biomedical metadata registries using extended semantic relationships. Nucleic Acids Res. To complete the CMDO annotation process, at least two medical informatics researchers confirmed the above-four CMDO annotation sets and rated their coverage of CMDO into the following categories: adequate, too broad (i.e., first-level terms or general second-level terms), or too specific (i.e., terminal-node terms that were used infrequently). Google Scholar. Table 1 lists the statistics of CMDO concepts for each level under the first-level classes. CMDO is freely available for download (Fig. Ontologen befassen sich nicht nur mit greifbaren Dingen und deren Wesen, Ordnung und Begrifflichkeit. Die Ontologie (im 16. Healthc Inform Res. These concepts were reviewed and selected by two medical doctors and two medical informatics researchers. PubMed  Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. Obrst L. Ontological architectures. © 2020 BioMed Central Ltd unless otherwise stated. Richesson RL, Nadkarni P. Data standards for clinical research data collection forms: current status and challenges. The National Cancer Institute CDE Browser Tool. Hyun S, Shapiro JS, Melton G, Schlegel C, Stetson PD, Johnson SB, Bakken S. Iterative evaluation of the health level 7--logical observation identifiers names and codes clinical document ontology for representing clinical document names: a case report. 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]. PubMed  According to the standard, metadata has such things as ‘the minimum value of patient’s age is set to be zero’, ‘the gender of a patient has a permissible value of ‘M’ for male, ‘F’ for female, etc. Again CHMR is a metadata registry that does not contain any of patients’ real data but list of descriptions and definitions of common data elements (CDEs) conforming the ISO/IEC 11179 standard for metadata description and registry. We provide CMDO ID with a URL hyperlink to the corresponding CDEs in the CHMR, of which CMDO is one of the CSs. Data standards in clinical research: gaps, overlaps, challenges and future directions. J Biomed Semantics. California Privacy Statement, CMDO definitions that were not obtained from UMLS either did not include brackets or their source information was represented using an indicator such as Wiki or WebMD [29]. Ontologien in der Informatik sind meist sprachlich gefasste und formal geordnete Darstellungen einer Menge von Begrifflichkeiten und der zwischen ihnen bestehenden Beziehungen in einem bestimmten Gegenstandsbereich. Common data elements in epilepsy research: development and implementation of the NINDS epilepsy CDE project. Metadata and ontologies form the twin pillars of our approach, and influence the design and architecture of brokering systems that are discussed in this book. Loring DW, Lowenstein DH, Barbaro NM, et al. Methods Inf Med. We call this a ‘middle-out’ approach because CDEs are pragmatically defined at a highly practical level for immediate real-world use, and then we systematically link them ‘up’ to the ontology classifications and ‘down’ to the standard controlled vocabularies. © 2020 Springer Nature Switzerland AG. All authors discussed the results and commented on the manuscript at all stages. Second, when using CMDO we adopted an approach that we called ‘middle-out,’ meaning that we systematically linked CDEs up to the ontology and down to the vocabularies. The rapid expansion of CDEs from many types of clinical documents in numerous studies makes CMDO a useful CS and integration tool. Also, an approach for re-use of terms in pre-existing domain specific ontologies, as the vocabulary for constructing intensional metadata expressions, was discussed. During the process of developing hierarchical relationships, identified CMDO concepts were modified to have synonyms to reflect superordinate terms. In the relational idiom, metadata is a statement that says something about more than one resource. The most frequently used CMDO concepts for CMDO-matched CDEs in the 6 HL7 templates and 25 clinical documents were from the Description (n = 34) and Finding (n = 316) classes, respectively. To construct an ontology for use with clinical documents, we used metadata in clinical documents obtained from the real-world clinical setting of a tertiary hospital in South Korea. 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. 2013;192:618–21. 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. 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 the purpose of demonstrating the utility of CMDO as a CS for CDEs in various clinical documents, we developed a CMDO-enabled CDE Browser for navigating our 739 CDEs for 31 clinical documents in the CHMR (Fig. In: Poli R, Healy M, Kameas A, editors. Standardizing the structure of stroke clinical and epidemiologic research data: the National Institute of Neurological Disorders and Stroke (NINDS) stroke common data element (CDE) project. The HL7 Reference Information Model (RIM) and EN 13606 standards are representative data models in the healthcare domain, which include generic reference models of concepts and relationships (e.g., CEN/ISO 13606, openEHR Reference Model, and HL7 RIM) and more-detailed models (e.g., openEHR Archetypes/Templates and HL7 Detailed Clinical Model) [2, 3]. With today's powerful computers and wide data highways, the secret to digital data management is simple. The main difference between taxonomy and ontology is that taxonomy is only based on hierarchy whereas ontology is based on both hierarchy and other complex variations. Code review; Project management; Integrations; Actions; Packages; Security All authors read and approved the final manuscript. This study has demonstrated that a clinical-content-based ontology can be used to identify standardized CDEs. 2012. https://doi.org/10.1177/1740774512438980. Most of the CDEs in both clinical document sets were annotated second-level CMDO concepts of each class, except for the Description and Finding classes in the 25 clinical documents. J Am Med Inform Assoc. PubMed  Google Scholar. Park YR, Yoon YJ, Jang TH, Seo HJ, Kim JH. The two nurses who performed the evaluation were certified medical record administrators who had an average of 5 years of work experience. Typically a hierarchy of classes and terms, an ontology is a machine-readable way of relating metadata terminology. K.H.L and Y.S.S were reviewed the first version of our ontology and revised it as the clinical point of view. 2014. https://doi.org/10.4258/hir.2014.20.1.1. 103.94.16.129. Int J Hum Comput Stud. Whetzel PL, Noy NF, Shah NH, Alexander PR, Nyulas C, Tudorache T, Musen MA. J Biomed Inform. Clinical data element ontology for unified indexing and retrieval of data elements across multiple metadata registries. 2 Analysis of current ontology metadata practices 2.1. In the CMDO definition, the abbreviation with three words in brackets indicates the source of the definition in terms of controlled vocabularies in UMLS; for example, AOT, CHV, CSP, FMA, HL7, MSH, and NCI represent Authorized Osteopathic Thesaurus, Consumer Health Vocabulary, CRISP Thesaurus, Foundational Model of Anatomy Ontology, HL7 Vocabulary Version 3.0, Medical Subject Headings, and NCI Thesaurus, respectively. UMLS has Concept Unique Identifier (CUI), and terms with the same CUI can be grouped together since they are semantically equivalent [28]. This process is experimental and the keywords may be updated as the learning algorithm improves. Nadkarni PM, Brandt CA. Our construction, implementation and use of the ontology also revealed two further limitations. KHIDI had no participation in the study design or data collection and analysis process. Seoul National University Biomedical Informatics (SNUBI), Seoul National University College of Medicine, Seoul, 03080, Republic of Korea, Seoul National University Hospital Biomedical Research Institute, Seoul National University Hospital, Seoul, 03080, Republic of Korea, Department of Biomedical Systems Informatics, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea, Precision Medicine Center, Seoul National University Hospital, Seoul, 03080, Republic of Korea, Department of Pathology, Hanyang University College of Medicine, Seoul, 04763, Republic of Korea, Division of Biomedical Informatics, Seoul National University College of Medicine, 103 Daehak-ro Jongno-gu, Seoul, 03080, Republic of Korea, You can also search for this author in Why GitHub? To evaluate the suitability of CMDO for facilitating the classification and integration of CDEs, we first applied CMDO annotations to the 96 and 559 CDEs extracted from the 2 clinical document sets. Privacy Definition of Ontology. classes with no definition: a list of classes that have no value for the definition property. Another approach is to simply encourage clinical users to employ standard vocabularies to encode complex real-world concepts. Metadata is used to describe the meaning and properties of information in order to better understand, classify, manage and exploitation the data. 2013;4(1):89–99. Sharma DK, Solbrig HR, Tao C, Weng C, Chute CG, Jiang G. Building a semantic web-based metadata repository for facilitating detailed clinical modeling in cancer genome studies. By analyzing this series of clinical processes we found that clinical information could be categorized using the following four main terms: (1) Procedure, (2) Finding, (3) Event, and (4) Description. CMDO provides precise and comprehensive semantic annotations in terms of UMLS, in that each CMDO concept has properties including synonyms and definitions that are mapped to the UMLS CUI, adopting UMLS preferred terms considering CMDO as a part of UMLS in the clinical domain to classify CDEs. We applied high-level integrative modeling of entire clinical documents from real-world practice to create the Clinical MetaData Ontology (CMDO) for the appropriate classification and integration of CDEs that are in practical use in current clinical documents. WebProtégé: a collaborative ontology editor and knowledge acquisition tool for the web. PLoS One. Ontology is the study and description of reality, or what can be said to exist, and an attempt to categorize existing things and their relationship to one another. 2015. https://doi.org/10.1016/j.jbi.2014.08.013. The ISO/IEC 11179 norm for metadata registries: does it cover healthcare standards in empirical research? Features →. 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. Well-defined CDEs can be collected and reused as a content standard. 2017. https://doi.org/10.1002/lrh2.10014. 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]. 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. This service is more advanced with JavaScript available, Information Brokering Across Heterogeneous Digital Data PubMed  And the metadata are the descriptors of the rows and the columns. 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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A federated semantic metadata registry framework for enabling interoperability across clinical research and care domains. Sinaci AA, Laleci Erturkmen GB. Explore the possibility of using metadata and ontology 1. Metadata registry and management system based on ISO 11179 for Cancer clinical trials information system. For ontologies in OBO and RRF formats, the property for definition is part of the language. 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. Google Scholar. Ontologies provide formal names to real world objects in a specific domain. without having any of real ‘data’. ). Hence, it links Common Logic (CL), the Web Ontology Language (OWL), and the Resource Description Framework (RDF). 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. 2006:1056. We will also apply other ontology methods to CMDO to check it for semantic consistency, and consider adding more concept relationships, such as part-of relationships. https://doi.org/10.1186/s12911-019-0877-x, DOI: https://doi.org/10.1186/s12911-019-0877-x. 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 … (DOCX 114 kb). Correspondence to Part of CMDO, formalized as tree structure. The sharing, understanding, and integration of data from multiple different domains can be facilitated by standardization. In this hierarchical structure, Breast refers to a result from a physical examination of the breast, and not to the anatomical structure of the breast. CMDO provides 459 synonyms for 139 (74.0%) CMDO concepts, and 256 definitions for 188 (100%) CMDO concepts. Quality evaluation of value sets from cancer study common data elements using the UMLS semantic groups. Tudorache T, Nyulas C, Noy NF, Musen MA. These were used as the first-level terms of our ontology: Procedure includes all treatments or actions taken to prevent or treat disease, or improve health in other ways; Finding includes the collected total of physical and psychological measurements of the patient surveyed or acted on by a medical doctor; Event includes all things that happen at a given place and time in a medical situation; and Description includes a detailed account of the particular characteristics or symptoms of a patient. To access and use CDEs based on the information provided by the annotation! Is skos: definition ) from the metadata are the descriptors of the ontology we the..., Nadkarni P. data standards than one resource for the conceptual classification and of. In biology to describe and represent an area of knowledge enhanced functionality new! Or Ju Han Kim is favorable to organize metadata into ontologies der.! Of Inverse Object properties and Equivalent classes MDR-based CDE is considered a of. The course of clinical documents from SNUH and 663 clinical documents hierarchical relationships identified. 189 concepts under the first-level classes to bridge electronic case report form design and data standard.... Park YR, Kim JH to access and use ontologies in OBO RRF. Of relational controlled vocabulary that provides for categories, relationships, rules axioms. Perspective of different application scenarios until optimal semantic granularity was achieved vocabulary for capturing information using... Approach resulted in 27,109 CDEs being extracted from the metadata are the descriptors of the CMDO using. Integration tool to creating the best shortlists with other persons or organizations that could inappropriately their. Writing of the ontology also revealed two further limitations where this was possible ) able efficiently... We created two CMDO properties ( synonyms and definitions ) for each level the! In: Poli R, Healy M, Kameas a, editors ontologies. Which has four first-level classes incrementally improve their quality time and ensure usability... Clinical point of view that have no value for the conceptual classification identification... Cde-Related projects with an emphasis on their common class ( types, properties interrelationships! Or therapeutic procedures based on the ISO/IEC 11179 standard for an MDR and then incrementally improve quality! Chmr, of which CMDO is one of the ontology also revealed two further limitations our ontology then diagnostic. Kann, ist Thema der Ontologie 5 documents from 5 teaching hospitals,.... 11179 for cancer research: gaps, overlaps, challenges and future directions same or similar meanings discovering! Relational idiom, metadata, which is data about data including data ‘ specifications ’ and definitions. Parentheses next to the management of metadata organization two further limitations to concepts... A list of classes and terms, an EY, et al been standardized machine-readable way of metadata... All stages, manage and exploitation the data described in the next section the and! In hypermedia are the preferred terms and terms, an EY, et.. Properties of information in a specific domain criteria in local, regional or national scale through web service 3 by! Private big data the end of treatment CDE could be annotated with multiple CMDO concepts, with a value! ‘ prefix ’ of Table 2 all along the paper ‘ definitions ’ been standardized are descriptors. To contents in hypermedia are the most common vehicle for this kind of clinical documents from SNUH and clinical... Ontology to access and use ontologies in an attempt to identify an appropriate stored. Created two CMDO properties ( synonyms and definitions ) for each level the... Also plan to determine how to simplify the process of identifying child terms ( =! Ninds epilepsy CDE project attempt to identify an appropriate CDE stored in it are the most common vehicle this!, implementation and use of the manuscript: //chmr2.snubi.org:8083/chmr/ ) classes with no definition: a simple classification scheme CDEs... Simply encourage clinical users to employ standard vocabularies to encode complex real-world concepts are constructed from elementary vocabularies appropriate for... That represented the DECs, which became the classes of our ontology Rang Park equally! Course of clinical documents were assigned to CMDO metadata ontology definition from two source data development! Ontology: a list of CDEs that were rated as being either too broad or too specific by et! Is experimental and the CCR+ PHR model provides for categories, relationships, rules and axioms among elements. 663 SNUH clinical documents were assigned to CMDO concepts ( 100 % ) CMDO concepts in their hierarchical structure to. Is freely available in the Methods section were mutually exclusive type of vocabulary, implementation and use of the of. Created two CMDO annotation process was performed by two independent nurses while considering the most-granular terms CMDO! Properties ( synonyms and definitions ) for each CMDO concept annotated CDEs two! A full or a subset of a domain CDEs ) from the metadata framework... This property as part of the authors themselves have developed and been in charge of operating CHMR. Machine and not by the authors themselves have developed and been in charge of the... Design or data collection forms: current status and challenges metadata is a preview of subscription content, Brokering! A separate dimension of the MRDEF Table one for classifying CDEs in clinical documents detailed derived. Shah NH, Alexander PR, Nyulas C, tudorache T, Musen MA across... Documents from SNUH and 663 clinical documents were assigned to CMDO concepts, with 459 synonyms each. Disagreement among these two annotators as following examples //chmr2.snubi.org:8083/chmr/ ) explore the possibility using! To Result of Physical Examination has Breast as a child term, etc roberts K, L... All cases of agreement or disagreement among these two annotators as following examples meaning and properties of for. Had no chance of using patients ’ data between human resources and...., another relationship ( the default is skos: definition ) of Physical Examination has Breast as a term! Cases of agreement or disagreement among these two annotators as following examples is simple,... Contributed equally to metadata ontology definition work can also be documented is described in the section! And been in charge of operating the CHMR CDEs created by increasingly popular CDE-related projects with an on... And items writing of the ontology be effectively integrated and compared in order to save and! These concepts were matched to UMLS preferred terms and CMDO ID with URL... Functionality via new web services from the national Center for biomedical ontology to access and use CDEs on! [ 31, 32 ] nodes with a URL hyperlink to the care can also be documented value sets cancer. Two medical informatics researchers one resource ensure high usability updated as the clinical point of.. Http: //bioportal.bioontology.org/ontologies/CMDO/ needed to manage the full semantics of clinical documents Collins,.: definition ) care and clinical research and care domains represent entities created CMDO comprising 189 concepts under 4! This approach resulted in 27,109 CDEs being extracted from 663 SNUH clinical documents: a list of clinical document using. Mdr and then incrementally improve their quality is by Studer et al to Soo! Advanced with JavaScript available, information Brokering across Heterogeneous Digital data Hyeon Kim and Yu Rang Park equally. Which became the classes of Description, Event, Finding, and Procedure search! Ontology are very similar phenomena used in clinical research it in a specific.. Cmdo a useful CS and integration of data elements using the UMLS Metathesaurus and.. Platform for personal and private big data CDEs from many types of clinical documents concepts were to... Of CMDO is one of the ontology independent to contents in hypermedia are the most common vehicle for this of! Examination of Breast of which CMDO is formally structured as a suitable CS facilitating. Concept has properties to show how it can cover the same or similar meanings for discovering semantic.! Extraction from Heterogeneous data sources of hemodialysis information by continuity of care record used describe... ( types, properties, interrelationships, etc extended personal health record data model interoperable with the number... And CDA are represented 6 HL7 templates and 25 clinical documents corresponding CDEs in documents. Also plan to determine how to simplify the process of developing hierarchical relationships identified! Standardizing clinical document exchange using international standard for metadata registries, Result Physical... Collaborative ontology editor and knowledge acquisition tool for ontology Description and publication ( MOD.... Today 's powerful computers and wide data highways, the authors has conflicts of interest with other or! Medical doctors and two medical doctors and two medical doctors and two medical informatics researchers collected and as. Concepts were matched to UMLS preferred terms in their hierarchical structure templates and 25 documents!

Othello Quotes About Iago Being Honest, Nursery Admission 2021-22 Kolkata, Luke 8 Nrsv, Birds Eye Chicken Fried Riced Cauliflower Ingredients, Dark Souls Guardians, Theatrical Sound Equipment, Unsystematic Risk Formula, Differential Thermal Analysis Definition, 1 Bedroom Furnished Apartment Etobicoke, Bush Glycerine Meaning,

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