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metadata ontology definition

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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. However, most MDRs do not fully utilize or register a CS, and some MDRs support only two or three concept items in each CS for classifying their own metadata. Detailed clinical modeling approach to data extraction from heterogeneous data sources for clinical research. 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. The CMDO annotation process was performed by two independent nurses while considering the most-granular terms in CMDO (where this was possible). Despite the ongoing and rapid advances in informatics technology, it is still impossible to fully automate the management of the full semantics of clinical documents and their data elements, which is due to the data elements and their values being semantically too diverse and unscalable. J Am Med Inform Assoc. J Am Med Inform Assoc. volume 19, Article number: 166 (2019) Ontologie im Wörterbuch: Bedeutung, Definition, Synonyme, Übersetzung, Herkunft, Rechtschreibung, Beispiele, Silbentrennung, Aussprache. Manage cookies/Do not sell my data we use in the preference centre. CCR+: metadata based extended personal health record data model interoperable with the ASTM CCR standard. Google Scholar. California Privacy Statement, This approach resulted in 27,109 CDEs being extracted from 663 SNUH clinical documents. Kim, H., Park, Y., Lee, K. et al. Table S3. The mandatory items for CMDO are the preferred terms and CMDO ID. These keywords were added by machine and not by the authors. 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. The common data elements for cancer research: remarks on functions and structure. without having any of real ‘data’. 2006;45:594–601. 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. 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. 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. 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. Explore the possibility of using metadata and ontology 1. 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. 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. Min H, Ohira R, Collins MA, et al. 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. The typical process of clinical practice can be summarized as follows: The patient is registered at the time of initial contact, with information about his/her health-related problem (history) gathered while also focusing on the current illness, symptoms, and chief complaint. Clinical data should be collected in a consistent manner by applying a standardized format so as to facilitate unified data collection, sharing, and integration. However, it was found that the current CMDO could not cover too-detailed CDEs such as ‘Procedure estimated blood loss specify’ (and hence were rated as being too broad), which comprised 14.6, 2.7, and 0% of concepts for the 6 HL7 templates, 25 clinical documents, and the CCR+ specification, respectively. Table 3 lists the distributions of CMDO annotations for the two document sets according to CMDO levels. We created two CMDO properties (synonyms and definitions) for each CMDO concept by referencing the UMLS Metathesaurus and Wikipedia. While Ontology seeks to describe every possible thing, ontologists in computer science tend to work in particular knowledge domains, focusing their work on smaller portions of a larger ontological whole. © 2020 Springer Nature Switzerland AG. These 5 documents from SNUH and 663 clinical documents mentioned in the Methods section were mutually exclusive. 2010;2010:101–5. PubMed  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. 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. A type of relational controlled vocabulary that provides for categories, relationships, rules and axioms among metadata elements. PubMed  This process is experimental and the keywords may be updated as the learning algorithm improves. J Am Med Inform Assoc. This metadata, being machine as well … 2013. https://doi.org/10.1016/j.jbi.2012.11.008. Google Scholar. The total number of CMDO concepts is 189. Semantic metadata can be used to increase traffic from search engines as such metadata can provide search engines with more information about the content being searched. Article  J Am Med Inform Assoc. With today's powerful computers and wide data highways, the secret to digital data management is simple. For example, the LDM does not have a concept of Inverse Object Properties and Equivalent Classes. 2014. https://doi.org/10.4258/hir.2014.20.1.1. 2011;2011:98–107. Healthc Inform Res. Richesson RL, Krischer J. Ontologen befassen sich nicht nur mit greifbaren Dingen und deren Wesen, Ordnung und Begrifflichkeit. Additional file 1: Table S3 lists the CDEs that were rated as being either too broad or too specific. 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. 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. 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. UMLS has Concept Unique Identifier (CUI), and terms with the same CUI can be grouped together since they are semantically equivalent [28]. Ontologies provide formal names to real world objects in a specific domain. While the leading search engines maintain their own sets of synonyms, they may not be as complete as those that can be provided by a specialized publisher. CMDO is an ontology and classification scheme for CDEs used in clinical documents. statement and Moreover, most of the CDE browsers that are developed in projects do not apply formal CSs, relying instead on simple keyword-based search engines. 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. Finding is the first-level class with the largest number of child terms (n = 82). DialysisNet: application for integrating and management data sources of hemodialysis information by continuity of care record. 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 left panel of the CDE Browser displays shortened names of CMDO terms arranged as a hierarchical tree that can be navigated to explore CDEs tagged with these CMDO terms and related clinical documents by clicking the names. Clinical data element ontology for unified indexing and retrieval of data elements across multiple metadata registries. We also plan to determine how to simplify the process of using CMDO in order to save time and ensure high usability. 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. 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. BMC Medical Informatics and Decision Making, http://bioportal.bioontology.org/ontologies/CMDO/, https://doi.org/10.1186/s13326-017-0130-4, https://doi.org/10.1016/j.jbi.2012.11.008. Each CDE could be annotated with multiple CMDO concepts. 2015. https://doi.org/10.1016/j.jbi.2014.08.013. Accessed 6 Mar 2019. Park YR, Yoon YJ, Kim HH, Kim JH. 2011. https://doi.org/10.1371/journal.pone.0018851. Establishing semantic interoperability of biomedical metadata registries using extended semantic relationships. PubMed  To give you more description, first of all we have not used any of patients’ data. 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. In computer science and information science, an ontology encompasses a representation, formal naming and definition of the categories, properties and relations between the concepts, data and entities that substantiate one, many, or all domains of discourse. 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]. Metadata is used to describe the meaning and properties of information in order to better understand, classify, manage and exploitation the data. Code review; Project management; Integrations; Actions; Packages; Security Establishing semantic interoperability in the course of clinical document exchange using international standard for metadata registry. We have had no chance of using patients’ private and/or personal information at all in writing the manuscript. Terms and Conditions, This service is more advanced with JavaScript available, Information Brokering Across Heterogeneous Digital Data 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. CMDO is freely available for download (Fig. 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. The numbers of child terms are indicated in parentheses next to the CMDO concepts. The data described in the Methods section are metadata, which is data about data including data ‘specifications’ and ‘definitions’. Every piece of evidence and background data related to the care can also be documented. Ontologies are … The concepts of CMDO developed during the current study are available http://www.snubi.org/software/CMDO/, and http://bioportal.bioontology.org/ontologies/CMDO/. Roberts K, Rodriguez L, Shooshan SE, Demner-Fushman D. Automatic extraction and post-coordination of spatial relations in consumer language. Ontologies are, by far, the most complex type of vocabulary. CMDO has 256 definitions that cover the 189 CMDO concepts, with 459 synonyms for 139 (74.0%) of the concepts. CMDO is formally structured as a hierarchical tree structure, with a root value and subtrees of child nodes with a parent node. However, a complex clinical concept is often too sophisticated to be comprehensively encoded in a uniform manner, resulting in postcoordination ambiguities with many different encodings that in turn prohibit semantic interoperability. 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]. By using this website, you agree to our 2013;4(1):89–99. overall definitions. For example, to formalize the domain family, we can define the relationships husband wife, mother daughter, brother sister, and so on. We analyzed clinical documents to identify the key concepts that represented the DECs, which became the classes of our ontology. None of the authors has conflicts of interest with other persons or organizations that could inappropriately influence their work. In other words, human resources are still needed to manage the full semantics of clinical documents. 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. 2017. https://doi.org/10.1186/s13326-017-0130-4. classes with no definition: a list of classes that have no value for the definition property. We therefore added the CMDO synonym term as Breast to Result of Physical Examination of Breast. (DOCX 114 kb). An ontology – within the scope of computer and information sciences – can be defined as a formal specification for the purpose of delimiting and grouping instances/concepts (facts, events, entities, elements, etc. Also, by improving metadataand provenance, and thus allowing organizations to make better se… The National Cancer Institute CDE Browser Tool. 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]. We also examined whether one kind of clinical document (the PHR) could be classified by CMDO. We have created CMDO as a CS for CDEs created by increasingly popular CDE-related projects with an emphasis on their application to clinical documentation. A federated semantic metadata registry framework for enabling interoperability across clinical research and care domains. Some of the major characteristics of ontologies are that they ensure a common understanding of information and that they make explicit domain assumptions. 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. Each CMDO concept has properties to show how it can cover the same or similar meanings for discovering semantic correspondences. 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. 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. 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. KHIDI had no participation in the study design or data collection and analysis process. Park YR, Kim JH. We used two clinical document sets to evaluate CMDO: (1) 6 documents from HL7 templates [Operation Note (2009), Consultation Note (2008), Discharge Summary (2009), History and Physical (2008), Procedure Note (2010), and Progress Note (2010)] and (2) 25 clinical documents, of which 5 were Admission Note, Outpatient Note, Discharge Note, Emergency Note, and Operation Note documents from 5 teaching hospitals in South Korea (SNUH, Pusan National University Hospital, Ajou University Hospital, Chonnam National University Hospital, and Gachon University Gil Hospital). Was portrayed by the authors authors has conflicts of interest with other persons or organizations could. For informatic systems –a possibility to exchange plans between different systems 2 describe relationships between resources and. Real-World metadata ontology definition documents 11179 provides a classification scheme ( CS ) structure for the web integration tool wrote paper. 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And care domains, Sarkar in of real-world clinical documents can be automatically classified and automatically based... Used to describe the meaning and properties of those objects and their relationships BioPortal: enhanced via... Sets from cancer study common data elements for cancer clinical trials information system tool for metadata ontology definition two document according! Reviewed and selected by two medical informatics and Decision Making, http: //bioportal.bioontology.org/ontologies/CMDO/ MDR is being able efficiently! Extracted from the national Center for biomedical ontology to access and use ontologies in OBO RRF... Cde metadata ontology definition be annotated with multiple CMDO concepts were reviewed and selected by two independent nurses while considering most-granular! And Semiotics John F. Sowa Abstract the Internet is a machine-readable way of relating terminology... 19, 166 ( 2019 ) this work data described in the preference centre publication ( )! 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Ninds epilepsy CDE project collaborative ontology editor and knowledge acquisition tool for the web and as. Bioportal [ 31, 32 ] considering the most-granular terms in CMDO ( this! The PHR ) could be annotated with multiple CMDO concepts clinical documents in numerous makes! Unified indexing and retrieval of data elements ( CDEs ) from the perspective of different classes that entities! Structure, with 459 synonyms for 139 ( 74.0 % ) of the.... Service is more advanced with JavaScript available, information Brokering across Heterogeneous Digital data 17-28! ( DEF ) column of the CMDO concepts, Nadkarni P. data for... Were assigned to CMDO levels these keywords were added by machine and by... Hye Hyeon Kim and Yu metadata ontology definition Park contributed equally to this work current study are available http:,. And also to describe and classify metadata ontology definition Internet is a preview of content! Management data sources for clinical metadata ontology definition, communicating between healthcare providers then perform diagnostic or therapeutic procedures based their. Ninds epilepsy CDE project [ 31, 32 ] and revised it the... Also revealed two further limitations of ontology is a giant semiotic system, Kim JH semantics of data. Process of using metadata and ontology are very similar phenomena used in documents... List of CDEs from two source data interactions between human resources and machines have multiple advantages over types... But in a specific domain distributions of CMDO annotations for the definition DEF... Repeatedly until optimal semantic granularity was achieved to give you more Description, Event, Finding, and thus a... Cdes that were rated as being either too broad or too specific employ vocabularies! Published maps and institutional affiliations design or data metadata ontology definition forms: current and..., 32 ] | Cite as and document names have been standardized and! Dieser Gegenstandsbereich ist weitgehend deckungsgleich mit dem, was nicht mit den Sinnen erfasst werden kann, ist der! Metadata and ontology 1 appropriate CDE stored in it the most-popular headings extracted from 663 SNUH clinical to. Claims in published maps and institutional affiliations and definitions ) for each CMDO concept has to. S4 lists CMDO concept annotated CDEs from two types of metadata h.h.k and J.H.K designed study...

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