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By using this website, you agree to our Kim JH. These classes are the different taxonomic ranks known … A classification of metadata based on information content captured was discussed, and domain specific metadata was identified as the most appropriate for information brokering. Lim Choi Keung SN, Zhao L, Rossiter J, McGilchrist M, Culross F, Ethier JF, Burgun A, Verheij RA, Khan N, Taweel A, Curcin V, Delaney BC, Arvanitis TN. 2011;2011:98–107. All authors discussed the results and commented on the manuscript at all stages. To give you more description, first of all we have not used any of patients’ data. Dordrecht: Springer; 2010. p. 27–66. 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. For example, an admission note and discharge summary may share many CDEs such as the chief complaint, present illness, and past history, making them structurally similar but with very different administrative roles. Download preview PDF. For example, Result of Physical Examination has Breast as a child term. BioPortal: enhanced functionality via new web services from the National Center for biomedical ontology to access and use ontologies in software applications. Not affiliated http://bioportal.bioontology.org/ontologies/CMDO/. A multi-technique approach to bridge electronic case report form design and data standard adoption. 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. This process involving procedures, observations, and testing is repeated until the end of treatment. CMDO web services: (a) CMDO Browser and (b) CMDO-enabled CDE Browser., (c) CMDO Download Function (OWL). Ontologies have multiple advantages over other types of metadata organization. We reviewed the existing upper level ontologies in an attempt to identify an appropriate one for classifying CDEs in clinical documents. Ontologies also provide descriptive properties of those objects and their relationships. Keywords Semantic Interoperability Document Type Definition Metadata Description Domain Specific Ontology Information Brokering However, clinical documents within the same DO classification may be semantically diverse, and those that are in different DO classifications may have a multitude of CDEs in common. Lin CH, Wu NY. 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. Metadata is used to describe the meaning and properties of information in order to better understand, classify, manage and exploitation the data. We created two CMDO properties (synonyms and definitions) for each CMDO concept by referencing the UMLS Metathesaurus and Wikipedia. Often, it is favorable to organize metadata into ontologies. However, a major problem of this top-down ontology-construction approach is that it takes an unacceptably long time for users to adopt and use them under all possible situations that are encountered in healthcare [4]. J Am Med Inform Assoc. We identified CMDO concepts using a representative concept (DEC) of data elements (CDEs) from the metadata registry (CHMR). These concepts were reviewed and selected by two medical doctors and two medical informatics researchers. Table S2. The ISO/IEC 11179 norm for metadata registries: does it cover healthcare standards in empirical research? For ontologies in OBO and RRF formats, the property for definition is part of the language. © 2020 BioMed Central Ltd unless otherwise stated. Int J Hum Comput Stud. Dolin RH, Alschuler L, Boyer S, Beebe C, Behlen FM, Biron PV, Shabo Shvo A. HL7 clinical document architecture, release 2. 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. Keyword searching suffers from imprecision and ambiguity; for example, documents containing synonyms of the query keywords will not be retrieved, and homonyms cannot be properly managed. CMDO provides 459 synonyms for 139 (74.0%) CMDO concepts, and 256 definitions for 188 (100%) CMDO concepts. Ontologies. Generally speaking, ontology is used to describe concepts and concepts’ relationships in a domain or an even wider Detailed labels derived from one ontology not only connect everything but are critical to creating the best shortlists. The main limitation we have experienced during the long-term use of an MDR is the lack of an ontology that can be used to semantically group, search, and integrate metadata. However, we found no multiple annotations in the CCR+ specification, and the CMDO concepts in the Description class (i.e., 8 concepts for 81 CDEs) were frequently used for annotating CDEs from there. Nucleic Acids Res. 2011;18:341–6. We also plan to determine how to simplify the process of using CMDO in order to save time and ensure high usability. 2006. https://doi.org/10.1197/jamia.M1888. PubMed  KHIDI did not participate in the writing of the manuscript. Accessed 6 Mar 2019. 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. For example, to formalize the domain family, we can define the relationships husband wife, mother daughter, brother sister, and so on. 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. Article  Cookies policy. PubMed Central  Clinical data element ontology for unified indexing and retrieval of data elements across multiple metadata registries. 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 Google Scholar. We also found definitions that were flagged in the definition (DEF) column of the MRDEF table. 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]. This is a preview of subscription content, Information Brokering Across Heterogeneous Digital Data. All authors read and approved the final manuscript. Ontologie im Wörterbuch: Bedeutung, Definition, Synonyme, Übersetzung, Herkunft, Rechtschreibung, Beispiele, Silbentrennung, Aussprache. Semant Web. In this chapter, we discussed issues related to the management of metadata from the perspective of different application scenarios. Additional file 1: Table S2 lists all of the CMDO concepts in their hierarchical structure. Table 3 lists the distributions of CMDO annotations for the two document sets according to CMDO levels. Richesson RL, Nadkarni P. Data standards for clinical research data collection forms: current status and challenges. 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. PubMed Central  For this purpose ISO/IEC 11179 provides a classification scheme (CS) structure for the conceptual classification and identification of data elements. 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. Jeong S, Kim HH, Park YR, Kim JH. 2010;2010:101–5. 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. 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. Whetzel PL, Noy NF, Shah NH, Alexander PR, Nyulas C, Tudorache T, Musen MA. 2012. https://doi.org/10.1136/amiajnl-2011-000739. Metadata for the relationship between Leia and Alderaan, such as the timespan when she lived there, can be added. 2014. https://doi.org/10.1136/amiajnl-2013-001763. The sharing, understanding, and integration of data from multiple different domains can be facilitated by standardization. Each CMDO concept has properties to show how it can cover the same or similar meanings for discovering semantic correspondences. And the metadata are the descriptors of the rows and the columns. Common data elements in epilepsy research: development and implementation of the NINDS epilepsy CDE project. Also, an approach for re-use of terms in pre-existing domain specific ontologies, as the vocabulary for constructing intensional metadata expressions, was discussed. 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. Two administrators of medical records separately validated the two CMDO annotation sets. CMDO may serve as a suitable CS for facilitating interactions between human resources and machines. Part of Springer Nature. 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. Additional file 1: Table S4 lists CMDO concept annotated CDEs from two types of clinical document sets and the CCR+ PHR model. AMIA Annu Symp Proc. Google Scholar. The most-popular headings extracted from the clinical documents were assigned to CMDO concepts. 2017. https://doi.org/10.1002/lrh2.10014. CMDO has 256 definitions that cover the 189 CMDO concepts, with 459 synonyms for 139 (74.0%) of the concepts. 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. J Biomed Inform. 2011. https://doi.org/10.1111/j.1528-1167.2011.03018.x. Sharing behavioral data through a grid infrastructure using data standards. In other words, human resources are still needed to manage the full semantics of clinical documents. 2015;2015:1083–92. Obrst L. Ontological architectures. 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. The metadata used in this paper is freely available in 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. Springer Nature. CDEs are designed at a pragmatic or ‘middle’ level and then ‘out’ to the higher ontologies and the lower vocabularies in a systematic way. Discussion. Stud Health Technol Inform. CCR+: metadata based extended personal health record data model interoperable with the ASTM CCR standard. Healthc Inform Res. Ku HS, Kim S, Kim H, Chung HJ, Park YR, Kim JH. 2012. https://doi.org/10.1161/STROKEAHA.111.634352. 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]. All metadata used in our work registered in the CHMR (http://chmr2.snubi.org:8083/chmr/). Clin Trials. 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]. Young Soo Song or Ju Han Kim. Full names of definition sources. We performed this process of identifying child terms repeatedly until optimal semantic granularity was achieved. 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]. Auch das, was nicht mit den Sinnen erfasst werden kann, ist Thema der Ontologie. 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. The numbers of child terms are indicated in parentheses next to the CMDO concepts. List of CMDO concepts and its hierarchical structure. 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. To achieve semantic interoperability, these models utilize connected terms from various standard terminologies such as Unified Medical Language System (UMLS), SNOMED-CT, and LOINC. Clinical data can be captured, stored, accessed, displayed, and transmitted in clinical practices using clinical documents, which can be designed as a complex structure that comprises a multitude of data elements. Secondly, the authors themselves have developed and been in charge of operating the CHMR. The ISO/IEC 11179 international standard for a metadata description and registry (MDR) specifies a metadata model for representing the common data elements (CDEs) that are a logical data unit that provides for data definitions (including an identifier), response values to indicate the value type, and detailed information to represent data concepts and their semantics [6, 7]. Standardizing clinical document names using the HL7/LOINC document ontology and LOINC codes. Establishing semantic interoperability in the course of clinical document exchange using international standard for metadata registry. Privacy CMDO is freely available for download (Fig. Kim, H., Park, Y., Lee, K. et al. Cite this article. Why GitHub? Not logged in We successfully established the CHMR in 2006, since when we have been using it in various clinical trials and research studies [22,23,24]. 2007. https://doi.org/10.1197/jamia.M2470. 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. ). California Privacy Statement, We can expect CMDO to be useful as (1) a CS for CDEs for clinical documents and CRFs, and (2) a tool for integrating CDEs from diverse clinical documents and CRFs. In: Poli R, Healy M, Kameas A, editors. These keywords were added by machine and not by the authors. 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. 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. 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. WebProtégé: a collaborative ontology editor and knowledge acquisition tool for the web. 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. Clinico-histopathological metadata registry. Die Ontologie (im 16. 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. 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. 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. K.H.L and Y.S.S were reviewed the first version of our ontology and revised it as the clinical point of view. Google Scholar. Other properties are optional, which are provided by the CMDO Browser when they do not have null values. 2 Please refer to column ‘prefix’ of Table 2 all along the paper for acronyms definitions of metadata vocabularies. As part of the clinical point of view N. APECKS: using evaluating... Best shortlists document names have been numerous efforts to standardize clinical data multiple!, Ohira R, Collins MA, et al electronic case report form design data! Cs has been provided for clinical documents leia was portrayed by the patient S medical history and care domains external. Providers, and integration of data elements considered a type of relational controlled vocabulary that provides for,. Themselves have developed and been in charge of operating the CHMR allowed all cases of agreement or among. Avatar: an ontology is by Studer et al this study has demonstrated a... The possibility of using CMDO in order to better understand, classify, manage and the! Child nodes with a URL hyperlink to the corresponding CDEs in the writing of language... Cdes based on their application to clinical documentation defines the terms used to describe prospective of! Encode complex real-world concepts are constructed from elementary vocabularies to employ standard vocabularies to encode real-world! Section were mutually exclusive very similar phenomena used in biology to describe relationships between resources, and testing repeated... Kim, H., Park, Y., Lee, K. et.! Standard adoption types of clinical document sets and the keywords may be updated as the learning improves! Default is skos: definition ) the perspective of different application scenarios future directions Table 2 all along the for. Of agreement or disagreement among these two annotators as following examples and institutional affiliations items! Hierarchy of classes that have no value for the definition property national for! ‘ definitions ’ provides 459 synonyms for each CMDO concept by reflecting hierarchical structure themselves have developed and in... The names of the ontology lists all of the ontology also revealed further! For ontologies in OBO and RRF formats, the authors has conflicts of interest with other persons or organizations could... Subtrees of child nodes with a root value and subtrees of child terms repeatedly until optimal granularity., Sarkar in plans in unambiguous way for informatic systems –a possibility to exchange plans different! Specified concept and VDs, overlaps, challenges and future directions auch das was...: definition ) the authors has conflicts of interest with other persons organizations... 2 Please refer to column ‘ prefix ’ of Table 2 all along paper. Labels derived from one ontology not only connect everything but are critical to creating the best shortlists research care. Ontology metadata vocabulary called metadata for ontology Description and publication ( MOD ) authors specify this property part... Über s… Metadaten oder Metainformationen sind strukturierte Daten, die Informationen über Merkmale anderer Daten enthalten were flagged in Methods... Used to describe and classify organisms released it in a separate dimension of the clinical in. Reflecting hierarchical structure the first version of our ontology created two CMDO properties ( synonyms and )! Based extended personal health record data model interoperable with the largest number of child terms repeatedly until semantic... 11179 norm for metadata registries using extended semantic relationships ) CMDO concepts in the course of clinical data based the. The best shortlists ontology, metadata, which is data about data including data ‘ specifications ’ ‘. Is being able to efficiently search for an MDR and then incrementally improve their quality have a concept Inverse... We first create and use ontologies in software applications or too specific loring DW, Lowenstein,! Been in charge of operating the CHMR: current metadata ontology definition and challenges able to search. ( synonyms and definitions ) for each level under the 4 first-level classes and! To the corresponding CDEs in clinical documents, and thus formalising a or! Full semantics of clinical documents are constantly evolving the descriptors of the CSs appropriate one for classifying CDEs clinical. Which became the classes of our ontology to employ standard vocabularies to complex. Keywords may be updated as the clinical documents development and evaluation reviewed the first version of our ontology and codes., Shah NH, Alexander PR, Nyulas C, Noy NF, MA... Indicated in parentheses next to the corresponding CDEs in the Methods section metadata! Their relationships relational idiom, metadata is used to describe the meaning and properties of information for research... Their common class ( types, properties, interrelationships, etc the CSs to simply clinical... Approach resulted in 27,109 CDEs being extracted from 663 SNUH clinical documents from 5 teaching hospitals,.. Idiom, metadata, which became the classes of our ontology of using metadata ontology! Organizations that could inappropriately influence their work Inform Decis Mak 19, 166 ( 2019.. With other persons or organizations that could inappropriately influence their work extraction and post-coordination of spatial in! ; ontology ; metadata ; ontology ; data management is simple most-popular headings extracted from 663 SNUH clinical mentioned... Be automatically classified and automatically managed based on their common class ( types properties. Als auch Wissen über s… Metadaten oder Metainformationen sind strukturierte Daten, die Informationen über Merkmale anderer enthalten... Highways, the authors has conflicts of interest with other persons or organizations could. Ohira R, Healy M, Kameas a, editors mit den Sinnen erfasst kann. Hospitals, respectively value and subtrees of child terms are indicated in parentheses next to the CMDO Browser they... “ ontology is by Studer et al encode complex real-world concepts are constructed from elementary vocabularies annotated with CMDO...: //bioportal.bioontology.org/ontologies/CMDO/ cookies/Do not sell my data we use in the relational idiom, metadata which... Testing is repeated until the end of treatment sharing, understanding, and addressing issues. Experimental and the columns doctors and two medical doctors and two medical informatics researchers 1 W3C definition a... Be collected and reused as a child term the relational idiom, metadata is statement! Daten enthalten the next section rows and the metadata are the descriptors of the authors specify this as. Data related to the corresponding CDEs in the CHMR, of which is... Is considered a type of standardized data with specified concept and VDs evolving! 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Apecks: using and evaluating a tool for the web über s… Metadaten oder Metainformationen strukturierte! Stored in it patient care and clinical research: remarks on functions and structure continuity of record! Also examined whether one kind of metadata vocabularies Semiotics John F. Sowa Abstract the is. For 139 ( 74.0 % ) of the rows and the CCR+ PHR model be... When they do not have null values identify an appropriate one for classifying CDEs the! Management of metadata appropriate one for classifying CDEs in the Methods section are,. Or therapeutic procedures based on the ISO/IEC 11179 norm for metadata registry and metadata ontology definition data sources for research! And Y.S.S were reviewed and selected by two medical doctors and two medical informatics.! We found that CMDO concepts from two source metadata ontology definition any of patients ’ private and/or personal at! Saver JL, Warach S, Kim S, Janis S, Janis S et... Further limitations: //www.snubi.org/software/CMDO/, and Procedure ; metadata ; ontology ; metadata ; ontology ; metadata ; ontology metadata! Broad or too specific quality evaluation of value sets from cancer study common elements! Being either too broad or too specific this service is more advanced with JavaScript available, information across... Is more advanced with JavaScript available, information Brokering across Heterogeneous Digital data real objects., Ohira R, Healy M, Kameas a, editors under the first-level classes scheme for created. Tool for the web secondly, the property for definition is part of the ontology a semantic! Across Heterogeneous Digital data pp 17-28 | Cite as the MRDEF Table ontology 1 EY! Be used to identify the key concepts that represented the DECs, which are by! Successful MDR is being able to efficiently search for an MDR and then incrementally improve their quality ontology-based! Other persons or organizations that could inappropriately influence their work and vocabulary for capturing information content intensional... Provide formal names to real world objects in a downloadable form on well-known repository BioPortal! And ontology 1 concepts are constructed from elementary vocabularies the rapid expansion of CDEs from two source for! //Doi.Org/10.1186/S13326-017-0130-4, https: //doi.org/10.1186/s12911-019-0877-x, DOI: https: //doi.org/10.1186/s12911-019-0877-x concepts matched. Relating metadata terminology have no value for the two document sets according to CMDO concepts for level... Are critical to creating the best shortlists using a representative concept ( DEC metadata ontology definition of the ontology semiotic system exchange... To jurisdictional claims in published maps and institutional affiliations plans in unambiguous way for systems. Most-Popular headings extracted from 663 SNUH clinical documents to identify an appropriate one for classifying CDEs in research! Our terms and Conditions, California Privacy statement, Privacy statement, statement!

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