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"Data dictionaries"
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The Semantic Data Dictionary – An Approach for Describing and Annotating Data
It is common practice for data providers to include text descriptions for each
column when publishing data sets in the form of data dictionaries. While these
documents are useful in helping an end-user properly interpret the meaning of a
column in a data set, existing data dictionaries typically are not
machine-readable and do not follow a common specification standard. We introduce
the Semantic Data Dictionary, a specification that formalizes the assignment of
a semantic representation of data, enabling standardization and harmonization
across diverse data sets. In this paper, we present our Semantic Data Dictionary
work in the context of our work with biomedical data; however, the approach can
and has been used in a wide range of domains. The rendition of data in this form
helps promote improved discovery, interoperability, reuse, traceability, and
reproducibility. We present the associated research and describe how the
Semantic Data Dictionary can help address existing limitations in the related
literature. We discuss our approach, present an example by annotating portions
of the publicly available National Health and Nutrition Examination Survey data
set, present modeling challenges, and describe the use of this approach in
sponsored research, including our work on a large National Institutes of Health
(NIH)-funded exposure and health data portal and in the RPI-IBM collaborative
Health Empowerment by Analytics, Learning, and Semantics project. We evaluate
this work in comparison with traditional data dictionaries, mapping languages,
and data integration tools.
Journal Article
A Common Data Dictionary and Common Data Model for Additive Manufacturing
Additive manufacturing (AM) leverages emerging technologies and well-adopted processes to produce near-net-shape products. The advancement of AM technology requires data management tools to collect, store, and share information through the product development lifecycle and across the material and machine value chain. To address the need for sharing data among AM developers and practitioners, an AM common data dictionary (AM-CDD) was first developed based on community consensus to provide a common lexicon for AM, and later standardized by ASTM International. Following the AM-CDD work, the development of a common data model (AM-CDM) defining the structure and relationships of the key concepts, and terms in the AM-CDD is being developed. These efforts have greatly facilitated system integrations and AM data exchanges among various organizations. This work outlines the effort to create the AM-CDD and AM-CDM, with a focus on the design of the AM-CDM. Two use cases are provided to demonstrate the adoption of these efforts and the interoperability enabled by the AM-CDM for different engineering applications managed by different types of database technology. In these case studies, the AM-CDM is implemented in two distinct formats to curate AM data from NIST—the first in XML from their additive manufacturing material database and the second in OWL from their 2022 AM bench database. These use cases present the power of the AM-CDM for data representation, querying, and seamless data exchange. Our implementation experiences and some challenges are highlighted that can assist others in future adoptions of the AM-CDM for data integration and data exchange applications.
Journal Article
Web-based interactive mapping from data dictionaries to ontologies, with an application to cancer registry
Background
The Kentucky Cancer Registry (KCR) is a central cancer registry for the state of Kentucky that receives data about incident cancer cases from all healthcare facilities in the state within 6 months of diagnosis. Similar to all other U.S. and Canadian cancer registries, KCR uses a data dictionary provided by the North American Association of Central Cancer Registries (NAACCR) for standardized data entry. The NAACCR data dictionary is not an ontological system. Mapping between the NAACCR data dictionary and the National Cancer Institute (NCI) Thesaurus (NCIt) will facilitate the enrichment, dissemination and utilization of cancer registry data. We introduce a web-based system, called Interactive Mapping Interface (IMI), for creating mappings from data dictionaries to ontologies, in particular from NAACCR to NCIt.
Method
IMI has been designed as a general approach with three components: (1) ontology library; (2) mapping interface; and (3) recommendation engine. The ontology library provides a list of ontologies as targets for building mappings. The mapping interface consists of six modules: project management, mapping dashboard, access control, logs and comments, hierarchical visualization, and result review and export. The built-in recommendation engine automatically identifies a list of candidate concepts to facilitate the mapping process.
Results
We report the architecture design and interface features of IMI. To validate our approach, we implemented an IMI prototype and pilot-tested features using the IMI interface to map a sample set of NAACCR data elements to NCIt concepts. 47 out of 301 NAACCR data elements have been mapped to NCIt concepts. Five branches of hierarchical tree have been identified from these mapped concepts for visual inspection.
Conclusions
IMI provides an interactive, web-based interface for building mappings from data dictionaries to ontologies. Although our pilot-testing scope is limited, our results demonstrate feasibility using IMI for semantic enrichment of cancer registry data by mapping NAACCR data elements to NCIt concepts.
Journal Article
Toolbox for Research, or how to facilitate a central data management in small-scale research projects
Background
In most research projects budget, staff and IT infrastructures are limiting resources. Especially for small-scale registries and cohort studies professional IT support and commercial electronic data capture systems are too expensive. Consequently, these projects use simple local approaches (e.g. Excel) for data capture instead of a central data management including web-based data capture and proper research databases. This leads to manual processes to merge, analyze and, if possible, pseudonymize research data of different study sites.
Results
To support multi-site data capture, storage and analyses in small-scall research projects, corresponding requirements were analyzed within the MOSAIC project. Based on the identified requirements, the Toolbox for Research was developed as a flexible software solution for various research scenarios. Additionally, the Toolbox facilitates data integration of research data as well as metadata by performing necessary procedures automatically. Also, Toolbox modules allow the integration of device data. Moreover, separation of personally identifiable information and medical data by using only pseudonyms for storing medical data ensures the compliance to data protection regulations. This pseudonymized data can then be exported in SPSS format in order to enable scientists to prepare reports and analyses.
Conclusions
The Toolbox for Research was successfully piloted in the German Burn Registry in 2016 facilitating the documentation of 4350 burn cases at 54 study sites. The Toolbox for Research can be downloaded free of charge from the project website and automatically installed due to the use of Docker technology.
Journal Article
How Can a Clinical Data Modelling Tool Be Used to Represent Data Items of Relevance to Paediatric Clinical Trials? Learning from the Conect4children (c4c) Consortium
Data dictionaries for clinical trials are often created manually, with data structures and controlled vocabularies specific for a trial or family of trials within a sponsor’s portfolio. Microsoft Excel is commonly used to capture the representation of data dictionary items but has limited functionality for this purpose. The conect4children (c4c) network is piloting the Direcht clinical data modelling tool to model their Cross Cutting Paediatric Data Dictionary (CCPDD) in a more formalised way. The first pilot had the key objective of testing whether a clinical data modelling tool could be used to represent data items from the CCPDD. The key objective of the second pilot is to establish whether a small team with little or no experience of clinical data modelling can use Direcht to expand the CCPDD. Clinical modelling is the process of structuring clinical data so it can be understood by computer systems and humans. The model contains all of the elements that are needed to define the data item. Results from the pilots show that Direcht creates a structured environment to build data items into models that fit into the larger CCPDD. Models can be represented as an HTML document, mind map, or exported in various formats for import into a computer system. Challenges identified over the course of both pilots are being addressed with c4c partners and external stakeholders.
Journal Article