Data Normalization Improves Semantic Annotation – a Case Study of Rare Disease Name Annotation

Abstract Objective In this study, we aimed to evaluate the capability of the Unified Medical Language System (UMLS) as one data standard to support data normalization and harmonization of datasets that have been developed for rare diseases. Through analysis of data mappings between multiple rare disease resources and the UMLS, we propose suggested extensions of the UMLS that will enable its adoption as a global standard in rare disease. Methods We analyzed data mappings between the UMLS and existing datasets on over 7,000 rare diseases that were retrieved from four publicly accessible resources: Genetic And Rare Diseases Information Center (GARD), Orphanet, Online Mendelian Inheritance in Men (OMIM), and the Monarch Disease Ontology (MONDO). Two types of disease mappings were assessed, (1) curated mappings extracted from those four resources; and (2) established mappings generated by querying the rare disease-based integrative knowledge graph developed in the previous study. Results We found that 100% of OMIM concepts, and over 50% of concepts from GARD, MONDO, and Orphanet were normalized by the UMLS and accurately categorized into the appropriate UMLS semantic groups. We analyzed 58,636 UMLS mappings, which resulted in 3,876 UMLS concepts across these resources. Manual evaluation of a random set of 500 UMLS mappings demonstrated a high level of accuracy (99%) of developing those mappings, which consisted of 414 mappings of synonyms (82.8%), 76 are subtypes (15.2%), and five are siblings (1%). Conclusion The mapping results illustrated in this study that the UMLS was able to accurately represent rare disease concepts, and their associated information, such as genes and phenotypes, and can effectively be used to support data harmonization across existing resources developed on collecting rare disease data. We recommend the adoption of the UMLS as a data standard for rare disease to enable the existing rare disease datasets to support future applications in a clinical and community settings.

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Simultaneous Occurrence of Choriocarcinoma in an Infant and Mother

International Journal of Environmental Research and Public Health ◽

10.3390/ijerph18041934 ◽

2021 ◽

Vol 18 (4) ◽

pp. 1934

Author(s):

Małgorzata Rzanny-Owczarzak ◽

Joanna Sawicka-Metkowska ◽

Katarzyna Jończyk-Potoczna ◽

Ewelina Gowin ◽

Patrycja Sosnowska-Sienkiewicz ◽

...

Keyword(s):

Rare Disease ◽

Organ Failure ◽

Liver Tumor ◽

Serum Levels ◽

Simultaneous Occurrence ◽

Positive History ◽

Multi Organ Failure ◽

History Of

Infantile choriocarcinoma is an extremely rare disease. We present a case study of a 1-month-old male with choriocarcinoma diagnosed simultaneously with his mother. On admission to hospital, the disease was very advanced and massive progression and multi-organ failure caused the death of the patient despite the implemented treatment. It was too late to save the child’s life, but early enough to save his mother. The authors believe that the serum levels of hCG should be determined in every newborn with anemia and liver tumor, especially when the mother has a positive history of miscarriage.

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Product Analysis and Variants Derivation Based on a Semantically Annotated Product Family Ontology

Volume 2: 29th Computers and Information in Engineering Conference, Parts A and B ◽

10.1115/detc2009-87160 ◽

2009 ◽

Cited By ~ 3

Author(s):

Soon Chong Johnson Lim ◽

Ying Liu ◽

Wing Bun Lee

Keyword(s):

Semantic Annotation ◽

Product Family ◽

Relevant Information ◽

Product Analysis ◽

Laptop Computer ◽

Family Analysis ◽

Design And Manufacturing ◽

Commonality Analysis ◽

Current Representation

In literature, there are a number of indexes suggested that serve as the indicator of commonality among product components, modules and variants. However, as these elements are increasingly interconnected with aspects other than the component view, the existing commonality metrics are unable to effectively model these aspects due to their limitation in capturing relevant information for analysis. Therefore, there exists a need to consider multiple design and manufacturing aspects in commonality metrics so that a comprehensive view of the commonality among product variants can be presented. In the current representation schemes proposed for product family modeling, ontology is one of the most promising ones to model the complex semantic relations among various elements in a product family. Nevertheless, the research and application of ontology in the analysis of a product family has so far received little attention. In this paper, we proposed a framework to generate a semantically annotated multi-facet product family ontology. Using a case study of a laptop computer family, we suggest and demonstrate a new commonality analysis approach based on the semantically annotated multi-facet laptop product family ontology. Together with a new method of deriving product variants based on the aforementioned ontology, our approach illustrates the merits of using semantic annotation in assisting ontology based product family analysis.

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Disclosure: A Case Study of Communication about Medically Acquired Risk for a Rare Disease

The Knowledgeable Patient ◽

10.1002/9781444346855.ch7 ◽

2011 ◽

pp. 82-93

Author(s):

Rebecca E. Ryan ◽

Jessica Kaufman ◽

Sophie Hill

Keyword(s):

Rare Disease

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Eight years after an international workshop on myotonic dystrophy patient registries: case study of a global collaboration for a rare disease

Orphanet Journal of Rare Diseases ◽

10.1186/s13023-018-0889-0 ◽

2018 ◽

Vol 13 (1) ◽

Cited By ~ 8

Author(s):

Libby Wood ◽

Guillaume Bassez ◽

Corinne Bleyenheuft ◽

Craig Campbell ◽

Louise Cossette ◽

...

Keyword(s):

Rare Disease ◽

Myotonic Dystrophy ◽

International Workshop ◽

Global Collaboration ◽

Patient Registries

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A Case of Acquired Amegakaryocytic Thrombocytopenia with Anti-c-mpl Autoantibody: Comparison with Idiopathic Thrombocytopenic Purpura

Acta Haematologica ◽

10.1159/000499523 ◽

2019 ◽

Vol 142 (4) ◽

pp. 239-243

Author(s):

Bora Son ◽

Hee sue Park ◽

Hye Sook Han ◽

Hee Kyung Kim ◽

Seung Woo Baek ◽

...

Keyword(s):

Bone Marrow ◽

Platelet Count ◽

Rare Disease ◽

Idiopathic Thrombocytopenic Purpura ◽

Immunosuppressive Treatment ◽

Severe Bleeding ◽

Severe Thrombocytopenia ◽

Thrombocytopenic Purpura ◽

Acquired Amegakaryocytic Thrombocytopenia

Acquired amegakaryocytic thrombocytopenia (AAMT) is a rare disease that causes severe bleeding. The pathogenesis and treatment of AAMT have not yet been defined. We report the case of a 60-year-old woman diagnosed with AAMT, who presented with severe thrombocytopenia, gastrointestinal bleeding, and significantly reduced bone marrow megakaryocytes. The patient was treated with methylprednisolone, cyclosporin, and intravenous immunoglobulin. After 2 weeks of treatment, her platelet count started to increase, and her bone marrow megakaryocyte count had normalized 3 months after diagnosis. At the time of diagnosis, the patient was seropositive for anti-c-mpl antibody but was seen to be seronegative once the platelet count recovered. In contrast, anti-c-mpl antibodies were not detected in the serum of 3 patients with idiopathic thrombocytopenic purpura. This case study suggests that anti-c-mpl antibody plays an important role in the development of AAMT, and that intensive immunosuppressive treatment is required for autoantibody clearance and recovery of megakaryocyte count.

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A bibliography of Canadian Inuit periodicals: a case study in Omeka.net migration

Digital Library Perspectives ◽

10.1108/dlp-06-2020-0054 ◽

2020 ◽

Vol ahead-of-print (ahead-of-print) ◽

Author(s):

Sharon Rankin

Keyword(s):

Design Methodology ◽

Data Normalization ◽

Dublin Core ◽

Content Type ◽

Descriptive Information ◽

Unique Application

Purpose This paper aims to describe the migration steps taken by a humanities librarian to create a new searchable website for an indigenous bibliography on the Omeka.net cloud-based service. Design/methodology/approach Using CSV files and Excel, the bibliography entries were moved from the old website to the new one, carefully mapping the descriptive information into Qualified Dublin Core metadata elements. Findings After resolving diacritic and other data normalization issues, the new site was created in Omeka.net with ease. The plugins available for Omeka.net allowed the editor to geolocate the site of publications. Using TimelineJS, the editor was able to create several timelines and link them to the new CanInuit website as an exhibition. Originality/value This is a unique application of the Omeka.net cloud-based service.

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Development of the Myasthenia Gravis (MG) Symptoms PRO: a case study of a patient-centred outcome measure in rare disease

Orphanet Journal of Rare Diseases ◽

10.1186/s13023-021-02064-0 ◽

2021 ◽

Vol 16 (1) ◽

Author(s):

Sophie Cleanthous ◽

Ann-Christin Mork ◽

Antoine Regnault ◽

Stefan Cano ◽

Henry J. Kaminski ◽

...

Keyword(s):

Literature Review ◽

Myasthenia Gravis ◽

Rare Disease ◽

Outcome Measures ◽

Patient Experience ◽

Muscle Weakness ◽

Symptom Severity ◽

Test Theory ◽

Concept Elicitation

Abstract Background Myasthenia gravis (MG) is a chronic autoimmune neuromuscular disease, characterised by fluctuating muscle weakness which makes it challenging to assess symptom severity. Mixed methods psychometrics (MMP), which combines evidence from qualitative research and modern psychometrics, is a versatile approach to the development of patient-centred outcome measures (PCOM) in the context of rare disease. Our objective was to develop the MG Symptom patient-reported outcome (PRO) to assess key aspects of MG severity from the patient perspective. Methods We used MMP to develop a novel PRO instrument in a multi-step process. An initial conceptual model for MG patient experience was developed and expanded based on preliminary literature review and two waves of concept elicitation interviews with people with MG (Step 1). Based on this, the novel PRO instrument, the MG Symptoms PRO, was drafted. The draft instrument was refined by combining qualitative and quantitative data collected in a Phase 2 clinical study (Step 2). Results Findings from the literature review and concept elicitation interviews (n = 96) indicated that patient experience in MG includes proximal muscle weakness symptoms related to several body parts, along with muscle weakness fatigability and general fatigue. Then, a set of 42 items across five scales (ocular-, bulbar-, and respiratory muscle weakness, physical fatigue, and muscle weakness fatigability) was developed. Qualitative evidence endorsed its relevance, clarity, and ease of completion; quantitative analysis with Rasch measurement theory methods demonstrated strong measurement properties, including good targeting and high reliability. Classical test theory analyses showed adequate reliability of the instrument and mild to moderate correlations with other widely used MG-specific outcome measures. Conclusions The MG Symptoms PRO has potential to be used both to measure treatment benefit in clinical trials and monitor symptom severity in clinical practice. Its component scales were purposefully designed to stand alone, enhancing interpretability of scores given the heterogeneity of MG, and enabling modular use. Compared with existing MG PROs, it contains more detailed assessments of muscle weakness and muscle weakness fatigability symptoms, which are of key importance to people with MG. The MMP approach used may serve as a case study for developing PCOMs across rare disease indications.

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