Leveraging the UMLS As a Data Standard for Rare Disease Data Normalization and Harmonization

2020 ◽  
Author(s):  
Qian Zhu ◽  
Dac-Trung Nguyen ◽  
Eric Sid ◽  
Anne Pariser
Keyword(s):  
Rare Disease ◽  
Rare Diseases ◽  
Mendelian Inheritance ◽  
Data Normalization ◽  
Community Settings ◽  
Unified Medical Language System ◽  
Data Standard ◽  
Medical Language ◽  
Disease Concepts ◽  
High Level

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.

scholarly journals Research and Management of Rare Diseases in the COVID-19 Pandemic Era: Challenges and Countermeasures

2021 ◽  
Vol 9 ◽  
Author(s):  
Sanjana Fatema Chowdhury ◽  
Syed Muktadir Al Sium ◽  
Saeed Anwar
Keyword(s):  
Rare Disease ◽  
Rare Diseases ◽  
Genetic Diseases ◽  
Management Strategies ◽  
Routine Care ◽  
Ongoing Research ◽  
The People ◽  
Number Of Patients ◽  
High Level ◽  
Disease Community

The ongoing coronavirus disease 2019 (COVID-19) pandemic has disrupted every aspect of our life. The need to provide high-level care for an enormous number of patients with COVID-19 infection during this pandemic has impacted resourcing for and restricted the routine care of all non-COVID-19 conditions. Since the beginning of the pandemic, the people living with rare disorders, who represent a marginalized group of the population even in a normal world, have not received enough attention that they deserve. Due to the pandemic situation, they have experienced (and experiencing) an extreme inadequacy of regular clinical services, counseling, and therapies they need, which have made their life more vulnerable and feel more marginalized. Besides, the clinicians, researchers, and scientists working on rare genetic diseases face extra challenges due to the pandemic. Many ongoing research projects and clinical trials for rare and genetic diseases were stalled to avoid patients' and research staff's transmission to COVID-19. Still, with all the odds, telehealth and virtual consultations for rare disease patients have shown hope. The clinical, organizational, and economic challenges faced by institutions, patients, their families, and the caregivers during the pandemic indicate the importance of ensuring continuity of care in managing rare diseases, including adequate diagnostics and priority management strategies for emergencies. In this review, we endeavored to shed light on the issues the rare disease community faces during the pandemic and the adaptations that could help the rare disease community to better sustain in the coming days.

Evaluation of a Tool to Enhance Searching for Useful Medical Information on the Internet

2011 ◽  
pp. 330-343
Author(s):  
David Parry
Keyword(s):  
Medical Information ◽  
Point Of Care ◽  
Health Sector ◽  
Sources Of Information ◽  
Unified Medical Language System ◽  
Professional Groups ◽  
Medical Language ◽  
High Quality Information ◽  
High Level ◽  
Based Medicine

Evidence-based medicine (EBM) requires appropriate information to be available to clinicians at the point of care. Electronic sources of information may fulfill this need but require a high level of skill to use successfully. This chapter describes the rationale and initial testing of a system to allow collaborative searching and ontology construction for professional groups in the health sector. The approach is based around the use of a browser using a fuzzy ontology based on the National library of medicine (NLM) unified medical language system (UMLS). The results suggest that a tool that can assist users in finding information by recording their preferences and preferred meaning of text words can be usable by healthcare professionals. This approach may provide high-quality information for professionals in the future.

scholarly journals Results of a Patient Reported Experience Measure (PREM) to measure the rare disease patients and caregivers experience: a Spanish cross-sectional study

2021 ◽  
Vol 16 (1) ◽  
Author(s):  
Mercedes Guilabert ◽  
Alba Martínez-García ◽  
Marina Sala-González ◽  
Olga Solas ◽  
José Joaquín Mira
Keyword(s):  
Rare Disease ◽  
Rare Diseases ◽  
Healthcare Services ◽  
Paediatric Population ◽  
Cross Sectional Study ◽  
Sectional Study ◽  
Optimal Care ◽  
Cross Sectional ◽  
Patient Reported ◽  
Mean Time

Abstract Objective To measure the experience of the person having a rare disease in order to identify objectives for optimal care in the health care received by these patients. Methods. A cross-sectional study was conducted in Spain involving patients associated with the Spanish Rare Diseases Federation [Federación Española de Enfermedades Raras] (FEDER). A modified version of the PREM IEXPAC [Instrumento para evaluar la Experiencia del Paciente Crónico] instrument was used (IEXPAC-rare-diseases). Scores ranged between 0 (worst experience) and 10 (best experience). Results A total of 261 caregivers (in the case of paediatric population) and patients with rare diseases (response rate 54.4%) replied. 232 (88.9%) were adult patients and 29 (11.1%) caregivers of minor patients. Most males, 227 (87%), with an average age of 38 (SD 13.6) years. The mean time since confirmation of diagnosis was 7.8 (SD 8.0) years. The score in this PREM was 3.5 points out to 10 (95%CI 3.2–3.8, SD 2.0). Caregivers of paediatric patients scored higher, except for coordination of social and healthcare services. Conclusions There are wide and important areas for improvement in the care of patients with rare diseases. This study involves a first assesment of the experience of patients with rare diseases in Spain.

Cooccurrence of Two Different Genetic Diseases: A Case of Valproic Acid Hepatotoxicity in Nicolaides–Baraitser Syndrome (SMARCA2 Mutation)—Due to a POLG1-Related Effect?

2019 ◽  
Vol 51 (01) ◽  
pp. 049-052
Author(s):  
Benedikt Hofmeister ◽  
Celina von Stülpnagel ◽  
Steffen Berweck ◽  
Angela Abicht ◽  
Gerhard Kluger ◽  
...  
Keyword(s):  
Valproic Acid ◽  
Literature Review ◽  
Rare Disease ◽  
Clinical Features ◽  
Rare Diseases ◽  
Rare Complication ◽  
Genetic Diseases ◽  
Related Effect ◽  
Higher Sensitivity ◽  
Polg1 Mutation

AbstractNicolaides–Baraitser syndrome (NCBRS) is a rare disease caused by a mutation in the SMARCA2 gene. Clinical features include craniofacial dysmorphia and abnormalities of the limbs, as well as intellectual disorder and often epilepsy. Hepatotoxicity is a rare complication of the therapy with valproic acid (VPA) and a mutation of the polymerase γ (POLG) might lead to a higher sensitivity for liver hepatotoxicity. We present a patient with the coincidence of two rare diseases, the NCBRS and additionally a POLG1 mutation in combination with a liver hepatotoxicity. The co-occurrence in children for two different genetic diseases is discussed with the help of literature review.

scholarly journals A resource to explore the discovery of rare diseases and their causative genes

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Friederike Ehrhart ◽  
Egon L. Willighagen ◽  
Martina Kutmon ◽  
Max van Hoften ◽  
Leopold M. G. Curfs ◽  
...  
Keyword(s):  
Rare Disease ◽  
Rare Diseases ◽  
Genetic Background ◽  
Gene Discovery ◽  
Google Scholar ◽  
Semantic Model ◽  
Causative Gene ◽  
Scientific Publications ◽  
Monogenic Diseases ◽  
First Time

AbstractHere, we describe a dataset with information about monogenic, rare diseases with a known genetic background, supplemented with manually extracted provenance for the disease itself and the discovery of the underlying genetic cause. We assembled a collection of 4166 rare monogenic diseases and linked them to 3163 causative genes, annotated with OMIM and Ensembl identifiers and HGNC symbols. The PubMed identifiers of the scientific publications, which for the first time described the rare diseases, and the publications, which found the genes causing the diseases were added using information from OMIM, PubMed, Wikipedia, whonamedit.com, and Google Scholar. The data are available under CC0 license as spreadsheet and as RDF in a semantic model modified from DisGeNET, and was added to Wikidata. This dataset relies on publicly available data and publications with a PubMed identifier, but by our effort to make the data interoperable and linked, we can now analyse this data. Our analysis revealed the timeline of rare disease and causative gene discovery and links them to developments in methods.

Current Advances in Clinical Trials for Rare Disease Populations: Spotlight on the Patient

2021 ◽  
Vol 16 ◽  
Author(s):  
Erica Winter ◽  
Scott Schliebner
Keyword(s):  
Clinical Trial ◽  
Clinical Trials ◽  
Drug Development ◽  
Rare Disease ◽  
Rare Diseases ◽  
Statistical Analyses ◽  
Clinical Trial Designs ◽  
Novel Approaches

: Characterized by small, highly heterogeneous patient populations, rare disease trials magnify the challenges often encountered in traditional clinical trials. In recent years, there have been increased efforts by stakeholders to improve drug development in rare diseases through novel approaches to clinical trial designs and statistical analyses. We highlight and discuss some of the current and emerging approaches aimed at overcoming challenges in rare disease clinical trials, with a focus on the ultimate stakeholder, the patient.

scholarly journals The case for open science: rare diseases

JAMIA Open ◽  
2020 ◽  
Vol 3 (3) ◽  
pp. 472-486
Author(s):  
Yaffa R Rubinstein ◽  
Peter N Robinson ◽  
William A Gahl ◽  
Paul Avillach ◽  
Gareth Baynam ◽  
...  
Keyword(s):  
Rare Disease ◽  
Rare Diseases ◽  
Medical Management ◽  
Open Science ◽  
Patient Data ◽  
Diagnosis And Treatment ◽  
Community Research ◽  
The Core ◽  
Delays In Diagnosis

Abstract The premise of Open Science is that research and medical management will progress faster if data and knowledge are openly shared. The value of Open Science is nowhere more important and appreciated than in the rare disease (RD) community. Research into RDs has been limited by insufficient patient data and resources, a paucity of trained disease experts, and lack of therapeutics, leading to long delays in diagnosis and treatment. These issues can be ameliorated by following the principles and practices of sharing that are intrinsic to Open Science. Here, we describe how the RD community has adopted the core pillars of Open Science, adding new initiatives to promote care and research for RD patients and, ultimately, for all of medicine. We also present recommendations that can advance Open Science more globally.

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