ArticleJournal of the American Medical Informatics Association : JAMIA2018
DataMed - an open source discovery index for finding biomedical datasets.
Article in Journal of the American Medical Informatics Association : JAMIA, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers, 2 of them syntheses that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
25 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- ImmuneData: an integrated data discovery system for immunology data repositories.Database : the journal of biological databases and curation · 2022Pooled it
- ENIGMA + COINSTAC: Improving Findability, Accessibility, Interoperability, and Re-usability.Neuroinformatics · 2022Pooled it
- Using semantic search to find publicly available gene-expression datasets.Bioinformatics (Oxford, England) · 2026Article
- Clinical Terminology Mapping Service Based on Information Retrieval.Methods of information in medicine · 2025Article
- Genomics and multiomics in the age of precision medicine.Pediatric research · 2025Review
- The Venus score for the assessment of the quality and trustworthiness of biomedical datasets.BioData mining · 2025Article
- Datagraphy: toward a systematic approach to dataset discovery.GigaScience · 2025Article
- BioBricks.ai: a versioned data registry for life sciences data assets.Frontiers in artificial intelligence · 2025Article
- Applying Findable, Accessible, Interoperable, and Reusable Principles to Biospecimens and Biobanks.Biopreservation and biobanking · 2024Article
- Towards Machine-FAIR: Representing software and datasets to facilitate reuse and scientific discovery by machines.Journal of biomedical informatics · 2024Article
- A hierarchical strategy to minimize privacy risk when linking "De-identified" data in biomedical research consortia.Journal of biomedical informatics · 2023Article
- Addressing barriers in FAIR data practices for biomedical data.Scientific data · 2023Article
- Developing a standardized but extendable framework to increase the findability of infectious disease datasets.Scientific data · 2023Article
- A repository for the publication and sharing of heterogeneous materials data.Scientific data · 2022Article
- SVAT: Secure outsourcing of variant annotation and genotype aggregation.BMC bioinformatics · 2022Article
- Dug: a semantic search engine leveraging peer-reviewed knowledge to query biomedical data repositories.Bioinformatics (Oxford, England) · 2022Article
- Challenges with organization, discoverability and access in Canadian open health data repositories.The journal of the Canadian Health Libraries Association · 2021Article
- Article
- An informatics research platform to make public gene expression time-course datasets reusable for more scientific discoveries.Database : the journal of biological databases and curation · 2020Article
- The Data Tags Suite (DATS) model for discovering data access and use requirements.GigaScience · 2020Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
24 authors.
Funding
Abstract
objectiveFinding relevant datasets is important for promoting data reuse in the biomedical domain, but it is challenging given the volume and complexity of biomedical data. Here we describe the development of an open source biomedical data discovery system called DataMed, with the goal of promoting the building of additional data indexes in the biomedical domain. MATERIALS AND
methodsDataMed, which can efficiently index and search diverse types of biomedical datasets across repositories, is developed through the National Institutes of Health-funded biomedical and healthCAre Data Discovery Index Ecosystem (bioCADDIE) consortium. It consists of 2 main components: (1) a data ingestion pipeline that collects and transforms original metadata information to a unified metadata model, called DatA Tag Suite (DATS), and (2) a search engine that finds relevant datasets based on user-entered queries. In addition to describing its architecture and techniques, we evaluated individual components within DataMed, including the accuracy of the ingestion pipeline, the prevalence of the DATS model across repositories, and the overall performance of the dataset retrieval engine. RESULTS AND
conclusionOur manual review shows that the ingestion pipeline could achieve an accuracy of 90% and core elements of DATS had varied frequency across repositories. On a manually curated benchmark dataset, the DataMed search engine achieved an inferred average precision of 0.2033 and a precision at 10 (P@10, the number of relevant results in the top 10 search results) of 0.6022, by implementing advanced natural language processing and terminology services. Currently, we have made the DataMed system publically available as an open source package for the biomedical community.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.