ArticleJournal of the American Medical Informatics Association : JAMIA2015
BiobankConnect: software to rapidly connect data elements for pooled analysis across biobanks using ontological and lexical indexing.
Article in Journal of the American Medical Informatics Association : JAMIA, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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
17 citing papers in PubMed.
- Pretrained language models for semantics-aware data harmonisation of observational clinical studies in the era of big data.BMC medical informatics and decision making · 2025Article
- A natural language processing approach to support biomedical data harmonization: Leveraging large language models.PloS one · 2025Article
- Clinical Research Informatics: a Decade-in-Review.Yearbook of medical informatics · 2024Review
- Current state of data stewardship tools in life science.Frontiers in big data · 2024Review
- Dug: a semantic search engine leveraging peer-reviewed knowledge to query biomedical data repositories.Bioinformatics (Oxford, England) · 2022Article
- Addressing the clinical unmet needs in primary Sjögren's Syndrome through the sharing, harmonization and federated analysis of 21 European cohorts.Computational and structural biotechnology journal · 2022Article
- Overcoming the Barriers That Obscure the Interlinking and Analysis of Clinical Data Through Harmonization and Incremental Learning.IEEE open journal of engineering in medicine and biology · 2020Article
- Pan-European Data Harmonization for Biobanks in ADOPT BBMRI-ERIC.Applied clinical informatics · 2019Article
- MOLGENIS research: advanced bioinformatics data software for non-bioinformaticians.Bioinformatics (Oxford, England) · 2019Article
- An ontology-guided semantic data integration framework to support integrative data analysis of cancer survival.BMC medical informatics and decision making · 2018Article
- BiobankUniverse: automatic matchmaking between datasets for biobank data discovery and integration.Bioinformatics (Oxford, England) · 2017Article
- Clinical Research Informatics Contributions from 2015.Yearbook of medical informatics · 2016Article
- Enhancing translational research in paediatric rheumatology through standardization.Nature reviews. Rheumatology · 2016Review
- MOLGENIS/connect: a system for semi-automatic integration of heterogeneous phenotype data with applications in biobanks.Bioinformatics (Oxford, England) · 2016Article
- OBIB-a novel ontology for biobanking.Journal of biomedical semantics · 2016Article
- Towards data integration automation for the French rare disease registry.AMIA ... Annual Symposium proceedings. AMIA Symposium · 2015Article
- SORTA: a system for ontology-based re-coding and technical annotation of biomedical phenotype data.Database : the journal of biological databases and curation · 2015Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
objectivePooling data across biobanks is necessary to increase statistical power, reveal more subtle associations, and synergize the value of data sources. However, searching for desired data elements among the thousands of available elements and harmonizing differences in terminology, data collection, and structure, is arduous and time consuming. MATERIALS AND
methodsTo speed up biobank data pooling we developed BiobankConnect, a system to semi-automatically match desired data elements to available elements by: (1) annotating the desired elements with ontology terms using BioPortal; (2) automatically expanding the query for these elements with synonyms and subclass information using OntoCAT; (3) automatically searching available elements for these expanded terms using Lucene lexical matching; and (4) shortlisting relevant matches sorted by matching score.
resultsWe evaluated BiobankConnect using human curated matches from EU-BioSHaRE, searching for 32 desired data elements in 7461 available elements from six biobanks. We found 0.75 precision at rank 1 and 0.74 recall at rank 10 compared to a manually curated set of relevant matches. In addition, best matches chosen by BioSHaRE experts ranked first in 63.0% and in the top 10 in 98.4% of cases, indicating that our system has the potential to significantly reduce manual matching work.
conclusionsBiobankConnect provides an easy user interface to significantly speed up the biobank harmonization process. It may also prove useful for other forms of biomedical data integration. All the software can be downloaded as a MOLGENIS open source app from http://www.github.com/molgenis, with a demo available at http://www.biobankconnect.org.
Indexed as
Identifiers
What OpenQuestion holds
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.