ArticleDatabase : the journal of biological databases and curation2019
GenoSurf: metadata driven semantic search system for integrated genomic datasets.
Article in Database : the journal of biological databases and curation, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers, 1 of them a synthesis that pooled it.
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Who cites it
15 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Understanding the Nature of Metadata: Systematic Review.Journal of medical Internet research · 2022Pooled it
- Toward a Common Set of Interface Requirements for Genomic Data Management: Scoping Review.Journal of medical Internet research · 2026Article
- PEPhub: a database, web interface, and API for editing, sharing, and validating biological sample metadata.bioRxiv : the preprint server for biology · 2024Article
- Joint Representation Learning for Retrieval and Annotation of Genomic Interval Sets.Bioengineering (Basel, Switzerland) · 2024Article
- PEPhub: a database, web interface, and API for editing, sharing, and validating biological sample metadata.GigaScience · 2024Article
- Processing genome-wide association studies within a repository of heterogeneous genomic datasets.BMC genomic data · 2023Article
- Ontologies for increasing the FAIRness of plant research data.Frontiers in plant science · 2023Review
- Challenges to sharing sample metadata in computational genomics.Frontiers in genetics · 2023Article
- Genomic data integration and user-defined sample-set extraction for population variant analysis.BMC bioinformatics · 2022Article
- Dug: a semantic search engine leveraging peer-reviewed knowledge to query biomedical data repositories.Bioinformatics (Oxford, England) · 2022Article
- GeMI: interactive interface for transformer-based Genomic Metadata Integration.Database : the journal of biological databases and curation · 2022Article
- High Performance Integration Pipeline for Viral and Epitope Sequences.Biotech (Basel (Switzerland)) · 2022Article
- EpiSurf: metadata-driven search server for analyzing amino acid changes within epitopes of SARS-CoV-2 and other viral species.Database : the journal of biological databases and curation · 2021Article
- A review on viral data sources and search systems for perspective mitigation of COVID-19.Briefings in bioinformatics · 2021Review
- ViruSurf: an integrated database to investigate viral sequences.Nucleic acids research · 2021Article
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Many valuable resources developed by world-wide research institutions and consortia describe genomic datasets that are both open and available for secondary research, but their metadata search interfaces are heterogeneous, not interoperable and sometimes with very limited capabilities. We implemented GenoSurf, a multi-ontology semantic search system providing access to a consolidated collection of metadata attributes found in the most relevant genomic datasets; values of 10 attributes are semantically enriched by making use of the most suited available ontologies. The user of GenoSurf provides as input the search terms, sets the desired level of ontological enrichment and obtains as output the identity of matching data files at the various sources. Search is facilitated by drop-down lists of matching values; aggregate counts describing resulting files are updated in real time while the search terms are progressively added. In addition to the consolidated attributes, users can perform keyword-based searches on the original (raw) metadata, which are also imported; GenoSurf supports the interplay of attribute-based and keyword-based search through well-defined interfaces. Currently, GenoSurf integrates about 40 million metadata of several major valuable data sources, including three providers of clinical and experimental data (TCGA, ENCODE and Roadmap Epigenomics) and two sources of annotation data (GENCODE and RefSeq); it can be used as a standalone resource for targeting the genomic datasets at their original sources (identified with their accession IDs and URLs), or as part of an integrated query answering system for performing complex queries over genomic regions and metadata.
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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 Socratic graph.