ArticleDatabase : the journal of biological databases and curation2012
Improving links between literature and biological data with text mining: a case study with GEO, PDB and MEDLINE.
Article in Database : the journal of biological databases and curation, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 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
14 citing papers in PubMed.
- Unlocking the potential of PubMed Central supplementary data files.Bioinformatics advances · 2025Article
- MicroRNA-107 promotes apoptosis of acute myelocytic leukemia cells by targeting RAD51.Archives of medical science : AMS · 2021Article
- A Review of Recent Advancement in Integrating Omics Data with Literature Mining towards Biomedical Discoveries.International journal of genomics · 2017Review
- Article
- Database citation in supplementary data linked to Europe PubMed Central full text biomedical articles.Journal of biomedical semantics · 2015Article
- PubServer: literature searches by homology.Nucleic acids research · 2014Article
- Mining locus tags in PubMed Central to improve microbial gene annotation.BMC bioinformatics · 2014Article
- BC4GO: a full-text corpus for the BioCreative IV GO task.Database : the journal of biological databases and curation · 2014Article
- Accessing biomedical literature in the current information landscape.Methods in molecular biology (Clifton, N.J.) · 2014Review
- Overview of the gene ontology task at BioCreative IV.Database : the journal of biological databases and curation · 2014Article
- PubTator: a web-based text mining tool for assisting biocuration.Nucleic acids research · 2013Article
- tmVar: a text mining approach for extracting sequence variants in biomedical literature.Bioinformatics (Oxford, England) · 2013Article
- Experimental design-based functional mining and characterization of high-throughput sequencing data in the sequence read archive.PloS one · 2013Article
- Database citation in full text biomedical articles.PloS one · 2013Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
Abstract
High-throughput experiments and bioinformatics techniques are creating an exploding volume of data that are becoming overwhelming to keep track of for biologists and researchers who need to access, analyze and process existing data. Much of the available data are being deposited in specialized databases, such as the Gene Expression Omnibus (GEO) for microarrays or the Protein Data Bank (PDB) for protein structures and coordinates. Data sets are also being described by their authors in publications archived in literature databases such as MEDLINE and PubMed Central. Currently, the curation of links between biological databases and the literature mainly relies on manual labour, which makes it a time-consuming and daunting task. Herein, we analysed the current state of link curation between GEO, PDB and MEDLINE. We found that the link curation is heterogeneous depending on the sources and databases involved, and that overlap between sources is low, <50% for PDB and GEO. Furthermore, we showed that text-mining tools can automatically provide valuable evidence to help curators broaden the scope of articles and database entries that they review. As a result, we made recommendations to improve the coverage of curated links, as well as the consistency of information available from different databases while maintaining high-quality curation. Database URLs: http://www.ncbi.nlm.nih.gov/PubMed, http://www.ncbi.nlm.nih.gov/geo/, http://www.rcsb.org/pdb/
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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.