ArticleBMC research notes2009
GenBank and PubMed: How connected are they?
Article in BMC research notes, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 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
15 citing papers in PubMed.
- Liberating links between datasets using lightweight data publishing: an example using plant names and the taxonomic literature.Biodiversity data journal · 2018Article
- A high-precision rule-based extraction system for expanding geospatial metadata in GenBank records.Journal of the American Medical Informatics Association : JAMIA · 2016Article
- Knowledge-driven geospatial location resolution for phylogeographic models of virus migration.Bioinformatics (Oxford, England) · 2015Article
- BioNames: linking taxonomy, texts, and trees.PeerJ · 2013Article
- SeedSeq: off-target transcriptome database.BioMed research international · 2013Article
- Detection of horizontal gene transfers from phylogenetic comparisons.International journal of evolutionary biology · 2012Article
- Metadata management and semantics in microarray repositories.Balkan journal of medical genetics : BJMG · 2011Article
- Marine natural products: a new wave of drugs?Future medicinal chemistry · 2011Article
- Linking NCBI to Wikipedia: a wiki-based approach.PLoS currents · 2011Article
- Article
- Aggregating, tagging and integrating biodiversity research.PloS one · 2011Article
- MeSHing molecular sequences and clinical trials: a feasibility study.Journal of biomedical informatics · 2010Article
- LINNAEUS: a species name identification system for biomedical literature.BMC bioinformatics · 2010Article
- LigerCat: using "MeSH Clouds" from journal, article, or gene citations to facilitate the identification of relevant biomedical literature.AMIA ... Annual Symposium proceedings. AMIA Symposium · 2009Article
- A vector space model approach to identify genetically related diseases.Journal of the American Medical Informatics Association : JAMIAArticle
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
backgroundGenBank is a public repository of all publicly available molecular sequence data from a range of sources. In addition to relevant metadata (e.g., sequence description, source organism and taxonomy), publication information is recorded in the GenBank data file. The identification of literature associated with a given molecular sequence may be an essential first step in developing research hypotheses. Although many of the publications associated with GenBank records may not be linked into or part of complementary literature databases (e.g., PubMed), GenBank records associated with literature indexed in Medline are identifiable as they contain PubMed identifiers (PMIDs).
resultsHere we show that an analysis of 87,116,501 GenBank sequence files reveals that 42% are associated with a publication or patent. Of these, 71% are associated with PMIDs, and can therefore be linked to a citation record in the PubMed database. The remaining (29%) of publication-associated GenBank entries either do not have PMIDs or cite a publication that is not currently indexed by PubMed. We also identify the journal titles that are linked through citations in the GenBank files to the largest number of sequences.
conclusionOur analysis suggests that GenBank contains molecular sequences from a range of disciplines beyond biomedicine, the initial scope of PubMed. The findings thus suggest opportunities to develop mechanisms for integrating biological knowledge beyond the biomedical field.
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.