ArticleBMC bioinformatics2009
Towards large-scale sample annotation in gene expression repositories.
Article in BMC bioinformatics, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
What it found
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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.
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Who cites it
5 citing papers in PubMed, 7 citations in OpenAlex.
- BioDataome: a collection of uniformly preprocessed and automatically annotated datasets for data-driven biology.Database : the journal of biological databases and curation · 2018Article
- Assessing the quality of annotations in asthma gene expression experiments.BMC bioinformatics · 2010Article
- Selected proceedings of the 2009 Summit on Translational Bioinformatics.BMC bioinformatics · 2009Article
- Evaluation of a large-scale biomedical data annotation initiative.BMC bioinformatics · 2009Article
- PhenDisco: phenotype discovery system for the database of genotypes and phenotypes.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
6 authors at 4 institutions in 3 countries.
Funding
Abstract
backgroundLarge repositories of biomedical research data are most useful to translational researchers if their data can be aggregated for efficient queries and analyses. However, inconsistent or non-existent annotations describing important sample details such as name of tissue or cell line, histopathological type, and subject characteristics like demographics, treatment, and survival are seldom present in data repositories, making it difficult to aggregate data.
resultsWe created a flexible software tool that allows efficient annotation of samples using a controlled vocabulary, and report on its use for the annotation of over 12,500 samples.
conclusionWhile the amount of data is very large and seemingly poorly annotated, a lot of information is still within reach. Consistent tool-based re-annotation enables many new possibilities for large scale interpretation and analyses that would otherwise be impossible.
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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.