Bioinformatics paper uses NCBI open data to analyze drug response

A study (PMID: 28158543) published in the July 2017 issue of Bioinformatics collects, classifies and analyzes single nucleotide variants (SNVs) that may affect response to currently approved drugs. They identified 2,640 SNVs of interest, most of which occur rarely in populations (minor … Continue reading

Expression teasers and indexing added to Gene

Last February, we added gene expression data to Gene. Now, you can access these data in a few new ways. Expression pattern “teasers” in Summary We’ve added a brief sentence describing the expression pattern to the Summary section. This teaser … Continue reading

Gene_orthologs file on Gene FTP site

For ease in accessing the orthology data subset, a new gene_orthologs FTP file has been created on the Gene FTP site. The file uses the same format as the gene_group file. As of January 31, 2018, the gene_group FTP file … Continue reading

5 NCBI articles in 2018 Nucleic Acids Research database issue

The 2018 Nucleic Acids Research database issue features several papers from NCBI staff that cover the status and future of databases including CCDS, ClinVar, GenBank and RefSeq. These papers are also available on PubMed. To read an article, click on … Continue reading

Updated HIV-1 interaction datasets in Gene

We recently updated the HIV-1 interaction datasets in Gene with data provided by the Southern Research Institute (SRI). The protein interactions dataset now has: 8,005 interactions, 16,215 interaction descriptions, 3,859 proteins encoded by 3,757 human genes, and 6,822 publications. The … Continue reading

A journal printed a sharp critique of a paper it had published. If only it had checked with the authors first.

In 2016, researchers published a paper showing that an RNA molecule may be overactive in breast tumor tissue. But after reading the paper, three biologists believed the data supported the opposite conclusion. What happened after that is a tale of misunderstandings and unnecessarily bruised feelings. We’ve seen plenty of cases where researchers ignore criticism, which […]

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September 2017: NCBI to present EDirect workshop at NLM

On September 18, 2017, NCBI staff will offer a workshop on EDirect, NCBI’s suite of programs for easy command line access to literature and biomolecular records. To join the workshop, please register. NOTE: This is an in-person workshop at the … Continue reading

Zebrafish (Danio rerio), 11 other organisms in June RefSeq genome annotations

In June, the NCBI Eukaryotic Genome Annotation Pipeline released new annotations in RefSeq for the following organisms, including Danio rerio (zebrafish): Bombyx mori (domestic silkworm) Numida meleagris (helmeted guineafowl) Herrania umbratica (eudicot) Sorghum bicolor (sorghum) Mizuhopecten yessoensis (Yesso scallop) Lonchura striata domestica (Bengalese finch) … Continue reading

RefSeq Functional Elements now public

NCBI is pleased to announce the initial data release of RefSeq Functional Elements, a resource that provides RefSeq and Gene records for experimentally validated human and mouse non-genic functional elements. Data can be accessed via Gene, Nucleotide, BLAST, BioProject, Graphical Displays and FTP. These records include known gene regulatory elements (e.g., … Continue reading

New pig (Sus scrofa) genome annotation in RefSeq

The new pig (Sus scrofa) genome annotation produced by the NCBI eukaryotic genome annotation pipeline is now available in RefSeq. This data is now available for download and can be explored in the Genome Data Viewer, with BLAST, and in the Gene database. In Annotation Release 106, a … Continue reading