NCBI previously announced improved search functionality to provide users with better results for common language queries.
We have expanded this search capability beyond queries for species-qualified gene symbols (e.g. human GhrI) to support species-qualified protein names (e.g. human obestatin) and gene names (e.g. human ghrelin and obestatin prepropeptide) in eukaryotes and viruses.
Whether you are searching for a gene, transcript, or protein, our updated featured results panel displays the relevant information. The results panel for the selected gene includes quick links to many resources including transcripts, protein products, and publications.
Try these example queries to see the improved search results.
Putting your schedule together for ASHG? Don’t forget to look at all of NCBI’s activities, which include 1 GRC Workshop, 1 Booth (#315), 2 Co-Labs, and 10 Poster presentations. We created a handy schedule below, with links to posts where we’ve highlighted events.
Booth #315, Exhibit Hall:
Wednesday, October 17, 10:00 AM – 4:30 PM
Thursday, October 18, 10:00 AM – 4:30 PM
Friday, October 19, 10:00 AM – 4:30 PM
Visit us at the booth to provide feedback, have questions answered or just to chat!
My Bibliography is a component of My NCBI and allows you to create an online collection of your published work. You can import citations directly from PubMed or add them manually. For accounts linked to eRA Commons, you can associate citations with awards and manage compliance with the NIH Public Access Policy.
Are you a My Bibliography user?
We are working on a new My Bibliography and want your feedback! The new trial version of My Bibliography is an NCBI Labs experiment. It incorporates many improved features over the existing My Bibliography, including a color-coded view of compliance status, filtering by compliance status, and functionality on your phone.
Anything you try or change in the NCBI Labs My Bibliography site will not affect content in your existing My Bibliography account, so feel free to experiment.
The RefSeq project at the NCBI and the Ensembl/GENCODE project at EMBL-EBI have provided independent high-quality human reference gene datasets to biologists since the sequencing of the human genome. Now we’re joining together on an exciting new project we’re calling Matched Annotation from the NCBI and EMBL-EBI or MANE, to provide a matched set of well-supported transcripts for human protein-coding genes and define one representative transcript for each gene. Both RefSeq and Ensembl will continue to provide a rich set of alternate transcripts per gene.
The MANE project builds on the successful CCDS collaboration (PMCID: PMC5753299) and incorporates feedback from RefSeq and Ensembl/GENCODE users who requested a common reference transcript dataset including one or a few key transcripts for each gene where the RefSeq and Ensembl/GENCODE transcripts are identical in length and sequence, and completely match the human reference genome sequence. We expect to later expand the project to include a larger subset of full-length transcripts that more fully represent the functional complexity of many genes. We’re leveraging public deep sequencing datasets to optimize 5’ and 3’ UTR endpoints to more accurately reflect transcriptional processes. To pick representative transcripts, we’ve developed computational methods to evaluate and integrate transcript expression levels, protein conservation, support from archived transcript submissions, clinical relevance, and other factors. Complex genes are subject to review by annotation experts from both groups to agree on a representative transcript and often make improvements to both annotation sets.
The unified, high-quality transcript set provided by the MANE project will simplify the task of choosing a transcript for comparative genomics, clinical reporting, and basic research. When integrated across different public genome resources, this minimal, identically annotated transcript set will eliminate the need to choose between RefSeq and Ensembl/GENCODE datasets for genomic analyses. This will also make it easy for researchers who currently prefer one dataset over the other to exchange data or translate coordinates (or HGVS variation expressions) between RefSeq and Ensembl annotation results. Furthermore, the perfect alignment of all MANE transcripts to GRCh38 will make the set compatible with NGS-based sequencing technologies and other resources that use the latest and highest-quality reference human genome assembly available.
Our goal is for the final MANE dataset to be stable, although individual sequences and the dataset as a whole will be versioned and allow for future updates and expansions as needed to incorporate significant new data and additional curation. We plan to release a partial “beta” transcript set by the end of the year for testing, and a large sequence update in the next few months to refine 5’ and 3’ RefSeq transcript ends and match the GRCh38 sequence. Ensembl plans to release similar updates in spring 2019.
We’re looking forward to your feedback! Next week, we will be presenting the project at the annual American Society for Human Genetics (ASHG) meeting in San Diego, CA, USA. Please attend our talks scheduled in the Genome Reference Consortium (GRC) workshop on Tuesday, October 16, at 1:00 PM, and in the Importance of Isoform Expression in Variant Interpretation Session (#94) on Saturday, October 20th at 9:15 AM. You can also visit us at the NCBI or Ensembl booths and posters throughout the meeting or send us feedback at firstname.lastname@example.org. We’re looking forward to your valuable input on our new initiative!
In 2016, NCBI introduced the Genome Data Viewer (GDV). This past May, the GDV replaced the aging Map Viewer. Over the past year, NCBI has kept you updated about GDV through announcements, webinars, and blogs. Now you can gather information and get an overview of all the changes to GDV in person at ASHG!
Check out Poster 1670F “What’s new with NCBI tools for genome visualization and analysis.” on Friday, Oct. 19 from 3 PM to 4 PM
(Exhibit Hall, Ground Level)
Thank you for your feedback! The community response to our launch of PubMed Labs has been outstanding. We are continuing to test new features at PubMed Labs, like the addition of a new view for search results.
In response to your input, we’ve added “Abstract” to the Display Options of your PubMed Labs search results.
Figure 1. PubMed Labs search. Click the ‘gear’ icon at the top of your results page and click “Abstract” to see the new view.
Be sure to let us know how this and other new features in PubMed Labs work for you.
Please note that PubMed Labs includes only a limited set of features, and not the full set of PubMed tools. The absence of a PubMed tool in PubMed Labs does not mean it is planned for elimination.
Next Wednesday, October 10, 2018, NCBI staff will show you how to use the NCBI resources MedGen, ClinVar, and GTR to locate records for a specified list of symptoms or clinical features, explore specific disease-causing variants, see the review status of the clinical significance for a genetic variant, and find tests relevant to a clinical feature, gene or disease. You will also learn which resource works best for different types of searches.
Date and time: Wed, Oct 10, 2018 12:00 PM – 12:45 PM EDT
After registering, you will receive a confirmation email with information about attending the webinar. A few days after the live presentation, you can view the recording on the NCBI YouTube channel. You can learn about future webinars on the Webinars and Courses page.