CNVs from Exome Aggregation Consortium (ExAC) added to dbVar in September 2017 data release

Posted on October 18, 2017 by NCBI Staff

Copy number variants (CNVs) from ExAC’s publication are now available at dbVar as nstd151. The data include approximately 50,000 CNV regions identified from 60,000 human exomes, providing a deep survey of common and rare copy number variation affecting protein-coding sequences in the human genome.

dbVar provides FTP files in VCF, GVF, and CSV formats, and include placements on GRCh37 as well as remapped placements on GRCh38. Tutorials for working with different formats are also available.

Follow the dbVar RSS feed for information on monthly releases.

Updated HIV-1 interaction datasets in Gene

Posted on October 18, 2017 by NCBI Staff

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 replication interactions dataset now has:

1,595 interactions,
1,854 interaction descriptions,
1,583 proteins encoded by 1,583 human genes,
and 229 publications.

Data are also available at the RefSeq HIV-1 website and the GeneRIF FTP site.

Try Our New, Experimental PubMed Search and User Interface in PubMed Labs

Posted on October 17, 2017 by NCBI Staff

NLM needs your input. We are experimenting with a new PubMed search algorithm, as well as a modern, mobile-first user interface, and want to know what you think. You can try out these experimental elements at PubMed Labs, a website we created for the very purpose of giving potential new PubMed features a test drive and gathering user opinions.

Please note that PubMed Labs includes only a limited set of features at this time and not the full set of PubMed tools. The absence of a feature or tool on PubMed Labs does not mean we plan to eliminate it from PubMed; it simply means we are not testing it now!

The key elements we are testing are:

In PubMed Labs, search results are listed by best match. The best match button is at the top right; you can also click the "most recent" button (to the right of "best match") to sort by date.

A new search algorithm for ranking (ordering) the best matches to your query

Based on analysis of data obtained from anonymous PubMed search logs, we have developed a new algorithm that we believe does a much better job of sorting search results by their relevance, or “best match,” to your query. This new algorithm incorporates machine learning to re-rank the top articles returned.

We were so excited by results with this algorithm that we already implemented it in PubMed, but it is still experimental and we would very much appreciate hearing what you think. Part of our test in PubMed Labs is having best match be the default sort, instead of PubMed’s default of sorting by most recent articles. If you find that you prefer to sort by the most recent articles instead, it takes only a simple click of a button to do so.

Interested in specifics about the new algorithm? You can read more in this NLM Technical Bulletin.

Continue reading →

GRAF, a new tool for finding duplicates and closely related samples in large genomic datasets

Posted on October 16, 2017 by NCBI Staff

Genome-wide association studies (GWAS) usually rely on the assumption that different samples aren’t from closely related individuals. If you’re using combined datasets that have been genotyped on different platforms, though, how do you detect duplicates and close relatives?

The dbGaP team at NCBI developed a new software tool and rapid statistical method called Genetic Relationship and Fingerprinting (GRAF) to do exactly that. At NCBI, we use GRAF as a quality assurance tool in dbGaP data processing. We’re presenting this tool publicly so any researcher can check the quality of their own data.

GRAF uses two statistical metrics to determine subject relationships directly from the observed genotypes, without estimating probabilities of identity by descent (IBD), or kinship coefficients, and compares the predicted relationships with those reported in the pedigree files. Please see the PLOS ONE article published in July 2017 for a detailed description of GRAF.

A recent update to GRAF adds the ability to determine subject ancestries. For more information on this addition, visit Poster #1322T, “Quickly determining subject ancestries in large datasets using genotypes of dbGaP fingerprint SNPs”, on Thursday, October 19^th from 3-4 in the Exhibit Hall at ASHG.

Genome Workbench v2.12.5

Posted on October 10, 2017 by NCBI Staff

Recent updates to Genome Workbench include a new navigation tutorial for Graphical Sequence View, and various bug fixes and improvements. You can see the full list of changes in the Genome Workbench release notes.

Genome Workbench is an integrated application for viewing and analyzing sequences. Genome Workbench can be used to browse data in GenBank and combine this data with your own private data.

PubMed Labs is now part of NCBI Labs

Posted on October 3, 2017 by NCBI Staff

About two years ago, NCBI launched PubMed Labs, a gathering place for discovering and experimenting with new features and content for NCBI’s family of websites. Over those years, we launched a few experiments that have helped us learn more about our customers and how we can serve them better.

Today we’re happy to announce that we’re expanding PubMed Labs to a broader set of experiments called NCBI Labs.

Why are we doing this?

To better convey the breadth of upcoming experiments on data, services, and websites that NCBI offers now and hopes to offer in the future. You can expect to see new features, content, and other experiments from NCBI Labs in the coming months.
To reserve the name “PubMed Labs” for an exciting new set of experiments around biomedical literature and especially literature search.

What Will Change?

This blog’s menu item and blog category “PubMed Labs” will now appear as “NCBI Labs”. Existing links will continue to work. We won’t be updating the old blog posts, for the most part, although some links on existing sites (e.g. on PubMed Journals) may be updated to use the new name.

October 11 NCBI Minute: Introducing the New RefSeq Functional Elements Project

Posted on October 2, 2017 by NCBI Staff

On October 11, 2017, NCBI will present a webinar on RefSeq Functional Elements. This NCBI Minute will introduce you to this project and its scope, describe how functional elements are curated and displayed, demonstrate how to access the data, and provide information on the current progress of the project.

Date and time: Wed, Oct 11, 2017 12:00 PM – 12:30 PM EDT

After registering, you will receive a confirmation email with information about attending the webinar. After the live presentation, the webinar will be uploaded to the NCBI YouTube channel. You can learn about future webinars on the Webinars and Courses page.

The new RefSeq Functional Elements project is an expansion of the NCBI RefSeq project to include non-genic functional genomic regions in human and mouse that have been experimentally validated and described in the scientific literature.

October 4th NCBI Minute: Create, link and share your bibliography (PubMed & ORCID)

Posted on September 27, 2017 by NCBI Staff

On October 4, 2017, NCBI staff will present a webinar on author disambiguation and the advantages of using an ORCID ID.

Disambiguating common author names is tough in any field, but if your published research is cited in PubMed, we can help you find your citations, create a bibliography, and share your publication list with others.

In this webinar, we’ll also talk about the advantage of quickly registering for a free, unique identifier that will remain constant – even if your name changes.

Date & time: Wednesday, October 4, 2017 12:00 PM – 12:30 PM EDT

Magic-BLAST 1.3.0 released with new features and improvements

Posted on September 26, 2017 by NCBI Staff

The newest version of Magic-BLAST (v. 1.3.0) offers improved sensitivity and faster run-times as well as a number of other new features and improvements. These include the ability to set the alignment cut-off score as a function of read length, a maximum edit distance option and optional local cacheing for SRA files. For more information on these and other improvements, see the release notes. You can download the new executables from the NCBI FTP site.

Magic-BLAST is a tool for mapping large next-generation RNA or DNA sequencing runs against a whole genome or transcriptome. Read more here.

14 new NCBI RefSeq genome annotations are available

Posted on September 21, 2017 by NCBI Staff

In August, the NCBI Eukaryotic Genome Annotation Pipeline released new annotations in RefSeq for the following organisms:

Spinacia oleracea (spinach)
Carica papaya (papaya)
Zootermopsis nevadensis (termites)
Acanthochromis polyacanthus (spiny chromis)
Folsomia candida (springtails)
Helianthus annuus (common sunflower)
Acanthaster planci (crown-of-thorns starfish)
Myzus persicae (green peach aphid)
Momordica charantia (bitter melon)
Pieris rapae (cabbage white)
Nilaparvata lugens (brown planthopper)
Drosophila obscura (a fly)
Canis lupus familiaris (dog)
Limulus polyphemus (Atlantic horseshoe crab)

See more details on the Eukaryotic RefSeq Genome Annotation Status page.

NCBI Insights

Providing insights into NCBI resources and the science behind them