PubMed Health to be discontinued October 31, 2018; content will continue to be available at NLM

Update #2: As announced July 31, 2018, the PubMed Health website has been shut down as of October 31, 2018.

NLM thanks you for using PubMed Health over the years.

Update #1: As reported previously, the PubMed Health website will shut down on October 31, 2018. This decision was made so the National Library of Medicine (NLM) can consolidate its consumer health and comparative effectiveness resources to make them easier to find.

In an effort to consolidate similar resources and make information easier to find, the National Library of Medicine will be retiring its PubMed Health website, effective October 31, 2018, and providing the same or similar content through more widely used NLM resources, namely PubMed, MedlinePlus, and Bookshelf.

PubMed Health content falls into two general categories: consumer health resources and systematic reviews/comparative effectiveness research (CER). A similar range of consumer health information to that in PubMed Health is available from NLM’s MedlinePlus, while the systematic reviews and CER in PubMed Health are searchable through PubMed, which links to the full text (when available) in Bookshelf, journals, and/or PubMed Central.

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Upcoming Changes to EST and GSS Databases

Update: NCBI is now in the process of merging EST and GSS records into the Nucleotide database, and we expect to complete this process in early 2019. Accession.version and GI identifiers will not change during this process.

As of December 1, 2018, all records from the databases for Expressed Sequence Tags (EST) and Genome Survey Sequences (GSS) will reside in NCBI’s Nucleotide database. This change will provide a single point of access for all GenBank sequence data with a common look and feel.

Read more to learn about how this change affects these resources:

  • Websites (Entrez)
  • APIs (E-utilities)
  • FTP sites
  • Submission procedures
  • TSA (have a look if you’re not familiar!)

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May – July annotations in RefSeq: ants, Chinese alligator & more

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

  • Alligator sinensis (Chinese alligator)
  • Athalia rosae (coleseed sawfly)
  • Bubalus bubalis (water buffalo)
  • Camponotus floridanus (Florida carpenter ant)
  • Canis lupus dingo (dingo)
  • Harpegnathos saltator (Jerdon’s jumping ant)
  • Melanaphis sacchari (aphid)
  • Pelodiscus sinensis (Chinese soft-shelled turtle)
  • Pogonomyrmex barbatus (red harvester ant)
  • Pomacea canaliculata (gastropod)
  • Sipha flava (yellow sugarcane aphid)
  • Theropithecus gelada (gelada)

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

NCBI implements new, natural language sequence search

In late May, we introduced a new type of search experience in NCBI Labs that uses natural language queries to make common tasks easier. The experience at NCBI Labs – where we experiment with potential new features and tools – proved successful. We’re pleased to announce that we added this simplified search capability to NCBI’s global search page. Some natural language queries now work in the “All Databases” search from the NCBI home page!

NCBI search bar, red arrow pointing to all databases

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NCBI scientists verify taxonomic identities in prokaryotic genomes

As of March 2018, there were 141,000 prokaryotic genomes in the Assembly database. As this database grows, misassigned prokaryotic genomes becomes a serious problem. Taxonomy misassignment can occur through simple submission error or can accumulate as new information adds greater specification to the taxonomic tree.

paper in the International Journal of Systematic and Evolutionary Microbiology presents the method NCBI scientists used to verify taxonomic identities in prokaryotic genomes. The authors used an Average Nucleotide Identity method with optimum threshold ranges for prokaryotic taxa to review all prokaryotic genome assemblies in GenBank. This method relies on Type strain information and is one outcome of a 2015 workshop involving several important parties in the bacteriology community.

Add your full-text book to the NCBI Bookshelf

Since 1999, the NCBI Bookshelf has made full-text books and documents on life sciences and health freely available. The most accessed books, viewed by hundreds of thousands of people each month, are textbooks. This blog post explores the NCBI Bookshelf’s free, online textbooks and discusses how publishers, editors, and authors can contribute to this successful resource.

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July 25 NCBI Minute: Five Teaching Examples Using NCBI BLAST

Next Wednesday, July 25, 2018, NCBI staff will show you a set of simple teaching examples that use BLAST and related alignment tools at NCBI to explore modern biology concepts and techniques including evolution, taxonomy, homology, multiple sequence alignment, phylogenetic trees, primer design and gene expression analysis. You can easily incorporate these examples into your undergraduate biology courses.

Date and time: Wed, July 25, 2018 12:00 PM – 12:30 PM EDT

Register here.

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 our Webinars and Courses page.

The new BLAST widget seamlessly integrates your results into NCBI’s Genome Data Viewer (GDV)

Want to analyze your BLAST results in the context of a genome browser? Want to compare those results against other genome assembly annotations? The BLAST widget, a new browser feature, lets you do that. It provides direct access within GDV to execute and manage BLAST queries (blastn, tblastn) aligned to the specific assembly displayed in GDV.

To learn about this tool, keep reading or watch this short introduction video. Further details are in GDV’s help documents.

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RefSeq release 89 is public

RefSeq release 89 is accessible online, via FTP and through NCBI’s programming utilities. This full release incorporates genomic, transcript, and protein data available as of July 9, 2018. It contains 163,859,625 records, including 113,429,348 proteins, 23,029,67 RNAs and sequences from 81,345 organisms. The release is in several directories as a complete dataset and as divided by logical groupings.

NYGC NCBI-style bioinformatics hackathon August 6-8, 2018

From August 6-8, 2018, the NCBI will help with a data science hackathon at the New York Genome Center in Manhattan. The hackathon will focus on genomics as well as general Data Science. This event is for researchers, including students and postdocs, who have already engaged in the use of large datasets or in the development of pipelines for analyses from high-throughput experiments. Some projects are available to other non-scientific developers, mathematicians, or librarians.

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