The NCBI homepage now has six prominent buttons on it: Submit, Download, Learn, Develop, Analyze, and Research. Each of these buttons leads to an action page devoted to a particular set of services.
Entrez Direct is a UNIX/LINUX command-line interface to E-utilities, the API to the NCBI Entrez system. One of Entrez Direct’s most useful features is its ability to parse and reformat complex XML data returns from EFetch. In this post, we will explore how to use these features to parse, reformat and process specific data from PubMed records downloaded in XML using EFetch. Though this post focuses on PubMed, the technique is universal and applies to any XML returned by E-utilities from any database. The example explored here is also presented briefly in the Entrez Direct documentation; here we’ll dive in a bit depeer to see how it works. Let’s get started! Continue reading
As a My NCBI account holder, you can invite other individuals to act as your delegate and grant them the ability to view and edit your My Bibliography collection (including Other Citations), as well as the ability to view, edit, and create profiles in your SciENcv.
Inviting a Delegate
The first step is to send a delegate invitation from your NCBI Account Settings page. After you’ve logged in to your NCBI account, click on your username in the top right corner of the screen to access your Account Settings. Then, under the “Delegates” section, click “Add a delegate” and enter the email address for your intended recipient. You can have multiple delegates on your account, and you can control what each delegate has access to from the Delegates section of your Account Settings page.
Acting as a Delegate
If a colleague invites you to become a delegate on their NCBI account, you will receive an email invitation. After you’ve accepted the delegation invitation, you will see your colleague’s Bibliography appear in your Collections list on your My NCBI landing page:
In addition, your colleague’s SciENcv will be available in your SciENcv portlet: Continue reading
Today, the NIH Manuscript Submission (NIHMS) system gets a new interface design, as well as updates that streamline the login and manuscript submission processes and provide relevant help information directly on each screen.
The NIHMS sign-in routes will now be available from the homepage. Select a route based on your funding agency (1) or sign in through NCBI if you are starting a deposit on an author’s behalf (2).
The homepage also includes a graphic overview of the NIHMS process (3). You can hover over each step for more information or click “Learn More” to read the complete overview in the FAQ.
Note: The steps of the NIHMS conversion process will remain the same. An author or PI (i.e., Reviewer) will still need to complete the Initial Approval and Final Approval steps. Updated help documentation and FAQs will help you navigate the process.
Once you are signed into NIHMS, you will be directed to your Manuscript List. From this page, you can manage and track your existing submissions (1), submit a new manuscript (2), and search for a record (3). You can also click on any headings in the information box (4) to expand a topic and read the help text.
Deposit a Manuscript
The initial deposit still requires you to enter a manuscript and journal title, deposit complete manuscript files, and specify funding information and the embargo.
Key updates include:
- assigning an NIHMSID to a record only after files have been uploaded, i.e., at the Check Files step (1);
- a streamlined deposit process with clearly defined and explained actions in each step (2);
- requiring the Submitter to open the PDF Receipt to review the uploaded files and confirm that the submission is complete before advancing to the next step (3);
- relevant help information available on each page, as in the previous example (4); and
- requiring the Reviewer to add funding before approving the initial deposit (not pictured).
Questions? Contact firstname.lastname@example.org.
A series of press releases, including one by Science Publishing, recently announced the first findings of the Avian Phylogenomics Consortium, who analyzed genome sequences and annotation data for 48 bird genomes representing all of the bird taxonomic orders. All of the sequenced genomes, along with any annotation provided by the submitter, are available in NCBI resources including Assembly, Nucleotide, Protein, the Sequence Read Archive (SRA), and BLAST, or from species-specific GenBank genomes FTP directories. RNA-Seq data for some of the bird species can be found in SRA.
With the exception of three very fragmented assemblies, NCBI annotated the genome assemblies submitted by the Avian Phylogenomics Consortium using NCBI’s Eukaryotic Genome Annotation Pipeline, and these annotations are now part of the RefSeq project. The RefSeq project also generated annotations for an additional 6 bird assemblies, for a total of 51 RefSeq genomes. A summary of all the bird genomes that have RefSeq annotation is here.
RNA-Seq data was used to generate annotations for 12 of the 51 bird assemblies. The number of protein-coding genes per genome ranges from >13,300 to >21,100 (chicken) with an average of 14,932 protein-coding genes. Orthology to human proteins was also calculated using simple metrics of local synteny and sequence similarity, and on average, roughly 11,000 orthologous proteins were identified per avian genome. These results are shown in the Homology section of NCBI Gene records (see Figure 2 below). Continue reading
A common task facing geneticists is to assay for sequence changes at particular locations in genes. These assays are often looking for changes in the coding exon of genes, and the target sequences are typically amplified using PCR from genomic DNA using a pair of specific primers. In this article, we will show you how to use NCBI Reference Sequences and Primer-BLAST, NCBI’s primer designer and specificity checker, to design a pair of primers that will amplify a single exon (exon 15) of the human breast cancer 1 (BRCA1) gene.
Here are the steps to follow to design primers to amplify exon 15 from human BRCA1. Continue reading
In an earlier blog post, we discussed how sequence updates in GRCh38, the most recent version of the human reference genome, filled in a gap in human chromosome 17 near position 21,300K and expanded the region by 500K (500,000 base pairs). In this post, we will again consider this same region, but with an emphasis now on how GRCh38 also improved the gene annotation.
Figure 1 shows a narrower area that corresponds to components AC068418.5 and AC233702.5 on GRCh38. The graphic display is configured so that it shows annotated gene models without the corresponding transcripts and proteins. The two assemblies share component AC068418.5 along with the five gene models annotated on it. That the same sequence would have the same annotation over time might seem an obvious outcome, but this is not always the case. Annotations on the same sequence (same assembly) can change from one annotation release to another if new transcript data support a new gene model, and this process of gathering and presenting new evidence for gene models is one of the major purposes of new annotation releases on a given assembly. Continue reading
NCBI has three relatively new online resources for information about genetic tests, genetic conditions, and genetic variations:
- The Genetic Testing Registry, or GTR – a registry of genetic tests for heritable and somatic changes in humans
- MedGen – a medical genetics portal that focuses on information about medical conditions with a genetic component
- ClinVar – an archival database that contains reported assertions about the relationship between genetic variations and phenotypes
This blog will provide a very brief overview of the three resources by outlining some of their content features. For a more thorough introduction to the three resources, including the types of information available in each and how to use them, we recommend viewing this approximately hour-long webinar that we conducted in June 2014.
The GTR, MedGen and ClinVar databases are all integrated, making it simple to navigate between them to find related information. They are also integrated with a number of other databases, such as OMIM, GeneReviews, PubMed, Genetics Home Reference, and others. This integration provides a rich information space for exploration, but it is nonetheless helpful to know where you might want to start based on the type of information you are seeking. Continue reading
“The NIH public access policy requires scientists to submit final peer-reviewed journal manuscripts that arise from NIH funds to PubMed Central immediately upon acceptance for publication.” – http://publicaccess.nih.gov/
To comply with NIH Public Access Policy, here are the steps you should take:
Determine if the Public Access Policy applies to your publication
Generally, the NIH Public Access Policy applies to any peer-reviewed journal article that was accepted for publication on or after April 7, 2008 and that arose from NIH funding in Fiscal Year 2008 or later.
Review your publication agreement
Before you sign a publication agreement or similar copyright transfer agreement, first make sure that the agreement allows the paper to be posted to PubMed Central (PMC) in accordance with the NIH Public Access Policy.
NCBI’s recent update to the SciENcv feature in MyNCBI gives researchers the ability to create multiple biosketches for grants from federal agencies engaged in scientific research, allowing a more tailored and convenient approach to the grant application process.
What is SciENcv?
SciENcv (Science Experts Network Curriculum Vitae) is designed to help researchers assemble an NIH biosketch by extracting information from NIH eRA Commons and PubMed. The SciENcv interagency working group includes NIH, as well as DOD, DOE, EPA, NSF, USDA and the Smithsonian. You can access SciENcv if you have a My NCBI account. My NCBI accounts are free and offer many useful features, such as saving searches, automated e-mail alerts and My Bibliography.
Create your biosketch
Based on user suggestions, we’ve made it possible to create biosketches in three ways: from scratch, from an external source, or by duplicating an existing profile (see Figure 1). While the eRA Commons data feed is currently the only external data option, we plan on adding other external data sources in a future release of SciENcv.