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.
Figure 1. The new NIH Manuscript Submission system homepage.
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.
Figure 2. The Manuscript List.
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.
Figure 3. A sample submission.
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.
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. Annotation of a region of chromosome 17 near the KCNJ12 and KCNJ18 genes. Top panel: Annotation release 105 on GRCh37.p13 represented by a configured graphic display of sequence record NC_000017.10. Bottom panel: Annotation release 106 on assembly GRCh38 represented by a configured graphic display of sequence record NC_000017.11. New gene models are circled.
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
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.
Figure 1. Three ways to create your NIH biosketches in SciENcv
NCBI, in collaboration with NLM and the National Network of Libraries of Medicine NLM Training Center (NTC) at the University of Utah, recently presented the second offering of A Librarian’s Guide to NCBI. Health Sciences Librarians from 17 universities and two federal agencies attended the five-day intensive course on the NIH campus. This second offering of the training continues to prepare health science librarians for supporting NCBI molecular databases and tools, and training patrons in the use of NCBI resources at their own institutions.
Participants and instructors from the 2014 “A Librarian’s Guide to NCBI” outside of the National Library of Medicine.
As before, all the course materials are available online. Feel free to learn from them, adapt them for your own teaching, and share them with others. You can use the links below to access the updated 2014 course materials. These include the slide sets with demonstrations and practice problems.
The NCBI in partnership with the National Library of Medicine Training Center (NTC) will offer the Librarian’s Guide to NCBI course on the NIH campus in April 2014. This will be the second presentation of the course; it was previously offered in the spring of 2013 (NCBI Insights April 11 and May 6, 2013). After the course, we will post lecture slides and hands-on practical exercises on the education area of the NCBI FTP site and video tutorials of the course lectures will be available on the NCBI YouTube channel. Materials from the 2013 course are available, as well as lecture videos for the expression module.
This month marks a major event in the realm of human genome research: the release of a new assembly of the genome, GRCh38. It has been over four years since the last major release (GRCh37 in March 2009), and we are going to explore several aspects of this new assembly in a series of blog posts over the coming weeks. In this initial post, we will give an overview of the data flow so that you will understand how NCBI received the data, where the data are at NCBI and what genome annotations you can expect from NCBI in the near future.
November 2013 marks 25 years since the founding of the National Center for Biotechnology Information (NCBI).
In honor of NCBI’s 25th anniversary, United States Senator Ben Cardin read a statement into the Congressional Record recognizing years of service in providing access to biomedical and genomic information to enhance the world’s science and health.
On November 1st an awards and recognition program was held on the NIH Campus in Bethesda, Maryland to commemorate this occasion.
Tony Hey, Ph.D., Vice President of Microsoft Research, presenting the Jim Gray eScience award to David Lipman, M.D., Director of the NCBI.
At this event, Tony Hey, PhD, Vice President of Microsoft Research, presented NCBI Director David Lipman, MD, with the Jim Gray eScience Award which recognizes researchers who have made outstanding contributions to the field of data-intensive computing in the pursuit of open, supportive, and collaborative research models. Continue reading
NCBI has released a pilot version of a new service in PubMed that allows researchers to post comments on individual PubMed abstracts. Called PubMed Commons, this service is an initiative of the NIH leadership in response to repeated requests by the scientific community for such a forum to be part of PubMed. We hope that PubMed Commons will leverage the social power of the internet to encourage constructive criticism and high quality discussions of scientific issues that will both enhance understanding and provide new avenues of collaboration within the community.