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.
In the July 19, 2013 issue of the journal Science, an interesting article describes the discovery and characterization of two “giant” viruses that are proposed to comprise the first members of the “Pandoravirus” genus.
Nadege Philippe and co-workers obtained the viruses from sediment samples in Chile and Australia and found that they have no morphological resemblance to any previously defined virus families. The investigators isolated the genomes of these viruses and sequenced them using a variety of NextGen methodologies. They then assembled the reads into contigs and characterized them using various sequence similarity algorithms (including NCBI’s BLAST and CD-Search). Interestingly, while related to each other, the genomes were not similar to those of any other organism or virus. Additionally, 93% of protein-coding sequences had no recognizable homologs.
NCBI, in collaboration with NLM and the National Network of Libraries of Medicine NLM Training Center (NTC) at the University of Utah, recently presented A Librarian’s Guide to NCBI. Thisnew course was designed to prepare health science librarians for supporting and training patrons about NCBI molecular databases and tools at their own institutions.
Participants, instructors, and organizers in the first offering of “A Librarian’s Guide to NCBI” outside the National Library of Medicine.
We have made all of the course materials available. Feel free to learn from these, adapt them for your own teaching, or share them with others. You can use the links below access the course materials, which include the slide sets with quizzes, demonstrations and practice problems, or visit the FTP site to get all the materials.