Legacy view will no longer be available effective late-March 2023
You asked, we listened! We appreciate your feedback since the launch of the updated PubMed Central (PMC) website in March 2022, and we made several improvements to help you better access PMC. These updates include:
Streamlined functionality to get formatted citation information that includes the PubMed format (NBIB file), that works easily on both web and mobile, and is consistent across the PubMed and PMC sites (see number 1 in the image below).
Updated functionality to easily add an article to your My NCBI collections through PMC’s new “Collections” button (number 2 below).
An improved “Resources” section that allows easy access to articles similar to the one you are viewing, other papers that cite that article, and links to related data records in other NCBI databases (number 3 below).
New article view in PMC. Updates are illustrated with yellow number squares: 1) “Cite” button provides formatted citation information; 2) “Collection” button adds the article to My NCBI collections; 3) “Resources” button finds related articles; 4) “Feedback” button to communicate with NCBI. Continue reading “New Enhancements to PMC Website”→
As a national resource for molecular biology information, our mission is to develop new information technologies to aid in the understanding of fundamental molecular and genetic processes that control health and disease. We provide access to biomedical and genomic information by creating, curating, and maintaining medical and scientific databases. Continue reading “What is NCBI and who works here?”→
In response to your feedback, we’ve made more whole genome cross-species alignments available in NCBI’s Comparative Genome Viewer (CGV). You can use these alignments to explore genome rearrangements between species. You can also zoom in to analyze regions of conserved gene synteny.
There are over 20 new cross-species alignments available, including human-mouse, mouse-rat, human-chimp, human-cattle, dog-cat, and others! These cross-species alignments provide additional opportunities to explore evolutionary relationships at the genomic and gene levels. We will add more cross-species alignments in the coming months.
The latest cross-species alignments added to CGV include imports from the UCSC Genomics Institute, as well as those generated at NCBI.
Check out two examples of cross-species whole-genome alignments in CGV below (Figure 1).
Figure 1. Whole genome alignments between (A) mouse and human (GRCm39 vs. GRCh38.p14) and (B) cat and dog (F.catus_Fca126_mat1.0 vs. ROS_Cfam_1.0). Colored bands connects aligned regions; green indicates same orientation, blue indicates opposite orientation.
When you zoom in on an alignment (Figure 2), you can compare gene annotation on the two assemblies and see the extent of conservation of synteny. You can also see which genes are missing from one or the other assembly, indicating changes in sequence or differences in annotation.
We recognize that the traditional influenza virus names like ‘Influenza A virus’ and ‘Influenza B virus’ are broadly used in public health, educational institutions, and research. To minimize the impact of this change to those who use NCBI resources, the taxonomy schema will keep the former names in the lineages for each species; however, they will be moved below the (new) species taxa in the hierarchy. See example below.
Historically, RefSeq EGAP has used an integer to identify a particular annotation release, such as Homo sapiens Annotation Release 110. This method provides no information on the assembly used for the annotation. In the new RefSeq naming system, annotation releases are designated by a combination of the assembly identifier (e.g., GCF_000001405.40) and an annotation name (e.g., RS_2022_04). The annotation name consists of an RS prefix to indicate RefSeq annotation, and the year and month that it was generated, RS_YYYY_MM. You should always use the annotation name in combination with the corresponding assembly accession.version, for example, GCF_026419915.1-RS_2022_12 (as shown in Figure 1). This ensures that you’re always using the name that defines a specific annotation for a specific genome assembly. If you use only part of the name, it will be ambiguous.
We are excited to celebrate ClinVar’s 10th anniversary and look forward to seeing you in-person at the 2023 ACMG Annual Clinical Genetics Meeting, March 14-18, 2023, in Salt Lake City, Utah. We will participate in a variety of events and activities featuring our clinical and human genetic resources.
Do you currently add an organism name(s)to focus your searches when using the BLAST standard nr database? You can now focus your searches by organism with the BLAST ClusteredNR database and get faster results with a better overview of protein homologs in a wider range of organisms. Your searches will be restricted to protein clusters that contain one or more sequences from the organism(s) you add.
Do you work with human-derived sequence data? Do you often struggle with the need to determine if your data is free of human sequence and therefore suitable for public distribution? We encourage submitters to screen for and remove contaminating human reads from data files prior to submission to SRA. To support investigators in this effort, we offer a tool to remove human sequence contamination from your SRA submissions!
ClinVar is NCBI’s archive of reports of the relationships among human genetic variations and diseases, with supporting evidence. To make ClinVar data more accurate and useful, we are introducing an enhanced data model to better accept and support classifications of somatic variants.