NCBI’s Genome Data Viewer (GDV) now supports visualization and analysis of nearly 400 submitter-annotated chromosome-level assemblies from the INSDC (GenBank/ENA/DDBJ). These submitter-annotated assemblies join more than 1,200 NCBI RefSeq-annotated assemblies available in GDV for hundreds of eukaryotes, spanning fungi, plants, fish, insects, and all major model organisms.
Figure 1 shows a GenBank apple assembly (GCA_004115385) displayed in GDV.
Figure 1. Submitter-annotated Malus domestica (apple) assembly displayed in GDV. GDV provides submitter-provided gene annotation, as well as some additional tracks including interspersed repeats identified by RepeatMasker and six-frame translations (not shown). Red boxes indicate useful tools and panels including a search box, an exon navigator, and interfaces to add user data and conduct NCBI BLAST searches.
The National Library of Medicine and its partners in the International Nucleotide Database Collaboration (INSDC) have joined together to issue a statement encouraging the scientific community to submit their SARS-CoV-2 sequences to INSDC databases. The databases offer broad open access and integrated data, literature and tools – features that we believe are critical as the research community works together to understand and combat COVID-19. Read the full statement below.
The databases of the International Nucleotide Sequence Database Collaboration (INSDC; http://www.insdc.org/) capture, organize, preserve and present nucleotide sequence data as part of the open scientific record. INSDC member institutions – the EMBL European Bioinformatics Institute (EMBL-EBI), the NIG DNA Data Bank of Japan (NIG-DDBJ) and the National Library of Medicine’s National Center for Biotechnology Information at NIH (NCBI) – are committed to the continued delivery of this critical element of scientific infrastructure.
The global COVID-19 crisis has brought an urgent need for the rapid open sharing of data relating to the outbreak. Most importantly, access to sequence data from the SARS-CoV-2 viral genome is essential for our understanding of the biology and spread of COVID-19. To aid in that effort, all three INSDC members have prioritized processing of SARS-CoV-2 sequence data and have streamlined the submission process.
Availability of data through INSDC databases provides:
- Rapid open access – INSDC quickly makes submitted data freely available to everyone, without restrictions on reuse
- Linkage of raw sequence read data to genome assemblies, providing researchers with the ability to validate the integrity of assemblies and investigate asserted mutations and changes in genome sequences
- Integration of SARS-CoV-2 sequences with entirety of INSDC data, including related coronaviruses genome sequences, enabling comparison across species
- Linkage of sequences to the published literature
- Tools – INSDC partners provide integrated data analysis tools, such as BLAST, enhancing the discovery process
In support of the global response to the COVID-19 crisis, the INSDC calls upon the research community to:
- Submit raw SARS-CoV-2 data to the databases of the INSDC
- Submit consensus/assembled SARS-CoV-2 data to the databases of the INSDC
- Provide information relating to the sequenced isolate or sample as part of the sequence submission; minimally the time and place of isolation/sampling and an isolate/sample identifier should be provided to maximize the value of the sequences.
- In cases where scientists have already established submissions to other databases, these submissions should continue in parallel to the INSDC submission
The integration of INSDC databases with the global bioinformatics data infrastructure, including tools, secondary databases, compute capacity and curation processes, assures the rapid dissemination of data and drives its maximal impact.
In addition to these fundamental roles of INSDC member institutions in the sharing of viral sequence data, each institution has rapidly established COVID-19-specific programs and resources: the European COVID-19 Data Platform from EMBL-EBI, the DDBJ’s Research Data Resources on New Coronavirus and the NCBI SARS-CoV-2 Resources. These resources both demonstrate the connectedness of INSDC databases to broader bioinformatics initiatives and serve to add immediate value to COVID-19 research.
Guy Cochrane (EMBL-EBI), Ilene Karsch-Mizrachi (NCBI-NLM-NIH), & Masanori Arita (DDBJ) on behalf of the International Nucleotide Sequence Database Collaboration
RefSeq release 84 is now accessible online, via FTP and through NCBI’s programming utilities.
This full release incorporates genomic, transcript, and protein data available, as of September 11, 2017, and contains 140,627,690 records, including 95,563,598 proteins, 20,356,598 RNAs, and sequences from 72,965 organisms.
The release is provided in several directories as a complete dataset and as divided by logical groupings. See the RefSeq release notes for more information.
Phasing out support for non-human organisms
As of September 1, 2017, the dbSNP and dbVar databases have stopped accepting submissions for non-human organisms. Submissions for non-human variation will now be accepted by the European Variation Archive, one of our partners in the International Nucleotide Sequence Database (INSDC).