Updates

UI-optimized

The new version of CNGBdb comes with a much better user interface, which has been re-revised, fully upgraded, becomes more easier to use and user-friendly.

Data retrieval service of China National GeneBank

Advanced search

CNGBdb's advanced search allows users to run queries over all fields in the database according to the data retrieval needs. For example, users can do a title search with keyword ‘rice’ in the Title field of the literature database, or search ‘Gigascience’ in the Journal field. BOOLEAN operations also can be used to improve search accuracy and search efficiency.

Text auto-completion

Users are offered ‘auto complete’ search service by CNGBdb. If users type partial keywords into the CNGBdb search bar, auto-complete will finish typing it for users.

Text auto-correction

Users are offered ‘auto correction’ search service by CNGBdb. With this search service, users will receive suggested spelling search results if they type their search queries incorrectly, which can help users find what they are looking for in an easy and fast way. For example, users type ‘lang cancer’ into the search bar, based on the algorithms analysis, CNGBdb predicts ‘lung cancer’ may be the term users think about actually, and provides search results of ‘lung cancer’.

Results filtering

Search and filter functions of CNGBdb in all databases can help users narrow down searches that brought back too many results and find results accurately and rapidly. For example, users can filter out full-text articles by selecting ‘Free full text’ in the search result page of literature database, and also can search for the newest papers by the year data of publication.

Excellent datasets recommendation

In search results, CNGBdb will give priority to recommend excellent datasets that match the user's search terms. For example, if users search for ‘the Ruili Botanical Garden’, the search results will give priority to recommend the Ruili Botanical Garden dataset, project ID of which is CNPhis0000538, containing 42TB sequencing data and 738 plant samples.

Data update

CNGBdb version 1.0 has increased data resources compared to the beta version. Up to February 2019, data resources of all databases are as follows:

  • Literature Library ( 29,198,501 )
  • Gene bank ( 33,171,984 )
  • mutation library ( 763,230,128 )
  • Protein Library ( 134,065,913 )
  • Sequence Library ( 2,136,651,182 )
  • Project Library ( 3,162 )
  • sample library ( 323,116 )
  • Experimental Library ( 430,586 )
  • Assembly library ( 2,346 )

Data resources will be updated periodically to ensure timeliness, such as daily updates of the literature database.

China National GeneBank Nucleotide Sequence Archive (CNSA)

Data submission interaction logic has been optimized, adding prompts.
Online batch submission efficiency optimization

The average submission time is reduced by 70% after optimization. Testing case: submission time-consuming(file size: 99kb; article number: 768) is 27s and 5s before and after optimization.

Upload ftp, MD5 verification speed has been accelerated to eight times.
New submission types (bulk/single) have been added in My Submission page, the number(e.g. sample ID) list also can be downloaded from this page.
Reviewer link generated automatically according to users’ requirements for article publication can be provided to the journal editors to review, which can help the article get approved and published more quickly.
Internal Users are offered auto data submission service via Cluster Upload.

Data Calculation and Analysis Service of China National GeneBank (BLAST)

BLAST has been upgraded to NCBI's latest V2.8.1.
The reference database has been upgraded to NCBI's latest V5 version, and the genome assembly data published by BGI has been added in CNGBdb Version1.0.

Based on big data and cloud computing technologies, China National GeneBank DataBase (CNGBdb) provides integrated data services such as data archiving, computational analysis, knowledge search, management authorization and visualization.

Data retrieval service of China National GeneBank

CNGBdb constructs multiple databases, including Literature, Gene, Variation, Protein, Sequence, Project, Sample, Experiment, Assembly, and allows cross-reference among those data sources to form data interconnection. CNGBdb offers a number of important performance advantages:3 billion data items; full-text search; second response time; retrieval keywords both in Chinese and English.

Data Calculation and Analysis Service of China National GeneBank (BLAST)

BLAST has been upgraded to NCBI's latest V2.8.1.
BLAST has been integrated with NCBI's nc and nr databases.
BLAST has been integrated with CNGB's multiple databases, such as ONEKP(BLAST for 1,000 Plants), B10K(The Bird 10,000 Genomes), PIRD(Pan immune repertoire database), containing 564,057,891 items of immune data.
  1. Batch submit and review data of projects, samples, experiments and assemblies online.
  2. CNSA provides archiving services of variation data for users.
  3. CNSA assigns DOI(digital object identifier) numbers for projects in order to help users cite, trace, retrieval and reuse data conveniently.
  1. Users can submit data of projects, samples, experiments and assemblies online.
  2. Reviewer can review data of projects, samples, experiments and assemblies online.
  3. English-Chinese bilingual interface, localized service.
  4. Open data retrieval service to users.
https://db.cngb.org