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On October 25, 2018, at the 13th International Conference on Genomics (ICG-13) hosted by BGI, with the witness of the guests at home and abroad, the China National GeneBank DataBase (CNGBdb) officially released and became a highlight of ICG-13.

Xiaofeng Wei, the head of the CNGBdb platform and the leader of the data application team in the Big Data Center of BGI, introduced CNGBdb. The platform was built to promote the sharing and utilization of biological data. Unlike other data platforms, based on the big data and cloud computing technologies, CNGBdb has integrated massive data from CNGB (China National GeneBank), NCBI (National Center for Biotechnology Information), EBI (European Bioinformatics Institute), OMIM (Online Mendelian Inheritance in Man), etc., to meet the multiple needs such as search, storage, computation and use, to broke the barriers of database decentralization in the field, to provide one-stop solution to all needs of users with a unified portal, so it is called “Google in the genetic world”.

The head of CNGBdb platform

What can CNGBdb do specifically? Xiaofeng Wei, the head of the platform, said that the platform provides data services such as data archive, knowledge search, computational analysis, management authorization, and visualization to researchers around the world, covering more than a dozen studies on maternal and child health, tumors, animal and plant diversity, and pathogenic microorganisms, which has formed a super large scientific research data system that integrates multiple research fields, multiple data types, and multiple analysis dimensions.

CNGBdb data structure

CNGBdb first solved the problem of “storage” for domestic researchers – the domestic localized data archive space. Its CNGB Nucleotide Sequence Archive (CNSA) provides English-Chinese bilingual interface, 1Gb bandwidth, and batch submission functions to ensure users can use easily, upload and download quickly, and strengthen the security of genetic data resources in China. At the same time, CNGBdb assigns each scientific data a unique "identity card" - DOI (Digital Object Identifier) identifier for easy retrieval, tracking and citation, increasing data exposure and citation rate. At present, the platform has supported nearly 3,000 projects and with an archived data volume of nearly 600TB.

CNSA

It is reported that another major advantage of CNGBdb is the distributed, AI-driven search engine. It is also the largest search engine in the vertical field of life science, and has realized the index of more than 3 billion data and interconnection of 10TB meta information. 12 data structures such as literature, variation, gene, protein, and sequence, etc., are linked to each other, and the related information is showed on the same page at the time of retrieval, which makes the efficiency of information collection and screening double. In addition, the CNGBdb search engine not only achieves second-level response speed, but also supports Chinese keywords and full-text search.

In terms of "computation", CNGBdb provides a series of data computing and analysis services, of which BLAST is one of the most recommended applications. It is a high-performance hybrid computing pool that integrates NCBI's latest nt, nr libraries and has CNGB's unique the 1, 000 Plants project (1KP) dataset, the Bird 10,000 Genomes (B10K) Project dataset, and the world's largest immune sequence dataset etc., to make it easy for users to search and compare nucleic acid or protein sequences.

CNGBdb BLAST

The release of CNGBdb is a great event in the field of life science, which has aroused strong repercussions from guests at home and abroad. The platform is now officially online, and users can access its features and services at db.cngb.org. Xiaofeng Wei, the head of the platform, said that GNGBdb will provide great convenience for scientific research in life science at home and abroad. The CNGB will further expand the data storage of the platform, and continue to strengthen the functions and services of the platform in combination with cutting-edge technologies to better promote the interoperability, open sharing and effective use of life multi-omics big data, and promote the rapid development of life science and bioindustry.

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China National GeneBank DataBase (CNGBdb)

Recently, the CNGB Nucleotide Sequence Archive (CNSA) has undergone a major upgrade. The batch submission function of sequencing data that many users are eagerly awaiting is finally realized for the first time in China. From now on, CNSA can not only complete data submission several times faster than before, but also greatly improve the operating experience.

With the development of biotechnology, a large number of biological research data have been produced. The massive achievement need to be shared, bring data security management and efficient transmission bottlenecks. CNSA established by China National GeneBank, built for the big data of life science, will solve the problems completely.

1 Solve the problem of local data submission

As a researcher, there is often a need to publish articles in authoritative scientific journals. When you submit sequencing data in advance, do you often encounter such problems?

• The submission process of international public database is complex and may require repeated communication changes if problems arise;
• Only English interfaces and services affect the efficiency of submission and communication to a certain extent;
• Data is transmitted very slowly across borders, with 5TB of data going to be transmitted for 2-3 months, which takes a lot of valuable time.

As a result, the data submission is time-consuming and laborious, which not only makes many researchers feel overwhelmed, but also has other hidden dangers such as sensitive data outflow.

CNSA released on October 25, 2017. With the recognition and support of many researchers, CNSA has supported more than 700 scientific research projects with a total archived data volume of nearly 600TB.

The CNSA system is easy to operate, supports high-speed upload and download, and provides domestic localized storage space for genomics data. In addition, CNGB systematically optimizes and enhances both information security management and technology, which has passed the three-level review of information security level protection and the protection capability review of trusted cloud service, providing powerful information security protection for data storage.

2 omnipotent platform to promote global information sharing

CNSA is dedicated to facilitating the storage and sharing of sequencing data, providing researchers worldwide with the most comprehensive data and information resources, and making it easier and more in-depth for researchers to access and use data. In order to fully meet the various needs of biological researchers for data, achieve complete archive of data from generation, submission, synchronization, search to download, and ensure the integrity of scientific research results, CNSA can not only archive data, but also provide other important services:

• Backup of large volumes of data;
• Data-controlled management, whether the data is public or not can be set at the time of submission;
• When submitting data, you can choose to synchronize to an international public database (NCBI or ENA);
• Ultra-fast download of massive public data files;
• Publish articles can reference to the CNSA accession number;
• A search engine that supports billions of data, with second level response.

Note: At present, CNSA does not accept relevant data covered by the Human Genetic Resources Regulations

3 Support the DOI index and publication of scientific research results

In addition to the above features, CNSA has a significant advantage, which can be identified using the DOI (Digital Object Identifier). At present, CNGB has become one of the first organizations to cooperate with the British Library on DataCite services and is the first data center in Asia to participate in the project. The use of unique DOI numbers to identify the data generated by scientific research and facilitate the retrieval, tracking and reference of data, can improve its exposure and citation rate, and will greatly facilitate the establishment of data sharing and sharing evaluation system.

CNSA follows the International Nucleotide Sequence Database Collaboration (INSDC) standard and the DataCite standard, and accepts sequencing data (including raw data and other supporting data) from around the world. Its data submission service can be used as a supplement to the literature publishing process to support early data sharing. CNSA will support the publication of global scientific research results, realize data sharing for different research types and scales, improve the reproducibility of scientific research results, and promote new discoveries in science and technology.

4 Batch submission, do more with less

In order to better meet the needs of large-scale data submission, the CNSA system has undergone a major upgrade. CNSA has realized the online batch submission function of nucleotide sequence archive system for the first time in China. At the same time, it also optimizes the operation experience. The submission process is clearer and consumes less time, so you can easily upload and archive large amounts of data.

CNSA link: https://db.cngb.org/cnsa/

Please contact us if any problem or suggestion.

Email:datasubs@cngb.org

On October 25, 2017, China National GeneBank released CNGB Nucleotide Sequence Archive (CNSA). CNSA is a convenient and fast online submission system for biological research projects, samples, experiments and other information data. CNSA is committed to the storage and sharing of biological sequencing information and data, and is designed to provide global researchers with the most comprehensive data and information resources, enabling researchers to access and use data easily and deeply.

With the development of biotechnology, a large number of biological research data have been produced. The massive achievement need to be shared, bring data security management and efficient transmission bottlenecks. CNSA established by China National GeneBank, built for the big data of life science, will solve the problems completely.

Combined with the international authority of the data structure standards to meet the global share of scientific research

CNSA accepts the submission of the raw reads and other support data, integrating with INSDC and Datacite standard, sharing different types of research and scale data.

Following the International data open protocol, Serving as a complement to the literature publication process of scientific research achievement all over the world.

CNSA follows the international data open protocol such as Fort Lauderdale Agreement, NHGRI Rapid Data Release Policies, Joint Data Archiving Policy, CC0-No Rights Reserved, accepting the submission of global scientific research sequencing data (including raw data and other support data), its data submission service can be used as a supplement to the literature publishing process to support early data sharing.

Following the user`s stated data permissions and rights constraints.

CNSA follows the "Interim Measures for the Management of Human Genetic Resources" and ethical norms of users` countries. Researchers need to send an electronic copy of the document that the Ethics Committee agrees to approve to the datasubs@cngb.org. For the data related to the collection, sale, export and exit approval of human genetic resources, researchers need to send an electronic copy of the document which the relevant department of human genetic resources management approve (Eg, a regional or national country with a human genetic resources management approach).

Ensuring a level of security，taking into account the categories of data

CNSA combines the data types and processing methods, using the corresponding technical and management measures to ensure that different levels of security.

Using high-performance distributed archiving system.

CNSA uses high-performance distributed for data archiving, with independent high availability backup storage system for secure data storage.

Having the high-speed internet network and logistics network

CNSA Relies on the high-speed internet network and logistics network of BGI and CNGB, covering the global multi-center, synchronizing the data to the to the global public databases quickly.

Having a full-text search engine

CNSA has a full-text search engine which can support Petabytes of data, combine any keywords and fast position.

Providing Localized Chinese language services, fastest feedback, zero-distance communication

CNSA provides Chinese and English artificial bilingual services and can contact us by phone, email, etc., to achieve barrier-free and zero-distance communication.

CNSA Quick Start Guide :

1. Raw sequence data submission

Raw data refers to all the original data generated by a sequencing without any filter theoretically.For raw sequence data submission, CNSA integrates data standards and structure of INSDC for data review and archiving, including projects, samples, experiments and data submission.

Fig 1. Raw sequence data submission process

2. Other support data submission

Other support data except the raw reads, which is related to articles or research, includes but not limited to process and result data, analysis methods, software programs, image files, audio files, video files, imaging files, electronic charts and word documents. CNSA cooperates with Gigascience GigaDB to archive the support data. With a link to DataCite, each dataset will be assigned with a DOI which can be directly referenced(Fig 2).

Fig 2. Other support data submission process

3. Data search and download