1. Practices of Science Data Sharing Platform for Bioinformation in SCBIT
Guoqing Zhang
Oct 7th 2010

2. Overview of SDSPB
Shanghai Center for BIoformation Technology(SCBIT) takes promoting Chinese bioinformation data sharing as a goal
Scientific Data Sharing Platform for Bioinformation(SDSPB) is the executive platform of data sharing in SCBIT
SDSPB is aimed to build and manage databases of biological data that servers the life science research community in China, especially in Yangtze River Delta

3. Data Transmission in SDSPB
Retrieve data from 3rd data centers, including EBI, NCBI, KEGG, and so on
Accept data submitted by users, including nucleotide sequences, protein sequences, proteomics, and other data
Supply download service

4. SDSPB had built many databases and online services in Chinese and/or English
SDSPB classify these resources as basic resources, subject resources, online services and metadata system

5. Basic Resources and Subject Resources
Collect various data from basic resources
Import related data to meet the need of subject resources
hepatitis B virus

6. Full Database Update
Taxonomy database as support data for all other resources
NT/NR databases for blast
UniProt database for protein identification
KEGG pathway database for pathway analysis
Entrez gene database for gene names
ID mapping database for database integration

7. Data Update for Basic Resources
Update as full database in weekly or monthly
Download automatically from background
Once finished, is sent to the curators
Once overtime or receive , the curators check the data manually
The speed is between 2-3kb/s, and no more than 100kb/s
About 1/5 data should be downloaded manually

8. Selective Database Update
Genome sequences for virus genomes, pathogen genomes
Other nucleotide sequences of special species
GEO profiles of special species
RPIDE experiments of special species
Structure data of special species
Literature resources for special issues

9. Data Update for Subject Resources
SDSPB build some subject databases and platforms
HBV drug resistance platform(in Chinese) includes HBV related genomes, protein sequences
Schistosome database collects protein sequences, EST and other data
Flu database …

10. How We get data selectively
Subject resources require to integrate necessary data
SDSPB define the data range, make the collecting strategy, and retrieve these data automate or manually
Data imported into basic resources
Subject resources integrate different data with local resources

11. Data Submission and download
Genome sequences and related data
NGS data
Proteomics data
Supply data download service, especial raw data submitted and allowed by users

12. Current situation of SDSPB
We wish to accept data by network
We accept data by express now
We retrieve data from 3rd data centers again and again
Robust scripts to struggle with complicated network

13. What we do
Introduce one line from CAS for data download (100M/s) to meet with the low speed
More human resources devoted to meet with the unstable network
More robust scripts written to check the network connection status

14. Thanks