Download Gene Set Knowledge Base (GSKB).

Core descriptors GSKB according to BioDBcore guideline (Gaudet et al.
Database, 2011)
1. Database name
Gene Set Knowledge Base (GSKB).
2. Main resource URL
http://bioinformatics.sdstate.edu/gskb/
3. Contact information (E-mail; postal mail)
Dr. Xijin Ge
[email protected]
South Dakota State University
Department of Mathematics and Statistics
Box 2220
Brookings, SD 57007
4. Date resource established (year)
2014
5. Conditions of use (Free, or type of license)
Free
6. Scope: data types captured, curation policy, standards used
Mostly gene lists, or gene sets and their annotation, source and publication information.
We tried to include all gene sets that we could find for mouse. This includes pathways such
those from KEGG, functional categories (Gene Ontology), and many other similar resources. In addition,
GSKB also includes over 8000 lists of differentially expressed genes from original gene expression
studies. The expression studies are retrieved from the datasets included in public data repositories
including Gene Expression Ominibus and ArrayExpress.
This database was constructed through a process similar to MSigDB and AraPath.
7. Standards: MIs, Data formats, Terminologies
Gene lists can be downloaded in GMT format. See description here:
http://www.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats
8. Taxonomic coverage
Primarily focused on mouse.
9. Data accessibility/output options
Data can be downloaded as either Excel file, or GMT file. Search results could be shown as html,
CSV, XML, or JSON.
10. Data release frequency
Data will be released as we update the database.
11. Versioning policy and access to historical files
Currently it is version 1.0. If we release new version, historical files will be available for
download.
12. Documentation available
Some documentation is available in the download page.
http://bioinformatics.sdstate.edu/gskb/db/ Further documentation will be provided.
13. User support options
We will provide supports to users if they have questions.
14. Data submission policy
We welcome user submissions of gene lists directly to our contact email.
15. Relevant publications
Under review in Databases.
16. Resource’s Wikipedia URL
Currently under preparation.
17. Tools available
We provide a searching tool for simple keyword search. The keyword can be a subject such as
“stem cell”, or a gene symbol “ACTB”. We also provide a similarity search, where users can upload a
gene list, and our web server will compare user’s gene lists with all the gene lists in our database and
return those that have statistically significant overlaps.