Hello
I am searching for a good genotype-phenotype database for human.
I know OMIM (http://www.ncbi.nlm.nih.gov/omim). But it seems not to include GWAS results.
I found GWASdb (http://jjwanglab.org/gwasdb) that collects only GWAS results.
I also found PheGenI http://www.ncbi.nlm.nih.gov/gap/phegeni on the NCBI website, but there is no downloadable dataset.
Merging OMIM and GWASdb will solve the problem, which, however, is not easy because their phenotype classification is different.
Does anyone know a human genotype-phenotype database that contains both OMIM-like and GWAS info.
Thank you.
Best,
Kyungtaek
Hi Kyungtaek Lim,
PhenomicDB is a comprehensive phenotype-genotype database
dbGap is another comprehensive database
and PheGenl is another comprehensive database
Check the following weblinks below:
http://www.nature.com/ejhg/journal/v22/n1/full/ejhg201396a.html
http://www.ncbi.nlm.nih.gov/gap
http://www.phenomicdb.de/
Kind regards
Olugbenga
Try http://genome.ucsc.edu/ is a very comprensive database although complex
The best suggestion would be ' The Phenomizer' in Human Phenotype Ontology website. In this try to go for a tabular column module, so that you can get the list of Genes involved in the phenotype that you focus for.
Good luck and Here you go with!
http://compbio.charite.de/phenomizer/
http://www.human-phenotype-ontology.org/
Dear Michel and Srinivasan
Thanks for your suggestions. I will check out those web-servers.
Best,
Kyungtaek
Have you tried the EGA European Genome-Phenome Archive available at CRG and EBI?
https://ega.crg.eu/
For genome-wide association data we provide the GWAS Central database: http://www.gwascentral.org/
Here you can search for GWAS results on physical location, or via phenotype (HPO and MeSH ontologies are both supported).
For other variation data, there is an extensive network of locus-specific and disease-specfic databases. Most of these can be searched via the variation discovery tool Cafe Variome: http://www.cafevariome.org/discover.
Dear Eva
Thanks. EGA seems very comprehensive. They have a strict policy in data access.
and Dear Adam
Thank you for the info. I'm impressed by GWAS central's RESTFUL-like service.
Best,
Kyungtaek
As far as I know, only dbGAP and EGA provide genotype data and/or raw data, but it is not open access. You need to apply it first, which may take several months. If you only want to check the final results, I think GWAS Catalog is good enough.
In addition to recently posted DataBases I use GWAS Integrator:
http://hugenavigator.net/HuGENavigator/gWAHitStartPage.do
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