Forum:Most useful public genomic/genetic databases/tools/applications

Question

[datanerd]

Hi guys,

I am looking for suggestions/recommendations from the research community regarding public databases that are most commonly used by researchers in their analysis. These could be the open access data or controlled access.

Also, what are some of the applications used most commonly in genetics/genomics analyses?

I want to compile a list of the most commonly used and was hoping to have a good resource setup to access it.

Just like GEO, GTex, TCGA, Gnomad, TopMed etc and databases from other countries (which Iam less familiar with and might need permissions/accesses)

[GenoMax]

So you are trying to recreate something like: https://elixir-europe.org/platforms

[datanerd]

This is great resource. Yes, I want to add databases that are consortium led or portals that deposit data too. But you are right, something similar to what they did there.

[WouterDeCoster]

even databases from other countries besides US.

Whoa, people do science outside of the US? Crazy. Not sure I would trust those databases!

[datanerd]

I don't want to make this platform a discussion for this but I would recommend a great Book, it gives a great perspective about how we are wrong regarding our assumptions about the world

[WouterDeCoster]

I am European, and I read that book. You started with writing 'even from other countries', like only the US matters ;-) So you may want to rephrase that. A database being from the US doesn't make it high quality.

[datanerd]

Ohh.. I absolutely didn't mean that. I meant it in a data compliance/regulations issue, and also Iam more familiar with ones here but need suggestions for one's outside US. Sorry, I should rephrase that.

[WouterDeCoster]

No worries then!

Answer 1

[Michael]

What you are asking sounds like the scope of Elixir, at least for European resources or "other countries besides US", see Elixir core data resources or Tools. Elixir has also published some papers about the identification process.

For US, I guess the top entry is GenBank/NCBI by far (if that counts, otherwise list DBs Nucleotide, Protein, Gene, etc separately). For all the bioinformatics tools of the world and all times it is probably NCBI Blast leading with a pretty large margin before anything else.

[datanerd]

Elixir is great. Thanks for bringing that up. I hope to achieve something similar with input from researchers regarding what they most frequently use. I know GEO is a great resource that researchers reuse and apply for new studies. I really appreciate any feedback.