Examples Of Useful, Concise And Cool Biological Database/Bioinformatics Tool Faqs?

Question

[Attila Csordas]

Hi,

Can you mention really good and informative FAQs from the biological database/bioinformatics world?

Answer 1

[Mary]

Sigh. Oh, man, this drives me insane. I'm sure I'll think of more over the next couple of days.

But here's the biggest example of #FAIL: https://www.icgc.org/node/1083?destination=icgc%2Fcontacts

And although it is not entirely up-to-date (some examples don't work), I really like examples like the BioMart FAQ. The reason I like this is because it provides "solved examples" that you can load up yourself. We find that end users who want to solve problems could use stuff like this--with the basic query features--and then modify them for their favorite gene, region, SNP, whatever. That button click to load the query is particularly handy.

However, I don't think that's all that I would have expected in the FAQ. I would have wanted more foundational questions about the site/data/etc. But I like the sample queries.

I'll keep thinking of other examples and come back and edit as I think of good ones.

EDIT: Ok, here's what I think of as a typical example--PDB. They have one for web site users, and one for depositors. I think that's nice too, to separate out the uses. http://www.pdb.org/pdb/static.do?p=home/faq.html That's the User's one.

Here's one we like: http://www.ncbi.nlm.nih.gov/Structure/biosystems/docs/biosystems_faq.html This is clean, covers the things we expect in a FAQ, and gives quick answers but offers more depth or the appropriate links to answers.

Let me add that one of the things I want the most in an FAQ is which paper to cite when using the site/data/etc.

[Attila Csordas]

I like the NCBI BioSystems Database FAQ.

Answer 2

[Pierre Lindenbaum]

The NCBI has a good(?) documentation for Entrez.

Some databases use and maintain a Wiki ( eg. the wiki for the UCSC).

The UCSC has a documentation for each mysql database: e.g: http://genome.ucsc.edu/cgi-bin/hgTables?hgta_doSchemaDb=hg18&hgta_doSchemaTable=snp130

[Attila Csordas]

those are the ones you found useful and concise or just the ones you are using most frequently?

[Pierre Lindenbaum]

I'm using the mysql schemas for the UCSC quite frequently.

[Andrea_Bio]

the ncbi has tonnes of documentation but personally i find it difficult to use. With good documentation its obvious where to look for information. I find the ncbi docs like looking for the proverbial needle. I guess that's why Pierre added a ? after good

Answer 3

[Thaman]

My choices are

• Ensembl documentation and FAQ
• PDB Wiki