Link this

You want to link to a NCBI resource, say a SNP record in dbSNP or a search of a term in Pubmed.

You could put this:

http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&cmd=search&term=transposon

or this:

http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?rs=41279541

But that’s kind of longish and gobblygook. There’s another choice though, a bit more clear and straightforward,

http://view.ncbi.nlm.nih.gov/pubmed/search/transposon

and

http://view.ncbi.nlm.nih.gov/snp/rs41279541

It’s the “NCBI Resource Locator” type link…

I only just found this. Ok, so I should have seen this earlier as much as I’ve used NCBI, but better late than never, so I’m assuming others haven’t found it either :).

The NCBI Resource Locator uses a ‘REST‘-based URL system. As it shows on the page NCBI Resource Locator the format is straightforward:

http://view.ncbi.nlm.nih.gov/<noun>/<verb>/<expression>

So, lets take these two links to explain the format:

http://view.ncbi.nlm.nih.gov/ (the homepage)

<noun>= pubmed or snp (these are ncbi resources, you can do others, gene, homologene, etc)

<verb>= search or get (so, ‘pubmed’ is ‘searched’. ‘get’ is default if you don’t put anything as I haven’t in the second link, it ‘gets’ the record)

<expression> = transposon or rs41279541 (the search term or record ID)

The nouns are the resource name, action, term. Pretty simple. You could just write one up without ever going to NCBI to search in the first place. Hmm, lets say I want to find the record for Danio rerio in the Taxonomy browser. So, here’s an experiment. I’m going to type this in right now, not having tried it before. Just guessing:

http://view.ncbi.nlm.nih.gov/taxonomy/search/danio rerio

Worked!

Anyway, nice way to clean up links, add a simple search to a script you might do, etc.