The paper makes it sound as though at least for the disease-miRNA link, that this is the proper tool, though perhaps not for keywords. It seems that the link to PhenomiR http://mips.helmholtz-muenchen.de/phenomir is down at the moment. Hopefully it is not another stale bioinformatics resource. Thanks.
Linking Mirnas With Disease Or Keywords
We have a list of about 30 miRNAs with accession number and name like so:
MIMAT0003313 miR-643
MIMAT0000446 miR-127-3p
MIMAT0002814 miR-432
MIMAT0000423 miR-125b
MIMAT0003214 miR-551a
MIMAT0004694 miR-342-5p
MIMAT0003284 miR-616*
I want to try to connect those miRNAs to diseases or key words--such as "circulating", "plasma", or "cancer". Programs like chilibot can do this well for genes since gene/protein names and aliases are well-mapped. I wonder if it is possible to do this for miRNAs, though. miRNA id's, family names, or aliases do not seem to have such a tool available as I can tell. If something exists which can mine Pubmed or other databases to look for matches between miRNAs in this list and certain keywords/diseases, that would be great. If there is another handy way you can think to do this, I'd love to hear suggestions.
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I think you will be interested in having a look at PhenomiR (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2847718/).
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Anthony Mathelier
If down you should email the authors but I guess it should fullfill your needs at least for the disease part. And you can also ask the authors if they are aware of other tools.
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Anthony Mathelier
You can use EUtils ESearch to search the NCBI nucleotide database for miRNAs, then link to PubMed using ELink.
Here's a quick example using the BioRuby implementation of EUtils. Search this site too (e.g. for "elink"); the topic has been covered before.
To search the Nucleotide database:
#!/usr/bin/ruby
require "rubygems" # ruby 1.8.7
require "bio"
require "open-uri"
require "crack" # for XML parsing
Bio::NCBI.default_email = "me@me.com"
ncbi = Bio::NCBI::REST.new
ncbi.esearch("miR-643", {"db" => "nucleotide", "retmax" => 200})
# => ["301172193", "270132492"]
To link nucleotide GI with PubMed UIDs:
# use ID 301172193 as example
base = "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/"
suff = "elink.fcgi?dbfrom=nucleotide&db=pubmed&id=301172193"
xml = open("#{base + suff}").read
xml = Crack::XML.parse(xml)
# ugly code to get the PubMed IDs
ids = xml['eLinkResult']['LinkSet']['LinkSetDb'].map {|ls| ls['Link'].map {|l| l['Id']} }
# => [["18760970", "16381832"], ["18760970", "16381832"]]
# more ugly code for unique IDs
ids = ids.flatten.uniq
=> ["18760970", "16381832"]
# do something with IDs e.g. EFetch
My colleague, Jingchun Sun, had some useful links toward this end including: HMDD The human microRNA disease database (HMDD) and miR2Disease base.
The former of them claims to be more up to date than the latter. I will update once I know more.
+1 for HMDD; they also provide PMID in one of the downloadable files.
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Khader Shameer
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