Is there a good overview of all the online bioinformatics databases available in this world? I often thought it would be helpful to have an up-to-date overview of what databases there are, if and by whom they are curated, what their specialization is, and potentially some qualitative assessment.
I am thinking of a very broad catalog of databases, from gene databases, and interaction databases, to literature databases, and whatever else you can think of.
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written
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Magdalena •
The closest thing is probably the annual NAR Database issue, which is easy to criticise, but does do a pretty good job of rounding things up. It is relatively easy to search, and seems to get more comprehensive every year.
On a related, but slightly off-topic note, there is BioCatalogue, which is a database of web services. I guess you're after something similar?
The NAR databases issue is published yearly and its list is available here: http://www.oxfordjournals.org/nar/database/c/
I'm currently working on adding all those databases in Wikipedia under http://en.wikipedia.org/wiki/Category:Biological_databases.
See also Jeremy's question :
"Which of the 2011 NAR Database Submissions are fully accessible?"
Which Of The 2011 Nar Database Submissions Are Fully Accessible?
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written
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Pierre Lindenbaum
That is NOT a database, it is just a listing which is output from a database, which is not the same. A database is much more than a web page listing.
Yes. Please check Bioinformatics Link Directory
Bioinformatics Link Directory covers all the resources in NAR and additional resources curated from literature. Developers can also submit the details about databases/tools which are not listed. Manuscript describing different version of Bioinformatics Link Directory are available here
There is also http://www.pathguide.org. They list and monitor pathway related databases.
Later ( Sept 2011). I wrote a template:Biological_database for wikipedia that has now been integrated into DBPedia. You can now query the databases through a SPARQL query. See my blog post: http://plindenbaum.blogspot.com/2011/09/wikipedia-templateinfoboxbiodatabase-is.html
e.g:
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX dbpedia: <http://dbpedia.org/ontology/>
SELECT ?title ?uri WHERE {
?uri a dbpedia:BiologicalDatabase .
OPTIONAL {
?uri dbpedia:title ?title.
}
} ORDER By ?uri
--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
| title | uri |
========================================================================================================================================================================================================
| "3did"@en | <http://dbpedia.org/resource/3did> |
| "ABCdb"@en | <http://dbpedia.org/resource/ABCdb> |
| "AREsite"@en | <http://dbpedia.org/resource/AREsite> |
| "AlloSteric Database"@en | <http://dbpedia.org/resource/ASD_%28database%29> |
| "AgBase"@en | <http://dbpedia.org/resource/AgBase> |
| "Allele frequency net"@en | <http://dbpedia.org/resource/Allele_frequency_net_database> |
| "ASTD"@en | <http://dbpedia.org/resource/Alternative_splicing_and_transcript_diversity_database> |
| "ASAP"@en | <http://dbpedia.org/resource/Alternative_splicing_annotation_project> |
| "AmoebaDB"@en | <http://dbpedia.org/resource/AmoebaDB> |
| "ArachnoServer"@en | <http://dbpedia.org/resource/ArachnoServer> |
| "ArtadeDB"@en | <http://dbpedia.org/resource/Artade> |
| "ASPicDB"@en | <http://dbpedia.org/resource/AspicDB> |
| "The Autophagy Database"@en | <http://dbpedia.org/resource/Autophagy_database>
(...) |
[?]
http://www.bioinformatics.fr/resources.php [?]Most of the resources are from the servers and databases issues from NAR. I just tried to link some tags to each resource. Tags are located on the right sidebar.[?]
Id say my favorites are the nar database listed above.
OBRC is great too: http://www.hsls.pitt.edu/obrc/
We have a curated one at http://www.openhelix.com that is publicly available. It has almost 700 and growing. The search ranks by several relevant criteria (keyword context), usage, etc.
A couple more possibilities for databases of databases:
Since directories, lists and wikis are being mentioned...
And finally lists of more lists, directories and wikis:
Well... now there is a database of databases, its human genomic only, but it is the largest portal for human genomic data in the world with 1.1 million datasets. And it's FREE! https://repositive.io
Take a look at the data here without needing an account: https://discover.repositive.io
Currently it has indexed 40 sources so you can search across them, you can take a look at which ones here: https://repositive.io/product/datasources/
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Magdalena, I suggest Pierre's answer of today to be picked as solution.