Database Of Databases?

Question

[Magdalena]

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.

[Egon Willighagen]

Magdalena, I suggest Pierre's answer of today to be picked as solution.

Answer 1

[Simon Cockell]

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?

Answer 2

[Pierre Lindenbaum]

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?

[michaelhavner]

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.

Answer 3

[Khader Shameer]

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

Answer 4

[Andra Waagmeester]

There is also http://www.pathguide.org. They list and monitor pathway related databases.

Answer 5

[Pierre Lindenbaum]

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>    
(...)                                                                    |

Answer 6

[Fred Fleche]

[?]

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.[?]

Answer 7

[Treylathe]

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.

Answer 8

[Hamish]

A couple more possibilities for databases of databases:

• Data Resource Catalogue: http://drcat.sourceforge.net/. Used in EMBOSS
• MIRIAM Registry: http://www.ebi.ac.uk/miriam/. Used by Identifiers.org
• UniProt database of cross-references: http://www.uniprot.org/docs/dbxref
• BIO_CATAL: ftp://ftp.ebi.ac.uk/pub/databases/bio_catal/. Rather old now but includes software, databases and web resources.

Since directories, lists and wikis are being mentioned...

• Bioinformatics.org Wiki: http://www.bioinformatics.org/wiki/. A bit more focused on software than databases but with some overlap.
• NeuroLex resources: http://neurolex.org/wiki/Category:Resource
• MetaBase: http://metadatabase.org/wiki/

And finally lists of more lists, directories and wikis:

• http://biowikifarm.net/meta/Other_science_wikis
• http://www.bioinfo-user.org.uk/dokuwiki/doku.php/hpm/links/bioinformatics/directories

Answer 9

[Yogesh Pandit]

Mother of All Databases

Answer 10

[craig]

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/