List of bioinformatics databases

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The following text is copied from the MetaBase article in WikiPedia. I like it because its organized better than the content here... I need to rewrite the resources page!

Contents

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Related Resources

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Link dump

http://biowiki.net/index.php/All_the_BioWiki_contest_sites http://biome.info/index.php/Main_Page http://biopedia.org/index.php/Main_Page http://bioprograms.net/ http://biocafe.net/index.php/Main_Page http://biodenmark.org/index.php/Main_Page http://bioindonesia.org/index.php/Main_Page http://bioinformatist.org/index.php/Main_Page http://biolive.org/index.php/Main_Page http://biopicture.net/index.php/Main_Page http://biosingapore.org/index.php/Main_Page http://biostructure.org/index.php/Main_Page http://web.archive.org/web/20070302150127rn_1/biotip.org/index.php/Main_Page http://biovideo.org/index.php/Main_Page http://biozine.org/index.php/Main_Page http://contactome.org/index.php/Main_Page http://diseasepedia.net/index.php/Main_Page http://ethnome.org/index.php/Main_Page http://evolomics.net/index.php/Main_Page http://expressome.org/index.php/Main_Page http://introductome.org/index.php/Main_Page http://koreansnp.org/index.php/Main_Page http://mitogenome.org/index.php/Main_Page http://mybio.net/biowiki/Main_Page http://networkbiology.org/index.php/Main_Page http://pharmanome.org/index.php/Main_Page http://primatome.org/index.php/Main_Page http://stemcellbiology.net/index.php/Main_Page http://proteinfunction.net/index.php/Main_Page http://www.bioforge.net/forge/index.jspa http://tech.groups.yahoo.com/group/biohacking/ http://biowaredb.org/site/ http://kk.org/cooltools/archives/000582.php http://ecolihub.org/ http://en.wikibooks.org/wiki/Future/Biotechnology http://en.wikibooks.org/wiki/General_Biology/Genetics/Recombinant_DNA_Technology http://www.nexusresearchgroup.com/technical_data/carter.htm http://openwetware.org/wiki/Main_Page http://rsss.anu.edu.au/~janeth/home.html http://biohackery.com/ http://web.archive.org/web/20070420204234/http://www.dnahack.com/ http://biobricks.org/ (Endy just added some new mailing lists!)

Some other stuff.

http://openprosthetics.org/ http://obofoundry.org/ http://www.open-bio.org/wiki/Main_Page http://www.bioconductor.org/ http://www.openehr.org/home.html http://openeeg.sourceforge.net/ http://open-rtms.sourceforge.net/ http://transcenmentalism.org/OpenStim/tiki-index.php http://biocyc.org/open-compounds.shtml http://opendoar.org/ http://www.opensearch.org/Home http://www.howtoforge.com/ http://www.openhardwarefoundation.org/ http://www.ohloh.net/ http://www.earlham.edu/~peters/

-- Kanzure 04:53, 28 January 2008 (KST)

Oops. Do not forget

http://en.wikipedia.org/wiki/Synthetic_biology http://syntheticbiology.org/ http://www.syntheticgenomics.com/ http://heybryan.org/forums.html <-- the list of forums that I monitor (inc. many bio related sites) -- Kanzure 04:58, 28 January 2008 (KST)

http://bionumbers.org/ ( http://bionumbers.hms.harvard.edu/ )

What do we do with those ?? Should we create a categoy and start to order them ? --Pingou 00:27, 29 January 2008 (KST)

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Second round (Return of the Linkdump)

Hey, I'd like to offer reactome.org and the following from the hplusroadmap wiki on computational biology:

-- Kanzure 05:56, 16 March 2008 (KST)




Note: This page is currently beta! Re-researching and re-writing this page is high on the TODO list - (ongoing). It is vital that we properly organize and reference the body of similar work so that we can most easily gain the most value from that work.


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Related Resources (in no particular order)

This list of links requires organization, but is none the less included as is for reference. Please support MetaBase by adding content!


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Projects with a similar philosophy

Header text. Header text. Header text. Header text.

The Bio Community Cluster 
Here is a description of BiO.CC, BioWiki and its sister sites. See also the detailed section below.
The Molecular and Cellular Biology 'WikiProject' 
This project aims to better organize information in articles related to molecular and cell biology on Wikipedia. Some pages relevant to the MetaBase project include;
The WikiData project 
A proposed wiki-like database for various types of structured content. See also the OmegaWiki project and WikiProteins.
EcoliWiki 
The goal for EcoliWiki is to generate community-based pages about everything related to E. coli K-12, its phages, plasmids, and mobile genetic elements. Of particular interest is the Database category of the wiki. See the internal link.
WikiOmics 
A collection of questions and answers about bioinformatics funded by the Godzik lab at the Burnham Institute for Medical Research in San Diego. See the internal link.
MyBio 
MyBio.net is a community-built directory of tools, databases, protocols and other web resources for life sciences researchers in a wiki format which everyone can edit! See the internal link.
OpenWetWare 
an effort to promote the sharing of information, know-how, and wisdom among researchers and groups who are working in biology & biological engineering. More
WikiPathways 
an open, public platform dedicated to the curation of biological pathways by and for the scientific community.
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Other bioinformatics database & resource lists

Header text. Header text. Header text. Header text.

Biomed Cetral Databases 
Oh yes! http://databases.biomedcentral.com/ http://databases.biomedcentral.com/home


The Health Sciences Library System (HSLS) Online Bioinformatics Resources Collection (OBRC) 
The Online Bioinformatics Resources Collection (OBRC) contains annotations and links for 1746 bioinformatics databases and software tools. See the internal link.
The Bioinformatics Links Directory 
Features curated links to molecular resources, tools and databases. See the internal link.
The Molecular Biology Database Collection 
A public on-line resource that lists the databases described in Nucleic Acids Research, together with other databases of value to the biologist. See the internal link.
CABRI 
Common Access to Biotechnological Resources and Information - an online service where users can search a number of European Biological Resource Centre catalogues. The catalogues may be searched independently, or as one, and the located materials ordered online or by post. See the internal link.
MetaBasis 
(Not to be confused with MetaBase!) - A database system for the effective management of metadata concerning software tools and databases in the field of Bioinformatics. See the internal link.
The DBD: Database of Biological Database 
Consists of 1200 Database entries covering wide range of databases useful for biological researchers. See the internal link.
The DoD: Database of Databases 
Links to all molecular biology databases that appear in the Nucleic Acids Research database issue. See the internal link.
BioWareDB.org 
Is an attempt to collect an exhaustive database of links to the vast amounts of freely available and commercial bioinformatics software. See the internal link, or link directly to the homepage.


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See also;

The following dynamically generated list of MetaBase resources in the 'database of databases' category.

<DPL> category = Database of databases mode = inline inlinetext =  |  </DPL>


Added 2008-07-10 thanks to Matthias Samwald on public-semweb-lifesci:

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Other interesting projects

Header text. Header text. Header text. Header text.

OReFiL 
an Online Resource Finder for Lifesciences. See the internal link.
The Database of Databases of Biology Databases 
There are biology databases. And then there databases of biology databases. This is a database of those database of biology databases! (A meta-meta-database!)
ChemXtreme : Harvesting Chemical Information from the Internet Using a Distributed Approach: ChemXtreme.
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BioWiki

There is a lot more work to go into this section!

BioWiki is a wiki farm that provides free hosting services to those who want to create wiki sites for biology. Its ultimate aim is to exchange knowledge and information among biologists towards collaborative development of biological knowledge bases that anyone can contribute. As a promotional activity, it also holds a contest called International BioWiki Contest.

BioWiki Contest

Here are some of the other entrants in the International BioWiki Contest;

http://Bioinformatist.org http://BioIndonesia.Org http://BioSingapore.org http://BioStructure.Org http://MitoGenome.org http://NetworkBiology.org http://PDBwiki.info http://biowiki.net/bioinformics

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BioWiki Contest

Here are some of the other entrants in the International Openfree Bioinformation Contents Competition;

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Rough Notes

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Important projects

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Things to classify

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Open Chemistry

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Others

Other MetaBase ideas / existing technology / Database Databases and resources (in no particular order);

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Other (new (to sort))

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Other (old (to sort))

  • Commercial GeneGo MetaBase™ : Arguably, the most comprehensive manually curated database of mammalian biology and medicinal chemistry data available today. http://www.genego.com/metabase.php
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Google?

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Literature

Links to literature relating to MetaBase

Time to Organize the Bioinformatics Resourceome [2] 
"We suggest that the full set of bioinformatics resources - the "resourceome" should be explicitly characterized and organized. A hierarchical and machine-understandable organization of the field, along with rich cross-links (an ontology!) would be a useful start. It is likely that a distributed development approach would be required so that those with focused expertise can classify resources in their area, while providing the metadata that would allow easier access to useful existing resources."
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Interfaces

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