From MetaBase

BiOFreedom!

Hello! If you like you can leave a message!

I maintain a profile on Nature Networks and OpenWetWare, which is actually a vain effort to beat my brothers Google rank.

[edit] My favourite databases

• PSIMAP (inc. PSIbase & InterPare)
• SCOP
• The PDB
• UniProt aka. Swiss-Prot
• SUPERFAMILY
• ENZYME
• The NCBI Taxonomy Database
• LIGAND
• BIND
• ...

[edit] Some databases that I have used

• VIPERdb | PubMed | VADAR | MolMovDB | AAindex | ASEdb | Decoys 'R' Us |...

[edit] Interesting databases

Here is a loose collection of databases that I have found using and developing MetaBase that look very interesting:

• POPSCOMP - predictions of protein complexes using surface area.
• PMDB - Protein Model Database
• SuperNatural - database of 50,000 natural compounds.
• ChEBI - Chemical Entities of Biological Interest
• PROCOGNATE - database of cognate ligands.
• SIMAP - a similarity matrix from > 4 million amino-acid sequences
• OReFiL - an On-line Resource Finder for Life-sciences
• SYSTERS - an automatically generated classification of protein sequences into disjoint protein family and superfamily clusters.
• BiologicalNetworks - A webservice for displaying / mapping expression data onto ... biological networks!
• ArchDB - Looks nice.
• Structural Biology Software Database - Looks amazingly cool!
• PINTS
• MatchMiner
• ...

[edit] My MetaBase convenience links

• Special:Listusers
• MediaWiki:Sidebar
• Special:Allmessages
  • MediaWiki:Newarticletext
• Special:Wantedpages
• Special:Version
• ...

[edit] MediaWiki bookmarks

• http://www.mediawiki.org/wiki/Manual:Interface/Sidebar
• http://static.wiki-tools.com/wiki/Extension:Wiki_Category_Tag_Cloud
• http://www.mediawiki.org/wiki/Extension:Hierarchy
• http://www.mediawiki.org/wiki/Extension:TagAsCategory
• ...

[edit] Cool stuff

• Category:NARDatabase:Drugs and drug design
• List of user contributed resources

[edit] Administrative queryies

SELECT
 *
FROM (
 SELECT
   rev_user_text, count(*) AS hits
 FROM
   Biodatabaserevision
 GROUP BY
   rev_user_text
) AS x
ORDER BY
 hits DESC
LIMIT
 20;
 
SELECT 
  RIGHT(user_email, length(user_email) - LOCATE("@", user_email)) AS domain, 
  count(*) AS domain_count 
FROM 
  Biodatabaseuser 
GROUP BY 
  domain 
HAVING 
  domain_count>1
 
SELECT 
  user_name, user_real_name, user_password, user_email 
FROM 
  Biodatabaseuser 
WHERE 
  user_email RLIKE "mail.ru"

[edit] YES!

The above uses:

• Template:Database/Create 'related' (generic) and
• Template:Database/Create 'related' (generic) Intro.

[edit] To Add

This is a MetaBase also http://www.up.univ-mrs.fr/~wabim/english/logligne.html albeit a static one. I would like to make an entry in MetaBase for all such web pages, each categorized as a Category:Database of databases. See also Category:Database pages to write

And;

• http://DBpedia.org
• http://BioWareDB.org
• http://carmen.org.uk
• http://sciencecommons.org
  • http://sciencecommons.org/projects/data
• http://OpenWetWare.Org
• http://Proteopedia.Org

Pages to add and/or categorize as NCBI 

NCBI resources include Entrez, the Entrez Programming Utilities, My NCBI, PubMed, PubMed Central, Entrez Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link (BLink), Electronic PCR, OrfFinder, Spidey, Splign, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, Cancer Chromosomes, Entrez Genome, Genome Project, the Trace, Assembly, and Short Read Archives, Map Viewer, Model Maker, Evidence Viewer, Clusters of Orthologous Groups, Viral Genotyping Tools, Influenza Viral Resources, HIV-1/Human Protein Interaction Database, Gene Expression Omnibus, Entrez Probe, GENSAT, Database of Genotype and Phenotype, Online Mendelian Inheritance in Man, Online Mendelian Inheritance in Animals, the Molecular Modeling Database, the Conserved Domain Database, the Conserved Domain Architecture Retrieval Tool, and the PubChem suite of small molecule databases.

ExPASy! 

Swiss-Flash reports news of databases, software and service developments from the groups at the Swiss Institute of Bioinformatics that are responsible for the ENZYME, PROSITE, SWISS-2DPAGE, Swiss-Prot and TrEMBL databases; the Melanie software package; the ExPASy WWW server the SWISS-MODEL, Swiss-Shop and other network-based computational tools; the Core Facilities services.

[edit] Databases to add

See Category...

• PDBTM
• TMPDB
• ChemXtreme or something...
• Hotsprint http://prism.ccbb.ku.edu.tr/hotsprint/

http://semantic-mediawiki.org/wiki/Image:Feed_icon.png

[edit] Important repositories

• See also: bioDBnet.
• See also: GO Database Abbreviations.
• See also: open helix thingy.
• See also: BioCatalogue thingy.

• ArrayExpress
• BioModels Database
• Database of Interacting Proteins
• DNA Data Bank of Japan
• EMBL Nucleotide Sequence Database
• GenBank
• Gene Expression Omnibus
• Protein Data Bank
• UniProtKB/Swiss-Prot
• ClinicalTrials.gov

• Ensembl
• Entrez Gene
• FlyBase
• InterPro
• Mouse Genome Database (MGD)
• Online Mendelian Inheritance in Man (OMIM)