User:DB

From MetaBase

[edit] Hello!

Speak!

I maintain a profile on Nature Networks and OpenWetWare

Contents 1 Hello! 1.1 My favourite databases 1.2 Additionally, a (partial) list of databases that I have used; 1.3 Here is a loose collection of databases that I have found using and developing MetaBase that look very interesting; 1.3.1 And 2 Internal convenience links 2.1 Also 2.2 YES! 3 Cool stuff 4 To Add 4.1 Databases to add

[edit] My favourite databases

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

[edit] Additionally, a (partial) list of databases that I have used;

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

[edit] Here is a loose collection of databases that I have found using and developing MetaBase that look very interesting;

• PMDB - Protein Model Database
• 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!
• ...

[edit] And

• PINTS
• MatchMiner
• ...

[edit] Internal convenience links

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

[edit] Also

• 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] YES!

The above uses:

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

[edit] Cool stuff

Category:NARDatabase:Drugs and drug design

[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/

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