User:DB
From MetaBase
| dan.bolser@gmail.com | |
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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.
Contents |
My favourite databases
- PSIMAP (inc. PSIbase & InterPare)
- SCOP
- The PDB
- UniProt aka. Swiss-Prot
- SUPERFAMILY
- ENZYME
- The NCBI Taxonomy Database
- LIGAND
- BIND
- ...
Some databases that I have used
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
- ...
My MetaBase convenience links
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
- ...
Cool stuff
Administrative queryies
<source lang="sql"> -- Top contributors: select
*
from (
select rev_user_text, count(*) as hits from mb_revision group by rev_user_text
) as x order by
hits desc
limit
20;
-- Top email domains: select
right(user_email, length(user_email) - LOCATE("@", user_email)) as domain,
count(*) as domain_count
from
mb_user
group by
domain
having
domain_count>1;
-- Select likely spammers (sorry!): select
user_name, user_real_name, user_password, user_email
from
mb_user
where
user_email rlike "mail.ru"
</source>
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://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.
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
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)
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