http://www.biomart.or Databases in Biomart format: Ensembl HapMap HTGT HGNC Dictybase Wormbase Gramene Europhenome UniPro Rat Genome Database DroSpeGe ArrayExpress DW Eurexpress GermOnLine PRIDE PepSeeker VectorBase Pancreatic Expression Database Reactome EU Rat Mart Paramecium DB “BioMart is a query-oriented data management system developed jointly by the Ontario Institute for Cancer Research (OICR) and the European Bioinformatics Institute (EBI).” Open Source – LGPL * Perl API → Web Interface, Web Services Interface, REST API * Java API → Mart Explorer GUI, MartShell * 3 rd Party Software → Bioclipse, biomaRt-BioConductor, Cytoscape, Galaxy, Taverna, WebLab
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Http:// Databases in Biomart format: EnsemblHapMapHTGTHGNCDictybaseWormbaseGramene EurophenomeUniProRat Genome Database DroSpeGeArrayExpress.
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http://www.biomart.org/
Databases in Biomart format:
EnsemblHapMap HTGT HGNC Dictybase Wormbase Gramene Europhenome UniPro Rat Genome Database DroSpeGe ArrayExpress DW Eurexpress GermOnLine PRIDE PepSeeker VectorBase Pancreatic Expression Database Reactome EU Rat Mart Paramecium DB
“BioMart is a query-oriented data management system developed jointly by the Ontario Institute for Cancer Research
(OICR) and the European Bioinformatics Institute (EBI).”
Open Source – LGPL
* Perl API → Web Interface, Web Services Interface, REST API
# Filters can be either numeric, string or boolean.# Boolean filters need a TRUE or FALSE value
# Determine type of filter with:
filterType('with_unigene', mart)
# Attributes and filters are organised into categories
# To get a list of the categories:attributeSummary(mart)filterSummary(mart) # You can then list attributes and filters limited to a # specified category:listAttributes(mart, category='Variations')
# Older versions of ensembl are archived, useful if you've # got genome positions to a previous build
Note that any of the _flank types need an 'upstream' or 'downstream' argument to determine the size of the flanking region. At the moment, you can't specify both.
Exporting Sequences:
# The exportFASTA function provides a quick way of saving # sequences in FASTA format:
res <- getSequence(id="BRCA1", type="mgi_symbol", seqType="peptide", mart = mart)
exportFASTA(res, file='sequence.fa')
Linking Datasets...
# Make mart connections for each of the datasets:mouse.mart<-useMart('ensembl', dataset="mmusculus_gene_ensembl")people.mart<-useMart('ensembl', dataset='hsapiens_gene_ensembl')
# In Ensembl, datasets are made of transcripts # from a single species. # Linking datasets amounts to homology
#eg. Get pos of mouse homolog to human 'TP53' gene
library(annotate)# Provides the htmlpage function. Salient args are:# genelist – a list or dataframe of IDs to be made into links# filename# title – for the table# othernames – a list of other things to add to the table as is# table.head – a character vector of col headers for the table.# repository – a list of repositories to use for creating links