### Check Available BioMarts ###

library(biomaRt)
listMarts()

### Select the Ensembl BioMart ###

ensembl = useMart("ensembl")
datasets = listDatasets(ensembl)
ensembl = useMart("ensembl",dataset="hsapiens_gene_ensembl")
attributes=listAttributes(ensembl)
filters=listFilters(ensembl)

### Task 1a ###

affyids = c("211550_at","202431_s_at","206044_s_at")
annotation = getBM(c("affy_hg_u133_plus_2","ensembl_gene_id","hgnc_symbol","chromosome_name","start_position","end_position","band","strand"), filters="affy_hg_u133_plus_2", values=affyids,mart = ensembl)
print(annotation)

### Task 1b ###

illuminaIDs = c("ILMN_1728071","ILMN_1662668")
goAnnot = getBM(c("illumina_humanwg_6_v2", "go_biological_process_id","go_biological_process_linkage_type"), filters="illumina_humanwg_6_v2", values=illuminaIDs, mart = ensembl)
print(goAnnot[1:5,])

### Task 2 ###

diab=getBM(c("ensembl_gene_id","hgnc_symbol"),filters=c("mim_morbid_accession","go"), values=list(c("125853","222100"),"GO:0003700"),mart=ensembl)
print(diab)

### Task 3 ###

miRNA = getBM(c("mirbase","ensembl_gene_id","start_position","chromosome_name"), filters=c("chromosome_name","with_mirbase"), values=list(13,TRUE), mart=ensembl)
miRNA[1:5,]

### Task 4 ###

filterOptions("snptype_filters",ensembl)
entrez = getBM("entrezgene",filters=c("chromosome_name","snptype_filters"), values=list(22,"NON_SYNONYMOUS_CODING"),mart=ensembl)
entrez[1:5,]

### Task 5 ###

seq = getSequence(id="CDH1", type="hgnc_symbol",seqType="gene_exon", mart = ensembl)
seq[1,]

### Task 6 ###

promoter=getSequence(id=c("APC","CUL1"), type="hgnc_symbol",seqType="coding_gene_flank",upstream =2000, mart=ensembl)

### Task 7 ###

human=useMart("ensembl", dataset="hsapiens_gene_ensembl")
chicken=useMart("ensembl", dataset="ggallus_gene_ensembl")
mapping = getLDS(attributes=c("affy_hg_u95av2","hgnc_symbol"), filters="affy_hg_u95av2", values=c("1888_s_at","1434_at"),mart=human,attributesL="affy_chicken", martL=chicken)

### Task 8 ###

snp=useMart("snp", dataset="hsapiens_snp")
out=getBM(attributes=c("refsnp_id","allele","chrom_start"), filters=c("chr_name","chrom_start","chrom_end"), values=list(8,148350,158612), mart=snp)
out[1:5,]

### Archives ###

listMarts(host="may2009.archive.ensembl.org/biomart/martservice/")
ensembl54=useMart("ENSEMBL_MART_ENSEMBL", host="may2009.archive.ensembl.org/biomart/martservice/")
listDatasets(ensembl54)
ensembl54=useMart("ENSEMBL_MART_ENSEMBL", host="may2009.archive.ensembl.org/biomart/martservice/", dataset='hsapiens_gene_ensembl')


listMarts(archive=TRUE)