Resources

Glossary of Genetics

NHGRI Genetics glossary

Annotation

The Ensembl public MySQL Servers

The following script gives information on genes from ENSEMBL as well as attributes (columns) that contains gene.

library(biomaRt)
listMarts()
mart <- useMart("ENSEMBL_MART_FUNCGEN")
listDatasets(mart)
mart <- useMart("ensembl")
listDatasets(mart)
ensembl <- useMart("ensembl", dataset="hsapiens_gene_ensembl", host="grch37.ensembl.org", path="/biomart/martservice")
attr <- listAttributes(ensembl)
attr_select <- c('ensembl_gene_id', 'chromosome_name', 'start_position', 'end_position', 'description', 'hgnc_symbol', 'transcription_start_site')
gene <- getBM(attributes = attr_select, mart = ensembl)
filter <- listFilters(ensembl)
searchFilters(mart = ensembl, pattern = "gene")

See also https://sites.google.com/site/jpopgen/wgsa for precompiled annotation. Alternatively, 

# GENCODE v19
url <- "ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_19/gencode.v19.chr_patch_hapl_scaff.annotation.gtf.gz"
gtf <- rtracklayer::import(url)
gencode <- as.data.frame(gtf)

Linkage disequilibrium

LDlink: https://ldlink.nci.nih.gov/?tab=home.

NyuWa Chinese Population Variant Database (NCVD): http://bigdata.ibp.ac.cn/NyuWa_variants/

EFO

https://www.ebi.ac.uk/efo/

Example code,

library(ontologyIndex)

id <- function(ontology)
{
  inflammatory <- grep(ontology$name,pattern="inflammatory")
  immune <- grep(ontology$name,pattern="immune")
  inf <- union(inflammatory,immune)
  list(id=ontology$id[inf],name=ontology$name[inf])
}
# GO
data(go)
goidname <- id(go)
# EFO
file <- "efo.obo"
get_relation_names(file)
efo <- get_ontology(file, extract_tags="everything")
length(efo) # 89
length(efo$id) # 27962
efoidname <- id(efo)
diseases <- get_descendants(efo,"EFO:0000408")
efo_0000540 <- get_descendants(efo,"EFO:0000540")
efo_0000540name <- efo$name[efo_0000540]
isd <- data.frame(efo_0000540,efo_0000540name)
save(efo,diseases,isd,efoidname,goidname, file="work/efo.rda")
write.table(isd,file="efo_0000540.csv",col.names=FALSE,row.names=FALSE,sep=",")
pdf("efo_0000540.pdf",height=15,width=15)
library(ontologyPlot)
onto_plot(efo,efo_0000540)
dev.off()

FUMA GWAS

https://fuma.ctglab.nl/ (https://github.com/Kyoko-wtnb/FUMA-webapp/)

GRCh38 reference genome

https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/GRCh38_reference_genome/

GTEx and eQTLGen

MetaMapLite

https://metamap.nlm.nih.gov/MetaMapLite.shtml

MR-Base/OpenGWAS

OmicsPred

https://www.omicspred.org/

PredictDB data repository

http://predictdb.org/

Proteomic researches

RegulomeDB

http://regulomedb.org/

Roadmap

http://www.roadmapepigenomics.org/

snakemake workflow catalogue

https://snakemake.github.io/snakemake-workflow-catalog/

TWAS

https://github.com/hakyimlab/MetaXcan

http://gusevlab.org/projects/fusion/

eQTL Catalog

https://www.ebi.ac.uk/eqtl/

GWAS Catalog

https://www.ebi.ac.uk/gwas/

PGS Catalog

https://www.pgscatalog.org/

PheWAS Catalog

https://phewascatalog.org/

rentrez

The relevant URLs are as follows,

with example code,

library(rentrez)
entrez_dbs()
entrez_db_links("pubmed")
pubmed_fields <- entrez_db_searchable("pubmed")
# set_entrez_key("")
Sys.getenv("ENTREZ_KEY")
term <- "pQTLs OR (protein AND quantitative AND trait AND loci) AND human [MH] AND (plasma OR Serum)"
r <- entrez_search(db="pubmed",term=term,use_history=TRUE)
class(r)
names(r)
with(r,web_history)
unlink(paste("pubmed",c("fetch","summary"),sep="."))
fields <- c("uid", "pubdate", "sortfirstauthor", "title", "source", "volume", "pages")
for(i in seq(1,with(r,count),50))
{
  cat(i+49, "records downloaded\r")
  f <- entrez_fetch(db="pubmed", web_history=with(r,web_history), rettype="text", retmax=50, retstart=i)
  write.table(f, col.names=FALSE, row.names=FALSE, file="pubmed.fetch", append=TRUE)
  s <- entrez_summary(db="pubmed", web_history=with(r,web_history), rettype="text", retmax=50, retstart=i)
  e <- extract_from_esummary(s, fields)
  write.table(t(e), col.names=FALSE, row.names=FALSE, file="pubmed.summary", append=TRUE, sep="\t")
}
id <- 600807
upload <- entrez_post(db="omim", id=id)
asthma_variants <- entrez_link(dbfrom="omim", db="clinvar", cmd="neighbor_history", web_history=upload)
asthma_variants
snp_links <- entrez_link(dbfrom="clinvar", db="snp", web_history=asthma_variants$web_histories$omim_clinvar, cmd="neighbor_history")
all_links <- entrez_link(dbfrom='pubmed', id=id, db='all')

Sequence Ontology

http://www.sequenceontology.org/

TWAS-hub

http://twas-hub.org/

Biobanks