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BRAVO API Basis Data.

Reference Data required by bravo2 data loading into mongo via load\_genes command of Bravo API.

Genenames: HUGO Gene Nomenclature Commitee (HGNC)

Can be obtained from genenames custom downloads Check the boxes for:

  • Approved symbol
  • Approved name
  • Previous symbols
  • Alias symbols
  • Ensembl gene ID boxes

The genenames set from all the chromosomes with the above columns is currently 2.8M and can be obtained using curl.

curl 'https://www.genenames.org/cgi-bin/download/custom?col=gd_app_sym&col=gd_app_name&col=gd_prev_sym&col=gd_aliases&col=gd_pub_ensembl_id&status=Approved&order_by=gd_app_sym_sort&format=text&submit=submit' > hgcn_custom_results.txt

A smaller subset was used for the chr11 vignette to test the pipeline. It used a few genes from chr11. In advanced filtering section, use the following "where clause" in the text box to cut down on the number of results to illustrate this example.

gd_app_sym IN ('HBB', 'HBD', 'HBM', 'HBZ', 'HBA1', 'HBA2' ,'HBE1' ,'HBG1' ,'HBG2' ,'HBQ1' ,'HBAP1' ,'HBBP1' ,'HBXP1')

Here is the smaller subset query url encoded

Tab delim results

Approved symbol	Approved name	Previous symbols	Alias symbols	Ensembl gene ID
HBB	hemoglobin subunit beta		CD113t-C, beta-globin	ENSG00000244734
HBBP1	hemoglobin subunit beta pseudogene 1		HBH1, HBHP	ENSG00000229988
HBD	hemoglobin subunit delta			ENSG00000223609
HBE1	hemoglobin subunit epsilon 1		HBE	ENSG00000213931
HBG1	hemoglobin subunit gamma 1		HBG-T2	ENSG00000213934
HBG2	hemoglobin subunit gamma 2		HBG-T1	ENSG00000196565

Headers need to be rewritten to match expected column names and the results gzipped

# Approved symbol
# Approved name
# Previous symbols
# Alias symbols
# Ensembl gene ID

echo -e "symbol\tname\talias_symbol\tprev_symbol\tensembl_gene_id" > hgcn_genenames.txt
tail -n +2 hgcn_custom_result.txt >> hgcn_genenames.txt
gzip hgcn_genenames.txt

Canonical Transcripts: Ensembl ID to Ensembl Transcript ID mapping

  • No headers
  • Two columns
  • Whitespace delimited
  • Order: gene_id transcript_id
  • Gzipped

Sourced from Ensembl's Biomart tool The following is the query xml for the Gene stable ID and Transcript stable ID of GRCh38.p13, and the curl command to retrieve the results from the REST endpoint.

read -r -d '' RAW_QUERY <<-HEREDOC 
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE Query>
<Query  virtualSchemaName = "default" formatter = "TSV" header = "0" uniqueRows = "0" count = "" datasetConfigVersion = "0.6" >
	<Dataset name = "hsapiens_gene_ensembl" interface = "default" >
		<Attribute name = "ensembl_gene_id" />
		<Attribute name = "ensembl_transcript_id" />
	</Dataset>
</Query>
HEREDOC

QUERY=$(echo "$RAW_QUERY" | tr -d '\n')

curl "http://www.ensembl.org/biomart/martservice" \
  --data-urlencode "query=${QUERY}" > canonical_transcripts.txt

QUERY_URL='http://useast.ensembl.org/biomart/martview/57c40cc27b63f390d259d9fd4894919f?VIRTUALSCHEMANAME=default&ATTRIBUTES=hsapiens_gene_ensembl.default.feature_page.ensembl_gene_id|hsapiens_gene_ensembl.default.feature_page.ensembl_transcript_id&FILTERS=&VISIBLEPANEL=attributepanel'
curl "${QUERY_URL}" > canonical_transcripts.txt
gzip canonical_transcripts.txt

OMIM File

Sourced from Ensembl's Biomart tool Required columns separated by tab: Gene stable ID, Transcript stable ID, MIM gene accession, MIM gene description. The following is the query xml wrapped in bash to facilitate pulling it from the biomart endpoint.

read -r -d '' XML_QUERY <<-HEREDOC 
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE Query>
<Query  virtualSchemaName = "default" formatter = "TSV" header = "1" uniqueRows = "0" count = "" datasetConfigVersion = "0.6" >
	<Dataset name = "hsapiens_gene_ensembl" interface = "default" >
		<Attribute name = "ensembl_gene_id" />
		<Attribute name = "ensembl_transcript_id" />
		<Attribute name = "mim_gene_accession" />
		<Attribute name = "mim_gene_description" />
	</Dataset>
</Query>
HEREDOC

curl "http://www.ensembl.org/biomart/martservice" \
  --data-urlencode "query=${XML_QUERY}" > omim_ensembl_refs.txt
gzip omim_ensembl_refs.txt

Gencode File

This file serves as the source list of genes to collate the other data

GEN_URL=ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_38/gencode.v38.annotation.gtf.gz
curl ${GEN_URL} > gencode.v38.annotation.gtf.gz

This same can be accessed on their webpage. GTF format comprehensive gene annotations for CHR region from gencode