In production, rather than starting with an empty database and then importing everything as unmapped terms from ClinVar, we want to initialise the database using all mappings which were curated previously using the spreadsheet approach.
This is a simple TSV file like this:
#clinvar_trait_name uri label
breast-ovarian cancer, familial 2 http://www.orpha.net/ORDO/Orphanet_145 Hereditary breast and ovarian cancer syndrome
pten hamartoma tumor syndrome http://www.orpha.net/ORDO/Orphanet_306498 PTEN hamartoma tumor syndrome
hereditary breast and ovarian cancer syndrome http://www.orpha.net/ORDO/Orphanet_145 Hereditary breast and ovarian cancer syndrome
We only need columns 1 and 2 from it. There needs to be a script which would take this TSV and load it into the database. All mappings should be considered already reviewed.
The complete, latest version of this file (as of 2020-08-01) is attached to the issue.
latest_mappings.tsv.gz
In production, rather than starting with an empty database and then importing everything as unmapped terms from ClinVar, we want to initialise the database using all mappings which were curated previously using the spreadsheet approach.
This is a simple TSV file like this:
We only need columns 1 and 2 from it. There needs to be a script which would take this TSV and load it into the database. All mappings should be considered already reviewed.
The complete, latest version of this file (as of 2020-08-01) is attached to the issue. latest_mappings.tsv.gz