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documentation:laertes_etl [2015/05/26 18:49] lee [EU SPC ADR data feed] |
documentation:laertes_etl [2015/05/26 18:49] lee [PUBMED / MEDLINE data feed] |
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* Run python scripts to convert the data into RDF ntriple graph data | * Run python scripts to convert the data into RDF ntriple graph data | ||
* Load the RDF ntriple graph data into the Virtuoso database | * Load the RDF ntriple graph data into the Virtuoso database | ||
+ | * Manually load the annotation URIs into the URL Shortener MySQL database using the MySQL command line client | ||
* Manually run Virtuoso SPARQL query to export the drug/hoi combinations along with the adverse event counts into an export file | * Manually run Virtuoso SPARQL query to export the drug/hoi combinations along with the adverse event counts into an export file | ||
* Run Python script to load the export file into the PostgreSQL public schema database | * Run Python script to load the export file into the PostgreSQL public schema database | ||
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The details for this data feed are documented and maintained here: | The details for this data feed are documented and maintained here: | ||
https://github.com/OHDSI/KnowledgeBase/tree/master/LAERTES/PubMed | https://github.com/OHDSI/KnowledgeBase/tree/master/LAERTES/PubMed | ||
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==== SPLICER SPL data feed ==== | ==== SPLICER SPL data feed ==== | ||
SPLICER Natural Language Processing extracted Adverse Drug Events from FDA Structured Product Labels (SPLs) | SPLICER Natural Language Processing extracted Adverse Drug Events from FDA Structured Product Labels (SPLs) |