documentation:laertes_etl
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documentation:laertes_etl [2015/05/26 18:49] lee [EU SPC ADR data feed] |
documentation:laertes_etl [2015/05/26 18:50] lee [SemMED 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 | ||
| Line 218: | Line 219: | ||
| 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 | ||
| - | |||
| ==== 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) | ||
| Line 227: | Line 227: | ||
| * 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 | ||
| Line 234: | Line 235: | ||
| 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/SPLICER | https://github.com/OHDSI/KnowledgeBase/tree/master/LAERTES/SPLICER | ||
| - | |||
| ==== SemMED data feed ==== | ==== SemMED data feed ==== | ||
| The Semantic MEDLINE Database is a repository of semantic predications (subject-predicate-object triples) extracted by SemRep, a semantic interpreter of biomedical text. | The Semantic MEDLINE Database is a repository of semantic predications (subject-predicate-object triples) extracted by SemRep, a semantic interpreter of biomedical text. | ||
| Line 244: | Line 244: | ||
| * 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 | ||
documentation/laertes_etl.txt · Last modified: 2015/06/23 10:58 by lee
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