Merge pull request #448 from bio2rdf/release3

Release3 - update linkedSPLs at Jan 18, 2017

Author: Yifan Ning

.gitignore

@@ -2,4 +2,18 @@
 .DS_Store
 *.lock
 *.log
-linkedSPLs/LinkedSPLs-activeMoiety/activeMoietySub-in-rdf.xml
+
+linkedSPLs/LinkedSPLs-activeMoiety/mergedActiveMoiety.csv
+linkedSPLs/LinkedSPLs-clinicalDrug/mergedClinicalDrug.tsv
+linkedSPLs/LinkedSPLs-activeMoiety/activeMoietySub-in-rdf.xml
+linkedSPLs/LinkedSPLs-clinicalDrug/clinicalDrugSub-in-rdf.xml
+
+linkedSPLs/LinkedSPLs-activeMoiety/mappings/
+linkedSPLs/LinkedSPLs-clinicalDrug/mappings/
+
+linkedSPLs/LinkedSPLs-activeMoiety/PT-RXCUI-UNII-DB.csv
+
+linkedSPLs/LinkedSPLs-update/data/
+linkedSPLs/LinkedSPLs-update/load-dailymed-spls/problematic-spls/
+linkedSPLs/LinkedSPLs-update/mappings/FDA-pharmacogenetic-info-mapping/cached-table-downloads/
+linkedSPLs/LinkedSPLs-update/mappings/PT-UNII-ChEBI-mapping/ChEBIJavaClient/bin/

linkedSPLs/LinkedSPLs-activeMoiety/README

@@ -4,67 +4,64 @@ OVERVIEW
 
 This folder will hold a graph that maps the active moiety components of an SPL to other drug resources
 
-Inputs are original mappings listed as belows:
-
-(1) PT to UNII
-(2) UNII to RxNORM
-(3) PT to Drugbank
-(4) PT to ChEBI
-(5) RxNORM to OMOP
-(6) RxNORM to DrOn
-(7) RxNORM to NDFRT (EPC)
-
 Outputs is a RDF/XML graph that represents all active moiety with linked resouces.
 
 
 ################################################################################
-Procedures to get active moieties RDF graph
+PRE-CONDITIONS:
 ################################################################################
 
-<1>: query to get omopid mapping and put in mapping folder
+------------------------------------------------------------------------
+python libraries:
+------------------------------------------------------------------------
+
+(1) Bio from "http://biopython.org/wiki/Download"
+(2) rdflib 
+(3) rdflib#jsonld from "https://github.com/RDFLib/rdflib-jsonld"
+(4) pandas
+
+------------------------------------------------------------------------
+Mappings from linkedSPLs core update
+------------------------------------------------------------------------
+
+Please ensure following mappings are available at specified path. They are should be automatically generated when core graph updated (refers to LinkedSPLs-update/README)
 
-mappings/active-ingredient-omopid-rxcui.dsv
+(1) PT (preferred term) to UNII: LinkedSPLs-update/data/FDA/FDAPreferredSubstanceToUNII.txt
+(2) UNII to RxNORM: LinkedSPLs-update/data/UMLS/UNIIs-Rxcuis-from-UMLS.txt
+(3) PT to Drugbank: LinkedSPLs-update/mappings/ChEBI-DrugBank-bio2rdf-mapping/fda-substance-preferred-name-to-drugbank.txt
+(4) PT to ChEBI: LinkedSPLs-update/mappings/PT-UNII-ChEBI-mapping/UNIIToChEBI.txt
+(5) RxNORM to DrOn: LinkedSPLs-update/mappings/DrOn-to-RxNorm/cleaned-dron-chebi-rxcui-ingredient.txt
+(6) RxNORM to NDFRT (EPC): LinkedSPLs-update/mappings/pharmacologic_class_indexing/EPC_extraction_most_recent.txt
+
+(7) OMOP concept Id from OHDSI or query OMOP CDM V5 (GeriOMOP) by SQL query
 
- 
 query OMOP CDM V5 (GeriOMOP) by SQL query below:
 SELECT cpt.CONCEPT_ID as omopid, cpt.CONCEPT_CODE as rxcui FROM
 CONCEPT cpt
 WHERE 
 cpt.CONCEPT_CLASS = 'Ingredient';
 
-09/04/2015: 17049 results
-
 right click result table and export to csv ('|' delimited) 
+save name as: active-ingredient-omopid-rxcui-<DATE>.dsv
+to dir: LinkedSPLs-activeMoiety/mappings/active-ingredient-omopid-rxcui.dsv
 
+01/18/2017: 17049 results
 
-<STEP 2>: run python script to merge those mappings together
+################################################################################
+Procedures to get active moieties RDF graph
+################################################################################
+
+(1) run python script to merge those mappings together
 
 $ python mergeToActiveMoiety.py
 
 outputs: mergedActiveMoiety.csv contains all joined mappings
 
 columns: pt, unii, db_uri1, db_uri2, rxcui, omopid, chebi, dron, nui, nameAndRole
 
-<STEP 3>: run python script to create RDF graph for all active moieties
+(2) run python script to create RDF graph for all active moieties
 
 $ python createActiveMoietySubInRDF.py
 
 outputs: activeMoietySub-in-rdf.xml
 
-
-################################################################################
-PRE-REQUISITES:
-################################################################################
-
-python libraries:
-
-(1) Bio 
-from "http://biopython.org/wiki/Download"
-
-(2) rdflib 
-
-(3) rdflib#jsonld
-from "https://github.com/RDFLib/rdflib-jsonld"
-
-(4) pandas
-