revise linkedSPLs README for update core, active moiety, clinical drug

Author: ningyifan

Diff for: linkedSPLs/LinkedSPLs-activeMoiety/README

@@ -33,7 +33,7 @@ Please ensure following mappings are available at specified path. They are shoul
 (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
+(7) OMOP concept Id from OHDSI or query OMOP CDM V5 (GeriOMOP) by SQL query (it's available if just updated linkedSPLs core graph)
 
 query OMOP CDM V5 (GeriOMOP) by SQL query below:
 SELECT cpt.CONCEPT_ID as omopid, cpt.CONCEPT_CODE as rxcui FROM
@@ -45,7 +45,6 @@ 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
 
 ################################################################################
 Procedures to get active moieties RDF graph

Diff for: linkedSPLs/LinkedSPLs-clinicalDrug/README

@@ -12,11 +12,11 @@ PRE-CONDITIONS:
 Mappings from linkedSPLs core update
 ------------------------------------------------------------------------
 
-(1) Dron to rxcui: linkedSPLs/LinkedSPLs-update/mappings/DrOn-to-RxNorm/cleaned-dron-to-rxcui-drug-<DATE>.txt
+(1) Dron to rxcui: LinkedSPLs-update/mappings/DrOn-to-RxNorm/cleaned-dron-to-rxcui.txt
 
-(2) Dailymed setid and rxcui: LinkedSPLs-update/mappings/RxNORM-mapping/converted_rxnorm_mappings_<DATE>.txt converted_rxnorm_mappings.txt
+(2) Dailymed setid and rxcui: 
 
-$ cat converted_rxnorm_mappings.txt | cut -f1,2 -d\| | sort | uniq > setid_rxcui.txt
+$ cat LinkedSPLs-update/mappings/RxNORM-mapping/converted_rxnorm_mappings.txt | cut -f1,2 -d\| | sort | uniq > LinkedSPLs-clinicalDrug/mappings/setid_rxcui.txt
 
 (3) Dailymed setid and drug fullname
 
@@ -25,9 +25,9 @@ $ use linkedSPLs;
 
 SELECT setId, fullName FROM linkedSPLs.structuredProductLabelMetadata INTO OUTFILE '/tmp/setid_fullname.txt' FIELDS TERMINATED BY ',' ENCLOSED BY '"' LINES TERMINATED BY '\n';
 
-$ cp /tmp/setid_fullname.txt ../linkedSPLs/LinkedSPLs-clinicalDrug/mappings/
+$ cp /tmp/setid_fullname.txt LinkedSPLs-clinicalDrug/mappings/
 
-(4) mappings of omopid and rxcui 
+(4) mappings of omopid and rxcui (it's available if just updated linkedSPLs core graph)
 
 query OMOP CDM V5 (GeriOMOP) by SQL query below:
 
@@ -36,8 +36,6 @@ CONCEPT cpt
 WHERE 
 cpt.CONCEPT_CLASS = 'Clinical Drug';
 
-01/18/2017: 120561 results
-
 right click result table and export to delimited ('|' delimited, none Left or Right Enclosure)
 save name as: clinical-drug-omopid-rxcui-<DATE>.dsv
 to dir: LinkedSPLs-clinicalDrug/mappings/

Diff for: linkedSPLs/LinkedSPLs-update/README

@@ -241,7 +241,7 @@ TESTING THE D2R SERVER ON THE DEVELOPMENT MACHINE
 ------------------------------------------------------------
 
 cd /home/PITT/rdb20/Downloads/D2R/d2rq-0.8.1
-./d2r-server --verbose -b http://130.49.206.86:2021/ -p 2021 dailymed_d2r_map_config_d2rq_8_1.n3 
+./d2r-server --verbose -b http://<host>:<port>/ -p 2021 dailymed_d2r_map_config_d2rq_8_1.n3 
 
 ------------------------------------------------------------
 MOVING THE DEVELOPMENT MODE RDB DATA TO THE PUBLIC SERVER

Diff for: linkedSPLs/LinkedSPLs-update/data-source.properties

@@ -8,13 +8,13 @@ SCHEMA_SQL = load-dailymed-spls/TableSchema.sql
 
 ## Mapping data sources:
 
-FDA_UNII_NAMES = data/FDA/UNIIs_10Nov2016_Names.txt
-FDA_UNII_RECORDS = data/FDA/UNIIs_10Nov2016_Records.txt
+FDA_UNII_NAMES = data/FDA/UNIIs_28Apr2017_Names.txt
+FDA_UNII_RECORDS = data/FDA/UNIIs_28Apr2017_Records.txt
 DRUGBANK_XML = data/DrugBank/drugbank.xml
 PG_CLASS_INDEXING_SPLS = data/dailymed-indexing/pharmacologic_class_indexing_spl_files/
 RXNORM_SETID = data/dailymed-mappings/rxnorm_mappings.txt
-RXNCONSO_RRF = data/UMLS/rrf/RXNCONSO.RRF
-RXNORM_FULL_SCHEMA = data/UMLS/scripts/mysql/Table_scripts_mysql_rxn.sql
+RXNCONSO_RRF = data/UMLS/rxnorm-full/rrf/RXNCONSO.RRF
+RXNORM_FULL_SCHEMA = data/UMLS/rxnorm-full/scripts/mysql/Table_scripts_mysql_rxn.sql
 UNIIS_RXCUIS_FROM_UMLS = data/UMLS/UNIIs-Rxcuis-from-UMLS.txt
 DRON_RXCUI_DRUG = data/umasdbmi/dron-rxnorm.owl
 DRON_RXCUI_INGREDIENT = data/umasdbmi/dron-ingredient.owl