revise README for dailymed indexing source

Author: ningyifan

linkedSPLs/LinkedSPLs-update/README

@@ -100,11 +100,9 @@ Put in folder at "bio2rdf/linkedSPLs/LinkedSPLs-update/data/dailymed-mappings/"
 
 Download pharmacologic_class_indexing_spl_files.zip from http://dailymed.nlm.nih.gov/dailymed/spl-resources-all-indexing-files.cfm
 
-Put in folder at "bio2rdf/linkedSPLs/LinkedSPLs-update/data/dailymed-indexings/"
+Put in folder at "bio2rdf/linkedSPLs/LinkedSPLs-update/data/dailymed-indexings/pharmacologic_class_indexing_spl_files"
 
-unzip XMLs to folder "pharmacologic_class_indexing_spl_files"
-
-$ cd pharmacologic_class_indexing_spl_files; unzip \*.zip; rm *.zip
+$ unzip pharmacologic_class_indexing_spl_files.zip -d pharmacologic_class_indexing_spl_files
 
 --------------------------------------------------------
 FDA (Preferred terms, UNIIs):
@@ -118,9 +116,9 @@ Downloads UNII List ('UNIIs <DATE> Names.txt' as UNII lists)
 (2) UNIIs_Records 
 Downloads UNII Data ('UNIIs <DATE> Records.txt' as UNII records) 
 
-Keep in directory LinkedSPLs-update/data/FDA
-
-(replace whitespace ' ' in file name to underscore '_')
+Put in directory LinkedSPLs-update/data/FDA
+Unzip UNII_Data.zip and UNIIs.zip in LinkedSPLs-update/data/FDA/
+Replace whitespace ' ' in file names to underscore '_'
 
 Edit LinkedSPLs-update/data-source.properties to reset FDA_UNII_NAMES and FDA_UNII_RECORDS 
 
@@ -130,15 +128,16 @@ Drugbank (Drug bank Id) :
 
 Download from http://www.drugbank.ca/downloads
 
-download drugbank.xml as drugbankX.X and keep in directory LinkedSPLs-update/data/DrugBank/drugbank.xml
+download and unzip drugbank.xml as drugbankX.X in directory:
+LinkedSPLs-update/data/DrugBank/drugbank.xml
 
 --------------------------------------------------------
 UMLS (rxcui):
 --------------------------------------------------------
 
 Download RXNORM mappings (full rxnorm) from UMLS at "http://www.nlm.nih.gov/research/umls/rxnorm/docs/rxnormfiles.html"
 
-keep in directory: "LinkedSPLs-update/data/UMLS"
+Unzip and keep in directory: "LinkedSPLs-update/data/UMLS/rxnorm-full/"
 
 ------------------------------------------------------------------------
 PharmagxTable && FDAPharmgxTableToOntologyMap
@@ -152,8 +151,8 @@ put at "LinkedSPLs-update/mappings/FDA-pharmacogenetic-info-mapping/"
 
 Edit data-source.properties
 ex.
-BIOMARKER = mappings/FDA-pharmacogenetic-info-mapping/biomarker-to-ontology-mapping-07242015.xlsx
-GENETIC= genetic-biomarker-table-update-07242015.csv
+BIOMARKER = mappings/FDA-pharmacogenetic-info-mapping/biomarker-to-ontology-mapping-01262017.csv
+GENETIC= mappings/FDA-pharmacogenetic-info-mapping/FDA_PGx_Table.csv
 
 --------------------------------------------------------
 umlsdbmi (DronId for drug and ingredient):
@@ -164,21 +163,21 @@ Code: https://bitbucket.org/uamsdbmi/dron/src
 Download repository from "https://bitbucket.org/uamsdbmi/dron/downloads"
 
 unzip repository and then:
-copy dron-rxnorm.owl at data/umasdbmi/dron-rxnorm.owl
-copy dron-ingredient.owl at data/umasdbmi/dron-ingredient.owl
+copy dron-rxnorm.owl from repository to data/umasdbmi/dron-rxnorm.owl
+copy dron-ingredient.owl from repository to data/umasdbmi/dron-ingredient.owl
 
 dron-rxnorm.owl for drug product
 dron-ingredient.owl for active ingredients
 
-
 ------------------------------------------------------------------------
 OMOP concept Id from OHDSI or query OMOP CDM V5 (GeriOMOP) by SQL query
 ----------------------------------------------------------------------- 
 
 Download from "https://github.com/OHDSI/KnowledgeBase/tree/master/LAERTES/terminology-mappings/StandardVocabToRxNorm/imeds_drugids_to_rxcuis.csv"
 
-OR
+OR query OMOP CDM vocabulary Version 5 (below example via client sqldeveloper)
 
+(1) For drug product
 SELECT cpt.CONCEPT_ID as omopid, cpt.CONCEPT_CODE as rxcui FROM
 CONCEPT cpt
 WHERE 
@@ -188,7 +187,7 @@ right click result table and export to delimited ('|' delimited, none Left or Ri
 save name as: clinical-drug-omopid-rxcui-<DATE>.dsv
 to dir: LinkedSPLs-clinicalDrug/mappings/
 
-AND
+(2) For active ingredient
 
 query OMOP CDM V5 (GeriOMOP) by SQL query below:
 SELECT cpt.CONCEPT_ID as omopid, cpt.CONCEPT_CODE as rxcui FROM