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revise README for clinical drug and active ingredient graph
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‎linkedSPLs/LinkedSPLs-activeMoiety/README

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

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Merge clinical drug mapping to create clinical drug RDF graph. Each clinical drug entity include attributes FDA preferred name, Rxcui, DrOn Id, OMOP concept Id.
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#############################################################
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update clinical drug entity graph
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#############################################################
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################################################################################
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OVERVIEW
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################################################################################
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<STEP1> update clinical drug mappings
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Merge clinical drug mapping to create clinical drug RDF graph. Each clinical drug entity include attributes FDA preferred name, Rxcui, DrOn Id, OMOP concept Id.
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mappings folder keep all orginal mappings from linkedSPLs
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################################################################################
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PRE-CONDITIONS:
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################################################################################
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----------------------------------------------------------
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mappings of omopid and rxcui
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----------------------------------------------------------
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OMOP concept Id and Rxcui mapping download from "https://github.com/OHDSI/KnowledgeBase/tree/master/LAERTES/terminology-mappings/StandardVocabToRxNorm/imeds_drugids_to_rxcuis.csv"
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------------------------------------------------------------------------
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Mappings from linkedSPLs core update
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------------------------------------------------------------------------
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OR
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(1) Dron to rxcui: linkedSPLs/LinkedSPLs-update/mappings/DrOn-to-RxNorm/cleaned-dron-to-rxcui-drug-<DATE>.txt
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query OMOP CDM V5 (GeriOMOP) by SQL query below:
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(2) Dailymed setid and rxcui: LinkedSPLs-update/mappings/RxNORM-mapping/converted_rxnorm_mappings_<DATE>.txt converted_rxnorm_mappings.txt
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SELECT cpt.CONCEPT_ID as omopid, cpt.CONCEPT_CODE as rxcui FROM
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CONCEPT cpt
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WHERE
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cpt.CONCEPT_CLASS = 'Clinical Drug';
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09/04/2015: 120561 results
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right click result table and export to csv ('|' delimited)
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----------------------------------------------------------
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cleaned-dron-to-rxcui-drug-<DATE>.txt
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----------------------------------------------------------
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mappings of DrOn Id and Rxcui available from "linkedSPLs/LinkedSPLs-update/mappings/DrOn-to-RxNorm/cleaned-dron-to-rxcui-drug-<DATE>.txt"
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$ cat converted_rxnorm_mappings.txt | cut -f1,2 -d\| | sort | uniq > setid_rxcui.txt
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----------------------------------------------------------
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converted_rxnorm_mappings_<DATE>.txt
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----------------------------------------------------------
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(3) Dailymed setid and drug fullname
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Dailymed product label indexing mapping from "linkedSPLs/LinkedSPLs-update/mappings/RxNORM-mapping/converted_rxnorm_mappings_<DATE>"
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$ mysql -u <username> -p
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$ use linkedSPLs;
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$ cd mappings
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SELECT setId, fullName FROM linkedSPLs.structuredProductLabelMetadata INTO OUTFILE '/tmp/setid_fullname.txt' FIELDS TERMINATED BY ',' ENCLOSED BY '"' LINES TERMINATED BY '\n';
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$ cp ../../LinkedSPLs-update/mappings/RxNORM-mapping/converted_rxnorm_mappings_10132015.txt converted_rxnorm_mappings.txt
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$ cp /tmp/setid_fullname.txt ../linkedSPLs/LinkedSPLs-clinicalDrug/mappings/
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$ cat converted_rxnorm_mappings.txt | cut -f1,2 -d\| | sort | uniq > setid_rxcui.txt
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(4) mappings of omopid and rxcui
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----------------------------------------------------------
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mappings of FDA preferred term and setId
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----------------------------------------------------------
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query OMOP CDM V5 (GeriOMOP) by SQL query below:
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$ mysql -u <username> -p
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SELECT cpt.CONCEPT_ID as omopid, cpt.CONCEPT_CODE as rxcui FROM
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CONCEPT cpt
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WHERE
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cpt.CONCEPT_CLASS = 'Clinical Drug';
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$ use linkedSPLs;
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01/18/2017: 120561 results
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SELECT setId, fullName FROM linkedSPLs.structuredProductLabelMetadata INTO OUTFILE '/tmp/setid_fullname.txt' FIELDS TERMINATED BY ',' ENCLOSED BY '"' LINES TERMINATED BY '\n';
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right click result table and export to delimited ('|' delimited, none Left or Right Enclosure)
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save name as: clinical-drug-omopid-rxcui-<DATE>.dsv
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to dir: LinkedSPLs-clinicalDrug/mappings/
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$ cp /tmp/setid_fullname.txt ../linkedSPLs/LinkedSPLs-clinicalDrug/mappings/
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################################################################################
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Procedures to get clinical drug RDF graph
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################################################################################
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<STEP 2> merge clinical drug mappings
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(1) merge clinical drug mappings
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$ python mergeToClinicalDrug.py
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output: mergedClinicalDrug.tsv
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<STEP 3> create clinical drug entity graph
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(2) create clinical drug entity graph
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$ python createClinicalDrugSubInRDF.py
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‎linkedSPLs/LinkedSPLs-clinicalDrug/mergeToClinicalDrug.py

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DRON_RXCUI = "../LinkedSPLs-update/mappings/DrOn-to-RxNorm/cleaned-dron-to-rxcui-drug.txt"
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SETID_RXCUI = "mappings/setid_rxcui.txt"
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FULLNAME_SETID = "mappings/setid_fullname.txt"
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#OMOP_RXCUI = "mappings/imeds_drugids_to_rxcuis.csv"
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OMOP_RXCUI = "mappings/clinical-drug-omopid-rxcui.dsv"
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## read mappings of dron and rxcui
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dron_rxcui_cols = ['dron', 'chebi', 'rxcui']

‎linkedSPLs/LinkedSPLs-core/linkedSPLs_dump_rdf_config.n3

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map:database a d2rq:Database;
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d2rq:jdbcDriver "com.mysql.jdbc.Driver";
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#d2rq:jdbcDSN "jdbc:mysql://136.142.148.191/linkedSPLs?autoReconnect=true&user=root&password=";
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d2rq:jdbcDSN "jdbc:mysql://localhost/linkedSPLs";
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d2rq:jdbcDriver "com.mysql.jdbc.Driver";
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d2rq:username "root";
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d2rq:password "";
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.
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# d2rq:resultSizeLimit 500;
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# d2rq:fetchSize 500;
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.
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#.
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map:DrugsRdfTypeBridge a d2rq:PropertyBridge;
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d2rq:belongsToClassMap map:structuredProductLabelMetadata;

‎linkedSPLs/LinkedSPLs-update/README

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Last updated Date: 01/18/2017
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################################################################################
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OVERVIEW
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################################################################################
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WHERE
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cpt.CONCEPT_CLASS = 'Ingredient';
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right click result table and export to delimited ('|' delimited, none Left or Right Enclosure)
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save name as: active-ingredient-omopid-rxcui-<DATE>.dsv
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to dir: LinkedSPLs-activeMoiety/mappings/
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On the public server:
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cd Downloads/d2rq-0.8.1/webapp/WEB-INF/templates
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...Then edit the root_page.vm file
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------------------------------------------------------------
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CREATING AN RDF DUMP OF THE DATA IN THE D2R SERVER
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------------------------------------------------------------
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$ cd <d2r server for linkedSPLs>
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$ ./dump-rdf -m <path to mapping file> -o linkedSPLs-dump.nt
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---------------------------------------------------------------------------------------
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LOADING AN RDF DUMP OF THE DATA INTO VIRTUOSO (tested with OpenLink Virtuoso in Ubuntu)
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---------------------------------------------------------------------------------------
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Initial load:
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$ isql-vt
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SQL> ld_dir ('/path/to/files', '*.n3', 'http://dbpedia.org');
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SQL> rdf_loader_run();
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SQL> select * from DB.DBA.load_list;
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Reloading (DELETE THE OLD GRAPH FIRST from Virtuoso composer!):
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$ isql-vt
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SQL> log_enable(3,1); # see http://www.openlinksw.com/dataspace/dav/wiki/Main/VirtTipsAndTricksGuideDeleteLargeGraphs
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SQL> SPARQL CLEAR GRAPH <http://dbmi-icode-01.dbmi.pitt.edu/linkedSPLs/>;
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SQL> update DB.DBA.load_list set ll_state = 0 where ll_file = '<name of RDF file>';
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SQL> rdf_loader_run();
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SQL> select * from DB.DBA.load_list;
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Graph list:
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http://purl.org/net/nlprepository/spl-core
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http://purl.org/net/nlprepository/spl-active-moiety
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http://purl.org/net/nlprepository/spl-clinical-drug
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- The D2R file has the mapping from RDB tables to RDF: ../LinkedSPLs-core/linkedSPLs_dump_rdf_config.n3
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...Then edit the root_page.vm file

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