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global configuration for TURBO R scripts
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| default: | |
| # replace <SECRET>s with settings appropriate for your environment | |
| # and save as ~/turbo_R_setup.yaml | |
| # | |
| # still need to make file paths relative | |
| # | |
| pds.host: <SECRET> | |
| pds.port: <SECRET> | |
| pds.database: <SECRET> | |
| pds.user: <SECRET> | |
| pds.pw: <SECRET> | |
| # | |
| rxnav.api.address: <SECRET> | |
| rxnav.api.port: <SECRET> | |
| # | |
| rxnav.mysql.user: <SECRET> | |
| rxnav.mysql.pw: <SECRET> | |
| rxnav.mysql.address: <SECRET> | |
| rxnav.mysql.port: <SECRET> | |
| # | |
| #my.bioportal.api.base: <SECRET> | |
| #my.apikey: <SECRET> | |
| # | |
| my.graphdb.base: <SECRET> | |
| my.selected.repo: <SECRET> | |
| my.graphdb.username: <SECRET> | |
| my.graphdb.pw: <SECRET> | |
| # | |
| med.map.kb.solr.host: <SECRET> | |
| med.map.kb.solr.port: <SECRET> | |
| med.map.kb.solr.core: <SECRET> | |
| # | |
| # for copying json to solr server | |
| ssh.user: <SECRET> | |
| ssh.host: <SECRET> | |
| # | |
| oracle.jdbc.path: "~/ojdbc8.jar" | |
| mysql.jdbc.path: "~/mysql-connector-java-8.0.19.jar" | |
| # | |
| source.medications.savepath: "source_medications.txt" | |
| source.medications.loadpath: "local/source_medications.txt" | |
| # | |
| normalization.file: "local/med_name_normalization.csv" | |
| # | |
| json.for.solr: "medlabels_for_chebi_for_solr.json" | |
| json.source: "/Users/markampa/cr3/med_mapping/" | |
| json.dest: "/project/turbo_graphdb_staging/" | |
| #### | |
| min.empi.count: 2 | |
| rxaui.asserted.strings.chunk.count: 3000 | |
| approximate.row.count: 5000 | |
| approximate.max.chars: 100 | |
| # tuning decoupled from training at this point | |
| tune.rf: FALSE | |
| train.split: 0.7 | |
| static.ntree: 351 | |
| static.mtry: 9 | |
| coverage.check.fraction: 0.1 | |
| my.pagesize: 4000 | |
| monitor.pause.seconds: 30 | |
| main.solr.query: | | |
| PREFIX mydata: <http://example.com/resource/> | |
| PREFIX obo: <http://purl.obolibrary.org/obo/> | |
| PREFIX owl: <http://www.w3.org/2002/07/owl#> | |
| PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> | |
| PREFIX rxn_tty: <http://example.com/resource/rxn_tty/> | |
| PREFIX rxnorm: <http://purl.bioontology.org/ontology/RXNORM/> | |
| PREFIX skos: <http://www.w3.org/2004/02/skos/core#> | |
| select (?iri_for_solr as ?mediri) ?definedin ?employment ?labelpred (lcase(str(?l)) as ?medlabel) | |
| where { | |
| { | |
| # only ChEBI, RxNorm and DrOn (subontologies) are included in this result at this point | |
| # skipping | |
| # <http://purl.obolibrary.org/obo/dron/dron-upper.owl> (contains dispositions... but just a few) | |
| # assuming that, in a given graph from a given definer) each term will have only one rdfs:label or skos:prefLabel | |
| # who has obo:IAO_0000118 alternative terms? just turbo, DrOn hand and DrOn upper | |
| { | |
| # for ChEBI ingredients and roles | |
| # ChEBI has synonyms with sources and types (sometimes) | |
| # rosuvastatin not in here because employment creation did not consider BioPortal mappings | |
| graph mydata:employment { | |
| values ?employment_iri { | |
| mydata:active_ingredient | |
| mydata:curated_role | |
| } | |
| ?iri_for_solr mydata:employment ?employment_iri . | |
| bind(replace(str( ?employment_iri ), "http://example.com/resource/", "") as ?employment) | |
| } | |
| values ?definedin { | |
| obo:chebi.owl | |
| } | |
| values ?labelpred { | |
| rdfs:label | |
| } | |
| graph ?definedin { | |
| ?iri_for_solr ?labelpred ?l . | |
| } | |
| } union { | |
| # for DrOn products | |
| graph mydata:employment { | |
| values ?employment_iri { | |
| mydata:product | |
| } | |
| ?iri_for_solr mydata:employment ?employment_iri . | |
| bind(replace(str( ?employment_iri ), "http://example.com/resource/", "") as ?employment) | |
| } | |
| values ?definedin { | |
| <http://purl.obolibrary.org/obo/dron/dron-rxnorm.owl> <http://purl.obolibrary.org/obo/dron/dron-hand.owl> | |
| } | |
| values ?labelpred { | |
| rdfs:label | |
| } | |
| graph ?definedin { | |
| ?iri_for_solr ?labelpred ?l . | |
| } | |
| } union { | |
| # for DrOn native ingredients | |
| graph mydata:employment { | |
| values ?employment_iri { | |
| mydata:active_ingredient | |
| } | |
| ?iri_for_solr mydata:employment ?employment_iri . | |
| bind(replace(str( ?employment_iri ), "http://example.com/resource/", "") as ?employment) | |
| } | |
| # the obo RxNorm graph name is liable to change (due to a typo from MAM) | |
| values ?definedin { | |
| <http://purl.obolibrary.org/obo/dron/dron-ingredient.owl> | |
| } | |
| values ?labelpred { | |
| rdfs:label | |
| } | |
| graph ?definedin { | |
| ?iri_for_solr ?labelpred ?l . | |
| } | |
| minus { | |
| graph obo:chebi.owl { | |
| ?iri_for_solr a owl:Class . | |
| } | |
| } | |
| } union { | |
| # RxNorm | |
| # BioPortal RxNorm RDF does have some alternative terms | |
| # but not as many as the NLM files/tables ? | |
| graph mydata:employment { | |
| # values ?employment_iri { | |
| # rxn_tty:IN rxn_tty:MIN rxn_tty:PIN rxn_tty:BN | |
| # rxn_tty:SBDF rxn_tty:SBDG rxn_tty:SCDF rxn_tty:SCDG | |
| # } | |
| ?iri_for_solr mydata:employment ?employment_iri . | |
| bind(replace(str( ?employment_iri ), "http://example.com/resource/rxn_tty/", "") as ?employment) | |
| } | |
| values ?definedin { | |
| rxnorm: | |
| } | |
| values ?labelpred { | |
| skos:prefLabel | |
| } | |
| graph rxnorm: { | |
| ?iri_for_solr ?labelpred ?l . | |
| } | |
| } | |
| } | |
| filter(isiri( ?iri_for_solr )) | |
| } | |
| clinrel_structclass.solr: | | |
| PREFIX obo: <http://purl.obolibrary.org/obo/> | |
| PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> | |
| select ?id ?definedin ?employment (lcase(str(?l)) as ?medlabel) | |
| where { | |
| values ?definedin { | |
| obo:chebi.owl | |
| } | |
| values ?labelpred { | |
| rdfs:label | |
| } | |
| values ?employment_iri { | |
| <http://example.com/resource/clinrel_structclass> | |
| } | |
| graph <http://example.com/resource/employment> { | |
| ?id <http://example.com/resource/employment> | |
| ?employment_iri . | |
| bind(replace(str( ?employment_iri ), "http://example.com/resource/", "") as ?employment) | |
| } | |
| graph ?definedin { | |
| ?id ?labelpred ?l . | |
| } | |
| } | |
| rxn.alt.lab.solr.query: | | |
| PREFIX mydata: <http://example.com/resource/> | |
| PREFIX rxn_tty: <http://example.com/resource/rxn_tty/> | |
| PREFIX rxnorm: <http://purl.bioontology.org/ontology/RXNORM/> | |
| PREFIX skos: <http://www.w3.org/2004/02/skos/core#> | |
| select distinct ?mediri ?medlabel | |
| where { | |
| graph rxnorm: { | |
| values ?labelpred { | |
| skos:altLabel | |
| } | |
| graph mydata:employment { | |
| # values ?employment_iri { | |
| # rxn_tty:IN rxn_tty:MIN rxn_tty:PIN rxn_tty:BN | |
| # rxn_tty:SBDF rxn_tty:SBDG rxn_tty:SCDF rxn_tty:SCDG | |
| # } | |
| ?mediri mydata:employment ?employment_iri . | |
| } | |
| ?mediri ?labelpred ?rawlab ; | |
| skos:prefLabel ?pl . | |
| bind(lcase(str(?rawlab)) as ?medlabel) | |
| filter(lcase(str(?rawlab)) != lcase(str(?pl))) | |
| } | |
| } | |
| #group by ?mediri ?labelpred | |
| chebi.synonym.query: | | |
| PREFIX obo: <http://purl.obolibrary.org/obo/> | |
| PREFIX owl: <http://www.w3.org/2002/07/owl#> | |
| PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> | |
| PREFIX oboInOwl: <http://www.geneontology.org/formats/oboInOwl#> | |
| PREFIX mydata: <http://example.com/resource/> | |
| select | |
| (?annsource as ?mediri) ?l (?annprop as ?synstrength) (?dbxr as ?synsource) ?syntype (?anntarg as ?synval) (strlen( ?anntarg ) as ?synlen) ?employment | |
| where { | |
| values ?employment { mydata:active_ingredient mydata:clinrel_structclass } | |
| graph mydata:employment { | |
| ?annsource mydata:employment ?employment | |
| } | |
| graph obo:chebi.owl { | |
| values ?annprop { | |
| oboInOwl:hasExactSynonym oboInOwl:hasRelatedSynonym | |
| } | |
| ?restr a owl:Axiom ; | |
| owl:annotatedSource ?annsource ; | |
| owl:annotatedProperty ?annprop ; | |
| owl:annotatedTarget ?anntarg . | |
| ?annsource rdfs:label ?l . | |
| filter( ?syntype != <http://purl.obolibrary.org/obo/chebi#IUPAC_NAME> ) | |
| filter( lcase(str(?l)) != lcase(str(?anntarg)) ) | |
| optional { | |
| ?restr oboInOwl:hasDbXref ?dbxr . | |
| } | |
| optional { | |
| ?restr oboInOwl:hasSynonymType ?syntype . | |
| } | |
| } | |
| } | |
| dron.additional.chebi.label.query: | | |
| PREFIX obo: <http://purl.obolibrary.org/obo/> | |
| PREFIX owl: <http://www.w3.org/2002/07/owl#> | |
| PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> | |
| PREFIX : <http://purl.obolibrary.org/obo/dron.owl#> | |
| select | |
| * | |
| where { | |
| graph <http://purl.obolibrary.org/obo/chebi.owl> { | |
| ?s a owl:Class ; | |
| rdfs:label ?cl . | |
| } | |
| graph <http://purl.obolibrary.org/obo/dron/dron-ingredient.owl> { | |
| # labels not asserted here | |
| ?s a owl:Class ; | |
| rdfs:label ?dl . | |
| } | |
| filter(lcase(str(?dl))!= lcase(str(?cl))) | |
| } | |
| chebi.role.syns: | | |
| PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> | |
| PREFIX oboInOwl: <http://www.geneontology.org/formats/oboInOwl#> | |
| PREFIX owl: <http://www.w3.org/2002/07/owl#> | |
| select | |
| distinct | |
| ?role ?at | |
| where { | |
| values ?dbxr { "ChEBI" "IUPHAR" } | |
| graph <http://example.com/resource/transitive_role_of_class> { | |
| ?ing <http://example.com/resource/transitive_role_of_class> ?role . | |
| } | |
| graph <http://purl.obolibrary.org/obo/chebi.owl> { | |
| ?ing rdfs:label ?il . | |
| ?role rdfs:label ?rl . | |
| ?an <http://www.w3.org/2002/07/owl#annotatedSource> ?role ; | |
| owl:annotatedProperty oboInOwl:hasRelatedSynonym ; | |
| owl:annotatedTarget ?at ; | |
| oboInOwl:hasDbXref ?dbxr . | |
| } | |
| } | |
| # | |
| target.col: "RELA" | |
| factor.levels: {"TTY.sr": ["AB","BD","BN","BPCK","CD","CDA","CDC","CDD","CE","DF","DFG","DP","GN","GPCK","IN","MH","MIN","MS","MTH_RXN_BD","MTH_RXN_CD","MTH_RXN_CDC","MTH_RXN_DP","NM","PCE","PEP","PIN","PSN","RXN_IN","RXN_PT","SBD","SBDC","SBDF","SC","SCD","SCDC","SCDF","SY"], "SAB.sr": ["ATC","CVX","DRUGBANK","GS","MMSL","MMX","MSH","MTHSPL","NDDF","RXNORM","USP","VANDF"], "RELA": ["consists_of","constitutes","contained_in","contains","form_of","has_form","has_ingredient","has_part","has_quantified_form","has_tradename","identical","ingredient_of","inverse_isa","isa","more distant","part_of","quantified_form_of","tradename_of"]} | |
| important.features: ["score","rank","rxcui.count","SAB.sr","TTY.sr","q.char","q.words","sr.char","sr.words","qgram","cosine","jaccard","jw"] | |
| testing.confusion.writepath: "rxnav_medication_mapping_confusion.csv" | |
| rf.model.savepath: "rxnav_med_mapping_rf.Rdata" | |
| rf.model.loadpath: "local/rxnav_med_mapping_rf.Rdata" | |
| allowed.synonym.sources: RXNORM | |
| excluded.term.types: | |
| - ET | |
| - FN | |
| - FSY | |
| - N1 | |
| - PM | |
| - PT | |
| - PTGB | |
| - SBDG | |
| - SCDG | |
| - SU | |
| - SYGB | |
| - TMSY | |
| final.predictions.writepath: "rxnav_medication_mapping_final_predictions.csv" | |
| # - 'ATC' | |
| # - 'NDFRT' | |
| my.source.ontolgies: | |
| - 'CHEBI' | |
| - 'DRON' | |
| - 'RXNORM' | |
| relevant.ontologies: | |
| - 'CHEBI' | |
| - 'DRON' | |
| - 'RXNORM' | |
| aceepted.mapping.sources: | |
| - 'CUI' | |
| - 'LOOM' | |
| bioportal.triples.destination: 'med_mapping_bioportal_mapping.ttl' | |
| # skipping http://purl.obolibrary.org/obo/dron/dron-ndc.owl , http://purl.obolibrary.org/obo/dron/dron-pro.owl | |
| # could possibly do some rewriting and not need http://purl.obolibrary.org/obo/dron/dron-chebi.owl ? | |
| my.import.urls: {"http://purl.obolibrary.org/obo/dron.owl":{"url":["https://bitbucket.org/uamsdbmi/dron/raw/master/dron-full.owl"],"format":[""]}, | |
| "http://purl.obolibrary.org/obo/dron/dron-hand.owl":{"url":["https://bitbucket.org/uamsdbmi/dron/raw/master/dron-hand.owl"],"format":[""]}, | |
| "http://purl.obolibrary.org/obo/dron/dron-ingredient.owl":{"url":["https://s3.amazonaws.com/drugontology/dron-ingredient.owl"],"format":[""]}, | |
| "http://purl.obolibrary.org/obo/dron/dron-rxnorm.owl":{"url":["https://s3.amazonaws.com/drugontology/dron-rxnorm.owl"],"format":[""]}, | |
| "https://raw.githubusercontent.com/PennTURBO/med_mapping/master/tmm_ontology/tmm_ontology.ttl":{"url":["https://raw.githubusercontent.com/PennTURBO/med_mapping/master/tmm_ontology/tmm_ontology.ttl"],"format":[""]}, | |
| "http://purl.obolibrary.org/obo/dron/dron-upper.owl":{"url":["https://bitbucket.org/uamsdbmi/dron/raw/master/dron-upper.owl"],"format":[""]}} | |
| # "http://purl.bioontology.org/ontology/NDFRT/":{"local.file":["/Users/markampa/med_mapping/local/NDFRT.ttl"],"format":["text/turtle"]}, | |
| # "http://purl.bioontology.org/ontology/UATC/":{"local.file":["/Users/markampa/med_mapping/local/ATC.ttl"],"format":["text/turtle"]}, | |
| my.import.files: {"http://example.com/resource/bioportal_mapping":{"local.file":["/Users/markampa/cr3/med_mapping/local/med_mapping_bioportal_mapping.ttl"],"format":["text/turtle"]}, | |
| "http://example.com/resource/classified_search_results":{"local.file":["/Users/markampa/cr3/med_mapping/local/classified_search_results_from_robot.ttl.gz"],"format":["text/turtle"]}, | |
| "http://example.com/resource/reference_medications":{"local.file":["/Users/markampa/cr3/med_mapping/local/reference_medications_from_robot.ttl"],"format":["text/turtle"]}, | |
| "http://purl.bioontology.org/ontology/RXNORM/":{"local.file":["/Users/markampa/cr3/med_mapping/local/RXNORM.ttl.gz"],"format":["text/turtle"]}, | |
| "http://purl.obolibrary.org/obo/chebi.owl":{"local.file":["/Users/markampa/cr3/med_mapping/local/chebi.owl.gz"],"format":["application/rdf+xml"]}} | |
| # | |
| # not asserting that http://example.com/resource/reference_medications | |
| # and | |
| # http://example.com/resource/classified_search_results | |
| # are owl:Ontology any more | |
| # | |
| # remove "blanknode an ontology", or use robot ontology annotations file | |
| # | |
| materializastion.projection.sparqls: | |
| #turbo_med_mapping_hand: | | |
| # PREFIX owl: <http://www.w3.org/2002/07/owl#> | |
| # insert data { | |
| # graph <http://example.com/resource/turbo_med_mapping_hand> { | |
| # <http://example.com/resource/reference_medications> a owl:Ontology . | |
| # <http://example.com/resource/classified_search_results> a owl:Ontology . | |
| # <http://example.com/resource/bioportal_mapping> a owl:Ontology . | |
| # <http://purl.obolibrary.org/obo/PDRO_0000024> <http://www.w3.org/1999/02/22-rdf-syntax-ns#comment> 'There are prescription "order names" like "wheelchair" in PDS and upstream sources that clearly do not denote a drug. So it may be more appropriator for Drivetrain to instantiate PDRO_0000001, "health care prescription"' ; | |
| # <http://www.w3.org/1999/02/22-rdf-syntax-ns#label> "drug prescription"@en . | |
| # <http://purl.obolibrary.org/obo/OBI_0001909> <http://www.w3.org/1999/02/22-rdf-syntax-ns#label> "conclusion based on data" . | |
| # } | |
| # } | |
| #remove_annonymous_ontologies: | | |
| # PREFIX owl: <http://www.w3.org/2002/07/owl#> | |
| # delete { | |
| # ?s a owl:Ontology . | |
| # } | |
| # where { | |
| # ?s a owl:Ontology . | |
| # filter(isblank(?s)) | |
| # } | |
| delete_useless_named_ind_assertions: | | |
| delete { | |
| ?s a <http://www.w3.org/2002/07/owl#NamedIndividual> | |
| } where { | |
| { | |
| graph <http://example.com/resource/classified_search_results> { | |
| ?s a <http://www.w3.org/2002/07/owl#NamedIndividual> | |
| } | |
| } union { | |
| graph <http://example.com/resource/reference_medications> { | |
| ?s a <http://www.w3.org/2002/07/owl#NamedIndividual> | |
| } | |
| } | |
| } | |
| # this could be a CRID symbol value | |
| standalone_source_med_ids: | | |
| PREFIX mydata: <http://example.com/resource/> | |
| PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> | |
| PREFIX obo: <http://purl.obolibrary.org/obo/> | |
| PREFIX skos: <http://www.w3.org/2004/02/skos/core#> | |
| insert { | |
| graph <http://example.com/resource/source_med_id> { | |
| ?s skos:notation ?extracted_id | |
| } | |
| } | |
| where { | |
| graph mydata:reference_medications { | |
| ?s a obo:PDRO_0000024 . | |
| } | |
| bind(strafter(str(?s),"http://example.com/resource/source_med_id/") as ?extracted_id) | |
| } | |
| reference_medications_labels: | | |
| PREFIX obo: <http://purl.obolibrary.org/obo/> | |
| PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> | |
| PREFIX skos: <http://www.w3.org/2004/02/skos/core#> | |
| insert { | |
| graph <http://example.com/resource/reference_medications_labels> { | |
| ?s rdfs:label ?bound . | |
| } | |
| } | |
| where { | |
| graph <http://example.com/resource/reference_medications> { | |
| ?s a obo:PDRO_0000024 ; | |
| <http://example.com/resource/source_full_name> ?source_full_name . | |
| } | |
| graph <http://example.com/resource/source_med_id> { | |
| ?s skos:notation ?extracted_id | |
| } | |
| bind(concat(?extracted_id, "|", ?source_full_name ) as ?bound) | |
| } | |
| classifications_labels: | | |
| PREFIX obo: <http://purl.obolibrary.org/obo/> | |
| PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> | |
| insert { | |
| graph <http://example.com/resource/classifications_labels> { | |
| ?s rdfs:label ?bound . | |
| } | |
| } | |
| where { | |
| graph <http://example.com/resource/classified_search_results> { | |
| ?s a obo:OBI_0001909 ; | |
| <http://example.com/resource/query_val> ?query_val . | |
| bind(concat(?query_val, "|", replace(str(?s), "http://example.com.resource/", "")) as ?bound) | |
| } | |
| } | |
| # if something is defined in ChEBI (XXX), remove assertion that it is also defined in DrOn-ChEBI (XXX)? | |
| defined_in: | | |
| PREFIX owl: <http://www.w3.org/2002/07/owl#> | |
| insert { | |
| graph <http://example.com/resource/defined_in> { | |
| ?s <http://example.com/resource/defined_in> ?g . | |
| } | |
| } | |
| where { | |
| graph ?g { | |
| ?s a owl:Class . | |
| filter (isuri(?s)) | |
| } | |
| # ?s a owl:Class? | |
| # ?s a ?c ; ?c a owl:Class ? | |
| } | |
| # # keep this, or just use BioPortal mappings? | |
| # materialized_rxcui: | | |
| # PREFIX obo: <http://purl.obolibrary.org/obo/> | |
| # insert { | |
| # graph <http://example.com/resource/materialized_rxcui> { | |
| # ?s <http://example.com/resource/materialized_rxcui> ?concat | |
| # } | |
| # } where { | |
| # { | |
| # graph <http://purl.obolibrary.org/obo/dron/dron-ingredient.owl> | |
| # { | |
| # ?s obo:DRON_00010000 ?o . | |
| # } | |
| # } | |
| # union | |
| # { | |
| # graph <http://purl.obolibrary.org/obo/dron/dron-rxnorm.owl> | |
| # { | |
| # ?s obo:DRON_00010000 ?o . | |
| # } | |
| # } | |
| # bind(uri(concat("http://purl.bioontology.org/ontology/RXNORM/",?o)) as ?concat) | |
| # } | |
| transitively_materialized_dron_ingredient: | | |
| PREFIX obo: <http://purl.obolibrary.org/obo/> | |
| PREFIX owl: <http://www.w3.org/2002/07/owl#> | |
| PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> | |
| PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> | |
| PREFIX xsd: <http://www.w3.org/2001/XMLSchema#> | |
| PREFIX ro: <http://www.obofoundry.org/ro/ro.owl#> | |
| insert { | |
| graph <http://example.com/resource/transitively_materialized_dron_ingredient> { | |
| ?dronsubprod <http://example.com/resource/transitively_materialized_dron_ingredient> ?droning . | |
| } | |
| } | |
| where { | |
| graph <http://purl.obolibrary.org/obo/dron/dron-ingredient.owl> { | |
| ?s a owl:Restriction ; | |
| owl:someValuesFrom ?droning ; | |
| owl:onProperty obo:BFO_0000071 . | |
| ?bt1 rdf:first ?s ; | |
| rdf:rest rdf:nil . | |
| ?bt2f a owl:Restriction ; | |
| owl:onProperty obo:BFO_0000053 ; | |
| owl:someValuesFrom obo:DRON_00000028 . | |
| ?bt2 rdf:rest ?bt1 ; | |
| rdf:first ?bt2f . | |
| ?bt3 rdf:rest ?bt2 ; | |
| rdf:first obo:OBI_0000576 . | |
| ?bt4 owl:intersectionOf ?bt3 ; | |
| rdf:type owl:Class . | |
| ?bt5 owl:someValuesFrom ?bt4 ; | |
| rdf:type owl:Restriction ; | |
| owl:onProperty ro:has_proper_part . | |
| ?dronprod rdfs:subClassOf ?bt5 ; | |
| a owl:Class . | |
| } | |
| ?dronsubprod rdfs:subClassOf* ?dronprod | |
| } | |
| transitively_materialized_drugrole: | | |
| PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> | |
| PREFIX obo: <http://purl.obolibrary.org/obo/> | |
| insert { | |
| graph <http://example.com/resource/transitively_materialized_drugrole> { | |
| ?nextdrugrole <http://example.com/resource/transitively_materialized_drugrole> ?subdrugrole . | |
| } | |
| } where { | |
| values ?valsource { | |
| obo:CHEBI_130181 obo:CHEBI_131699 obo:CHEBI_131770 obo:CHEBI_131787 obo:CHEBI_139503 obo:CHEBI_22333 obo:CHEBI_22586 | |
| obo:CHEBI_23018 obo:CHEBI_23354 obo:CHEBI_23357 obo:CHEBI_23366 obo:CHEBI_23888 obo:CHEBI_24020 obo:CHEBI_24621 | |
| obo:CHEBI_24869 obo:CHEBI_25435 obo:CHEBI_25491 obo:CHEBI_25728 obo:CHEBI_27026 obo:CHEBI_27314 obo:CHEBI_33229 | |
| obo:CHEBI_33280 obo:CHEBI_35195 obo:CHEBI_35221 obo:CHEBI_35522 obo:CHEBI_35530 obo:CHEBI_35544 obo:CHEBI_35569 | |
| obo:CHEBI_35660 obo:CHEBI_35856 obo:CHEBI_35941 obo:CHEBI_36413 obo:CHEBI_37153 obo:CHEBI_37670 obo:CHEBI_37699 | |
| obo:CHEBI_37700 obo:CHEBI_37733 obo:CHEBI_37886 obo:CHEBI_37887 obo:CHEBI_37890 obo:CHEBI_37955 obo:CHEBI_37956 | |
| obo:CHEBI_37961 obo:CHEBI_38157 obo:CHEBI_38161 obo:CHEBI_38215 obo:CHEBI_38234 obo:CHEBI_38324 obo:CHEBI_38325 | |
| obo:CHEBI_38462 obo:CHEBI_38623 obo:CHEBI_38632 obo:CHEBI_38633 obo:CHEBI_38637 obo:CHEBI_38706 obo:CHEBI_38808 | |
| obo:CHEBI_38809 obo:CHEBI_39000 obo:CHEBI_47958 obo:CHEBI_48001 obo:CHEBI_48279 obo:CHEBI_48561 obo:CHEBI_48578 | |
| obo:CHEBI_48873 obo:CHEBI_48876 obo:CHEBI_48878 obo:CHEBI_49020 obo:CHEBI_49103 obo:CHEBI_49159 obo:CHEBI_49200 | |
| obo:CHEBI_50103 obo:CHEBI_50112 obo:CHEBI_50113 obo:CHEBI_50114 obo:CHEBI_50137 obo:CHEBI_50183 obo:CHEBI_50188 | |
| obo:CHEBI_50218 obo:CHEBI_50276 obo:CHEBI_50390 obo:CHEBI_50502 obo:CHEBI_50509 obo:CHEBI_50510 obo:CHEBI_50566 | |
| obo:CHEBI_50568 obo:CHEBI_50629 obo:CHEBI_50630 obo:CHEBI_50683 obo:CHEBI_50696 obo:CHEBI_50745 obo:CHEBI_50750 | |
| obo:CHEBI_50781 obo:CHEBI_50790 obo:CHEBI_50837 obo:CHEBI_50844 obo:CHEBI_50902 obo:CHEBI_50904 obo:CHEBI_50905 | |
| obo:CHEBI_50908 obo:CHEBI_50910 obo:CHEBI_51060 obo:CHEBI_51065 obo:CHEBI_51373 obo:CHEBI_52209 obo:CHEBI_52210 | |
| obo:CHEBI_52290 obo:CHEBI_53559 obo:CHEBI_53756 obo:CHEBI_55322 obo:CHEBI_59282 obo:CHEBI_59517 obo:CHEBI_59826 | |
| obo:CHEBI_59897 obo:CHEBI_60186 obo:CHEBI_60311 obo:CHEBI_60605 obo:CHEBI_60606 obo:CHEBI_60643 obo:CHEBI_60798 | |
| obo:CHEBI_60807 obo:CHEBI_60832 obo:CHEBI_61015 obo:CHEBI_61016 obo:CHEBI_61115 obo:CHEBI_61908 obo:CHEBI_61951 | |
| obo:CHEBI_62488 obo:CHEBI_62872 obo:CHEBI_64571 obo:CHEBI_64909 obo:CHEBI_64911 obo:CHEBI_65023 obo:CHEBI_65259 | |
| obo:CHEBI_68495 obo:CHEBI_68563 obo:CHEBI_70727 obo:CHEBI_70781 obo:CHEBI_71232 obo:CHEBI_73240 obo:CHEBI_73263 | |
| obo:CHEBI_73333 obo:CHEBI_73913 obo:CHEBI_74213 obo:CHEBI_74234 obo:CHEBI_76779 obo:CHEBI_76797 obo:CHEBI_76932 | |
| obo:CHEBI_77194 obo:CHEBI_77255 obo:CHEBI_77402 obo:CHEBI_77748 obo:CHEBI_78444 obo:CHEBI_85234 obo:CHEBI_86385 | |
| obo:CHEBI_90414 obo:CHEBI_90415 obo:CHEBI_91079 obo:CHEBI_35664 | |
| } | |
| ?subdrugrole rdfs:subClassOf* ?valsource . | |
| ?nextdrugrole rdfs:subClassOf* ?subdrugrole . | |
| } | |
| transitive_role_of_class: | | |
| PREFIX owl: <http://www.w3.org/2002/07/owl#> | |
| PREFIX obo: <http://purl.obolibrary.org/obo/> | |
| PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> | |
| insert { | |
| graph <http://example.com/resource/transitive_role_of_class> { | |
| ?chebidrugsubclass <http://example.com/resource/transitive_role_of_class> ?superrole . | |
| } | |
| } where { | |
| graph <http://example.com/resource/transitively_materialized_drugrole> { | |
| ?drugrole <http://example.com/resource/transitively_materialized_drugrole>* ?superrole . | |
| } | |
| graph obo:chebi.owl { | |
| ?restr a owl:Restriction ; | |
| owl:someValuesFrom ?drugrole ; | |
| owl:onProperty obo:RO_0000087 . | |
| ?chebidrugclass rdfs:subClassOf ?restr . | |
| ?chebidrugsubclass rdfs:subClassOf* ?chebidrugclass . | |
| filter(isuri(?chebidrugsubclass)) | |
| } | |
| } | |
| # # I don't think we're actually using this | |
| # materialize_cuis: | | |
| # insert { | |
| # graph <http://example.com/resource/cui> { | |
| # ?materialized a <http://purl.obolibrary.org/obo/IAO_0000578> ; | |
| # <http://purl.obolibrary.org/obo/IAO_0000219> ?s . | |
| # } | |
| # } | |
| # where { | |
| # ?s <http://bioportal.bioontology.org/ontologies/umls/cui> ?cui . | |
| # bind(uri(concat("http://example.com/resource/cui/",?cui)) as ?materialized ) | |
| # } | |
| elected_mappings: | | |
| PREFIX mydata: <http://example.com/resource/> | |
| PREFIX obo: <http://purl.obolibrary.org/obo/> | |
| insert { | |
| graph mydata:elected_mapping { | |
| ?wasinner mydata:elected_mapping ?outermrxc | |
| } | |
| } | |
| where | |
| { | |
| { | |
| select | |
| (?innersm as ?wasinner) ?outermrxc ?innerpimax (sum(?outerpi) as ?outersum) | |
| where { | |
| graph mydata:classified_search_results { | |
| ?doublecheck mydata:source_id_uri ?innersm ; | |
| mydata:prob_identical ?outerpi ; | |
| mydata:match_rxcui ?outermrxc . | |
| } | |
| { | |
| select (?sourcemed as ?innersm) (max(?pisum) as ?innerpimax) | |
| where | |
| { | |
| select ?sourcemed ?match_rxcui (sum( ?prob_identical ) as ?pisum) | |
| where { | |
| graph mydata:reference_medications { | |
| ?sourcemed a obo:PDRO_0000024 ; | |
| mydata:source_count ?source_count . | |
| } | |
| graph mydata:classified_search_results { | |
| ?classified_search_result mydata:source_id_uri ?sourcemed ; | |
| mydata:prob_more_distant ?prob_more_distant ; | |
| mydata:prob_identical ?prob_identical ; | |
| mydata:match_rxcui ?match_rxcui . | |
| } | |
| } | |
| group by ?sourcemed ?match_rxcui | |
| order by desc (sum( ?prob_identical )) | |
| } | |
| group by ?sourcemed | |
| } | |
| } | |
| group by ?innersm ?innerpimax ?outermrxc | |
| } | |
| filter(?innerpimax = ?outersum) | |
| } | |
| ing.prod.employment: | | |
| PREFIX owl: <http://www.w3.org/2002/07/owl#> | |
| PREFIX ro: <http://www.obofoundry.org/ro/ro.owl#> | |
| PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> | |
| PREFIX obo: <http://purl.obolibrary.org/obo/> | |
| PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> | |
| PREFIX mydata: <http://example.com/resource/> | |
| PREFIX oboInOwl: <http://www.geneontology.org/formats/oboInOwl#> | |
| insert { | |
| graph mydata:employment { | |
| ?dronprod mydata:employment mydata:product . | |
| ?acting mydata:employment mydata:active_ingredient . | |
| } | |
| } | |
| where { | |
| graph <http://purl.obolibrary.org/obo/dron/dron-ingredient.owl> { | |
| ?r a owl:Restriction ; | |
| owl:onProperty ro:has_proper_part ; | |
| owl:someValuesFrom ?hpp_valsource . | |
| ?hpp_valsource owl:intersectionOf ?hpp_intersection . | |
| ?hpp_intersection rdf:first obo:OBI_0000576 ; | |
| rdf:rest ?sma_intersection . | |
| ?sma_intersection rdf:first ?sma_intersection_first ; | |
| rdf:rest ?acting_intersection . | |
| ?sma_intersection_first a owl:Restriction ; | |
| owl:onProperty obo:BFO_0000053 ; | |
| owl:someValuesFrom obo:DRON_00000028 . | |
| ?acting_intersection rdf:first ?acting_first ; | |
| rdf:rest rdf:nil . | |
| ?acting_first a owl:Restriction ; | |
| owl:onProperty obo:BFO_0000071 ; | |
| owl:someValuesFrom ?acting . | |
| } | |
| # was constraining the subacting asn product graphs more for performance that truth? | |
| # acutally added in some junk?! | |
| # or was that from subacting? | |
| ?dronprod rdfs:subClassOf* ?r . | |
| filter( isiri(?dronprod)) | |
| } | |
| # todo how did I choose these roles? | |
| # bootstapped from common roles of ingredients with lots of products? | |
| # or lots of patients? | |
| curated.role.employment: | | |
| PREFIX mydata: <http://example.com/resource/> | |
| PREFIX obo: <http://purl.obolibrary.org/obo/> | |
| PREFIX owl: <http://www.w3.org/2002/07/owl#> | |
| PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> | |
| PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> | |
| insert { | |
| graph mydata:employment { | |
| ?role mydata:employment mydata:curated_role | |
| } | |
| } | |
| where { | |
| values ?valsource { | |
| obo:CHEBI_130181 obo:CHEBI_131699 obo:CHEBI_131770 obo:CHEBI_131787 obo:CHEBI_139503 obo:CHEBI_22333 obo:CHEBI_22586 | |
| obo:CHEBI_23018 obo:CHEBI_23354 obo:CHEBI_23357 obo:CHEBI_23366 obo:CHEBI_23888 obo:CHEBI_24020 obo:CHEBI_24621 | |
| obo:CHEBI_24869 obo:CHEBI_25435 obo:CHEBI_25491 obo:CHEBI_25728 obo:CHEBI_27026 obo:CHEBI_27314 obo:CHEBI_33229 | |
| obo:CHEBI_33280 obo:CHEBI_35195 obo:CHEBI_35221 obo:CHEBI_35522 obo:CHEBI_35530 obo:CHEBI_35544 obo:CHEBI_35569 | |
| obo:CHEBI_35660 obo:CHEBI_35856 obo:CHEBI_35941 obo:CHEBI_36413 obo:CHEBI_37153 obo:CHEBI_37670 obo:CHEBI_37699 | |
| obo:CHEBI_37700 obo:CHEBI_37733 obo:CHEBI_37886 obo:CHEBI_37887 obo:CHEBI_37890 obo:CHEBI_37955 obo:CHEBI_37956 | |
| obo:CHEBI_37961 obo:CHEBI_38157 obo:CHEBI_38161 obo:CHEBI_38215 obo:CHEBI_38234 obo:CHEBI_38324 obo:CHEBI_38325 | |
| obo:CHEBI_38462 obo:CHEBI_38623 obo:CHEBI_38632 obo:CHEBI_38633 obo:CHEBI_38637 obo:CHEBI_38706 obo:CHEBI_38808 | |
| obo:CHEBI_38809 obo:CHEBI_39000 obo:CHEBI_47958 obo:CHEBI_48001 obo:CHEBI_48279 obo:CHEBI_48561 obo:CHEBI_48578 | |
| obo:CHEBI_48873 obo:CHEBI_48876 obo:CHEBI_48878 obo:CHEBI_49020 obo:CHEBI_49103 obo:CHEBI_49159 obo:CHEBI_49200 | |
| obo:CHEBI_50103 obo:CHEBI_50112 obo:CHEBI_50113 obo:CHEBI_50114 obo:CHEBI_50137 obo:CHEBI_50183 obo:CHEBI_50188 | |
| obo:CHEBI_50218 obo:CHEBI_50276 obo:CHEBI_50390 obo:CHEBI_50502 obo:CHEBI_50509 obo:CHEBI_50510 obo:CHEBI_50566 | |
| obo:CHEBI_50568 obo:CHEBI_50629 obo:CHEBI_50630 obo:CHEBI_50683 obo:CHEBI_50696 obo:CHEBI_50745 obo:CHEBI_50750 | |
| obo:CHEBI_50781 obo:CHEBI_50790 obo:CHEBI_50837 obo:CHEBI_50844 obo:CHEBI_50902 obo:CHEBI_50904 obo:CHEBI_50905 | |
| obo:CHEBI_50908 obo:CHEBI_50910 obo:CHEBI_51060 obo:CHEBI_51065 obo:CHEBI_51373 obo:CHEBI_52209 obo:CHEBI_52210 | |
| obo:CHEBI_52290 obo:CHEBI_53559 obo:CHEBI_53756 obo:CHEBI_55322 obo:CHEBI_59282 obo:CHEBI_59517 obo:CHEBI_59826 | |
| obo:CHEBI_59897 obo:CHEBI_60186 obo:CHEBI_60311 obo:CHEBI_60605 obo:CHEBI_60606 obo:CHEBI_60643 obo:CHEBI_60798 | |
| obo:CHEBI_60807 obo:CHEBI_60832 obo:CHEBI_61015 obo:CHEBI_61016 obo:CHEBI_61115 obo:CHEBI_61908 obo:CHEBI_61951 | |
| obo:CHEBI_62488 obo:CHEBI_62872 obo:CHEBI_64571 obo:CHEBI_64909 obo:CHEBI_64911 obo:CHEBI_65023 obo:CHEBI_65259 | |
| obo:CHEBI_68495 obo:CHEBI_68563 obo:CHEBI_70727 obo:CHEBI_70781 obo:CHEBI_71232 obo:CHEBI_73240 obo:CHEBI_73263 | |
| obo:CHEBI_73333 obo:CHEBI_73913 obo:CHEBI_74213 obo:CHEBI_74234 obo:CHEBI_76779 obo:CHEBI_76797 obo:CHEBI_76932 | |
| obo:CHEBI_77194 obo:CHEBI_77255 obo:CHEBI_77402 obo:CHEBI_77748 obo:CHEBI_78444 obo:CHEBI_85234 obo:CHEBI_86385 | |
| obo:CHEBI_90414 obo:CHEBI_90415 obo:CHEBI_91079 obo:CHEBI_35664 | |
| } | |
| graph obo:chebi.owl { | |
| ?role rdfs:subClassOf* ?valsource ; | |
| rdfs:label ?rolelab . | |
| } | |
| } | |
| # # this is an attempt to get knowledge about clinically relevant | |
| # # structural classes in ChEBI | |
| # # like statins, cardiac glycosides, benzodiazepines, etc. | |
| # # macrolide antibiotics may be especially tricky | |
| # # and or use ATC/NDFRT in the future | |
| # Added 333 statements. Update took 18m, minutes ago. | |
| # does the rest of the R script need to be blocked until this is complete? | |
| assert_clinrel_structclass: | | |
| PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> | |
| PREFIX owl: <http://www.w3.org/2002/07/owl#> | |
| PREFIX obo: <http://purl.obolibrary.org/obo/> | |
| insert { | |
| graph <http://example.com/resource/employment> { | |
| ?molent <http://example.com/resource/employment> <http://example.com/resource/clinrel_structclass> | |
| } | |
| } | |
| where { | |
| graph <http://example.com/resource/employment> { | |
| ?superrole <http://example.com/resource/employment> <http://example.com/resource/curated_role> . | |
| } | |
| graph <http://purl.obolibrary.org/obo/chebi.owl> { | |
| ?subrole rdfs:subClassOf* ?superrole . | |
| ?restr a owl:Restriction ; | |
| owl:someValuesFrom ?subrole ; | |
| owl:onProperty obo:RO_0000087 . | |
| ?molent rdfs:subClassOf ?restr ; | |
| rdfs:label ?ml . | |
| ?anything rdfs:subClassOf ?molent . | |
| } | |
| } | |
| per.task.columns: 'med_map_csv_cols.csv' | |
| tasks: | |
| - reference_medications | |
| - classified_search_results | |
| reference_medications: | |
| current.file.base.name: 'reference_medications' | |
| my.numericals: | |
| - source_count | |
| my.class: 'http://purl.obolibrary.org/obo/PDRO_0000024' | |
| classified_search_results: | |
| current.file.base.name: 'classified_search_results' | |
| my.numericals: | |
| - match_chars | |
| - match_words | |
| - query_chars | |
| - query_words | |
| - match_rank | |
| - match_rxaui | |
| - match_score | |
| - prob_consists_of | |
| - prob_constitutes | |
| - prob_contained_in | |
| - prob_contains | |
| - prob_form_of | |
| - prob_has_form | |
| - prob_has_ingredient | |
| - prob_has_part | |
| - prob_has_quantified_form | |
| - prob_has_tradename | |
| - prob_identical | |
| - prob_ingredient_of | |
| - prob_inverse_isa | |
| - prob_isa | |
| - prob_more_distant | |
| - prob_part_of | |
| - prob_quantified_form_of | |
| - prob_tradename_of | |
| - rxaui_freq | |
| - rxcui_freq | |
| - sd_cosine | |
| - sd_jaccard | |
| - sd_jw | |
| - sd_lcs | |
| - sd_lv | |
| - sd_qgram | |
| my.class: 'http://purl.obolibrary.org/obo/OBI_0001909' | |
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