Merge pull request #35 from andrewsu/main

create DrugCentral_subset

config/DrugCentral_subset/README.md

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+# DrugCentral Creative Mode -- SUBSET
+
+##Goal
+A benchmark data set for returning drugs that treat an indication.  Indications are drawn from DrugCentral. This benchmark is a very small subset of the full DrugCentral benchmark.
+
+##Data Description
+DrugCentral provides ~10k indications for ~3000 drugs. `get_indications.py` retrieves these indications and parses out chemical and disease identifiers. It removes cases where one disease has many known drugs. It also samples 5 indications that it writes to `data.tsv`.
+
+##Benchmarks
+This data set is used to create the following benchmarks:
+
+### Treats
+A creative mode query looking for small molecules connected to the indication via a treats predicate
+
+
+##Data Creation
+created from DrugCentral via mychem.info using `get_indications.py`.

config/DrugCentral_subset/data.tsv

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+_id	chebi	drug_umls	disease_umls	drug_name	disease_name
+ZZHLYYDVIOPZBE-UHFFFAOYSA-N	CHEBI:9725	UMLS:C0041031	UMLS:C0002994	alimemazine,alimemazine tartrate,temaril,trimeprazine tartrate,trimeprazine,alimezine,methylpromazine,teralene	Angioedema
+UREBDLICKHMUKA-DVTGEIKXSA-N	CHEBI:3077	UMLS:C0005308	UMLS:C0002994	betamethasone,betadexamethasone,betametasone,betamethazone,bethamethasone	Angioedema
+ITRJWOMZKQRYTA-RFZYENFJSA-N	CHEBI:3897	UMLS:C0056391	UMLS:C0002994	cortisone acetate,cortone acetate,irisone acetate,adrenalex	Angioedema
+UREBDLICKHMUKA-CXSFZGCWSA-N	CHEBI:41879	UMLS:C0011777	UMLS:C0002994	dexamethasone,dexasone,dexmethsone	Angioedema
+ALEXXDVDDISNDU-JZYPGELDSA-N	CHEBI:17609	UMLS:C0063077	UMLS:C0002994	hydrocortisone acetate,cortisol acetate,hydroxycorticosterone acetate	Angioedema
+VWQWXZAWFPZJDA-CGVGKPPMSA-N	CHEBI:5782	UMLS:C0056387	UMLS:C0002994	hydrocortisone sodium succinate,hydrocortisone succinate,hydrocortisone hemisuccinate	Angioedema
+JYGXADMDTFJGBT-VWUMJDOOSA-N	CHEBI:17650	UMLS:C0020268	UMLS:C0002994	hydrocortisone,17-hydroxycorticosterone,acticort,cetacort,hydracort,hydrasson,hydrocortisyl,cortisol	Angioedema
+CBHCDHNUZWWAPP-UHFFFAOYSA-N	CHEBI:135324	UMLS:C0065954	UMLS:C0002994	mepazine,mepazin,mepazine base,meprazine,mesapin,nothiazine,pecazine,mepazine acetate	Angioedema
+HTMIBDQKFHUPSX-UHFFFAOYSA-N	CHEBI:6823	UMLS:C0066101	UMLS:C0002994	methdilazine,methdilazine hydrochloride,methdilazine HCl	Angioedema
+VHRSUDSXCMQTMA-PJHHCJLFSA-N	CHEBI:6888	UMLS:C0721647	UMLS:C0002994	methylprednisolone,medralone,metilbetasone	Angioedema
+YNDXUCZADRHECN-JNQJZLCISA-N	CHEBI:71418	UMLS:C2608734	UMLS:C0002994	nasacort,triamcinolone acetonide,aristicort,allernaze	Angioedema
+OIGNJSKKLXVSLS-VWUMJDOOSA-N	CHEBI:8378	UMLS:C0032950	UMLS:C0002994	prednisolone,prenolone,deltahydrocortisone,hydroretrocortin,hydroretrocortine,metacortandralone	Angioedema
+XOFYZVNMUHMLCC-ZPOLXVRWSA-N	CHEBI:8382	UMLS:C0032952	UMLS:C0002994	prednisone anhydrous,prednisone,1,2-dehydrocortisone,dehydrocortisone	Angioedema
+ZGUGWUXLJSTTMA-UHFFFAOYSA-N	CHEBI:8459	UMLS:C0033399	UMLS:C0002994	promazine,prazin,prazine,romtiazin,promazine hydrochloride,promazine HCl	Angioedema
+XGMPVBXKDAHORN-RBWIMXSLSA-N	CHEBI:9669	UMLS:C0137442	UMLS:C0002994	triamcinolone diacetate,aristocort diacetate,polcortolon	Angioedema
+GFNANZIMVAIWHM-OBYCQNJPSA-N	CHEBI:9667	UMLS:C0040864	UMLS:C0002994	triamcinolone,triamcinlon,triamcinolon,rodinolone	Angioedema
+KDLRVYVGXIQJDK-AWPVFWJPSA-N	CHEBI:3745	UMLS:C0008947	UMLS:C0014013	clindamycin hydrochloride hydrate,clindamycin,7-Chloro-7-deoxylincomycin,7-Chlorolincomycin,7-Deoxy-7(S)-chlorolincomycin,chlolincocin,clincin,clinimycin,Dalacin C,dalacine,clindamycin hydrochloride,clindamycin HCl	Empyema of pleura
+UFUVLHLTWXBHGZ-MGZQPHGTSA-N	CHEBI:3746	UMLS:C1119917	UMLS:C0014013	clindamycin phosphate,cleocin phosphate,clindagel,clindamycin-2-phosphate	Empyema of pleura
+OHKOGUYZJXTSFX-KZFFXBSXSA-N	CHEBI:9587	UMLS:C0040193	UMLS:C0014013	ticarcillin,ticarcillin disodium,ticarcillin sodium	Empyema of pleura
+JCQLYHFGKNRPGE-RUKGUBFJSA-N	CHEBI:6359	UMLS:C0719221	UMLS:C0019151	lactulose,bifiteral,cephulac,D-Lactulose,isolactose,lactulose hydrate	Hepatic encephalopathy
+057Y626693	CHEBI:7507	UMLS:C0027607	UMLS:C0019151	neomycin sulfate,neomycin,bykomycin,endomixin,fradiomycin sulfate,mycerin sulfate,neomycin sulphate	Hepatic encephalopathy
+C0027607	CHEBI:7507	UMLS:C0027607	UMLS:C0019151	neomycin sulfate,neomycin,bykomycin,endomixin,fradiomycin sulfate,mycerin sulfate,neomycin sulphate	Hepatic encephalopathy
+I16QD7X297	CHEBI:7507	UMLS:C0027607	UMLS:C0019151	neomycin sulfate,neomycin,bykomycin,endomixin,fradiomycin sulfate,mycerin sulfate,neomycin sulphate	Hepatic encephalopathy
+NZCRJKRKKOLAOJ-XRCRFVBUSA-N	CHEBI:75246	UMLS:C0073374	UMLS:C0019151	rifaximine,rifaximin,xifaxan,refaximin	Hepatic encephalopathy
+BJOLKYGKSZKIGU-UHFFFAOYSA-N	CHEBI:4753	UMLS:C0301366	UMLS:C0271093	echothiophate,ecothiopate,ecothiophate,phospholine,echothiophate iodide	Stargardt's disease
+ZKHQWZAMYRWXGA-KQYNXXCUSA-N	CHEBI:15422	UMLS:C0001480	UMLS:C0428974	adenosine triphosphate,ATP,triphosphoric acid adenosine ester,adenosine triphosphate disodium hydrate	Supraventricular arrhythmia
+CJDRUOGAGYHKKD-RQBLFBSQSA-N	CHEBI:28462	UMLS:C0001888	UMLS:C0428974	ajmaline hydrochloride,ajmaline HCl,aritmina,rauverid,ajmaline,(+)-Ajmaline,ajmalin,cardiorythmine,gilurytmal,raugalline	Supraventricular arrhythmia
+NZLBHDRPUJLHCE-UHFFFAOYSA-N	CHEBI:135370	UMLS:C1448442	UMLS:C0428974	aprindine,aprindin,aprinidine,aprindine hydrochloride,aprindine HCl,amidonal,fiboran	Supraventricular arrhythmia
+IXLGLCQSNUMEGQ-PYJPINIGSA-N	CHEBI:135740	UMLS:C0075765	UMLS:C0428974	detajmium,detajmium bitartrate,tachmalcor,detajmium bitartrate hydrate	Supraventricular arrhythmia
+PQXGNJKJMFUPPM-UHFFFAOYSA-N	CHEBI:134732	UMLS:C0059688	UMLS:C0428974	ethacizine,ethacizine hydrochloride,etacizin,ethacizin,ethacizine HCl	Supraventricular arrhythmia

config/DrugCentral_subset/sample_cases.sh

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+#!/bin/bash
+
+# get header
+head -1 ../DrugCentral_creative/data_full.tsv > data.tsv
+
+# sample five random UMLS disease IDs
+awk -F"\t" -v OFS="\t" '{print $4}' ../DrugCentral_creative/data_full.tsv | sort -u | shuf | head -5 | sort > selected_diseases.txt
+
+# retrieve all records for those selected diseases
+sort -t $'\t' -k4 ../DrugCentral_creative/data_full.tsv  > data_full_sorted.tsv
+join -t $'\t' -1 1 -2 4 -o 2.1 2.2 2.3 2.4 2.5 2.6 selected_diseases.txt data_full_sorted.tsv >> data.tsv
+
+# cleanup 
+rm data_full_sorted.tsv 

config/DrugCentral_subset/selected_diseases.txt

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+UMLS:C0002994
+UMLS:C0014013
+UMLS:C0019151
+UMLS:C0271093
+UMLS:C0428974

config/DrugCentral_subset/templates/treats.json

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+{
+  "message": {
+    "query_graph": {
+      "nodes": {
+        "disease_umls": {
+          "ids": [],
+	  "categories": [
+            "biolink:DiseaseOrPhenotypicFeature"
+	  ]
+        },
+        "chebi": {
+          "categories": [
+            "biolink:SmallMolecule"
+          ]
+        }
+      },
+      "edges": {
+        "e01": {
+          "object": "disease_umls",
+          "subject": "chebi",
+          "predicates": [
+            "biolink:treats"
+          ],
+	  "knowledge_type": "inferred"
+        }
+      }
+    }
+  }
+}

config/benchmarks.json

@@ -11,6 +11,12 @@
             "templates": ["treats"]
         }
     ],
+    "DrugCentral_subset": [
+        {
+            "source": "DrugCentral_subset",
+            "templates": ["treats"]
+        }
+    ],
     "DrugCentral_creative": [
         {
             "source": "DrugCentral_creative",