Enables new experiments

This refs bst-mug#107, bst-mug#82 and bst-mug#70.
michelole · Jul 29, 2017 · 074ae82 · 074ae82
1 parent 3417df3
commit 074ae82
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Showing 4 changed files with 188 additions and 2 deletions.
diff --git a/src/main/java/at/medunigraz/imi/bst/trec/Experimenter.java b/src/main/java/at/medunigraz/imi/bst/trec/Experimenter.java
@@ -14,7 +14,9 @@ public static void main(String[] args) {
 		final File boostKeywordsTemplate = new File(
 				RunnerDemo.class.getResource("/templates/boost-keywords.json").getFile());
 		final File relaxedTemplate = new File(RunnerDemo.class.getResource("/templates/relaxed.json").getFile());
-		final File simplifiedTemplate = new File(RunnerDemo.class.getResource("/templates/simplified.json").getFile());
+		final File englishTemplate = new File(RunnerDemo.class.getResource("/templates/english.json").getFile());
+		final File b0Template = new File(RunnerDemo.class.getResource("/templates/b0.json").getFile());
+		final File synonymTemplate = new File(RunnerDemo.class.getResource("/templates/synonym.json").getFile());
 		final Gene.Field[] expandTo = { Gene.Field.SYMBOL, Gene.Field.DESCRIPTION };
 
 		ExperimentsBuilder builder = new ExperimentsBuilder();
@@ -36,7 +38,13 @@ public static void main(String[] args) {
 				.withKeyword(String.valueOf(2)).withTemplate(relaxedTemplate).withWordRemoval();
 
 		builder.newExperiment().withGoldStandard(Experiment.GoldStandard.FINAL).withTarget(Experiment.Task.PUBMED)
-				.withTemplate(simplifiedTemplate).withWordRemoval();
+				.withTemplate(englishTemplate).withWordRemoval();
+
+		builder.newExperiment().withGoldStandard(Experiment.GoldStandard.FINAL).withTarget(Experiment.Task.PUBMED)
+				.withTemplate(b0Template).withWordRemoval();
+
+		builder.newExperiment().withGoldStandard(Experiment.GoldStandard.FINAL).withTarget(Experiment.Task.PUBMED)
+				.withTemplate(synonymTemplate).withWordRemoval();
 
 		Set<Experiment> experiments = builder.build();
 

diff --git a/src/main/resources/templates/b0.json b/src/main/resources/templates/b0.json
@@ -0,0 +1,89 @@
+{
+	"bool": {
+		"must": [
+			{
+				"multi_match": {
+					"query": "{{disease}}",
+					"fields": [
+						"title.b0_bm25^2",
+						"abstract.b0_bm25",
+						"keyword",
+						"meshTags.b0_bm25"
+					],
+					"tie_breaker": 0.3,
+					"type": "best_fields",
+					"boost": 1
+				}
+			},
+			{
+				"multi_match": {
+					"query": "{{gene}}",
+					"fields": [
+						"title.b0_bm25^2",
+						"abstract.b0_bm25",
+						"keyword",
+						"meshTags.b0_bm25"
+					],
+					"tie_breaker": 0.3,
+					"type": "best_fields"
+				}
+			}
+		],
+		"should": [
+			{
+				"match": {
+					"_type": "extra"
+				}
+			},
+			{
+				"bool": {
+					"should": {
+						"multi_match": {
+							"query": "cancer carcinoma tumor",
+							"fields": [
+								"title.b0_bm25^2",
+								"abstract.b0_bm25",
+								"keyword",
+								"meshTags.b0_bm25"
+							],
+							"tie_breaker": 0.3,
+							"type": "best_fields"
+						}
+					}
+				}
+			},
+			{
+				"bool": {
+					"should": {
+						"multi_match": {
+							"query": "gene genotype DNA base",
+							"fields": [
+								"title.b0_bm25^2",
+								"abstract.b0_bm25",
+								"keyword",
+								"meshTags.b0_bm25"
+							],
+							"tie_breaker": 0.3,
+							"type": "best_fields"
+						}
+					}
+				}
+			},
+			{
+				"bool": {
+					"should": {
+						"multi_match": {
+							"query": "therapy treatment prognosis prognostic survival patient resistance recurrence targets malignancy study therapeutical outcome",
+							"fields": [
+								"title.b0_bm25^2",
+								"abstract.b0_bm25"
+							],
+							"tie_breaker": 0.3,
+							"type": "best_fields"
+						}
+					}
+				}
+			}
+		]
+	}
+}
diff --git a/src/main/resources/templates/simplified.json → src/main/resources/templates/english.json b/src/main/resources/templates/simplified.json → src/main/resources/templates/english.json
diff --git a/src/main/resources/templates/synonym.json b/src/main/resources/templates/synonym.json
@@ -0,0 +1,89 @@
+{
+	"bool": {
+		"must": [
+			{
+				"multi_match": {
+					"query": "{{disease}}",
+					"fields": [
+						"title.synonym^2",
+						"abstract.synonym",
+						"keyword",
+						"meshTags.synonym"
+					],
+					"tie_breaker": 0.3,
+					"type": "best_fields",
+					"boost": 1
+				}
+			},
+			{
+				"multi_match": {
+					"query": "{{gene}}",
+					"fields": [
+						"title.synonym^2",
+						"abstract.synonym",
+						"keyword",
+						"meshTags.synonym"
+					],
+					"tie_breaker": 0.3,
+					"type": "best_fields"
+				}
+			}
+		],
+		"should": [
+			{
+				"match": {
+					"_type": "extra"
+				}
+			},
+			{
+				"bool": {
+					"should": {
+						"multi_match": {
+							"query": "cancer carcinoma tumor",
+							"fields": [
+								"title.synonym^2",
+								"abstract.synonym",
+								"keyword",
+								"meshTags.synonym"
+							],
+							"tie_breaker": 0.3,
+							"type": "best_fields"
+						}
+					}
+				}
+			},
+			{
+				"bool": {
+					"should": {
+						"multi_match": {
+							"query": "gene genotype DNA base",
+							"fields": [
+								"title.synonym^2",
+								"abstract.synonym",
+								"keyword",
+								"meshTags.synonym"
+							],
+							"tie_breaker": 0.3,
+							"type": "best_fields"
+						}
+					}
+				}
+			},
+			{
+				"bool": {
+					"should": {
+						"multi_match": {
+							"query": "therapy treatment prognosis prognostic survival patient resistance recurrence targets malignancy study therapeutical outcome",
+							"fields": [
+								"title.synonym^2",
+								"abstract.synonym"
+							],
+							"tie_breaker": 0.3,
+							"type": "best_fields"
+						}
+					}
+				}
+			}
+		]
+	}
+}