Merge branch 'master' of https://github.com/hpi-dhc/trec-pm

README.md

@@ -2,7 +2,7 @@
 
 A repository containing support code and resources initially developed at the [Institute for Medical Informatics, Statistics and Documentation at the Medical University of Graz (Austria)](https://www.medunigraz.at/imi/en/) for participation at the [2017 TREC Precision Medicine Track](http://trec-cds.appspot.com/2017.html). For further information on this track and the final results please check the official [TREC-PM 2017 overview paper](https://trec.nist.gov/pubs/trec26/papers/Overview-PM.pdf). Team name: **imi_mug**
 
-It was then further improved for participation at the [2018 TREC Precision Medicine Track](http://trec-cds.appspot.com/2018.html).
+It was then further improved for participation at the [2018 TREC Precision Medicine Track](http://trec-cds.appspot.com/2018.html), team: **dhc-hpi**. Improvements include: support for subtemplates and the possibility to use disjunctive queries (_dis\_max_) allowing e.g. synonyms and hypernyms to have different weights.
 
 If you use data or code in your work, please cite our [TREC 2017 proceedings paper](https://trec.nist.gov/pubs/trec26/papers/imi_mug-PM.pdf):
 
@@ -14,6 +14,9 @@ Also of interest:
 
 * [Our TREC 2017 presentation slides](https://github.com/bst-mug/trec2017/blob/master/docs/presentation.pdf)
 * [Our TREC 2017 Poster](https://github.com/bst-mug/trec2017/blob/master/docs/poster.pdf)
+* [Our TREC 2018 presentation slides](https://github.com/hpi-dhc/trec-pm/blob/master/docs/2018/presentation.pdf)
+* [Our TREC 2018 Poster](https://github.com/hpi-dhc/trec-pm/blob/master/docs/2018/poster.pdf)
+* [Our TREC 2018 Data Artifacts](https://figshare.com/projects/TREC_PM_2018_Data_hpi-dhc_/56882)
 
 ## Code Dependencies
 
@@ -24,6 +27,34 @@ Also of interest:
 - perl (for `sample_eval` tool)
 - Elasticsearch 5.4.0+
 
+## Some Examples on How to Run Experiments
+
+```
+# All executions should be run where the pom file is, usually the root of the project
+
+# How to run the pubmed experimenter
+# Necessary to define the year and type of gold-standard (for evaluation)
+
+mvn clean install
+mvn exec:java -Dexec.mainClass="at.medunigraz.imi.bst.trec.PubmedExperimenter"
+
+# How to run the clinical trials experimenter
+# Necessary to define the year and type of gold-standard (for evaluation)
+
+mvn clean install
+mvn exec:java -Dexec.mainClass="at.medunigraz.imi.bst.trec.ClinicalTrialsExperimenter"
+
+# How to run the KeywordExperimenter
+# Necessary to define the year and type of gold-standard (for evaluation)
+# For positive booster, in the keyword template leave boost = 1
+# For negative booster, in the keyword template leave boost = -1
+# Also, in the KeywordExperimenter the keywordsSource needs to be specified
+
+mvn clean install
+mvn exec:java -Dexec.mainClass="at.medunigraz.imi.bst.trec.KeywordExperimenter" > out.txt &
+cat out.txt | grep -e "\(^[0-9\.]*\)\(\;.*\)\(with.*\)\(\\[.*\\]\)\(.*\)" | sed -r "s/"\(^[0-9\.]*\)\(\;.*\)\(with.*\)\(\\[.*\\]\)\(.*\)"/\1 \2 \4/" > results.txt
+```
+
 [![Codacy Badge](https://api.codacy.com/project/badge/Grade/00d52e98173d4629be22a4224a48a223)](https://www.codacy.com/app/michelole/trec-pm)
 [![Build Status](https://travis-ci.com/bst-mug/trec-pm.svg?branch=master)](https://travis-ci.com/bst-mug/trec-pm)
 [![Coverage Status](https://coveralls.io/repos/github/bst-mug/trec-pm/badge.svg?branch=master)](https://coveralls.io/github/bst-mug/trec-pm?branch=master)