From cc0dc70dad491747712849955b8e65ae5aac8e4e Mon Sep 17 00:00:00 2001 From: Ferhat Aydin Date: Mon, 28 Nov 2016 22:30:31 +0200 Subject: [PATCH] update readme --- README.md | 7 +++++++ src/main/scala/com/ferhtaydn/biocemid/package.scala | 8 ++++---- 2 files changed, 11 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index 4f33361..254819a 100644 --- a/README.md +++ b/README.md @@ -2,6 +2,13 @@ [BioCreative V - BioC Track (I) - Task 6 Implementation](http://www.biocreative.org/tasks/biocreative-v/track-1-bioc/) +- The code is under [source](src/main/scala/com/ferhtaydn/biocemid/) directory. +- Target experimental methods from PSI-MI ontology are in [methods file](src/main/resources/methods.conf). +- The [main](src/main/scala/com/ferhtaydn/biocemid/Main.scala) class is `com.ferhtaydn.biocemid.Main`. +You may need to modify annotation and evaluation configurations in order to obtain your desired operation. +- All the resources related to word2vecs, raw and annotated articles are located under [files](files/) directory. +- The published data set, consists of 30 articles, is located in [published dataset](files/published_dataset/) directory. + The versions of the libraries which are used: * [Java Version: 1.8.0_91](http://download.oracle.com/otn-pub/java/jdk/8u91-b14/jdk-8u91-macosx-x64.dmg) * [Scala Version: 2.11.8](http://search.maven.org/#search|ga|1|g%3A%22org.scala-lang%22%20AND%20v%3A%222.11.8%22) diff --git a/src/main/scala/com/ferhtaydn/biocemid/package.scala b/src/main/scala/com/ferhtaydn/biocemid/package.scala index e9c8861..d28d2c4 100644 --- a/src/main/scala/com/ferhtaydn/biocemid/package.scala +++ b/src/main/scala/com/ferhtaydn/biocemid/package.scala @@ -122,15 +122,15 @@ package object biocemid { } } - // gold_set_13, gold_set_17 and gold_set_30 files contains the articles from $manualAnnotationStatistics - val goldResultDirectory = "files/gold_set_13" + // gold_set_13, gold_set_17 and gold_set_30 files contains the articles from $publishedDataSet + val goldResultDirectory = "files/gold_set_17" val publishedDataSet = "files/published_dataset" - val word2vecResultDirectory = "files/results/word2vec/pure-baseline/config_3b_13_articles_genia0_ino1" + val word2vecResultDirectory = "files/results/word2vec/pure-baseline/config_3b_17_articles_genia0_ino1" val tfrfResultDirectory = "files/results/tfrf/pure-baseline/manual/config_1_17_articles" val pureBaselineResultDirectory = "files/results/pure-baseline/pure-baseline_17_articles_genia0_ino1" - val rawDirectory = "files/manual_annotation_raw_13" + val rawDirectory = "files/manual_annotation_raw_17" val oaWord2vecsDirectory = "files/oa_word2vecs" val oaWord2vecsPureBaselineDirectory = "files/oa_word2vecs_pure_baseline"