From 8f88c2d35bf18ab8eca544ccbf6bd38801bf1af0 Mon Sep 17 00:00:00 2001
From: "louise.deleger" <louise.deleger@inra.fr>
Date: Thu, 25 Nov 2021 15:49:13 +0100
Subject: [PATCH 1/6] Removed &ontobiotope; entity

---
 plans/tomap-habitats.plan             | 22 +++++++++++-----------
 plans/tomap-microbial-phenotypes.plan | 26 +++++++++++++-------------
 plans/use-extraction.plan             |  4 ++--
 process_PubMed_corpus.snakefile       | 16 ++++++++++++----
 4 files changed, 38 insertions(+), 30 deletions(-)

diff --git a/plans/tomap-habitats.plan b/plans/tomap-habitats.plan
index 46bbb98..205a5fa 100644
--- a/plans/tomap-habitats.plan
+++ b/plans/tomap-habitats.plan
@@ -7,14 +7,14 @@
     <targetLayerName>habitats</targetLayerName>
     <conceptFeature>concept-id</conceptFeature>
     <explanationFeaturePrefix>explain_</explanationFeaturePrefix>
-    <tomapClassifier empty-words="ancillaries/stopwords_EN.ttg" graylist="ancillaries/graylist_extended.heads" whole-proxy-distance="false">&ontobiotope;-Habitat.tomap</tomapClassifier>
+    <tomapClassifier empty-words="ancillaries/stopwords_EN.ttg" graylist="ancillaries/graylist_extended.heads" whole-proxy-distance="false">ancillaries/BioNLP-OST+EnovFood-Habitat.tomap</tomapClassifier>
     <lemmaKeys/>
     <subject feature="lemma" layer="words"/>
     <scoreFeature>score</scoreFeature>
   </tomap>
 
   <concept-names class="OBOMapper">
-    <oboFiles>&ontobiotope;-Habitat.obo</oboFiles>
+    <oboFiles>ancillaries/BioNLP-OST+EnovFood-Habitat.obo</oboFiles>
     <idKeys/>
     <target>documents.sections.layer:habitats</target>
     <form>@concept-id</form>
@@ -30,14 +30,14 @@
       <targetLayerName>habitats2</targetLayerName>
       <conceptFeature>concept-id</conceptFeature>
       <explanationFeaturePrefix>explain_</explanationFeaturePrefix>
-      <tomapClassifier empty-words="ancillaries/stopwords_EN.ttg" graylist="ancillaries/graylist_extended.heads" whole-proxy-distance="false">&ontobiotope;-Habitat.tomap</tomapClassifier>
+      <tomapClassifier empty-words="ancillaries/stopwords_EN.ttg" graylist="ancillaries/graylist_extended.heads" whole-proxy-distance="false">ancillaries/BioNLP-OST+EnovFood-Habitat.tomap</tomapClassifier>
       <lemmaKeys/>
       <subject feature="lemma2" layer="words"/>
       <scoreFeature>score</scoreFeature>
     </tomap>
 
     <concept-names class="OBOMapper">
-      <oboFiles>&ontobiotope;-Habitat.obo</oboFiles>
+      <oboFiles>ancillaries/BioNLP-OST+EnovFood-Habitat.obo</oboFiles>
       <idKeys/>
       <target>documents.sections.layer:habitats2</target>
       <form>@concept-id</form>
@@ -62,13 +62,13 @@
       <targetLayerName>habitats3</targetLayerName>
       <conceptFeature>concept-id</conceptFeature>
       <explanationFeaturePrefix>explain_</explanationFeaturePrefix>
-      <tomapClassifier empty-words="ancillaries/stopwords_EN.ttg" graylist="ancillaries/graylist_extended.heads" whole-proxy-distance="false">&ontobiotope;-Habitat.tomap</tomapClassifier>
+      <tomapClassifier empty-words="ancillaries/stopwords_EN.ttg" graylist="ancillaries/graylist_extended.heads" whole-proxy-distance="false">ancillaries/BioNLP-OST+EnovFood-Habitat.tomap</tomapClassifier>
       <subject feature="lemma" layer="words"/>
       <scoreFeature>score</scoreFeature>
     </tomap>
 
     <concept-names class="OBOMapper">
-      <oboFiles>&ontobiotope;-Habitat.obo</oboFiles>
+      <oboFiles>ancillaries/BioNLP-OST+EnovFood-Habitat.obo</oboFiles>
       <idKeys/>
       <target>documents.sections.layer:habitats3</target>
       <form>@concept-id</form>
@@ -93,14 +93,14 @@
       <targetLayerName>habitats4</targetLayerName>
       <conceptFeature>concept-id</conceptFeature>
       <explanationFeaturePrefix>explain_</explanationFeaturePrefix>
-      <tomapClassifier empty-words="ancillaries/stopwords_EN.ttg" graylist="ancillaries/graylist_extended.heads" whole-proxy-distance="false">&ontobiotope;-Habitat.tomap</tomapClassifier>
+      <tomapClassifier empty-words="ancillaries/stopwords_EN.ttg" graylist="ancillaries/graylist_extended.heads" whole-proxy-distance="false">ancillaries/BioNLP-OST+EnovFood-Habitat.tomap</tomapClassifier>
       <lemmaKeys/>
       <subject feature="variant" layer="words"/>
       <scoreFeature>score</scoreFeature>
     </tomap>
 
     <concept-names class="OBOMapper">
-      <oboFiles>&ontobiotope;-Habitat.obo</oboFiles>
+      <oboFiles>ancillaries/BioNLP-OST+EnovFood-Habitat.obo</oboFiles>
       <idKeys/>
       <target>documents.sections.layer:habitats4</target>
       <form>@concept-id</form>
@@ -125,13 +125,13 @@
       <targetLayerName>habitats5</targetLayerName>
       <conceptFeature>concept-id</conceptFeature>
       <explanationFeaturePrefix>explain_</explanationFeaturePrefix>
-      <tomapClassifier empty-words="ancillaries/stopwords_EN.ttg" graylist="ancillaries/graylist_extended.heads" whole-proxy-distance="false">&ontobiotope;-Habitat.tomap</tomapClassifier>
+      <tomapClassifier empty-words="ancillaries/stopwords_EN.ttg" graylist="ancillaries/graylist_extended.heads" whole-proxy-distance="false">ancillaries/BioNLP-OST+EnovFood-Habitat.tomap</tomapClassifier>
       <subject feature="form" layer="words"/>
       <scoreFeature>score</scoreFeature>
     </tomap>
 
     <concept-names class="OBOMapper">
-      <oboFiles>&ontobiotope;-Habitat.obo</oboFiles>
+      <oboFiles>ancillaries/BioNLP-OST+EnovFood-Habitat.obo</oboFiles>
       <idKeys/>
       <target>documents.sections.layer:habitats5</target>
       <form>@concept-id</form>
@@ -714,7 +714,7 @@
 
 <!-- Add concept-path in case some are missing -->
     <concept-path class="OBOMapper">
-      <oboFiles>&ontobiotope;-Habitat.obo</oboFiles>
+      <oboFiles>ancillaries/BioNLP-OST+EnovFood-Habitat.obo</oboFiles>
       <idKeys/>
       <target>documents.sections.layer:habitats</target>
       <form>@concept-id</form>
diff --git a/plans/tomap-microbial-phenotypes.plan b/plans/tomap-microbial-phenotypes.plan
index 1748164..275e64c 100644
--- a/plans/tomap-microbial-phenotypes.plan
+++ b/plans/tomap-microbial-phenotypes.plan
@@ -6,14 +6,14 @@
     <targetLayerName>phenotypes</targetLayerName>
     <conceptFeature>concept-id</conceptFeature>
     <explanationFeaturePrefix>explain_</explanationFeaturePrefix>
-    <tomapClassifier empty-words="ancillaries/stopwords_EN.ttg" whole-proxy-distance="false">&ontobiotope;-Phenotype.tomap</tomapClassifier>
+    <tomapClassifier empty-words="ancillaries/stopwords_EN.ttg" whole-proxy-distance="false">ancillaries/BioNLP-OST+EnovFood-Phenotype.tomap</tomapClassifier>
     <lemmaKeys/>
     <subject feature="lemma" layer="words"/>
     <scoreFeature>score</scoreFeature>
   </tomap>
 
   <concept-names class="OBOMapper">
-    <oboFiles>&ontobiotope;-Phenotype.obo</oboFiles>
+    <oboFiles>ancillaries/BioNLP-OST+EnovFood-Phenotype.obo</oboFiles>
     <idKeys/>
     <target>documents.sections.layer:phenotypes</target>
     <form>@concept-id</form>
@@ -29,14 +29,14 @@
       <targetLayerName>phenotypes2</targetLayerName>
       <conceptFeature>concept-id</conceptFeature>
       <explanationFeaturePrefix>explain_</explanationFeaturePrefix>
-      <tomapClassifier empty-words="ancillaries/stopwords_EN.ttg" whole-proxy-distance="false">&ontobiotope;-Phenotype.tomap</tomapClassifier>
+      <tomapClassifier empty-words="ancillaries/stopwords_EN.ttg" whole-proxy-distance="false">ancillaries/BioNLP-OST+EnovFood-Phenotype.tomap</tomapClassifier>
       <lemmaKeys/>
       <subject feature="lemma2" layer="words"/>
       <scoreFeature>score</scoreFeature>
     </tomap>
 
     <concept-names class="OBOMapper">
-      <oboFiles>&ontobiotope;-Phenotype.obo</oboFiles>
+      <oboFiles>ancillaries/BioNLP-OST+EnovFood-Phenotype.obo</oboFiles>
       <idKeys/>
       <target>documents.sections.layer:phenotypes2</target>
       <form>@concept-id</form>
@@ -61,13 +61,13 @@
       <targetLayerName>phenotypes3</targetLayerName>
       <conceptFeature>concept-id</conceptFeature>
       <explanationFeaturePrefix>explain_</explanationFeaturePrefix>
-      <tomapClassifier empty-words="ancillaries/stopwords_EN.ttg" whole-proxy-distance="false">&ontobiotope;-Phenotype.tomap</tomapClassifier>
+      <tomapClassifier empty-words="ancillaries/stopwords_EN.ttg" whole-proxy-distance="false">ancillaries/BioNLP-OST+EnovFood-Phenotype.tomap</tomapClassifier>
       <subject feature="lemma" layer="words"/>
       <scoreFeature>score</scoreFeature>
     </tomap>
 
     <concept-names class="OBOMapper">
-      <oboFiles>&ontobiotope;-Phenotype.obo</oboFiles>
+      <oboFiles>ancillaries/BioNLP-OST+EnovFood-Phenotype.obo</oboFiles>
       <idKeys/>
       <target>documents.sections.layer:phenotypes3</target>
       <form>@concept-id</form>
@@ -93,14 +93,14 @@
       <targetLayerName>phenotypes4</targetLayerName>
       <conceptFeature>concept-id</conceptFeature>
       <explanationFeaturePrefix>explain_</explanationFeaturePrefix>
-      <tomapClassifier empty-words="ancillaries/stopwords_EN.ttg" whole-proxy-distance="false">&ontobiotope;-Phenotype.tomap</tomapClassifier>
+      <tomapClassifier empty-words="ancillaries/stopwords_EN.ttg" whole-proxy-distance="false">ancillaries/BioNLP-OST+EnovFood-Phenotype.tomap</tomapClassifier>
       <lemmaKeys/>
       <subject feature="variant" layer="words"/>
       <scoreFeature>score</scoreFeature>
     </tomap>
 
     <concept-names class="OBOMapper">
-      <oboFiles>&ontobiotope;-Phenotype.obo</oboFiles>
+      <oboFiles>ancillaries/BioNLP-OST+EnovFood-Phenotype.obo</oboFiles>
       <idKeys/>
       <target>documents.sections.layer:phenotypes4</target>
       <form>@concept-id</form>
@@ -125,13 +125,13 @@
       <targetLayerName>phenotypes5</targetLayerName>
       <conceptFeature>concept-id</conceptFeature>
       <explanationFeaturePrefix>explain_</explanationFeaturePrefix>
-      <tomapClassifier empty-words="ancillaries/stopwords_EN.ttg" whole-proxy-distance="false">&ontobiotope;-Phenotype.tomap</tomapClassifier>
+      <tomapClassifier empty-words="ancillaries/stopwords_EN.ttg" whole-proxy-distance="false">ancillaries/BioNLP-OST+EnovFood-Phenotype.tomap</tomapClassifier>
       <subject feature="form" layer="words"/>
       <scoreFeature>score</scoreFeature>
     </tomap>
 
     <concept-names class="OBOMapper">
-      <oboFiles>&ontobiotope;-Phenotype.obo</oboFiles>
+      <oboFiles>ancillaries/BioNLP-OST+EnovFood-Phenotype.obo</oboFiles>
       <idKeys/>
       <target>documents.sections.layer:phenotypes5</target>
       <form>@concept-id</form>
@@ -394,7 +394,7 @@
   <!--    <idFeature>molecule-id</idFeature> -->
   <!--    <nameFeature>molecule-name</nameFeature> -->
   <!--    <pathFeature>molecule-path</pathFeature> -->
-  <!--    <oboFiles>&ontobiotope;-Molecule.obo</oboFiles> -->
+  <!--    <oboFiles>ancillaries/BioNLP-OST+EnovFood-Molecule.obo</oboFiles> -->
   <!--    <subject feature="lemma" layer="words"/> -->
   <!--    <targetLayerName>molecules</targetLayerName> -->
   <!--  </molecule-projection-on-lemmas> -->
@@ -404,7 +404,7 @@
   <!--    <idFeature>molecule-id</idFeature> -->
   <!--    <nameFeature>molecule-name</nameFeature> -->
   <!--    <pathFeature>molecule-path</pathFeature> -->
-  <!--    <oboFiles>&ontobiotope;-Molecule.obo</oboFiles> -->
+  <!--    <oboFiles>ancillaries/BioNLP-OST+EnovFood-Molecule.obo</oboFiles> -->
   <!--    <subject feature="form" layer="words"/> -->
   <!--    <targetLayerName>molecules2</targetLayerName> -->
   <!--  </molecule-projection-on-words> -->
@@ -469,7 +469,7 @@
 
 <!-- Add concept-path in case some are missing -->
     <concept-path class="OBOMapper">
-      <oboFiles>&ontobiotope;-Phenotype.obo</oboFiles>
+      <oboFiles>ancillaries/BioNLP-OST+EnovFood-Phenotype.obo</oboFiles>
       <idKeys/>
       <target>documents.sections.layer:phenotypes</target>
       <form>@concept-id</form>
diff --git a/plans/use-extraction.plan b/plans/use-extraction.plan
index 5d12302..87195d8 100644
--- a/plans/use-extraction.plan
+++ b/plans/use-extraction.plan
@@ -2,7 +2,7 @@
 <alvisnlp-plan id="Use-extraction">
 
   <exact-match class="OBOProjector">
-    <oboFiles>&ontobiotope-use;.obo</oboFiles>
+    <oboFiles>ancillaries/Use_V2.obo</oboFiles>
     <targetLayerName>uses</targetLayerName>
     <subject feature="form" layer="words"/>
     <idFeature>concept-id</idFeature>
@@ -12,7 +12,7 @@
   </exact-match>
 
   <exact-match-2 class="OBOProjector">
-    <oboFiles>&ontobiotope-use;.obo</oboFiles>
+    <oboFiles>ancillaries/Use_V2.obo</oboFiles>
     <targetLayerName>uses2</targetLayerName>
     <subject feature="lemma" layer="words"/>
     <idFeature>concept-id</idFeature>
diff --git a/process_PubMed_corpus.snakefile b/process_PubMed_corpus.snakefile
index 7fd42f3..2d25617 100644
--- a/process_PubMed_corpus.snakefile
+++ b/process_PubMed_corpus.snakefile
@@ -47,8 +47,13 @@ rule run_pubmed_entities:
 		batch="{B}",
 		corpus='pubmed',
                 inhibitSyntax='inhibit-syntax',
-		onto='ancillaries/BioNLP-OST+EnovFood',
-                ontobiotopeUse='ancillaries/Use_V2',
+		onto_habitat='ancillaries/BioNLP-OST+EnovFood-Habitat.obo',
+        tomap_habitat='ancillaries/BioNLP-OST+EnovFood-Habitat.tomap',
+        onto_pheno='ancillaries/BioNLP-OST+EnovFood-Phenotype.obo',
+        tomap_pheno='ancillaries/BioNLP-OST+EnovFood-Phenotype.tomap',
+        graylist='ancillaries/graylist_extended.heads',
+		emptywords='ancillaries/stopwords_EN.ttg',
+        ontobiotopeUse='ancillaries/Use_V2.obo',
 		plan='plans/entities.plan',
 		dir='corpora/pubmed/batches/{B}/',
 		taxid_microorganisms='ancillaries/extended-microorganisms-taxonomy/taxid_microorganisms.txt',
@@ -65,8 +70,11 @@ rule run_pubmed_entities:
 		-environmentEntities \
 		-entity corpus {params.corpus} \
 		-feat inhibit-syntax {params.inhibitSyntax} \
-		-entity ontobiotope {params.onto} \
-		-entity ontobiotope-use {params.ontobiotopeUse} \
+        -alias ontobiotope-habitat {params.onto_habitat} \
+        -xalias '<ontobiotope-tomap-habitat empty-words="{params.emptywords}" graylist="{params.graylist}" whole-proxy-distance="false">{params.tomap_habitat}</ontobiotope-tomap-habitat>' \
+        -alias ontobiotope-phenotypes {params.onto_pheno} \
+        -xalias '<ontobiotope-tomap-phenotypes empty-words="{params.emptywords}" whole-proxy-distance="false">{params.tomap_pheno}</ontobiotope-tomap-phenotypes>' \
+		-alias ontobiotope-use {params.ontobiotopeUse} \
 		-entity batch {params.batch} \
 		-alias taxid_microorganisms {params.taxid_microorganisms} \
 		-alias taxa+id_full {params.taxa_id_full} \
-- 
GitLab


From cc295712a16652db30acd30e64abe3cdc9061445 Mon Sep 17 00:00:00 2001
From: "louise.deleger" <louise.deleger@inra.fr>
Date: Fri, 26 Nov 2021 14:29:24 +0100
Subject: [PATCH 2/6] removed &corpus; and &batch; entities

---
 plans/entities.plan                   | 141 +++++++++++++++++---------
 plans/tomap-habitats.plan             |  24 ++---
 plans/tomap-microbial-phenotypes.plan |  12 +--
 process_PubMed_corpus.snakefile       |  14 ++-
 4 files changed, 122 insertions(+), 69 deletions(-)

diff --git a/plans/entities.plan b/plans/entities.plan
index f98ea1c..b32f10c 100644
--- a/plans/entities.plan
+++ b/plans/entities.plan
@@ -17,6 +17,10 @@
   <param name="input-xslt">
     <alias module="read.pubmed" param="xslTransform"/>
   </param>
+    
+  <param name="batch">
+    <alias module="read.pubmed" param="constantDocumentFeatures"/>
+  </param>
 
   <param name="outputDir">
     <alias module="output.doc-mesh" param="outDir"/>
@@ -37,6 +41,23 @@
     <alias module="words" param="outDir"/>
     <alias module="success" param="outDir"/>
   </param>
+    
+  <param name="bionlp-output">
+    <alias module="bionlp-st-a2.microorganisms" param="outDir"/>
+    <alias module="bionlp-st-a2.habitats" param="outDir"/>
+    <alias module="bionlp-st-a2.phenotypes" param="outDir"/>
+    <alias module="bionlp-st-a2.obt" param="outDir"/>
+    <alias module="bionlp-st-a2.taxid" param="outDir"/>
+    <alias module="bionlp-st-a2.lives-in" param="outDir"/>
+    <alias module="bionlp-st-a2.exhibits" param="outDir"/>
+  </param>
+    
+  <param name="adbIndex">
+    <alias module="adb.index" param="indexDir"/>
+  </param>
+  <param name="index">
+    <alias module="index" param="indexDir"/>
+  </param>
 
   <param name="doc-mesh">
     <alias module="output.doc-mesh" param="fileName"/>
@@ -140,7 +161,28 @@
     <alias module="habitats.tomap-habitats.map-living-organisms" param="mappingFile"/>
   </param>
 
-
+  <!-- yatea -->
+  <param name="yatea-file">
+    <alias module="term-extraction.yatea" param="xmlTermsFile"/>
+  </param>
+  <param name="yatea-var-file">
+    <alias module="term-extraction.yatea-var" param="xmlTermsFile"/>
+  </param>
+  <param name="yatea-tomap">
+    <alias module="habitats.tomap-habitats.tomap" param="yateaFile"/>
+    <alias module="habitats.tomap-habitats.tomap-on-alternative-lemmas.tomap" param="yateaFile"/>
+    <alias module="habitats.tomap-habitats.tomap-no-lemmakeys.tomap" param="yateaFile"/>
+    <alias module="habitats.tomap-habitats.tomap-no-lemmakeys-word-form.tomap" param="yateaFile"/>
+    <alias module="tomap-phenotypes.tomap" param="yateaFile"/>
+    <alias module="tomap-phenotypes.tomap-on-alternative-lemmas.tomap" param="yateaFile"/>
+    <alias module="tomap-phenotypes.tomap-no-lemmakeys.tomap" param="yateaFile"/>
+    <alias module="tomap-phenotypes.tomap-no-lemmakeys-word-form.tomap" param="yateaFile"/>
+  </param>
+  <param name="yatea-var-tomap">
+    <alias module="habitats.tomap-habitats.tomap-on-variants.tomap" param="yateaFile"/>
+    <alias module="tomap-phenotypes.tomap-on-variants.tomap" param="yateaFile"/>
+  </param>
+    
   <!-- habitats-->
   <param name="ontobiotope-habitat">
     <alias module="habitats.tomap-habitats.concept-names" param="oboFiles"/>
@@ -195,14 +237,15 @@
 
   <read>
     <pubmed class="XMLReader">
-      <sourcePath>corpora/&corpus;/batches/&batch;/batch.xml</sourcePath>
-      <xslTransform>ancillaries/&corpus;-pubmed2alvisnlp.xslt</xslTransform>
+      <sourcePath>corpora/pubmed/batches/0000/batch.xml</sourcePath>
+      <xslTransform>ancillaries/microbes-2019-pubmed2alvisnlp.xslt</xslTransform>
+      <constantDocumentFeatures>batch=0000</constantDocumentFeatures>
     </pubmed>
 
     <bionlp-st class="BioNLPSTReader">
       <active>true</active>
       <sectionName>abstract</sectionName>
-      <textDir>corpora/&corpus;/batches/&batch;/bionlp-st</textDir>
+      <textDir>corpora/BioNLP-OST-2019/batches/BB19-kb+ner/bionlp-st</textDir>
     </bionlp-st>
   </read>
 
@@ -404,7 +447,7 @@
     <!-- Run Yatea term extractor -->
     <yatea class="YateaExtractor">
       <sectionFilter>@name == "title" or @name == "abstract"</sectionFilter>
-      <xmlTermsFile>corpora/&corpus;/batches/&batch;/yatea/candidates.xml</xmlTermsFile>
+      <xmlTermsFile>yatea/candidates.xml</xmlTermsFile>
       <posFeature>tt_pos</posFeature>
       <configDir>ancillaries/YaTeA/config-habitats</configDir>
       <localeDir>ancillaries/YaTeA/locale</localeDir>
@@ -415,7 +458,7 @@
     <!-- Run Yatea term extractor on variants -->
     <yatea-var class="YateaExtractor">
       <sectionFilter>@name == "title" or @name == "abstract"</sectionFilter>
-      <xmlTermsFile>corpora/&corpus;/batches/&batch;/yatea-var/candidates.xml</xmlTermsFile>
+      <xmlTermsFile>yatea-var/candidates.xml</xmlTermsFile>
       <posFeature>tt_pos</posFeature>
       <lemmaFeature>variant</lemmaFeature>
       <configDir>ancillaries/YaTeA/config-habitats</configDir>
@@ -669,12 +712,12 @@
 
   <output>
     <doc-mesh class="TabularExport">
-      <outDir>corpora/&corpus;/batches/&batch;</outDir>
+      <outDir>.</outDir>
       <files>$</files>
       <fileName>"doc-mesh.txt"</fileName>
       <lines>documents.sections:mesh</lines>
       <columns separator=";">
-	"&batch;";
+	document.@batch;
 	document.@id;
 	@UI;
 	@mesh-name;
@@ -683,12 +726,12 @@
     </doc-mesh>
 
     <taxa class="TabularExport">
-      <outDir>corpora/&corpus;/batches/&batch;</outDir>
+      <outDir>.</outDir>
       <files>$</files>
       <fileName>"taxa.txt"</fileName>
       <lines>documents.sections.layer:taxa</lines>
       <columns separator=";">
-	"&batch;";
+	document.@batch;
 	section.document.@id;
 	section.@name;
 	start ^ "-" ^ end;
@@ -702,12 +745,12 @@
     </taxa>
 
     <microorganisms class="TabularExport">
-      <outDir>corpora/&corpus;/batches/&batch;</outDir>
+      <outDir>.</outDir>
       <files>$</files>
       <fileName>"microorganisms.txt"</fileName>
       <lines>documents.sections.layer:microorganism</lines>
       <columns separator=";">
-	"&batch;";
+	document.@batch;
 	section.document.@id;
 	section.@name;
 	start ^ "-" ^ end;
@@ -721,12 +764,12 @@
     </microorganisms>
 
     <microorganisms-short class="TabularExport">
-      <outDir>corpora/&corpus;/batches/&batch;</outDir>
+      <outDir>.</outDir>
       <files>$</files>
       <fileName>"microorganisms-short.txt"</fileName>
       <lines>documents.sections.layer:microorganism[outside:words and not @form == outside:words.@form]</lines>
       <columns separator=";">
-	"&batch;";
+	document.@batch;
 	section.document.@id;
 	section.@name;
 	start ^ "-" ^ end;
@@ -740,12 +783,12 @@
     </microorganisms-short>
 
     <bacteria class="TabularExport">
-      <outDir>corpora/&corpus;/batches/&batch;</outDir>
+      <outDir>.</outDir>
       <files>$</files>
       <fileName>"bacteria.txt"</fileName>
       <lines>documents.sections.layer:bacteria</lines>
       <columns separator=";">
-	"&batch;";
+	document.@batch;
 	section.document.@id;
 	section.@name;
 	start ^ "-" ^ end;
@@ -759,12 +802,12 @@
     </bacteria>
 
     <habitats class="TabularExport">
-      <outDir>corpora/&corpus;/batches/&batch;</outDir>
+      <outDir>.</outDir>
       <files>$</files>
       <fileName>"habitats.txt"</fileName>
       <lines>documents.sections.layer:habitats</lines>
       <columns separator=";">
-	"&batch;";
+	document.@batch;
 	section.document.@id;
 	section.@name;
 	start ^ "-" ^ end;
@@ -780,12 +823,12 @@
     </habitats>
 
     <phenotypes class="TabularExport">
-      <outDir>corpora/&corpus;/batches/&batch;</outDir>
+      <outDir>.</outDir>
       <files>$</files>
       <fileName>"phenotypes.txt"</fileName>
       <lines>documents.sections.layer:phenotypes</lines>
       <columns separator=";">
-	"&batch;";
+	document.@batch;
 	section.document.@id;
 	section.@name;
 	start ^ "-" ^ end;
@@ -801,12 +844,12 @@
     </phenotypes>
 
     <uses class="TabularExport">
-      <outDir>corpora/&corpus;/batches/&batch;</outDir>
+      <outDir>.</outDir>
       <files>$</files>
       <fileName>"uses.txt"</fileName>
       <lines>documents.sections.layer:uses</lines>
       <columns separator=";">
-	"&batch;";
+	document.@batch;
 	section.document.@id;
 	section.@name;
 	start ^ "-" ^ end;
@@ -822,12 +865,12 @@
     </uses>
 
     <geo class="TabularExport">
-      <outDir>corpora/&corpus;/batches/&batch;</outDir>
+      <outDir>.</outDir>
       <files>$</files>
       <fileName>"geo.txt"</fileName>
       <lines>documents.sections.layer:Geographical</lines>
       <columns separator=";">
-	"&batch;";
+	document.@batch;
 	section.document.@id;
 	section.@name;
 	start ^ "-" ^ end;
@@ -837,12 +880,12 @@
     </geo>
 
     <relations class="TabularExport">
-      <outDir>corpora/&corpus;/batches/&batch;</outDir>
+      <outDir>.</outDir>
       <files>$</files>
       <fileName>"relations.txt"</fileName>
       <lines>documents.sections.relations:CooccurrenceLocalization.tuples</lines>
       <columns separator=";">
-	"&batch;";
+	document.@batch;
 	section.document.@id;
 	section.@name;
 	args:Bacterium.@taxid;
@@ -860,12 +903,12 @@
     </relations>
 
     <relations-pheno class="TabularExport">
-      <outDir>corpora/&corpus;/batches/&batch;</outDir>
+      <outDir>.</outDir>
       <files>$</files>
       <fileName>"phenotype-relations.txt"</fileName>
       <lines>documents.sections.relations:PhenotypeRelation.tuples</lines>
       <columns separator=";">
-	"&batch;";
+	document.@batch;
 	section.document.@id;
 	section.@name;
 	args:Microorganism.@taxid;
@@ -883,12 +926,12 @@
     </relations-pheno>
 
     <relations-use class="TabularExport">
-      <outDir>corpora/&corpus;/batches/&batch;</outDir>
+      <outDir>.</outDir>
       <files>$</files>
       <fileName>"uses-relations.txt"</fileName>
       <lines>documents.sections.relations:UseRelation.tuples</lines>
       <columns separator=";">
-	"&batch;";
+	document.@batch;
 	section.document.@id;
 	section.@name;
 	args:Microorganism.@taxid;
@@ -974,7 +1017,7 @@
       </index-sentences>
 
       <sentences class="TabularExport">
-	<outDir>corpora/&corpus;/batches/&batch;</outDir>
+	<outDir>.</outDir>
 	<files>$</files>
 	<fileName>"sentences.txt"</fileName>
 	<lines>documents.sections.layer:sentences[@name != "author"]</lines>
@@ -995,7 +1038,7 @@
       </sentences>
 
       <anaphora class="TabularExport">
-	<outDir>corpora/&corpus;/batches/&batch;</outDir>
+	<outDir>.</outDir>
 	<files>$</files>
 	<fileName>"anaphora.txt"</fileName>
 	<lines>documents.sections.relations:coreferences.tuples[args:Ante]</lines>
@@ -1028,7 +1071,7 @@
       </anaphora>
 
       <dependencies class="TabularExport">
-	<outDir>corpora/&corpus;/batches/&batch;</outDir>
+	<outDir>.</outDir>
 	<files>$</files>
 	<fileName>"dependencies.txt"</fileName>
 	<lines>documents.sections[@name != "author"].relations:dependencies.tuples</lines>
@@ -1247,11 +1290,11 @@
     </habitat-ancestors>
     
     <index class="AlvisDBIndexer">
-      <indexDir>corpora/&corpus;/batches/&batch;/adb</indexDir>
+      <indexDir>.</indexDir>
       <elements>
 	<relations>
 	  <items>documents.sections.relations:CooccurrenceLocalization.tuples[args:Bacterium[@bacteria == "true"]]</items>
-	  <id>"&batch;_" ^ id:unique</id>
+	  <id>section.document.@batch ^ id:unique</id>
 	  <name>"Localization"</name>
 	  <type>"localization"</type>
 	  <args>args:Bacterium|args:Localization</args>
@@ -1267,7 +1310,7 @@
   </adb>
 
   <index class="AlvisIRIndexer">
-    <indexDir>corpora/&corpus;/batches/&batch;/index</indexDir>
+    <indexDir>.</indexDir>
     <tokenPositionGap>9216</tokenPositionGap>
     <fieldNames>title,abstract,author,full-author,pmid,year,journal,mesh,url</fieldNames>
     <relations>
@@ -1404,8 +1447,8 @@
     </documents>
   </index>
 
-  <index-food class="AlvisIRIndexer">
-    <indexDir>corpora/&corpus;/batches/&batch;/index-food</indexDir>
+<!--  <index-food class="AlvisIRIndexer">
+    <indexDir>.</indexDir>
     <tokenPositionGap>9216</tokenPositionGap>
     <fieldNames>title,abstract,author,full-author,pmid,year,journal,mesh,url</fieldNames>
     <relations>
@@ -1538,7 +1581,7 @@
 	<keyword>document.@url</keyword>
       </fields>
     </documents>
-  </index-food>
+  </index-food>-->
 
   <!-- HTML visualization -->
   <add-feature class="Action">
@@ -1563,14 +1606,14 @@
   </add-feature3>
   <html class="QuickHTML">
     <active>false</active>
-    <outDir>corpora/&corpus;/batches/&batch;/html</outDir>
+    <outDir>./html</outDir>
     <classFeature>ne-type</classFeature>
     <layers>phenotypes,microorganism,habitats</layers>
     <colors>#99cc00,#ffcc99,#ffd333,#ffd666</colors>
   </html>
 
   <words class="TabularExport">
-    <outDir>corpora/&corpus;/batches/&batch;</outDir>
+    <outDir>.</outDir>
     <files>$</files>
     <fileName>"words.txt"</fileName>
     <lines>documents.sections[@name == "title" or @name == "abstract"].layer:words</lines>
@@ -1582,7 +1625,7 @@
 
   <bionlp-st-a2>
     <habitats class="TabularExport">
-      <outDir>corpora/&corpus;/batches/&batch;/a2</outDir>
+      <outDir>.</outDir>
       <files>documents.sections</files>
       <fileName>document.@id ^ ".a2"</fileName>
       <lines>layer:habitats</lines>
@@ -1595,7 +1638,7 @@
     
     <phenotypes class="TabularExport">
       <append/>
-      <outDir>corpora/&corpus;/batches/&batch;/a2</outDir>
+      <outDir>.</outDir>
       <files>documents.sections</files>
       <fileName>document.@id ^ ".a2"</fileName>
       <lines>layer:phenotypes</lines>
@@ -1608,7 +1651,7 @@
     
     <microorganisms class="TabularExport">
       <append/>
-      <outDir>corpora/&corpus;/batches/&batch;/a2</outDir>
+      <outDir>.</outDir>
       <files>documents.sections</files>
       <fileName>document.@id ^ ".a2"</fileName>
       <lines>layer:microorganism</lines>
@@ -1621,7 +1664,7 @@
 
     <obt class="TabularExport">
       <append/>
-      <outDir>corpora/&corpus;/batches/&batch;/a2</outDir>
+      <outDir>.</outDir>
       <files>documents.sections</files>
       <fileName>document.@id ^ ".a2"</fileName>
       <lines>layer:habitats|layer:phenotypes</lines>
@@ -1633,7 +1676,7 @@
 
     <taxid class="TabularExport">
       <append/>
-      <outDir>corpora/&corpus;/batches/&batch;/a2</outDir>
+      <outDir>.</outDir>
       <files>documents.sections</files>
       <fileName>document.@id ^ ".a2"</fileName>
       <lines>layer:microorganism</lines>
@@ -1645,7 +1688,7 @@
 
     <lives-in class="TabularExport">
       <append/>
-      <outDir>corpora/&corpus;/batches/&batch;/a2</outDir>
+      <outDir>.</outDir>
       <files>documents.sections</files>
       <fileName>document.@id ^ ".a2"</fileName>
       <lines>relations:CooccurrenceLocalization.tuples[args:Localization.@concept-id != ""]</lines>
@@ -1657,7 +1700,7 @@
 
     <exhibits class="TabularExport">
       <append/>
-      <outDir>corpora/&corpus;/batches/&batch;/a2</outDir>
+      <outDir>.</outDir>
       <files>documents.sections</files>
       <fileName>document.@id ^ ".a2"</fileName>
       <lines>relations:PhenotypeRelation.tuples</lines>
@@ -1670,7 +1713,7 @@
 
 
   <success class="TabularExport">
-    <outDir>corpora/&corpus;/batches/&batch;</outDir>
+    <outDir>.</outDir>
     <files>$</files>
     <fileName>"success.txt"</fileName>
     <lines>documents</lines>
diff --git a/plans/tomap-habitats.plan b/plans/tomap-habitats.plan
index 205a5fa..da458fd 100644
--- a/plans/tomap-habitats.plan
+++ b/plans/tomap-habitats.plan
@@ -3,7 +3,7 @@
 
   <!-- ToMap on lemmas -->
   <tomap class="TomapProjector">
-    <yateaFile output-feed="true">corpora/&corpus;/batches/&batch;/yatea/candidates.xml</yateaFile>
+    <yateaFile output-feed="true">yatea/candidates.xml</yateaFile>
     <targetLayerName>habitats</targetLayerName>
     <conceptFeature>concept-id</conceptFeature>
     <explanationFeaturePrefix>explain_</explanationFeaturePrefix>
@@ -26,7 +26,7 @@
   <tomap-on-alternative-lemmas>
 
     <tomap class="TomapProjector">
-      <yateaFile output-feed="true">corpora/&corpus;/batches/&batch;/yatea/candidates.xml</yateaFile>
+      <yateaFile output-feed="true">yatea/candidates.xml</yateaFile>
       <targetLayerName>habitats2</targetLayerName>
       <conceptFeature>concept-id</conceptFeature>
       <explanationFeaturePrefix>explain_</explanationFeaturePrefix>
@@ -58,7 +58,7 @@
   <tomap-no-lemmakeys>
 
     <tomap class="TomapProjector">
-      <yateaFile output-feed="true">corpora/&corpus;/batches/&batch;/yatea/candidates.xml</yateaFile>
+      <yateaFile output-feed="true">yatea/candidates.xml</yateaFile>
       <targetLayerName>habitats3</targetLayerName>
       <conceptFeature>concept-id</conceptFeature>
       <explanationFeaturePrefix>explain_</explanationFeaturePrefix>
@@ -89,7 +89,7 @@
   <tomap-on-variants>
 
     <tomap class="TomapProjector">
-      <yateaFile output-feed="true">corpora/&corpus;/batches/&batch;/yatea-var/candidates.xml</yateaFile>
+      <yateaFile output-feed="true">yatea-var/candidates.xml</yateaFile>
       <targetLayerName>habitats4</targetLayerName>
       <conceptFeature>concept-id</conceptFeature>
       <explanationFeaturePrefix>explain_</explanationFeaturePrefix>
@@ -121,7 +121,7 @@
   <tomap-no-lemmakeys-word-form>
 
     <tomap class="TomapProjector">
-      <yateaFile output-feed="true">corpora/&corpus;/batches/&batch;/yatea/candidates.xml</yateaFile>
+      <yateaFile output-feed="true">yatea/candidates.xml</yateaFile>
       <targetLayerName>habitats5</targetLayerName>
       <conceptFeature>concept-id</conceptFeature>
       <explanationFeaturePrefix>explain_</explanationFeaturePrefix>
@@ -196,7 +196,7 @@
   <bioyatea-projection class="YateaTermsProjector">
     <targetLayerName>yateaTerms</targetLayerName>
     <!--<yateaFile inhibitCheck="true">words_prepro/default/xml/candidates_pp.xml</yateaFile>-->
-    <yateaFile output-feed="yes">corpora/&corpus;/batches/&batch;/yatea/candidates.xml</yateaFile> <!-- ??? -->
+    <yateaFile output-feed="yes">yatea/candidates.xml</yateaFile> <!-- ??? -->
     <subject layer="words"/>
     <termLemma>lemma</termLemma>
   </bioyatea-projection>
@@ -388,20 +388,20 @@
       <removeFromLayer/>
    </delete-not-selected>
 
-<rule-for-food-corpus>
-   <tag-overlap-food class="Action">
+ <!-- <rule-for-food-corpus>
+   <tag-overlap-food class="Action"> -->
       <!-- <target>documents.sections.layer:habitats[not @concept-path =~ "OBT:000008/"]</target> -->
-      <target>documents[@id in "corpora/&corpus;/food-pmids.txt"].sections.layer:habitats[not @concept-path =~ "OBT:000008/"]</target>
+ <!--       <target>documents[@id in "corpora/&corpus;/food-pmids.txt"].sections.layer:habitats[not @concept-path =~ "OBT:000008/"]</target>
       <action>set:feat:overlap-food(span:habitats[@score == target.@score and @concept-path =~ "OBT:000008/"])</action>
       <setFeatures/>
     </tag-overlap-food>
    <remove-overlap-food class="Action">
-     <target>documents[@id in "corpora/&corpus;/food-pmids.txt"].sections.layer:habitats[not @concept-path =~ "OBT:000008/" and not @overlap-food == ""]</target>
+     <target>documents[@id in "corpora/&corpus;/food-pmids.txt"].sections.layer:habitats[not @concept-path =~ "OBT:000008/" and not @overlap-food == ""]</target>-->
      <!-- <target>documents.sections.layer:habitats[not @concept-path =~ "OBT:000008/" and not @overlap-food == ""]</target> -->
-      <action>remove:habitats</action>
+  <!--      <action>remove:habitats</action>
       <removeFromLayer/>
     </remove-overlap-food>
-</rule-for-food-corpus>
+</rule-for-food-corpus>-->
 
  <!-- Keep only the highest scored concepts -->
     <keep-highest class="Action">
diff --git a/plans/tomap-microbial-phenotypes.plan b/plans/tomap-microbial-phenotypes.plan
index 275e64c..f55357a 100644
--- a/plans/tomap-microbial-phenotypes.plan
+++ b/plans/tomap-microbial-phenotypes.plan
@@ -2,7 +2,7 @@
   
   <!-- ToMap on lemmas -->
   <tomap class="TomapProjector">
-    <yateaFile output-feed="true">corpora/&corpus;/batches/&batch;/yatea/candidates.xml</yateaFile>
+    <yateaFile output-feed="true">yatea/candidates.xml</yateaFile>
     <targetLayerName>phenotypes</targetLayerName>
     <conceptFeature>concept-id</conceptFeature>
     <explanationFeaturePrefix>explain_</explanationFeaturePrefix>
@@ -25,7 +25,7 @@
   <tomap-on-alternative-lemmas>
 
     <tomap class="TomapProjector">
-      <yateaFile output-feed="true">corpora/&corpus;/batches/&batch;/yatea/candidates.xml</yateaFile>
+      <yateaFile output-feed="true">yatea/candidates.xml</yateaFile>
       <targetLayerName>phenotypes2</targetLayerName>
       <conceptFeature>concept-id</conceptFeature>
       <explanationFeaturePrefix>explain_</explanationFeaturePrefix>
@@ -57,7 +57,7 @@
   <tomap-no-lemmakeys>
 
     <tomap class="TomapProjector">
-      <yateaFile output-feed="true">corpora/&corpus;/batches/&batch;/yatea/candidates.xml</yateaFile>
+      <yateaFile output-feed="true">yatea/candidates.xml</yateaFile>
       <targetLayerName>phenotypes3</targetLayerName>
       <conceptFeature>concept-id</conceptFeature>
       <explanationFeaturePrefix>explain_</explanationFeaturePrefix>
@@ -89,7 +89,7 @@
   <tomap-on-variants>
 
     <tomap class="TomapProjector">
-      <yateaFile output-feed="true">corpora/&corpus;/batches/&batch;/yatea-var/candidates.xml</yateaFile>
+      <yateaFile output-feed="true">yatea-var/candidates.xml</yateaFile>
       <targetLayerName>phenotypes4</targetLayerName>
       <conceptFeature>concept-id</conceptFeature>
       <explanationFeaturePrefix>explain_</explanationFeaturePrefix>
@@ -121,7 +121,7 @@
   <tomap-no-lemmakeys-word-form>
 
     <tomap class="TomapProjector">
-      <yateaFile output-feed="true">corpora/&corpus;/batches/&batch;/yatea/candidates.xml</yateaFile>
+      <yateaFile output-feed="true">yatea/candidates.xml</yateaFile>
       <targetLayerName>phenotypes5</targetLayerName>
       <conceptFeature>concept-id</conceptFeature>
       <explanationFeaturePrefix>explain_</explanationFeaturePrefix>
@@ -166,7 +166,7 @@
   <bioyatea-projection class="YateaTermsProjector">
     <targetLayerName>yateaTerms</targetLayerName>
     <!--<yateaFile inhibitCheck="true">words_prepro/default/xml/candidates_pp.xml</yateaFile>-->
-    <yateaFile output-feed="yes">corpora/&corpus;/batches/&batch;/yatea/candidates.xml</yateaFile> <!-- ??? -->
+    <yateaFile output-feed="yes">yatea/candidates.xml</yateaFile> <!-- ??? -->
     <subject layer="words"/>
     <termLemma>lemma</termLemma>
   </bioyatea-projection>
diff --git a/process_PubMed_corpus.snakefile b/process_PubMed_corpus.snakefile
index 2d25617..6b7d9e1 100644
--- a/process_PubMed_corpus.snakefile
+++ b/process_PubMed_corpus.snakefile
@@ -47,6 +47,8 @@ rule run_pubmed_entities:
 		batch="{B}",
 		corpus='pubmed',
                 inhibitSyntax='inhibit-syntax',
+        yatea="corpora/pubmed/batches/{B}/yatea/candidates.xml",
+        yatea_var="corpora/pubmed/batches/{B}/yatea-var/candidates.xml",
 		onto_habitat='ancillaries/BioNLP-OST+EnovFood-Habitat.obo',
         tomap_habitat='ancillaries/BioNLP-OST+EnovFood-Habitat.tomap',
         onto_pheno='ancillaries/BioNLP-OST+EnovFood-Phenotype.obo',
@@ -56,6 +58,8 @@ rule run_pubmed_entities:
         ontobiotopeUse='ancillaries/Use_V2.obo',
 		plan='plans/entities.plan',
 		dir='corpora/pubmed/batches/{B}/',
+        adbIndex='corpora/pubmed/batches/{B}/adb',
+        bionlp='corpora/pubmed/batches/{B}/a2',
 		taxid_microorganisms='ancillaries/extended-microorganisms-taxonomy/taxid_microorganisms.txt',
         taxa_id_full='ancillaries/extended-microorganisms-taxonomy/taxa+id_full.txt',
 		dummy='corpora/pubmed/batches/{B}/bionlp-st'
@@ -66,16 +70,22 @@ rule run_pubmed_entities:
 		-alias format pubmed \
 		-alias input {input.file} \
 		-alias input-xslt {input.xslt} \
+        -alias batch batch={params.batch} \
 		-alias outputDir {params.dir} \
+        -alias adbIndex {params.adbIndex} \
+        -alias index {output.index} \
+        -alias bionlp-output {params.bionlp} \
 		-environmentEntities \
-		-entity corpus {params.corpus} \
 		-feat inhibit-syntax {params.inhibitSyntax} \
+        -alias yatea-file {params.yatea} \
+        -alias yatea-var-file {params.yatea_var} \
+        -xalias '<yatea-tomap output-feed="true">{params.yatea}</yatea-tomap>' \
+        -xalias '<yatea-var-tomap output-feed="true">{params.yatea_var}</yatea-var-tomap>' \
         -alias ontobiotope-habitat {params.onto_habitat} \
         -xalias '<ontobiotope-tomap-habitat empty-words="{params.emptywords}" graylist="{params.graylist}" whole-proxy-distance="false">{params.tomap_habitat}</ontobiotope-tomap-habitat>' \
         -alias ontobiotope-phenotypes {params.onto_pheno} \
         -xalias '<ontobiotope-tomap-phenotypes empty-words="{params.emptywords}" whole-proxy-distance="false">{params.tomap_pheno}</ontobiotope-tomap-phenotypes>' \
 		-alias ontobiotope-use {params.ontobiotopeUse} \
-		-entity batch {params.batch} \
 		-alias taxid_microorganisms {params.taxid_microorganisms} \
 		-alias taxa+id_full {params.taxa_id_full} \
 		{params.plan}
-- 
GitLab


From d2b71ddb7a7f4fa003aabc28077c1c0176aa193c Mon Sep 17 00:00:00 2001
From: "louise.deleger" <louise.deleger@inra.fr>
Date: Fri, 26 Nov 2021 15:04:15 +0100
Subject: [PATCH 3/6] use -outputDir

---
 plans/entities.plan             | 57 ++++++---------------------------
 process_PubMed_corpus.snakefile | 15 ++-------
 2 files changed, 11 insertions(+), 61 deletions(-)

diff --git a/plans/entities.plan b/plans/entities.plan
index b32f10c..55e0338 100644
--- a/plans/entities.plan
+++ b/plans/entities.plan
@@ -41,23 +41,6 @@
     <alias module="words" param="outDir"/>
     <alias module="success" param="outDir"/>
   </param>
-    
-  <param name="bionlp-output">
-    <alias module="bionlp-st-a2.microorganisms" param="outDir"/>
-    <alias module="bionlp-st-a2.habitats" param="outDir"/>
-    <alias module="bionlp-st-a2.phenotypes" param="outDir"/>
-    <alias module="bionlp-st-a2.obt" param="outDir"/>
-    <alias module="bionlp-st-a2.taxid" param="outDir"/>
-    <alias module="bionlp-st-a2.lives-in" param="outDir"/>
-    <alias module="bionlp-st-a2.exhibits" param="outDir"/>
-  </param>
-    
-  <param name="adbIndex">
-    <alias module="adb.index" param="indexDir"/>
-  </param>
-  <param name="index">
-    <alias module="index" param="indexDir"/>
-  </param>
 
   <param name="doc-mesh">
     <alias module="output.doc-mesh" param="fileName"/>
@@ -160,28 +143,6 @@
   <param name="NCBI_taxa_ontobiotope">
     <alias module="habitats.tomap-habitats.map-living-organisms" param="mappingFile"/>
   </param>
-
-  <!-- yatea -->
-  <param name="yatea-file">
-    <alias module="term-extraction.yatea" param="xmlTermsFile"/>
-  </param>
-  <param name="yatea-var-file">
-    <alias module="term-extraction.yatea-var" param="xmlTermsFile"/>
-  </param>
-  <param name="yatea-tomap">
-    <alias module="habitats.tomap-habitats.tomap" param="yateaFile"/>
-    <alias module="habitats.tomap-habitats.tomap-on-alternative-lemmas.tomap" param="yateaFile"/>
-    <alias module="habitats.tomap-habitats.tomap-no-lemmakeys.tomap" param="yateaFile"/>
-    <alias module="habitats.tomap-habitats.tomap-no-lemmakeys-word-form.tomap" param="yateaFile"/>
-    <alias module="tomap-phenotypes.tomap" param="yateaFile"/>
-    <alias module="tomap-phenotypes.tomap-on-alternative-lemmas.tomap" param="yateaFile"/>
-    <alias module="tomap-phenotypes.tomap-no-lemmakeys.tomap" param="yateaFile"/>
-    <alias module="tomap-phenotypes.tomap-no-lemmakeys-word-form.tomap" param="yateaFile"/>
-  </param>
-  <param name="yatea-var-tomap">
-    <alias module="habitats.tomap-habitats.tomap-on-variants.tomap" param="yateaFile"/>
-    <alias module="tomap-phenotypes.tomap-on-variants.tomap" param="yateaFile"/>
-  </param>
     
   <!-- habitats-->
   <param name="ontobiotope-habitat">
@@ -1290,7 +1251,7 @@
     </habitat-ancestors>
     
     <index class="AlvisDBIndexer">
-      <indexDir>.</indexDir>
+      <indexDir>adb</indexDir>
       <elements>
 	<relations>
 	  <items>documents.sections.relations:CooccurrenceLocalization.tuples[args:Bacterium[@bacteria == "true"]]</items>
@@ -1310,7 +1271,7 @@
   </adb>
 
   <index class="AlvisIRIndexer">
-    <indexDir>.</indexDir>
+    <indexDir>index</indexDir>
     <tokenPositionGap>9216</tokenPositionGap>
     <fieldNames>title,abstract,author,full-author,pmid,year,journal,mesh,url</fieldNames>
     <relations>
@@ -1625,7 +1586,7 @@
 
   <bionlp-st-a2>
     <habitats class="TabularExport">
-      <outDir>.</outDir>
+      <outDir>a2</outDir>
       <files>documents.sections</files>
       <fileName>document.@id ^ ".a2"</fileName>
       <lines>layer:habitats</lines>
@@ -1638,7 +1599,7 @@
     
     <phenotypes class="TabularExport">
       <append/>
-      <outDir>.</outDir>
+      <outDir>a2</outDir>
       <files>documents.sections</files>
       <fileName>document.@id ^ ".a2"</fileName>
       <lines>layer:phenotypes</lines>
@@ -1651,7 +1612,7 @@
     
     <microorganisms class="TabularExport">
       <append/>
-      <outDir>.</outDir>
+      <outDir>a2</outDir>
       <files>documents.sections</files>
       <fileName>document.@id ^ ".a2"</fileName>
       <lines>layer:microorganism</lines>
@@ -1664,7 +1625,7 @@
 
     <obt class="TabularExport">
       <append/>
-      <outDir>.</outDir>
+      <outDir>a2</outDir>
       <files>documents.sections</files>
       <fileName>document.@id ^ ".a2"</fileName>
       <lines>layer:habitats|layer:phenotypes</lines>
@@ -1676,7 +1637,7 @@
 
     <taxid class="TabularExport">
       <append/>
-      <outDir>.</outDir>
+      <outDir>a2</outDir>
       <files>documents.sections</files>
       <fileName>document.@id ^ ".a2"</fileName>
       <lines>layer:microorganism</lines>
@@ -1688,7 +1649,7 @@
 
     <lives-in class="TabularExport">
       <append/>
-      <outDir>.</outDir>
+      <outDir>a2</outDir>
       <files>documents.sections</files>
       <fileName>document.@id ^ ".a2"</fileName>
       <lines>relations:CooccurrenceLocalization.tuples[args:Localization.@concept-id != ""]</lines>
@@ -1700,7 +1661,7 @@
 
     <exhibits class="TabularExport">
       <append/>
-      <outDir>.</outDir>
+      <outDir>a2</outDir>
       <files>documents.sections</files>
       <fileName>document.@id ^ ".a2"</fileName>
       <lines>relations:PhenotypeRelation.tuples</lines>
diff --git a/process_PubMed_corpus.snakefile b/process_PubMed_corpus.snakefile
index 6b7d9e1..5710034 100644
--- a/process_PubMed_corpus.snakefile
+++ b/process_PubMed_corpus.snakefile
@@ -46,9 +46,7 @@ rule run_pubmed_entities:
 	params:
 		batch="{B}",
 		corpus='pubmed',
-                inhibitSyntax='inhibit-syntax',
-        yatea="corpora/pubmed/batches/{B}/yatea/candidates.xml",
-        yatea_var="corpora/pubmed/batches/{B}/yatea-var/candidates.xml",
+        inhibitSyntax='inhibit-syntax',
 		onto_habitat='ancillaries/BioNLP-OST+EnovFood-Habitat.obo',
         tomap_habitat='ancillaries/BioNLP-OST+EnovFood-Habitat.tomap',
         onto_pheno='ancillaries/BioNLP-OST+EnovFood-Phenotype.obo',
@@ -58,8 +56,6 @@ rule run_pubmed_entities:
         ontobiotopeUse='ancillaries/Use_V2.obo',
 		plan='plans/entities.plan',
 		dir='corpora/pubmed/batches/{B}/',
-        adbIndex='corpora/pubmed/batches/{B}/adb',
-        bionlp='corpora/pubmed/batches/{B}/a2',
 		taxid_microorganisms='ancillaries/extended-microorganisms-taxonomy/taxid_microorganisms.txt',
         taxa_id_full='ancillaries/extended-microorganisms-taxonomy/taxa+id_full.txt',
 		dummy='corpora/pubmed/batches/{B}/bionlp-st'
@@ -71,16 +67,9 @@ rule run_pubmed_entities:
 		-alias input {input.file} \
 		-alias input-xslt {input.xslt} \
         -alias batch batch={params.batch} \
-		-alias outputDir {params.dir} \
-        -alias adbIndex {params.adbIndex} \
-        -alias index {output.index} \
-        -alias bionlp-output {params.bionlp} \
+        -outputDir {params.dir} \
 		-environmentEntities \
 		-feat inhibit-syntax {params.inhibitSyntax} \
-        -alias yatea-file {params.yatea} \
-        -alias yatea-var-file {params.yatea_var} \
-        -xalias '<yatea-tomap output-feed="true">{params.yatea}</yatea-tomap>' \
-        -xalias '<yatea-var-tomap output-feed="true">{params.yatea_var}</yatea-var-tomap>' \
         -alias ontobiotope-habitat {params.onto_habitat} \
         -xalias '<ontobiotope-tomap-habitat empty-words="{params.emptywords}" graylist="{params.graylist}" whole-proxy-distance="false">{params.tomap_habitat}</ontobiotope-tomap-habitat>' \
         -alias ontobiotope-phenotypes {params.onto_pheno} \
-- 
GitLab


From bf4c4556640c75cd9a7481c9b94284f4bef01b70 Mon Sep 17 00:00:00 2001
From: "louise.deleger" <louise.deleger@inra.fr>
Date: Fri, 26 Nov 2021 15:48:06 +0100
Subject: [PATCH 4/6] removed entities

---
 process-evaluate_BioNLP-OST.snakefile | 23 ++++++++++++++---------
 1 file changed, 14 insertions(+), 9 deletions(-)

diff --git a/process-evaluate_BioNLP-OST.snakefile b/process-evaluate_BioNLP-OST.snakefile
index c6b4373..e50a8be 100644
--- a/process-evaluate_BioNLP-OST.snakefile
+++ b/process-evaluate_BioNLP-OST.snakefile
@@ -39,9 +39,14 @@ rule run_bionlp_prediction:
 	params:
 		batch="{B}",
 		corpus='BioNLP-OST-2019',
-                inhibitSyntax='inhibit-syntax',
-		onto='ancillaries/BioNLP-OST+EnovFood',
-                ontobiotopeUse='ancillaries/Use_V2',
+        inhibitSyntax='inhibit-syntax',
+		onto_habitat='ancillaries/BioNLP-OST+EnovFood-Habitat.obo',
+        tomap_habitat='ancillaries/BioNLP-OST+EnovFood-Habitat.tomap',
+        onto_pheno='ancillaries/BioNLP-OST+EnovFood-Phenotype.obo',
+        tomap_pheno='ancillaries/BioNLP-OST+EnovFood-Phenotype.tomap',
+        graylist='ancillaries/graylist_extended.heads',
+		emptywords='ancillaries/stopwords_EN.ttg',
+        ontobiotopeUse='ancillaries/Use_V2.obo',
 		plan='plans/entities.plan',
 		dir='corpora/BioNLP-OST-2019/batches/{B}/',
 		taxid_microorganisms='ancillaries/extended-microorganisms-taxonomy/taxid_microorganisms.txt',
@@ -52,14 +57,14 @@ rule run_bionlp_prediction:
 		-log {log} \
 		-alias format bionlp-st \
 		-alias input-dir {input.dir} \
-		-alias input-xslt {input.xslt} \
-		-alias outputDir {params.dir} \
+		-outputDir {params.dir} \
 		-environmentEntities \
-		-entity corpus {params.corpus} \
 		-feat inhibit-syntax {params.inhibitSyntax} \
-		-entity ontobiotope {params.onto} \
-		-entity ontobiotope-use {params.ontobiotopeUse} \
-		-entity batch {params.batch} \
+        -alias ontobiotope-habitat {params.onto_habitat} \
+        -xalias '<ontobiotope-tomap-habitat empty-words="{params.emptywords}" graylist="{params.graylist}" whole-proxy-distance="false">{params.tomap_habitat}</ontobiotope-tomap-habitat>' \
+        -alias ontobiotope-phenotypes {params.onto_pheno} \
+        -xalias '<ontobiotope-tomap-phenotypes empty-words="{params.emptywords}" whole-proxy-distance="false">{params.tomap_pheno}</ontobiotope-tomap-phenotypes>' \
+		-alias ontobiotope-use {params.ontobiotopeUse} \
 		-alias taxid_microorganisms {params.taxid_microorganisms} \
 		-alias taxa+id_full {params.taxa_id_full} \
 		{params.plan}	    
-- 
GitLab


From f8db036f901025cb56740d9505e3b4a4a820d588 Mon Sep 17 00:00:00 2001
From: "louise.deleger" <louise.deleger@inra.fr>
Date: Fri, 26 Nov 2021 15:49:48 +0100
Subject: [PATCH 5/6] changed default values

---
 plans/entities.plan | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/plans/entities.plan b/plans/entities.plan
index 55e0338..8523ddb 100644
--- a/plans/entities.plan
+++ b/plans/entities.plan
@@ -198,9 +198,9 @@
 
   <read>
     <pubmed class="XMLReader">
-      <sourcePath>corpora/pubmed/batches/0000/batch.xml</sourcePath>
+      <sourcePath>corpora/pubmed/batches/0001/batch.xml</sourcePath>
       <xslTransform>ancillaries/microbes-2019-pubmed2alvisnlp.xslt</xslTransform>
-      <constantDocumentFeatures>batch=0000</constantDocumentFeatures>
+      <constantDocumentFeatures>batch=0001</constantDocumentFeatures>
     </pubmed>
 
     <bionlp-st class="BioNLPSTReader">
-- 
GitLab


From 7f044808cfeec89c8bf45de76916ef53c7cbac75 Mon Sep 17 00:00:00 2001
From: "louise.deleger" <louise.deleger@inra.fr>
Date: Fri, 26 Nov 2021 17:07:10 +0100
Subject: [PATCH 6/6] Changed plan used for mapping habitats

---
 plans/map_habitats.plan          |  6 +--
 process_CIRM_corpus.snakefile    | 69 ++++++++++++++++++--------------
 process_DSMZ_corpus.snakefile    |  7 +++-
 process_GenBank_corpus.snakefile |  7 +++-
 4 files changed, 52 insertions(+), 37 deletions(-)

diff --git a/plans/map_habitats.plan b/plans/map_habitats.plan
index 0777778..5aff349 100644
--- a/plans/map_habitats.plan
+++ b/plans/map_habitats.plan
@@ -168,7 +168,7 @@
 
     <!-- Run Yatea term extractor -->
     <yatea class="YateaExtractor">
-      <xmlTermsFile>ancillaries/yatea/candidates.xml</xmlTermsFile>
+      <xmlTermsFile>yatea/candidates.xml</xmlTermsFile>
       <posFeature>tt_pos</posFeature>
       <configDir>ancillaries/YaTeA/config-habitats</configDir>
       <localeDir>ancillaries/YaTeA/locale</localeDir>
@@ -178,7 +178,7 @@
 
     <!-- Run Yatea term extractor on variants -->
     <yatea-var class="YateaExtractor">
-      <xmlTermsFile>ancillaries/yatea-var/candidates.xml</xmlTermsFile>
+      <xmlTermsFile>yatea-var/candidates.xml</xmlTermsFile>
       <posFeature>tt_pos</posFeature>
       <lemmaFeature>variant</lemmaFeature>
       <configDir>ancillaries/YaTeA/config-habitats</configDir>
@@ -258,7 +258,7 @@
       <setFeatures/>
     </add-score>
     
-    <tomap-habitats file="plans/tomap-habitats-generic.plan"/>
+    <tomap-habitats file="plans/tomap-habitats.plan"/>
 
     <!-- <remove-living-org-overlapping-geo class="Action"> -->
     <!--   <target>documents.sections.layer:habitats[@concept-path ?= "OBT:000002" and span:Geographical]</target> -->
diff --git a/process_CIRM_corpus.snakefile b/process_CIRM_corpus.snakefile
index 2b172cf..f9f49e7 100644
--- a/process_CIRM_corpus.snakefile
+++ b/process_CIRM_corpus.snakefile
@@ -24,8 +24,8 @@ rule get_cirm_bia_taxa_habitats:
 		strain_index='1',
 		habitat_index='15'
 	output:
-		taxa='corpora/cirm/bia_taxa.txt',
-		habitats='corpora/cirm/bia_habitats.txt',
+		taxa='corpora/cirm/bia/bia_taxa.txt',
+		habitats='corpora/cirm/bia/bia_habitats.txt',
 		tsv='corpora/cirm/BIA_2021/florilege_export_final_17_02_21.tsv'
 	conda: 'softwares/envs/python3_pandas_env.yaml'
 	shell: """
@@ -42,8 +42,8 @@ rule get_cirm_yeast_taxa_habitats:
 		taxa_index='1',
 		habitat_index='10,11'
 	output:
-		taxa='corpora/cirm/yeast_taxa.txt',
-		habitats='corpora/cirm/yeast_habitats.txt',
+		taxa='corpora/cirm/levures/yeast_taxa.txt',
+		habitats='corpora/cirm/levures/yeast_habitats.txt',
 		tsv='corpora/cirm/Levures_2021/Florilege_21012021.tsv'
 	conda: 'softwares/envs/python3_pandas_env.yaml'
 	shell: """
@@ -61,8 +61,8 @@ rule get_cirm_cfbp_taxa_habitats:
 		strain_index='1',
 		habitat_index='6,10,13,14'
 	output:
-		taxa='corpora/cirm/cfbp_taxa.txt',
-		habitats='corpora/cirm/cfbp_habitats.txt',
+		taxa='corpora/cirm/cfbp/cfbp_taxa.txt',
+		habitats='corpora/cirm/cfbp/cfbp_habitats.txt',
 		tsv='corpora/cirm/CFBP_2021/20210617_PPortier.tsv'
 	conda: 'softwares/envs/python3_pandas_env.yaml'
 	shell: """
@@ -75,9 +75,9 @@ map microorganisms
 '''
 rule map_cirm_bia_microorganisms:
 	input:
-		taxa='corpora/cirm/bia_taxa.txt'
+		taxa='corpora/cirm/bia/bia_taxa.txt'
 	output:
-		mapped_taxaids='corpora/cirm/mapped_bia_taxa.txt'
+		mapped_taxaids='corpora/cirm/bia/mapped_bia_taxa.txt'
 	params:
 		plan='plans/map_microorganisms.plan',
 		taxid_microorganisms='ancillaries/extended-microorganisms-taxonomy/taxid_microorganisms.txt',
@@ -96,9 +96,9 @@ map microorganisms (CIRM Levures)
 '''
 rule map_cirm_yeast_microorganisms:
 	input:
-		taxa='corpora/cirm/yeast_taxa.txt'
+		taxa='corpora/cirm/levures/yeast_taxa.txt'
 	output:
-		mapped_taxaids='corpora/cirm/mapped_yeast_taxa.txt'
+		mapped_taxaids='corpora/cirm/levures/mapped_yeast_taxa.txt'
 	params:
 		plan='plans/map_microorganisms.plan',
 		taxid_microorganisms='ancillaries/extended-microorganisms-taxonomy/taxid_microorganisms.txt',
@@ -118,9 +118,9 @@ map microorganisms (CIRM CFBP)
 '''
 rule map_cirm_cfbp_microorganisms:
 	input:
-		taxa='corpora/cirm/cfbp_taxa.txt'
+		taxa='corpora/cirm/cfbp/cfbp_taxa.txt'
 	output:
-		mapped_taxa='corpora/cirm/mapped_cfbp_taxa.txt'
+		mapped_taxa='corpora/cirm/cfbp/mapped_cfbp_taxa.txt'
 	params:
 		plan='plans/map_microorganisms.plan',
 		taxid_microorganisms='ancillaries/extended-microorganisms-taxonomy/taxid_microorganisms.txt',
@@ -139,19 +139,22 @@ map habitats of microorganisms
 '''
 rule map_cirm_habitats:
 	input:
-		habitats='corpora/cirm/bia_habitats.txt'
+		habitats='corpora/cirm/bia/bia_habitats.txt'
 	output:
-		mapped_habitats='corpora/cirm/mapped_bia_habitats.txt'
+		mapped_habitats='corpora/cirm/bia/mapped_bia_habitats.txt'
 	params:
 		plan='plans/map_habitats.plan',
 		onto='ancillaries/BioNLP-OST+EnovFood-Habitat.obo',
 		tomap='ancillaries/BioNLP-OST+EnovFood-Habitat.tomap',
 		graylist='ancillaries/graylist_extended.heads',
-		emptywords='ancillaries/stopwords_EN.ttg'
+		emptywords='ancillaries/stopwords_EN.ttg',
+		outdir='corpora/cirm/bia',
+		outfile='mapped_bia_habitats.txt'
 	singularity:config["SINGULARITY_IMG"]
 	shell: """alvisnlp -J-Xmx32g -cleanTmp -verbose \
 	-alias input {input.habitats} \
-	-alias output {output.mapped_habitats} \
+    -outputDir {params.outdir} \
+	-alias output {params.outfile} \
 	-alias ontobiotope {params.onto} \
 	-xalias '<ontobiotope-tomap empty-words="{params.emptywords}" graylist="{params.graylist}" whole-proxy-distance="false">{params.tomap}</ontobiotope-tomap>' \
 	{params.plan}
@@ -162,19 +165,22 @@ map habitats of microorganisms (CIRM Levures)
 '''
 rule map_cirm_yeast_habitats:
 	input:
-		habitats='corpora/cirm/yeast_habitats.txt'
+		habitats='corpora/cirm/levures/yeast_habitats.txt'
 	output:
-		mapped_habitats='corpora/cirm/mapped_yeast_habitats.txt'
+		mapped_habitats='corpora/cirm/levures/mapped_yeast_habitats.txt'
 	params:
 		plan='plans/map_habitats.plan',
 		onto='ancillaries/BioNLP-OST+EnovFood-Habitat.obo',
 		tomap='ancillaries/BioNLP-OST+EnovFood-Habitat.tomap',
 		graylist='ancillaries/graylist_extended.heads',
-		emptywords='ancillaries/stopwords_EN.ttg'
+		emptywords='ancillaries/stopwords_EN.ttg',
+		outdir='corpora/cirm/levures',
+		outfile='mapped_yeast_habitats.txt'
 	singularity:config["SINGULARITY_IMG"]
 	shell: """alvisnlp -J-Xmx32g -cleanTmp -verbose \
 	-alias input {input.habitats} \
-	-alias output {output.mapped_habitats} \
+    -outputDir {params.outdir} \
+	-alias output {params.outfile} \
 	-alias ontobiotope {params.onto} \
 	-xalias '<ontobiotope-tomap empty-words="{params.emptywords}" graylist="{params.graylist}" whole-proxy-distance="false">{params.tomap}</ontobiotope-tomap>' \
 	{params.plan}
@@ -185,19 +191,22 @@ map habitats of microorganisms (CIRM CFBP)
 '''
 rule map_cirm_cfbp_habitats:
 	input:
-		habitats='corpora/cirm/cfbp_habitats.txt'
+		habitats='corpora/cirm/cfbp/cfbp_habitats.txt'
 	output:
-		mapped_habitats='corpora/cirm/mapped_cfbp_habitats.txt'
+		mapped_habitats='corpora/cirm/cfbp/mapped_cfbp_habitats.txt'
 	params:
 		plan='plans/map_habitats.plan',
 		onto='ancillaries/BioNLP-OST+EnovFood-Habitat.obo',
 		tomap='ancillaries/BioNLP-OST+EnovFood-Habitat.tomap',
 		graylist='ancillaries/graylist_extended.heads',
-		emptywords='ancillaries/stopwords_EN.ttg'
+		emptywords='ancillaries/stopwords_EN.ttg',
+		outdir='corpora/cirm/cfbp',
+		outfile='mapped_cfbp_habitats.txt'
 	singularity:config["SINGULARITY_IMG"]
 	shell: """alvisnlp -J-Xmx32g -cleanTmp -verbose \
 	-alias input {input.habitats} \
-	-alias output {output.mapped_habitats} \
+    -outputDir {params.outdir} \
+	-alias output {params.outfile} \
 	-alias ontobiotope {params.onto} \
 	-xalias '<ontobiotope-tomap empty-words="{params.emptywords}" graylist="{params.graylist}" whole-proxy-distance="false">{params.tomap}</ontobiotope-tomap>' \
 	{params.plan}
@@ -209,8 +218,8 @@ format results
 rule format_cirm_results:
 	input:
 		file='corpora/cirm/BIA_2021/florilege_export_final_17_02_21.tsv',
-		taxa='corpora/cirm/mapped_bia_taxa.txt',
-		habitats='corpora/cirm/mapped_bia_habitats.txt'
+		taxa='corpora/cirm/bia/mapped_bia_taxa.txt',
+		habitats='corpora/cirm/bia/mapped_bia_habitats.txt'
 	output:
 		result='corpora/florilege/cirm/cirm-bia-results.txt'
 	params:
@@ -226,8 +235,8 @@ format results (CIRM Levures)
 rule format_cirm_yeast_results:
 	input:
 		file='corpora/cirm/Levures_2021/Florilege_21012021.tsv',
-		taxa='corpora/cirm/mapped_yeast_taxa.txt',
-		habitats='corpora/cirm/mapped_yeast_habitats.txt'
+		taxa='corpora/cirm/levures/mapped_yeast_taxa.txt',
+		habitats='corpora/cirm/levures/mapped_yeast_habitats.txt'
 	output:
 		result='corpora/florilege/cirm/cirm-yeast-results.txt'
 	params:
@@ -242,8 +251,8 @@ format results (CIRM CFBP)
 rule format_cirm_cfbp_results:
 	input:
 		file='corpora/cirm/CFBP_2021/20210617_PPortier.tsv',
-		taxa='corpora/cirm/mapped_cfbp_taxa.txt',
-		habitats='corpora/cirm/mapped_cfbp_habitats.txt'
+		taxa='corpora/cirm/cfbp/mapped_cfbp_taxa.txt',
+		habitats='corpora/cirm/cfbp/mapped_cfbp_habitats.txt'
 	output:
 		result='corpora/florilege/cirm/cirm-cfbp-results.txt'
 	params:
diff --git a/process_DSMZ_corpus.snakefile b/process_DSMZ_corpus.snakefile
index b4fa67f..8fde651 100644
--- a/process_DSMZ_corpus.snakefile
+++ b/process_DSMZ_corpus.snakefile
@@ -35,11 +35,14 @@ rule map_dsmz_habitats:
 		onto='ancillaries/BioNLP-OST+EnovFood-Habitat.obo',
 		tomap='ancillaries/BioNLP-OST+EnovFood-Habitat.tomap',
 		graylist='ancillaries/graylist_extended.heads',
-		emptywords='ancillaries/stopwords_EN.ttg'
+		emptywords='ancillaries/stopwords_EN.ttg',
+		outdir='corpora/dsmz',
+		outfile='mapped_habitats.txt'
 	singularity:config["SINGULARITY_IMG"]
 	shell: """alvisnlp -J-Xmx32g -cleanTmp -verbose \
 	-alias input {input.habitats} \
-	-alias output {output.mapped_habitats} \
+    -outputDir {params.outdir} \
+	-alias output {params.outfile} \
 	-alias ontobiotope {params.onto} \
 	-xalias '<ontobiotope-tomap empty-words="{params.emptywords}" graylist="{params.graylist}" whole-proxy-distance="false">{params.tomap}</ontobiotope-tomap>' \
 	{params.plan}
diff --git a/process_GenBank_corpus.snakefile b/process_GenBank_corpus.snakefile
index 388f9ab..888835e 100644
--- a/process_GenBank_corpus.snakefile
+++ b/process_GenBank_corpus.snakefile
@@ -79,11 +79,14 @@ rule map_genbank_habitats:
 		tomap='ancillaries/BioNLP-OST+EnovFood-Habitat.tomap',
 		graylist='ancillaries/graylist_extended.heads',
 		emptywords='ancillaries/stopwords_EN.ttg',
-		inhibitSyntax='inhibit-syntax'
+		inhibitSyntax='inhibit-syntax',
+		outdir='corpora/genbank',
+		outfile='mapped_habitats.txt'
 	singularity:config["SINGULARITY_IMG"]
 	shell: """alvisnlp -J-Xmx32g -cleanTmp -verbose \
 	-alias input {input.habitats} \
-	-alias output {output.mapped_habitats}\
+    -outputDir {params.outdir} \
+	-alias output {params.outfile} \
 	-alias ontobiotope {params.onto} \
 	-feat inhibit-syntax {params.inhibitSyntax} \
 	-xalias '<ontobiotope-tomap empty-words="{params.emptywords}" graylist="{params.graylist}" whole-proxy-distance="false">{params.tomap}</ontobiotope-tomap>' \
-- 
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