diff --git a/plans/entities.plan b/plans/entities.plan
index 8523ddb14c67d45b2edc40e07b71539e55ef52cd..f98ea1c1a7e009f4d9006ca56f147057fbb3ad01 100644
--- a/plans/entities.plan
+++ b/plans/entities.plan
@@ -17,10 +17,6 @@
   <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"/>
@@ -143,7 +139,8 @@
   <param name="NCBI_taxa_ontobiotope">
     <alias module="habitats.tomap-habitats.map-living-organisms" param="mappingFile"/>
   </param>
-    
+
+
   <!-- habitats-->
   <param name="ontobiotope-habitat">
     <alias module="habitats.tomap-habitats.concept-names" param="oboFiles"/>
@@ -198,15 +195,14 @@
 
   <read>
     <pubmed class="XMLReader">
-      <sourcePath>corpora/pubmed/batches/0001/batch.xml</sourcePath>
-      <xslTransform>ancillaries/microbes-2019-pubmed2alvisnlp.xslt</xslTransform>
-      <constantDocumentFeatures>batch=0001</constantDocumentFeatures>
+      <sourcePath>corpora/&corpus;/batches/&batch;/batch.xml</sourcePath>
+      <xslTransform>ancillaries/&corpus;-pubmed2alvisnlp.xslt</xslTransform>
     </pubmed>
 
     <bionlp-st class="BioNLPSTReader">
       <active>true</active>
       <sectionName>abstract</sectionName>
-      <textDir>corpora/BioNLP-OST-2019/batches/BB19-kb+ner/bionlp-st</textDir>
+      <textDir>corpora/&corpus;/batches/&batch;/bionlp-st</textDir>
     </bionlp-st>
   </read>
 
@@ -408,7 +404,7 @@
     <!-- Run Yatea term extractor -->
     <yatea class="YateaExtractor">
       <sectionFilter>@name == "title" or @name == "abstract"</sectionFilter>
-      <xmlTermsFile>yatea/candidates.xml</xmlTermsFile>
+      <xmlTermsFile>corpora/&corpus;/batches/&batch;/yatea/candidates.xml</xmlTermsFile>
       <posFeature>tt_pos</posFeature>
       <configDir>ancillaries/YaTeA/config-habitats</configDir>
       <localeDir>ancillaries/YaTeA/locale</localeDir>
@@ -419,7 +415,7 @@
     <!-- Run Yatea term extractor on variants -->
     <yatea-var class="YateaExtractor">
       <sectionFilter>@name == "title" or @name == "abstract"</sectionFilter>
-      <xmlTermsFile>yatea-var/candidates.xml</xmlTermsFile>
+      <xmlTermsFile>corpora/&corpus;/batches/&batch;/yatea-var/candidates.xml</xmlTermsFile>
       <posFeature>tt_pos</posFeature>
       <lemmaFeature>variant</lemmaFeature>
       <configDir>ancillaries/YaTeA/config-habitats</configDir>
@@ -673,12 +669,12 @@
 
   <output>
     <doc-mesh class="TabularExport">
-      <outDir>.</outDir>
+      <outDir>corpora/&corpus;/batches/&batch;</outDir>
       <files>$</files>
       <fileName>"doc-mesh.txt"</fileName>
       <lines>documents.sections:mesh</lines>
       <columns separator=";">
-	document.@batch;
+	"&batch;";
 	document.@id;
 	@UI;
 	@mesh-name;
@@ -687,12 +683,12 @@
     </doc-mesh>
 
     <taxa class="TabularExport">
-      <outDir>.</outDir>
+      <outDir>corpora/&corpus;/batches/&batch;</outDir>
       <files>$</files>
       <fileName>"taxa.txt"</fileName>
       <lines>documents.sections.layer:taxa</lines>
       <columns separator=";">
-	document.@batch;
+	"&batch;";
 	section.document.@id;
 	section.@name;
 	start ^ "-" ^ end;
@@ -706,12 +702,12 @@
     </taxa>
 
     <microorganisms class="TabularExport">
-      <outDir>.</outDir>
+      <outDir>corpora/&corpus;/batches/&batch;</outDir>
       <files>$</files>
       <fileName>"microorganisms.txt"</fileName>
       <lines>documents.sections.layer:microorganism</lines>
       <columns separator=";">
-	document.@batch;
+	"&batch;";
 	section.document.@id;
 	section.@name;
 	start ^ "-" ^ end;
@@ -725,12 +721,12 @@
     </microorganisms>
 
     <microorganisms-short class="TabularExport">
-      <outDir>.</outDir>
+      <outDir>corpora/&corpus;/batches/&batch;</outDir>
       <files>$</files>
       <fileName>"microorganisms-short.txt"</fileName>
       <lines>documents.sections.layer:microorganism[outside:words and not @form == outside:words.@form]</lines>
       <columns separator=";">
-	document.@batch;
+	"&batch;";
 	section.document.@id;
 	section.@name;
 	start ^ "-" ^ end;
@@ -744,12 +740,12 @@
     </microorganisms-short>
 
     <bacteria class="TabularExport">
-      <outDir>.</outDir>
+      <outDir>corpora/&corpus;/batches/&batch;</outDir>
       <files>$</files>
       <fileName>"bacteria.txt"</fileName>
       <lines>documents.sections.layer:bacteria</lines>
       <columns separator=";">
-	document.@batch;
+	"&batch;";
 	section.document.@id;
 	section.@name;
 	start ^ "-" ^ end;
@@ -763,12 +759,12 @@
     </bacteria>
 
     <habitats class="TabularExport">
-      <outDir>.</outDir>
+      <outDir>corpora/&corpus;/batches/&batch;</outDir>
       <files>$</files>
       <fileName>"habitats.txt"</fileName>
       <lines>documents.sections.layer:habitats</lines>
       <columns separator=";">
-	document.@batch;
+	"&batch;";
 	section.document.@id;
 	section.@name;
 	start ^ "-" ^ end;
@@ -784,12 +780,12 @@
     </habitats>
 
     <phenotypes class="TabularExport">
-      <outDir>.</outDir>
+      <outDir>corpora/&corpus;/batches/&batch;</outDir>
       <files>$</files>
       <fileName>"phenotypes.txt"</fileName>
       <lines>documents.sections.layer:phenotypes</lines>
       <columns separator=";">
-	document.@batch;
+	"&batch;";
 	section.document.@id;
 	section.@name;
 	start ^ "-" ^ end;
@@ -805,12 +801,12 @@
     </phenotypes>
 
     <uses class="TabularExport">
-      <outDir>.</outDir>
+      <outDir>corpora/&corpus;/batches/&batch;</outDir>
       <files>$</files>
       <fileName>"uses.txt"</fileName>
       <lines>documents.sections.layer:uses</lines>
       <columns separator=";">
-	document.@batch;
+	"&batch;";
 	section.document.@id;
 	section.@name;
 	start ^ "-" ^ end;
@@ -826,12 +822,12 @@
     </uses>
 
     <geo class="TabularExport">
-      <outDir>.</outDir>
+      <outDir>corpora/&corpus;/batches/&batch;</outDir>
       <files>$</files>
       <fileName>"geo.txt"</fileName>
       <lines>documents.sections.layer:Geographical</lines>
       <columns separator=";">
-	document.@batch;
+	"&batch;";
 	section.document.@id;
 	section.@name;
 	start ^ "-" ^ end;
@@ -841,12 +837,12 @@
     </geo>
 
     <relations class="TabularExport">
-      <outDir>.</outDir>
+      <outDir>corpora/&corpus;/batches/&batch;</outDir>
       <files>$</files>
       <fileName>"relations.txt"</fileName>
       <lines>documents.sections.relations:CooccurrenceLocalization.tuples</lines>
       <columns separator=";">
-	document.@batch;
+	"&batch;";
 	section.document.@id;
 	section.@name;
 	args:Bacterium.@taxid;
@@ -864,12 +860,12 @@
     </relations>
 
     <relations-pheno class="TabularExport">
-      <outDir>.</outDir>
+      <outDir>corpora/&corpus;/batches/&batch;</outDir>
       <files>$</files>
       <fileName>"phenotype-relations.txt"</fileName>
       <lines>documents.sections.relations:PhenotypeRelation.tuples</lines>
       <columns separator=";">
-	document.@batch;
+	"&batch;";
 	section.document.@id;
 	section.@name;
 	args:Microorganism.@taxid;
@@ -887,12 +883,12 @@
     </relations-pheno>
 
     <relations-use class="TabularExport">
-      <outDir>.</outDir>
+      <outDir>corpora/&corpus;/batches/&batch;</outDir>
       <files>$</files>
       <fileName>"uses-relations.txt"</fileName>
       <lines>documents.sections.relations:UseRelation.tuples</lines>
       <columns separator=";">
-	document.@batch;
+	"&batch;";
 	section.document.@id;
 	section.@name;
 	args:Microorganism.@taxid;
@@ -978,7 +974,7 @@
       </index-sentences>
 
       <sentences class="TabularExport">
-	<outDir>.</outDir>
+	<outDir>corpora/&corpus;/batches/&batch;</outDir>
 	<files>$</files>
 	<fileName>"sentences.txt"</fileName>
 	<lines>documents.sections.layer:sentences[@name != "author"]</lines>
@@ -999,7 +995,7 @@
       </sentences>
 
       <anaphora class="TabularExport">
-	<outDir>.</outDir>
+	<outDir>corpora/&corpus;/batches/&batch;</outDir>
 	<files>$</files>
 	<fileName>"anaphora.txt"</fileName>
 	<lines>documents.sections.relations:coreferences.tuples[args:Ante]</lines>
@@ -1032,7 +1028,7 @@
       </anaphora>
 
       <dependencies class="TabularExport">
-	<outDir>.</outDir>
+	<outDir>corpora/&corpus;/batches/&batch;</outDir>
 	<files>$</files>
 	<fileName>"dependencies.txt"</fileName>
 	<lines>documents.sections[@name != "author"].relations:dependencies.tuples</lines>
@@ -1251,11 +1247,11 @@
     </habitat-ancestors>
     
     <index class="AlvisDBIndexer">
-      <indexDir>adb</indexDir>
+      <indexDir>corpora/&corpus;/batches/&batch;/adb</indexDir>
       <elements>
 	<relations>
 	  <items>documents.sections.relations:CooccurrenceLocalization.tuples[args:Bacterium[@bacteria == "true"]]</items>
-	  <id>section.document.@batch ^ id:unique</id>
+	  <id>"&batch;_" ^ id:unique</id>
 	  <name>"Localization"</name>
 	  <type>"localization"</type>
 	  <args>args:Bacterium|args:Localization</args>
@@ -1271,7 +1267,7 @@
   </adb>
 
   <index class="AlvisIRIndexer">
-    <indexDir>index</indexDir>
+    <indexDir>corpora/&corpus;/batches/&batch;/index</indexDir>
     <tokenPositionGap>9216</tokenPositionGap>
     <fieldNames>title,abstract,author,full-author,pmid,year,journal,mesh,url</fieldNames>
     <relations>
@@ -1408,8 +1404,8 @@
     </documents>
   </index>
 
-<!--  <index-food class="AlvisIRIndexer">
-    <indexDir>.</indexDir>
+  <index-food class="AlvisIRIndexer">
+    <indexDir>corpora/&corpus;/batches/&batch;/index-food</indexDir>
     <tokenPositionGap>9216</tokenPositionGap>
     <fieldNames>title,abstract,author,full-author,pmid,year,journal,mesh,url</fieldNames>
     <relations>
@@ -1542,7 +1538,7 @@
 	<keyword>document.@url</keyword>
       </fields>
     </documents>
-  </index-food>-->
+  </index-food>
 
   <!-- HTML visualization -->
   <add-feature class="Action">
@@ -1567,14 +1563,14 @@
   </add-feature3>
   <html class="QuickHTML">
     <active>false</active>
-    <outDir>./html</outDir>
+    <outDir>corpora/&corpus;/batches/&batch;/html</outDir>
     <classFeature>ne-type</classFeature>
     <layers>phenotypes,microorganism,habitats</layers>
     <colors>#99cc00,#ffcc99,#ffd333,#ffd666</colors>
   </html>
 
   <words class="TabularExport">
-    <outDir>.</outDir>
+    <outDir>corpora/&corpus;/batches/&batch;</outDir>
     <files>$</files>
     <fileName>"words.txt"</fileName>
     <lines>documents.sections[@name == "title" or @name == "abstract"].layer:words</lines>
@@ -1586,7 +1582,7 @@
 
   <bionlp-st-a2>
     <habitats class="TabularExport">
-      <outDir>a2</outDir>
+      <outDir>corpora/&corpus;/batches/&batch;/a2</outDir>
       <files>documents.sections</files>
       <fileName>document.@id ^ ".a2"</fileName>
       <lines>layer:habitats</lines>
@@ -1599,7 +1595,7 @@
     
     <phenotypes class="TabularExport">
       <append/>
-      <outDir>a2</outDir>
+      <outDir>corpora/&corpus;/batches/&batch;/a2</outDir>
       <files>documents.sections</files>
       <fileName>document.@id ^ ".a2"</fileName>
       <lines>layer:phenotypes</lines>
@@ -1612,7 +1608,7 @@
     
     <microorganisms class="TabularExport">
       <append/>
-      <outDir>a2</outDir>
+      <outDir>corpora/&corpus;/batches/&batch;/a2</outDir>
       <files>documents.sections</files>
       <fileName>document.@id ^ ".a2"</fileName>
       <lines>layer:microorganism</lines>
@@ -1625,7 +1621,7 @@
 
     <obt class="TabularExport">
       <append/>
-      <outDir>a2</outDir>
+      <outDir>corpora/&corpus;/batches/&batch;/a2</outDir>
       <files>documents.sections</files>
       <fileName>document.@id ^ ".a2"</fileName>
       <lines>layer:habitats|layer:phenotypes</lines>
@@ -1637,7 +1633,7 @@
 
     <taxid class="TabularExport">
       <append/>
-      <outDir>a2</outDir>
+      <outDir>corpora/&corpus;/batches/&batch;/a2</outDir>
       <files>documents.sections</files>
       <fileName>document.@id ^ ".a2"</fileName>
       <lines>layer:microorganism</lines>
@@ -1649,7 +1645,7 @@
 
     <lives-in class="TabularExport">
       <append/>
-      <outDir>a2</outDir>
+      <outDir>corpora/&corpus;/batches/&batch;/a2</outDir>
       <files>documents.sections</files>
       <fileName>document.@id ^ ".a2"</fileName>
       <lines>relations:CooccurrenceLocalization.tuples[args:Localization.@concept-id != ""]</lines>
@@ -1661,7 +1657,7 @@
 
     <exhibits class="TabularExport">
       <append/>
-      <outDir>a2</outDir>
+      <outDir>corpora/&corpus;/batches/&batch;/a2</outDir>
       <files>documents.sections</files>
       <fileName>document.@id ^ ".a2"</fileName>
       <lines>relations:PhenotypeRelation.tuples</lines>
@@ -1674,7 +1670,7 @@
 
 
   <success class="TabularExport">
-    <outDir>.</outDir>
+    <outDir>corpora/&corpus;/batches/&batch;</outDir>
     <files>$</files>
     <fileName>"success.txt"</fileName>
     <lines>documents</lines>
diff --git a/plans/map_habitats.plan b/plans/map_habitats.plan
index 5aff349486ac1d6145c03930300193eeb36b05e4..07777780e184fa6ede0bf8d55785a7e3a463d7f9 100644
--- a/plans/map_habitats.plan
+++ b/plans/map_habitats.plan
@@ -168,7 +168,7 @@
 
     <!-- Run Yatea term extractor -->
     <yatea class="YateaExtractor">
-      <xmlTermsFile>yatea/candidates.xml</xmlTermsFile>
+      <xmlTermsFile>ancillaries/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>yatea-var/candidates.xml</xmlTermsFile>
+      <xmlTermsFile>ancillaries/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.plan"/>
+    <tomap-habitats file="plans/tomap-habitats-generic.plan"/>
 
     <!-- <remove-living-org-overlapping-geo class="Action"> -->
     <!--   <target>documents.sections.layer:habitats[@concept-path ?= "OBT:000002" and span:Geographical]</target> -->
diff --git a/plans/tomap-habitats.plan b/plans/tomap-habitats.plan
index da458fd1932cceace194e9cae09134bd2bf10027..46bbb98d0e1a2aadb023988465071097e7a11a72 100644
--- a/plans/tomap-habitats.plan
+++ b/plans/tomap-habitats.plan
@@ -3,18 +3,18 @@
 
   <!-- ToMap on lemmas -->
   <tomap class="TomapProjector">
-    <yateaFile output-feed="true">yatea/candidates.xml</yateaFile>
+    <yateaFile output-feed="true">corpora/&corpus;/batches/&batch;/yatea/candidates.xml</yateaFile>
     <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">ancillaries/BioNLP-OST+EnovFood-Habitat.tomap</tomapClassifier>
+    <tomapClassifier empty-words="ancillaries/stopwords_EN.ttg" graylist="ancillaries/graylist_extended.heads" whole-proxy-distance="false">&ontobiotope;-Habitat.tomap</tomapClassifier>
     <lemmaKeys/>
     <subject feature="lemma" layer="words"/>
     <scoreFeature>score</scoreFeature>
   </tomap>
 
   <concept-names class="OBOMapper">
-    <oboFiles>ancillaries/BioNLP-OST+EnovFood-Habitat.obo</oboFiles>
+    <oboFiles>&ontobiotope;-Habitat.obo</oboFiles>
     <idKeys/>
     <target>documents.sections.layer:habitats</target>
     <form>@concept-id</form>
@@ -26,18 +26,18 @@
   <tomap-on-alternative-lemmas>
 
     <tomap class="TomapProjector">
-      <yateaFile output-feed="true">yatea/candidates.xml</yateaFile>
+      <yateaFile output-feed="true">corpora/&corpus;/batches/&batch;/yatea/candidates.xml</yateaFile>
       <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">ancillaries/BioNLP-OST+EnovFood-Habitat.tomap</tomapClassifier>
+      <tomapClassifier empty-words="ancillaries/stopwords_EN.ttg" graylist="ancillaries/graylist_extended.heads" whole-proxy-distance="false">&ontobiotope;-Habitat.tomap</tomapClassifier>
       <lemmaKeys/>
       <subject feature="lemma2" layer="words"/>
       <scoreFeature>score</scoreFeature>
     </tomap>
 
     <concept-names class="OBOMapper">
-      <oboFiles>ancillaries/BioNLP-OST+EnovFood-Habitat.obo</oboFiles>
+      <oboFiles>&ontobiotope;-Habitat.obo</oboFiles>
       <idKeys/>
       <target>documents.sections.layer:habitats2</target>
       <form>@concept-id</form>
@@ -58,17 +58,17 @@
   <tomap-no-lemmakeys>
 
     <tomap class="TomapProjector">
-      <yateaFile output-feed="true">yatea/candidates.xml</yateaFile>
+      <yateaFile output-feed="true">corpora/&corpus;/batches/&batch;/yatea/candidates.xml</yateaFile>
       <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">ancillaries/BioNLP-OST+EnovFood-Habitat.tomap</tomapClassifier>
+      <tomapClassifier empty-words="ancillaries/stopwords_EN.ttg" graylist="ancillaries/graylist_extended.heads" whole-proxy-distance="false">&ontobiotope;-Habitat.tomap</tomapClassifier>
       <subject feature="lemma" layer="words"/>
       <scoreFeature>score</scoreFeature>
     </tomap>
 
     <concept-names class="OBOMapper">
-      <oboFiles>ancillaries/BioNLP-OST+EnovFood-Habitat.obo</oboFiles>
+      <oboFiles>&ontobiotope;-Habitat.obo</oboFiles>
       <idKeys/>
       <target>documents.sections.layer:habitats3</target>
       <form>@concept-id</form>
@@ -89,18 +89,18 @@
   <tomap-on-variants>
 
     <tomap class="TomapProjector">
-      <yateaFile output-feed="true">yatea-var/candidates.xml</yateaFile>
+      <yateaFile output-feed="true">corpora/&corpus;/batches/&batch;/yatea-var/candidates.xml</yateaFile>
       <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">ancillaries/BioNLP-OST+EnovFood-Habitat.tomap</tomapClassifier>
+      <tomapClassifier empty-words="ancillaries/stopwords_EN.ttg" graylist="ancillaries/graylist_extended.heads" whole-proxy-distance="false">&ontobiotope;-Habitat.tomap</tomapClassifier>
       <lemmaKeys/>
       <subject feature="variant" layer="words"/>
       <scoreFeature>score</scoreFeature>
     </tomap>
 
     <concept-names class="OBOMapper">
-      <oboFiles>ancillaries/BioNLP-OST+EnovFood-Habitat.obo</oboFiles>
+      <oboFiles>&ontobiotope;-Habitat.obo</oboFiles>
       <idKeys/>
       <target>documents.sections.layer:habitats4</target>
       <form>@concept-id</form>
@@ -121,17 +121,17 @@
   <tomap-no-lemmakeys-word-form>
 
     <tomap class="TomapProjector">
-      <yateaFile output-feed="true">yatea/candidates.xml</yateaFile>
+      <yateaFile output-feed="true">corpora/&corpus;/batches/&batch;/yatea/candidates.xml</yateaFile>
       <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">ancillaries/BioNLP-OST+EnovFood-Habitat.tomap</tomapClassifier>
+      <tomapClassifier empty-words="ancillaries/stopwords_EN.ttg" graylist="ancillaries/graylist_extended.heads" whole-proxy-distance="false">&ontobiotope;-Habitat.tomap</tomapClassifier>
       <subject feature="form" layer="words"/>
       <scoreFeature>score</scoreFeature>
     </tomap>
 
     <concept-names class="OBOMapper">
-      <oboFiles>ancillaries/BioNLP-OST+EnovFood-Habitat.obo</oboFiles>
+      <oboFiles>&ontobiotope;-Habitat.obo</oboFiles>
       <idKeys/>
       <target>documents.sections.layer:habitats5</target>
       <form>@concept-id</form>
@@ -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">yatea/candidates.xml</yateaFile> <!-- ??? -->
+    <yateaFile output-feed="yes">corpora/&corpus;/batches/&batch;/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">
@@ -714,7 +714,7 @@
 
 <!-- Add concept-path in case some are missing -->
     <concept-path class="OBOMapper">
-      <oboFiles>ancillaries/BioNLP-OST+EnovFood-Habitat.obo</oboFiles>
+      <oboFiles>&ontobiotope;-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 f55357aa56a7004280b8a5bae6cef17a501a97fe..17481643bb3b90c66ab16caa337ee600eb2f1f0f 100644
--- a/plans/tomap-microbial-phenotypes.plan
+++ b/plans/tomap-microbial-phenotypes.plan
@@ -2,18 +2,18 @@
   
   <!-- ToMap on lemmas -->
   <tomap class="TomapProjector">
-    <yateaFile output-feed="true">yatea/candidates.xml</yateaFile>
+    <yateaFile output-feed="true">corpora/&corpus;/batches/&batch;/yatea/candidates.xml</yateaFile>
     <targetLayerName>phenotypes</targetLayerName>
     <conceptFeature>concept-id</conceptFeature>
     <explanationFeaturePrefix>explain_</explanationFeaturePrefix>
-    <tomapClassifier empty-words="ancillaries/stopwords_EN.ttg" whole-proxy-distance="false">ancillaries/BioNLP-OST+EnovFood-Phenotype.tomap</tomapClassifier>
+    <tomapClassifier empty-words="ancillaries/stopwords_EN.ttg" whole-proxy-distance="false">&ontobiotope;-Phenotype.tomap</tomapClassifier>
     <lemmaKeys/>
     <subject feature="lemma" layer="words"/>
     <scoreFeature>score</scoreFeature>
   </tomap>
 
   <concept-names class="OBOMapper">
-    <oboFiles>ancillaries/BioNLP-OST+EnovFood-Phenotype.obo</oboFiles>
+    <oboFiles>&ontobiotope;-Phenotype.obo</oboFiles>
     <idKeys/>
     <target>documents.sections.layer:phenotypes</target>
     <form>@concept-id</form>
@@ -25,18 +25,18 @@
   <tomap-on-alternative-lemmas>
 
     <tomap class="TomapProjector">
-      <yateaFile output-feed="true">yatea/candidates.xml</yateaFile>
+      <yateaFile output-feed="true">corpora/&corpus;/batches/&batch;/yatea/candidates.xml</yateaFile>
       <targetLayerName>phenotypes2</targetLayerName>
       <conceptFeature>concept-id</conceptFeature>
       <explanationFeaturePrefix>explain_</explanationFeaturePrefix>
-      <tomapClassifier empty-words="ancillaries/stopwords_EN.ttg" whole-proxy-distance="false">ancillaries/BioNLP-OST+EnovFood-Phenotype.tomap</tomapClassifier>
+      <tomapClassifier empty-words="ancillaries/stopwords_EN.ttg" whole-proxy-distance="false">&ontobiotope;-Phenotype.tomap</tomapClassifier>
       <lemmaKeys/>
       <subject feature="lemma2" layer="words"/>
       <scoreFeature>score</scoreFeature>
     </tomap>
 
     <concept-names class="OBOMapper">
-      <oboFiles>ancillaries/BioNLP-OST+EnovFood-Phenotype.obo</oboFiles>
+      <oboFiles>&ontobiotope;-Phenotype.obo</oboFiles>
       <idKeys/>
       <target>documents.sections.layer:phenotypes2</target>
       <form>@concept-id</form>
@@ -57,17 +57,17 @@
   <tomap-no-lemmakeys>
 
     <tomap class="TomapProjector">
-      <yateaFile output-feed="true">yatea/candidates.xml</yateaFile>
+      <yateaFile output-feed="true">corpora/&corpus;/batches/&batch;/yatea/candidates.xml</yateaFile>
       <targetLayerName>phenotypes3</targetLayerName>
       <conceptFeature>concept-id</conceptFeature>
       <explanationFeaturePrefix>explain_</explanationFeaturePrefix>
-      <tomapClassifier empty-words="ancillaries/stopwords_EN.ttg" whole-proxy-distance="false">ancillaries/BioNLP-OST+EnovFood-Phenotype.tomap</tomapClassifier>
+      <tomapClassifier empty-words="ancillaries/stopwords_EN.ttg" whole-proxy-distance="false">&ontobiotope;-Phenotype.tomap</tomapClassifier>
       <subject feature="lemma" layer="words"/>
       <scoreFeature>score</scoreFeature>
     </tomap>
 
     <concept-names class="OBOMapper">
-      <oboFiles>ancillaries/BioNLP-OST+EnovFood-Phenotype.obo</oboFiles>
+      <oboFiles>&ontobiotope;-Phenotype.obo</oboFiles>
       <idKeys/>
       <target>documents.sections.layer:phenotypes3</target>
       <form>@concept-id</form>
@@ -89,18 +89,18 @@
   <tomap-on-variants>
 
     <tomap class="TomapProjector">
-      <yateaFile output-feed="true">yatea-var/candidates.xml</yateaFile>
+      <yateaFile output-feed="true">corpora/&corpus;/batches/&batch;/yatea-var/candidates.xml</yateaFile>
       <targetLayerName>phenotypes4</targetLayerName>
       <conceptFeature>concept-id</conceptFeature>
       <explanationFeaturePrefix>explain_</explanationFeaturePrefix>
-      <tomapClassifier empty-words="ancillaries/stopwords_EN.ttg" whole-proxy-distance="false">ancillaries/BioNLP-OST+EnovFood-Phenotype.tomap</tomapClassifier>
+      <tomapClassifier empty-words="ancillaries/stopwords_EN.ttg" whole-proxy-distance="false">&ontobiotope;-Phenotype.tomap</tomapClassifier>
       <lemmaKeys/>
       <subject feature="variant" layer="words"/>
       <scoreFeature>score</scoreFeature>
     </tomap>
 
     <concept-names class="OBOMapper">
-      <oboFiles>ancillaries/BioNLP-OST+EnovFood-Phenotype.obo</oboFiles>
+      <oboFiles>&ontobiotope;-Phenotype.obo</oboFiles>
       <idKeys/>
       <target>documents.sections.layer:phenotypes4</target>
       <form>@concept-id</form>
@@ -121,17 +121,17 @@
   <tomap-no-lemmakeys-word-form>
 
     <tomap class="TomapProjector">
-      <yateaFile output-feed="true">yatea/candidates.xml</yateaFile>
+      <yateaFile output-feed="true">corpora/&corpus;/batches/&batch;/yatea/candidates.xml</yateaFile>
       <targetLayerName>phenotypes5</targetLayerName>
       <conceptFeature>concept-id</conceptFeature>
       <explanationFeaturePrefix>explain_</explanationFeaturePrefix>
-      <tomapClassifier empty-words="ancillaries/stopwords_EN.ttg" whole-proxy-distance="false">ancillaries/BioNLP-OST+EnovFood-Phenotype.tomap</tomapClassifier>
+      <tomapClassifier empty-words="ancillaries/stopwords_EN.ttg" whole-proxy-distance="false">&ontobiotope;-Phenotype.tomap</tomapClassifier>
       <subject feature="form" layer="words"/>
       <scoreFeature>score</scoreFeature>
     </tomap>
 
     <concept-names class="OBOMapper">
-      <oboFiles>ancillaries/BioNLP-OST+EnovFood-Phenotype.obo</oboFiles>
+      <oboFiles>&ontobiotope;-Phenotype.obo</oboFiles>
       <idKeys/>
       <target>documents.sections.layer:phenotypes5</target>
       <form>@concept-id</form>
@@ -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">yatea/candidates.xml</yateaFile> <!-- ??? -->
+    <yateaFile output-feed="yes">corpora/&corpus;/batches/&batch;/yatea/candidates.xml</yateaFile> <!-- ??? -->
     <subject layer="words"/>
     <termLemma>lemma</termLemma>
   </bioyatea-projection>
@@ -394,7 +394,7 @@
   <!--    <idFeature>molecule-id</idFeature> -->
   <!--    <nameFeature>molecule-name</nameFeature> -->
   <!--    <pathFeature>molecule-path</pathFeature> -->
-  <!--    <oboFiles>ancillaries/BioNLP-OST+EnovFood-Molecule.obo</oboFiles> -->
+  <!--    <oboFiles>&ontobiotope;-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>ancillaries/BioNLP-OST+EnovFood-Molecule.obo</oboFiles> -->
+  <!--    <oboFiles>&ontobiotope;-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>ancillaries/BioNLP-OST+EnovFood-Phenotype.obo</oboFiles>
+      <oboFiles>&ontobiotope;-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 87195d8d5434aaa4ac887c01765ea83e3c1d4a05..5d12302993b0490526cb682ad0934cca5820bda1 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>ancillaries/Use_V2.obo</oboFiles>
+    <oboFiles>&ontobiotope-use;.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>ancillaries/Use_V2.obo</oboFiles>
+    <oboFiles>&ontobiotope-use;.obo</oboFiles>
     <targetLayerName>uses2</targetLayerName>
     <subject feature="lemma" layer="words"/>
     <idFeature>concept-id</idFeature>
diff --git a/process-evaluate_BioNLP-OST.snakefile b/process-evaluate_BioNLP-OST.snakefile
index 629e84b58eea01802d1b2c754c720a8783456ecc..a237c0749b04326ee1aae3462fb93dfee352bd44 100644
--- a/process-evaluate_BioNLP-OST.snakefile
+++ b/process-evaluate_BioNLP-OST.snakefile
@@ -41,14 +41,9 @@ rule run_bionlp_prediction:
 	params:
 		batch="{B}",
 		corpus='BioNLP-OST-2019',
-        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',
+                inhibitSyntax='inhibit-syntax',
+		onto='ancillaries/BioNLP-OST+EnovFood',
+                ontobiotopeUse='ancillaries/Use_V2',
 		plan='plans/entities.plan',
 		dir='corpora/BioNLP-OST-2019/batches/{B}/',
 		taxid_microorganisms='ancillaries/extended-microorganisms-taxonomy/taxid_microorganisms.txt',
@@ -59,14 +54,14 @@ rule run_bionlp_prediction:
 		-log {log} \
 		-alias format bionlp-st \
 		-alias input-dir {input.dir} \
-		-outputDir {params.dir} \
+		-alias input-xslt {input.xslt} \
+		-alias outputDir {params.dir} \
 		-environmentEntities \
+		-entity corpus {params.corpus} \
 		-feat inhibit-syntax {params.inhibitSyntax} \
-        -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 ontobiotope {params.onto} \
+		-entity ontobiotope-use {params.ontobiotopeUse} \
+		-entity batch {params.batch} \
 		-alias taxid_microorganisms {params.taxid_microorganisms} \
 		-alias taxa+id_full {params.taxa_id_full} \
 		{params.plan}	    
diff --git a/process_CIRM_corpus.snakefile b/process_CIRM_corpus.snakefile
index f9f49e74a7c963826b96a1eed27b4ebbecd48f8c..2b172cf78ac91f2f0387201244ff924c6a48a7ee 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/bia_taxa.txt',
-		habitats='corpora/cirm/bia/bia_habitats.txt',
+		taxa='corpora/cirm/bia_taxa.txt',
+		habitats='corpora/cirm/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/levures/yeast_taxa.txt',
-		habitats='corpora/cirm/levures/yeast_habitats.txt',
+		taxa='corpora/cirm/yeast_taxa.txt',
+		habitats='corpora/cirm/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/cfbp_taxa.txt',
-		habitats='corpora/cirm/cfbp/cfbp_habitats.txt',
+		taxa='corpora/cirm/cfbp_taxa.txt',
+		habitats='corpora/cirm/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/bia_taxa.txt'
+		taxa='corpora/cirm/bia_taxa.txt'
 	output:
-		mapped_taxaids='corpora/cirm/bia/mapped_bia_taxa.txt'
+		mapped_taxaids='corpora/cirm/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/levures/yeast_taxa.txt'
+		taxa='corpora/cirm/yeast_taxa.txt'
 	output:
-		mapped_taxaids='corpora/cirm/levures/mapped_yeast_taxa.txt'
+		mapped_taxaids='corpora/cirm/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/cfbp_taxa.txt'
+		taxa='corpora/cirm/cfbp_taxa.txt'
 	output:
-		mapped_taxa='corpora/cirm/cfbp/mapped_cfbp_taxa.txt'
+		mapped_taxa='corpora/cirm/mapped_cfbp_taxa.txt'
 	params:
 		plan='plans/map_microorganisms.plan',
 		taxid_microorganisms='ancillaries/extended-microorganisms-taxonomy/taxid_microorganisms.txt',
@@ -139,22 +139,19 @@ map habitats of microorganisms
 '''
 rule map_cirm_habitats:
 	input:
-		habitats='corpora/cirm/bia/bia_habitats.txt'
+		habitats='corpora/cirm/bia_habitats.txt'
 	output:
-		mapped_habitats='corpora/cirm/bia/mapped_bia_habitats.txt'
+		mapped_habitats='corpora/cirm/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',
-		outdir='corpora/cirm/bia',
-		outfile='mapped_bia_habitats.txt'
+		emptywords='ancillaries/stopwords_EN.ttg'
 	singularity:config["SINGULARITY_IMG"]
 	shell: """alvisnlp -J-Xmx32g -cleanTmp -verbose \
 	-alias input {input.habitats} \
-    -outputDir {params.outdir} \
-	-alias output {params.outfile} \
+	-alias output {output.mapped_habitats} \
 	-alias ontobiotope {params.onto} \
 	-xalias '<ontobiotope-tomap empty-words="{params.emptywords}" graylist="{params.graylist}" whole-proxy-distance="false">{params.tomap}</ontobiotope-tomap>' \
 	{params.plan}
@@ -165,22 +162,19 @@ map habitats of microorganisms (CIRM Levures)
 '''
 rule map_cirm_yeast_habitats:
 	input:
-		habitats='corpora/cirm/levures/yeast_habitats.txt'
+		habitats='corpora/cirm/yeast_habitats.txt'
 	output:
-		mapped_habitats='corpora/cirm/levures/mapped_yeast_habitats.txt'
+		mapped_habitats='corpora/cirm/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',
-		outdir='corpora/cirm/levures',
-		outfile='mapped_yeast_habitats.txt'
+		emptywords='ancillaries/stopwords_EN.ttg'
 	singularity:config["SINGULARITY_IMG"]
 	shell: """alvisnlp -J-Xmx32g -cleanTmp -verbose \
 	-alias input {input.habitats} \
-    -outputDir {params.outdir} \
-	-alias output {params.outfile} \
+	-alias output {output.mapped_habitats} \
 	-alias ontobiotope {params.onto} \
 	-xalias '<ontobiotope-tomap empty-words="{params.emptywords}" graylist="{params.graylist}" whole-proxy-distance="false">{params.tomap}</ontobiotope-tomap>' \
 	{params.plan}
@@ -191,22 +185,19 @@ map habitats of microorganisms (CIRM CFBP)
 '''
 rule map_cirm_cfbp_habitats:
 	input:
-		habitats='corpora/cirm/cfbp/cfbp_habitats.txt'
+		habitats='corpora/cirm/cfbp_habitats.txt'
 	output:
-		mapped_habitats='corpora/cirm/cfbp/mapped_cfbp_habitats.txt'
+		mapped_habitats='corpora/cirm/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',
-		outdir='corpora/cirm/cfbp',
-		outfile='mapped_cfbp_habitats.txt'
+		emptywords='ancillaries/stopwords_EN.ttg'
 	singularity:config["SINGULARITY_IMG"]
 	shell: """alvisnlp -J-Xmx32g -cleanTmp -verbose \
 	-alias input {input.habitats} \
-    -outputDir {params.outdir} \
-	-alias output {params.outfile} \
+	-alias output {output.mapped_habitats} \
 	-alias ontobiotope {params.onto} \
 	-xalias '<ontobiotope-tomap empty-words="{params.emptywords}" graylist="{params.graylist}" whole-proxy-distance="false">{params.tomap}</ontobiotope-tomap>' \
 	{params.plan}
@@ -218,8 +209,8 @@ format results
 rule format_cirm_results:
 	input:
 		file='corpora/cirm/BIA_2021/florilege_export_final_17_02_21.tsv',
-		taxa='corpora/cirm/bia/mapped_bia_taxa.txt',
-		habitats='corpora/cirm/bia/mapped_bia_habitats.txt'
+		taxa='corpora/cirm/mapped_bia_taxa.txt',
+		habitats='corpora/cirm/mapped_bia_habitats.txt'
 	output:
 		result='corpora/florilege/cirm/cirm-bia-results.txt'
 	params:
@@ -235,8 +226,8 @@ format results (CIRM Levures)
 rule format_cirm_yeast_results:
 	input:
 		file='corpora/cirm/Levures_2021/Florilege_21012021.tsv',
-		taxa='corpora/cirm/levures/mapped_yeast_taxa.txt',
-		habitats='corpora/cirm/levures/mapped_yeast_habitats.txt'
+		taxa='corpora/cirm/mapped_yeast_taxa.txt',
+		habitats='corpora/cirm/mapped_yeast_habitats.txt'
 	output:
 		result='corpora/florilege/cirm/cirm-yeast-results.txt'
 	params:
@@ -251,8 +242,8 @@ format results (CIRM CFBP)
 rule format_cirm_cfbp_results:
 	input:
 		file='corpora/cirm/CFBP_2021/20210617_PPortier.tsv',
-		taxa='corpora/cirm/cfbp/mapped_cfbp_taxa.txt',
-		habitats='corpora/cirm/cfbp/mapped_cfbp_habitats.txt'
+		taxa='corpora/cirm/mapped_cfbp_taxa.txt',
+		habitats='corpora/cirm/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 8fde651932d3c4255ef92b8bbbfb11f822308cf3..b4fa67fa3a0830be87fa78e37a69270333359c55 100644
--- a/process_DSMZ_corpus.snakefile
+++ b/process_DSMZ_corpus.snakefile
@@ -35,14 +35,11 @@ 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',
-		outdir='corpora/dsmz',
-		outfile='mapped_habitats.txt'
+		emptywords='ancillaries/stopwords_EN.ttg'
 	singularity:config["SINGULARITY_IMG"]
 	shell: """alvisnlp -J-Xmx32g -cleanTmp -verbose \
 	-alias input {input.habitats} \
-    -outputDir {params.outdir} \
-	-alias output {params.outfile} \
+	-alias output {output.mapped_habitats} \
 	-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 888835e413b1864c216cebcf38a65355270f103e..388f9ab1da3af0ffa392a81c44802b85b812d21b 100644
--- a/process_GenBank_corpus.snakefile
+++ b/process_GenBank_corpus.snakefile
@@ -79,14 +79,11 @@ rule map_genbank_habitats:
 		tomap='ancillaries/BioNLP-OST+EnovFood-Habitat.tomap',
 		graylist='ancillaries/graylist_extended.heads',
 		emptywords='ancillaries/stopwords_EN.ttg',
-		inhibitSyntax='inhibit-syntax',
-		outdir='corpora/genbank',
-		outfile='mapped_habitats.txt'
+		inhibitSyntax='inhibit-syntax'
 	singularity:config["SINGULARITY_IMG"]
 	shell: """alvisnlp -J-Xmx32g -cleanTmp -verbose \
 	-alias input {input.habitats} \
-    -outputDir {params.outdir} \
-	-alias output {params.outfile} \
+	-alias output {output.mapped_habitats}\
 	-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>' \
diff --git a/process_PubMed_corpus.snakefile b/process_PubMed_corpus.snakefile
index 5710034a3d3862750f5fcff9027c2a2411ed89db..7fd42f33b809b64d119f5f88c543976bf8ebc097 100644
--- a/process_PubMed_corpus.snakefile
+++ b/process_PubMed_corpus.snakefile
@@ -46,14 +46,9 @@ rule run_pubmed_entities:
 	params:
 		batch="{B}",
 		corpus='pubmed',
-        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',
+                inhibitSyntax='inhibit-syntax',
+		onto='ancillaries/BioNLP-OST+EnovFood',
+                ontobiotopeUse='ancillaries/Use_V2',
 		plan='plans/entities.plan',
 		dir='corpora/pubmed/batches/{B}/',
 		taxid_microorganisms='ancillaries/extended-microorganisms-taxonomy/taxid_microorganisms.txt',
@@ -66,15 +61,13 @@ rule run_pubmed_entities:
 		-alias format pubmed \
 		-alias input {input.file} \
 		-alias input-xslt {input.xslt} \
-        -alias batch batch={params.batch} \
-        -outputDir {params.dir} \
+		-alias outputDir {params.dir} \
 		-environmentEntities \
+		-entity corpus {params.corpus} \
 		-feat inhibit-syntax {params.inhibitSyntax} \
-        -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 ontobiotope {params.onto} \
+		-entity ontobiotope-use {params.ontobiotopeUse} \
+		-entity batch {params.batch} \
 		-alias taxid_microorganisms {params.taxid_microorganisms} \
 		-alias taxa+id_full {params.taxa_id_full} \
 		{params.plan}