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Commit bf4c4556 authored by Louise Deleger's avatar Louise Deleger
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removed entities

parent d2b71ddb
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3 merge requests!44Revert "Merge branch '40-evaluate-pubmed-pipeline-with-bb' into 'master'",!42From ld,!39Remove entities in plans
......@@ -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}
......
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