diff --git a/.gitignore b/.gitignore
index cf2817aecc6ae86c9d0f7f2cab2e8f9d5356996f..7b829ec7858ac542d09b369d49277eed61cee8d8 100644
--- a/.gitignore
+++ b/.gitignore
@@ -27,36 +27,37 @@ corpora/genbank/mapped_habitats.txt
corpora/genbank/mapped_taxids.txt
corpora/genbank/taxids.txt
corpora/genbank/test-3.2.txt
-corpora/*-2019/batch/*/adb/
-corpora/*-2019/batch/*/alvisnlp.log
-corpora/*-2019/batch/*/anaphora.txt
-corpora/*-2019/batch/*/bacteria.txt
-corpora/*-2019/batch/*/dependencies.txt
-corpora/*-2019/batch/*/doc-mesh.txt
-corpora/*-2019/batch/*/geo.txt
-corpora/*-2019/batch/*/habitats.txt
-corpora/*-2019/batch/*/index-food/
-corpora/*-2019/batch/*/index/
-corpora/*-2019/batch/*/microorganisms-short.txt
-corpora/*-2019/batch/*/microorganisms.txt
-corpora/*-2019/batch/*/phenotype-relations.txt
-corpora/*-2019/batch/*/phenotypes.txt
-corpora/*-2019/batch/*/relations.txt
-corpora/*-2019/batch/*/sentences.txt
-corpora/*-2019/batch/*/success.txt
-corpora/*-2019/batch/*/taxa.txt
-corpora/*-2019/batch/*/uses-relations.txt
-corpora/*-2019/batch/*/uses.txt
-corpora/*-2019/batch/*/words.txt
-corpora/*-2019/batch/*/yatea-var/
-corpora/*-2019/batch/*/yatea/
-corpora/*-2019/expander/
-corpora/*-2019/batch/*/a2/
+corpora/*/batch/*/adb/
+corpora/*/batch/*/alvisnlp.log
+corpora/*/batch/*/anaphora.txt
+corpora/*/batch/*/bacteria.txt
+corpora/*/batch/*/dependencies.txt
+corpora/*/batch/*/doc-mesh.txt
+corpora/*/batch/*/geo.txt
+corpora/*/batch/*/habitats.txt
+corpora/*/batch/*/index-food/
+corpora/*/batch/*/index/
+corpora/*/batch/*/microorganisms-short.txt
+corpora/*/batch/*/microorganisms.txt
+corpora/*/batch/*/phenotype-relations.txt
+corpora/*/batch/*/phenotypes.txt
+corpora/*/batch/*/relations.txt
+corpora/*/batch/*/sentences.txt
+corpora/*/batch/*/success.txt
+corpora/*/batch/*/taxa.txt
+corpora/*/batch/*/uses-relations.txt
+corpora/*/batch/*/uses.txt
+corpora/*/batch/*/words.txt
+corpora/*/batch/*/yatea-var/
+corpora/*/batch/*/yatea/
+corpora/*/expander/
+corpora/*/batch/*/a2/
corpora/BioNLP-OST-2019/batch/*/eval.json
corpora/BioNLP-OST-2019/batch/*/predictions.zip
corpora/microbes-2019/*.full.txt
corpora/microbes-2019/index/
.snakemake/
+ancillaries/extended-microorganisms-taxonomy
ancillaries/BioNLP-OST+EnovFood-Habitat.json
ancillaries/BioNLP-OST+EnovFood-Habitat.paths
ancillaries/BioNLP-OST+EnovFood-Habitat.tomap
diff --git a/all-bis.snakefile b/all-bis.snakefile
index 76a93b1340c43ca1e932276fe0d21ecdb7dfc99c..9ce4cd9183fe8d00bc6aa384b81b3d5fbbfb5921 100644
--- a/all-bis.snakefile
+++ b/all-bis.snakefile
@@ -21,7 +21,7 @@ rule preprocess_ontology:
input:
ontobiotope='ancillaries/BioNLP-OST+EnovFood.obo',
use_onto='ancillaries/Use_V2.obo',
- names='ancillaries/supertaxo/names.dmp'
+ names='ancillaries/extended-microorganisms-taxonomy/names.dmp'
output:
'ancillaries/BioNLP-OST+EnovFood-Habitat.json',
'ancillaries/BioNLP-OST+EnovFood-Phenotype.json',
diff --git a/all.snakefile b/all.snakefile
index 0eb24d3cc92c49b1ae71b1e6063ae6145128c19e..2a495be8533f55b624404131ee3ed638c92eb985 100644
--- a/all.snakefile
+++ b/all.snakefile
@@ -21,7 +21,7 @@ rule preprocess_ontology:
input:
ontobiotope='ancillaries/BioNLP-OST+EnovFood.obo',
use_onto='ancillaries/Use_V2.obo',
- names='ancillaries/supertaxo/names.dmp'
+ names='ancillaries/extended-microorganisms-taxonomy/names.dmp'
output:
'ancillaries/BioNLP-OST+EnovFood-Phenotype.json',
'ancillaries/Use_V2.json',
diff --git a/ancillaries/ncbi-taxonomy-prefix/dsmz-match/bacdive-to-taxid.txt b/ancillaries/ncbi-taxonomy-prefix/dsmz-match/bacdive-to-taxid.txt
deleted file mode 100644
index ed63d7d612dd11fa2acdd71d62f68d872123340c..0000000000000000000000000000000000000000
--- a/ancillaries/ncbi-taxonomy-prefix/dsmz-match/bacdive-to-taxid.txt
+++ /dev/null
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-137944 cip:102248
-137905 cip:102156
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-137469 cip:a107
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-137401 cip:55.115
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-1922 dsm:6756
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diff --git a/ancillaries/supertaxo/bacdive-to-taxid.txt b/ancillaries/supertaxo/bacdive-to-taxid.txt
deleted file mode 100644
index bce3aa2b38a31209a42787eebec54ea39c81453e..0000000000000000000000000000000000000000
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-137630 cip:102485
-137624 cip:101873
-137650 cip:103784
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-136740 cip:60.53
-136756 cip:104929
-136770 cip:107049
-136717 cip:pat271
-136757 cip:104927
-136764 cip:102140
-136750 cip:64.15
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-121169 st:009557
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-121113 st:003928
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-2985 ncbi:866565
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-2951 dsm:18833
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-2964 dsm:650
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-2957 ncbi:491745
-2913 dsm:6577
-2989 ncbi:28066
-2962 dsm:12828
-3004 dsm:1071
-2914 dsm:6781
-2943 dsm:8370
-2997 dsm:12826
-2992 ncbi:76731
-2995 ncbi:215580
-2944 dsm:12586
-2924 dsm:6838
-2998 ncbi:80882
-2970 ncbi:249410
-2916 dsm:11414
-3000 dsm:645
-2919 dsm:14802
-2994 dsm:15264
-2933 ncbi:363952
-2909 ncbi:491919
-2927 ncbi:32013
-2953 dsm:23722
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-2907 dsm:18852
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-2910 dsm:1455
-2991 dsm:13235
-2922 dsm:50242
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-2978 ncbi:263067
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-2942 dsm:6411
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-2921 dsm:50241
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-2946 dsm:17854
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-2940 dsm:1621
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-2929 ncbi:108437
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-2925 dsm:15091
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-2955 dsm:13225
-2918 dsm:14576
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-2917 dsm:12678
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-2938 ncbi:663949
-2906 ncbi:179636
-2963 ncbi:65657
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-2949 dsm:12781
-2939 ncbi:80879
-2966 ncbi:47421
-2923 ncbi:285
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-2987 ncbi:94132
-2960 ncbi:314202
-2993 dsm:11814
-2959 ncbi:80883
-2941 ncbi:80866
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-158675 ncbi:1925763
-158636 ncbi:2047982
-158612 ncbi:2070451
-158661 cgmcc:1.16115
-158601 ncbi:2060098
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-158669 ncbi:1981892
-158617 ncbi:2021220
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-158623 ncbi:2056779
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-158664 ncbi:1656885
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-158630 ncbi:2078954
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-158639 ncbi:1678728
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-158600 ncbi:1758255
-158629 ncbi:2078952
-158625 ncbi:2072922
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-135627 cip:62.19
-135694 cip:76.12
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-135622 cip:61.2
-135617 cip:60.73
-135691 cip:75.19
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-135643 cip:76.58
-135653 cip:67.11
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-135626 cip:61.18
-135615 cip:59.46
-135664 cip:70.3
-135623 cip:61.3
-135618 cip:60.72
-135612 cip:59.26
-135644 cip:64.63
-135676 cip:76.60
-135673 cip:70.79
-135598 cip:57.12
-135606 cip:58.25
-135683 cip:73.13
-135604 cip:58.16
-135628 cip:62.20
-135696 cip:76.103
-135636 cip:63.65
-135672 cip:70.71
-135677 cip:71.38
-135647 cip:a169
-135639 cip:63.69
-135669 cip:70.41
-135697 cip:76.104
-135611 cip:59.25
-135682 cip:73.12
-135638 cip:63.68
-135608 cip:58.19
-135665 cip:70.5
-135654 cip:a174
-135686 cip:73.28
-135609 cip:58.35
-135692 cip:75.18
-135599 cip:a112
-135605 cip:58.10
-135602 cip:57.39
-135681 cip:72.10
-135625 cip:61.5
-135649 cip:a170
-135629 cip:62.22
-135690 cip:74.21
-135616 cip:60.31
-135610 cip:58.36
-135657 cip:68.26
-135600 cip:57.33
-135646 cip:66.30
-135693 cip:76.5
-135630 cip:62.23
-135613 cip:59.38
-135695 cip:76.44
-135621 cip:62.1
-135620 cip:61.7
-135631 cip:63.3
-135662 cip:70.37
-135637 cip:63.67
-135658 cip:68.30
-135659 cip:69.26
-135642 cip:65.21
-135650 cip:66.29
-135670 ccug:9696
-135601 cip:57.36
-135648 cip:66.32
-135661 cip:70.10
-135634 cip:63.34
-135624 cip:61.4
-135685 cip:73.27
-135687 cip:74.14
-135656 cip:68.23
-135651 cip:66.48
-135668 cip:72.8
-135641 cip:100644
-135674 cip:71.20
-135684 cip:73.14
-135632 cip:63.4
-135688 cip:74.15
-135679 cip:72.12
-135635 cip:63.35
-135640 cip:63.70
-135667 cip:70.21
-135633 cip:63.30
-135666 cip:70.7
-135614 cip:59.45
-135619 cip:60.74
-135652 cip:66.49
-139599 cip:109982
-139688 dsm:103904
-139602 cip:105831
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-139696 dsm:16815
-139616 ncbi:1678752
-139606 cip:70.31
-139670 cip:111184
-139691 dsm:16146
-139650 cip:110516
-139617 ncbi:1776859
-139687 dsm:103922
-139678 cip:58.14
-139633 cip:101447
-139655 cip:110533
-139640 cip:a179
-139669 cip:60.23
-139689 dsm:16285
-139608 cip:56.2
-139685 dsm:4222
-139607 cip:101934
-139609 cip:102595
-139601 cip:105827
-139676 cip:102328
-139656 ncbi:60217
-139657 cip:108286
-139684 dsm:26354
-139661 cip:105701
-139613 cip:102529
-139667 cip:104725
-139647 cip:110512
-139598 cip:105150
-139666 cip:107050
-139654 cip:110529
-139677 cip:52.55
-139614 cip:105630
-139668 cip:105091
-139651 cip:110520
-139658 ncbi:153266
-139629 cip:110534
-139663 ncbi:171194
-139694 dsm:16490
-139603 cip:53.82
-139662 cip:109753
-139646 cip:110511
-139665 cip:106754
-139605 cip:64.7
-139638 cip:54.166
-139615 cip:106179
-139621 cip:100825
-139680 cip:55.119
-139618 ncbi:1744846
-139693 dsm:16489
-139623 cip:105242
-139630 cip:100357
-139627 cip:101511
-139652 cip:110521
-139639 cip:60.42
-139644 cip:110505
-139643 cip:110504
-139611 cip:111047
-139622 cip:62.21
-139660 cip:109835
-139648 cip:110514
-139653 cip:110523
-139620 cip:100358
-139674 cip:102283
-139636 cip:53.119
-139631 cip:100529
-139664 cip:103659
-139641 cip:110371
-139635 cip:101606
-139682 dsm:17946
-139686 dsm:106266
-139679 cip:109783
-139697 dsm:16818
-139681 dsm:30190
-139637 cip:54.158
-139612 cip:101966
-139642 cip:110503
-139619 ncbi:574964
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-139626 cip:100668
-139604 cip:102136
-139692 dsm:16207
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-139632 cip:101418
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-139610 cip:108653
-139628 cip:101720
-139673 cip:102376
-139675 cip:102323
-139634 cip:101499
-139690 dsm:16286
-139672 cip:104220
-139659 ncbi:510946
-139683 dsm:18537
-139625 cip:101087
-139671 cip:107234
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-14420 ncbi:69969
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-136118 cip:102649
-136117 cip:102623
-136140 cip:102826
-136139 cip:102804
-136150 cip:102863
-136174 cip:103124
-136102 cip:102490
-136168 cip:103086
-136142 cip:102812
-136146 cip:110440
-136123 cip:102617
-136182 cip:52.220
-136148 cip:107345
-136122 cip:102664
-136131 cip:102723
-136195 cip:103314
-136134 cip:102746
-136149 cip:102859
-136166 cip:103077
-136121 cip:102659
-136147 cip:52.181
-136180 cip:103196
-136103 cip:102497
-136143 cip:102814
-136183 cip:103204
-136112 cip:102570
-136100 cip:102475
-136101 cip:102489
-136116 cip:102616
-136138 cip:102778
-136181 cip:103211
-136109 cip:102549
-136163 cip:52.205
-136162 cip:103059
-136175 cip:52.214
-136193 cip:52.229
-136170 cip:a42
-136104 cip:52.149
-136111 cip:102560
-136132 cip:102724
-136108 cip:102565
-136171 cip:103100
-136194 cip:52.231
-136179 cip:52.218
-136136 cip:52.174
-136128 cip:55.18
-136144 cip:102815
-136137 cip:102777
-136161 cip:52.204
-136120 cip:102658
-136178 cip:103184
-136176 cip:52.215
-136159 cip:103035
-136184 cip:103326
-136135 cip:52.173
-136124 cip:55.16
-136187 cip:52.223
-136133 cip:102736
-136125 cip:102668
-136177 cip:104926
-136169 cip:103097
-136189 cip:103245
-136188 cip:52.224
-136145 cip:52.180
-136152 cip:102927
-136157 cip:103058
-136192 cip:52.227
-136173 cip:103121
-136130 cip:102721
-136110 cip:52.154
-136156 cip:103011
-136155 cip:52.198
-136105 cip:102505
-136153 cip:52.193
-136107 cip:102535
-136164 cip:103074
-136158 cip:52.201
-136172 cip:103102
-136099 cip:102474
-136197 cip:103321
-136115 cip:102614
-136165 cip:52.206
-136196 cip:52.230
-136186 cip:52.222
-136126 cip:102669
-136098 cip:102473
-136185 cip:103213
-136154 cip:52.197
-136191 cip:52.226
-136127 cip:102702
-136113 cip:102587
-136190 cip:52.225
-136160 cip:103057
-136151 cip:102904
-136106 cip:102530
-136167 cip:103083
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diff --git a/ancillaries/supertaxo/names.dmp b/ancillaries/supertaxo/names.dmp
deleted file mode 100644
index 322d0035335fbee22096242aa064ceabecd1fa10..0000000000000000000000000000000000000000
Binary files a/ancillaries/supertaxo/names.dmp and /dev/null differ
diff --git a/ancillaries/supertaxo/taxa+id_microorganisms.txt b/ancillaries/supertaxo/taxa+id_microorganisms.txt
deleted file mode 100644
index d81f2194fa1ea739e28796191238c54e56d1ad12..0000000000000000000000000000000000000000
Binary files a/ancillaries/supertaxo/taxa+id_microorganisms.txt and /dev/null differ
diff --git a/ancillaries/supertaxo/taxid_microorganisms.txt b/ancillaries/supertaxo/taxid_microorganisms.txt
deleted file mode 100644
index 7fa4366de3cddfaf7a647d9eb01988d05501d5a7..0000000000000000000000000000000000000000
Binary files a/ancillaries/supertaxo/taxid_microorganisms.txt and /dev/null differ
diff --git a/plans/entities.plan b/plans/entities.plan
index 32b2d8b8872324188edb906dbdcaffc7f28afffb..ea2f03d6364c709e7e884ded2174e41fb43f51e3 100644
--- a/plans/entities.plan
+++ b/plans/entities.plan
@@ -195,14 +195,14 @@
<read>
<pubmed class="XMLReader">
- <sourcePath>corpora/&corpus;/batches/&batch;/batch.xml</sourcePath>
+ <sourcePath>corpora/&corpus;/batch/&batch;/batch.xml</sourcePath>
<xslTransform>ancillaries/&corpus;-pubmed2alvisnlp.xslt</xslTransform>
</pubmed>
<bionlp-st class="BioNLPSTReader">
<active>true</active>
<sectionName>abstract</sectionName>
- <textDir>corpora/&corpus;/batches/&batch;/bionlp-st</textDir>
+ <textDir>corpora/&corpus;/batch/&batch;/bionlp-st</textDir>
</bionlp-st>
</read>
@@ -304,10 +304,6 @@
<taxids class="FileMapper">
<target>documents.sections.layer:taxa</target>
<form>@taxid</form>
- <!--<operator>prefix</operator>-->
- <mappingFile>ancillaries/ncbi-taxonomy-prefix/taxid_microorganisms.txt</mappingFile>
- <!--<mappingFile>ancillaries/microorganisms.txt</mappingFile>-->
- <!--keyColumn>1</keyColumn-->
<targetFeatures>microorganism</targetFeatures>
</taxids>
diff --git a/plans/map_microorganisms.plan b/plans/map_microorganisms.plan
index 199e88cdebc3c21e64721660a9cbeb58e60423cd..06d8a3c4c19b3b40370497547b51feae2cd9e95d 100644
--- a/plans/map_microorganisms.plan
+++ b/plans/map_microorganisms.plan
@@ -38,10 +38,6 @@
<taxids class="FileMapper">
<target>documents.sections.layer:taxa</target>
<form>@taxid</form>
- <!--<operator>prefix</operator>-->
- <mappingFile>ancillaries/ncbi-taxonomy-prefix/taxid_microorganisms.txt</mappingFile>
- <!--<mappingFile>ancillaries/microorganisms.txt</mappingFile>-->
- <!--keyColumn>1</keyColumn-->
<targetFeatures>microorganism</targetFeatures>
</taxids>
diff --git a/plans/map_taxid.plan b/plans/map_taxid.plan
index 6522b46d4a8eaeeefbc6457cddcf82383f7069d8..eb1fa8f9f41eaef7448b6f1a92c5e666246df5c9 100644
--- a/plans/map_taxid.plan
+++ b/plans/map_taxid.plan
@@ -21,7 +21,6 @@
<taxids class="FileMapper">
<target>documents.sections</target>
<form>"ncbi:" ^ str:normalizeSpace(contents)</form>
- <mappingFile>ancillaries/ncbi-taxonomy-prefix/taxa+id_full.txt</mappingFile>
<keyColumn>1</keyColumn>
<targetFeatures>,taxid,canonical-name,path,pos,rank</targetFeatures>
</taxids>
diff --git a/plans/strains-1.plan b/plans/strains-1.plan
index 47eb3ff0dafc9f80edebd7692999b8e929188e15..52a1f3d46c1743de9c4f8ae6a5bef45622bda21a 100644
--- a/plans/strains-1.plan
+++ b/plans/strains-1.plan
@@ -11,7 +11,7 @@
</strainRegExp1>
<strainRegExp2 class="RegExp">
- <pattern>(?<=[Ss]train\s)((ATCC|DSMZ|family|mc)[\- ]?[0-9]+)</pattern>
+ <pattern>(?<=[Ss]train\s)?(([A-Z]{3,}|family|mc)[\- ]?[0-9]+)</pattern>
<targetLayerName>strainRE2</targetLayerName>
<constantAnnotationFeatures>subtype=strain</constantAnnotationFeatures>
</strainRegExp2>
diff --git a/plans/strains-2.plan b/plans/strains-2.plan
index c411f17867d546d75d15c26a9789b99960065b96..fd762088e170048ad3d5f9e0a43777f09b87299f 100644
--- a/plans/strains-2.plan
+++ b/plans/strains-2.plan
@@ -7,7 +7,7 @@
(bact:
[@microorganism]
)
- [@form=="strain" or @form=="Strain"]
+ [@form=="strain" or @form=="Strain"]?
(strain:
[@subtype=="strain"]
)
@@ -18,6 +18,24 @@
</actions>
</strainPattern1>
+ <strainPattern1-enum class="PatternMatcher">
+ <layerName>words</layerName>
+ <pattern>
+ (bact:
+ [@microorganism]
+ )
+ [ @form == "," or @subtype=="strain" ]+
+ [@form=="strain" or @form=="Strain"]?
+ (strain:
+ [@subtype=="strain"]
+ )
+ </pattern>
+ <actions>
+ <createAnnotation features="taxid=group:bact.@taxid,canonical-name=group:bact.@canonical-name,path=group:bact.@path,rank=group:bact.@rank" group="strain" layer="strains"/>
+ <createAnnotation features="taxid=group:bact.@taxid,canonical-name=group:bact.@canonical-name,path=group:bact.@path,rank=group:bact.@rank" group="strain" layer="shortNames"/>
+ </actions>
+ </strainPattern1-enum>
+
<strainPattern2 class="PatternMatcher">
<layerName>words</layerName>
<pattern>
diff --git a/plans/taxa.plan b/plans/taxa.plan
index 16f6ccb44e7ccfbca8ab228ef74f94b43855c101..df5d51b3df34d67169a3dd693646582639e464de 100644
--- a/plans/taxa.plan
+++ b/plans/taxa.plan
@@ -3,9 +3,8 @@
<dict class="TabularProjector">
<sectionFilter>@name == "title" or @name == "abstract" or @name == "text"</sectionFilter>
<targetLayerName>taxa</targetLayerName>
- <dictFile>ancillaries/ncbi-taxonomy-prefix/taxa+id_full.txt</dictFile>
- <!--<trieSink>ancillaries/ncbi-taxonomy-prefix/taxa+id_full.trie</trieSink>-->
- <!--<trieSource>ancillaries/ncbi-taxonomy-prefix/taxa+id_full.trie</trieSource>-->
+ <dictFile>ancillaries/extended-microorganisms-taxonomy/taxa+id_full.txt</dictFile>
+ <!--<trieSource>ancillaries/extended-microorganisms-taxonomy/taxa+id_full.trie</trieSource>-->
<matchStartCaseInsensitive/>
<valueFeatures>,taxid,canonical-name,path,pos,rank,species-taxid,species-name</valueFeatures>
<constantAnnotationFeatures>source=NCBI</constantAnnotationFeatures>
@@ -51,9 +50,6 @@
<taxids class="FileMapper">
<target>documents.sections.layer:taxa</target>
<form>@taxid</form>
- <!--<operator>prefix</operator>-->
- <mappingFile>ancillaries/ncbi-taxonomy-prefix/taxid_microorganisms.txt</mappingFile>
- <!--keyColumn>1</keyColumn-->
<targetFeatures>microorganism</targetFeatures>
</taxids>
diff --git a/plans/taxa_generic.plan b/plans/taxa_generic.plan
index 80f757396cee2bc2f22af4d51e1343690e3f5a86..c7b8d74c4df46fd58f2dcf47104289316b3cf390 100644
--- a/plans/taxa_generic.plan
+++ b/plans/taxa_generic.plan
@@ -1,7 +1,6 @@
<alvisnlp-plan id="taxa">
<dict class="TabularProjector">
<targetLayerName>taxa</targetLayerName>
- <dictFile>ancillaries/ncbi-taxonomy-prefix/taxa+id_full.txt</dictFile>
<matchStartCaseInsensitive/>
<valueFeatures>,taxid,canonical-name,path,pos,rank,species-taxid,species-name</valueFeatures>
<constantAnnotationFeatures>source=NCBI</constantAnnotationFeatures>
@@ -47,9 +46,6 @@
<taxids class="FileMapper">
<target>documents.sections.layer:taxa</target>
<form>@taxid</form>
- <!--<operator>prefix</operator>-->
- <mappingFile>ancillaries/ncbi-taxonomy-prefix/taxid_microorganisms.txt</mappingFile>
- <!--keyColumn>1</keyColumn-->
<targetFeatures>microorganism</targetFeatures>
</taxids>
diff --git a/preprocess-ontology.snakefile b/preprocess-ontology.snakefile
index 66d87f6b7144599c21176ad0635af41d44f0754a..d77135abd33f3a4d0001471c9c4d0e2eba812311 100644
--- a/preprocess-ontology.snakefile
+++ b/preprocess-ontology.snakefile
@@ -136,7 +136,7 @@ get ncbi names
'''
rule get_ncbi_names:
input:
- names='ancillaries/supertaxo/names.dmp'
+ names='ancillaries/extended-microorganisms-taxonomy/names.dmp'
output:
common_names='ancillaries/NCBI_common_names'
shell: 'grep "common name" {input.names} |cut -f1,2 -d"|" |perl -npe "s/\s+\|\s+/\t/; s/\s+\n/\n/;" > {output.common_names}'
diff --git a/process-evaluate_BioNLP-OST.snakefile b/process-evaluate_BioNLP-OST.snakefile
index 6cbeb4ff747c963df4a3c5b3e3c86b22db5a5ab2..3566f70de874447f2e6b1c2fe70c3ba62351edde 100644
--- a/process-evaluate_BioNLP-OST.snakefile
+++ b/process-evaluate_BioNLP-OST.snakefile
@@ -44,8 +44,8 @@ rule run_bionlp_prediction:
ontobiotopeUse='ancillaries/Use_V2',
plan='plans/entities.plan',
dir='corpora/BioNLP-OST-2019/batches/{B}/',
- taxid_microorganisms='ancillaries/supertaxo/taxid_microorganisms.txt',
- taxa_id_full='ancillaries/supertaxo/taxa+id_full.txt'
+ taxid_microorganisms='ancillaries/extended-microorganisms-taxonomy/taxid_microorganisms.txt',
+ taxa_id_full='ancillaries/extended-microorganisms-taxonomy/taxa+id_full.txt'
singularity:config["SINGULARITY_IMG"]
shell:"""
alvisnlp -J-XX:+UseSerialGC -J-Xmx10g -cleanTmp -verbose \
diff --git a/process_CIRM_corpus.snakefile b/process_CIRM_corpus.snakefile
index 42a9effcb0ee41d931355b5a970f02826994c58b..e699bd4b10b2d950ebebc6f965aeec32aa5ac5a2 100644
--- a/process_CIRM_corpus.snakefile
+++ b/process_CIRM_corpus.snakefile
@@ -80,8 +80,8 @@ rule map_cirm_bia_microorganisms:
mapped_taxaids='corpora/cirm/mapped_bia_taxa.txt'
params:
plan='plans/map_microorganisms.plan',
- taxid_microorganisms='ancillaries/supertaxo/taxid_microorganisms.txt',
- taxa_id_full='ancillaries/supertaxo/taxa+id_full.txt'
+ taxid_microorganisms='ancillaries/extended-microorganisms-taxonomy/taxid_microorganisms.txt',
+ taxa_id_full='ancillaries/extended-microorganisms-taxonomy/taxa+id_full.txt'
singularity:config["SINGULARITY_IMG"]
shell: """alvisnlp -J-Xmx32g -cleanTmp -verbose \
-alias input {input.taxa} \
@@ -101,8 +101,8 @@ rule map_cirm_yeast_microorganisms:
mapped_taxaids='corpora/cirm/mapped_yeast_taxa.txt'
params:
plan='plans/map_microorganisms.plan',
- taxid_microorganisms='ancillaries/supertaxo/taxid_microorganisms.txt',
- taxa_id_full='ancillaries/supertaxo/taxa+id_full.txt'
+ taxid_microorganisms='ancillaries/extended-microorganisms-taxonomy/taxid_microorganisms.txt',
+ taxa_id_full='ancillaries/extended-microorganisms-taxonomy/taxa+id_full.txt'
singularity:config["SINGULARITY_IMG"]
shell: """alvisnlp -J-Xmx32g -cleanTmp -verbose \
-alias input {input.taxa} \
@@ -123,8 +123,8 @@ rule map_cirm_cfbp_microorganisms:
mapped_taxa='corpora/cirm/mapped_cfbp_taxa.txt'
params:
plan='plans/map_microorganisms.plan',
- taxid_microorganisms='ancillaries/supertaxo/taxid_microorganisms.txt',
- taxa_id_full='ancillaries/supertaxo/taxa+id_full.txt'
+ taxid_microorganisms='ancillaries/extended-microorganisms-taxonomy/taxid_microorganisms.txt',
+ taxa_id_full='ancillaries/extended-microorganisms-taxonomy/taxa+id_full.txt'
singularity:config["SINGULARITY_IMG"]
shell: """alvisnlp -J-Xmx32g -cleanTmp -verbose \
-alias input {input.taxa} \
diff --git a/process_DSMZ_corpus.snakefile b/process_DSMZ_corpus.snakefile
index dbcdbec84d6cdf745fde0c99f72c58bd0b26ffb6..b4fa67fa3a0830be87fa78e37a69270333359c55 100644
--- a/process_DSMZ_corpus.snakefile
+++ b/process_DSMZ_corpus.snakefile
@@ -56,8 +56,8 @@ rule format_dsmz_results:
output:
result='corpora/florilege/dsmz/dsmz-results.txt'
params:
- taxa_id_full='ancillaries/supertaxo/taxa+id_full.txt',
- bacdive_taxid='ancillaries/supertaxo/bacdive-to-taxid.txt',
+ taxa_id_full='ancillaries/extended-microorganisms-taxonomy/taxa+id_full.txt',
+ bacdive_taxid='ancillaries/extended-microorganisms-taxonomy/bacdive-to-taxid.txt',
conda: 'softwares/envs/obo-utils-env.yaml'
shell: 'python softwares/Florilege/scripts/format-dsmz-results.py --bacdive-taxid {params.bacdive_taxid} --taxonomy {params.taxa_id_full} --dsmz-habitats {input.habitats_file} --mapped-habitats {input.habitats} > {output.result}'
diff --git a/process_GenBank_corpus.snakefile b/process_GenBank_corpus.snakefile
index 0b7d1d182a1d28b0a2934116e748f501f062b3df..2478b080a60cd8c3bd85e95a9cfcc9fefd2af1a1 100644
--- a/process_GenBank_corpus.snakefile
+++ b/process_GenBank_corpus.snakefile
@@ -17,7 +17,7 @@ extract genbank data
'''
rule extract_genbank_data:
input:
- taxa_microorganisms='ancillaries/supertaxo/taxa+id_microorganisms.txt',
+ taxa_microorganisms='ancillaries/extended-microorganisms-taxonomy/taxa+id_microorganisms.txt',
db_path='/db/genbank/current/flat'
output:
genbank_data='corpora/genbank/GenBank_extraction_20210127.tsv'
@@ -55,7 +55,7 @@ rule map_genbank_taxid:
output:
mapped_taxids='corpora/genbank/mapped_taxids.txt'
params:
- taxa_id_full='ancillaries/supertaxo/taxa+id_full.txt',
+ taxa_id_full='ancillaries/extended-microorganisms-taxonomy/taxa+id_full.txt',
plan='plans/map_taxid.plan'
singularity:config["SINGULARITY_IMG"]
shell: """alvisnlp -J-Xmx32g -cleanTmp -verbose \
diff --git a/process_PubMed_corpus.snakefile b/process_PubMed_corpus.snakefile
index aaef2bbc38b72b93000c9d11c4f188733370833f..3bc43eb12de2176a1f37991a66870918915e9ee4 100644
--- a/process_PubMed_corpus.snakefile
+++ b/process_PubMed_corpus.snakefile
@@ -52,8 +52,8 @@ rule run_pubmed_entities:
ontobiotopeUse='ancillaries/Use_V2',
plan='plans/entities.plan',
dir='corpora/pubmed/batches/{B}/',
- taxid_microorganisms='ancillaries/supertaxo/taxid_microorganisms.txt',
- taxa_id_full='ancillaries/supertaxo/taxa+id_full.txt',
+ 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'
singularity:config["SINGULARITY_IMG"]
shell:"""
@@ -124,7 +124,7 @@ create the expander
rule create_pubmed_expander:
input:
expander="ancillaries/expander.xml",
- taxa_id_microorganisms="ancillaries/supertaxo/taxa+id_microorganisms.txt",
+ taxa_id_microorganisms="ancillaries/extended-microorganisms-taxonomy/taxa+id_microorganisms.txt",
onto_habitat="ancillaries/BioNLP-OST+EnovFood-Habitat.obo",
onto_phenotype="ancillaries/BioNLP-OST+EnovFood-Phenotype.obo",
onto_use="ancillaries/Use_V2.obo"