diff --git a/ancillaries/default-taxon-disambiguation.txt b/ancillaries/default-taxon-disambiguation.txt new file mode 100644 index 0000000000000000000000000000000000000000..79d4a88ad96a2e7bc7c18ae85d88eff537067371 --- /dev/null +++ b/ancillaries/default-taxon-disambiguation.txt @@ -0,0 +1,4 @@ +E. coli ncbi:562 +E. faecalis ncbi:1351 +HIV ncbi:11676 +Plasmodium ncbi:5820 diff --git a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner/eval.json b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner/eval.json index 82b42c488e831803b5c5dba20f41cea75a03b722..b016a28eca6a4b78d303c577e634f7e0547a3d3e 100644 --- a/corpora/BioNLP-OST-2019/batches/BB19-kb+ner/eval.json +++ b/corpora/BioNLP-OST-2019/batches/BB19-kb+ner/eval.json @@ -1,6 +1,6 @@ { "evaluation": { - "submission-id": 19587, + "submission-id": 554, "global-evaluations": [{ "name": "Standard pairing", "scorings": [{ @@ -8,15 +8,15 @@ "measures": [ { "name": "mean-references", - "value": 0.33271664391893746 + "value": 0.3306756747299038 }, { "name": "Predictions", - "value": 506 + "value": 476 }, { "name": "False Negatives", - "value": 290 + "value": 293 } ] }] @@ -25,33 +25,51 @@ "messages": [ { "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-kb+ner\/a2\/BB-kb+ner-12417169.a2", - "lineno": 53, + "lineno": 47, "level": "SERIOUS", "body": "referent bd:15573 is not in the vocabulary" }, + { + "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-kb+ner\/a2\/BB-kb+ner-14657131.a2", + "lineno": 26, + "level": "SERIOUS", + "body": "referent bd:5616 is not in the vocabulary" + }, + { + "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-kb+ner\/a2\/BB-kb+ner-14657131.a2", + "lineno": 27, + "level": "SERIOUS", + "body": "referent bd:5616 is not in the vocabulary" + }, + { + "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-kb+ner\/a2\/BB-kb+ner-14657131.a2", + "lineno": 28, + "level": "SERIOUS", + "body": "referent bd:5616 is not in the vocabulary" + }, { "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-kb+ner\/a2\/BB-kb+ner-15273106.a2", - "lineno": 51, + "lineno": 21, "level": "SERIOUS", "body": "referent bd:14460 is not in the vocabulary" }, { "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-kb+ner\/a2\/BB-kb+ner-15273106.a2", - "lineno": 53, + "lineno": 23, "level": "SERIOUS", "body": "referent bd:14460 is not in the vocabulary" }, { "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-kb+ner\/a2\/BB-kb+ner-15273106.a2", - "lineno": 54, + "lineno": 24, "level": "SERIOUS", "body": "referent bd:14460 is not in the vocabulary" }, { - "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-kb+ner\/a2\/BB-kb+ner-15460321.a2", - "lineno": 44, + "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-kb+ner\/a2\/BB-kb+ner-20672296.a2", + "lineno": 39, "level": "SERIOUS", - "body": "referent 2770636 is not in the vocabulary" + "body": "referent bd:133179 is not in the vocabulary" }, { "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-kb+ner\/a2\/BB-kb+ner-21511409.a2", @@ -61,15 +79,33 @@ }, { "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-kb+ner\/a2\/BB-kb+ner-23645023.a2", - "lineno": 46, + "lineno": 37, "level": "SERIOUS", - "body": "referent bd:6553 is not in the vocabulary" + "body": "referent bd:133442 is not in the vocabulary" }, { "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-kb+ner\/a2\/BB-kb+ner-23645023.a2", - "lineno": 47, + "lineno": 38, + "level": "SERIOUS", + "body": "referent bd:14416 is not in the vocabulary" + }, + { + "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-kb+ner\/a2\/BB-kb+ner-23645023.a2", + "lineno": 43, "level": "SERIOUS", - "body": "referent bd:6553 is not in the vocabulary" + "body": "referent bd:134026 is not in the vocabulary" + }, + { + "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-kb+ner\/a2\/BB-kb+ner-23645023.a2", + "lineno": 44, + "level": "SERIOUS", + "body": "referent bd:134026 is not in the vocabulary" + }, + { + "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-kb+ner\/a2\/BB-kb+ner-23645023.a2", + "lineno": 45, + "level": "SERIOUS", + "body": "referent bd:134026 is not in the vocabulary" }, { "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-kb+ner\/a2\/BB-kb+ner-25046729.a2", @@ -101,27 +137,51 @@ "level": "SERIOUS", "body": "referent bd:4466 is not in the vocabulary" }, + { + "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-kb+ner\/a2\/BB-kb+ner-8406892.a2", + "lineno": 23, + "level": "SERIOUS", + "body": "referent bd:11824 is not in the vocabulary" + }, + { + "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-kb+ner\/a2\/BB-kb+ner-8406892.a2", + "lineno": 24, + "level": "SERIOUS", + "body": "referent bd:11824 is not in the vocabulary" + }, + { + "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-kb+ner\/a2\/BB-kb+ner-8406892.a2", + "lineno": 32, + "level": "SERIOUS", + "body": "referent bd:11824 is not in the vocabulary" + }, { "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-kb+ner\/a2\/BB-kb+ner-9575437.a2", - "lineno": 69, + "lineno": 59, "level": "SERIOUS", "body": "referent bd:14460 is not in the vocabulary" }, { "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-kb+ner\/a2\/BB-kb+ner-9575437.a2", - "lineno": 71, + "lineno": 61, "level": "SERIOUS", "body": "referent bd:14460 is not in the vocabulary" }, { "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-kb+ner\/a2\/BB-kb+ner-9575437.a2", - "lineno": 76, + "lineno": 63, + "level": "SERIOUS", + "body": "referent bd:5712 is not in the vocabulary" + }, + { + "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-kb+ner\/a2\/BB-kb+ner-9575437.a2", + "lineno": 66, "level": "SERIOUS", "body": "referent bd:12888 is not in the vocabulary" }, { "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-kb+ner\/a2\/BB-kb+ner-F-25064656-015.a2", - "lineno": 30, + "lineno": 28, "level": "SERIOUS", "body": "referent bd:2623 is not in the vocabulary" }, diff --git a/corpora/BioNLP-OST-2019/batches/BB19-norm+ner/eval.json b/corpora/BioNLP-OST-2019/batches/BB19-norm+ner/eval.json index 30bb62bcb3f998759c1dac8d863f7deebb7ed13a..621531e146b6e743efd706acd1479efbdedb8076 100644 --- a/corpora/BioNLP-OST-2019/batches/BB19-norm+ner/eval.json +++ b/corpora/BioNLP-OST-2019/batches/BB19-norm+ner/eval.json @@ -1,6 +1,6 @@ { "evaluation": { - "submission-id": 19588, + "submission-id": 544, "global-evaluations": [ { "name": "Standard pairing", @@ -10,39 +10,39 @@ "measures": [ { "name": "SER", - "value": 0.6547872340425532 + "value": 0.6712765957446809 }, { "name": "ISER", - "value": 0.6043072966891675 + "value": 0.5983450031826861 }, { "name": "Mismatches", - "value": 219.18358890632828 + "value": 201.16921626551257 }, { "name": "Matches", - "value": 1023.8164110936716 + "value": 965.8307837344876 }, { "name": "Insertions", - "value": 375 + "value": 348 }, { "name": "Deletions", - "value": 637 + "value": 713 }, { "name": "Recall", - "value": 0.5445831973902509 + "value": 0.5137397785821742 }, { "name": "Precision", - "value": 0.6327666323199453 + "value": 0.6375120684716089 }, { "name": "Predictions", - "value": 1618 + "value": 1515 } ] }, @@ -51,39 +51,39 @@ "measures": [ { "name": "SER", - "value": 0.639344262295082 + "value": 0.6533957845433255 }, { "name": "ISER", - "value": 0.61 + "value": 0.6048158640226629 }, { "name": "Mismatches", - "value": 180.56822947976318 + "value": 176.9852608459769 }, { "name": "Matches", - "value": 468.4317705202377 + "value": 455.01473915402397 }, { "name": "Insertions", - "value": 161 + "value": 160 }, { "name": "Deletions", - "value": 205 + "value": 222 }, { "name": "Recall", - "value": 0.5485149537707702 + "value": 0.532804144208459 }, { "name": "Precision", - "value": 0.5783108278027626 + "value": 0.5745135595379091 }, { "name": "Predictions", - "value": 810 + "value": 792 } ] }, @@ -92,39 +92,39 @@ "measures": [ { "name": "SER", - "value": 0.7423887587822015 + "value": 0.7576112412177985 }, { "name": "ISER", - "value": 0.5739247311827956 + "value": 0.5689540306462358 }, { "name": "Mismatches", - "value": 268.9403822157718 + "value": 265.51403207161377 }, { "name": "Matches", - "value": 380.0596177842278 + "value": 366.48596792838583 }, { "name": "Insertions", - "value": 161 + "value": 160 }, { "name": "Deletions", - "value": 205 + "value": 222 }, { "name": "Recall", - "value": 0.44503468124616835 + "value": 0.4291404776678991 }, { "name": "Precision", - "value": 0.46920940467188615 + "value": 0.46273480799038613 }, { "name": "Predictions", - "value": 810 + "value": 792 } ] }, @@ -215,39 +215,39 @@ "measures": [ { "name": "SER", - "value": 0.746875 + "value": 0.828125 }, { "name": "ISER", - "value": 0.5724508050089445 + "value": 0.5470085470085471 }, { "name": "Mismatches", - "value": 22.817223677933953 + "value": 10.24749951153148 }, { "name": "Matches", - "value": 97.182776322066 + "value": 62.7525004884685 }, { "name": "Insertions", - "value": 17 + "value": 8 }, { "name": "Deletions", - "value": 200 + "value": 247 }, { "name": "Recall", - "value": 0.30369617600645626 + "value": 0.19610156402646406 }, { "name": "Precision", - "value": 0.7093633308180001 + "value": 0.7747222282526975 }, { "name": "Predictions", - "value": 137 + "value": 81 } ] }, @@ -256,39 +256,39 @@ "measures": [ { "name": "SER", - "value": 0.884375 + "value": 0.85625 }, { "name": "ISER", - "value": 0.5306799336650083 + "value": 0.5387205387205387 }, { "name": "Mismatches", - "value": 66.026938747527 + "value": 19.026938747526984 }, { "name": "Matches", - "value": 53.97306125247301 + "value": 53.973061252473016 }, { "name": "Insertions", - "value": 17 + "value": 8 }, { "name": "Deletions", - "value": 200 + "value": 247 }, { "name": "Recall", - "value": 0.16866581641397815 + "value": 0.16866581641397818 }, { "name": "Precision", - "value": 0.3939639507479782 + "value": 0.6663340895367039 }, { "name": "Predictions", - "value": 137 + "value": 81 } ] }, @@ -338,39 +338,39 @@ "measures": [ { "name": "SER", - "value": 0.8247422680412371 + "value": 0.7647058823529411 }, { "name": "ISER", - "value": 0.5480225988700566 + "value": 0.5666666666666667 }, { "name": "Mismatches", - "value": 43 + "value": 5.999999999999999 }, { "name": "Matches", - "value": 21 + "value": 21.000000000000004 }, { "name": "Insertions", - "value": 4 + "value": 2 }, { "name": "Deletions", - "value": 33 + "value": 58 }, { "name": "Recall", - "value": 0.21649484536082475 + "value": 0.2470588235294118 }, { "name": "Precision", - "value": 0.3088235294117647 + "value": 0.7241379310344829 }, { "name": "Predictions", - "value": 68 + "value": 29 } ] }, @@ -379,39 +379,39 @@ "measures": [ { "name": "SER", - "value": 0.6695059625212947 + "value": 0.7018739352640545 }, { "name": "ISER", - "value": 0.5989795918367347 + "value": 0.5875875875875876 }, { "name": "Mismatches", - "value": 203.38545315769696 + "value": 187.2327603575084 }, { "name": "Matches", - "value": 565.6145468423034 + "value": 517.767239642492 }, { "name": "Insertions", - "value": 178 + "value": 168 }, { "name": "Deletions", - "value": 405 + "value": 469 }, { "name": "Recall", - "value": 0.4817841114500029 + "value": 0.441028313153741 }, { "name": "Precision", - "value": 0.5972698488303099 + "value": 0.5930896215836106 }, { "name": "Predictions", - "value": 947 + "value": 873 } ] }, @@ -420,39 +420,39 @@ "measures": [ { "name": "SER", - "value": 0.7810902896081772 + "value": 0.7844974446337308 }, { "name": "ISER", - "value": 0.5614538498326159 + "value": 0.560381861575179 }, { "name": "Mismatches", - "value": 334.9673209632992 + "value": 284.5409708191408 }, { "name": "Matches", - "value": 434.0326790367008 + "value": 420.4590291808588 }, { "name": "Insertions", - "value": 178 + "value": 168 }, { "name": "Deletions", - "value": 405 + "value": 469 }, { "name": "Recall", - "value": 0.3697041559086038 + "value": 0.3581422735782443 }, { "name": "Precision", - "value": 0.45832384269978965 + "value": 0.4816254629792197 }, { "name": "Predictions", - "value": 947 + "value": 873 } ] }, @@ -502,15 +502,15 @@ "measures": [ { "name": "SER", - "value": 0.7870967741935484 + "value": 0.7718120805369127 }, { "name": "ISER", - "value": 0.5595667870036101 + "value": 0.5643939393939393 }, { "name": "Mismatches", - "value": 133.2604323172907 + "value": 96.2604323172907 }, { "name": "Matches", @@ -518,23 +518,23 @@ }, { "name": "Insertions", - "value": 16 + "value": 14 }, { "name": "Deletions", - "value": 95 + "value": 120 }, { "name": "Recall", - "value": 0.2636760247829332 + "value": 0.2742938512842594 }, { "name": "Precision", - "value": 0.35385094234939096 + "value": 0.425726915014111 }, { "name": "Predictions", - "value": 231 + "value": 192 } ] }, @@ -543,39 +543,39 @@ "measures": [ { "name": "SER", - "value": 0.6288951841359773 + "value": 0.6189801699716714 }, { "name": "ISER", - "value": 0.6139130434782609 + "value": 0.6176727909011374 }, { "name": "Mismatches", - "value": 15.798135748631427 + "value": 13.936455908004215 }, { "name": "Matches", - "value": 458.2018642513687 + "value": 448.06354409199594 }, { "name": "Insertions", - "value": 197 + "value": 180 }, { "name": "Deletions", - "value": 232 + "value": 244 }, { "name": "Recall", - "value": 0.6490111391662446 + "value": 0.634650912311609 }, { "name": "Precision", - "value": 0.6828641792121739 + "value": 0.6979182929781869 }, { "name": "Predictions", - "value": 671 + "value": 642 } ] }, @@ -584,39 +584,39 @@ "measures": [ { "name": "SER", - "value": 0.6 + "value": 0.6202127659574468 }, { "name": "ISER", - "value": 0.625 + "value": 0.6172028890347997 }, { "name": "Mismatches", - "value": 116.43610313177439 + "value": 105.61611607079135 }, { "name": "Matches", - "value": 1126.5638968682263 + "value": 1061.3838839292084 }, { "name": "Insertions", - "value": 375 + "value": 348 }, { "name": "Deletions", - "value": 637 + "value": 713 }, { "name": "Recall", - "value": 0.5992361153554395 + "value": 0.5645658957070258 }, { "name": "Precision", - "value": 0.696269404739324 + "value": 0.7005834217354511 }, { "name": "Predictions", - "value": 1618 + "value": 1515 } ] }, @@ -625,39 +625,39 @@ "measures": [ { "name": "SER", - "value": 0.5468384074941453 + "value": 0.5655737704918032 }, { "name": "ISER", - "value": 0.6464799394398183 + "value": 0.6387434554973822 }, { "name": "Mismatches", - "value": 101.7468805450224 + "value": 101.03373686364789 }, { "name": "Matches", - "value": 547.2531194549778 + "value": 530.9662631363523 }, { "name": "Insertions", - "value": 161 + "value": 160 }, { "name": "Deletions", - "value": 205 + "value": 222 }, { "name": "Recall", - "value": 0.6408116152868593 + "value": 0.6217403549605999 }, { "name": "Precision", - "value": 0.6756211351296022 + "value": 0.6704119484044851 }, { "name": "Predictions", - "value": 810 + "value": 792 } ] }, @@ -666,39 +666,39 @@ "measures": [ { "name": "SER", - "value": 0.689695550351288 + "value": 0.7072599531615925 }, { "name": "ISER", - "value": 0.5918225918225918 + "value": 0.5857338820301784 }, { "name": "Mismatches", - "value": 223.5333333333331 + "value": 222.8666666666664 }, { "name": "Matches", - "value": 425.46666666666624 + "value": 409.1333333333328 }, { "name": "Insertions", - "value": 161 + "value": 160 }, { "name": "Deletions", - "value": 205 + "value": 222 }, { "name": "Recall", - "value": 0.49820452771272394 + "value": 0.4790788446526145 }, { "name": "Precision", - "value": 0.5252674897119336 + "value": 0.5165824915824909 }, { "name": "Predictions", - "value": 810 + "value": 792 } ] }, @@ -707,39 +707,39 @@ "measures": [ { "name": "SER", - "value": 0.721875 + "value": 0.809375 }, { "name": "ISER", - "value": 0.5807622504537205 + "value": 0.5526770293609672 }, { "name": "Mismatches", - "value": 14.689222586751914 + "value": 4.582379207143451 }, { "name": "Matches", - "value": 105.31077741324808 + "value": 68.41762079285654 }, { "name": "Insertions", - "value": 17 + "value": 8 }, { "name": "Deletions", - "value": 200 + "value": 247 }, { "name": "Recall", - "value": 0.32909617941640024 + "value": 0.21380506497767668 }, { "name": "Precision", - "value": 0.7686918059361173 + "value": 0.8446619850969943 }, { "name": "Predictions", - "value": 137 + "value": 81 } ] }, @@ -748,15 +748,15 @@ "measures": [ { "name": "SER", - "value": 0.871875 + "value": 0.84375 }, { "name": "ISER", - "value": 0.5342237061769616 + "value": 0.5423728813559322 }, { "name": "Mismatches", - "value": 62 + "value": 15 }, { "name": "Matches", @@ -764,11 +764,11 @@ }, { "name": "Insertions", - "value": 17 + "value": 8 }, { "name": "Deletions", - "value": 200 + "value": 247 }, { "name": "Recall", @@ -776,11 +776,11 @@ }, { "name": "Precision", - "value": 0.4233576642335766 + "value": 0.7160493827160493 }, { "name": "Predictions", - "value": 137 + "value": 81 } ] }, @@ -789,39 +789,39 @@ "measures": [ { "name": "SER", - "value": 0.5954003407155025 + "value": 0.6320272572402045 }, { "name": "ISER", - "value": 0.6268019220501868 + "value": 0.6127348643006263 }, { "name": "Mismatches", - "value": 116.43610313177439 + "value": 105.61611607079135 }, { "name": "Matches", - "value": 652.5638968682249 + "value": 599.3838839292084 }, { "name": "Insertions", - "value": 178 + "value": 168 }, { "name": "Deletions", - "value": 405 + "value": 469 }, { "name": "Recall", - "value": 0.5558465901773636 + "value": 0.5105484530913189 }, { "name": "Precision", - "value": 0.689085424359266 + "value": 0.6865794775821402 }, { "name": "Predictions", - "value": 947 + "value": 873 } ] }, @@ -830,39 +830,39 @@ "measures": [ { "name": "SER", - "value": 0.7393526405451448 + "value": 0.7444633730834753 }, { "name": "ISER", - "value": 0.574926542605289 + "value": 0.5732421875 }, { "name": "Mismatches", - "value": 285.5333333333333 + "value": 237.8666666666664 }, { "name": "Matches", - 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"lineno": 41, - "level": "SERIOUS", - "body": "unknown type: NCBI_Taxonomy" - }, - { - "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-F-25064656-010.a2", - "lineno": 42, - "level": "SERIOUS", - "body": "unknown type: NCBI_Taxonomy" - }, { "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-F-25064656-011.a2", "lineno": 5, @@ -9413,6 +8837,18 @@ "level": "SERIOUS", "body": "unknown type: NCBI_Taxonomy" }, + { + "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-F-25064656-013.a2", + "lineno": 26, + "level": "SERIOUS", + "body": "unknown type: OntoBiotope" + }, + { + "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-F-25064656-013.a2", + "lineno": 27, + "level": "SERIOUS", + "body": "unknown type: OntoBiotope" + }, { "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-F-25064656-013.a2", "lineno": 28, @@ -9513,13 +8949,13 @@ "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-F-25064656-013.a2", "lineno": 44, "level": "SERIOUS", - "body": "unknown type: OntoBiotope" + "body": "unknown type: NCBI_Taxonomy" }, { "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-F-25064656-013.a2", "lineno": 45, "level": "SERIOUS", - "body": "unknown type: OntoBiotope" + "body": "unknown type: NCBI_Taxonomy" }, { "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-F-25064656-013.a2", @@ -9552,28 +8988,16 @@ "body": "unknown type: NCBI_Taxonomy" }, { - "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-F-25064656-013.a2", - "lineno": 51, - "level": "SERIOUS", - "body": "unknown type: NCBI_Taxonomy" - }, - { - "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-F-25064656-013.a2", - "lineno": 52, - "level": "SERIOUS", - "body": "unknown type: NCBI_Taxonomy" - }, - { - "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-F-25064656-013.a2", - "lineno": 53, + "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-F-25064656-014.a2", + "lineno": 15, "level": "SERIOUS", - "body": "unknown type: NCBI_Taxonomy" + "body": "unknown type: OntoBiotope" }, { - "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-F-25064656-013.a2", - "lineno": 54, + "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-F-25064656-014.a2", + "lineno": 16, "level": "SERIOUS", - "body": "unknown type: NCBI_Taxonomy" + "body": "unknown type: OntoBiotope" }, { "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-F-25064656-014.a2", @@ -9615,13 +9039,13 @@ "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-F-25064656-014.a2", "lineno": 23, "level": "SERIOUS", - "body": "unknown type: OntoBiotope" + "body": "unknown type: NCBI_Taxonomy" }, { "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-F-25064656-014.a2", "lineno": 24, "level": "SERIOUS", - "body": "unknown type: OntoBiotope" + "body": "unknown type: NCBI_Taxonomy" }, { "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-F-25064656-014.a2", @@ -9648,28 +9072,10 @@ "body": "unknown type: NCBI_Taxonomy" }, { - "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-F-25064656-014.a2", - "lineno": 29, - "level": "SERIOUS", - "body": "unknown type: NCBI_Taxonomy" - }, - { - "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-F-25064656-014.a2", - "lineno": 30, - "level": "SERIOUS", - "body": "unknown type: NCBI_Taxonomy" - }, - { - "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-F-25064656-014.a2", - "lineno": 31, - "level": "SERIOUS", - "body": "unknown type: NCBI_Taxonomy" - }, - { - "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-F-25064656-014.a2", - "lineno": 32, + "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-F-25064656-015.a2", + "lineno": 17, "level": "SERIOUS", - "body": "unknown type: NCBI_Taxonomy" + "body": "unknown type: OntoBiotope" }, { "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-F-25064656-015.a2", @@ -9723,7 +9129,7 @@ "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-F-25064656-015.a2", "lineno": 26, "level": "SERIOUS", - "body": "unknown type: OntoBiotope" + "body": "unknown type: NCBI_Taxonomy" }, { "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-F-25064656-015.a2", @@ -9762,16 +9168,10 @@ "body": "unknown type: NCBI_Taxonomy" }, { - "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-F-25064656-015.a2", - "lineno": 33, - "level": "SERIOUS", - "body": "unknown type: NCBI_Taxonomy" - }, - { - "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-F-25064656-015.a2", - "lineno": 34, + "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-F-25064656-016.a2", + "lineno": 28, "level": "SERIOUS", - "body": "unknown type: NCBI_Taxonomy" + "body": "unknown type: OntoBiotope" }, { "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-F-25064656-016.a2", @@ -9861,7 +9261,7 @@ "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-F-25064656-016.a2", "lineno": 43, "level": "SERIOUS", - "body": "unknown type: OntoBiotope" + "body": "unknown type: NCBI_Taxonomy" }, { "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-F-25064656-016.a2", @@ -9930,16 +9330,10 @@ "body": "unknown type: NCBI_Taxonomy" }, { - "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-F-25064656-016.a2", - "lineno": 55, - "level": "SERIOUS", - "body": "unknown type: NCBI_Taxonomy" - }, - { - "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-F-25064656-016.a2", - "lineno": 56, + "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-F-25064656-017.a2", + "lineno": 9, "level": "SERIOUS", - "body": "unknown type: NCBI_Taxonomy" + "body": "unknown type: OntoBiotope" }, { "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-F-25064656-017.a2", @@ -9975,23 +9369,11 @@ "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-F-25064656-017.a2", "lineno": 15, "level": "SERIOUS", - "body": "unknown type: OntoBiotope" - }, - { - "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-F-25064656-017.a2", - "lineno": 16, - "level": "SERIOUS", "body": "unknown type: NCBI_Taxonomy" }, { "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-F-25064656-017.a2", - "lineno": 17, - "level": "SERIOUS", - "body": "unknown type: NCBI_Taxonomy" - }, - { - "source": "predictions.zip\/corpora\/BioNLP-OST-2019\/batches\/BB19-rel+ner\/a2\/BB-rel+ner-F-25064656-017.a2", - "lineno": 18, + "lineno": 16, "level": "SERIOUS", "body": "unknown type: NCBI_Taxonomy" }, diff --git a/plans/taxa.plan b/plans/taxa.plan index e45c93f1016d19f1b78d8a321aeaf94f1a833f5a..cd7850e63732b92cc9989351517d088c1ef2d2f4 100644 --- a/plans/taxa.plan +++ b/plans/taxa.plan @@ -27,30 +27,45 @@ <disambiguate> <not-ambiguous class="Action"> <target>documents.sections.layer:taxa[not span:taxa]</target> - <action>set:feat:not-ambiguous("yes")</action> + <action>set:feat:not-ambiguous("yes") | set:feat:disambiguation-method("never-ambiguous")</action> <setFeatures/> </not-ambiguous> <disambiguate-coreferences class="Action"> - <target>documents.sections.layer:taxa[@not-ambiguous != "yes" and $ as x.(section.nav:sections-before.layer:taxa|before:taxa)[@not-ambiguous == "yes" and @taxid == x.@taxid]]</target> - <action>set:feat:not-ambiguous("yes")</action> + <target>documents.sections.layer:taxa[@not-ambiguous != "yes" and not (span:taxa[@not-ambiguous == "yes"]) and $ as x.(section.nav:sections-before.layer:taxa|before:taxa)[@not-ambiguous == "yes" and @taxid == x.@taxid]]</target> + <action>set:feat:not-ambiguous("yes") | set:feat:disambiguation-method("coreference-exact") | set:feat:coreference-of((section.nav:sections-before.layer:taxa|before:taxa)[@not-ambiguous == "yes" and target.@taxid == @taxid].@form)</action> <setFeatures/> </disambiguate-coreferences> - <disambiguate-coreferences-more-specific class="Action"> - <target>documents.sections.layer:taxa[@not-ambiguous != "yes" and $ as x.(section.nav:sections-before.layer:taxa|before:taxa)[@not-ambiguous == "yes" and x.@path ^= @path]]</target> - <action>set:feat:not-ambiguous("yes")</action> + <disambiguate-coreference-more-specific class="Action"> + <target>documents.sections.layer:taxa[@not-ambiguous != "yes" and not (span:taxa[@not-ambiguous == "yes"]) and $ as x.(section.nav:sections-before.layer:taxa|before:taxa|outside:taxa)[@not-ambiguous == "yes" and @path ^= x.@path]]</target> + <action>set:feat:not-ambiguous("yes") | set:feat:disambiguation-method("coreference-specific") | set:feat:coreference-of((section.nav:sections-before.layer:taxa|before:taxa)[@not-ambiguous == "yes" and @path ^= target.@path].@form)</action> <setFeatures/> - </disambiguate-coreferences-more-specific> + </disambiguate-coreference-more-specific> - <disambiguate-coreference-more-general class="Action"> - <target>documents.sections.layer:taxa[@not-ambiguous != "yes" and $ as x.(section.nav:sections-before.layer:taxa|before:taxa)[@not-ambiguous == "yes" and @path ^= x.@path]]</target> - <action>set:feat:not-ambiguous("yes")</action> + <disambiguate-coreferences-more-general class="Action"> + <target>documents.sections.layer:taxa[@not-ambiguous != "yes" and not (span:taxa[@not-ambiguous == "yes"]) and $ as x.(section.nav:sections-before.layer:taxa|before:taxa)[@not-ambiguous == "yes" and x.@path ^= @path]]</target> + <action>set:feat:not-ambiguous("yes") | set:feat:disambiguation-method("coreference-general") | set:feat:coreference-of((section.nav:sections-before.layer:taxa|before:taxa)[@not-ambiguous == "yes" and target.@path ^= @path].@form)</action> <setFeatures/> - </disambiguate-coreference-more-general> + </disambiguate-coreferences-more-general> + + <default-disambiguation> + <map class="FileMapper"> + <mappingFile>ancillaries/default-taxon-disambiguation.txt</mappingFile> + <target>documents.sections.layer:taxa[@not-ambiguous != "yes" and not (span:taxa[@not-ambiguous == "yes"])]</target> + <form>@form</form> + <targetFeatures>,default-taxid</targetFeatures> + </map> + + <disamiguate class="Action"> + <target>documents.sections.layer:taxa[@taxid == @default-taxid]</target> + <action>set:feat:not-ambiguous("yes") | set:feat:disambiguation-method("default")</action> + <setFeatures/> + </disamiguate> + </default-disambiguation> <remove-alternative-to-not-ambiguous class="Action"> - <target>documents.sections.layer:taxa[@not-ambiguous == "yes"].span:taxa[@not-ambiguous != "yes"]</target> + <target>documents.sections.layer:taxa[@not-ambiguous == "yes"].(span:taxa|inside:taxa|overlapping:taxa)[@not-ambiguous != "yes"]</target> <action>remove:taxa</action> <removeFromLayer/> </remove-alternative-to-not-ambiguous>