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Finalized changes to the descriptors. #20
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,139 +1,113 @@ | ||
| configuration: | ||
| name: bioqa-development-test | ||
| name: bioqa-test-06 | ||
| author: yanfang | ||
|
|
||
| persistence-provider: | ||
| inherit: bioqa.db.cse-persistence-provider | ||
| inherit: bioqa.persistence.peace-persistence-provider | ||
|
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| async-configuration: | ||
| inherit: bioqa.async.cse-broker | ||
|
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||
| collection-reader: | ||
| inherit: bioqa.db.collection-reader-consumer | ||
| inherit: bioqa.collection.db-collection-reader-producer | ||
| dataset: BIO-COMBINED | ||
| sequence-start: 160 | ||
| sequence-end: 187 | ||
| #sequence-end: 160 | ||
|
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||
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| pipeline: | ||
| - inherit: internal.cse.phase | ||
| - inherit: jdbc.cse.phase | ||
| name: keyterm-extractor | ||
| option-timeout: 2 | ||
| options: | | ||
| - inherit: default.keyterm.default | ||
| - inherit: bioqa.keyterm.default | ||
| - inherit: internal.cse.phase | ||
| - inherit: jdbc.cse.phase | ||
| option-timeout: 2 | ||
| name: pos-tagger | ||
| options: | | ||
| - inherit: bioqa.keyterm.lingpipe-hmm | ||
| - inherit: bioqa.keyterm.pos.lingpipe-hmm | ||
| - inherit: internal.cse.phase | ||
| - inherit: jdbc.cse.phase | ||
| option-timeout: 2 | ||
| name: name-entity-recognizer | ||
| options: | | ||
| - inherit: bioqa.keyterm.lingpipe-abbreviation | ||
| - inherit: bioqa.keyterm.ner.lingpipe-acronym | ||
| - inherit: internal.cse.phase | ||
| - inherit: jdbc.cse.phase | ||
| option-timeout: 2 | ||
| name: name-entity-recognizer | ||
| name: lexical-variants-resolver | ||
| options: | | ||
| - inherit: bioqa.keyterm.syn-lexical-variants | ||
| - inherit: bioqa.keyterm.ner.lexical-variants | ||
| - inherit: internal.cse.phase | ||
| name: restore | ||
| - inherit: jdbc.cse.phase | ||
| name: keyterm-restore | ||
| options: | | ||
| - inherit: bioqa.keyterm.io.restore | ||
| #- inherit: internal.cse.phase | ||
| # option-timeout: 2 | ||
| #name: synonyms | ||
| #options: | | ||
| # - inherit: bioqa.keyterm.kb.mesh | ||
| - inherit: bioqa.keyterm.io.restore-06 | ||
| #- inherit: internal.cse.phase | ||
| # option-timeout: 2 | ||
| #name: synonyms | ||
| #options: | | ||
| # - inherit: bioqa.keyterm.kb.entrezgene | ||
|
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||
| - inherit: internal.cse.phase | ||
| - inherit: jdbc.cse.phase | ||
| option-timeout: 2 | ||
| name: synonyms | ||
| name: umls-synonyms | ||
| options: | | ||
| - inherit: bioqa.keyterm.kb.umls | ||
| # - inherit: internal.cse.phase | ||
| # option-timeout: 2 | ||
| # name: store | ||
| # options: | | ||
| # - inherit: bioqa.keyterm.io.backup | ||
|
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||
| - inherit: internal.cse.phase | ||
| option-timeout: 2 | ||
| - inherit: jdbc.cse.phase | ||
| name: keyterm-refiner | ||
| option-timeout: 2 | ||
| lazy-load-options: true | ||
| options: | | ||
| - inherit: bioqa.keyterm.keyterm-refiner | ||
| - inherit: bioqa.keyterm.kb.keyterm-refiner | ||
| - inherit: internal.cse.phase | ||
| - inherit: jdbc.cse.phase | ||
| name: retrieval-strategist | ||
| option-timeout: 8 | ||
| options: | | ||
| - inherit: bioqa.retrieval.BasicIndriRetrieval | ||
| options: | | ||
| - inherit: bioqa.retrieval.indri | ||
| - inherit: internal.cse.phase | ||
| - inherit: jdbc.cse.phase | ||
| name: passage-extractor | ||
| option-timeout: 20 | ||
| options: | | ||
| - inherit: bioqa.ie.IndriLegalSpan | ||
| options: | | ||
| - inherit: bioqa.ie.indri-legalspan | ||
| - inherit: internal.cse.phase | ||
| - inherit: jdbc.cse.phase | ||
| name: passage-span | ||
| option-timeout: 5 | ||
| lazy-load-options: true | ||
| options: | | ||
| - inherit: bioqa.ie.span.important-sentence@peace | ||
| - inherit: base.noop | ||
| - inherit: internal.cse.phase | ||
| - inherit: jdbc.cse.phase | ||
| name: passage-rank | ||
| option-timeout: 5 | ||
| lazy-load-options: true | ||
| options: | | ||
| - inherit: base.noop | ||
| - inherit: bioqa.ie.rank.proximity@peace | ||
| #- inherit: base.noop | ||
| - inherit: base.noop | ||
| - inherit: internal.cse.phase | ||
| - inherit: jdbc.cse.phase | ||
| name: score-combine | ||
| option-timeout: 5 | ||
| options: | | ||
| - inherit: base.noop | ||
| - inherit: bioqa.ie.rank.combine | ||
| #- inherit: base.noop | ||
| - inherit: base.noop | ||
| - inherit: internal.cse.phase | ||
| - inherit: jdbc.cse.phase | ||
| name: passage-overlap | ||
| option-timeout: 5 | ||
| options: | | ||
| options: | | ||
| - inherit: bioqa.ie.overlap.merge | ||
| - inherit: bioqa.ie.overlap.filter | ||
| #- inherit: bioqa.ie.overlap.merge | ||
| #- inherit: base.noop | ||
| - inherit: internal.eval.cse-retrieval-aggregator-consumer | ||
| - inherit: internal.eval.cse-passage-map-aggregator-consumer | ||
| - inherit: jdbc.eval.retrieval-aggregator-consumer | ||
| - inherit: bioqa.eval.passage-map-aggregator-consumer | ||
|
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||
| post-process: | ||
| - inherit: internal.eval.cse-retrieval-evaluator-consumer | ||
| post-process: | ||
| - inherit: jdbc.eval.retrieval-evaluator-consumer | ||
| - inherit: report.csv-report-generator | ||
| builders: | | ||
| - inherit: internal.report.f-measure-report-component | ||
| - inherit: internal.eval.cse-passage-map-evaluator-consumer | ||
| - inherit: jdbc.report.f-measure-report-component | ||
| - inherit: bioqa.eval.passage-map-evaluator-consumer | ||
| - inherit: report.csv-report-generator | ||
| builders: | | ||
| - inherit: internal.report.map-report-component | ||
|
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||
|
|
||
| - inherit: bioqa.report.map-report-component |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,126 +1,113 @@ | ||
| configuration: | ||
| name: bioqa-development-test | ||
| name: bioqa-test-06 | ||
| author: yanfang | ||
|
|
||
| persistence-provider: | ||
| inherit: bioqa.db.peace-persistence-provider | ||
| inherit: bioqa.persistence.peace-persistence-provider | ||
|
|
||
| async-configuration: | ||
| inherit: bioqa.async.cse-broker | ||
|
|
||
| collection-reader: | ||
| inherit: bioqa.db.collection-reader-producer | ||
| inherit: bioqa.collection.db-collection-reader-consumer | ||
| dataset: BIO-COMBINED | ||
| sequence-start: 160 | ||
| sequence-end: 187 | ||
| #sequence-end: 160 | ||
|
|
||
|
|
||
| pipeline: | ||
| - inherit: internal.cse.phase | ||
| - inherit: jdbc.cse.phase | ||
| name: keyterm-extractor | ||
| option-timeout: 2 | ||
| options: | | ||
| - inherit: default.keyterm.default | ||
| - inherit: bioqa.keyterm.default | ||
| - inherit: internal.cse.phase | ||
| - inherit: jdbc.cse.phase | ||
| option-timeout: 2 | ||
| name: pos-tagger | ||
| options: | | ||
| - inherit: bioqa.keyterm.lingpipe-hmm | ||
| - inherit: bioqa.keyterm.pos.lingpipe-hmm | ||
| - inherit: internal.cse.phase | ||
| - inherit: jdbc.cse.phase | ||
| option-timeout: 2 | ||
| name: name-entity-recognizer | ||
| options: | | ||
| - inherit: bioqa.keyterm.lingpipe-abbreviation | ||
| - inherit: bioqa.keyterm.ner.lingpipe-acronym | ||
| - inherit: internal.cse.phase | ||
| - inherit: jdbc.cse.phase | ||
| option-timeout: 2 | ||
| name: name-entity-recognizer | ||
| name: lexical-variants-resolver | ||
| options: | | ||
| - inherit: bioqa.keyterm.syn-lexical-variants | ||
| - inherit: bioqa.keyterm.ner.lexical-variants | ||
| - inherit: internal.cse.phase | ||
| name: restore | ||
| - inherit: jdbc.cse.phase | ||
| name: keyterm-restore | ||
| options: | | ||
| - inherit: bioqa.keyterm.io.restore | ||
| #- inherit: internal.cse.phase | ||
| # option-timeout: 2 | ||
| #name: restore | ||
| #options: | | ||
| # - inherit: bioqa.keyterm.restore | ||
| - inherit: bioqa.keyterm.io.restore-06 | ||
| - inherit: internal.cse.phase | ||
| name: synonyms | ||
| - inherit: jdbc.cse.phase | ||
| option-timeout: 2 | ||
| name: umls-synonyms | ||
| options: | | ||
| - inherit: bioqa.keyterm.kb.umls | ||
| - inherit: internal.cse.phase | ||
| option-timeout: 2 | ||
| - inherit: jdbc.cse.phase | ||
| name: keyterm-refiner | ||
| option-timeout: 2 | ||
| lazy-load-options: true | ||
| options: | | ||
| - inherit: bioqa.keyterm.keyterm-refiner | ||
| - inherit: bioqa.keyterm.kb.keyterm-refiner | ||
| - inherit: internal.cse.phase | ||
| - inherit: jdbc.cse.phase | ||
| name: retrieval-strategist | ||
| option-timeout: 8 | ||
| options: | | ||
| - inherit: bioqa.retrieval.BasicIndriRetrieval | ||
| options: | | ||
| - inherit: bioqa.retrieval.indri | ||
| - inherit: internal.cse.phase | ||
| - inherit: jdbc.cse.phase | ||
| name: passage-extractor | ||
| option-timeout: 20 | ||
| options: | | ||
| - inherit: bioqa.ie.IndriLegalSpan | ||
| options: | | ||
| - inherit: bioqa.ie.indri-legalspan | ||
| - inherit: internal.cse.phase | ||
| - inherit: jdbc.cse.phase | ||
| name: passage-span | ||
| option-timeout: 5 | ||
| lazy-load-options: true | ||
| options: | | ||
| - inherit: bioqa.ie.span.important-sentence@peace | ||
| - inherit: base.noop | ||
| - inherit: internal.cse.phase | ||
| - inherit: jdbc.cse.phase | ||
| name: passage-rank | ||
| option-timeout: 5 | ||
| lazy-load-options: true | ||
| options: | | ||
| - inherit: base.noop | ||
| - inherit: bioqa.ie.rank.proximity@peace | ||
| #- inherit: base.noop | ||
| - inherit: internal.cse.phase | ||
| - inherit: base.noop | ||
| - inherit: jdbc.cse.phase | ||
| name: score-combine | ||
| option-timeout: 5 | ||
| options: | | ||
| - inherit: base.noop | ||
| - inherit: bioqa.ie.rank.combine | ||
| #- inherit: base.noop | ||
| - inherit: base.noop | ||
| - inherit: internal.cse.phase | ||
| - inherit: jdbc.cse.phase | ||
| name: passage-overlap | ||
| option-timeout: 5 | ||
| options: | | ||
| - inherit: bioqa.ie.overlap.merge | ||
| - inherit: bioqa.ie.overlap.filter | ||
| #- inherit: bioqa.ie.overlap.merge | ||
| #- inherit: bioqa.ie.overlap.merge | ||
| #- inherit: base.noop | ||
| - inherit: internal.eval.cse-retrieval-aggregator-consumer | ||
| - inherit: internal.eval.cse-passage-map-aggregator-consumer | ||
| - inherit: jdbc.eval.retrieval-aggregator-consumer | ||
| - inherit: bioqa.eval.passage-map-aggregator-consumer | ||
|
|
||
| post-process: | ||
| - inherit: internal.eval.cse-retrieval-evaluator-consumer | ||
| post-process: | ||
| - inherit: jdbc.eval.retrieval-evaluator-consumer | ||
| - inherit: report.csv-report-generator | ||
| builders: | | ||
| - inherit: internal.report.f-measure-report-component | ||
| - inherit: internal.eval.cse-passage-map-evaluator-consumer | ||
| - inherit: jdbc.report.f-measure-report-component | ||
| - inherit: bioqa.eval.passage-map-evaluator-consumer | ||
| - inherit: report.csv-report-generator | ||
| builders: | | ||
| - inherit: internal.report.map-report-component | ||
| - inherit: bioqa.report.map-report-component |
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