├── Dockerfile ├── GSC+.rar ├── GSC_v2.rar ├── LICENSE ├── README.md ├── bin ├── Tokenizer.jar ├── base.old.prop ├── base.prop ├── default.properties └── florchebi.jar ├── corpora ├── .gitkeep ├── hpo │ ├── .gitkeep │ ├── test_ann │ │ └── .gitkeep │ ├── test_corpus │ │ └── .gitkeep │ ├── train_ann │ │ └── .gitkeep │ └── train_corpus │ │ └── .gitkeep └── test_suite │ └── test_suites │ └── .gitkeep ├── data ├── annotation_gazette.txt ├── gazette.txt ├── paths ├── paths_stanford └── stopwords.txt ├── models ├── .gitkeep ├── hpo_train.bilou └── hpo_train.ser.gz ├── requirements.txt ├── settings.json ├── settings_base.json └── src ├── __init__.py ├── classification ├── __init__.py ├── __init__.pyc ├── model.py ├── model.pyc ├── ner │ ├── __init__.py │ ├── __init__.pyc │ ├── crfsuitener.py │ ├── crfsuitener.pyc │ ├── matcher.py │ ├── matcher.pyc │ ├── mirna_matcher.py │ ├── mirna_matcher.pyc │ ├── simpletagger.py │ ├── simpletagger.pyc │ ├── stanfordner.py │ ├── stanfordner.pyc │ ├── taggercollection.py │ └── taggercollection.pyc ├── results.py ├── results.pyc └── rext │ ├── __init__.py │ ├── __init__.pyc │ ├── crfre.py │ ├── crfre.pyc │ ├── ddi_kernels.py │ ├── ddi_kernels.pyc │ ├── jsrekernel.py │ ├── jsrekernel.pyc │ ├── kernelmodels.py │ ├── kernelmodels.pyc │ ├── multir.py │ ├── multir.pyc │ ├── relations.py │ ├── relations.pyc │ ├── rules.py │ ├── rules.pyc │ ├── scikitre.py │ ├── scikitre.pyc │ ├── stanfordre.py │ ├── stanfordre.pyc │ ├── svmtk.py │ └── svmtk.pyc ├── client.py ├── config ├── __init__.py ├── __init__.pyc ├── config.py ├── config.pyc └── hindex.py ├── crossvalidation.py ├── evaluate.py ├── evaluate.pyc ├── fuzzy_test.py ├── main.py ├── main.pyc ├── mirna_base.py ├── mirna_base.pyc ├── normalize.py ├── other ├── __init__.pyc ├── _init_.py ├── cross_validation.py ├── dictionary.py ├── dictionary.pyc └── word_lists │ ├── definingwords.txt │ ├── go_words.txt │ ├── pos_go_words.txt │ ├── pre_entity_terms.txt │ ├── removewords.txt │ ├── stopwords.txt │ └── suffixes.txt ├── postprocessing ├── __init__.py ├── __init__.pyc ├── chebi_resolution.py ├── ensemble_ner.py ├── ensemble_ner.pyc ├── hpo_resolution.py ├── mirna_resolution.py └── ssm.py ├── reader ├── __init__.py ├── __init__.pyc ├── chebi_corpus.py ├── chebi_corpus.pyc ├── chemdner_corpus.py ├── chemdner_corpus.pyc ├── ddi_corpus.py ├── ddi_corpus.pyc ├── genia_corpus.py ├── genia_corpus.pyc ├── gpro_corpus.py ├── gpro_corpus.pyc ├── hpo_corpus.py ├── hpo_corpus.pyc ├── jnlpba_corpus.py ├── jnlpba_corpus.pyc ├── mirna_corpus.py ├── mirna_corpus.pyc ├── mirtext_corpus.py ├── mirtext_corpus.pyc ├── pubmed.py ├── pubmed.pyc ├── pubmed_corpus.py ├── pubmed_corpus.pyc ├── seedev_corpus.py ├── seedev_corpus.pyc ├── tempEval_corpus.py ├── tempEval_corpus.pyc ├── test_suite.py ├── test_suite.pyc ├── transmir.py ├── transmir_corpus.py └── transmir_corpus.pyc ├── seedev_evaluation.py ├── server.py ├── text ├── __init__.py ├── chemical_entity.py ├── corpus.py ├── dna_entity.py ├── document.py ├── entity.py ├── event_entity.py ├── hpo_document.py ├── hpo_entity.py ├── mirna_entity.py ├── offset.py ├── pair.py ├── protein_entity.py ├── sentence.py ├── time_entity.py ├── tlink.py └── token2.py ├── word2vec_experiments.py └── word2vec_experiments.pyc /Dockerfile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/Dockerfile -------------------------------------------------------------------------------- /GSC+.rar: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/GSC+.rar -------------------------------------------------------------------------------- /GSC_v2.rar: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/GSC_v2.rar -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/README.md -------------------------------------------------------------------------------- /bin/Tokenizer.jar: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/bin/Tokenizer.jar -------------------------------------------------------------------------------- /bin/base.old.prop: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/bin/base.old.prop -------------------------------------------------------------------------------- /bin/base.prop: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/bin/base.prop -------------------------------------------------------------------------------- /bin/default.properties: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/bin/default.properties -------------------------------------------------------------------------------- /bin/florchebi.jar: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/bin/florchebi.jar -------------------------------------------------------------------------------- /corpora/.gitkeep: -------------------------------------------------------------------------------- 1 | 2 | -------------------------------------------------------------------------------- /corpora/hpo/.gitkeep: -------------------------------------------------------------------------------- 1 | 2 | -------------------------------------------------------------------------------- /corpora/hpo/test_ann/.gitkeep: -------------------------------------------------------------------------------- 1 | 2 | -------------------------------------------------------------------------------- /corpora/hpo/test_corpus/.gitkeep: -------------------------------------------------------------------------------- 1 | 2 | -------------------------------------------------------------------------------- /corpora/hpo/train_ann/.gitkeep: -------------------------------------------------------------------------------- 1 | 2 | -------------------------------------------------------------------------------- /corpora/hpo/train_corpus/.gitkeep: -------------------------------------------------------------------------------- 1 | 2 | -------------------------------------------------------------------------------- /corpora/test_suite/test_suites/.gitkeep: -------------------------------------------------------------------------------- 1 | 2 | -------------------------------------------------------------------------------- /data/annotation_gazette.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/data/annotation_gazette.txt -------------------------------------------------------------------------------- /data/gazette.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/data/gazette.txt -------------------------------------------------------------------------------- /data/paths: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/data/paths -------------------------------------------------------------------------------- /data/paths_stanford: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/data/paths_stanford -------------------------------------------------------------------------------- /data/stopwords.txt: -------------------------------------------------------------------------------- 1 | 2 | -------------------------------------------------------------------------------- /models/.gitkeep: -------------------------------------------------------------------------------- 1 | 2 | -------------------------------------------------------------------------------- /models/hpo_train.bilou: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/models/hpo_train.bilou -------------------------------------------------------------------------------- /models/hpo_train.ser.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/models/hpo_train.ser.gz -------------------------------------------------------------------------------- /requirements.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/requirements.txt -------------------------------------------------------------------------------- /settings.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/settings.json -------------------------------------------------------------------------------- /settings_base.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/settings_base.json -------------------------------------------------------------------------------- /src/__init__.py: -------------------------------------------------------------------------------- 1 | 2 | -------------------------------------------------------------------------------- /src/classification/__init__.py: -------------------------------------------------------------------------------- 1 | 2 | -------------------------------------------------------------------------------- /src/classification/__init__.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/src/classification/__init__.pyc -------------------------------------------------------------------------------- /src/classification/model.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/src/classification/model.py -------------------------------------------------------------------------------- /src/classification/model.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/src/classification/model.pyc -------------------------------------------------------------------------------- /src/classification/ner/__init__.py: -------------------------------------------------------------------------------- 1 | 2 | -------------------------------------------------------------------------------- /src/classification/ner/__init__.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/src/classification/ner/__init__.pyc -------------------------------------------------------------------------------- /src/classification/ner/crfsuitener.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/src/classification/ner/crfsuitener.py -------------------------------------------------------------------------------- /src/classification/ner/crfsuitener.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/src/classification/ner/crfsuitener.pyc -------------------------------------------------------------------------------- /src/classification/ner/matcher.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/src/classification/ner/matcher.py -------------------------------------------------------------------------------- /src/classification/ner/matcher.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/src/classification/ner/matcher.pyc -------------------------------------------------------------------------------- /src/classification/ner/mirna_matcher.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/src/classification/ner/mirna_matcher.py -------------------------------------------------------------------------------- /src/classification/ner/mirna_matcher.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/src/classification/ner/mirna_matcher.pyc -------------------------------------------------------------------------------- /src/classification/ner/simpletagger.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/src/classification/ner/simpletagger.py -------------------------------------------------------------------------------- /src/classification/ner/simpletagger.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/src/classification/ner/simpletagger.pyc -------------------------------------------------------------------------------- /src/classification/ner/stanfordner.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/src/classification/ner/stanfordner.py -------------------------------------------------------------------------------- /src/classification/ner/stanfordner.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/src/classification/ner/stanfordner.pyc -------------------------------------------------------------------------------- /src/classification/ner/taggercollection.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/src/classification/ner/taggercollection.py -------------------------------------------------------------------------------- /src/classification/ner/taggercollection.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/src/classification/ner/taggercollection.pyc -------------------------------------------------------------------------------- /src/classification/results.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/src/classification/results.py -------------------------------------------------------------------------------- /src/classification/results.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/src/classification/results.pyc -------------------------------------------------------------------------------- /src/classification/rext/__init__.py: -------------------------------------------------------------------------------- 1 | 2 | -------------------------------------------------------------------------------- /src/classification/rext/__init__.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/src/classification/rext/__init__.pyc -------------------------------------------------------------------------------- /src/classification/rext/crfre.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/src/classification/rext/crfre.py -------------------------------------------------------------------------------- /src/classification/rext/crfre.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/src/classification/rext/crfre.pyc -------------------------------------------------------------------------------- /src/classification/rext/ddi_kernels.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/src/classification/rext/ddi_kernels.py -------------------------------------------------------------------------------- /src/classification/rext/ddi_kernels.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/src/classification/rext/ddi_kernels.pyc -------------------------------------------------------------------------------- /src/classification/rext/jsrekernel.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/src/classification/rext/jsrekernel.py -------------------------------------------------------------------------------- /src/classification/rext/jsrekernel.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/src/classification/rext/jsrekernel.pyc -------------------------------------------------------------------------------- /src/classification/rext/kernelmodels.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/src/classification/rext/kernelmodels.py -------------------------------------------------------------------------------- /src/classification/rext/kernelmodels.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/src/classification/rext/kernelmodels.pyc -------------------------------------------------------------------------------- /src/classification/rext/multir.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/src/classification/rext/multir.py -------------------------------------------------------------------------------- /src/classification/rext/multir.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/src/classification/rext/multir.pyc -------------------------------------------------------------------------------- /src/classification/rext/relations.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/src/classification/rext/relations.py -------------------------------------------------------------------------------- /src/classification/rext/relations.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/src/classification/rext/relations.pyc -------------------------------------------------------------------------------- /src/classification/rext/rules.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/src/classification/rext/rules.py -------------------------------------------------------------------------------- /src/classification/rext/rules.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/src/classification/rext/rules.pyc -------------------------------------------------------------------------------- /src/classification/rext/scikitre.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/src/classification/rext/scikitre.py -------------------------------------------------------------------------------- /src/classification/rext/scikitre.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/src/classification/rext/scikitre.pyc -------------------------------------------------------------------------------- /src/classification/rext/stanfordre.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/src/classification/rext/stanfordre.py -------------------------------------------------------------------------------- /src/classification/rext/stanfordre.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/src/classification/rext/stanfordre.pyc -------------------------------------------------------------------------------- /src/classification/rext/svmtk.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/src/classification/rext/svmtk.py -------------------------------------------------------------------------------- /src/classification/rext/svmtk.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/src/classification/rext/svmtk.pyc -------------------------------------------------------------------------------- /src/client.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/src/client.py -------------------------------------------------------------------------------- /src/config/__init__.py: -------------------------------------------------------------------------------- 1 | 2 | -------------------------------------------------------------------------------- /src/config/__init__.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/src/config/__init__.pyc -------------------------------------------------------------------------------- /src/config/config.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/src/config/config.py -------------------------------------------------------------------------------- /src/config/config.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/src/config/config.pyc -------------------------------------------------------------------------------- /src/config/hindex.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/src/config/hindex.py -------------------------------------------------------------------------------- /src/crossvalidation.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/src/crossvalidation.py -------------------------------------------------------------------------------- /src/evaluate.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/src/evaluate.py -------------------------------------------------------------------------------- /src/evaluate.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/src/evaluate.pyc -------------------------------------------------------------------------------- /src/fuzzy_test.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/src/fuzzy_test.py -------------------------------------------------------------------------------- /src/main.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/src/main.py -------------------------------------------------------------------------------- /src/main.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/src/main.pyc -------------------------------------------------------------------------------- /src/mirna_base.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/src/mirna_base.py -------------------------------------------------------------------------------- /src/mirna_base.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/src/mirna_base.pyc -------------------------------------------------------------------------------- /src/normalize.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/src/normalize.py -------------------------------------------------------------------------------- /src/other/__init__.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/src/other/__init__.pyc -------------------------------------------------------------------------------- /src/other/_init_.py: -------------------------------------------------------------------------------- 1 | 2 | -------------------------------------------------------------------------------- /src/other/cross_validation.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/src/other/cross_validation.py -------------------------------------------------------------------------------- /src/other/dictionary.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/src/other/dictionary.py -------------------------------------------------------------------------------- /src/other/dictionary.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/src/other/dictionary.pyc -------------------------------------------------------------------------------- /src/other/word_lists/definingwords.txt: -------------------------------------------------------------------------------- 1 | group 2 | type 3 | -------------------------------------------------------------------------------- /src/other/word_lists/go_words.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/src/other/word_lists/go_words.txt -------------------------------------------------------------------------------- /src/other/word_lists/pos_go_words.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/src/other/word_lists/pos_go_words.txt -------------------------------------------------------------------------------- /src/other/word_lists/pre_entity_terms.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/src/other/word_lists/pre_entity_terms.txt -------------------------------------------------------------------------------- /src/other/word_lists/removewords.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/src/other/word_lists/removewords.txt -------------------------------------------------------------------------------- /src/other/word_lists/stopwords.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/src/other/word_lists/stopwords.txt -------------------------------------------------------------------------------- /src/other/word_lists/suffixes.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/src/other/word_lists/suffixes.txt -------------------------------------------------------------------------------- /src/postprocessing/__init__.py: -------------------------------------------------------------------------------- 1 | 2 | -------------------------------------------------------------------------------- /src/postprocessing/__init__.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/src/postprocessing/__init__.pyc -------------------------------------------------------------------------------- /src/postprocessing/chebi_resolution.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/src/postprocessing/chebi_resolution.py -------------------------------------------------------------------------------- /src/postprocessing/ensemble_ner.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/src/postprocessing/ensemble_ner.py -------------------------------------------------------------------------------- /src/postprocessing/ensemble_ner.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/src/postprocessing/ensemble_ner.pyc -------------------------------------------------------------------------------- /src/postprocessing/hpo_resolution.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/src/postprocessing/hpo_resolution.py -------------------------------------------------------------------------------- /src/postprocessing/mirna_resolution.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/src/postprocessing/mirna_resolution.py -------------------------------------------------------------------------------- /src/postprocessing/ssm.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/src/postprocessing/ssm.py -------------------------------------------------------------------------------- /src/reader/__init__.py: -------------------------------------------------------------------------------- 1 | 2 | -------------------------------------------------------------------------------- /src/reader/__init__.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/src/reader/__init__.pyc -------------------------------------------------------------------------------- /src/reader/chebi_corpus.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/src/reader/chebi_corpus.py -------------------------------------------------------------------------------- /src/reader/chebi_corpus.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/src/reader/chebi_corpus.pyc -------------------------------------------------------------------------------- /src/reader/chemdner_corpus.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/src/reader/chemdner_corpus.py -------------------------------------------------------------------------------- /src/reader/chemdner_corpus.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/src/reader/chemdner_corpus.pyc -------------------------------------------------------------------------------- /src/reader/ddi_corpus.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/src/reader/ddi_corpus.py -------------------------------------------------------------------------------- /src/reader/ddi_corpus.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/src/reader/ddi_corpus.pyc -------------------------------------------------------------------------------- /src/reader/genia_corpus.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/src/reader/genia_corpus.py -------------------------------------------------------------------------------- /src/reader/genia_corpus.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/src/reader/genia_corpus.pyc -------------------------------------------------------------------------------- /src/reader/gpro_corpus.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/src/reader/gpro_corpus.py -------------------------------------------------------------------------------- /src/reader/gpro_corpus.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/src/reader/gpro_corpus.pyc -------------------------------------------------------------------------------- /src/reader/hpo_corpus.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/src/reader/hpo_corpus.py -------------------------------------------------------------------------------- /src/reader/hpo_corpus.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/src/reader/hpo_corpus.pyc -------------------------------------------------------------------------------- /src/reader/jnlpba_corpus.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/src/reader/jnlpba_corpus.py -------------------------------------------------------------------------------- /src/reader/jnlpba_corpus.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/src/reader/jnlpba_corpus.pyc -------------------------------------------------------------------------------- /src/reader/mirna_corpus.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/src/reader/mirna_corpus.py -------------------------------------------------------------------------------- /src/reader/mirna_corpus.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/src/reader/mirna_corpus.pyc -------------------------------------------------------------------------------- /src/reader/mirtext_corpus.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/src/reader/mirtext_corpus.py -------------------------------------------------------------------------------- /src/reader/mirtext_corpus.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/src/reader/mirtext_corpus.pyc -------------------------------------------------------------------------------- /src/reader/pubmed.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/src/reader/pubmed.py -------------------------------------------------------------------------------- /src/reader/pubmed.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/src/reader/pubmed.pyc -------------------------------------------------------------------------------- /src/reader/pubmed_corpus.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/src/reader/pubmed_corpus.py -------------------------------------------------------------------------------- /src/reader/pubmed_corpus.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/src/reader/pubmed_corpus.pyc -------------------------------------------------------------------------------- /src/reader/seedev_corpus.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/src/reader/seedev_corpus.py -------------------------------------------------------------------------------- /src/reader/seedev_corpus.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/src/reader/seedev_corpus.pyc -------------------------------------------------------------------------------- /src/reader/tempEval_corpus.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/src/reader/tempEval_corpus.py -------------------------------------------------------------------------------- /src/reader/tempEval_corpus.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/src/reader/tempEval_corpus.pyc -------------------------------------------------------------------------------- /src/reader/test_suite.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/src/reader/test_suite.py -------------------------------------------------------------------------------- /src/reader/test_suite.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/src/reader/test_suite.pyc -------------------------------------------------------------------------------- /src/reader/transmir.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/src/reader/transmir.py -------------------------------------------------------------------------------- /src/reader/transmir_corpus.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/src/reader/transmir_corpus.py -------------------------------------------------------------------------------- /src/reader/transmir_corpus.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/src/reader/transmir_corpus.pyc -------------------------------------------------------------------------------- /src/seedev_evaluation.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/src/seedev_evaluation.py -------------------------------------------------------------------------------- /src/server.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/src/server.py -------------------------------------------------------------------------------- /src/text/__init__.py: -------------------------------------------------------------------------------- 1 | 2 | -------------------------------------------------------------------------------- /src/text/chemical_entity.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/src/text/chemical_entity.py -------------------------------------------------------------------------------- /src/text/corpus.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/src/text/corpus.py -------------------------------------------------------------------------------- /src/text/dna_entity.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/src/text/dna_entity.py -------------------------------------------------------------------------------- /src/text/document.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/src/text/document.py -------------------------------------------------------------------------------- /src/text/entity.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/src/text/entity.py -------------------------------------------------------------------------------- /src/text/event_entity.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/src/text/event_entity.py -------------------------------------------------------------------------------- /src/text/hpo_document.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/src/text/hpo_document.py -------------------------------------------------------------------------------- /src/text/hpo_entity.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/src/text/hpo_entity.py -------------------------------------------------------------------------------- /src/text/mirna_entity.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/src/text/mirna_entity.py -------------------------------------------------------------------------------- /src/text/offset.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/src/text/offset.py -------------------------------------------------------------------------------- /src/text/pair.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/src/text/pair.py -------------------------------------------------------------------------------- /src/text/protein_entity.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/src/text/protein_entity.py -------------------------------------------------------------------------------- /src/text/sentence.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/src/text/sentence.py -------------------------------------------------------------------------------- /src/text/time_entity.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/src/text/time_entity.py -------------------------------------------------------------------------------- /src/text/tlink.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/src/text/tlink.py -------------------------------------------------------------------------------- /src/text/token2.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/src/text/token2.py -------------------------------------------------------------------------------- /src/word2vec_experiments.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/src/word2vec_experiments.py -------------------------------------------------------------------------------- /src/word2vec_experiments.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lasigeBioTM/IHP/HEAD/src/word2vec_experiments.pyc --------------------------------------------------------------------------------