Method List
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BC2GM Biocreative
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BC2GM_eval Biocreative
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#abstract PubMed::Article
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#add Dictionary
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#add Dictionary::KL
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#add Dictionary::TF_IDF
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add_description Rake::Pipeline::Step
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add_file FileCache
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add_name DictionaryNER
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#aka Entrez::Gene
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all Organism
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#appearence_order Normalizer
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append Open
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#arabic String
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#author PubMed::Article
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#best Dictionary::KL
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#best Dictionary::TF_IDF
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#bibentry PubMed::Article
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#bibtex PubMed::Article
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#bigrams String
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bigrams BagOfWords
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build_re RegExpNER
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build_re_old RegExpNER
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cachedir Rbbt
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#chunk Array
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chunk DictionaryNER
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citation_link GoogleScholar
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#classify Classifier
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#classify_feature_array Classifier
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#classify_feature_hash Classifier
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#classify_text_array Classifier
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#classify_text_hash Classifier
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clean ArrayHash
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#clean ArrayHash
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#clean CueIndex
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#comentaries Entrez::Gene
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#config NERFeatures
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#config CueIndex
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#config SimpleDSL
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#context NERFeatures
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count BagOfWords
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create_model Classifier
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#cues CueIndex
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#data ArrayHash
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datadir Rbbt
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#define CueIndex
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#define NERFeatures
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del_file FileCache
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#description Entrez::Gene
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#df Dictionary::TF_IDF
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#direction NERFeatures
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#docs Dictionary::TF_IDF
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#downcase_first String
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entrez2native Entrez
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entrez2pubmed Entrez
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#entrez_score Normalizer
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escape_title PubMed::Article
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#extract Abner
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#extract NER
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#extract Banner
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#features NERFeatures
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features BagOfWords
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#field_pos ArrayHash
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#fields ArrayHash
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fields Open
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full_text_url GoogleScholar
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func_match_field Open
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gene_filename Entrez
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gene_literature Organism
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gene_literature_go Organism
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gene_text_similarity Entrez
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get_article PubMed
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get_best Normalizer
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get_gene Entrez
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goterms GO
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goterms Organism
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#gscholar_pdf PubMed::Article
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guessIdFormat Organism
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id2ancestors GO
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id2name GO
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id2namespace GO
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id_formats Organism
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id_index Organism
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id_position Organism
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#idf Dictionary::TF_IDF
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index Index
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#infile Rake::Pipeline
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info GO
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#info Rake::Pipeline
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info_file Rake::Pipeline::Info
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init GO
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#initialize RegExpNER
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#initialize Banner
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#initialize Normalizer
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#initialize Abner
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#initialize NER
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#initialize SimpleDSL
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#initialize NERFeatures
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#initialize ArrayHash
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#initialize Dictionary
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#initialize Dictionary::KL
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#initialize PubMed::Article
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#initialize Dictionary::TF_IDF
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#initialize Classifier
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#initialize CueIndex
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#initialize DictionaryNER
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#initialize Entrez::Gene
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#input Rake::Pipeline
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#is_binary? Rake::Pipeline
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#is_special? String
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#journal PubMed::Article
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#kl Dictionary::KL
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lexicon Organism
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literature Organism
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#load CueIndex
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load DictionaryNER
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load_config Rbbt
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load_info Rake::Pipeline::Info
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#load_input Rake::Pipeline
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#main ArrayHash
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match Polysearch
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match DictionaryNER
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#match RegExpNER
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#match Normalizer
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#match CueIndex
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#match DictionaryNER
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#match_hash RegExpNER
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match_re RegExpNER
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#merge ArrayHash
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merge ArrayHash
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merge_values ArrayHash
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merge_values_string ArrayHash
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name Organism
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name Polysearch
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name2org Organism
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#neg_dict Dictionary::KL
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ner Organism
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norm Organism
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#num_docs Dictionary::TF_IDF
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number_cites GoogleScholar
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#organism Entrez::Gene
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#outfile Rake::Pipeline
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#parse SimpleDSL
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parse_xml PubMed::Article
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path FileCache
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#pdf_url PubMed::Article
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#pmc_pdf PubMed::Article
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#pmid PubMed::Article
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#pos_dict Dictionary::KL
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position Biocreative
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#process ArrayHash
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process ArrayHash
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#protnames Entrez::Gene
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pullout ArrayHash
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query BioMart
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query PubMed
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random_name TmpFile
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read Open
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#remove ArrayHash
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#resolve Normalizer
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#reverse NERFeatures
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reverse NERFeatures
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rootdir Rbbt
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save_info Rake::Pipeline::Info
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#save_output Rake::Pipeline
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#select Normalizer
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simplify DictionaryNER
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#step Rake::Pipeline
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#step_def Rake::Pipeline
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step_def Rake::Pipeline::Step
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step_descriptions Rake::Pipeline::Step
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#step_descriptions Rake::Pipeline
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#summary Entrez::Gene
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supported_ids Organism
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#symbol Entrez::Gene
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#tagged_features NERFeatures
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#template NERFeatures
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#terms Dictionary::KL
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#terms Dictionary::TF_IDF
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#terms Dictionary
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#terms Classifier
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terms BagOfWords
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#text PubMed::Article
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#text Entrez::Gene
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#text_features NERFeatures
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#tf Dictionary::TF_IDF
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#tf_idf Dictionary::TF_IDF
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#title PubMed::Article
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tmp_file TmpFile
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tmpdir Rbbt
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to_hash Open
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#token_score Normalizer
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tokens NERFeatures
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#total_terms Dictionary::TF_IDF
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#train NERFeatures
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type_index Polysearch
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type_names Polysearch
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user_agent GoogleScholar
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#weights Dictionary::KL
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#weights Dictionary::TF_IDF
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#window NERFeatures
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with_file TmpFile
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#words String
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words BagOfWords
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write Open