Index

A

add_data() (Dataset method) add_end_character() (in module oats.nlp.small) add_prefix_safely() (in module oats.nlp.small) all_fuzzy_matches() (in module oats.nlp.search) all_rabinkarp_matches() (in module oats.nlp.search) annotate_using_fuzzy_matching() (in module oats.annotation.annotation)

annotate_using_noble_coder() (in module oats.annotation.annotation) annotate_using_rabin_karp() (in module oats.annotation.annotation) annotations() (Dataset method) any_fuzzy_matches() (in module oats.nlp.search) any_rabinkarp_matches() (in module oats.nlp.search) AnyInteractions (class in oats.biology.relationships)

B

binary_fuzzy_match() (in module oats.nlp.search)

binary_robinkarp_match() (in module oats.nlp.search)

C

capitalize_sentence() (in module oats.nlp.small)

concatenate_texts() (in module oats.nlp.preprocess) concatenate_with_delim() (in module oats.nlp.preprocess)

D

Dataset (class in oats.biology.dataset) depth() (Ontology method) descendants() (Ontology method)

describe() (Dataset method) (Groupings method) descriptions() (Dataset method)

F

filter_by_species() (Dataset method) filter_has_annotation() (Dataset method) filter_has_description() (Dataset method) filter_randomly() (Dataset method)

filter_with_ids() (Dataset method) flatten() (in module oats.utils.utils) function_wrapper() (in module oats.utils.utils) function_wrapper_with_duration() (in module oats.utils.utils)

G

Gene (class in oats.biology.gene) genes() (Dataset method) get_dataframe_for_kegg() (Groupings static method) get_dataframe_for_plantcyc() (Groupings static method) get_df() (AnyInteractions method) (ProteinInteractions method) get_distance() (SquarePairwiseDistances method) get_distances() (SquarePairwiseDistances method) get_gene_names_from_group_id() (Groupings method) get_group_id_to_ids_dict() (Groupings method) get_group_ids_from_gene_name() (Groupings method) get_group_ids_from_gene_obj() (Groupings method) get_groupings_for_dataset() (Groupings method) get_id_to_group_ids_dict() (Groupings method) get_ids() (AnyInteractions method) (ProteinInteractions method)

get_name_to_id_dictionary() (Dataset method) get_nearest_neighbor_ids() (RectangularPairwiseDistances method) (SquarePairwiseDistances method) get_ontology_ids() (in module oats.nlp.small) get_overrepresented_tokens() (in module oats.nlp.vocabulary) get_species_to_name_to_ids_dictionary() (Dataset method) get_vector() (RectangularPairwiseDistances method) (SquarePairwiseDistances method) get_vocab_from_tokens() (in module oats.nlp.vocabulary) get_word2vec_related_words_from_doc() (in module oats.nlp.vocabulary) get_word2vec_related_words_from_word() (in module oats.nlp.vocabulary) get_wordnet_related_words_from_doc() (in module oats.nlp.vocabulary) get_wordnet_related_words_from_word() (in module oats.nlp.vocabulary) Groupings (class in oats.biology.groupings)

I

ic() (Ontology method)

ids() (Dataset method) inherited() (Ontology method)

L

load_from_pickle() (in module oats.utils.utils)

O

oats (module) oats.annotation (module) oats.annotation.annotation (module) oats.annotation.ontology (module) oats.biology (module) oats.biology.dataset (module) oats.biology.gene (module) oats.biology.groupings (module) oats.biology.relationships (module) oats.distances (module)

oats.distances.distances (module) oats.distances.pairwise (module) oats.nlp (module) oats.nlp.preprocess (module) oats.nlp.search (module) oats.nlp.small (module) oats.nlp.vocabulary (module) oats.utils (module) oats.utils.constants (module) oats.utils.utils (module) Ontology (class in oats.annotation.ontology)

P

ProteinInteractions (class in oats.biology.relationships)

R

read_annotations_from_file() (in module oats.annotation.annotation) RectangularPairwiseDistances (class in oats.distances.distances) reduce_vocab_connected_components() (in module oats.nlp.vocabulary) reduce_vocab_linares_pontes() (in module oats.nlp.vocabulary) remove_duplicates_retain_order() (in module oats.utils.utils)

remove_enclosing_brackets() (in module oats.nlp.small) remove_newlines() (in module oats.nlp.small) remove_punctuation() (in module oats.nlp.small) remove_text_duplicates_retain_order() (in module oats.nlp.preprocess) replace_delimiter() (in module oats.nlp.preprocess)

S

save_all_kegg_pathway_files() (Groupings static method) save_to_pickle() (in module oats.utils.utils) similarity_ic() (Ontology method)

similarity_jaccard() (Ontology method) species() (Dataset method) SquarePairwiseDistances (class in oats.distances.distances) subtract_string_lists() (in module oats.nlp.preprocess)

T

term_enrichment() (in module oats.annotation.annotation) to_csv() (Dataset method) to_hms() (in module oats.utils.utils) to_json() (Dataset method)

to_pandas() (Dataset method) (Groupings method) token_enrichment() (in module oats.nlp.vocabulary) tokens() (Ontology method)

V

vectorize_with_bert() (in module oats.distances.pairwise) vectorize_with_doc2vec() (in module oats.distances.pairwise)

vectorize_with_ngrams() (in module oats.distances.pairwise) vectorize_with_similarities() (in module oats.distances.pairwise) vectorize_with_word2vec() (in module oats.distances.pairwise)

W

with_annotations() (in module oats.distances.pairwise) with_bert() (in module oats.distances.pairwise) with_doc2vec() (in module oats.distances.pairwise) with_ngrams() (in module oats.distances.pairwise)

with_precomputed_vectors() (in module oats.distances.pairwise) with_similarities() (in module oats.distances.pairwise) with_topic_model() (in module oats.distances.pairwise) with_word2vec() (in module oats.distances.pairwise) write_annotations_to_file() (in module oats.annotation.annotation)