Ontologies and annotation corpora included in fastSemSim

This module contains a set of embedded ontologies and annotation corpora, and a class for keeping track and easily find the required datasets.

fastsemsim.data.dataset submodule

class fastsemsim.data.dataset.Dataset(descriptor=None)

Bases: object

This class keeps track of the dataset of ontologies and annotation corpora included in fastSemSim. The file data/dataset.txt is read to collect the list of embedded ontologies and annotation corpora.

get_annotation_corpus(dataset_name)

Return the required annotation corpus

get_annotation_corpus_by_species(ontology=None, species=None)

Return the annotation corpus for the selected species, and compatible with the ontology specified by the ontology parameter.

get_dataset(dataset_name)

Return the required dataset

get_default_annotation_corpus(ontology=None, species=None)

Return the default annotation corpus for the selected species, and compatible with the ontology specified by the ontology parameter.

get_default_ontology(ontology_type)

Return the default embedded ontology of the ontology_type type

get_ontology(dataset_name)

Return the required ontology

populate(descriptor=None)

Initialize class structures. Use the descriptor parameter to specify a dataset descriptor file. By default, the file data/dataset.txt will be used.