.. py:currentmodule:: orangecontrib.bio.go .. py:module:: orangecontrib.bio.go ========================= Gene Ontology (:mod:`go`) ========================= Provides access to `Gene Ontology`_ and its gene annotations. .. _Gene Ontology: http://geneontology.org/ .. autoclass:: orangecontrib.bio.go.Ontology(filename=None, progress_callback=None, rev=None) :members: defined_slims_subsets, named_slims_subset, set_slims_subset, slims_for_term, extract_super_graph, extract_sub_graph, __getitem__, __len__, __iter__, __contains__ Ontology supports a subset of the Mapping protocol: >>> term_ids = list(ontology) >>> term = ontology[term_ids[0]] .. autoclass:: orangecontrib.bio.go.Term .. attribute:: id The term id. .. attribute:: namespace The namespace of the term. .. attribute:: def_ The term definition (Note the use of trailing underscore to avoid conflict with a python keyword). .. attribute:: is_a List of term ids this term is a subterm of (parent terms). .. attribute:: related List of (rel_type, term_id) tuples with rel_type specifying the relationship type with term_id. .. autoclass:: orangecontrib.bio.go.Annotations(filename_or_organism=None, ontology=None, genematcher=None, progress_callback=None, rev=None) :members: :member-order: bysource :exclude-members: set_ontology, load, Load, parse_file, ParseFile, RemapGenes, AddAnnotation, DrawEnrichmentGraph, GetAllAnnotations, GetAllGenes, GetAnnotatedTerms, GetEnrichedTerms, GetGeneNamesTranslator, GetOntology, SetOntology, aliasMapper, allAnnotations, geneAnnotations, geneNames, geneNamesDict, termAnnotations .. autoclass:: orangecontrib.bio.go.AnnotationRecord :members: from_string, DB, DB_Object_ID, DB_Object_Symbol, Qualifier, GO_ID, DB_Reference, Evidence_Code, With_From, Aspect, DB_Object_Name, DB_Object_Synonym, DB_Object_Type, Taxon, Date, Assigned_By, Annotation_Extension, Gene_Product_Form_ID Example ------- Load the ontology and print out some terms:: from orangecontrib.bio import go ontology = go.Ontology() term = ontology["GO:0097194"] # execution phase of apoptosis # print a term print(term) # access fields by name print(term.id, term.name) # note the use of underscore due to a conflict with a python def keyword print(term.def_) Searching the annotation (part of :download:`code/go_gene_annotations.py`) .. literalinclude:: code/go_gene_annotations.py Term enrichment (part of :download:`code/go_enrichment.py`) .. literalinclude:: code/go_enrichment.py :lines: 6-