An R object that contains information on Gene Ontology Biological Process terms. These terms are organised as a direct acyclic graph (DAG), which is further stored as an object of the class 'igraph' (see http://igraph.org/r/doc/aaa-igraph-package.html). This data is prepared based on http://www.geneontology.org/ontology/obo_format_1_2/gene_ontology.1_2.obo. Only the edges with the relation (either 'is_a' or 'part_of') are retained.
an object of S4 class Onto. It has slots for "nodeInfo" and "adjMatrix"
nodeInfo: an object of S4 class InfoDataFrame,
describing information on nodes/terms including: "term_id" (i.e. Term
ID), "term_name" (i.e. Term Name), "term_namespace" (i.e. Term
Namespace), and "term_distance" (i.e. Term Distance: the distance to
the root; always 0 for the root itself)
adjMatrix: an object of S4 class AdjData,
containing adjacency data matrix, with rows for parent (arrow-outbound)
and columns for children (arrow-inbound)
Ashburner et al. (2000) Gene ontology: tool for the unification of
biology. Nat Genet, 25:25-29.
Fang H and Gough J. (2013) dcGO: database of domain-centric ontologies on functions, phenotypes, diseases and more. Nucleic Acids Res, 41(Database issue):D536-44.
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