dipper.models.assoc.OrthologyAssoc module

class dipper.models.assoc.OrthologyAssoc.OrthologyAssoc(graph, definedby, gene1, gene2, rel=None)

Bases: dipper.models.assoc.Association.Assoc

add_gene_family_to_graph(family_id)

Make an association between a group of genes and some grouping class. We make the assumption that the genes in the association are part of the supplied family_id, and that the genes have already been declared as classes elsewhere. The family_id is added as an individual of type DATA:gene_family.

Triples: <family_id> a DATA:gene_family <family_id> RO:has_member <gene1> <family_id> RO:has_member <gene2>

Parameters:

• family_id –
• g – the graph to modify

Returns:

ortho_rel = {'has_member': 'RO:0002351', 'homologous': 'RO:HOM0000019', 'in_paralogous': 'RO:HOM0000023', 'least_diverged_orthologous': 'RO:HOM0000020', 'ohnologous': 'RO:HOM0000022', 'orthologous': 'RO:HOM0000017', 'paralogous': 'RO:HOM0000011', 'xenologous': 'RO:HOM0000018'}

terms = {'gene_family': 'DATA:3148'}