dipper.sources.GeneOntology module

class dipper.sources.GeneOntology.GeneOntology(graph_type, are_bnodes_skolemized, tax_ids=None)

Bases: dipper.sources.Source.Source

This is the parser for the [Gene Ontology Annotations](http://www.geneontology.org), from which we process gene-process/function/subcellular location associations.

We generate the GO graph to include the following information: * genes * gene-process * gene-function * gene-location

We process only a subset of the organisms:

Status: IN PROGRESS / INCOMPLETE

clean_db_prefix(db)

Here, we map the GO-style prefixes with Monarch-style prefixes that are able to be processed by our curie_map. :param db: :return:

fetch(is_dl_forced=False)

abstract method to fetch all data from an external resource. this should be overridden by subclasses :return: None

files = {'10090': {'url': 'http://geneontology.org/gene-associations/gene_association.mgi.gz', 'file': 'gene_association.mgi.gz'}, '10116': {'url': 'http://geneontology.org/gene-associations/gene_association.rgd.gz', 'file': 'gene_association.rgd.gz'}, '4896': {'url': 'http://geneontology.org/gene-associations/gene_association.pombase.gz', 'file': 'gene_association.pombase.gz'}, '559292': {'url': 'http://geneontology.org/gene-associations/gene_association.sgd.gz', 'file': 'gene_association.sgd.gz'}, '6239': {'url': 'http://geneontology.org/gene-associations/gene_association.wb.gz', 'file': 'gene_association.wb.gz'}, '7227': {'url': 'http://geneontology.org/gene-associations/gene_association.fb.gz', 'file': 'gene_association.fb.gz'}, '7955': {'url': 'http://geneontology.org/gene-associations/gene_association.zfin.gz', 'file': 'gene_association.zfin.gz'}, '9031': {'url': 'http://geneontology.org/gene-associations/goa_chicken.gaf.gz', 'file': 'gene_association.goa_ref_chicken.gz'}, '9606': {'url': 'http://geneontology.org/gene-associations/goa_human.gaf.gz', 'file': 'gene_association.goa_ref_human.gz'}, '9615': {'url': 'http://geneontology.org/gene-associations/goa_dog.gaf.gz', 'file': 'gene_association.goa_dog.gz'}, '9823': {'url': 'http://geneontology.org/gene-associations/goa_pig.gaf.gz', 'file': 'gene_association.goa_ref_pig.gz'}, '9913': {'url': 'http://geneontology.org/gene-associations/goa_cow.gaf.gz', 'file': 'goa_cow.gaf.gz'}, 'go-references': {'url': 'http://www.geneontology.org/doc/GO.references', 'file': 'GO.references'}, 'id-map': {'url': 'ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/idmapping_selected.tab.gz', 'file': 'idmapping_selected.tab.gz'}}

getTestSuite()

An abstract method that should be overwritten with tests appropriate for the specific source. :return:

get_uniprot_entrez_id_map()

map_files = {'eco_map': 'http://purl.obolibrary.org/obo/eco/gaf-eco-mapping.txt'}

parse(limit=None)

abstract method to parse all data from an external resource, that was fetched in fetch() this should be overridden by subclasses :return: None

process_gaf(file, limit, id_map=None, eco_map=None)