dipper.sources.KEGG module

class dipper.sources.KEGG.KEGG(graph_type, are_bnodes_skolemized)

Bases: dipper.sources.Source.Source

fetch(is_dl_forced=False)

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

files = {'cel_orthologs': {'url': 'http://rest.kegg.jp/link/orthology/cel', 'file': 'cel_orthologs'}, 'disease': {'url': 'http://rest.genome.jp/list/disease', 'file': 'disease'}, 'disease_gene': {'url': 'http://rest.kegg.jp/link/disease/hsa', 'file': 'disease_gene'}, 'dme_orthologs': {'url': 'http://rest.kegg.jp/link/orthology/dme', 'file': 'dme_orthologs'}, 'dre_orthologs': {'url': 'http://rest.kegg.jp/link/orthology/dre', 'file': 'dre_orthologs'}, 'hsa_gene2pathway': {'url': 'http://rest.kegg.jp/link/pathway/hsa', 'file': 'human_gene2pathway'}, 'hsa_genes': {'url': 'http://rest.genome.jp/list/hsa', 'file': 'hsa_genes'}, 'hsa_orthologs': {'url': 'http://rest.kegg.jp/link/orthology/hsa', 'file': 'hsa_orthologs'}, 'mmu_orthologs': {'url': 'http://rest.kegg.jp/link/orthology/mmu', 'file': 'mmu_orthologs'}, 'ncbi': {'url': 'http://rest.genome.jp/conv/ncbi-geneid/hsa', 'file': 'ncbi'}, 'omim2disease': {'url': 'http://rest.genome.jp/link/disease/omim', 'file': 'omim2disease'}, 'omim2gene': {'url': 'http://rest.genome.jp/link/omim/hsa', 'file': 'omim2gene'}, 'ortholog_classes': {'url': 'http://rest.genome.jp/list/orthology', 'file': 'ortholog_classes'}, 'pathway': {'url': 'http://rest.genome.jp/list/pathway', 'file': 'pathway'}, 'pathway_disease': {'url': 'http://rest.kegg.jp/link/pathway/ds', 'file': 'pathway_disease'}, 'pathway_ko': {'url': 'http://rest.kegg.jp/link/pathway/ko', 'file': 'pathway_ko'}, 'pathway_pubmed': {'url': 'http://rest.kegg.jp/link/pathway/pubmed', 'file': 'pathway_pubmed'}, 'rno_orthologs': {'url': 'http://rest.kegg.jp/link/orthology/rno', 'file': 'rno_orthologs'}}

getTestSuite()

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

parse(limit=None)

Parameters:limit – Returns:

test_ids = {'disease': ['ds:H00015', 'ds:H00026', 'ds:H00712', 'ds:H00736', 'ds:H00014'], 'genes': ['hsa:100506275', 'hsa:285958', 'hsa:286410', 'hsa:6387', 'hsa:1080', 'hsa:11200', 'hsa:1131', 'hsa:1137', 'hsa:126', 'hsa:1277', 'hsa:1278', 'hsa:1285', 'hsa:1548', 'hsa:1636', 'hsa:1639', 'hsa:183', 'hsa:185', 'hsa:1910', 'hsa:207', 'hsa:2099', 'hsa:2483', 'hsa:2539', 'hsa:2629', 'hsa:2697', 'hsa:3161', 'hsa:3845', 'hsa:4137', 'hsa:4591', 'hsa:472', 'hsa:4744', 'hsa:4835', 'hsa:4929', 'hsa:5002', 'hsa:5080', 'hsa:5245', 'hsa:5290', 'hsa:53630', 'hsa:5630', 'hsa:5663', 'hsa:580', 'hsa:5888', 'hsa:5972', 'hsa:6311', 'hsa:64327', 'hsa:6531', 'hsa:6647', 'hsa:672', 'hsa:675', 'hsa:6908', 'hsa:7040', 'hsa:7045', 'hsa:7048', 'hsa:7157', 'hsa:7251', 'hsa:7490', 'hsa:7517', 'hsa:79728', 'hsa:83893', 'hsa:83990', 'hsa:841', 'hsa:8438', 'hsa:8493', 'hsa:860', 'hsa:9568', 'hsa:9627', 'hsa:9821', 'hsa:999', 'hsa:3460'], 'orthology_classes': ['ko:K00010', 'ko:K00027', 'ko:K00042', 'ko:K00088'], 'pathway': ['path:map00010', 'path:map00195', 'path:map00100', 'path:map00340', 'path:hsa05223']}