本文整理汇总了Python中dipper.models.Dataset.Dataset类的典型用法代码示例。如果您正苦于以下问题：Python Dataset类的具体用法？Python Dataset怎么用？Python Dataset使用的例子？那么, 这里精选的类代码示例或许可以为您提供帮助。
在下文中一共展示了Dataset类的15个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的Python代码示例。
示例1: __init__
def __init__(self):
Source.__init__(self, 'mpd')
# @N, not sure if this step is required
self.namespaces.update(curie_map.get())
self.stdevthreshold = 2
self.nobnodes = True # FIXME
# update the dataset object with details about this resource
# @N: Note that there is no license as far as I can tell
self.dataset = Dataset(
'mpd', 'MPD', 'http://phenome.jax.org', None, None)
# TODO add a citation for mpd dataset as a whole
self.dataset.set_citation('PMID:15619963')
self.assayhash = {}
self.idlabel_hash = {}
# to store the mean/zscore of each measure by strain+sex
self.score_means_by_measure = {}
# to store the mean value for each measure by strain+sex
self.strain_scores_by_measure = {}
self.geno = Genotype(self.graph)
self.gu = GraphUtils(curie_map.get())
return示例2: __init__
def __init__(self, tax_ids=None):
super().__init__("biogrid")
self.tax_ids = tax_ids
self.load_bindings()
self.dataset = Dataset(
"biogrid",
"The BioGrid",
"http://thebiogrid.org/",
None,
"http://wiki.thebiogrid.org/doku.php/terms_and_conditions",
)
# Defaults
# taxids = [9606,10090,10116,7227,7955,6239,8355] #our favorite animals
if self.tax_ids is None:
self.tax_ids = [9606, 10090, 7955]
if "test_ids" not in config.get_config() or "gene" not in config.get_config()["test_ids"]:
logger.warn("not configured with gene test ids.")
else:
self.test_ids = config.get_config()["test_ids"]["gene"]
# data-source specific warnings (will be removed when issues are cleared)
logger.warn("several MI experimental codes do not exactly map to ECO; using approximations.")
return示例3: __init__
def __init__(self):
Source.__init__(self, 'ctd')
self.dataset = Dataset(
'ctd', 'CTD', 'http://ctdbase.org', None,
'http://ctdbase.org/about/legal.jsp')
if 'test_ids' not in config.get_config() \
or 'gene' not in config.get_config()['test_ids']:
logger.warning("not configured with gene test ids.")
self.test_geneids = []
else:
self.test_geneids = config.get_config()['test_ids']['gene']
if 'test_ids' not in config.get_config() \
or 'disease' not in config.get_config()['test_ids']:
logger.warning("not configured with disease test ids.")
self.test_diseaseids = []
else:
self.test_diseaseids = config.get_config()['test_ids']['disease']
self.gu = GraphUtils(curie_map.get())
self.g = self.graph
self.geno = Genotype(self.g)
return示例4: __init__
def __init__(self):
Source.__init__(self, 'hpoa')
self.load_bindings()
self.dataset = Dataset(
'hpoa', 'Human Phenotype Ontology',
'http://www.human-phenotype-ontology.org', None,
'http://www.human-phenotype-ontology.org/contao/index.php/legal-issues.html')
self.replaced_id_count = 0
if 'test_ids' not in config.get_config()\
or 'disease' not in config.get_config()['test_ids']:
logger.warning("not configured with disease test ids.")
self.test_ids = []
else:
self.test_ids = config.get_config()['test_ids']['disease']
# data-source specific warnings to be removed when issues are cleared
logger.warning(
"note that some ECO classes are missing for ICE, PCS, and ITM;" +
" using temporary mappings.")
return示例5: __init__
def __init__(self, tax_ids=None):
super().__init__('biogrid')
self.tax_ids = tax_ids
self.load_bindings()
self.dataset = Dataset(
'biogrid', 'The BioGrid', 'http://thebiogrid.org/', None,
'http://wiki.thebiogrid.org/doku.php/terms_and_conditions')
# Defaults
# our favorite animals
# taxids = [9606,10090,10116,7227,7955,6239,8355]
if self.tax_ids is None:
self.tax_ids = [9606, 10090, 7955]
if 'test_ids' not in config.get_config() or \
'gene' not in config.get_config()['test_ids']:
logger.warning("not configured with gene test ids.")
else:
self.test_ids = config.get_config()['test_ids']['gene']
# data-source specific warnings
# (will be removed when issues are cleared)
logger.warning(
"several MI experimental codes do not exactly map to ECO; "
"using approximations.")
return示例6: __init__
def __init__(self, graph_type, are_bnodes_skolemized):
super().__init__(graph_type, are_bnodes_skolemized, 'ctd')
self.dataset = Dataset(
'ctd', 'CTD', 'http://ctdbase.org', None,
'http://ctdbase.org/about/legal.jsp')
if 'test_ids' not in config.get_config() \
or 'gene' not in config.get_config()['test_ids']:
logger.warning("not configured with gene test ids.")
self.test_geneids = []
else:
self.test_geneids = config.get_config()['test_ids']['gene']
if 'test_ids' not in config.get_config() \
or 'disease' not in config.get_config()['test_ids']:
logger.warning("not configured with disease test ids.")
self.test_diseaseids = []
else:
self.test_diseaseids = config.get_config()['test_ids']['disease']
self.g = self.graph
self.geno = Genotype(self.graph)
self.pathway = Pathway(self.graph)
return示例7: __init__
def __init__(self, graph_type, are_bnodes_skolemized):
super().__init__(graph_type, are_bnodes_skolemized, 'mmrrc')
self.strain_hash = {}
self.id_label_hash = {}
self.dataset = Dataset(
'mmrrc', 'Mutant Mouse Regional Resource Centers',
'https://www.mmrrc.org', None,
'https://www.mmrrc.org/about/data_download.php')
return示例8: __init__
def __init__(self):
Source.__init__(self, 'wormbase')
# update the dataset object with details about this resource
# NO LICENSE for this resource
self.dataset = Dataset(
'wormbase', 'WormBase', 'http://www.wormbase.org', None, None,
'http://www.wormbase.org/about/policies#012')
self.version_num = None
return示例9: __init__
def __init__(self):
Source.__init__(self, 'mmrrc')
self.strain_hash = {}
self.id_label_hash = {}
self.load_bindings()
self.dataset = Dataset(
'mmrrc', 'Mutant Mouse Regional Resource Centers',
'https://www.mmrrc.org', None,
'https://www.mmrrc.org/about/data_download.php')
return示例10: __init__
def __init__(self, graph_type, are_bnodes_skolemized):
super().__init__(graph_type, are_bnodes_skolemized, 'wormbase')
# update the dataset object with details about this resource
# NO LICENSE for this resource
self.dataset = Dataset(
'wormbase', 'WormBase', 'http://www.wormbase.org', None, None,
'http://www.wormbase.org/about/policies#012')
self.version_num = None
return示例11: __init__
def __init__(self):
Source.__init__(self, 'coriell')
self.load_bindings()
self.dataset = Dataset('coriell', 'Coriell', 'http://ccr.coriell.org/', None)
# data-source specific warnings (will be removed when issues are cleared)
logger.warn('We assume that if a species is not provided, that it is a Human-derived cell line')
logger.warn('We map all omim ids as a disease/phenotype entity, but should be fixed in the future')
# check if config exists; if it doesn't, error out and let user know
if 'dbauth' not in config.get_config() or 'coriell' not in config.get_config()['dbauth']:
logger.error("not configured with FTP user/password.")
return示例12: __init__
def __init__(self):
Source.__init__(self, 'eom')
self.namespaces.update(curie_map.get())
# update the dataset object with details about this resource
# TODO put this into a conf file?
self.dataset = Dataset('eom', 'EOM', 'http://elementsofmorphology.nih.gov', None,
'http://www.genome.gov/copyright.cfm',
'https://creativecommons.org/publicdomain/mark/1.0/')
# check if config exists; if it doesn't, error out and let user know
if 'dbauth' not in config.get_config() or 'disco' not in config.get_config()['dbauth']:
logger.error("not configured with PG user/password.")
# source-specific warnings. will be cleared when resolved.
return示例13: __init__
def __init__(self, graph_type, are_bnodes_skolemized):
super().__init__(graph_type, are_bnodes_skolemized, 'genereviews')
self.dataset = Dataset(
'genereviews', 'Gene Reviews', 'http://genereviews.org/',
None, 'http://www.ncbi.nlm.nih.gov/books/NBK138602/')
self.dataset.set_citation('GeneReviews:NBK1116')
self.book_ids = set()
self.all_books = {}
if 'test_ids' not in config.get_config() or\
'disease' not in config.get_config()['test_ids']:
logger.warning("not configured with disease test ids.")
self.test_ids = list()
else:
# select ony those test ids that are omim's.
self.test_ids = config.get_config()['test_ids']['disease']
return示例14: __init__
def __init__(self, graph_type, are_bnodes_skolemized):
Source.__init__(self, graph_type, are_bnodes_skolemized, 'mpd')
# @N, not sure if this step is required
self.stdevthreshold = 2
# update the dataset object with details about this resource
# @N: Note that there is no license as far as I can tell
self.dataset = Dataset(
'mpd', 'MPD', 'http://phenome.jax.org', None, None)
# TODO add a citation for mpd dataset as a whole
self.dataset.set_citation('PMID:15619963')
self.assayhash = {}
self.idlabel_hash = {}
# to store the mean/zscore of each measure by strain+sex
self.score_means_by_measure = {}
# to store the mean value for each measure by strain+sex
self.strain_scores_by_measure = {}
return示例15: __init__
def __init__(self):
Source.__init__(self, 'genereviews')
self.load_bindings()
self.dataset = Dataset(
'genereviews', 'Gene Reviews', 'http://genereviews.org/',
None, 'http://www.ncbi.nlm.nih.gov/books/NBK138602/')
self.dataset.set_citation('GeneReviews:NBK1116')
self.gu = GraphUtils(curie_map.get())
self.book_ids = set()
self.all_books = {}
if 'test_ids' not in config.get_config() or\
'disease' not in config.get_config()['test_ids']:
logger.warning("not configured with disease test ids.")
self.test_ids = list()
else:
# select ony those test ids that are omim's.
self.test_ids = config.get_config()['test_ids']['disease']
return