def __init__(self, graph_type, are_bnodes_skolemized, tax_ids=None):
super().__init__(
graph_type,
are_bnodes_skolemized,
'biogrid',
ingest_title=
'Biological General Repository for Interaction Datasets',
ingest_url='http://thebiogrid.org',
license_url=
'https://wiki.thebiogrid.org/doku.php/terms_and_conditions'
# data_rights=None,
# file_handle=None
)
self.tax_ids = tax_ids
# 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
def __init__(self, graph_type, are_bnodes_skolemized, tax_ids=None):
super().__init__(
graph_type,
are_bnodes_skolemized,
'go',
ingest_title='Gene Ontology',
ingest_url='http://www.geneontology.org',
license_url=None,
data_rights='http://geneontology.org/page/use-and-license'
# file_handle=None
)
# Defaults
self.tax_ids = tax_ids
self.test_ids = list()
if self.tax_ids is None:
self.tax_ids = [9606, 10090, 7955]
logger.info("No taxa set. Defaulting to %s", str(tax_ids))
else:
logger.info("Filtering on the following taxa: %s", str(tax_ids))
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']
# build the id map for mapping uniprot ids to genes ... ONCE
self.uniprot_entrez_id_map = self.get_uniprot_entrez_id_map()
self.eco_map = self.get_eco_map(self.map_files['eco_map'])
return
def __init__(self, tax_ids=None, gene_ids=None):
Source.__init__(self, 'ensembl')
self.tax_ids = tax_ids
self.gene_ids = gene_ids
self.load_bindings()
self.dataset = Dataset(
'ensembl', 'ENSEMBL', 'http://www.ensembl.org', None)
# Defaults
if self.tax_ids is None:
self.tax_ids = [9606, 10090, 7955]
self.gene_ids = []
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.gene_ids = config.get_config()['test_ids']['gene']
self.properties = Feature.properties
logger.setLevel(logging.INFO)
return
def __init__(self,
graph_type,
are_bnodes_skolemized,
method,
tax_ids=None):
super().__init__(
graph_type,
are_bnodes_skolemized,
# method ??? this should be lowercase ingest name/identifier
'oma',
'Ortholgous MAtrix Hierarchical Orthologous Groups',
'https://omabrowser.org/',
license_url=None,
data_rights="https://creativecommons.org/licenses/by-sa/2.5/",
# file_handle=None
)
self.tax_ids = tax_ids
self._map_orthology_code_to_RO_FOO = {
'orthologGroup': OrthologyAssoc.ortho_rel['orthologous'],
'paralogGroup': OrthologyAssoc.ortho_rel['paralogous']
}
if 'test_ids' not in config.get_config() \
or 'protein' not in config.get_config()['test_ids']:
logger.warning("not configured with gene test ids.")
else:
self.test_ids = config.get_config()['test_ids']['protein']
return
def __init__(self, graph_type, are_bnodes_skolemized):
super().__init__(
graph_type,
are_bnodes_skolemized,
'coriell',
ingest_title='Coriell Institute for Medical Research',
ingest_url='https://ccr.coriell.org/'
# website disclaimer 'https://www.coriell.org/1/About-Us/Legal-Notice'
# wet material https://www.coriell.org/1/NINDS/About/Shared-Usage-Guidelines
# license_url=None,
# data_rights=None,
# file_handle=None
)
# data-source specific warnings
# (will be removed when issues are cleared)
LOG.warning('We assume that if a species is not provided, '
'that it is a Human-derived cell line')
LOG.warning('We map all omim ids as a disease/phenotype entity, '
'but should be fixed in the future') # TODO
# 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']:
LOG.error("not configured with FTP user/password.")
# raise error
return
def __init__(self,
graph_type,
are_bnodes_skolemized,
tax_ids=None,
gene_ids=None):
super().__init__(
graph_type,
are_bnodes_skolemized,
'hgnc',
ingest_title='HGNC',
ingest_url='https://www.genenames.org/',
license_url='ftp://ftp.ebi.ac.uk/pub/databases/genenames/README.txt'
# data_rights=None,
# file_handle=None
)
self.tax_ids = tax_ids
self.gene_ids = gene_ids
self.gene_ids = []
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.gene_ids = config.get_config()['test_ids']['gene']
self.hs_txid = self.globaltt['H**o sapiens']
return
def __init__(self, graph_type, are_bnodes_skolemized):
super().__init__(
graph_type,
are_bnodes_skolemized,
'genereviews',
ingest_title='Gene Reviews',
ingest_url='http://genereviews.org/',
license_url=None,
data_rights='http://www.ncbi.nlm.nih.gov/books/NBK138602/',
# file_handle=None
)
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']:
LOG.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']
self.omim_replaced = {} # id_num to SET of id nums
self.omim_type = {} # id_num to onto_term
return
def fetch(self, is_dl_forced=False):
'''connection details for DISCO'''
cxn = {}
cxn['host'] = 'nif-db.crbs.ucsd.edu'
cxn['database'] = 'disco_crawler'
cxn['port'] = '5432'
cxn['user'] = config.get_config()['user']['disco']
cxn['password'] = config.get_config()['keys'][cxn['user']]
self.dataset.setFileAccessUrl(
'jdbc:postgresql://'+cxn['host']+':'+cxn['port']+'/'+cxn['database'],
is_object_literal=True)
# process the tables
# self.fetch_from_pgdb(self.tables,cxn,100) #for testing
self.fetch_from_pgdb(self.tables, cxn)
self.get_files(is_dl_forced)
# FIXME: Everything needed for data provenance?
fstat = os.stat('/'.join((self.rawdir, 'dvp.pr_nlx_157874_1')))
filedate = datetime.utcfromtimestamp(fstat[ST_CTIME]).strftime("%Y-%m-%d")
self.dataset.setVersion(filedate)
return
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
def __init__(self, graph_type, are_bnodes_skolemized):
super().__init__(
graph_type,
are_bnodes_skolemized,
'coriell',
ingest_title='Coriell Institute for Medical Research',
ingest_url='https://ccr.coriell.org/'
# website disclaimer 'https://www.coriell.org/1/About-Us/Legal-Notice'
# wet material https://www.coriell.org/1/NINDS/About/Shared-Usage-Guidelines
# license_url=None,
# data_rights=None,
# file_handle=None
)
# data-source specific warnings
# (will be removed when issues are cleared)
LOG.warning(
'We assume that if a species is not provided, '
'that it is a Human-derived cell line')
LOG.warning(
'We map all omim ids as a disease/phenotype entity, '
'but should be fixed in the future') # TODO
# 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']:
LOG.error("not configured with FTP user/password.")
# raise error
return
def __init__(self, graph_type, are_bnodes_skolemized, tax_ids=None):
super().__init__(graph_type, are_bnodes_skolemized, 'go')
# Defaults
self.tax_ids = tax_ids
if self.tax_ids is None:
self.tax_ids = [9606, 10090, 7955]
logger.info("No taxa set. Defaulting to %s", str(tax_ids))
else:
logger.info("Filtering on the following taxa: %s", str(tax_ids))
# update the dataset object with details about this resource
# NO LICENSE for this resource
self.dataset = Dataset(
'go', 'GeneOntology', 'http://www.geneontology.org', None,
"https://creativecommons.org/licenses/by/4.0/legalcode",
'http://geneontology.org/page/use-and-license')
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']
return
def __init__(self,
graph_type,
are_bnodes_skolemized,
tax_ids=None,
gene_ids=None):
super().__init__(graph_type, are_bnodes_skolemized, 'ensembl')
self.tax_ids = tax_ids
self.gene_ids = gene_ids
self.dataset = Dataset('ensembl', 'ENSEMBL',
'http://uswest.ensembl.org', None)
# Defaults
if self.tax_ids is None:
self.tax_ids = [9606, 10090, 7955]
self.gene_ids = []
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.gene_ids = config.get_config()['test_ids']['gene']
self.properties = Feature.properties
logger.setLevel(logging.INFO)
return
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
def __init__(self, graph_type, are_bnodes_skolemized, tax_ids=None, gene_ids=None):
super().__init__(
graph_type,
are_bnodes_skolemized,
'ensembl',
ingest_title='ENSEMBL',
ingest_url='http://uswest.ensembl.org'
# license_url=None,
# data_rights=None,
# file_handle=None
)
self.tax_ids = tax_ids
self.gene_ids = gene_ids
# Defaults
if self.tax_ids is None:
self.tax_ids = [9606, 10090, 7955]
self.gene_ids = []
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.gene_ids = config.get_config()['test_ids']['gene']
logger.setLevel(logging.INFO)
return
def __init__(self, graph_type, are_bnodes_skolemized):
super().__init__(
graph_type,
are_bnodes_skolemized,
'kegg',
ingest_title='Kyoto Encyclopedia of Genes and Genomes',
ingest_url='http://www.genome.jp/kegg/',
license_url='http://www.kegg.jp/kegg/legal.html'
# data_rights=None,
# file_handle=None
)
# check to see if there are any ids configured in the config;
# otherwise, warn
if 'test_ids' not in config.get_config() or\
'disease' not in config.get_config()['test_ids']:
LOG.warning("not configured with disease test ids.")
else:
self.test_ids['disease'] += \
config.get_config()['test_ids']['disease']
self.label_hash = {}
self.omim_disease_hash = {} # to hold the mappings of omim:kegg ids
self.kegg_disease_hash = {} # to hold the mappings of kegg:omim ids
return
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
def __init__(self, graph_type, are_bnodes_skolemized,
tax_ids=None, gene_ids=None):
super().__init__(graph_type, are_bnodes_skolemized, 'ncbigene')
self.tax_ids = tax_ids
self.gene_ids = gene_ids
self.filter = 'taxids'
self.dataset = Dataset(
'ncbigene', 'National Center for Biotechnology Information',
'http://ncbi.nih.nlm.gov/gene', None,
'http://www.ncbi.nlm.nih.gov/About/disclaimer.html',
'https://creativecommons.org/publicdomain/mark/1.0/')
# Defaults
if self.tax_ids is None:
self.tax_ids = [9606, 10090, 7955]
logger.info("No taxa set. Defaulting to %s", str(tax_ids))
else:
logger.info("Filtering on the following taxa: %s", str(tax_ids))
self.gene_ids = []
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.gene_ids = config.get_config()['test_ids']['gene']
self.properties = Feature.properties
self.class_or_indiv = {}
return
def __init__(self,
graph_type,
are_bnodes_skolemized,
data_release_version=None):
super().__init__(
graph_type=graph_type,
are_bnodes_skolemized=are_bnodes_skolemized,
data_release_version=data_release_version,
name='omim',
ingest_title='Online Mendelian Inheritance in Man',
ingest_url='http://www.omim.org',
ingest_logo='source-omim.png',
# ingest_desc=None,
license_url=None,
data_rights='http://omim.org/help/agreement',
# file_handle=None
)
self.omim_ncbigene_idmap = {}
# check if config exists; if it doesn't, error out and let user know
if 'keys' not in config.get_config() and \
'omim' not in config.get_config()['keys']:
LOG.error("not configured with API key.")
if 'disease' in self.all_test_ids:
# local_id (numeric) portion of omim identifier
self.test_ids = [
x[5:] for x in self.all_test_ids['disease'] if x[:5] == 'OMIM:']
else:
LOG.warning("not configured with gene test ids.")
self.test_ids = []
self.disorder_regex = re.compile(r'(.*), (\d{6})\s*(?:\((\d+)\))?')
self.nogene_regex = re.compile(r'(.*)\s+\((\d+)\)')
def __init__(self, graph_type, are_bnodes_skolemized, tax_ids=None, gene_ids=None):
super().__init__(graph_type, are_bnodes_skolemized, 'ensembl')
self.tax_ids = tax_ids
self.gene_ids = gene_ids
self.dataset = Dataset(
'ensembl', 'ENSEMBL', 'http://uswest.ensembl.org', None)
# Defaults
if self.tax_ids is None:
self.tax_ids = [9606, 10090, 7955]
self.gene_ids = []
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.gene_ids = config.get_config()['test_ids']['gene']
self.properties = Feature.properties
logger.setLevel(logging.INFO)
return
def fetch(self, is_dl_forced=False):
'''connection details for DISCO'''
cxn = {}
cxn['host'] = 'nif-db.crbs.ucsd.edu'
cxn['database'] = 'disco_crawler'
cxn['port'] = '5432'
cxn['user'] = config.get_config()['user']['disco']
cxn['password'] = config.get_config()['keys'][cxn['user']]
self.dataset.setFileAccessUrl('jdbc:postgresql://' + cxn['host'] +
':' + cxn['port'] + '/' +
cxn['database'],
is_object_literal=True)
# process the tables
# self.fetch_from_pgdb(self.tables,cxn,100) #for testing
self.fetch_from_pgdb(self.tables, cxn)
self.get_files(is_dl_forced)
# FIXME: Everything needed for data provenance?
fstat = os.stat('/'.join((self.rawdir, 'dvp.pr_nlx_157874_1')))
filedate = datetime.utcfromtimestamp(
fstat[ST_CTIME]).strftime("%Y-%m-%d")
self.dataset.setVersion(filedate)
def __init__(self, graph_type, are_bnodes_skolemized, tax_ids=None):
super().__init__(graph_type, are_bnodes_skolemized, 'go')
# Defaults
self.tax_ids = tax_ids
if self.tax_ids is None:
self.tax_ids = [9606, 10090, 7955]
logger.info("No taxa set. Defaulting to %s", str(tax_ids))
else:
logger.info("Filtering on the following taxa: %s", str(tax_ids))
# update the dataset object with details about this resource
# NO LICENSE for this resource
self.dataset = Dataset(
'go', 'GeneOntology', 'http://www.geneontology.org', None,
"https://creativecommons.org/licenses/by/4.0/legalcode",
'http://geneontology.org/page/use-and-license')
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']
return
def __init__(self, graph_type, are_bnodes_skolemized):
super().__init__(graph_type, are_bnodes_skolemized, 'omim')
self.dataset = Dataset(
'omim', 'Online Mendelian Inheritance in Man',
'http://www.omim.org', None,
'http://omim.org/help/agreement')
self.omim_ncbigene_idmap = {}
# data-source specific warnings
# (will be removed when issues are cleared)
# check if config exists; if it doesn't, error out and let user know
if 'keys' not in config.get_config() and \
'omim' not in config.get_config()['keys']:
logger.error("not configured with API key.")
# check to see if there's any ids configured in the config;
# otherwise, warn
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.")
else:
# select ony those test ids that are omim's.
self.test_ids += \
[obj.replace('OMIM:', '')
for obj in config.get_config()['test_ids']['disease']
if re.match(r'OMIM:', obj)]
return
def __init__(self, graph_type, are_bnodes_skolemized, tax_ids=None):
super().__init__(graph_type, are_bnodes_skolemized, 'biogrid')
self.tax_ids = tax_ids
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
def __init__(self, tax_ids=None, gene_ids=None):
Source.__init__(self, 'ncbigene')
self.tax_ids = tax_ids
self.gene_ids = gene_ids
self.filter = 'taxids'
self.load_bindings()
self.dataset = Dataset('ncbigene', 'National Center for Biotechnology Information',
'http://ncbi.nih.nlm.gov/gene', None,
'http://www.ncbi.nlm.nih.gov/About/disclaimer.html',
'https://creativecommons.org/publicdomain/mark/1.0/')
# data-source specific warnings (will be removed when issues are cleared)
# Defaults
if self.tax_ids is None:
self.tax_ids = [9606, 10090, 7955]
logger.info("No taxa set. Defaulting to %s", str(tax_ids))
else:
logger.info("Filtering on the following taxa: %s", str(tax_ids))
self.gene_ids = []
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.gene_ids = config.get_config()['test_ids']['gene']
self.properties = Feature.properties
return
def __init__(self, graph_type, are_bnodes_skolemized, method, tax_ids=None):
super().__init__(graph_type, are_bnodes_skolemized, method)
self.tax_ids = tax_ids
self._map_orthology_code_to_RO = {
'orthologGroup': OrthologyAssoc.ortho_rel['orthologous'],
'paralogGroup': OrthologyAssoc.ortho_rel['paralogous']}
if 'test_ids' not in config.get_config() \
or 'protein' not in config.get_config()['test_ids']:
logger.warning("not configured with gene test ids.")
else:
self.test_ids = config.get_config()['test_ids']['protein']
return
def __init__(self, graph_type, are_bnodes_skolemized):
super().__init__(graph_type, are_bnodes_skolemized, 'orphanet')
self.dataset = Dataset(
'orphanet', 'Orphanet', 'http://www.orpha.net', None,
'http://creativecommons.org/licenses/by-nd/3.0/',
'http://omim.org/help/agreement')
# check to see if there's any ids configured in the config;
# otherwise, warn
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.")
return
def __init__(self, graph_type, are_bnodes_skolemized):
super().__init__(graph_type, are_bnodes_skolemized, 'orphanet')
self.dataset = Dataset(
'orphanet', 'Orphanet', 'http://www.orpha.net', None,
'http://creativecommons.org/licenses/by-nd/3.0/',
'http://omim.org/help/agreement')
# check to see if there's any ids configured in the config;
# otherwise, warn
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.")
return
def fetch(self, is_dl_forced=False):
'''create the connection details for DISCO'''
cxn = config.get_config()['dbauth']['disco']
cxn.update({
'host': 'nif-db.crbs.ucsd.edu',
'database': 'disco_crawler',
'port': 5432
})
self.dataset.setFileAccessUrl(''.join(
('jdbc:postgresql://', cxn['host'], ':', str(cxn['port']), '/',
cxn['database'])),
is_object_literal=True)
# process the tables
# self.fetch_from_pgdb(self.tables,cxn,100) #for testing
self.fetch_from_pgdb(self.tables, cxn)
self.get_files(is_dl_forced)
# FIXME: Everything needed for data provenance?
st = os.stat('/'.join((self.rawdir, 'dvp.pr_nlx_157874_1')))
filedate = datetime.utcfromtimestamp(st[ST_CTIME]).strftime("%Y-%m-%d")
self.dataset.setVersion(filedate)
return
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
def __init__(self):
Source.__init__(self, 'orphanet')
self.load_bindings()
self.dataset = Dataset(
'orphanet', 'Orphanet', 'http://www.orpha.net', None,
'http://creativecommons.org/licenses/by-nd/3.0/',
'http://omim.org/help/agreement')
# check to see if there's any ids configured in the config;
# otherwise, warn
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.")
return
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
def __init__(self, tax_ids=None, gene_ids=None):
Source.__init__(self, 'hgnc')
self.tax_ids = tax_ids
self.gene_ids = gene_ids
self.load_bindings()
self.dataset = Dataset('hgnc', 'HGNC', 'http://www.genenames.org', None)
self.gene_ids = []
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.gene_ids = config.get_config()['test_ids']['gene']
self.properties = Feature.properties
return
def __init__(self, graph_type, are_bnodes_skolemized):
super().__init__(graph_type, are_bnodes_skolemized, 'eom')
# 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
def __init__(self):
Source.__init__(self, 'gwascatalog')
self.load_bindings()
self.dataset = Dataset(
'gwascatalog', 'GWAS Catalog', 'http://www.ebi.ac.uk/gwas/',
'The NHGRI-EBI Catalog of published genome-wide association studies',
'http://creativecommons.org/licenses/by/3.0/', None)
# 'http://www.ebi.ac.uk/gwas/docs/about' # TODO add this
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']
return
def __init__(self,
graph_type,
are_bnodes_skolemized,
method,
tax_ids=None):
super().__init__(graph_type, are_bnodes_skolemized, method)
self.tax_ids = tax_ids
self._map_orthology_code_to_RO = {
'orthologGroup': OrthologyAssoc.ortho_rel['orthologous'],
'paralogGroup': OrthologyAssoc.ortho_rel['paralogous']
}
if 'test_ids' not in config.get_config() \
or 'protein' not in config.get_config()['test_ids']:
logger.warning("not configured with gene test ids.")
else:
self.test_ids = config.get_config()['test_ids']['protein']
return
def __init__(self):
Source.__init__(self, 'kegg')
# update the dataset object with details about this resource
self.dataset = Dataset('kegg', 'KEGG', 'http://www.genome.jp/kegg/', None, None,
'http://www.kegg.jp/kegg/legal.html')
# source-specific warnings. will be cleared when resolved.
# check to see if there's any ids configured in the config; otherwise, warn
if 'test_ids' not in config.get_config() or 'disease' not in config.get_config()['test_ids']:
logger.warn("not configured with disease test ids.")
else:
self.test_ids['disease'] += config.get_config()['test_ids']['disease']
self.label_hash = {}
self.omim_disease_hash = {} # to hold the mappings of omim:kegg ids
self.kegg_disease_hash = {} # to hold the mappings of kegg:omim ids
return
def __init__(self):
Source.__init__(self, "orphanet")
self.load_bindings()
self.dataset = Dataset(
"orphanet",
"Orphanet",
"http://www.orpha.net",
None,
"http://creativecommons.org/licenses/by-nd/3.0/",
"http://omim.org/help/agreement",
)
# check to see if there's any ids configured in the config; otherwise, warn
if "test_ids" not in config.get_config() or "disease" not in config.get_config()["test_ids"]:
logger.warn("not configured with disease test ids.")
return
def __init__(self, graph_type, are_bnodes_skolemized, tax_ids=None):
super().__init__(graph_type, are_bnodes_skolemized, 'panther')
self.tax_ids = tax_ids
self.dataset = Dataset(
'panther', 'Protein ANalysis THrough Evolutionary Relationships',
'http://pantherdb.org/', None,
'http://www.pantherdb.org/terms/disclaimer.jsp')
# # Defaults
# if self.tax_ids is None:
# self.tax_ids = [9606, 10090, 7955]
if 'test_ids' not in config.get_config() \
or 'protein' not in config.get_config()['test_ids']:
logger.warning("not configured with gene test ids.")
else:
self.test_ids = config.get_config()['test_ids']['protein']
return
def __init__(self, graph_type, are_bnodes_skolemized,
tax_ids=None, gene_ids=None):
super().__init__(graph_type, are_bnodes_skolemized, 'hgnc')
self.tax_ids = tax_ids
self.gene_ids = gene_ids
self.dataset = Dataset(
'hgnc', 'HGNC', 'http://www.genenames.org', None)
self.gene_ids = []
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.gene_ids = config.get_config()['test_ids']['gene']
self.properties = Feature.properties
return
def __init__(self, graph_type, are_bnodes_skolemized):
super().__init__(graph_type, are_bnodes_skolemized, 'decipher')
self.dataset = Dataset(
'decipher', 'Development Disorder Genotype – Phenotype Database',
'https://decipher.sanger.ac.uk/', None,
'https://decipher.sanger.ac.uk/legal')
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']
self.g = self.graph
self.geno = Genotype(self.g)
self.model = Model(self.g)
return
def __init__(self, graph_type, are_bnodes_skolemized):
super().__init__(graph_type, are_bnodes_skolemized, 'coriell')
self.dataset = Dataset('coriell', 'Coriell', 'http://ccr.coriell.org/',
None)
# data-source specific warnings
# (will be removed when issues are cleared)
logger.warning('We assume that if a species is not provided, '
'that it is a Human-derived cell line')
logger.warning('We map all omim ids as a disease/phenotype entity, '
'but should be fixed in the future') # TODO
# 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
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
def __init__(self, graph_type, are_bnodes_skolemized):
super().__init__(
graph_type,
are_bnodes_skolemized,
'orphanet',
ingest_title='Orphanet',
ingest_url='http://www.orpha.net',
license_url='http://creativecommons.org/licenses/by-nd/3.0/',
data_rights='http://omim.org/help/agreement'
# file_handle=None
)
# check to see if there's any ids configured in the config;
# otherwise, warn
# TODO remove
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.")
return
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
def __init__(self, graph_type, are_bnodes_skolemized):
super().__init__(
graph_type,
are_bnodes_skolemized,
'eom',
ingest_title='Elements of Morphology',
ingest_url='http://elementsofmorphology.nih.gov',
data_rights='http://www.genome.gov/copyright.cfm',
license_url='https://creativecommons.org/publicdomain/mark/1.0/'
# file_handle=None
)
# 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
def __init__(self, tax_ids=None):
super().__init__('panther')
self.tax_ids = tax_ids
self.load_bindings()
self.dataset = Dataset('panther', 'Protein ANalysis THrough Evolutionary Relationships',
'http://pantherdb.org/', None,
'http://www.pantherdb.org/terms/disclaimer.jsp')
# # Defaults
# if self.tax_ids is None:
# self.tax_ids = [9606, 10090, 7955]
if 'test_ids' not in config.get_config() or 'protein' not in config.get_config()['test_ids']:
logger.warn("not configured with gene test ids.")
else:
self.test_ids = config.get_config()['test_ids']['protein']
# data-source specific warnings (will be removed when issues are cleared)
return
def __init__(self, graph_type, are_bnodes_skolemized,
tax_ids=None, gene_ids=None):
super().__init__(graph_type, are_bnodes_skolemized, 'clinvar')
self.tax_ids = tax_ids
self.gene_ids = gene_ids
self.filter = 'taxids'
self.dataset = Dataset(
'ClinVar', 'National Center for Biotechnology Information',
'http://www.ncbi.nlm.nih.gov/clinvar/', None,
'http://www.ncbi.nlm.nih.gov/About/disclaimer.html',
'https://creativecommons.org/publicdomain/mark/1.0/')
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.gene_ids = 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.")
else:
self.disease_ids = config.get_config()['test_ids']['disease']
self.properties = Feature.properties
return
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
def __init__(self, graph_type, are_bnodes_skolemized):
super().__init__(graph_type,
are_bnodes_skolemized,
'ctd',
ingest_title='Comparative Toxicogenomics Database',
ingest_url='http://ctdbase.org',
license_url='http://ctdbase.org/about/legal.jsp'
# data_rights=None,
# file_handle=None
)
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.geno = Genotype(self.graph)
self.pathway = Pathway(self.graph)
return
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
def __init__(self,
graph_type,
are_bnodes_skolemized,
tax_ids=None,
gene_ids=None):
super().__init__(graph_type, are_bnodes_skolemized, 'clinvar')
self.tax_ids = tax_ids
self.gene_ids = gene_ids
self.filter = 'taxids'
self.dataset = Dataset(
'ClinVar', 'National Center for Biotechnology Information',
'http://www.ncbi.nlm.nih.gov/clinvar/', None,
'http://www.ncbi.nlm.nih.gov/About/disclaimer.html',
'https://creativecommons.org/publicdomain/mark/1.0/')
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.gene_ids = 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.")
else:
self.disease_ids = config.get_config()['test_ids']['disease']
self.properties = Feature.properties
return
def __init__(self, graph_type, are_bnodes_skolemized):
super().__init__(graph_type, are_bnodes_skolemized, 'kegg')
# update the dataset object with details about this resource
self.dataset = Dataset('kegg', 'KEGG', 'http://www.genome.jp/kegg/',
None, None,
'http://www.kegg.jp/kegg/legal.html')
# check to see if there are any ids configured in the config;
# otherwise, warn
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.")
else:
self.test_ids['disease'] += \
config.get_config()['test_ids']['disease']
self.label_hash = {}
self.omim_disease_hash = {} # to hold the mappings of omim:kegg ids
self.kegg_disease_hash = {} # to hold the mappings of kegg:omim ids
return
def __init__(self):
Source.__init__(self, 'decipher')
self.load_bindings()
self.dataset = Dataset(
'decipher', 'Development Disorder Genotype – Phenotype Database',
'https://decipher.sanger.ac.uk/', None,
'https://decipher.sanger.ac.uk/legal')
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']
self.gu = GraphUtils(curie_map.get())
self.g = self.graph
self.geno = Genotype(self.g)
return
def __init__(self,
graph_type,
are_bnodes_skolemized,
tax_ids=None,
gene_ids=None):
super().__init__(
graph_type,
are_bnodes_skolemized,
'ncbigene',
ingest_title='National Center for Biotechnology Information',
ingest_url='http://ncbi.nih.nlm.gov/gene',
# ingest_desc=None,
license_url='https://creativecommons.org/publicdomain/mark/1.0/',
data_rights='http://www.ncbi.nlm.nih.gov/About/disclaimer.html'
# file_handle=None
)
self.tax_ids = tax_ids
self.gene_ids = gene_ids
self.id_filter = 'taxids' # 'geneids
# Defaults
if self.tax_ids is None:
self.tax_ids = [9606, 10090, 7955]
logger.info("No taxa set. Defaulting to %s", str(tax_ids))
else:
logger.info("Filtering on the following taxa: %s", str(tax_ids))
self.gene_ids = []
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.gene_ids = config.get_config()['test_ids']['gene']
self.class_or_indiv = {}
return
def __init__(self):
Source.__init__(self, 'omim')
self.load_bindings()
self.dataset = Dataset('omim', 'Online Mendelian Inheritance in Man', 'http://www.omim.org',
None, 'http://omim.org/help/agreement')
# data-source specific warnings (will be removed when issues are cleared)
# check if config exists; if it doesn't, error out and let user know
if 'keys' not in config.get_config() and 'omim' not in config.get_config()['keys']:
logger.error("not configured with API key.")
# check to see if there's any ids configured in the config; otherwise, warn
if 'test_ids' not in config.get_config() or 'disease' not in config.get_config()['test_ids']:
logger.warn("not configured with disease test ids.")
else:
# select ony those test ids that are omim's.
self.test_ids += [obj.replace('OMIM:', '') for obj in config.get_config()['test_ids']['disease']
if re.match('OMIM:', obj)]
return
def __init__(self, graph_type, are_bnodes_skolemized):
super().__init__(graph_type, are_bnodes_skolemized, 'gwascatalog')
if graph_type != 'rdf_graph':
raise ValueError("UDP requires a rdf_graph")
self.dataset = Dataset(
'gwascatalog', 'GWAS Catalog', 'http://www.ebi.ac.uk/gwas/',
'The NHGRI-EBI Catalog of published genome-wide association studies',
'http://creativecommons.org/licenses/by/3.0/', None)
# 'http://www.ebi.ac.uk/gwas/docs/about' # TODO add this
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']
# build a dictionary of genomic location to identifiers,
# to try to get the equivalences
self.id_location_map = dict()
return
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