from pathlib import Path
import rdflib
from pyontutils.core import Ont, OntGraph
from pyontutils.config import auth
from pyontutils.sheets import Sheet
from pyontutils.namespaces import owl, rdf, rdfs, ilxtr, NIFRID, OntCuries, skos, makeNamespaces
from neurondm import OntTerm, OntId
from neurondm.models.allen_cell_types import AllenCellTypes
from neurondm.core import log
log = log.getChild('indicators')
OntCuries(AllenCellTypes.prefixes) # FIXME BAD
OntCuries({'TEMPIND': 'http://uri.interlex.org/temp/uris/phenotype-indicators/'})
NIFRAW, NIFTTL = makeNamespaces('NIFRAW', 'NIFTTL')
a = rdf.type
# TODO the proper way to do this in the future will be to write a populateIndicators
# for Neuron and Phenotype
class PhenotypeIndicators(Sheet):
name = 'phenotype-indicators'
sheet_name = 'indicators'
@property
def things(self):
def process(k, v):
if ',' in v:
#!/usr/bin/env python3
import rdflib
import ontquery
from neurondm.lang import *
from neurondm import *
from pyontutils.core import OntId, OntTerm
from pyontutils.utils import relative_path
from pyontutils.namespaces import makePrefixes, makeNamespaces, OntCuries
from pyontutils.namespaces import interlex_namespace, PREFIXES
from pyontutils.namespaces import NIFRID, ilxtr, hasRole, definition
from pyontutils.namespaces import rdf, rdfs, owl
from pyontutils.combinators import restriction
swanr = rdflib.Namespace(interlex_namespace('swanson/uris/readable/'))
NIFRAW, = makeNamespaces('NIFRAW')
config = Config(
'basic-neurons',
prefixes={
'swanr':
swanr,
'SWAN':
interlex_namespace('swanson/uris/neuroanatomical-terminology/terms/'),
'SWAA':
interlex_namespace(
'swanson/uris/neuroanatomical-terminology/appendix/'),
},
source_file=relative_path(__file__))
class NeuronSWAN(NeuronEBM):
owlClass = ilxtr.NeuronSWAN
if def_:
yield from olit(subject, definition, def_)
if synonyms:
if not isinstance(synonyms, tuple):
# this is why python sucks and racket is awesome if this was racket
# the error would show up on the line where the problem was :/
raise TypeError(
f'Type of {synonyms!r} should not be {type(synonyms)}!')
yield from olit(subject, NIFRID.synonym, *synonyms)
if comment:
yield from olit(subject, rdfs.comment, comment)
obo, RO, prov, *_ = makeNamespaces('obo', 'RO', 'prov')
filename = 'methods-core'
prefixes = None
OntCuries['HBP_MEM'] = 'http://www.hbp.FIXME.org/hbp_measurement_methods/'
imports = NIFTTL['nif_backend.ttl'],
#imports = obo['bfo.owl'], obo['ro.owl']
#imports = tuple()
comment = 'The core components for modelling techniques and methods.'
branch = 'methods'
_repo = True
debug = True
triples = (
# data properties
odp(ilxtr.hasAspectValue),
odp(ilxtr.hasConstrainingAspect_value,
from datetime import datetime
from getpass import getuser
from collections import OrderedDict
import rdflib
from docopt import docopt
from pyontutils.core import OntId
from pyontutils.utils import makeSimpleLogger
from pyontutils.qnamefix import cull_prefixes
from pyontutils.namespaces import makeNamespaces, NIFRID, definition
from pyontutils.namespaces import TEMP, PREFIXES as uPREFIXES
from pyontutils.closed_namespaces import rdf, rdfs, owl, oboInOwl
from IPython import embed
log = makeSimpleLogger('obo-io')
fobo, obo, NIFSTD, NOPE = makeNamespaces('fobo', 'obo', 'NIFSTD', '')
N = -1 # use to define 'many ' for tag counts
TW = 4 # tab width
class od(OrderedDict):
pass
od.__repr__ = dict.__repr__
# this is our current (horrible) conversion from obo to ttl
obo_tag_to_ttl = {
#'id': (lambda s, p: rdflib.URIRef(s), rdf.type, owl.Class), '%s rdf:type owl:Class ;\n',
'name': rdfs.label,