Using datasource: dbi:Pg:dbname=fb_2020_02_05;host=deneb.pdn.cam.ac.uk;port=5432
./get_vfb_exp_list.pl started at: Mon Feb 24 12:41:53 2020
The following papers require vfb expression curation. They have already been thin curated.
Prefix(:=<http://www.semanticweb.org/davidos/ontologies/2020/9/untitled-ontology-21#>) | |
Prefix(owl:=<http://www.w3.org/2002/07/owl#>) | |
Prefix(rdf:=<http://www.w3.org/1999/02/22-rdf-syntax-ns#>) | |
Prefix(xml:=<http://www.w3.org/XML/1998/namespace>) | |
Prefix(xsd:=<http://www.w3.org/2001/XMLSchema#>) | |
Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>) | |
Ontology(<http://www.semanticweb.org/davidos/ontologies/2020/9/untitled-ontology-21> |
Prefix(:=<http://www.semanticweb.org/davidos/ontologies/2020/9/untitled-ontology-21#>) | |
Prefix(owl:=<http://www.w3.org/2002/07/owl#>) | |
Prefix(rdf:=<http://www.w3.org/1999/02/22-rdf-syntax-ns#>) | |
Prefix(xml:=<http://www.w3.org/XML/1998/namespace>) | |
Prefix(xsd:=<http://www.w3.org/2001/XMLSchema#>) | |
Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>) | |
Ontology(<http://www.semanticweb.org/davidos/ontologies/2020/9/untitled-ontology-21> |
Prefix(:=<http://purl.org/phenoscape/demo/presence_absence.owl#>) | |
Prefix(owl:=<http://www.w3.org/2002/07/owl#>) | |
Prefix(rdf:=<http://www.w3.org/1999/02/22-rdf-syntax-ns#>) | |
Prefix(xml:=<http://www.w3.org/XML/1998/namespace>) | |
Prefix(xsd:=<http://www.w3.org/2001/XMLSchema#>) | |
Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>) | |
Ontology(<http://purl.org/phenoscape/demo/presence_absence.owl> | |
Annotation(<http://purl.org/dc/terms/creator> <http://orcid.org/0000-0001-7972-3866>) |
from vfb_connect.cross_server_tools import VfbConnect | |
vc = VfbConnect() | |
out = set() | |
for x in vc.oc.lookup.keys(): | |
m = re.findall('[^A-Za-z0-9 ]', x) | |
if m: | |
out.update(m) | |
import rdflib | |
from SPARQLWrapper import SPARQLWrapper, JSON | |
import time | |
g = rdflib.Graph() | |
g.parse('http://purl.org/ccf/latest/ccf.owl') | |
ccf_po_query = """ | |
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> | |
PREFIX ccf: <https://purl.org/ccf/latest/ccf.owl#> |
Using datasource: dbi:Pg:dbname=fb_2020_02_05;host=deneb.pdn.cam.ac.uk;port=5432
./get_vfb_exp_list.pl started at: Mon Feb 24 12:41:53 2020
The following papers require vfb expression curation. They have already been thin curated.
from vfb_connect.neo.neo4j_tools import Neo4jConnect, dict_cursor | |
nc = Neo4jConnect('http://kb.virtualflybrain.org', 'neo4j', 'neo4j') | |
query = """MATCH (f:Feature)<-[]-(ep:Class)-[dbx:hasDbXref]->(s:Site) | |
WHERE (s.short_form = 'FlyLight') OR (s.short_form = 'FlyLightSplit') | |
WITH f, ep MATCH (ep)<-[:INSTANCEOF]-(i:Individual) | |
<-[]-(channel:Individual)-[irw:in_register_with]->(t:Individual) | |
WITH distinct f.short_form AS `#FlyBase ID`, | |
collect(i.short_form)[0] AS DBURL, ep.label AS epl, t.label as template |
'abnormal Harderian gland pigmentation' | |
'abnormal agouti pigmentation' | |
'abnormal choroid melanin granule morphology' | |
'abnormal choroid melanocyte morphology' | |
'abnormal choroid pigmentation' | |
'abnormal ciliary body pigmentation' | |
'abnormal coat/hair pigmentation' | |
'abnormal dermal melanocyte morphology' | |
'abnormal dermal pigmentation' | |
'abnormal digit pigmentation' |
{ | |
"cells": [ | |
{ | |
"cell_type": "code", | |
"execution_count": 17, | |
"metadata": {}, | |
"outputs": [ | |
{ | |
"name": "stdout", | |
"output_type": "stream", |
from jsonpath_rw import parse | |
import json | |
vfbsf = open("./json_schema/vfb_termInfo.json", "r") | |
vfbs = json.loads(vfbsf.read()) | |
R = parse('*..required') | |
P = parse('*..properties') | |
Rs = [match for match in R.find(vfbs)] | |
Ps = [match for match in P.find(vfbs)] |