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.
David Osumi-Sutherland dosumis
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| 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> |
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| 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> |
dosumis
/ presence_absence_morphology.owl
Created
August 28, 2020 08:38
Extension of presence_absence.owl from http://purl.org/phenoscape/demo/presence_absence.owl to include grouping and morphology phenotypes
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| 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>) |
dosumis
/ special_char_in_VFB_labels.py
Created
July 14, 2020 12:37
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| 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) | |
dosumis
/ uber_check.py
Created
June 2, 2020 08:45
Validate ccf.owl partonomy against Uberon using renci uberongraph endpoint. (secondary checks for overlaps and subClassOf)
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| 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#> |
dosumis
/ FlyBase_linkout_gen.py
Created
March 25, 2020 17:58
Scripts for generating FB->VFB linkouts
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| 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 |
dosumis
/ MEl_phenotype_x_pigmentation_proc
Last active
March 10, 2020 12:54
MP_proc_x_ME_phenotype_breakdown
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| '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' |
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| { | |
| "cells": [ | |
| { | |
| "cell_type": "code", | |
| "execution_count": 17, | |
| "metadata": {}, | |
| "outputs": [ | |
| { | |
| "name": "stdout", | |
| "output_type": "stream", |
dosumis
/ JSON_schema_test_required.py
Last active
December 17, 2018 16:09
A quick demo of how to use JPATH to test whether JSON schema required fields are all valid property keys
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| 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)] |
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