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first attempt at creating the ontology file
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Marie-Angélique Laporte
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48119
documentation.html
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48119
documentation.html
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233
idss application profile.ipynb
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233
idss application profile.ipynb
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{
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"cells": [
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{
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"cell_type": "code",
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"execution_count": 118,
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"id": "solid-grove",
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"metadata": {},
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"outputs": [],
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"source": [
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"from rdflib import Graph\n",
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"from rdflib.namespace import OWL, DC, DCTERMS, RDF, RDFS, SKOS, XSD\n",
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"from rdflib import URIRef, BNode, Literal\n",
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"import json\n",
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"import os\n",
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"import pandas as pd\n",
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"import pylode"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 134,
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"id": "spiritual-geography",
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"metadata": {},
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"outputs": [],
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"source": [
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"g = Graph()\n",
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"\n",
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"##namespace\n",
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"NS = \"http://idss.org/terms/\"\n",
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"## create ontology\n",
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"iseal = URIRef(NS)\n",
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"g.add((iseal, RDF.type, OWL.Ontology)) "
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]
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},
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{
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"cell_type": "code",
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"execution_count": 135,
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"id": "competitive-turkish",
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"metadata": {},
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"outputs": [],
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"source": [
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"df = pd.read_excel('./idss_schema_fields.xlsx')\n",
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"df.dropna(how='all', axis=1)\n",
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"df.fillna('', inplace=True)\n",
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"\n",
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"\n",
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"for index, row in df.iterrows() :\n",
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" element_name = row['element name']\n",
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" element_description = row['element description']\n",
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" comment = row['element guidance']\n",
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" example = row['element link for more information']\n",
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" cardinality = row['element options']\n",
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" prop_type = row['element type']\n",
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" controlled_vocab = row['element controlled values or terms']\n",
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" module = row['idss module']\n",
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" module_cat = row['idss module category']\n",
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" \n",
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" ##module\n",
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" moduleUri = URIRef(NS+module)\n",
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" if not (None, SKOS.prefLabel, Literal(module)) in g:\n",
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" ##create module as skos concept\n",
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" g.add((moduleUri, RDF.type, OWL.Class)) ## SKOS.Concept\n",
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" g.add((moduleUri, SKOS.prefLabel, Literal(module)))\n",
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" ##element\n",
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" if '-' in element_name:\n",
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" concept = element_name.split(' - ')[0]\n",
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" element = element_name.split(' - ')[1]\n",
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" \n",
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" conceptUri = URIRef(NS+concept.replace(\" \", \"_\"))\n",
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" if not (None, SKOS.prefLabel, Literal(concept)) in g:\n",
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" ##create concept as skos concept\n",
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" g.add((conceptUri, RDF.type, OWL.Class)) ## SKOS.Concept\n",
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" g.add((conceptUri, SKOS.prefLabel, Literal(concept)))\n",
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" g.add((conceptUri, RDFS.subClassOf, moduleUri))\n",
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" \n",
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" ## create properties\n",
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" elementURI = URIRef(NS+element.replace(\" \", \"_\"))\n",
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" if prop_type == 'CONTROLLED VALUE': ## object property\n",
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" g.add((elementURI, SKOS.prefLabel, Literal(element)))\n",
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" g.add((elementURI, RDF.type, OWL.ObjectProperty))\n",
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" g.add((elementURI, OWL.domain, conceptUri))\n",
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" \n",
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" ## create controlled vocab\n",
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" cvURI = URIRef(NS+\"VOCAB_\"+element.replace(\" \", \"_\"))\n",
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" g.add((cvURI, RDF.type, OWL.Class)) ## SKOS.Concept ## SKOS.Collection??\n",
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" g.add((cvURI, SKOS.prefLabel, Literal(\"VOCAB \"+element)))\n",
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" for term in controlled_vocab.split(\"||\"):\n",
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" termURI = URIRef(NS+term.replace(\" \", \"_\").replace(\"|\", \"\"))\n",
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" g.add((termURI, RDF.type, OWL.Class)) ## SKOS.Concept\n",
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" g.add((termURI, SKOS.prefLabel, Literal(term)))\n",
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" g.add((termURI, RDFS.subClassOf, cvURI)) ## SKOS.member???\n",
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" g.add((elementURI, OWL.range, cvURI))\n",
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" \n",
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" ## cardinality\n",
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" if cardinality == 'MULTI SELECT FROM CONTROL LIST':\n",
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" br = BNode()\n",
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" g.add((br, RDF.type, OWL.Restriction))\n",
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" g.add((br, OWL.onProperty, elementURI))\n",
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" g.add((br, OWL.someValuesFrom, cvURI))\n",
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" g.add((conceptUri, RDFS.subClassOf, br))\n",
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" else:\n",
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" br = BNode()\n",
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" g.add((br, RDF.type, OWL.Restriction))\n",
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" g.add((br, OWL.onProperty, elementURI))\n",
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" g.add((br, OWL.maxQualifiedCardinality, Literal(1)))\n",
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" g.add((br, OWL.onClass, cvURI))\n",
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" g.add((conceptUri, RDFS.subClassOf, br))\n",
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" \n",
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" #elif prop_type == 'URL': ## object property\n",
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" # g.add((elementURI, RDF.type, OWL.ObjectProperty))\n",
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" # g.add((elementURI, OWL.domain, conceptUri))\n",
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" # g.add((elementURI, OWL.range, URIRef(\"\") ))\n",
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" # g.add((elementURI, SKOS.prefLabel, Literal(element)))\n",
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" else: ## datatype properties\n",
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" g.add((elementURI, SKOS.prefLabel, Literal(element)))\n",
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" g.add((elementURI, RDF.type, OWL.DatatypeProperty))\n",
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" g.add((elementURI, OWL.domain, conceptUri))\n",
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" range = None\n",
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" if prop_type == 'DATE':\n",
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" g.add((elementURI, OWL.range, XSD.date ))\n",
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" range = XSD.date\n",
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" elif prop_type == 'NUMERIC VALUE':\n",
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" g.add((elementURI, OWL.range, XSD.float))\n",
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" range = XSD.float\n",
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" else:\n",
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" g.add((elementURI, OWL.range, XSD.string))\n",
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" range = XSD.string\n",
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" ##cardinality\n",
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" if cardinality == 'REPEAT VALUES':\n",
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" br = BNode()\n",
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" g.add((br, RDF.type, OWL.Restriction))\n",
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" g.add((br, OWL.onProperty, elementURI))\n",
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" g.add((br, OWL.someValuesFrom, range))\n",
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" g.add((conceptUri, RDFS.subClassOf, br))\n",
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" else:\n",
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" br = BNode()\n",
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" g.add((br, RDF.type, OWL.Restriction))\n",
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" g.add((br, OWL.onProperty, elementURI))\n",
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" g.add((br, OWL.maxQualifiedCardinality, Literal(1)))\n",
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" g.add((br, OWL.onDataRange, range))\n",
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" g.add((conceptUri, RDFS.subClassOf, br))\n",
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" \n",
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" \n",
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" if comment:\n",
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" g.add((elementURI, SKOS.scopeNote, Literal(comment)))\n",
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" if example:\n",
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" g.add((elementURI, RDFS.comment, Literal(example)))\n",
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" if element_description:\n",
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" g.add((elementURI, SKOS.definition, Literal(element_description)))\n",
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" else:\n",
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" print(element_name)\n",
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" \n",
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" \n",
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" \n",
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" "
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "subject-asian",
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"metadata": {},
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"outputs": [],
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"source": []
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},
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{
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"cell_type": "code",
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"execution_count": 136,
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"id": "sudden-elite",
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"metadata": {},
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"outputs": [],
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"source": [
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"## save graph\n",
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"g.serialize(destination='idds.ttl', format='turtle')"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 137,
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"id": "subsequent-zealand",
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"metadata": {},
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"outputs": [],
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"source": [
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"html = pylode.MakeDocco(\n",
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" input_data_file=\"idds.ttl\",\n",
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" outputformat=\"html\",\n",
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" profile=\"ontdoc\"\n",
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").document()"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 138,
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"id": "occupied-caribbean",
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"metadata": {},
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"outputs": [],
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"source": [
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"f = open('documentation.html', 'w' )\n",
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"f.write( html )\n",
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"f.close()"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "abstract-consortium",
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"metadata": {},
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"outputs": [],
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"source": []
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}
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],
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"metadata": {
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"kernelspec": {
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"display_name": "Python 3",
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"language": "python",
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"name": "python3"
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},
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"language_info": {
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"codemirror_mode": {
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"name": "ipython",
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"version": 3
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},
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"file_extension": ".py",
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"mimetype": "text/x-python",
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.9.2"
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}
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},
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"nbformat": 4,
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"nbformat_minor": 5
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}
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