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{
"cells": [
{
"cell_type": "markdown",
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"id": "mechanical-johns",
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"metadata": {},
"source": [
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"## Mapping *Multilingual Data Stewardship terminology* and *SSHOC Multilingual Metadata* to SKOS resources\n",
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"\n",
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"This Notebook implements a simple parser used to transform the SSHOC Multilingual Data Stewardship Terminology and the SSHOC Multilingual Metadata, created in the Task 3.1 of the SSHOC project and published as spreadsheets, into SKOS resources. The parser reads the spreadsheets and transforms the content in SKOS data following a set of mapping rules, the result is stored in two Turtle files.\n",
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"\n"
]
},
{
"cell_type": "code",
"execution_count": 1,
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"id": "aware-comparison",
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"metadata": {},
"outputs": [],
"source": [
"import pandas as pd\n",
"import rdflib\n",
"import itertools\n",
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"import yaml\n",
"import datetime"
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]
},
{
"cell_type": "markdown",
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"id": "failing-shift",
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"metadata": {},
"source": [
"The file *config.yaml* contains the external information used in the parsing, including the position of the spreadsheets. Set the correct values before running the Notebook."
]
},
{
"cell_type": "code",
"execution_count": 2,
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"id": "cutting-triangle",
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"metadata": {},
"outputs": [],
"source": [
"try:\n",
" with open(\"config.yaml\", 'r') as stream:\n",
" try:\n",
" conf=yaml.safe_load(stream)\n",
" except yaml.YAMLError as exc:\n",
" print(exc)\n",
"except FileNotFoundError:\n",
" print('Warning config.yaml file not present! Please store it in the same directory as the notebook')\n",
"#print (conf)"
]
},
{
"cell_type": "markdown",
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"id": "cardiac-angel",
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"metadata": {},
"source": [
"The following cells defines the *Namespaces* used in the parsing"
]
},
{
"cell_type": "code",
"execution_count": 3,
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"id": "neural-career",
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"metadata": {},
"outputs": [],
"source": [
"from rdflib.namespace import DC, DCAT, DCTERMS, OWL, \\\n",
" RDF, RDFS, SKOS, \\\n",
" XMLNS, XSD, XMLNS\n",
"from rdflib import Namespace\n",
"from rdflib import URIRef, BNode, Literal\n",
"\n",
"sshocterm = Namespace(conf['Namespaces']['SSHOCTERM'])\n",
"sshoccmd= Namespace(conf['Namespaces']['SSHOCCMD'])\n",
"dc11=Namespace(\"http://purl.org/dc/elements/1.1/\");\n",
"dct = Namespace(\"http://purl.org/dc/terms/\")\n",
"iso369=Namespace(\"http://id.loc.gov/vocabulary/iso639-3\");"
]
},
{
"cell_type": "markdown",
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"id": "virtual-conducting",
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"metadata": {},
"source": [
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"Download **Data Stewardship terminology** spreadsheet"
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]
},
{
"cell_type": "code",
"execution_count": 4,
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"id": "systematic-bachelor",
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"metadata": {},
"outputs": [],
"source": [
"url=conf['Source']['VOCABULARYSOURCE']\n",
"df_data=pd.read_csv(url)"
]
},
{
"cell_type": "code",
"execution_count": 5,
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"id": "sealed-complexity",
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"metadata": {},
"outputs": [],
"source": [
"df_data.rename(columns = {'Unnamed: 0': 'Concept ID', 'Unnamed: 1':'Subject', 'Unnamed: 2':'Term',\n",
" 'Unnamed: 3':'Source of definition', 'Translations':'Dutch', 'Unnamed: 5':'French', \n",
" 'Unnamed: 6':'German', 'Unnamed: 7':'Greek',\n",
" 'Unnamed: 8':'Italian', 'Unnamed: 9':'Slovenian',\n",
" 'Linking':'Loterre Open Science Thesaurus', 'Unnamed: 11':'Terms4FAIRSkills',\n",
" 'Unnamed: 12':'CCR metadata', 'Unnamed: 13':'Linked Open Vocabularies',\n",
" 'Unnamed: 14':'LOV 2', 'Unnamed: 15':'ISO',\n",
" 'Unnamed: 16':'Broader Concept'}, inplace = True)\n",
"df_data=df_data.drop(0)"
]
},
{
"cell_type": "markdown",
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"id": "impossible-romantic",
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"metadata": {},
"source": [
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"Create a graph for the SKOS data and bind the namespaces to it"
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]
},
{
"cell_type": "code",
"execution_count": 6,
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"id": "southeast-cholesterol",
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"metadata": {},
"outputs": [],
"source": [
"c1rdf = rdflib.Graph()\n",
"c1rdf.bind(\"sshocterm\", sshocterm)\n",
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"c1rdf.bind(\"sshoccmd\", sshoccmd)\n",
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"c1rdf.bind(\"dc11\", dc11)\n",
"c1rdf.bind(\"dct\", dct)\n",
"c1rdf.bind(\"iso369-3\", iso369)\n",
"c1rdf.bind(\"skos\", SKOS)\n",
"c1rdf.bind(\"dc\", DC)\n",
"c1rdf.bind(\"rdf\", RDF)\n",
"c1rdf.bind(\"owl\", OWL)\n",
"c1rdf.bind(\"xsd\", XSD)\n"
]
},
{
"cell_type": "markdown",
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"id": "duplicate-oregon",
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"metadata": {},
"source": [
"Insert in the graph the *SKOS.ConceptScheme*"
]
},
{
"cell_type": "code",
"execution_count": 7,
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"id": "hydraulic-raising",
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"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
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"<Graph identifier=Nfbc9b96ef4c047d9a72e68d22f8fc441 (<class 'rdflib.graph.Graph'>)>"
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]
},
"execution_count": 7,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
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"now = datetime.datetime.today()\n",
"today_date=now.date()\n",
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"title=Literal(conf['Texts']['VOCABULARYTITLE'], lang=conf['Texts']['LANG'])\n",
"description=Literal(conf['Texts']['VOCABULARYDESCRIPTION'], lang=conf['Texts']['LANG'])\n",
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"identifier=Literal(conf['Texts']['VOCABULARYID'], lang=conf['Texts']['LANG'])\n",
"#identifier=URIRef(conf['Texts']['VOCABULARYID'])\n",
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"createddate= Literal(conf['Texts']['VOCABULARYCREATEDATE'],datatype=XSD.date)\n",
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"moddate= Literal(today_date,datatype=XSD.date)\n",
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"version= Literal(conf['Texts']['VOCABULARYVERSION'],datatype=XSD.string)\n",
"\n",
"c1rdf.add((sshocterm[''], RDF.type, SKOS.ConceptScheme))\n",
"c1rdf.add((sshocterm[''], DC.title, title))\n",
"c1rdf.add((sshocterm[''], DC.identifier, identifier))\n",
"c1rdf.add((sshocterm[''], DC.description, description))\n",
"c1rdf.add((sshocterm[''], dct.created, createddate))\n",
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"c1rdf.add((sshocterm[''], dct.modified, moddate))\n",
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"c1rdf.add((sshocterm[''], OWL.versionInfo, version))\n",
"c1rdf.add((sshocterm[''], dct.language, iso369.eng))\n",
"c1rdf.add((sshocterm[''], dct.language, iso369.ger))\n",
"c1rdf.add((sshocterm[''], dct.language, iso369.fra))\n",
"c1rdf.add((sshocterm[''], dct.language, iso369.ell))\n",
"c1rdf.add((sshocterm[''], dct.language, iso369.ita))\n",
"c1rdf.add((sshocterm[''], dct.language, iso369.dut))\n",
"c1rdf.add((sshocterm[''], dct.language, iso369.slv))"
]
},
{
"cell_type": "code",
"execution_count": 8,
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"id": "level-score",
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"metadata": {},
"outputs": [],
"source": [
"#c1rdf.serialize(destination='data/skostest.rdf', format=\"n3\");#format=\"pretty-xml\")\n",
"#comrdf.serialize(destination='data/parsed_rdf/prima_cantica_forme_com.rdf', format=\"n3\");"
]
},
{
"cell_type": "markdown",
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"id": "detailed-official",
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"metadata": {},
"source": [
"The following cell implements the mapping rules for creating SKOS resources."
]
},
{
"cell_type": "code",
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"execution_count": null,
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"id": "failing-relative",
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"metadata": {},
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"outputs": [],
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"source": [
"for index, row in df_data.iterrows():\n",
" \n",
" if row.Subject.lower()==\"preflabel\":\n",
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" label=URIRef(row[\"Concept ID\"].strip())\n",
" \n",
" \n",
" c1rdf.add((sshocterm[''], SKOS.hasTopConcept, sshocterm[label]))\n",
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" enlabel=Literal(row[\"Term\"].strip(), lang='en')\n",
" frlabel=Literal(row[\"French\"].strip(), lang='fr')\n",
" nllabel=Literal(row['Dutch'].strip(), lang='nl')\n",
" delabel=Literal(row['German'].strip(), lang='de')\n",
" itlabel=Literal(row['Italian'].strip(), lang='it')\n",
" sllabel=Literal(row['Slovenian'].strip(), lang='sl')\n",
" ellabel=Literal(row['Greek'].strip(), lang='el')\n",
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" c1rdf.add((sshocterm[label], RDF.type, SKOS.Concept))\n",
" c1rdf.add((sshocterm[label], SKOS.inScheme, sshocterm['']))\n",
" c1rdf.add((sshocterm[label], SKOS.topConceptOf, sshocterm['']))\n",
" c1rdf.add((sshocterm[label], SKOS.prefLabel, enlabel))\n",
" c1rdf.add((sshocterm[label], SKOS.prefLabel, frlabel))\n",
" c1rdf.add((sshocterm[label], SKOS.prefLabel, nllabel))\n",
" c1rdf.add((sshocterm[label], SKOS.prefLabel, delabel))\n",
" c1rdf.add((sshocterm[label], SKOS.prefLabel, itlabel))\n",
" c1rdf.add((sshocterm[label], SKOS.prefLabel, sllabel))\n",
" c1rdf.add((sshocterm[label], SKOS.prefLabel, ellabel))\n",
" if row.Subject.lower()==\"altlabel\":\n",
" if not pd.isna(row['Term']):\n",
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" c1rdf.add((sshocterm[label], SKOS.altLabel, Literal(row[\"Term\"].strip(), lang='en')))\n",
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" if not pd.isna(row['French']):\n",
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" c1rdf.add((sshocterm[label], SKOS.altLabel, Literal(row[\"French\"].strip(), lang='fr')))\n",
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" if not pd.isna(row['Dutch']):\n",
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" c1rdf.add((sshocterm[label], SKOS.altLabel, Literal(row[\"Dutch\"].strip(), lang='nl')))\n",
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" if not pd.isna(row['German']):\n",
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" c1rdf.add((sshocterm[label], SKOS.altLabel, Literal(row[\"German\"].strip(), lang='de')))\n",
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" if not pd.isna(row['Italian']):\n",
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" c1rdf.add((sshocterm[label], SKOS.altLabel, Literal(row[\"Italian\"].strip(), lang='it')))\n",
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" if not pd.isna(row['Slovenian']):\n",
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" c1rdf.add((sshocterm[label], SKOS.altLabel, Literal(row[\"Slovenian\"].strip(), lang='sl')))\n",
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" if not pd.isna(row['Greek']):\n",
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" c1rdf.add((sshocterm[label], SKOS.altLabel, Literal(row[\"Greek\"].strip(), lang='el')))\n",
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" \n",
" if row.Subject.lower()==\"definition\":\n",
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" endef=Literal(row[\"Term\"].strip(), lang='en')\n",
" frdef=Literal(row[\"French\"].strip(), lang='fr')\n",
" nldef=Literal(row['Dutch'].strip(), lang='nl')\n",
" dedef=Literal(row['German'].strip(), lang='de')\n",
" itdef=Literal(row['Italian'].strip(), lang='it')\n",
" sldef=Literal(row['Slovenian'].strip(), lang='sl')\n",
" eldef=Literal(row['Greek'].strip(), lang='el')\n",
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" \n",
" c1rdf.add((sshocterm[label], SKOS.definition, endef))\n",
" c1rdf.add((sshocterm[label], SKOS.definition, frdef))\n",
" c1rdf.add((sshocterm[label], SKOS.definition, nldef))\n",
" c1rdf.add((sshocterm[label], SKOS.definition, dedef))\n",
" c1rdf.add((sshocterm[label], SKOS.definition, itdef))\n",
" c1rdf.add((sshocterm[label], SKOS.definition, sldef))\n",
" c1rdf.add((sshocterm[label], SKOS.definition, eldef))\n",
" if not pd.isna(row['Source of definition']):\n",
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" source=Literal(row['Source of definition'].strip(), datatype=XSD.string)\n",
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" #print (f'{label}, {source}')\n",
" c1rdf.add((sshocterm[label], dct.source, source))\n",
" if not pd.isna(row['Loterre Open Science Thesaurus']):\n",
" lote=URIRef(row['Loterre Open Science Thesaurus'])\n",
" c1rdf.add((sshocterm[label], SKOS.exactMatch, lote))\n",
" \n",
" if not pd.isna(row['Linked Open Vocabularies']):\n",
" lov=URIRef(row['Linked Open Vocabularies'])\n",
" c1rdf.add((sshocterm[label], SKOS.exactMatch, lov))\n",
" \n",
" if not pd.isna(row['LOV 2']):\n",
" lov2=URIRef(row['LOV 2'])\n",
" c1rdf.add((sshocterm[label], SKOS.exactMatch, lov2))\n",
" #Terms4FAIRSkills ISO \n",
" if not pd.isna(row['Terms4FAIRSkills']):\n",
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" t4fs=Literal(row['Terms4FAIRSkills'].strip())\n",
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" c1rdf.add((sshocterm[label], SKOS.note, t4fs))\n",
" if not pd.isna(row['ISO']):\n",
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" tiso=Literal(row['ISO'].strip())\n",
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" c1rdf.add((sshocterm[label], SKOS.note, tiso))\n",
" if not pd.isna(row['Broader Concept']):\n",
" broc=URIRef(row['Broader Concept'])\n",
" c1rdf.add((sshocterm[label], SKOS.broadMatch, broc))\n",
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"\n",
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"print(len(c1rdf))"
]
},
{
"cell_type": "code",
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"execution_count": null,
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"id": "earlier-slovak",
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"metadata": {},
"outputs": [],
"source": [
"#for s, p, o in c1rdf.triples((None, None, None)):\n",
"# print(\"{} {}\".format(s, o.n3))"
]
},
{
"cell_type": "markdown",
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"id": "arabic-buyer",
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"metadata": {},
"source": [
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"Create a *Turtle* file and an *rdf* file in the **/data** directory with the SKOS resource for the **SSHOC Multilingual Data Stewardship Terminology** "
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]
},
{
"cell_type": "code",
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"execution_count": null,
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"id": "treated-spotlight",
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"metadata": {},
"outputs": [],
"source": [
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"c1rdf.serialize(destination='data/mdstskos.ttl', format=\"n3\");#format=\"pretty-xml\")\n",
"c1rdf.serialize(destination='data/mdstskos.rdf', format=\"pretty-xml\");#format=\"pretty-xml\")"
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]
},
{
"cell_type": "markdown",
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"id": "ruled-america",
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"metadata": {},
"source": [
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"Download **SSHOC Multilingual Metadata** spreadsheet"
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]
},
{
"cell_type": "code",
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"execution_count": null,
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"id": "olive-archive",
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"metadata": {},
"outputs": [],
"source": [
"mdurl=conf['Source']['METADATASOURCE']\n",
"df_metadata=pd.read_csv(mdurl)"
]
},
{
"cell_type": "code",
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"execution_count": null,
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"id": "square-michael",
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"metadata": {},
"outputs": [],
"source": [
"df_metadata.rename(columns = {'English': 'Englishterm', 'Unnamed: 1':'Englishdefinition', 'Unnamed: 2':'source',\n",
" 'Unnamed: 3':'URI', 'Dutch':'Dutchterm', 'Unnamed: 5':'Dutchdefinition', \n",
" 'French':'Frenchterm', 'Unnamed: 7':'Frenchdefinition',\n",
" 'Greek':'Greekterm', 'Unnamed: 9':'Greekdefinition',\n",
" 'Italian':'Italianterm', 'Unnamed: 11':'Italiandefinition'}, inplace = True)\n",
"df_metadata=df_metadata.drop(0)\n"
]
},
{
"cell_type": "markdown",
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"id": "explicit-routine",
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"metadata": {},
"source": [
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"Create a graph for the SKOS data and bind the namespaces to it"
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]
},
{
"cell_type": "code",
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"execution_count": null,
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"id": "patient-winner",
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"metadata": {},
"outputs": [],
"source": [
"ccr = rdflib.Graph()\n",
"ccr.bind(\"sshoccmd\", sshoccmd)\n",
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"ccr.bind(\"sshocterm\", sshocterm)\n",
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"ccr.bind(\"dc11\", dc11)\n",
"ccr.bind(\"dct\", dct)\n",
"ccr.bind(\"iso369-3\", iso369)\n",
"ccr.bind(\"skos\", SKOS)\n",
"ccr.bind(\"dc\", DC)\n",
"ccr.bind(\"rdf\", RDF)\n",
"ccr.bind(\"owl\", OWL)\n",
"ccr.bind(\"xsd\", XSD)\n"
]
},
{
"cell_type": "code",
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"execution_count": null,
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"id": "least-waterproof",
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"metadata": {},
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"outputs": [],
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"source": [
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"now = datetime.datetime.today()\n",
"today_date=now.date()\n",
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"title=Literal(conf['Texts']['METADATATITLE'], lang=conf['Texts']['LANG'])\n",
"description=Literal(conf['Texts']['METADATADESCRIPTION'], lang=conf['Texts']['LANG'])\n",
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"identifier=Literal(conf['Texts']['METADATAID'], lang=conf['Texts']['LANG'])\n",
"#identifier=URIRef(conf['Texts']['METADATAID'])\n",
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"createddate= Literal(conf['Texts']['METADATACREATEDATE'],datatype=XSD.date)\n",
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"moddate= Literal(today_date,datatype=XSD.date)\n",
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"version= Literal(conf['Texts']['METADATAVERSION'],datatype=XSD.string)\n",
"\n",
"ccr.add((sshoccmd[''], RDF.type, SKOS.ConceptScheme))\n",
"ccr.add((sshoccmd[''], DC.title, title))\n",
"ccr.add((sshoccmd[''], DC.description, description))\n",
"ccr.add((sshoccmd[''], DC.identifier, identifier))\n",
"ccr.add((sshoccmd[''], dct.created, createddate))\n",
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"ccr.add((sshoccmd[''], dct.modified, moddate))\n",
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"ccr.add((sshoccmd[''], OWL.versionInfo, version))\n",
"ccr.add((sshoccmd[''], dct.language, iso369.eng))\n",
"ccr.add((sshoccmd[''], dct.language, iso369.ger))\n",
"ccr.add((sshoccmd[''], dct.language, iso369.fra))\n",
"ccr.add((sshoccmd[''], dct.language, iso369.ell))\n",
"ccr.add((sshoccmd[''], dct.language, iso369.ita))\n",
"ccr.add((sshoccmd[''], dct.language, iso369.dut))\n",
"ccr.add((sshoccmd[''], dct.language, iso369.slv))"
]
},
{
"cell_type": "markdown",
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"id": "passing-onion",
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"metadata": {},
"source": [
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"The following cell implements the mapping rules for creating a SKOS resource."
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]
},
{
"cell_type": "code",
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"execution_count": null,
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"id": "confirmed-montana",
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"metadata": {},
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"outputs": [],
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"source": [
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"topconcepts=[]\n",
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"for index, row in df_metadata.iterrows():\n",
" \n",
" label=row[\"URI\"]\n",
" urilabel=URIRef(label)\n",
" lastslash=label.rfind('/')\n",
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" label=URIRef('sshoc_'+label[lastslash+1:])\n",
" ccr.add((sshoccmd[''], SKOS.hasTopConcept, sshoccmd[label]))\n",
" #topconcepts.append(Literal(sshoccmd[label]))\n",
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" \n",
" strsource=row['source']\n",
" \n",
" strsource=strsource.replace('(source: ','')\n",
" strsource=strsource.replace(')','')\n",
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" source=Literal(strsource.strip())\n",
" enterm=Literal(row[\"Englishterm\"].strip(), lang='en')\n",
" frterm=Literal(row[\"Frenchterm\"].strip(), lang='fr')\n",
" nlterm=Literal(row['Dutchterm'].strip(), lang='nl')\n",
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" #determ=Literal(row['Germanterm'], lang='de')\n",
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" itterm=Literal(row['Italianterm'].strip(), lang='it')\n",
" #slterm=Literal(row['Slovenianterm'].strip(), lang='sl')\n",
" elterm=Literal(row['Greekterm'].strip(), lang='el')\n",
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" \n",
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" endef=Literal(row[\"Englishdefinition\"].strip(), lang='en')\n",
" frdef=Literal(row[\"Frenchdefinition\"].strip(), lang='fr')\n",
" nldef=Literal(row['Dutchdefinition'].strip(), lang='nl')\n",
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" #dedef=Literal(row['Germandefinition'], lang='de')\n",
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" itdef=Literal(row['Italiandefinition'].strip(), lang='it')\n",
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" #sldef=Literal(row['Sloveniandefinition'], lang='sl')\n",
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" eldef=Literal(row['Greekdefinition'].strip(), lang='el')\n",
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" \n",
" ccr.add((sshoccmd[label], RDF.type, SKOS.Concept))\n",
" ccr.add((sshoccmd[label], SKOS.prefLabel, enterm))\n",
" ccr.add((sshoccmd[label], SKOS.prefLabel, frterm))\n",
" ccr.add((sshoccmd[label], SKOS.prefLabel, nlterm))\n",
" #ccr.add(sshoccmd[label], SKOS.prefLabel, determ))\n",
" ccr.add((sshoccmd[label], SKOS.prefLabel, itterm))\n",
" #ccr.add((sshoccmd[label], SKOS.prefLabel, slterm))\n",
" ccr.add((sshoccmd[label], SKOS.prefLabel, elterm))\n",
" \n",
" ccr.add((sshoccmd[label], SKOS.definition, endef))\n",
" ccr.add((sshoccmd[label], SKOS.definition, frdef))\n",
" ccr.add((sshoccmd[label], SKOS.definition, nldef))\n",
" #ccr.add(sshoccmd[label], SKOS.definition, dedef))\n",
" ccr.add((sshoccmd[label], SKOS.definition, itdef))\n",
" #ccr.add((sshoccmd[label], SKOS.definition, sldef))\n",
" ccr.add((sshoccmd[label], SKOS.definition, eldef))\n",
" \n",
" ccr.add((sshoccmd[label], dct.source, source))\n",
" ccr.add((sshoccmd[label], SKOS.exactMatch, urilabel))\n",
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" ccr.add((sshoccmd[label], SKOS.topConceptOf, sshoccmd['']))\n",
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" \n",
"print(len(ccr))"
]
},
{
"cell_type": "markdown",
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"id": "connected-honey",
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"metadata": {},
"source": [
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"Create a *Turtle* file and an *rdf* file in the **/data** directory with the SKOS resource for **SSHOC Multilingual Metadata** "
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]
},
{
"cell_type": "code",
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"execution_count": null,
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"id": "greater-thunder",
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"metadata": {},
"outputs": [],
"source": [
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"ccr.serialize(destination='data/skosccr.rdf', format=\"pretty-xml\");#format=\"n3\")\n",
"ccr.serialize(destination='data/skosccr.ttl', format=\"n3\");#format=\"n3\")"
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]
},
{
"cell_type": "code",
"execution_count": null,
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"id": "elementary-graphics",
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"metadata": {},
"outputs": [],
"source": []
}
],
"metadata": {
"kernelspec": {
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"display_name": "Python 3 (ipykernel)",
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"language": "python",
"name": "python3"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
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"version": "3.11.1"
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}
},
"nbformat": 4,
"nbformat_minor": 5
}
