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Update the notebooks and benchamrk results.
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Sheeba Samuel committed Sep 27, 2024
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"id": "0fbe88f1-2838-4ebb-8152-6b433c3b0650",
"metadata": {},
"source": [
"# FAIR Jupyter\n",
"FAIR Jupyter is a knowledge graph for semantic sharing and granular exploration of a computational notebook reproducibility dataset. This notebook provides some SPARQL queries to query the FAIR Jupyter SPARQL Endpoint.\n",
"# FAIR Jupyter: SPARQL Queries\n",
"FAIR Jupyter is a knowledge graph for semantic sharing and granular exploration of a computational notebook reproducibility dataset. This notebook provides some SPARQL queries to query the FAIR Jupyter SPARQL Endpoint. These SPARQL queries include queries that reproduce the original results, as well as additional queries that were not included in the [publication](https://doi.org/10.1093/gigascience/giad113). It also supports federated queries to external resources such as [Wikidata](https://query.wikidata.org/) and [MaRDI](https://www.mardi4nfdi.de).\n",
"\n",
"More Information on FAIR Jupyter Ontology and Knowledge Graph: https://w3id.org/fairjupyter\n",
"More Information on FAIR Jupyter Ontology and Knowledge Graph: [https://w3id.org/fairjupyter](https://w3id.org/fairjupyter).\n",
"\n",
"## Prerequisites\n",
"The notebook is written in Python and besides Jupyter and Wikidata, it has the following direct dependencies:\n",
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"results"
]
},
{
"cell_type": "markdown",
"id": "394e55cb-bc73-4982-a80c-ec140c9b6e6a",
"metadata": {},
"source": [
"# Match articles between FAIR Jupyter and MaRDI via DOI and get co-used software"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "3e52189b-5fa8-4708-8e65-c72f39e4edb6",
"execution_count": 27,
"id": "567161d1-c9f6-41d5-81c4-6d97d94ce9ca",
"metadata": {},
"outputs": [],
"source": []
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Results written to results/fairjupyter_mardi_match_articles_doi_software.csv\n"
]
},
{
"data": {
"text/html": [
"<div>\n",
"<style scoped>\n",
" .dataframe tbody tr th:only-of-type {\n",
" vertical-align: middle;\n",
" }\n",
"\n",
" .dataframe tbody tr th {\n",
" vertical-align: top;\n",
" }\n",
"\n",
" .dataframe thead th {\n",
" text-align: right;\n",
" }\n",
"</style>\n",
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th>title</th>\n",
" <th>doi</th>\n",
" <th>method</th>\n",
" <th>methodLabel</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
" <td>Phase Portraits of Bi-dimensional Zeta Values</td>\n",
" <td>10.1007/978-3-030-52200-1_39</td>\n",
" <td>https://portal.mardi4nfdi.de/entity/Q17941</td>\n",
" <td>mpmath</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
" <td>Phase Portraits of Bi-dimensional Zeta Values</td>\n",
" <td>10.1007/978-3-030-52200-1_39</td>\n",
" <td>https://portal.mardi4nfdi.de/entity/Q33077</td>\n",
" <td>Jupyter</td>\n",
" </tr>\n",
" <tr>\n",
" <th>2</th>\n",
" <td>Phase Portraits of Bi-dimensional Zeta Values</td>\n",
" <td>10.1007/978-3-030-52200-1_39</td>\n",
" <td>https://portal.mardi4nfdi.de/entity/Q34954</td>\n",
" <td>GitHub</td>\n",
" </tr>\n",
" <tr>\n",
" <th>3</th>\n",
" <td>Phase Portraits of Bi-dimensional Zeta Values</td>\n",
" <td>10.1007/978-3-030-52200-1_39</td>\n",
" <td>https://portal.mardi4nfdi.de/entity/Q54519</td>\n",
" <td>ipywidgets</td>\n",
" </tr>\n",
" <tr>\n",
" <th>4</th>\n",
" <td>Seminator 2 can complement generalized Büchi a...</td>\n",
" <td>10.1007/978-3-030-53291-8_2</td>\n",
" <td>https://portal.mardi4nfdi.de/entity/Q21456</td>\n",
" <td>SPOT</td>\n",
" </tr>\n",
" <tr>\n",
" <th>5</th>\n",
" <td>Polymake.jl: A New Interface to polymake</td>\n",
" <td>10.1007/978-3-030-52200-1_37</td>\n",
" <td>https://portal.mardi4nfdi.de/entity/Q13478</td>\n",
" <td>polymake</td>\n",
" </tr>\n",
" <tr>\n",
" <th>6</th>\n",
" <td>Polymake.jl: A New Interface to polymake</td>\n",
" <td>10.1007/978-3-030-52200-1_37</td>\n",
" <td>https://portal.mardi4nfdi.de/entity/Q19386</td>\n",
" <td>alphaCertified</td>\n",
" </tr>\n",
" <tr>\n",
" <th>7</th>\n",
" <td>Polymake.jl: A New Interface to polymake</td>\n",
" <td>10.1007/978-3-030-52200-1_37</td>\n",
" <td>https://portal.mardi4nfdi.de/entity/Q25895</td>\n",
" <td>Julia</td>\n",
" </tr>\n",
" <tr>\n",
" <th>8</th>\n",
" <td>Polymake.jl: A New Interface to polymake</td>\n",
" <td>10.1007/978-3-030-52200-1_37</td>\n",
" <td>https://portal.mardi4nfdi.de/entity/Q33896</td>\n",
" <td>HomotopyContinuation</td>\n",
" </tr>\n",
" <tr>\n",
" <th>9</th>\n",
" <td>FunGrim: A Symbolic Library for Special Functions</td>\n",
" <td>10.1007/978-3-030-52200-1_31</td>\n",
" <td>https://portal.mardi4nfdi.de/entity/Q13684</td>\n",
" <td>SymPy</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
"text/plain": [
" title \\\n",
"0 Phase Portraits of Bi-dimensional Zeta Values \n",
"1 Phase Portraits of Bi-dimensional Zeta Values \n",
"2 Phase Portraits of Bi-dimensional Zeta Values \n",
"3 Phase Portraits of Bi-dimensional Zeta Values \n",
"4 Seminator 2 can complement generalized Büchi a... \n",
"5 Polymake.jl: A New Interface to polymake \n",
"6 Polymake.jl: A New Interface to polymake \n",
"7 Polymake.jl: A New Interface to polymake \n",
"8 Polymake.jl: A New Interface to polymake \n",
"9 FunGrim: A Symbolic Library for Special Functions \n",
"\n",
" doi method \\\n",
"0 10.1007/978-3-030-52200-1_39 https://portal.mardi4nfdi.de/entity/Q17941 \n",
"1 10.1007/978-3-030-52200-1_39 https://portal.mardi4nfdi.de/entity/Q33077 \n",
"2 10.1007/978-3-030-52200-1_39 https://portal.mardi4nfdi.de/entity/Q34954 \n",
"3 10.1007/978-3-030-52200-1_39 https://portal.mardi4nfdi.de/entity/Q54519 \n",
"4 10.1007/978-3-030-53291-8_2 https://portal.mardi4nfdi.de/entity/Q21456 \n",
"5 10.1007/978-3-030-52200-1_37 https://portal.mardi4nfdi.de/entity/Q13478 \n",
"6 10.1007/978-3-030-52200-1_37 https://portal.mardi4nfdi.de/entity/Q19386 \n",
"7 10.1007/978-3-030-52200-1_37 https://portal.mardi4nfdi.de/entity/Q25895 \n",
"8 10.1007/978-3-030-52200-1_37 https://portal.mardi4nfdi.de/entity/Q33896 \n",
"9 10.1007/978-3-030-52200-1_31 https://portal.mardi4nfdi.de/entity/Q13684 \n",
"\n",
" methodLabel \n",
"0 mpmath \n",
"1 Jupyter \n",
"2 GitHub \n",
"3 ipywidgets \n",
"4 SPOT \n",
"5 polymake \n",
"6 alphaCertified \n",
"7 Julia \n",
"8 HomotopyContinuation \n",
"9 SymPy "
]
},
"execution_count": 27,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"query_string = \"\"\"\n",
"PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>\n",
"PREFIX wikibase: <http://wikiba.se/ontology#>\n",
"PREFIX mardi_wd: <https://portal.mardi4nfdi.de/entity/>\n",
"PREFIX mardi_wdt: <https://portal.mardi4nfdi.de/prop/direct/>\n",
"\n",
"PREFIX bd: <http://www.bigdata.com/rdf#>\n",
"PREFIX wikibase: <http://wikiba.se/ontology#>\n",
"\n",
"SELECT DISTINCT ?title ?doi ?method ?methodLabel\n",
"\n",
"WHERE {\n",
" ?fj_article <https://w3id.org/reproduceme/doi> ?doi .\n",
"\n",
" service <http://query.portal.mardi4nfdi.de/proxy/wdqs/bigdata/namespace/wdq/sparql> {\n",
" ?mardi_paper mardi_wdt:P27 ?doi .\n",
" ?mardi_paper mardi_wdt:P159 ?title .\n",
" \n",
" ?mardi_paper mardi_wdt:P1463 ?method .\n",
" ?method rdfs:label ?methodLabel .\n",
" }\n",
"\n",
"}\n",
"LIMIT 10\n",
"\"\"\"\n",
"csv_filename = 'fairjupyter_mardi_match_articles_doi_software'\n",
"results = query_and_display_results(query_string, csv_filename)\n",
"results"
]
}
],
"metadata": {
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