{ "cells": [ { "cell_type": "markdown", "source": [ "List of Publications\n", "===================" ], "metadata": { "collapsed": false } }, { "cell_type": "code", "execution_count": 20, "metadata": { "ExecuteTime": { "start_time": "2023-04-28T14:48:38.871405Z", "end_time": "2023-04-28T14:48:39.447825Z" }, "tags": [ "remove-input" ] }, "outputs": [ { "data": { "text/plain": "", "text/markdown": "* The application of the open pharmacological concepts triple store (Open PHACTS) to support drug discovery research (DOI, Wikidata)\n* Identifying sigma factors in Mycobacterium smegmatis by comparative genomic analysis (DOI, Wikidata)\n* The public road to high-quality curated biological pathways (DOI, Wikidata)\n* Centralizing content and distributing labor: a community model for curating the very long tail of microbial genomes (DOI, Wikidata)\n* Centralizing content and distributing labor: a community model for curating the very long tail of microbial genomes (DOI, Wikidata)\n* Wikidata: A platform for data integration and dissemination for the life sciences and beyond (DOI, Wikidata)\n* Scientific Lenses to Support Multiple Views over Linked Chemistry Data (DOI, Wikidata)\n* Wikidata as a semantic framework for the Gene Wiki initiative (DOI, Wikidata)\n* WikiPathways: capturing the full diversity of pathway knowledge (DOI, Wikidata)\n* Using the Semantic Web for Rapid Integration of WikiPathways with Other Biological Online Data Resources (DOI, Wikidata)\n* The ChEMBL database as linked open data (DOI, Wikidata)\n* Applying linked data approaches to pharmacology: Architectural decisions and implementation (DOI, Wikidata)\n* Pathway enrichment based on text mining and its validation on carotenoid and vitamin A metabolism (DOI, Wikidata)\n* The FAIR Guiding Principles for scientific data management and stewardship (DOI, Wikidata)\n* Nature Europe site should highlight most productive countries. (DOI, Wikidata)\n* Opportunities and challenges presented by Wikidata in the context of biocuration (DOI, Wikidata)\n* WikiGenomes: an open Web application for community consumption and curation of gene annotation data in Wikidata (DOI, Wikidata)\n* WikiGenomes: an open Web application for community consumption and curation of gene annotation data in Wikidata (DOI, Wikidata)\n* The role of bioinformatics in pathway curation (DOI, Wikidata)\n* The distinction between linguistic and conceptual semantics in medical terminology and its implication for NLP-based knowledge acquisition. (DOI, Wikidata)\n* WikiPathways: a multifaceted pathway database bridging metabolomics to other omics research (DOI, Wikidata)\n* Using Shape Expressions (ShEx) to Share RDF Data Models and to Guide Curation with Rigorous Validation (DOI, Wikidata)\n* Measuring impact in online resources with the CInumber (the CitedIn Number for online impact) (DOI, Wikidata)\n* Acknowledging contributions to online expert assistance (DOI, Wikidata)\n* Acknowledging contributions to online expert assistance (DOI, Wikidata)\n* Exposing WikiPathways as Linked Open Data (DOI, Wikidata)\n* Explicit interaction information from WikiPathways in RDF facilitates drug discovery in the Open PHACTS Discovery Platform (DOI, Wikidata)\n* Wikidata as an intuitive resource towards semantic data modeling in data FAIRification (DOI, Wikidata)\n* Addendum: The FAIR Guiding Principles for scientific data management and stewardship (DOI, Wikidata)\n* Using Shape Expressions (ShEx) to Share RDF Data Models and to Guide Curation with Rigorous Validation (DOI, Wikidata)\n* Wikidata as a linked-data hub for Biodiversity data (DOI, Wikidata)\n* FAIR Principles: Interpretations and Implementation Considerations (DOI, Wikidata)\n* Wikidata as a knowledge graph for the life sciences (DOI, Wikidata)\n* WikiPathways: connecting communities (DOI, Wikidata)\n* A protocol for adding knowledge to Wikidata: aligning resources on human coronaviruses (DOI, Wikidata)\n* Knowledge graphs and wikidata subsetting (DOI, Wikidata)\n* Participative Decision Making and the Sharing of Benefits: Laws, ethics, and data protection for building extended global communities (DOI, Wikidata)\n* Complex Portal 2022: new curation frontiers (DOI, Wikidata)\n* Ten simple rules for creating reusable pathway models for computational analysis and visualization (DOI, Wikidata)\n* Understanding signaling and metabolic paths using semantified and harmonized information about biological interactions (DOI, Wikidata)\n* Using Crowd-sourcing Platforms to Increase and Spread Knowledge on the Biodiversity in Sub-Saharan Africa (DOI, Wikidata)\n* Fairmetrics/Metrics: Proposed Fair Metrics And Results Of The Metrics Evaluation Questionnaire (DOI, Wikidata)\n" }, "metadata": {}, "output_type": "display_data" } ], "source": [ "from wikidataintegrator import wdi_core\n", "from IPython.display import Markdown, display\n", "\n", "# Set up the SPARQL endpoint URL\n", "sparql = \"https://query.wikidata.org/sparql\"\n", "\n", "# Set up the SPARQL query\n", "query = \"\"\"\n", "SELECT ?publication ?publicationLabel ?doi\n", "WHERE\n", "{\n", " ?publication wdt:P50 wd:Q19845625.\n", " ?publication wdt:P31 wd:Q13442814.\n", " OPTIONAL { ?publication wdt:P356 ?doi. }\n", " SERVICE wikibase:label { bd:serviceParam wikibase:language \"en\". }\n", "}\n", "\"\"\"\n", "\n", "results = wdi_core.WDItemEngine.execute_sparql_query(query, as_dataframe=False, endpoint=sparql)\n", "\n", "# Print the list of publications with their DOI and QID\n", "\n", "md = \"\"\n", "for result in results[\"results\"][\"bindings\"]:\n", " publication_name = result[\"publicationLabel\"][\"value\"]\n", " publication_doi = result[\"doi\"][\"value\"] if \"doi\" in result else \"N/A\"\n", " publication_qid = result[\"publication\"][\"value\"].split(\"/\")[-1]\n", " if publication_doi and publication_qid:\n", " md += f\"* {publication_name} (DOI, Wikidata)\\n\"\n", " elif publication_qid:\n", " md += f\"* {publication_name} (Wikidata)\\n\"\n", " else:\n", " md += f\"* {publication_name}\\n\"\n", "display(Markdown(md))" ] }, { "cell_type": "code", "execution_count": null, "outputs": [], "source": [], "metadata": { "collapsed": false } } ], "metadata": { "celltoolbar": "Tags", "kernelspec": { "display_name": "Python 3 (ipykernel)", "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", "version": "3.9.6" } }, "nbformat": 4, "nbformat_minor": 1 }