A Python Parser for PubMed Open-Access XML Subset and MEDLINE XML Dataset
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Jul 31, 2025 - Python
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pubmed-parser
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NLP framework in python for entity recognition and relationship extraction
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Dec 8, 2022 - Python
A Model Context Protocol (MCP) server enabling AI agents to intelligently search, retrieve, and analyze biomedical literature from PubMed via NCBI E-utilities. Includes a research agent scaffold. STDIO & HTTP
mcp pubmed pubmed-parser ncbi ai-agents ai-tools pubmed-api model-context-protocol mcp-server bio-medical-research
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Sep 26, 2025 - TypeScript
A clinical BERT-based NLP tool for parsing clinical trial abstracts following the PICO framework
natural-language-processing tensorflow information-extraction pubmed-parser bert pico pubmed-abstracts lstm-crf evidence-based-medicine pico-element rct-abstracts pico-framework bluebert pico-parser
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Oct 15, 2020 - Python
Tools to create a clinical knowledge graph from biomedical literature. Includes wrappers for NCBI Eutils, cTakes annotator and Neo4J
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Jun 27, 2024 - Java
ScrapeMed: Data scraping for PubMed Central.
python data-science data scraping pubmed embeddings pubmed-central pubmed-parser data-scraper medical-data scraping-python scrapemed
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Jan 6, 2024 - Python
Write PubMed search results with two display options (citation or listview) to PDF or Word
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Oct 18, 2020 - Python
Is a Django Python web application to download PubMed data into a Microsoft Excel spreadsheet and XML files.
javascript python django excel xlsx pubmed pubmed-parser xlsxwriter pubmed-abstracts pubmed-articles-grabber pubmed-xml
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Aug 27, 2025 - XSLT
We employed pre-trained BERT models (distillBERT, BioBert, and SciBert) for text-classifications of the titles and abstracts of clinical trials in medical psychology. The average score of AUC is 0.92. A stacked model was then built by featuring the probability predicted by distillBERT and keywords of search domains. The AUC improved to 0.96 with...
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Aug 18, 2021 - Jupyter Notebook
PubMed/Medline query transpiler
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Dec 26, 2019 - Go
A clinical BERT-based NLP tool for parsing clinical trial abstracts following the PICO framework
natural-language-processing information-extraction pubmed-parser named-entity-recognition clinical-trials abstract evidence-based-medicine pico-frameworks
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Jun 2, 2020 - Python
It provides a method of how to fetch articles along with their features and text from PubMed API.
pubmed-parser biopython fetch-api pubmed-abstracts pubmed-records cysticfibrosis entrezegquery medline-parse pubmed-keywords
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Apr 20, 2020 - Jupyter Notebook
A Gradio bot to retrieve PubMed papers' title, doi, authors and publication date based on general search terms or on specific publication names
python automation scraping pubmed-parser papers gradio biomedical academic-resources academic-research
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Nov 5, 2024 - Python
Python functions to curate data from NCBI and EUROPMC API.
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May 22, 2021 - Python
Simple R interface for PubMed data retrieval: abstracts, full-text (PMC), bibliometrics (iCite), and entity annotations (PubTator3).
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Jan 30, 2026 - R
A tool capable of parsing datasets of papers from pubmed, annotating entities that appear using bio-BERT, creating a network of cooccurrences on which to perform analysis with various algorithms
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Nov 22, 2023 - TeX
Identify PICO elements and formulate Medical Evidence Propositions from clinical trial abstracts
natural-language-processing pubmed information-extraction pubmed-parser clinical-trials knowledge-representation evidence-based-medicine bert-model pico-framework
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Mar 2, 2021 - Python
BIOF 309 Intro to Python Final Project
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Jun 13, 2018 - Jupyter Notebook
Pubmed Parser to get author emails in csv
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Dec 21, 2018 - Python
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