📋 A Python Parser for PubMed Open-Access XML Subset and MEDLINE XML Dataset
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Updated
Oct 16, 2024 - Python
📋 A Python Parser for PubMed Open-Access XML Subset and MEDLINE XML Dataset
An R package that provides streamlined access to multiple PubMed databases, including abstracts, bibliometrics, NER annotations, and full texts.
A Python tool for systematic review scraping PubMed articles based on specified search queries.
I'm passionate about Cloud and DevOps, and for the moment I'm posting some of my work and personal projects here to showcase that. If its useful for you, feel free to integrate or contribute!
Is a Django Python web application to download PubMed data into a Microsoft Excel spreadsheet and XML files.
Tools to create a clinical knowledge graph from biomedical literature. Includes wrappers for NCBI Eutils, cTakes annotator and Neo4J
ScrapeMed: Data scraping for PubMed Central.
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
get document info from pubmedapi if PMID is known
Project from the course 'E-health methods and applications' @ Politecnico di Milano
Parse PubMed data and get it into csv or plain text
NLP framework in python for entity recognition and relationship extraction
Update PubMed articles daily on HDFS by using Spark Cluster
Script that creates automatic searches based on author names, grant numbers, or organizations.
Reference conversion library for NodeJS. Import, Export and Convert between BibTex, EndNote, XML, JSON, and more...
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…
Python functions to curate data from NCBI and EUROPMC API.
Identify PICO elements and formulate Medical Evidence Propositions from clinical trial abstracts
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