Medical Abstract Segmentation NLP Tools

Tools for structurally parsing and classifying sections of medical research abstracts (Background, Methods, Results, etc.). Does NOT include general document parsing, biomedical relationship extraction, or PubMed data collection infrastructure.

There are 35 medical abstract segmentation tools tracked. 1 score above 50 (established tier). The highest-rated is titipata/pubmed_parser at 62/100 with 727 stars.

Get all 35 projects as JSON

curl "https://pt-edge.onrender.com/api/v1/datasets/quality?domain=nlp&subcategory=medical-abstract-segmentation&limit=20"

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#	Tool	Score	Tier	Stars	Language
1	titipata/pubmed_parser :clipboard: A Python Parser for PubMed Open-Access XML Subset and MEDLINE XML Dataset	62	Established	727	Python
2	nfflow/pubmedflow Data Collection API for pubmed	47	Emerging	41	Python
3	greenelab/snorkeling Extracting biomedical relationships from literature with Snorkel 🏊	43	Emerging	58	Jupyter Notebook
4	purplepotion/sadrat Smart Adverse Drug Reaction Assessment Tools.	39	Emerging	19	Jupyter Notebook
5	KarelDO/BioDEX BioDEX: Large-Scale Biomedical Adverse Drug Event Extraction for Real-World...	36	Emerging	60	Jupyter Notebook
6	databricks-industry-solutions/adverse-drug-events To ensure ongoing drug safety, pharma companies need to monitor and report...	36	Emerging	7	Python
7	nasa-petal/PeTaL-labeller The PeTaL labeler labels journal articles with biomimicry functions.	35	Emerging	6	Jupyter Notebook
8	jind11/PubMed-PICO-Detection PubMed PICO Element Detection Dataset	34	Emerging	57	—
9	andreped/adverse-events IEEE BIBM 2021: Bayesian optimization-guided topic modeling for automatic...	34	Emerging	7	Python
10	techthumb1/Drug-Safety-Monitoring-Application A real-time application that scrapes public health databases, employs NLP...	32	Emerging	3	Python
11	greenelab/snorkeling-full-text This is an upgraded version of the original snorkeling project.	31	Emerging	4	Jupyter Notebook
12	OdedMous/Medical-Text-Classification Developed an NLP classifier for detecting medical domains in texts using a...	27	Experimental	9	Jupyter Notebook
13	Ferrariic/pubwords All non-duplicated words as scraped from every publicly available PubMed abstract.	27	Experimental	2	Python
14	sergiog95/csabstracts Dataset of scientific abstracts for the purpose of sentence classification	26	Experimental	10	—
15	ncbi/biocreative_litcovid Evaluation scripts of the Biocreative LitCovid track	23	Experimental	4	Python
16	knowlab/ACE-NLP Identify Adverse Childhood Experiences from free-text data using NLP	22	Experimental	2	—
17	pszemraj/pubmed-text-classification ETHZ Machine Learning for Healthcare Problem 2: classification of pubmed...	22	Experimental	1	Jupyter Notebook
18	johndef64/grpm_bertopic paper: https://link.springer.com/chapter/10.1007/978-3-031-78093-6_1	21	Experimental	3	Jupyter Notebook
19	cognitive-metascience/psychological_abstract_crawler Retrieves scientific article abstracts, applies tagging to categorize them,...	21	Experimental	3	Python
20	qanastek/BioCreative-VII-Track-5 [BioCreative VII] Track 5 - LitCovid track Multi-label topic classification...	21	Experimental	1	Python
21	MTG-Lab/gpad Genotype-Phenotype Association Discovery: An ML tool to search and visualize...	20	Experimental	5	Python
22	p-karisani/illness-dataset A dataset for evaluating text classification, domain adaptation, and active...	19	Experimental	4	—
23	AswaniSahoo/biodiversity-publication-analyzer NLP-powered tool to discover and classify biodiversity genomics publications...	19	Experimental	—	Python
24	harshd23/Paper_Peek Paper Peek is a project based on Natural Language Processing which helps the...	18	Experimental	2	Jupyter Notebook
25	Shr3yash/eSKIMo eSKIMo is a text skimmer and labelling tool built using TensorFlow in...	18	Experimental	2	Jupyter Notebook
26	MatthewJansen/Medical-Abstract-Segmentation A Natural Language Processing (NLP) model with TensorFlow to segment text...	18	Experimental	2	Jupyter Notebook
27	smellycloud/pubmed_literature_scan Sequential Sentence Classification in Medical Abstracts with TensorFlow	17	Experimental	1	Jupyter Notebook
28	JatinPhogat/Durg-Safety-Monitoring-Tool AI-powered tool for detecting and analyzing Adverse Drug Reactions (ADRs)...	15	Experimental	—	Python
29	MariaZentsova/label-with-snorkel Semi-supervised labelling of news snippets to extract cleantech news	11	Experimental	3	Jupyter Notebook
30	MPKuchciak/PubMedResearch This repository focuses on processing and analyzing PubMed abstracts to...	11	Experimental	—	Jupyter Notebook
31	arifbinazhar/Network-Validation This Repository deals with our project on literature based validation of...	11	Experimental	—	Python
32	mrpranavr/Project_Med_Skim A project that makes use of Natural Language Processing in order to skim...	11	Experimental	3	Jupyter Notebook
33	Ryaaad/DDI Code for my Master thesis on "Intelligent Drug-Drug Interaction Extraction:...	11	Experimental	3	Python
34	abhi24112/PubMed-Literature-Skimmer I recently worked on a project to simplify the process of reading PubMed...	10	Experimental	1	Jupyter Notebook
35	tomwalczak/PubMed-Abstract-Analyzer NLP - exploring models across various tasks using PubMed RTC 200k dataset	10	Experimental	2	Python