A framework for keeping biomedical text mining result up-to-date
☆43Jul 11, 2020Updated 6 years ago
Alternatives and similar repositories for pubrunner
Users that are interested in pubrunner are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Text-mined knowledgebase for drivers, oncogenes and tumor suppressors in cancer☆42Dec 16, 2025Updated 9 months ago
- Analysis code for knowledge discovery project☆12Sep 25, 2018Updated 7 years ago
- Named Entity Recognition for biomedical entities☆48Jan 11, 2023Updated 3 years ago
- A Python biomedical relation extraction package that uses a supervised approach (i.e. needs training data).☆157Mar 12, 2023Updated 3 years ago
- Generate mutated sequence files from a reference genome.☆11Jun 12, 2026Updated 3 months ago
- Proton VPN Special Offer - Get 70% off • AdSpecial partner offer. Trusted by over 100 million users worldwide. Tested, Approved and Recommended by Experts.
- BioBTree v2: An MCP-enabled biomedical graph database unifying 70+ datasets.☆20Sep 2, 2026Updated 3 weeks ago
- NLP framework in python for entity recognition and relationship extraction☆116Dec 8, 2022Updated 3 years ago
- Tools for working with PubMed data.☆15Sep 26, 2020Updated 5 years ago
- Lookup PubMed records and make Publication objects with info about a scientific publication☆41Nov 23, 2022Updated 3 years ago
- This repository contains the corpora and supplementary data, along with instructions for recreating the experiments, for our paper: "Towa…☆15Jul 26, 2019Updated 7 years ago
- ☆18Mar 11, 2018Updated 8 years ago
- An example of a data analysis pipeline using Make☆17Jul 26, 2016Updated 10 years ago
- Text mining cancer biomarkers for the CIVIC database☆23Dec 16, 2025Updated 9 months ago
- Implementing semantically rich NeXML I/O in R☆15May 6, 2024Updated 2 years ago
- Deploy open-source AI quickly and easily - Special Bonus Offer • AdRunpod Hub is built for open source. One-click deployment and autoscaling endpoints without provisioning your own infrastructure.
- Hominid: host-microbiome interaction identification☆16Jun 17, 2024Updated 2 years ago
- Reproducible Phylogenomics☆22Jun 28, 2016Updated 10 years ago
- Crowdsourced ground truth for medical relation extraction.☆69Mar 18, 2019Updated 7 years ago
- Translates LinkML schemas into Datalog programs and executes them using Souffle, enabling advanced validation and inference over instance…☆21Feb 14, 2024Updated 2 years ago
- Minimal scripts to reproduce the RADICL-seq analysis of the Nature Communications manuscript☆11Jan 30, 2020Updated 6 years ago
- [NAACL(2019)] Generating Knowledge Graph Paths from Textual Definitions using Sequence-to-Sequence Models☆11Apr 27, 2022Updated 4 years ago
- Table compiling the list of biomedically-related corpora available for named entity recognition (and some also suitable for association d…☆18Mar 15, 2018Updated 8 years ago
- Retrieve PubMed articles, text-mining annotations, or molecular data from >35 Entrez databases via easy to use Python package - built on …☆82Nov 2, 2023Updated 2 years ago
- A project to capture biological pathway data from academic papers☆29Mar 24, 2025Updated last year
- Deploy open-source AI quickly and easily - Special Bonus Offer • AdRunpod Hub is built for open source. One-click deployment and autoscaling endpoints without provisioning your own infrastructure.
- provides common tools and lookup tables used primarily by the hgvs and uta packages☆25Jan 12, 2026Updated 8 months ago
- A CRF-biLSTM based Biomedical NER model in Bioinformatics 2018.☆24Jul 31, 2018Updated 8 years ago
- Biomedical wordlists (of drugs, genes, etc) for several text mining projects☆19Apr 3, 2023Updated 3 years ago
- 🎬 analyzing three decades of movie data☆14Dec 9, 2022Updated 3 years ago
- ☆15Sep 20, 2019Updated 7 years ago
- SciAI is an extension for the text editors like Google Docs to create structured semantic biomedical papers directly at the moment of wri…☆22Jul 11, 2023Updated 3 years ago
- ☆124May 2, 2018Updated 8 years ago
- BioAssay Research Database☆20Jan 29, 2019Updated 7 years ago
- genomic alignment similarity search tool☆20Jun 26, 2026Updated 2 months ago
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- ☆10Nov 19, 2019Updated 6 years ago
- JavaScript library for biological data visualization☆20Oct 12, 2018Updated 7 years ago
- Simple rust implementation of semantic similarity☆16Feb 20, 2026Updated 7 months ago
- micca - MICrobial Community Analysis☆19Feb 12, 2020Updated 6 years ago
- jinja2-enabled jupyter notebooks☆37Feb 13, 2026Updated 7 months ago
- blast, shmlast☆21Oct 5, 2020Updated 5 years ago
- A gene-targeted assembler tool☆19Oct 27, 2017Updated 8 years ago