Named Entity Linking from Raw Biomedical Text using SciSpacy, AIM AHEAD DICB Program, Laboratory of Experimental Medicine, University of Hawaii, John A. Burns School of Medicine
Created by AI Navigator
Sun Aug 3, 2025
Register now to attend the virtual ARCH Workshop, "Named Entity Linking from Raw Biomedical Text using SciSpacy," hosted by Billy Troy Wooton.
Workshop Description:
Explore how to extract and normalize medical entities from raw biomedical text using SciSpacy, a robust Python library for biomedical NLP. In this hands-on workshop, you'll work with real and synthetic clinical notes to identify concepts and link them to standardized biomedical vocabularies such as UMLS, MeSH, and SNOMED CT.
Date/Time: Thursday, August 28, 2025 - 1:00 PM PT / 3:00 PM CT / 4:00 PM ET
Location: Virtual Workshop. The Zoom link will be provided upon registration.
Prerequisites for Workshop:
Access to a computer and a stable internet connection. Basic familiarity with Python and Jupyter notebooks is helpful but not required.
Datasets and Tools:
What You'll Learn:
Tools: Python, Jupyter, Google Colab, SciSpacy, HuggingFace Datasets
Datasets: Augmented Clinical Notes dataset (includes PMC-Patients notes, synthetic NoteChat dialogues, and GPT-generated structured summaries)
What You'll Learn:
Participants will gain practical experience in processing clinical text data, identifying biomedical entities, and linking them to UMLS Concept Unique Identifiers (CUIs). By the end of the workshop, attendees will understand how to apply named entity linking techniques to biomedical text, which can be utilized in downstream analyses and machine learning.
About ARCH:
The AI Resource Concierge for Health (ARCH) is supported by the National Institutes of Health AIM-AHEAD program.
ARCH Mission:
Support academic and community stakeholders in the adoption of AI/ML tools to advance their health and disease research goals.
ARCH Vision:
ARCH provides expert technical assistance, guidance, and collaboration to facilitate the adoption of AI/ML tools, supporting the AIM-AHEAD and wider research communities in leveraging these technologies to improve the health of the Nation.
Need Support?
Contact the AI Navigators HelpDesk to request support here: https://helpdesk.aim-ahead.net/ticket/create/35bD542BF0
Interested in learning more?
See a schedule of all upcoming ARCH Workshop details here: https://www.arch.health/stakeholder-engagement-workshops
