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Welcome to NLP@UCSF community knowledge base!

This Wiki space is used to document shared and curated knowledge UCSF NLP community generates as we experiment, learn and implement NLP tools in various clinical and biomedical research and innovation projects. Everyone involved with NLP work at UCSF and affiliate organizations is encouraged to contribute content here. Space administrators will help organize and categorize the knowledge based on community input to make it accessible and usable for UCSF community. 

Next NLP@UCSF Tech Meetup

Next meetup is Friday, August 30 10:30 -12 pm at Mission Hall Room 2103

  • Optional NLP@UCSF group lunch right after

August 2019 Meetup

August 30, 2019 10:30am-12:00pm

Mission Hall Room 2103 or Zoom 

*Optional NLP group lunch 12:00-1pm - place TBD


  • 10:30-11:30 Brainstorm NLP-driven research project with a UCSF research team!
    • The UCSF SIREN team is interested in abstracting social risk factors (such as homelessness and social isolation) from free text clinical notes using NLP. The team is working on several projects that involve using abstracted social risk factors as either predictors (e.g. does homelessness identified in a physician note predict readmission within 30 days of discharge) or outcomes (e.g. does universal screening for food insecurity in a clinic increase the likelihood that physicians write about food insecurity in their notes). In one pending project, the researchers hope to use NLP, specifically, to examine how clinical initiatives to systematically collect social risk data at the point of care change clinician’s social risk charting behaviors.
      NLP@UCSF organizers believe our group  has the collective power to help this research team brainstorm and identify most promising NLP approaches to their projects. Please join this brainstorm and contribute your knowledge, ideas and insight to advance UCSF research!
      *** Learners and beginners are welcome to participate

  • 11:30-12:00 Summer of NLP Contest: last progress check-in before final presentation!

Zoom for remote attendees:

View June 2019 Meetup presentation and notes here. 

June 2019 Meetup

June 20, 2019 3:30-5:00pm

Mission Hall Room 2103 or Zoom 


  • Featured Presentation: Food and Nutrition Information Extraction and Data Management. Tome Eftimov, Postdoctoral Research Fellow, Biomedical Data Sciences, Stanford
    • Nowadays, there is a high demand for facilitating the Food and Nutrition Sciences with the tools for knowledge discovery maximizing the community engagement. To make this possible, a good food and nutrition data management is a requirement. The data management process should address several questions: i) how to deal with heterogeneous data and ii) how to match and aggregate heterogeneous data that are described and classified in various ways. In order to understand the processes that are crucial for the management, we are going to discuss several use cases, such as information extraction of food- and nutrition-related entities from textual data (i.e. unstructured data) and its harmonization using a unified classification system (i.e. an ontology). Understanding these steps will lead to an efficient data management system that satisfies the requirement for interoperability, which means the ability of data and tools from heterogeneous sources to integrate or work together with a minimal effort.
  • Summer of NLP Learning Project - Projects Check-in, Questions, Discussions.
  • ** 5-5:30 pm - Optional social time

Zoom for remote attendees:

View May meetup notes (Summer of NLP 2019) here. Join us next time!

Spring 2018 NLP@UCSF Symposium 

Congratulations and many thanks to the speakers and the organizing team for the inspiring and informative event. The feedback so far has been wonderful and we are planning to follow up shortly on questions and suggestions. Stay tuned.

  • Presentations are now available (Part 1 and Part 2), as well as the video recording.
  • Thank you to everyone who attended!

On the morning of May 18, 2018 we hosted an NLP@UCSF Symposiumfocused on Natural Language Processing of clinical and biomedical text. The meeting featured NLP-enabled research, as well as a technical methods discussion. 

Monthly Meetups

NLP@UCSF community organizers are pleased to announce monthly practitioner meetups for those of us who implement or use NLP to enable research or support clinical work. Ongoing meetups are usually scheduled for the last Thursday of every month at 3:30pm. Locations will rotate. This regular meeting is an opportunity for UCSF NLP practitioners to ask questions, discuss approaches and solutions, share best practices as well as the latest news from the field.

To learn what you've missed at the previous meetups and to discuss the upcoming meetup, visit the Monthly Meetups page

NLP-Biomed Slack Channel

Did you know there is a Slack channel for biomedical NLP practitioners on UC Tech Slack? It is envisioned as a space for instant communications, practice Q&A, announcements for UCSF (and other UCs) community of practice around NLP! If you are interested/involved in NLP work, it is probably a good idea to join the channel. Here is how.

NLP@UCSF Email List

Sign up for our email list! You will receive periodic email with updates from NLP@UCSF community, including a digest of activity on our Slack channel. 

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