Data Core Services

 

 

 

  • Clinical data extraction

 

CLARITY/APEX data extractions are our “core competency”. If needed, we can also explore extracting data from other databases (e.g. Syngo, OMOP…)

 

  • Data visualization

We offer help with descriptive statistics if needed (e.g. Table 1, graphs). However, we do not offer biostatistical support at this time.

 

  • Tableau dashboards

We create automatically-updating Tableau dashboards for operations, QI, and research purposes (including for study recruitment)

 

  • Recurring reports

We can create reports (using RMarkdown) that include tables, graphs, and text. These reports can also be updated automatically and sent out on a predetermined schedule.

 

  • Natural Language Processing (NLP) – 3 options
  1. Option #1: We can extract clinical note text from CLARITY and filter the text for matches on a key word or phrase. This method is can be used to search a large body of notes, but the data accuracy is highly dependent on the chosen phrase (the more unique the better). This method also struggles with negation (e.g. “no evidence of…”) and misspellings, among other issues.
  2. Option #2: We can run note texts through a clinical NLP software called CTAKES, which UCSF holds a license for. This is a much more robust approach to NLP that does attempt to account for negation and extracts clinical concepts. However, it has two significant limitations: 1) It is slow, ~3-5 seconds to process a note, 2) We are limited to the terms coded into the CTAKES program; while this covers most medical terminology, it does not cover everything.
  3. Option #3: We can run note texts through Versa, which is UCSF's HIPAA-compliant version of ChatGPT. Among other things, Versa can provide clinical summarization based on notes.
  • Automated messaging

Data Core has developed a platform called “Murmur” that can send automated messages (email, Voalte message, or text message) based on triggers derived from the EHR, Amion, or other sources. Some examples of this include sending surveys to providers currently on service, or notifying a discharging provider that their patient has been readmitted.

 

  • Automatically updating REDCap databases

Data Core can write code to extract relevant variables from Clarity, clean them, and then automatically upload them to REDCap using the REDCap API. This process can be automated to repeat on a set interval (e.g. monthly), and requires IRB approval.