Project Meeting -- 07/01/2019 @ 16:00

Meeting Date: 07/01/2019 Topic: Post-NLM Check-In Attendees: @tdbennett

Proposed Agenda:

[x] Discuss NLM Slides (briefly)
- Follow-up Meeting with Titus Schleyer to discuss applications of this work in his LHS
[x] Proposed Outline for Thesis Update Talk (scheduled 07/08/19)
- Title: Integrating Inferred Molecular Features into a Phenotype Vector Space, with Applications
- Outline:
  - Computational phenotyping is much more than just genotype-phenotype correlations or finding disease-gene relationships using GWAS. The future of computational phenotyping will have diverse applications including everything from next-generation clinical trial recruitment and precision subphenotyping for improved clinical care to EHR-driven phenotyping in order to support the development of learning health systems.
  - Unfortunately, there are many problems with traditional approaches to computational phenotyping that we would like to overcome, which include:
    1. Generalizability, Translatability, and Scalability (PheKnowVec work)
      - Generalizability - will have some preliminary results to review (similar to those in the NLM slides, but more than ADHD -- in progress)
      - Translatability -- I'd like to talk about the mapping work and the verification (including the survey) that has been done there. I will include the LOINC2HPO paper and
      - Scalability -- will just mention this and with that include how it will be applied to the pediatric asthma mechanisms that Stan has been developing.
    2. Assuming we could address the first problem, the majority of electronic phenotypes, like those developed by the eMERGE consortium, lack inclusion of important biological mechanisms, which is likely a result of the fact that most hospital patients are not currently genetic tested. This is where Med2Mech and PheKnowLator come in. The combined work of these projects aim to produce "right" level for better phenotype identification.
      - PheKnowLator - This is the knowledge graph path embedding work, which aims to imitate molecular mechanisms of human disease. I would like to present the knowledge representation we have been developing. I will mention preliminary results of work I am doing with Ignacio to validate the KG I created (paper being submitted by end of month).
      - Med2Mech - This work while similar to the work we did with HPO using lab tests, but we take it 1 step further going beyond manifestation in an effort to get closer to modeling mechanistic causation. I will present the preliminary results, which were presented at AMIA JS.

callahantiff / PheKnowVec

Project Meeting -- 07/01/2019 @ 16:00 #97