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PrioritiesSprint4.md

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These are the priorities for Sprint number 4, which runs from June 17, 2024 to July 19, 2024.

In this sprint, the builds are in these environments:

  • PROD: Octopus
  • TEST: Eel
  • CI: Fugu
  • DEV: Guppy

Each priority has a list of subtasks that are to be completed within this sprint.

Note that ARAs will be required to implement at least one of MCQ, Pathfinder, or LLM.

Develop Pathfinder Query

Pre-development work:

  • Develop automated tests

Fugu (CI) work:

  • Implement Constraints
  • Improve Results
  • Evaluate walltime performance and set goals

MultiCURIE Query (MCQ)

Pre-development work:

  • Develop automated tests
  • Develop Drug Side Effect Use Case

Fugu (CI):

  • ARA Implementation of Creative Mode
  • Improve KP results for Phenotypes to Disease
  • Implement Set IDs in NodeNorm

LLM Summarization

Pre-development work:

  • Experiment with and refine the summarization idea: Decide whether we will implement single-answer summarization, all-answers summarization, user querying over answers (RAG-like), or other approaches.

O&O Based grouping in the UI

Pre-development work:

  • User testing to determine effectiveness of chemical grouping based on ATC and Chebi roles
  • User testing to determine effectiveness of gene grouping based on Genetics KP Gene Sets and PFOCR

Fugu (CI):

  • Implementation of Gene Set grouping API (Genetics KP)

Display Full KL/AT in the UI

Pre-Development

  • Begin QA of KP implementation

Fugu (CI):

  • Remaining KPs implement KL/AT

Develop Automated Tests

Pre-Development

  • Add MVP2 tests to Benchmarking Suite
  • Implement automated tests for MCQ
  • Revise test cases based on ARA feedback

Fix Failing Automated Tests

Fugu (CI):

  • Each ARA is expected to pass 40 tests from the Sprint 4 test suite, which focuses on TopAnswer results.

Collect Feedback Issues

Eel (TEST):

  • Each team must perform manual testing of the Eel release in TEST and report issues to the Feedback repo between June 26 and July 3, 2024
  • TAQA will review and prioritize the discovered issues

Fix Feedback issues

Pre-development

  • Each team will review Feedback issues that they are responsible for and label them with either Eel, Fugu, Guppy, Hammerhead, or Phase 3, indicating the release in which a fix is expected.

Fugu (CI):

  • Each team will fix issues they own that are labeled with Fugu, and close the issue.

Eel (TEST):

  • Each team will fix issues labled with Eel, and close the issue. Eel fixes are reserved for high-priority show stoppers.

Technical Debt

Pre-development

  • Each team will assess technical debt items and create issues in their project repos tagged with "debt"
  • Each team will link each debt issue to a grouping issue in the Feedback repo based on the expected release in which the issue will be closed. (Fugu, Guppy, or Hammerhead)

Fugu (CI):

  • Each team closes Fugu debt issues

CLEAN-UP EFFORT: Documentation

Pre-development

  • Assess all documentation including (wiki pages, GH readme, GH pages, TRAPI docs, etc) and decide what requires effort in upcoming sprints.
  • For infores/wiki:
    1. get new UI MVP1/MVP2 dump from Andy;
    2. reconcile new dump with previous G-sheet and Infores Catalog;
    3. identify gaps in those primary knowledge sources that are being exposed via the UI in Octopus PROD release;
    4. highlight ARA wiki pages for review

Publications

Pre-development

  • Identify target journal
  • Form core writing team
  • Define scope of MS