A solution for finding an interesting set of publications based on enrichment analysis of the relationship between Genes and MeSHTerms using Chi-Square statistics. Built over publicly available datasets from NCBI and uses technologies Springboot, AWS batch, Docker, ECR, ECS, Spark, React, and Postgres.

1. Winnow
GeneFunctionNavigationMadeSimple
Pulkit Bhanot, Lila Mullany, Ed Santora, Mason Tan,
and Andrew Vennekotter

2. 01 BackgroundIntroduction to problem domain

3. HowGenesareRelatedtoDiseases
Transcription Translation Pathway Phenotype
DNA is transcribed
into RNA
RNA is translated
into protein
Proteins interact
within pathways
Pathways converge
in diseases

4. OrthologousGenes
● Orthologs are sequences in different
species that share a common ancestor
● Non-human species used for genetic
research, often before research is done
on humans; effects possibly comparable
to human
● Key starting point for the literature
review
Ancestral Gene

5. TypicalResearchProcess
Researcher enters
gene symbol on
NCBI Gene Database
GeneQuery
Link out to PubMed
and read
publications for gene
IdentifyPublications
Use MeSH annotations to
identify diseases; use
other genes to expand
analysis
Extrapolate
Compile a list of MeSH terms and
genes that are represented in
publications
IdentifyMeSHterms&Co-occurringGenes
Filter for species of
interest
IdentifyGeneRecord
0201 03 04 05

6. ResearchScale
● 30,000,000+ total publications in PubMed
● 27,044,830 total gene IDs on NCBI Gene
● 29,351 total MeSH terms
● BRCA1
○ 322 gene IDs; 16,892 publications
● GRM5
○ 352 gene IDs; 1,035 publications
● MeSH terms link genes to diseases
○ ~10-15 per publication: possibly thousands of disease associations per gene

7. WinnowConnectstheDots
Genes
Genetic information for various
species are stored, including gene
id, species, symbol, description,
etc.
MeSHTerms~Diseases
Medical subheadings (MeSH terms)
are standardized annotations assigned
to PubMed articles; give insight into
diseases
Publications
Publications are annotated with
MeSH terms and linked to genes via
the ‘gene2pubmed’ dataset
ConnectGenesto
Diseases

8. Demo
02

9. OurSolution 03

10. Winnow
A Web Application to
● streamline literature review process
● winnow down the set of useful relationships
Goal
● Automate all aspects: raw data → enrichment analysis
of NCBI Gene and PubMed datasets.

11. KeyAspects
DataQuerying&API
Data
Aggregation
Data
Analysis
DataCleaning
Data
Processing
● Process multiple formats from
multiple sources
● Remove discrepancies in data
● Select a statistical method
● Use complex filtering and
rollups at scale
● Simplify access to raw and
enriched data

12. Design04 Languages, platform,
infrastructure, tools, etc.

13. DataProcessingArchitecture

14. TechnologyStack
Aspect Choice
Language Java
Backend Framework Spring Boot
Front End UI React
Computation Framework Spark
Database Postgresql

15. DeploymentStack

16. 05
Development
ProcessChallenges, adaptations, and lessons
learned

17. ● Initial customer meeting, and once more with each milestone
● User requirements as user stories in Trello
● Planning poker for estimation and re-estimation
● Agile, one week sprint length, ~25 points/week
● Bi-weekly standing meetings
○ Sprint retrospective and planning on Saturdays
○ TA meeting on Wednesdays
● Stand-up via Slack 4x weekly
● Pair programming zoom meetings as needed
DevelopmentProcess

18. Estimation(BurndownChart)

19. NotableChallenges
DataIngestionTransformations
Custom marshalling and conversion
of attributes to ingest relationship
and varied data formats
DataComputation
Imprecision of computing large
factorials led to the use of Spark and
Pearson’s chi-squared test
MeSHTermTreeRecursion
Initial race conditions, difficulty
triggering page refresh

20. Tools
Aspect Choice
Environment Parity Docker, Test Data, Gradle
Version Control GitHub
Sprint Management Trello
Online collaboration Slack
Static Code Test SpotBugs
Code Coverage Jacoco
UI Testing Jest/Enzyme

21. Testing
06
Summary & Coverage

22. Unit&IntegrationTesting

23. CodeCoverage

24. UITesting

25. StaticCodeTesting

26. PerformanceTesting

27. LoadTesting

28. UserAcceptanceTesting
An iterative process of UI changes and bug fixes over several
days
Final customer acceptance on 12 May 2020

29. ● Links genes to diseases in a curated subset of
approximately 900,000 PubMed articles related to the
human genome and its orthologs
● Identifies genes co-occuring in publications
● Helps researchers expedite their literature reviews
● Helps researchers develop new hypotheses more
quickly
● Allows users to export the results of their searches
Winnow

30. CREDITS: This presentation template was
created by Slidesgo, including icons by
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THANK YOU
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