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Enhancing Biological Data Visualization with Vlad: A Directed Acyclic Graph Tool for MGI

Vlad is a novel Visual Annotation Display Tool developed to enhance the visualization of biological data, specifically involving Directed Acyclic Graphs (DAGs) in the Mouse Genome Informatics (MGI) context. Initially conceived to visualize MGI annotations against Gene Ontology (GO), it has evolved to support various applications. With its emphasis on user-friendly data display for curators, Vlad provides graphical representation of complex data through intuitive visualization. This includes color coding and node collapsing techniques to highlight significant biological features and facilitate deeper analysis.

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Enhancing Biological Data Visualization with Vlad: A Directed Acyclic Graph Tool for MGI

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  1. Vlad: A Visual Annotation Display Tool Joel RichardsonMouse Genome Informatics The Jackson Laboratory

  2. Directed (Acyclic) Graphs • Becoming commonplace • ontologies • gene families • strain histories • metabolic pathways • … • Need frameworks for dealing with them

  3. DAGs in MGI • MGI has general framework supporting: • DAGs with any kind of node • Vocabularies, which may have DAG structures • Annotations, associating vocabulary terms with objects such as genes • software infrastructure to support loading, querying, updating, etc. • Used for growing number of applications in MGI: • GO, mouse adult anatomy, phenotype ontology, etc.

  4. Vlad 0.1 • Visualization is an increasingly important theme • Vlad began as an experiment: • visualize MGI annotations against the GO • emphasis on data display, intended for users and curators of MGI • Vlad stands for VisuaL Annotation Display • implement in Python, use GraphViz • rough out an architecture for visualizing DAGs • Short talk presented at GO Meeting in Bar Harbor

  5. Visual Techniques • All intended to help focus attention on “hot” spots • All based on scores • Coloring (HSV) • nodes in a DAG have same color hue • intensity varies by score • Collapsing • draw more important nodes at full size, including labels and scores; • draw less important nodes as small circles • Pruning/abridging • remove uninteresting nodes • reattach unpruned descendents -> abridged edges

  6. Vlad 1.0 • Differences: • reimplemented in Java • not specific to MGI • annotations read from flat file - user chooses • GO structures read from MGI • added P-value scoring

  7. proto.informatics.jax.org • A new MGI web site • For deploying prototype tools, early access to upcoming releases, getting user feedback • Currently: • mockups of MGI 3.0 release • GO tools installed/developed by Mary Dolan • Vlad

  8. Demo

  9. Software Architecture • Directed graphs • Graph traversals and transformations • GraphViz interface • Support for DOT language constructs • Statistics • Specific “stylists” • Java/CGI

  10. Other Tools • GO::Term Finder • GO Miner • GenNav • Gene Ontology Tree Machine

  11. Similarities to GO::Term Finder • Computes P-values for annotations • Displays results as image and as table • Useful in contexts such as interpreting microarray results • Tools intended both as apps and as libraries

  12. Differences from GO::Term Finder • Supports raw counts • Doesn’t implement correction • More emphasis on the image • Not yet available for download • Web installation supports multispecies • Java vs. Perl • Architecture

  13. Vlad To Do (partial) • Finish adapting for stand-alone config • Make available for download • source code • shrink-wrapped app • Explore precomputing/caching to improve performance • Making results downloadable • Lots o’ tweaks

  14. Further Work • Adapt for doing cross-species comparisons • Apply infrastructure to build other analysis and visualization tools for MGI • e.g., expression data against anatomy

  15. Credits • MGI, especially: • Judy Blake • Carol Bult • David Hill • Harold Drabkin • Mary Dolan • Gary Churchill

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