The document discusses upcoming new features and pages for the Pombase website including publication details, genotype descriptions, phenotype annotations, and building curated networks that connect genes and gene products through their biological activities and processes to represent pathways in a visual format. It also outlines current limitations and plans to further develop network displays and features to better represent curated gene interaction and regulation data.

1. Welcome to
pombase-
preview.babraham.ac.uk/
New features
Arriving soon
Example pages
Feedback
Antonia’s poster P132

2. ● New website pages & features to display existing content
● New displays from novel approaches to curation to build networks
Overview

3. Current System
- Slow development
- Large Bug fix:New
feature ratio
- Long update cycle
Unnecessary
Architecture
Lots of “moving parts”
Large maintenance
Overhead (e.g. Drupal
web content management)
Redundancy

4. Simplified
Removed unnecessary
infrastructure:
● Increased robustness
(fewer bugs)
● Easy to implement new
features
● Nightly updates

5. New Pages
Publication
Citation details
Attribution
Abstract
Annotation

6. New Pages
Genotype
Name(description)
Allele type, expression
Annotations, filters

7. ● Single/Multi-allele
● Population/Cell
New Features
● Filter on term “class”
● Non redundant
annotation display in
summary view
(click the gene page to
play the movie)
Phenotypes

8. Building Curated
Networks
Traditionally annotations/gene/gene
pages unconnected.
We grouped gene products by common
activities and processes - accessible via
linked lists
e.g.
Pom1 protein kinase activity
Pom1 regulation of G2/M
Cdr2 protein kinase activity
Etc
But how these were connected
biologically was not evident

9. Pom1 Cdr2 Wee1 Cdc2
Cell size pathway
involved in negative regulation of G2/M
Pom1 ---------- Cdr2 Wee1 ----------- Cdc2
Cell size pathway
involved in positive regulation of G2/M
P
P
P
By capturing gene product
“inputs” and “outputs” we
can represent pathways
and processes as
biological network
diagrams.
Building Curated
Networks

10. Pom1 Cdr2 Wee1 Cdc2
Cdr2 Wee1
We now capture inputs and
outputs to provide
“functional” connections
between genes (pages).
PomBase is the first MOD
to make use of these
curated connections
between effectors and
substrates to build
networks.
Making Connections

11. Moving towards detailed
network displays
P
P P
P
P
Building Networks

12. Making
Connections
Making connections
between effectors and
substrates
(click the gene page
to play the movie)

13. Making
Connections
Processes and
Subprocesses
(click the gene page to
play the movie)

14. Currently generate networks
for GO slim terms only.
Will gradually fill in for all
terms with enough curated
data.
Add more notation.
(click the gene page to play
the movie)

15. Currently generate networks for
“GO slim” processes only
Future
● All processes
● Inhibition and activation
● Activities, modifications
(Annotation practice supports
this, we are working on the
display)
Future Displays
P
P P
P
P
P

16. Future
JBrowse
Protein feature viewer
New Query interface
Network viewer

17. Acknowledgements
Website Developer: Kim Rutherford
Curators: Midori Harris, Antonia Lock,
Jacky Hayles, Val Wood
The community curators (212 of you!)
PIs: Jürg Bähler, Steve Oliver