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Welcome to
pombase-
preview.babraham.ac.uk/
New features
Arriving soon
Example pages
Feedback
Antonia’s poster P132
● New website pages & features to display existing content
● New displays from novel approaches to curation to build networks
Overview
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
Simplified
Removed unnecessary
infrastructure:
● Increased robustness
(fewer bugs)
● Easy to implement new
features
● Nightly updates
New Pages
Publication
Citation details
Attribution
Abstract
Annotation
New Pages
Genotype
Name(description)
Allele type, expression
Annotations, filters
● 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
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
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
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
Moving towards detailed
network displays
P
P P
P
P
Building Networks
Making
Connections
Making connections
between effectors and
substrates
(click the gene page
to play the movie)
Making
Connections
Processes and
Subprocesses
(click the gene page to
play the movie)
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)
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
Future
JBrowse
Protein feature viewer
New Query interface
Network viewer
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

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New PomBase website features

Editor's Notes

  1. Ensembl not a good fit for a model organism database
  2. Lists are getting long, cdc2 single allele 250 annotations to over 100 phenotype terms
  3. b
  4. b