using annotation to drive ontology development. comprehensive annotation can drive ontology...
DESCRIPTION
Middle of November: Decided to focus on genes having to do with blood pressure regulation We had three terms in the ontology To describe blood pressure regulationTRANSCRIPT
Using Annotation to Drive Ontology Development
Comprehensive Annotation can Drive Ontology Development
Blood Pressure RegulationReal-world Example
Middle of November: Decided to focus on genes having to do with blood
pressure regulation
We had three terms in the ontologyTo describe blood pressure
regulation
Next step-READ!
Used a standardmedical textbookto learn about the
physiology of blood pressure
December 1, 2005
Propose a basic structure in a SourceForge item
December 1-19,2005
Lots of DiscussionConsult outside experts.
December 19, 2005
Added 43 new terms
Harold adds the new termsAnd relationships to
The “live” GO.
December 20, 2005-, 2006Read Papers and Annotate Genes!
December 22, 2005- five new termsDecember 23, 2005- two new synonyms,
two new termsDecember 27, 2005- six new termsDecember 28, 2005- three new termsFebruary 27, 2006- seven new GO terms
Not all of these were about blood-pressure regulation, some of themwere needed to annotate genes that are involved in other processes
Annotating Papers Results In
Improvement in parts of the GO outside the area of focus– If the original first pass was good, most of
these are new leaf nodesMore genes than the initial set that have to
do with the process of interest.Annotations of genes to processes other
than the one of primary interest
Steps in Comprehensive Annotation
Identify papers
Read papers
Modify GOCurate papers
A BC
DE
Where are we now?The Good News
On December 1st-– 14 genes annotated to blood pressure regulation– 65 annotations to those genes
Two weeks ago– 23 genes annotated to blood pressure regulation– 264 annotations to those genes– 5 genes have all literature annotated
Other genes get annotated as papers get annotatedNot all annotations have to do with blood pressure!
Where are we now?The Bad News
There is still an outstanding Sourceforge
Item about the terms in this part of the graph
WHAT HAPPENED?
I short-circuited the process!
Steps in Comprehensive Annotation
Identify papers
Read papers
Modify GOCurate papers
A BC
DE
X
X
Why was the process short-circuitedThe ontology issues outstanding are
relatively minorI could still annotate papers as the
ontology stoodI felt that my time could now be spent on
annotations-I switched my primary role from an ontology developer to an annotator.
How can we prevent short Circuits?Clearly there has to be an assignment of
responsibility for the ontology development– The responsibility begins with expert curators
representing the biology– The responsibility continues with ontology developers
who must point out major logical issues• Major logical issues should be dealt with by expert curators
– Minor issues should be then addressed as concrete proposals by ontology developers
• Minor issues are either accepted or rejected by curators– Final decisions are made based on whether the
ontology represents the biology
A Proposal
Given that we plan to go the route of reference genome annotation, let’s try an experiment
Neurobiology Interest Group Meeting: June 14-15,2006
Focus on Central Nervous System Development
Identify Reviews That Will Serve as the First Step of Ontology Development
Use Reviews to Create the First Pass
Triage the Literature in the Reviews
This review cites 291 references!
What does triage mean?
Identify papers that are of useIdentify reference-genome organisms that
are studied in those papersIdentify genes that are in those papers
Assign Papers to Curation Team MembersCurators are responsible for fully curating papers
that are assigned to themCurators are responsible for adding to/modifying
the ontology as necessaryTrack progress of genes, annotations and termsCurators are then responsible for assessing the
completeness of gene annotation in their MOD.