Agenda

Standing items

Was in a car accident; will need to minimize work load and screen time (emergencies only for now)
Should we put the next build (WS256) on hold? Probably not. OICR won't need to start the working on WS256 for ~4 weeks
Sibyl could possibly attempt to stage WS256, Juancarlos could provide assistance

Have had 2 meetings so far
Having some difficulty in defining the scope of user stories/use cases for the AGR portal
Also, not clear if there is a development group we should be immediately handing off use-cases to
We've done a cross-comparison of data presented on gene pages at each MOD
Started building wire-frame diagrams for the process of querying AGR on a gene and arriving at a gene page
We have identified several input/output pairs of data; input is what query is based on/seeded with; output is what data a user is attempting to retrieve
We are individually working on defining many user stories starting with different input data types
We will sort and prioritize the list of user stories and start developing use-cases for the top user stories
It may be best use of time to first outline what is on a gene page and how users would query for genes

2 meetings so far
What objects do people curate to?
What are the ontologies and controlled vocabularies that are used?
There's a mixed bag; group will work on defining standards that everyone can use
The Disease Ontology (DO) was decided to be a central ontology to use; some funding for DO in question
Mouse group has been working heavily with DO and OMIM
OMIM have their own curators and annotation style, not quite ready for receiving input from outside databases/groups
Discussing curation of NOTs; when a disease model might be expected, capture when it doesn't turn out to be

Only 3 members (PIs) up until this week; others joined this week
Currently working on defining canonical protein sets
Would use UniProt reference proteome; up to date for some organisms (yeast, fly, worm), not all (not mouse, zebrafish, rat)
UniProt working on getting up to date
Canonical zebrafish protein set defined by Ensembl/Havana(sp?)
Why doesn't UniProt have an up to date protein set for zebrafish?
Mouse: money/effort spent on curating protein sets for mouse at EBI; not clear how mouse databases (MGI) use the Ensembl data
Rat canonical protein set also not clearly defined in UniProt
Will learn more in upcoming meeting

What do we think about mapping sequence reads from these data sets?
We will try to incoporate all available data; some back log to work through
Each paper has their own pipelines/processes for analysis of data; how do we want to capture/accommodate this data?