RefG Bar Harbor May 20-21 2010

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Agenda

May 20th, morning

Introduction

  • 8:15 - 8:45 Arrive: coffee
    • Rm ERB 2535
  • 8:45 - 9:00 Welcome: Judy
    • Introductions
  • 9:00 - 9:30 Overview: Pascale
    • Description of the rationale and strategy for carrying out integrated biocuration projects

(see http://gocwiki.geneontology.org/index.php/Strategy_for_establishing_RefG_annotation_priorities)

How the GO represents lung branching morphogenesis

  • 9:30 - 10:15 David
    • Will include live review of GO structures in several areas
    • Including epithelial-mesenchymal transition

Seminar: Zena Werb

  • 10:30 - 11:30
  • CC Little Auditorium
  • '"Of mice and women: How studying mammary development gives us insights into breast cancer"


Rationale for target selection

  • 11:30 - 12:15 Target Selection: Carol
    • Review of basic biology involved in branching morphogenesis, specifically in the lung. .
    • Why/How was this particular set of genes chosen?
    • How do the selected targets relate to one another biologically? (viz. a diagram showing their relationships to one another)

Lunch 12:15 - 1:30 Roscoe's

May 20th, afternoon

Status of the completed MOD experiment-based annotations

  • 1:30 - 2:15 Li, wiki pages
    • Question from Mike L.: How do we interpret lung-specific annotations when it comes to propagating annotations to zebrafish?

Action item We need a lung page similar to the heart page.

Tree review: FOXF1A & related members

Mike

Possible topics for discussion:

Action Items:

  • Is there TPV for transcription factor complex? How are transcription factors represented in bacteria? Is there a mitochondrial TF complex?
  • Arjun's Q- how do you know a TF complex is in the nucleus. Arjun is questioning the experimental data. If there is inconsistency in the exp data, MikeL contacts the curators.
  • Hernan (KrasnowLab)-These are stronger inferences than based on Sequence similarity. Should you come up with a new evidence called 'Inferred from Phylogenetic analysis'? Good question.
  • Transcription factor activity part of the ontology is wrong. High priority.
  • if you use external information (example-posum), then document it.
  • Chris- taxon triggers- while propagating, look at the taxon data to check which term is applicable for which species, and if you find something new that is not already in the taxon file, feed it back to Chris.
  • Perhaps incorporate these taxon constraints into PAINT.

May 21th, morning

Tree review: DUSP6 & related members

PTHR10159

Pascale

Tree review: TAP2 & related members

Li


May 21th, afternoon

Summary

Paul

  • If this process is to be effective then what changes and improvements do we need to make?
  • File structure must be simpler for MODs to import (ie, not one GAF per family - but concatenate one file per MOD)
  • New evidence codes must be accepted
  • References must be publicly available
  • It must be clear what data each MOD needs to import
  • Reach out beyond MODs for importing PAINT-generated GAF files

Preparatory materials

Goals for this Meeting

  1. This meeting is the first result from a 'topic' approach to selection of ref genome target sets
  2. We want a method that results in a 'set' of annotations that could result in a 'story'with potential new information and 'publication'
  3. We want to evaluate confirm the PAINT Annotation process that generates inferential annotations based on the MOD experimental annotations

Background reading

  • PMID 18463632
  • PMID 16613830
  • PMID 17237346

Attendees

from away

  • Pascale Gaudet
  • Suzi Lewis
  • Mike Livstone
  • Paul Thomas
  • Chris Mungall
  • Rama Balakrishnan
  • Hernan Espinoza [Krasnow lab]
  • Arjun Guha [Cardoso lab]


local

  • Li Ni
  • Judy Blake
  • Carol Bult
  • David Hill
  • Mary Dolan
  • Randy Babiuk

others from Jax have been invited to attend as they wish.