RefG Bar Harbor May 20-21 2010: Difference between revisions

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* 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.
* 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.
* Transcription factor activity part of the ontology is wrong. High priority.
* if you use external information (example-posum), then document it.


==May 21th, morning==
==May 21th, morning==

Revision as of 15:08, 20 May 2010

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.

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.