RefG Bar Harbor May 20-21 2010: Difference between revisions
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* if you use external information (example-posum), then document it. | * 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 | * Chris- taxon triggers- while propagating, look at the taxon data to check which term is applicable for which species | ||
* Perhaps incorporate these taxon constraints into PAINT. | |||
==May 21th, morning== | ==May 21th, morning== |
Revision as of 15:23, 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.
Mike
Possible topics for discussion:
- Topology issues for FOXF1 (AN812) and FOXI (AN619) clades
- No lung-specific cilium terms. E.G.: GO:0042384 "cilium assembly" has a "sensory" child, but no lung, airway, epithelium, etc child. Possible issue for Foxj1. May also be an issue for gut cilia.
- Choosing structured notes vs. specific GO terms: several SF items.
- Can the notes be used in PAINT?
- https://sourceforge.net/tracker/?func=detail&atid=1040173&aid=2997217&group_id=36855 . Should we use a lung-specific child term or an "in lung" note on the parental term?
- https://sourceforge.net/tracker/?func=detail&atid=1040173&aid=2998363&group_id=36855
- https://sourceforge.net/tracker/?func=detail&atid=1040173&aid=3000642&group_id=36855
- Scope of propagation: the FoxC1/C2 clade
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
- Perhaps incorporate these taxon constraints into PAINT.
May 21th, morning
PTHR10159
Pascale
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
- This meeting is the first result from a 'topic' approach to selection of ref genome target sets
- We want a method that results in a 'set' of annotations that could result in a 'story'with potential new information and 'publication'
- 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.