Cardiovascular physiology/development

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Introduction

The goal of this project is to improve the representation of cardiovascular and renal physiology in the GO.

Personnel

  • David Hill (GO)
  • Jen Clark (GO)
  • Judith Blake (GO)
  • Victoria Petri (RGD)
  • Mary Shimoyama (RGD)
  • Simon Twigger (RGD)
  • Diane Munzenmaier (MCW)
  • Mingyu Liang (MCW)
  • Ruth Lovering (UCL)
  • Kieth Dipetrillo (Novartis)

Requirements:

  1. Sample graphs will be made available in Mid May
  2. GO numbers used for this project: GO:0003008-GO:0003672
  3. Header for file originally used for edits:

format-version: 1.2
date: 25:04:2007 10:28
saved-by: dph
auto-generated-by: OBO-Edit 1.100
subsetdef: goslim_generic "Generic GO slim"
subsetdef: goslim_goa "GOA and proteome slim"
subsetdef: goslim_plant "Plant GO slim"
subsetdef: goslim_yeast "Yeast GO slim"
subsetdef: gosubset_prok "Prokaryotic GO subset"
default-namespace: gene_ontology
remark: cvs version: $Revision: 5.297 $

On 28th August the file was converted using OBO2OBO so the consider and replaced_by tags were parsed into comments.


Preliminary Meetings

  • April 26, 2007

Webex meeting (D Hill, S Twigger, M Shimoyama, D Munzenmaier, M Liang, V Petri)
This meeting was just to touch base and get overall impressions. The overall feeling was that the organization of the physiology nodes should be represented in a more organ/system view.

  • April 30, 2007

Face-to-face at MCW (D Hill, S Twigger, M Shimoyama, D Munzenmaier, R Lovering, V Petri)
During this 1-day meeting we added the term 'system process' to the graph and added the more global system processes under this node. In particular we added cardiovascular, renal and muscle processes. We rearranged some of the top levels of each of these nodes.

June 2007 Meeting Report

A 1.5 day meeting was held at the Medical College of Wisconsin to expand and refine the representation of blood pressure regulation in the Biological Process ontology. The meeting was attended by: Diane Munzenmaier, Kieth Depetrillo, Mingyu Liang, Simon Twigger, Mary Shimoyama, Jennifer Smith, Stan Laulederkind, Victoria Petri, Ruth Lovering and David Hill. The meeting was also attended virtually by Judith Blake and Jennifer Deegan.

The on-site personnel used Webex and Skype to communicate with the offsite attendees. Jennifer Deegan edited the ontologies live as discussion progressed. This was the first time we tried to have a virtual atendee at one of these meetings. The technology worked well. The only issue was the size of the room was too large for only one microphone. In the future, we might want more than one conference microphone attached in series. A large part of the reason why this worked so well was the help that RGD curators gave in prior technology testing. Jennifer Smith and Victoria Petri were particularly helpful in making several complete technical rehearsals with Jen Deegan and making sure the necessary technology was in place. The system would not have worked without this. Jen Deegan found remote editing very much better than on site editing as she lost very little normal work time other than the time when the meeting was actually going on. She needed about 4 hours for technical rehearsals before the meeting to make sure everything went smoothly, and then she was back to normal work straight after the meeting. Working a late shift (UK)presented no problem at all.

The meeting covered a review of previous changes to the 'regulation of blood pressure' portion of the ontology that had been made over the last few months based on face-to-face and virtual meetings. Since blood pressure regulation is a complex biological process, the GOC members stepped through the graph and elicited comments from the physiology experts about term relationships and definitions. Many of the current terms in the ontology were renamed to a string that was more "useful" for a physiologist. Definitions were also refined to more accurately reflect what the terms were meant to represent. The meeting itself focused mostly on the renal control of blood pressure, which was previously only minimally represented in GO. By the end of the meeting approximately 100 new terms had been added to the ontology and approximately 1200 edits were made to the ontology. The project is not complete and GOC curators are continuing to work from recommendations that were made by physiologists. Some major outstanding issues are the standardization of all term names and the addition of synonyms as well as the further expansion of some parts of the graph. The current graph can be found in the CVS scratch directory. As the graph is changed, CVS will be updated and graphical representations of the ontology will be posted on the MGI ftp site. We will continue to hold virtual meetings until the new version of blood pressure is committed to the Biological Process ontology.

For minutes of skype calls in the run up to the file commit to live please see http://wiki.geneontology.org/index.php/Muscle_Implementation_after_Content_Meeting


muscle and cardiovascular physiology commit