Content Meeting Participants Information: Difference between revisions

Latest revision as of 18:14, 22 April 2014

Grading of Options

 Quick and Easy

 Technical or Time-consuming

The Gene Ontology Project Website

http://www.geneontology.org/

Browsing GO

AmiGO

AmiGO is the GO Consortium Browser that allows you to view the gene ontologies and annotations online.

http://amigo.geneontology.org/cgi-bin/amigo/go.cgi

Recent tutorial:
http://www.geneontology.org/teaching_resources/tutorials/2006-03_pombe-workshop_AmiGO_jlomax.ppt

AmiGO Help Guide: http://www.geneontology.org/amigo/help-front.shtml

QuickGO

Another GO browser, is developed by GOA, the GO Annotation group affiliated with UniProt at the EBI in Cambridge, UK.

The browser can be found here:

http://www.ebi.ac.uk/ego/

This browser is similar AmiGO but is very fast, and has an easy-access graph view similar to the one we have already seen in OBO-Edit. You can also search annotations in QuickGO using UniProt identifiers.

Send Us Your Ideas

Option 1

You can send your ideas for new GO terms or annotations directly to us by e-mail:

Midori: midori at ebi.ac.uk
Jennifer: jdeegan at ebi.ac.uk

Or via the GO-Help system: go-help at geneontology.org

Option 2

Alternatively you can enter your suggestions in the online tracker systems which are linked from:
http://www.geneontology.org/GO.sourceforge.links.shtml

For Term requests use 'GO curator requests tracker'.
For Annotation ideas use 'GO annotation tracker'.

The advantage of using this system is that you can then easily take part in online discussions amongst the GO Consortium staff, and you will be automatically notified as terms are added.

OBO-Edit

The advantage of using OBO-Edit is that you can view and edit the ontology file that worked on at the muscle meeting long before our work is integrated into the live GO file. You can also carry out far more sophisticated searches than in the browsers above. The application is a little more time-consuming and technical to use than AmiGO as you have to download it and the ontology file. You also have do some installation and configuring if you want to use the graph view (shown above).

*All information on OBO-Edit can be found here: http://oboedit.org/
*Download: http://oboedit.org/docs/html/The_Graph_Viewer_Plugin.htm
*Getting started: http://oboedit.org/docs/html/Getting_Started.htm
*Help Guide: http://oboedit.org/docs/index.html
*Graphviewer setup guide: http://oboedit.org/docs/html/The_Graph_Viewer_Plugin.htm

Muscle meeting ontology file - The latest version is at the top of the list:

http://cvsweb.geneontology.org/cgi-bin/cvsweb.cgi/go/scratch/gene_ontology_cardio.obo

OBO-Edit tutorial in Italian:

http://www.geneontology.org/teaching_resources/tutorials/2007_08_Italian_oboedit_tutorial.pdf

The Teaching Resources Page

This page contains all of our recent teaching materials and so provides an easy way into learning about GO.
http://www.geneontology.org/GO.teaching.resources.shtml

@@ Line 1: / Line 1: @@
-This page gives some introductory information for content meeting participants who may wish to carry on looking at the ontologies and thinking about annotation after the meeting is finished.
+[[Category:GO Editors]]
+'''Grading of Options'''<br>
+ [[Image:star.png]] Quick and Easy
+ [[Image:star.png]][[Image:star.png]]
+ [[Image:star.png]][[Image:star.png]][[Image:star.png]] Technical or Time-consuming
-== AmiGO ==
-AmiGO is a browser that allows you to view the Gene Ontologies and annotations online.
+== [[Image:star.png]] The Gene Ontology Project Website ==
+http://www.geneontology.org/
+== Browsing GO ==
+=== [[Image:star.png]] AmiGO  ===
+[[Image:amigo.PNG]]
+AmiGO is the GO Consortium Browser that allows you to view the gene ontologies and annotations online.
 http://amigo.geneontology.org/cgi-bin/amigo/go.cgi
-There is a recent tutorial on how to use it available at:
+Recent tutorial:<br>
+http://www.geneontology.org/teaching_resources/tutorials/2006-03_pombe-workshop_AmiGO_jlomax.ppt
-[[Image:Amigo.PNG]]
+AmiGO Help Guide: http://www.geneontology.org/amigo/help-front.shtml
-== OBO-Edit ==
-This is a standalone programme that you can install on your computer. It is the programme that we used for editing the ontologies live at the content meeting so you will know it well. It is a bit more difficult to use than AmiGO but has the advantage that you can edit any ontology on it and that you can download and the view the latest version of the muscle meeting ontology file on your own computer.
+=== [[Image:star.png]] QuickGO  ===
-The file from the muscle meeting can be downloaded at:
+Another GO browser, is developed by GOA, the GO Annotation group affiliated with UniProt at the EBI in Cambridge, UK.
+[[Image:quickgo.png]]
+The browser can be found here:
+http://www.ebi.ac.uk/ego/
+This browser is similar AmiGO but is very fast, and has an easy-access graph view similar to the one we have already seen in OBO-Edit. You can also search annotations in QuickGO using UniProt identifiers.
+==Send Us Your Ideas==
+[[Image:star.png]]''' Option 1 '''
+You can send your ideas for new GO terms or annotations directly to us by e-mail:
+Midori: midori at ebi.ac.uk<br>
+Jennifer: jdeegan at ebi.ac.uk
+Or via the GO-Help system: go-help at geneontology.org
+[[Image:star.png]][[Image:star.png]] '''Option 2'''
+Alternatively you can enter your suggestions in the online tracker systems which are linked from:<br>
+http://www.geneontology.org/GO.sourceforge.links.shtml
+For Term requests use 'GO curator requests tracker'.<br>
+For Annotation ideas use 'GO annotation tracker'.
+The advantage of using this system is that you can then easily take part in online discussions amongst the GO Consortium staff, and you will be automatically notified as terms are added.
+== [[Image:star.png]][[Image:star.png]][[Image:star.png]]OBO-Edit ==
+[[Image:oboedit.PNG]]
+The advantage of using OBO-Edit is that you can view and edit the ontology file that worked on at the muscle meeting long before our work is integrated into the live GO file. You can also carry out far more sophisticated searches than in the browsers above. The application is a little more time-consuming and technical to use than AmiGO as you have to download it and the ontology file. You also have do some installation and configuring if you want to use the graph view (shown above).
+ *All information on OBO-Edit can be found here: http://oboedit.org/
+ *Download: http://oboedit.org/docs/html/The_Graph_Viewer_Plugin.htm
+ *Getting started: http://oboedit.org/docs/html/Getting_Started.htm
+ *Help Guide: http://oboedit.org/docs/index.html
+ *Graphviewer setup guide: http://oboedit.org/docs/html/The_Graph_Viewer_Plugin.htm
+*Muscle meeting ontology file - The latest version is at the top of the list:
 http://cvsweb.geneontology.org/cgi-bin/cvsweb.cgi/go/scratch/gene_ontology_cardio.obo
-The latest version is at the top of the list.
+* OBO-Edit tutorial in Italian:<br>
+http://www.geneontology.org/teaching_resources/tutorials/2007_08_Italian_oboedit_tutorial.pdf
+== [[Image:star.png]] The Teaching Resources Page  ==
-There is an OBO-Edit tutorial in Italian here:
+This page contains all of our recent teaching materials and so provides an easy way into learning about GO.<br>
-http://www.geneontology.org/GO.teaching.resources.shtml#tut
+http://www.geneontology.org/GO.teaching.resources.shtml
-(OBO-Edit tutorial<br>
-Erica Feltrin <br>
-University of Padova, Italy <br>
-Tutorial in Italian on using OBO-Edit)