May 27th, 2010 8:30am (PDT) - Revision history

Cooperl: /* Other Items? */

2010-05-27T18:48:51Z

Other Items?

Cooperl: /* Discussion items: */

2010-05-27T18:48:39Z

Discussion items:

Cooperl: /* Discussion items: */

2010-05-27T18:47:55Z

Discussion items:

Cooperl at 18:44, 27 May 2010

2010-05-27T18:44:09Z

Cooperl at 18:22, 27 May 2010

2010-05-27T18:22:50Z

Cooperl at 18:17, 27 May 2010

2010-05-27T18:17:06Z

Cooperl: Created page with ' In attendance: == Discussion items: == '''1. Overview and introduction to the [http://soybase.org/ontology.php SoyBase Ontology]- Rex Nelson''' *Rex has re-named and re-numbe…'

2010-05-27T18:14:55Z

Created page with ' In attendance: == Discussion items: == '''1. Overview and introduction to the [http://soybase.org/ontology.php SoyBase Ontology]- Rex Nelson''' *Rex has re-named and re-numbe…'

New page

In attendance:

== Discussion items: ==

'''1. Overview and introduction to the [http://soybase.org/ontology.php SoyBase Ontology]- Rex Nelson'''
*Rex has re-named and re-numbered the soybean ontology. The prefix was changed back to "SOY" and the growth and development and trait ontology terms' accession number was changed to come after the whole growth terms.

* We need to check that the accession numbers that the PO Whole Plant Growth Stage Ontology have for soybean synonyms '''are unchanged''' and they refer to the proper terms.

'''2. List of terms to be added to the Trait Ontology from Rex'''

-Submit to [https://sourceforge.net/tracker/?func=browse&group_id=76834&atid=835557 TO SourceForge term request tracker]?

'''3. Possibility of hosting the SoyBase Ontology on the PO SVN.'''

We upload and store ("commit") all the ontology files in the svn repository on our server, instead of maintaining on our standalone machines. Every time we make a change it gets deposited back to the repository, so it will track the changes we just did. The link to the SVN can be accessed over the web anonymously, in addition to the command line via ssh/svn client.

For example, take a look at: [http://palea.cgrb.oregonstate.edu/viewsvn/Poc/trunk/ontology/OBO_format/po_anatomy.obo PO SVN]

We can help by creating a SOY or SoyBase directory under the
http://palea.cgrb.oregonstate.edu/viewsvn/Poc/trunk/ontology/collaborators_ontology/ for which you will have the read and write access and you will be the maintainer of it.

==Other Items?==

← Older revision		Revision as of 18:48, 27 May 2010
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	-Submit to [https://sourceforge.net/tracker/?func=browse&group_id=76834&atid=835557 TO SourceForge term request tracker]?		-Submit to [https://sourceforge.net/tracker/?func=browse&group_id=76834&atid=835557 TO SourceForge term request tracker]?
−
−	~~==Other Items?==~~

@@ Line 26: / Line 26: @@
 (Note: Is it important that the number is changed to SOY:0000001?- that number is currently 'Germination')
-*Add text to some of the term names thta currently consist of numbers only such as "SOY:0000403:m1-F0.1'
+*Add text to some of the term names that currently consist of numbers only such as "SOY:0000403:m1-F0.1'
-*Work to resolve the overlap between the plant structure Growth and Development Ontology and the whole plant Growth and Development Ontologies.
+*Work to resolve the overlap between the plant structure Growth and Development Ontology and the Whole Plant Growth and Development Ontologies.

@@ Line 11: / Line 11: @@
 *Rex has re-named and re-numbered the soybean ontology.  The prefix was changed back to "SOY" and the growth and development and trait ontology terms' accession number was changed to come after the whole growth terms.
 * We need to check that the accession numbers that the PO Whole Plant Growth Stage Ontology have for soybean synonyms '''are unchanged''' and they refer to the proper terms.
 *Terms in the SoyBase ontology should have a direct mapping to terms in the PO and or TO
@@ Line 18: / Line 17: @@
 see: [http://palea.cgrb.oregonstate.edu/viewsvn/Poc/trunk/associations/po_anatomy_gene_oryza_gramene.assoc?revision=760&view=markup PO_anatomy_Oryza QTL]
@@ Line 28: / Line 28: @@
 *Add text to some of the term names thta currently consist of numbers only such as "SOY:0000403:m1-F0.1'
 *Work to resolve the overlap between the plant structure Growth and Development Ontology and the whole plant Growth and Development Ontologies.
-'''3.  Possibility of hosting the SoyBase Ontology on the PO SVN.'''
+'''3.  Hosting the SoyBase Ontology on the PO SVN.'''
 We upload and store ("commit") all the ontology files in the svn repository on our server, instead of maintaining on our standalone machines. Every time we make a change it gets deposited back to the repository, so it will track the changes we just did. The link to the SVN can be accessed over the web anonymously, in addition to the command line via ssh/svn client.
@@ Line 40: / Line 36: @@
 For example, take a look at: [http://palea.cgrb.oregonstate.edu/viewsvn/Poc/trunk/ontology/OBO_format/po_anatomy.obo PO SVN]
-We can help by creating a SOY or SoyBase directory under the
+Laurel will create a SOY or SoyBase directory under the
 http://palea.cgrb.oregonstate.edu/viewsvn/Poc/trunk/ontology/collaborators_ontology/ for which you will have the read and write access and you will be the maintainer of it.
 ==Other Items?==

← Older revision		Revision as of 18:17, 27 May 2010
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		+	==POC-SoyBase Webex Conference Call, May 27th, 2010 8:30am (PDT)==
		+

	In attendance:		In attendance:

@@ Line 1: / Line 1: @@
 ==POC-SoyBase Webex Conference Call, May 27th, 2010 8:30am (PDT)==
 == Discussion items: ==
@@ Line 11: / Line 13: @@
 * We need to check that the accession numbers that the PO Whole Plant Growth Stage Ontology have for soybean synonyms '''are unchanged''' and they refer to the proper terms.
 '''2.  List of terms to be added to the Trait Ontology from Rex'''