Difference between revisions of "May 27th, 2010 8:30am (PDT)"
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*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. | *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. | ||
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* 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. | * 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 | *Terms in the SoyBase ontology should have a direct mapping to terms in the PO and or TO | ||
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see: [http://palea.cgrb.oregonstate.edu/viewsvn/Poc/trunk/associations/po_anatomy_gene_oryza_gramene.assoc?revision=760&view=markup PO_anatomy_Oryza QTL] | see: [http://palea.cgrb.oregonstate.edu/viewsvn/Poc/trunk/associations/po_anatomy_gene_oryza_gramene.assoc?revision=760&view=markup PO_anatomy_Oryza QTL] | ||
| + | *We need a mapping file that links the growth stages in PO to the more specific growth stages in SOYBase | ||
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*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 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. | *Work to resolve the overlap between the plant structure Growth and Development Ontology and the whole plant Growth and Development Ontologies. | ||
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| − | '''3. | + | '''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. | 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. | ||
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For example, take a look at: [http://palea.cgrb.oregonstate.edu/viewsvn/Poc/trunk/ontology/OBO_format/po_anatomy.obo PO SVN] | For example, take a look at: [http://palea.cgrb.oregonstate.edu/viewsvn/Poc/trunk/ontology/OBO_format/po_anatomy.obo PO SVN] | ||
| − | + | 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. | 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. | ||
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| + | '''4. List of terms to be added to the Trait Ontology from Rex'''- tabled for future discussions | ||
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| + | -Submit to [https://sourceforge.net/tracker/?func=browse&group_id=76834&atid=835557 TO SourceForge term request tracker]? | ||
==Other Items?== | ==Other Items?== | ||
Revision as of 18:47, 27 May 2010
POC-SoyBase Webex Conference Call, May 27th, 2010 8:30am (PDT)
In attendance: POC members: Laurel Cooper (OSU), Ramona Walls (NYBG), Pankaj Jaiswal (OSU), SOYBase members: Rex Nelson and David Grant-SOYBase, USDA-ARS, Ames, Iowa
Discussion items:
1. Overview and introduction to the 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.
- Terms in the SoyBase ontology should have a direct mapping to terms in the PO and or TO
- QTL associations can be uploaded (committed) to the PO SVN repository using the standard GO association format.
see: PO_anatomy_Oryza QTL
- We need a mapping file that links the growth stages in PO to the more specific growth stages in SOYBase
2. Suggestions for reorganization of the Soybean_Ontology:
-top level term " SOY:0000000:Soybean Growth and Trait Ontology V1.0" should be renamed " SOY:0000001:Soybean_Ontology" with three separate namespaces created under that using the Metadata/Namespace Manager in OBO-Edit. Lol and Ramona can assist with that is needed.
(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'
- Work to resolve the overlap between the plant structure Growth and Development Ontology and the whole plant Growth and Development Ontologies.
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.
For example, take a look at: PO SVN
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.
4. List of terms to be added to the Trait Ontology from Rex- tabled for future discussions
-Submit to TO SourceForge term request tracker?
