Plant Ontology Webinar- May 2011 release - Revision history

Cooperl: /* 4. Q&A */

2011-07-19T22:21:02Z

4. Q&A

2011-07-19T22:18:13Z

4. Q&A

2011-07-19T22:01:29Z

4. Q&A

2011-07-19T21:59:36Z

4. Q&A

2011-07-19T21:54:52Z

4. Q&A

2011-07-19T21:11:00Z

4. Q&A

2011-07-19T21:10:29Z

4. Q&A

2011-07-19T20:59:50Z

4. Q&A

2011-07-11T18:57:55Z

2011-06-21T19:08:30Z

Navigating the PO

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 MH: Can you make links to gene expression data on GeneVestigator?  We are in touch with as GV as they use our terms.
-Gramene is collaborating with EBI Atlas project- [http://www.ebi.ac.uk/arrayexpress/ ArrayExpress]- Expression libraries and
+Physcomitrella is currently been incorporated in Genevestigator, so maybe the easiest thing to get the expression data into PO would to cross connect with them? Problem is that it is proprietory database.  Need to get the PO updated at GV.  PJ will contact them and see if we can get the terms updated.
 Us the webservices to display the expression data on the genome.

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 Sharing data with Gramene, as well- Gramene is hosting the Physcomitrella genome, as part of the collaboration with Plant Ensemble in Hinxton
-SR: Had contacted Plant Ensemble a few years ago, Gramene annotations of Physco are not coordinated with their group- concern that there will be more than 1 version out there.
+SR: Had contacted Plant Ensemble a few years ago. Gramene tried to do annotations/predictions of Physco are not coordinated with their group- concern that there will be more than 1 version out there. Physco annotations came from JGI, not the recent version.  PJ will help coordinate with the Gramene genome team and get the correct version.
 ==5. Outreach==

← Older revision		Revision as of 22:01, 19 July 2011
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	Sharing data with Gramene, as well- Gramene is hosting the Physcomitrella genome, as part of the collaboration with Plant Ensemble in Hinxton		Sharing data with Gramene, as well- Gramene is hosting the Physcomitrella genome, as part of the collaboration with Plant Ensemble in Hinxton
		+
		+	SR: Had contacted Plant Ensemble a few years ago, Gramene annotations of Physco are not coordinated with their group- concern that there will be more than 1 version out there.

	==5. Outreach==		==5. Outreach==

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 - SR: we are currently using GO for bias and cross-species analysis would like to annotate all data sets with the new PO terms.  Would like to expand to anatomy and developmental processes. So far the annotations are not being submitted to GO.
-May be able to display GO functions in the PO site as well at some point in the future.
+May be able to display GO functions in the PO site as well at some point in the future. Get the complete picture.
 ==5. Outreach==

← Older revision		Revision as of 21:54, 19 July 2011
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	-contributors are responsible for their own data updates, database is populated with a "snapshot" at the time of the release.		-contributors are responsible for their own data updates, database is populated with a "snapshot" at the time of the release.
		+
		+	- SR: we are currently using GO for bias and cross-species analysis would like to annotate all data sets with the new PO terms. Would like to expand to anatomy and developmental processes. So far the annotations are not being submitted to GO.
		+
		+	May be able to display GO functions in the PO site as well at some point in the future.

	==5. Outreach==		==5. Outreach==

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 -Functional annotations and expression profiling data are the logical place to start to link to the PO
--creation of mapping file
+-creation of mapping file has been mostly already done
 -annotate library, above the level of significant expresed

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 ==4. Q&A ==
-SR: Are there tools for creating annotations on a genome-wide scale or for large datasets?
+SR: Are there tools for creating annotations on a genome-wide scale or for large data sets?
-[http://www.taylor-design.com/textspresso/overview.htm TextSpresso]- Text mining tool
+[http://www.taylor-design.com/textspresso/overview.htm TextSpresso]- Text mining tool- need a library of gene names and symbols
 ==5. Outreach==

← Older revision		Revision as of 20:59, 19 July 2011
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	==4. Q&A ==		==4. Q&A ==
		+	SR: Are there tools for creating annotations on a genome-wide scale or for large datasets?
		+
		+	[http://www.taylor-design.com/textspresso/overview.htm TextSpresso]- Text mining tool

	==5. Outreach==		==5. Outreach==

← Older revision		Revision as of 18:57, 11 July 2011
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	Expertise: Physcomitrella genomics, Moss Ontology		Expertise: Physcomitrella genomics, Moss Ontology
		+
		+
		+	Link to ppt presentation:
		+	[[File:PO-Physco_Webinar_6_21_11.pdf]]
		+
		+	Streaming recording link: [https://ontology.webex.com/ontology/ldr.php?AT=pb&SP=MC&rID=54336702&rKey=38cc8899c41b7748]
		+
		+	Download recording link: [https://ontology.webex.com/ontology/lsr.php?AT=dw&SP=MC&rID=54336702&rKey=42d398c4f0781895]

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 =Navigating the PO=
+==Browsing and searching on AmiGO==
 ==Downloading the Ontology File==
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 *Commenting on current trackers
 =Important changes that had to be made to accommodate mosses and other non-angiosperm plants=