Difference between revisions of "POC Conf. Call 11-15-11"

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(Created page with ''''POC meeting, Webex Conference Call; Date: Tuesday Nov 15th, 2011 10am (PDT)''' In attendance: POC members: Absent: Collaborators: none Any changes or corrections (a…')
 
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Need to look at seed and leaf dev stages, see where trichomes will fit in; add tuber dev stages (under plant organ dev stage).
 
Need to look at seed and leaf dev stages, see where trichomes will fit in; add tuber dev stages (under plant organ dev stage).
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 +
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==Status of New Annotation Files for data release in Dec:==
 +
 +
This content below needs updating:  Copied from 9-27-11 meeting
 +
 +
===Physcomitrella Annotations===
 +
 +
From 9-20-11 meeting: PJ will reply to SR about the Physco annotations- re: they should be using the actual gene ids rather than the microarray probe ids''
 +
 +
What link do we need to use for these and how do we get AmiGO to recognize it?
 +
 +
Need to set up SVN access for SR or whoever will be sending the files.
 +
 +
''PJ will contact SR about the files''
 +
 +
===Gramene Annotations===
 +
Regarding the following tech section from today's mtg agenda:
 +
 +
Two of the Gramene dbxrefs in PO_DBXref.txt are not working:
 +
 +
GR: http://www.gramene.org/perl/protein_search?acc=P93436
 +
 +
GR_MUT: http://www.gramene.org/perl/mutant/search_mutant?id=GR:0060198
 +
 +
Don’t know if it is because the urls are wrong, or if it is because the ids are bad. If someone from Gramene can provide the correct urls, we can write new stanzas for the dbxref file.
 +
 +
 +
''JP hunted down the correct link templates and confirmed them with Ken:''
 +
 +
http://www.gramene.org/db/protein/protein_search?acc=# (e.g. P93436)
 +
 +
http://www.gramene.org/db/genes/search_gene?acc=GR:# (e.g. GR:0060198 ...yes, Ken says mutant searches should be processed via the gene search)
 +
 +
JP and JE and I will work to get these implemented in the AmiGO codebase. RW will update the xref file.
 +
 +
''New annotations should be coming from Gramene in the next 1-2 weeks''
 +
 +
===Grape and Strawberry===
 +
* LC working on grape file, see sample
 +
 +
* Strawberry is on SVN: [http://palea.cgrb.oregonstate.edu/viewsvn/Poc/trunk/associations/po_anatomy_gene_fragaria_jaiswallab.assoc?view=log strawberry]
 +
 +
What links do we need to use for these and how do we get AmiGO to recognize them?
 +
 +
''See notes above''
 +
 +
===Potato Annotations===
 +
 +
LC has been in contact with the group who published the [http://www.nature.com/nature/journal/v475/n7355/full/nature10158.html#/f4 potato genome paper] and they are interested in collaborating with us to assign ontology terms to the annotations.
 +
 +
From Dr. Richard Finker (Wageningen, The Netherlands):
 +
 +
"We are also interested to use trait ontologies to assist in candidate gene selection within regions of interest, I'm eager to discuss with you on the efforts of cross linking ontologies to biological relevant entities. e.g. a metabolite content trait to its e.g. chebi ontology ID, form which we could obtain info about the pathway."
 +
 +
''This will go in the next release, do they have expression data- RNA Seq?''
 +
 +
===Comments from PJ about Annotation Guidelines===
 +
 +
Ask MS if she can write up a small blurb on how she created the Maize annotations.  Maize probe ids => gene ids  methods and cut-offs, a guide for other collaborators and  a page for the info.
 +
Maybe co-author it with SR
 +
 +
-This will also be helpful when applying for new grants
 +
 +
-it would be helpful to have a detailed guide on our wiki for collaborators

Revision as of 19:32, 7 November 2011

POC meeting, Webex Conference Call; Date: Tuesday Nov 15th, 2011 10am (PDT)

In attendance:

POC members:

Absent:


Collaborators: none


Any changes or corrections (additions/deletions, etc) needed in the minutes from the POC_Conf._Call_11-8-11?

Back to POC Meetings Minutes


PGDSO revisions

sub-types of whole plant development stage: vegetative, reproductive, senescent, and dormant stages

Continued from POC_Conf._Call_11-8-11.

other gametophyte stages

proposed definition, gametophyte dormant development stage: A gametophyte development stage that has as a participant a whole plant during the interval between a suspension of physiological activity and the reactivation of physiological activity.

proposed definition, gametophyte vegetative development stage: A gametophyte development stage that succeeds spore germination and ends with the formation of gametangia.

proposed definition, gametophyte reproductive development stage: A gametophyte development stage that is initiated with the development of a gametangium and terminated with fertilization.

Comment: Some gametophytes may die before fertilization.

Plant structure development stages (other than whole plant)

Need to get these in order so we can deal with user requests.

Need to look at seed and leaf dev stages, see where trichomes will fit in; add tuber dev stages (under plant organ dev stage).


Status of New Annotation Files for data release in Dec:

This content below needs updating: Copied from 9-27-11 meeting

Physcomitrella Annotations

From 9-20-11 meeting: PJ will reply to SR about the Physco annotations- re: they should be using the actual gene ids rather than the microarray probe ids

What link do we need to use for these and how do we get AmiGO to recognize it?

Need to set up SVN access for SR or whoever will be sending the files.

PJ will contact SR about the files

Gramene Annotations

Regarding the following tech section from today's mtg agenda:

Two of the Gramene dbxrefs in PO_DBXref.txt are not working:

GR: http://www.gramene.org/perl/protein_search?acc=P93436

GR_MUT: http://www.gramene.org/perl/mutant/search_mutant?id=GR:0060198

Don’t know if it is because the urls are wrong, or if it is because the ids are bad. If someone from Gramene can provide the correct urls, we can write new stanzas for the dbxref file.


JP hunted down the correct link templates and confirmed them with Ken:

http://www.gramene.org/db/protein/protein_search?acc=# (e.g. P93436)

http://www.gramene.org/db/genes/search_gene?acc=GR:# (e.g. GR:0060198 ...yes, Ken says mutant searches should be processed via the gene search)

JP and JE and I will work to get these implemented in the AmiGO codebase. RW will update the xref file.

New annotations should be coming from Gramene in the next 1-2 weeks

Grape and Strawberry

  • LC working on grape file, see sample

What links do we need to use for these and how do we get AmiGO to recognize them?

See notes above

Potato Annotations

LC has been in contact with the group who published the potato genome paper and they are interested in collaborating with us to assign ontology terms to the annotations.

From Dr. Richard Finker (Wageningen, The Netherlands):

"We are also interested to use trait ontologies to assist in candidate gene selection within regions of interest, I'm eager to discuss with you on the efforts of cross linking ontologies to biological relevant entities. e.g. a metabolite content trait to its e.g. chebi ontology ID, form which we could obtain info about the pathway."

This will go in the next release, do they have expression data- RNA Seq?

Comments from PJ about Annotation Guidelines

Ask MS if she can write up a small blurb on how she created the Maize annotations. Maize probe ids => gene ids methods and cut-offs, a guide for other collaborators and a page for the info. Maybe co-author it with SR

-This will also be helpful when applying for new grants

-it would be helpful to have a detailed guide on our wiki for collaborators

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