Difference between revisions of "POC Conf. Call 9-15-10"

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(Created page with ''''POC meeting, Webex Conference Call; Date: Sept 15th, 2010 10am (PDT)''' In attendance: POC members: Absent: Collaborators: none Acceptance of the minutes from the …')
 
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Acceptance of the minutes from the 9-8-10 meeting?
 
Acceptance of the minutes from the 9-8-10 meeting?
 +
 +
 +
==Status and Update of Progress: PO Release==
 +
 +
 +
 +
 +
'''B.  Response emails'''
 +
 +
After the meeting po-discuss@plantontology was set up and the members of po-internal were added to it.  This is the address that will be used in the letters to the reviewers.  Thanks to Chris Sullivan and Justin Elser for helping with this on short notice.
 +
 +
Also, the feedback box on the beta browser will direct responses there
 +
 +
 +
 +
 +
(Note: We need to define the function of each of the mailing lists: po, po-dev, po-announce, po-internal).  I think po-announce, po-internal are fine, but what are the other 2 supposed to be for?
 +
 +
We all agreed (last week) that these need to be reviewed and we need to deal with the spam problem as well.
 +
 +
''No changes or actions taken.''
 +
 +
 +
=== Annotations that have no term associated with them===
 +
 +
-Laurel and Ramona compiled a list of the 10 terms that have been obsoleted and how many annotations that are associated with them.
 +
 +
There were only 10 and only 5 of them are problematic: floral bud, gametophyte, leaf whorl, seedling and sporophyte.  [[File:Obseleted_terms_(LC_8-10-10).pdf‎]]
 +
 +
''In progress....''
 +
 +
Laurel sent a spreadsheet to TAIR and Gramene listing the annotations that were affected on 8/13/10, with our recommendations or suggestions on where they should be moved to.
 +
 +
'''A.  TAIR'''
 +
- 8/13/10 message sent to Donghui, Kate and Tanya:
 +
 +
"The main issues are with the annotations associated with the following PO terms which were obsoleted in the beta version:
 +
 +
PO:0009003: sporophyte  1  (from: po_anatomy_gene_arabidopsis_tair.assoc)
 +
 +
PO:0000056: floral bud  54: (from:  po_anatomy_gene_arabidopsis_tair.assoc)
 +
 +
PO:0008037:  seedling 16  (from po_anatomy_gene_arabidopsis_tair.assoc)
 +
 +
The first three will need to be looked at to determine where to best put them.  We have put our recommendations or suggestions on the spreadsheet
 +
 +
 +
PO:0008034: leaf whorl  15,802: (from po_anatomy_gene_arabidopsis_tair.assoc) These ones are pretty straightforward- we recommend to move them all to the new term collective leaf structure PO:0025022
 +
 +
Spreadsheet: [[File:TAIR_dangling_annotations_(LC_8-13-10).pdf]]
 +
 +
 +
'''
 +
*Comments:'''
 +
Response from Tanya Berardini@ TAIR 8/16/10:
 +
 +
"Hi Laurel,
 +
 +
Thanks for the update and for the spreadsheet.  We should be able to handle the transition for the obsoleted terms pretty easily as we already have a mechanism set up for automated transfer of annotations from an obsolete term to a replacement term, if that replacement term is suggested in the OBO stanza. 
 +
 +
Comments:
 +
 +
'''(1) sporophyte''' - suggestions are fine, annotations should move '''if replacement term is in OBO stanza'''  (see below:)
 +
 +
'''(2) floral bud'''
 +
 +
Why was 'floral bud' removed as a parent term for both 'axillary floral bud' and 'terminal floral bud'? I'm not sure I understand why this potentially useful grouping term was deemed no longer useful.  I am not sure that we'll be able to move all our annotations to the more specific terms as the publications do not always specify whether axillary or terminal flower buds were used or whether the DNA/RNA/protein sample was obtained from a mixture of both.
 +
 +
'''(3) seedling''' - suggestions are fine, annotations should move if replacement term is in OBO stanza
 +
 +
'''(4) leaf whorl''' - suggestion is fine, annotations should move if replacement term is in OBO stanza
 +
 +
When do you anticipate the public release of the new version of the PO vocabularies?  We will monitor the annotations that we have to the terms that you highlighted to make sure that the appropriate transfers and updates occur.
 +
 +
Thank you for your help,
 +
 +
Tanya"
 +
 +
Laurel replied and provided more  explanation and invited her to review that section and possibly attend the conference call.
 +
 +
 +
 +
'''B.  Gramene'''
 +
- 8/13/10 message sent to gramene@gramene.org contact email.  Ken replied and said that Pankaj was the best person to look at these.
 +
 +
[[File:Gramene_dangling_annotations_(LC_8-13-10).pdf‎]]
 +
 +
''
 +
 +
 +
'''C. Issues Arising:'''
 +
 +
'''*Changes to the annotation files:'''
 +
 +
- what is the mechanism for making these changes? Are we doing them here or is TAIR/Gramene going to send us new files? 
 +
 +
 +
See comments from CM about replacing the terms: 
 +
On Aug 17, 2010, at 6:51 AM, Walls, Ramona begin_of_the_skype_highlighting    end_of_the_skype_highlighting wrote:
 +
> We have put the replacement terms in the obo stanza as "consider" terms for all of these (check on this)
 +
 +
>>CM: note that where the replacement is clear you can use replaced_by - 
 +
this means the replacement can happen automatically without a human  having to make a choice
 +
 +
- Is there a script for making the changes?  Does this apply to the annotation files or just the OBO files?
 +
 +
 +
'''*sporphytic phase and gametophytic phase '''
 +
 +
> RW: in several cases (sporphytic phase for sporophyte, gametophytic phase for gametophyte, and seedling growth stage for seedling),
 +
we cannot currently add the 'consider' term to the po_anatomy_test file because the consider terms are in a different file (po_temporal_test). Probably the easiest way to solve this would be to merge the two files before the live release.
 +
 +
 +
'''*Do we want to do the merge before the release?? it seems like this should have been done before sending out to the reviewers.''' 
 +
We do not want to delay the process any further-
 +
What are other options?
 +
 +
CM: As an interim strategy you could embed the id in the comments using a standard syntax, then parse the tags out once you merge files.
 +
 +
What about a "bridge file"  We have discussed this in the past but have not implemented it.
 +
 +
 +
'''*floral bud'''
 +
 +
> > 2. Based on the response from TAIR (see above), we may want to reconsider obsoleting the term floral bud. Perhaps keeping this term for users is more important that getting rid of it to solve an ontological problem (term have multiple parentage).
 +
 +
 +
CM: Multiple Inheritance isn't an ontological problem, it's an engineering problem for you, in that manually maintaining MI is tedious and error prone. You should move to towards using the reasoner to infer all these, but in the meantime your asserted links /must/ reflect the biology, which in many cases means asserting MI.
 +
 +
''Those present at the meeting felt it was preferable to keep the current structure for floral bud. We were concerned about instituting a policy of changing the ontology here and there to fit the convenience of individual users, unless the change is biologically appropriate. Laurel will follow up with TAIR to see if they can work with the new structure for floral bud, and also to find out the status of their annotation files.''
 +
 +
''Barry described using axioms for terms with multiple inheritance, rather than using asserted relations. Not certain how this translates in OboEdit -- perhaps through the use of intersection of relations. There was a question of whether or not annotations would be passed on (to parent terms) using axiomatic relations -- no one knew the answer.
 +
''
 +
''Justin P. raised the issue that we should be mindful as to whether or not the utilities we use (like Amigo) will be able to support our future analysis needs (for example, implied relations do not show up in the Amigo browser).''
 +
 +
 +
'''D.  Resolution:'''
 +
 +
 +
''We still need to find out (maybe from Justin E. or Pankaj) what the procedure is for updating annotations before the release.''
 +
 +
'''A.  Feedback Box:'''
 +
 +
New link to [http://beta.plantontology.org:8080/db/feedback/send_feedback feedback box] on beta site- emails will go to '''po-discuss'''
 +
 +
*Laurel and Ramona are working on some changes to customize this with additional fields and boxes for more directed responses
 +
 +
 +
Note: It would be better if the feedback box could fill in the relative link automatically from the page.  Is this possible??
 +
"eg: Refer to URL:    http://www.plantontology.org/index.html "
 +
 +
''Apparently this got broken when it was moved to the new spot on the beta browser.  JE is looking at getting it to capture the url of the current page being viewed.''
 +
 +
 +
''No new news on this to report.''
 +
 +
 +
 +
 +
 +
 +
 +
Announcement for Plant Sciences Bulletin: Note: that this is not for the beta version but the live version due to the timing. Sent to PJ for review 8/12/10
 +
 +
Dennis will also send this to the BSA for posting on their website- but should wait to do this until after the release comes out~ mid September.
 +
 +
Ramona will follow up with Dennis and see what the status of this is.

Revision as of 20:02, 9 September 2010

POC meeting, Webex Conference Call; Date: Sept 15th, 2010 10am (PDT)

In attendance:

POC members:

Absent:

Collaborators: none


Acceptance of the minutes from the 9-8-10 meeting?


Status and Update of Progress: PO Release

B. Response emails

After the meeting po-discuss@plantontology was set up and the members of po-internal were added to it. This is the address that will be used in the letters to the reviewers. Thanks to Chris Sullivan and Justin Elser for helping with this on short notice.

Also, the feedback box on the beta browser will direct responses there



(Note: We need to define the function of each of the mailing lists: po, po-dev, po-announce, po-internal). I think po-announce, po-internal are fine, but what are the other 2 supposed to be for?

We all agreed (last week) that these need to be reviewed and we need to deal with the spam problem as well.

No changes or actions taken.


Annotations that have no term associated with them

-Laurel and Ramona compiled a list of the 10 terms that have been obsoleted and how many annotations that are associated with them.

There were only 10 and only 5 of them are problematic: floral bud, gametophyte, leaf whorl, seedling and sporophyte. File:Obseleted terms (LC 8-10-10).pdf

In progress....

Laurel sent a spreadsheet to TAIR and Gramene listing the annotations that were affected on 8/13/10, with our recommendations or suggestions on where they should be moved to.

A. TAIR - 8/13/10 message sent to Donghui, Kate and Tanya:

"The main issues are with the annotations associated with the following PO terms which were obsoleted in the beta version:

PO:0009003: sporophyte 1 (from: po_anatomy_gene_arabidopsis_tair.assoc)

PO:0000056: floral bud 54: (from: po_anatomy_gene_arabidopsis_tair.assoc)

PO:0008037: seedling 16 (from po_anatomy_gene_arabidopsis_tair.assoc)

The first three will need to be looked at to determine where to best put them. We have put our recommendations or suggestions on the spreadsheet


PO:0008034: leaf whorl 15,802: (from po_anatomy_gene_arabidopsis_tair.assoc) These ones are pretty straightforward- we recommend to move them all to the new term collective leaf structure PO:0025022

Spreadsheet: File:TAIR dangling annotations (LC 8-13-10).pdf


  • Comments:

Response from Tanya Berardini@ TAIR 8/16/10:

"Hi Laurel,

Thanks for the update and for the spreadsheet. We should be able to handle the transition for the obsoleted terms pretty easily as we already have a mechanism set up for automated transfer of annotations from an obsolete term to a replacement term, if that replacement term is suggested in the OBO stanza.

Comments:

(1) sporophyte - suggestions are fine, annotations should move if replacement term is in OBO stanza (see below:)

(2) floral bud

Why was 'floral bud' removed as a parent term for both 'axillary floral bud' and 'terminal floral bud'? I'm not sure I understand why this potentially useful grouping term was deemed no longer useful. I am not sure that we'll be able to move all our annotations to the more specific terms as the publications do not always specify whether axillary or terminal flower buds were used or whether the DNA/RNA/protein sample was obtained from a mixture of both.

(3) seedling - suggestions are fine, annotations should move if replacement term is in OBO stanza

(4) leaf whorl - suggestion is fine, annotations should move if replacement term is in OBO stanza

When do you anticipate the public release of the new version of the PO vocabularies? We will monitor the annotations that we have to the terms that you highlighted to make sure that the appropriate transfers and updates occur.

Thank you for your help,

Tanya"

Laurel replied and provided more explanation and invited her to review that section and possibly attend the conference call.


B. Gramene - 8/13/10 message sent to gramene@gramene.org contact email. Ken replied and said that Pankaj was the best person to look at these.

File:Gramene dangling annotations (LC 8-13-10).pdf


C. Issues Arising:

*Changes to the annotation files:

- what is the mechanism for making these changes? Are we doing them here or is TAIR/Gramene going to send us new files?


See comments from CM about replacing the terms: On Aug 17, 2010, at 6:51 AM, Walls, Ramona begin_of_the_skype_highlighting end_of_the_skype_highlighting wrote: > We have put the replacement terms in the obo stanza as "consider" terms for all of these (check on this)

>>CM: note that where the replacement is clear you can use replaced_by - this means the replacement can happen automatically without a human having to make a choice

- Is there a script for making the changes? Does this apply to the annotation files or just the OBO files?


*sporphytic phase and gametophytic phase

> RW: in several cases (sporphytic phase for sporophyte, gametophytic phase for gametophyte, and seedling growth stage for seedling), we cannot currently add the 'consider' term to the po_anatomy_test file because the consider terms are in a different file (po_temporal_test). Probably the easiest way to solve this would be to merge the two files before the live release.


*Do we want to do the merge before the release?? it seems like this should have been done before sending out to the reviewers. We do not want to delay the process any further- What are other options?

CM: As an interim strategy you could embed the id in the comments using a standard syntax, then parse the tags out once you merge files.

What about a "bridge file" We have discussed this in the past but have not implemented it.


*floral bud

> > 2. Based on the response from TAIR (see above), we may want to reconsider obsoleting the term floral bud. Perhaps keeping this term for users is more important that getting rid of it to solve an ontological problem (term have multiple parentage).


CM: Multiple Inheritance isn't an ontological problem, it's an engineering problem for you, in that manually maintaining MI is tedious and error prone. You should move to towards using the reasoner to infer all these, but in the meantime your asserted links /must/ reflect the biology, which in many cases means asserting MI.

Those present at the meeting felt it was preferable to keep the current structure for floral bud. We were concerned about instituting a policy of changing the ontology here and there to fit the convenience of individual users, unless the change is biologically appropriate. Laurel will follow up with TAIR to see if they can work with the new structure for floral bud, and also to find out the status of their annotation files.

Barry described using axioms for terms with multiple inheritance, rather than using asserted relations. Not certain how this translates in OboEdit -- perhaps through the use of intersection of relations. There was a question of whether or not annotations would be passed on (to parent terms) using axiomatic relations -- no one knew the answer. Justin P. raised the issue that we should be mindful as to whether or not the utilities we use (like Amigo) will be able to support our future analysis needs (for example, implied relations do not show up in the Amigo browser).


D. Resolution:


We still need to find out (maybe from Justin E. or Pankaj) what the procedure is for updating annotations before the release.

A. Feedback Box:

New link to feedback box on beta site- emails will go to po-discuss

  • Laurel and Ramona are working on some changes to customize this with additional fields and boxes for more directed responses


Note: It would be better if the feedback box could fill in the relative link automatically from the page. Is this possible?? "eg: Refer to URL: http://www.plantontology.org/index.html "

Apparently this got broken when it was moved to the new spot on the beta browser. JE is looking at getting it to capture the url of the current page being viewed.


No new news on this to report.




Announcement for Plant Sciences Bulletin: Note: that this is not for the beta version but the live version due to the timing. Sent to PJ for review 8/12/10

Dennis will also send this to the BSA for posting on their website- but should wait to do this until after the release comes out~ mid September.

Ramona will follow up with Dennis and see what the status of this is.

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