POC Conf. Call 9-15-10

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

Items Arising from reviews, as of 9/8/2010: From Paula Rudell, Kew Gardens

Flower; PO: 0009046 [A heterosporangiate strobilus, typically consisting of androecium, gynoecium, usually surrounded by a perianth and borne on an axis or receptacle. ]

New SF tracker for this term flower

Proposed Def'n: A determinate shoot system that has as part at least one carpel or at least one stamen and does not contain any other determinate shoot system as a part. Comment: may be have as part one or more petals, sepals or tepals.

Last week's minutes stated this should be a 'child of shoot system', but it is part_of inflorescence, which in turn is part_of shoot system.

rest ok

• Also note that we need to add a inflorescence has_part flower (can't use flower part_of inflorescence, because not all flowers are part of an inflorescence).

From Farshid Ahrestani (Columbia, TraitNet) Ramona responded to him that we agree that the terms he requested should be added to the ontology, but due to time constraints, we will not be adding any new terms to this release, but we will aim to add them before the next release.

Rich Zobel (Root terms) We have an open term request root terms from Rich Zobel from last November.

Upper level term that need to be added: 'basal root' (along with its children 'internode root' and 'non-pericyclic basal root') Modification of 'shoot-borne root (PO: 0000042) and taproot/primary root (PO: 0000042).

It may be possible to incorporate these changes into this release, (depending upon the amount of discussion generated)? Should I open individual SF trackers for each of these?

Naama Menda (tuber terms) Waiting for response from her on these.

Alejandra will follow up with Gar Rothwell Waiting for response

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:

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

*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.

*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:

Other Items:

A. Feedback page on Beta site fixed

Justin Elser fixed refer_to_url variable on the feedback page for the beta site. It is now working from within the AmiGO browser. Now it will capture the url of the page the person is looking at. Thanks Justin!

B. 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~ end of September.

Ramona will follow up with Dennis after he gets back to see what the status of this is.

Next meeting scheduled for: Weds, Sept 22nd, 10am PDT