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).
*floral bud
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. Will correct seed coat p_o plant tissue and add wood as synonym for secondary xylem for this 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
-There are 10 terms that have been obsoleted from this version of the PO.
PO:0025003 compound plant organ
PO:0025002 simple plant organ
PO:0009014 dermal tissue
PO:0000057 inflorescence bud
PO:0000058 vegetative bud
PO:0008034 leaf whorl
PO:0008037 seedling
PO:0009004 gametophyte
PO:0009003 sporophyte
PO:0000056 floral bud
Only the last 5 of them are problematic: leaf whorl, seedling, gametophyte, sporophyte and floral bud.
PO:0008034 leaf whorl
Annotations: 15,802: (from po_anatomy_gene_arabidopsis_tair.assoc)
- These ones are pretty straightforward- we recommended to TAIR to move them all to the new term 'collective leaf structure' PO:0025022
PO:0008037: seedling
16 (from po_anatomy_gene_arabidopsis_tair.assoc)
-Recommended to TAIR that they should be moved to seedling stage. Should they also belong to whole plant (PO:0000003) in PSO?
PO:0009004 gametophyte 1 is directly on gametophyte, 40- female gametophyte and 12, 441 to male gametophyte.
Will have to check annotations to see if they belong to whole plant or gametophytic stage.
PO:0009003: sporophyte
1 (from: po_anatomy_gene_arabidopsis_tair.assoc)
*sporphytic phase and gametophytic phase
> We have put the replacement terms in the obo stanza as "consider" terms for all of these (check on this)
> 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).
PO:0000056: floral bud 54: (from: po_anatomy_gene_arabidopsis_tair.assoc)
Question from TAIR (Tanya Berardini@ TAIR 8/16/10) 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.
*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:
Priorities for the Next Round of Revisions
-Merging the plant structure and plant developmental stages ontologies
-Adding Musa terms requested by Rosemary Shrestha
-Root terms- Rich Zobel
-Others??
-What is the target date for the next release?
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.
C. POC meeting to be held at NYBG in fall 2010. Date TBD.
Should we invite outside experts, scientists, students and postdocs?
Please fill out Doodle Poll re. dates that you are or are not available: http://www.doodle.com/6n4pmknkeebk9khg
We need to pick a date for this meeting ASAP so folks who are flying in can get tickets
