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 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. *See note below that it should not be part_of inflorescence, and it still needs an is_a parent (not enough to be part_of something).

• 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. 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'

Source: TAIR

These ones are pretty straightforward- we recommended to TAIR to move them all to the new term 'collective leaf structure' PO:0025022

Response from TAIR (Tanya Berardini 8/16/10): - suggestion is fine, annotations should move if replacement term is in OBO stanza- it is.

PO:0008037: seedling

• 16 annotations from 'po_anatomy_gene_arabidopsis_tair.assoc'

Source: TAIR

-Recommended to TAIR that they should be moved to seedling growth stage (PO:0007131) in PGDSO. Should they also belong to whole plant (PO:0000003) in PSO?

Response from TAIR (Tanya Berardini 8/16/10):- suggestions are fine, annotations should move if replacement term is in OBO stanza

Note: We cannot put in the consider link for this term as the seedling growth stage is in the PGDSO. These will have to be reassigned manually.

PO:0009003: sporophyte

• 1 annotation from: 'po_anatomy_gene_arabidopsis_tair.assoc'

Source: TAIR

-Recommended to TAIR that they should be moved to sporophytic growth phase (PO:0028002) in PGDSO. Should they also belong to whole plant (PO:0000003) in PSO?

Response from TAIR (Tanya Berardini 8/16/10): - suggestion is fine, annotation should move if replacement term is in OBO stanza

Note: We cannot put in the consider link for this term as the sporophytic growth phase is in the PGDSO. These will have to be reassigned manually

• 116 annotations from 'po_anatomy_gene_oryza_gramene.assoc' and 'po_anatomy_qtl_oryza_gramene.assoc'

Source: Gramene

Suggested that the associations for genes be moved to PO:0000003 whole plant, plus sporophytic growth phase (PO:0028002) for genes;

Seedling vigor QTLs are already associated with PO:0007131 seedling growth, suggested adding association to whole plant PO:0000003 as well, if appropriate

Note: We cannot put in the consider link for this term as the sporophytic growth phase is in the PGDSO. These will have to be reassigned manually

PO:0009004 gametophyte

• 1 annotation from 'po_anatomy_gene_oryza_gramene.assoc'

Source: Gramene

Suggested that this association be moved to male gametophyte (PO:0020091) or female gametophyte (PO:00290092) or to gametophytic phase (PO:0028003) and/or to to whole plant PO:0000003

Note: It is already associated with the megagametophytic stage (PO:000721) and pollen developmental stage (PO:0001007) in the PDGSO.

PO:0000056: floral bud

• 54 annotations from: po_anatomy_gene_arabidopsis_tair.assoc

Source: TAIR

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.

Resolution:

This was discussed at the 9-8-10 meeting. All those present felt it was preferable to keep the current structure for floral bud. For more detailed information and graphics, please see the [Summary of Changes] page

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 (can they be annotated to both axillary and terminal bud terms?), and also to find out the status of their annotation files.

Annotation File formats

We have had a question from Tanya Berardini@TAIR about whether or not we are planning to transition to the GAF 2.0 format or not.

GAF 2.0

This will affect how they modify the above files

Should we get one and test it first? Will it matter if there are some in GAF 1.0 and some in 2.0?

Maybe a goal for the next version?

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

-Legume terms submitted by Austin Mast

-New terms requested by reviewers (from Ahrestani and Kramer)

-is_a parents for remaining terms (will require work on upper level structure for non-material entities)

-convert to intersection_of relations?

-work on PGDSO

-tuber growth and development stages, open on SF since 6/2009

-add links to more images

-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

Upcoming meetings 2010-2011:

• Latin American Congress of Botany

LACB. La Serena, Chile, October 4-10;

Dennis is attending LACB. We will consider having a presentation at this meeting. Alejandra will not be able to attend.

* Infectious Disease Ontology Workshop

Dallas, Dec. 8th and 9th, 2010

Organized by Lindsay Cowall (Duke University) and others, under the auspices of the National Center for Biomedical Ontology. IDO Workshop December 2010. Note that relations between the IDO and other ontologies is one of their provisional goals.

Pankaj will represent the PO with regard to plant infectious diseases. This is especially relevant to the PO as infectious disease agents (viruses and bacteria) are widely used in plant genetic research.

For additional information on the IDO see http://www.infectiousdiseaseontology.org/Home.html

*Plant and Animal Genome XIX Conference

January 15-19, 2011 PAG 2011

Registration is open, abstract deadline Nov 1, 2010.

* International Botanical Congress (IBC2011)

July 23rd-30th 2011, Melbourne, Australia

Registration is open- deadline for abstracts: 31 October 2010, Important dates

Dennis and Alejandra are planning to attend IBC2011 and speak in other symposia.

Symposium proposal was accepted, 'Bio-Ontologies for the Plant Sciences' under the genetics, genomics and bioinformatics theme.

Ramona contacted the organizers about whether or not it is possible to get a room with Internet for outreach activities, but hasn't gotten a response yet. Is this something we still want to pursue?

Pankaj, Ramona, and Angelica Cibrian (Harvard and ANMH, Genomics of Seed Plants) are scheduled to give talks and must submit abstracts by October 31st. Three additional speakers will be chosen from abstracts that are submitted.

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