POC Conf. Call 1-4-11

POC meeting, Webex Conference Call; Date: Tuesday Jan 4th, 2011 10am (PST)

In attendance:

POC members: Laurel Cooper (OSU), Ramona Walls (NYBG), Pankaj Jaiswal (OSU), Dennis Stevenson (NYBG), Justin Preece (OSU), Justin Elser (OSU), Maire Alejandra Gandolfo; (Cornell University),

Absent: Chris Mungall (Lawrence Berkeley National Lab) Barry Smith (University at Buffalo, NY),

Collaborators: None

Acceptance of the minutes from the POC Conf. Call 12-28-10? There were no additions, deletions or changes to the minutes of the last meeting.

Completion of Changes for the Next Release:

*Timeline and Plan for Upcoming Release:

- We completed all the changes discussed last week, and the merged plant_ontology.obo file was loaded on the *Beta* browser (Thanks Justin E!)

• Internal review before full release:

- Annotations that need to be moved:

- List of changes: Summary_of_Changes_to_PO_Jan2011 (still under construction)

-see also Jan 2011_Release_Page

List of things to fix:

*Beta browser is not working, so everyone in the group should go over file on dev brower before the release. RW will make final changes on Wednesday, then LC will put the file up on the dev browser for viewing after Wednesday afternoon.

DWS commented that we should review whatw e planned to do in the original grant proposal, and make sure we are not forgetting anything. All agreed it was a good idea and we will put it on the agenda for next time.

Issues arising from last week's meeting:

inflorescence and infructescence branch orders, secondary inflorescence

Should the sub-inflorescences that arise from the main inflorescence axis be named 'primary inflorescence' or 'secondary inflorescence'?

We decided it should be consistent with how we describe branching orders.

We don't have terms for different vegetative branching orders (outside the inflorescence), but the stem is defined as the primary (not zero order) axis of the plant, which makes the first-order branches secondary axes.

We do have terms for inflorescence branch orders:

inflorescence axis (PO:0020122): A shoot axis that is part of an inflorescence. [describes any order axis in an inflorescence]

inflorescence branch (PO:0009081): Any branch forming from the primary or the higher order inflorescence axis.

second order inflorescence branch (PO:0006321): Any branch forming from the primary or first order inflorescence branch.

third order inflorescence branch (PO:0006322): Any branch forming from the second order inflorescence branch.

• We don't have terms for 'first order inflorescence branch' or 'primary inflorescence axis', so it is unclear if the use of the phrase "first order branch" in the definition of second order inflorescence branch refers to the main axis or a branch from this axis.

This makes all of the definitions ambiguous, but since they have annotation attached to them, we cannot change them until it is clear what they mean.

• All of the annotations for 'second order inflorescence branch' are from QTL, and most of them are for genes called "primary branch" or "primary branch length"

• Most of the annotations for 'third order inflorescence branch' are for a gene called "secondary branch."

This suggests that they are using our term 'second order inflorescence branch' as the first branch from the main inflorescence axis and 'third order inflorescence branch' as the second order branch from the main inflorescence.

Here is an image we can look at for discussion purposes:

• Also need to add terms for infructescence axis and branches, in order to add a terms for "hand of fruit" (see Musa fruit terms).

• Proposed term names and definitions (may change, depending on resolution of inflorescence branch order names):

secondary inflorescence: A reproductive shoot system that is part of an inflorescence and has a parts a second order inflorescence branch and any shoot axes and flowers that arise from that branch. part_of inflorescence, has_part inflorescence branch, flower

secondary infructescence: A reproductive shoot system that is part of an infructescence and has as parts a second order infructescence branch and any shoot axes and fruits that arise from that branch. part_of infructescence, has_part infructescence branch, fruit

We agreed on the following naming convention:

inflorescence axis (PO:0020122) and inflorescence branch (PO:0009081) will remain as is.

New term will be added for first-order inflorescence axis (syn: primary inflorescence axis). This will be the main axis of the inflorescence (A in diagram). The penduncle is A up to the point where it branches. Need to redefine peduncle as a shoot axis where the transition from vegetative to reproductive growth occurs. All subsequent branches from the peduncle are reproductive.

Old term second order inflorescence branch (PO:0006321) will be renamed "second order inflorescence axis," defined as an inflorescence branch that branches from the primary inflorescence axis. It will have the exact synonym primary inflorescence branch, but also keep the old name secondary inflorescence branch as a related synonym, with comment that that was the old name.

Old term third order inflorescence branch (PO:0006322) will be renamed "third order inflorescence axis," defined as an inflorescence branch that branches from a secondary inflorescence axis. It will have the exact synonym secondary inflorescence branch, but also keep the old name third order inflorescence branch as a related synonym, with comment that that was the old name.

Inflorescence axes up to the ninth order will be named (create new terms). After the 9th order, will have a term for Nth order inflorescence axis.

Similar terms will be created for infructescence branches.

New terms for sub-parts of inflorescences or infructescences will be named "second order inflorescence" or "second order infructescene," to parallel the axes names. Definitions will be as above, except the phrase "has a parts a second order inflorescence branch" will be replaced by "has a parts a second order inflorescence axis."

Comment from RW after meeting: pedicel and paraclade should be moved from children of branch to children of inflorescence branch. Peduncle should be a child of shoot axis, not branch. Need to work on definition of peduncle.

Comment from Justin Preece (from chat): something to chew on: just have a single inflorescence branch term, and perhaps use a PATO xref term to represent DEGREE of ordinality (1st, 2nd, 3rd...Nth), and use that to characterize any annotations. what you lose with this approach is the ability to reason up and down the PO on the basis of ordinality parentage, but it's a cleaner way to represent an infinite number of ordinal inflorescence branches. it depends on whether the priority is annotative accuracy or reasoning capacity.

sensu terms

• RW replaced all of the ~80 term names that were structure (sensu Taxon) with Taxon structure. However, there were three terms that were obsoleted and replaced with new terms in November, rather than being renamed:

-floret (sensu Poaceae), floret meristem (sensu Poaceae) and gynoecium (sensu Poaceae)

Either we should unobsolete these terms and rename them or obsolete all the terms with sensu in their names. BS suggested that we obsolete and rename at the 10-26-10 meeting, but with ~80 terms, this might not be the best solution.

Also, as a test, gynoecium (sensu Zea) was made obsolete, because it is not different from gynoecium (sensu Poaceae). Perhaps it should be merged with gynoecium (sensu Poaceae instead).

Action:

We decided that there should be a page on the PO wiki (under developers guidelines) with "SOPs" or guidelines on when terms should be obsoleted, destroyed, or merged and the steps to take in each case.

Old terms [floret (sensu Poaceae), florest meristem (sensu Poaceae), and gynoecium (sensu Poaceae)] should be unobsoleted, then new terms (Poaceae floret, Poaceae floret meristem, and Poaceae gynoecium) should be merged with the old terms, so old number is primary number. Primary name will be changed to new names.

There was a general discussion of taxon-specific terms and subsets. We agreed that in principle they should use scientific rather than common names, and that subset names should agree with term names. This means, for example, that the subset for maize should be the subset for Zea mays spp. mays.

Also, since terms like "Zea anther" are referring only to anthers in Zea mays, and not in all Zea species, they should have names like "Zea mays anther." However, since we have on our agenda to try to get away from terms with taxon names in them, I (RW) will not change the names until we decide on a final policy on how to deal with these terms.

PJ suggested that all terms that are in the subset for maize or rice should also be in the subset for Poaceae. RW asked if Justin E or Justin P could write a script to do this automatically, as doing it manually is bound to miss some terms.

Action:

We had a further discussion of the method GO uses to associated terms with taxa. That method has the advantage of automatically including any term from a sub-clade in the set of terms for a larger clade. PJ asked how this information is encoded in the obo file.

LC posted a link to one of the GO-taxonomy papers in the chat:Deegan et al; 2010

RW forwarded an additional paper that describes the method.Kusnierczyk, 2008

• Elizabeth Arnaud confirmed we should use Musa as their terms encompass banana and plantain

TIPS proposal

An abstract/proposal was been submitted to Trends in Plant Science on Dec 31st, 2010. It was sent out to everyone by email.

Upcoming meetings 2011:

• Plant and Animal Genome XIX Conference January 15-19, 2011 PAG 2011

Laurel, Ramona, DWS and Justin Preece are attending. PJ will attend for the weekend only as he is teaching. Alejandra cannot attend.

PO Activities at PAG:

• Computer Demonstration: Ramona will present.

Saturday - Early Afternoon, January 15, 2011 -- 1:30 pm - 3:00 pm (third in series of seven)

Outline for PAG2011 Computer Demo

• Plant Phenotypes workshop and panel discussion: Laurel will present.

" The Plant Ontology: Linking phenotypes and genomics across plant taxa"

Sunday Morning, 16 January 2011 -- 8:00 am - 10:10 am

• PAG_2011_Collaborators_Workshop and meeting with collaborators

Sunday Late Morning:

Time: 10:30-1:00 pm (to include lunch, will wrap up in time to get to 1:30 sessions)

PO Workshop Reg'n site and Survey

• Poster: PO Poster Monday 3:00 pm - 4:30 pm

• Outreach Booth being organized by MaizeGBD- More info TBA

• Phenotype Ontology RCN Summit

The Phenotype Ontology RCN

February 25-27, 2010 at the National Evolutionary Synthesis Center in Durham, NC,

Laurel and Pankaj will be attending.

* International Botanical Congress (IBC2011)

July 23rd-30th 2011, Melbourne, Australia

Registration is open 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.

Pankaj will give the introductory talk on general use of ontologies, GO, genomics, etc, and Ramona will present the talk on the Plant Ontology. Abstracts have been submitted.

No additional abstracts were submitted for our proposal, and Angelica does not think she will be able to attend because of lack of funds.

Dennis will speak in place of Angelica. PJ invited two other speakers. Gavin Kennedy will talk about the ontology application in large scale phenomics projects. Rudi Appels will speak on crop genomics and phenomics. Ramona has contacted these speakers to get their information and abstract; waiting for responses from them.

We received permission to use the 6th time slot for a discussion session. PJ will lead the discussion.