POC Conf. Call 7-05-11

POC meeting, Webex Conference Call; Date: Tuesday June 14th, 2011 10am (PDT)

In attendance:

POC members: Laurel Cooper (OSU), Ramona Walls (NYBG), Pankaj Jaiswal (OSU), Barry Smith (University at Buffalo, NY), Justin Elsner (OSU), Justin Preece (OSU)

Absent: Chris Mungall (Lawrence Berkeley National Lab), Dennis Stevenson (NYBG), Marie Alejandra Gandolfo (Cornell University)

Collaborators: none

Acceptance of the minutes from the POC_Conf._Call_6-28-11? There were no changes, additions, or deletions.

Meeting with Morphobank this afternoon

Time: 2:30pmPT/ 5:30pmET/10:30pm England/11:30 Europe

The purpose of this meeting is to discuss potential collaboration between the Plant Ontology and Morphobank.

For more details, see meeting page: POC-Morphobank_Webex_meeting_07-05-2011

PO wants to develop a matrix of plant phenotype characters (character on Y axis, states on X axis), with ontologies integrated into character descriptions. Need tools to help people describe phenotypes. Should be useable by both taxonomists and people doing large-scale phenotype screens.

There was some discussion of how this project relates to PO collaboration with FNA, and their need for plant-specific characters from PO and PATO. Both FNA and taxonomic studies (like Morphobank normally deals with) have traditionally used free text definitions.

There was some discussion of working with PATO to incorporate new terms for plants. Georgios Gkoutos is doing the day-to-day operations of PATO. We need to work with him to make sure plants terms are represented correctly. He won't be at the ICBO meeting, but CM will be, and we could talk to him about it. BS also expressed concern about how large PATO is growing and the need for some modularization. We need to set up a meeting with Georgios.

We can at least associate to PATO at a coarse level (e.g., to shape or size), even if we can't have the specific types of shape or size descriptors we need.

Action items:

Set up meeting with Georgios Gkoutos to discuss PATO

In the meantime, we need to start compiling a list of characters people will need.

PJ will start collecting terms and definitions over the next few months. We can also contribute to upper level of PATO. BS will assist working on a possibly a new branch of the PO utilizing the upper level PATO

All of our phenotype characters should have an xref to PATO. Upper-level PATO must be organism-neutral.

Compliance with OBO Foundry guidelines

- All but 3 terms now have is_a parents. The last three will be dealt with when we restructure the PGDSO

- Restructuring of PGDSO should make PO compliant with BFO (see item below).

- need to double check that all terms have text definitions

PJ is working on this.

User requests, Plant Anotomy Ontology:

Legume terms submitted by Austin Mast

Several terms have already been dealt with (Taproot, Stem Hair, Prickles, Anther pore and anther slit).

Remaining:

fascicle

The term fascicle can refer to different structures in different taxa. Suggest we use the term floral fascicle or flower fascicle in this case, to distinguish it from a "leaf fascicle," which we may want to add for describing gymnosperms.

From Tucker, 2003, Flora: (in the Papilionoideae) "Pseudoracemes (Fig. 5B) differ from racemes in that two to several flowers are initiated in each bract axil rather than just one as in a raceme. The cluster of flowers at each node is called a fascicle. The order of initiation among flowers at a node (Fig. 5B, Psoralea macrostachys DC) shows the fascicle to be a short shoot topped by a second order inflorescence apical meristem. This meristem initiates flowers in a bilaterally symmetrical order: a single abaxial flower, then two lateral flowers, another median abaxial, then two more laterals. The number of flowers per fascicle depends on the duration of the axillary inflorescence apex of the short shoot, which ceases activity after initiating the few flowers in the fascicle. No flowers are initiated adaxially (toward the first order axis) on the short shoot (Tucker, 1987b; Tucker and Stirton, 1991). The short shoot in a pseudoraceme can be distinguished from a cyme in that every flower is bract subtended in a pseudoraceme."

Proposed def: A reproductive shoot system that is a second or higher order inflorescence in which the second or higher order inflorescence branch bears two or more flowers but is not elongated.

Comment: A fascicle appears to be a cluster of flowers in an axil of a single bract of the main inflorescence. Fascicles are common in some sections of the Fabaceae, where they are second order inflorescences.

is_a reproductive shoot system, part_of inflorescence

Okay to call it a floral fascicle. Definition is okay. This is similar to the description of a hand of fruit which is a second order infructescence.

phyllode

Proposed def: A leaf in which the laminar development is a median plane (perpendicular to the axis), rather than the more common state of in a transverse plane (tangent to the axis).

Comment: Lamina development in a phyllode may occur in the region of the leaf that would normally develop into a petiole. In some leaves, the petiole may twist giving the appearance that the lamina is a phyllode, but it is not.

See references by Boke 1940 (http://www.jstor.org/stable/2436690, DOI:10.2307/2436690) and Kaplan 1970

How to cite articles without a PMID? Can we use DOI?

Unifacial leaf as synonym? Not the same, but similar development.

Okay to use DOI as a dbxref, but need to check with GO to make sure it is in the dbxref database, or request it.

Should be a child of vascular leaf, rather than leaf.

We looked at examples of leaves where the petiole is a phyllode, but there is lamina development (with leaflets) beyond the lamina. In this case, the phyllode only represents the petiole portion of the leaf. We need a term to describe this, as well as when the whole leaf develops as a phyllode. Revisit this next week.

 The rest of these items were tabled for next week...

banner, wing and keel

reference: Lawrence, Taxonomy of Vascular Plants (1955)

Banner (as in a legume flower) - suggest using name banner petal

Proposed def: A petal that is the top-most petal of a papilionaceous corolla.

Comment: Usually larger than the adjacent wing petals. Found in the flowers of some Fabaceae.

Synonyms vexillum (exact), standard (broad)

Wing (as in a legume flower) - suggest using name wing petal

Proposed def: One of two lateral petals that is adjacent to the banner petal of a papilionaceous corolla .

Comment: The wing petals are usually much smaller than the banner petal and the corolla keel. Found in the flowers of some Fabaceae.

Keel (as in a legume flower) - suggest using name corolla keel and adding term for keel petal.

Two new terms:

corolla keel: A boat-shaped collective phyllome structure that consists of the two lowest petals of a papilionaceous corolla.

Comment: The two petals of the keel are often fused at the apex and free at the base. The keel projects toward the front of the flower. Found in the flowers of some Fabaceae.

is_a collective phyllome structure, part_of corolla

keel petal: A petal that is one of the two lowest petals of a papilionaceous corolla.

Comment: The keel petals are usually larger than the adjacent wing petals. They are often partially fused to each other. Each petal is shaped like half a boat and projects toward the front of the flower.

bristle

More complicated, because it is a phenotype term, and applies to structures other than stipules.

Will discuss at a future meeting.

TraitNet requests:

postponed for a future meeting

root terms submitted by Rich Zobel (Nov 2009)

postponed for a future meeting

Tech issues

Getting Spanish Synonyms into the Plant Ontology File

-JE has gotten the script to work to integrate the list of Spanish synonyms into the plant_ontology.obo file

Some of these are duplicates, because they represent a live and an obsolete term. These are not a problem.

RW will review these synonyms with MAG to determine if any of them should be changed. See updated list at duplicated Spanish synonyms May2011.

There are a couple of other issues I still need to work out, and haven't tested the Japanese translations, but it should be the same as the Spanish, so I am not too worried about it. (JE)

The Japanese synonyms will stay in the main PO file, then we can strip them out when we go to load it onto AmiGO (rather than maintaining a separate file for Japanese users, as we discussed earlier). JE will try putting them in the file, and see if there are any problems.

• Status update:

RW and MAG are planning to go over list of duplicate synonyms tomorrow.

Will get back to Justin with answers.

Problem with how annotations move through relations

-LC contacted TB at TAIR to let her know we are working on it. They said thought that we had a good plan in mind and appreciated the updates.

TB thought that it would helpful tothem if we just provided the ontology file (without the extra relations) on our SVN for use on their system.

• Status update:

RW added a file to the SVN (tags/live) called "plant_ontology_assert_basic.obo". This is the same as plant_ontology_assert.obo but with only the is_a, part_of and disjoint_from relations. Left in disjoint_from, because it doesn't seem to be causing any problems (Amigo ignores it and TAIR has never reported a problem with it in the past). Should we remove disjoint_from too?

We should take out disjoint_from relations as well. Although it doesn't cause problems with AmiGO, they may be problematic for other applications.

We should also create a "readme" file to the live folder, explaining what the different folders are. Also put this on the download page on the webiste. Every folder should have a readme file by default.

Publications

• Plant Physiology: RW and LC are working on a manuscript to submit to Plant Physiology. This will be a more detailed description of the changes made to the PO in the past year, focusing on restructuring of PAO . Will focus on how PO is now applicable to a wider range of plant species.

Please send comments by Wednesday night. LC and RW will review all comments, condense into one draft, and send it out again.

Agreed to use "type" and "term" in the way BS suggested based on the Hill et al. 2008 gene annotation paper.

• Short topics paper for American Journal of Botany

The editor of AJBOT asked Dennis to put together a short paper for them- can focus on PO. This would be consistent with the goals of the Phenotype RCN to reach out more to the botany community.

Upcoming meetings 2011:

• Botany 2011 Meeting [Botany 2011] St. Louis, MO at the Chase Park Plaza, July 9-13.

Societies participating: Society for Economic Botany, the American Fern Society (AFS), the American Society of Plant Taxonomists (ASPT), and the Botanical Society of America (BSA).

DWS is attending, but will not present. Many people from the BSA will be at the IBC meeting in Melbourne.

• ICBO 2011 Second International Conference on Biomedical Ontology

July 26-30, 2011 Buffalo, New York ICBO

-LC will present the PO on Friday July 29th, 3:30pm in the session: "Parallel Sessions on Special Topics: The OBO Foundry, featuring discussions of the Infectious Disease Ontology, the Ontology for Biomedical Investigations, the Ontology for General Medical Sciences and the Plant Ontology"

Link to program: [1]

LC is co-organizing the workshop "From Fins to Limbs to Leaves: Facilitating anatomy ontology interoperability" along with Melissa Haendel, Chris Mungall, Alan Ruttenberg, David Osumi-Sutherland.

Date: July 27 8.30am-4pm Facilitating Anatomy Ontology Interoperability

• Plant Biology 2011, Aug 6-10th, Minneapolis, Minn

Plant Biology 2011

Gramene and Plant Ontology are hosting a [Data Curation Workshop] again, focusing on pathway curations.

LC and PJ will present a PO poster.

TAIR (Kate Dreher) is organizing an Plant_Biology_2011_Outreach_Booth and we are invited to take part. We are hosting the website.

• International Botanical Congress (IBC2011)

July 23rd-30th 2011, Melbourne, Australia

Registration is open Important dates

Symposium 'Bio-Ontologies for the Plant Sciences' under the Genetics, Genomics and Bioinformatics theme, wiil be held on Thursday, 27 July, from 13:30 to 15:30.

Dennis, Alejandra, Pankaj and Ramona are planning to attend.

See IBC 2011 Bio-Ontologies Symposium wiki page for more details

• POC Meeting at New York Botanic Garden Tentative dates, Sept 9th-11th, 2011

DWS will look into booking the apartments at the NYBG for accommodations

More details TBA....