POC Conf. Call 9-22-10

POC meeting, Webex Conference Call; Date: Sept 22nd, 2010 10am (PDT)

In attendance:

POC members: Laurel Cooper, Alejandra Gandolfo, Dennis Stevenson, Ramona Walls, Pankaj Jaiswal.

Absent: Chris Mungal, Barry Smith, Justin Preece, Justin Elser

Collaborators: none

Acceptance of the minutes from the 9-15-10 meeting?

There were no additions, deletions or changes to the minutes of the last meeting.

Status and Update of Progress: PO Release

Flower (PO:0009046)

Proposed def'n (from 9/15/10 mtg): A determinate reproductive 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. May contain pistillode or staminode or other aborted organs that don't show up in mature form.

From SourceForge tracker: RW:Having the word reproductive in the definition is redundant, because it is already implied by the presence of a carpel or stamen. Also, some flowers are sterile, and not involved in reproduction. Instead we can keep the original comment: "The characteristic reproductive structure of angiosperms."

However, if we have add the term 'reproductive shoot system,' then it is appropriate to keep it in the name. We will add reproductive shoot system, and keep this wording.

DWS: Gnetum- does it have a stamen? Gnetum has filament with a microsporangium on the end, which fits our current def. of stamen. We should look at the definition of stamen. it needs to be specific to Angiosperms

Need: synonyms of flower: staminate or pistillate flower, double flower, perfect, imperfect, diclinous, monoclinous

secondary xylem (PO:0009046)

New proposed def: A portion of xylem tissue that develops from a vascular cambium.

Comment:It is absent in some dicots and most monocots; the "wood" of dicot angiosperm trees, shrubs, and lianas.

Exact synonym: wood

• From SourceForge tracker:

RW: Should also apply to gymnosperms. The comment has been reworded slightly to "It is absent in some dicots and most monocots. The "wood" of gymnosperm and dicot angiosperm trees, shrubs, and lianas".

This item is okay. Will accept on SF tracker.

basal root (PO:0025002)

Proposed def'n (from 9/15/10 mtg): A root that arises from a part of the hypocotyl.

We will deal with synonyms and child term (non-pericyclic basal root) of basal root in next round of revisions.

Adventitious root will be broad synonym of both basal root and shoot-borne root.

primary root (PO:0000042) to 'taproot'

Current def'n: A root that develops directly from a embryonic radicle. Tap root is given as a related synonym.

We will leave this as is for now. Tap root may be a type of primary root or may be an exact synonym. Will get more feeback from others.

Comment: Often is the central axis of the root system.

No changes to this item. Okay as is.

shoot-borne root (PO:0000042)

Current Def'n: A post-embryonic root that develops from shoot tissue. [source: GR:pj, TAIR:ki]

Hyphen was added to the name, as suggested.

• From SourceForge tracker:

RW: Adventitious root is already a related synonym of shoot-borne root in the PO. If we remove it, it won't show up in searches. Rather than removing it, I suggest following Rich's suggestion of making it a broad synonym of both shoot-borne root and basal root (it's okay for multiple terms to share a broad synonym).

Adventitious root will be broad synonym of both basal root and shoot-borne root. Last week we decided to put this on the list for the next round of discussions/revisions. It may need to be a term

subterranean tuber axillary shoot (PO:0025081)

Proposed def'n: An axillary shoot that develops from a subterranean tuber axillary bud.

New term for tuber sprout (exact synonym)

From 9-15-10 meeting: Can have 'swollen eye' as synonym of tuber axillary bud. (note there is no term 'tuber axillary bud', it should go on 'subterranean tuber axillary vegetative bud' or the new term 'subterranean tuber axillary shoot' ). We will ask Naama if it is more like a bud or a shoot.

Will add term subterranean tuber axillary shoot, with synonym sprout. Will not add swollen eye as synonym for now, until we hear from Naama where it should go (maybe broad synonym of both bud and shoot?).

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

(These two were never in the live version, so they were actually destroyed, not obsoleted)

PO:0009014 dermal tissue

PO:0008034 leaf whorl

PO:0008037 seedling

PO:0009004 gametophyte

PO:0009003 sporophyte

• PO:0000056 floral bud

• PO:0000057 inflorescence bud

• PO:0000058 vegetative bud

• These look like they are not going to be obsoleted after all (see below)

Only 5 of them are problematic: leaf whorl, seedling, gametophyte, sporophyte and floral bud* because there were annotations associated with them.

TAIR (Tanya Berardini 9/16/10): -suggested that we handle moving these annotations for now, since we want to include them in the new release.

Before the changes were made in the files, Laurel obtained up-to-date files from TAIR as the existing ones were 18 months old and committed them to the SVN. Note that the numbers of annotations has changed in this new version.

The indicated changes were made in the files and they were committed back to the SVN.

leaf whorl PO:0008034

• Annotations: 15,786, from 'po_anatomy_gene_arabidopsis_tair.assoc'

Source: TAIR

These ones are pretty straightforward- we decided at the 4-27-10 meeting that leaf whorl would be 'replaced-by' 'collective leaf structure' PO:0025022.

Annotations were moved to collective leaf structure' (PO:0025022) in 'po_anatomy_gene_arabidopsis_tair.assoc'

• Laurel also changed the consider relation to 'replaced_by 'collective leaf structure'(PO:0025022)' in the PSO.

seedling PO:0008037

• 53 annotations from 'po_anatomy_gene_arabidopsis_tair.assoc'

• 53 annotations to 'po_temporal_gene_arabidopsis_tair.assoc'

Source: TAIR

Annotations in 'po_anatomy_gene_arabidopsis_tair.assoc' were moved to whole plant (PO:0000003)in and also copied to the 'po_temporal_gene_arabidopsis_tair.assoc' and assigned to seedling growth stage (PO:0007131).

A 'consider' whole plant (PO:0000003) relation was added in the PSO. We did not use 'replaced_by as this might not appropriate in all cases.

This should be replacd_by, rather than consider. Need to investigate whether it is better to use replaced_by or to merge terms.

Seedling should be a narrow synonym of whole plant. We will need to work on the former part_of chidren of seedling (embryo axis and cotyledon) for the next round of revisions.

sporophyte PO:0009003

• 1 annotation from: 'po_anatomy_gene_arabidopsis_tair.assoc'

Source: TAIR

-One annotation in 'po_anatomy_gene_arabidopsis_tair.assoc' was moved to whole plant (PO:0000003) and also copied to the 'po_temporal_gene_arabidopsis_tair.assoc' and assigned to sporphytic growth phase (PO:0007131).

We have added the consider relation to whole plant in the PSO.

• 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, if appropriate.

The Gramene files are about a year old as well, Pankaj is checking on the Gramene files to see if there are more up-to-date ones.

gametophyte PO:0009004

• 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)Note: This appears to be an error and pollen developmental stage (PO:0001007) in the PDGSO.

Note: This annotation is concerning rice anthers so it should be moved to male gametophyte (PO:0020091) and to gametophytic phase (PO:0028003).

In the ontology, LC -Added replaced_by 'gametophytic phase' (PO:0028003)' comment -Added the consider 'whole plant'(PO:0000003) relation -Added consider 'male gametophyte (PO:0020091)' relation -added consider 'female gametophyte' (PO:0020092)'

Laurel is working on getting the updated files from Gramene, since the ones on the SVN are about 11 months old. See above.

floral bud PO:0000056

• 54 annotations from: po_anatomy_gene_arabidopsis_tair.assoc

Source: TAIR

In order to get a better understanding of the issue, Laurel went through the annotations associated with the term 'floral bud' and looked at each paper to see how they describe the plant tissue samples. Most of them refer to "floral bud", "flower bud", or simply "buds". In a few cases they seem to be referring to the whole inflorescence.

In light of this, we reopened the discussion of the bud structure and will reexamine these terms.

At the 9-15 meeting, We discussed of bud terms. Since all floral buds are at the end of a shoot (since they are determinate) they should all be terminal buds, but then those terminal buds can arise either at the end of a shoot or in an axil.

In response to the above concern: Rather than terminal and axillary bud being defined as being at the end of a shoot or in an axil, They can be defined as developing from the SAM or an axillary bud meristem. This way, a floral bud can be axillary or terminal, depending on whether it develops from an axillary bud meristem or an SAM, and you don’t have to worry about when a floral bud (or any other kind of bud) that develops in a leaf axil transitions from being axillary to terminal.

Below is a proposed version the PO branch for bud. Basically, this is the same structure as the original ontology, but with the new term reproductive bud as a parent of floral, inflorescence and strobilus bud. Also, new terms have been added for vegetative shoot system and reproductive shoot system, and new develops from relations have been added.

For easier viewing, here is the same structure, with only terms related to inflorescence bud:

In general, all were in favor of the proposed schema, but PJ felt that the develops_from relationship should be left off for now, until we have time to look in depth at the terms. We will need to consider if there should be terms like terminal flower and axillary flower, etc. to parallel the structure of bud. If so, then the develops_from relations should be at that level. DWS: We will also need to consider compound versus simple strobilus.

Annotation Errors

In the course of investigating where annotations for obsolete terms should be moved to, Laurel and Ramona came across several annotations that appear to be incorrect.

Laurel corrected any she ran across in the process of updating the files.

Is there a process for checking annotations or reporting incorrect annotations? maybe on the Feedback box?

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)

-add terms for non-angiosperm structures

-better organization of descendants of portion of plant tissue

-convert to intersection_of relations?

-Convert existing definitions to genus-differentia form?

-work on PGDSO

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

-add links to more images through PlantSystematics.org

-Others??- PJ: Lol and Ramona will focus more on adding annotations

-What is the target date for the next release?

Other Items

We have been contacted by Stefan Rensing, University of Freiburg, Germany

re: setting up an ontology for bryophytes with a focus on the model moss Physcomitrella patens.

Ramona and Dennis will respond to him. PJ: Should show him examples of papers that that study gametophyte or sporophyte in Physco and how that would be annotated.

We felt that the Amigo browser should be able to display obsolete terms that match search criterea, possibly as a search option. Laurel will post request on Amigo feature request tracker at Source Forge.

PO slims

GO includes reduced versions of their ontologies (Go slims) for some user groups. The slims are developed and maintained by the users, but publicly accessable as part of the GO flat file. We have one user group (TraitNet) that is interested in creating a PO slim. We should decide if we want to include that in the PO flat file, and if we want to have any other policies regarding slims. For example, GO also maintains a generic slim. Should we make something similar (especially as the PO gets more detailed and adds more taxon specific terms)?

Upcoming meetings 2010-2011:

• Phenote Meeting at OSU This week-

Thursday afternoon, Sept 23 Suzi Lewis, Chris Mungall and Nomi Harris will visit with Pankaj, Laurel, Justin P and Justin E.

• 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.

From last week: Lol and Ramona should plan on attending and meeting with collaborators. Set up a computer demonstration, and possibly a Phenote workshop. Perhaps Dennis and Alejandra could also attend, and we could all meet there. PJ is not attending as he is teaching.

* 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.

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

Next meeting scheduled for: Weds, Sept 29th, 10am PDT