POC Conf. Call 12-1-10

POC meeting, Webex Conference Call; Date: Wednesday Dec 1st, 2010 10am (PST)

In attendance:

POC members: Laurel Cooper (OSU), Ramona Walls (NYBG), Pankaj Jaiswal (OSU), Dennis Stevenson (NYBG)

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

Collaborators: none

Acceptance of the minutes from the POC Conf. Call 11-17-10?

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

Priorities for next release- (from 10-13-10 Minutes):

Overall priorities for next two releases: completed is_a parents, restructuring of the PGDSO and the addition of non-angiosperm terms to the PSO.

Target date for next release: End of December (see below)

From PJ (10-13-10): Top priority for the short term (mid-December) should be addressing the term that are lacking is_a parents. This will require work on upper level structure for non-material entities.

-The longer term (mid-February) goal for the next release will involve restructuring of the PGDSO, but we should begin working on that now. The next revision with the completed is_a parents should be ready by early/mid December so release can go out before PAG in mid January. Then the longer term goal will be revision of the PGDSO upper levels to accommodate non-flowering plants.

We all agreed that these were still reasonable goals if we prioritize the terms and people follow and respond to the items on the SF tracker. RW and LC will be the only ones on the conference call next week. RW and DWS will discuss the terms that need to be focused on

Top Level PSO structure -- anatomical spaces, portion of plant substance, plant anatomical entity

Pores and anatomical space (Approval of changes from 11-5)

New top level term (sibling to plant structure) called plant anatomical space. This term would be parent to pore and slit. This would allow us to add new terms for slits or fissures as they come up.

Suggested definitions:

plant anatomical space: An anatomical space (CARO:0000005) that is part of a plant.

Ref. anatomical space (CARO:0000005): Non-material anatomical entity of three dimensions, that is generated by morphogenetic or other physiologic processes; is surrounded by one or more anatomical structures; contains one or more organism substances or anatomical structures.

We decided that we do not really need the terms 'pore' and 'slit' at this time. the definitions of their children will be reworded

Children of plant anatomical space:

• pore (PO:0025118): A plant anatomical space that is roughly circular and forms an opening in a plant structure.

• slitNew term,

proposed def'n: A plant anatomical space that is roughly linear and forms an opening in a plant structure.

This will allow us to create is_a parents for the following terms:

• micropyle (PO:0020025): "A small canal or opening through the integument(s) at the apex of an ovule." [APWeb:Glossary]

comment: In a mature seed the micropyle may remain visible as an occluded pore or may be obliterated. The micropyle originates as an opening in the integuments of an ovule through which the pollen tube usually enters the embryo sac. subset: reference

Suggested def: A pore that forms an opening in the integuments at the apex of an ovule. part_of integument. Comment: The micropyle originates as an opening in the integuments of an ovule through which the pollen tube usually enters the embryo sac. In a mature seed the micropyle may remain visible as an occluded pore or may be obliterated.

• seed micropyle (PO:0006334): "A pore on the seed coat which is a remnant of the ovular micropyle." [GR:pj]

relationship: develops_from PO:0020025 micropyle; part_of seed coat

Current definition is okay

• stomatal pore (PO:0008032): "The space of variable size controlled by stomatal guard cells in response to environmental clues." [GR:cwt]

synonym: "stomatal aperture" RELATED; relationship: part_of PO:0002000 stomatal complex

Suggested def'n: A pore in an epidermis, flanked by two guard cells. Comment: The size of the stomatal pore is variable and controlled by movement of the guard cells in response to environmental cues. part_of stomatal complex

• floral stomatal pore (PO:0008046): "The space of variable size controlled by floral stomatal guard cells in response to environmental clues." [GR:cwt] relationship: part_of PO:0008044 ! floral stomatal complex

Proposed def'n: A stomatal pore that is part of a floral stomatal complex. part_of floral stomatal complex

• stomium (PO:0020101): "A fissure or pore in the anther lobe through which the pollen is released."

[GR:pj] subset: reference, relationship: part_of PO:0005011 ! anther dehiscence zone

Proposed def'n: A slit in an anther lobe formed from when a dehiscence zone dehisces. Comment: Pollen may be released through the stomium. part_of anther

• anther pore (requested by TraitNet)

Proposed def'n: A pore at the apex of an anther. Comment: Pollen may be released through the anther pore. part_of anther

Plant body substance/portion of plant substance

Last week, we discussed adding a new upper level term for plant body substances. Perhaps a more consistent name would be portion of plant substance.

Possible children: Latex, xylem sap, phloem sap, resin, mucilage, oil, cuticle, cutin, sporopollenin.

We can add the upper level term now, but suggest waiting to populate it, as this is not a priority for this release.

Suggested definition: plant body substance: A portion of organism substance (CARO:0000004) that is or was part of a plant.

Ref.: portion of organism substance (CARO:0000004): Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body.

All in agreement: but keep the name 'portion of plant substance', Dbx ref to CARO:0000004; RW will ask them to modify their def'n to include substances taken up from the environment

Anatomical entity

At the 11-10-10 meeting, Barry suggested that we have only two branches in the ontology (one for independent continuants and one for occuraents). Should we make a new top level term plant anatomical entity, which would be parent to plant structure, plant anatomical space, and portion of plant substance?

Suggested def: An anatomical entity (CARO:0000000) that is or was part of a plant. [source: CARO:0000000].

Comment: Includes both material entities such as plant structures and immaterial entities such as plant anatomical spaces.

We all agreed that this parent term was needed, to be consistent with other ontologies and have a top level parent terms for the PSO. PJ suggested CARO should not use the CARO:0000000 number;

Continuation of older agenda items (needed for terms without is_a parents)

Primordium, (approval of changes from 11-5-10)

At the POC meeting on 11-5-2010, we agreed to add the new term 'primordium', child of portion of plant tissue.

Proposed def: A portion of plant tissue that differentiates and develops from meristem tissue into a new plant structure.

There was some discussion of whether or not we should keep the comment "A visible primordium of an organ is the first distinct stage of the respective organ development.

Have deleted is_a relations between 'primordia' and the structures they develop into and replaced with develops_from relations (e.g., 'leaf' develops from 'leaf primordium').

Although we have the term 'adventitious root primordium', can’t add 'adventitious root' develops_from 'adventitious root primordium', b/c adventitious root is a synonym for several terms.

Also added new term: phyllome primordium, which is parent to leaf primordium, petal primordium, etc. Fine

Reworded the comment: The primordium is the first distinct form in the development of an organ.- to differentiate it from a process or stage.

Parts of root tip (continued from meeting on 10-26-10)

Proposed new parent term: root parenchyma (PO:0025095): A portion of parenchyma tissue that is part of a root system. all agreed

root cap: PO:0020123

original def: "A group of cells that covers the apical meristem of the root." [APWeb:Glossary], subset: reference

Suggest: is_a root parenchyma, part_of root tip

Proposed definition: A portion of root parenchyma tissue that is part of the root tip and covers the root apical meristem. Comment: Often composed of living and dead parenchyma cells. Protects the root apical meristem.

all agreed, accepted

central root cap: PO:0020130

original def: "The central part of a root cap in which the cells are arranged in longitudinal files." [GR:pj], synonym: "columella cells" RELATED [] plus columella root cap, relationship: part_of PO:0020123 ! root cap

Suggest: is_a root parenchyma, part_of root cap

Proposed definition: A portion of root parenchyma tissue that is the central part of a root cap in which the cells are arranged in longitudinal files.

all agreed, accepted

lateral root cap: PO:0020131

original def: "The part of the root cap that is parallel to the sides of the axis." [ISBN:0122151704], synonym: "peripheral cells" RELATED [], relationship: part_of PO:0020123 ! root cap

Suggest: is_a root parenchyma, part_of root cap

Proposed definition: A portion of parenchyma tissue that is part of a root cap and is parallel to the sides of a root axis. comment: This is the general term for the lateral portion of any root cap and not the term for a root cap of lateral root (PO:0003018) or lateral root cap of lateral root (PO:0003020).

Revised de'fn: A portion of root parenchyma tissue that is part of a root cap and is parallel to the sides of a root axis. all agreed, accepted

quiescent center: PO:0020149 part of: new children of portion of plant tissue

original def: "Hemispherically shaped aggregation of mitotically and metabolically inactive cells positioned behind the root cap." [ISBN:0122151704]

Suggest: is_a meristem, part_of root apical meristem

Proposed definition: A hemispherically shaped portion of meristem tissue consisting of mitotically and metabolically inactive cells that is part of the root apical meristem and is positioned behind the root cap.

revised def'n: A portion of meristem tissue that is part of the root apical meristem, consists of mitotically and metabolically inactive cells and is positioned behind the root cap.

Comment from DWS??

all agreed, accepted

differentiation zone: PO:0020135, alt_id: PO:0003002

original def: "The portion of the root located behind the elongation zone containing cells that are differentiating into their final form and function."

[GR:pj], subset: reference, synonym: "maturation zone" RELATED, synonym: "specialization zone" RELATED

Suggest: is_a cardinal organ part, part_of root

Proposed new name: root differentiation zone; Proposed definition: A cardinal organ part that is the part of a root and is located behind the elongation zone and contains cells that are differentiating into their final form and function.

Comment: Most of the primary tissues of a root mature in the differentiation zone. This zone is where root hairs are produced.

Could add new parent term "shoot axis differentiation zone" to be parent to this term and to stem internode differentiation zone (PO:0008042)

all agreed to the rename, accepted

elongation zone: PO:0020125

original def: "The portion of the root that includes small, densely cytoplasmic cells that are dividing and expanding in size." [GR:pj],

subset: reference, synonym: "region of cell elongation" RELATED, synonym: "region of radial enlargement" RELATED

Suggest: obsoleting this term, because the definition is wrong, and making a new term, root elongation zone;

is_a cardinal organ part, part_of root tip

root elongation zone: Proposed definition: A cardinal organ part that is part of a root that is located directly behind a root apical meristem, in which the cells are undergoing longitudinal expansion.

Comment: The elongation zone is only a few millimeters in length and is the only portion of the root in which cell elongation generally occurs. Root hairs are not yet produced in this region. Primary root tissue begin to differentiate in the root elongation zone.

all agreed to the obsoleting the term 'elongation zone' and creating a new term; 'root elongation zone'. accepted

Could add new parent term "shoot axis elongation zone" to be parent to this term and to stem internode elongation zone (PO:0008041)

all agreed, accepted

New from SF- Revisiting bract

bract should be a phyllome, not a leaf. We had revised the def'n [1]

Current def'n: A leaf, usually different in form from the foliage leaves, subtending a flower or inflorescence

SF Comment: This fits vascular bracts, so maybe should be a child of vascular leaf, but sometimes the term bract is used in bryophytes.

Bract is_a phyllome bract

Proposed new def'n: A phyllome, usually different in form from the foliage leaves, subtending a flower or inflorescence note: this should be modified to include bryophytes and gymnosperms

Revised new def'n: bract (PO:0009055) A phyllome, usually different in form from the foliage leaves, subtending a reproductive structure.

Revised new def'n: leaf (PO:0025034): A phyllome that is not part of a reproductive structure.

all agreed, accepted

Restructuring PGDSO for Occurents

Suggested New "working" Structure of the PGDSO:

• The root term, plant growth and development stage, would be replaced by 'plant life cycle process' (an "Occurrent").

LC, BS and RW met on 11-30 to discuss this restructuring, and changed the upper level term from plant life cycle process to plant process, plus several other changes.

The top level structure would have three branches, as below

None of the old term names or definitions have been changed yet, except to put (phase) on the end of some term names that did not have stage in their names.

Most of the terms from PGDSO went under plant structure development phase, but a few went under plant structure development process. In the case of seedling development (which went under plant structure development process) we added a new phase called seedling phase. Something like imbibition is not a phase, but a developmental process, so it went under plant structure development process. Could add a germination phase that begins with imbibition and ends with emergence of the radicle.

From last meeting:

-Add corresponding phases for each of the developmental processes.

For example: gametophytic phase corresponds to gametophyte development and leaf development phase could correspond to leaf development.

Then it would be possible to move the developmental processes to GO, but keep the phases in PO.

At the POC meeting on 11-10-10, we reviewed this proposed structure, and decided to experiment with how it will work for existing PGDSO terms. Barry suggested that his goal was to have all PO terms in one of two branches: plant structures (plant anatomical entity = independent continuant) and plant processes (plant life cycle process = occurent)

Lol and Ramona will work on moving all of the ~120 terms from the PGDSO into one of the three new plant life cycle process branches, to see where they can fit.

• Can delete existing relations for those terms, but will still be able to compare to old structure by comparing dev to live browser.

Note from BS: Keep in mind where there might be potential overlaps with the GO- we will need to figure out how to split the process terms, ie: will they reside in the PO or in GO? Make a list as we go along.

-Stage term names need to be rewritten as nouns, for example: "whole plant in the phase where 1 leaf is visible

-Complex terms could be rendered using post coordination; ie: 'on the fly' for users, but some may need to have actual PO IDs in order to accommodate annotations.

changes in new PGDSO version

Collaboration with Physco group to cover mosses in PO

Email from Stefan Rensing:

"We have now completely reworked the mapping of bryophyte terms to the new version of the PO. We would be happy to make this mapping available to you on the condition that we will be co-authoring the eventually resulting publication. Would that be ok for you?

Of course, we are willing and interested to continue discussion on this topic, e.g. on how to broaden term definitions that to our opinion are currently too narrow to accommodate bryophytes."

MossOntology wiki

How do we want to proceed? Should we set up a Webex or Skype meeting?

Pankaj will respond to Rensing (copy to po-internal). Lol will invite Rensing or someone from Physco group to present at the PO workshop at PAG. We will not do a meeting at this time.

Rensing is still waiting for a response. Someone needs to email him asap.

Upcoming meetings 2010-2011:

* 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.

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 will give the introductory talk on general use of ontologies, GO, genomics, etc, and Ramona will present the talk on the Plant Ontology, and 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. This means that as of now, only Ramona and Pankaj are giving talks (two of the six slots are filled). Dennis might be able to give a talk, and we are allowed to request other speakers (but they would have to be willing to travel to the meeting). Do we still want to go ahead with attending this meeting? Should we ask the organizers if we can use part of the time to do a computer demonstration of annotation workshop for the PO? Need an answer on this today.

• Plant and Animal Genome XIX Conference

January 15-19, 2011 PAG 2011

PO Activities at PAG: -PAG_2011_Collaborators_Workshop and meeting with collaborators

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

-Computer demonstration:

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

Poster:

-Outreach booth being organized by MaizeGBD

-Plant Phenotypes workshop and panel discussion (Laurel):

-Laurel is organizing a mini-symposium for the PO on Sunday morning.

POC workshop

• 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