POC Conf. Call 2-15-11

POC meeting, Webex Conference Call; Date: Tuesday Feb 15th, 2011 10am (PST)

In attendance:

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

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

Collaborators: none

Acceptance of the minutes from the POC_Conf._Call_2-08-11? There were no changes, additions, or deletions.

Update on Progress of Publications

Target journal for a major, detailed paper: This is the top priority right now:

-Plant Physiology:

RW and LC are working on an outline for a manuscript to submit to Plant Physiology. This will be a more detailed description of the changes made to the PSO in the past year, including restructuring.

Will focus on how PO is now applicable to a wider range of plant species. Note: having the MO terms included will be very helpful to this. Once our draft is prepared, we will work with Nick Provart of BAR to collaborate on the analysis section.

Plant_Physiology_paper-_2011

Possible target journals for a short paper: PO_Paper_Winter_2011

• Paper for ICBO meeting- suggestion from BS, ICBO call for papers, deadline is March 1st. could be expanded for submission to journal later

Wrapping up the TAIR requests on SF:

xylem pole pericycle cell

- xylem pole pericycle cell (PO:0000064): A pericycle cell that is adjacent to a xylem cell.

Comment: Xylem pole pericycle cells may retain some meristematic activity and are the site of lateral root initiation. ref: PMID: 17993548

- phloem pole pericycle cell (PO:0000065): A pericycle cell that is adjacent to a phloem cell.

Comment: Phloem pole pericycle cells are distinct from xylem pole pericycle cells in that they display cytoplasmic characteristics of a more differentiated status. ref: PMID: 17993548

Should a xylem pole pericycle cell should be defined as a pericycle cell that is next to a xylem pole, instead of next to a xylem cell? Generally, we agreed that the xylem pole and phloem pole are not structures per se, but more of a way of describing the orientation of the vascular bundle.

There are pericycle cells that are adjacent to xylem cells that are not adjacent to the xylem pole, so we will need a more specific description of the location of xylem pole pericycle cell.

The xylem pole is the really the protoxylem cells in the vascular bundle.

Proposed new definition for xylem pole pericycle cell: A pericycle cell that is adjacent to a protoxylem cell.

Comment: Xylem pole pericycle cells are cells in the pericycle that are adjacent to the protoxylem pole of a vascular bundle. Pericycle cells that are adjacent to other xylem cells in the vascular bundle are not considered xylem pole pericycle cells. Xylem pole pericycle cells may retain some meristematic activity and are the site of lateral root initiation.

This definition was approved. Definition of phloem pole pericycle cell should be similar.

locule

Also see original term request.

At least week's meeting, we decided on the following new terms:

locule

> sporangium locule

> sporophyll locule

> > ovary locule

> > anther locule

However, this structure is a problem, because an anther locule is both a sporophyll locule and a sporangium locule (because a pollen sac is a microsporangium). Suggest the following revised structure and definitions:

locule

> ovary locule

> sporangium locule

> > anther locule

This hierarchy was approved.

locule: A plant anatomical space that is a cavity a reproductive structure.

Comment: May be a cavity in a sporophyll, within several fused sporophylls, or within a sporangium. In many instances, the locules are filled with seeds or other plant structures.

ovary locule: A locule that is a cavity in an ovary.

Comment: Generally contains at least one ovule, but ovules may be absent in sterile fruits. An ovary locule may be part of a single carpel, in the case of unicarpellate flowers. An ovary that is part of a syncarpous gynoecium may have multiple locules, or the anatomical spaces of multiple carpels may be fused to form a single locule.

Sporophyll locule should be a broad synonym of ovary locule. Will get rid of comment about sterile fruit.

sporangium locule: A locule that is a cavity in a sporangium or several fused sporangia.

anther locule: A sporangium locule that is part of an anther and is a cavity within a single pollen sac or two or more fused pollen sacs.

PJ: Link to image: anther schematic

We need to look at the existing term 'pollen sac'- def'n needs to be rewritten. then anther locule could be part of it. We will reopen the tracker for pollen sac

exact synonym: pollen sac locule

Do we want at term for fruit locule?

Yes, add term for fruit locule. Add develops_from ovary locule relation.

We could also add the term spore capsule locule for mosses, if we wanted to.

spore capsule locule: A sporangium locule that is a cavity in a spore capsule. part_of spore capsule (PO:0025232).

Okay to add spore capsule locule.

carpel/ovary septum and replum

We agreed to obsolete carpel septum (PO:0005009). Also suggest that we obsolete fruit septum (PO:0005008), for the same reason and add consider relations to new terms fruit septum (PO:0025268) and fruit replum (PO:0025267).

ovary septum(PO:0025262): A septum that divides a multilocular ovary. part_of gynoecium

Comment: Found in species with syncarpous gynoecia (fused carpels). An ovary septum is derived from the fused walls of two adjacent carpels, while a replum (PO:0005016) develops from early contact of placental tissue from opposite sides of the ovary. Annotations for Arabidopsis should go under replum, not here.

New term, fruit septum (PO:0025268): A septum that divides a cavity or mass of tissue in a fruit and develops from an ovary septum.

Comment: Annotations for Arabidopsis should go under fruit replum (PO:0025267), not under fruit septum. The partition between two sections of an orange is a fruit septum.

The definitions for ovary septum and fruit septum were approved.

New definition for replum (PO:0005016): A portion of ovary placenta tissue that divides an ovary into two or more chambers and develops from contact of the placental tissue from opposite sides of the ovary early in gynoecium development. synonyms: false ovary septum, placental septum

Comment: A replum develops along with the ovary and has no suture line in its center, while a true ovary septum (PO:0025262) is derived from the fusion two adjacent carpel walls. Common in Brassicaceae. Annotations for Arabidopsis should go here, and not under ovary septum.

NOTES ON REPLUM: replum was develops_from ovary placenta, changed to is_a portion of ovary placenta.

Made replum part of the Arabidopsis subset, but not ovary septum.

Suggest adding synonym ovary replum.

Current TAIR annotations to carpel septum (PO:0005009) should move to replum.

from PJ Arabidopsis replum

Note: highlight the changes in the ontology terms in presentations at meetings- explain how authors may not be using them correctly. Use replum/spetum as an example

Replum has part_of relation to fruit, but because it is_a portion of ovary placenta tissue, it is by default part of ovary. Suggest making a new term for fruit replum.

New term fruit replum (PO:0025267): A portion of fruit placenta tissue that divides a fruit into two or more chambers and develops from a replum. is_a fruit placenta (by transitivity, part of fruit), develops_from ovary placenta.

Should obsolete replum (PO:0005016) and replace it with new term ovary replum, exact synonym replum. Add term for fruit replum -- develops from ovary replum.

Ovary

Ovary (PO:0009072) was part of carpel. Last week we agreed that it should be part_of gynoecium, because it can be part of multiple carpels. Made it is_a plant structure, rather than cardinal organ part, because it can be part of one carpel or more.

Current def. of ovary: The basal portion of a carpel or group of fused carpels, that encloses the ovule(s). [source: APWeb:Glossary, TAIR:lr]

New definition: A plant structure that is the basal portion of a carpel or group of fused carpels and encloses the ovule(s). part_of gynoecium, is_a plant structure

Comment: May not contain ovules in the case of sterile fruit.

Get rid of commment about sterile fruit (ovules present but aborted).

Collective organ part structure?

Last week we discussed adding a new upper level term for structures that are composed of parts of multiple organs (collective organ part structure). Children would be septum and pseudostem. Will probably find others.

Last we considered this structure:

plant structure

> collective plant structure

> > collective plant organ structure

> > > collective phyllome structure

> > > shoot system

> > > etc.

> > collective organ part structure

> > > septum

> > > pseudostem

We liked the proposed structure, but felt it was not good to change upper level term names or definitions.

Collective organ part structure was added as sibling of collective plant structure (child of plant structure), and collective plant organ structure was added as synonym of collective plant structure (PO:0025007). This gives the following structure:

plant structure

> collective plant structure (existing term, synonym collective plant organ structure)

> > collective phyllome structure

> > shoot system

> > etc.

> collective organ part structure (new term)

> > septum

> > pseudostem

Proposed definition of collective organ part structure: A plant structure composed of two or more cardinal organ parts from adjacent organs and any associated portions of plant tissue.

Comment: A collective organ part structure is composed of parts of multiple organs, but no complete organs. The organ parts are often of the same type (e.g., petioles, carpel walls), but may be of different types. Includes plant structures like a septum that consists of the walls of two fused carpels or a pseudostem that consist of multiple, overlapping leaf sheaths.

Should we add a disjoint_from collective plant structure relation?

The new structure and definition were approved. Can add disjoint from relation, but will send email to Barry to find out what is the policy on when to use it. Also check if GO already has an icon for disjoint_from.

dispersed meristematic cell

On 2/1/11 we decided to add three new terms:

-procambial cell (PO:0025258): A meristematic cell that is part of a portion of procambium. part_of procambium

-leaf procambium (PO:0025259): A portion of shoot procambium tissue that is part of a leaf. part_of leaf

-leaf procambial cell (PO:0000063): A procambial cell that is part of a leaf procambium. part_of leaf procabium, syn: DMC, dispersed meristematic cell

Comment: Leaf procambial cells may differentiate in the mesophyll tissue layer and divide to form and extend the vascular tissue network of the leaf.

These definitions were approved.

Problem that arose during editing:

procambium (PO:0006074) is defined as "A portion of primary cambium that undergoes differentiation to form the primary vascular tissue. is_a cambium, part_of apical meristem," but cambium is defined as a lateral meristem (which procambium isn't), and procambium is defined as part_of apical meristem (which it isn't always -- think of leaves).

Suggest making procambium is_a meristem, similar to protoderm.

Proposed new def: procambium: A portion of meristem tissue that undergoes differentiation to form primary vascular tissue. Comment: May occur in an apical meristem or in the mesophyll of a developing phyllome.

Is this is a substantial change in the definition? Should we obsolete the new term and create a new term with the same name?

New definition was approved. Will ask Barry whether or not we should obsolete (PO:0006074) and make new term for procambium. Add comment: Gives rise to the primary xylem and primary phloem.

Need to revisit cambium/vascular cambium. Cannot just add relation vascular cambium develops_from procambium (that is from the procambial strands), because part of it develops from the procambium, but part of it develops from parenchyma cells in the interfascicular region. Probably need to add separate terms for fascicular and interfascicular cambium, plus a term that combines the two of them for wood. Will create new SF tracker for this.

I think it is okay to have root procambium and shoot axis procambium as part of (root or shoot axis) apical meristem, but not leaf procambium. Right now, root procambium is part_of root meristem, should be part_of root apical meristem.

Current term shoot procambium (PO:0006306): A derivative of the apical meristem which undergoes differentiation to form the primary vascular tissue of a shoot)

The definition is vague, because it does not specify shoot system or shoot axis. This is a carry-over from before we clarified the difference between shoot system and shoot axis. Changed definition to make it clear it is for a shoot system (any above ground part of plant), then made leaf procambium a child of shoot procambium, and also added new term for shoot axis procambium.

Proposed def'n: shoot procambium (PO:0006306) A portion of procambium tissue that is part of a shoot system.

Proposed def'n: shoot axis procambium (new term): A portion of shoot procambium that is part of a shoot apical meristem and gives rise to the primary vascular tissue of a shoot axis.

New definition of shoot procambium was appproved. Okay to add shoot axis procambium. Should also add stem and branch procambium.

Also found that root initial cell (PO:0000059) is_a root apical meristem. Changed it to is_a initial cell, part_of root apical meristem.

Okay to change. Should be more specific and make root initial cell part_of quiescent center, rather than part of root apical meristem.

Need to revisit initial cell and have a discussion of initial cell versus stem cell, and totipotency versus pluripotency.

Restructuring descendants of leaf (PO:0025034)

-Some of the part_of children of vascular leaf can also be part of non-vascular leaf. This needs to be done before we can add terms for bryophytes.

-Need to double check the is_a children of leaf.

current is_a children of leaf

• prophyll (PO:0009042) is_a phyllome and scale leaf (PO:0006003) is_a phyllome (see prophyll and scale leaf).

Suggest making prophyll a child of vascular leaf.

Suggest making scale leaf is_a leaf (because the term could be used to refer to non-vascular leaves, even though it is usually used for vascular leaves.

We decided it was best to leave prophyll as a phyllome. It is the first leaf on a shoot system in vascular plants, but it may not be a true vascular leaf/may not have fully developed vascular system. Better to leave it with a more general parent since exact nature of organ is not known.

We decided to leave scale leaf as a phyllome too, because it is not clear whether it is a true leaf or a bract. Definition of scale leaf needs to be redone. Will post new definition on SF.

There was a discussion about whether or not Psilotum (fern) has scale leaves.

PJ posted a link to a pdf concerning Psilotum in which they refer to the outgrowths as prophylls, but this is the wrong use of the word prophyll.

• non-vascular leaf - ok as is - Physco group has asked us to add phyllid as exact synonym. Can also add gametophyll.

• vascular leaf - ok as is - Suggest adding frond and needle as exact synonyms of vascular leaf

We did not have time to address synonyms of non-vascular leaf and vascular leaf this week.

Question from sharon.lewis@syngenta.com to Pankaj:Re: changing name of "leaf" to "vascular leaf"

"> We are just updating our internal copies of some ontologies, and noticed some changes in the Plant Structure ontology from the Plant Ontology Consortium. (As you know we also use the Trait Ontology.)

"> We don’t so much like the change of “leaf” to “vascular leaf” for several reasons. If we use “vascular leaf” in an alphabetically ordered pulldown menu, users will miss it if they’re looking for leaf. Could you use “leaf, vascular” instead?

"> I think I understand why the increased granularity was added in this area. (Sort of – if mosses aren’t really plants, why does the POC care about them?) I understand that the old “leaf” really meant leaf of a vascular plant, and the new “leaf” is supposed to mean something else.

"> It causes search problems for us when a term is added that is the same term as a previous one, but with a different code. Do you know how others handle this situation?"

Possible solution: if we make "leaf vascular" (I don't think we should put punctuation in the name) an exact synonym, and they add exact synonyms to their pull-down menu, it will solve the problem. Sharon said that would work, because they include exact synonyms.

Note from PJ: GO has examples of terms which use commas in the name, so we should be able to do this if we need to

from chat window: [Term] id: GO:0001867 name: complement activation, lectin pathway namespace: biological_process def: "Any process involved in the activation of any of the steps of the lectin pathway of the complement cascade which allows for the direct killing of microbes and the regulation of other immune processes." [GOC:add, ISBN:0781735149 "Fundamental Immunology"] comment: Note that proteins such as mannose-binding lectin (MBL) and certain serum ficolins can activate the lectin complement pathway. synonym: "complement cascade, lectin pathway" EXACT [GOC:add]

Ramona will send a response to Sharon Lewis, telling her that we are adding "leaf, vascular" as a synonym, and asking her to be sure to sign in when submitting requests on SF.

current part_of children of leaf

• leaf apex - ok as is - applies to both vascular and non-vascular leaf

• leaf base - ok as is - applies to both vascular and non-vascular leaf

• leaf epidermis - ok as is - The term may be used for non-vascular leaves, even though many are only one cell thick.

Need to consider if the definition of epidermis works bryophytes (see section below on Physco terms).

• leaf endodermis -- Is there ever an endodermis in non-vascular leaves? This should probably be part_of vascular leaf, not leaf.

current is_a children of vascular leaf

Is there heteroblasty in non-vascular leaves? do these terms apply?

• juvenile leaf

• transition leaf

• adult leaf

Physco group has included these terms in their ontology, but said they are not sure if they are necessary. Said there are differences among phyllids based on their position on the stem (more basal versus more terminal), but the terms juvenile and adult are not normaly used to describe them. If we want to use them for non-vascular leaves, we either need to make them children of leaf instead of vascular leaf, or add separate terms for vascular and non-vascular juvenile, transition and adult leaves.

Do we want to keep these (as phenotype terms)? At one point we discussed getting rid of them.

• simple leaf

• compound leaf

Terms that are probably okay as children of vascular leaf:

• cotyledon - ok

• leaf spine - ok

• cigar leaf - ok

• rosette leaf - probably ok as child of vascular leaf - Are there ever rosette's in gametophytes?

• cauline leaf - definition is a bit weird, actually applies to leaves that are part of an inflorescence (which we define as bracts)

Current def: Leaf or pairs/whorls of leaves borne on the stem. [source: TAIR:ki]. Comment: In Arabidopsis, refers to the leaves that are borne on the elongated inflorescence branches.

Suggest we flag this definition for later, but not deal with it for now, and leave it as is_a vascular leaf.

current part_of children of vascular leaf

Terms that are probably okay (only occur in vascular leaves):

• auricle - ok

• bundle sheath - ok

• leaf abscission zone - ok

• leaf collar - ok

• leaf vascular system - ok

• ligule - ok

• petiole - ok

• stipule - ok

• leaf intercalary meristem - probably ok - does it ever occur in non-vascular leaves? Normal growth in non-vascular leaves if from the tip.

• leaf sheath - probably ok - does it ever occur in non-vascular leaves?

(see part_of children of leaf)

Terms I'm not sure about:

• leaf aerenchyma- is there ever aerenchyma in non-vascular leaves?

• leaf mesophyll - should probably be part of leaf. Is there a mesophyll in non-vascular leaves?

Terms that are part of vascular leaf but should be part of leaf:

• leaf lamina - should be part_of leaf

• leaf margin - should be part_of leaf

• leaf base and leaf apex are already part of leaf (rather than vascular leaf)

Do we keep these terms for vascular leaf and rename them, move them to non-vascular leaf, or obsolete them and create new children of leaf?

Plant cells and embyronic plant cell

Rachael Huntley from EBI/Uniprot is working on annotations that involve plant cells. She would like to be able to import all plant cell types by only using the plant cell branch of the ontology, but this would miss embryonic plant cell (PO:0025028), which is a child of embryonic plant structure. She has requested that we make embyronic plant cell is a plant cell.

Current def. of embryonic plant cell: An embryonic plant structure that is a plant cell that is found only in an embryo.

Her point that an embryonic plant cell is still a plant cell is correct (based on the definition), but have tried to avoid dual parentage.

Embryonic plant cell has three is_a children: apical cell (PO:0004000), basal cell (PO:0002002), and hypophysis (PO:0020109)

We can either:

Make embryonic cell a child of both plant cell and embryonic plant structure

or

Make embryonic cell a child of plant cell, and add intersection of relations:

embryonic plant cell [intersection_of] plant cell and part_of embryo,

plus embryonic plant structure [intersection_of] plant structure and part_of embryo.

Then the reasoner would figure out that embryonic plant cell is an embryonic plant structure, with the relation being asserted.

Physcomitrella terms:

postponed until next week

See Terms requested by Physco group for a list of terms.

-This was identified as a priority, since if we can get their terms in by the next release, they will use PO instead of continuing to develop their own ontology.

The Moss Ontology (MO) has about 65 PSO terms. About 20 of those already exist or are trival to add to the PO (e.g. non-vascular leaf base, non-vascular leaf apex). Many of the terms will be fairly straight-forward to add, but some will require discussion.

They have requested about about 35 PGDSO terms. About 10 of those already exist. The others should be fairly easy to add once the PGDSO is restructured.

• Do we want to give MO/Physco terms their own number space? Maybe a subset of the NYBG number space.

Term requested by MO that are already in PO but need some work

epidermis (PO:0005679)

Current def: A portion of plant tissue composed of epidermal cells that develops from the protoderm and covers the surface of a plant structure. [source: POC:curators].

Comment: The epidermis can be composed of one or more layers of cells. In some species, the epidermis is replaced by periderm. Epidermis can also include trichomes and stomatal pores (add root hairs and rhizoids too).

Is there a protoderm in non-vascular plants? (def: A portion of meristem tissue that develops from the outer layer of an apical meristem and gives rise to a portion of epidermis.)

phyllid base and phyllid apex

We already have the terms leaf base (PO:0020040) and leaf apex (PO:0020137). The choice is to make phyllid base (=non-vascular leaf base) and phyllid apex (=non-vascular leaf apex) synonyms of these terms, or to make them is_a children (see discussion of part_of children of leaf, above).

The same issue also applies for phyllid trichome/leaf trichome.

spore capsule

We have the term moss capsule (PO:0025232), but having a taxon name in the term name is not desirable, nor is having it defined based on its taxa. Suggest renaming it spore capsule and defining it based on its unique characteristics.

Current definition: A sporangium in mosses.

Proposed def.: A sporangium...

Comment: Found in mosses.

transfer cell

We have the term transfer cell (PO:0000078). Def: A cell with wall ingrowths (or invaginations) that increase the surface of the plasmalemma. [source: ISBN:0471245208] Comment: Appears to be specialized for short-distance transfer of solutes.

MO suggested definition: Specialized cell at the junction of the gametophyte and sporophyte that function in nourishing the sporophyte. [source: Bill and Nancy Malcolm (2006): Mosses and other Bryophytes, an illustrated glossary, second edition]

Are transfer cells always at the junction between the sporophyte and gametophyte? Do we want to include that in the definition or in a comment?

Do we want to add a specialized term for transfer cells in mosses? Are they different from other transfer cells?

Basal endosperm transfer cell (PO:0009018) is currently the only is_a child of transfer cell.

New items for Physco

Shoot apical meristem/apical cell/phyllome

MO has requested the term apical cell.

We already have the term apical cell (PO:0004000), which is an embryonic cell: "An embryonic plant cell that is the uppermost cell formed after the first division of the zygote." Suggest renaming PO:0004000 "embryonic apical cell" for clarity. The embryonic apical cell can also be found in non-angiosperms.

Growth in mosses (and other bryophytes?) results from divisions of a single apical cell. Branches or leaves form from division and differentiation of sub-apical cells. Mosses do not have an apical meristem in the same sense as vascular plants.

If we define apical cell as is_a meristematic cell, we will have a problem. Even though apical cell is consistent with the definition of meristematic cell (synthesizing protoplasm and producing new cells by division and with only a primary cell wall), it is not consistent with the relation meristematic cell part_of meristem. A meristem is a portion of tissue and therefore two or more cells. We could solve this problem by changing meristematic cell part_of meristem to meristem has_part meristematic cell.

Proposed def. of apical cell: A meristematic cell at the apex of a gametophore or non-vascular leaf (phyllid).

Comment: Occurs in mosses and other bryophytes.

Apical cells also cause an issue with or definition of phyllome (PO:0006001): "A lateral plant organ produced by a shoot apical meristem." This definition is not strictly applicable to non-vascular leaves, which are phyllomes. Suggest we tweak the definition of phyllome to allow for this.

Proposed def. of phyllome: A plant organ produced by the lateral portion of a shoot apex.

Comment: In vascular plants, phyllomes arise from the shoot apical meristem. In non-vascular plants, phyllomes arise from division of a sub-apical cell (sometimes referred to as a leaf initial).

Upcoming meetings 2011:

• 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.

From RW: -What is official PO strategy for dealing with phenotypes?

-Should it differ between description of mutant phenotypes and descriptions needed for systematic studies?

-Should PO develop a list of terms to be submitted to PATO (rather than our current piecemeal suggestions)?

-Possible case study: description of inflorescence types.

* ICBO 2011 Second International Conference on Biomedical Ontology July 26-30, 2011 Buffalo, New York

ICBO

CALL FOR WORKSHOP AND TUTORIAL PROPOSALS: The deadline for workshop and tutorial proposals for the ICBO conference has been extended to February 15th, 2011

- We decided we are too shorthanded to put together a PO workshop, but Melissa, Alan and Chris are organizing an anatomy ontology workshop.

- LC will attend and represent the PO. Invite other plant people?

-BS suggested we might want to submit a short paper which could be published in longer form later- see above

* International Botanical Congress (IBC2011)

July 23rd-30th 2011, Melbourne, Australia

Registration is open Important dates

Symposium proposal was accepted, 'Bio-Ontologies for the Plant Sciences' under the Genetics, Genomics and Bioinformatics theme.

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

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