POC Conf. Call 7-19-11

POC meeting, Webex Conference Call; Date: Tuesday July 19th, 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_7-12-11? There were no changes, additions, or deletions.

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Tech Talk

A web service for PO terms

Justin Preece will demonstrate a prototype web service providing PO terms from the AmiGO database. This was originally built for his annotation wiki project, but could be expanded for general use and advertised as POC "technical outreach", to be consumed by other people's applications wanting to use PO data.

Example screenshots

• PO term autocompletion in raw JSON format
• Term detail in raw JSON format
• Autocompletion, as used by another web application (outside of plantontology.org)
• Term details, retrieved and used by another web application

JP and JE propose to add such a web service to plantontology.org.

For those interested in some technical background info: see Wikipedia's entries for web service, RESTful web services, and JSON.

JP: Purpose of these web services would include: data accessibility, potential to increase exposure of the PO to more users and application, technical outreach tool development

Questions: Do the keyword searches include synonyms? That should be possible if the terms are in the database

What about alternate spellings? add the British spellings in the synonym filed

Talk with the other groups at ICBO about how they deal with this issue.

Comments: BS shared a link with us to a Microsoft Word plugin that will give you a drop down list of terms from ontologies when you are writing a paper.

Update on the Translations:

details TBA...

JE has tested script for Japanese terms. Some problems putting them in alphabetical order, because it doesn't recognize UTF8 characters. Should work okay as long as there is only one synonym for each term (which is the case for Japanese synonyms).

Letter for OBO-Foundry acceptance

Comments from BS:

* Should go through list of OBO Foundry criteria. Order the points in the letter as the same order as the criteria. * Most important is proving a multiplicity of independent users. Not a problem for PO, but needs to be included. * Also should mention that PO is supporting tool development. Not in the OBO Foundry criteria, but will impress reviewers with good citizenship. *Need to make the discussion of the relations consistent- derives_from an experimental manipulations

Plant Physiology Publication

Comment on relations from BS (re. the letter and the paper): In RO, derives_from does not refer to manipulated material, but PO manuscript describes it that way. We should have a more specific relation for this. Need to see what others are using. Check with OBI.

RW:We have only been using develops_from for in vitro structures, but we did not necessarily mean to define it in terms of manipulations.

We reviewed the differences between transformation and derivation. Transformation is always one to one. Deriviation always involves a fusion or a fission. Classic example of transformation is zygote to embryo to child to adult. Example of derivation is zygote from egg cell and sperm cell.

Develops_from can be use when we don't know or don't want to specify if there is a transformation or derivation. This is not necessarily recommended, except that people really want to use it.

Transformation_of is a little vague, because there are underlying derivations that happen during a transformation (to the parts of the thing that is transforming). For this reason, develops_from might be better to use.

Talked about adding a new relation called "experimentally_derived_from" or maybe better "derived_from_by_manipulation.

Action items:

-Check with OBI to find out if they have a relation similar to what we need for in vitro structure.

-Rework the manuscript re. develops_from and derives_from so that is consistent with what we are doing.

-Be sure descriptions of relations in the OBO Foundry letter are consistent with the manuscript, and that all are accurate.

see additional notes in text below

Issues from last week's discussion

Use of develops_from and derives_from relations in PO

Last week we discussed how develops_from can be used to mean either transformation_of or derives_from.

From RO:

transformation_of: Relation between two classes, in which instances retain their identity yet change their classification by virtue of some kind of transformation.

And: ...one and the same continuant entity instantiates distinct classes at different times in virtue of phenotypic changes.

derives_from: Derivation on the instance level (*derives_from*) holds between distinct material continuants when one succeeds the other across a temporal divide in such a way that at least a biologically significant portion of the matter of the earlier continuant is inherited by the later.

And: ...from c derives_from c1 we can infer that c and c1 are not identical and that there is some instant of time t such that c1 exists only prior to and c only subsequent to t.

From http://www.berkeleybop.org/ontologies/obo-all/ro_proposed/ro_proposed.obo

id: OBO_REL:develops_from

alt_id: OBO_REL:0000038

name: develops_from

def: "A relation between two continuants, C and D. C develops_from D if C derived_from D or C transformation_of D. On the class level: C develops from D if and only if, for any x and any time t, the following holds: if x instantiates C at time t, then 1. either for some time t1, x instantiates D at t1 and t1 precedes t, and there is no time interval t2 such that x instantiates C at t2 and x instantiates D at t2 ; 2. or for some time t1 , there is some y such that y instantiates D at t1 and x derived_from y. On the instance level: x develops_from y is indistinguishable from x derives_from y" [GOC:cjm]

comment: Examples: eye develops_from eye disc; erythrocyte develops_from reticulocyte. Note that ontologies should use either derives_from or transformation_of where appropriate, but the develops_from relation can be used where one does not want to differentiate between these 2 cases

is_transitive: true

! domain: snap:IndependentContinuant

! range: snap:IndependentContinuant

We decided we needed to examine the instances of each of these relation in the PO on a case by case basis.

derives_from relations in PO:

lateral root primordium (PO:0000016) derives_from pericycle (PO:0006203) This one should be develops_from

leaf-derived cultured plant cell (PO:0000007) derives_from leaf (PO:0025034)

root-derived cultured plant cell (PO:0000008) derives_from root (PO:0009005)

change the latter two to something like derives_by_manipulation_from

develops_from relations in the PO:

See list of develops_from relation in PO 07-2011

participates_in relation

We use the participates_in relation to describe the whole plant growth phase in which an anatomical entity occurs. For example:

sporangium participates_in sporophyte phase.

There is no restriction on the participates_in relation that says that just because A participates_in B, it cannot also participate in C.

Saying sporangium participates_in sporophyte phase does not preclude the possibility of sporangium participates_in gametophyte phase (although of course it doesn't).

What we really want to say is sporangium participates_in_only sporophyte phase. Should we create a more specific relation to say this? This would be much more powerful for reasoning than the regular participates_in relation.

From CM (via email):

adding the only qualifier is easy in OWL, but not in OboEdit. Also, although we want to exclude structures from participating in other whole plant growth stages, we don't want to exclude them from participating in other processes (which the only qualifier would do).

In OWL, we cold say: sporangium SubClassOf participates_in only ('sporophyte phase' or not 'life cycle stage'

but this is difficult in OboEdit.

Chris recommends that we:

i. Create a shortcut relation called (OK, we need a better name here!) "participationally_disjoint_from".

ii. Add a macro expansion definition to this (tech. spec. is here: http://oboformat.googlecode.com/svn/trunk/doc/obo-syntax.html#7 -- but I can do this for you)

iii. Make direct triples between sporophyte and gametophyte in OE using this relation (note this is not an all-some relationship, it's a direct relationship at the class level. confused yet?)

which would be similar to creating an OWL axiom that says: (participates_in some sporophyte) DisjointWith (participates_in gametophyte)

This proposal is okay to use tentatively, but we should not go into too much detail about the participates_in relation in the current manuscript, because our usage of it may change as we rework the PGDSO. We can describe it more in the next manuscript.

We still need to use or mention participates_in in the paper, in order to say how we would describe a gametophyte or sporophyte, but don't make it a focus.

A sporophytes is a whole plant during the time it participates_in the sporophyte phase. We need a solution for this temporal issue.

Request from Cell Ontology (CL)

CL plans to obsolete most of its plant cell types, and add xrefs to those for PO terms.

CL will provide bridge files as part of the CL release process. An example of this is provided in the WOMBO paper (upcoming at IBCO).

PO has appropriate terms for all but four of the CL terms, although two of the terms are obsolete (PO:0000373 mucilage cell and PO:0000020 starch sheath cell).

four problematic terms

PO does not have equivalent terms for these CL terms, because it was set up for only angiosperms. Suggest we add terms like these when we work on the revisions of conducting tissue and cells. The CL terms come form Esau's Anatomy of Seed Plants. For now, Terry has removed the problematic xrefs from CL, will update them if we add new terms.

CL:0000399 phloem element (PO could add phloem element, similar to xylem element, parent to sieve element and phloem fiber)

CL:0000364 ray cell (PO has ray wood parenchyma, but ray cell could be parent to both ray wood parenchyma and ray tracheary element)

CL:0000294 sieve cell (could add this term for gymnosperms, if still used, see Esau)

CL:0000268 sieve element (PO has sieve tube member, but sieve element could be parent to both sieve tube member and sieve cell)

okay. we can contact them if we add terms for these.

epidermal cell

CM writes:

CL:0000362 ! epidermal cell [DEF: "An epithelial cell of the integument (the outer layer of an organism)."]

GO uses "epidermis" in this way. However, I would prefer something like:

integumental cell (functionally defined, lives in CL or FUNCARO)

epidermal cell (vertebrate sense, lives in CL)

plant epidermal cell (lives in PO with name "epidermal cell", imported into pan-euk view with obofoundry unique label "plant epidermal cell")

PJ would prefer that they just take the PO branch for plant cells and import it into the CL.

They still need to obosolete (or merge) their terms, so there are not duplicates.

We confirmed our decision last week that epidermal cell should be renamed "plant epidermal cell" When other ontologies import PO terms, they will have to remove "plant" from the name before appending "plant" to all of the PO term names.

We need to talk to CL about how they will link to PO terms. Lol will see Terry Meehan at ICBO meeting, and/or we could set up a phone meeting with them.

User requests, Plant Anatomy Ontology:

Legume terms submitted by Austin Mast

Remaining:

phyllode

Last week, we looked at examples of leaves where the petiole has phyllode development, but there is normal lamina development (with leaflets) beyond the petiole. We need a term to describe this, as well as when the whole leaf develops as a phyllode.

Background:

Boke 1940 (http://www.jstor.org/stable/2436690, DOI:10.2307/2436690) uses the term phyllode to refer only to those leaves without leaflets:

"The seedling usually displays 1 even-pinnate leaf, 1 bipinnate leaf, and several transition forms. Pinnate leaves and transition forms possess an apical pointlet like that of the phyllode."

The main reference people cite for phyllodes is: D.R. Kaplan 1980, Heteroblastic leaf development in Acacia: morphological and morphogenetic implications, La Cellule 73, pp. 137–203.

Kaplan say: "The present developmental comparisons between phyllodes and pinnatifid leaves in seedlings of Acacia have demonstrated unequivically that the blade of the phyllode is the longitudinal positional homologue of the lamina of the fully pinnate leaf, at all stages of development. At no stage is the phyllode blade merely a petiolar derivative, nor is there evidence of lamina suppression in favor of petiolar elaboration as suggested in the classical developmental paradigm."

Some more contemporary uses of the term phyllode:

Gardner et al. 2005 (http://www.publish.csiro.au/view/journals/dsp_journal_fulltext.cfm?nid=150&f=SB04052):

"A phyllode usually consists of a pulvinus and photosynthetic region, although it can be sessile, decurrent with the stem, or reduced to scales. The photosynthetic region is highly variable and ranges from vertically flattened, through terete, quadrangular and triquetrous to horizontally flattened. Phyllodes usually possess at least one extra-floral nectary on the adaxial nerve, and sometimes up to five. Boughton (1981, 1985) observed three types of extra-floral nectaries. She also investigated the indumentum and found almost all species have two kinds of trichomes, one glandular and one non-glandular (Boughton 1989). According to Arber (1918), the chief anatomical feature by which phyllodes differ from true leaf laminae is the occurrence of two opposing series of vascular bundles."

and later in the paper:

"Previous approaches, such as basic anatomy and inferences from the sequence of heteroblastic leaf development in acacias, have led researchers to state that the phyllode is homologous with the petiole of a bipinnate leaf (e.g. Mann 1894; Goebel 1905; Troll 1939), or with the petiole and rachis (e.g. Bentham 1875; Reinke 1897), and make comparisons with the monocotyledonous leaf. Investigating the developmental morphology of phyllodes, Kaplan (1980) proposed a new model: that the phyllode is actually the positional homologue of the lamina of a bipinnate leaf. In essence, this suggests that the phyllode is directly comparable to a simple leaf. Kaplan’s theory does not, however, address the issue of the opposing vascular bundles found in phyllodes.

"The pattern of branching observed in the vascular bundles of A. verniciflua phyllodes suggests that the abaxial marginal nerve is homologous to the mid-rib in a simple leaf. This implies that laminar expansion occurs on both sides of the ‘mid-rib’, but vertically, and fused together. The emergence of the adaxial marginal nerve as two separate bundles, originating on opposing sides that eventually fuse rather than directly from the vascular ring found in the pulvinus, supports our interpretation and has been observed (together with other patterns) in several other Acacia species (von Wartburg 1991)."

Leroy and Heuret 2007 (doi:10.1016/j.crvi.2007.11.006): "The subgenera Phyllodineae... as the species are characterised by a polymorphism of vegetative characters where bi-pinnate leaves are replaced by a type of foliar organ called a phyllode." and "...the different transitional forms range from pinnate leaves to phyllodes..."

See fig. 1 in this paper. They refer a "flattened petiole" and a "flattened rachis" in transitional leaves.

Yang et al. 2008 (DOI: 10.1007/s11240-008-9424-7) use leaf as synonym for phyllode in Acacia. Refer specifically to phyllodes without any pinnate (sic) on top of them.

Forster and Bonser 2009, Annals of Botany, use the term phyllode to refer to adult leaves without leaflets: "Acacia implexa (Mimosaceae) is a heteroblastic species that develops compound (juvenile), transitional and phyllode (adult) leaves that differ dramatically in form and function."

RW did not find any contemporary papers that said that a phyllode is a petiole.

Leaves that have phyllode-type development toward the base with leaflet development toward the tip are a type of transition leaf.

Unifacial leaf as synonym? No- not exactly the same, but similar development. See Kaplan 1970 (http://www.jstor.org/stable/2485311). Might be better to make a parent term ensiform leaf which has children phyllode and unifacial leaf.

Proposed terms and definitions:

ensiform leaf: A vascular leaf that has increased activity of the adaxial meristem early in development, leading to abscense of an abaxial surface on the leaf. (ref: Lawrence, Kaplan 1970 fig. 1, Sajo and Rudall 1999)

Comment: Common in many monocots and some dicots. An ensiform leaf may be round in cross-section (unifacial) or it may be laminar, in which case lamina development is in a median plane (perpendicular to the axis), rather than a transverse plane (tangent to the axis). Ensiform leaves are often bifacial at the leaf base.

synonym: unifacial leaf

phyllode: An adult ensiform leaf with a lamina that develops in a median plane (perpendicular to the axis), rather a transverse plane (tangent to the axis) throughout the length of the leaf.

Comment: Common in legumes of the genus Acacia. Similar development occurs in some monocot leaves, but they are not called phyllodes. Transitional leaves also occur, in which the basal portion of the leaf develops similar to a phyllode, but the apical portion of the leaf develops normal leaflets (see PO:xxxxxxx, transitional phyllode-type leaf). In some leaves, the petiole may twist giving the appearance that the lamina is a phyllode, but it is not. Phyllodes are generally xeromorphic.

is_a vascular leaf, is_a adult leaf (unless we add a term adult vascular leaf)

phyllode-type transition leaf: A transitional vascular leaf in which the basal portion of the leaf has lamina development is a median plane, similar to a phyllode, and the apical portion of the leaf develops leaflets similar to a juvenile leaf.

Comment: Common in seedlings of legumes of the genus Acacia.

is_a transitional leaf, is_a vascular leaf

Maize GDB

transition leaf - definition

From Mary at MaizeGDB: It would be helpful to add some insights on the transition leaf. For example - Leaves that have mosaics of juvenile and adult tissues. In maize, the juvenile will be at the tip, which differentiates first, with adult at the base. Other grasses may have other arrangements, eg Brachypodium, which may have both juvenile and adult across the breadth of a leaf. Provided by Erin Irish, who references t his paper: Irish, E. E. and Karlen, S. (1998) Restoration of juvenility in maize shoots by meristem culture. International Journal of Plant Science 159, 695-701. The Brachy. information is more recent.

Suggest adding to the comment of juvenile leaf, transition leaf and adult leaf: Many species have juvenile leaves are at the base of the stem, adult leaves at the apex, and transition leaves in between. In maize, juvenile leaves will be at the tip of the stem, which differentiates first, with adult at the base, while other grasses may have other arrangements. Transition leaves may have mosaics of juvenille and adult tissues, as in Brachypodium.

Can add Irish and Karlen reference to definition dbxrefs if it is appropriate.

leaf base

See tracker item for details.

I think Mary's questions have been answered, and this item can be closed. We can add a comment to it once we resolve the issue of transferring annotations for parts of leaf.

style, silk, Poaceae style

From Mary at MaizeGDB: Suggest that you merge these, keeping style, obsoleting silk and Poaceae style. Do the same for other floral parts that have a species spin on them, but are really the same as other more generic names for flower parts.

From PJ: Poaceae / Zea was necessary in some terms because often detail structures referred to parts of tassel/ear floret and it has conflict with floret compositeae besides the spatial aspects.

Rather than working on this piecemeal, we need to have an organized approach to eliminating the Poacaeae/Zea terms. Need to look at the structure from the top down and ensure part_of relations remain correct. Do we want to allocate time to this now or wait for next release?

See page for Eliminating Zea/Poaceae terms from PO

42 terms in PAO with Poaceae in the name.

28 terms in PAO with Zea in the name.

Only on Poaceae terms in PGDSO, and it is on today's agenda to merge with another term.

Upcoming meetings 2011:

• 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, will be held on Thursday, 27 July, from 1:30pm to 3:30pm.

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

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

PJ is staying at the Best Western. RW is staying at Hotel Enterprize. DWS is staying with a friend, and MAG has an apartment/suite nearby.

• ICBO 2011 Second International Conference on Biomedical Ontology

July 26-30, 2011 Buffalo, New York ICBO

-LC will present the Plant Ontology on Thursday, July 28th, 3:40pm in the session: "Introduction to The OBO Foundry Initiative":

Also presenting will be: The Ontology for Biomedical Investigations,the Ontology for General Medical Sciences and the Infectious Disease Ontology. Link: ICBO Program

July 27 8.30am-4pm: 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.

• 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.

• 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.

We agreed that the PO meeting will be all day Saturday Sep. 10 and morning of Sunday Sep. 11. DWS, PJ, BS, LC, and RW can make it. Need to find out if MAG can attend.

RW has reserved the NYBG apartment for the nights of Sep. 9 and 10.