POC Conf. Call 4-19-11

POC meeting, Webex Conference Call; Date: Tuesday Apr 19th, 2011 10am (PDT)

In attendance: Laurel Cooper (OSU), Ramona Walls (NYBG), Barry Smith (University at Buffalo, NY), Justin Preece (OSU), Justin Elser (OSU), Dennis Stevenson (NYBG),

Absent: Pankaj Jaiswal (OSU), Marie Alejandra Gandolfo (Cornell University), Chris Mungall (Lawrence Berkeley National Lab),

Collaborators: none

Acceptance of the minutes from the POC_Conf._Call_4-14-11? There were no changes, additions or deletions.

Tech issues:

*Update on the OBO to OWL conversion:

JE now has an owl version of the live plant_ontology file that has the definitions and other information. It is available at: http://palea.cgrb.oregonstate.edu/svn/Poc/tags/live/plant_ontology.owl

Still working with Damon and Shuly on getting the SSWAP components to work properly from their end.

'PO will host the owl file and the SSWAP components of it (?), they have software that enables us to do it. (need more accurate details)

* progress on has_parts?

Currently, the existing has parts in the ontology do not seem to be causing any problems, now that we removed the reciprocal relations. The problem still exists that the annotations do not flow in the right direction.

JE still needs a test file that has fewer terms and annotations, because testing with the live version takes about 10 hours to load.

*Changing the namespace from Plant Structure Ontology (PSO) to Plant Anatomy Ontology (PAO) This was discussed at the POC_Conf._Call_3-29-11

Action taken: -LC talked with CM, we all agreed that it would not be too much of an issue to do so.

-Change was made in the plant_ontology.OBO development file, version #1068 and on the SourceForge term tracker "group"

-Still needs to be changed on the PO webpage and in other spots where the individual files are linked to (such as Bioportal)- so it should also change in those places.

-Will also need to be changed on the AmiGO Browser (eg search page)- how difficult is this?

JE was able to modify the drop down menu on the Amigo browser to say "plant anatomy" instead of "plant structure" while we spoke.

*Review for OBO Foundry Acceptance

BS brought up the topic of review for OBO Foundry acceptance. He suggested that the PO can be submitted for OBO Foundry membership within the next weeks

Asked if we have one ontology or two? We have one, because all have same id space (PO). We have been using the word 'namespace' to mean a branch of the ontology, which is really a line in the obo stanza generated by OboEdit. Namespace may mean something different in the Obo Foundry. The default namespace for the PO is still plant ontology. We should be careful in how we refer to parts of the PO. For example, GO has been merged into one file, but old literature says there were three ontologies, so that is how people still talk about it. BS will send a copy of OBO foundry principles so we can check if we are in compliance and what needs to be done.

By email after the call: BS sent us a link to the list of principles: [OBO_Foundry_Principles] and then CM sent:"Use the list here": [Accepted]

Issues arising from last week's meeting:

plant embryo (PO:0009009)

current definition: A whole plant in the post-zygotic stage that does not yet consist of fully differentiated tissues.

Comment: Adventitious embryos and somatic embryos do not arise from zygotes. Cultured embryos (PO:0000010), including haploid embryos, are in vitro plant structures. Embryos occur prior to germination in vascular plants.

This is not really consistent with the fact that we have tissues like embryonic epidermis and embryonic cortex.

Logically, an embryo could be treated like a sporophyte or gametophyte, that is, a whole plant in the embryonic life cycle phase. However, since we don't have embryonic phase yet, and so much research is done on embryos, it seems appropriate to pre-compose the term embryo and use that for now.

Proposed definition of plant embryo: A whole plant in the early part of a sporophytic phase after the first cell division.

Comment: An embryo is generally formed after the first division of a zygote, but in the case of adventitious embryos, somatic embryos, embryos that arise through apogamy and cultured haploid embryos, it is formed after the division of a single cell that is not a zygote. In seed plants, the embryonic phase ends with germination. In non-seed plants and cultured embryos of seed plants, the end of the embryonic phase is less clearly defined and varies among taxa.

Proposed definition is workable for now. In the comment, we should be more specific about the end of the embryonic phase in different taxa, to the extent that we know about it. We discussed that the word 'early' is quite vague, but we can't say pre-seedling stage- restricted to seed plants

We discussed the possibility of describing the end of the embryonic phase as 'before any organs or non-embryonic organs are formed'. Problems: Cotyledons are formed in pteridophyte embryos (and many seed plants too), and they are organs. Also, the foot in a bryophyte or pteridophyte organ.

new proposed comment: An embryo is generally formed after the first division of a zygote, but in the case of adventitious embryos, somatic embryos, other embryos that arise through apogamy, and cultured haploid embryos, it is formed after the division of a single cell that is not a zygote. The end of the embryonic phase varies among taxa. In seed plants, the embryonic phase ends with germination. In pteridophytes, the embryonic phase ends with the formation of the first true leaf after the cotyledon(s). In bryophytes, the embryonic phase ends when the apical cell stops dividing and the sporangium begins to develop.

Can we say when the embryonic phase ends for cultured embryos? Yes, when roots and shoots form

Other issues:

• on 4-12-11, PJ suggested we could add zygotic embryo- the one in the seed and also a cultured one. Also, we need haploid embryo as child of cultured embryo? Do haploid embryos ever form in nature?

We discussed whether or not the original intent was to describe an embryo derived from a zygote and grown in culture? BS suggested it would be better to call it: "cultured zygote-derived (plant) embryo", as the name 'zygotic embryo' is a little misleading, because it implies that it is an embryo that is a zygote. May want to rename "zygote-derived embryo" or similar, but should keep (cultured) zygotic embryo as synonym because it is widely used.''

Need to add the term: zygotic (plant) embryo, is_a plant embryo, then 'cultured zygote-derived (plant) embryo' is_a zygotic (plant) embryo, and is_a cultured embryo.

We will also add 'haploid embryo' (microspore-derived HE?) as child of cultured embryo. Needs to be defined. Can add the naturally arising one later if needed.

*adventitious embryo (PO:0004537): Embryo derived directly from nucellus cells without involving embryo sac cells

Is this always true? Need to check on it.

It was suggested that adventitious embryo should be a synonym for somatic embryo, or maybe a child of somatic embryo. LC pointed out that adventitious embryos are really those embryos that arise where embryos normally would not arise, i.e.: on the edges of leaves on Kalanchoe or ferns. There was general agreement on this.

DS pointed out that somatic or adventitious embryos are all embryos that are derived from apogamy, so we could use the word apogamy in the definition for clarity.

Adventitious embryo should be merged into the new term 'somatic plant embryo' Need to work on the definition of 'somatic plant embryo'.

Note: BS: We need to remember to put 'plant' in the all these names.

• Note: Adventitious embryos, somatic embryos, embryos that arise through apogamy, and cultured haploid embryos, embryos cannot be considered in the sporophytic phase (as it it defined now), since they are not the product of fertilization.

Suggest that we rework the definition of sporophytic phase with a comment about apogamy. see SF tracker and/or future meeting:

cultured plant embryo and its children

*cultured plant embryo (PO:0000010):

Current Def’n: In vitro isolated and maintained mature or immature zygotic embryos, somatic embryos or haploid embryos (derived from male gametophyte). [source: TAIR:ki] Comment: None

Rename: cultured plant embryo (PO:0000010)

Proposed def’n: A plant embryo that is grown or maintained in vitro.

Comment: Includes isolated and maintained mature or immature zygotic embryos, somatic embryos or haploid embryos (derived from male gametophyte).

parentage: is_a plant embryo (PO:0009009) and is_a in vitro plant structure

PJ: We should we have a cultured zygotic embryo, any annotation to cultured ZE should go there

see the discussion above about this

*cultured somatic embryo: (PO:0000011): Child of cultured plant embryo

Current Def’n: An embryo arising from previously differentiated somatic cells in vitro, rather than from fused haploid gametes, i.e., zygote.

Proposed def’n: A plant somatic embryo that is grown or maintained in vitro.

new proposed def’n: A plant embryo arising from previously differentiated somatic cells in vitro, rather than from the zygote or from gametes.

is_a: plant embryo, and need a new term "somatic (plant) embryo"

See new proposed definition of embryo above.

embryonic plant structures

Definition of embryonic plant structure:

embryonic plant structure (PO:0025099): A plant structure that is part of an embryo.

Comment: Includes organs, tissues and cell types that are unique to embryos, not plant structures that can occur in both embryos and mature plant structures.

Changed definition from "proper part of" to "part of", so it would be consistent with the intersection of term. Think part_of is better anyway, because technically an embryo is an embryonic plant structure.

We discussed how to deal with structures that are part of an embryo when the plant is in the embryonic phase but are also part of a plant after it passes out of the embryonic phase, like hypocotyl root junction or coleorhiza.

Ideally, we would define embryonic plant structure as "A plant structure that is part of an embryo when a plant is in the embryonic phase," but we don't have a mechanism whereby the reasoner could infer that. Humans may know that a radicle is part of an embryo when the plant is an embryo and part of a seedling when a plant is a seedling, but the reasoner could only infer it after an annotation is made, and only if the user specified the phase that the structure was taken from. Since we can't count on that, and we don't yet have embryonic phase and seedling phase, it is not a practical solution for now.

An alternative solution is to specify sibling terms like embryonic radicle and seedling radicle, with the correct part_of or participates_in relations. We will try this, because there are only 5-10 terms where this should be necessary. We should add appropriate develops from relations (e.g., seedling radicle develops_from embyronic radicle).

Some terms were left as is_a children of embryonic plant structure:

embryo proper (PO:0000001): An embryonic plant structure that is the body of a developing embryo attached to the maternal tissue in an ovule by a suspensor.

scutellum (PO:0020110): An embryonic plant structure that is a more or less shield-shaped and absorptive portion of an embryo of Poaceae.

suspensor (PO:0020108): An embryonic plant structure at the base of an embryo that develops from a basal cell and connects an embryo proper to the wall of a megagametophyte.

New definitions for embryonic plant cells and tissues

Both now have cross-product definitions, and no asserted is_a children

embryonic plant cell (PO:0025028): A plant cell that is part of an embryo.

is_a embryonic plant structure, intersection_of: is_a plant cell, intersection_of: part_of embryo

Made apical cell (PO:0004000, now embryonic apical cell) is_a apical cell part_of embryo (still dev_from zygote). Should probably obsolete and replace with new term to avoid confusion

Made basal cell (PO:0002002, now embryonic basal cell) is_a plant cell, part of embryo (still dev_from zygote)

Made hypophysis (PO:0020109, now embryonic hypophysis) is_a plant cell, part_of embryo.

(portion of) embryonic plant tissue (PO:0025233): A portion of plant tissue that is part of an embryo.

is_a embryonic plant structure, intersection_of: is_a portion of plant tissue, intersection_of: part_of embryo

Should we add the portion of prefix to the name?

coleorhiza (PO:0020034), embryo cortex (PO:0005014), embryo epidermis (PO:0005015), embryonic shoot apical meristem (PO:0006362), epiblast (PO:0020036), scutellar epithelium (PO:0008048), and scutellum epidermis (PO:0006049) are now inferred children of embryonic plant tissue.

Technically, we could get rid of the is_a embryonic plant structure relation for both, because it would be inferred, but is makes it easier to work with the reasoner off when the relations are there.

Here is a picture of some plant tissues, to show how it works:

Proposed changes/questions for structures that were is_a embryonic plant structure:

Discussion of specific terms was postponed until the next meeting. For more details please see next week's agenda

coleoptile (PO:0020033)

coleorhiza (PO:0020034)

hypocotyl (PO:0020100)

epicotyl (PO:0020035)

mesocotyl (PO:0020037)

hypocotyl-root junction PO:0004724

plumule(PO:0020032)

scutellar node (PO:0004708)

embryonic root (PO:0000045)

radicle (PO:0020031)

embryonic leaf (PO:0006338)

New Physcomitrella and related terms

Collective plant structures:

Discussion of specific terms was postponed until the next meeting. For more details please see next week's agenda

vascular and non-vascular shoot systems

The Moss Ontology did not request these terms, but we may want to add them in order to classify shoot systems.

non-vascular shoot system (PO:0030017): A shoot system that does not have as part vascular tissue.

comment: Does not have any xylem of phloem, but may have other conducting cells, such hydroids or leptoids. Can occur in both the gametophytic and sporophytic phases of non-vascular plants.

vascular shoot system (PO:0030016): A shoot system that has as part vascular tissue.

comment: Has xylem and/or phloem. Occurs only in the sporophytic phase of vascular plants.

participates_in sporophytic phase, has_part vascular system

gametophore (PO:0030018)

Proposed def.: A non-vascular shoot system that consists of the shoot axes and non-vascular leaves of a plant in the gametophytic phase.

participates_in gametophytic phase, develops_from gametophore bud

Comment: A gametophore is the leafy part of the gametophyte of mosses and leafy liverworts, excluding the protonema. Develop from buds that form on the protonema. Antheridia and archegonia arise on the gametophore.

subset for bryophytes

gametophore bud (PO:0030026)

Suggest a new term gametophore bud. This could be a child of bud (PO:0000055: An undeveloped shoot system).

Proposed def'n: A vegetative bud that develops into a gametophore.

Comment: Occurs in mosses and leafy liverworts. Develops from a caulonema cell in mosses.

participates_in gametophytic phase, has_part gametophore apical cell

synonym: brown bud

thallus (PO:0030027)

proposed def: A whole plant in the gametophytic phase that has a flat growth form and no distinct organs.

Comment: A thallus is a gametophyte of liverworts and pteridophytes and develops from a short-lived protonema. Roughly two dimensional growth results from division of a single apical cell. Thalli may be ribbon or heart shaped or almost filamentous. Although there are no distinct organs, there may be tissue differentiation and dichotomous branching.

Other gametophyte terms

We need to keep in mind terms for other types of gametophytes, such as the subterranean, heterotrophic gametophytes of some ferns. RW, DWS, and MAG will maintain a list of terms that we don't need to add yet, but may want to add as time allows or need demands. Can use this list, for example, for writing a renewal of things that still need to be done.

Upcoming meetings 2011:

2011 Semantic Web Workshop June 6th and 7th, Santa Fe, NM.

Hosted by Damian Gessler and the iPlant Collaborative, this two-day workshop will focus on biological applications for semantic web services.

-JE and JP will be attending

-JE has already worked with Damian to implement a SSWAP web service for PO terms, so further collaboration with him and iPlant will benefit the POC going forward.

For more Workshop details: Semantic web.

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

ICBO

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.

Full-Day Workshops Schedule:

July 26 9am-6pm The Ontological Representation of Adverse Events: Working with Multiple Biomedical Ontologies

July 27 8.30am-4pm Facilitating Anatomy Ontology Interoperability

July 26 6.30pm-9pm Evening Workshop: Common Logic

July 27 4pm-8pm Evening Workshop: Doctoral and Post-Doctoral Consortium

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

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

Plant Biology 2011

Early-bird registration ends May 13.

Gramene will be putting together a workshop again, focusing on pathways. PJ will present a PO poster.

TAIR (Kate Dreher) is organizing an Outreach Booth and we are invited to take part.

For inclusion on the program memory stick and in the program book, abstracts must be submitted by May 27.

* 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