POC Conf. Call 5-22-12

POC meeting, Webex Conference Call; Date: Tuesday May 22nd, 2012 10am PDT/1pm EDT

In attendance:

POC members: Laurel Cooper (OSU), Ramona Walls (NYBG), Marie Alejandra Gandolfo (Cornell), Pankaj Jaiswal (OSU), Barry Smith (University at Buffalo, NY), Justin Preece (OSU)

Absent: Justin Elser (OSU), Dennis Stevenson (NYBG), Chris Mungall (Lawrence Berkeley National Lab)

Collaborators: none

Any changes or corrections (additions/deletions, etc) needed in the minutes from the POC_Conf._Call_5-8-12?

Back to POC Meetings Minutes

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Update and Progress report from Cornell (MAG)

• We have now ~330 slides and more than 5000 photos in CUPAC.bh.cornell.edu

Photos have been calibrated based upon the magnifications

Also have ~200 boxes of additional slides (?) that cover taxa from algae to angiosperms, not including fungi. Contacting other groups at Cornell ...rose (??), who work on Physcomitrella and tomato. CUPAC will be the repository. Collection from Germany may also be included.

KN will provide everyone with a password, so everyone will be able to edit the information of the photo or slide- this week or next week

• All the images are now available and they are all calibrated (measuring tool is completely functional).

Pictures are available for each of the 1200 terms in PAE in the PO (or at least the majority of them, especially the Angiosperms).

e.g. Capsella embryos and flowers

PJ: Can we remove the copyright stamp on the images? Better to have it along the bottom of the image, credit the projects CUPAC and PO, use Creative Commons license like on the PO website.

• RW and MAG will start editing the images as planned. Tool for measuring and putting on arrows to the parts.
• This will include a description of the slide, with taxon name, structure and type of tissue/cell type, etc, based on PO numbers. Not clear where this info will be displayed.

PJ: what are the plans for prioritizing the annotations of the images? Should look through the list of genomes at Phytozome.net and focus on the ones in that list first, and the ones we have data for in the PO. Well-known, well-studied species, Brassicaea, Oryza. e.g. Zea mays,

Do we have a mapping between the terms used in the "Slide Description' and the PO ids? It would be good to use the PO terms with ids, if available.

Currently, will be done using annotation tool at Cornell, will move towards using the new PO desktop tool as it is developed.

Needs: A prioritized timeline to cover the PO terms and species of interest

Need a URL that has the POid in it, so we can search the images by the PO:id.

Meeting report: Semantics of Biodiversity Workshop

May 16 - 18, 2012

University of Kansas Biodiversity Institute, Lawrence, Kansas

The goals of this workshop:

1) Clarification of terms used in the biodiversity, genomics, and ecological communities

2) Steps to take in building a Biocollections Ontology.

BS, MAG and RW attended

The purpose of this meeting was to discuss if and how the Darwin Core terminology should be converted to and OWL ontology.

From the Darwin Core home page:

"The Darwin Core is body of standards. It includes a glossary of terms (in other contexts these might be called properties, elements, fields, columns, attributes, or concepts) intended to facilitate the sharing of information about biological diversity by providing reference definitions, examples, and commentaries. The Darwin Core is primarily based on taxa, their occurrence in nature as documented by observations, specimens, and samples, and related information. Included are documents describing how these terms are managed, how the set of terms can be extended for new purposes, and how the terms can be used. The Simple Darwin Core [SIMPLEDWC] is a specification for one particular way to use the terms - to share data about taxa and their occurrences in a simply structured way - and is probably what is meant if someone suggests to "format your data according to the Darwin Core"."

BS gave a presentation on the advantages of using the BFO as an upper level ontology and following the guidelines of the OBO Foundry.

The collection of Google docs on from the meeting can be viewed at: https://docs.google.com/folder/d/0B6UQCyNEE7qESzNvWmZFbVlTS21PZElVNUZ0Mm1PZw/edit?pli=1

There was some discussion of setting up a biodiversity ontology governing body, similar to OBO Foundry, but for ontologies within the biodiversity domain. Would overlap with some of the OBO Foundry ontologies, such as anatomy ontologies, EnvO, PCO. TWDG (Biodiversity Information Standards, also known as the Taxonomic Databases Working Group) currently oversees Darwin Core standards.

Open Items from Past Meetings:

ovule

At the POC_Conf._Call_4-17-12, we agreed to make ovule a plant organ, instead of a cardinal organ part.

It may be part of carpel, which is a plant organ, but we already have other examples of organs that are part of other organs (e.g., nucellus and pollen sac).

Also, ovule is currently part_of ovary, but that is only true for angiosperms. Ovules can be found in all seed plants.

proposed def: ovule (PO:0020003): A plant organ (PO:0009008) that has as parts a nucellus (PO:0020020) containing a female gametophyte (PO:0025279), one or two integuments (PO:0020021), and a funicle (PO:0020006).

comment: A seed (PO:0009010) develops from an ovule. In angiosperms, an ovule is part of an (plant) ovary (PO:0009072). In gymnosperms, an ovule is part of an ovuliferous scale (add term).

Comment should say: should be in conifers, not gymnosperms, as Gingko have a naked ovule, ovary has_part ovule

RW: It would be more correct to say ovary has_part ovarian ovule, but that would conflict with the relation ovarian ovule part_of ovary.

PJ requested separate subtypes for ovarian ovule and non-ovarian ovule, to make annotation easier. Suggest using ovuliferous scale ovule instead of non-ovarian ovule. See Items_for_future_meetings#ovuliferous_scale.

Proposed def: ovarian ovule (PO:0025490): An ovule (PO:0020006) that is part of an ovary (PO:0009072).

comment: Found in angiosperms.

Accepted proposed def'ns; but suggested we should use "plant ovule", "plant ovary ovule" and similarly, "plant ovary"

Proposed def: ovuliferious scale ovule (PO:0025491): An ovule (PO:0020006) that is part of an ovuliferous scale (add).

Comment: Found in gymnosperms. replace with conifer

Made embryo sac part of ovarian ovule, instead of part_of ovule, but it should really be located_in.

Located_in is more appropriate for one organism located another organism, example the fetus and the mother.

Located_in vs contained_in: original idea was that a solid object that is part_of another object is located_in and contained_in was for when the object was not a part of other object.

Examples are plant substances such as cuticle (currently adjacent_to) and xylem sap (when added)- could be located_in or maybe contained_in. Need to clarify

BS: A is located_in B means either: A is a part of B and is inside B, or it is contained in B (like a fetus). Located_in and part of or just located_in.

embryo sac is only in the angiosperms, in gymnosperms the megagametophyte is in the archegonium

Made funicle (PO:0020006) part of ovule.

Antiraphe, chalaza, integument, nucellus, and raphe and funicle are part_of ovule. Will need to add comment to each of these saying: "If you are annotating to this structure for an angiosperm, please add an additional annotation to plant ovary ovule (PO:0025490). If you are annotating to this structure for an gymnosperm, please add an additional annotation to ovuliferous scale ovule (PO:0025491)." --okay

Questions about the PO tuber terms

Root primordia and roots

lateral root

lateral root (PO:0020121), current def.: A root that develops from a lateral root primordium located in the pericycle layer of a primary root.

proposed def.: A root (PO:0009005) that develops from a lateral root primordium (PO:0000016) that is part of another root.

comment: A lateral root primordium may develops on any root, including a primary root (PO:0020127), on an existing lateral root (PO:0020121), or a shoot-borne root (PO:0000042) . In seed plants, a lateral root primordium generally develops from pericycle cells (PO:0025261), but cells of an endodermis (PO:0000252) may also participate in its formation in some species. In ferns, lateral root primordia develop from the endodermis.

This is consistent with the definition of lateral root suggested by Rich Zobel (A root developing from a parent root.) He also suggested we add a new term called "non-pericyclic lateral root" (RZ's def.: A lateral root that does not arise from pericycle tissues.), as a subtype of lateral root. If we add this term, we should add the sibling term "pericyclic lateral root" (A lateral root that develops from a root primordium that is part of a pericycle.).

Okay to add pericyclic and non-pericyclic lateral root as subtypes of lateral root, plus corresponding lateral root primordium types.

root anlagen

Root anlagen is_a portion of pericycle tissue, but this is not always true. Lateral roots can also develop from endodermis, and shoot-borne root develop from parenchyma cells on a stem or branch (or elsewhere).

New proposed definition for root anlagen (PO:0025433): A portion of plant tissue (PO:0009007 that is committed to the development of a root primordium (PO:0005029).

Comment: Only detectable by gene expression, not morphology. May arise in a pericycle (PO:0006203), as for lateral roots in most seed plants, an endodermis (PO:0000252), as for lateral roots in ferns, or from parenchyma cells (PO:0000074) that are part a shoot axis (PO:0025029), in the case of a basal root (PO:0025002) or shoot-borne root (PO:0000042).

okay

root primordium

root primordium (PO:0005029), new def.: A primordium (PO:0025127) that develops from a root anlagen (PO:0025433) and is committed to the development of a root (PO:0009005).

Comment: Root primordia may arise from pericycle cells (PO:0025261), as in most seed plants, cells of an endodermis (PO:0000252), as in ferns, or from cells on a shoot axis (PO:0025029), in the case of basal root primordia (PO:0025479) and shoot-borne root primordia (PO:0025480). Transition from root primordium to root occurs with the formation of a root cap (PO:0020123), shortly after the development of a root apical meristem (PO:0020147).

ref.: Steves and Sussex, ISBN:0521288959, POC:curators

added root primordium develops from root anlagen (PO:0025433).

okay

adventitious root primordium (PO:0008038): We don't actually have a term for adventitious root. This term has been obsoleted. There are no annotations on adventitious root primordium.

basal root primordium, new term (PO:0025479): A root primordium (PO:0005029) that is committed to the development of a basal root (PO:0025002).

comment: Transition from basal root primordium to basal root occurs with the formation of a root cap (PO:0020123), shortly after the development of a root apical meristem (PO:0020147).

synonym: adventitious root primordium (broad)

added basal root develops_from basal root primordium

Looked at the term for "crown root". Crown roots are similar to basal roots, in that they arise from the base of the stem, but they are found in grasses, which don't have a hypocotyl. Need to look at the definition of crown root and all of the development stage terms that refer to it. Maybe add comment to basal root that you don't use it for grasses. See if RZ's treatment addresses crown roots. Check definitions with Mary Schaeffer.

shoot-borne root primordium, new term (PO:0025480): A root primordium (PO:0005029) that is committed to the development of a shoot-borne root (PO:0000042).

comment: Transition from shoot-borne root primordium to shoot-borne root occurs with the formation of a root cap (PO:0020123), shortly after the development of a root apical meristem (PO:0020147).

synonym: adventitious root primordium (broad)

added shoot-borne root develops_from shoot-borne root primordium

okay

lateral root primordium (PO:0000016), existing def.: A root primordium that is derived from a root pericycle and will develop into a lateral root.

lateral root primordium (PO:0000016), proposed def.: A root primordium (PO:0005029) that is committed to the development of a lateral root (PO:0020121).

comment: In seed plants, a lateral root primordium generally develops from pericycle cells (PO:0025261), but cells of an endodermis (PO:0000252) may also participate in the formation of a lateral root primordium in some species, and in ferns lateral root primordia develop from the endodermis. Transition from lateral root primordium to lateral root occurs with the formation of a root cap (PO:0020123), shortly after the development of a root apical meristem (PO:0020147), which can occur before the lateral root penetrates the exterior of the parent root.

>Removed the relation lateral root primordium develops_from pericycle (PO:0006203), because it is not always true.

>Added relation lateral root primordium part_of root, because that is what makes it a lateral root primorodium.

>If we decide to add terms for non-pericyclic and pericyclic lateral roots, we could add corresponding primordia types. It would make it easier to define the root types.

primary shoot (PO:0006341) vs stem (PO:0009047)

We need to look at primary shoot (PO:0006341) (CPS > shoot system) vs stem (PO:0009047) (plant organ > plant axis > shoot axis).

PO:0006341 has always been a subtype of shoot system PO:0009006. They were originally called "shoot" and "primary shoot". PO:0009006 was renamed "shoot system" to distinguish it from shoot axis and make it clear that it was referring to the system, not the organ. Presumably when shoot system was renamed, the child term, primary shoot, did not get renamed. The definitions of PO:0006341 should say "A shoot system developing from the embryonic shoot apical meristem." The ontology structure and the fact that we have a separate term for stem indicate that this terms is referring to a type of shoot system.

Propose new name and definition: primary shoot system (PO:0006341): A shoot system (PO:0009006) developing from the embryo shoot apical meristem (PO:0006362).

PO-CARO

Post-poned to future meeting. Some of this will be part of the discussion of how to deal with seeds, etc.

The Common Anatomy Reference Ontology (CARO) is undergoing a major revision as CARO 2.

Since all of the PAE root terms are defined based on CARO, it would be good to review their proposed definitions and provide them with feedback before their release.

This will be especially important if we want to include structures that were part of a plant, as this may not be covered by their definition.

Also, it is not clear how or if in vitro plant structures would fit into CARO.

Upcoming meetings and Presentations 2012:

MOSS 2012 and The 3rd International Symposium on Molecular Systematics of Bryophytes

Thursday, June 14, 2012 - Friday, June 22, 2012

The New York Botanical Garden

Attendees have the option of registering for MOSS 2102 ($225), the Symposium on Molecular Systematics of Bryophytes ($225) or both ($400).

RW submitted an abstract for a poster File:PO poster Moss 2012.pdf.

Crop Ontology Workshop

For more information see the wiki page: Crop_Ontology_Workshop_at_OSU,_2012

Dates TBA: probably Sept. 13-15th

The focus of the workshop will be on mostly development stages and traits for the crop plants

Botany 2012

July 7 - 11, 2012 - Columbus, Ohio

• PO workshop on Sunday, July 8th, 9:00AM - 12:00PM

see: Botany 2012 workshops

This is a half-day (morning) workshop. The schedule now links to the correct abstract.

An announcement has been posted on the PO home page and FB page.

Goal of workshop: Will be to teach people (mostly botanists) how to access and use the PO, including how to send feedback, suggest new terms, etc.

PJ: suggest that we go there with a 'draft' version of the Plant Phenotype Ontology and show them how to use these in character matrices.

A desktop version of the image annotation software should be ready to demo at this meeting.

exhibitor's booth

We should also consider hosting an outreach booth.

Not a bad deal for non-profits: $500 for A 10 x 10 Booth Space at Botany 2012, and 2 complimentary registrations for the conference. (plus all the extras!)

• 2 months of Rotating Banner Ads in the online American Journal of Botany

• A Rotating Banner Ad in one edition of the online Plant Science Bulletin

• A Rotating Banner Ad on the Botany 2012 abstract submission site

• A Rotating Banner Ad on the 2012 Conference Registration site.

PJ will check with Gramene and Doreen Ware to see if they want to co-host a booth.

We should do the booth. PJ will attend to host the booth for both Gramene and PO.

Bio-Ontologies SIG 2012

Where: July 13 - 14, 2012, Long Beach, CA. Co-located with ISMB 2012

When: Submissions Due: April 13th, 2012 (Fri)

See: Bio-Ontologies SIG 2012

Three types of submissions.

- Short papers, up to 4 pages. - Poster abstracts, up to 1 page. - Flash updates, up to 1 page

Successful papers will be presented at the Bio-Ontologies SIG.

Poster abstracts: time will be allocated during the 2 days for at least one poster session.

Flash updates are for short talks (5 min) giving the salient new developments on existing public ontologies. Authors of posters can also provide a flash update. Unsuccessful papers will automatically be considered for poster presentation.

ASPB Plant Biology 2012

July 20 - 24, 2012 - Plant Biology 2012, Austin, TX

Link to meeting page: ASPB2012

Abstract was submitted for submission for minisymposia consideration.

Joint workshop is planned with PO, Gramene and TAIR

Registration is open, Advance Discounted: May 12-June 15

ICBO 2012

International Conference on Biomedical Ontologies (ICBO 2012), July 22nd-25th, Graz, Austria

co-located with the 7th International Conference on Formal Ontologies in Information Systems (FOIS 2012)

RW and BS (with JE, AG, DWS and PJ) submitted a short paper describing a plant disease extension of the Infectious Disease Ontology. This paper was accepted and is being revised. Wiki page for notes on Plant Disease Ontology.

Relevant dates

• Feb. 28th, 2012: Notification of paper acceptance
• April 15th, 2012: Poster, early career symposium, software demonstrations and workshop papers submission deadline
• May 15th, 2012: Notification of poster, early career symposium, software demonstrations and workshop paper acceptance
• June 30th 2012: Deadline for all camera-ready copies for the proceedings

RW sent around a draft of an abstract for a poster summarizing the PO-FNA collaboration, with the folks from FNA.

BS will be organizing an OBO Foundry meeting the afternoon of the day before the conference starts

Anatomy Ontology Course at NESCent, July 30th- Aug 3rd, 2012

Link to: Anatomy Ontology course

from Paula Mabee: Opening are available the Anatomy Ontology course.

Link to Course materials

This course aims to teach proper ontology design principles and practices such that anatomical interoperability across evolutionarily disparate taxa is achieved. It further seeks to promote community growth and adoption of ontology-based methods and tools. The subsequent benefit is in the form of shared access to the unique data store of each community (e.g. genetic, genomic, developmental, and evolutionary data).

Apply here: [1]

Application deadline is April 4th, 2012 (extended through mid-April)

Next meeting scheduled for Tuesday, June 5, 2012 at 10am PDT/1pm EDT

See: POC_Conf._Call_6-5-12