POC Conf. Call 4-17-12

POC meeting, Webex Conference Call; Date: Tuesday Apr 17th, 2012 10am PDT/1pm EDT

In attendance:

POC members: Laurel Cooper (OSU), Ramona Walls (NYBG), Justin Preece (OSU), Pankaj Jaiswal (OSU), Justin Elser (OSU), Marie Alejandra Gandolfo (Cornell).

Absent: Dennis Stevenson (NYBG), Chris Mungall (Lawrence Berkeley National Lab), Barry Smith (University at Buffalo, NY)

Collaborators: none

Any changes or corrections (additions/deletions, etc) needed in the minutes from the POC_Conf._Call_4-10-12?

Back to POC Meetings Minutes

Streaming recording link: https://ontology.webex.com/ontology/ldr.php?AT=pb&SP=MC&rID=64088372&rKey=8d6313b4d2894779

Download recording link: https://ontology.webex.com/ontology/lsr.php?AT=dw&SP=MC&rID=64088372&rKey=63402cb01828c48f

Open items and user requests:

root cambial zone

There are is_a AND part_of relationships between 'root cambial zone' and 'root'.

JE can you make this change without having to reload everything?

ie: remove the is_a relationship between 'root cambial zone' and >'root'

Fixed in dev file?

This relation should have read "root cambial zone part_of root" instead of "root cambial zone is_a root". However, it is not necessary to change it to part of in live, because the part_of relation is inferred by the reasoner (and therefor already there in plant_ontology_assert.obo).

RW will remove the relation "root cambial zone is_a root" from the various files in the live tag, as well as from the dev version.

JE will try to remove just that relation from the database, but if that doesn't work, he will reload the database with the new file onto Beta, then move it over to live when it is ready.

Separate Aspect Files on Bioportal

Are we going to keep generating these and posting them there?

Bioportal is having issues as all three files have the PO abbreviation.

We will keep generating these and posting them on Bioportal through the next release #18. After that people will have to come to the SVN to obtain them.

check for details...

On recording: Alert users that we will stop supplying these files after release 18.

Ask BioPortal to stop serving them now. Bioportal should only server plant_ontology.obo (or does it serve plant_ontology_assert.obo?)

• Need to check with Gramene and TAIR and SGN to see if they are still using those files

• note that these are derived from the plant _ontology assert_basic file.

add top-level plant ontology term

This is in reference to the issues raised by NM of SGN:

LC suggest we make a root term "plant entity' This would be consistent with BFO and avoid the problems above.

from RW: I think it would be good to incorporate some of the BFO and CARO terms.

For example:

BFO:entity

> BFO:continuant

>> BFO:independent continuant

>>> CARO:anatomical entity

>>>> PO:plant anatomical entity

> BFO:occurent

>> BFO:processual occurent

>>> PO:plant structure development stage

GO has links between aspects only as bridge files.

SGN currently has to run script to strip out cross-aspect relations (has_participant and participates_in).

PJ does not want to add an upper-level terms, because in some applications, only the upper-level term will show up, so it won't be clear that there are two different branches. We will look into how other sites are handling the cross-aspect relations and

PJ suggested creating another file that strips out cross-aspect relations and presenting them as a bridge file.

Create another file called something like "plant_ontology_assert_no_hp or pi.obo" (will need to work out name and provide this on the download page. Alternative is to automatically generate a separate file that inserts a top level term and provide that to SGN.

PJ and JE will look at options- one would be for JE to write a script to add in a top level term "entity" that gets added after each commit.

One solution would be for them to load the separate aspect files.

We still need to revisit the issue of changing names of all the files, if that is something we want to do. (see last week's minutes).

Download ontologies page must be updated for the next release, along with tutorials

areole bud and lamina areole

At the POC meeting on 11-8-11 we to add a term for areole, refering to a type of bud in cacti. However, this term is also used to refer to a part of a leaf (or other phyllome) lamina. The term for lamina areole was requested by one of our Arabidopsis users (Dora).

Suggest we add a general term for lamina areole, which will cover petals, etc., and a more specific term for leaf lamina areole.

Proposed definition for lamina areole (PO:0025391): A cardinal organ part that is the smallest part of a lamina that is completely surrounded by veins.

Comment: Any order of vein can form the sides of an areole. Taken together, the areoles form a contiguous field of polygons over the area of a lamina. part_of lamina

Proposed definition for leaf lamina areole (PO:0025392): A lamina areole that is the smallest part of a leaf lamina that is completely surrounded by leaf veins.

Comment: Any order of leaf vein can form the sides of an areole. Taken together, the areoles form a contiguous field of polygons over the area of a leaf lamina. Free ending veinlets (PO:0025390) may be found within a leaf lamina areole. part_of leaf lamina

Ref: ISBN:9780801475184

"smallest part" is subjective. PJ suggested instead to say that it is a unit part of a lamina. However, that is equally subject. Will post new proposed definition on SF.

Proposed definition, bud areole (PO:0025353): An axillary bud that does not elongate, in which the leaves develop as spine leaves.

Comment: Found in Cactaceae. Appears as a cluster of spines. May be covered in trichomes. In species with tubercles, the areole is often found at the distal end of the tubercle. The areole originates in the axil of the leaf that becomes the tubercle but is displaced to the tip of a tubercle through adnation.

is_a axillary bud

ref.: Bell and Bryan, ISBN:9780881928501

Should be called areole bud.

Cannot know if a bud is going to elongate or not. Can only say that it is not elongated.

Should be an axillary vegetative bud (PO:0004712), but need to fix definition of axillary vegetative bud so it matches vegetative bud.

Is not adnation, but elongation of the tubercle that displaces areole.

new proposed definition, areole bud: An axillary vegetative bud (PO:0004712) that is not elongated, in which the vascular leaves (PO:0009025) develop as spine leaves (PO:0025173).

Comment: Found in Cactaceae. Appears as a cluster of spine leaves. May be covered in trichomes (PO:0000282). In species with tubercles (PO:0025352), the areole bud is often found at the distal end of the tubercle. The areole bud originates in a leaf axil (PO:0009023) of a leaf that becomes a tubercle but is displaced to the tip of a tubercle through elongation of the tubercle.

Could add subset for Cactaceae.

primordium

primordium (PO:0025127), current def.: A portion of plant tissue that differentiates and develops from meristem tissue into a new plant structure. [source: POC:Curators]

Comment: The primordium is the first distinct form in the development of a plant structure.

An issues with this definition came up while we were working on new term requests for Agron-Omics. We felt primordium should probably be an organ, because all primordia have at least two types of tissue - protoderm and ground meristem. Primodia represent plant structures in the earliest stages of development.

There are four types of primordia that are not for organs: flower primordium, ovule primordium, anther primordium and ligule primordium. Therefor, it will be a problem to make primordium is_a plant organ.

For ovule primordium (PO:0000018): We will make ovule a subtype of plant organ, because it fits the definition of plant organ. Will post new proposed definition on SF.

okay

For flower primordium (PO:0004706): We will obsolete this term and replace with "floral organ primordium" (a bin term for petal, sepal, etc. primordium) and add "flower primordium" and "floral primordium" as related synonyms of flower meristem (PO:0000229).

See for example PMID:17272833 and PMID:19717616, two of the PO annotations for flower primordium, which are really referring to floral organ primordia.

There a number of annotations on flower primordium that will have to be moved.

Okay. Also checked this with Amy Litt at NYBG, and she said it made sense to her.

For anther primordium (PO:0009066): Anther is a collective plant structure (4 pollen sacs, which are plant organs). Not much we can do about this.

For ligule primordium (PO:0020105): Ligule is a cardinal organ part ("A membranous or hairy appendage on the adaxial/upper surface of a leaf, at the junction between sheath and blade, especially in grasses." part_of vascular leaf).

Even though we don't have a PO term for it, people also use the term "leaflet primordium", which is also a cardinal organ part. (We have a term for formation of leaflet primordium).

proposed definition, primordium (PO:0025127): A plant organ/plant structure/portion of meristem tissue in an early stage of development after a protoderm has begun to develop and before anatomical structure morphogenisis (GO:0009653).

new proposed def.: A portion of meristem tissue (PO:0009013) that has been committed to the formation of a particular plant structure.

Maybe say composed of ground meristem and protoderm. Primordium stage ends when non-meristematic cells start to develop. Can still have meristematic cells present after primordium stage ends.

stem cells - anlagen - primordium - organ or organ part

Need to look at which tissue form first. Maybe epidermis.

How does this relate to plasitchrons?

Will post proposed definitions for primordium and subtypes for next week.

subtypes of primordium

Need a little work too. Will be discussed at future meeting.

New items for the July 2012 Release

Page set up with goals and priorities etc.

Need to update tutorials and dowload page on PO website.

Upcoming meetings and Presentations 2012:

Semantics of Biodiversity Workshop

May 16 - 18, 2012

University of Kansas Biodiversity Institute, Lawrence, Kansas

The goals of this workshop (still being refined): 1) Clarification of terms used in the biodiversity, genomics, and ecological communities, and 2) Steps to take in building a Biocollections Ontology.

BS, MAG, and RW are attending.

SPNHC 2012

Annual meeting of the Society for the Preservation of Natural History Collections

Yale University, New Haven Connecticut June 11-16, 2012

Any interest in making a PO presentation at this meeting? Perhaps RW and/or DWS could just go for the day of the presentation, since it is local (New Haven, CT).

The theme for the meeting is "Emerging Technology and Innovation in Natural History Collections Management" (focus on the tools, innovative methods and collaborations that will move the natural history collections community forward).

From PJ: If we can show progress in the FNA work or Morphobank yes we should

Crop Ontology Workshop

For more information see the wiki page: Crop_Ontology_Workshop_at_OSU,_2012

Dates TBA: probably Aug 6th to 8th or in Sept.

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

Ruth Bastow is contacting some of the interested people to see which of these dates work best.

Can we consider September? RB is available 12th -25th September

Botany 2012

July 7 - 11, 2012 - Columbus, Ohio

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

see: Botany 2012 workshops

The meeting web site has been fixed so this is now listed as a half-day (morning) workshop. The schedule now links to the correct abstract.

RW will prepare an announcement for the PO home page and FB page.

Workshop goal 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, early Bird Registration: by May 11

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)

LC will forward email to PO announce list and post on PO Facebook page.