POC Conf. Call 6-19-12

POC meeting, Webex Conference Call; Date: Tuesday June 19th, 2012 10am PDT/1pm EDT

In attendance: Laurel Cooper (OSU), Ramona Walls (NYBG), Pankaj Jaiswal (OSU), Justin Preece (OSU), Justin Elser (OSU), Dennis Stevenson (NYBG), Barry Smith (University at Buffalo, NY), Marie Alejandra Gandolfo (Cornell)

Absent: Chris Mungall (Lawrence Berkeley National Lab)

Collaborators: none

Streaming recording link: https://ontology.webex.com/ontology/ldr.php?AT=pb&SP=MC&rID=65969132&rKey=9f9f445660d68cfa

Download recording link: https://ontology.webex.com/ontology/lsr.php?AT=dw&SP=MC&rID=65969132&rKey=701561c108bc5518

Any changes or corrections (additions/deletions, etc) needed in the minutes from the POC_Conf._Call_6-12-12?

Back to POC Meetings Minutes

Report from Moss 2012 meeting

-Great feedback on PO poster.

-People would like to be able to search the ontology using a gene sequence, rather than a gene name (eliminate the step of having to find the orthologs and names for all other species first).

-Maybe we could have a link out to something like Biomart, have search tools that link to other databases.

-People like the idea of having on site to search across all ontologies for plant data.

-Many people interested in using PO to find data. Lots of interest in having more data for bryophytes associated with ontology terms, but no good solutions about who will do those annotations. SR felt that it was not going to be possible to get funding for a database, so it will have to be done another way. He said people can contribute annotations through the Cosmoss site, but no one does it. In crops, there is an incentive for breeders to create annotations, but for mosses, it is more of an "academic exercise", so there is less incentive.

-DWS suggested that there may be alternative sources (like NGOs) for database money.

-No news about releasing the rest of the annotation data to the PO yet.

Upcoming Release:

At the POC_Conf._Call_4-10-12 we decide that the next release would be in late June to early July, before the BSA meetings. We have a number of important changes that have taken place,

• 20 new PAE terms, including the new upper-level level terms for the PAE

For more information about the changes see: Summary of Changes to PO July 2012 and New terms and obsolete terms July 2012 Release

Only have obsoleted two terms:

• flower primordium (PO:0004706)

consider flower meristem (PO:0000229) or floral structure primordium (PO:0025477) instead.

This has 27 annotations, mostly from TAIR, one Gramene and one SGN

• adventitious root primordium (PO:0008038) - consider basal root primordium (PO:0025479) and consider shoot-borne root primordium (PO:0025480)

LC has sent an email to TAIR and SGN to inform them of the upcoming changes.

• Propose we go ahead and do this release, so we have an updated version on the live site.

We will make the release asap, and update the manuscripts to match the upcoming release. It will not be in review before the release is out.

JE will look into whether or not he can make the changes to the website and server at the same time as the release.

What other things should be included in it- open trackers that need to be dealt with:

We will finish edits this week, so the ontology can be reviewed next week and preparations made for the release. Should try to have release out before the Botany meeting (before July 4th).

Only the changes on today's agenda will go into the next release. Other items (including ovary) can wait until the next release.

Ale will need a list of new terms (RW will send to her in the next few days).

Update and Progress report from Cornell (MAG)

last update was on POC_Conf._Call_5-22-12

From MAG: "I started editing the photos and I am focusing on all the ones with "parenchyma" terms. Ramona will present in BSA the "parenchyma" example so I am working on those.

We have added more taxa since the last time (my technician is in vacation this week) so I do not have the exact number."

Update on Semantic Image Annotation (SIA)

From JP:

• The image annotation app has been named SIA (Semantic Image Annotator, pronounced "see-yah").
• We have functional Windows XP and Linux packages. Working on the Mac and Windows 7 builds -- priority is on the Mac build due to RW's July 8 demo in Columbus.
• Nikhil and I met with PJ last week to go over the application's features in detail. PJ is working on user documentation to go with the application.
• I am working with JE to get a bug report/feature request system in place before we hand it over to Ale and her group.

MAG has an XP laptop, and RW or DWS could install a windows desktop on their machines if needed. If necessary, JP can send a computer from OSU for us to use.

New upper level terms for Plant Anatomical Entity branch of the PO

New proposed hierarchy:

New proposed term: multi-tissue plant structure (MTPS) (PO:0025496)

proposed def., MTPS: A plant structure (PO:0009011) that has as parts two or more portions of plant tissue (PO:0009007) of at least two different types and which through specific morphogenetic processes forms a single, distinct structural unit demarcated by bona-fide boundaries from other distinct structural units of different types.

• Added definition dbxref to CARO:0000055.

BS suggested we should think about not saying "distinct" twice- maybe should see if CARO will revise theirs as well.

Also, could say more than one, instead of two or more, but it is good to try to stay close to CARO's definition.

Revised proposed def.: A plant structure (PO:0009011) that has as parts two or more portions of plant tissue (PO:0009007) of at least two different types and which through specific morphogenetic processes forms a single structural unit demarcated by bona-fide boundaries from other structural units of different types.

Sub-classes of MTPS:

plant organ (PO:0009008):

new proposed def'n: plant organ (PO:0009008): A multi-tissue plant structure (PO:0025496) that is a functional unit, is a proper part of a whole plant (PO:0000003), and includes portions of plant tissue (PO:0009007) of at least two different types that derive from a common developmental path.

new proposed comment: Examples include stem (PO:0009047), leaf (PO:0025034), and root (PO:0009005). May include individual cell types that are not part of tissues (e.g., idioblasts (PO:0000283)). A plant organ may have one or more different plant organs as parts, such as sporophyll (PO:0009026) that may have as part a sporangium (PO:0025094) or a carpel that may have as part an plant ovule (PO:0020003).

Comment should say "individual plant cells (PO:id)" instead of "individual cell types".

seed (PO:0009010):

Current def'n: A plant structure that develops from an ovule and has as parts an embryo enclosed in a seed coat.

propose revised def'n: A multi-tissue plant structure (PO:0025496) that develops from a plant ovule (PO:0020003) and has as parts a plant embryo (PO:0009009) enclosed in a seed coat (PO:0009088).

okay

fruit (PO:0009001)

proposed def.: A multi-tissue plant structure (PO:0025496) that develops from a gynoecium (PO:0009062) and has as parts one or more plant embryos (PO:0009009) located within it.

comment: A fruit may contain additional plant structures that were part of the flower that mature along with the gynoecium, such as a receptacle. A fruit may develop without fertilization in cases of parthenocarpy, apomixis, or other hormone-induced conditions. Fruits only occur in angiosperms.

The embryos, are actually located in the seeds, which are part of a fruit. Why not say a fruit has as parts one or more seeds, instead of saying it has one or more embryos located in it. Seems like we are adding an extra layer. Then we could add to the commment that it may not contain seeds under special circumstances.

revised def.: A multi-tissue plant structure (PO:0025496) that develops from a gynoecium (PO:0009062) and may have as parts one or more seeds (PO:0009010).

comment: A fruit may contain additional plant structures that were part of the flower that mature along with the gynoecium, such as a receptacle. A fruit may develop without fertilization in cases of parthenocarpy, apomixis, or other hormone-induced conditions and may not always contain seeds. Fruits only occur in angiosperms.

New term: collective plant structure (PO:0025497)

This is a general term, parent to collective plant organ structure (PO:0025007) and collective organ part structure (PO:0025269); see below. The important part of a collective plant structure is that it is a collection of two or more similar structures that are not tissues (e.g., two organs, two cardinal organ parts). We decided last week that CPS should not be subtypes of MTPS, because not all CPS's are distinct structural units.

proposed definition: A plant structure (PO:0009011) that is a proper part of a whole plant (PO:0000003) and includes two or more adjacent plant organs (PO:0009008) or adjacent cardinal organ parts (PO:0025001), along with any associated portions of plant tissue (PO:0009007).

okay

Sub-classes of collective plant structure (PO:0025497)

collective plant organ structure (PO:0025007)

This is currently named collective plant structure. At the POC meeting on 5-?-12, we discussed renaming it "collective plant organ structure", which is clearer.

New proposed def.: A collective plant structure (PO:PO:0025497) that is a proper part of a whole plant (PO:0000003), and is composed of two or more adjacentplant organs (PO:0009008) and the associated portions of plant tissue (PO:0009007).

comment: A collective plant organ structure must have as parts at least two plant organs (PO:0009008) that do not have a part_of relation between them, that is, one must be adjacent to the other, rather than one part of the other. The plant organs in a collective plant structure can be of the same type, such as the corolla (PO:0009059) composed of multiple petals (PO:0009032), or of different types, such as a shoot system (PO:0009006), composed of shoot axes (PO:0025029) and phyllomes (PO:0006001). Other examples include flower (PO:0009046), perianth (PO:0009058), and inflorescence (PO:0009049). See also collective organ part structure (PO:0025269), for collective plant structures composed of parts of multiple organs, but no complete organs.

We had some discussion about obsoleting terms. We have been following the policy that a term is only obsoleted when the definition associated with an ID changes. We do not obsolete terms for name changes. BS suggested that we check with CM about whether or not a name change merits obsoletion. In this case, it can be confusing because there is a new term with the same name.

BS also asked how we make sure users start using the new name. We can't make them, but we do have a detailed list of changes with each release, including name changes. We do this on already the release wiki pages. The SF tracker also documents everything.

collective organ part structure (PO:0025269)

This is the existing term that is currently defined as: "A plant structure composed of two or more cardinal organ parts from adjacent organs and any associated portions of plant tissue." examples are septum, pseudostem etc.

propose revised def'n: A collective plant structure (PO:0025497) composed of two or more cardinal organ parts (PO:0025001) from adjacent plant organs (PO:0009008) and any associated portions of plant tissue (PO:0009007).

comment stays as is

Remove "from"

revised def: A collective plant structure (PO:0025497) composed of two or more cardinal organ parts (PO:0025001) that are part of adjacent plant organs (PO:0009008) and any associated portions of plant tissue (PO:0009007).

Sub-classes of plant structure, for the parts of the various multi-tissue plant structures

cardinal part of multi-tissue plant structure (PO:0025498)

This is similar to "cardinal plant organ" (or cardinal part of plant organ) but includes parts of multi-tissue plant structures that are not organs (e.g., aril, which is part of seed).

Proposed def.: A plant structure (PO:0009011) that is a proper part of a multi-tissue plant structure (PO:0025496) and includes portions of plant tissue (PO:0009007) of at least two different types.

Comment: Includes cardinal parts of plant organs (PO:0025001) as well as other multi-tissue plant structures. Cardinal refers to the fact that these are biologically meaningful parts, not arbitrary. Includes parts with both fiat boundaries, such as leaf base (PO:id), and bona-fide boundaries, such as leaflet (PO:id).

Add to comment something about the fact that even parts with bona fide boundaries usually also have tiny fiat boundaries. Actually, most COPs have both fiat and bonafide boundaries. Say something about boundaries primarily being of one type or the other. Would be good to add some more examples as well.

cardinal organ part (PO:0025001)

Do we want to rename this cardinal part of plant organ? No, add it as a synonym

proposed new def.: A cardinal part of multi-tissue plant structure (PO:0025498) that is a proper part of a plant organ (PO:0009008) and includes portions of plant tissue (PO:0009007) of at least two different types.

revised comment: Cardinal refers to the fact that these are biologically meaningful parts, not arbitrary. Examples include petiole (PO:0020038), lamina (PO:0025060), and leaflet (PO:0020049). See also collective organ part structure (PO:0025269), for plant structures composed of parts of multiple organs.

In comment, say "biologically meaningful and not arbitrary parts of a plant organ".

Re: fiat versus bona-fide boundaries:

CARO has terms for "organism subdivision", which includes things like appendages that are separated by fiat boundaries, and "multi-tissue structure", which includes things like organs that are separated by bona-fide boundaries. However, it does not appear to have any terms of for organ parts.

We are checking with CARO to found out how they plan to deal with organ parts.

FMA has the following hierarchy for organ parts (definitions paraphrased):

anatomical structure

>cardinal organ part: any part of an organ that has two or more tissues

>>organ component: a cardinal organ part which is bounded predominantly by bonafide boundaries

>>organ region: a cardinal organ part which is a fiat subdivision of an organ (includes organ segments and organ zones)

>>region of organ component: a cardinal organ part which is a fiat subdivision of an organ component. (RW: This seems redundant with organ region to me)

FMA:cardinal organ part is directly parallel to PO:cardinal organ part (or cardinal part of plant organ)

vascular system

current def., vascular system (PO:0000034): A plant structure that includes the totality of the portions of vascular tissue in their specific arrangement in a whole plant or in a constituent part thereof.

We originally decided that vascular system was not a child of portion of vascular tissue, because it can contain portions of other tissue. However, vascular tissue, as it is now defined, can contain portions of other tissues or other cell types. See definition of portion of vascular tissue.

Vascular system (PO:0000034) is actually the maximal portion of vascular tissue in a plant structure.

New proposed name and def., plant vascular system (PO:0000034): A portion of vascular tissue (PO:0009015) that is the maximal portion vascular tissue in a whole plant or in a constituent part thereof.

comment: A vascular system consist of the totality of the portions of vascular tissue in their specific arrangement in a plant structure. May include other types of tissues or cells, such as parenchyma (PO:0005421) or fiber cells (PO:0025407).

BS: How small does the constituent part have to be? If the plant part is one cm of leaf vein, then the maximal portion of vascular tissue in it cannot be a vascular system. We need to define it as being part of a whole plant, multi-tissue plant structure, or cardinal part of a multitissue plant structure. Need to make sure this covers all examples. Can't just say in a plant structure, because that includes tissues.

New proposed def.: A maximal portion of vascular tissue (PO:0009015) in a whole plant, multi-tissue plant structure, or cardinal part of a multitissue plant structure (add ids).

New located_in relation

Need icon

The located_in relation has been to the PO file. Right now it is only used for embryo sac located in plant ovary ovule, but should be applied whenever there are two plant structures that are parts of different organisms.

Located_in replaces contained_in. Located_in can be used for both part_of and contained_in, but in the PO, we should use part_of when it is more appropriate.

Could also add the "inverse located in" relation. For example, we now have seed has_part plant embryo, but this should really be inverse_located_in. This is a terrible name for the relation.

BS is not in charge of BFO relation names.

Need to check with CM about correct xrefs for located_in.

Located in is used when there are two different organisms (embryo located in seed) while part of is used when two structures are part of the same organism (petiole part of leaf).

plant ovary (PO:0009072) and similar

current def'n: A plant structure that is the basal portion of a carpel or group of fused carpels and encloses the ovule(s).

note: An ovary is either the basal part of a carpel (in an apocarpous gyneocium) or the basal part of a syncarpous gynoecium. This is how it is defined in Esau, Raven, Weberling, etc

Cardinal part of MTPS does not work as a parent for this, because it is not part of a MTPS. Still have the issue that ovary can be part of either carpel (a plant organ/MTPS) or gyneocium (a CPOS).

Ovary wall (PO:0005022), style (PO:0009074) and stigma (PO:0009073) have the same problem (part of either a single organ organs).

See more at Items_for_future_meetings#ovary_and_the_like

We will leave this as for now, and deal with it during the next release.

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.

Botany 2012

July 7 - 11, 2012 - Columbus, Ohio

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

see: link on Botany 2012 workshops schedule to view the abstract.

Wiki page for workshop: Plant Ontology Workshop, Botany 2012

Goal of workshop: 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.

Announcement has been posted on the PO home page and FB page.

exhibitor's booth

We had considered 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)

We decided that there were not enough people at the conference to man a booth and we could put up a display at the NYBG booth

RW will look into purchasing a TV/monitor (~22") that could display a rotating slideshow. Could also be used for future presentations

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: Poster Number: P28002

Plant Informatics Workshop is planned with TAIR, Gramene and PO : Saturday, July 21, 2012, 7:30 PM - 10:30 PM

LC and PJ are attending

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. 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 will present the IDO-Plant paper and a poster on the PO-FNA collaboration.

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)

LM will be attending

Crop Ontology Workshop

For more information see the wiki page: Plant Ontology Crop Annotation Workshop at OSU, 2012

Dates: Sept. 13-15th

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

Next meeting scheduled for Tuesday, June 26, 2012 at 10am PDT/1pm EDT

See: POC_Conf._Call_6-26-12