POC Conf. Call 3-13-12

POC meeting, Webex Conference Call; Date: Tuesday Mar 13th, 2012 10am PST/1pm EST

In attendance:

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

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

Collaborators: none

Any changes or corrections (additions/deletions, etc) needed in the minutes from the POC_Conf._Call_3-8-12?

Back to POC Meetings Minutes

part 1: 18 minutes

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part 2: 41 minutes

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Notes on the in-progress papers

IAWA meeting report

Some wood anatomists take issue with the idea that a vessel is a portion of xylem tissue. They think it should be part of xylem, but don't have a suggestion for what the is_a parent should be, because that is not the way they traditionally think of it.

We will need to talk more about the definitions of xylem and phloem, plus vessel and sieve tube. For the short publications, there is not a lot of space to go into a detail explanation of how the PO defines a portion of tissue, but we should talk about how the classic or conventional way of learning that says vessel is part of xylem, but the ontology defines it as a type of xylem.

For this short paper, should use a simple image, perhaps just showing tracheid is_a tracheary element, and removing vessel.

RW will make new, simpler figure, and LC will set up a conference call with the whole group for next week.

AJB and PO anatomy papers

LC is putting together figures from the data analysis for the PO anatomy paper. Should have draft ready by next week (but see discussion below about release, in which we decide to have paper ready by April 15).

The two papers should fit together nicely, so that they are complimentary. We need to make sure that the content is not overlapping too much.

Finishing up the wood types:

Started discussing this on POC Conf. Call 3-8-12

sapwood (PO:0004513):

Current def.: Outer part of the wood of stem or root containing living cells and reserves and in which conduction of water takes place. Generally lighter colored than the heartwood.

Proposed def.: A portion of secondary xylem (PO:0005848) that has as parts living secondary xylem parenchyma cells (PO:0004525).

comment: Sapwood contains reserve materials and may function in the conduction of water and minerals. It is generally lighter colored than the heartwood (PO:0004512) and is located between the heartwood and the vascular cambium (PO:0005598) of a plant axis (PO:0025004). Sapwood forms during a secondary xylem development stage (PO:xxxx).

Could use secondary xylem in these names, but these are the names in common use.

Add relation secondary xylem development stage has_participant sapwood.

These don't currently have part_of relation to anything, because the part_of relation could be in secondary xylem. However, it turns out that we can't put secondary xylem part_of plant axis, because DWS showed us some examples of plants that have secondary xylem in their needles, and multiple examples of petioles with a vascular cambium that produce secondary xylem.

We can put sapwood and heartwood part_of plant axis.

In the actual definition, we can say they are part of root axis and shoot axis. We should go back and change other definitions of secondary xylem to say root axis or shoot axis, plus need to put in comment that it can be in other organs.

heartwood (PO:0004512)

Current def.: The inner layers of secondary xylem that have largely ceased to function in storage and conduction and in which reserve materials have been removed or converted into heartwood substances; generally darker colored than the functioning sapwood.

Proposed def.: A portion of secondary xylem (PO:0005848) that lacks living secondary xylem parenchyma cells (PO:0004525).

comment: Heartwood has ceased to function in storage and conduction, and the reserve materials have been removed or converted into heartwood substances. It is generally darker colored than sapwood (PO:0004513) and is found in the center of a plant axis (PO:0025004), interior to the sapwood. Heartwood forms at the end of a cell death stage of secondary xylem (PO:xxxx).

OK. Say shoot axis or root.

early wood (PO:0004515):

Current def.: The wood formed in first part of a growth ring and characterized by a lower density and larger cells than the late wood.

Proposed def.: A portion of secondary xylem (PO:0005848) that has lower density and larger cells than late wood (PO:0004516) and is formed in the first part of a growing season.

Comment: The transition from early wood to late wood may be gradual and is not always easy to distinguish.

part_of growth ring

synonyms: earlywood, spring wood

Change "first part of growing season" to "early part of growing season".

In the tropics, the growing season is based on rain rather than temperature. Some species don't have growth ring.

Don't want to say annual growing season, because growing season does not always correspond with one year. May get two rings in one year or one ring for two or three years.

Instead of saying larger cells, should say cells with larger lumens. Proportion of vessel elements versus tracheids may vary as well.

We should add terms for early wood tracheary element and late wood tracheary element: A tracheary element that is part of a portion of early/late wood. Put in comment about the difference in sizes.

Change definitions to say tracheary element lumen, instead of cell size.

Given that early wood and late wood have the same kinds of cells, are these traits or are they PO terms? They are entities (PO terms), but it is true that they represent the same kinds of cells at different stages.

late wood (PO:0004516):

Current def.: The secondary xylem formed in the later part of a growth ring; denser and composed of smaller cells than the early wood.

Proposed def.: A portion of secondary xylem (PO:0005848) that has higher density and smaller cells than early wood (PO:0004515) and is formed in the later part of a growing season.

Comment: The transition from early wood to late wood may be gradual and is not always easy to distinguish.

part_of growth ring

synonyms: latewood, summer wood

growth ring/layer (PO:0004514):

Current def., growth ring: A growth layer of secondary xylem or secondary phloem as seen in transection of stem or root; may be an annual ring or a false annual ring.

Would "growth layer" be a better primary name? This is a layer of tissue that looks like a ring when viewed in transverse section.

Proposed def.: A portion of secondary xylem (PO:0005848) that has as parts a single layer of early wood (PO:0004515) and a single layer of late wood (PO:0004516) from the same growth season and is part of a plant axis (PO:0025004).

comment: Forms a ring in a plant axis when viewed in transverse section. May be an annual ring or a false annual ring.

Will keep growth ring as a primary name, because it is used more commonly. Add growth layer as synonym.

New comment: Appears as a ring in a transverse section of plant axis. May be an annual ring (one growth ring per year) or a false annual ring (more or less than one growth ring per year).

Add annual ring and false annual ring as synonyms.

growth ring boundary (PO:0004517):

Current def.: Boundary between two growth rings.

The boundary is the transition between the outermost late wood of one growth ring and the earliest early wood of the next growth ring. This is not a portion of tissue, but an anatomical surface (CARO:0000010). Alternative is to define it as the portion of tissue that includes the latest part of one ring and the earliest part of the next ring.

Could use anatomical surface (CARO:0000010) or BFO:object_boundary as a parent. However, some species have indistinct boundaries, which makes them harder to define.

object boundary (from BFO):An independent continuant [snap:IndependentContinuant] that is a lower dimensional part of a spatial entity, normally a closed two-dimensional surface. Boundaries are those privileged parts of object [snap:Object] entities that exist at exactly the point where the object [snap:Object] is separated off from the rest of the existing entities in the world.

comment: Boundaries are theoretically difficult entities to account for, however the intuitive notion of a physical boundary as a surface of some sort (whether inside or outside of a thing) will generally serve as a good guide for the use of this universal. Definition: An independent continuant [snap:IndependentContinuant] that is a lower dimensional part of a spatial entity, normally a closed two-dimensional surface. Boundaries are those privileged parts of object [snap:Object] entities that exist at exactly the point where the object [snap:Object] is separated off from the rest of the existing entities in the world. Examples: the surface of the skin, the surface of the earth, the surface of the interior of the stomach, the outer surface of a cell or cell wall Synonyms: substance boundary.

Proposed def.: A plant anatomical surface that is the boundary between the outermost (last formed) late wood (PO:0004516) of one growth ring and the innermost (earliest formed) early wood (PO:0004515) of the next growth ring (PO:0004514).

Alternative def.: A portion of secondary xylem that includes the outermost (last formed) late wood (PO:0004516) of one growth ring and the innermost (earliest formed) early wood (PO:0004515) of the next growth ring (PO:0004514).

Will use alternative definition, because it lets us cover non-distinct boundaries. Innnermost and outermost is a little confusing.

Revised definition: A portion of secondary xylem that includes the last-formed late wood (PO:0004516) of one growth ring and the earliest-formed early wood (PO:0004515) of the next growth ring (PO:0004514).

Open SourceForge Tracker for coleoptile emergence:

This section was moved to Items_for_future_meetings- will be wrapped up on 3-20-12.

Update on linking to images from PlantSystematics.org

This was discussed at the Monday Ontology Development meeting- see the associated wiki page: PO_PlantSystematics_conference_call_03-11-12#Links_to_images_from_PO

KN will be visiting the NYBG next week

What is the status of the images and the annotation software?

It would be good to have a set of test or sample images in the Ontology for the upcoming release. This wil help move it forward.

PJ will talk to MAG separately about the image annotation software. If necessary, we can set up conference call with KN re. informatics issues.

Next PO Release:

On POC_Conf._Call_2-21-12, we set the following goals: Need to be revised...

Timeline:

• Target date for finishing edits: March 21st

• Target date for release: Before March 30th

We should aim to have to release out by the end of this month, so we can then focus on the paper to have manuscripts ready by April 15th.

We probably want to have this release out before we submit, so reviewers and editors can look at the web site. If we get feedback from reviewers on manuscripts, we can work those into the next release in two months.

We can get this week's changes, plus the wood development stages and the coleoptile emergence terms in the file by next week, and review them at next week's meeting.

icons

LC should send email to PJ about which icons are needed, what letters he should use.

Goals and Priorities:

First major revisions of PSDS (formerly PGDSO):

• Status to 2-30-11: This needs to be updated...

-22 new terms added, many existing terms have been modified, eg changed all the 'phase' names to 'stage'

All terms PSDS terms names are now singular. Some still need to have "stage" appended.

-most of the recent work has been on the whole plant development stage (PO:0007033) and its children

* Addition of Wood development stages (See: SF tracker), started at the NYBG Workshop

New and Revised Terms for the PAE

• Addition of new terms and revisions to existing terms to encompass wood- see Goal_1._Anatomical_Entities

• Please see New terms and obsolete terms-March 2012 Release for a complete list

• Complete old user requests/SF tracker items:

- This is an ongoing process

New association files:

• Physcomitrella (released Jan 2012), small set of cotton annotations (TBA Feb 2012)

Glossary of PO terms

See PO Glossary on dev

This was discussed at the RCN meetings 2011, plan is to eventually replace APWeb Glossary. This will be useful for users of APWeb Glossary who need a glossary, but don't want to use AmiGO browser. We could eventually incorporate other terms from APweb into PO if needed.

what is the status of this?

This is ready to go, and can go out with the next release.

Other Items

• from POC_Conf._Call_10-18-11

• Fix dbxrefs for Fragaria annotations

• ABRC annotations to PO and TO terms: These are descriptions of mutant phenotypes from Arabidopsis stock center, based on free text descriptions

• Links to images on PlantSystematics.org - Update? See notes above

Translations

Will need to update translations for PAE terms before release. Can JE generate a file (after we stop editing) that includes all terms without Spanish or Japanese translations?

Collaborative projects:

• Mapping of Flora of North America Glossary to PO terms:

We now have id's for FNA terms. Can finish adding synonyms before this release. Still need to add new terms from the FNA list and create mapping file.

Are we okay with using these FNA ids? They are UUID and are very long and contain dashes (e.g., 40b5fa5d-a75b-49d8-8328-b4c28d54ea66). See antheridium (PO:0025125) on dev browser for an example of how it will look.

Where did this synonym go? It is still there, just doesn't show up in AmiGO.

RW is working on modifying a perl script from JE to insert FNA synonyms into the PO file. May needs some help from JE.

-What are the plans after this?

Once mappings are done, want to see how PO shows up in their data base. Show utility of PO for recovering descriptors from free text.

FNA is using natural language processing to map their descriptions to PO. We are starting with plant structures and later will add phenotype descriptors. We will start with leaf characters.

Will use PATO as it has terms available, and add PO terms as needed. Will also help show utility of PO to systematists.

-Others (These may be longer term than the next release):

• Linking ontology terms to character matrices using Morphobank.

Upcoming meetings and Presentations 2012:

Maize Genetics Meeting, March 15-18, 2012

The maize meetings are being held in Portland, OR this year.

For more info see: Maize Genetics Meeting 2012

Registration Link

LC will present a short talk abstract Friday march 16th, 5:45pm

No PO-Gramene workshop is planned

Katherine Esau Research Symposium

Integrating Plant Structure with Function, Development and Evolution

Hosted by the Katherine Esau Fellowship Program,

Date and location: Thursday, March 29, 2012, 1002 Giedt Hall, UC Davis

Space is limited and registration will close at 5 pm on March 10th.

Organizer; Neelima Sinha (Sinha@ucdavis.edu) The PO will not take part this year, because the timing is too short. We will look at attending next year.

5th International Biocuration Conference

April 2-4, 2012, Washington DC

• Abstract was submitted and has been selected for a poster presentation.

See link: File:Abs Biocuration 2012 (LC 12-9-11).pdf

• PJ is planning to attend, may do a talk. LC is planning to attend

The early bird registration is now closed.

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

We are looking at the tentative dates of either: June 11-13th or Aug 6th to 8th

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 for Sunday, July 8th

The organizer have listed it as a whole day workshop, but it is planned for a half day and will be changed on the schedule. Also need to correct link to abstract (currently goes to wrong abstract).

see: Botany 2012 workshops

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.

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.

• Annotation wiki: JP may also give a talk on the new annotation wiki at this meeting, as part of the genomics section.

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 is working on an abstract summarizing the PO-FNA collaboration, with the folks from FNA. Will circulate soon. This will be either for a poster or a short talk in the Early Career Researcher session.

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