POC Conf. Call 2-14-12

POC meeting, Webex Conference Call; Date: Tuesday Feb 14th, 2012 10am (PST)

In attendance:

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

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

Collaborators: none

Any changes or corrections (additions/deletions, etc) needed in the minutes from the POC_Conf._Call_1-31-12? none

Back to POC Meetings Minutes

News and Report from the Wood Ontology Meeting:

This discussion was postponed until PJ was present.

We had a successful meeting last week at the NYBG with the group of wood experts we invited.

• Link to the Wood_anatomy_ontology_meeting,_2012_at_NYBG,_agenda

• Overall objective was to raise awareness and encourage the wood research community to get involved with the development and use of the Plant Ontology

Specific Goals with links to the pages:

To develop PO terms and definitions to describe:

1. Wood structures (PAE branch of PO) Goal_1._Anatomical_Entities

2. Stages of wood development (PSDS branch of PO) Goal_2._Plant_Structure_Development_Stages

3. Wood qualities and phenotypes (to go into TO and/or PATO) Goal_3._Wood_qualities_and_phenotypes

4. To obtain association data linked to the PO terms to be hosted in our database Developing_and_incorporating_new_annotations_for_woody_plants

• Links to flash presentations by all the participants:

Wood_anatomy_ontology_meeting,_2012_at_NYBG,_agenda#2:00PM-2:45PM_Flash_talks_by_participants

• Link to wrap up and action items: Wood_anatomy_ontology_meeting,_2012_at_NYBG,_agenda#10:40AM-11:20PM_Wrap_up

Questions Arising from the the Workshop

• How is the best way to redirect users to terms that are in GO? For example; casparian strip or pit membranes?

Added a note to the AmiGO2 wish list POC_Technical_Issues_Page#AmiGo_2_Wishlist: for a means of redirection.

One possibility is to have a PO slim in GO that could load with PO. This could cause problems with keeping the slim up to date. We could load the slim without GO annotations.

JP suggested that maybe we could incorporate a look-up service, so that when a search fails for PO terms, it automatically searches other ontologies.

BS suggested that we should keep track of people's searches on the PO web page, so we can add new terms that people are searching for.

There has been no activity on AmiGO revisions lately. In the interim, are we planning to upgrade to an intermediate version of AmiGO. It may not be worth it to have to modify AmiGO twice for PO.

The search function does not have to wait for AmiGO 2. The search takes you into AmiGO, but it is a separate chunk of code.

• How are we going to deal with terms that contain adjectives; such as 'storied cambium', 'early wood', 'late wood' etc? These are commonly used terms in this community and we need them.

BS raised the concern that having terms with adjectives can cause problems with multiple inheritance -- two different ways of classifying wood leads to two different parents. Suggest that we put all the adjectives in a phenotype ontology to which we can refer.

However, there are instances where the terms need to be in the PO, particularly for adjectives that are used only for particular plant structures (like epigynous flower). On the other hand, some adjectives can be used for many different structures (like variegated), and terms like "variegated leaf" probably shouldn't go in the PO. Adjectives like "storied" are somewhere in between -- it can apply multiple tissue types, but not hundreds of them. We will need to examine these terms on a case by case basis.

BS, best practice: Terms like "septate" should go into PATO, and we include terms for fiber types and instruct people how to post compose terms as they need them. Some communities would eventually create compound terms like "septate phloem fiber", but they will not live in PO.

We will probably not be able to live up to this best practice, but at a minimum, when we do add terms with synonyms, we should introduce the synonym into PATO and add xrefs to them.

Note, latewood and earlywood should be one word.

• How do we want to approach the TO terms, since this is a complex area and officially outside the mandate of the PO?

Where does this fit into our list of top priorities?? Discussion of this question was postponed.

Revisions of existing terms:

leaf vein, primary vein, mid vein

These changes have already been made in the dev file.

• leaf vein (PO:0020138)

Suggest: rename "leaf lamina vein" (not changed yet)

revised def'n, leaf (lamina) vein (PO:0020138): A vascular bundle (PO:0005020) that is part of a leaf lamina vascular system (PO:0000048).

part_of leaf lamina vascular system

synonym: leaf lamina vascular bundle

Changes are okay. We also need a term for petiole vascular bundle.

• Proposed new term: primary leaf vein (PO:0025413)

proposed def'n: A leaf lamina vein (PO:0020138) that connects directly to a petiole vascular system (PO:0000052) or a shoot axis vascular system (PO:0000039).

Comment: Generally the largest and most prominent of the leaf veins. A leaf may have more than one primary vein. The central primary vein is the leaf midvein (PO:0020139). Vein orders only apply to hierarchically branching vein patterns, not to dichotomously branching vein patterns, as in some ferns and gymnosperms.

okay

• midvein (PO:0020139)

revised def.: A primary leaf vein (PO:0025413) that is the central vein of a vascular leaf (PO:0009025).

Comment: Often the most prominent vein of a vascular leaf. See costa (PO:0030072) for the central conductive strand of a non-vascular leaf (PO:0025075).

broad synonyms: mid rib, midrib, mid-rib; exact synonym: vascular leaf midvein; related synonym: costa, Hickey and Peterson 1978 doi:10.1139/b78-128

Rename "leaf midvein".

We already have terms for secondary, tertiary, quaternary, and higher order veins. Do we want to make their naming consistent with the changes suggested above for primary leaf vein? --Yes!

PO terms for lateral meristems

These edits have been done in the dev obo file, except as noted below.

See Items_for_future_meetings#Primary_and_secondary_growth.2C_etc. for more details on terms that will be requested in GO.

The PO has a general term for lateral meristem, of which cambium is a subtype:

lateral meristem (PO:0020145)

revised def'n: A portion of meristem (PO:0009013) tissue located parallel to the circumference of a plant organ (PO:0009008).

comment: Participates in lateral growth (request has been made for lateral growth in GO) of a plant organ, primarily shoot axes (PO:0025029) and roots (PO:0009005). Contrast with apical meristem (PO:0020144).

New proposed def.: A portion of meristem (PO:0009013) tissue located parallel to the sides of a plant axis (PO:0025004), the cells of which undergo periclinal and anticlinal (tangential?) division.

New comment: Participates in lateral growth (request has been made for lateral growth in GO) of a shoot axis (PO:0025029) or root (PO:0009005), leading to an increase in the cross-sectional area. Contrast with apical meristem (PO:0020144) or intercalary meristem (PO:0006073).

Add lateral meristem part_of plant axis.

May want to add periclinal, anticlinal cell division to GO (or maybe just add periclinal and anticlinal to PATO).

Definition of intercalary meristem need a little work too, to distinguish it from lateral meristem.

cambium (PO:0005597)

revised def'n: A lateral meristem (PO:0020145) that is part of a plant axis (PO:0025004) and has as part a single layer of cambial initial cells (PO:0000295) and their derivatives, arranged orderly in radial files. (Ref.: Esau)

comment: This term is applied to only two types of meristems: vascular cambium (PO:0005598) and cork cambium/phellogen (PO:0005599).

Changed cambial initial from part_of vascular cambium to part_of cambium, because that is how it was defined.

New proposed def.: A lateral meristem (PO:0020145) that has as part a single layer of cambial initial cells (PO:0000295) and their derivatives, arranged orderly in radial files.

Also need to add term for cambial zone, is a cardinal organ part.

vascular cambium (PO:0005598)

revised def'n: A cambium (PO:0005597) that is located between and gives rise to secondary xylem (PO:0005848) and secondary phloem (PO:0005043).

comment: Vascular cambium gives off cells in both directions by periclinal division, leading to an increase in girth of a plant axis (PO:0025004).

Got rid of relation vascular cambium part_of vascular bundle.

No one likes "gives off" or "girth".

New proposed comment: A vascular cambium produces cells in both directions by periclinal division, leading to an increase in the cross-sectional area of a plant axis (PO:0025004).

cork cambium/phellogen (PO:0005599)

revised def'n: A cambium (PO:0005597) that is part of a periderm (PO:0005046) and produces phellem (PO:0004003) and phelloderm (PO:0005050).

comment: Cork cambium is located between the phellem and phelloderm and produces phellem toward the outside and phelloderm toward the inside of a plant axis.

Definition okay. Phellogen should change from related synonym to exact synonym.

primary thickening meristem (PO:0005039)

Esau defines it as originating in the apical meristem, but Rudall's review shows that in some species, it is discontinuous with the SAM.

revised def'n: A shoot lateral meristem (PO:0006344) that is part of a stem (PO:0009047) and has a parts multiple layers of meristematic cells (PO:0004010) located near the shoot apical meristem (PO:0020148).

comment: Contributes to primary thickening of a stem (PO:0009047), adventitious (shoot-borne) root (PO:0000042) formation, and formation of linkages between shot axis (PO:0000039), leaf (PO:0000036), and root (PO:0003011) vascular systems. Contiguous with the shoot apical meristem (PO:0020148) in some species, but not all. Produces more or less distinct vascular bundles (PO:0005020) surrounded by ground tissue (PO:0025059), as opposed to the more or less continuous xylem (PO:0005352) and phloem (PO:0005417) produced by a vascular cambium (PO:0005598). A primary thickening meristem is a multi-layered structure, compared to the single layer of a cambium. Found in many monocotyledons.

DWS was skeptical about whether or not the PTM is actually discontinuous with the SAM in some species, but we will leave the comment in for now, since it is described in Rudall's review.

Need to add synonyms PTM, meristematic cap, and collar meristem.

Definition okay.

secondary thickening meristem (new term)

proposed def'n: A shoot lateral meristem (PO:0006344) that is part of a stem (PO:0025029) that is not contiguous with the shoot apical meristem (PO:0020148) and has a parts multiple layers of meristematic cells (PO:0004010).

comment: Contributes mainly to formation of the body of a stem (PO:0009047), but may also produce adventitious (shoot-borne) roots (PO:0000042). May be continuous or discontinuous with the primary thickening meristem (PO:0005039). Found in some monocot species of the Liliales and Asperigales.

There are also secondary thickening meristems in roots of some monocots (Cheadle 1937, JSTOR:2471543), so this should be lateral meristem, rather than a shoot lateral meristem.

Other types of lateral meristems: (have not done these edits yet)

*root lateral meristem (PO:0006308)

This is just a lateral meristem in the root, which is only the cambium (vascular cambium and phellogen). Therefore, it makes more sense to call it a root cambium.

proposed new name and def'n: root cambium: A cambium that is part of a root.

This terms has six annotations. These should be checked, because it is not obvious what some of them have to do with roots.

Suggest that we also add root vascular cambium and root cork cambium, plus shoot axis vascular cambium and shoot axis cork cambium. Set up root cambium and shoot lateral meristem as XPs, so we don't have multiple inheritance.

DWS will check if there are secondary thickening meristems in some kinds of monocots. In that case, we should leave the general term for root lateral meristem.

New proposed def., root lateral meristem: A lateral meristem that is part of a root.

This will be an XP of is_a lateral meristem and part_of root. We will make new terms for root vascular cambium and root cork cambium that are subtypes of vascular cambium and cork cambium, respectively, and will be inferred children of root lateral meristem.

• PO has the terms shoot lateral meristem (PO:0006344), inflorescence lateral meristem (PO:0009105), ear lateral meristem (PO:0009110) and tassel meristem (PO:0009107), plus their subtypes.

Shoot lateral meristem is okay, but inflorescence lateral meristem and all the others are misleading. Inflorescence branches develop from apical meristems, not a lateral meristem.

There are three annotations on shoot lateral meristem and two on inflorescence lateral meristem that should be moved to shoot apical meristem.

Shoot lateral meristem should be set up as an xp, so subtypes and be inferred, just like root lateral meristem. Will create new terms for shoot vascular cambium and shoot cork cambium, as per root terms.

inflorescence lateral meristem (PO:0009105)

current def'n: The meristem which gives rise to the lateral structures of the inflorescence and contributes to their apical growth.

This should be called inflorescence branch meristem, and be a subtype of inflorescence meristem (PO:0000230), which should in turn be an apical meristem.

revised def: An inflorescence meristem that gives rise to an inflorescence branch.

ear lateral meristem (PO:0009110)

This should be called ear inflorescence branch meristem, and be a subtype of inflorescence branch meristem (PO:0009105). Will need to add XP definitions to the different types of meristems so that they don't have dual parentage (e.g., ear inflorescence meristem XP of is_a inflorescence meristem and part_of ear inflorescence).

revised def.: An inflorescence branch meristem that gives rise to a branch of an ear inflorescence.

okay

Primary and secondary growth, etc.

request has been made to GO.

These terms are for GO, not PO. Definitions are here for reference.

proposed terms for GO

primary growth (new term):

proposed definition: Growth of a plant structure from the time of its initiation by an apical meristem until its expansion is completed. Ref: Esau (ISBN:0471245208 or 9780471245209)

comment: Has its inception in the apical meristems (PO:0020144) and continues in their derivative meristems - protoderm (PO:0006210) and procambium (PO:0025275) - even in older tissues. Primary and secondary growth can occur simultaneously in the same organism.

is_a growth (GO:0040007)

secondary versus lateral growth

GO currently defines secondary growth as: Increase in plant girth due to the activity of lateral meristems (vascular and cork cambium). Source: PMID:19074290

Secondary growth from the vascular cambium does not occur in monocots, but there is a secondary thickening meristem that may be discontinuous from apical meristem that can contribute to another kind of secondary growth. See paper by Rudall et al. in Botanical Review (JSTOR:4354165).

I suggest that GO add a general term for lateral growth (to mirror PO, see below), with specific subtypes for growth from the vascular cambium and growth from other types of lateral meristems.

lateral growth (GO:new term): Growth of a plant axis (shoot axis or root) that originates from a lateral meristem (PO:0020145).

Comment: Includes thickening of plant axes (PO:0025004) due to the activity of a cambium (PO:0005597), known as secondary growth and found in most gymnosperms and dicotyledons, a primary thickening meristem (PO:0005039) as found in many monocotyledons, some ferns and some cycads, or secondary thickening meristem, (PO:0025414) as found in some monocotyledons.

proposed new def., secondary growth (GO:0080117): Lateral growth of a plant axis (PO:0025004, shoot axis or root) that is an increase in thickness resulting from formation of secondary vascular tissues by the vascular cambium (PO:0005598). Ref: Esau (ISBN:0471245208 or 9780471245209)

Comment: Occurs in vascular plants, including gymnosperms and most dicotyledons. Commonly supplemented by activity of the cork cambium or phellogen (PO:0005599). Monocotyledons do not have secondary growth, but may undergo primary thickening (GO:xxx) or secondary thickening (GO:xxx), which can give the appearance of secondary growth. Primary and secondary growth can occur simultaneously in the same organism.

Add exact synonym "cambial secondary growth", which is makes the meaning clearer.

secondary thickening (GO:new term): Lateral growth of a plant axis (PO:0025004, shoot axis or root) that is an increase in thickness resulting from formation of tissue from a secondary thickening meristem (PO:0025414).

comment: Occurs in shoot axes in some monocotyledons such as Dracaena, and rarely in roots of monocotyledons. Distinct from primary thickening, because it is distant from and generally discontinuous with the apical meristem.

References: Fahn 1990, ISBN:0080374903; Rudall 1991, JSTOR:4354165

primary thickening (GO:new term): Lateral growth of a plant axis (PO:0025004, shoot axis or root) that is an increase in thickness resulting from the activity of a primary thickening meristem (PO:0005039)

comment: Occurs in shoot axes and rarely in roots in many monocotyledons.

Ref: JSTOR:4354165, Rudall 1991; and Esau ISBN:0471245208

diffuse secondary thickening (GO:new term): Lateral growth of the older parts of a stem that occurs when the central parenchyma cells and the not yet fully differentiated fiber cells of the bundle sheaths continue to undergo cell division and expansion for a long period of time, leading to an increase in girth of the stem.

comment: Occurs in the stems (PO:0009047) of some Arecaceae (palms).

Ref.: Fahn 1990, ISBN:0080374903

vascular and related cell types

Postponed for a future meeting.

Upcoming meetings and Presentations 2012:

Phenotype RCN meeting, February 23rd-25th, 2012

The dates: February 23-25, 2012 (Thursday, Friday, 1/2 Saturday) have been confirmed for the next annual Phenotype RCN meeting.

It will be held again at NESCent (Durham, NC).

This meeting will focus on bringing in new people and training them on how to develop and use anatomy ontologies. RW offered to help with the training.

The projects of the Plant Working Group that we started in CO will be worked on during the next meeting, in the fall.

RW will attend, the RCN is covering her air travel.

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: 2012 Maize Genetics Conference Registration Page will open on December 30, 2011.

Deadlines: Advance meeting registration is due by January 31, 2012.

LC submitted an abstract for consideration for a short talk

The PO and Gramene will most likely be co-hosting a workshop. Details TBA....

Katherine Esau Research Symposium

Integrating Plant Structure with Function, Development and Evolution

Thursday, March 29, 2012

1002 Giedt Hall, UC Davis

We will keep a track of this symposium and request if we can be invited for a short presentation. Esau's work has helped us build the ontology to a greater extent.

5th International Biocuration Conference

April 2-4, 2012, Washington DC

• Abstract was submitted December 9, 2011 for consideration for a talk (or else a poster). MS was co-author.

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

• Notification date: February 3, 2012

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

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

Botany 2012

July 7 - 11, 2012 - Columbus, Ohio

Call for Symposia, Colloquia and Workshops:

RW, DWS and MAG put together a proposal for a half day hands-on workshop. The goal will be to teach people (mostly botanists) how to access and use the PO, including how to send feedback, suggest new terms, etc.

Proposal was submitted, waiting for news.

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

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

Link to meeting page: ASPB2012

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

Joint workshop is planned with PO, Gramene and TAIR

Registration scheduled to open first week in January.

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)

Relevant dates

• Paper submission deadline extended to...Feb. date?
• Feb. 28th, 2012: Notification of paper acceptance
• March 15th, 2012: Poster, early career symposium, software demonstrations and workshop papers submission deadline
• April 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

BS would like to collaborate on a preliminary paper on Plant Disease Ontology. RW will review IDO and summarize what is there already for plants, what is needed, how it will link to PO. LC will also collaborate.

RW will circulate a draft of a manuscript for a plant disease extension of the Infectious Disease Ontology. Must be submitted by Jan. 31, 2012.

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