POC Conf. Call 2-14-12

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

In attendance:

POC members:

Absent:

Collaborators: none

Any changes or corrections (additions/deletions, etc) needed in the minutes from the POC_Conf._Call_1-31-12?

Back to POC Meetings Minutes

Upcoming PO Release:

In October, we had planned the next release for Feb 2012:

POC_Conf._Call_10-18-11#Next_PO_Release

Goals and Priorities:

• First major Revisions of PSDS (formerly PGDSO):

Status to 1-30-11:

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

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

-will be working on wood development at the NYBG next week

• Complete old user requests/SF tracker items:

- This is an ongoing process, we have added about 50 new PAE terms recently

• 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?

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?

Timeline:

• Target date for finishing edits:

• Target date for release:

Collaborative projects:

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

RW: We now have id's for FNA terms. Can finish adding synonyms before this release, and probably mapping file for existing terms.

-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):

• Leaf character ontology for Phenotype RCN? see notes above

• Linking ontology terms to character matrices using Morphobank?

Also need to work on providing PO in glossary form, to eventually replace APWeb Glossary. PJ has hired new grad student who will be working on this. 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.

Review of terms from last meeting:

Vascular tissues and cell types

leaf vein, primary vein, mid vein

These changes have already been made in the dev file, unless otherwise noted

• 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

• Proposed new term: primary leaf vein (PO:000xxxx)

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 midvein (PO:0020139). Vein orders only apply to hierarchically branching vein patterns, not to dichotomously branching vein patterns, as in some ferns and gymnosperms.

Is this a revision of the existing term 'primary vein' (PO:0025413) or a new term?  Cannot find 'primary leaf vein' in the dev file

• midvein (PO:0020139)

revised def'n: 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

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?

Primary and secondary growth, etc.

request has been made to GO.

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

PO terms for lateral meristems

These edits have been done in the 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).

cambium (PO:0005597)

revised def'n: A lateral meristem that is part of a plant axis (PO:0025004) and has as part a single layer of cambial initial cells 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.

root lateral meristem (PO:0006308)

didn't do this edit yet

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.

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.

cork cambium/phellogen (PO:0005599)

revised def'n: A cambium (PO:0005597) that is part of a shoot axis periderm (PO:0005048) 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.

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.

secondary thickening meristem (new term)

proposed def'n: A shoot lateral meristem (PO:0006344) that is part of a stem (PO:0025029) 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.

Other types of lateral meristems

didn't do these edits yet

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. Same for root meristem and shoot meristem.

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.

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'n: An inflorescence branch meristem that gives rise to the branches of an ear inflorescence.

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