POC Conf. Call 1-24-12

POC meeting, Webex Conference Call; Date: Tuesday Jan 24th, 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_1-17-12?

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Interim Data Release 16A, January 2012

The Plant Ontology is pleased to announce the availability of the January 2012, Interim Data Release 16A on our web page.

Through a collaborative effort with the Moss Computational Biology Resource (COSMOSS and University of Freiburg), this interim data release adds approximately 82,000 new annotations for genes expressed in the model moss species; Physcomitrella patens.

Links from annotations on the PO terms; gametophore (PO:0030018), spore (PO:0025017), protonema (PO:0030003) and protoplast (PO:0030003) will take you to the Cosmoss site (cosmoss.org) for further info.

This work is the result of a process that has been undergone for the past year, adding more than 80 new terms and revising the structure of the Plant Anatomy branch of the ontology to accommodate non-vascular plants.

There are no changes to the ontology file relative to version #16.

Demonstration of Image Annotation Tool

JP and Nikhil (CS student) will demonstrate an image annotation application currently under development. It is intended to be used by curators for segmenting and tagging images of plant specimens with PO terms.

Updates from PAG 2012

January 14-18, 2012, San Diego, California

PO was represented at the following events:

• Ontology workshop, Saturday January 14th from 10:20am-12:30pm: Use of Ontologies for Organizing Plant and Animal Genomics Data.

We had 5 speakers and a panel discussion at the end

 For more info, see the PAG 2012 Ontology workshop wiki page.

• Non-Seed Plant Workshop on Saturday, Jan 14th, (3:50pm-6pm)
• Plant Phenotypes workshop on Sunday, Jan. 15th, (8:00am - 10:10am)
• Computer demo Monday 12:50 pm for the PO.

• The PO also took part in an Outreach booth organized by MaizeGDB

Wood Anatomy Ontology Meeting

Please see the Wood_Anatomy and the Wood anatomy ontology meeting, 2012 at NYBG, agenda wiki pages for more information.

Confirmed dates are Feb. 5th-7th, 2012 (Sun-Tues)

Update and status:

Attendees:

• Frederic Lens: Netherlands Centre for Biodiversity Naturalis
• Barb Lachenbruch link
• Elisabeth Wheeler (paleobotanist and wood anatomist at NC State
• Rachel Spicer Connecticut College
• John Carlson (jec16@psu.edu) link
• Meg (Margeret) Staton (mestato@yahoo.com) Clemson University (the lead on both the hardwoods website and the Fagaceae Genomics Web

Hotel is booked and flights have been arranged for all except for Rachel spicer, who is driving

 Barry, please send me flight info so we can coordinate shuttle

BS will give his presentation on Sunday morning (see: Wood anatomy ontology meeting, 2012 at NYBG, agenda). This will be open to the public and notices have been sent out.

Vascular tissues and cell types

These terms will need to be fixed before the Wood Ontology meeting in February.

vascular tissue types

For vascular plants, we have the class:

portion of vascular tissue (PO:0009015): A portion of plant tissue that has parts xylem and phloem. [APweb:Glossary]

Comment: Functions in conduction and support. In the stem it is often found as a stele, surrounded by the cortex and surrounding the pith.

part_of vascular bundle (which is part_of vascular system)

This is okay, but suggest that we change definition to include xylem or phloem, and it may not always be part_of vascular bundle.

Proposed definition: A portion of plant tissue that has as parts tracheary elements or sieve elements.

Comment: Functions in conduction and support. In shoot axes, vascular tissue is often found as part of a stele or as scattered vascular bundles. May include other types of tissues or cells, such as parenchyma or fibers.

part_of vascular system (should add vascular system participates_in sporophytic phase)

vascular bundle (PO:0005020) current def.: A unit strand of the vascular system containing the vascular tissues, xylem and phloem. In addition vascular cambium is often present. [GR:pj]

This currently is_a portion of plant tissue. Should be is_a portion of vascular tissue.

proposed definition: A portion of vascular tissue that is a unit strand of the vascular system and has as part xylem or phloem.

Comment: Usually contains both xylem and phloem. May also contain other types of cells or tissue such as fibers, vascular cambium, or portions of ground tissue.

part_of vascular system

add vein as exact synonym -- can be in any organ

primary and secondary vascular tissue

primary vascular tissue: A portion of vascular tissue that develops from a procambium. (ref: Esau)

comment: Forms as part of primary growth (GO:xxxx).

secondary vascular tissue: A portion of vascular tissue that develops from a vascular cambium. (ref: Esau)

comment: Forms as part of secondary growth (GO:0080117) in vascular plants. Often differentiated into the axial system and ray system.

If we set both of these up as a cross products, then primary and secondary xylem and phloem will be inferred children.

phloem

phloem (PO:0005417) current def.: A portion of vascular tissue whose principal function is conducting organic substances. [GR:pj]

proposed definition: A portion of vascular tissue that has as parts sieve elements.

Comment: Functions in the conduction of organic substances in vascular plants.

Note: currently, sieve element is listed as a synonym of sieve tube member, but this does not correctly follow Esau's usage. It was okay when we only had angiosperms in PO, but is no longer valid. Suggest we make a new term for sieve element, rather than have it as synonym. See below under conductive_and_related_cell_types.

metaphloem (PO:0006076) current def.: Part of the primary phloem that differentiates after the protophloem and before the secondary phloem, if any of the latter is formed.

proposed definition: A portion of primary phloem that differentiates after the protophloem.

Comment: Differentiates before the secondary phloem, if any is formed.

protophloem (PO:0006077) current def.: The first-formed elements of the primary phloem.

proposed definition: A portion of primary phloem tissue that has as parts the first-formed sieve elements of the primary phloem.

primary phloem (PO:0006075) current def.: A portion of phloem tissue of the primary plant body.

proposed definition: A portion of phloem tissue that develops from the procambium.

Comment: Primary phloem develops as part of GO:xxxx primary growth. (see below)

develops_from PO:0025275 procambium

secondary phloem (PO:0005043) current def.: A portion of phloem tissue formed by the activity of the vascular cambium.

proposed definition: A portion of phloem tissue that develops from the vascular cambium.

Comment: Secondary phloem develops as part of GO:0080117 secondary growth.

develops_from PO:0005598 vascular cambium

xylem

xylem (PO:0005352) current def.: A portion of vascular tissue composed of xylem elements.

comment: The principal function is the upward translocation of water and solutes. See also primary xylem and secondary xylem.

proposed definition: A portion of vascular tissue that has as parts tracheary elements.

comment: Functions in the translocation of water and solutes from roots to the shoot system and in support.

primary xylem (PO:0005849) current def.: A portion of xylem tissue of the primary plant body. [source: GR:Pankaj_Jaiswal, ISBN:0122151704, ISBN:0471245194]

Comment: In stem or root it is differentiated behind the apical meristem.

proposed definition: A portion of xylem tissue that differentiates from the procambium.

Comment: Primary xylem develops as part of GO:xxxx primary growth.

develops_from PO:0025275 procambium

protoxylem (PO:0000272) current def.: A portion of xylem tissue composed of any of the first formed elements of the primary xylem. [source: ISBN:047125208]

proposed definition: A portion of primary xylem that has as parts the first formed xylem elements of the primary xylem.

metaxylem (PO:0000372) current def.: A portion of xylem tissue that is part of the primary xylem and differentiates after the protoxylem and before the secondary xylem, if any of the latter is formed. [source: ISBN:047125208]

proposed definition: A portion of primary xylem that differentiates after the protoxylem.

Comment: Differentiates before the secondary xylem, if any is formed.

secondary xylem (PO:0005848) current def.: A portion of xylem tissue that develops from a vascular cambium. [source: ISBN:0471245194, POC:Curators]

Comment: Absent in some dicots and most monocots. The "wood" of gymnosperm and dicot angiosperm trees, shrubs, and lianas.

Existing definition is okay.

New comment: Secondary xylem develops as part of GO:0080117 secondary growth. Found in gymnosperms and most dicots. Secondary xylem is the "wood" of gymnosperm and dicot angiosperm trees, shrubs, and lianas. May be organized into axial and ray systems. Some monocots have a primary peripheral thickening meristem, located near shoot apical meristem, that gives the appearance of secondary growth and may produce lignified tissue that appears woody, but is not composed of secondary xylem.

develops_from PO:0005598 vascular cambium

Note: exarch, endarch, mesarch are descriptors for different types of xylem development.

tracheid bar (PO:0019026) current def.: A distinct ring-like structure, composed of tracheid cells, which surrounds the hilum of some taxa e.g., Phaseolus, and forms a groove in the surface of the pericarp (immediately adjacent to the hilum). [ISBN:0080280293]

proposed definition: A portion of xylem tissue that is a distinct ring-like structure, composed of tracheid cells, which surrounds the hilum and forms a groove in the surface of the pericarp immediately adjacent to the hilum.

Comment: Found some taxa such as Phaseolus. [ISBN:0080280293]

part_of seed; adjacent_to hilum

leaf vein, midrib

• leaf vein (PO:0020138), current def: A strand of vascular tissue in the leaf blade.

is_a portion of vascular tissue; part_of leaf vascular system

proposed definition, leaf vein (PO:0020138): A vascular bundle that is part of a leaf lamina in a vascular leaf.

part_of leaf vascular system, part_of leaf lamina

synonym: leaf vascular bundle

Suggest new term primary leaf vein: A leaf vein that originates from the base of a leaf lamina where it attaches to the petiole or to the shoot axis if no petiole is present.

Comment: A leaf may have more than one primary vein. The central primary vein is the midvein (PO:0020139).

• midvein (PO:0020139): The central, and usually the most prominent, vein of a leaf or leaf-like organ. [source: APWeb:Glossary]

Since midvein is_a leaf vein, it should say just "leaf" instead of "leaf or leaf-like organ.

proposed definition: A primary leaf vein that is the central vein of a vascular leaf.

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

broad synonyms: mid rib, midrib, mid-rib, 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.

Primary and secondary growth, lateral meristems, etc.

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 and continues in their derivative meristems - protoderm and procambium - even in older tissues. Primary and secondary growth can occur simultaneously in the same organism.

is_a growth (GO:0040007)

secondary or 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.

Perhaps GO should have 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 due to the activity of a cambium (secondary growth, found in most gymnosperms and dicotyledons), a primary thickening meristem (found in many monocotyledons, some ferns and some cycads), or secondary thickening meristem (in some monocotyledons).

proposed new def., secondary growth (GO:0080117): Lateral growth of a plant axis (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 (phellogen). 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 synonym "cambial secondary growth", which is makes the meaning clearer.

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

comment: Occurs 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 (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 fibers 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 of some Arecaceae (palms).

Ref.: Fahn 1990, ISBN:0080374903

PO terms for lateral meristems

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

lateral meristem (PO:0020145)

current def.: A meristem containing cells along the stem or root that first differentiate and function as members of a mature tissue system but then again take up meristematic activity.

proposed def.: A meristem located parallel to the circumference of a plant organ.

comment: Participates in lateral growth (GO:xxxx) of a plant organ, primarily shoot axes and roots. Contrast with apical meristem (PO:0020144).

root lateral meristem (PO:0006308)

current def.: Meristem of the root located parallel to the sides of the axis.

comment: Generally causes root thickening. Not to be confused with lateral root meristem, which is the meristem of the lateral root.

This is just a cambium in the root, which also has vascular cambium and phellogen.

proposed new name and def.: 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.

If we are going to have this term, maybe we should have root vascular cambium and root cork cambium, plus shoot axis vascular cambium and shoot axis cork cambium?

cambium (PO:0005597)

current def.: A lateral meristem, the cells of which divide mostly periclinally. [source: ISBN:0080374913]

proposed def.: A lateral meristem that has a 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).

vascular cambium (PO:0005598)

current def.: A lateral meristem, the cells of which give rise to secondary xylem and phloem, leading to an increase in girth.

Current definition is okay, but needs minor changes.

proposed def.: A cambium that gives rise to secondary xylem and secondary phloem.

comment: Vascular cambium is located between the secondary xylem and secondary phloem and gives off cells in both directions by periclinal division, leading to an increase in girth of a plant axis.

cork cambium/phellogen (PO:0005599)

current def.: Lateral meristem which produces the phellem (cork) and the phelloderm.

proposed def.: A cambium that is part of a periderm and produces phellem (cork) and phelloderm.

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)

current def.: A meristem that develops from a peripheral zone of a shoot apical meristem and is responsible for the primary increase in thickness of a shoot axis.

comment: May appear as a distinct mantle like zone. Often found in monocotyledons.

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

proposed def.: A lateral meristem that has a parts multiple layers of cells located near the shoot apical meristem.

comment: Contributes to primary thickening of the stem, adventitious root formation, and formation of linkages between the stem, leaf, and root vasculature. Contiguous with the shoot apical meristem in some species, but not all. Produces more or less distinct vascular bundles surrounded by ground tissue, as opposed to the more or less continuous xylem and phloem produced by a vascular cambium. 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.: A lateral meristem has a parts multiple layers of cells in a shoot axis...

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

Other types of lateral meristems

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

Shoot lateral meristem is okay, but inflorescence lateral meristem and all the others are misleading. Inflorescence branches generall 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.

inflorescence lateral meristem (PO:0009105)

current def.: 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)

current def.: The meristem that gives rise to the lateral structures of a maize ear.

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).

proposed def.: 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).

RW has a friend there she can stay with and is interested in going.

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.

Eva said that they can cover RW's plane fare from NY.

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.

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

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

From 9-27-11: PJ is planning to attend and will be running a biocuration workshop- is this happening?

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.

ASPB Plant Biology 2012

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

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

• Jan. 31st, 2012: Paper submission deadline
• 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