POC Conf. Call 1-31-12

POC meeting, Webex Conference Call; Date: Tuesday Jan 31st, 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_1-24-12?

Back to POC Meetings Minutes

Upcoming PO Release:

Items below copied from: POC_Conf._Call_10-18-11#Next_PO_Release, need to be updated....

Goals and Priorities:

• First major revision of PSDS (formerly PGDSO) this is top priority

• Complete old user requests/SF tracker items this is top priority

• New association files: Physcomitrella, grape, potato (?)

• 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 - Skype meeting with KN scheduled for 2:00/11:00 on Friday, October 21 PJ will confirm that he can make it on Friday. JE and JP can attend.

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.

Timeline

We will have an interim release in December to add new data (data release). Have new data sets ready by December 15, so release can happen before holidays and is out in year 2011.

• Target date for finishing edits: late January

• Target date for release: February 15

Items from old meetings

spore (PO:0025017)

May need to be more specific in definition. Maybe add something about the exine?

New proposed definition, plant spore: A whole plant that arises through meiosis and develops into a gametophyte.

Comment: A spore is usually single-celled in homosporous ferns but may be multicellular in heterosporous plants.

Vascular tissues and meristems

POIDs will be added to comments as needed. These notes were types a while ago.

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

RW: protoxylem and metaxylem have the same issues as proto and metaphloem, from last week's discussion.

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, primary vein, midvein

See POC Conf. Call 1-31-12

• 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

• primary leaf vein (new term)

proposed definition: A leaf vein that connect directly to the vasculature of a petiole or a shoot axis, if no petiole is present.

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).

• 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; 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.

PO terms for lateral meristems

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

RW: I still need to make the SF tracker for these items. Will do on Monday.

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 (PO:xxx), 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 that is part of a shoot axis not contiguous with the shoot apical meristem and has a parts multiple layers of cells.

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 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).

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.

RW will attend.

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

• 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