POC Conf. Call 2-21-12
POC meeting, Webex Conference Call; Date: Tuesday Feb 21st, 2012 10am (PST)
In attendance:
POC members: Laurel Cooper (OSU), Justin Elser (OSU), Justin Preece (OSU), Ramona Walls (NYBG), Dennis Stevenson (NYBG), Pankaj Jaiswal (OSU)
Absent: Barry Smith (University at Buffalo, NY), 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_2-14-12?
Back to POC Meetings Minutes
Follow up from the Wood Ontology Meeting:
This was discussed briefly on the POC_Conf._Call_2-14-12
* Question: 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??
PJ: The TO will be moving into the domain of the PO, so it is important to continue developing this for the wood community. LC will take the lead on organizing and directing this effort.
LC has updated the notes on the TO and PATO discussion: Goal_3._Wood_qualities_and_phenotypes, adding links to references and and list of questions and tasks to proceed with.
* RW will assist adding the needed terms discussed at the meeting to GO - should be referenced to the PO
* Question: How do we want to proceed with the IAWA short publication and more extensive paper later.
At the Workshop, we decided FL would take the lead in sending a short announcement of the Wood Ontology Meeting for IAWA Journal. Pieter Baas, editor-in-chief of IAWA Journal, was 'really excited' about the content of this short text and suggested that with minor adjustments (e.g., maybe adding few sentences, some key references and a general scheme), this short text could be published as a mini paper. This should still be a meeting report, rather than an short paper. Want to be able a cite it. Needs a paragraph describing the Plant (and Trait) Ontology, what was discussed at the meeting, what is available for the wood science community, focus on trees in general, feedstock for biofuels, cite the PO papers.
We will remove the reference to the plant cell- GO example, and replace it with a more wood-oriented example. eg sieve tube elements, part of phloem
People will be directed to the feedback link on the website to make inquiries.
Suggested title: "Plant Ontology Embraces Tree Species"'
For the future renewal: "Ontologies for Plant Biology": all hosted under our umbrella: PO, TO, GO, Plant PATO and Plant Disease Ontology
- may be able to use web services, but limited by AmiGO at this time
- Need to look at "tension wood, immature xylem, immature phloem"- is this an anatomical structure or a trait?
Tension wood is the reaction wood of angiosperms, develops on the upper side of leaning trunks or limbs. (Raven et al., 5th edition)
Eucalyptus annotations are being developed and they measured the tensile strength of the wood. This is definitely a trait
PJ will get more information regarding how the gene expression analysis was done and send it out so we can assist with the mapping to the PO terms.
Revisions of existing terms:
Changes to lateral meristems from last week
lateral meristem (PO:0020145)
From POC_Conf._Call_2-14-12: revised 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 division as part of lateral growth.
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).
Lateral growth can arise from meristems other than the "lateral meristem" for example, the stem gets thicker as the growth proceeds from the shoot apical meristem as the cells increase in size and width and also divide. Also, growth from phyllome marginal meristem contributes to expansion of the phyllome lamina. That said, lateral meristems as we are defining them are distinct from the SAM that give rise to branches or lateral roots.
Revised def'n: A portion of meristem (PO:0009013) tissue located parallel to the sides of a shoot axis (PO:0025029) or root (PO:0009005) that participates in lateral growth (GO:xxxxxxx, requested).
Revised comment: Lateral meristems contribute to an increase in the cross-sectional area of a shoot axis or root. Examples of lateral meristems are: cambium (PO:0005597), (includes cork cambium (PO:0005599) and vascular cambium (PO:0005598), shoot lateral meristem (PO:0006344) (includes primary thickening meristem (PO:0005039)), root lateral meristem (PO:0006308) and secondary thickening meristem (PO:0025414). Contrasts with apical meristem (PO:0020144), phyllome marginal meristem (PO:0025404) or intercalary meristem (PO:0006073).
'lateral growth' has been requested from GO:
From POC_Conf._Call_2-14-12: Proposed def'n: lateral growth (GO:xxxxxxx): 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.
Note: Plant axis (PO:0025004) includes the children: antheridiophore (PO:0030033), archegoniophore (PO:0030034), embryo axis (PO:0019018) and seta (PO:0030032). May have to revise this def and comment.
In order to help clarify things for the users, for the time being, we will add "lateral growth meristem" as a synonym.
could also use "editor's preferred names"
intercalary meristem (PO:0006073)
Current def.: A shoot meristem separated from the apical meristem in the primary body by more or less mature tissues.
Current definition is okay, but we need to distinguish it from lateral meristem.
From POC_Conf._Call_2-14-12: Proposed def.: A shoot meristem (PO:0006079) that is separated from an apical meristem (PO:0020144) by more or less mature tissues, the cells of which undergo (longitudinal?) division as part of primary growth.
An intercalary meristem in a leaf is intercalated between the leaf apex and base, so it is not really appropriate to talk about it as being separated from the SAM
Proposed def.: A shoot meristem (PO:0006079) that is intercalated between two portions of non-meristematic tissue and results in an increase in length as part of primary growth.
Comments: See subtypes: leaf intercalary meristem (PO:0006346) and stem intercalary meristem (PO:0006347), not known to occur in roots
Add "shoot system meristem" as synonym of shoot meristem.
cambium: (PO:0005597)
From POC_Conf._Call_2-14-12:
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.
Definition was okay with minor changes
vascular cambium (PO:0005598)
From POC_Conf._Call_2-14-12:
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 shoot axis (PO:0025029) or root (PO:0009005).
Got rid of relation vascular cambium part_of vascular bundle.
No one liked "gives off" or "girth"
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).
Definition was okay
Revised comment: A vascular cambium produces cells in both directions, centrifugally and centrifically, leading to an increase in the cross-sectional area of a plant axis (PO:0025004).
cork cambium/phellogen (PO:0005599)
From POC_Conf._Call_2-14-12:
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 was okay. Phellogen was changed from related synonym to exact synonym.
primary thickening meristem (PO:0005039)
From POC_Conf._Call_2-14-12:
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).
Added synonyms: PTM, meristematic cap, and collar meristem.
OK
secondary thickening meristem (PO:0025414)
From POC_Conf._Call_2-14-12:
revised def.: A lateral meristem (PO:0020145) 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) and may also be found in the roots (PO:0009005) of some species. May be continuous or discontinuous with the primary thickening meristem (PO:0005039). Found in some monocot species of the Liliales and Asperigales.
Added Cheadle 1937, JSTOR:2471543 as definition dbxref.
revised def'n: A lateral meristem (PO:0020145) that is not contiguous with an apical meristem (PO:0020144) and has a parts multiple layers of meristematic cells (PO:0004010).
modified to include roots as well
RW: also added root STM and stem STM
root lateral meristem (PO:0006308)
revised def.: A lateral meristem (PO:0020145) that is part of a root (PO:0009005).
Comment: Not to be confused with lateral root apical meristem (PO:0006020), which is an apical meristem (PO:0020144) of a lateral root (PO:0020121).
Set up root lateral meristem as XP, so we don't have multiple inheritance.
This terms has six annotations. These should be checked, because it is not obvious what some of them have to do with roots.
Add "root lateral growth meristem" as a synonym.
shoot lateral meristem (PO:0006344)
revised def.: A lateral meristem (PO:0020145) that is part of a shoot axis (PO:0025029).
Set up shoot lateral meristem as an xp, so subtypes and be inferred, just like root lateral meristem.
Annotations that should be moved to shoot apical meristem:
- three annotations on shoot lateral meristem
- two annotations on inflorescence lateral meristem
We will ask TAIR to take a look at these annotations for the next release
Add "shoot lateral growth meristem" as a synonym.
new terms:
shoot axis cork cambium (PO:0025435): A cork cambium (PO:0005599) that is part of a shoot axis (PO:0025029).
root cork cambium (PO:0025436): A cork cambium (PO:0005599) that is part of a root (PO:0009005).
shoot axis vascular cambium (PO:0025437): A vascular cambium (PO:0005598) that is part of a shoot axis (PO:0025029).
root vascular cambium (PO:0025438): A cork cambium (PO:0005599) that is part of a root (PO:0009005).
proposed def.: A cardinal organ part that is part of a shoot axis and has as parts a cambium and adjacent cells.
Comment: This term is used for the cambium and surrounding area, especially when the borders of the cambium are not clear.
revised def'n: A cardinal organ part (PO:0025001) that is part of a plant axis (PO:0025004) and has as parts a cambium (PO:0005597) and adjacent cells.
should have two children: shoot cambial zone and root cambial zone
This will be useful when people are sampling by just peeling back the bark and scraping the innner layer, or in girdling experiments
What about the hypocotyl?
Hypocotyl is stem internode, which is part of a stem, and therefor covered by shoot axis.
inflorescence meristems
Tangled mess of multiple parentage, need to start making XPs
These terms are under the tracker for lateral meristems, because that's where they were originally classified. A new tracker for inflorescence meristems has not been started yet, and no changes have been made to those terms yet.
inflorescence branch meristem (PO:0009105)
Was: inflorescence lateral meristem
revised def: An inflorescence meristem (PO:0009108) that gives rise to an inflorescence branch (PO:0009081).
Normally, no lateral growth in inflorescence's, is_a apical meristem
ear inflorescence branch meristem (PO:0009110)
Was ear lateral meristem
revised def.: An inflorescence branch meristem (PO:0009105) that gives rise to a branch of an ear inflorescence (PO:0020136).
tassel inflorescence branch meristem (PO:0009107)
Was: tassel lateral meristem
revised def.: An inflorescence branch meristem (PO:0009105) that gives rise to the long lateral tassel branch (PO:0009101), short tassel branch (PO:0009102), and tassel spikelets (PO:0006309) in a tassel inflorescence (PO:0020126).
There are a lot of other changes needed to inflorescence meristems. Rife with multiple inheritance, which could be fixed with cross products.
These were tabled for next week's discussion:
axial cell
New proposed hierarchy (children of plant cell)
sieve element and associated terms:
Definitions from Esau's Anatomy of Seed Plants:
sieve element (PO:0025406)
proposed def.: A plant cell that is part of a portion of phloem tissue, has sieve areas in its walls, and lacks a nucleus in its mature protoplast.
Comment: Sieve elements function mainly in longitudinal conduction of organic solutes. Classified into sieve cells and sieve tube members based on the presence of sieve plates and specialization of sieve areas in different parts of the cell. Develops from either a cambial initial or a cell of the procambium.
part_of phloem, participates_in sporophyte stage
The loss of the nucleus and other organelles is characteristic across plants, P-protein (aka slime, mostly actin) is present in angiosperms, in sieve tube elements only
sieve cell (PO:0025415)
proposed def.: A sieve element (PO:0025406) in which the sieve areas are not aggregated into sieve plates. [source: ISBN:0471245208]
Comment: Sieve areas in sieve cells generally have narrow pores and thin connecting strands, and they are not highly specialized, but instead are fairly uniform throughout the cell wall. Typical of gymnosperms and non-seed vascular plants. Differ from sieve tube members, which have sieve plates and more pronounced specialization of sieve areas.
Should we add comment that in sieve cells the pores in sieve areas appear blocked by endoplasmic reticulum? DS: This is just an artifact of fixation due to turgor change that slams cell contents into pores.
Ferns also have sieve cells. Leptoids in bryophytes are identical to sieve cells. Could look at book on phloem by Esau.
sieve tube member (PO:0000289)
proposed def.: A sieve element that is part of a sieve tube and has sieve areas aggregated into sieve plates.
Comment: Sieve tube members have sieve areas that are specialized into those with wide pores in sieve plates and those with with narrow pores in lateral sieve areas. Sieve tube members may have inclined end walls with compound or simple sieve plates. Typical of angiosperms. Differ from sieve cells, which have less pronounced specialization of sieve areas and no sieve plates.
syn.: sieve tube element, sieve tube segment
part_of sieve tube (new term)
switch the name and the synonym so primary name is sieve tube element
Sieve elements can also have starch or crystals in them, but we don't need to put that in the comment.
sieve tube (PO:0025416):
proposed def'n: A portion of phloem tissue that has as parts a series of sieve tube members arranged end to end and interconnected through sieve plates.
Comment: A sieve plate (GO:0097218) is part of a sieve tube member.
companion cell (PO:0000071)
proposed definition: A parenchyma cell (PO:0000074) that is adjacent to a sieve-tube member (PO:0000289) and arises from the same initial cell (PO:0004011) as the sieve-tube member.
comment: Found in angiosperms. Compare to albuminous cells (PO:0025412), which are found in gymnosperms.
Maybe add comment that it is connected to a sieve element through numerous plasmodesmata and aids in phloem loading.
Currently part_of primary phloem and part_of secondary phloem, which can't be true. Changed to part_of phloem.
Added relation companion cell adjacent_to sieve tube member.
Need to look at definition of phloem mother cell. Does it only differentiate into secondary phloem, or can it be for primary phloem too?
Do we want to add a separate term for "intermediary cell", the type of companion cell found in apoplastic loaders? See, for example Amiard et al..
All companion cells have plasmodesmatal connections to sieve tube element, but not all of them have plasmodesmatal connections to adjacent parenchyma cells -- they use apoplastic loading.
Create two kind of companion cells:
- input from source is symplastic and loading to phloem is symplastic.
- input from source is apoplastic and loading to phloem is symplastic.
Need to research definition of (phloem) intermediary cell in primary literature. Slides from PJ show that it is a phloem parenchyma cell that is adjacent to a companion cell. Some people are calling the adjacent phloem parenchyma cells companion cells, but that is not correct. This is the case in the Amiard et al. paper, above.
albuminous cell (new term)
proposed def.: A parenchyma cell (PO:0000074) that is morphologically and physiologically associated with a sieve cell (PO:0025415) but does is not derived from the same initial cell (PO:0004011) as the sieve cell.
comment: May be found in the ray system (PO:0025411) and sometimes the axial system (PO:0025410) of gymnosperms. Compare to companion cells (PO:0000071), which are found in angiosperms.
is_a parenchyma cell, part_of phloem, adjacent_to sieve cell.
other
Need to request lateral sieve area and sieve plate pore for GO.
Is P-protein a cellular component (for GO) or just a protein (for PRO)? Need to find out.
Next PO Release:
In October, we had planned the next release for Feb 2012:
POC_Conf._Call_10-18-11#Next_PO_Release
We will aim for the second week of March- would be great to have it done for the presentation at the Maize Genetics Meeting, March 16th.
Timeline:
- Target date for finishing edits: March 2nd
- Target date for release: Before March 16th
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
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
- 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?
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 ther, 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:
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. Planning to talk with George Gkoutos re. plant quality terms and with Bruce Kirchoff re. images in ontologies.
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
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.
LC contacted the organizer; Neelima Sinha (Sinha@ucdavis.edu) and she said a short presentation was a possibility and would be pleased if a couple of PO people could attend.
LC may be interested in attending if we can get a slot. Could also combine the visit with a follow up meeting with Jill Wegrzyn and Andrew Groover about the wood terms and data for the PO.
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 ends this Friday, February 25.
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
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)
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 submission for minisymposia consideration ends March 2!
Joint workshop is planned with PO, Gramene and TAIR
Registration scheduled 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.
Relevant dates
- 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
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
