POC Conf. Call 1-31-12
POC meeting, Webex Conference Call; Date: Tuesday Jan 31st, 2012 10am (PST)
In attendance:
POC members: Laurel Cooper (OSU), Pankaj Jaiswal (OSU), Justin Elser (OSU), Justin Preece (OSU), Ramona Walls (NYBG)
Absent: Dennis Stevenson (NYBG), Marie Alejandra Gandolfo (Cornell University), Barry Smith (University at Buffalo, NY), Chris Mungall (Lawrence Berkeley National Lab)
Collaborators: none
Any changes or corrections (additions/deletions, etc) needed in the minutes from the POC_Conf._Call_1-24-12? No additions, changes, or deletions.
Back to POC Meetings Minutes
Streaming recording link:
https://ontology.webex.com/ontology/ldr.php?AT=pb&SP=MC&rID=61902932&rKey=eca857eefea40919 Download recording link:
https://ontology.webex.com/ontology/lsr.php?AT=dw&SP=MC&rID=61902932&rKey=b4449adc3cd01a81
Miscellaneous
Genvestigator: Should send an email to them and ask if there is a mechanism to search their database using PO ids. This means we would be better able to support any need they have for new terms.
Ensembl Plants - Has a listing for PO, but nothing there yet?
PJ: All the genomes that have PO annotation (Arabidopsis, rice) are in Ensemble plants.
Except there are none for Physcomitrella yet. You cannot search by PO ID there either. ie: it can return a list of Arabidopsis ids, but where is the PO info?
Adding top level parent term- Plant Ontology
See discussion with Naama from SGN
Is there any reason why we should not do this??
Do we want to use plant ontology as NM suggested or adopt the BFO/CARO top levels?
Test on dev browser.
AmiGO automatically inserts the generic parent "all". GO uses this too.
If we bring in top-level terms, it could create problems with dangling parents. Also, BFO terms could be confusing for users who aren't familiar with the other ontologies.
We used to have plant ontology at top level, but removed it at CM's request. Plant ontology doesn't really work as a top level term, because it is not a parent of the different ontology terms.
Should ask Naama how their software deals with GO. They now have cross-reference relations as well. See SGN
Rather than us adding top level terms, it might be better to have it be part of the browser. Otherwise, they will have to put a root level term in everyone ontology that is hosted on the browser.'
Another option is to create a top level term with a PO-id, like "plant entity", but this may be counter to the idea of re-using upper-level ontology terms.
JE can respond to the SF tracker in technical terms, suggesting that we keep it the way it is, and they should modify their browser to add "all" or something similar.
Other groups are asking about this as well, but the solution should be in the software, rather than hard coding it in the ontology, which creates problems.
Adding PO Ids to terms in comments and definitions:
-add on first instance of the term in the comment agreed
This example shows how it looks in the comment, but term ids in the definitions do not currently work as links. We decided back in ....(date ref?) NOT to put ids from other ontologies in the definitions to avoid cluttering them up.
See: plant cell and PAE
-update our PO_Developers_Guide to reflect this change in policy
-This might be a good task for a student- go through and add the po ids to the comments
-We will have to run a check at each release to update any ids that have been changed or obsoleted.- should be added to the PO_Release_SOP_Page
The disadvantage of having id's in the definition is that it clutters them and may be redundant with the existing relations. Also provides mark-ups for NLPs. The advantage is that people who are not looking at the tree while they read the definition will be able to see that we are referring to PO terms.
Adding them is hard, but taking them out is easy, if we decide we don't like them. For now, we will add them to both definitions and comments for new terms, and see how we like it.
We will need to institute a new check with each release to these links. We should still be checking for references to obsolete terms in definitions, whether they have id's or not, and having them as numbers makes the check easier.
This also makes it more likely that the name we used in the comments or definitions matches the PO term name.
New relations
- need an icon for has_participant
- for example see: seed trichome
-already using Hp for has part, suggestions?
PJ will make the icon.
'Has_participant could be "hP" in a circle, (to distinguish it from has_part). It would be good to relate the new icon visually to the reciprocal participates_in- it could also be a circle.
Dark background with white letters is more visible.
Should create a link from the legend on PO tree viewer page to a wiki page for all the relations. This should go to the separate page Relations_in_the_Plant_Ontology and link there from developers' guide, with subheading for each relation. However, link form PO page should just go to the relations page (not separate links for each relation), so we don't have to update the links every time we have change a relation.
See the test version on dev.
Items from past meetings:
From POC_Conf._Call_1-17-12:
Revised def'n, plant spore (PO:0025017): A whole plant that arises through meiosis and develops into a gametophyte.
Comment: A spore is usually single-celled in homosporous plants but may be multicellular in heterosporous plants.
May need to be more specific in definition. Maybe add something about sporopollenin in the spore wall (GO:0031160)?
Revised definition: A whole plant that arises through meiosis and is contained in a spore wall.'
comment: A spore is usually single-celled in homosporous plants but may be multicellular in heterosporous plants. May have a spore wall (GO:0031160) made of sporopollenin.
Keep this term as is, and add specific terms for uni- and multicellular spores, since most spores are a single cell. Add single celled mega and microspores now, since that covers the majority of plants.
From POC_Conf._Call_1-24-12:
protophloem (PO:0006077)
revised def'n: A portion of primary phloem tissue that does not have companion cells or albuminous cells associated with the sieve cells and has as parts the first-formed sieve elements at a particular location.
comment: Protophloem is the first primary phloem to differentiate in any particular level of a vascular bundle. Sieve elements in the protophloem are smaller than in the metaphloem. The protophloem only lasts a short time before it is replaced by metaphloem.
Note: Xylem and phloem development stages need to be addressed in the PSDS branch. Can be used to clarify these tissues.
Revised definition: A portion of primary phloem tissue has as parts the first-formed sieve elements at a particular location and does not have companion cells (in angiosperms) or albuminous cells (in gymnosperms) associated with the sieve cells.
metaphloem (PO:0006076)
revised def'n: A portion of primary phloem that has as parts companion cells or albuminous cells and develops after the protophloem.
Comment: Metaphloem develops after the vascular tissue has stopped elongating, in the same location as the primary phloem, replacing the protophloem. Sieve elements in the metaphloem are larger than in the protophloem. Differentiates before the secondary phloem, if any is formed.
Revised definition: A portion of primary phloem that has as parts companion cells (in angiosperms) or albuminous cells (in gymnosperms) associated with the sieve cells that develops after the protophloem.
General comment: Sometimes it is a better idea to repeat some of the definition from the parent terms, to help educate the readers. Not everyone will know to or take the time to read the definitions of the genus terms.
Esau: Strasburger cells, synonym for albuminous cells
Vascular tissues and meristems
PO IDs will be added to comments and definitions as needed (these notes were typed a while ago).
xylem
xylem (PO:0005352)
revised def'n: 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.
Add comments to this and other xylem terms that the cells are dead at maturity. We already have this comment on tracheary element. Also add comment about cell walls (see TE's for comment)
primary xylem (PO:0005849)
revised def'n: 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
Add comment that it is not differentiated into axial and ray systems.
protoxylem (PO:0000272)
revised def'n: A portion of primary xylem that has as parts tracheary elements with only annular or helical secondary wall thickening that are the first formed tracheary elements at a particular location.
Comment: Tracheary elements in protoxylem are always smaller than in metaxylem.
Add to comment: develops while VB is still expanding.
metaxylem (PO:0000372)
revised def'n: A portion of primary xylem that develops after the vascular bundle has stopped elongating and after the protoxylem.
Comment: Differentiates before the secondary xylem, if any is formed. Tracheary elements in metaxylem are always larger than in protoxylem and can have any type of secondary wall thickening.
secondary xylem (PO:0005848) current def.: A portion of xylem tissue that develops from a vascular cambium. [source: ISBN:0471245194, POC:Curators]
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)
revised def'n: 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
- leaf vein (PO:0020138)
revised 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 def'n: 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)
revised def'n: 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.
The PO has a general term for lateral meristem, of which cambium is a subtype:
lateral meristem (PO:0020145)
revised def'n: 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)
This is just a cambium in the root, which also has vascular cambium and phellogen.
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.
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)
revised def'n: 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)
revised def'n: 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)
revised def'n: 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)
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 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'n: 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 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.
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 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.
The PO and Gramene will most likely be co-hosting a workshop. Details TBA....
LC will submit a proposal for a talk at this meeting.
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 doing 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.
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
