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

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:

phyllome adaxial meristem

-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.

Links to sources

• Need to create a POC:curators, po-ref page with a list of who the curators are
• Link to list of ISBN #s with the references

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:

• plant spore (PO:0025017)

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. Maybe add single celled mega and microspores now, since that covers the majority of plants.

From POC_Conf._Call_1-24-12:

• phloem and its children

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 and 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: A portion of xylem (PO:0005352) tissue that develops from a vascular cambium (PO:0005598).

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

The following items were postponed until next week's discussion:

Details moved to Items for future meetings

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 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.

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