POC Conf. Call 8-2-11

POC meeting, Webex Conference Call; Date: Tuesday Aug 2nd, 2011 10am (PDT)

In attendance:

POC members: Laurel Cooper (OSU), Ramona Walls (NYBG), Barry Smith (University at Buffalo, NY), Justin Elsner (OSU), Justin Preece (OSU)

Absent: Pankaj Jaiswal (OSU), Chris Mungall (Lawrence Berkeley National Lab), Dennis Stevenson (NYBG), Marie Alejandra Gandolfo (Cornell University)

Collaborators: none

Acceptance of the minutes from the POC_Conf._Call_7-19-11? There were no changes, additions, or deletions.

Conference/Meetings updates:

IBC 2011, Melbourne, Australia

The POC hosted the IBC_2011_Bio-Ontologies_Symposium on Thursday, July 28th.

The PO and our symposium (and the MaizeCyc database) were publicized in the conference newspaper.

Both PJ and MAG had their research mentioned during the plenary lectures!

Throughout the meeting, RW and DWS spoke to a number of people from the plant systematics community who are interested in potential uses of the PO.

PO will also look into collaboration with/tagging terms in JStor Plant Science. See page for Jstor_Herbarium_annotations

Talked to Rudi Appels about using PO terms for wheat gene expression data. See page for Wheat_Gene_Catalogue

Bruce Kirchoff would like to have a conference call with POC to discuss image annotation.

Should follow up on the interest from the person in Melbourne setting up a Plant Phenomics center- PJ should know the name

ICBO, 2011, Buffalo, NY

ICBO 2011 Second International Conference on Biomedical Ontology July 26-30, 2011 Buffalo, New York ICBO

-LC presented the Plant Ontology on Thursday, July 28th, 3:40pm in the session: "Introduction to The OBO Foundry Initiative"

Link: ICBO Program

July 27 8.30am-4pm: LC co-organized the workshop "From Fins to Limbs to Leaves: Facilitating Anatomy Ontology Interoperability and the OBO to OWL workshop, along with Melissa Haendel, Chris Mungall, Alan Ruttenberg, David Osumi-Sutherland.

LC had many discussions with various groups about ontology interoperability,

• ICBO proceedings. This includes all papers from the main conference, conference workshops, and other associated events.

Link to the slides: ICBO slides

CL has obsoleted all their plant cell terms. We should create a subset for them, and look over the plant cell terms and add any that are missing (see notes on last meeting's agenda)

CM still thinks we should remove "plant" as prefix from term names, but we still feel it is right to keep it. We will be responsible for looking after the plant cell terms. Also, if we want to import terms from other ontologies (like cell from GO), it would cause conflicts if they have the same name.

The presentation for OBO Foundry acceptance went well. No one brought up any objections to LC. OBO Foundry is working to schedule a meeting in Europe (probably England) in the fall. Ontologies will make a presentation similar to ICBO, followed by a review by the OBO Foundry committee. Would be good (but not absolutely necessary) if someone form PO could go.

The letter for OBO Foundry acceptance is still under work. Some presenters at ICBO (not PO) misunderstood the principles of Collaboration and Locus of Authority. Have been clarified on the OBO Foundry page, so we can use the wording from there in the letter. Will take up after ASPB meeting

MaizeGDB mappings for Annotations

• See also collaborator page: Submission of Association files for the Kaeppler gene expression data from MaizeGDB- Aug 2011 for details from the 8-4-11 conference call.

Mary Schaeffer of MaizeGDB is preparing a large number of annotations to our terms from a large microarray data set. As part of that, she has prepared a mapping between the samples in the studies and our terms. We need to look these over and make sure they make sense.

File:Maize Atlas2011.pdf

How will PO users be able to access the comments in Mary's mapping file? There is not space for them in the annotation file. Each annotation links back to the contributor's page for the gene. Can they also link back to the rows of their mapping spread sheet? (RW: or does it make more sense for the link to be from the PO structure or growth stage term?

BS: There is software available that will convert each row of a spreadsheet to a web page, making it easy to convert their mappings to links from PO.

Here is the link to their tissue pages: Maize Developmental Gene Atlas

There is a page for each tissue, for example: anthers R1 B73, with links to the PO terms and photos

Use of column 16: Not completely clear what they want to use it for. Have to make sure it doesn't interfere with our plan to use it adding annotations for vascular/non-vascular leaves for similar.

There are different ways to describe growth stages if they both map to the same PO term, then they should just be added a synonyms to the PO term, rather than going into column 16.

There was also some question about the significance cutoff they are using, and how to convey that to users. Maybe MaizeGDB can create a page showing the methods they used. This question also came up for the Physco data. Not every experiment needs to use the same methods, but we need to have a page that explains what statistical tools were used for any experiment.

Action: We are working on setting up a Submission of Association files for the Kaeppler gene expression data from MaizeGDB- Aug 2011 with Mary Schaffer to discuss the mappings and how the information can be presented.

We should deal with these SF requests from them as well:

PAO terms for MaizeGDB

transition leaf - definition

From Mary at MaizeGDB: It would be helpful to add some insights on the transition leaf.

For example - Leaves that have mosaics of juvenile and adult tissues. In maize, the juvenile will be at the tip, which differentiates first, with adult at the base. Other grasses may have other arrangements, eg Brachypodium, which may have both juvenile and adult across the breadth of a leaf.

Provided by Erin Irish, who references this paper: Irish, E. E. and Karlen, S. (1998) Restoration of juvenility in maize shoots by meristem culture. International Journal of Plant Science 159, 695-701. The Brachy. information is more recent.

Suggest adding to the comment of juvenile leaf, transition leaf and adult leaf: Many species have juvenile leaves are at the base of the stem, adult leaves at the apex, and transition leaves in between. In maize, juvenile leaves will be at the tip of the stem, which differentiates first, with adult at the base, while other grasses may have other arrangements. Transition leaves may have mosaics of juvenile and adult tissues, as in Brachypodium.

Can add Irish and Karlen reference to definition dbxrefs if it is appropriate.

It is okay to add the comment. Fix grammar. Should say "stalk (stem)" for maize instead of "stem", because maize researchers use the term stalk.

leaf base

See tracker item for details.

I think Mary's questions have been answered, and this item can be closed. We can add a comment to it once we resolve the issue of transferring annotations for parts of leaf.

We should check with her during the conference call to make sure everything is clear about how to annotate the parts of the leaf.

style, silk, Poaceae style

From Mary at MaizeGDB: Suggest that you merge these, keeping style, obsoleting silk and Poaceae style. Do the same for other floral parts that have a species spin on them, but are really the same as other more generic names for flower parts.

From PJ: Poaceae / Zea was necessary in some terms because often detail structures referred to parts of tassel/ear floret and it has conflict with floret compositeae besides the spatial aspects.

Rather than working on this piecemeal, we need to have an organized approach to eliminating the Poacaeae/Zea terms. Need to look at the structure from the top down and ensure part_of relations remain correct. Do we want to allocate time to this now or wait for next release?

See page for Eliminating Zea/Poaceae terms from PO

42 terms in PAO with Poaceae in the name.

28 terms in PAO with Zea in the name.

Only one Poaceae term in PGDSO (PO:0007012 Poaceae inflorescence visible), and there is a Source Forge item requesting that we merge it with another term.

We need to be careful about merging terms to ensure that partonomy remains consistent and doesn't cause conflicts among taxa.

We should begin by looking at the terms in Mary's mapping spread sheet to see which ones need to be done first. We can at least begin by merging the terms needed for their current annotations.

RW will go over the spread sheet, and make some notes on the Eliminating Zea/Poaceae terms from PO page. Can at least see what the ramifications are of making the specific changes she requested.

Comments from BS: problems with combinatorial explosion of terms if you try to add species-specific terms for every organism. Can be problems if you don't know what structures are homologous. Should keep working on being a species-neutral reference ontology, but create synonyms and slims for organisms as needed.

RW: later: maybe conflict with Poaceae/Asteraceae floret was due to the old use of the part_of relation to mean either part_of or has_part. Now that we have clarified that part_of means only part_of, that might not be a problem.

PGDSO terms for MaizeGDB

We can discuss these items, if time allows.

See: Items_for_future_meetings#Maize_GDB

Upcoming meetings 2011:

• Plant Biology 2011, Aug 6-10th, Minneapolis, Minn

Plant Biology 2011

Gramene and Plant Ontology are hosting a Data Curation Workshop again, focusing on pathway curations.

LC and PJ will present a PO poster.

TAIR (Kate Dreher) is organizing an Plant_Biology_2011_Outreach_Booth and we are invited to take part. We are hosting the website.

• POC Meeting at New York Botanic Garden Tentative dates, Sept 10th-11th, 2011

DWS will look into booking the apartments at the NYBG for accommodations.

We agreed that the PO meeting will be all day Saturday Sep. 10 and morning of Sunday Sep. 11. DWS, PJ, BS, LC, MAG and RW can make it.

RW has reserved the NYBG apartment for the nights of Sep. 9 and 10.

BS suggested that we should have a public lecture at the garden at some point. Perhaps it could be part of the public lecture series that is already held at the garden.

Maybe we could have some of the more plant-biology oriented parts of the meeting at the end, so Barry could leave earlier if necessary.

LC may stay in NYC until Monday, and host the presentation for Physco from the NYBG.

Probably start the first day talking about the PGDSO, then go from there.

See: POC Meeting at NYBG; Sept 10th-11th, 2011