POC Conf. Call 9-8-10

POC meeting, Webex Conference Call; Date: Sept 8th, 2010 10am (PDT)

In attendance:

POC members: Laurel Cooper, Alejandra Gandolfo, Justin Preece, Justin Elser, Ramona Walls, Barry Smith.

Absent: Pankaj Jaiswal, Chris Mungal, Dennis Stevenson.

Collaborators: none

Acceptance of the minutes from the 8-18-10 meeting? All in favor? No changes were made.

Status and Update of Progress: PO Release

Feedback Box:

New link to feedback box on beta site- emails will go to po-discuss

• This could be customized in the future with additional fields and boxes for more directed responses

Note: It would be better if the feedback box could fill in the relative link automatically from the page. Is this possible?? "eg: Refer to URL: http://www.plantontology.org/index.html "

Apparently this got broken when it was moved to the new spot on the beta browser. JE is looking at getting it to capture the url of the current page being viewed.

feedback box on the live site has been fixed so it sends message to PO-internal

No other news on this to report.

Annotations that have no term associated with them

-Laurel and Ramona compiled a list of the 10 terms that have been obsoleted and how many annotations that are associated with them.

There were only 10 and only 5 of them are problematic: floral bud, gametophyte, leaf whorl, seedling and sporophyte. File:Obseleted terms (LC 8-10-10).pdf

In progress....

Laurel sent a spreadsheet to TAIR and Gramene listing the annotations that were affected on 8/13/10, with our recommendations or suggestions on where they should be moved to.

A. TAIR - 8/13/10 message sent to Donghui, Kate and Tanya:

"The main issues are with the annotations associated with the following PO terms which were obsoleted in the beta version:

PO:0009003: sporophyte 1 (from: po_anatomy_gene_arabidopsis_tair.assoc)

PO:0000056: floral bud 54: (from: po_anatomy_gene_arabidopsis_tair.assoc)

PO:0008037: seedling 16 (from po_anatomy_gene_arabidopsis_tair.assoc)

The first three will need to be looked at to determine where to best put them. We have put our recommendations or suggestions on the spreadsheet

PO:0008034: leaf whorl 15,802: (from po_anatomy_gene_arabidopsis_tair.assoc) These ones are pretty straightforward- we recommend to move them all to the new term collective leaf structure PO:0025022

Spreadsheet: File:TAIR dangling annotations (LC 8-13-10).pdf

• Comments:

Response from Tanya Berardini@ TAIR 8/16/10:

"Hi Laurel,

Thanks for the update and for the spreadsheet. We should be able to handle the transition for the obsoleted terms pretty easily as we already have a mechanism set up for automated transfer of annotations from an obsolete term to a replacement term, if that replacement term is suggested in the OBO stanza.

Comments:

(1) sporophyte - suggestions are fine, annotations should move if replacement term is in OBO stanza (see below:)

(2) floral bud

Why was 'floral bud' removed as a parent term for both 'axillary floral bud' and 'terminal floral bud'? I'm not sure I understand why this potentially useful grouping term was deemed no longer useful. I am not sure that we'll be able to move all our annotations to the more specific terms as the publications do not always specify whether axillary or terminal flower buds were used or whether the DNA/RNA/protein sample was obtained from a mixture of both.

(3) seedling - suggestions are fine, annotations should move if replacement term is in OBO stanza

(4) leaf whorl - suggestion is fine, annotations should move if replacement term is in OBO stanza

When do you anticipate the public release of the new version of the PO vocabularies? We will monitor the annotations that we have to the terms that you highlighted to make sure that the appropriate transfers and updates occur.

Thank you for your help,

Tanya"

Laurel replied and provided more explanation and invited her to review that section and possibly attend the conference call. Will follow up with them to get this resolved

B. Gramene - 8/13/10 message sent to gramene@gramene.org contact email. Ken replied and said that Pankaj was the best person to look at these.

File:Gramene dangling annotations (LC 8-13-10).pdf

C. Issues Arising:

*Changes to the annotation files:

See comments from CM about replacing the terms: On Aug 17, 2010, at 6:51 AM, Walls, Ramona

> We have put the replacement terms in the obo stanza as "consider" terms for all of these (check on this)

>>CM: note that where the replacement is clear you can use replaced_by - this means the replacement can happen automatically without a human having to make a choice

- Is there a script for making the changes? Does this apply to the annotation files or just the OBO files?

No more info on this

*sporphytic phase and gametophytic phase

> RW: in several cases (sporphytic phase for sporophyte, gametophytic phase for gametophyte, and seedling growth stage for seedling), we cannot currently add the 'consider' term to the po_anatomy_test file because the consider terms are in a different file (po_temporal_test). Probably the easiest way to solve this would be to merge the two files before the live release.

*Do we want to do the merge before the release?? it seems like this should have been done before sending out to the reviewers. We do not want to delay the process any further- What are other options?

we all agreed that this is a good idea, but it will have to wait for the next release.

*floral bud

> > 2. Based on the response from TAIR (see above), we may want to reconsider obsoleting the term floral bud (or not). Perhaps keeping this term for users is more important that getting rid of it to solve an ontological problem (term have multiple parentage).

(from email): CM: Multiple Inheritance isn't an ontological problem, it's an engineering problem for you, in that manually maintaining MI is tedious and error prone. You should move to towards using the reasoner to infer all these, but in the meantime your asserted links /must/ reflect the biology, which in many cases means asserting MI.

Those present at the meeting felt it was preferable to keep the current structure for floral bud. We were concerned about instituting a policy of changing the ontology here and there to fit the convenience of individual users, unless the change is biologically appropriate. Laurel will follow up with TAIR to see if they can work with the new structure for floral bud, and also to find out the status of their annotation files.

Barry described using axioms for terms with multiple inheritance, rather than using asserted relations. Not certain how this translates in OboEdit -- perhaps through the use of intersection of relations. There was a question of whether or not annotations would be passed on (to parent terms) using axiomatic relations -- no one knew the answer. Justin P. raised the issue that we should be mindful as to whether or not the utilities we use (like Amigo) will be able to support our future analysis needs (for example, implied relations do not show up in the Amigo browser).

BS pointed out that having a single inheritance rule will make us examine the biology more closely and avoid 'catch all' terms.

D. Resolution: - What is the mechanism for making these changes? Are we doing them here or is TAIR/Gramene going to send us new files?

The annotation files need to be updated and tested on the beta version before releasing the new version of the database. The association file from TAIR (PO_anatomy_gene_arabidopsis_tair.assoc) on our SVN site have not been updated since 2-10-2009- 18 months ago.

We still need to find out (maybe from Justin E. or Pankaj) what the procedure is for updating annotations before the release. We do not want to have to hold up our release waiting for their files.

Feedback on the Beta Release

The review request letters were sent out by email (copied to po-discuss) on Thurs 8-19 and Friday 8/20.

*Potential reviewer, institution, email address, suggestions for portions to review:

Sarah Hake*, UC Berkeley, The Plant Gene Expression Center, hake@berkeley.edu, flower (PO:0009046), collective phyllom structure PO:0025023

Quentin Cronk*, Biodiversity Research Center, University of British Columbia, Quentin.cronk@ubc.ca,collective plant structure (PO:0025007)

Paula Rudall*, Head of Micromorphology Section, Royal Botanic Garden, Kew p.rudall@kew.org plant cell (PO:0009002), male gametophyte (PO:0020091) and female gametophyte (PO:0020092)

Sarah Mathews*, Harvard University, Arnold Arboretum, smathews@oeb.harvard.edu, shoot system (PO:0009006), plant tissue (PO:0009007), how does our terminology relate to gene annotation, especially with respect to gymnosperms

Elena Kramer*, Harvard University, Organismic and Evolutionary Biology, ekramer@oeb.harvard.edu, plant organ (PO:0009008), flower (PO:0009046)

Neelima Sinha, UC Davis, nrsinha@ucdavis.edu, plant organ (PO:0009008), especially phyllome (PO:0006001)

Chelsea Specht*, UC Berkeley, Plant and Microbial Biology, cdspecht@berkeley.edu, plant organ (PO:0009008), especially plant axis (PO:0025004)

Rob Martienssen*, Cold Spring Harbor Laboratory, martiens@cshl.edu, shoot system (PO:0009006), how does our terminology relate to gene annotation

Peter Raven*, Missouri Botanical Garden peter.raven@mobot.org, upper level structure [direct children of plant structure (PO:0009011)]

Gar Rothwell*, Ohio University, Department of Environmental and Plant Biology, rothwell@ohio.edu, plant life cycle phase (PO:0028001); upper level structure [direct children of plant structure (PO:0009011)], especially how it relates to fossil taxa; suggestions for terms that might be missing for fossils

Peter Linder*, Universität Zürich, Institut für Systematische Botanik, director of botanical garden, peter.linder@systbot.uzh.ch vascular system, PO:0000034); review the ontology from an ecological perspective

Chris Hardy*, Millersville University, Herbarium, christopher.hardy@millersville.edu, cardinal organ part (PO:0025001); review ontology from a teaching perspective; how will it appeal to the next generation of plant scientists?

Rob Last, Michigan State University, Biochemistry and Molecular Biology, lastr@msu.edu, plant cell (PO:0009002), trichomes (PO:0000282)

Robert Stevens, University of Manchester, Bio and Health Informatics Group, robert.stevens@manchester.ac.uk, entire ontology, upper level structure

Farshid Ahrestani*, Columbia University, TraitNet, fa2260@columbia.edu, entire ontology, with reference to whatever structures of interest to Traitnet

yes, will do review of the PO

Sandy Knapp*, British Museum, s.knapp@nhm.ac.uk, plant tissue (PO:0009007), overall structure of the ontology

Richard Halse, Oregon State University, email:halser@science.oregonstate.edu, Research area: Taxonomy of the Hydrophyllaceae; ecology and taxonomy of Sidalcea; floristics of Oregon.

collective plant structure (PO:0025007), cardinal organ part (PO:0025001)?

Rich Zobel, USDA, rich.zobel@ars.usda.gov, root system (PO:0025025), root (PO:0009005); note that he has already submitted suggestions

yes, will do review of roots

Austin Mast*, Robert K. Godfrey Herbarium, Florida State University amast@bio.fsu.edu, cardinal organ part (PO:0025001)

Lukas Mueller and Naama Menda, Solanum Genomics Network, Need email, tuber (PO:0004543) and all of its part_of and is_a children

yes, Naama will do review of tuber terms

Responses, as of 8/7/2010:

From Paula Rudall (Kew)

1. Flower; PO: 0009046 [A heterosporangiate strobilus, typically consisting of androecium, gynoecium, usually surrounded by a perianth and borne on an axis or receptacle. ]

Does the definition make sense? There is no mention of determinacy, which is an important defining feature of the flower. I would prefer "bisexual" to "heterosporangiate", but not all flowers are bisexual (or heterosprangiate). The flower is notoriously difficult to define. Bateman et al. (2006: J Exp Bot 57: 3471-3503) discussed earlier definitions, and suggested the following: '. . . a determinate axis terminating in megasporangia that are surrounded by microsporangia and are collectively subtended by at least one sterile laminar organ'

Is it appropriate for all plants (not just angiosperms)? Not really, because the terms androecium and gynoecium are applied only to angiosperms. Flowers are not necessarily restricted to angiosperms.

Those present felt that the current definition of flower was not acceptable (it is inaccurate), and that we needed to come up with a new working definition before the release.

PROPOSED DEFINITION: A determinate shoot system that has as part at least one carpel or at least one stamen and does not contain any other determinate shoot system as a part. Comment: may be have as part one or more petals, sepals or tepals.

Child of shoot system

Also note that we need to add a inflorescence has_part flower (can't use flower part_of inflorescence, because not all flowers are part of an inflorescence).

RW opened a SF tracker for this term flower

2. Collective phyllome structure; PO:0052023 [A collective plant structure that consists of two or more phyllomes originating from the same node or from one or more adjacent nodes with compressed internodes.]

Does the definition make sense? It is not clear to me why the word collective occurs in both the term and the definition. It seems rather a strange term; at first I couldn't see what it would be used for, but when I found the discussion (e.g. the definition of the androecium as "A collective phyllome structure composed of two or more stamens") it made more sense. However, I'm not sure that this term needs to be defined separately.

Is it appropriate for all plants (not just angiosperms)? yes

We agreed to keep collective phyllome structure as it is for this release.

3. Central cell; PO: 0020090 [The largest cell of the mature embryo sac. Contains two polar nuclei, which (after double fertilization) will develop into the endosperm.]

Does the definition make sense? Yes, but see below.

Is it appropriate for all plants (not just angiosperms)? No; in a gymnosperm archegonium, the central cell is the cell that will divide to form the ventral canal cell and the egg cell (see Rudall 2006, Bioessays 28: 1067-1071).

This will be an issue when we add terms for gymnosperms, so we will address it in the next release.

From Elena Kramer (Harvard)

Does the definition of each term make sense?

For collective tepal structure PO:0025021 - This seems like an odd term that's never commonly used. I realize that the difficulty is finding a parallel collective concept for calyx and corolla. What if the first level under perianth was differentiated perianth and undifferentiated perianth. Then the first option would break down to calyx-->sepal and corolla-->petal while the second would just break down to tepal. I realize that structure is still not entirely parallel but at least it doesn't introduce terms that will never be used elsewhere.

The consensus was that the term undifferentiated perianth is not in use either, so it would better to keep collective tepal structure.

For hypanthium PO:0009065, I honestly wasn't sure what "cardinal" meant in the definition "A cup- or tube-shaped cardinal organ part". Does that refer to it being in the outer whorl?

We noted that both Kramer and Rudall appeared to misunderstand the genus/differentia form that uses the parent term in the definitions (comment on use of collective by Rudall and use of cardinal by Kramer). Perhaps we should add a glossary, FAQ link, or some other type of instructions to the web browser, to help novice users. There is some information available on the documentation page, but it inadequate, and it is not obvious when you are browsing the ontology.

The meaning of the term cardinal is described in the comment for cardinal organ part. Perhaps there should be a cross-reference to it in the child terms.

Is it appropriate for all plants (not just angiosperms)?

Since I only looked at floral terms, no, they are just appropriate for angiosperms, although the micro/megasporophyll definitions would be comparable for gymnosperms.

Coverage: Are the terms included under the node(s) you are reviewing (its descendent terms) sufficient?

Well, we work on petal spurs and they were missing under petal, so that would be a big problem for describing Aquilegia. Also, I wondered if there was some way to incorporate corolla tubes vs. free petals, inferior vs. superior ovaries, and the phenomenon of common primordia (that last one would only apply to the development ontology).

A spur is a part of a petal, so we could add a term for it under cardinal organ part. The other terms are phenotypic descriptors, and could be annotated using a combination of PO and PATO terms.

From Farshid Ahrestani (Columbia, TraitNet)

There is a possibility that we (TraitNet and partners) may incorporate a slim-version of the PO for a Plant Functional Trait ontology that we are developing.

The following terms could be included in the ontology, depending on their relevance and importance:

Corm - Maybe as a synonym of stem.

Spine

Podaria (which is synonym to Tubercle)

Pneumatophore

Stele

Diaspore

Cone

Sorus

Shoot - Subclasses of the shoot are included, such as shoot apex and shoot axis

Tendril

Wood - Although sapwood, late wood, early wood, heartwood present

- Seed coat is present, but is part-of of Plant tissue. Is that correct?

- Pollen Tube (and maybe others at that same level in the ontology) could do with a parent.

By slims, they are referring to something similar to a GO slim (based on conversations with Ramona), which they would develop using selected terms from the PO.

Shoot is a synonym of shoot system, and wood is a synonym of secondary xylem. Other terms can be added for the next release. Can fix seed coat part_of portion of plant tissue for this release.

Laurel will follow-up with Rich Zobel (Root terms) and Naama Menda (tuber terms), Alejandra will follow up with Gar Rothwell

Updates to the PO Web pages

• So the reviewers can access the obo and OWL files, they should be made available on the download page (http://www.plantontology.org/download/download.html#download).

On all three sites or just on the beta site??** It should be on both Live and the Beta at least.

Next meeting scheduled for: Weds, Sept 15th, 10am