POC Conf. Call 9-15-10

POC meeting, Webex Conference Call; Date: Sept 15th, 2010 10am (PDT)

In attendance:

POC members: Laurel Cooper, Alejandra Gandolfo, Justin Preece, Justin Elser, Ramona Walls, Pankaj Jaiswal.

Absent: Chris Mungal, Dennis Stevenson, Barry Smith.

Collaborators: none

Acceptance of the minutes from the 9-8-10 meeting? No changes or additions.

Status and Update of Progress: PO Release

Items Arising from reviews, as of 9/14/2010:

From Paula Rudell, Kew Gardens

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

New SF tracker for this term flower

Proposed Def'n: 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 have as part one or more petals, sepals or tepals.

This should be a 'child of shoot system', rather than part_of inflorescence (can't use flower part_of inflorescence, because not all flowers are part of an inflorescence),

• Also note that we need to add a inflorescence has_part flower .

perhaps we should have a reproductive shoot system? (which is a term we don't have at the moment).

New proposed definition: A determinate reproductive 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 have as part one or more petals, sepals or tepals. May contain pistillode or staminode or other aborted organs that don't show up in mature form.

Need to look at terms like lemma, palea, lodicule and nectary for next round of revisions.

From Farshid Ahrestani (Columbia, TraitNet) Ramona responded to him that we agree that the terms he requested should be added to the ontology, but due to time constraints, we will not be adding any new terms to this release, but we will aim to add them before the next release.

• Will correct seed coat part_of plant tissue and add wood as synonym for secondary xylem for this release.

Seed coat is not part_of plant tissue, but is_a, which is correct, so no need to fix it.

Re. definition of secondary xylem: should add that it develops from vascular cambium, and add develops_from relation. Fix typo in comment (tress). SF tracker: secondary xylem

Rich Zobel (Root terms)

We have an open term request root terms from Rich Zobel from last November. We requested Rich's help with the review process, so it makes sense to deal with the open tracker.

There are a couple of upper level term that need to be added: 'basal root' (along with its child: 'non-pericyclic basal root') Modification of 'shoot borne root (PO: 0000042) and taproot/primary root (PO:0000042).

It should be possible to incorporate these changes into this release, (depending upon the amount of discussion generated). The essential issues are that there are 3 distinct types of roots: basal roots, shoot-borne roots, and taproot (primary root)

1. new term 'basal root'. I looked around in the literature and this is being used. We will have to work on the definition though. Seems pretty straightforward, also suggested a child term: 'non-pericyclic basal root')

2. Change name of primary root (PO:0000042) to 'taproot'. This one I am not too sure about- is the primary root always a taproot? What about in the grasses? I propose we leave this as is for now and keep taproot as a synonym.

Should it be 'tap root' or 'taproot'? It is used both ways.

3.'shoot-borne root- addition of hyphen, problem with the synonym 'adventitious'- too broad. seems pretty straightforward.

LC opened individual SF trackers for each of these.

We will add basal root as new term. New proposed definition: A root that develops from one of the of hypocotyl (which layer?) or "A root that arises from a part of the hypocotyl" ?. Will deal with synonyms and child terms of basal root in next round of revisions.

Decided to leave primary root named as is for now, keeping tap root as synonym, but will seek more outside input into what the best name should be. Will add comment: Is often the central axis of the root system.

Okay to add hyphen to shoot-borne root. Should add hyphens to other -borne terms in the ontology for consistency. We felt that adventitious root should not be a synonym, because some basal roots may be adventitious roots. Need to give adventitious roots further consideration, and maybe add as its own term for next round of revisions.

PJ: We also should discuss root terms with Phil Benfey (Duke) and Leon Kochian (Cornell). They are developing software for root type recognition. Should work to integrate PO with their software. Don't know if Rich is involved in discussions with them.

Naama Menda (tuber terms)

Naama's response:

NM:"I think the new hierarchy is better than the previous one (branch vs shoot). The child terms in the tuber node seem complete to me, at least from looking at the features that are being evaluated by the potato breeders community (mostly tuber skin, flesh, eyes)"

NM: subterranean tuber axillary vegetative bud (PO:0025042): the term 'sprout' is often used by potato breeders. One example is the trait 'heat sprout rating' which measures new sprouts on the tuber. These range from 'swollen eyes' to 'chain tubers'. I'm not sure if 'tuber sprout' should be a synonym or a child term (develops from the axillary vegetative bud)"

The 'sprouts' are buds (eyes) that begin to grow. Since they actually develop from an existing axillary vegetative bud, perhaps the term 'sprout' is more like a shoot than a bud? If so, they perhaps they should be an axillary shoot (PO:0006343)? Or maybe we need a new term 'subterranean tuber axillary shoot' ?

Can have swollen eye as synonym of tuber axillary bud. Sprout should be added a synonym of axillary shoot or better yet, add new term subterranean tuber axillary shoot.

Link to SF tracker for request for new term subterranean tuber axillary shoot

NM: "tuber epidermis and tuber periderm: 'potato skin' is a synonym for both terms. I see the clarification in the comment field, but I think it would be clearer to have a synonym of 'mature potato tuber skin' and 'young potato tuber skin'. Queries using 'potato skin' should still pick up both terms".

We agreed this is a good suggestion, and will fix.

NM: "Are any plans to add tuber developmental and growth stages to PO? Currently this is the only portion I think is missing from the ontology. Data we have from potato breeders usually refers to fully mature tubers, but molecular biologist do look at gene expression during different growth stages". (See below under Priorities for next round of revisions)

Alejandra will follow up with Gar Rothwell

Waiting for response from Gar Rothwell and Peter Linder. MAG will copy responses to po-discuss.

Annotations that have no term associated with them

-There are 10 terms that have been obsoleted from this version of the PO.

PO:0025003 compound plant organ

PO:0025002 simple plant organ

(These two were never in the live version, so they were actually destroyed, not obsoleted)

PO:0009014 dermal tissue

PO:0000057 inflorescence bud

PO:0000058 vegetative bud

PO:0008034 leaf whorl

PO:0008037 seedling

PO:0009004 gametophyte

PO:0009003 sporophyte

PO:0000056 floral bud

Only the last 5 of them are problematic: leaf whorl, seedling, gametophyte, sporophyte and floral bud.

PO:0008034 leaf whorl

• Annotations: 15,802, from 'po_anatomy_gene_arabidopsis_tair.assoc'

Source: TAIR

These ones are pretty straightforward- we recommended to TAIR to move them all to the new term 'collective leaf structure' PO:0025022

Response from TAIR (Tanya Berardini 8/16/10): -suggestion is fine, annotations should move if replacement term is in OBO stanza- it is.

PO:0008037: seedling

• 16 annotations from 'po_anatomy_gene_arabidopsis_tair.assoc'

Source: TAIR

-Recommended to TAIR that they should be moved to seedling growth stage (PO:0007131) in PGDSO and also to whole plant (PO:0000003)in PSO.

Response from TAIR (Tanya Berardini 8/16/10):- suggestions are fine, annotations should move if replacement term is in OBO stanza

Laurel will add the consider relation to seedling growth stage in the PGDSO, but we need to clarify whether or not this works for TAIR's script.

PO:0009003: sporophyte

• 1 annotation from: 'po_anatomy_gene_arabidopsis_tair.assoc'

Source: TAIR

-Recommended to TAIR that they should be moved to sporophytic growth phase (PO:0028002) in PGDSO and also to whole plant (PO:0000003)in PSO.

Response from TAIR (Tanya Berardini 8/16/10): - suggestion is fine, annotation should move if replacement term is in OBO stanza

Laurel will add the consider relation to seedling growth stage in the PGDSO, but we need to clarify whether or not this works for TAIR's script.

Yes -- these annotations should also be attached to whole plant.

• 116 annotations from 'po_anatomy_gene_oryza_gramene.assoc' and 'po_anatomy_qtl_oryza_gramene.assoc'

Source: Gramene

Suggested that the associations for genes be moved to PO:0000003 whole plant, plus sporophytic growth phase (PO:0028002) for genes;

Seedling vigor QTLs are already associated with PO:0007131 seedling growth, suggested adding association to whole plant PO:0000003 as well, if appropriate

PO:0009004 gametophyte

• 1 annotation from 'po_anatomy_gene_oryza_gramene.assoc'

Source: Gramene

Suggested that this association be moved to male gametophyte (PO:0020091) or female gametophyte (PO:00290092) or to gametophytic phase (PO:0028003) and/or to to whole plant PO:0000003

Note: It is already associated with the megagametophytic stage (PO:000721)Note: This appears to be an error and pollen developmental stage (PO:0001007) in the PDGSO.

Note: This annotation is concerning rice anthers so it should be moved to male gametophyte (PO:0020091) and to gametophytic phase (PO:0028003).

PO:0000056: floral bud

• 54 annotations from: po_anatomy_gene_arabidopsis_tair.assoc

Source: TAIR

Question from TAIR (Tanya Berardini@ TAIR 8/16/10)

"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."

This was discussed at the 9-8-10 meeting. All those present felt it was preferable to keep the current structure for floral bud. For more detailed information and graphics, please see the [Summary of Changes] page We were concerned about instituting a policy of changing the ontology, unless the change is biologically appropriate.

Response: TB: "The PO suggestion "...to move the annotations to both axillary floral bud and terminal floral bud, if that is appropriate. " is not necessarily practical as this information is not always available and I would be reluctant to move the annotations to the child terms if I wasn't sure that these were correct."

In order to get a better understanding of the issue, Laurel went through the annotations associated with the term 'floral bud' and looked at each paper to see how they describe the plant tissue samples. Most of them refer to "floral bud", "flower bud", or simply "buds". In a few cases they seem to be referring to the whole inflorescence.

In light of this, we need to reopen the discussion of the bud structure and will reexamine these terms.

We had some discussion of bud terms. Since all floral buds are at the end of a shoot (since they are determinate) they should all be terminal buds, but then those terminal buds can arise either at the end of a shoot or in an axil. Pankaj and Lol will work on sketching new structures for bud terms that includes the categories reproductive bud and floral bud. Will re-open SF tracker so we can work on this more.

Annotation File formats

We have had a question from Tanya Berardini@TAIR about whether or not we are planning to transition to the GAF 2.0 format or not.

GAF 2.0

This will affect how they modify the above files

Should we get one and test it first? Will it matter if there are some in GAF 1.0 and some in 2.0?

Maybe a goal for the next version?

Lol talked to Justin and Chris before meeting, and they say new format should work fine, so TAIR can send us the files in GAF 2.0

Priorities for the Next Round of Revisions

-Merging the plant structure and plant developmental stages ontologies

-Adding Musa terms requested by Rosemary Shrestha

-Root terms- Rich Zobel

-Legume terms submitted by Austin Mast

-New terms requested by reviewers (from Ahrestani and Kramer)

-is_a parents for remaining terms (will require work on upper level structure for non-material entities)

-convert to intersection_of relations?

-work on PGDSO

-tuber growth and development stages, open on SF since 6/2009

-add links to more images

-Others??- PJ: Lol and Ramona will focus more on adding annotations (~50% of time)

-What is the target date for the next release?

Other Items:

Alejandra has the first set of images ready to load onto PlantSystematic.org. Alejandra, her technician, and Ramona (and anyone else who is interested) will try to meet by phone next week to go over the progress.

A. Feedback page on Beta site fixed

Justin Elser fixed refer_to_url variable on the feedback page for the beta site. It is now working from within the AmiGO browser. Now it will capture the url of the page the person is looking at. Thanks Justin!

B. Announcement for Plant Sciences Bulletin: Note: that this is not for the beta version but the live version due to the timing. Sent to PJ for review 8/12/10

Dennis will also send this to the BSA for posting on their website- but should wait to do this until after the release comes out~ end of September.

Ramona will follow up with Dennis after he gets back to see what the status of this is.

C. POC meeting to be held at NYBG in fall 2010. Date TBD.

Should we invite outside experts, scientists, students and postdocs?

Please fill out Doodle Poll re. dates that you are or are not available: http://www.doodle.com/6n4pmknkeebk9khg

We need to pick a date for this meeting ASAP so folks who are flying in can get tickets

Pankaj will check his calender to see if this is possible. Ramona will follow up with Dennis when he returns.

Upcoming meetings 2010-2011:

• Latin American Congress of Botany

LACB. La Serena, Chile, October 4-10;

Dennis is attending LACB. We will consider having a presentation at this meeting. Alejandra will not be able to attend.

* Infectious Disease Ontology Workshop

Dallas, Dec. 8th and 9th, 2010

Organized by Lindsay Cowall (Duke University) and others, under the auspices of the National Center for Biomedical Ontology. IDO Workshop December 2010. Note that relations between the IDO and other ontologies is one of their provisional goals.

Pankaj will represent the PO with regard to plant infectious diseases. This is especially relevant to the PO as infectious disease agents (viruses and bacteria) are widely used in plant genetic research.

For additional information on the IDO see http://www.infectiousdiseaseontology.org/Home.html

*Plant and Animal Genome XIX Conference

January 15-19, 2011 PAG 2011

Registration is open, abstract deadline Nov 1, 2010.

Lol and Ramona should plan on attending and meeting with collaborators. Set up a computer demonstration, and possibly a Phenote workshop. Perhaps Dennis and Alejandra could also attend, and we could all meet there. PJ is not attending as he is teaching.

* International Botanical Congress (IBC2011)

July 23rd-30th 2011, Melbourne, Australia

Registration is open- deadline for abstracts: 31 October 2010, Important dates

Dennis and Alejandra are planning to attend IBC2011 and speak in other symposia.

Symposium proposal was accepted, 'Bio-Ontologies for the Plant Sciences' under the genetics, genomics and bioinformatics theme.

Ramona contacted the organizers about whether or not it is possible to get a room with Internet for outreach activities, but hasn't gotten a response yet. Is this something we still want to pursue?

Pankaj, Ramona, and Angelica Cibrian (Harvard and ANMH, Genomics of Seed Plants) are scheduled to give talks and must submit abstracts by October 31st. Three additional speakers will be chosen from abstracts that are submitted.

Ramona and Pankaj will switch talks, so that Pankaj gives the introductory talk on general use of ontologies, GO, genomics, etc, and Ramona gives the talk on the Plant Ontology.

Next meeting scheduled for: Weds, Sept 22nd, 10am PDT