POC Conf. Call 6-7-11

POC meeting, Webex Conference Call; Date: Tuesday June 7th, 2011 10am (PDT)

In attendance:

POC members: Laurel Cooper (OSU), Ramona Walls (NYBG), Pankaj Jaiswal (OSU), Barry Smith (University at Buffalo, NY), Marie Alejandra Gandolfo (Cornell University)

Absent: Chris Mungall (Lawrence Berkeley National Lab), Justin Elsner (OSU), Dennis Stevenson (NYBG),Justin Preece (OSU)

Collaborators: none

Acceptance of the minutes from the POC_Conf._Call_5-24-11? No additions, deletions, or changes.

New release (Version #15, May 2011) is available on the Live Plant Ontology browser site

Comments on release?

Process went much more smoothly than the Jan 2011 release, although we did not get everything in that we would have liked to.

Still need to get the Spanish translations in, JE is working on the script

Rescheduling the webinar with the Physcomitrella group for June 21st

For future release, RW and MAG thought it will be easier to add translated synonyms for all new terms once for each release, rather than trying to add them as the new terms are added.

Items arising from the reviews:

Children of Leaf

The issue:

Non-vascular leaf was added in the fall 2010 round of revisions. There are a number of terms (~25) that can be part of either non-vascular leaf or vascular leaf (for eg. leaf apex, leaf tip etc).

-Rather than make all these specific children for each type of leaf, we felt it was better to ask annotators to annotate to the specific term and the correct type of leaf (ie vascular or non vascular).

-We also have a similar situation with two terms that are children of vascular leaf: rosette leaf and cauline leaf.

Feedback from TAIR:

The following is a summary from the email correspondence, from Tanya Berardini:

• TAIR strongly supports creating specific vascular and non-vascular children for leaf apex and similar terms that are part_of leaf, like those describing the leaf apex in rosette leaves and cauline leaves.

• TAIR proposes we create more specific terms for the is_a children of vascular leaf, like cauline leaf. For example, 'cauline leaf margin' and 'rosette leaf margin'.

• PO looks like it has not addressed the fact that rosette leaves have leaf apices, etc.

• TAIR suggests creating the terms which already have annotations attached to them, like 'vascular leaf margin' (current Arabidopsis, rice, maize annotations to 'leaf margin') and adding other terms upon request by annotators or users.

this fits the pattern we have been using

• TAIR strongly supports Taxon id checks, as a quality control to make sure that species/taxa-specific terms are not being erroneously applied

Their Reasons:

- Much easier for annotators to choose the specific term they need as opposed to having to remember to co-annotate or having a script go in after and clean up

- Benefits for the researcher who is looking for very specific information

- The added granularity of these terms will be a benefit when people want to describe structures such as the leaf apex in rosette leaves and cauline leaves.

- They are not worried about term inflation

- A researcher browsing through the ontology would not know to look at annotations to see that there are combinations of annotations that give the 'same' result ('leaf apex' + 'rosette leaf')

-The current functionality of AmiGO does not allow a search for gene products annotated to Term A AND Term B.

- The combinatorial solution work will not work if a gene is expressed only in the 'leaf margin of cauline leaves' and in the 'leaf apex of rosette leaves'. How do we know which 'part' goes with which 'leaf'?

- Unless the co-annotations are captured in a single line in the gaf file (possible with column 16), this could lead to misinformation.

Comment from BS: This is a common problem for many ontologies and there is no single or standard way to deal with it. It would not do any harm to add those extra terms, as long as you are careful. It is messy but would not hurt anything. Annotators like pre-composed terms. On the other hand post-compositional terms (compound terms created 'on-the-fly') are better, but then if an annotation is attached to it it becomes a pre-composed term. Treat each case on its own merit.

Discussion:

See notes on Summary_of_Changes_to_PO_May_2011#Changes_to_children_of_leaf_.28PO:0025034.29

Problem with creating these specific children, is where do you stop? Do we create leaf apex of the sixth stem leaf, for example?

If we are not going to create specific children, we shouldn't have any, so that terms for vascular leaf apical cell and non-vascular leaf apical cell should be merged into leaf apical cell. Don't think there are any other examples of specific children.

PJ: There is an issue of training, and it can be kind of difficult for the users. Annotators will have to be taught to annotate to the part of the leaf and the type of leaf. The same applies of other types of plant structures as well. We need to provide a script to add the extra lines to the ontology.

Our responsibility is to the extra rows for annotations if needed. We need to mention this when writing the paper. A similar situation is the mitochondria in cells. Should GO make a separate term for all mitochondria in each type of cell?

We should add disjoint_from relations between vascular leaf and non-vascular leaf. In OWL you have to do that, because if you don't assert it, OWL assumes they are not disjoint.

We have inflated in one case. We have both non-vascular leaf meristematic apical cell and vascular leaf meristematic apical cell. Perhaps we should merge those with leaf apical cell.

We could use a script to move annotation from the parts of leaf to the appropriate type of leaf, but this effectively creates another line in the annotation file, and does not solve the problem of how to associate two different annotations (like the annotation to leaf margin with the annotation to rosette leaf). To do this, we need to have the information in the same row of the annotation file.

Does the GAF format allow us to put the PO id for the type of leaf in column 16? If we put the PO id in column 16, will that create an annotation to that term? Probably we will still have to make a separate line for that annotation. See: GO annotation file GAF 2.0 format guide.

BS: We need to work with TAIR to avoid alienating them, as they are important contributors to the annotation database and may just go create their own mini-ontology to satisfy their needs if we cannot provide it.

rosette leaf and cauline leaf

On a related note: PJ suggested that we make rosette leaf and cauline leaf is_a children of leaf, rather than is_a children of vascular leaf. Then we could make children vascular rosette leaf and vascular cauline leaf.

Do we need these parent terms if rosette leaf and cauline leaf only occur in vascular leaves? (RW: We should create a SF tracker for this.)

Also, we need to work on the definitions of rosette leaf and cauline leaf. Should link them to growth stages, because (at least in Arabidopsis and other Brassicaceae) they are the same leaves at different times.

Proposal: move all leaf parts to part_of leaf

-This was proposed so that users could find all of the parts in one place. This might also force them to make the second annotation to the type of leaf.

VL and NVL should only have is_a children, the part_of children should go to leaf (?)

Would this make it clearer?

Would this prevent curators from making an association to the wrong type of leaf?

Problem with this is that we intentionally omit information that we know to be true (e.g., we would leave out leaf vascular system part_of vascular leaf). That is not necessarily bad, but we need to have a good reason for it.

BS: proceed empirically: Need to make a list of all the part_of children of each VL and NVL

PJ suggested that we could use disjoint_from relation, for example: have leaf vascular system be a part_of leaf (instead of part_of vascular leaf) then make it disjoint_from non-vascular leaf.

eg. leaf vein part_of_leaf, disjoint between leaf vein and NVL. Does this work?

do we need to also assert leaf vein part_of vascular leaf?

BS: we should err of the side of saying things that are true, but, NOT saying something that is true can be ok if you have a good enough reason. Otherwise we should assert that leaf vein is part_of vascular leaf

PJ: examples are vascular tissues in the Vas and the hydroids and leptoids in NV plants

• should add a disjoint between NVL and VL.

Action Items:

• Need to make a list of all the part_of children of each VL and NVL

• Work with the existing list of terms that need the annotations- find the right solution

• Need to work on the definition of rosette and cauline leaves

• Rather than setting a strict policy about when to inflate or not, we should probably consider it on a case by case basis

• We need to have the script for transferring the annotations up and running, and that we test out whether or not we can use column 16 for associating leaf types before we meet with them

• We also need to consider processing of the annotation files that happens with each release

• Add a disjoint between NVL and VL

• We need a demo to show TAIR

• Set up a meeting with TAIR to explain to them why we don't want to add all of the specific terms, and to work them on the solution

List of annotations on terms that are part_of leaf

In vascular plants, these structures may be part_of a vascular leaf. In non-vascular plants, they may be part_of a non-vascular leaf.

In the last round of revisions, we decided that Any existing annotation for these terms should also be copied to vascular leaf. Future annotations should go to both the part and to the appropriate leaf type.

• We need to decide if we are going to create more specific terms for all these- see comments from TAIR above

Term name (id) number of annotations (from live AmiGO (version 14), not from most recent association files)

• leaf aerenchyma (PO:0006215) 1

• leaf apex (PO:0020137) 12890

• leaf base (PO:0020040) 5

• leaf epidermis (PO:0006016)365

includes:

buliform cell (PO:0004001) 1

leaf abaxial epidermis (PO:0006019) 4

leaf adaxial epidermis (PO:0006018) 4

leaf lamina epidermis (PO:0000047) 1

leaf trichome (PO:0006504) 63

• leaf intercalary meristem (PO:0006346) 1

• leaf lamina (PO:0020039) 12800

includes:

leaf lamina base (PO:0008019) 12614

leaf lamina vascular system (PO:0000048) 1

• leaf margin (PO:0020128) 100

• leaf mesophyll (PO:0005645) 762

includes:

palisade mesophyll cell (PO:0006206) 1

spongy mesophyll (PO:0005647) 1

spongy mesophyll cell (PO:0006205) 2

• leaf prickle (PO:0025175) 0

• leaf sheath (PO:0020104) 205

includes:

• leaf sheath pulvinus (PO:0008017) 2

• leaf stomatal complex (PO:0025183) 0

PO Webinar for review of the Physcomitrella terms

We will hold a wenbinar wiht the Physcomitrella group to demonstrate the new plant anatomy terms that have been added to accommodate mosses and give reviewers a brief tutorial on how to use PO. Goal is to encourage and facilitate them to send annotations to us.

-This webinar was postponed until June 2011. Do we want to plan this for June 21st?

Webinar took place June 21st, 2011 Plant Ontology Webinar- May 2011 release

Report from the Phenotype RCN Meeting: June 1-3rd, Boulder CO

PJ, LC and RW attended

Agenda:

Overall goals for the Plant Working Group meeting:

• Discuss how PO (Plant Ontology) can serve as the reference ontology for all plants and come up with a list of specific changes that will be needed.

• Explore how links can be made to taxonomic databases like RegNum to define the taxonomic scope of terms.

• Clarify the role of TO (Trait Ontology) - should it be used as a set of pre-composed EQ terms for all plant taxa and all areas of plant biology including systematics?

See discussion: POC_Conf._Call_5-24-11#Review_of_leaf_terms_for_Phenotype_RCN_meeting_next_week

Different communities were determining if PO was robust enough to support annotations and use by systematics and taxonomy or ecology communities. They are happy with PO and we should work with them to enrich the PO for their different needs. PO will be the reference ontology.

Suggestions from the meeting:

• Provide a web page that is the PO terms listed as a glossary (alphabetical). Must update whenever file updates. Must link back to PO page for each term.

Work with PS to create and include the terms from his glossary, will eventually be retired. Use definitions that are worded in a more user-friendly style than the standard genus-differentia definitions.

• Jquery widget for search field for autofill. (there is also something similar available from Bioportal)

• Add a place for commentary on the website

• Link persons name to the definitions that they work on

• Do more outreach: Maybe host workshops at Botany meetings on Sunday before sessions (NC)

Wrap-up:

Achievements: - We agreed (more or less) that PO is the central reference ontology for plants, the TO needs work

- Developed new collaborations

- Improved communication between the different groups- ecology, systematics, taxonomy HPT phenotyping,

Goals: - Character atlas or matrix focused on leaf, between FNA and sources from books etc.

- Develop Use Case- how will this be developed? focus on leaves,

- PJ: HALS demo leaf development genes, examples of mutations -eg. peltate leaves

- Improve outreach- get workshops out to more groups eg. Botany meetings

- Link images associated with the terms, layers with labels

PJ described his plan to set up a matrix of leaf characters, with entities on the y axis, and characters or states on the x axis. Ontologies is not being used directly to make phylogenies, only to describe characters, which may or may not be used to construct phylogenies.

There was general agreement that developing a use case was a good idea.

Other possible goals for next release, arising from the RCN meeting: see above

• Provide a web page that is the PO terms listed as a glossary (alphabetical). Must update whenever file updates. Must link back to PO page for each term.

• Character atlas or matrix focused on leaf, between Flora of North America and sources from books etc.

• Develop a use case for ecologists and/or evolutionary biologists.

Goals for the Next Release:

Priorities for this release (from PJ): publish a paper, address the concerns with parts of leaf.

From BS: OBO Foundry acceptance should also be a priority. We cannot complete this before the IBCO, but the request should go in immediately.

Need to come up with a plan on how to respond to TAIR.

Discussion of other items was postponed until future meetings.

• Target date: mid-September????

Tech Issues:

- Upgrade to new version AmiGO browser

- Need to get the translations into the OBO file

Priorities for the Next Round of Revisions (from POC_Conf._Call_1-25-11)

High priority

* Publications:

-Plant Physiology: RW and LC are working on an outline for a manuscript to submit to Plant Physiology. This will be a more detailed description of the changes made to the PO in the past year, focusing on restructuring of PSO . Will focus on how PO is now applicable to a wider range of plant species.

-Others? Maybe a short topics paper for American Journal of Botany?

The editor of AJBOT asked Dennis to put together a short paper for them- can focus on PO. This would be consistent with the

* Compliance with OBO Foundry guidelines

- All but 3 terms now have is_a parents. The last three will be dealt with when we restructure the PGDSO

- Restructuring of PGDSO should make PO compliant with BFO (see item below).

-need to double check that all terms have text definitions

* User requests, Plant Anotomical Ontology:

• root terms submitted by Rich Zobel (Nov 2009)

• TraitNet requests: corm, podarium, pneumatophore, diaspore, cone, sorus, tendril

• Legume terms submitted by Austin Mast. Several terms have already been dealt with (Taproot, Stem Hair, Prickles, Anther pore and anther slit). Remaining: fascicle, bristle (used in key as "Stipules spinose or bristles"; might be thought of as a quality, rather than a structure), phyllode, banner, wing and keel

User requests: Plant Growth and Developmental Stage Ontology:

• terms for seed trichome development stages. This item has been open on SF since 7/2010. Fiona McCarthy- AgBase

• tuber growth and development stages. This item has been open on SF since 6/2009.

Reproductive structures across plants: RW and DWS (and MAG?) could work together to add the terms using the NYBG numberspace.

- terms used by model systems (Physcomitrella, Selaginella, Loblolly pine, poplar etc.), and terms are needed for the EST library from the Genomics of Seed Plants project.

- Many of these terms were added during the last round of revision (e.g., terms related to sporangium and gametangium).

* Plant Growth and Development Stage Ontology restructuring

A. overall structure:

In the fall LC, RW and BS worked on restructuring PGDSO to meet BFO standards. Have a proposal to show group.

B. Framework for non-angiosperm terms

As we work on a new overall structure to the PGDSO, need to be sure it provides a framework for non-angiosperm terms

New terms for non-angiosperm structures

- Ramona has a long list of new terms to add, but we need to choose an area for focus. See: File:NewTermsToAdd RW06-07-2011.pdf

- Many of these terms were added by request from the Physco group, but could add more. May want to focus on terms for ferns or gymnosperms.

Medium Priority

• Adding links to images through PlantSystematics.org

-Ramona visited with Ale in October 20th, 2010 to work on this and we discussed it at the November, 2010 POC meeting at NYBG.

-Images should be linked to the PO ids - have PO ids embedded in the Plantsystematics.org database.

• Removing taxon names from terms

-Most (all?) of the terms with Zea or Poaceae in their name could be merged with other PO terms (e.g., Zea gynoecium merge with gynoecium)

-RW spoke to Mary Schaeffer (from MaizeGDB) at PAG, and she was happy to see the taxon specific terms go

Low Priority

• Better organization of descendants of portion of plant tissue:

Needs to be organized better, add some new categories for tissue types.

Some work was done on this during last round of revisions. May be okay as is.

• Adding annotations

LC set up a call with RW and PJ to discuss RW and LC adding more annotations. 1-2 days per week? EST libraries, RNA seq datasets.

• Convert existing definitions to genus-differentia form

Ongoing.

Other

• Add taxonomic relations?

• Add replaced_by relations for older terms that were made obsolete (e.g., fleshy fruit replaced_by fruit).

Upcoming meetings 2011:

2011 Semantic Web Workshop June 6th and 7th, Santa Fe, NM.

Hosted by Damian Gessler and the iPlant Collaborative, this two-day workshop will focus on biological applications for semantic web services.

-JE and JP are attending

-JE has already worked with Damian to implement a SSWAP web service for PO terms, so further collaboration with him and iPlant will benefit the POC going forward.

For more Workshop details: Semantic web.

* Botany 2011 Meeting [Botany 2011] St. Louis, MO at the Chase Park Plaza, July 9-13.

Societies participating: Society for Economic Botany, the American Fern Society (AFS), the American Society of Plant Taxonomists (ASPT), and the Botanical Society of America (BSA).

Anybody going??

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

ICBO

LC is co-organizing the workshop "From Fins to Limbs to Leaves: Facilitating anatomy ontology interoperability" along with Melissa Haendel, Chris Mungall, Alan Ruttenberg, David Osumi-Sutherland.

Full-Day Workshops Schedule:

July 26 9am-6pm The Ontological Representation of Adverse Events: Working with Multiple Biomedical Ontologies

July 27 8.30am-4pm Facilitating Anatomy Ontology Interoperability

July 26 6.30pm-9pm Evening Workshop: Common Logic

July 27 4pm-8pm Evening Workshop: Doctoral and Post-Doctoral Consortium

- LC will attend and represent the PO. Invite other plant people?

* International Botanical Congress (IBC2011)

July 23rd-30th 2011, Melbourne, Australia

Registration is open Important dates

Symposium 'Bio-Ontologies for the Plant Sciences' under the Genetics, Genomics and Bioinformatics theme, wiil be held on Thursday, 27 July, from 13:30 to 15:30.

Dennis, Alejandra, Pankaj and Ramona are planning to attend.

See IBC 2011 Bio-Ontologies Symposium wiki page for more details

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

Plant Biology 2011

For inclusion on the program memory stick and in the program book, abstracts must be submitted by May 27.

Gramene will be putting together a workshop again, focusing on pathways. LC and PJ will present a PO poster.

TAIR (Kate Dreher) is organizing an Outreach Booth and we are invited to take part.