POC Conf. Call 6-28-11

POC meeting, Webex Conference Call; Date: Tuesday June 21st, 2011 10am (PDT)

In attendance:

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

Absent: Chris Mungall (Lawrence Berkeley National Lab), Marie Alejandra Gandolfo (Cornell University)

Collaborators: none

Acceptance of the minutes from the POC_Conf._Call_6-7-11? No additions, deletions, or changes.

Tech issues

Getting Spanish Synonyms into the Plant Ontology File

-JE has gotten the script to work to integrate the list of Spanish synonyms into the plant_ontology.obo file

-There seems to be some duplicates, for example:

synonym: "c&#233lula latic&#237fera" EXACT Spanish [POC:mag]

synonym: "c&#233lula procambial de la hoja" EXACT Spanish [POC:mag]

synonym: "caliptra de la ra&#237z lateral" EXACT Spanish [POC:mag]

synonym: "columela" EXACT Spanish [POC:mag]

synonym: "endotecio" EXACT Spanish [POC:mag]

synonym: "estambre" EXACT Spanish [POC:mag]

synonym: "exotecio" EXACT Spanish [POC:mag]

synonym: "floema interno" EXACT Spanish [POC:mag]

synonym: "gluma inferior del penacho (borla) de la espiguilla" EXACT Spanish [POC:mag]

synonym: "inflorescencia" EXACT Spanish [POC:mag]

synonym: "tricoma del s&#233palo" EXACT Spanish [POC:mag]

Some of these are duplicates, because they represent a live and an obsolete term. These are not a problem.

RW will review these synonyms with MAG to determine if any of them should be changed.

There are a couple of other issues I still need to work out, and haven't tested the Japanese translations, but it should be the same as the Spanish, so I am not too worried about it. (JE)

PJ: We should keep the Japanese terms in the main PO file, then strip them out when we go to load it onto AmiGO (rather than maintaining a separate file for Japanese users, as we discussed earlier). JE will try putting them in the file, and see if there are any problems.

New xref in database for SF tracker:

A stanza for our SF tracker has been added to GO.xrf_abbs (thanks to Becky Foulger):

abbreviation: OBO_SF_PO

database: Source Forge OBO Plant Ontology (PO) term request tracker

object: Term request

example_id: OBO_SF_PO:3184921

generic_url: http://sourceforge.net/tracker/?func=browse&group_id=76834&atid=835555

url_syntax: https://sourceforge.net/tracker/index.php?func=detail&aid=[example_id]&group_id=76834&atid=835555

url_example: https://sourceforge.net/tracker/index.php?func=detail&aid=3184921&group_id=76834&atid=835555

see GO page: http://www.geneontology.org/cgi-bin/xrefs.cgi#ref-s

RW also updated the file at http://plantontology.org/docs/dbxref/PO_DBXref.txt.

• Do we need to do anything else to get the new xrefs to link automatically? (it is not working in the browser at the moment)

We need to determine how AmiGO is reading the dbxref file. Is it reading them on the fly, or do they have to be imported into AmiGO. PJ will talk to GO folks about that.

The xrefs are already in the correct format in the obo file. Source Forge xrefs are in for most of the tracker items -- all of the newer ones, and all but about 50 of the older ones.

Problem with how annotations move through relations

This has been discussed in the past and has also been recently raised by TAIR.

Excerpts from Tanya's message:

"We're working on integrating the new relationships that PO is using into our local system and were wondering about handling annotation count propagation over some of these relationships.

For example, anther wall endothecium and anther wall middle layer are adjacent. When you look for annotations to anther wall endothecium, one also retrieves annotations to anther wall middle layer: http://plantontology.org/amigo/go.cgi?view=assoc&search_constraint=terms&query=PO:0020002 Somehow, this does not seem like the expected (or desired) result.

Would consider producing a file of the PO that does not contain the 'trickier to count' new relationships?"

• Do we want to create a file without has_part, develops_from, derives_from, and adjacent_to?

This is a major problem with AmiGO and ontology use. Having only is_a and part_of relations avialable in GO has limited development throughout the bio-ontology community.

Everyone agreed that the ideal solution would be to fix AmiGO so that it treats different relations differently. However, this is unlikely to happen in the next few months.

As a short-term solution, we discussed having two versions of the browser, one with all of the relations but no associations, and one with the associations but only is_a and part_of relations.

Does the cost of maintaining two browsers outweigh the advantage users will get from having two file.

Drawbacks of this solutions are that it would require maintaining another browser (we already have 3, with live, dev and beta). Also we would have to create a new, stripped-down file whenever a new release comes out, and maintain that too. It is not clear how we communicate to users that there are two browsers. May create some confusion about which browser to use and what the differences are.

If we create a second file, we should also remove the participates_in relation. Even though annotations can move through participates_in the same as for is_a or part_of, some people may be using software that doesn't know how to handle different types of relations, so we should take out everything but is_a and part_of.

Question about whether or not webProtege allows annnotations. RW thinks it can handle different relations differently, but can't deal with annotations. Will check on it.

Although it is not ideal, having two browsers may be the only solution at the moment. Main site would have annotations but limited relations, link to alternate site with all relations.

PJ will talk to someone at GO about when the new version of AmiGO will come out.

LC will get back to Tanya at TAIR to let her know we are working on it.

Items arising from previous meetings: Dealing with children of leaf

This is a continuation of the discussion on POC_Conf._Call_6-7-11 Please review the minutes from last meeting.

Action Items from 6-7-11 meeting:

• 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

Questions and suggestions from the last meeting:

-We could create specific child terms, but at what level should we stop?

-Users could post-compose terms, but then, those terms ultimately would need to go into the PO so that future work could reference the definitions, so it doesn't save much over precomposing the terms (but it does provide a guide for when to stop adding term: you stop at what the users need.

-There is an issue of training. 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 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.

-Rather than setting a strict policy about when to inflate or not, we should probably consider it on a case by case basis. We could start by adding pre-composed terms for those structures that already have annotations associated with them (see below), then asking TAIR and other users to use column 16 to post-compose any other term they might need. They can also use column 16 to associate a structure with a growth or developmental stage. See below for more details.

-We should set up a meeting with TAIR to explain to them why we don't want to add all of the specific children, and to work them on a solution. It is important that we have the script for transferring annotation up and running, and that we test out how we can use column 16 for associating leaf types before we meet with them.

-Need to consider how this will affect the processing of the annotation files that happens with each release.

Other related suggestions:

1. 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.

2. Move all leaf parts (be they part_of vascular leaf, part_of non-vascular leaf or part_of leaf) to be part_of leaf, 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. 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. This would prevent curators form 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.

3. 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.

4. We have both non-vascular leaf meristematic apical cell and vascular leaf meristematic apical cell. We should merge those with leaf apical cell if we are going to be strict about not making any specific part_of children of different leaf types.

Proposed solutions:

All: Create specific children for all of the parts of leaf, for each type of leaf. This is pretty much what we did for tuber, although it only has 2 is_a descendents and 8 part_of descendents. There are 15 is_a descendents of leaf (juvenile leaf, transition leaf, adult leaf, transition leaf, non-vascular leaf, vascular leaf, simple leaf, compound leaf, rosette leaf, cauline leaf, cigar leaf, embyro leaf, leaf spine, cotyledon, and flag leaf) and about 30 part_of descendents (not counting those that are only part of vascular or non-vascular leaf), so if we created all of the combinations of child terms it would add about 450 new terms.

Nothing: Do not create any specific part_of children for vascular leaf and other types of leaves. Keep or move all part_of children under leaf, and use column 16 to create cross-products to the correct type of leaf.

Somewhere in between: There are 21 part_of descendents of leaf that currently have annotations associated with them. All of these annotations come from vascular plants. We could create specific part_of vascular leaf children only for these 21 terms, and then add others as annotations for them arise.

We could adopt a policy of only adding specific part_of children for vascular leaf and non-vascular leaf. All other leaf types could be considered phenotypes (e.g. compound or simple leaf, spine leaf) or growth-stage specific forms (e.g., embryo leaf or cotyledon), and we could ask annotators to use column 16 to associate the part of the leaf to the type of leaf in these cases.

Unless we adopt the "All" strategy (which seems impractical), we will need a mechanism for associating the annotation that is on the part_of a leaf to the correct type of leaf. Such a mechanism would be very useful for other types of structures, as it would allow users to create new cross-product terms on the fly. It could also be used to more accurately annotate gene expression that occurs in a structures at a specific growth stage (right now, users simply put the annotation on both the structure and the growth stage, without any link between them). Annotation extensions (Column 16) allow us to do this.

See PO_Annotation_Extensions_(column_16) for a full explanation of how this would work.

PJ needs to work with JE to set up a test file before we make a final decision on how to go forward. We need to be able to automate the process of filling in column 16 based on the taxon ID, as well as the process of creating a new line in the annotation file from column 16. This will also provide a benefit for automated text mining. For example, papers will probably never use the term "vascular leaf tip", they will just say "leaf tip" and the species. Therefore, having a specific term for vascular leaf tip will not help the automated date mining, but having a script that autofills column 16 then creates the new annotation row will.

PJ will get back to us in a week.

Annotations on terms that are part_of leaf

The list below contains all of the terms that are part_of leaf and have annotations associated with them.

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. However, we have not actually transferred any of the annotation yet.

term name - (id) - number of annotations (from 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 (already shows up under vascular leaf)

• 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 sheath (PO:0020104) 205, includes:

• • leaf sheath pulvinus (PO:0008017) 2

If we were to adopt a policy of only creating specific terms when they are needed for annotation, we would have to create a vascular leaf child for each of these 20 terms.

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

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)

Number one priority should be getting the manuscript out. We need to write it based on what is working in the PO now. After that, revising the PGDSO should be the next priority. We can continue to address user requests for the PAO as time allows, as well as any user request for PGDSO that can fit into current structure.

LC and RW should send around a draft of the manuscript for review for next week.

PJ is preparing a document for OBO Foundry review. BS suggested that we use the PO presentation at the ICBO to lay out the condition of the PO, and the audience can serve as a kind of preliminary review panel. They should let us know if there are any issues we need to address for foundry acceptance. LC will work with BS on the slides for the presentation to make sure it covers the correct material.

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).

• Fix structure of conductive tissue, so e.g., phloem and leptome can group together. Need to fix definitions for many of these terms.

Other

Consortium Meeting for 2011

We should plan on meeting in NYC on Sep. 10-11 (Sat and Sun), right after the NSF meeting in Washington. We should reserve the garden apartment as far in advance as possible.

Stipule

It has been resolved on SF. Will be a cardinal organ part.

Someone asked PJ how the ontology will deal with a case when there are stipules but no leaf lamina development. DS: This is why we need to get images into the PO. We should prioritize (start making a list) of terms that are problematic.

Meeting with Morphobank

DWS will be gone next week, but can call in if the time is right (6 hour different). PJ will be available next week - afternoons are better. RW will contact Maureen, and set up a Doodle poll if necessary.

Paper for AJB'

RW has prepared an outline. DWS and RW will work on it a little more, then send it around to the group.

Upcoming meetings 2011:

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?

*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.

* 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