POC Conf. Call 5-24-11

POC meeting, Webex Conference Call; Date: Tuesday May 24th, 2011 10am (PDT)

In attendance:

POC members: Laurel Cooper (OSU), Ramona Walls (NYBG), Justin Elsner (OSU), Pankaj Jaiswal (OSU), Dennis Stevenson (NYBG)

Absent: Chris Mungall (Lawrence Berkeley National Lab), Barry Smith (University at Buffalo, NY), Marie Alejandra Gandolfo (Cornell University)

Collaborators: none

Acceptance of the minutes from the POC_Conf._Call_5-17-11? No additions, deletions, or changes.

Review of Plant Ontology for upcoming release

Curators: Please review the release file on the beta browser to see if you can find any errors.

If you have problems with that site, you can view the dev version

Please take a look at: Summary_of_Changes_to_PO_May_2011

Let us know if you think any important changes are missing or if you disagree with any of the explanations on that page.

Details for the Upcoming Release:

• See the List of changes on our wiki which is available from the May_2011_Release_Page. In progress...

• List of terms that have been obsoleted or merged: New_terms_and_obsolete_terms_for_May2011_release. In progress...

• Reviews of the new version for release and the associated webinar: Plant_Ontology_Webinar-_May_2011_release postponed till June 21st?

new relations in release

- a question and reminder from PJ, Are other ontologies using these? New relations

- update on PO_Developers_Guide and we need to update our links from the PO page to here.

We need to add a page for all the PO relations on the wiki.

Should include links to RO if that is possible, plus logical definitions and examples from the PO.

Include RO id.

Try to get BS to approve the definitions on this page. Need to confirm that adjacent_to is in the RO

Be sure web page is updated too.

relation icons will be stored on the SVN in the icons folder

Annotations on parts of leaf

see: New_terms_and_obsolete_terms_for_May2011_release#List_of_terms_that_are_part_of_leaf

How will we communicate this?

We don't really know how annotators search for terms to attach annotations too, and whether or not they would find vascular or non-vascular leaf.

Eventually, we can try to automate the gathering of annotations to vascular or non-vascular leaf. In the mean time, we can ask users to put annotations on both terms (the part of and the correct leaf.

We should add a comment to each of the terms on the list saying:

"If you are annotating to this term, please add an additional annotation to vascular leaf (PO:0009025) or non-vascular leaf (PO:0025075), depending on the species. All annotations for angiosperms, gymnosperms, and pteridophytes should go to vascular leaf and all annotations for bryophytes should go to non-vascular leaf."

RW (after meeting): actually, there is a much longer list of terms that are part_of leaf, because the list on New_terms_and_obsolete_terms_for_May2011_release#List_of_terms_that_are_part_of_leaf was only for terms with annotations. The comment will need to go to all of the part_of descendents, and all of the is_a descendents, except vascular and non-vascular leaf and their descendents.

We could also consider adding cross-product terms (pre- or post-compositionally).

We will not try to copy these annotations before this release -- leave at it is for now and they will be caught by TAIR or other for the next release.

translation synonyms

-SVN folder has been created and the translation files are in it.

-we have a file of the Spanish synonyms, including ASCII characters for almost all the terms in the release, but the script to add them to the OBO file is not ready.

-File of the Japanese synonyms is based on the live version (Jan 2011 release, Version #14)

These can go in the next release

Timeline for release:

* Week of May 9th to 13th:

*Completed required edits and changes?

-All edits as per minutes are done :-)

-All known errors are fixed (sure others will show up)

-LC, RW, JE and PJ met on 5-12 to make a decision about the translations and the nouns vs adjectives in names (see below)- done

-Need to assert implied relations- done, will do again on final version for release

-Reassigning annotations from terms that been obsoleted New_terms_and_obsolete_terms_for_May2011_release along with database groups TAIR, Gramene, SGN and MaizeGDB.

in progress, see below...

* Week of May 16th to 20th:

-Load new file onto Beta browser to check for any issues with loading, annotations

- send link to reviewers- Physcomitrella group, po-internal, done

- Schedule a Plant Ontology Webinar- May 2011 release 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. postponed till June 21st

JE ran the script to give LC a list of the annotations attached to the obsoleted terms and LC reassigned them to the new terms and they were loaded on the beta browser

* Week of May 23-26th:

*fix any final issues that have come up:

-add comments to the part_of children of leaf to remind users to annotate to either vascular or non-vascular leaf

-typo in definition of leptoid?, others?

- problem with the annotations loading- only about half are being displayed (~22,000 out of ~46,000)

JE is working on sorting out why the annotations are not loaded, will reload the beta browser to test

PJ is preparing a few annotations to Physcomitrella genes for demonstration

* prepare release notices, Send out announcements to the mailing lists

PJ suggested we should have a count of the terms associated with the new relations and provide a few examples

* Release on live browser by the end of this week

-update live link used by many users

Update the release pages on browser

* update on PO page, Facebook

Review of leaf terms for Phenotype RCN meeting next week

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

PJ, LC and RW will attend, DWS will skype in as needed

From preliminary agenda:

Overall goals for this 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 taxanomic 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?

Tasks:

1. Examine the children of ‘leaf’ in PO (PO:0025034), looking at terms, definitions and relationships to determine what’s missing or in need of updating, generate a list of changes needed for this subsection of PO to serve as a reference anatomy ontology for all plants, look for terms with homology relationships and examine how these terms are related within PO.

See obo file with only descendents of leaf (both is_a and part_of).

Possible new terms to add: lobe, tooth, mucro, areole, sinus, domatia, pinna, pinnule, others?

There was some discussion of whether something like lobe or tooth is an entity in the PO, or a phenotype. For example, you could say "leaf margin lobed" as a phenotype. But then how to annotate expression to a lobe? You could put the the annotation on leaf margin, but the expression isn't really the whole margin, and may extend in past the margin into the lobe.

Tendril is another structure we will need, but it has already been requested on SF.

2. Within ‘leaf’ subsection of PO, find terms where database cross-references to taxonomic nodes within RegNum would be useful for delimiting which taxa the term applies to. Find appropriate IDs within RegNum that could be used as dbxrefs for these PO terms.

Can we get a look at RegNum before the meeting?

3. Examine a list of leaf-related characters (from RegNum or other sources), determine whether entity and attribute terms exist in PO and PATO that could be used to construct these characters, discuss whether the precomposed character terms should be housed in TO or elsewhere (review TO ‘leaf anatomy and morphology trait’ as needed), set up a character matrix and determine whether the value terms needed to populate the matrix exist in PATO.

See list of characters in Harris and Haris at google books.

Could supply list of characters from Manual of Leaf Architecture. This is mainly for dictos, but it is a starting point.

Does DWS have a matrix of leaf characters for monocots or gymonosperms?

Could also get non-vascular leaf characters from glossaries in Parihar, Schofeld, Crum, etc..

We reviewed list of leaf descriptors from Harris and Harris that LC had converted to a spread sheet. We could also use images from Lawrence's "Vascular Plant Anatomy," since they are older and past copyright. We also discussed the possibility of using something like Morphobank or Delta to construct character matrix based on PO terms. These allow you to insert images into cells. (Could even use Mesquite).

Need to set up a matrix with PO terms in first column, different characters across the other columns, then character states in each cell.

We will probably need to create an ontology of phenotypic descriptors for plants that is maintained by PO. It should be based on PATO. PATO could host it, but they may not be able to get the terms in fast enough.

4. Using the character matrix, discuss what ontology terms and other resources will be needed for annotation of quantitative traits (e.g. leaf length, width, area, dry weight, specific leaf area)

Other items

replaced_by relations for obsolete terms

-RW: All of the terms we have made obsolete in the past year have up-to-date replacement or consider relations (I added the relation for seedling).

- Added a few obvious replacement relations of the older obsolete terms:

• ground tissue (PO:0009016) replaced_by portion of ground tissue (PO:0025059)
• L1 (PO:0006303), L2 (PO:0006304), and L3 (PO:0006305) replaced by meristem L1 (PO:0009020), meristem L2 (PO:0009021), and meristem L3 (PO:0009022)

-There are a number of other terms that were made obsolete because they were phenotype terms (fleshy fruit, lacunar collenchyma, etc.). For these, we could add replaced by relations to the more general term, such as fleshy fruit replaced_by fruit.

Upcoming meetings 2011:

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

PJ, LC and RW will attend

From preliminary agenda:

Overall goals for this 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 taxanomic 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 above

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 will be 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?

*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