POC Conf. Call 5-17-11

POC meeting, Webex Conference Call; Date: Tuesday May 17th, 2011 10am (PDT)

In attendance:

POC members:

Absent:

Collaborators:

Acceptance of the minutes from the POC_Conf._Call_5-10-11?

Tech Issues:

from POC_Conf._Call_5-10-11, Also added to the POC Technical Issues Page

These are ranked in terms of priority for the release:

* Asserted relationships need to be checked

At the POC_Conf._Call_3-29-11 we agreed to start using intersection_of relations:

Problem: The inferred relations are not displayed in AmiGO

Solution proposed: (from POC_Conf._Call_3-29-11)

-For each new live release, we will create a version of the plant_ontology file that asserts the relations implied by the reasoner.

For the time being, we should do the assertions manually (either in OboEdit, or with a script, which we manually check), to be sure that they are relations we want.

This would also normally be done regularly while editing, by using the reasoner.

RW suggests that it would be easier and less-error prone if the relations were asserted with a script. GO does this, so CM should have a script that we can use. Then we can check the file to make sure nothing odd was asserted.

Do we want to release two versions -- one with implied links asserted and one without -- or should we keep the file without only for curators?

* Problem on the dev browser- can't filter by the new 'plant anatomy' name

Looked at filtering problem on dev browser. It does not seem to be related to differences in capitalization or word form, as these also exist on the live browser, with no problem.

Updates:

JE is looking into it.

* Proper Flow of Annotations through the Relations

• has_parts -need to go the opposite direction, (see the tech issues page for more info)

• develops_from and adjacent_to -neither of these should be transitive

* New images needed for browser

We need images for participates_in and adjacent_to.

RW sent the image for participates_in to JE.

Still need image for adjacent_to, RW requested help from PJ about this

* Inserting the translations as synonyms into the obo file:

Spanish:

-We have a list of translations of the PO terms into Spanish, but without the accented characters. MAG is going to replace those with the accented characters and add the new terms. Then RW will put the accented characters in as ASCII text.

Once that is done, then we can insert them into the OBO file using the script.

Problem: The synonym type does not appear in AmiGO, so we should append (Sp.) or (Spanish) to the synonym

RW will check with CM and ask if he can suggest the best way to display synonym types in AmiGO

Japanese:

-We have a list of translations of the PO terms into Japanese from Yukiko Yamakazi, but the Japanese characters will not display correctly on the AmiGO browser

-JE is still waiting to hear from Yukiko about altering AmiGO loading script to display Japanese characters.

We decided at the 5-10 meeting that putting in the Japanese synonyms will take more work and testing. Best to leave that for the next release.

But after the meeting PJ suggested that we go ahead and put in the Japanese translations and then have JE run a script to remove them in our version for the browser. That way YY can use them right away for their users.

Issue: -Would we host two separate version of the live file? These translations will most likely be a problem for other groups who are using our ontology, such as the SGN. Problematic for maintenance.

How does GO deal with this?

Alternatively, We might be better to send YY a special version of the file containing them and this can be done once the release is out.

Others:

-PJ mentioned someone at FAO for translation mechanism for about seven languages. Will contact him after this release.

-Also at AToL put in link:

* Problems displaying AmiGO Browser in Internet Explorer

PJ sent a note out by email that some users are having problems displaying AmiGO Browser in Internet Explorer: IE views are not similar to the ones in Firefox.

-See the comment at:link "On my computer, this displays correctly in FireFox 3.6.13, but not Internet Explorer 8.0.6' on this page."

- RW confirmed it: "The Amigo browser tree view does not display correctly in Internet Explorer on my PC either. All of the terms at one level of the tree are displayed on one line, instead of in a hierarchy. I'm sure I've griped about this before, but don't know if I have a written record. It works fine on Safari and Firefox on my Mac."

Status Report for Upcoming Release:

* Highlights and Major Accomplishments in this Release:

-Addition of 41 new terms requested by the Physcomitrella group, 44 associated new terms that can be used for pteridophytes, and the addition of synonyms or minor modifications to 21 existing terms to make them applicable to a broader range of plants.

-Renamed Plant Structure Ontology to Plant Anatomy Ontology- note this is just the branch of the Plant Ontology, all terms still have the PO:xxxxxxx identifier

See note above about filtering issue on 'plant anatomy'

-Revised the in vitro plant structures branch and the embryonic plant structures branch

-many other minor changes and fixes- see below for more details

-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...

Timeline for release:

* Week of May 9th to 13th:

-Completed required edits and changes?

RW: need to approve idioblast. Need to assert implied relations. Need two more definition dbxrefs. Other edits done.

-Reassign annotations from terms that been obsoleted (about 10), along with database groups TAIR, Gramene, SGN, MaizeGDB, etc

* 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, others??

- 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.

-prepare release notices, update on PO page, facebook

* Week of May 23-27th:

-fix any final issues that have come up

-Release on live browser

-Send out announcements

Items arising from previous meetings:

Adjective form vs Noun form in term names

Do we need to use the adjective form for some, e.g., antheridial wall versus antheridium wall?

The advantage of using adjectives is that they often seem more grammatically correct.

The advantage of using nouns is that if the differntia is another PO class, then the noun will match that class name (for example, antheridium wall automatically matches to the PO class antheridium).

At the POC meeting on 5-10-11, we agree to use the noun form for all primary term names, and add the adjective form as an exact synonym.

The obo file has been changed to reflect this. Terms that had antheridial, archegonial, floral, extrafloral, embryonic, gametophytic, and sporophytic have been changed to antheridium, archegonium, flower, extraflower, embryo, gametophyte and sporophyte, and the adjective forms made exact synonyms.

Maybe this does not work for every case? For example, should be we change apical meristem to apex meristem or meristematic apical cell to meristem apex cell?

What about terminal bud to terminus bud or axillary bud to axil bud? Basal endosperm transfer cell to base endosperm transfer cell? Cultured plant cell to culture plant cell?

Others that are probably okay to change: cambial/procambial, epidermal

idioblast

We use the term idioblast in the comments for plant cell and plant organ. At an earlier meeting, we discussed adding a term for idioblast.

idioblast (PO:0000283) was in the PO before. Def.: A cell in a tissue that markedly differs in form, size, or contents from other cells in the same tissue. [ISBN:0471245208]

PO:0000283 is obsolete: "This term was made obsolete because its a kind of attribute for a cell type."

Should we reinstate this term?

Upcoming meetings 2011:

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

Goals of the Plant Working Group at this meeting (from the Phenotype RCN webpage):

"Plants – Go through relevant parts of Plant Ontology in order to develop proofs of concept; explore how to make links to homology. Examine existing annotations and determine kinds of info can be extracted. Analyze quantitative data and look for ways to annotate them."

PJ will attend

More details TBA

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

Early-bird registration ends May 13.

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

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

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

* 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.

Scott Schuette from the Department of Plant Biology at Southern Illinois University has been added as the sixth speaker in our symposium. He will speak on "Predicted Protein-Protein Interactions in the Moss Physcomitrella patens: A New Bioinformatic Resource".

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