POC Conf. Call 5-17-11

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

In attendance:

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

Absent: Chris Mungall (Lawrence Berkeley National Lab), Justin Preece (OSU),

Collaborators: none

Acceptance of the minutes from the POC_Conf._Call_5-10-11? No additions, deletions, or changes.

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:

* Asserting Implied Relationships

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: -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 will 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.

-5-13-11: RW created a version of the plant_ontology.obo file with all of the implied is_a relations asserted (plant_ontology_assert1.obo).

-JE tested the loading of this file onto the dev browser- results: worked fine, no errors

Details from email: 5-13-11 RW: There were 46 implied is_a links. Two are a bit odd:

• Poaceae ovary epidermis is_a carpel epidermis even though ovary epidermis is not
• Poaceae integument epidermis is_a carpel epidermis, even though integument epidermis is not a carpel epidermis.

"This is b/c Poaceae ovary is part of Poaceae carpel, but ovary is not part of carpel (it is part of gynoecium). Technically, the Poaceae integument epidermis and the Poaceae ovary epidermis are portions of carpel epidermis (that is, a portion of epidermis that is part of a carpel), so the relation is correct. The only problem is the inconsistency.

The inconsistency will go away when we get rid of the Poaceae terms, so I am okay with just leaving it for now."

See Media:poaceae_ovary_epidermis1.jpg

• Once all corrections have been made to the plant_ontology.obo file, the relations can be asserted for a final version.

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?. What is the best way to maintain both files

We will continue as we have been with having the live version (with the asserted relations) on the browser and we will continue to work on the dev version with the implied relations. At the time of the each release, we will finalize the edits, assert the relations and put it up on the live site. We could also supply the final/stable file in the same folder with only the implied relations.

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

The filtering problem on the dev browser 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:

-5-13 JE and JP were able to find the problem and we thought it was fixed.

-RW, 5-16: If I do a search first, and then set the filter, it seems to work fine, but if there is more than one page of results, when I go to page two, it reverts to all the results. Also, if I set the filter first, and then to a search, it reverts to "all" and gives me all the results (maybe this is the normal behavior.

-JE will have to redo the fix once the live browser is updated to the new version, but it should be easier, now that it is fixed on the dev browser.

-Still don't know if loading the annotations will complicate this, but will test on beta.

JE is continuing to work on the filtering issue, it may be a problem with the beta/live browser when we switch over to them with the new namespace.

• Also, graphical viewer is not working on dev browser:

error " Can't use an undefined value as a symbol reference at (eval 36) line 50. "

This has apparently not worked for a while, JE is not sure why. Lower priority

* 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,

Will follow up with PJ about

* Inserting the translations as synonyms into the obo file:

Spanish:

-We have a list of translations of the PO terms into Spanish, with the accented characters replaced ASCII text.

Needs to be inserted into the OBO file using a script, then tested on the dev or beta browser.

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

RW asked CM if he can suggest the best way to display synonym types in AmiGO (no response)

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/question: -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.

Action items:

• Create a branch on SVN for the translation files. done

Then people who do the translations can access and update them.

done- we should set it up that they have access to commit the new versions

• Add a dbxref to foreign synonyms to give credit to the translators, for example: POC:mag for the Spanish synonyms. see below

RW sent JE a line of syntax which should be appended with [POC:mag] for each of the spanish synonyms.

-JE created a folder on trunk for the translation files and converted the file to a tab-delimited file. Posted the file from MAG/RW which has the terms in the ascii characters, should put the other one in as well. Need to add the Japanese translation file to the folder. MAG can work from the file with the ASCI characters. Not a problem. This file corresponds to the current dev version (except the 6 terms from today)

JE is working on the script to insert the translated term names as synonyms- High priority for the release

• Note: It would be helpful to be able to generate a list of the new terms whenever we are ready for a new release. It should contain the ID, English name, foreign name and definition.

Discussion about this- JE can generate this table/tab-delimited file as part of the release pipeline. Currently the script just returns just a count of the terms. Could he also generate the ID, English name, foreign name and definition? These could be sent to the translators, with spaces for the above info.

Discussion about a proposal by BS to have an interim/beta release on a weekly (or monthly ?) basis similar to the model that Zfin uses. They post the new terms each week and have the collaborators look at them and respond, move annotations etc. Do they need to be updated. Could get extra points from the OBO Foundry as well.

Could do it weekly and put it out for feedback from the collaborators, faster access to the terms

* 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

These are major programming problems that cannot be fixed for this release. Can include a disclaimer.

New terms requested by Moss Ontology

leaflet

As a related synonym of non-vascular leaf (in the sense that it is a small leaf)

this refers to a 'little leaf', not part of a compound leaf. Will add a related synonym, " non-vascular leaflet".

leaflet midrib

As a related synonym of costa (not as a new term for a midrib in a non-vascular leaflet).

Will add non-vascular leaflet midrib as a related synonym to costa.

amphithecium

We have the term exothecium (PO:0030073): A portion of epidermis that is the outermost layer of a sporangium.

Sporangium epidermis, epithecium, and amphithecium are currently synonyms of exothecium. However, "these two (amphithecium and exothecium) are not synonymes - exothecium may develop from the amphithecium but not necessarily" (from Stefan)

We also have endothecium (PO:0030049): A portion of ground tissue that is the sub-epidermal layer of a sporangium wall. Comment: The outermost layer of a sporangium wall, internal to the exothecium.

The problem is that the terms endothecium and amphithecium are used differently by the bryophyte community than for vascular plants.

Campbell, Crum, Parihar, Smith, and Schofeld all use endothecium and amphithecium to describe the inner and outer layers of the sporangium early in its development.

For example:

Campbell, p. 13: "the outer tissue (amphithecium) of the embryo"

Campbell, p. 179: "The terms endothecium and amphithecium have been given respectively to these two primary parts of the young Moss sporangium." (the inner and outer parts)

Both Parihar and Smith: "the amphithecium gives rise to the sporangium jacket layer" (which is equivalent to the sporangium wall).

Definitions from Crum (Definitions from Schofeld are similar):

amphithecium: tissue of the embryo external to the endothecium, giving rise to the capsule wall and the peristome of true mosses and, in hornworts and peat mosses, spores.

endothecium: in bryophyte capsule, the embryonic tissue internal to the amphitecium; in liverworts the endothecium produces sporogenous tissue; in Sphagnum, Andreaea, and hornworts, it produces columella and sporogenous tissue.

exothecial cells/exothecium: the outer layer of cells of a capsule wall.

Proposed solution

Create new terms for amphithecium and endothecium in bryophytes, with different names to distinguish the different types of tissue.

Proposed definitions (new or modified):

amphithecium (PO:0030053): A portion of plant tissue that is the outer layer or layers of a sporangium early in sporangium development.

Comment: Term used for bryophytes. May have one or more layers. An amphithecium may give rise to an exothecium and other layer of a sporangium wall (jacket layer or layers). In true mosses, the amphithecium gives rise to the sporangium wall and the peristome. In hornworts and peat mosses, it gives rise to the sporangium wall and sporogenous tissue.

accepted

early sporangium endothecium (PO:0030085): A portion of ground tissue that is the tissue internal to an amphithecium early in sporangium development.

Comment: Term used for bryophytes. In liverworts an early sporangium endothecium produces sporogenous tissue. In Sphagnum, Andreaea, and hornworts, it produces columella and sporogenous tissue.

disjoint_from sporangium wall endodethecium

synonym: endothecium of early sporangium

A better name would be protosporangium endothecium. The term protosporangium is preferable to the term used in most older literature, which is "embryonic sporangium". The PO uses embryonic only to refer to structures that are part of the embryo, not, as others sometimes do, to refer to structures such as leaves, flowers or sporangia, early in their development. Users searching for endothecium will be offered the two choices, and have to decide which is correct for their species.

sporangium wall endothecium (PO:0030049): A portion of ground tissue that is the sub-epidermal layer of a sporangium wall.

Comment: Term used for vascular plants to describe the outermost layer of a sporangium wall that is internal to the exothecium.

adjacent_to exothecium, disjoint_from early sporangium endothecium

synonym: endothecium of sporangium wall

accepted

exothecium (PO:0030073): A portion of epidermis that is the outermost layer of a sporangium.

Add comment: Develops from the outermost layer of an amphithecium in bryophytes.

accepted

sporangium wall (PO:0025306): Add sporangium jacket layers and sporangium jacket layer as exact synonyms.

accepted

New apical cells

Proposed definitions:

caulonema meristematic apical cell (PO:0030081): A protonema meristematic apical cell that is part of a caulonema.

chloronema meristematic apical cell (PO:0030082): A protonema meristematic apical cell that is part of a chloronema.

rhizoid meristematic apical cell (PO:0030080): A gametophytic meristematic apical cell that is part of a rhizoid.

accepted

gametophore bud initial (PO:0030083)

Proposed definition: A protonemal side branch initial that gives rise to a gametophore bud.

Sibling of protonemal side branch rhizoid initial (PO:0030077)

Add gametophore bud develops_from gametophore bud initial.

This was accepted at the meeting, but afterwards, Stefan said it was not appropriate as child of side branch initial, should be sibling instead. See full comment on SF tracker.

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 In progress...

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 (see below)- in progress...

-Reassigning annotations from terms that been obsoleted. in progress...

See the page: along with database groups TAIR, Gramene, SGN, MaizeGDB, etc

-JE ran the script to give LC a list of the annotations attached to the obsoleted terms- 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, 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,embryonic, gametophytic, and sporophytic have been changed to antheridium, archegonium, flower, 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

We decided the make it a policy to use the noun name when the term refers to another term in the ontology. In the other cases such as for descriptors "extrafloral", we will use the form of the word that is in common use and makes the most sense.

Other items:

OBO Foundry Acceptance:

See summary page: [OBO Foundry]

Need to display a list of webpages that use the PO and encourage other groups to link to the PO and where the PO is integrated into their search engines.

Need an impressive web page, volunteer to link to them

-need collaborator pages for SSWAP and NASC- others??

-1000 Transcriptome project- DWS will encourage them to have a link to PO, adopt the PO rather than free text for annotations

BS: Need to demonstrate utility, will help with getting refunded

Update from MAG about photos

-MAG: "We are finalizing the info for the photos and pictures and should have it up on Plantsystematics.org in a couple of weeks. Will have about 6000 images- will do a selection of the ones that are the best for the PO- examples for the terms we have. They will have connections between the pics and the terms." RW: "Need a practical way to display them on AmiGO"

PJ: "Need a mapping file of the PO ids terms and the corresponding image ID in Plantsystematics.org, and a list of the keywords/ to the existing PO IDs. Could KS generate the list of keywords? Ask the curators at Plantsystematics.org to try to start using the PO terms/ids rather than their free test keywords. MAG will talk to KS@ it.

MAG and RW will meet next Monday (depending upon the webinar schedule) to start working on it.

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

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.

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