POC Conf. Call 5-10-11

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

In attendance:

POC members: Laurel Cooper (OSU), Ramona Walls (NYBG), Justin Preece (OSU), 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_5-06-11? No additions, deletions, or changes.

Tech Issues:

Also added to the POC Technical Issues Page

New images needed for browser

JE: I noticed in the server logs that errors are being created because we are missing images for participates_in and adjacent_to. Can someone create these for me to add to the browser?

We have an image for participates_in, need one for adjacent_to. Will send to JE.

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. JE is looking into it.

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."

Items arising from previous meetings:

Review of apical cell (PO:0030007) and its descendents

(This is a continuation of the discussion from POC_Conf._Call_4-28-11#apical_cell)

The problem:

Moss Ontology requested the term apical cell. Apical growth in byrophytes is via division of a single cell at the tip of the shoot apical meristem. They also requested shoot apical cell and phyllid apical cell.

The existing term in the PO, "apical cell (PO:0004000)" referred to "An embryonic plant cell that is the uppermost cell formed after the first division of the zygote". This term was obsoleted and replaced by embryonic apical cell (PO:0025284) for clarity.

A new term apical cell (PO:0030007) was created to be the general class for all apical cell types.

At the POC meeting on 4/28/11, we decided to name this term meristematic apical cell

meristematic apical cell (PO:0030007): New proposed def'n: A single meristematic cell at the tip of a plant structure where apical growth occurs.

is_a meristematic cell, sibling to initial cell

Proposed revised comment, for clarity: Meristematic apical cells occur only at the tip of a shoot axis apex, leaf apex, root apex, thallus apex or protonema in bryophytes and some pteridophytes. Apical growth in these structures results from division of a single meristematic cell located at the tip of an apical meristem or plant organ, (rather than from a population of meristematic cells located at the tip of an apical meristem). The meristematic apical cell may be tetrahedral shaped, with three (in shoots) or four (in roots) cutting faces, or wedge-shaped with two cutting faces (in non-vascular leaves or thalli) and may be established upon germination of a spore or upon the first cell division of an embryo or later.

Do we need a citation for this comment? (RW: Yes! Will add definition dbxrefs that cover this)

See: Apical cells

The issue:

At the POC_Conf._Call_4-28-11, there was an extensive discussion about whether to modify the definition of the existing 'apical cell' to refer to a general class encompassing the cell at the very tip of an angiosperm leaf or other any other structure.

The problem of adding a generic term for an "apical cell" is that it would cause confusion and it may not be biologically accurate.

The issue was raised that a scientist might isolate such a cell from the tip of a vascular leaf or root and be confused as to where the annotation should go.

Is there actually a single cell at the tip of a vascular leaf or root?

See the ppt below showing SAM and RAM tissues of angiosperms. There are references to stem cells in the central zone of the SAM, initial cells in the quiescent center of the RAM.

File:20-growth and development-02-A.pdf

See P.13: "The root apical meristem (RAM) is subterminal, but like the shoot apical meristem has a layered structure and a center of slowly dividing cells (the Quiescent Center (QC, shown in blue) surrounded by the initials for individual tissue (shown in green). (from Current Opinion in Genetics & Development 2003, 13:551–557)

The solution:

We can use the existing PO terms for cells at the leaf apex (PO:0020137) and leaf tip (PO:0025142),

For more precise work, we have the 'shoot apical meristem'(PO:0020148) and its part_of children (only some shown):

PO:0000224: central zone

PO:0009020: meristem L1

PO:0009021: meristem L2

PO:0009022: meristem L3

PO:0000225: peripheral zone

And the 'root apical meristem' (PO:0020147): and its part_of children (only some shown):

PO:0020149 : quiescent center (and its part_of child: root initial cell (PO:0000059))

PO:0006307 : root procambium

PO:0030008 : root apical cell ???? Should this be part_of RAM or part of root tip? Might be confusing if we make it part of RAM.

Although the term apical meristem is used to include the portion of tissue at the tip of a fern root that includes the root apical cell, using part_of RAM could lead to confusion. For now, we will make root apical cell part_of root tip. If it becomes widely accepted that there are apical meristems in plants that grow from apical cells, we can change it later.

RW: By the same reasoning, shoot axis apical cell should be part of shoot apex, not part of SAM.

We could also use always_in and never_in taxon relations to help clarify which taxa these are from. (once those relations are added)

There was a discussion of the nature of apical cells. Although they divide infrequently, it is still legitimate to call them meristematic cells. We should look at Steves and Sussex to see what they say about the apical meristem in plants that grow with apical cells. We accepted the above name and definition. Will try it and see if it works for our users.

New terms and definitions for apical cells

The definitions for the descendents of apical cell (listed below) were approved, pending approval of final definition of meristematic apical cell.

See above and POC_Conf._Call_4-26-11#apical_cell for more details.

We decided that we should append the names of the child terms with 'meristematic' in their names, except for embryonic apical cell, to ensure clarity.

gametophytic apical cell (PO:0030014) > gametophytic meristematic apical cell

sporophytic apical cell (PO:0030015) > sporophytic meristematic apcial cell

thallus apical cell (PO:0030025) > thallus meristematic apical cell

root apical cell (PO:0030008) > root meristematic apical cell

shoot apical cell (PO:0030009) > etc.

gametophore apical cell (PO:0030019)

leaf apical cell (PO:0030011)

non-vascular leaf apical cell (PO:0030013)

vascular leaf apical cell (PO:0030012)

shoot axis apical cell (PO:0030010)

gametophore axis apical cell (PO:0030023)

vascular shoot axis apical cell (PO:0030024)

seta apical cell (PO:0030016)

embryonic apical cell (PO:0025284, replaces PO:0004000)

Also need to add a term for protonema meristematic apical cell.

Should add term for protonema meristematic apical cell.

perianth calyptra (PO:0025299)

Proposed definition: A perianth that is composed of fused perianth parts and located on top of a gynoecium that contains an inferior ovary. (accepted at the POC meeting on 4-28-11)

Comment: May be composed of fused petals, sepals or tepals, but is generally formed from fused petals in Eucalyptus and other Myrtaceae. Sometimes erroneously referred to as part of a fruit. Not the same structure as a spore capsule calyptra.

is_a perianth, disjoint_from spore capsule calyptra

synonyms: floral calyptra (exact) and floral operculum (related)

Should we rename calytpra perianth? This would be more consistent with our usual naming practice of have the qualifiers first, and the is_a parent last.

We already have "angiosperm calyptra" as a narrow synonym of corolla (PO:0009059). In the synonym dbxref comment, it says: In angiosperms, the petals may be fused into a calyptra, which is different than a calytra in mosses. Note: this text does not show up on the Amigo browser, but it is in the obo file.

Suggest we remove this synonym, as it is redundant with the new term PO:0025299.

We will remove angiosperm calyptra as a synonym of perianth, and add it as a synonym of PO:0025299.

PO:0025299 will be renamed calyptra perianth.

Rhizoids

On 5/6/11, we agreed to add the term cotyledonary node rhizoid (PO:0025320).

In that case, we should also add the term cotyldonary node (PO:0025321)

Proposed definition: A stem node from which one or more cotyledons grow.

Agreed

Issues that still need to be dealt with:

gametophytic phase and sporophytic phase

sporophytic phase (PO:0028002)

Current definition: A plant life cycle phase that is the product of fertilization. [source: POC:rw]

Comment: During the sporophtyic phase, a plant may produce meiospores by meiosis.

Proposed definition: A plant life cycle phase (or a whole plant growth stage) that begins with fertilization or the division of a non-fertilized embryogenic cell.

Comment: During the sporophtyic phase, a plant may produce meiospores by meiosis. A whole plant in the sporophytic phase usually has twice the chromosome complement of a plant in the gametophytic phase, but may not in the case of apogamy or in vitro culture of haploid embryos.

New proposed definition: A whole plant growth stage that begins with fertilization or apogamy.

This covers the example of in vitro fusion of two haploid cells or two protoplasts. May need to update comment.

Will check that apospory and apogamy are in the GO Biological process ontology

gametophytic phase (PO:0028003)

Current definition: A plant life cycle phase that arises through meiosis. [source: POC:rw]

Comment: During the gametophytic phase, a plant may produce gametes by mitosis.

Proposed definition: A plant life cycle phase (or a whole plant growth stage) that begins with meiosis.

Comment: During the gametophytic phase, a plant may produce gametes by mitosis. In bryophytes and pteridophytes, a gametophytic phase may begin without meiosis by apospory. This usually occurs when damage to a plant in the sporophytic phase leads directly to the growth of a plant that is in the gametophytic phase but bears the chromosome complement that would normally be found in the sporophytic phase. A whole plant in the gametophytic phase usually has half the chromosome complement of a plant in the sporophytic phase, but not in the case of apospory.

New proposed definition: A whole plant growth stage that begins with meiosis or apospory.

Comment okay.

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:

-Complete required edits and changes (by the end of this week)

This should be possible.

Week of May 16th to 20th:

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

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

- send link to reviewers- Physcomitrella group, po-internal, others??

-prepare release notices, update on PO page

PJ suggested that we schedule a webex session to give reviewers a brief tutorial on how to use PO. This should make it easier for them to do a more useful review.

The idea would be to demonstrate the new plant anatomy terms that have been added to accommodate mosses

People to invite: Physco group (Stefan Rensing, Daniel Lang, others), Scott Schuette (Southern Illinois University -- will present talk on Physco bioinformatics at our symposium at the IBC), Brent Mischler, Bill Buck (NYBG), M.L. Christianson (University of Kansas), B. Crandall-Stotler (Southern Illinois University), B. Goffinet (University of Connecticut), others.

Week of May 23-27th:

-fix any final issues that have come up

-Release on live browser

-Send out announcements

Other Issues:

Foreign language synonyms

Should we add foreign synonyms for this release? JE can easily insert the Spanish synonyms into the obo file, once RW sends him a final list. Need to add accents where needed, and replace with ASCII characters.

Should we append (Sp.) or (Spanish) to the synonym, because right now the synonym type does not appear in AmiGO?

Would be better to append something like "SPANISH:spanish synonym"- but maybe not in capital letters

Should email CM and ask if he can suggest the best way to display synonym types in AmiGO.

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

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

We should try to get Spanish synonyms in this release, but not delay the release because of them. Putting in the Japanese synonyms will take more work and testing. Best to leave that for the next release"

After the meeting PJ suggested that we go ahead and put in the Japanese translations and then remove them in our version for the browser. That way YY can use them right away for their users. Alternatively, We might be better to send them a special version of the file containing them or we may have offer two versions

Monocot and gymnosperm AToL meetings

PJ suggested that we should try to attend any upcoming monocot or gymnosperm AToL meetings, to see how they work, and how the PO could fit in with what they are doing.

DS will find out if they are meeting at the BSA conference this summer and/or at the IBC in Melbourne.

Maybe we could use one of their character matrices as a test case for how to describe plant phenotypes for systematics using PO.

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? As is done in the literature?

Problem: We have not been consistent in using adjectives versus nouns and differentiae in names. PO is a mix of both. In some cases, we provide both (one as primary name, one as synonym).

As far as I can tell, OBO foundry naming conventions (http://www.obofoundry.org/wiki/index.php/Naming) don't offer any guidance in this matter.

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).

If the term name is widely used in the literature, that provides a clue, but often, our term names are something we invented, and not widely used.

Barry and Chris, can you make any suggestions about this?

There was some discussion of which way was better, but no one had a strong argument or opinion for doing it one way or the other. We agree to use the noun form for all primary term names, and add the adjective form as an exact synonym. Will try to get all these fixed for the upcoming release.

Stable URIs for OWL RDF version of PO terms

Question from Steve Baskauf of the Live Plant Image Group (via email earlier this week)

"We are working on creating and defining standardized views for live plant images. We have compiled a consensus list of views and have moved into the stage of creating technical definitions for them. We are considering using Plant Ontology terms to indicate the plant part that is the subject of the image.

However, we will probably create the technical definitions in RDF and therefore are interested in URIs to serve as objects of the descriptive properties used in the term definitions. Although the form of the PO identifiers suggests a URI (i.e. a namespace prefix of "PO:"), after surfing through the PO website for some time, I have not been able to find any actual namespace definition for "PO:" in the form of an HTTP URI. Is there one?

Also, the representation of the ontology is apparently OBO format. We are interested in an OWL representation of PO. I realize that there are tools which can do an OBO to OWL conversion, but it would be more straightforward (from our point of view) to be able to refer to a URI which resolves to OWL RDF.

Does that exist? In particular, we would like the end LPIG product to be usable by the LOD/Semantic Web, hence our interest in dereferencable HTTP URIs."

JE responded to them and send them the existing link: PO Owl files with a note of explanation:

"The files available from here correspond to the live version of the PO (ie, not the development version which undergoes frequent changes). However, we are working on updating the system we use to generate these files because much of the information was lost in the obo-owl conversion (such as definitions). I'm not sure if the information you are looking for is currently missing, but just letting you know that we are aware that some info is missing from those files."

PJ suggested that we should create a collaborator page Live_Plant_Image_Group for these folks and this question in case others ask it as well. Done

Review for OBO Foundry Acceptance

See summary page: [OBO Foundry]

BS brought up the topic of review for OBO Foundry acceptance at the POC_Conf._Call_4-19-11. He suggested that the PO can be submitted for OBO Foundry membership within the next few weeks.

List of Foundry Principles:[Accepted] with a brief summary of each:

• FP 001 open:

The ontology must be open and available to be used by all without any constraint other than (a) its origin must be acknowledged and (b) it is not to be altered and subsequently redistributed under the original name or with the same identifiers.

• FP 002 format:

The ontology is in, or can be expressed in, a common shared syntax. This may be either the OBO syntax, extensions of this syntax, or OWL.

• FP 003 URIs:

The ontology possesses a unique identifier space within the OBO Foundry. The identifier uniquely and persistently identifies a definition, which itself unambiguous identifies some type of biological entity. The identifier is for the definition: it is NOT the name and it is NOT an identifier for the name.

• FP 004 versioning:

The ontology provider has procedures for identifying distinct successive versions.

• FP 005 delineated content:

The ontology has a clearly specified and clearly delineated content. The ontology must be orthogonal to other ontologies already lodged within OBO.

• FP 006 textual definitions:

The ontologies include textual definitions for all terms.

• FP 007 relations:

The ontology uses relations which are unambiguously defined following the pattern of definitions laid down in the OBO Relation Ontology.

• FP 008 documented:

The ontology is well documented.

• FP 009 users:

The ontology has a plurality of independent users.

• FP 010 collaboration:

The ontology will be developed collaboratively with other OBO Foundry members.

• FP 011 locus of authority:

single locus of authority, tracker (SOP), responsive help desk

• FP 012 naming conventions:

See naming conventions

• FP 016 maintenance

OBO is an open community and, by joining the initiative, the authors of an ontology commit to its maintenance in light of scientific advance and to working with other members to ensure the improvement of these principles over time

We reviewed the list and feel that we are in compliance on all of them, although the PGDSO still needs to be completely revised. LC will contact BS (since he was not present) and find out what the procedure is for applying for OBO Foundry acceptance. PJ thought we just send an email with a request to be considered.

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.

* 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