POC Conf. Call 9-20-11

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POC meeting, Webex Conference Call; Date: Tuesday Sept 20th, 2011 10am (PDT)

In attendance:

POC members:

Absent:


Collaborators: none


Acceptance of the minutes from the POC Meeting at NYBG; Sept 10th-11th, 2011?

Summary of Discussions at NYBG; Sept 10th-11th, 2011

  • Main topics of discussion was the revision of the PGDSO and the upcoming release.
  • We made some significant steps on the PGDSO- see complete details: here [Saturday_Sept_10th,_2011]
  • The revision of the PGDSO will be the focus of the next major release later this fall.

Upcoming Release

Major changes for this release are:

1. Inclusion of Spanish synonyms.

They seem to be working fine, except that we still should have the descriptor "(Spanish:)" preceding them.

Not clear if this is a problem with just the dev browser.

2. Eliminating_Zea/Poaceae_terms_from_PO

This is more or less complete. PGDSO may change as we go forward, but we can use as is for now.

3. New annotation files:

We are working on getting the new set of MaizeGDB annotations in.

Addition of new annotations for grape (LC working on) and strawberry

What is the status of the Physcomitrella annotations?

4. Other changes

  • Japanese synonyms?

Will have Japanese synonyms in obo file, but JE will strip them out before the file gets loaded on AmiGO.

Japanese synonyms are not currently in the editors' file. Should be added.

5. For more details see: Summary_of_Changes_to_PO_September_2011

Target dates:

We discussed having a release in September, 2011

  • Finish all edits: 9/26/2011
  • Update annotation files and test on beta browser:
  • Other tasks?
  • Final release: First week of October?

Tech issues:

these have been posted on the POC_Technical_Issues_Page

Adding Dbx Refs

for MaizeGDB

See notes from the Follow_up_meeting_re:_Association_files_for_the_Kaeppler_data_set_Sept_15,_2011

We can use one database abbreviation to access all MaizeGDB pages. It uses their url for anything with a MaizeGDB id, but also works for gene model names.

File format (modified from http://www.geneontology.org/cgi-bin/xrefs.cgi - changed object to include gene model name):

abbreviation: MaizeGDB

database: Maize Genetics and Genomics Database

object: MaizeGDB Object ID Number or Gene Model Name

example_id: MaizeGDB:881225

generic_url: http://www.maizegdb.org/

url_syntax: http://www.maizegdb.org/cgi-bin/id_search.cgi?id=[example_id]

url_example: http://www.maizegdb.org/cgi-bin/id_search.cgi?id=881225


Mary will update all of the xrefs in MaizeGDB's old association files to use this abbreviation when she does her next update. Until then, we should keep the other MaizeGDB abbreviation in the dbxref file, so the links will still work.

Existing MaizeGDB stanzas are incorrectly formatted. We cannot add the new stanza to http://plantontology.org/docs/dbxref/PO_DBXref.txt without removing at least one of the old ones. Not sure what repurcussions this will have.

Gramene

Two of the Gramene dbxrefs in PO_DBXref.txt are not working:

GR: http://www.gramene.org/perl/protein_search?acc=P93436

GR_MUT: http://www.gramene.org/perl/mutant/search_mutant?id=GR:0060198

Don’t know if it is because the urls are wrong, or if it is because the ids are bad. If someone from Gramene can provide the correct urls, we can write new stanzas for the dbxref file.

Others

We are also working on adding new annotation files for Physcomitrella, grape and strawberry. We will need to add DBXrefs for these sources as well.

dbxref file

Does PO's version of AmiGO read from http://plantontology.org/docs/dbxref/PO_DBXref.txt? This file seems very out of date and appears to have incorrect formatting in a number of places.

OWL version stamp

Request from Gavin Kennedy:

"Would it be possible to add an owl:versionInfo attribute to the OWL Plant Ontology so that we can track the changes in versions. This could be the version number or a date stamp, etc."

filter translation

from Mary Schaeffer at MaizeGDB

comments: It would help to have a link to what the filters mean from all pages where one can set the filters. A click on the help box seemed to missing this information, or require reading pages of stuff to find out it wasn't there.

For example - most folks will not know that MGCSC refers to the maize mutant stock collection at Illinois.

Edits to complete before release: PAO

New children of calyptra perianth

This was raised at the POC meeting POC_Conf._Call_8-23-11

Existing terms:

  • fruit operculum (PO:0025298): A collective organ part structure that is the apical part of a circumsessile capsular fruit that separates from the rest of the capsule during dehiscence. [source: POC:curators]

Comment: Develops from the apical portion of a gynoecium. Found in Eucalyptus and other Myrtaceae.

and

  • calyptra perianth (PO:0025299): A perianth that is composed of fused perianth parts and located on top of a gynoecium that contains an inferior ovary. [source: POC:curators]

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.

Synonyms: related: floral operculum; exact: angiosperm calyptra; exact: floral calyptra (suggest we add flower operculum as related and flower calyptra as exact)

Proposed changes: More specific terms for calyptra

At the 8/23/11 meeting, there was a request for more specific terms for calyptras formed of fused petals or fused sepals.

In Eucalyptus, there may be one or two calyptras: an inner operculum or calyptra composed of fused petals and an outer operculum or calyptra composed of fused sepals. In many species, the sepals to do not fuse, and there is no outer operculum.

Our current definition of calyptra perianth includes fused tepals, which would encompass the existing term "fused collective tepal structure" (PO:0025138), but to my knowledge, tepals are not present in Eucalyptus. (The ANBG provides EUCLID, an excellent resource for description of Eucatypus morphology.)

Suggest adding a new term "fused perianth", that is consistent with our other terms such as "fused collective tepal structure". This would be a more general term, and could include perianths that are partially fused.

Proposed new terms and ontology structure:

perianth

> fused perianth (new)

>> fused collective tepal structure (PO:0025138)

>> calyptra perianth (flower operculum) (PO:0025299)

>>> calyptra calyx (outer operculum) (new)

>>> calyptra corolla (inner operculum) (new)

  • Should we also add terms for fused petal and fused sepal (already have fused tepal)?

terms and definitions

These changes are in the editor's file

  • fused perianth: A perianth that is composed of two or more fused perianth parts (sepals, petals or tepals).

Comment: Perianth parts may be partially or wholly fused.

  • calyptra perianth (PO:0025299): A fused perianth that is composed of fused sepals or petals and located on top of a gynoecium that contains an inferior ovary.

Comment: Found in Eucalyptus and other Myrtaceae. The petals are generally completely fused. Sometimes erroneously referred to as part of a fruit. Not the same structure as a spore capsule calyptra or fruit operculum. Use the more specific term (calyptra corolla or calyptra calyx) if possible. Species of the subgenus Monocalyptrus have only a calyptra corolla (inner operculum) while in most other species, a calyptra calyx is also present, at least early in flower development.

Synonyms: flower operculum, floral operculum, floral calyptra, flower calyptra, angiosperm calyptra

  • calyptra calyx: A calyptra perianth composed of fused sepals.

Comment: Sometimes found in Eucalyptus and other Myrtaceae, covering an inner operculum or calyptra corolla. The sepals are generally completely fused.

Synonyms: outer operculum, operculum calyx

  • calyptra corolla: A calyptra perianth composed of fused petals.

Comment: Often found in Eucalyptus and other Myrtaceae. The petals are generally completely fused. If an outer operculum (calyptra calyx) is present, it covers the inner operculum (calyptra corolla).

Synonyms: inner operculum, operculum corolla

  • fused collective tepal structure (PO:0025138), calyptra calyx and calyptra corolla all have dual parentage (is_a fused perianth and is_a collective tepal structure, calyx, or corolla. If we were to import PATO:0000642 (fused with), we could make cross product definitions and infer one of the relations.

floret

floret is currently a synonym of flower (as decided at the POC_Conf._Call_8-30-11).

We could add a new term floret, is_a flower, part_of inflorescence. Def: A small flower that is part of an inflorescence.


Edits for release: PGDSO

Edits requested by MS for MaizeGDB

We don't need to fix the definitions of coleoptile emergence PO:0007045 before this release, because Mary decided she should use "radicle emergence" (PO:0007015) instead.

5 fruit formation; FF.00 fruit size 10%

Initial Comment from MS:

"There are currently five stages based on size of final fruit, starting at 10%, etc. There is not any term for very early stage and 10% is already pretty far along from a developmental biology view. Since there seem to be no annotations for any of these stages, suggest instead of introducing new terms to change the definitions a tad. So for FF.00 fruit size 10%, define as up to 10% final size. For the case of the FF.00 fruit size term, the related term for maize would be 6.1 dilatory."

Fruitsize.jpg

current def'n:FF.00 fruit size 10% (PO:0007032): The stage when the size of the fruit is about 10% of final fruit size. [source: GR:ap, ISBN:3826331524]

Synonyms: related: 7.01 Pod 10% of final length in soybean, related: FF.00 fruit size 10% in Solanaceae, related: stage R3 in soybean, related: tomato immature green

All the other sizes are defined similarly.

proposed def'n.: (based on Mary's suggestion): A fruit formation stage that begins with the formation of a fruit and ends when the fruit has reached 10% of its final size.

Comment: This stage can only be used when the final size of the fruit is known.

At the POC meeting on 9-11-11, we agreed that these stages could be up to and including the % size for now. Should rename terms "fruit size up to 10%", etc.

RW: When does formation of a fruit occur? Should we say fertilization of an ovary instead?

new proposed: FF.00 fruit size up to 10% (PO:0007032): A fruit formation stage that begins with fertilization of an ovary and ends when the fruit has reached 10% of its final size.

Comment: A fruit development stage may begin without fertilization in cases of parthenocarpy, apomixis, or other hormone-induced conditions.

New names:

Fruit formation.jpg

These edits are already in the file.

PGDSO terms without is_a parents

As discussed at the NYBG meeting, we can fix the three remaining PO terms without is_a parents: shoot emergence, seedling growth and imbibition.

Shoot emergence is part_of seedling growth, but has no is_a parent, and seedling growth has no is_a parent. Imbibition (sibling of shoot emergence) also has no is_a parent.

current structure:

Germination stages.jpg

Shoot emergence (stage) should be is_a seedling growth (stage). Seedling growth (stage) should be is_a vegetative growth stage.

Imbitition (stage) should be is_a germination (stage). Will deal with definitions of imbibition and germination later.

current and proposed terms and definitions

0 germination (PO:0007057): rename "(0) germination stage".

imbibition (PO:0007022): rename "imbibition stage" and make is_a child of "germination stage".

NOTE: RW tried the parentheses around the zero, and they display fine in the dev browser. Will leave it up so we can look at it, but should remove them before release until we are ready to change them all.

current: seedling growth (PO:0007131): Growth of embryo after imbibition up to the development of the first adult leaves. part_of germination

new proposed name and def.: seedling development stage: A vegetative growth stage that has as a participant a whole plant during the interval between germination and development of the first adult leaves.

Comment: This terms is used only for seed plants, although non-seed plants may have a comparable phase during which they produce juvenile or transition leaves.

Note: After the PGDSO is revised, the parent of seedling growth stage will be sporophyte vegetative development stage, so definition will change slightly. Also, the numbering of the children of vegetative growth stage is messed up now. Should we renumber the stages?


shoot emergence (PO:0007030): Shoot or leaf breaks through the soil surface.

Propose that we rename shoot emergence stage and make it is_a seedling growth stage, instead of part of seedling growth stage. Can work on definition when we revise the PGDSO.


These edits are already in the file.

Upcoming meetings and Presentations 2011/2012:

* 2011 CGRB Fall Conference Oregon State University, on Sunday-Monday, September 18-19, 2011.

Two posters related to the Plant Ontology will be presented.

JP will present a poster at the regarding the development of a semantic web application for annotation curation. This web application makes use of PO data via a newly created web service, and includes an initial data set built from PO GAF (.assoc) files for Oryza sativa.

Additionally, he and PJ will host a web presentation for Syngenta employees on the same topic on Sept 26.

LC will present the poster: Expanding the Plant Ontology: Linking Plant Anatomy and Development to Genomics Across Plant Taxa.

PAG 2012

January 14-18, 2012, San Diego, California

Registration and Abstract submissions open on Sept 22nd

LC is presenting in the Plant Phenotypes workshop on Sunday Morning, 15 January 2012 -- 8:00 am - 10:10 am.

The PO will take part in an Outreach booth organized by MaizeGDB

Other activities?

*5th International Biocuration Conference

April 2-4, 2012, Washington DC

Call for abstracts is now open: Need to clarify the deadlines

There are three submission categories for abstracts:

1. Talk or Poster (with consideration for oral presentation)

2. Poster only

3. Workshop only

• Submission deadline November 30, 2011

• Notification of acceptance February 3, 2012

Instructions

There are seven topic sessions from which submitters are invited to select: 

  1. Ontologies, standards and best practices, including gold standard datasets.
  2. Protein annotation; sequences, structures and pathways.
  3. Community annotation and Wikis.
  4. Genomics and metagenomics data curation.
  5. High throughput proteomics data (focus on NGS and MS data) curation and presentation.
  6. Literature collection, text mining and curation.
  7. Tools to assist curation, including automated pipelines.

There are four submission tracks: 

  1. Paper, with consideration for oral presentation
  2. Talk
  3. Workshop
  4. Poster

From the Instructions page: For authors wishing to submit to DATABASE for the 2012 BIOCURATION VIRTUAL ISSUE:

  • Submission deadline: October 15, 2011
  • First decisions: November 15, 2011
  • Revisions deadline: December 15, 2011
  • Final decisions: January 10, 2012
  • Conference: April 2-4 2012


Botany 2012

July 7 - 11, 2012 - Columbus, Ohio

Call for Symposia, Colloquia and Workshops:

Submission site now open

Next meeting scheduled for Tuesday, Sept. 27th, 2011 at 10am PDT/1pm EDT

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