POC Conf. Call 9-20-11

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

In attendance: Laurel Cooper (OSU), Ramona Walls (NYBG), Pankaj Jaiswal (OSU),Justin Preece (OSU), Dennis Stevenson (NYBG), Marie Alejandra Gandolfo (Cornell University), Barry Smith (University at Buffalo, NY).

POC members: Chris Mungall (Lawrence Berkeley National Lab), Justin Elsner (OSU)

Absent: no additions, deletions, or changes

Collaborators: none

Acceptance of the minutes from the POC Meeting at NYBG; Sept 10th-11th, 2011? no additions, deletions, or changes


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. 9-21-11: this has been fixed

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

For the release, we will highlight this new feature as we are the first ontology to offer spanish (and possibly Japanese) translations. Will send out the announcements in Spanish as well.

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? PJ will reply to SR about the Physco annotations- re: they should be using the actual gene ids rather than the microarray probe ids


We will move ahead with the release with the maizeGDB anatomy annotations (in SVN already), may need some minor fixing

There is increasing interest in the OBOEdit community to be able to include non-standard characters. JP will bring it up ont he next AmiGO development meeting


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. What is the status on this?


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: By Monday 9/26/2011 Or weds 9/28/11, after our meeting next week
  • Update annotation files and test on beta browser: Grape annotation file is almost done, will ask JE to load on beta to test.
  • Other tasks?
  • Final release: First week of Oct, by Friday, October 7th.

Note: Need to make sure all the Ontology QCs are run first, loading the annotations will be a big job

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.


PJ will work with the JE/JP to get the Dbxrefs working.

PJ: The local file is not used. The major library of Dbxrefs is coming from GO, as part of AmiGO. For JP: when you are working with CM on the new AmiGO, need to make sure that the local installations, can amend the library of cross refs from GO with the ones from the local databse.

RW: The problem we are having is that even if we request new DBxrefs to be added to the GO file, they are not showing up in our browser. It appears that our version of AmiGO has a built-in set of refs and it is not reading the current GO file. Go is using an updated version of AmiGO, we are using a customized version of the older version. Suggestion is to have the new AmiGO read the common file.

LC will send PJ the broken Gramene links, need new ones for the new files. JP will set up meeting with JE and CM to work on this

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 Eucalyptus 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.

These edits will be fixed in the editors file for the release.

If there is a case where things may change from being fused to unfused (or visa versa), then we should use a cross ref to the PATO Id#, and make it an inferred class rather than an asserted class. This is what was done for fused collective tepal structure (FCTS).

Suggestion: Get rid of fused perianth and make calyptra perianth is_a perianth (as it was before). So FCTS is_a collective tepal structure. Makes it more general than having the specific term calyptra. Calyptra is specific to certain species

MAG: Tubiliform (tube-shaped)corolla is also a case. You cannot tell where the petals start and end. Calyptra is a specific case, ansd in some cases they are not completely fused.

Suggestion: get rid of calyptra perianth, avoid dual parentage, keep calyptra calyx (is_a calyx) and calyptra corolla (is_a corolla). Make calyptra perianth a broad (RW: should be narrow) synonym of perianth. Will also add the synonyms from MAG: calyptra calyx: calycine operculum; outer operculum and for calyptra corolla: corolline operculum; inner operculum

floret

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

Background Comment: In the live version, we had the term floret (PO:0009082). Def'n: Small flowers, especially of the spikelets of Poaceae and Cyperaceae. After the 8-30-11 POC meeting, it was been renamed 'spikelet floret' (see below) and we added "ray flower", "disk flower" as narrow synonyms of flower and "disk floret", "ray floret" and floret as related synonyms.


Since then there was a suggestion that we needed a general term 'floret':

proposed def'n: A small flower that is part of an inflorescence. Inheritance: is_a flower, part_of inflorescence.

Spikelet floret would then be a child of floret.


In the dev file:, note: We should make these def'ns consistent and in the g-d format.

  • spikelet floret (PO:0009082): Def'n: A small flower that is part of a spikelet. [source: APWeb:Glossary, PMID:20197291]

Comment: Found in Poaceae, Cyperaceae and other Poales. Lemma, palea and lodicule are associated with a spikelet floret, but since it is not clear what they correspond to in conventional flowers, no assumptions of homology are made at the present time. To describe a ray or disk floret of the Asteraceae, use flower (PO:0009046).

  • ear floret (PO:0006354): def'n: Small flowers of the spikelets of maize ear. [source: GR:pj]

proposed def'n: A spikelet floret found specifically in the Zea mays ear.

What about other grasses. Some references to ears in the grains.

new proposed def: A spikelet floret that is part of an ear spikelet (this way it is not specific to Zea mays, but any species that has an ear).


  • tassel floret (PO:0006310): def"n: Flowers of the spikelets of maize tassel. [source: GR:pj]

proposed def'n: A spikelet floret found specifically in the Zea mays tassel.

new proposed def: A spikelet floret that is part of a tassel spikelet.

  • Will update definitions of all children of ear and tassel floret as well.


PJ: we need to have the terms 'ray flower' and 'disc flower', they would be is_a flower, do not need the specific term floret. Synonyms are ray floret, disc floret.

We will need to change the comment for spikelet floret to match the above changes.

This edit is not in the file, will be added for the release.

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.

proposed def'n: 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.


new proposed def'n: FF.00 fruit size up to 10% (PO:0007032): A fruit formation stage that begins the formation of the zygote and ends when the fruit has reached 10% of its final size.

We will put the old term names as synonyms.

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

'Problem with staging reproductive development across different species is there is no consistency. Hard to find landmarks.

Proposed new names were rejected. The stages will be up to 10%, then 10%-30%, etc:

Fruit formation.jpg


These edits will be fixed in the file for the release.

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

  • germination (PO:0007057): rename "(0) germination stage". (Tested the parentheses around the zero, and they display fine in the dev browser. Will remove them before release until we are ready to change them all).

This was discussed at the NYBG meeting

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

We will rename these:"seed germination stage" and "seed imbibition stage"


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

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?

this was not discussed at the meeting- should leave till after the release is out


  • 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.


We will rename thie term "seedling shoot emergence stage". We will check to make sure GO Biol processes has seed imbibition. Definitions need further reworking for the next release.


These edits will be made in the file for upcoming release.

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.

Plant Genomes & Biotechnology: From Genes to Networks, CSHL

Dates: November 30 - December 3, 2011 Abstract Deadline: September 9, 2011

  • Pricing

Academic Package $1055

Graduate/PhD Student Package $880

Corporate Package $1340

Academic/Student No-Housing Package $720

Corporate No-Housing Package $905


DWS will be away, but RW could attend

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

PJ planning to attend, LC and RW can go. Check with Pascal to confirm dates

Botany 2012

July 7 - 11, 2012 - Columbus, Ohio

Call for Symposia, Colloquia and Workshops:

Submission site now open

RW and DWS will look at putting in a proposal for a half day workshop.

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

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