POC Conf. Call 9-29-10

POC meeting, Webex Conference Call; Date: Sept 29th, 2010 10am (PDT)

In attendance:

POC members:

Absent:

Collaborators:

Acceptance of the minutes from the 9-22-10 meeting?

Status and Update of Progress: PO Release

• Swollen eye:

From 9-15-10 meeting: Can have 'swollen eye' as synonym of tuber axillary bud. (note there is no term 'tuber axillary bud', it should go on 'subterranean tuber axillary vegetative bud' or the new term 'subterranean tuber axillary shoot' ). We will ask Naama if it is more like a bud or a shoot.

Response from Naama: "I think since a 'swollen eye' is not yet a sprout, and might not develop into a sprout, it should be a synonym of vegetative bud. It seems to me more like a term used by breeders to evaluate the quality of tubers. It's a bit difficult to differentiate a small 'sprout' from a 'swollen eye', so a broad synonym of 'sprout' might do too. These terms are a bit artificial, since they were created to help breeders score tuber appearance in the field, and might not reflect on distinct developmental staged or plant organs."

Here is the scale that the breeders use to rate the buds/sprouts of the tubers. 1 none 2 swollen eyes 3 sprouts ca. 1/4" 4 sprouts ca. 1/2" 5 sprouts ca. 1" 6 sprouts ca. 2" 7 sprouts ca. 3" 8 new top growth 9 chain tubers

Therefore, 'swollen eye' should be a broad synonym of 'subterranean tuber axillary vegetative bud' (PO:0025042) (eye)

On a related note (from DWS), using the word sprout could be problematic, since a sprout can be used in many contexts. Suggest we change the synonym of subterranean tuber axillary shoot to 'tuber sprout'.

Comments from other reviewers

-Alejandra or Dennis will follow up with Gar Rothwell

Waiting for response from Gar Rothwell and Peter Linder, will copy responses to po-discuss.

-Dennis will check whether there are any other outstanding reviews to come in yet from the folks he contacted. Chris Hardy?

Obseleting terms in the Ontology

For our future work, we need to know: Is it better to use replaced_by or to merge terms.

What are the advantages and disadvantages of each? Merging (from OBO-Edit User guide)

When term A is merged into term B, the following things happen:

• A's id is assigned as an alternate id of B
• All of A's synonyms are copied to B
• All of A's dbxrefs are copied to B
• A & B's comments are merged
• A & B's definitions are merged
• A's name is assigned as an exact synonym of B.
• All of A's parents become parents of B
• All of A's children become parents of B
• All of A's parent relationships are deleted
• All of A's child relationships are deleted
• A is destroyed

In progress..

Updating and Fixing the Annotations

We need to formalize the procedures in place for making updates to the annotation files on the SVN and in our ontologies.

Current status:

• TAIR-

Summarized from Email correspondence with Tanya Bernadini: They would prefer us to set up an script to automatically retrieve the files from their FTP site (there was apparently some agreement to do this in the past). They are updated weekly- do we want to reload the files between releases to keep the annotations more up-to-date?

• MaizeGDB-

Summarized from Email correspondence with Mary Schaeffer: "We prefer to supply them when there are major updates, such as phenotype-stock associations to add for genetic stocks, etc. In general, we are not doing a lot of hand curation. The next major update will probably be between Feb and June, 2011, when the new set of gene models is released, along with their PO associations."

• Gramene-??

• Solanaceae Genomics network (SGN)-

Naama Menda has obtained SVN access rights (thanks Justin E) and she will look after submitting up-dated files directly to our SVN repository when they are available. She is working on updating them before the release.

Updates to the PO Web pages

List of Priorities:

• Download Page

The OBO and OWL files, are available on the download page

On all three sites or just on the beta site?? It should be on both Live and the Beta at least.

• We discussed moving the supplemental information on the PO web page (like the links under "Documentation") to the PO wiki. That way, when we update, we will only have to do it on one site. Should we do this?'

Ramona and Laurel have been gradually updating the documents and other web pages. Will continue to work on this.

Other Items

• POC meeting to be held at NYBG in fall 2010. Date TBD. Are we still planning to do this??

Should we invite outside experts, scientists, students and postdocs? Time to do so is getting short.

Please fill out Doodle Poll re. dates that you are or are not available: http://www.doodle.com/6n4pmknkeebk9khg

We need to pick a date for this meeting ASAP so folks who are flying in can get tickets

From 9-15 meeting: Pankaj will check his calender to see if this is possible. Ramona will follow up with Dennis when he returns.

• Plans for a publication to detail the updates in the PO

-This was discussed a bit in May/June, but we have not made any detailed steps towards getting it done yet

-We have been keeping track of the changes on the 'Summary of Changes' page

-Target journal: Current Opinions in Plant Biology or Plant Physiology

-List of action items to move this ahead:

• We have been contacted by Stefan Rensing, University of Freiburg, Germany re: setting up an ontology for bryophytes with a focus on the model moss Physcomitrella patens.

Ramona and Dennis will respond to him.

Issues arising from this:

• Setting up conference call with Bruce Kirchoff to discuss the Plant Ontology and the issues he raised at the Botany Meeting

His comments: "I hope you understand that my comments were not directed at you, or the work that you are doing with the plant ontology. I do understand the need for the ontology, at least from a database perspective, and I think that the improvements that you and the plant ontology group have made to the initial ontology are important, and substantial. However, I feel that there are still serious problems with any attempt to bring all aspects of plant morphology together under a unifying ontology. Perhaps the word "ontology" was coined for these controlled vocabularies with tongue-in-cheek, but the attempts to extend the ontology beyond their use in databases tends to remove the jest, at least in my opinion. I very much believe in open discussion as a way of advancing science. It was for this reason that I convinced the Botanical Society to institute the discussion sections that now are a standard part of the annual program. I would be interested in continuing the discussion of plant trait ontology at the next botanical society meetings, in a discussion session. Perhaps you and your colleagues would be interested in organizing one of these sessions with me."

This was scheduled to be done after Sept 20th, so we should probably decide when we want to do it. Doodle poll?? Who all wants to take part?

• Setting the AmiGO browser to display terms that have been obsoleted.

Laurel posted a message on the AmiGO SF tracker and has been discussing this possibility with Seth Carbon at the Berkeley Bioinformatics group.

In summary, it appears there may* be a variable in the config.pl file that can be set before installation or reinstsllstion.

$ENV{AMIGO_OBSOLETE_BEHAVIOUR}

The options are: 'ignore','include_commented', and 'include_all'.

However, Seth was not sure how much of this is in the current version of AmiGO. Chris- Perhaps you know better??

• Status of BSA announcement for bulletin? Did it ever get sent?

• Mailing lists

We need to define the function of each of the mailing lists: po, po-dev, po-announce, po-internal. I think po-announce, po-internal are fine, but what are the other 2 supposed to be for?

In mid-August the new list po-discuss@plantontology was set up and the members of po-internal were added to it. This is the address that will be used in the letters to the reviewers.

We all agreed that these need to be reviewed and we need to deal with the spam problem as well.

• New curator hired at NYBG: She has been hired and will be a split appointment between Genomics of Seed Plants project (with Gloria Coruzzi, Virtual Plant) and the PO (?). She will spend part of her time NYBG and rest at NYU. Dennis is this accurate?

• Fall exhibition at NYBG- DWS: ask PJ about the details of this? Look for details in the grant.

PO slims

GO includes reduced versions of their ontologies (Go slims) for some user groups. The slims are developed and maintained by the users, but publicly accessible as part of the GO flat file. We have one user group (TraitNet) that is interested in creating a PO slim.

We should decide if we want to include that in the PO flat file, and if we want to have any other policies regarding slims.

For example, GO also maintains a generic slim. Should we make something similar (especially as the PO gets more detailed and adds more taxon specific terms)?

Priorities for the Next Round of Revisions

Target date for the next release?

-Merging the plant structure and plant developmental stages ontologies

-Adding Musa terms requested by Rosemary Shrestha

-Root terms- submitted by Rich Zobel, adventitious roots

-Legume terms submitted by Austin Mast

-New terms requested by reviewers (from Ahrestani and Kramer)

-is_a parents for remaining terms (will require work on upper level structure for non-material entities)

-add terms for non-angiosperm structures

-better organization of descendants of portion of plant tissue

-convert to intersection_of relations?

-Convert existing definitions to genus-differentia form?

-work on PGDSO

-tuber growth and development stages, open on SF since 6/2009

-add links to more images through PlantSystematics.org

PJ: Lol and Ramona will focus more on adding annotations

-Others??-

Upcoming meetings 2010-2011:

• Latin American Congress of Botany

LACB. La Serena, Chile, October 4-10;

Dennis is attending LACB. We will consider having a presentation at this meeting. Alejandra will not be able to attend.

• Infectious Disease Ontology Workshop

Dallas, Dec. 8th and 9th, 2010

Organized by Lindsay Cowall (Duke University) and others, under the auspices of the National Center for Biomedical Ontology. IDO Workshop December 2010. Note that relations between the IDO and other ontologies is one of their provisional goals.

Pankaj will represent the PO with regard to plant infectious diseases. This is especially relevant to the PO as infectious disease agents (viruses and bacteria) are widely used in plant genetic research.

For additional information on the IDO see http://www.infectiousdiseaseontology.org/Home.html

• Plant and Animal Genome XIX Conference

January 15-19, 2011 PAG 2011

Registration is open, abstract deadline Nov 1, 2010.

Lol and Ramona should plan on attending and meeting with collaborators. Set up a computer demonstration, and possibly a Phenote workshop. Perhaps Dennis and Alejandra could also attend, and we could all meet there. PJ is not attending as he is teaching.

* International Botanical Congress (IBC2011)

July 23rd-30th 2011, Melbourne, Australia

Registration is open- deadline for abstracts: 31 October 2010, Important dates

Dennis and Alejandra are planning to attend IBC2011 and speak in other symposia.

Symposium proposal was accepted, 'Bio-Ontologies for the Plant Sciences' under the genetics, genomics and bioinformatics theme.

Ramona contacted the organizers about whether or not it is possible to get a room with Internet for outreach activities, but hasn't gotten a response yet. Is this something we still want to pursue?

Pankaj, Ramona, and Angelica Cibrian (Harvard and ANMH, Genomics of Seed Plants) are scheduled to give talks and must submit abstracts by October 31st. Three additional speakers will be chosen from abstracts that are submitted.

Pankaj will give the introductory talk on general use of ontologies, GO, genomics, etc, and Ramona will present the talk on the Plant Ontology.