POC Conf. Call 9-29-10

From Plant Ontology Wiki
Jump to navigationJump to search

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

Steps to get the release out - by the end of the week

-Updating the annotation files: TAIRs are done, waiting for files from SGN,

Gramene- Updates have been made to the files on the SVN.

-updating the AmiGO browser?

-The revised ontology files from the dev browser should be combined with the updated annotation files on the Beta browser for review.

-If everything looks good, we will ask Justin E to load them on the live browser

-We will send out announcements to the mail lists and user groups.

-Update info on the release notes page


  • Swollen eye:

-Has been made a synonym of 'subterranean tuber axillary vegetative bud' after discussing this with Naama. This is a term that the breeders use and swollen eyes may or may not develop into shoots.

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 narrow 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. We already refer to the synonym of 'subterranean tuber axillary shoot' as '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?

Obsoleting 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 children* of B (Note there is a typo in the user guide here)
  • All of A's parent relationships are deleted
  • All of A's child relationships are deleted
  • A is destroyed

What happens to the annotations?

  • One advantage of merging is that the comments from the obsoleted term are merged into the comments of the replacement term. But a big disadvantage is that the term is destroyed.

Destroying terms:(from OBO-Edit User guide)

"It is dangerous to use the Destroy command. If a term is destroyed, its id goes back into circulation for use in new term creation, and that id will probably be reused immediately. If the term that was destroyed was ever included in a publicly available version of your ontology, external database and applications that use your ontology may become confused by this id reuse. For example, tools like obodiff will think that instead of destroying a term and creating a new term somewhere else, you have kept the old term in the ontology but changed all its parents, children, its name, its definition, and all its other attributes."

"Applications assume that a term id will be used for a single term and never again. That is why terms are obsoleted instead of destroyed: we need to keep an audit trail of ids that have been used. If it is possible to reuse an id through the use of the destroy command or ontology filtering, this assumption does not hold, and applications everywhere become deeply confused."


Are these terms really 'destroyed' when they are merged? NO, since the ID becomes an alternate ID, and that ID will not go back into use. The alternate IDs show up in the browser as synonyms, so you can find them in the search. Also the definition and synonyms become part of the term that was merged into, so they don't just go away, as in destroying.


Replaced_by: (from OBO-Edit User guide)

  • "If an obsolete term is perfectly supplanted by another term, the new term may be specified as a replacement term. Note that a replacement term should only be specified if the obsolete term can be replaced by exactly this term in every case. If this criterion is not met, use a "consider" term instead."

"Replacement terms should be specified when possible, because replacement terms can be used by software agents to do automatic corrections in databases when a term becomes obsolete."


  • Also, it is possible to edit the definition and comments of an obsolete term, whereas the destroyed terms are gone forever (but merging does not really destroy the term).

-seedling, gametophyte, and sporophyte are narrow synonyms of whole plant

-leaf whorl is a narrow synonym of collective leaf structure

thus, these terms should probably not be merged.


In progress...


  • 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??

Updating and Fixing the Annotations

Obsoleted terms:

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

'po_anatomy_gene_arabidopsis_tair.assoc'

'po_temporal_gene_arabidopsis_tair.assoc'

Laurel obtained up-to-date files from TAIR as the existing ones were 18 months old and committed them to the SVN. Note that the numbers of annotations has changed in this new version.

The changes were made in the files and they were committed back to the SVN. TB sent us a link to a script to run on the files to check them for errors. JE will run the check on them?

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. In order to do so, she will load the po-dev version of po_anatomy_test.obo (from the SVN, version #936) onto their database. That way they can access the tuber terms that we have added for them in the past few months. She is aware that this is still our dev version and said it is not a big issue for them to update their database once it goes on the live site.

Updates to the PO Web pages

List of Priorities:


  • Download Page

The OBO and OWL files, are available on the download page from all three sites.

  • Flat files are being retired?
  • 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. Dennis will look at Doodle poll for availability in November.


  • 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 responded to him with an explanation of why we chose the current structure. He responded:

'We will aim to setup bryophyte terms with regard to the new structure and (if possible) suggest terms that are broad enough to cover all land plants in the process.'

'FYI, the current, but now obsolete, PO-MO term mapping is at Moss_Ontology'

This site has a list of moss tissue and cell types, as well as life cycle/developmental stages that we could use a a guide for adding new terms.


Issues arising from this:

This groups is setting up their own ontology for their immediate needs, but as the PO includes more moss terms, it will probably become redundant. Should we work with this group to meet their needs quickly, so they don't have to develop their own ontology? They may be able to develop a moss PO slim.


  • 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.

Laurel can set up a Doodle poll?? Who wants to take part?


  • Status of BSA announcement for bulletin

Notice came out in this quarter's issue of the Plant Science Bulletin. Can be viewed online at: http://www.botany.org/plantsciencebulletin/PSB-2010-56-3.pdf on p. 102 (great location - on the first page).

We can also post an online announcement with the BSA when the final release is ready.


  • 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. May be able to use images instead of textual links to email addresses.

We will need to update the links to this lists on the PO web site (http://plantontology.org/mailarchs/mail_list.html)


  • New curator hired at NYBG: Angelica Cibrian has been hired and will be a split appointment between Genomics of Seed Plants project (3/4 time) and the PO (1/4). She will spend part of her time NYBG and rest at NYU. She has been working on using GO terms and annotations to analyze the Seed Plant data, and so can act as an interface between the Seed Plant project and the PO, perhaps provide annotations to the PO.


  • Fall exhibition at NYBG- DWS: ask PJ about the details of this?

From the grant:

(2) Dr. Stevenson, a co-PI from NY Botanical Garden (NYBG), will involve PO project in the ongoing outreach activities of the NYBG in developing Plant Biology tools for 6-12 teachers in NY City public schools as well as the general public and education programs at NYBG for K-12. NYBG being a Museum gives us an opportunity to reach out to parents and students alike and in ways that a university setting like Cornell may not provide. He will organize three annual exhibitions (one per year) at NYBG.

Deliverables: Years 2-4: Student workshop at NYBG.

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)?


Looks like this can be done in OE see: Creating Your Own GO Slim in OBO-Edit. This actually describes how to create slims in an older version of OE. It is similar to creating subsets in the current OE. It does not have the capability to check if the subset will function independently, as needed for a slim.

Berkeley BOP has an online tool for creating slims (http://berkeleybop.org/galaxy/) but the server has been unavailable for the past week and a half.

Priorities for the Next Round of Revisions

Target date for the next release?

-Merging the plant structure and plant developmental stages ontologies

-Complete compliance with OBO foundry principles

-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. To qualify for reduced registration rates, must register by October 15th.

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.

Next meeting scheduled for: Weds, Oct 6th, 10am PDT

Retrieved from "http://wiki.plantontology.org/index.php?title=POC_Conf._Call_9-29-10&oldid=2785"