POC Conf. Call 10-20-10

POC meeting, Webex Conference Call; Date: Oct 20th, 2010 10am (PDT)

In attendance:

POC members:

Absent:

Collaborators:

Acceptance of the minutes from the 10-13-10 meeting?

Adding links to more images through PlantSystematics.org

Goal is to add links between PO terms and images on PlantSystematics.org. With current technology, we can add html links to specific pages on PlantSystematics.org. If we register PlantSystematics.org with the GO database directory, we could make those links automatic (need to talk with Chris about this).

PlantSystematic terms could also be linked to the PO ids - have PO ids embedded in the Plantsystematics.org database.

We also need to discuss how to create annotations to areas within individual images, using HTML labels.

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. This is basically done by creating a subset, which can then be extracted to make a smaller file.

The problem with users creating and maintaining subsets, is that whenever the plant_ontology file changes, their file will become out of date. This problem can be overcome if we maintain the subset within the main plant_ontology file.

We need to decide if we want to include users subsets in the PO flat file, and if we want to have any other policies regarding slims. For example, GO also maintains a generic slim. PO has a 'reference plant structure' subset, but we have not been maintaining it.

We need to decide asap about whether or not to maintain Traitnet's subset, because they are beginning work on it now.

Status and Update of Progress: PO Release

• The new release is on the live, public PO web page! Thanks to everyone for all their hard work, it has definitely been a team effort.

Issues:

• Amigo browser: There are no icons for relations that we added (has_part, derives_from). Show up as question marks.

What about participates_in? We have also created the participates_in and derives_from relations, but they are not currently in use. Will need to create icons for them if we use them in the next release.

Might be possible to make icons in OboEdit. Justin E. said that if we can figure out how to make the icons, he can probably figure out how to get them on to Amigo.

Barry said to contact Chris Mungall to be sure whatever icons we use are consistent with Obo Foundry use.

From CM: OE should come with a set of images you can use, including all letters of the alphabet plus greek

recommended:

H - has_part

D - develops/derives from

are you sure you want participates in rather than capable of? (note from RW: participates_in relation is for structures that occur during a particular growth or development stage. This relation was recommended by Chris)

Perhaps move on to the greek for participates_in (so as not to confuse it with P for part_of)

RW: I didn't get any other responses from the OE users group re. standard icons. Guess we can pick the color and shape.

*The new species annotated by SGN are not reflected in the drop down box on the advanced search page.

Missing: Anisodus acutangulus, Atropa baetica, Coffea arabica (coffee), Nicotiana tabacum (tobacco), Physalis spp., Solanum insanum (eggplant)

We do not have Lycopersicum esculentum tomato, (but we do have Solanum lycopersicum)

This is another issue with the browser. Need to request a feature on AmiGO SF tracker for the script to pull in all synonyms based on the NCBI taxon ID and should display common names as well. Annotation files should just use NCBI id.

• The top level parent term "all" is problematic and should have a comment that states :'this is an artefact created by the AmiGO browser. Inclusion is required. All should be redefined as 'an entity that exists'."

Not sure how we do this since it does not show up in OE. It is present in GO, but does not have a definition there. May have to be done in Amigo

• PO Web page things that still need to be fixed:

See the detailed discussion of this on [9-29-10 Conf Call]

-The PO front page, release notes, acknowledgments pages have all been revised.

-Still need to do minor fixes to front page, add About us tab to top of page

-Download Ontologies page: links have been updated (thanks Justin), needs minor text edits. Has a link to the page "ontology concepts and how they are organized." That page needs to be updated.

-Documentation page: the table itself is okay. Suggest mirroring this table on the PO wiki, then moving all of the links form the table to the PO wiki, so it is easier for Ramona and Lol to update. Many of the documents linked from this table need to be updated.

-There are plans to move the entire web site to a new application(?). This might make editing easier. Before this is done, we should decide what is going on the web page, and what is on the wiki. Files will have to be renamed and reorganized for this move. Some of the current names are not intuitive, and this would be a good opportunity to fix them (e.g. release notes is really release statistics, ontology_doc is really the developers guide, but links through "concepts", the file with the old announcements is called "new" ).

Laurel and Ramona- Adding Annotations

10/14/10-LC, RW and PJ had a conf call discuss.

Summary: Laurel will work on annotating rice flowering time genes using the Phenote configuration from the ASPB workshop.

Note: Check that it is properly installed and working on Laurel's computer. Beta 1.7 ver 18?

Coordinate with the work going on in the lab by Mamatha, Keshvan and Gina - have list of ~270 flowering time genes and the associated references. Link those to the PO.

Ramona will focus on the gymnosperm EST datasets. Exclude plastid/ mitochodrial data sets. Can also search Pubmed for papers on gymnosperms, e.g. Wuschel gene in Picea. Will coordinate with Dennis and Manny(?) about getting EST info from GenBank - need description of libraries (description, tissues, stage, evironment, treatment, variety or germplasm name, accession number) and genbank ids that belong to them.

Note: will need a special config in order to use Phenote for EST annotation.

Also: Coordinating with Rensing and the moss ontology folks as well to add annotations from their work. Probably will need to add terms for them see: Moss_Ontology-_Stefan_Rensing,_Daniel_Lang

Can sign up on the Physcomitrella ontology website to follow.

We should follow up with them - upcoming Annotation Jamboree

Priorities for next release

The next revision with the completed is_a parents should be ready by early/mid December so release can go out before PAG in mid January. Then the longer term goal will be revision of the PGDSO upper levels to accommodate non-flowering plants

High Priority items:

• Merging the plant structure and plant developmental stages ontologies-

Done- New merged file called plant_ontology.obo. (Don't need to use 'test' suffix any more)

Now available on the dev browser. This is the one we will work on from now till the next release.

Reminder: PO terms added by POC curators to the Plant structure namespace should be in the PO:0025001-PO:0028000 range and ones in the PGDSO namespace should be PO:0028001-PO:0030000

*is_a parents for remaining terms

~50 terms. Link to list of terms without is_a parents.

Most of the terms that still lack a parent are the difficult ones, so this may take some time. We will need to address the issue of how to categorize non-material entities and trichomes.

Ramona is working on suggestions for is_a parents, as well as new classes where needed. They are being posted on next week's agenda and Source Forge.

Plans for a publication to detail the updates in the PO

-This is a priority for the fall to detail the changes in the PSO and promote its application

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

FIrst manuscript will target journal: 'Trends in Plant science' or 'Current Opinions in Plant Biology' may also consider 'Trends in Ecology and Evolution'

-Laurel and Ramona will prepare a summary preproposal (300-400 words) to be sent to Trends in Plant Science for their consideration. Focus will be on the benefits and usefulness of the PO, global perspective, links between PO and GO

-two papers to consider when writing this He et al, 2009 and Vincent etal, 2003

Second manuscript will be a full paper to Plant Physiology- Bioinformatics section, target date after the new year, once we complete more revisions. Use info from the grant proposal. Focus will be on updates to PO, and how it is now applicable to all plants.

-Compare to previous publication Ilic et al, Plant Phys.

Other Items

• 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)

Upcoming meetings 2010-2011:

• 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 are planning on attending and setting up a PAG_2011_Collaborators_Workshop half day workshop and meeting with collaborators. We will present a computer demonstration,and poster and possibly a Phenote workshop. Alejandra cannot attend. PJ is not attending as he is teaching. DWS will attend also Justin Preece. Abstract under construction....

* 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.

Ramona sent out abstract for review. Any comments?

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