POC Conf. Call 3-20-12

POC meeting, Webex Conference Call; Date: Tuesday Mar 20th, 2012 10am PST/1pm EST

In attendance:

POC members:

Absent:

Collaborators: none

Any changes or corrections (additions/deletions, etc) needed in the minutes from the POC_Conf._Call_3-13-12?

Back to POC Meetings Minutes

Next PO Release:

Apache update:

JE has managed to port the website code to work with Apache2. Please check http://beta.plantontology.org (no port 8080).

Question: Should we wait until after the release to update? Probably could update with only minor disruption, but there could be unforeseen difficulties. Most of it could be done in parallel to minimize downtime however.

After the switch, all links to :8080 addresses will have to be fixed. There are only about 30, and most of them seem to be links to wiki.plantontology.org.

Timeline:

• Target date for finishing edits: March 21st

• Target date for release: Before March 30th

We should aim to have to release out by the end of this month, so we can then focus on the paper to have manuscripts ready by April 15th.

We probably want to have this release out before we submit, so reviewers and editors can look at the web site. If we get feedback from reviewers on manuscripts, we can work those into the next release in two months.

We can get this week's changes, plus the wood development stages and the coleoptile emergence terms in the file by next week, and review them at next week's meeting.

Goals and Priorities:

For more details see: New terms and obsolete terms-March 2012 Release

PO_Release_SOP_Page

After the release in October 2011, LC put toghether this page to help facilitate the releases

Revisions of PSDS (formerly PGDSO):

Status to 3-19-12

• ~34 new terms added
• many existing terms have been modified, eg changed all the 'phase' names to 'stage'
• all PSDS terms names are now singular. Some still need to have "stage" appended
• focus has been on the whole plant development stage (PO:0007033) and its children
• Addition of Wood development stages: (See: SF tracker), started at the NYBG Workshop

New and Revised Terms for the PAE

• Addition of new terms and revisions to existing terms to encompass wood- see Goal_1._Anatomical_Entities

• Please see New terms and obsolete terms-March 2012 Release for a complete list

• Complete old user requests/SF tracker items:

- This is an ongoing process

New association files:

• Physcomitrella (released Jan 2012)

• Small set of cotton annotations (TBA Feb 2012)

• Updated annotations from SGN received

Glossary of PO terms

See PO Glossary on dev

This was discussed at the RCN meetings 2011, plan is to eventually replace APWeb Glossary. This will be useful for users of APWeb Glossary who need a glossary, but don't want to use AmiGO browser. We could eventually incorporate other terms from APweb into PO if needed.

• What is the status of this? PJ will follow up with the developers. It should be updated to the version for the release.

Other Items

• from POC_Conf._Call_10-18-11

• Fix dbxrefs for Fragaria annotations

• ABRC annotations to PO and TO terms: These are descriptions of mutant phenotypes from Arabidopsis stock center, based on free text descriptions

• Links to images on PlantSystematics.org - Update? See notes above

Translations

Will need to update translations for PAE terms before release. Can JE generate a file (after we stop editing) that includes all terms without Spanish or Japanese translations?

icon for has_participant relation

We need an icon for the has_participant relation so it can be included in the upcoming release. According to discussion of POC_Conf._Call_1-31-12 we decided:

It would be good to relate the new icon visually to the reciprocal 'participates_in':

has_participant should be "hP" in a circle, (to distinguish it from has_part: Hp) and that a dark background with white letters is more visible

sent reminder after meeting on 3-13-12

• derives by manipulation from icon is present but not showing up in de browser?

Collaborative projects:

• Mapping of Flora of North America Glossary to PO terms:

See the collaborators page: Flora_of_North_America-_FNA

We now have id's for FNA terms. Can finish adding synonyms before this release. Still need to add new terms from the FNA list and create mapping file.

Are we okay with using these FNA ids? They are UUID and are very long and contain dashes (e.g., 40b5fa5d-a75b-49d8-8328-b4c28d54ea66). See antheridium (PO:0025125) on dev browser for an example of how it will look.

Where did this synonym go? It is still there, just doesn't show up in AmiGO.

RW is working on modifying a perl script from JE to insert FNA synonyms into the PO file. May needs some help from JE.

-What are the plans after this?

Once mappings are done, want to see how PO shows up in their data base. Show utility of PO for recovering descriptors from free text.

FNA is using natural language processing to map their descriptions to PO. We are starting with plant structures and later will add phenotype descriptors. We will start with leaf characters.

Will use PATO as it has terms available, and add PO terms as needed. Will also help show utility of PO to systematists.

-Others (These may be longer term than the next release):

• Linking ontology terms to character matrices using Morphobank.

wood development stages

Will move here from Items for future meetings after Monday.

Upcoming meetings and Presentations 2012:

Katherine Esau Research Symposium

Integrating Plant Structure with Function, Development and Evolution

Hosted by the Katherine Esau Fellowship Program,

Date and location: Thursday, March 29, 2012, 1002 Giedt Hall, UC Davis

Space is limited and registration will close at 5 pm on March 10th.

Organizer; Neelima Sinha (Sinha@ucdavis.edu) The PO will not take part this year, because the timing is too short. We will look at attending next year.

5th International Biocuration Conference

April 2-4, 2012, Washington DC

• Abstract was submitted and has been selected for a poster presentation.

See link: File:Abs Biocuration 2012 (LC 12-9-11).pdf

• LC is attending and is taking part in the BioCreative workshop

The early bird registration is now closed.

SPNHC 2012

Annual meeting of the Society for the Preservation of Natural History Collections

Yale University, New Haven Connecticut June 11-16, 2012

Any interest in making a PO presentation at this meeting? Perhaps RW and/or DWS could just go for the day of the presentation, since it is local (New Haven, CT).

The theme for the meeting is "Emerging Technology and Innovation in Natural History Collections Management" (focus on the tools, innovative methods and collaborations that will move the natural history collections community forward).

From PJ: If we can show progress in the FNA work or Morphobank yes we should

Crop Ontology Workshop

For more information see the wiki page: Crop_Ontology_Workshop_at_OSU,_2012

We are looking at the tentative dates of either: June 11-13th or Aug 6th to 8th

The focus of the workshop will be on mostly development stages and traits for the crop plants

Botany 2012

July 7 - 11, 2012 - Columbus, Ohio

• PO workshop for Sunday, July 8th

The organizer have listed it as a whole day workshop, but it is planned for a half day and will be changed on the schedule. Also need to correct link to abstract (currently goes to wrong abstract).

see: Botany 2012 workshops

Workshop goal will be to teach people (mostly botanists) how to access and use the PO, including how to send feedback, suggest new terms, etc.

PJ: suggest that we go there with a 'draft' version of the Plant Phenotype Ontology and show them how to use these in character matrices.

exhibitor's booth

We should also consider hosting an outreach booth.

Not a bad deal for non-profits: $500 for A 10 x 10 Booth Space at Botany 2012, and 2 complimentary registrations for the conference. (plus all the extras!)

• 2 months of Rotating Banner Ads in the online American Journal of Botany

• A Rotating Banner Ad in one edition of the online Plant Science Bulletin

• A Rotating Banner Ad on the Botany 2012 abstract submission site

• A Rotating Banner Ad on the 2012 Conference Registration site.

PJ will check with Gramene and Doreen Ware to see if they want to co-host a booth.

• Annotation wiki: JP may also give a talk on the new annotation wiki at this meeting, as part of the genomics section.

Bio-Ontologies SIG 2012

Where: July 13 - 14, 2012, Long Beach, CA. Co-located with ISMB 2012

When: Submissions Due: April 13th, 2012 (Fri)

See: Bio-Ontologies SIG 2012

Three types of submissions.

- Short papers, up to 4 pages. - Poster abstracts, up to 1 page. - Flash updates, up to 1 page

Successful papers will be presented at the Bio-Ontologies SIG.

Poster abstracts: time will be allocated during the 2 days for at least one poster session.

Flash updates are for short talks (5 min) giving the salient new developments on existing public ontologies. Authors of posters can also provide a flash update. Unsuccessful papers will automatically be considered for poster presentation.

ASPB Plant Biology 2012

July 20 - 24, 2012 - Plant Biology 2012, Austin, TX

Link to meeting page: ASPB2012

Abstract was submitted for submission for minisymposia consideration.

Joint workshop is planned with PO, Gramene and TAIR

Registration is open, early Bird Registration: by May 11

Advance Discounted: May 12-June 15

ICBO 2012

International Conference on Biomedical Ontologies (ICBO 2012), July 22nd-25th, Graz, Austria

co-located with the 7th International Conference on Formal Ontologies in Information Systems (FOIS 2012)

RW and BS (with JE, AG, DWS and PJ) submitted a short paper describing a plant disease extension of the Infectious Disease Ontology. This paper was accepted and is being revised. Wiki page for notes on Plant Disease Ontology.

Relevant dates

• Feb. 28th, 2012: Notification of paper acceptance
• April 15th, 2012: Poster, early career symposium, software demonstrations and workshop papers submission deadline
• May 15th, 2012: Notification of poster, early career symposium, software demonstrations and workshop paper acceptance
• June 30th 2012: Deadline for all camera-ready copies for the proceedings

RW is working on an abstract summarizing the PO-FNA collaboration, with the folks from FNA. Will circulate soon. This will be either for a poster or a short talk in the Early Career Researcher session.

BS will be organizing an OBO Foundry meeting the afternoon of the day before the conference starts