POC Conf. Call 7-31-12

POC meeting, Webex Conference Call; Date: Tuesday July 31st, 2012 10am PDT/1pm EDT

In attendance:

POC members:

Absent:

Collaborators: none

Any changes or corrections (additions/deletions, etc) needed in the minutes from the POC_Conf._Call_7-3-12?

Back to POC Meetings Minutes

Meeting reports

ICBO 2012

Disease ontology

RW presented a paper on a plant disease extension of the Infectious Disease Ontology (IDOplant). The paper was well received, and there was a lot of discussion (after the talk) about how to model disease symptoms. The IDOplant manuscript defined "plant disase symptom", but did not include a term for it in the ontology. The Ontology for General Medical Science (OGMS) is planning to remove their term for symptom, for similar reasons -- a symptom can really be anything.

Symptoms should be modeled as dispositions. An infectious disease is a disposition, which is borne by some plant and has as a material basis some infectious disorder. As a result of having the infection, that plant also bears the disposition to undergo certain processes, which may lead to measurable/observable changes in the plant. For example, infection by a particular microbe results in the disposition to lose chlorophyll, which may lead to yellow leaves. Of course, the mechanisms could be modeled in even more detail, for example, at the molecular level. As dispositions, symptoms or signs are mechanistically linked to a disease, but it is never stated that every instance of the disease course will display a particular symptom. This way of modeling diseases and symptoms requires that we think carefully about the processes involved in a disease course, which is what we will need if we want to use ontologies to learn something new about diseases.

New tools for ontology editing

RW attended an OBI workshop while at IBCO. This included presentation of some of the tools being developed by Oliver He's lab. These may be of general interest to the PO curators.

• Ontobee: A web server aimed to facilitate ontology visualization, query, and development. This is already familiar to many people in the ontology community.
• Ontofox: An easy-to-use web-based tool for importing ontology terms using the MIREOT process.
• Ontodog: A web-based tool for generating community views of ontologies. Allows users to create subsets of an ontology with their own preferred term names. This could be very helpful for PO users who represent specific parts of the plant science community. RW: I haven't tried this one yet, so not sure how easy it is to use.

ASPB 2012

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

Link to meeting page: ASPB2012

Helped organize an Outreach booth- ASPB Plant Biology 2012 along with Gramene, TAIR, BAR, iPlant,

Plant Informatics Workshop is planned with TAIR, Gramene and PO : Saturday, July 21, 2012, 7:30 PM - 9:00 PM

LC is attending

Upcoming meetings and Presentations 2012:

Anatomy Ontology Course at NESCent, July 30th- Aug 3rd, 2012

Link to: Anatomy Ontology course

from Paula Mabee: Opening are available the Anatomy Ontology course.

Link to Course materials

This course aims to teach proper ontology design principles and practices such that anatomical interoperability across evolutionarily disparate taxa is achieved. It further seeks to promote community growth and adoption of ontology-based methods and tools. The subsequent benefit is in the form of shared access to the unique data store of each community (e.g. genetic, genomic, developmental, and evolutionary data).

Apply here: [1]

LM will be attending

Online Ontology Workshops at The University at Buffalo

The University at Buffalo is pleased to announce two on-line tutorials in ontology:

1. Introduction to Protégé for absolute beginners:

Saturday and Sunday, August 11-12, 2012.

Faculty: Ron Rudnicki (CUBRC, Buffalo), Alan Ruttenberg (University at Buffalo), Barry Smith (University at Buffalo)

This course will provide an introduction to the Protégé 4.2 ontology editor. It will begin with a brief introduction to ontology building, and to the use and importance of ontologies. This will be followed by an introduction to the Web Ontology Language (OWL). The bulk of the course will consist of an interactive introduction to the use of Protégé in building an ontology. No background in the use of computer languages and programming is presupposed. All sessions will be highly interactive.

2. Basic Formal Ontology 2.0

Saturday and Sunday, August 18-19, 2012

Faculty: Alan Ruttenberg and Barry Smith (University at Buffalo)

Basic Formal Ontology is currently being used by over 100 ontology-based research projects in biomedical informatics and increasingly in other fields. The tutorial will provide an introduction to the content and use of BFO in ontology development. Participants will acquire knowledge of the ontology and of its use as top-level ontology in multiple ontology development projects in a variety of fields. They will learn about the most recent developments in the new version 2.0 of the BFO ontology, including new formalizations of BFO in first-order logic and in OWL.

Both tutorials are also open for face-to-face participation.

PO/TO Crop Annotation Workshop at OSU

For more information see the wiki page: Plant_Ontology_and_Crop_Annotation_Workshop_OSU_2012

Dates: Sept. 13-15th

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

Next meeting scheduled for Tuesday, Aug 14th, 2012 at 10am PDT/1pm EDT

See: POC_Conf._Call_8-14-12