Botany 2012 PO workshop planning page

This page is for internal use, for preparing for the PO workshop at the Botany 2012 meeting.

For a description of the workshop, see Plant Ontology Workshop, Botany 2012.

Topics

• Introductions of presenters and participants
  • determine participants' needs and interests
• Brief introduction to the principles and content of the PO.
• Tutorial on how to access the various resources available through the PO website:
  • how to navigate the website
  • how to interpret an ontology (including relations, definitions, and external references)
  • how to browse or search for ontology terms or annotations
  • how to submit feedback (including requests for new terms or revised definitions)
  • how to download and work with ontology and annotation files.
• Discussion of ontology terms and definitions
• Supplemental: Instruction will be available on how to generate association files for genomic projects interested in contributing and maintaining new PO annotations. Do we have any material available for this?

Agenda

This will be flexible, depending on participant's needs.

9:00 - 9:30 Introductions and assessing needs and interests of participants

• Introduction of PO curators (Dennis, Ale, and Ramona, plus those who are not present)
• Introduction of attendees: Name, affiliation, why attending this workshop, requests

9:30 - 10:00 Introduction to ontologies and to the PO

Intro to ontologies

1. What is an ontology and what is it for?

2. Ontology success stories in the life sciences

3. The bio-ontologies landscape

• Open Biomedical Ontologies (OBO) Foundry
• National Center for Biomedical Ontology (NCBO) and its Bioportal
• Ontologies and the Semantic Web

Intro to the PO

1. What is the Plant Ontology and what is it for?

2. How the Plant Ontology is structured: anatomy and development stages

3. Plant Ontology relations and definitions

4. Neighboring ontologies of the PO: Traits (TO) and Phenotypes (PATO)

5. Different types of plant data made available through the Plant Ontology

10:00 - 10:45 Hands-on tutorials

How to navigate the PO website:

• browse - tree view, graph view, icons, annotation data

Need to update images on browser users' guide: http://plantontology.org/amigo_user_guide/index.html#intro

We also need a link to this page from the "docs" page.

• search - for terms, for annotations, advanced search

• downloading and working with files - ontology file and annotation file (only if people want to be able to do this)

Need to correct spelling mistake and remove DagEdit, put in links to OBOEdit: http://www.plantontology.org/download/svn_doc.html Developers guide

Need to fix download page: http://www.plantontology.org/download/download.html, but only if PJ allows us to get rid of the out of date tables. Otherwise, it is functional.

Need to update tutorials.

Other hi-priority pages to fix:

• http://plantontology.org/docs/otherdocs/principles_rationales.html - Out of date.
• http://plantontology.org/docs/growth/growth_stages.html - Out of date. Should merge with page for development stages.
• http://plantontology.org/docs/faq/growth_faq.html - Out of date. Should merge with page for development stages.
• http://plantontology.org/docs/development/developmental_stages.html - Out of date. Should merge with page for growth stages.

• http://plantontology.org/docs/otherdocs/ontology_doc.html Developers' guide. Content is not too bad, but this should be only on the wiki, and not on the web page since it is only for developers -- most users never need to see this.

11:00 - 11:30 PO and images

• CUPAC images and PO terms
• SIA demonstration

11:30 - 11:50 Flexible time

Will continue hands-on tutorials if needed, or have a discussion of ontology terms