Difference between revisions of "Botany 2012 PO workshop planning page"
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How to navigate the PO website: | How to navigate the PO website: | ||
*browse - tree view, graph view, icons, annotation data | *browse - tree view, graph view, icons, annotation data | ||
| − | ''[http://plantontology.org/amigo_user_guide/index.html | + | ''[http://plantontology.org/amigo_user_guide/index.html Browser users' guide] has been updated and a link it was added to the "docs" page.'' |
''A brochure will also be available to participants.'' | ''A brochure will also be available to participants.'' | ||
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*search - for terms, for annotations, advanced search | *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) | + | *downloading and working with files - ontology file and annotation file (only if people want to be able to do this) [http://www.plantontology.org/download/download.html Download page] |
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=Links= | =Links= | ||
| + | Plant Ontology [http://plantontology.org/amigo_user_guide/index.html browser users' guide]. Help on how to navigate the PO AmiGO browser. | ||
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| + | The [http://www.plantontology.org/download/svn_doc.html developers guide to SVN] provides instructions on how to check out a copy of the PO's SVN repository. For individual users, it is probably easier to just download a copy of the file you want directly from the [http://palea.cgrb.oregonstate.edu/viewsvn/Poc/ PO SVN site]. | ||
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| + | You can download the latest version of the PO in OBOF, OWL, or table format from our [http://www.plantontology.org/download/download.html download page]. | ||
Revision as of 19:11, 3 July 2012
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. Anyone who wants to contribute annotation files should contact Lol directly. See Annotation_Association_File_Format.
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
- Pass around sign-up sheet for po-announce mailing list.
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. Annotation data made available through the Plant Ontology
-What is an annotation?
-How are annotation files generated?
-How to access existing annotations.
10:00 - 10:45 Hands-on tutorials
How to navigate the PO website:
- browse - tree view, graph view, icons, annotation data
Browser users' guide has been updated and a link it was added to the "docs" page.
A brochure will also be available to participants.
- 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) Download page
Tutorials are still out of date.
10:45 - 11:00 Break and re-assessment of needs
11:00 - 11:30 PO and images
- Presenation of CUPAC images: How PO terms can be used to annotate diverse anatomical data. Show how the ontology applies across species.
- Image markup software: SIA demonstration.
11:30 - 11:50 Flexible time
Will continue hands-on tutorials if needed, or have a discussion of ontology terms
11:50 - 12:00 Wrap up
Links
Plant Ontology browser users' guide. Help on how to navigate the PO AmiGO browser.
The developers guide to SVN provides instructions on how to check out a copy of the PO's SVN repository. For individual users, it is probably easier to just download a copy of the file you want directly from the PO SVN site.
You can download the latest version of the PO in OBOF, OWL, or table format from our download page.
