Difference between revisions of "Botany 2012 PO workshop planning page"
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==9:00 - 9:30 Introductions and assessing needs and interests of participants== | ==9:00 - 9:30 Introductions and assessing needs and interests of participants== | ||
| − | *Introduction of | + | *Introduction of [[Plant Ontology curators]] (Dennis and Ramona, plus those who are not present) |
*Introduction of attendees: Name, affiliation, why attending this workshop, requests | *Introduction of attendees: Name, affiliation, why attending this workshop, requests | ||
*Pass around sign-up sheet for po-announce mailing list. | *Pass around sign-up sheet for po-announce mailing list. | ||
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1. What is the Plant Ontology and what is it for? | 1. What is the Plant Ontology and what is it for? | ||
| − | 2. How the Plant Ontology is structured: | + | 2. How the Plant Ontology is structured: anatomical entities and development stages |
3. Plant Ontology relations and definitions | 3. Plant Ontology relations and definitions | ||
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[http://www.plantontology.org/download/download.html Download page] | [http://www.plantontology.org/download/download.html Download page] | ||
| − | [http://palea.cgrb.oregonstate.edu/viewsvn/Poc/trunk/associations/ | + | Association files as spread sheets, [http://palea.cgrb.oregonstate.edu/viewsvn/Poc/trunk/associations/ from SVN] |
===Working with annotation files=== | ===Working with annotation files=== | ||
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**Original terminology: http://www.maizegdb.org/cgi-bin/displayrefrecord.cgi?id=9021423 | **Original terminology: http://www.maizegdb.org/cgi-bin/displayrefrecord.cgi?id=9021423 | ||
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*How to create an annotation file (''with help from [http://phenote.org/ Phenote], if there is interest''). | *How to create an annotation file (''with help from [http://phenote.org/ Phenote], if there is interest''). | ||
Latest revision as of 11:13, 8 July 2012
This page has a tinyurl: http://tinyurl.com/PO-Botany2012
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 us directly. See also Annotation_Association_File_Format.
Agenda
This will be flexible, depending on participant's needs. We do not anticipate using the full three hours.
9:00 - 9:30 Introductions and assessing needs and interests of participants
- Introduction of Plant Ontology curators (Dennis 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
- What is an ontology and what is it for?
- The bio-ontologies landscape
- Open Biomedical Ontologies (OBO) Foundry
- National Center for Biomedical Ontology (NCBO) and its Bioportal
Intro to the PO
1. What is the Plant Ontology and what is it for?
2. How the Plant Ontology is structured: anatomical entities 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
- browse - tree view, graph view, icons, annotation data
A brochure is also be available for participants. (Media:PO_users_guide_brochure.pdf)
- search - for terms, for annotations, advanced search
- downloading and working with files - ontology file and annotation files (only if people want to be able to do this)
Association files as spread sheets, from SVN
Working with annotation files
- Annotation_Association_File_Format
- Example: Maize expression data set from Sekhon et al.
- Original terminology: http://www.maizegdb.org/cgi-bin/displayrefrecord.cgi?id=9021423
- How to create an annotation file (with help from Phenote, if there is interest).
10:45 - 11:00 Break and re-assessment of needs
11:00 - 11:30 PO and images
- Presentation of CUPAC images: How PO terms can be used to annotate diverse anatomical data from across all plant species.
- Image markup software: SIA demonstration.
11:30 - 11:50 Flexible time
Will continue hands-on tutorials if needed, or have a discussion.
11:50 - 12:00 Wrap up
Links
A slide show with an [http://plantontology.org/docs/presentations/demo/poc-demo-1.html introduction to the Plant Ontology}.
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.
