Difference between revisions of "Botany 2012 PO workshop planning page"

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This page is for internal use, for preparing for the PO workshop at the Botany 2012 meeting.
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This page has a tinyurl: http://tinyurl.com/PO-Botany2012
  
 
For a description of the workshop, see [[Plant Ontology Workshop, Botany 2012]].
 
For a description of the workshop, see [[Plant Ontology Workshop, Botany 2012]].
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**how to download and work with ontology and annotation files.  
 
**how to download and work with ontology and annotation files.  
 
*Discussion of ontology terms and definitions
 
*Discussion of ontology terms and definitions
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*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?'''
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*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 [http://plantontology.org/db/feedback/send_feedback?refer_to=/ contact us] directly. See also [[Annotation_Association_File_Format]].''
  
 
=Agenda=
 
=Agenda=
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''This will be flexible, depending on participant's needs.''
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''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==
 
==9:00 - 9:30 Introductions and assessing needs and interests of participants==
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*Introduction of PO curators (Dennis, Ale, and Ramona, plus those who are not present)
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*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
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*Pass around sign-up sheet for po-announce mailing list.
  
 
==9:30 - 10:00 Introduction to ontologies and to the PO==
 
==9:30 - 10:00 Introduction to ontologies and to the PO==
 
===Intro to ontologies===
 
===Intro to ontologies===
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1. What is an ontology and what is it for?
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* What is an ontology and what is it for?
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2. Ontology success stories in the life sciences
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*The bio-ontologies landscape
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3. The bio-ontologies landscape
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**Open Biomedical Ontologies (OBO) Foundry
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*Open Biomedical Ontologies (OBO) Foundry
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**National Center for Biomedical Ontology (NCBO) and its Bioportal
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*National Center for Biomedical Ontology (NCBO) and its Bioportal
 
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*Ontologies and the Semantic Web
 
  
 
===Intro to the PO===
 
===Intro to the PO===
 
1. What is the Plant Ontology and what is it for?
 
1. What is the Plant Ontology and what is it for?
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2. How the Plant Ontology is structured: anatomy and development stages
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2. How the Plant Ontology is structured: anatomical entities and development stages
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3. Plant Ontology relations and definitions
 
3. Plant Ontology relations and definitions
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4. Neighboring ontologies of the PO: Traits (TO) and Phenotypes (PATO)
 
4. Neighboring ontologies of the PO: Traits (TO) and Phenotypes (PATO)
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5. Different types of plant data made available through the Plant Ontology
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5. Annotation data made available through the Plant Ontology
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-What is an annotation?
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 +
-How are annotation files generated?
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-How to access existing annotations.
  
 
==10:00 - 10:45 Hands-on tutorials==
 
==10:00 - 10:45 Hands-on tutorials==
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How to navigate the PO website:
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===How to navigate the PO website===
 
*browse - tree view, graph view, icons, annotation data
 
*browse - tree view, graph view, icons, annotation data
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''Need to update images on browser users' guide: http://plantontology.org/amigo_user_guide/index.html#intro''
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[http://plantontology.org/amigo_user_guide/index.html Browser users' guide]
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A brochure is also be available for participants. ([[Media:PO_users_guide_brochure.pdf]])
  
 
*search - for terms, for annotations, advanced search
 
*search - for terms, for annotations, advanced search
  
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*downloading and working with files - ontology file and annotation file (only if people want to be able to do this)
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*downloading and working with files - ontology file and annotation files (only if people want to be able to do this)  
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''Need to correct spelling mistake and remove DagEdit, put in links to OBOEdit: http://www.plantontology.org/download/svn_doc.html Developers guide''
 
  
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''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.''
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[http://www.plantontology.org/download/download.html Download page]
  
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Association files as spread sheets, [http://palea.cgrb.oregonstate.edu/viewsvn/Poc/trunk/associations/ from SVN]
  
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===Working with annotation files===
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*[[Annotation_Association_File_Format]]
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*Example: Maize expression data set from Sekhon et al.
  
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''Need to update tutorials.''
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**Original terminology: http://www.maizegdb.org/cgi-bin/displayrefrecord.cgi?id=9021423
  
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Other hi-priority pages to fix:
 
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*http://plantontology.org/docs/otherdocs/principles_rationales.html - Out of date.
 
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*http://plantontology.org/docs/growth/growth_stages.html - Out of date. Should merge with page for development stages.
 
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*http://plantontology.org/docs/faq/growth_faq.html - Out of date. Should merge with page for development stages.
 
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*http://plantontology.org/docs/development/developmental_stages.html - Out of date. Should merge with page for growth stages.
 
  
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*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.
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*How to create an annotation file (''with help from [http://phenote.org/ Phenote], if there is interest'').
  
 
==10:45 - 11:00 Break and re-assessment of needs==
 
==10:45 - 11:00 Break and re-assessment of needs==
  
 
==11:00 - 11:30 PO and images==
 
==11:00 - 11:30 PO and images==
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*CUPAC images and PO terms
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*Presentation of CUPAC images: How PO terms can be used to annotate diverse anatomical data from across all plant species.
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*SIA demonstration
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*Image markup software: SIA demonstration.
  
 
==11:30 - 11:50 Flexible time==
 
==11:30 - 11:50 Flexible time==
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Will continue hands-on tutorials if needed, or have a discussion of ontology terms
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Will continue hands-on tutorials if needed, or have a discussion.
  
 
==11:50 - 12:00 Wrap up==
 
==11:50 - 12:00 Wrap up==
  
 
=Links=
 
=Links=
 +
A slide show with an [http://plantontology.org/docs/presentations/demo/poc-demo-1.html introduction to the Plant Ontology}.
 +
 +
Plant Ontology [http://plantontology.org/amigo_user_guide/index.html browser users' guide]. Help on how to navigate the PO AmiGO browser.
 +
 +
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].
 +
 +
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].

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

How to navigate the PO website

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

Browser users' guide

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)

Download page

Association files as spread sheets, from SVN

Working with annotation files


  • 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.

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