Botany 2012 PO workshop planning page - Revision history

Rwalls: /* Working with annotation files */

2012-07-08T11:13:18Z

Working with annotation files

Rwalls: /* How to navigate the PO website */

2012-07-08T11:09:19Z

How to navigate the PO website

Rwalls: /* Intro to the PO */

2012-07-08T11:08:26Z

Intro to the PO

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

2012-07-08T03:37:58Z

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

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

2012-07-08T03:37:24Z

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

Rwalls: /* Topics */

2012-07-08T03:36:58Z

Topics

Rwalls: /* Working with annotation files */

2012-07-08T03:35:43Z

Working with annotation files

Rwalls at 03:24, 8 July 2012

2012-07-08T03:24:42Z

Rwalls: /* Agenda */

2012-07-08T03:11:58Z

Agenda

Rwalls: /* Agenda */

2012-07-08T02:59:49Z

Agenda

@@ Line 69: / Line 69: @@
 **Original terminology: http://www.maizegdb.org/cgi-bin/displayrefrecord.cgi?id=9021423
-**Mapped to PO terms:
 *How to create an annotation file (''with help from [http://phenote.org/ Phenote], if there is interest'').

@@ Line 62: / Line 62: @@
 [http://www.plantontology.org/download/download.html Download page]
-[http://palea.cgrb.oregonstate.edu/viewsvn/Poc/trunk/associations/ Association files as spread sheets, from SVN]
+Association files as spread sheets, [http://palea.cgrb.oregonstate.edu/viewsvn/Poc/trunk/associations/ from SVN]
 ===Working with annotation files===

@@ Line 34: / Line 34: @@
 . What is the Plant Ontology and what is it for?
-. How the Plant Ontology is structured: anatomy and development stages
+. How the Plant Ontology is structured: anatomical entities and development stages
 . Plant Ontology relations and definitions

@@ Line 20: / Line 20: @@
 ==9:00 - 9:30 Introductions and assessing needs and interests of participants==
-*Introduction of PO curators (Dennis and Ramona, plus those who are not present)
+*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.

@@ Line 20: / Line 20: @@
 ==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 PO 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.

@@ Line 14: / Line 14: @@
 **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]].''
+*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=

@@ Line 67: / Line 67: @@
 *[[Annotation_Association_File_Format]]
 *Example: Maize expression data set from Sekhon et al.
 *How to create an annotation file (''with help from [http://phenote.org/ Phenote], if there is interest'').

@@ Line 1: / Line 1: @@
-This page is for internal use, for preparing for the PO workshop at the Botany 2012 meeting.
+This page has a tinyurl: http://tinyurl.com/PO-Botany2012
 For a description of the workshop, see [[Plant Ontology Workshop, Botany 2012]].
@@ Line 58: / Line 58: @@
 *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) [http://www.plantontology.org/download/download.html Download page]
+*downloading and working with files - ontology file and annotation files (only if people want to be able to do this)
 ===Working with annotation files===

@@ Line 51: / Line 51: @@
 ===How to navigate the PO website===
 *browse - tree view, graph view, icons, annotation data
-A brochure is also be available for participants.
+[http://plantontology.org/amigo_user_guide/index.html Browser users' guide]
 *search - for terms, for annotations, advanced search
@@ Line 60: / Line 61: @@
 ===Working with annotation files===
-*Annotation file format
+*[[Annotation_Association_File_Format]]
 *Example: Maize expression data set from Sekhon et al.
-*How to create an annotation file (''with help from Phenote, if there is interest'').
+*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==

@@ Line 17: / Line 17: @@
 =Agenda=
-''This will be flexible, depending on participant's needs.''
+''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==
@@ Line 26: / Line 26: @@
 ==9:30 - 10:00 Introduction to ontologies and to the PO==
 ===Intro to ontologies===
-. What is an ontology and what is it for?
+* What is an ontology and what is it for?
+*The bio-ontologies landscape
-. Ontology success stories in the life sciences
+**Open Biomedical Ontologies (OBO) Foundry
+**National Center for Biomedical Ontology (NCBO) and its Bioportal
 ===Intro to the PO===
@@ Line 57: / Line 53: @@
 ''[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 (upload pdf) is also be available for participants.
+A brochure is also be available for participants.
 *search - for terms, for annotations, advanced search
@@ Line 66: / Line 62: @@
 *Annotation file format
 *Example: Maize expression data set from Sekhon et al.
-*How to create an annotation file with help from Phenote.
+*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==
-*Presenation of CUPAC images: How PO terms can be used to annotate diverse anatomical data. Show how the ontology applies across species.
+*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 of ontology terms
+Will continue hands-on tutorials if needed, or have a discussion.
 ==11:50 - 12:00 Wrap up==