Difference between revisions of "PAG 2012 Ontology workshop"
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| − | + | =PAG 2012 Ontology workshop= | |
| − | + | Link to workshop page on PAG site: [http://pag.confex.com/pag/xx/webprogrampreliminary/Session1272.html Use of Ontologies for Organizing Plant and Animal Genomics Data] | |
| + | Organizers: | ||
| + | Laurel Cooper (Oregon State University) and Pankaj Jaiswal(Oregon State University) | ||
| + | Date: Saturday, January 14, 2012, Time: 10:20 AM-12:30 PM | ||
| − | |||
| − | + | 10:20 AM '''Introductory Remarks: Pankaj Jaiswal''' | |
| + | |||
| + | |||
| + | 10:25 AM W732 '''"GO and PO Facilitate Integration and Mining of Arabidopsis Data"''' | ||
| + | |||
| + | Eva Huala, [http://www.arabidopsis.org/ TAIR] Carnegie Institution for Science | ||
| + | |||
| + | |||
| + | 10:45 AM W733 '''"Protein Ontology (PRO) for integration of knowledge on proteins, complexes and PTMs"''' | ||
| + | |||
| + | Cathy H. Wu, University of Delaware, [http://pir.georgetown.edu/pirwww/index.shtml PIR] | ||
| + | |||
| + | |||
| + | 11:05 AM W734 '''"Expanding the Plant Ontology: Linking Plant Anatomy and Development to Genomics Across Plant Taxa"''' | ||
| + | |||
| + | Laurel Cooper, Oregon State University | ||
| + | |||
| + | |||
| + | 11:25 AM W735 '''"B73 Maize Gene Expression Atlas – a Plant Ontology Use Case"''' | ||
| + | |||
| + | Mary Schaeffer, USDA-ARS and University of Missouri, [http://www.maizegdb.org/ MaizeGDB] | ||
| + | |||
| + | 11:45 AM W736 '''"NCBO Web Services and Development of Semantic Applications"''' | ||
| + | Trish Whetzel, [http://www.bioontology.org/ The National Center for Biomedical Ontology] | ||
| − | |||
| − | + | ==Panel Discussion== | |
| − | + | Questions and discussion: | |
| − | + | There was interest arising from the Eva's presentation regarding their work on developing Journal collaborations for annotations. Since 2008 they now have working with Journals to have authors annotate their own research material as part of the submission process. This started in 2008 with Plant Physiology and now includes about 8 or 10 journals. This started as an excel spreadsheet, but they now have an online submission form. **Currently this does not include PO annotations (this was one of the questions that was asked). | |
| − | |||
| − | + | Once the information is received it is reviewed by the TAIR curator teams. | |
| − | =Suggestions for speakers:= | + | ==Suggestions for speakers for next year:== |
| + | Should have talks from people working on ontology applications, rather than ontology development, to show utility. | ||
| − | + | Procedure: LC should contact potential speakers and ask them to submit an abstract to us and to the organizers. | |
==Text mining applications: TextPresso== | ==Text mining applications: TextPresso== | ||
| Line 34: | Line 58: | ||
[http://www.textpresso.org/arabidopsis/ Arabidopsis] | [http://www.textpresso.org/arabidopsis/ Arabidopsis] | ||
| + | |||
| + | See the article from [http://www.hhmi.org/news/sternberg2.html HHMI] | ||
==Phenolog== | ==Phenolog== | ||
| − | == | + | ==Someone from Grape Genome Initiative?== |
| + | They are featuring both PO and GO on their [http://genomes.cribi.unipd.it/cgi-bin/pqs2/query.pl?release=v1#Ontologies Genome Browser Query page]. We are working to add annotations from them as well to our database. | ||
| + | |||
| + | They also have a workshop: Date: Sunday, January 15, 2012, 1:30 PM-3:40 PM, | ||
| + | |||
| + | Organizer: Grant Cramer (University of Nevada, Reno) | ||
Latest revision as of 18:50, 25 January 2012
PAG 2012 Ontology workshop
Link to workshop page on PAG site: Use of Ontologies for Organizing Plant and Animal Genomics Data
Organizers: Laurel Cooper (Oregon State University) and Pankaj Jaiswal(Oregon State University)
Date: Saturday, January 14, 2012, Time: 10:20 AM-12:30 PM
10:20 AM Introductory Remarks: Pankaj Jaiswal
10:25 AM W732 "GO and PO Facilitate Integration and Mining of Arabidopsis Data"
Eva Huala, TAIR Carnegie Institution for Science
10:45 AM W733 "Protein Ontology (PRO) for integration of knowledge on proteins, complexes and PTMs"
Cathy H. Wu, University of Delaware, PIR
11:05 AM W734 "Expanding the Plant Ontology: Linking Plant Anatomy and Development to Genomics Across Plant Taxa"
Laurel Cooper, Oregon State University
11:25 AM W735 "B73 Maize Gene Expression Atlas – a Plant Ontology Use Case"
Mary Schaeffer, USDA-ARS and University of Missouri, MaizeGDB
11:45 AM W736 "NCBO Web Services and Development of Semantic Applications"
Trish Whetzel, The National Center for Biomedical Ontology
Panel Discussion
Questions and discussion: There was interest arising from the Eva's presentation regarding their work on developing Journal collaborations for annotations. Since 2008 they now have working with Journals to have authors annotate their own research material as part of the submission process. This started in 2008 with Plant Physiology and now includes about 8 or 10 journals. This started as an excel spreadsheet, but they now have an online submission form. **Currently this does not include PO annotations (this was one of the questions that was asked).
Once the information is received it is reviewed by the TAIR curator teams.
Suggestions for speakers for next year:
Should have talks from people working on ontology applications, rather than ontology development, to show utility.
Procedure: LC should contact potential speakers and ask them to submit an abstract to us and to the organizers.
Text mining applications: TextPresso
Main Page: TextPresso
See the article from HHMI
Phenolog
Someone from Grape Genome Initiative?
They are featuring both PO and GO on their Genome Browser Query page. We are working to add annotations from them as well to our database.
They also have a workshop: Date: Sunday, January 15, 2012, 1:30 PM-3:40 PM,
Organizer: Grant Cramer (University of Nevada, Reno)
