Mar 1st, 2016 Ontology Working Group Meeting: Difference between revisions

From Planteome.org
Jump to navigation Jump to search
No edit summary
Line 8: Line 8:


==Agenda:==
==Agenda:==
=== 1. recent updates on the TO ===
=== 1. Recent updates on the TO ===
* revisions to equivalence axioms- ''occurs_in'' and ''composition''
* revisions to equivalence axioms- ''occurs_in'' and ''composition''
* Stem and culm
* Stem and culm
Line 24: Line 24:
=== 3. Update on AmiGO APIs- Justin Elser ===
=== 3. Update on AmiGO APIs- Justin Elser ===


=== Visit to IRRI===
=== 4. Visit to IRRI===
* Leo, Marie-Angelique and Austin will visit IRRI Monday March 7th to Friday March 11th
* Leo, Marie-Angelique and Austin will visit IRRI Monday March 7th to Friday March 11th
* Goals: TD revision and data annotation-  
* Goals: TD revision and data annotation-  
Line 33: Line 33:
* EA- the need for an annotation tool: "We discussed the visit of Marie, Léo and Austin and the agenda we prepared. I indicated Mau that the team would like to see how IRRI data annotations could go on Planteome. Mau asked where Planteome stands with the annotations tools because this what IRRI is waiting for long. Would you have any points you want the team to share with IRRI on that aspect?"
* EA- the need for an annotation tool: "We discussed the visit of Marie, Léo and Austin and the agenda we prepared. I indicated Mau that the team would like to see how IRRI data annotations could go on Planteome. Mau asked where Planteome stands with the annotations tools because this what IRRI is waiting for long. Would you have any points you want the team to share with IRRI on that aspect?"
* MAL/LV: "We need a simple tool that scientists will be able to use to easily annotate their data. Adhoc scripts are short term and one-shot solutions that will serve Planteome but not necessarily serve IRRI because: The GAF2 format that amiGO2 requires is not known by the breeding community and the annotated data will be published on Planteome and not in the IRRI information systems. We should take the opportunity of being at IRRI to provide some guidance on how to include the ontologies in their data model. Annotating the data at the source is beneficial for everyone. IRRI information systems will have interoperable and discoverable data. And Planteome can easily add future annotations from the IRRI systems."
* MAL/LV: "We need a simple tool that scientists will be able to use to easily annotate their data. Adhoc scripts are short term and one-shot solutions that will serve Planteome but not necessarily serve IRRI because: The GAF2 format that amiGO2 requires is not known by the breeding community and the annotated data will be published on Planteome and not in the IRRI information systems. We should take the opportunity of being at IRRI to provide some guidance on how to include the ontologies in their data model. Annotating the data at the source is beneficial for everyone. IRRI information systems will have interoperable and discoverable data. And Planteome can easily add future annotations from the IRRI systems."


==[http://www.phenotypercn.org/?page_id=2750 Phenotype RCN meeting February 26-28, 2016] ==
==[http://www.phenotypercn.org/?page_id=2750 Phenotype RCN meeting February 26-28, 2016] ==

Revision as of 22:04, 29 February 2016

Planteome Ontology WG Zoom Meeting

  • Date: Tuesday Mar. 1st, 2016
  • Time: 8:15am PST (GMT-8)
  • Connection details: Join from PC, Mac, Linux, iOS or Android: https://zoom.us/j/762470789
  • Links to recordings:
  • Attendees:

Agenda:

1. Recent updates on the TO

  • revisions to equivalence axioms- occurs_in and composition
  • Stem and culm
  • anther morphology traits, incl. anther number
  • biochemical branch

2. Changes and updates in the CO files

  • rice
  • cassava
  • lentil
  • newly mapped and added- wheat--- TBA


3. Update on AmiGO APIs- Justin Elser

4. Visit to IRRI

  • Leo, Marie-Angelique and Austin will visit IRRI Monday March 7th to Friday March 11th
  • Goals: TD revision and data annotation-
    • MAL, and Leo will be working on trait dictionary
    • AM: annotate 140K+ germplasm entries with PD and TO mapping data

Discussion from email:

  • EA- the need for an annotation tool: "We discussed the visit of Marie, Léo and Austin and the agenda we prepared. I indicated Mau that the team would like to see how IRRI data annotations could go on Planteome. Mau asked where Planteome stands with the annotations tools because this what IRRI is waiting for long. Would you have any points you want the team to share with IRRI on that aspect?"
  • MAL/LV: "We need a simple tool that scientists will be able to use to easily annotate their data. Adhoc scripts are short term and one-shot solutions that will serve Planteome but not necessarily serve IRRI because: The GAF2 format that amiGO2 requires is not known by the breeding community and the annotated data will be published on Planteome and not in the IRRI information systems. We should take the opportunity of being at IRRI to provide some guidance on how to include the ontologies in their data model. Annotating the data at the source is beneficial for everyone. IRRI information systems will have interoperable and discoverable data. And Planteome can easily add future annotations from the IRRI systems."

Phenotype RCN meeting February 26-28, 2016

  • PJ attended

Status of second year funding

  • Bioversity is getting impatient, PJ will follow up with NSF and find out

Upcoming Meetings and Workshops

Biocuration 2016, April 10th-14th,2016; Geneva, Switzerland

GARNet/Egenis Workshop: Integrating Large Data into Plant Science, April 21st-22nd 2016, Dartington Hall, Totnes, Devon

  • Elizabeth and George are going, EA will present Planteome as part of her talk

Meeting in Montpellier, May 2016- website??

BioOntologies SIG of the Intelligent Systems for Molecular Biology (ISMB); July 8-12, 2016, Orlando, Florida

  • Dates: July 8th and 9th, with July 9th being the “Phenotype Day”, focused on the systematic description of phenotypes.
    • Short papers, up to 4 pages (will be published in JBMS)
    • Poster abstracts, up to 1 page
    • Flash updates, up to 1 page

7th International Conference on Biological Ontology and BioCreative 2016 Aug 1st to 4th, Corvallis, OR

Retrieved from "https://wiki.planteome.org/index.php?title=Mar_1st,_2016_Ontology_Working_Group_Meeting&oldid=2542"