Jan 21st, 2016 Ontology Working Group Meeting
Planteome Ontology WG Zoom Meeting
- Date: Thursday Jan. 21st, 2016
- Time: 8:15am PST (GMT-8)
- Connection details: Join from PC, Mac, Linux, iOS or Android: Join from PC, Mac, Linux, iOS or Android: https://zoom.us/j/757453328
- Attendees: LC, AM, JE, PJ, EA, MAL, BS, GG.
File:Ontology WG Meeting 1-21-2016 video.mp4
File:Ontology WG Meeting 1-21-2016 audio.m4a
Report on PAG 2016
- strong emphasis on high throughput phenotyping, machine learning is hot right now
- data standardization, field scale measurements
- Utilization of ontologies for data annotation
- everyone wants specialized ontologies for THEIR data, not something predefined
- we need to demonstrate how ontologies are useful.
Planteome Collaborators Workshop Monday Jan 11th
- http://planteome.org/outreach/workshops/PAG_2016
- Goals of the Meeting:
- Introduce the Planteome project and launch Planteome 1.0 beta
- Provide an update on the progress of the collaboration with the Crop Ontology to map crop-specific trait dictionaries to the Reference Trait Ontology
- Provide a summary report and overview of the Planteome Curators Workshop, held Nov 2015 in Corvallis, OR
- Engage Planteome collaborators and the plant genomics community by demonstrating use cases of data annotation for rice, cassava and lentils
- Seek engagement of the plant genomics community through tools and applications to integrate into your workflow
- Who attended?
- 29 attendees (link to spreadsheet: Participants list CO-Planteome Meeting PAG 2016)
- Representatives from: CG centers (IITA, CIP, CIMMYT, IRRI) and Bioversity; INRA, IRD, LIRMM, USDA-ARS databases (SoyBase, MaizeGDB, GDR, PeanutBase, LegumeInfo), EBI, Transplant, ELIXIR Consortium, Rothamsted Research.
Comments and feedback
- People are concerned about the GAF2 format, but hopefully it will be expanding to more than 16 columns- modification of the GAF2 format
- we will develop standards for conversion to GAF2
Data download functionality on the browser needs to be refined
- PJ: Suggest to have the column headings displayed- that would help people (JE open issue @ column headings)
- Modification and customization of the fields for download ( open issue @)
- figure out what format people want to download data in, allow for download in this format
- GeneBanks use the MCPD format (?)
- Need a few use-cases for questions that researchers will be trying to answer
Update on browsers
- Main Planteome website: http://planteome.org/
- drupal front pages and AmiGO2 browser serving ontologies and annotation data
- Development site: http://dev.planteome.org/amigo
- Currently just ontology files but can also load annotations on there to test
- loads nightly with all the ontologies
Issues being sorted out:
- Many of our relations are not being recognized and displayed in AmiGO 2.0 (https://github.com/Planteome/planteome-ontology-browsers/issues/20)
- only showing up- is_a, part_of and occurs_in; this is an issues for the Gene Ontology as well
- Gene Ontology tracker:
- Synonym scopes are not being displayed- all the broad, narrow, related and exact synonyms are being lumped together- (https://github.com/Planteome/planteome-ontology-browsers/issues/17)
From MAL:
- The CO terms are showing up as subclasses, but they get confused with other things that are subclasses
- Perhaps they should be 'taxonomic equivalents' AND subclasses; perhaps you can have double-relationships??? (Suggestion from BS)
- Perhaps color coding in combination with changing CO_### to the correct name
- Visualization: Need a better way to view trees.
- Choices now are OLS-vis, or the static .png display
- OLS-Vis tool (http://ols.wordvis.com/)- pulls all the ontologies from the urls
- Could this be modified to display the planteome ones specifically on our browser??