Jan 21st, 2016 Ontology Working Group Meeting: Difference between revisions
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<big> Main Planteome website: http://planteome.org/</big> | <big> Main Planteome website: http://planteome.org/</big> | ||
* drupal front pages and AmiGO2 browser serving ontologies and annotation data | * drupal front pages and AmiGO2 browser serving ontologies and annotation data | ||
<big> Development site: http://dev.planteome.org/amigo</big> | <big> Development site: http://dev.planteome.org/amigo</big> | ||
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** loads nightly with all the ontologies | ** loads nightly with all the ontologies | ||
** would be good if it was a different color or if there was a banner to alert users that it is the dev site. '''Done''' | ** would be good if it was a different color or if there was a banner to alert users that it is the dev site. '''Done''' | ||
==Issues being sorted out:== | ==Issues being sorted out:== | ||
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From MAL: | From MAL: | ||
* '''The CO terms are showing up as subclasses, but they get confused with other things that are subclasses''' | * '''The CO terms are showing up as subclasses, but they get confused with other things that are subclasses'''- We need special relationship to link the CO and TO classes | ||
* Currently, the method_of, scale_of and variable_of relations are not being displayed- MAL will post a comment on the tracker: (https://github.com/Planteome/planteome-ontology-browsers/issues/20) | |||
** Perhaps they should be 'taxonomic equivalents' AND subclasses; perhaps you can have double-relationships??? (Suggestion from BS) | ** Perhaps they should be 'taxonomic equivalents' AND subclasses? ; perhaps you can have double-relationships??? (Suggestion from BS) | ||
''This requires further discussion'' | |||
* '''Suggestions for improving the display:''' | * '''Suggestions for improving the display:''' | ||
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** How could this be done? | ** How could this be done? | ||
* | |||
* The breeders and data managers from the CG centers will maintain their Trait Dictionaries (TDs), which should include the mappings | * Merged version of TO will contain all the mappings to the Crop specific ontologies, so they will not have to be loaded individually (From PJ) | ||
* MAL's script will convert from the TD to the | * The breeders and data managers from the CG centers will maintain their Trait Dictionaries (TDs), which should include the mappings to the TO | ||
* MAL's script will convert from the TD to the ontology file | |||
* We should work on creating and testing a merged version with cassava, rice and lentil | * We should work on creating and testing a merged version with cassava, rice and lentil | ||
* Visualization: need a better way to view the ontology trees | * '''Visualization: need a better way to view the ontology trees ''' | ||
** Choices now are OLS-vis, or the static .png display (note: OLS-Vis is currently only on the dev site) | ** Choices now are OLS-vis, or the static .png display (note: OLS-Vis is currently only on the dev site) | ||
** OLS-Vis tool (http://ols.wordvis.com/)- pulls all the ontologies from the urls, so it is the Release version. | ** OLS-Vis tool (http://ols.wordvis.com/)- pulls all the ontologies from the urls, so it is the Release version. | ||
** Could this be modified to display the planteome ones specifically on our browser?? | ** Could this be modified to display the planteome ones specifically on our browser?? ''Does not appear to be available for local install.'' | ||
==Trait vs descriptors- from EA- breeder terminology is important== | |||
* Descriptors (need to avoid this word), these are not traits | * Descriptors (need to avoid this word), these are not traits | ||
** Usually measured on a small number of plants, and locations, with no stress | ** Usually measured on a small number of plants, and locations, with no stress | ||
** qualitative scale, but may be converted to ??? | ** qualitative scale, but may be converted to ??? | ||
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** evaluation: happens at multiple times | ** evaluation: happens at multiple times | ||
==AberOWL- Georgios V. Gkoutos== | |||
* An ontology repository and semantic search engine- link to paper on PubMed: http://www.ncbi.nlm.nih.gov/pubmed/25627673 | * An ontology repository and semantic search engine- link to paper on PubMed: http://www.ncbi.nlm.nih.gov/pubmed/25627673 | ||
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* can use SPQL | * can use SPQL | ||
==Next meetings:== | |||
* need to break up the calls into: | * need to break up the calls into: | ||
** Ontology- Tuesday | ** Ontology- Tuesday Feb 2nd | ||
** technical things (mappings and such)?? | ** technical things (mappings and such)?? | ||
** Browser/annotation ?? | ** Browser/annotation ?? |
Latest revision as of 21:51, 7 February 2017
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 (as always)
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)
From JE: Can't really do it as the "download" is actually a direct query to the solr and can't add stuff to it. However, there is a "Gaf chunk download" button that should actually have the gaf format, but again for technical reasons, we can't add a header line to. But, that button currently doesn't work, and a ticket has been created for it. Apparently, that button is not used much as it is broken on their end as well: https://github.com/geneontology/amigo/issues/293
- 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 Planteome 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
- would be good if it was a different color or if there was a banner to alert users that it is the dev site. Done
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: https://github.com/geneontology/amigo/issues/220
- 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)
- Working with CM and Seth on resolving this. It may require us fixing it on our end
- Links to GitHub trackers are not functional-
- Need to add these as dbxrefs in the AmiGO file- AM will do
- CM has suggested going to using the url of the issue instead. LC will test, could write a script to implement this.
From MAL:
- The CO terms are showing up as subclasses, but they get confused with other things that are subclasses- We need special relationship to link the CO and TO classes
- Currently, the method_of, scale_of and variable_of relations are not being displayed- MAL will post a comment on the tracker: (https://github.com/Planteome/planteome-ontology-browsers/issues/20)
- Perhaps they should be 'taxonomic equivalents' AND subclasses? ; perhaps you can have double-relationships??? (Suggestion from BS)
This requires further discussion
- Suggestions for improving the display:
- Perhaps color coding in the graph
- Changing CO_### to the correct name- e.g. CO_334:0000432 Plant Height ---> lentil plant height
- How could this be done?
- Merged version of TO will contain all the mappings to the Crop specific ontologies, so they will not have to be loaded individually (From PJ)
- The breeders and data managers from the CG centers will maintain their Trait Dictionaries (TDs), which should include the mappings to the TO
- MAL's script will convert from the TD to the ontology file
- We should work on creating and testing a merged version with cassava, rice and lentil
- Visualization: need a better way to view the ontology trees
- Choices now are OLS-vis, or the static .png display (note: OLS-Vis is currently only on the dev site)
- OLS-Vis tool (http://ols.wordvis.com/)- pulls all the ontologies from the urls, so it is the Release version.
- Could this be modified to display the planteome ones specifically on our browser?? Does not appear to be available for local install.
Trait vs descriptors- from EA- breeder terminology is important
- Descriptors (need to avoid this word), these are not traits
- Usually measured on a small number of plants, and locations, with no stress
- qualitative scale, but may be converted to ???
- Often used for taxonomic reasons, measured at their maximum
- breeder evaluation of trait: done at multiple sites, multiple generations, include stress evaluations
- are traits, looking for stability
- indexed or quantitative, can be categorical scale
- evaluation: happens at multiple times
AberOWL- Georgios V. Gkoutos
- An ontology repository and semantic search engine- link to paper on PubMed: http://www.ncbi.nlm.nih.gov/pubmed/25627673
- semantic queries looking at relationships
- can search over all ontologies in obo
- reasoner is run, then query.
- can use SPQL
Next meetings:
- need to break up the calls into:
- Ontology- Tuesday Feb 2nd
- technical things (mappings and such)??
- Browser/annotation ??
- Planning
Upcoming meetings and workshops
- Phenotype RCN meeting Feb 2016
- GARNet/Egenis Workshop: Integrating Large Data into Plant Science: From Big Data to Discovery
April 21st-22nd 2016 (Link)
- Meeting in Montpellier, May 2016
- ICBO 2016 Corvallis