Oct 5th, 2017 Ontology Working Group Meeting: Difference between revisions
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* Meeting Recordings: | * Meeting Recordings: | ||
** | ** [[File:Ontology WG Meeting 10-5-17 audio only.m4a|thumb|Ontology WG Meeting 10-5-17 audio]] | ||
** | ** [[File:Ontology WG Meeting video 10-5-17.mp4|thumb|Ontology WG Meeting video 10-5-17]] | ||
=Agenda= | =Agenda and Notes= | ||
PJ | PJ | ||
* Applying for no cost extension, should be planning to start applying for renewal by spring | * Applying for no cost extension, should be planning to start applying for renewal by spring | ||
| Line 27: | Line 27: | ||
EA | EA | ||
phenotyping platforms, automating annotations | * phenotyping platforms, automating annotations | ||
MIAPPE meeting, concern about having ontology terms for the environment and experimental conditions | * MIAPPE meeting, concern about having ontology terms for the environment and experimental conditions | ||
* Setting up collaboration with groups doing High Throughput Phenotyping | |||
** French group at Agropolis in Montpellier | |||
** John Doonan | |||
** PODD- Australian group | |||
* Invite them to one of our calls | |||
GG: - most of the data is proprietary | GG: - most of the data is proprietary | ||
* Can we partner with them? Use the data/images with the sources removed, feed back to them? | |||
Find phenotypic features | * Find phenotypic features | ||
Machine learning as an approach | * Machine learning as an approach | ||
PJ: Set up separate call with George and John to see what we can get working on | PJ: Set up separate call with George and John to see what we can get working on | ||
Need the data | * Need the data | ||
Also would like to have Bjorn Usadel come to one of our meetings | * Also would like to have Bjorn Usadel come to one of our meetings | ||
EA: | EA: | ||
HTP work going on at IRRI and other sites, that data may be more available | * HTP work going on at IRRI and other sites, that data may be more available | ||
Will work on setting up a conf call with the folks French group at Agropolis in Montpellier | * Will work on setting up a conf call with the folks French group at Agropolis in Montpellier | ||
MAL: | MAL: | ||
Breeding API | * Breeding API | ||
Mapping CO to TO will facilitate finding the data | * Mapping CO to TO will facilitate finding the data | ||
Next two CO vocabs are groundnut and Musa | * Next two CO vocabs are groundnut and Musa | ||
Working with Ethy Cannon on traits from PeanutBase, follow up with Steve Cannnon as well | * Working with Ethy Cannon on traits from PeanutBase, follow up with Steve Cannnon as well | ||
Do we have any peanut data?- Not at this time | * Do we have any peanut data?- Not at this time | ||
PJ: demo of the Ontology Enrichment Tool http://planteome.org/oat/ | PJ: demo of the Ontology Enrichment Tool http://planteome.org/oat/ | ||
Demo of the tool, | * Demo of the tool, | ||
test with the input gene example sets available from the bottom right hand side of the gene list box. Or add your own gene IDs from another species to test. | * test with the input gene example sets available from the bottom right hand side of the gene list box. Or add your own gene IDs from another species to test. | ||
Similar to AgriGO, but revised the methods | * Similar to AgriGO, but revised the methods | ||
Collaboration with software development company Sanmita | * Collaboration with software development company Sanmita | ||
Developing the ability to edit genes, add info etc | * Developing the ability to edit genes, add info etc | ||
May be able to merge with Noctua at some point in the future | * May be able to merge with Noctua at some point in the future | ||
Community engagement portal | * Community engagement portal | ||
AM: Update on OoPS | AM: Update on OoPS | ||
Samara scrape for APS and germplasm | * Samara scrape for APS and germplasm | ||
GRIN descriptors converted to gaf files | * GRIN descriptors converted to gaf files | ||
Mapping files, | * Mapping files, | ||
Using INCA tool -https://planteome.github.io/planteome-inca-form | * Using INCA tool -https://planteome.github.io/planteome-inca-form | ||
Some steps need to be done manually- like pushing to GH | * Some steps need to be done manually- like pushing to GH | ||
Plant disease patterns, issues with names that are obtained from script | * Plant disease patterns, issues with names that are obtained from script | ||
Probably need to have meeting with Dan Keith and CM to see what needs to be done on the INCA tool to get it configured | * Probably need to have meeting with Dan Keith and CM to see what needs to be done on the INCA tool to get it configured | ||
Scrape of diseases had about 11,000 lines, narrowed down to about 7000 as there are redundancies | * Scrape of diseases had about 11,000 lines, narrowed down to about 7000 as there are redundancies | ||
GG interested in doing text mining on the data set, or maybe a test set | * GG interested in doing text mining on the data set, or maybe a test set | ||
MAL- Crop dictionaries may also be helpful | * MAL- Crop dictionaries may also be helpful | ||
LC: | LC: | ||
NAR paper in review | * NAR paper in review | ||
Collaboration with Hong Cui and James Macklin- they have digitized the flora of North America descriptions | * Collaboration with Hong Cui and James Macklin- they have digitized the flora of North America descriptions | ||
Working on TO and PECO revisions | * Working on TO and PECO revisions | ||
Latest revision as of 19:27, 5 October 2017
Planteome Ontology WG Zoom Meeting
- Date: Thursday Oct 5th, 2017
- Time: 8:15am PDT (GMT-7)
- Meeting Recordings:
Agenda and Notes
PJ
- Applying for no cost extension, should be planning to start applying for renewal by spring
- Ideally should include people who may have their own sources of funding
- Planning for a database release by Dec 15th, in advance of PAG 2018
- Metadata annotations automated,
- Neural network approach
- Using the images- recognition of leaf, flower, stem- ~ 60% accuracy
- Need to bring in engineering/computing folks, people doing high throughput phenotyping
GG
- Working to develop Plant PhenomeNet further, but need a good source of annotated data
- Qualities vs values in the data annotations
- New person hired…
- Luke Slater working on AberOwl
- Also focusing on updating PATO
- How to convert quantitative data to qualitative data??
EA
- phenotyping platforms, automating annotations
- MIAPPE meeting, concern about having ontology terms for the environment and experimental conditions
- Setting up collaboration with groups doing High Throughput Phenotyping
- French group at Agropolis in Montpellier
- John Doonan
- PODD- Australian group
- Invite them to one of our calls
GG: - most of the data is proprietary
- Can we partner with them? Use the data/images with the sources removed, feed back to them?
- Find phenotypic features
- Machine learning as an approach
PJ: Set up separate call with George and John to see what we can get working on
- Need the data
- Also would like to have Bjorn Usadel come to one of our meetings
EA:
- HTP work going on at IRRI and other sites, that data may be more available
- Will work on setting up a conf call with the folks French group at Agropolis in Montpellier
MAL:
- Breeding API
- Mapping CO to TO will facilitate finding the data
- Next two CO vocabs are groundnut and Musa
- Working with Ethy Cannon on traits from PeanutBase, follow up with Steve Cannnon as well
- Do we have any peanut data?- Not at this time
PJ: demo of the Ontology Enrichment Tool http://planteome.org/oat/
- Demo of the tool,
- test with the input gene example sets available from the bottom right hand side of the gene list box. Or add your own gene IDs from another species to test.
- Similar to AgriGO, but revised the methods
- Collaboration with software development company Sanmita
- Developing the ability to edit genes, add info etc
- May be able to merge with Noctua at some point in the future
- Community engagement portal
AM: Update on OoPS
- Samara scrape for APS and germplasm
- GRIN descriptors converted to gaf files
- Mapping files,
- Using INCA tool -https://planteome.github.io/planteome-inca-form
- Some steps need to be done manually- like pushing to GH
- Plant disease patterns, issues with names that are obtained from script
- Probably need to have meeting with Dan Keith and CM to see what needs to be done on the INCA tool to get it configured
- Scrape of diseases had about 11,000 lines, narrowed down to about 7000 as there are redundancies
- GG interested in doing text mining on the data set, or maybe a test set
- MAL- Crop dictionaries may also be helpful
LC:
- NAR paper in review
- Collaboration with Hong Cui and James Macklin- they have digitized the flora of North America descriptions
- Working on TO and PECO revisions