Mar 15th, 2016 Ontology Working Group Meeting: Difference between revisions
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=Agenda= | =Agenda= | ||
=='''Update and report on the visit to IRRI by Austin, Marie-Angelic and Le'''o== | =='''Update and report on the visit to IRRI by Austin, Marie-Angelic and Le'''o== | ||
* Austin: annotations- progress report and issues with webservices and dbxref urls | * '''Austin: annotations- progress report and issues with webservices and dbxref urls''' | ||
- Currently we have a small test set of the annotations from The Rice SNP-Seek database (http://oryzasnp.org/iric-portal/index.zul). | - Currently we have a small test set of the annotations from The Rice SNP-Seek database (http://oryzasnp.org/iric-portal/index.zul). | ||
Test files on dev.planteome see awn color: http://dev.planteome.org/amigo/search/bioentity?q=awn%20color | - Test files on dev.planteome see awn color: http://dev.planteome.org/amigo/search/bioentity?q=awn%20color | ||
- AM will see if they can add the dashes in from their end at IRRI, otherwise we need to just link to the generic Home page we the user could run the search | - AM will see if they can add the dashes in from their end at IRRI, otherwise we need to just link to the generic Home page we the user could run the search | ||
- IRIC site is very slow- Amazon cloud issue? | - IRIC site is very slow- Amazon cloud issue? | ||
- Accessing the API- AM can from here, MAL cannot | - Accessing the API- AM can from here, MAL cannot | ||
- Sources: GRIN System: 124,000 germplasm accessions | - Sources: GRIN System: 124,000 germplasm accessions | ||
- Genesys, accessing the database- in MS access | - Genesys, accessing the database- in MS access | ||
- IR64 mutant lines- database not being maintained. | - IR64 mutant lines- database not being maintained. | ||
* '''MAL/Leo: Update on the revisions to the Rice Trait dictionary''' | * '''MAL/Leo: Update on the revisions to the Rice Trait dictionary''' | ||
- Leo has completed cleaning the TD and will post to GH soon. MAL will create the OBO file with the mapping to the TO on the CO traits | |||
- | - All the traits from IRIS - so genebank traits are covered | ||
- some traits from GRiSP | - some traits from GRiSP, next version will have the core traits from the Breeding for Rice - BPI(?) | ||
- the variable will be a sbclass of so that it shows up in the browser | |||
- apiculus traits in the TO are linked to the lemma apiculus, but the PO only includes palea apiculus. | - apiculus traits in the TO are linked to the lemma apiculus, but the PO only includes palea apiculus. | ||
- shouldn't be "plaleal", should be non-adjective | - shouldn't be "plaleal", should be non-adjective form | ||
- add lemma apiculus to the PO | |||
Photo of rice grain from AM (from IRRI) | |||
==Recent updates on the TO == | ==Recent updates on the TO == | ||
Revision as of 18:32, 15 March 2016
Planteome Ontology WG Zoom Meeting
- Date: Tuesday Mar. 15th, 2016
- Time: 8:15am PDT (GMT-7)
- Connection details: Join from PC, Mac, Linux, iOS or Android: https://zoom.us/j/762470789
- attendees: AM, MAL, LC, PJ, JE
- Links to recordings:
- Planteome Ontology WG Zoom Meeting:
- Planteome IRRI meeting Thursday March 10th:
Agenda
Update and report on the visit to IRRI by Austin, Marie-Angelic and Leo
- Austin: annotations- progress report and issues with webservices and dbxref urls
- Currently we have a small test set of the annotations from The Rice SNP-Seek database (http://oryzasnp.org/iric-portal/index.zul).
- Test files on dev.planteome see awn color: http://dev.planteome.org/amigo/search/bioentity?q=awn%20color - AM will see if they can add the dashes in from their end at IRRI, otherwise we need to just link to the generic Home page we the user could run the search
- IRIC site is very slow- Amazon cloud issue? - Accessing the API- AM can from here, MAL cannot - Sources: GRIN System: 124,000 germplasm accessions - Genesys, accessing the database- in MS access - IR64 mutant lines- database not being maintained.
- MAL/Leo: Update on the revisions to the Rice Trait dictionary
- Leo has completed cleaning the TD and will post to GH soon. MAL will create the OBO file with the mapping to the TO on the CO traits - All the traits from IRIS - so genebank traits are covered - some traits from GRiSP, next version will have the core traits from the Breeding for Rice - BPI(?) - the variable will be a sbclass of so that it shows up in the browser
- apiculus traits in the TO are linked to the lemma apiculus, but the PO only includes palea apiculus.
- shouldn't be "plaleal", should be non-adjective form
- add lemma apiculus to the PO
Photo of rice grain from AM (from IRRI)
Recent updates on the TO
- revisions to equivalence axioms- occurs_in and composition
- Stem and culm
- anther morphology traits, incl. anther number
- biochemical branch
- Resolving issues between PO and TO- e.g stem/ culm, grain/kernel/caryopsis and fruit, pistil/carpel etc
- revisions to the equivalence axioms etc
AmiGO2 issues continued..
Tabled for next meeting
Other items?
OBA development- Chris Mungall
Tabled for next meeting...
Upcoming Meetings and Workshops
Biocuration 2016, April 10th-14th, 2016; Geneva, Switzerland
- MAL is going
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, 9-13 May 2016
Link to tentative agenda/website: [1]
DivSeek Partner Assembly, Friday, June 17th, Saskatoon, Canada
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
- Link to program: ICBO + BioCreative Program
- Link to Easy Chair site: https://easychair.org/conferences/conference_info.cgi?a=10776589
Update on the plans for the Meeting in Montpellier, 9-13 May 2016
Upcoming Meetings and Workshops
Biocuration 2016, April 10th-14th, 2016; Geneva, Switzerland
- MAL is going
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, 9-13 May 2016
Link to tentative agenda/website: [2]
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
- Link to program: ICBO + BioCreative Program
- Link to Easy Chair site: https://easychair.org/conferences/conference_info.cgi?a=10776589