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- | =='''Update and report on the visit to IRRI by Austin, Marie-Angelique 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). | - 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: | |||
- Sources: GRIMS System: 124,000 germplasm accessions (http://www.irgcis.irri.org:81/grc/IRGCISHome.html) | |||
- 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=== | |||
- 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 | - 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 | - 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(?) | - some traits from GRiSP, next version will have the core traits from the Breeding for Rice - BPI(?) | ||
- the variable will be a subclass of so that it shows up in the browser | |||
* Mapping issues: | |||
- 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 " | |||
- shouldn't be "paleal", should be non-adjective form | |||
- add lemma apiculus to the PO | - add lemma apiculus to the PO | ||
* Discussion of how to express the scale, esp the categorical ones- CO rice trait file does not have the scale info in it. MAL will fix it the next time. | |||
* Link to summary report (https://docs.google.com/document/d/1SYt5MC4kw87UxMsCOElg2yJQaE4nsEzVuXdNYq30ixU/edit?ts=56e6fbb5) | |||
Photo of rice grain from AM (from IRRI) | Photo of rice grain from AM (from IRRI) | ||
| Line 45: | Line 59: | ||
==Recent updates on the TO == | ==Recent updates on the TO == | ||
* revisions to equivalence axioms- ''occurs_in'' and ''composition'' | * revisions to equivalence axioms- ''occurs_in'' and ''composition'' | ||
* anther morphology traits, incl. anther number | * anther morphology traits, incl. anther number | ||
* biochemical branch | * biochemical branch | ||
* revisions to the equivalence axioms etc | |||
* Resolving issues between PO and TO- e.g stem/ culm, grain/kernel/caryopsis and fruit, pistil/carpel etc | |||
** ''Go ahead and make a "culm" term -PJ or not... Stay out of the granularity | |||
- panicle traits- inflorescence | |||
- annotation to the trait- CO/TO | |||
- prefer to annotate to the CO trait, not to the variable | |||
- can we use relationships, or annotation extension column eg: CO_320:0000184("2") | |||
- not sure how, or if this will work. Try with the cassava data set (where is this data?) | |||
- the relationships between CO traits, variables, scales, and methods are not working in the Planteome browser yet, but they should eventually. | |||
- traits for cassava- data set.Play with the annotations to get them to fit into GAF | |||
== | ==Other items:== | ||
=== Update on the plans for the Meeting in Montpellier, 9-13 May 2016=== | |||
''Tabled for next meeting'' | ''Tabled for next meeting'' | ||
== | ===AmiGO2 issues continued.. === | ||
''Tabled for next meeting'' | |||
==OBA development- Chris Mungall== | ===OBA development- Chris Mungall=== | ||
Tabled for next meeting... | Tabled for next meeting... | ||
| Line 74: | Line 97: | ||
==DivSeek Partner Assembly, Friday, June 17th, Saskatoon, Canada== | ==DivSeek Partner Assembly, Friday, June 17th, Saskatoon, Canada== | ||
==[http://www.bio-ontologies.org.uk/call-for-participation BioOntologies SIG] of the [http://www.iscb.org/ismb2016 Intelligent Systems for Molecular Biology (ISMB)]; July 8-12, 2016, Orlando, Florida == | ==[http://www.bio-ontologies.org.uk/call-for-participation BioOntologies SIG] of the [http://www.iscb.org/ismb2016 Intelligent Systems for Molecular Biology (ISMB)]; July 8-12, 2016, Orlando, Florida == | ||
Latest revision as of 22:53, 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-Angelique 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: GRIMS System: 124,000 germplasm accessions (http://www.irgcis.irri.org:81/grc/IRGCISHome.html)
- 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 subclass of so that it shows up in the browser
- Mapping issues:
- apiculus traits in the TO are linked to the lemma apiculus, but the PO only includes palea apiculus.
- shouldn't be "paleal", should be non-adjective form
- add lemma apiculus to the PO
- Discussion of how to express the scale, esp the categorical ones- CO rice trait file does not have the scale info in it. MAL will fix it the next time.
- Link to summary report (https://docs.google.com/document/d/1SYt5MC4kw87UxMsCOElg2yJQaE4nsEzVuXdNYq30ixU/edit?ts=56e6fbb5)
Photo of rice grain from AM (from IRRI)
Recent updates on the TO
- revisions to equivalence axioms- occurs_in and composition
- anther morphology traits, incl. anther number
- biochemical branch
- revisions to the equivalence axioms etc
- Resolving issues between PO and TO- e.g stem/ culm, grain/kernel/caryopsis and fruit, pistil/carpel etc
- Go ahead and make a "culm" term -PJ or not... Stay out of the granularity
- panicle traits- inflorescence - annotation to the trait- CO/TO - prefer to annotate to the CO trait, not to the variable
- can we use relationships, or annotation extension column eg: CO_320:0000184("2")
- not sure how, or if this will work. Try with the cassava data set (where is this data?)
- the relationships between CO traits, variables, scales, and methods are not working in the Planteome browser yet, but they should eventually.
- traits for cassava- data set.Play with the annotations to get them to fit into GAF
Other items:
Update on the plans for the Meeting in Montpellier, 9-13 May 2016
Tabled for next meeting
AmiGO2 issues continued..
Tabled for next meeting
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