Planteome.org - User contributions [en]

April 11th, 2017 Ontology Working Group Meeting

2017-04-11T14:46:21Z

Marieangelique.laporte: /* Agenda */

=Planteome Ontology WG Zoom Meeting=
* Date: Tuesday April 4th, 2017
* Time: 8:15am PST (GMT-8)

* Connection details: Join from PC, Mac, Linux, iOS or Android: https://zoom.us/j/151299709

* Attendees:

* Regrets:

* Recordings:

=Agenda=
* Proposed additions of new inflorescence types and related terms. See notes here: [https://docs.google.com/document/d/18HF9rV18-nUZ6KBp-mi2p1CKHi-pF_eRRmecj582VCo/edit?usp=sharing Inflorescence Types]

* RDA and IGAD meetings:
** agrisemantics group : agricultural data semantics landscape
** wheat and rice groups
** side discussions: agGateway (will be at EBI next week)

= Upcoming Meetings and Workshops=
==AgBioData Workshop, Salt Lake City, April 18-19th, 2017==
* The purpose of this meeting is to bring together personnel from agricultural scientific databases to plan common projects, establish proof of principle for data sharing, and to establish standards and guidelines for agricultural genomic, genetic and breeding databases.

Link to folder on Google drive: [https://drive.google.com/drive/folders/0B1a8eLRiK74ARnF0eXdnWmd0OHM?usp=sharing AgBioData Ontology Working Group Notes]

== 2017 Gene Ontology Consortium Meeting, June 1-5th, 2017, Corvallis ==
* [https://sites.google.com/s/0BxnW-HvvUL8iMkM5VmxxWTBsYzg/p/0BxnW-HvvUL8iRnB0S1dtYUJXYUE/edit GO Meeting Corvallis]
* [https://docs.google.com/forms/d/1cJWCL0mL3X3rXrNsIcmLtkAf9et6TfhyYbHX9ouLwZs/edit Registration]
* [https://docs.google.com/forms/d/1F9BUTwzPqeyYQW81BXY1Qfj63OwCwWj9e0zC6sTt2jk/edit Travel plans]

* Dates: June 1-5, 2017 (Details)
** Arrive (May 31) View travel directions
** GOC meeting (June 1-3)
** Noctua gene annotation jamboree (June 4)
** Reactome Pathway curation jamboree (June 5)
** Depart (June 5 late evening / June 6 anytime)

==Plant Biology 2017, June 24th-28th, Honolulu, Hawaii==
* Important deadlines:
** April 30, 2017: Deadline for early-bird registration rates for Plant Biology 2017 and iMOSS 2017.
** May 24, 2017: Deadline for submission of abstracts to be included in the online program book and to receive a poster number.
** May 27, 2017: Deadline for discount hotel rates. (Please note: Our discounted room block may fill up long before this deadline.)
** June 12, 2017: Final deadline for Plant Biology 2017 abstract submissions.
** June 12, 2017: Deadline for standard registration rates for Plant Biology 2017 and iMOSS 2017.
** June 24–28, 2017: Onsite registration during Plant Biology 2017!

== [http://www.ibc2017.cn XIX International Botanical Congress], July 23-29, 2017, Shenzhen, China ==
* Workshop proposal accepted-

* T5-06:Ontologizing botanical knowledge (two sessions)
** Organizer: Hong Cui (University of Arizona, USA)
** James Macklin (Agriculture Agri-Food Canada, Canada)
** Pankaj Jaiswal (Oregon State University, USA)

* T5-18: Bioinformatics resources for comparative functional and phylogenetic analysis of plant genomes, pathways and diversity
** Organizer: Pankaj Jaiswal (Oregon State University, USA)
** Sushma Naithani (Oregon State University, USA)

* Deadline for the abstract submission for oral presentations has been extended for 39 of the 212 [http://www.ibc2017.cn/Symposia/ general symposia] where one or a few speaker slots are available
* New deadline: February 15, 2017 for those 39 symposia and for posters only

* Abstract submitted?

==ICBO 2017, Sept 12th-15th, 2017==
* Newcastle, GB
* http://icbo.buffalo.edu/
* Important dates:
** Mar 29, 2017: Workshops and tutorials proposals submission deadline
** Apr 19, 2017: Notification of acceptance of workshops and tutorials
** Jun 02, 2017: Paper and Poster Deadline
** Jun 16, 2017: Paper Reviews Due

Oct 11th, 2016 Ontology Working Group Meeting

2016-10-07T22:51:13Z

Marieangelique.laporte: /* CO mappings */

=Planteome Ontology WG Zoom Meeting=
* Date: Tuesday Oct 11th, 2016
* Time: 8:15am PDT (GMT-7)
* Connection details: Join from PC, Mac, Linux, iOS or Android:

* Attendees:
* Regrets: rest

Recordings:

=Agenda=

== Suggest adding a new relation between the morphology trait and a quality trait ==
Many of these are currently is a children resulting in dual parentage

e.g. pericarp texture (TO:0002623):
* is_a pericarp morphology trait (TO:0000945)
* is_a fruit quality trait (TO:0002728)

== Harmonisation between TO and PO ==
PO defines classes with sometimes a lot of synonyms (broad and narrow).
e.g. PO fruit (http://browser.planteome.org/amigo/term/PO:0009001)
In TO, the classes 'fruit weight' and 'grain weight' exist. How to harmonise that?
* use subClassOf instead of equivalentClass for the DP when narrow synonyms
* keep only 'fruit weight'. 'grain weight' will then become a synonym of 'fruit weight'
* keep 'fruit weight' in TO. 'grain weight' will then be in CO and imported in TO. The CO class 'grain weight' will use the same DP than 'fruit weight' + a taxon constraint. Related question: should all the CO class have a taxon constraint? or only the classes with a species-specific entity (i.e. synonyms narrow or broad) should have one?

== CO mappings ==
* 8 crops have been mapped to TO so far: lentil, cassava, wheat and rice are part of the planteome release. New crops added: sweet potato, maize, soybean and pigeonpea.
* statistics are available here: [[https://docs.google.com/spreadsheets/d/1BbM5QT7idUr8MTbSd9SGnJlJRl7OaLUlrkjKQJzJ3fI/edit?usp=sharing]]
* attempt of a visualisation [[http://mariealaporte.github.io]] (avoid this if you have ocean sickness!). Feedback welcome.

= Upcoming Meetings and Workshops=
==IC-FOODS Conference November 7-9,2016 Davis, California ==
* http://www.ic-foods.org/conference
* Matthew Lange is organizing
* BS cannot attend, will be at ISO meeting in Europe
* MAL and PJ will attend

== 4th International Plant Phenotyping Symposium, CIMMYT, December 13 – 15, 2016 ==
* International Maize and Wheat Improvement Center (CIMMYT)
* El Batan, Texcoco, México (Near Mexico City)
* Early bird registration deadline: October 16, 2016
* http://www.cimmyt.org/event/4th-international-plant-phenotyping-symposium/

==Plant and Animal Genome 2017, Jan 14-18, 2017, San Diego, CA, USA==
http://www.intlpag.org/
* October 31 early registration deadline
* Deadline for workshop abstract submissions is December 2, 2016.
* Deadline for changes to program (posting speakers) is November 30, 2016
* Poster Abstracts Submission Deadline is October 28, 2016

== Phenome 2017, Feb 10th to 14th, 2017==
http://www.phenome2017.org/#homepage
* DWS will attend- evo devo presentation
* CM will attend and present Planteome and pheno-BLASTing

== [http://www.ibc2017.cn XIX International Botanical Congress], July 23-29, 2017, Shenzhen, China ==
Workshop proposal accepted

Oct 11th, 2016 Ontology Working Group Meeting

2016-10-07T22:49:27Z

Marieangelique.laporte: /* CO mappings */

=Planteome Ontology WG Zoom Meeting=
* Date: Tuesday Oct 11th, 2016
* Time: 8:15am PDT (GMT-7)
* Connection details: Join from PC, Mac, Linux, iOS or Android:

* Attendees:
* Regrets: rest

Recordings:

=Agenda=

== Suggest adding a new relation between the morphology trait and a quality trait ==
Many of these are currently is a children resulting in dual parentage

e.g. pericarp texture (TO:0002623):
* is_a pericarp morphology trait (TO:0000945)
* is_a fruit quality trait (TO:0002728)

== Harmonisation between TO and PO ==
PO defines classes with sometimes a lot of synonyms (broad and narrow).
e.g. PO fruit (http://browser.planteome.org/amigo/term/PO:0009001)
In TO, the classes 'fruit weight' and 'grain weight' exist. How to harmonise that?
* use subClassOf instead of equivalentClass for the DP when narrow synonyms
* keep only 'fruit weight'. 'grain weight' will then become a synonym of 'fruit weight'
* keep 'fruit weight' in TO. 'grain weight' will then be in CO and imported in TO. The CO class 'grain weight' will use the same DP than 'fruit weight' + a taxon constraint. Related question: should all the CO class have a taxon constraint? or only the classes with a species-specific entity (i.e. synonyms narrow or broad) should have one?

== CO mappings ==
* 8 crops have been mapped to TO so far: lentil, cassava, wheat and rice are part of the planteome release. New crops added: sweet potato, maize, soybean and pigeonpea.
* statistics are available [[https://docs.google.com/spreadsheets/d/1BbM5QT7idUr8MTbSd9SGnJlJRl7OaLUlrkjKQJzJ3fI/edit?usp=sharing|here]]
* attempt of a visualisation [[mariealaporte.github.io|here]] (avoid this if you have ocean sickness!). Feedback welcome.

= Upcoming Meetings and Workshops=
==IC-FOODS Conference November 7-9,2016 Davis, California ==
* http://www.ic-foods.org/conference
* Matthew Lange is organizing
* BS cannot attend, will be at ISO meeting in Europe
* MAL and PJ will attend

== 4th International Plant Phenotyping Symposium, CIMMYT, December 13 – 15, 2016 ==
* International Maize and Wheat Improvement Center (CIMMYT)
* El Batan, Texcoco, México (Near Mexico City)
* Early bird registration deadline: October 16, 2016
* http://www.cimmyt.org/event/4th-international-plant-phenotyping-symposium/

==Plant and Animal Genome 2017, Jan 14-18, 2017, San Diego, CA, USA==
http://www.intlpag.org/
* October 31 early registration deadline
* Deadline for workshop abstract submissions is December 2, 2016.
* Deadline for changes to program (posting speakers) is November 30, 2016
* Poster Abstracts Submission Deadline is October 28, 2016

== Phenome 2017, Feb 10th to 14th, 2017==
http://www.phenome2017.org/#homepage
* DWS will attend- evo devo presentation
* CM will attend and present Planteome and pheno-BLASTing

== [http://www.ibc2017.cn XIX International Botanical Congress], July 23-29, 2017, Shenzhen, China ==
Workshop proposal accepted

Oct 11th, 2016 Ontology Working Group Meeting

2016-10-07T22:46:54Z

Marieangelique.laporte: /* CO mappings */

=Planteome Ontology WG Zoom Meeting=
* Date: Tuesday Oct 11th, 2016
* Time: 8:15am PDT (GMT-7)
* Connection details: Join from PC, Mac, Linux, iOS or Android:

* Attendees:
* Regrets: rest

Recordings:

=Agenda=

== Suggest adding a new relation between the morphology trait and a quality trait ==
Many of these are currently is a children resulting in dual parentage

e.g. pericarp texture (TO:0002623):
* is_a pericarp morphology trait (TO:0000945)
* is_a fruit quality trait (TO:0002728)

== Harmonisation between TO and PO ==
PO defines classes with sometimes a lot of synonyms (broad and narrow).
e.g. PO fruit (http://browser.planteome.org/amigo/term/PO:0009001)
In TO, the classes 'fruit weight' and 'grain weight' exist. How to harmonise that?
* use subClassOf instead of equivalentClass for the DP when narrow synonyms
* keep only 'fruit weight'. 'grain weight' will then become a synonym of 'fruit weight'
* keep 'fruit weight' in TO. 'grain weight' will then be in CO and imported in TO. The CO class 'grain weight' will use the same DP than 'fruit weight' + a taxon constraint. Related question: should all the CO class have a taxon constraint? or only the classes with a species-specific entity (i.e. synonyms narrow or broad) should have one?

== CO mappings ==
* 8 crops have been mapped to TO so far: lentil, cassava, wheat and rice are part of the planteome release. New crops added: sweet potato, maize, soybean and pigeonpea.
* statistics are available here: https://docs.google.com/spreadsheets/d/1BbM5QT7idUr8MTbSd9SGnJlJRl7OaLUlrkjKQJzJ3fI/edit?usp=sharing
* attempt of a visualisation here: [[mariealaporte.github.io]] (avoid this if you have ocean sickness!). Feedback welcome.

= Upcoming Meetings and Workshops=
==IC-FOODS Conference November 7-9,2016 Davis, California ==
* http://www.ic-foods.org/conference
* Matthew Lange is organizing
* BS cannot attend, will be at ISO meeting in Europe
* MAL and PJ will attend

== 4th International Plant Phenotyping Symposium, CIMMYT, December 13 – 15, 2016 ==
* International Maize and Wheat Improvement Center (CIMMYT)
* El Batan, Texcoco, México (Near Mexico City)
* Early bird registration deadline: October 16, 2016
* http://www.cimmyt.org/event/4th-international-plant-phenotyping-symposium/

==Plant and Animal Genome 2017, Jan 14-18, 2017, San Diego, CA, USA==
http://www.intlpag.org/
* October 31 early registration deadline
* Deadline for workshop abstract submissions is December 2, 2016.
* Deadline for changes to program (posting speakers) is November 30, 2016
* Poster Abstracts Submission Deadline is October 28, 2016

== Phenome 2017, Feb 10th to 14th, 2017==
http://www.phenome2017.org/#homepage
* DWS will attend- evo devo presentation
* CM will attend and present Planteome and pheno-BLASTing

== [http://www.ibc2017.cn XIX International Botanical Congress], July 23-29, 2017, Shenzhen, China ==
Workshop proposal accepted

Oct 11th, 2016 Ontology Working Group Meeting

2016-10-07T22:45:24Z

Marieangelique.laporte: /* Agenda */

=Planteome Ontology WG Zoom Meeting=
* Date: Tuesday Oct 11th, 2016
* Time: 8:15am PDT (GMT-7)
* Connection details: Join from PC, Mac, Linux, iOS or Android:

* Attendees:
* Regrets: rest

Recordings:

=Agenda=

== Suggest adding a new relation between the morphology trait and a quality trait ==
Many of these are currently is a children resulting in dual parentage

e.g. pericarp texture (TO:0002623):
* is_a pericarp morphology trait (TO:0000945)
* is_a fruit quality trait (TO:0002728)

== Harmonisation between TO and PO ==
PO defines classes with sometimes a lot of synonyms (broad and narrow).
e.g. PO fruit (http://browser.planteome.org/amigo/term/PO:0009001)
In TO, the classes 'fruit weight' and 'grain weight' exist. How to harmonise that?
* use subClassOf instead of equivalentClass for the DP when narrow synonyms
* keep only 'fruit weight'. 'grain weight' will then become a synonym of 'fruit weight'
* keep 'fruit weight' in TO. 'grain weight' will then be in CO and imported in TO. The CO class 'grain weight' will use the same DP than 'fruit weight' + a taxon constraint. Related question: should all the CO class have a taxon constraint? or only the classes with a species-specific entity (i.e. synonyms narrow or broad) should have one?

== CO mappings ==
* 8 crops have been mapped to TO so far: lentil, cassava, wheat and rice are part of the planteome release. New crops added: sweet potato, maize, soybean and pigeonpea.
* statistics are available here: https://docs.google.com/spreadsheets/d/1BbM5QT7idUr8MTbSd9SGnJlJRl7OaLUlrkjKQJzJ3fI/edit?usp=sharing
* attempt of a visualisation here: mariealaporte.github.io (avoid this if you have ocean sickness!). Feedback welcome.

= Upcoming Meetings and Workshops=
==IC-FOODS Conference November 7-9,2016 Davis, California ==
* http://www.ic-foods.org/conference
* Matthew Lange is organizing
* BS cannot attend, will be at ISO meeting in Europe
* MAL and PJ will attend

== 4th International Plant Phenotyping Symposium, CIMMYT, December 13 – 15, 2016 ==
* International Maize and Wheat Improvement Center (CIMMYT)
* El Batan, Texcoco, México (Near Mexico City)
* Early bird registration deadline: October 16, 2016
* http://www.cimmyt.org/event/4th-international-plant-phenotyping-symposium/

==Plant and Animal Genome 2017, Jan 14-18, 2017, San Diego, CA, USA==
http://www.intlpag.org/
* October 31 early registration deadline
* Deadline for workshop abstract submissions is December 2, 2016.
* Deadline for changes to program (posting speakers) is November 30, 2016
* Poster Abstracts Submission Deadline is October 28, 2016

== Phenome 2017, Feb 10th to 14th, 2017==
http://www.phenome2017.org/#homepage
* DWS will attend- evo devo presentation
* CM will attend and present Planteome and pheno-BLASTing

== [http://www.ibc2017.cn XIX International Botanical Congress], July 23-29, 2017, Shenzhen, China ==
Workshop proposal accepted

Apr. 26th, 2016 Ontology Working Group Meeting

2016-04-26T14:47:37Z

Marieangelique.laporte: /* 2. Update on the plans for the PhenoHarmonIS Meeting in Montpellier, 9-13 May 2016 */

=Planteome Ontology WG Zoom Meeting=
* Date: Tuesday Apr. 26th, 2016
* Time: 8:15am PDT (GMT-7)

* Connection details: Join from PC, Mac, Linux, iOS or Android: https://zoom.us/j/695257950

* attendees:

[[File:xyz|thumbnail|xyz]]

[[File:xyz|thumbnail|xyz]]

=Agenda=
==1. Update from [https://www.isb-sib.ch/events/biocuration2016/home Biocuration 2016, April 10th-14th, 2016; Geneva, Switzerland]==
* MAL attended and presented a talk
* Abstract: https://easychair.org/conferences/submission.cgi?a=10690939;submission=2641703
** Feedback on the presentation?
***question from someone working on GO (GO curator): How do we annotate the data related to a subspecies (e.g. variety, cultivar, form...)?
** Potential collaborators
***Petra Ten Hoopen (EBI): works on a controlled list of traits that should be measured by the partners of her project. She might need some help to map the list to TO.
***KE Lin (Rijk Zwaan): works on vegetable varieties. Interested in the approach in order to map his species specific breeders traits.
***Sebastien Briois (Syngenta): was interested in using Planteome data.
***Melissa Haedel (OHSU): phenopackets to annotate the breeders data.

===Talks of Interest:===
* Link to https://www.isb-sib.ch/events/biocuration2016/oral-presentations#

* Why the world needs phenopacketeers, and how to be one Melissa Haendel
** PhenoPackets: https://github.com/phenopackets- Chris Mungall

* Noctua: http://noctua.berkeleybop.org/

* LEGO: expressing complex biological models using the Gene Ontology

*Wikidata initiative: http://database.oxfordjournals.org/content/2016/baw015.full

*Pubtator: Text mining genotype-phenotype associations at PubMed scale for database curation and precision medicine

==2. Update on the plans for the PhenoHarmonIS Meeting in Montpellier, 9-13 May 2016==
* Link to website: https://sites.google.com/a/cgxchange.org/cropontologycommunity/home
* http://tinyurl.com/hzsho6v

* LC, AM will go from OSU

* About 70+ Participants are signed up:
** [https://sites.google.com/a/cgxchange.org/cropontologycommunity/workshop-on-harmonization-semantic-and-integration-of-phenotypic-and-agronomic-data-9-13-may-2016-montpellier-france/list-of-participants PhenoHarmonIS_List-of-participants]

* Link to the agenda:
** [https://sites.google.com/a/cgxchange.org/cropontologycommunity/workshop-on-harmonization-semantic-and-integration-of-phenotypic-and-agronomic-data-9-13-may-2016-montpellier-france/agenda PhenoHarmonIS Agenda]

Planteome Presentations:
* Monday afternoon 2:50pm: Planteome presentation- 10 minutes, LC
* Monday late afternoon (~5pm) 5-mns Lightning talks- AM "Annotating germplasm using the Plant Trait Ontology in Planteome" (or maybe Tues am)
* Monday Poster presentation: (~5pm to 7pm)
* Tuesday morning: Austin (10 min + questions): Detailed 10-mn presentations on systems using selected tools for annotations and understanding of the opportunities and bottlenecks Followed by questions
* Tuesday afternoon : Hands on Trait Dictionaries: includes validation of mappings CO -TO MAL. Groups: Tree species, CWR, Barley, Cacao, Wheat, Rice, Potato, Sweet Potato
* Wednesday morning: FOCUS ON TRAIT - Intra and interspecies Trait Harmonization Mapping techniques MAL (10 min)
* Thursday 2pm: Hands-on Planteome Data Annotation- AM, LC, MAL

==3. ICBO 2016 Call for Papers is open==
* ICBO call for papers is open- http://icbo.cgrb.oregonstate.edu/ICBO_submission

http://icbo.cgrb.oregonstate.edu/ICBO_submission

'''Deadline is May 5th'''

Proposed Topics, with suggested lead:
* Planteome paper- LC
* Mappings- MAL
* Annotations project on rice, cassava and lentil, etc - AM

Formats:
* Extended Abstract- up to 2 pages
* Short Papers- up to 4 pages
* Full Papers- up to 6 pages

https://easychair.org/conferences/?conf=icbo2016

Papers will be published in a book of proceedings, not in a journal

== 4. Plant Trait Ontology updates==
* Recent revisions and changes to the equivalence axioms etc

* Plans to do release

More details TBA:

==5. AmiGO2 Update: ==
* New version of AmiGO is being tested on the dev.planteome site- http://dev.planteome.org

* You can preview the new drill down browser here: http://dev.planteome.org/amigo/dd_browse

* GO version: http://tomodachi.berkeleybop.org/amigo/landing

* Issues of the relations and some things showing up in weird places

* Significant changes:
** Actual browser functionality
** Neighborhood tab (was ancestors and children)
** All relations will be displayed..?????
** annotations by species

==Other Items==
Tabled from previous meetings:

===OBA development- Chris Mungall===
* CM: If there is time I would like to walk through the procedure we use to develop OBA.

* Part of this was covered in the tutorial on template-based ontology development, but we had to rush this part due to lack of time:
https://github.com/Planteome/protege-tutorial/tree/master/template-examples

* For OBA, the source of the ontology is primarily in TSVs, found here:
https://github.com/obophenotype/bio-attribute-ontology/tree/master/src/ontology/modules

* The design patterns are specified here:
https://github.com/obophenotype/bio-attribute-ontology/tree/master/src/ontology/patterns

* Together these are used to build the ontology with equivalence axioms, with the entire ontology hierarchy being inferred automatically, e.g:
http://www.ebi.ac.uk/ols/beta/ontologies/oba/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FOBA_VT0000017

= Upcoming Meetings and Workshops=

==[http://blog.garnetcommunity.org.uk/garnetegenis-workshop-integrating-large-data-plant-science-big-data-discovery/ 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: [https://sites.google.com/a/cgxchange.org/cropontologycommunity/home]

==[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 ==
* 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

== [http://icbo.cgrb.oregonstate.edu/ 7th International Conference on Biological Ontology and BioCreative 2016] Aug 1st to 4th, Corvallis, OR==
* Link to program: [http://icbo.cgrb.oregonstate.edu/node/20 ICBO + BioCreative Program]
* Link to Easy Chair site: https://easychair.org/conferences/conference_info.cgi?a=10776589

Apr. 26th, 2016 Ontology Working Group Meeting

2016-04-26T14:47:03Z

Marieangelique.laporte: /* 2. Update on the plans for the PhenoHarmonIS Meeting in Montpellier, 9-13 May 2016 */

=Planteome Ontology WG Zoom Meeting=
* Date: Tuesday Apr. 26th, 2016
* Time: 8:15am PDT (GMT-7)

* Connection details: Join from PC, Mac, Linux, iOS or Android: https://zoom.us/j/695257950

* attendees:

[[File:xyz|thumbnail|xyz]]

[[File:xyz|thumbnail|xyz]]

=Agenda=
==1. Update from [https://www.isb-sib.ch/events/biocuration2016/home Biocuration 2016, April 10th-14th, 2016; Geneva, Switzerland]==
* MAL attended and presented a talk
* Abstract: https://easychair.org/conferences/submission.cgi?a=10690939;submission=2641703
** Feedback on the presentation?
***question from someone working on GO (GO curator): How do we annotate the data related to a subspecies (e.g. variety, cultivar, form...)?
** Potential collaborators
***Petra Ten Hoopen (EBI): works on a controlled list of traits that should be measured by the partners of her project. She might need some help to map the list to TO.
***KE Lin (Rijk Zwaan): works on vegetable varieties. Interested in the approach in order to map his species specific breeders traits.
***Sebastien Briois (Syngenta): was interested in using Planteome data.
***Melissa Haedel (OHSU): phenopackets to annotate the breeders data.

===Talks of Interest:===
* Link to https://www.isb-sib.ch/events/biocuration2016/oral-presentations#

* Why the world needs phenopacketeers, and how to be one Melissa Haendel
** PhenoPackets: https://github.com/phenopackets- Chris Mungall

* Noctua: http://noctua.berkeleybop.org/

* LEGO: expressing complex biological models using the Gene Ontology

*Wikidata initiative: http://database.oxfordjournals.org/content/2016/baw015.full

*Pubtator: Text mining genotype-phenotype associations at PubMed scale for database curation and precision medicine

==2. Update on the plans for the PhenoHarmonIS Meeting in Montpellier, 9-13 May 2016==
* Link to website: https://sites.google.com/a/cgxchange.org/cropontologycommunity/home
* http://tinyurl.com/hzsho6v

* LC, AM will go from OSU

* About 70+ Participants are signed up:
** [https://sites.google.com/a/cgxchange.org/cropontologycommunity/workshop-on-harmonization-semantic-and-integration-of-phenotypic-and-agronomic-data-9-13-may-2016-montpellier-france/list-of-participants PhenoHarmonIS_List-of-participants]

* Link to the agenda:
** [https://sites.google.com/a/cgxchange.org/cropontologycommunity/workshop-on-harmonization-semantic-and-integration-of-phenotypic-and-agronomic-data-9-13-may-2016-montpellier-france/agenda PhenoHarmonIS Agenda]

Planteome Presentations:
* Monday afternoon 2:50pm: Planteome presentation- 10 minutes, LC
* Monday late afternoon (~5pm) 5-mns Lightning talks- AM "Annotating germplasm using the Plant Trait Ontology in Planteome" (or maybe Tues am)
* Monday Poster presentation: (~5pm to 7pm)
* Tuesday morning: Brainstorming : Austin (10 min + questions): Detailed 10-mn presentations on systems using selected tools for annotations and understanding of the opportunities and bottlenecks Followed by questions
* Tuesday afternoon : Hands on Trait Dictionaries: includes validation of mappings CO -TO MAL. Groups: Tree species, CWR, Barley, Cacao, Wheat, Rice, Potato, Sweet Potato
* Wednesday morning: FOCUS ON TRAIT - Intra and interspecies Trait Harmonization Mapping techniques MAL (10 min)
* Thursday 2pm: Hands-on Planteome Data Annotation- AM, LC, MAL

==3. ICBO 2016 Call for Papers is open==
* ICBO call for papers is open- http://icbo.cgrb.oregonstate.edu/ICBO_submission

http://icbo.cgrb.oregonstate.edu/ICBO_submission

'''Deadline is May 5th'''

Proposed Topics, with suggested lead:
* Planteome paper- LC
* Mappings- MAL
* Annotations project on rice, cassava and lentil, etc - AM

Formats:
* Extended Abstract- up to 2 pages
* Short Papers- up to 4 pages
* Full Papers- up to 6 pages

https://easychair.org/conferences/?conf=icbo2016

Papers will be published in a book of proceedings, not in a journal

== 4. Plant Trait Ontology updates==
* Recent revisions and changes to the equivalence axioms etc

* Plans to do release

More details TBA:

==5. AmiGO2 Update: ==
* New version of AmiGO is being tested on the dev.planteome site- http://dev.planteome.org

* You can preview the new drill down browser here: http://dev.planteome.org/amigo/dd_browse

* GO version: http://tomodachi.berkeleybop.org/amigo/landing

* Issues of the relations and some things showing up in weird places

* Significant changes:
** Actual browser functionality
** Neighborhood tab (was ancestors and children)
** All relations will be displayed..?????
** annotations by species

==Other Items==
Tabled from previous meetings:

===OBA development- Chris Mungall===
* CM: If there is time I would like to walk through the procedure we use to develop OBA.

* Part of this was covered in the tutorial on template-based ontology development, but we had to rush this part due to lack of time:
https://github.com/Planteome/protege-tutorial/tree/master/template-examples

* For OBA, the source of the ontology is primarily in TSVs, found here:
https://github.com/obophenotype/bio-attribute-ontology/tree/master/src/ontology/modules

* The design patterns are specified here:
https://github.com/obophenotype/bio-attribute-ontology/tree/master/src/ontology/patterns

* Together these are used to build the ontology with equivalence axioms, with the entire ontology hierarchy being inferred automatically, e.g:
http://www.ebi.ac.uk/ols/beta/ontologies/oba/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FOBA_VT0000017

= Upcoming Meetings and Workshops=

==[http://blog.garnetcommunity.org.uk/garnetegenis-workshop-integrating-large-data-plant-science-big-data-discovery/ 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: [https://sites.google.com/a/cgxchange.org/cropontologycommunity/home]

==[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 ==
* 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

== [http://icbo.cgrb.oregonstate.edu/ 7th International Conference on Biological Ontology and BioCreative 2016] Aug 1st to 4th, Corvallis, OR==
* Link to program: [http://icbo.cgrb.oregonstate.edu/node/20 ICBO + BioCreative Program]
* Link to Easy Chair site: https://easychair.org/conferences/conference_info.cgi?a=10776589

Apr. 26th, 2016 Ontology Working Group Meeting

2016-04-26T14:08:18Z

Marieangelique.laporte: /* 1. Update from Biocuration 2016, April 10th-14th, 2016; Geneva, Switzerland */

=Planteome Ontology WG Zoom Meeting=
* Date: Tuesday Apr. 26th, 2016
* Time: 8:15am PDT (GMT-7)

* Connection details: Join from PC, Mac, Linux, iOS or Android: https://zoom.us/j/695257950

* attendees:

[[File:xyz|thumbnail|xyz]]

[[File:xyz|thumbnail|xyz]]

=Agenda=
==1. Update from [https://www.isb-sib.ch/events/biocuration2016/home Biocuration 2016, April 10th-14th, 2016; Geneva, Switzerland]==
* MAL attended and presented a talk
* Abstract: https://easychair.org/conferences/submission.cgi?a=10690939;submission=2641703
** Feedback on the presentation?
***question from someone working on GO (GO curator): How do we annotate the data related to a subspecies (e.g. variety, cultivar, form...)?
** Potential collaborators
***Petra Ten Hoopen (EBI): works on a controlled list of traits that should be measured by the partners of her project. She might need some help to map the list to TO.
***KE Lin (Rijk Zwaan): works on vegetable varieties. Interested in the approach in order to map his species specific breeders traits.
***Sebastien Briois (Syngenta): was interested in using Planteome data.
***Melissa Haedel (OHSU): phenopackets to annotate the breeders data.

===Talks of Interest:===
* Link to https://www.isb-sib.ch/events/biocuration2016/oral-presentations#

* Why the world needs phenopacketeers, and how to be one Melissa Haendel
** PhenoPackets: https://github.com/phenopackets- Chris Mungall

* Noctua: http://noctua.berkeleybop.org/

* LEGO: expressing complex biological models using the Gene Ontology

*Wikidata initiative: http://database.oxfordjournals.org/content/2016/baw015.full

*Pubtator: Text mining genotype-phenotype associations at PubMed scale for database curation and precision medicine

==2. Update on the plans for the PhenoHarmonIS Meeting in Montpellier, 9-13 May 2016==
* Link to website: https://sites.google.com/a/cgxchange.org/cropontologycommunity/home
* http://tinyurl.com/hzsho6v

* LC, AM will go from OSU

* About 70+ Participants are signed up:
** [https://sites.google.com/a/cgxchange.org/cropontologycommunity/workshop-on-harmonization-semantic-and-integration-of-phenotypic-and-agronomic-data-9-13-may-2016-montpellier-france/list-of-participants PhenoHarmonIS_List-of-participants]

* Link to the agenda:
** [https://sites.google.com/a/cgxchange.org/cropontologycommunity/workshop-on-harmonization-semantic-and-integration-of-phenotypic-and-agronomic-data-9-13-may-2016-montpellier-france/agenda PhenoHarmonIS Agenda]

Planteome Presentations:
* Monday afternoon 2:50pm: Planteome presentation- 10 minutes, LC
* Monday late afternoon (~5pm) 5-mns Lightning talks- AM "Annotating germplasm using the Plant Trait Ontology in Planteome" (or maybe Tues am)
* Monday Poster presentation: (~5pm to 7pm)
* Thursday 2pm: Hands-on Planteome Data Annotation- AM, LC, MAL

==3. ICBO 2016 Call for Papers is open==
* ICBO call for papers is open- http://icbo.cgrb.oregonstate.edu/ICBO_submission

http://icbo.cgrb.oregonstate.edu/ICBO_submission

'''Deadline is May 5th'''

Proposed Topics, with suggested lead:
* Planteome paper- LC
* Mappings- MAL
* Annotations project on rice, cassava and lentil, etc - AM

Formats:
* Extended Abstract- up to 2 pages
* Short Papers- up to 4 pages
* Full Papers- up to 6 pages

https://easychair.org/conferences/?conf=icbo2016

Papers will be published in a book of proceedings, not in a journal

== 4. Plant Trait Ontology updates==
* Recent revisions and changes to the equivalence axioms etc

* Plans to do release

More details TBA:

==5. AmiGO2 Update: ==
* New version of AmiGO is being tested on the dev.planteome site- http://dev.planteome.org

* You can preview the new drill down browser here: http://dev.planteome.org/amigo/dd_browse

* GO version: http://tomodachi.berkeleybop.org/amigo/landing

* Issues of the relations and some things showing up in weird places

* Significant changes:
** Actual browser functionality
** Neighborhood tab (was ancestors and children)
** All relations will be displayed..?????
** annotations by species

==Other Items==
Tabled from previous meetings:

===OBA development- Chris Mungall===
* CM: If there is time I would like to walk through the procedure we use to develop OBA.

* Part of this was covered in the tutorial on template-based ontology development, but we had to rush this part due to lack of time:
https://github.com/Planteome/protege-tutorial/tree/master/template-examples

* For OBA, the source of the ontology is primarily in TSVs, found here:
https://github.com/obophenotype/bio-attribute-ontology/tree/master/src/ontology/modules

* The design patterns are specified here:
https://github.com/obophenotype/bio-attribute-ontology/tree/master/src/ontology/patterns

* Together these are used to build the ontology with equivalence axioms, with the entire ontology hierarchy being inferred automatically, e.g:
http://www.ebi.ac.uk/ols/beta/ontologies/oba/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FOBA_VT0000017

= Upcoming Meetings and Workshops=

==[http://blog.garnetcommunity.org.uk/garnetegenis-workshop-integrating-large-data-plant-science-big-data-discovery/ 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: [https://sites.google.com/a/cgxchange.org/cropontologycommunity/home]

==[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 ==
* 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

== [http://icbo.cgrb.oregonstate.edu/ 7th International Conference on Biological Ontology and BioCreative 2016] Aug 1st to 4th, Corvallis, OR==
* Link to program: [http://icbo.cgrb.oregonstate.edu/node/20 ICBO + BioCreative Program]
* Link to Easy Chair site: https://easychair.org/conferences/conference_info.cgi?a=10776589

Apr. 26th, 2016 Ontology Working Group Meeting

2016-04-26T14:07:37Z

Marieangelique.laporte: /* 1. Update from Biocuration 2016, April 10th-14th, 2016; Geneva, Switzerland */

=Planteome Ontology WG Zoom Meeting=
* Date: Tuesday Apr. 26th, 2016
* Time: 8:15am PDT (GMT-7)

* Connection details: Join from PC, Mac, Linux, iOS or Android: https://zoom.us/j/695257950

* attendees:

[[File:xyz|thumbnail|xyz]]

[[File:xyz|thumbnail|xyz]]

=Agenda=
==1. Update from [https://www.isb-sib.ch/events/biocuration2016/home Biocuration 2016, April 10th-14th, 2016; Geneva, Switzerland]==
* MAL attended and presented a talk
* Abstract: https://easychair.org/conferences/submission.cgi?a=10690939;submission=2641703
** Feedback on the presentation?
question from someone working on GO (GO curator): How do we annotate the data related to a subspecies (e.g. variety, cultivar, form...)?
** Potential collaborators
Petra Ten Hoopen (EBI): works on a controlled list of traits that should be measured by the partners of her project. She might need some help to map the list to TO.
KE Lin (Rijk Zwaan): works on vegetable varieties. Interested in the approach in order to map his species specific breeders traits.
Sebastien Briois (Syngenta): was interested in using Planteome data.
Melissa Haedel (OHSU): phenopackets to annotate the breeders data.

===Talks of Interest:===
* Link to https://www.isb-sib.ch/events/biocuration2016/oral-presentations#

* Why the world needs phenopacketeers, and how to be one Melissa Haendel
** PhenoPackets: https://github.com/phenopackets- Chris Mungall

* Noctua: http://noctua.berkeleybop.org/

* LEGO: expressing complex biological models using the Gene Ontology

*Wikidata initiative: http://database.oxfordjournals.org/content/2016/baw015.full

*Pubtator: Text mining genotype-phenotype associations at PubMed scale for database curation and precision medicine

==2. Update on the plans for the PhenoHarmonIS Meeting in Montpellier, 9-13 May 2016==
* Link to website: https://sites.google.com/a/cgxchange.org/cropontologycommunity/home
* http://tinyurl.com/hzsho6v

* LC, AM will go from OSU

* About 70+ Participants are signed up:
** [https://sites.google.com/a/cgxchange.org/cropontologycommunity/workshop-on-harmonization-semantic-and-integration-of-phenotypic-and-agronomic-data-9-13-may-2016-montpellier-france/list-of-participants PhenoHarmonIS_List-of-participants]

* Link to the agenda:
** [https://sites.google.com/a/cgxchange.org/cropontologycommunity/workshop-on-harmonization-semantic-and-integration-of-phenotypic-and-agronomic-data-9-13-may-2016-montpellier-france/agenda PhenoHarmonIS Agenda]

Planteome Presentations:
* Monday afternoon 2:50pm: Planteome presentation- 10 minutes, LC
* Monday late afternoon (~5pm) 5-mns Lightning talks- AM "Annotating germplasm using the Plant Trait Ontology in Planteome" (or maybe Tues am)
* Monday Poster presentation: (~5pm to 7pm)
* Thursday 2pm: Hands-on Planteome Data Annotation- AM, LC, MAL

==3. ICBO 2016 Call for Papers is open==
* ICBO call for papers is open- http://icbo.cgrb.oregonstate.edu/ICBO_submission

http://icbo.cgrb.oregonstate.edu/ICBO_submission

'''Deadline is May 5th'''

Proposed Topics, with suggested lead:
* Planteome paper- LC
* Mappings- MAL
* Annotations project on rice, cassava and lentil, etc - AM

Formats:
* Extended Abstract- up to 2 pages
* Short Papers- up to 4 pages
* Full Papers- up to 6 pages

https://easychair.org/conferences/?conf=icbo2016

Papers will be published in a book of proceedings, not in a journal

== 4. Plant Trait Ontology updates==
* Recent revisions and changes to the equivalence axioms etc

* Plans to do release

More details TBA:

==5. AmiGO2 Update: ==
* New version of AmiGO is being tested on the dev.planteome site- http://dev.planteome.org

* You can preview the new drill down browser here: http://dev.planteome.org/amigo/dd_browse

* GO version: http://tomodachi.berkeleybop.org/amigo/landing

* Issues of the relations and some things showing up in weird places

* Significant changes:
** Actual browser functionality
** Neighborhood tab (was ancestors and children)
** All relations will be displayed..?????
** annotations by species

==Other Items==
Tabled from previous meetings:

===OBA development- Chris Mungall===
* CM: If there is time I would like to walk through the procedure we use to develop OBA.

* Part of this was covered in the tutorial on template-based ontology development, but we had to rush this part due to lack of time:
https://github.com/Planteome/protege-tutorial/tree/master/template-examples

* For OBA, the source of the ontology is primarily in TSVs, found here:
https://github.com/obophenotype/bio-attribute-ontology/tree/master/src/ontology/modules

* The design patterns are specified here:
https://github.com/obophenotype/bio-attribute-ontology/tree/master/src/ontology/patterns

* Together these are used to build the ontology with equivalence axioms, with the entire ontology hierarchy being inferred automatically, e.g:
http://www.ebi.ac.uk/ols/beta/ontologies/oba/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FOBA_VT0000017

= Upcoming Meetings and Workshops=

==[http://blog.garnetcommunity.org.uk/garnetegenis-workshop-integrating-large-data-plant-science-big-data-discovery/ 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: [https://sites.google.com/a/cgxchange.org/cropontologycommunity/home]

==[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 ==
* 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

== [http://icbo.cgrb.oregonstate.edu/ 7th International Conference on Biological Ontology and BioCreative 2016] Aug 1st to 4th, Corvallis, OR==
* Link to program: [http://icbo.cgrb.oregonstate.edu/node/20 ICBO + BioCreative Program]
* Link to Easy Chair site: https://easychair.org/conferences/conference_info.cgi?a=10776589

Mar 1st, 2016 Ontology Working Group Meeting

2016-03-01T15:54:03Z

Marieangelique.laporte: /* Meeting in Montpellier, 9 - 13 May 2016 */

==Planteome Ontology WG Zoom Meeting==
* Date: Tuesday Mar. 1st, 2016
* Time: 8:15am PST (GMT-8)
* Connection details: Join from PC, Mac, Linux, iOS or Android: https://zoom.us/j/762470789

* Links to recordings:
* Attendees:

==Agenda:==
=== 1. Recent updates on the TO ===
* revisions to equivalence axioms- ''occurs_in'' and ''composition''
* Stem and culm
* anther morphology traits, incl. anther number
* biochemical branch

=== 2. Changes and updates in the CO files ===
* rice
* cassava
* lentil

* newly mapped and added- wheat--- TBA

=== 3. Update on AmiGO APIs- Justin Elser ===
* API code changes have been merged into our version of AmiGO (dev.planteome.org)
* Does not work on browser.planteome.org as it will require a reload of all data to work because of a schema change to SOLR
* Small issue with main readme page not showing up, but the API itself is working
** ie. http://dev.planteome.org/api doesn't work
** http://dev.planteome.org/api/entity/term/GO:0022008 works and returns JSON

* Still testing out speed and working on readme page not working

=== 4. Visit to IRRI===
* Leo, Marie-Angelique and Austin will visit IRRI Monday March 7th to Friday March 11th
* Goals: TD revision and data annotation-
** MAL, and Leo will be working on trait dictionary
** AM: annotate 140K+ germplasm entries with PD and TO mapping data

Discussion from email:
* EA- the need for an annotation tool: "We discussed the visit of Marie, Léo and Austin and the agenda we prepared. I indicated Mau that the team would like to see how IRRI data annotations could go on Planteome. Mau asked where Planteome stands with the annotations tools because this what IRRI is waiting for long. Would you have any points you want the team to share with IRRI on that aspect?"
* MAL/LV: "We need a simple tool that scientists will be able to use to easily annotate their data. Adhoc scripts are short term and one-shot solutions that will serve Planteome but not necessarily serve IRRI because: The GAF2 format that amiGO2 requires is not known by the breeding community and the annotated data will be published on Planteome and not in the IRRI information systems. We should take the opportunity of being at IRRI to provide some guidance on how to include the ontologies in their data model. Annotating the data at the source is beneficial for everyone. IRRI information systems will have interoperable and discoverable data. And Planteome can easily add future annotations from the IRRI systems."

== 5. [http://www.phenotypercn.org/?page_id=2750 Phenotype RCN meeting February 26-28, 2016] ==
* PJ attended

== 6. Status of second year funding==
* Bioversity is getting impatient, PJ will follow up with NSF and find out

= Upcoming Meetings and Workshops=
==[https://www.isb-sib.ch/events/biocuration2016/home Biocuration 2016, April 10th-14th,2016; Geneva, Switzerland]==
* MAL is going
** [https://www.isb-sib.ch/events/biocuration2016/key-dates key dates]
** Abstract submitted: https://easychair.org/conferences/submission.cgi?a=10690939;submission=2641703

==[http://blog.garnetcommunity.org.uk/garnetegenis-workshop-integrating-large-data-plant-science-big-data-discovery/ 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 [https://sites.google.com/a/cgxchange.org/cropontologycommunity/home]==

==[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 ==
* 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

== [http://icbo.cgrb.oregonstate.edu/ 7th International Conference on Biological Ontology and BioCreative 2016] Aug 1st to 4th, Corvallis, OR==
* Link to program: [http://icbo.cgrb.oregonstate.edu/node/20 ICBO + BioCreative Program]
* Link to Easy Chair site: https://easychair.org/conferences/conference_info.cgi?a=10776589

Mar 1st, 2016 Ontology Working Group Meeting

2016-03-01T15:52:43Z

Marieangelique.laporte: /* Meeting in Montpellier, May 2016- website?? */

==Planteome Ontology WG Zoom Meeting==
* Date: Tuesday Mar. 1st, 2016
* Time: 8:15am PST (GMT-8)
* Connection details: Join from PC, Mac, Linux, iOS or Android: https://zoom.us/j/762470789

* Links to recordings:
* Attendees:

==Agenda:==
=== 1. Recent updates on the TO ===
* revisions to equivalence axioms- ''occurs_in'' and ''composition''
* Stem and culm
* anther morphology traits, incl. anther number
* biochemical branch

=== 2. Changes and updates in the CO files ===
* rice
* cassava
* lentil

* newly mapped and added- wheat--- TBA

=== 3. Update on AmiGO APIs- Justin Elser ===
* API code changes have been merged into our version of AmiGO (dev.planteome.org)
* Does not work on browser.planteome.org as it will require a reload of all data to work because of a schema change to SOLR
* Small issue with main readme page not showing up, but the API itself is working
** ie. http://dev.planteome.org/api doesn't work
** http://dev.planteome.org/api/entity/term/GO:0022008 works and returns JSON

* Still testing out speed and working on readme page not working

=== 4. Visit to IRRI===
* Leo, Marie-Angelique and Austin will visit IRRI Monday March 7th to Friday March 11th
* Goals: TD revision and data annotation-
** MAL, and Leo will be working on trait dictionary
** AM: annotate 140K+ germplasm entries with PD and TO mapping data

Discussion from email:
* EA- the need for an annotation tool: "We discussed the visit of Marie, Léo and Austin and the agenda we prepared. I indicated Mau that the team would like to see how IRRI data annotations could go on Planteome. Mau asked where Planteome stands with the annotations tools because this what IRRI is waiting for long. Would you have any points you want the team to share with IRRI on that aspect?"
* MAL/LV: "We need a simple tool that scientists will be able to use to easily annotate their data. Adhoc scripts are short term and one-shot solutions that will serve Planteome but not necessarily serve IRRI because: The GAF2 format that amiGO2 requires is not known by the breeding community and the annotated data will be published on Planteome and not in the IRRI information systems. We should take the opportunity of being at IRRI to provide some guidance on how to include the ontologies in their data model. Annotating the data at the source is beneficial for everyone. IRRI information systems will have interoperable and discoverable data. And Planteome can easily add future annotations from the IRRI systems."

== 5. [http://www.phenotypercn.org/?page_id=2750 Phenotype RCN meeting February 26-28, 2016] ==
* PJ attended

== 6. Status of second year funding==
* Bioversity is getting impatient, PJ will follow up with NSF and find out

= Upcoming Meetings and Workshops=
==[https://www.isb-sib.ch/events/biocuration2016/home Biocuration 2016, April 10th-14th,2016; Geneva, Switzerland]==
* MAL is going
** [https://www.isb-sib.ch/events/biocuration2016/key-dates key dates]
** Abstract submitted: https://easychair.org/conferences/submission.cgi?a=10690939;submission=2641703

==[http://blog.garnetcommunity.org.uk/garnetegenis-workshop-integrating-large-data-plant-science-big-data-discovery/ 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==

==[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 ==
* 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

== [http://icbo.cgrb.oregonstate.edu/ 7th International Conference on Biological Ontology and BioCreative 2016] Aug 1st to 4th, Corvallis, OR==
* Link to program: [http://icbo.cgrb.oregonstate.edu/node/20 ICBO + BioCreative Program]
* Link to Easy Chair site: https://easychair.org/conferences/conference_info.cgi?a=10776589

Feb 18th, 2016 Ontology Working Group Meeting

2016-02-17T13:03:53Z

Marieangelique.laporte:

Planteome Ontology WG Zoom Meeting
* Date: Thursday Feb 18th, 2016
* Time: 8:15am PST (GMT-8)
* Connection details: Join from PC, Mac, Linux, iOS or Android: https://zoom.us/j/627445291

Agenda: In progress

Possible agenda (EA & MAL)
* Status of the possible ICBO paper: Comparison of ontology mapping techniques to map traits (MAL)
** bottleneck: needs of a collaborative revision of the design patterns
* Current progress of the TO cleaning (LC)
* agreement on a timeline

* Display of the Crop Ontologies in amiGO2
** crop specific names

* Visit to IRRI: 7-11 March: TD revision and data annotation

Oct 20th, 2015 Ontology Working Group Meeting

2015-10-19T08:21:40Z

Marieangelique.laporte:

Who: participants: AM, LC, CM, PJ, JE, EA, MAL

Absent: DWS, ...

* Link to recording- Video: tba
* Link to recording- Audio: tba

==1. Training workshop in Corvallis==
* Location: Corvallis, 2nd week of Nov
* notes are on the wiki- dates, accommodations

Oct 20th, 2015 Ontology Working Group Meeting

2015-10-19T07:09:39Z

Marieangelique.laporte:

Who: participants: AM, LC, CM, PJ, JE, MAL

Absent: DWS, EA, ...

* Link to recording- Video: tba
* Link to recording- Audio: tba

==1. Training workshop in Corvallis==
* Location: Corvallis, 2nd week of Nov
* notes are on the wiki- dates, accommodations

Sept 22nd, 2015- Ontology Working Group Meeting

2015-09-25T08:31:45Z

Marieangelique.laporte: /* From the breeders group, EA, MAL: */

=Agenda=
Connection details: Join from PC, Mac, iOS or Android: https://zoom.us/j/655429261
* In attendance: LC, AM, EA, MAL, PJ, CM, BS

* Link to recording- Video: [[File:Ontology WG Meeting 9-22-15-video.mp4|thumb|Ontology WG 9-22-15 video]]
* Link to recording- Audio: [[File:Ontology WG Meeting 9-22-15-audio.m4a|thumb|Ontology WG 9-22-15 audio]]

== 1. Ontology Development Meeting in Corvallis- November 2015 ==
* Discussion of Workshop scheduling and what would be covered (and other strategy meetups):
Date planning: Week 2 Nov (9th-13th)
* Issues
* EA - tentatively will be traveling week 2 of Nov., but will check on the dates.
* CM - week 1 doesn't work, week 2 works.
* PJ - week1 in Dec doesn't work.
* BS - comes for first/second half for a few days for the strategic planning.

* Agenda of workshop: Three parts:
'''1. Strategic planning (core group and PIs)'''
* Coordination between the Crop Ontology and Planteome
* Plan to have strategic discussions with the PI team to clarify the plans and details - can be on Zoom (difficult to schedule with that number of people)
** LC will send a doodle poll to set up

'''2. Curator training: GitHub, Protege, TermGenie'''
* Ontology development training
* CM is fine training twice, exposure, then larger group
* First training: week 2 of Nov.
* Second stage 2-3 days before or after PAG
* Who? Curators from IITA and CIP are interested- Afola and Reinhard

'''3. Hands on curation/annotation'''

'''4. Software team: AmiGO2 '''
* CM and SC could attend and work with JE in person on the AmiGO2

===From the breeders group, EA, MAL:===
* Cassava file has been posted on the GitHub- from the meeting between CassavaBase and CO in Montpellier
* Naama Menda uses the Cassava OBO file generated from Java (Marie's code), not created and edited in OE
** Afola maintains OBO file- so where is it? Is it the same one??? The files that Afola was maintaining has been modified in order to be compliant with the notion of the variable. Now, the file on Github that Naama uploaded is the one that is maintained by Afola.

* Both Afola, Naama and Reinhard would prefer to use the OBO file or even better, work in Protege

* They discussed how to harmonize efforts between CO, CassavaBase and Breeding Management System- traits and variables, common semantics
* Developed an agreed-upon process that involves MAL's script to transform the excel file to OBO
* This addresses the needs- will start with CassavaBase, move to roots/tuber crops in the RTB program

* new 9/10 annotation file for Cassava conversion is up
* An OBO file will be maintained

* Will this work? Them in OBO/excel, us in OWL.
* Would general ontology training/OBO training help?
* Can we convert from excel to OWL : Yes.

* Unfortunately, the early November dates may not work for Afola and Reinhard, but may be able to join meeting at PAG

* PAG- will be used as a second meeting/continuation of the OSU workshop
** Continue strategy and OWL training for those who make it to OSU in Nov, and fill in people who couldn't make it.
** PJ probably not going to PAG- or perhaps just for the weekend
** Can use travel funding to fly curators out to PAG if they can't make OSU workshop

Please see the notes here: [[Planteome_Curator_workshop_Fall_2015]]

==2. Annual report due now ==
* Year 1 final report due
* next 2 weeks (it's been due since Sept started)
* put it on the Drive, so everyone can add their components
* components:
** who has been listed and working on the project
** Time that people have spent on the project- email addresses
** Might be asking for additions

== 3. Update from Bioversity: ==
* Progress on mapping the CO vocabularies and creating cross products
On going results are in repo ibp-crossproducts: https://github.com/Planteome/ibp-crossproducts

The formal definitions are based on BFO.

Review of existing ontologies (trait, phenotype, ...) are described here : https://github.com/Planteome/ibp-crossproducts/wiki/Related-work

Formal definitions by trait types are described here: https://github.com/Planteome/ibp-crossproducts/wiki/Rules-used-to-build-formal-defintions

Plant Trait definition (what I understand of what is a trait): A plant trait is a quality of Process or a quality of a plant Entity.

Plant Trait definition (Manchester syntax): supposed to be the translation of the above definition (what do you think?)
Quality and s_depends_on some (Process or (Plant Entity or part_of some Plant Entity))
Intersection of a quality and either a Process or a Plant Entity.

Stat: about 25% of the traits that are in TD version 5 (9 crops) are currently defined with a formal definition. I based this work on the content if the columns 'Entity' and 'Attribute' of the TD version 5.

Question: Traits are classified under PATO Quality, e.g. Seed Color in under PATO color. Does this sound good?

Note: I didn't find the URIs of the BFO properties (MAL)

=== Examples ===
'''Seed Color'''
color and ('inheres in' some seed)
Intersection of Color (specifically dependent continuant) and a specifically dependent continuant (indeed, the domain of inheres_in is specifically dependent continuant) that exists only if seed exists.

'''Aluminium Tolerance'''
'tolerant to' and ('inheres in' some ('aluminum nutrient regimen' and 'whole plant'))
Intersection of Tolerant to and a specifically dependent continuant that depends on both the presence of a plant and an aluminum nutrient regimen

'''Amylose content (of the tuberous root)'''
composition and ('inheres in' some (amylose and ('continuant part of' some 'tuberous root')))
Intersection of Composition and a specifically dependent continuant that exists only if ( the intersection of amylose and a continuant (which is a part of a tuberous root) )exists.

'''Flowering Time'''
time and ('s depends on' some (flowering and ('has participant' some 'flowering stage')))
Intersection of Time and a specifically dependent continuant that exists only if the intersection of (the Process Flowering and A Process that exists only the Flowering stage exists) exists

=== From OBA: ===

Plant trait:
'biological attribute' and ('occurs in' some 'whole plant') and ('has quality' some quality)
Intersection of a biological attribute and a process (domain of occurs in a process) and an independent continuant (I assume that the domain of has quality is an independent continuant)

seed color
'biological attribute' and ('has quality' some color) and ('attribute of' some 'seed coat')
Intersection of an Biological Attribute and an independent continuant (I assume that the domain of has quality is an independent continuant, so something that have a color) and something that have an attribute (attribute of is not described, and I am not able to guess the domain of the property)

== 4. ICBO Meeting, 2016, Corvallis ==
* Need to create a web page and send out a notice
* ICBO conference

* JE will set up a site - ICBO-2016-conference.com
** might need to host on our stuff, can be complicated.
** a portal exists ICBO-conference.org
** can link to that domain name ^

* BS will work with PJ on the details for the committee
** Get the announcement out as soon as possible, so people have plenty of warning

* OBO started as Open Biological Ontologies, and now it's "Biomedical"
** need to make it clear we are not making biomedical assumptions
** change the name to just use 'Biological'
** already a CSO (chief science officer) lined up as potential headline speaker
** USDA chief science officer also an option

==Next meeting: [[Sept_29th,_2015_Ontology_Working_Group_Meeting]]==

Sept 15th, 2015- Ontology Working Group Meeting

2015-09-18T15:10:57Z

Marieangelique.laporte: /* Examples */

'''Time: 8:15am PDT (GMT-7:00) Pacific Time (US and Canada)'''

Connection details: Join from PC, Mac, iOS or Android: https://zoom.us/j/655429261

* In attendance: LC, MAL, AM, PJ, BS, CM

* Link to recording- Video: [[File:Ontology WG 9-15-15.mp4|thumb|Ontology WG 9-15-15 video]]
* Link to recording- Audio: [[File:Ontology WG 9-15-15 audio.m4a|thumb|Ontology WG 9-15-15 audio]]

=Agenda=
== 1. Upcoming Plant Ontology Release #21 ==
- Many changes and updates to the PO which will accompany the PSDS paper submission
* Transition to GitHub complete, and working well- required many updated Xrefs and links in the various browsers, ontology files and pages.
* PO Live Browser updated for the transition to GitHub with links to the new Issue Tracker and association repository on the SVN-
* Timeline- within the next 2 weeks
* For more information: [http://wiki.plantontology.org/index.php/Release_21 Plant_Ontology_Release_#21]

* New association data developed from the [http://wiki.plantontology.org/index.php/Plant_Pheontype_Pilot_Project_2015] paper published in Feb 2015: http://www.plantmethods.com/content/11/1/10/abstract
** Six plant species: Rice, Maize, Arabidopsis, soybean, Medicago, tomato ~ 4,193 new direct associations

==2. Planteome.org Update:==
* Once the Plant Ontology update is pushed out, we will be rolling all the data files and updated ontologies to the Planteome web page: Planteome.org for our Planteome 1.0 release.
* This is important as we are getting ready to submit our first annual report and people are using the Planteome site, so we want to make sure it is all working well.
* We are diligently working to make sure all the dbxrefs and links are updated, so if you find any issues, please let us know.

* New association data developed from MaizeGDB (Mary Schaeffer)
* Based on data set from Scott Stelpfulg et al (Kaeppler group): "An expanded maize gene expression atlas based on RNA-sequencing and its use to explore root development"
** [https://dl.sciencesocieties.org/publications/tpg/first-look The Plant Genome doi:10.3835/plantgenome2015.04.0025]
** Accepted paper, posted 08/07/2015.
** Update of the Nimblegen Microarray data - more tissues, not so much background noise

== 3. Plant Trait Ontology: ==
Questions from Barry about how to define the traits:

===Anatomy and Morphology traits===
'''> Are there any traits which are not anatomy and morphology traits?'''

''There are 8 different branches in the TO, anatomy and morphology trait is just one.''

[[File:TO-top level.png|TO-top level.png.jpg]]

''* Note that there is a still a class "other miscellaneous traits" which we are planning to get rid of soon. ''

'''> Is there a definition of 'anatomy trait' and of 'morphology trait'?'''
* LC: My understanding of the meaning of anatomy and morphology in botany are as follows: the anatomy is the internal structure and the morphology is the external structure. This is consistent with the definitions of plant anatomy and morphology in common use:

* '''From Evert, RF and Eichhorn, SE (2006). Esau's Plant Anatomy: Meristems, Cells, And Tissues Of The Plant Body: Their Structure, Function, And Development''', 3rd Edition. Wiley-Liss. ISBN:0471738433: "Anatomy is the study of the internal structure of organism, morphology is the study of their external structure.

* Morphology (biology): Morphology is a branch of biology dealing with the study of the form and structure of organisms and their specific structural features.[http://www.oxforddictionaries.com]. This includes aspects of the outward appearance (shape, structure, colour, pattern,size), i.e., external morphology (eidonomy) as well as the form and structure of the internal parts like bones and organs, i.e., internal morphology or anatomy.

* morphology (PATO:0000051): A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure.

'''> Are they logically disjoint? '''
* Based on some definitions, they are logically disjoint, but others define morphology to encompass both internal and external features.

'''> The term 'anatomy and morphology trait' really means 'anatomy trait or morphology trait', right?'''
* ''The class is designed to be inclusive- covering physical traits that are either internal (anatomy) or external (morphology), so 'anatomy trait or morphology trait' would perhaps be more correct. Even better would be to call them plant''

====Test classification of some of the subclasses of PSA+M traits as either anatomy or morphology traits:====

===== Examples of morphological (external) trait classes =====
* awn length, width, thickness, color, presence (?)
* leaf margin serrated
* seedling hypocotyl size
* axillary bud shape
* plant cell shape, size, length
* embryo shape, shootless embryo
* flower or floret color, type, diameter, length, number, shape, etc
* chasmogamous flower, cleistogamus flower
* ear (infructescence) circumference, aspect, color, length, weight, position shape, diameter, circumference
* inflorescence (incl. panicle, spikelet, tassel) size, width, branching, color, density, depth, diameter, exsertion, number, presence, shape, texture, type, waxiness, weight, etc
* axillary bud number, shape, size, prominence
* leaf attitude, color, weight, cover, volume, flexibility, height, number, pubescence, adherence, shape, size, rolling, phyllotaxy, area, nitrogen content, pigment content, gloss, drying, stomatal frequency, temperature, necrosis,
* leaf lamina area, color, length, splitting, width, pubescence, joint bending, etc

===== Examples of anatomy (internal) trait classes: =====
* leaf vein color, size
* leaf midvein thickness

''Thus I feel that we could change the name of this class to "plant morphological trait", which would encompass both the internal and external structure, appearance and form. '''

* Current term name def'n: '''anatomy and morphology trait (TO:0000017): A plant trait (TO:0000387) which is associated with the anatomy or morphology of a plant anatomical entity (PO:0025131) or one or more constituent cellular components (GO:0005575) contained therein.'''
** Comment: Includes traits of plant structures (PO:0009011) such as plant cell (PO:0009002), plant organ (PO:0009008), portion of plant tissue (PO:0009007), vascular system (PO:0000034), whole plant (PO:0000003) and seed (PO:0009010), as well as those of plant anatomical spaces (PO:0025117) and portions of plant substance (PO:0025161).

* ''This definition will need to be revised if we keep this name for the class. It could be rewritten with a definition of what the

* Proposed revised name and def'n: plant morphological trait (TO:0000017): A plant trait (TO:0000387) which is "associated with" physical traits that are either internal (anatomy) or external (morphology) of a plant anatomical entity (PO:0025131) or one or more constituent cellular components (GO:0005575) contained therein.'''

cell wall (GO:0005618); chloroplast (GO:0009507)

== Objection to using: 'associated with' ==
> BS: (a) it is vague (b) it will block reasoning
''I agree that it is vague and would prefer a more precise statement, although textual definition will not block reasoning.''

Example anatomy and morphology trait classes:
* stem number (TO:0000953): A shoot system anatomy and morphology trait (TO:0000077) which is associated with the number of stems (PO:0009047).
* stem size (TO:0000954): A stem anatomy and morphology trait (TO:0000361) which is associated with the size of a stem (PO:0009047).

> Suggestions:
* "stem number =def. a trait of a plant which is the number of stems of the plant" and so on for the other cases
''the trait is not the number of stems on the plant, but it describes the number of stems. This is not in the genus-differentia format ''

''stem number (TO:0000953): A shoot system anatomy and morphology trait (TO:0000077) which '''is''' the number of stems (PO:0009047) in the shoot system of a plant.''

* Examples from other from [http://obofoundry.github.io/ OBO_Foundry_Ontologies] that concern traits:

e.g. Vertebrate Trait Ontology: [http://www.berkeleybop.org/ontologies/vt.owl] -- “related to”
* body size trait (VT:0100005): Any measurable or observable characteristic '''related to''' the overall physical magnitude of an organism.
* body temperature trait (VT:0005535): Any measurable or observable characteristic '''related to''' the level of heat maintained by a living being.

e.g. Animal Trait Ontology:
[http://147.99.159.184:8080/webprotege/#ATOL] -- “related to”

How are traits defined using formal relations?

* name: has_quality (id: RO:0000086)
* def: "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence"
* property_value: IAO:0000112 "this apple has quality this red color" xsd:string
* property_value: IAO:0000116 "A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the
* bearer does not exist." xsd:string
* property_value: IAO:0000118 "has_quality" xsd:string

Possible solution using relations from RO:

ear shape (TO:0000964): An infructescence anatomy or morphology trait (TO:0000920)
an ear infructescence (PO:0025597) has_quality shape.

e.g.

inheres_in

Example from BATTO: http://www.ontobee.org/browser/index.php?o=oba

[Term]
id: TO:0000431 ! ear length
intersection_of: BATTO:0000001 ! biological attribute
intersection_of: affects_quality PATO:0000122 ! length
intersection_of: attribute_of PO:0020136 ! ear (sensu Zea)

== 4. Update from Bioversity: ==
* Progress on mapping the CO vocabularies and creating cross products
On going results are in repo ibp-crossproducts: https://github.com/Planteome/ibp-crossproducts

The formal definitions are based on BFO.

Review of existing ontologies (trait, phenotype, ...) are described here : https://github.com/Planteome/ibp-crossproducts/wiki/Related-work

Formal definitions by trait types are described here: https://github.com/Planteome/ibp-crossproducts/wiki/Rules-used-to-build-formal-defintions

Plant Trait definition (what I understand of what is a trait): A plant trait is a quality of Process or a quality of a plant Entity.

Plant Trait definition (Manchester syntax): supposed to be the translation of the above definition (what do you think?)
Quality and s_depends_on some (Process or (Plant Entity or part_of some Plant Entity))
Intersection of a quality and either a Process or a Plant Entity.

Stat: about 25% of the traits that are in TD version 5 (9 crops) are currently defined with a formal definition. I based this work on the content if the columns 'Entity' and 'Attribute' of the TD version 5.

Question: Traits are classified under PATO Quality, e.g. Seed Color in under PATO color. Does this sound good?

Note: I didn't find the URIs of the BFO properties

=== Examples ===
'''Seed Color'''
color and ('inheres in' some seed)
Intersection of Color (specifically dependent continuant) and a specifically dependent continuant (indeed, the domain of inheres_in is specifically dependent continuant) that exists only if seed exists.

'''Aluminium Tolerance'''
'tolerant to' and ('inheres in' some ('aluminum nutrient regimen' and 'whole plant'))
Intersection of Tolerant to and a specifically dependent continuant that depends on both the presence of a plant and an aluminum nutrient regimen

'''Amylose content (of the tuberous root)'''
composition and ('inheres in' some (amylose and ('continuant part of' some 'tuberous root')))
Intersection of Composition and a specifically dependent continuant that exists only if ( the intersection of amylose and a continuant (which is a part of a tuberous root) )exists.

'''Flowering Time'''
time and ('s depends on' some (flowering and ('has participant' some 'flowering stage')))
Intersection of Time and a specifically dependent continuant that exists only if the intersection of (the Process Flowering and A Process that exists only the Flowering stage exists) exists

=== From OBA: ====

Plant trait:
'biological attribute' and ('occurs in' some 'whole plant') and ('has quality' some quality)
Intersection of a biological attribute and a process (domain of occurs in a process) and an independent continuant (I assume that the domain of has quality is an independent continuant)

seed color
'biological attribute' and ('has quality' some color) and ('attribute of' some 'seed coat')
Intersection of an Biological Attribute and an independent continuant (I assume that the domain of has quality is an independent continuant, so something that have a color) and something that have an attribute (attribute of is not described, and I am not able to guess the domain of the property)

== 5. Proposed: Ontology Development Meeting in Corvallis early November- ==
Please see the notes here: [[Planteome_Curator_workshop_Fall_2015]]

== 5. TermGenie Demo ==
* A tool for creating new ontology terms for either GO (Gene Ontology) or OBA (Ontology of Biological Attributes). It uses a pattern-based approach to rapidly generate new terms and place them appropriately within the ontology structure. All terms are reviewed by a senior editor before the final commit to the ontology.

* Two instances of TermGenie exist: for OBA and GO:
** [http://go.termgenie.org/ TermGenie GO]

** [http://go.termgenie.org/ TermGenie OBO]

* Citation: [http://www.ncbi.nlm.nih.gov/pubmed/25937883 TermGenie - a web-application for pattern-based ontology class generation]

''Discussion of TermGenie tabled for next meeting"

==Next meeting: Sept 29th==

Sept 15th, 2015- Ontology Working Group Meeting

2015-09-18T13:55:47Z

Marieangelique.laporte: /* 4. Update from Bioversity: */

'''Time: 8:15am PDT (GMT-7:00) Pacific Time (US and Canada)'''

Connection details: Join from PC, Mac, iOS or Android: https://zoom.us/j/655429261

* In attendance: LC, MAL, AM, PJ, BS, CM

* Link to recording- Video: [[File:Ontology WG 9-15-15.mp4|thumb|Ontology WG 9-15-15 video]]
* Link to recording- Audio: [[File:Ontology WG 9-15-15 audio.m4a|thumb|Ontology WG 9-15-15 audio]]

=Agenda=
== 1. Upcoming Plant Ontology Release #21 ==
- Many changes and updates to the PO which will accompany the PSDS paper submission
* Transition to GitHub complete, and working well- required many updated Xrefs and links in the various browsers, ontology files and pages.
* PO Live Browser updated for the transition to GitHub with links to the new Issue Tracker and association repository on the SVN-
* Timeline- within the next 2 weeks
* For more information: [http://wiki.plantontology.org/index.php/Release_21 Plant_Ontology_Release_#21]

* New association data developed from the [http://wiki.plantontology.org/index.php/Plant_Pheontype_Pilot_Project_2015] paper published in Feb 2015: http://www.plantmethods.com/content/11/1/10/abstract
** Six plant species: Rice, Maize, Arabidopsis, soybean, Medicago, tomato ~ 4,193 new direct associations

==2. Planteome.org Update:==
* Once the Plant Ontology update is pushed out, we will be rolling all the data files and updated ontologies to the Planteome web page: Planteome.org for our Planteome 1.0 release.
* This is important as we are getting ready to submit our first annual report and people are using the Planteome site, so we want to make sure it is all working well.
* We are diligently working to make sure all the dbxrefs and links are updated, so if you find any issues, please let us know.

* New association data developed from MaizeGDB (Mary Schaeffer)
* Based on data set from Scott Stelpfulg et al (Kaeppler group): "An expanded maize gene expression atlas based on RNA-sequencing and its use to explore root development"
** [https://dl.sciencesocieties.org/publications/tpg/first-look The Plant Genome doi:10.3835/plantgenome2015.04.0025]
** Accepted paper, posted 08/07/2015.
** Update of the Nimblegen Microarray data - more tissues, not so much background noise

== 3. Plant Trait Ontology: ==
Questions from Barry about how to define the traits:

===Anatomy and Morphology traits===
'''> Are there any traits which are not anatomy and morphology traits?'''

''There are 8 different branches in the TO, anatomy and morphology trait is just one.''

[[File:TO-top level.png|TO-top level.png.jpg]]

''* Note that there is a still a class "other miscellaneous traits" which we are planning to get rid of soon. ''

'''> Is there a definition of 'anatomy trait' and of 'morphology trait'?'''
* LC: My understanding of the meaning of anatomy and morphology in botany are as follows: the anatomy is the internal structure and the morphology is the external structure. This is consistent with the definitions of plant anatomy and morphology in common use:

* '''From Evert, RF and Eichhorn, SE (2006). Esau's Plant Anatomy: Meristems, Cells, And Tissues Of The Plant Body: Their Structure, Function, And Development''', 3rd Edition. Wiley-Liss. ISBN:0471738433: "Anatomy is the study of the internal structure of organism, morphology is the study of their external structure.

* Morphology (biology): Morphology is a branch of biology dealing with the study of the form and structure of organisms and their specific structural features.[http://www.oxforddictionaries.com]. This includes aspects of the outward appearance (shape, structure, colour, pattern,size), i.e., external morphology (eidonomy) as well as the form and structure of the internal parts like bones and organs, i.e., internal morphology or anatomy.

* morphology (PATO:0000051): A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure.

'''> Are they logically disjoint? '''
* Based on some definitions, they are logically disjoint, but others define morphology to encompass both internal and external features.

'''> The term 'anatomy and morphology trait' really means 'anatomy trait or morphology trait', right?'''
* ''The class is designed to be inclusive- covering physical traits that are either internal (anatomy) or external (morphology), so 'anatomy trait or morphology trait' would perhaps be more correct. Even better would be to call them plant''

====Test classification of some of the subclasses of PSA+M traits as either anatomy or morphology traits:====

===== Examples of morphological (external) trait classes =====
* awn length, width, thickness, color, presence (?)
* leaf margin serrated
* seedling hypocotyl size
* axillary bud shape
* plant cell shape, size, length
* embryo shape, shootless embryo
* flower or floret color, type, diameter, length, number, shape, etc
* chasmogamous flower, cleistogamus flower
* ear (infructescence) circumference, aspect, color, length, weight, position shape, diameter, circumference
* inflorescence (incl. panicle, spikelet, tassel) size, width, branching, color, density, depth, diameter, exsertion, number, presence, shape, texture, type, waxiness, weight, etc
* axillary bud number, shape, size, prominence
* leaf attitude, color, weight, cover, volume, flexibility, height, number, pubescence, adherence, shape, size, rolling, phyllotaxy, area, nitrogen content, pigment content, gloss, drying, stomatal frequency, temperature, necrosis,
* leaf lamina area, color, length, splitting, width, pubescence, joint bending, etc

===== Examples of anatomy (internal) trait classes: =====
* leaf vein color, size
* leaf midvein thickness

''Thus I feel that we could change the name of this class to "plant morphological trait", which would encompass both the internal and external structure, appearance and form. '''

* Current term name def'n: '''anatomy and morphology trait (TO:0000017): A plant trait (TO:0000387) which is associated with the anatomy or morphology of a plant anatomical entity (PO:0025131) or one or more constituent cellular components (GO:0005575) contained therein.'''
** Comment: Includes traits of plant structures (PO:0009011) such as plant cell (PO:0009002), plant organ (PO:0009008), portion of plant tissue (PO:0009007), vascular system (PO:0000034), whole plant (PO:0000003) and seed (PO:0009010), as well as those of plant anatomical spaces (PO:0025117) and portions of plant substance (PO:0025161).

* ''This definition will need to be revised if we keep this name for the class. It could be rewritten with a definition of what the

* Proposed revised name and def'n: plant morphological trait (TO:0000017): A plant trait (TO:0000387) which is "associated with" physical traits that are either internal (anatomy) or external (morphology) of a plant anatomical entity (PO:0025131) or one or more constituent cellular components (GO:0005575) contained therein.'''

cell wall (GO:0005618); chloroplast (GO:0009507)

== Objection to using: 'associated with' ==
> BS: (a) it is vague (b) it will block reasoning
''I agree that it is vague and would prefer a more precise statement, although textual definition will not block reasoning.''

Example anatomy and morphology trait classes:
* stem number (TO:0000953): A shoot system anatomy and morphology trait (TO:0000077) which is associated with the number of stems (PO:0009047).
* stem size (TO:0000954): A stem anatomy and morphology trait (TO:0000361) which is associated with the size of a stem (PO:0009047).

> Suggestions:
* "stem number =def. a trait of a plant which is the number of stems of the plant" and so on for the other cases
''the trait is not the number of stems on the plant, but it describes the number of stems. This is not in the genus-differentia format ''

''stem number (TO:0000953): A shoot system anatomy and morphology trait (TO:0000077) which '''is''' the number of stems (PO:0009047) in the shoot system of a plant.''

* Examples from other from [http://obofoundry.github.io/ OBO_Foundry_Ontologies] that concern traits:

e.g. Vertebrate Trait Ontology: [http://www.berkeleybop.org/ontologies/vt.owl] -- “related to”
* body size trait (VT:0100005): Any measurable or observable characteristic '''related to''' the overall physical magnitude of an organism.
* body temperature trait (VT:0005535): Any measurable or observable characteristic '''related to''' the level of heat maintained by a living being.

e.g. Animal Trait Ontology:
[http://147.99.159.184:8080/webprotege/#ATOL] -- “related to”

How are traits defined using formal relations?

* name: has_quality (id: RO:0000086)
* def: "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence"
* property_value: IAO:0000112 "this apple has quality this red color" xsd:string
* property_value: IAO:0000116 "A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the
* bearer does not exist." xsd:string
* property_value: IAO:0000118 "has_quality" xsd:string

Possible solution using relations from RO:

ear shape (TO:0000964): An infructescence anatomy or morphology trait (TO:0000920)
an ear infructescence (PO:0025597) has_quality shape.

e.g.

inheres_in

Example from BATTO: http://www.ontobee.org/browser/index.php?o=oba

[Term]
id: TO:0000431 ! ear length
intersection_of: BATTO:0000001 ! biological attribute
intersection_of: affects_quality PATO:0000122 ! length
intersection_of: attribute_of PO:0020136 ! ear (sensu Zea)

== 4. Update from Bioversity: ==
* Progress on mapping the CO vocabularies and creating cross products
On going results are in repo ibp-crossproducts: https://github.com/Planteome/ibp-crossproducts

The formal definitions are based on BFO.

Review of existing ontologies (trait, phenotype, ...) are described here : https://github.com/Planteome/ibp-crossproducts/wiki/Related-work

Formal definitions by trait types are described here: https://github.com/Planteome/ibp-crossproducts/wiki/Rules-used-to-build-formal-defintions

Plant Trait definition (what I understand of what is a trait): A plant trait is a quality of Process or a quality of a plant Entity.

Plant Trait definition (Manchester syntax): supposed to be the translation of the above definition (what do you think?)
Quality and s_depends_on some (Process or (Plant Entity or part_of some Plant Entity))
Intersection of a quality and either a Process or a Plant Entity.

Stat: about 25% of the traits that are in TD version 5 (9 crops) are currently defined with a formal definition. I based this work on the content if the columns 'Entity' and 'Attribute' of the TD version 5.

Question: Traits are classified under PATO Quality, e.g. Seed Color in under PATO color. Does this sound good?

Note: I didn't find the URIs of the BFO properties

=== Examples ===
Seed Color:
color and ('inheres in' some seed)
Intersection of Color (specifically dependent continuant) and a specifically dependent continuant (indeed, the domain of inheres_in is specifically dependent continuant) that exists only if seed exists.

=== From OBA: ====

Plant trait:
'biological attribute' and ('occurs in' some 'whole plant') and ('has quality' some quality)
Intersection of a biological attribute and a process (domain of occurs in a process) and an independent continuant (I assume that the domain of has quality is an independent continuant)

seed color
'biological attribute' and ('has quality' some color) and ('attribute of' some 'seed coat')
Intersection of an Biological Attribute and an independent continuant (I assume that the domain of has quality is an independent continuant, so something that have a color) and something that have an attribute (attribute of is not described, and I am not able to guess the domain of the property)

== 5. Proposed: Ontology Development Meeting in Corvallis early November- ==
Please see the notes here: [[Planteome_Curator_workshop_Fall_2015]]

== 5. TermGenie Demo ==
* A tool for creating new ontology terms for either GO (Gene Ontology) or OBA (Ontology of Biological Attributes). It uses a pattern-based approach to rapidly generate new terms and place them appropriately within the ontology structure. All terms are reviewed by a senior editor before the final commit to the ontology.

* Two instances of TermGenie exist: for OBA and GO:
** [http://go.termgenie.org/ TermGenie GO]

** [http://go.termgenie.org/ TermGenie OBO]

* Citation: [http://www.ncbi.nlm.nih.gov/pubmed/25937883 TermGenie - a web-application for pattern-based ontology class generation]

''Discussion of TermGenie tabled for next meeting"

==Next meeting: Sept 29th==

Sept 15th, 2015- Ontology Working Group Meeting

2015-09-17T14:09:27Z

Marieangelique.laporte: /* 4. Update from Bioversity: */

'''Time: 8:15am PDT (GMT-7:00) Pacific Time (US and Canada)'''

Connection details: Join from PC, Mac, iOS or Android: https://zoom.us/j/655429261

* In attendance: LC, MAL, AM, PJ, BS, CM

* Link to recording- Video: [[File:Ontology WG 9-15-15.mp4|thumb|Ontology WG 9-15-15 video]]
* Link to recording- Audio: [[File:Ontology WG 9-15-15 audio.m4a|thumb|Ontology WG 9-15-15 audio]]

=Agenda=
== 1. Upcoming Plant Ontology Release #21 ==
- Many changes and updates to the PO which will accompany the PSDS paper submission
* Transition to GitHub complete, and working well- required many updated Xrefs and links in the various browsers, ontology files and pages.
* PO Live Browser updated for the transition to GitHub with links to the new Issue Tracker and association repository on the SVN-
* Timeline- within the next 2 weeks
* For more information: [http://wiki.plantontology.org/index.php/Release_21 Plant_Ontology_Release_#21]

* New association data developed from the [http://wiki.plantontology.org/index.php/Plant_Pheontype_Pilot_Project_2015] paper published in Feb 2015: http://www.plantmethods.com/content/11/1/10/abstract
** Six plant species: Rice, Maize, Arabidopsis, soybean, Medicago, tomato ~ 4,193 new direct associations

* New association data developed from MaizeGDB (Mary Schaeffer)
* Based on data set from Scott Stelpfulg et al (Kaeppler group): "An expanded maize gene expression atlas based on RNA-sequencing and its use to explore root development"
** [https://dl.sciencesocieties.org/publications/tpg/first-look The Plant Genome doi:10.3835/plantgenome2015.04.0025]
** Accepted paper, posted 08/07/2015.
** Update of the Nimblegen Microarray data - more tissues, not so much background noise

==2. Planteome.org Update:==
* Once the Plant Ontology update is pushed out, we will be rolling all the data files and updated ontologies to the Planteome web page: Planteome.org for our Planteome 1.0 release.
* This is important as we are getting ready to submit our first annual report and people are using the Planteome site, so we want to make sure it is all working well.
* We are diligently working to make sure all the dbxrefs and links are updated, so if you find any issues, please let us know.

== 3. Plant Trait Ontology: ==
Questions from Barry about how to define the traits:

===Anatomy and Morphology traits===
'''> Are there any traits which are not anatomy and morphology traits?'''

''There are 8 different branches in the TO, anatomy and morphology trait is just one.''

[[File:TO-top level.png|TO-top level.png.jpg]]

''* Note that there is a still a class "other miscellaneous traits" which we are planning to get rid of soon.

'''> Is there a definition of 'anatomy trait' and of 'morphology trait'?'''
* LC: My understanding of the meaning of anatomy and morphology in botany are as follows: the anatomy is the internal structure and the morphology is the external structure. This is consistent with the definitions of plant anatomy and morphology in common use:

* '''plant anatomy:''' "The general term for the study of the internal structure of plants. While originally it included plant morphology, which is the description of the physical form and external structure of plants, since the mid-20th century the investigations of plant anatomy are considered a separate, distinct field, and plant anatomy refers to just the internal plant structures.[1][2] Plant anatomy is now frequently investigated at the cellular level, and often involves the sectioning of tissues and microscopy.[3] (from : https://en.wikipedia.org/wiki/Plant_anatomy)

* '''Plant morphology:''' "The study of the physical form and external structure of plants.[1] This is usually considered distinct from plant anatomy,[1] which is the study of the internal structure of plants, especially at the microscopic level.[2] Plant morphology is useful in the visual identification of plants." (from https://en.wikipedia.org/wiki/Plant_morphology)

* Current def'n: '''anatomy and morphology trait (TO:0000017): A plant trait (TO:0000387) which is associated with the anatomy or morphology of a plant anatomical entity (PO:0025131) or one or more constituent cellular components (GO:0005575) contained therein.'''
** Comment: Includes traits of plant structures (PO:0009011) such as plant cell (PO:0009002), plant organ (PO:0009008), portion of plant tissue (PO:0009007), vascular system (PO:0000034), whole plant (PO:0000003) and seed (PO:0009010), as well as those of plant anatomical spaces (PO:0025117) and portions of plant substance (PO:0025161).

'''> Are they logically disjoint? '''
* Based on the definitions above, they are logically disjoint

'''> The term 'anatomy and morphology trait' really means 'anatomy trait or morphology trait', right?'''
* ''The class is designed to be inclusive- covering physical traits that are either internal (anatomy) or external (morphology), so 'anatomy trait or morphology trait' would perhaps be more correct.''
* ''If we say "anatomy and morphology trait", does that mean that the trait in question is both an anatomical and a morphological trait?''

====Test classification of some of the subclasses of PSA+M traits as either anatomy or morphology traits:====

===== Examples of morphological trait classes =====
* awn length, width, thickness, color, presence (?)
* leaf margin serrated
* seedling hypocotyl size
* axillary bud shape
* plant cell shape, size, length
* embryo shape, shootless embryo
* flower or floret color, type, diameter, length, number, shape, etc
* chasmogamous flower, cleistogamus flower
* ear (infructescence) circumference, aspect, color, length, weight, position shape, diameter, circumference
* inflorescence (incl. panicle, spikelet, tassel) size, width, branching, color, density, depth, diameter, exsertion, number, presence, shape, texture, type, waxiness, weight, etc
* axillary bud number, shape, size, prominence
* leaf attitude, color, weight, cover, volume, flexibility, height, number, pubescence, adherence, shape, size, rolling, phyllotaxy, area, nitrogen content, pigment content, gloss, drying, stomatal frequency, temperature, necrosis,
* leaf lamina area, color, length, splitting, width, pubescence, joint bending, etc

===== Examples of anatomy trait classes: =====
* leaf vein color, size
* leaf midvein thickness

* Question: Would either of these classes include traits such as fruit color or leaf color? This is more a quality or atribute than an anatomical or morphological trait.

== Objection to using: 'associated with' ==
> BS: (a) it is vague (b) it will block reasoning
''I agree that it is vague and would prefer a more precise statement, although textual definition will not block reasoning.''

Example anatomy and morphology trait classes:
* stem number (TO:0000953): A shoot system anatomy and morphology trait (TO:0000077) which is associated with the number of stems (PO:0009047).
** Added Xrefs to: number (PATO:0001555); TO_GIT:157

* stem size (TO:0000954):A stem anatomy and morphology trait (TO:0000361) which is associated with the size of a stem (PO:0009047).
** Added Xrefs to: size (PATO:0000117); TO_GIT:157
** Added narrow synonym: stalk size

Suggestions:
* "stem number =def. a trait of a plant which is the number of stems of the plant"
and so on for the other cases

* "infructescence axis shape: An infructescence axis anatomy and morphology trait (TO:0000921) that describes the shape of the infructescence axis" [or specify the 'of' further]

synonym: cob shape

Examples from other from [http://obofoundry.github.io/ OBO_Foundry_Ontologies] that concern traits:

Vertebrate Trait Ontology:
http://www.berkeleybop.org/ontologies/vt.owl -- “related to”

Animal Trait Ontology:
http://147.99.159.184:8080/webprotege/#ATOL -- “related to”

* name: has_quality (id: RO:0000086)
* def: "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence"
property_value: IAO:0000112 "this apple has quality this red color" xsd:string
property_value: IAO:0000116 "A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist." xsd:string
property_value: IAO:0000118 "has_quality" xsd:string

Possible solution using relations from RO:

ear shape (TO:0000964): An infructescence anatomy or morphology trait (TO:0000920)
an ear infructescence (PO:0025597) has_quality shape.

Added dXrefs: shape (PATO:0000052);

Example from BATTO: http://www.ontobee.org/browser/index.php?o=oba

[Term]
id: TO:0000431 ! ear length
intersection_of: BATTO:0000001 ! biological attribute
intersection_of: affects_quality PATO:0000122 ! length
intersection_of: attribute_of PO:0020136 ! ear (sensu Zea)

== 4. Update from Bioversity: ==
* Progress on mapping the CO vocabularies and creating cross products
On going results are in repo ibp-crossproducts: https://github.com/Planteome/ibp-crossproducts

The formal definitions are based on BFO.

Review of existing ontologies (trait, phenotype, ...) are described here : https://github.com/Planteome/ibp-crossproducts/wiki/Related-work

Formal definitions by trait types are described here: https://github.com/Planteome/ibp-crossproducts/wiki/Rules-used-to-build-formal-defintions

Trait definition (Manchester syntax):
Quality and s_depends_on some (Process or (Plant Entity or part_of some Plant Entity))

Stat: about 25% of the traits that are in TD version 5 (9 crops) are currently defined with a formal definition. I based this work on the content if the columns 'Entity' and 'Attribute' of the TD version 5.

Question: Traits are classified under PATO Quality, e.g. Seed Color in under PATO color. Does this sound good?

Note: I didn't find the URIs of the BFO properties

== 5. Proposed: Ontology Development Meeting in Corvallis early November- ==
Please see the notes here: [[Planteome_Curator_workshop_Fall_2015]]

== 5. TermGenie Demo ==
* A tool for creating new ontology terms for either GO (Gene Ontology) or OBA (Ontology of Biological Attributes). It uses a pattern-based approach to rapidly generate new terms and place them appropriately within the ontology structure. All terms are reviewed by a senior editor before the final commit to the ontology.

* Two instances of TermGenie exist: for OBA and GO:
** [http://go.termgenie.org/ TermGenie GO]

** [http://go.termgenie.org/ TermGenie OBO]

* Citation: [http://www.ncbi.nlm.nih.gov/pubmed/25937883 TermGenie - a web-application for pattern-based ontology class generation]

''Discussion of TermGenie tabled for next meeting"

==Next meeting: Sept 29th==

Sept 15th, 2015- Ontology Working Group Meeting

2015-09-17T14:08:54Z

Marieangelique.laporte: /* 4. Update from Bioversity: */

'''Time: 8:15am PDT (GMT-7:00) Pacific Time (US and Canada)'''

Connection details: Join from PC, Mac, iOS or Android: https://zoom.us/j/655429261

* In attendance: LC, MAL, AM, PJ, BS, CM

* Link to recording- Video: [[File:Ontology WG 9-15-15.mp4|thumb|Ontology WG 9-15-15 video]]
* Link to recording- Audio: [[File:Ontology WG 9-15-15 audio.m4a|thumb|Ontology WG 9-15-15 audio]]

=Agenda=
== 1. Upcoming Plant Ontology Release #21 ==
- Many changes and updates to the PO which will accompany the PSDS paper submission
* Transition to GitHub complete, and working well- required many updated Xrefs and links in the various browsers, ontology files and pages.
* PO Live Browser updated for the transition to GitHub with links to the new Issue Tracker and association repository on the SVN-
* Timeline- within the next 2 weeks
* For more information: [http://wiki.plantontology.org/index.php/Release_21 Plant_Ontology_Release_#21]

* New association data developed from the [http://wiki.plantontology.org/index.php/Plant_Pheontype_Pilot_Project_2015] paper published in Feb 2015: http://www.plantmethods.com/content/11/1/10/abstract
** Six plant species: Rice, Maize, Arabidopsis, soybean, Medicago, tomato ~ 4,193 new direct associations

* New association data developed from MaizeGDB (Mary Schaeffer)
* Based on data set from Scott Stelpfulg et al (Kaeppler group): "An expanded maize gene expression atlas based on RNA-sequencing and its use to explore root development"
** [https://dl.sciencesocieties.org/publications/tpg/first-look The Plant Genome doi:10.3835/plantgenome2015.04.0025]
** Accepted paper, posted 08/07/2015.
** Update of the Nimblegen Microarray data - more tissues, not so much background noise

==2. Planteome.org Update:==
* Once the Plant Ontology update is pushed out, we will be rolling all the data files and updated ontologies to the Planteome web page: Planteome.org for our Planteome 1.0 release.
* This is important as we are getting ready to submit our first annual report and people are using the Planteome site, so we want to make sure it is all working well.
* We are diligently working to make sure all the dbxrefs and links are updated, so if you find any issues, please let us know.

== 3. Plant Trait Ontology: ==
Questions from Barry about how to define the traits:

===Anatomy and Morphology traits===
'''> Are there any traits which are not anatomy and morphology traits?'''

''There are 8 different branches in the TO, anatomy and morphology trait is just one.''

[[File:TO-top level.png|TO-top level.png.jpg]]

''* Note that there is a still a class "other miscellaneous traits" which we are planning to get rid of soon.

'''> Is there a definition of 'anatomy trait' and of 'morphology trait'?'''
* LC: My understanding of the meaning of anatomy and morphology in botany are as follows: the anatomy is the internal structure and the morphology is the external structure. This is consistent with the definitions of plant anatomy and morphology in common use:

* '''plant anatomy:''' "The general term for the study of the internal structure of plants. While originally it included plant morphology, which is the description of the physical form and external structure of plants, since the mid-20th century the investigations of plant anatomy are considered a separate, distinct field, and plant anatomy refers to just the internal plant structures.[1][2] Plant anatomy is now frequently investigated at the cellular level, and often involves the sectioning of tissues and microscopy.[3] (from : https://en.wikipedia.org/wiki/Plant_anatomy)

* '''Plant morphology:''' "The study of the physical form and external structure of plants.[1] This is usually considered distinct from plant anatomy,[1] which is the study of the internal structure of plants, especially at the microscopic level.[2] Plant morphology is useful in the visual identification of plants." (from https://en.wikipedia.org/wiki/Plant_morphology)

* Current def'n: '''anatomy and morphology trait (TO:0000017): A plant trait (TO:0000387) which is associated with the anatomy or morphology of a plant anatomical entity (PO:0025131) or one or more constituent cellular components (GO:0005575) contained therein.'''
** Comment: Includes traits of plant structures (PO:0009011) such as plant cell (PO:0009002), plant organ (PO:0009008), portion of plant tissue (PO:0009007), vascular system (PO:0000034), whole plant (PO:0000003) and seed (PO:0009010), as well as those of plant anatomical spaces (PO:0025117) and portions of plant substance (PO:0025161).

'''> Are they logically disjoint? '''
* Based on the definitions above, they are logically disjoint

'''> The term 'anatomy and morphology trait' really means 'anatomy trait or morphology trait', right?'''
* ''The class is designed to be inclusive- covering physical traits that are either internal (anatomy) or external (morphology), so 'anatomy trait or morphology trait' would perhaps be more correct.''
* ''If we say "anatomy and morphology trait", does that mean that the trait in question is both an anatomical and a morphological trait?''

====Test classification of some of the subclasses of PSA+M traits as either anatomy or morphology traits:====

===== Examples of morphological trait classes =====
* awn length, width, thickness, color, presence (?)
* leaf margin serrated
* seedling hypocotyl size
* axillary bud shape
* plant cell shape, size, length
* embryo shape, shootless embryo
* flower or floret color, type, diameter, length, number, shape, etc
* chasmogamous flower, cleistogamus flower
* ear (infructescence) circumference, aspect, color, length, weight, position shape, diameter, circumference
* inflorescence (incl. panicle, spikelet, tassel) size, width, branching, color, density, depth, diameter, exsertion, number, presence, shape, texture, type, waxiness, weight, etc
* axillary bud number, shape, size, prominence
* leaf attitude, color, weight, cover, volume, flexibility, height, number, pubescence, adherence, shape, size, rolling, phyllotaxy, area, nitrogen content, pigment content, gloss, drying, stomatal frequency, temperature, necrosis,
* leaf lamina area, color, length, splitting, width, pubescence, joint bending, etc

===== Examples of anatomy trait classes: =====
* leaf vein color, size
* leaf midvein thickness

* Question: Would either of these classes include traits such as fruit color or leaf color? This is more a quality or atribute than an anatomical or morphological trait.

== Objection to using: 'associated with' ==
> BS: (a) it is vague (b) it will block reasoning
''I agree that it is vague and would prefer a more precise statement, although textual definition will not block reasoning.''

Example anatomy and morphology trait classes:
* stem number (TO:0000953): A shoot system anatomy and morphology trait (TO:0000077) which is associated with the number of stems (PO:0009047).
** Added Xrefs to: number (PATO:0001555); TO_GIT:157

* stem size (TO:0000954):A stem anatomy and morphology trait (TO:0000361) which is associated with the size of a stem (PO:0009047).
** Added Xrefs to: size (PATO:0000117); TO_GIT:157
** Added narrow synonym: stalk size

Suggestions:
* "stem number =def. a trait of a plant which is the number of stems of the plant"
and so on for the other cases

* "infructescence axis shape: An infructescence axis anatomy and morphology trait (TO:0000921) that describes the shape of the infructescence axis" [or specify the 'of' further]

synonym: cob shape

Examples from other from [http://obofoundry.github.io/ OBO_Foundry_Ontologies] that concern traits:

Vertebrate Trait Ontology:
http://www.berkeleybop.org/ontologies/vt.owl -- “related to”

Animal Trait Ontology:
http://147.99.159.184:8080/webprotege/#ATOL -- “related to”

* name: has_quality (id: RO:0000086)
* def: "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence"
property_value: IAO:0000112 "this apple has quality this red color" xsd:string
property_value: IAO:0000116 "A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist." xsd:string
property_value: IAO:0000118 "has_quality" xsd:string

Possible solution using relations from RO:

ear shape (TO:0000964): An infructescence anatomy or morphology trait (TO:0000920)
an ear infructescence (PO:0025597) has_quality shape.

Added dXrefs: shape (PATO:0000052);

Example from BATTO: http://www.ontobee.org/browser/index.php?o=oba

[Term]
id: TO:0000431 ! ear length
intersection_of: BATTO:0000001 ! biological attribute
intersection_of: affects_quality PATO:0000122 ! length
intersection_of: attribute_of PO:0020136 ! ear (sensu Zea)

== 4. Update from Bioversity: ==
* Progress on mapping the CO vocabularies and creating cross products
On going results are in repo ibp-crossproducts: https://github.com/Planteome/ibp-crossproducts

The formal definitions are based on BFO.

Review of existing ontologies (trait, phenotype, ...) are described here : https://github.com/Planteome/ibp-crossproducts/wiki/Related-work

Formal definitions by trait types are described here: https://github.com/Planteome/ibp-crossproducts/wiki/Rules-used-to-build-formal-defintions

Trait definition (Manchester syntax):
Quality and s_depends_on some (Process or (Plant Entity or part_of some Plant Entity))

Stat: about 25% of the traits that are in TD version 5 (9 crops) are currently defined with a formal definition. I based this work on the content if the columns 'Entity' and 'Attribute' of the TD version 5.

Question: Traits are classified under PATO Quality, e.g. Seed Color in under PATO color.

Note: I didn't find the URIs of the BFO properties

== 5. Proposed: Ontology Development Meeting in Corvallis early November- ==
Please see the notes here: [[Planteome_Curator_workshop_Fall_2015]]

== 5. TermGenie Demo ==
* A tool for creating new ontology terms for either GO (Gene Ontology) or OBA (Ontology of Biological Attributes). It uses a pattern-based approach to rapidly generate new terms and place them appropriately within the ontology structure. All terms are reviewed by a senior editor before the final commit to the ontology.

* Two instances of TermGenie exist: for OBA and GO:
** [http://go.termgenie.org/ TermGenie GO]

** [http://go.termgenie.org/ TermGenie OBO]

* Citation: [http://www.ncbi.nlm.nih.gov/pubmed/25937883 TermGenie - a web-application for pattern-based ontology class generation]

''Discussion of TermGenie tabled for next meeting"

==Next meeting: Sept 29th==

Sept 15th, 2015- Ontology Working Group Meeting

2015-09-17T14:03:35Z

Marieangelique.laporte: /* 4. Update from Bioversity: */

'''Time: 8:15am PDT (GMT-7:00) Pacific Time (US and Canada)'''

Connection details: Join from PC, Mac, iOS or Android: https://zoom.us/j/655429261

* In attendance: LC, MAL, AM, PJ, BS, CM

* Link to recording- Video: [[File:Ontology WG 9-15-15.mp4|thumb|Ontology WG 9-15-15 video]]
* Link to recording- Audio: [[File:Ontology WG 9-15-15 audio.m4a|thumb|Ontology WG 9-15-15 audio]]

=Agenda=
== 1. Upcoming Plant Ontology Release #21 ==
- Many changes and updates to the PO which will accompany the PSDS paper submission
* Transition to GitHub complete, and working well- required many updated Xrefs and links in the various browsers, ontology files and pages.
* PO Live Browser updated for the transition to GitHub with links to the new Issue Tracker and association repository on the SVN-
* Timeline- within the next 2 weeks
* For more information: [http://wiki.plantontology.org/index.php/Release_21 Plant_Ontology_Release_#21]

* New association data developed from the [http://wiki.plantontology.org/index.php/Plant_Pheontype_Pilot_Project_2015] paper published in Feb 2015: http://www.plantmethods.com/content/11/1/10/abstract
** Six plant species: Rice, Maize, Arabidopsis, soybean, Medicago, tomato ~ 4,193 new direct associations

* New association data developed from MaizeGDB (Mary Schaeffer)
* Based on data set from Scott Stelpfulg et al (Kaeppler group): "An expanded maize gene expression atlas based on RNA-sequencing and its use to explore root development"
** [https://dl.sciencesocieties.org/publications/tpg/first-look The Plant Genome doi:10.3835/plantgenome2015.04.0025]
** Accepted paper, posted 08/07/2015.
** Update of the Nimblegen Microarray data - more tissues, not so much background noise

==2. Planteome.org Update:==
* Once the Plant Ontology update is pushed out, we will be rolling all the data files and updated ontologies to the Planteome web page: Planteome.org for our Planteome 1.0 release.
* This is important as we are getting ready to submit our first annual report and people are using the Planteome site, so we want to make sure it is all working well.
* We are diligently working to make sure all the dbxrefs and links are updated, so if you find any issues, please let us know.

== 3. Plant Trait Ontology: ==
Questions from Barry about how to define the traits:

===Anatomy and Morphology traits===
'''> Are there any traits which are not anatomy and morphology traits?'''

''There are 8 different branches in the TO, anatomy and morphology trait is just one.''

[[File:TO-top level.png|TO-top level.png.jpg]]

''* Note that there is a still a class "other miscellaneous traits" which we are planning to get rid of soon.

'''> Is there a definition of 'anatomy trait' and of 'morphology trait'?'''
* LC: My understanding of the meaning of anatomy and morphology in botany are as follows: the anatomy is the internal structure and the morphology is the external structure. This is consistent with the definitions of plant anatomy and morphology in common use:

* '''plant anatomy:''' "The general term for the study of the internal structure of plants. While originally it included plant morphology, which is the description of the physical form and external structure of plants, since the mid-20th century the investigations of plant anatomy are considered a separate, distinct field, and plant anatomy refers to just the internal plant structures.[1][2] Plant anatomy is now frequently investigated at the cellular level, and often involves the sectioning of tissues and microscopy.[3] (from : https://en.wikipedia.org/wiki/Plant_anatomy)

* '''Plant morphology:''' "The study of the physical form and external structure of plants.[1] This is usually considered distinct from plant anatomy,[1] which is the study of the internal structure of plants, especially at the microscopic level.[2] Plant morphology is useful in the visual identification of plants." (from https://en.wikipedia.org/wiki/Plant_morphology)

* Current def'n: '''anatomy and morphology trait (TO:0000017): A plant trait (TO:0000387) which is associated with the anatomy or morphology of a plant anatomical entity (PO:0025131) or one or more constituent cellular components (GO:0005575) contained therein.'''
** Comment: Includes traits of plant structures (PO:0009011) such as plant cell (PO:0009002), plant organ (PO:0009008), portion of plant tissue (PO:0009007), vascular system (PO:0000034), whole plant (PO:0000003) and seed (PO:0009010), as well as those of plant anatomical spaces (PO:0025117) and portions of plant substance (PO:0025161).

'''> Are they logically disjoint? '''
* Based on the definitions above, they are logically disjoint

'''> The term 'anatomy and morphology trait' really means 'anatomy trait or morphology trait', right?'''
* ''The class is designed to be inclusive- covering physical traits that are either internal (anatomy) or external (morphology), so 'anatomy trait or morphology trait' would perhaps be more correct.''
* ''If we say "anatomy and morphology trait", does that mean that the trait in question is both an anatomical and a morphological trait?''

====Test classification of some of the subclasses of PSA+M traits as either anatomy or morphology traits:====

===== Examples of morphological trait classes =====
* awn length, width, thickness, color, presence (?)
* leaf margin serrated
* seedling hypocotyl size
* axillary bud shape
* plant cell shape, size, length
* embryo shape, shootless embryo
* flower or floret color, type, diameter, length, number, shape, etc
* chasmogamous flower, cleistogamus flower
* ear (infructescence) circumference, aspect, color, length, weight, position shape, diameter, circumference
* inflorescence (incl. panicle, spikelet, tassel) size, width, branching, color, density, depth, diameter, exsertion, number, presence, shape, texture, type, waxiness, weight, etc
* axillary bud number, shape, size, prominence
* leaf attitude, color, weight, cover, volume, flexibility, height, number, pubescence, adherence, shape, size, rolling, phyllotaxy, area, nitrogen content, pigment content, gloss, drying, stomatal frequency, temperature, necrosis,
* leaf lamina area, color, length, splitting, width, pubescence, joint bending, etc

===== Examples of anatomy trait classes: =====
* leaf vein color, size
* leaf midvein thickness

* Question: Would either of these classes include traits such as fruit color or leaf color? This is more a quality or atribute than an anatomical or morphological trait.

== Objection to using: 'associated with' ==
> BS: (a) it is vague (b) it will block reasoning
''I agree that it is vague and would prefer a more precise statement, although textual definition will not block reasoning.''

Example anatomy and morphology trait classes:
* stem number (TO:0000953): A shoot system anatomy and morphology trait (TO:0000077) which is associated with the number of stems (PO:0009047).
** Added Xrefs to: number (PATO:0001555); TO_GIT:157

* stem size (TO:0000954):A stem anatomy and morphology trait (TO:0000361) which is associated with the size of a stem (PO:0009047).
** Added Xrefs to: size (PATO:0000117); TO_GIT:157
** Added narrow synonym: stalk size

Suggestions:
* "stem number =def. a trait of a plant which is the number of stems of the plant"
and so on for the other cases

* "infructescence axis shape: An infructescence axis anatomy and morphology trait (TO:0000921) that describes the shape of the infructescence axis" [or specify the 'of' further]

synonym: cob shape

Examples from other from [http://obofoundry.github.io/ OBO_Foundry_Ontologies] that concern traits:

Vertebrate Trait Ontology:
http://www.berkeleybop.org/ontologies/vt.owl -- “related to”

Animal Trait Ontology:
http://147.99.159.184:8080/webprotege/#ATOL -- “related to”

* name: has_quality (id: RO:0000086)
* def: "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence"
property_value: IAO:0000112 "this apple has quality this red color" xsd:string
property_value: IAO:0000116 "A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist." xsd:string
property_value: IAO:0000118 "has_quality" xsd:string

Possible solution using relations from RO:

ear shape (TO:0000964): An infructescence anatomy or morphology trait (TO:0000920)
an ear infructescence (PO:0025597) has_quality shape.

Added dXrefs: shape (PATO:0000052);

Example from BATTO: http://www.ontobee.org/browser/index.php?o=oba

[Term]
id: TO:0000431 ! ear length
intersection_of: BATTO:0000001 ! biological attribute
intersection_of: affects_quality PATO:0000122 ! length
intersection_of: attribute_of PO:0020136 ! ear (sensu Zea)

== 4. Update from Bioversity: ==
* Progress on mapping the CO vocabularies and creating cross products
On going results are in repo ibp-crossproducts: https://github.com/Planteome/ibp-crossproducts

The formal definitions are based on BFO.

Review of existing ontologies (trait, phenotype, ...) are described here : https://github.com/Planteome/ibp-crossproducts/wiki/Related-work

Formal definitions by trait types are described here: https://github.com/Planteome/ibp-crossproducts/wiki/Rules-used-to-build-formal-defintions

Trait definition (Manchester syntax):
Quality and s_depends_on some (Process or (Plant Entity or part_of some Plant Entity))

Stat: about 25% of the traits that are in TD version 5 (9 crops) are currently defined with a formal definition. I based this work on the content if the columns 'Entity' and 'Attribute' of the TD version 5.

== 5. Proposed: Ontology Development Meeting in Corvallis early November- ==
Please see the notes here: [[Planteome_Curator_workshop_Fall_2015]]

== 5. TermGenie Demo ==
* A tool for creating new ontology terms for either GO (Gene Ontology) or OBA (Ontology of Biological Attributes). It uses a pattern-based approach to rapidly generate new terms and place them appropriately within the ontology structure. All terms are reviewed by a senior editor before the final commit to the ontology.

* Two instances of TermGenie exist: for OBA and GO:
** [http://go.termgenie.org/ TermGenie GO]

** [http://go.termgenie.org/ TermGenie OBO]

* Citation: [http://www.ncbi.nlm.nih.gov/pubmed/25937883 TermGenie - a web-application for pattern-based ontology class generation]

''Discussion of TermGenie tabled for next meeting"

==Next meeting: Sept 29th==

Crop Ontology Pages

2015-09-10T09:55:47Z

Marieangelique.laporte:

==Introduction to [http://www.cropontology.org/ The Crop Ontology]==

The Crop Ontology website consists of 5 sections:
# Phenotypes and Traits Ontology
##crop specific trait ontologies. contains also the methods and the scales of measurement
## crop list: Maize, Rice, Wheat, Cassava, Cowpea, Chickpea, Potato, Sorghum, Soybean, Barley, Common Bean, Groundnut, Pearl millet, Pigeon Pea, Musa, Sweet Potato, Yam, Oat, Vitis
# Plant Anatomy & Development Ontology
##Banana anatomy
##Plant Ontology (PO)
##Wheat Plant Anatomy and Development Ontology: Defines growth stages of wheat
# General Germplasm Ontology
##FAO/IPGRI Multi-Crop Passport Descriptor ontology : Adapted from FAO/Bioversity Multi-Crop Passport Descriptors, 2004
##GCP Germplasm ontology: General germplasm descriptors
##ICIS germplasm methods ontology: adaptation of the ICIS germplasm methods table
# Location and Environmental Ontology
##Country and Location ontology: Official ISO 3166-1 alpha-2, alpha-3 and numeric country codes
##Crop Research ontology: Describes experimental design, environmental conditions and methods associated with the crop study/experiment/trail and their evaluation
# Structural and Functional Genomic Ontology
##Bioversity molecular markers ontology: Adapted from Descriptors for Genetic Markers Technologies (2004)

===There are 3 ways of creating “ontologies” on the Crop Ontology website===
# Upload a Trait Dictionary (TD) in Excel. (Note, the TD is only used to store and load information about traits, thus it cannot be used for uploading ontologies that would belong to the other categories)
# Upload an OBO file. They can be used to create ontologies in any of the 5 sections
# Ontologies can be built from scratch using the website dedicated interface. ''Are there any examples of these?''

===Storage and Downloading===
* Once the files are uploaded or some terms are submitted using the web interface, the data are stored in a noSQL database (Google App Engine Datastore).
* The ontologies can be downloaded in various formats: CSV, OBO, SKOS and JSON. The structures of the different formats are described in the following sections.
* Note that because there is no exact mapping between the different formats some compromises has been made. Not all the information is available in the different formats.

=List of Crops and IDs=
According to the project timeline, the crops that will be linked to the reference ontologies are:
{| {{table}}
| align="center" style="background:#f0f0f0;"|'''CROPS'''
| align="center" style="background:#f0f0f0;"|'''Crop Ids'''
| align="center" style="background:#f0f0f0;"|'''Prefixes'''
| align="center" style="background:#f0f0f0;"|'''Map to prefixes recommended by Chris'''
|-
| Maize||322||CO_322||IBPCO:322xxxx
|-
| Rice||320||CO_320||IBPCO:320xxxx
|-
| Wheat||321||CO_321||IBPCO:321xxxx
|-
| Cassava||334||CO_334||IBPCO:334xxxx
|-
| Cowpea||340||CO_340||IBPCO:340xxxx
|-
| Chickpea||338||CO_338||IBPCO:338xxxx
|-
| Potato||330||CO_330||IBPCO:330xxxx
|-
| Sorghum||324||CO_324||IBPCO:324xxxx
|-
| Soybean||336||CO_336||IBPCO:336xxxx
|-
| Barley||323||CO_323||IBPCO:323xxxx
|-
| Common Bean||335||CO_335||IBPCO:335xxxx
|-
| Groundnut||337||CO_337||IBPCO:337xxxx
|-
| Pearl millet||327||CO_327||IBPCO:327xxxx
|-
| Pigeon Pea||341||CO_341||IBPCO:341xxxx
|-
| Musa||325 (traits) and 125 (anatomy)||CO_325 and CO_125||IBPCO:325xxxx and IBPCO:125xxxx
|-
| Sweet Potato||331||CO_331||IBPCO:331xxxx
|-
| Yam||333||CO_333||IBPCO:333xxxx
|-
| Other crops ???||||||
|}

=Trait Dictionary V5=
== Mapping TD to OBO ==
{| {{table}}
| align="center" style="background:#f0f0f0;"|'''TDv5 Elements'''
| align="center" style="background:#f0f0f0;"|'''Description'''
| align="center" style="background:#f0f0f0;"|'''Stored in CO website'''
| align="center" style="background:#f0f0f0;"|'''OBO element'''
|-
| Curation||Comments for curation||NO||NO
|-
| Trait ID||Term ID for trait as generated by the system. Use an existing ID to modify data for that trait. If left blank the system will automatically generate a new ID.||Yes||Ontology ID (trait namespace)
|-
| Trait||Trait name (property)||Yes||name (trait namespace)
|-
| Entity||A trait must follow the convention "Trait" = "Entity" + "Attribute", eg for "grain colour", attribute = "grain"||Yes||Crossproduct to PO
|-
| Attribute||eg for "grain colour", entity = "colour"||Yes||Crossproduct to PATO
|-
| Trait synonyms||Acronym/abbreviated name.||Yes||synonym (trait namespace)
|-
| Trait abbreviation||Trait name abbreviation. If several abbrevations, separate with comas. The recommended abbreviation must be the first in the list.||Yes||synonym (trait namespace)
|-
| Trait description||Textual description of trait.||Yes||def (trait namespace)
|-
| Trait class||General class to which trait belongs. Concensus trait classes are morphological, phenological, agronomical, physiological, abiotic stress, biotic stress, biochemical, quality traits and fertility traits||Yes||is_a
|-
| Trait status||Status of the trait. Trait can be tagged as recommended, standard for , deprecated, legacy||Yes||is_obsolete
|-
| Trait Xref||Cross reference of the trait e.g., Xref to TO||Yes||xref
|-
| Method ID|| Term ID for method as generated by the system. Use an existing ID to modify data for that method. If left blank the system will automatically generate a new ID. ||Yes||id
|-
| Method|| (Short) method name. ||Yes||name (method namespace)
|-
| Method description|| Textual description of method. ||Yes||def (method namespace)
|-
| Formula|| For computational methods, express the formula using variable names ||Yes||NO
|-
| Method class|| Measurement, Counting, Estimation, Computation ||Yes||NO
|-
| Method reference|| Biobliographical reference describing method. ||Yes||Xref
|-
| Scale id||Term ID for scale as generated by the system. Use an existing ID to modify data for that scale. If left blank the system will automatically generate a new ID.||Yes||id
|-
| Scale name||[Guidelines to be defined for naming the scale]||Yes||name (scale namespace)
|-
| Scale class||Numerical, Nominal, Ordinal, Text, Code, Time, Duration||Yes||NO
|-
| Decimal places||For numerical, number of decimal places of report||Yes||NO
|-
| Lower limit||Minimum value (used for validation) for numerical and date||Yes||NO
|-
| Upper limit||Maximum value (used for validation).||Yes||NO
|-
| Scale Xref||Cross reference to the scale, eg to a unit repository like "improved UO"||Yes||Xref
|-
| Category n||If the scale is categorical, class value and meaning of the n-th category. It possible to create as many category columns as necessary, as long as they are called "Category "||Yes||Yes
|-
| Variable ID||Term ID for method as generated by the system. Use an existing ID to modify data for that method. If left blank the system will automatically generate a new ID.||Yes||Ontology ID (variable namespace)
|-
| Variable name (abbreviated)||Name of the variable following the convetion __. Variable name must be unique.||Yes||synonym (variable namespace)
|-
| Variable synonyms||Other names given to this variable||Yes||synonym (variable namespace)
|-
| Context of use||Indication of how trait is routinely used. If several context of use, separate with ","||Yes||NO
|-
| Growth stage|| Growthstage at which measurement is made. Follow standards. If variable used in time series, leave blank ||Yes||NO
|-
| Variable status||Obsolete, Legacy, Standard for , Recommended, Experimental, Revision||Yes||is_obsolete
|-
| CV Term ID||ID generated by BMS||Yes||NO
|-
| Variable Xref||||Yes||Xref
|-
| Scientist||Name of scientist submitting variable.||Yes||NO
|-
| Institution||Name of institution submitting variable||Yes||NO
|-
| Language||2 letter ISO code for language in which variable data is submitted.||Yes||NO
|-
| Date||Date the variable was submitted.||Yes||NO
|-
| Crop||Crop name.||Yes||Yes
|-
| Full variable name||||||customized name. For new variables -> concatenation of by in
|-
| variable definition||||||T: /n M: /n S:
|}
=OBO files=
==OBO file structure==
OBO files are created using the obo2owl library (which should sound familiar ;-)).

The main issue with the Trait Template is that because different IDs can be created for the same “thing” (e.g. the term “cm” will get different IDs if different traits are measured in cm), different obo terms can have the same name (but different IDs).

That is a problem when our users tried to import the OBO files in a Chado database.

* Consequently, I created a little script that created OBO files where all the names are unique in a given namespace. The script has not be inserted in the website yet but it will be soon. Example of an OBO files on Github. (MAL)

{| border="1" class="sortable"
!TD column!!OBO element
|-
|Crop||Used for setting up the namespace
|-
|Name of Trait||name
|-
|Trait ID for modification, Blank for New||Term + id
|-
|Description of Trait||definition
|-
|Trait Class||Term +id + name + is-a
|-
|Language of submission (only in ISO 2 letter codes)||We have only English OBO files.
|-
|Name of submitting scientist||created_by
|-
|Institution||Not used
|-
|Date of submission||creation_date
|-
|Abbreviated name||synonym [EXACT]
|-
|Synonyms (separate by commas)||synonym [EXACT]
|-
|How is this trait routinely used||Not used
|-
|Name of method||name
|-
|Method ID for modification, Blank for New||Term + id + method_of
|-
|Describe how measured (method||definition
|-
|Bibliographic Reference||xref
|-
|Growth Stage||Not used
|-
|Comments||Not used
|-
|Scale ID for modification, Blank for New||Term + id + scale_of
|-
|Type of Measure (Continuous, Discrete or Categorical||Not used
|-
|For Continuous: units of measurement||name
|-
|For Discrete: Name of scale or units of measurement||name
|-
|For Categorical: Name of rating scale||name
|-
|For Categorical: Class 1 - value = meaning||Term + name + is-a
|-
|For Categorical: Class 2 - value = meaning ||Term + name + is-a
|-
|For Categorical: Class 3 - value = meaning||Term + name + is-a
|-
|For Categorical: Class 4 - value = meaning||Term + name + is-a
|}

=SKOS files=
==SKOS file structure==
{| border="1" class="sortable"
!TD column!!SKOS
|-
|Crop||Used for setting up the namespace
|-
|Name of Trait||skos:prefLabel
|-
|Trait ID for modification, Blank for New||Local Name (URI) + rdf: type skos:concept
|-
|Description of Trait||skos:definition
|-
|Trait Class||rdf:type Skos:Concept + skos:broader
|-
|Language of submission (only in ISO 2 letter codes)||xml:lang of the literals. SKOS files are multilingual (if we have the info)
|-
|Name of submitting scientist||foaf:Person (not set so far but will be soon)
|-
|Institution||foaf:Organization (not set so far but will be soon)
|-
|Date of submission||dc:date (not set so far but will be soon)
|-
|Abbreviated name||skos:altLabel
|-
|Synonyms (separate by commas)||skos:altLabel
|-
|How is this trait routinely used||Not used
|-
|Name of method||skos:prefLabel
|-
|Method ID for modification, Blank for New||Local Name (URI) + rdf: type skos:concept
|-
|Describe how measured (method||skos:definition
|-
|Bibliographic Reference||Not set (dc: bibliographicCitation?)
|-
|Growth Stage||skos:related (not set so far)
|-
|Comments||skos:editorialNote
|-
|Scale ID for modification, Blank for New||Local Name (URI) + rdf: type skos:concept
|-
|Type of Measure (Continuous, Discrete or Categorical||Not used
|-
|For Continuous: units of measurement||skos:prefLabel
|-
|For Discrete: Name of scale or units of measurement||skos:prefLabel
|-
|For Categorical: Name of rating scale||skos:prefLabel
|-
|For Categorical: Class 1 - value = meaning||Local Name (URI) + rdf: type skos:concept
|-
|For Categorical: Class 2 - value = meaning ||Local Name (URI) + rdf: type skos:concept
|-
|For Categorical: Class 3 - value = meaning||Local Name (URI) + rdf: type skos:concept
|-
|For Categorical: Class 4 - value = meaning||Local Name (URI) + rdf: type skos:concept
|}

Thursday Aug 20th, 2015

2015-08-27T08:29:53Z

Marieangelique.laporte: /* Updates from Bioversity: Marie-Angelique */

=Agenda=
Topic: Planteome Project All Hands Meeting
Time: Aug 20, 2015 8:00 AM (GMT-7:00) Pacific Time (US and Canada)
Join from PC, Mac, iOS or Android: https://zoom.us/j/431144926

* Who: LC, PJ, AM, JE, JP, MAL, GG, JD, CM, EZ
* Regrets: BS, EA, DWS

* Link to recording- Video: TBA
* Link to recording- Audio: TBA

= A. General Comments and Updates:=
== Introductions: ==

* Any new faces? - Updates on new hires:
** Georgios moving to University of Birmingham, UK
** Has not hired a postdoc, will re-advertise, joint position with John Doonan
** No Updates from NYBG

* New Postdoc Curator has joined the team since late June: Austin Meier
* Austin's Background: Born: Omaha, NE
** Undergraduate: BS biology (genetics): University of Iowa, Iowa City
** Internship: Monsanto, Huxley IA
** Graduate: PhD Plant Breeding, Plant Genetics: University of Wisconsin, Madison.

==News and Announcements:==
===NSF PI meeting Sept 9th to 11th, Washington DC===
* Need 2 pager report- PJ and LC are working on, will circulate
* Poster for presenting- needs photos of all participants
* End of Year One coming up- will need to prepare annual report soon

=== Ontology Development Workshop planned for this fall: ===
* Dates: Possibly Nov-Dec, in Corvallis or maybe another central location
* See wiki page for more details:
* Goal: Focus on ontology training (OWL/Protege), but stay for a several days to a week total for actual hands on, get people actually comfortable in the system.
* Bring in OSU Conferences coordinators to help manage logistics
* may be able to utilize OSU Conference people to help organize.

=== Birmingham/Montpellier Meeting ~May 2016 ===
* Will be in conjunction with another meeting, GG and JD are working with Ruth Bastow to organize
* Goal of the meeting is to ...??

===ICBO Meeting Aug 1-4th, 2016===
* http://icbo.buffalo.edu/index.html
* Location- to be held in Corvallis
* May include an Annotation Jamboree??

=== Other items:===
* GG and JD could show their data structure at a future meeting- When, next all hands meeeting

* Chris could demo update of new AmiGO curation NGS Annotation for the GO annotation with pathway curation, possibly in the next week
* Next Data viz meeting next 11am next Wed

* Next All Hands: planned for Sept 24th- LC will send out a doodle poll, GG has a conflict on the 24th. EA and MAL have also conflict on the 24th (RDA meeting, Paris)

== B. Update from Ontologies Working Group:==
=== Updates from OSU: Laurel===
* All the ontology development work and files have been moved from SVN to the new Planteome Site on Github (https://github.com/Planteome)
* Reference Ontologies: PO, TO, PSO, EO
* Ontology files and issue trackers, Association files are still on the SVN as they are too large for GH
* Some Crop Ontology (IBP- maize, wheat, rice, cassava)
* Everyone needs github IDs for access to our project- JD and GG still need GH ids
'''GG has a GitHub id, will send, JD will get one''

=== Updates from Bioversity: Marie-Angelique ===
* Crop Ontology webpage: http://www.cropontology.org/
** Curation efforts have been going on during the summer to update them to the new Trait Template Ver. 5
** Nine of the CO vocabs are done- will be uploaded - ''Where, to the CO site or to GH??'' We are planning to upload the curated ontologies on both Github (probably the rdf version, maybe the Excel Template even if changes cannot be tracked) and CO website.

====Mapping between Crop Ontologies and the Ref Ontologies:====
* MAL continues to work on the mapping between crop ontologies and ref. ontologies
* Priority is mapping, using an automated tool: Agreement Maker Light (AML) (http://agreementmaker.org/) tool
''For details of the mapping algorithm- see the Ontology working group meeting June 21st''

* Need to check on which of the files have been updated... ''not sure what this is referring to''

* The CO vocabs are being revised to include fields in TT spreadsheet for the enttiy and attribute
* Mappings will be added as they are developed, based on the E + A

* MAL has tried tools, CM has tools, need to find out what tool works best
* New version of the TT has more information

* From CM: Prospective mapping is better than retrospective mapping- by creating logical definitions
* It would be good to work with CM to develop a workflow, power comes from the cross products
* Will review the workflow at the next ontology call

''Ask CM to show us the mapping tool and if he has a more up to date version of the XP file, the one on the SVN is quite old''

* Pankaj: Ideal goal is to have a tool available for the workflow by the curators
** Suggestion to each run a common panel of files through and compare the results- e.g. rice and maize
''Need to get the most recent version of the CO file- Updated TT version 5. Are these on the GH repository?''
* Goal is to map back to reference ontologies through the XPs. If the terms are composed in the XPs then we are
* Suggestion: A Term Genie instance for the generation of the terms for the CO vocabs.

* MAL will share her slides to illustrate, that were presented for the RTB meeting.

====Roots, Tubers, Banana Development (TRB) meeting in Montpellier:====
* Funded by Bill Gates Foundation, three days week of Aug 20th
** Discussing NGS and ontologies
** Development and curation for the RTB crops with Boyce Thompson Institute will split the work
* Cassava has been uploaded, but it is not the up to date version, still needs to be finalized and now has a Read-Me file

''Question: which of the CO species does this include? cassava, potato, banana, others? '' BTI only works so far on the Cassava ontology. The other RTB crops that will be used by BTI nextgen project, will be the Crop Ontologies (Sweat Potato, Yam, Banana, Potato)

== C. Update from IT group- Data Store, AmiGO2- Justin Elser==

=== Migration to github- See above ===
* Almost complete. Let me know if there are any more files to transfer with history
* All files (minus SVN) are over on github (almost, still moving a few extras)

* Association files: moving to iPlant eventually?
** Where are we going to put the association files?- the association files are too big for Github
** They are cluttered within the SVN- JE will move them all to a new SVN repository

** Keep association files on SVN, but keep them alone, not mixed with things that have migrated to Github.
* Irods: iPlant's 'big iron' is a possibility, but lacks any version control system
* In the long run, it makes more sense to keep annotation/association files on iPlant
* Mirror the latest version from version control (SVN) over on iPlant for 'bulk download' options for end users.

=== AmiGO 2 ===
Fixed annotation loading issue (well, a workaround)
* Working on bisecting issue so we can stay current with Owltools and AmiGO 2 development
''Not sure what this is referring to''

* Loading is far far faster, but issue is that it won't load any annotations
** JE found a workaround with an old version of OWLtools, but its "not ideal"
** GO doesn't have this issue- Can Chris or Seth help?
** CM can't help until the beginning of Sept.
** If JE can't figure it out by sept, Chris can help

* Post issues to Github's issues tracker on the Planteome-amigo2 repository
** JE will have it up and down frequently, so be wary when you're 'testing' it.

* Migrating live version to iPLant- need to check on virtual machines
* Need to work on customization and tools
* iPlant won't get looked at until it is working on the live version (????)

== D. Update from AISO/BisQue group- Justin Preece==
* Main goal: getting a web module for people to segment images, and link those segments to ontology terms/metadata
** There are desktop programs/algorithms that work, they are moving them to the web as 'modules'
** TL;DR-Newer/better/shinier graph cuts
** putting a module on iPlant BisQue that allows you to segment an image, and annotate it with ontologies.
** Doing a test environment locally, will expand to testing groups that are larger

* Working with two students from Comp Sci- Sinisa's Lab
* 1. C++ and Matlab under the hood
* 2. Matlab and python on the surface for UI

==E. Other Comments:==

==Next meeting TBA==
Planned for Sept 24th- LC will send out a doodle poll as GG has a conflict

Thursday Aug 20th, 2015

2015-08-27T08:27:24Z

Marieangelique.laporte: /* Roots, Tubers, Banana Development (TRB) meeting in Montpellier: */

=Agenda=
Topic: Planteome Project All Hands Meeting
Time: Aug 20, 2015 8:00 AM (GMT-7:00) Pacific Time (US and Canada)
Join from PC, Mac, iOS or Android: https://zoom.us/j/431144926

* Who: LC, PJ, AM, JE, JP, MAL, GG, JD, CM, EZ
* Regrets: BS, EA, DWS

* Link to recording- Video: TBA
* Link to recording- Audio: TBA

= A. General Comments and Updates:=
== Introductions: ==

* Any new faces? - Updates on new hires:
** Georgios moving to University of Birmingham, UK
** Has not hired a postdoc, will re-advertise, joint position with John Doonan
** No Updates from NYBG

* New Postdoc Curator has joined the team since late June: Austin Meier
* Austin's Background: Born: Omaha, NE
** Undergraduate: BS biology (genetics): University of Iowa, Iowa City
** Internship: Monsanto, Huxley IA
** Graduate: PhD Plant Breeding, Plant Genetics: University of Wisconsin, Madison.

==News and Announcements:==
===NSF PI meeting Sept 9th to 11th, Washington DC===
* Need 2 pager report- PJ and LC are working on, will circulate
* Poster for presenting- needs photos of all participants
* End of Year One coming up- will need to prepare annual report soon

=== Ontology Development Workshop planned for this fall: ===
* Dates: Possibly Nov-Dec, in Corvallis or maybe another central location
* See wiki page for more details:
* Goal: Focus on ontology training (OWL/Protege), but stay for a several days to a week total for actual hands on, get people actually comfortable in the system.
* Bring in OSU Conferences coordinators to help manage logistics
* may be able to utilize OSU Conference people to help organize.

=== Birmingham/Montpellier Meeting ~May 2016 ===
* Will be in conjunction with another meeting, GG and JD are working with Ruth Bastow to organize
* Goal of the meeting is to ...??

===ICBO Meeting Aug 1-4th, 2016===
* http://icbo.buffalo.edu/index.html
* Location- to be held in Corvallis
* May include an Annotation Jamboree??

=== Other items:===
* GG and JD could show their data structure at a future meeting- When, next all hands meeeting

* Chris could demo update of new AmiGO curation NGS Annotation for the GO annotation with pathway curation, possibly in the next week
* Next Data viz meeting next 11am next Wed

* Next All Hands: planned for Sept 24th- LC will send out a doodle poll, GG has a conflict on the 24th. EA and MAL have also conflict on the 24th (RDA meeting, Paris)

== B. Update from Ontologies Working Group:==
=== Updates from OSU: Laurel===
* All the ontology development work and files have been moved from SVN to the new Planteome Site on Github (https://github.com/Planteome)
* Reference Ontologies: PO, TO, PSO, EO
* Ontology files and issue trackers, Association files are still on the SVN as they are too large for GH
* Some Crop Ontology (IBP- maize, wheat, rice, cassava)
* Everyone needs github IDs for access to our project- JD and GG still need GH ids
'''GG has a GitHub id, will send, JD will get one''

=== Updates from Bioversity: Marie-Angelique ===
* Crop Ontology webpage: http://www.cropontology.org/
** Curation efforts have been going on during the summer to update them to the new Trait Template Ver. 5
** Twelve of the CO vocabs are done- will be uploaded - ''Where, to the CO site or to GH??''

====Mapping between Crop Ontologies and the Ref Ontologies:====
* MAL continues to work on the mapping between crop ontologies and ref. ontologies
* Priority is mapping, using an automated tool: Agreement Maker Light (AML) (http://agreementmaker.org/) tool
''For details of the mapping algorithm- see the Ontology working group meeting June 21st''

* Need to check on which of the files have been updated... ''not sure what this is referring to''

* The CO vocabs are being revised to include fields in TT spreadsheet for the enttiy and attribute
* Mappings will be added as they are developed, based on the E + A

* MAL has tried tools, CM has tools, need to find out what tool works best
* New version of the TT has more information

* From CM: Prospective mapping is better than retrospective mapping- by creating logical definitions
* It would be good to work with CM to develop a workflow, power comes from the cross products
* Will review the workflow at the next ontology call

''Ask CM to show us the mapping tool and if he has a more up to date version of the XP file, the one on the SVN is quite old''

* Pankaj: Ideal goal is to have a tool available for the workflow by the curators
** Suggestion to each run a common panel of files through and compare the results- e.g. rice and maize
''Need to get the most recent version of the CO file- Updated TT version 5. Are these on the GH repository?''
* Goal is to map back to reference ontologies through the XPs. If the terms are composed in the XPs then we are
* Suggestion: A Term Genie instance for the generation of the terms for the CO vocabs.

* MAL will share her slides to illustrate, that were presented for the RTB meeting.

====Roots, Tubers, Banana Development (TRB) meeting in Montpellier:====
* Funded by Bill Gates Foundation, three days week of Aug 20th
** Discussing NGS and ontologies
** Development and curation for the RTB crops with Boyce Thompson Institute will split the work
* Cassava has been uploaded, but it is not the up to date version, still needs to be finalized and now has a Read-Me file

''Question: which of the CO species does this include? cassava, potato, banana, others? '' BTI only works so far on the Cassava ontology. The other RTB crops that will be used by BTI nextgen project, will be the Crop Ontologies (Sweat Potato, Yam, Banana, Potato)

== C. Update from IT group- Data Store, AmiGO2- Justin Elser==

=== Migration to github- See above ===
* Almost complete. Let me know if there are any more files to transfer with history
* All files (minus SVN) are over on github (almost, still moving a few extras)

* Association files: moving to iPlant eventually?
** Where are we going to put the association files?- the association files are too big for Github
** They are cluttered within the SVN- JE will move them all to a new SVN repository

** Keep association files on SVN, but keep them alone, not mixed with things that have migrated to Github.
* Irods: iPlant's 'big iron' is a possibility, but lacks any version control system
* In the long run, it makes more sense to keep annotation/association files on iPlant
* Mirror the latest version from version control (SVN) over on iPlant for 'bulk download' options for end users.

=== AmiGO 2 ===
Fixed annotation loading issue (well, a workaround)
* Working on bisecting issue so we can stay current with Owltools and AmiGO 2 development
''Not sure what this is referring to''

* Loading is far far faster, but issue is that it won't load any annotations
** JE found a workaround with an old version of OWLtools, but its "not ideal"
** GO doesn't have this issue- Can Chris or Seth help?
** CM can't help until the beginning of Sept.
** If JE can't figure it out by sept, Chris can help

* Post issues to Github's issues tracker on the Planteome-amigo2 repository
** JE will have it up and down frequently, so be wary when you're 'testing' it.

* Migrating live version to iPLant- need to check on virtual machines
* Need to work on customization and tools
* iPlant won't get looked at until it is working on the live version (????)

== D. Update from AISO/BisQue group- Justin Preece==
* Main goal: getting a web module for people to segment images, and link those segments to ontology terms/metadata
** There are desktop programs/algorithms that work, they are moving them to the web as 'modules'
** TL;DR-Newer/better/shinier graph cuts
** putting a module on iPlant BisQue that allows you to segment an image, and annotate it with ontologies.
** Doing a test environment locally, will expand to testing groups that are larger

* Working with two students from Comp Sci- Sinisa's Lab
* 1. C++ and Matlab under the hood
* 2. Matlab and python on the surface for UI

==E. Other Comments:==

==Next meeting TBA==
Planned for Sept 24th- LC will send out a doodle poll as GG has a conflict

Thursday Aug 20th, 2015

2015-08-27T08:23:00Z

Marieangelique.laporte: /* Other items: */

=Agenda=
Topic: Planteome Project All Hands Meeting
Time: Aug 20, 2015 8:00 AM (GMT-7:00) Pacific Time (US and Canada)
Join from PC, Mac, iOS or Android: https://zoom.us/j/431144926

* Who: LC, PJ, AM, JE, JP, MAL, GG, JD, CM, EZ
* Regrets: BS, EA, DWS

* Link to recording- Video: TBA
* Link to recording- Audio: TBA

= A. General Comments and Updates:=
== Introductions: ==

* Any new faces? - Updates on new hires:
** Georgios moving to University of Birmingham, UK
** Has not hired a postdoc, will re-advertise, joint position with John Doonan
** No Updates from NYBG

* New Postdoc Curator has joined the team since late June: Austin Meier
* Austin's Background: Born: Omaha, NE
** Undergraduate: BS biology (genetics): University of Iowa, Iowa City
** Internship: Monsanto, Huxley IA
** Graduate: PhD Plant Breeding, Plant Genetics: University of Wisconsin, Madison.

==News and Announcements:==
===NSF PI meeting Sept 9th to 11th, Washington DC===
* Need 2 pager report- PJ and LC are working on, will circulate
* Poster for presenting- needs photos of all participants
* End of Year One coming up- will need to prepare annual report soon

=== Ontology Development Workshop planned for this fall: ===
* Dates: Possibly Nov-Dec, in Corvallis or maybe another central location
* See wiki page for more details:
* Goal: Focus on ontology training (OWL/Protege), but stay for a several days to a week total for actual hands on, get people actually comfortable in the system.
* Bring in OSU Conferences coordinators to help manage logistics
* may be able to utilize OSU Conference people to help organize.

=== Birmingham/Montpellier Meeting ~May 2016 ===
* Will be in conjunction with another meeting, GG and JD are working with Ruth Bastow to organize
* Goal of the meeting is to ...??

===ICBO Meeting Aug 1-4th, 2016===
* http://icbo.buffalo.edu/index.html
* Location- to be held in Corvallis
* May include an Annotation Jamboree??

=== Other items:===
* GG and JD could show their data structure at a future meeting- When, next all hands meeeting

* Chris could demo update of new AmiGO curation NGS Annotation for the GO annotation with pathway curation, possibly in the next week
* Next Data viz meeting next 11am next Wed

* Next All Hands: planned for Sept 24th- LC will send out a doodle poll, GG has a conflict on the 24th. EA and MAL have also conflict on the 24th (RDA meeting, Paris)

== B. Update from Ontologies Working Group:==
=== Updates from OSU: Laurel===
* All the ontology development work and files have been moved from SVN to the new Planteome Site on Github (https://github.com/Planteome)
* Reference Ontologies: PO, TO, PSO, EO
* Ontology files and issue trackers, Association files are still on the SVN as they are too large for GH
* Some Crop Ontology (IBP- maize, wheat, rice, cassava)
* Everyone needs github IDs for access to our project- JD and GG still need GH ids
'''GG has a GitHub id, will send, JD will get one''

=== Updates from Bioversity: Marie-Angelique ===
* Crop Ontology webpage: http://www.cropontology.org/
** Curation efforts have been going on during the summer to update them to the new Trait Template Ver. 5
** Twelve of the CO vocabs are done- will be uploaded - ''Where, to the CO site or to GH??''

====Mapping between Crop Ontologies and the Ref Ontologies:====
* MAL continues to work on the mapping between crop ontologies and ref. ontologies
* Priority is mapping, using an automated tool: Agreement Maker Light (AML) (http://agreementmaker.org/) tool
''For details of the mapping algorithm- see the Ontology working group meeting June 21st''

* Need to check on which of the files have been updated... ''not sure what this is referring to''

* The CO vocabs are being revised to include fields in TT spreadsheet for the enttiy and attribute
* Mappings will be added as they are developed, based on the E + A

* MAL has tried tools, CM has tools, need to find out what tool works best
* New version of the TT has more information

* From CM: Prospective mapping is better than retrospective mapping- by creating logical definitions
* It would be good to work with CM to develop a workflow, power comes from the cross products
* Will review the workflow at the next ontology call

''Ask CM to show us the mapping tool and if he has a more up to date version of the XP file, the one on the SVN is quite old''

* Pankaj: Ideal goal is to have a tool available for the workflow by the curators
** Suggestion to each run a common panel of files through and compare the results- e.g. rice and maize
''Need to get the most recent version of the CO file- Updated TT version 5. Are these on the GH repository?''
* Goal is to map back to reference ontologies through the XPs. If the terms are composed in the XPs then we are
* Suggestion: A Term Genie instance for the generation of the terms for the CO vocabs.

* MAL will share her slides to illustrate, that were presented for the RTB meeting.

====Roots, Tubers, Banana Development (TRB) meeting in Montpellier:====
* Funded by Bill Gates Foundation, three days week of Aug 20th
** Discussing NGS and ontologies
** Development and curation for the RTB crops with Boyce Thompson Institute will split the work
* Cassava has been uploaded, but it is not the up to date version, still needs to be finalized and now has a Read-Me file

''Question: which of the CO species does this include? cassava, potato, banana, others? ''

== C. Update from IT group- Data Store, AmiGO2- Justin Elser==

=== Migration to github- See above ===
* Almost complete. Let me know if there are any more files to transfer with history
* All files (minus SVN) are over on github (almost, still moving a few extras)

* Association files: moving to iPlant eventually?
** Where are we going to put the association files?- the association files are too big for Github
** They are cluttered within the SVN- JE will move them all to a new SVN repository

** Keep association files on SVN, but keep them alone, not mixed with things that have migrated to Github.
* Irods: iPlant's 'big iron' is a possibility, but lacks any version control system
* In the long run, it makes more sense to keep annotation/association files on iPlant
* Mirror the latest version from version control (SVN) over on iPlant for 'bulk download' options for end users.

=== AmiGO 2 ===
Fixed annotation loading issue (well, a workaround)
* Working on bisecting issue so we can stay current with Owltools and AmiGO 2 development
''Not sure what this is referring to''

* Loading is far far faster, but issue is that it won't load any annotations
** JE found a workaround with an old version of OWLtools, but its "not ideal"
** GO doesn't have this issue- Can Chris or Seth help?
** CM can't help until the beginning of Sept.
** If JE can't figure it out by sept, Chris can help

* Post issues to Github's issues tracker on the Planteome-amigo2 repository
** JE will have it up and down frequently, so be wary when you're 'testing' it.

* Migrating live version to iPLant- need to check on virtual machines
* Need to work on customization and tools
* iPlant won't get looked at until it is working on the live version (????)

== D. Update from AISO/BisQue group- Justin Preece==
* Main goal: getting a web module for people to segment images, and link those segments to ontology terms/metadata
** There are desktop programs/algorithms that work, they are moving them to the web as 'modules'
** TL;DR-Newer/better/shinier graph cuts
** putting a module on iPlant BisQue that allows you to segment an image, and annotate it with ontologies.
** Doing a test environment locally, will expand to testing groups that are larger

* Working with two students from Comp Sci- Sinisa's Lab
* 1. C++ and Matlab under the hood
* 2. Matlab and python on the surface for UI

==E. Other Comments:==

==Next meeting TBA==
Planned for Sept 24th- LC will send out a doodle poll as GG has a conflict

Ontology Working Group Meeting, Tuesday July 21st, 2015

2015-08-03T09:44:36Z

Marieangelique.laporte: /* Workshop planning */

'''Time: 8am PDT (GMT-7:00) Pacific Time (US and Canada)'''

* In attendance: LC, MAL, AM, EA
[[File:Ontology WG July 21st audio only.m4a|thumb|Ontology WG_July 21st_audio_only.m4a]]

- Participants: Maria-Angelique, Elizabeth Arnaud, Lol, Austin

== Planning and formulating a vision for the workplan- Planteome Ontologies ==

== Priority 1 ==
* Improving the IBP/CO trait dictionaries with trait names and methods and scales from the curators
* Will eventually make sure the trait is mapped to the ontologies
* lentil, pigeonpea, cowpea, 3 dictionaries need to upload
* OBO files generated computationally are intersection of trait and scale
* By the end of July: all trait dictionaries revised and sent to BIPP ''(no idea on this acronym)''
"Running a little behind schedule, but should have 10 done by end of Aug."
* For rest, waiting on validation of variables, and structure by the curators
"variables = how the trait is measured."
* MAL- working on the file and OBO structure
"still wanting to work on the mapping"
- Mapping will not be a separate file, it will be imbedded
- Needs to be validated first (the trait dictionary).
- some already on Github
- trait name, variable name, scale
- Priority 2:
"PDO"
- Disease ontology needs reviewed.
- plan for overall structure needs made (next week)
- Share google spreadsheet with us from the CO, done by french group
- need to unify a plan from the 3 ontologies
- Early August deadline

- OSU's targets
- look at stress traits in TO
- TO has been switched to Github
"no longer updating the SVN"
- Need to migrate the trackers
-
- migrate PO and EO
- identify overall plan for PDO pathogens
- unclear as what should be a synonym
- Migrate PDO

* JE- working with seth and chris to fix AmiGO2
- OWL conversion from OBO in process

* Upper level conversation
- what dictionaries become ontologies?
== Workshop planning ==
- PJ and EA need to figure out who is getting trained on OWL
- sessions for mapping? Or just ontology demo
- AM + MAL
- train for OWL
- Need to know when
- Austin
- Afola Agbona ("Afolabi, Agbona (IITA)" <A.Afolabi@cgiar.org>)
"cassava guy"
- only one still using OBO
- PAG meeting another option for OWL training
"not ideal"
- Teach someone OWL in 3 days? This is tough for people with little exposure
- need goals
- Clear goals will be key
- nama working with afula, and soon to CIP
- should ask her how far everyone she works with needs training in.
- Maybe just CIP and banana people need the training
- possible that no one needs to be upgraded
- Better to try and teach OWL, or just stick to teaching OBO
- if they are going to work in Planteome, OWL would be nice
- the endgame of each person should determine what should be taught (OBO or OWL)
- Background can decide what each person needs
- bioinformaticist- easy to learn programs, tougher to learn biology
- format
- trait dictionary
- excel
- ontology format?
- enriched relationships

== Schedule: ==
- rice/wheat - still getting worked on
"end of July is the goal"
- rosemary and kate in charge of this
- Kate- working on the dictionary and data management
- rosemary is in charge of it

* Get George to join an ontology meeting
"also his postdoc"
- just get him in one of these meetings, and ask him about what he's doing, and find out if he can help us.
- been difficult because of everyone's schedule.
- Lets get a meeting going at PAG

Wednesday June 24th, 2015

2015-06-24T08:26:16Z

Marieangelique.laporte: /* Agenda */

=Agenda=
Planteome Project is inviting you to a scheduled Zoom meeting.
Join from PC, Mac, iOS or Android: https://zoom.us/j/667957473

* Who: LC, MAL, PJ, JP,
* Not available: EA (COPO workshop)
(Others: GG, JE, DWS, EZ, ST? )

== A. General Comments and Updates:==
=== Introductions: ===
* Any new faces?
===Updates on new hires===
* New postdoc at OSU: details TBA
===Workshop and travels: Elizabeth's questions===

a. What will be the objective of the workshop?

b. Who will be the attendees ? data manager, ontology curators, researchers?

I propose to consider: Use of Protégé; Discussion on Traits/trait mapping; Discussion on possible annotation pipelines and test on data sets

c. Travel budget: shall we keep our travel budget for this workshop or can we use it entirely for visit to CGIAR centers on our side

== B. Update from IT group- Data Store, AmiGO2- Justin Elser==

* AmiGO 2 progress
** Fixed issue with loading both EO and TO together. Issue was that they were both trying to use the "TEMP" namespace after the conversion to OWL. Wrote a little script to fix it.
** Wrote an importer owl file (planteome.owl) that is used when loading. We can add new ontologies simply by adding a line to the import list.

* Git migration
** Working on using Chris Mungall's [https://github.com/cmungall/gosf2github/ script] to migrate TO term requests from sourceforge to github.

== C. Update from AISO/BisQue group- Justin Preece:==

== D. Update from Ontologies Working Group:==

==E. Other Comments:==

==Next meeting Thursday July 23rd, 2015==

Ontology Working Group Meeting, Tuesday June 23rd, 2015

2015-06-23T15:16:01Z

Marieangelique.laporte: /* Mappings from CO to TO: MAL */

'''Time: 8:15am PDT (GMT-7:00) Pacific Time (US and Canada)'''

Connection details: Join from PC, Mac, iOS or Android: https://zoom.us/j/985703701

* Who will attend: LC, MAL, DWS, PJ, BS, AM
* Others: GG, JE ?
* Regrets: EA, CM

==Summary from last meeting [[Ontology_Working_Group_Meeting,_Tuesday_June_9th,_2015| June 9th]]: ==
* new [[Crop_Ontology_Pages]] on the wiki (MAL)
* Agrovoc discussion- Part of FAO
* Updates on Plant Disease Ontology and future plans for Plant Stress Ontology (Laurel)

== Updates on New Hires, etc==
* '''OSU: New Postdoc Curator has joined the team: Austin Meier'''
** Austin's Background:

* NYBG: - Offer to postdoc candidate has been made, waiting for confirmation, graduate student will be joining to help with the imaging work, and a summer undergrad intern to help with the imaging

==Report from Bioversity team: Marie_Angelique==

==Mappings from CO to TO: MAL==
From [[Ontology_Working_Group_Meeting,_Tuesday_May_26th,_2015]] :
* Marie-Angelique is testing Mapping to TO using the program Agreement Maker Light (AML) (http://agreementmaker.org/) tool
* Import as OWL or OBO, * Needs to make the product using owl files??
* Add mapping to terms, structure or words

===Results of mapping to [http://www.cropontology.org/ontology/CO_321/Wheat Wheat Ontology CO:321]===
* The Wheat Ontology CO:321 has 240 trait terms, with 46 xrefs to the TO (done by Rosemary Shrestha)
* The manually created '''Xrefs to TO''' can be used to double check the AML mappings (a caution as they were created some time ago- may be out of date)
* The AML tool found about 73 mapping, case independent
* Results on [https://github.com/Planteome/ibp-wheat-traits/tree/master/mappings Github]

* Results: color coding:
** Green- Xref and AML in agreement
** Orange- Xref and AML NOT in agreement
** No color- new mapping that the AML tool found- about 30 new ones identified, need to be verified.

* Mapping to PO was complicated by the presence of the synonyms, and issue of AML did not want to use the PO terms more than once.

Examples of lack of agreement:
* CO term: CO:321:0000040 grain size
* Xref to: seed size TO:0000391
* AML maps it to: TO:0000397 grain size (which is correct)

Note: Xref Links CO trait definitions which are mapped to Gramene right have been changed to the Planteome page- ''Are these only in the wheat file right now?''

===Test of a brand new algorithm developed at LASIGE in Lisbon===
*compound matching [http://ceur-ws.org/Vol-1317/om2014_poster2.pdf Poster]
*We ran first tests with TO-PO-PATO and COWheat-PO-PATO. The idea is to only look at the top results first to check if the things are ok. The top results were good for TO-PO-PATO. But we did not get result for COWheat-PO-PATO. Therefore we are working on that

==Next Meeting Tuesday July 21st==

Back to the [[Planteome_Ontology_Development_and_Coordination_Working_Group]] page

Ontology Working Group Meeting, Tuesday June 23rd, 2015

2015-06-22T11:51:27Z

Marieangelique.laporte:

'''Time: 8:15am PDT (GMT-7:00) Pacific Time (US and Canada)'''

Connection details: TBA

* Who will attend: LC, MAL, DWS, PJ, BS
* Others: CM, GG, JE ?
* Regrets: EA

==Summary from last meeting [[Ontology_Working_Group_Meeting,_Tuesday_June_9th,_2015| June 9th]]: ==
* TBA...

==Discussion of Timeline and Plan==
==Mappings from CO to TO: MAL==
From [[Ontology_Working_Group_Meeting,_Tuesday_May_26th,_2015]] :
* Marie-Angelique is testing Mapping to TO using the program Agreement Maker Light (AML) (http://agreementmaker.org/) tool
* Import as OWL or OBO, * Needs to make the product using owl files??
* Add mapping to terms, structure or words

===Results of mapping to [http://www.cropontology.org/ontology/CO_321/Wheat Wheat Ontology CO:321]===
* The Wheat Ontology CO:321 has 240 trait terms, with 46 xrefs to the TO (done by Rosemary Shrestha)
* The manually created '''Xrefs to TO''' can be used to double check the AML mappings (a caution as they were created some time ago- may be out of date)
* The AML tool found about 73 mapping, case independent
* Results on [https://github.com/Planteome/ibp-wheat-traits/tree/master/mappings Github]

* Results: color coding:
** Green- Xref and AML in agreement
** Orange- Xref and AML NOT in agreement
** No color- new mapping that the AML tool found- about 30 new ones identified, need to be verified.

* Mapping to PO was complicated by the presence of the synonyms, and issue of AML did not want to use the PO terms more than once.

Examples of lack of agreement:
* CO term: CO:321:0000040 grain size
* Xref to: seed size TO:0000391
* AML maps it to: TO:0000397 grain size (which is correct)

Note: Xref Links CO trait definitions which are mapped to Gramene right have been changed to the Planteome page- ''Are these only in the wheat file right now?''

==Next Meeting Tuesday July 21st==

Back to the [[Planteome_Ontology_Development_and_Coordination_Working_Group]] page

Ontology Working Group Meeting, Tuesday June 23rd, 2015

2015-06-22T11:39:31Z

Marieangelique.laporte: /* Mappings from CO to TO: MAL */

'''Time: 8:15am PDT (GMT-7:00) Pacific Time (US and Canada)'''

Connection details: TBA

* Who will attend: LC, MAL, DWS, PJ, BS
* Others: CM, GG, JE, EA ?
* Regrets:

==Summary from last meeting [[Ontology_Working_Group_Meeting,_Tuesday_June_9th,_2015| June 9th]]: ==
* TBA...

==Discussion of Timeline and Plan==
==Mappings from CO to TO: MAL==
From [[Ontology_Working_Group_Meeting,_Tuesday_May_26th,_2015]] :
* Marie-Angelique is testing Mapping to TO using the program Agreement Maker Light (AML) (http://agreementmaker.org/) tool
* Import as OWL or OBO, * Needs to make the product using owl files??
* Add mapping to terms, structure or words

===Results of mapping to [http://www.cropontology.org/ontology/CO_321/Wheat Wheat Ontology CO:321]===
* The Wheat Ontology CO:321 has 240 trait terms, with 46 xrefs to the TO (done by Rosemary Shrestha)
* The manually created '''Xrefs to TO''' can be used to double check the AML mappings (a caution as they were created some time ago- may be out of date)
* The AML tool found about 73 mapping, case independent
* Results on [https://github.com/Planteome/ibp-wheat-traits/tree/master/mappings Github]

* Results: color coding:
** Green- Xref and AML in agreement
** Orange- Xref and AML NOT in agreement
** No color- new mapping that the AML tool found- about 30 new ones identified, need to be verified.

* Mapping to PO was complicated by the presence of the synonyms, and issue of AML did not want to use the PO terms more than once.

Examples of lack of agreement:
* CO term: CO:321:0000040 grain size
* Xref to: seed size TO:0000391
* AML maps it to: TO:0000397 grain size (which is correct)

Note: Xref Links CO trait definitions which are mapped to Gramene right have been changed to the Planteome page- ''Are these only in the wheat file right now?''

==Next Meeting Tuesday July 21st==

Back to the [[Planteome_Ontology_Development_and_Coordination_Working_Group]] page

Ontology Working Group Meeting, Tuesday June 9th, 2015

2015-06-22T11:36:41Z

Marieangelique.laporte: /* Agrovoc discussion- Part of FAO */

'''Time: 8:15am PDT (GMT-7:00) Pacific Time (US and Canada)'''
Connection details:
Join from PC, Mac, iOS or Android: https://zoom.us/j/834566681

* Who will attend: LC, MAL, DWS, PJ, BS
* Others?: , CM, GG
* Regrets: JE, EA

* Link to recording- Video: File: [[File:Ontology WG 6-9-15 audio only.m4a|thumbnail|Ontology WG 6-9-15 audio only.m4a]]
* Link to recording- Audio: File: [[File:Ontology WG 6-9-15 video.mp4|thumbnail|Ontology WG 6-9-15 video.mp4]]

=Agenda=

==Summary from last meeting [[Ontology_Working_Group_Meeting,_Tuesday_May_26th,_2015| May 26th]]: ==
* Report form UN meeting- BS- ''need links to publication''
* Updates underway to the Trait Template (Leo)
* Discussion of the id space for Crop Ontologies
* Discussion of the hierarchy of the CO Vocabs- not a problem if the terms have logical def'ns, just import as flat file.
* Mapping to TO with Agreement Maker Light - see below
* Progress on AmiGO2 browser development: http://dev.planteome.org/amigo
* Updates on the transition to Github: https://github.com/Planteome

== Other Updates, etc==
* OSU: Offer has been made to postdoc, waiting for confirmation, hopefully will start around the end of June, undergraduate student hired for summer, another one joining in August
* NYBG: - Offer to postdoc candidate has been made, waiting for confirmation, graduate student will be joining to help with the imaging work, and a summer undergrad intern to help with the imaging
** Also working with the AISO-Bisque team to generate images. Idea to do a use case study involving ''in situ'' analysis- leaf development or procambium development- link GO and PO to the image. Requires color recognition
** NYBG has received a new 5 year DOE grant to work on epiphytic plants in Chile and California and the effects of nitrogen stress. DWS' group is doing the molecular genetic characterization and is planning to use the ontologies such as the Stress Ontology, should be able to link the expressed genes and GO terms to the stresses.
*

==Report from Bioversity team: Marie_Angelique==
* MAL reported that the Github repository names for the CO will be changed to IBP from CGIAR- ''Done. New names are of the form: "IBP-wheat-traits"''
* The Xrefs to the TO term Ids in the wheat and maize ontologies have been updated to link to the TO on the Planteome site and XRef name has been changed from "Gramene Trait Ontology" to "Plant Trait Ontology". ''Files on Github should be updated to the newest version''
* [http://www.cropontology.org/ontology/CO_322/Maize]
* Need to work on the coordination between EO, ENVO and CR (BS)

===Introduce new [[Crop_Ontology_Pages]] on the wiki (MAL) ===
As a follow up from the discussion last week, Marie-Angelique has created an informative page on the wiki with information about the structure and format of the CO vocabularies.
* Current structure of the Trait template (v.4)
* Future structure of the Trait Template (v.5)

==== Agrovoc discussion- Part of FAO ====
Agrovoc is maintained by FAO as a SKOS Thesaurus. Agrovoc covers area related to Agriculture, including food, nutrition, agriculture, fisheries, forestry, environment etc... Agrovoc is mainly used by Agris (multilingual bibliographic database of FAO) to index bibliographic documents.
* Uses SKOS versions of the ontologies?
* Johannes Keizer
* [http://www.slideshare.net/CIARD_/the-gacs-project-by-caterina-caracciolo GACs project] info (from web)
* GACS beta release [http://aims.fao.org/activity/blog/global-agricultural-concept-scheme-gacs-beta-10-released]: "GACS explored the possibility of creating a global repository of concepts and terminology in the area of agriculture. This first beta is the result of the first experimental attempt, and it went very well! We now have a pool of concepts based on a mapping between AGROVOC, the CAB Thesaurus and the NAL Thesaurus."

* Bill & Melinda Gates Foundation Project- $18.5M project funded to Cornell: [http://cornellcals.tumblr.com/post/115963302150/18-5-million-grant-to-boost-breeding-of-global Genomic and Open-source Breeding Informatics Initiative (GOBII)]
** Stan Wood, Simon Leu

== Updates on work on Plant Disease Ontology and future plans for Plant Stress Ontology (Laurel)==
* Discussion of overall structure and goals:
* See Google doc: [https://docs.google.com/document/d/1b-t1MNYcQznBe6mTM_Evb9r4XBe-z1jyKoFV2gTyAzc/edit?usp=sharing Notes on the development of the Plant Stress Ontology]]
* View the current version on the AmiGO Dev browser: [http://palea.cgrb.oregonstate.edu/trait_ontology/cgi-bin/trait_amigo/go.cgi Trait and Stress Dev Ontology]

'''Discussion Points:'''
* Started building a Plant Disease Ontology by adding diseases and pathogens causal agents from the [http://www.apsnet.org/publications/commonnames/Pages/default.aspx APS "Common Names of Plant Diseases" pages]. Currently has branches for the causal agents, host species and plant diseases, linked by relationships
* Adding in information from a number of additional sources now, as the APS is a bit outdated and not comprehensive e.g. NCBI, PHI-base, MaizeGDB, Rice SES, EOL
* Disease names are based on the common name in use with the host species and disease causal agent type added. e.g. "Bacterial blight (APS)" --> rice bacterial blight disease (PDO).

* Ideally we would like to have the disease causal agents and host plant species in a separate ontology or taxonomy that we would not be responsible for maintaining, such as NCBI, but it is too large to import into the AmiGO browser.
* In order to create a slim we need to have a list of the names of the pathogens. One suggestion was to use the [http://www.obofoundry.org/cgi-bin/detail.cgi?id=ncbi_taxonomy NCBI Taxon ontology], but we would need to create a slim.

* Suggestion from MAL after the call: There is also the [http://www.uniprot.org/taxonomy/ Uniprot Taxonomy] which has URIs for taxon along with some synonyms.
* Compare with approach in the Human Disease Ontology- flat list of diseases and the "Plant Infectious Disease Ontology"

==Mappings from CO to TO: MAL==
Tabled for next meeting....

==Next Meeting Tuesday June 23rd==

Back to the [[Planteome_Ontology_Development_and_Coordination_Working_Group]] page

Crop Ontology Pages

2015-06-22T11:24:43Z

Marieangelique.laporte: /* Introduction to The Crop Ontology */

Crop Ontology Pages

2015-06-22T08:25:07Z

Marieangelique.laporte: /* List of Crops and IDs */

==Introduction to [http://www.cropontology.org/ The Crop Ontology]==

The Crop Ontology website consists of 5 sections:
# Phenotypes and Traits Ontology
# Plant Anatomy & Development Ontology
# General Germplasm Ontology
# Location and Environmental Ontology
# Structural and Functional Genomic Ontology

===There are 3 ways of creating “ontologies” on the Crop Ontology website===
# Upload a Trait Dictionary (TD) in Excel. (Note, the TD is only used to store and load information about traits, thus it cannot be used for uploading ontologies that would belong to the other categories)
# Upload an OBO file. They can be used to create ontologies in any of the 5 sections
# Ontologies can be built from scratch using the website dedicated interface. ''Are there any examples of these?''

===Storage and Downloading===
* Once the files are uploaded or some terms are submitted using the web interface, the data are stored in a noSQL database (Google App Engine Datastore).
* The ontologies can be downloaded in various formats: CSV, OBO, SKOS and JSON. The structures of the different formats are described in the following sections.
* Note that because there is no exact mapping between the different formats some compromises has been made. Not all the information is available in the different formats.

=List of Crops and IDs=
According to the project timeline, the crops that will be linked to the reference ontologies are:
{| {{table}}
| align="center" style="background:#f0f0f0;"|'''CROPS'''
| align="center" style="background:#f0f0f0;"|'''Crop Ids'''
| align="center" style="background:#f0f0f0;"|'''Prefixes'''
| align="center" style="background:#f0f0f0;"|'''Map to prefixes recommended by Chris'''
|-
| Maize||322||CO_322||IBPCO:322xxxx
|-
| Rice||320||CO_320||IBPCO:320xxxx
|-
| Wheat||321||CO_321||IBPCO:321xxxx
|-
| Cassava||334||CO_334||IBPCO:334xxxx
|-
| Cowpea||340||CO_340||IBPCO:340xxxx
|-
| Chickpea||338||CO_338||IBPCO:338xxxx
|-
| Potato||330||CO_330||IBPCO:330xxxx
|-
| Sorghum||324||CO_324||IBPCO:324xxxx
|-
| Soybean||336||CO_336||IBPCO:336xxxx
|-
| Barley||323||CO_323||IBPCO:323xxxx
|-
| Common Bean||335||CO_335||IBPCO:335xxxx
|-
| Groundnut||337||CO_337||IBPCO:337xxxx
|-
| Pearl millet||327||CO_327||IBPCO:327xxxx
|-
| Pigeon Pea||341||CO_341||IBPCO:341xxxx
|-
| Musa||325 (traits) and 125 (anatomy)||CO_325 and CO_125||IBPCO:325xxxx and IBPCO:125xxxx
|-
| Sweet Potato||331||CO_331||IBPCO:331xxxx
|-
| Yam||333||CO_333||IBPCO:333xxxx
|-
| Other crops ???||||||
|}

=OBO files=
==OBO file structure==
OBO files are created using the obo2owl library (which should sound familiar ;-)).

The main issue with the Trait Template is that because different IDs can be created for the same “thing” (e.g. the term “cm” will get different IDs if different traits are measured in cm), different obo terms can have the same name (but different IDs).

That is a problem when our users tried to import the OBO files in a Chado database.

* Consequently, I created a little script that created OBO files where all the names are unique in a given namespace. The script has not be inserted in the website yet but it will be soon. Example of an OBO files on Github. (MAL)

{| border="1" class="sortable"
!TD column!!OBO element
|-
|Crop||Used for setting up the namespace
|-
|Name of Trait||name
|-
|Trait ID for modification, Blank for New||Term + id
|-
|Description of Trait||definition
|-
|Trait Class||Term +id + name + is-a
|-
|Language of submission (only in ISO 2 letter codes)||We have only English OBO files.
|-
|Name of submitting scientist||created_by
|-
|Institution||Not used
|-
|Date of submission||creation_date
|-
|Abbreviated name||synonym [EXACT]
|-
|Synonyms (separate by commas)||synonym [EXACT]
|-
|How is this trait routinely used||Not used
|-
|Name of method||name
|-
|Method ID for modification, Blank for New||Term + id + method_of
|-
|Describe how measured (method||definition
|-
|Bibliographic Reference||xref
|-
|Growth Stage||Not used
|-
|Comments||Not used
|-
|Scale ID for modification, Blank for New||Term + id + scale_of
|-
|Type of Measure (Continuous, Discrete or Categorical||Not used
|-
|For Continuous: units of measurement||name
|-
|For Discrete: Name of scale or units of measurement||name
|-
|For Categorical: Name of rating scale||name
|-
|For Categorical: Class 1 - value = meaning||Term + name + is-a
|-
|For Categorical: Class 2 - value = meaning ||Term + name + is-a
|-
|For Categorical: Class 3 - value = meaning||Term + name + is-a
|-
|For Categorical: Class 4 - value = meaning||Term + name + is-a
|}

=SKOS files=
==SKOS file structure==
{| border="1" class="sortable"
!TD column!!SKOS
|-
|Crop||Used for setting up the namespace
|-
|Name of Trait||skos:prefLabel
|-
|Trait ID for modification, Blank for New||Local Name (URI) + rdf: type skos:concept
|-
|Description of Trait||skos:definition
|-
|Trait Class||rdf:type Skos:Concept + skos:broader
|-
|Language of submission (only in ISO 2 letter codes)||xml:lang of the literals. SKOS files are multilingual (if we have the info)
|-
|Name of submitting scientist||foaf:Person (not set so far but will be soon)
|-
|Institution||foaf:Organization (not set so far but will be soon)
|-
|Date of submission||dc:date (not set so far but will be soon)
|-
|Abbreviated name||skos:altLabel
|-
|Synonyms (separate by commas)||skos:altLabel
|-
|How is this trait routinely used||Not used
|-
|Name of method||skos:prefLabel
|-
|Method ID for modification, Blank for New||Local Name (URI) + rdf: type skos:concept
|-
|Describe how measured (method||skos:definition
|-
|Bibliographic Reference||Not set (dc: bibliographicCitation?)
|-
|Growth Stage||skos:related (not set so far)
|-
|Comments||skos:editorialNote
|-
|Scale ID for modification, Blank for New||Local Name (URI) + rdf: type skos:concept
|-
|Type of Measure (Continuous, Discrete or Categorical||Not used
|-
|For Continuous: units of measurement||skos:prefLabel
|-
|For Discrete: Name of scale or units of measurement||skos:prefLabel
|-
|For Categorical: Name of rating scale||skos:prefLabel
|-
|For Categorical: Class 1 - value = meaning||Local Name (URI) + rdf: type skos:concept
|-
|For Categorical: Class 2 - value = meaning ||Local Name (URI) + rdf: type skos:concept
|-
|For Categorical: Class 3 - value = meaning||Local Name (URI) + rdf: type skos:concept
|-
|For Categorical: Class 4 - value = meaning||Local Name (URI) + rdf: type skos:concept
|}

Wednesday June 24th, 2015

2015-06-22T07:29:06Z

Marieangelique.laporte: /* A. General Comments and Updates: */

=Agenda=
Planteome Project is inviting you to a scheduled Zoom meeting.
Join from PC, Mac, iOS or Android: https://zoom.us/j/667957473

* Who: LC, MAL, PJ, JP,
* Not available:
(Others: GG, JE, DWS, EZ, ST? )

== A. General Comments and Updates:==
=== Introductions: ===
* Any new faces?
===Updates on new hires===
* New postdoc at OSU: details TBA
===Workshop and travels: Elizabeth's questions===

a. What will be the objective of the workshop?

b. Who will be the attendees ? data manager, ontology curators, researchers?

I propose to consider: Use of Protégé; Discussion on Traits/trait mapping; Discussion on possible annotation pipelines and test on data sets

c. Travel budget: shall we keep our travel budget for this workshop or can we use it entirely for visit to CGIAR centers on our side

== B. Update from IT group- Data Store, AmiGO2- Justin Elser==

* AmiGO 2 progress

* Git migration
== C. Update from AISO/BisQue group- Justin Preece:==

== D. Update from Ontologies Working Group:==

==E. Other Comments:==

==Next meeting Thursday July 23rd, 2015==

Ontology Working Group Meeting, Tuesday June 23rd, 2015

2015-06-22T07:28:19Z

Marieangelique.laporte: /* Workshop and travels: Elizabeth's questions */

'''Time: 8:15am PDT (GMT-7:00) Pacific Time (US and Canada)'''

Connection details: TBA

* Who will attend: LC, MAL, DWS, PJ, BS
* Others: CM, GG, JE, EA ?
* Regrets:

==Summary from last meeting [[Ontology_Working_Group_Meeting,_Tuesday_June_9th,_2015| June 9th]]: ==
* TBA...

==Discussion of Timeline and Plan==
==Mappings from CO to TO: MAL==
From [[Ontology_Working_Group_Meeting,_Tuesday_May_26th,_2015]] :
* Marie-Angelique is testing Mapping to TO using the program Agreement Maker Light (AML) (http://agreementmaker.org/) tool
* Import as OWL or OBO, * Needs to make the product using owl files??
* Add mapping to terms, structure or words

===Results of mapping to [http://www.cropontology.org/ontology/CO_321/Wheat Wheat Ontology CO:321]===
* The Wheat Ontology CO:321 has 240 trait terms, with 46 xrefs to the TO (done by Rosemary Shrestha)
* The manually created '''Xrefs to TO''' can be used to double check the AML mappings (a caution as they were created some time ago- may be out of date)
* The AML tool found about 73 mapping, case independent

* Results: color coding:
** Green- Xref and AML in agreement
** Orange- Xref and AML NOT in agreement
** No color- new mapping that the AML tool found- about 30 new ones identified, need to be verified.

* Mapping to PO was complicated by the presence of the synonyms, and issue of AML did not want to use the PO terms more than once.

Examples of lack of agreement:
* CO term: CO:321:0000040 grain size
* Xref to: seed size TO:0000391
* AML maps it to: TO:0000397 grain size (which is correct)

Note: Xref Links CO trait definitions which are mapped to Gramene right have been changed to the Planteome page- ''Are these only in the wheat file right now?''

==Next Meeting Tuesday July 21st==

Back to the [[Planteome_Ontology_Development_and_Coordination_Working_Group]] page

Crop Ontology Pages

2015-06-03T08:52:59Z

Marieangelique.laporte: /* Structure of the Trait Template V5 (Léo is still working on it with Julian Pietragalla from CIMMYT) */

There are 3 ways of creating “ontologies” on the Crop Ontology website.
*First, one can choose to upload a Trait Dictionary in Excel. The TD is only used to store and load information about traits, thus it cannot be used for uploading ontologies that would belong to the other categories (Note, there are 5 sections on the CO website: General Germplasm Ontology, Phenotypes and Traits Ontology, Structural and Functional Genomic Ontology, Location and Environmental Ontology and Plant Anatomy & Development Ontology).
*OBO files can be uploaded as well. They can be used to create ontologies in any of the 5 sections.
*Finally, ontologies can be built from scratch using the website dedicated interface.

Once the files are uploaded or some terms are submitted using the web interface, the data are stored in a noSQL database (Google App Engine Datastore).
The ontologies can be downloaded in various formats: CSV, OBO, SKOS and JSON. The structures of the different formats are described in the following sections. Note that because there is no exact mapping between the different formats some compromises has been made. Not all the information is available in the different formats.

=Trait Template=
==Structure of the Trait Template V4==
So far, the Trait Template V4 is uploaded into the CO website. The Trait Template is used to gather information on traits along with their methods and scales of measurement. For each trait, some meta-information is added (5 first columns). An (unique) ID is created by the system for each trait, method and scale (several IDs are created when the scale is categorical). But for now, if two methods or scales are the same (seed length and leaf length are measured in centimeters), different IDs are created, which is far from being ideal or even ontologically correct.
The Trait Template V4 columns are:
*IBFieldbook
*Name of submitting scientist
*Institution
*Language of submission (only in ISO 2 letter codes)
*Date of submission
*Crop
*Name of Trait
*Abbreviated name
*Synonyms (separate by commas)
*Trait ID for modification, Blank for New
*Description of Trait
*How is this trait routinely used?
*Trait Class
*Method ID for modification, Blank for new
*Name of Method
*Describe how measured (method)
*Growth Stage
*Bibliographic Reference
*Comments
*Scale ID for modification, Blank for new
*Type of Measure (Continuous, Discrete or Categorical)
*For Continuous: units of measurement
*For Continuous: reporting units (if different from measurement)
*For Continuous: minimum
*For Continuous: maximum
*For Discrete: Name of scale or units of measurement
*For Categorical: Name of rating scale
*For Categorical: Class 1 - value = meaning
*For Categorical: Class 2 - value = meaning
*For Categorical: Class 3 - value = meaning
*For Categorical: Class 4 - value = meaning
*For Categorical: Class 5 - value = meaning

==Structure of the Trait Template V5 (Léo is still working on it with Julian Pietragalla from CIMMYT) ==
Note the structure can still evolve. Template V5 is still a draft
{| {{table}}
| align="center" style="background:#f0f0f0;"|'''Column'''
| align="center" style="background:#f0f0f0;"|'''Description'''
|-
| Curation||Comments for curation
|-
| Scientist||Name of scientist submitting variable.
|-
| Institution||Name of institution submitting variable
|-
| Language||2 letter ISO code for language in which variable data is submitted.
|-
| Date||Date the variable was submitted.
|-
| Crop||Crop name.
|-
| Trait ID||Term ID for trait as generated by the system. Use an existing ID to modify data for that trait. If left blank the system will automatically generate a new ID.
|-
| Trait||Trait name (property)
|-
| Entity||A trait must follow the convention "Trait" = "Entity" + "Attribute", eg for "grain colour", attribute = "grain"
|-
| Attribute||eg for "grain colour", entity = "colour"
|-
| Trait synonyms||Acronym/abbreviated name.
|-
| Trait abbreviation||Recommended trait name abbreviation
|-
| Trait abbreviation synonyms||Other trait name abbreviations
|-
| Trait description||Textual description of trait.
|-
| Trait class||General class to which trait belongs.
|-
| Trait status||recommended, standard, obsolete,
|-
| Trait Xref||Cross reference of the trait e.g., Xref to TO
|-
| Method ID|| Term ID for method as generated by the system. Use an existing ID to modify data for that method. If left blank the system will automatically generate a new ID.
|-
| Method|| (Short) method name.
|-
| Method description|| Textual description of method.
|-
| Formula|| For computational methods, express the formula using variable names
|-
| Method class|| Measurement, Counting, Rating, Estimation, Scoring, Computation
|-
| Method reference|| Biobliographical reference describing method.
|-
| Scale id||Term ID for scale as generated by the system. Use an existing ID to modify data for that scale. If left blank the system will automatically generate a new ID.
|-
| Scale name||[Guidelines to be defined for naming the scale]
|-
| Scale class||Numerical, Nominal, Ordinal, Text, Code, Time, Duration
|-
| Decimal places||For numerical, number of decimal places of report
|-
| Lower limit||Minimum value (used for validation) for numerical and date
|-
| Upper limit||Maximum value (used for validation).
|-
| Scale Xref||Cross reference to the scale, eg to a unit repository like "improved UO"
|-
| Categorie i||Class value and meaning of the category "i" with "i" a positive integer
|-
| Variable name||Name of the variable, it follows a naming convention described in guidelines
|-
| Variable synonyms||Other names given to this variable
|-
| Context of use||Indication of how trait is routinely used. If several context of use, separate with ","
|-
| Growth stage|| Growthstage at which measurement is made. Follow standards. If variable used in time series, leave blank
|-
| Variable status||Obsolete, Legacy, Standard // institution1, institution2, Recommended, Experimental, Revision
|-
| CV Term ID||ID generated by BMS
|-
| Variable Xref||
|}

=OBO files=
==OBO file structure==
OBO files are created using the obo2owl library (which should sound familiar ;-)).
The main issue with the Trait Template is that because different IDs can be created for the same “thing” (e.g. the term “cm” will get different IDs if different traits are measured in cm), different obo terms can have the same name (but different IDs). That is a problem when our users tried to import the OBO files in a Chado database.
Consequently, I created a little script that created OBO files where all the names are unique in a given namespace. The script has not be inserted in the website yet but it will be soon. Example of an OBO files on Github.

{| border="1" class="sortable"
!TD column!!OBO element
|-
|Crop||Used for setting up the namespace
|-
|Name of Trait||name
|-
|Trait ID for modification, Blank for New||Term + id
|-
|Description of Trait||definition
|-
|Trait Class||Term +id + name + is-a
|-
|Language of submission (only in ISO 2 letter codes)||We have only English OBO files.
|-
|Name of submitting scientist||created_by
|-
|Institution||Not used
|-
|Date of submission||creation_date
|-
|Abbreviated name||synonym [EXACT]
|-
|Synonyms (separate by commas)||synonym [EXACT]
|-
|How is this trait routinely used||Not used
|-
|Name of method||name
|-
|Method ID for modification, Blank for New||Term + id + method_of
|-
|Describe how measured (method||definition
|-
|Bibliographic Reference||xref
|-
|Growth Stage||Not used
|-
|Comments||Not used
|-
|Scale ID for modification, Blank for New||Term + id + scale_of
|-
|Type of Measure (Continuous, Discrete or Categorical||Not used
|-
|For Continuous: units of measurement||name
|-
|For Discrete: Name of scale or units of measurement||name
|-
|For Categorical: Name of rating scale||name
|-
|For Categorical: Class 1 - value = meaning||Term + name + is-a
|-
|For Categorical: Class 2 - value = meaning ||Term + name + is-a
|-
|For Categorical: Class 3 - value = meaning||Term + name + is-a
|-
|For Categorical: Class 4 - value = meaning||Term + name + is-a
|}

=SKOS files=
==SKOS file structure==
{| border="1" class="sortable"
!TD column!!SKOS
|-
|Crop||Used for setting up the namespace
|-
|Name of Trait||skos:prefLabel
|-
|Trait ID for modification, Blank for New||Local Name (URI) + rdf: type skos:concept
|-
|Description of Trait||skos:definition
|-
|Trait Class||rdf:type Skos:Concept + skos:broader
|-
|Language of submission (only in ISO 2 letter codes)||xml:lang of the literals. SKOS files are multilingual (if we have the info)
|-
|Name of submitting scientist||foaf:Person (not set so far but will be soon)
|-
|Institution||foaf:Organization (not set so far but will be soon)
|-
|Date of submission||dc:date (not set so far but will be soon)
|-
|Abbreviated name||skos:altLabel
|-
|Synonyms (separate by commas)||skos:altLabel
|-
|How is this trait routinely used||Not used
|-
|Name of method||skos:prefLabel
|-
|Method ID for modification, Blank for New||Local Name (URI) + rdf: type skos:concept
|-
|Describe how measured (method||skos:definition
|-
|Bibliographic Reference||Not set (dc: bibliographicCitation?)
|-
|Growth Stage||skos:related (not set so far)
|-
|Comments||skos:editorialNote
|-
|Scale ID for modification, Blank for New||Local Name (URI) + rdf: type skos:concept
|-
|Type of Measure (Continuous, Discrete or Categorical||Not used
|-
|For Continuous: units of measurement||skos:prefLabel
|-
|For Discrete: Name of scale or units of measurement||skos:prefLabel
|-
|For Categorical: Name of rating scale||skos:prefLabel
|-
|For Categorical: Class 1 - value = meaning||Local Name (URI) + rdf: type skos:concept
|-
|For Categorical: Class 2 - value = meaning ||Local Name (URI) + rdf: type skos:concept
|-
|For Categorical: Class 3 - value = meaning||Local Name (URI) + rdf: type skos:concept
|-
|For Categorical: Class 4 - value = meaning||Local Name (URI) + rdf: type skos:concept
|}

=List of Crops and IDs=
According to the project timeline, the crops that will be linked to the reference ontologies are:
{| border="1" class="sortable"
|-
! Crops
! Prefixes
|-
| Maize
| 322
|-
| Rice
| 320
|-
| Wheat
| 321 (traits) and 121 (anatomy)
|-
| Cassava
| 334
|-
| Cowpea
| 340
|-
| Chickpea
| 338
|-
| Potato
| 330
|-
| Sorghum
| 324
|-
| Soybean
| 336
|-
| Barley
| 323
|-
| Common Bean
| 335
|-
| Groundnut
| 337
|-
| Pearl Millet
| 327
|-
| Pigeon Pea
| 341
|-
| Musa
| 325 (traits) and 125 (anatomy)
|-
| Sweet Potato
| 331
|-
| Yam
| 333
|-
| Other crops ?????
|
|}

The trait ontologies start with 3XX whereas the anatomy ontologies start with 1XX.

Crop Ontology Pages

2015-06-03T08:50:13Z

Marieangelique.laporte: /* Trait Template */

There are 3 ways of creating “ontologies” on the Crop Ontology website.
*First, one can choose to upload a Trait Dictionary in Excel. The TD is only used to store and load information about traits, thus it cannot be used for uploading ontologies that would belong to the other categories (Note, there are 5 sections on the CO website: General Germplasm Ontology, Phenotypes and Traits Ontology, Structural and Functional Genomic Ontology, Location and Environmental Ontology and Plant Anatomy & Development Ontology).
*OBO files can be uploaded as well. They can be used to create ontologies in any of the 5 sections.
*Finally, ontologies can be built from scratch using the website dedicated interface.

Once the files are uploaded or some terms are submitted using the web interface, the data are stored in a noSQL database (Google App Engine Datastore).
The ontologies can be downloaded in various formats: CSV, OBO, SKOS and JSON. The structures of the different formats are described in the following sections. Note that because there is no exact mapping between the different formats some compromises has been made. Not all the information is available in the different formats.

=Trait Template=
==Structure of the Trait Template V4==
So far, the Trait Template V4 is uploaded into the CO website. The Trait Template is used to gather information on traits along with their methods and scales of measurement. For each trait, some meta-information is added (5 first columns). An (unique) ID is created by the system for each trait, method and scale (several IDs are created when the scale is categorical). But for now, if two methods or scales are the same (seed length and leaf length are measured in centimeters), different IDs are created, which is far from being ideal or even ontologically correct.
The Trait Template V4 columns are:
*IBFieldbook
*Name of submitting scientist
*Institution
*Language of submission (only in ISO 2 letter codes)
*Date of submission
*Crop
*Name of Trait
*Abbreviated name
*Synonyms (separate by commas)
*Trait ID for modification, Blank for New
*Description of Trait
*How is this trait routinely used?
*Trait Class
*Method ID for modification, Blank for new
*Name of Method
*Describe how measured (method)
*Growth Stage
*Bibliographic Reference
*Comments
*Scale ID for modification, Blank for new
*Type of Measure (Continuous, Discrete or Categorical)
*For Continuous: units of measurement
*For Continuous: reporting units (if different from measurement)
*For Continuous: minimum
*For Continuous: maximum
*For Discrete: Name of scale or units of measurement
*For Categorical: Name of rating scale
*For Categorical: Class 1 - value = meaning
*For Categorical: Class 2 - value = meaning
*For Categorical: Class 3 - value = meaning
*For Categorical: Class 4 - value = meaning
*For Categorical: Class 5 - value = meaning

==Structure of the Trait Template V5 (Léo is still working on it with Julian Pietragalla from CIMMYT) ==
Note the structure can still evolve. Template V5 is still a draft

=OBO files=
==OBO file structure==
OBO files are created using the obo2owl library (which should sound familiar ;-)).
The main issue with the Trait Template is that because different IDs can be created for the same “thing” (e.g. the term “cm” will get different IDs if different traits are measured in cm), different obo terms can have the same name (but different IDs). That is a problem when our users tried to import the OBO files in a Chado database.
Consequently, I created a little script that created OBO files where all the names are unique in a given namespace. The script has not be inserted in the website yet but it will be soon. Example of an OBO files on Github.

{| border="1" class="sortable"
!TD column!!OBO element
|-
|Crop||Used for setting up the namespace
|-
|Name of Trait||name
|-
|Trait ID for modification, Blank for New||Term + id
|-
|Description of Trait||definition
|-
|Trait Class||Term +id + name + is-a
|-
|Language of submission (only in ISO 2 letter codes)||We have only English OBO files.
|-
|Name of submitting scientist||created_by
|-
|Institution||Not used
|-
|Date of submission||creation_date
|-
|Abbreviated name||synonym [EXACT]
|-
|Synonyms (separate by commas)||synonym [EXACT]
|-
|How is this trait routinely used||Not used
|-
|Name of method||name
|-
|Method ID for modification, Blank for New||Term + id + method_of
|-
|Describe how measured (method||definition
|-
|Bibliographic Reference||xref
|-
|Growth Stage||Not used
|-
|Comments||Not used
|-
|Scale ID for modification, Blank for New||Term + id + scale_of
|-
|Type of Measure (Continuous, Discrete or Categorical||Not used
|-
|For Continuous: units of measurement||name
|-
|For Discrete: Name of scale or units of measurement||name
|-
|For Categorical: Name of rating scale||name
|-
|For Categorical: Class 1 - value = meaning||Term + name + is-a
|-
|For Categorical: Class 2 - value = meaning ||Term + name + is-a
|-
|For Categorical: Class 3 - value = meaning||Term + name + is-a
|-
|For Categorical: Class 4 - value = meaning||Term + name + is-a
|}

=SKOS files=
==SKOS file structure==
{| border="1" class="sortable"
!TD column!!SKOS
|-
|Crop||Used for setting up the namespace
|-
|Name of Trait||skos:prefLabel
|-
|Trait ID for modification, Blank for New||Local Name (URI) + rdf: type skos:concept
|-
|Description of Trait||skos:definition
|-
|Trait Class||rdf:type Skos:Concept + skos:broader
|-
|Language of submission (only in ISO 2 letter codes)||xml:lang of the literals. SKOS files are multilingual (if we have the info)
|-
|Name of submitting scientist||foaf:Person (not set so far but will be soon)
|-
|Institution||foaf:Organization (not set so far but will be soon)
|-
|Date of submission||dc:date (not set so far but will be soon)
|-
|Abbreviated name||skos:altLabel
|-
|Synonyms (separate by commas)||skos:altLabel
|-
|How is this trait routinely used||Not used
|-
|Name of method||skos:prefLabel
|-
|Method ID for modification, Blank for New||Local Name (URI) + rdf: type skos:concept
|-
|Describe how measured (method||skos:definition
|-
|Bibliographic Reference||Not set (dc: bibliographicCitation?)
|-
|Growth Stage||skos:related (not set so far)
|-
|Comments||skos:editorialNote
|-
|Scale ID for modification, Blank for New||Local Name (URI) + rdf: type skos:concept
|-
|Type of Measure (Continuous, Discrete or Categorical||Not used
|-
|For Continuous: units of measurement||skos:prefLabel
|-
|For Discrete: Name of scale or units of measurement||skos:prefLabel
|-
|For Categorical: Name of rating scale||skos:prefLabel
|-
|For Categorical: Class 1 - value = meaning||Local Name (URI) + rdf: type skos:concept
|-
|For Categorical: Class 2 - value = meaning ||Local Name (URI) + rdf: type skos:concept
|-
|For Categorical: Class 3 - value = meaning||Local Name (URI) + rdf: type skos:concept
|-
|For Categorical: Class 4 - value = meaning||Local Name (URI) + rdf: type skos:concept
|}

=List of Crops and IDs=
According to the project timeline, the crops that will be linked to the reference ontologies are:
{| border="1" class="sortable"
|-
! Crops
! Prefixes
|-
| Maize
| 322
|-
| Rice
| 320
|-
| Wheat
| 321 (traits) and 121 (anatomy)
|-
| Cassava
| 334
|-
| Cowpea
| 340
|-
| Chickpea
| 338
|-
| Potato
| 330
|-
| Sorghum
| 324
|-
| Soybean
| 336
|-
| Barley
| 323
|-
| Common Bean
| 335
|-
| Groundnut
| 337
|-
| Pearl Millet
| 327
|-
| Pigeon Pea
| 341
|-
| Musa
| 325 (traits) and 125 (anatomy)
|-
| Sweet Potato
| 331
|-
| Yam
| 333
|-
| Other crops ?????
|
|}

The trait ontologies start with 3XX whereas the anatomy ontologies start with 1XX.

Crop Ontology Pages

2015-05-29T13:39:56Z

Marieangelique.laporte: /* SKOS file structure */

There are 3 ways of creating “ontologies” on the Crop Ontology website.
*First, one can choose to upload a Trait Dictionary in Excel. The TD is only used to store and load information about traits, thus it cannot be used for uploading ontologies that would belong to the other categories (Note, there are 5 sections on the CO website: General Germplasm Ontology, Phenotypes and Traits Ontology, Structural and Functional Genomic Ontology, Location and Environmental Ontology and Plant Anatomy & Development Ontology).
*OBO files can be uploaded as well. They can be used to create ontologies in any of the 5 sections.
*Finally, ontologies can be built from scratch using the website dedicated interface.

Once the files are uploaded or some terms are submitted using the web interface, the data are stored in a noSQL database (Google App Engine Datastore).
The ontologies can be downloaded in various formats: CSV, OBO, SKOS and JSON. The structures of the different formats are described in the following sections. Note that because there is no exact mapping between the different formats some compromises has been made. Not all the information is available in the different formats.

=Trait Template=
==Structure of the Trait Template V4==
So far, the Trait Template V4 is uploaded into the CO website. The Trait Template is used to gather information on traits along with their methods and scales of measurement. For each trait, some meta-information is added (5 first columns). An (unique) ID is created by the system for each trait, method and scale (several IDs are created when the scale is categorical). But for now, if two methods or scales are the same (seed length and leaf length are measured in centimeters), different IDs are created, which is far from being ideal or even ontologically correct.
The Trait Template V4 columns are:
*IBFieldbook
*Name of submitting scientist
*Institution
*Language of submission (only in ISO 2 letter codes)
*Date of submission
*Crop
*Name of Trait
*Abbreviated name
*Synonyms (separate by commas)
*Trait ID for modification, Blank for New
*Description of Trait
*How is this trait routinely used?
*Trait Class
*Method ID for modification, Blank for new
*Name of Method
*Describe how measured (method)
*Growth Stage
*Bibliographic Reference
*Comments
*Scale ID for modification, Blank for new
*Type of Measure (Continuous, Discrete or Categorical)
*For Continuous: units of measurement
*For Continuous: reporting units (if different from measurement)
*For Continuous: minimum
*For Continuous: maximum
*For Discrete: Name of scale or units of measurement
*For Categorical: Name of rating scale
*For Categorical: Class 1 - value = meaning
*For Categorical: Class 2 - value = meaning
*For Categorical: Class 3 - value = meaning
*For Categorical: Class 4 - value = meaning
*For Categorical: Class 5 - value = meaning

=OBO files=
==OBO file structure==
OBO files are created using the obo2owl library (which should sound familiar ;-)).
The main issue with the Trait Template is that because different IDs can be created for the same “thing” (e.g. the term “cm” will get different IDs if different traits are measured in cm), different obo terms can have the same name (but different IDs). That is a problem when our users tried to import the OBO files in a Chado database.
Consequently, I created a little script that created OBO files where all the names are unique in a given namespace. The script has not be inserted in the website yet but it will be soon. Example of an OBO files on Github.

{| border="1" class="sortable"
!TD column!!OBO element
|-
|Crop||Used for setting up the namespace
|-
|Name of Trait||name
|-
|Trait ID for modification, Blank for New||Term + id
|-
|Description of Trait||definition
|-
|Trait Class||Term +id + name + is-a
|-
|Language of submission (only in ISO 2 letter codes)||We have only English OBO files.
|-
|Name of submitting scientist||created_by
|-
|Institution||Not used
|-
|Date of submission||creation_date
|-
|Abbreviated name||synonym [EXACT]
|-
|Synonyms (separate by commas)||synonym [EXACT]
|-
|How is this trait routinely used||Not used
|-
|Name of method||name
|-
|Method ID for modification, Blank for New||Term + id + method_of
|-
|Describe how measured (method||definition
|-
|Bibliographic Reference||xref
|-
|Growth Stage||Not used
|-
|Comments||Not used
|-
|Scale ID for modification, Blank for New||Term + id + scale_of
|-
|Type of Measure (Continuous, Discrete or Categorical||Not used
|-
|For Continuous: units of measurement||name
|-
|For Discrete: Name of scale or units of measurement||name
|-
|For Categorical: Name of rating scale||name
|-
|For Categorical: Class 1 - value = meaning||Term + name + is-a
|-
|For Categorical: Class 2 - value = meaning ||Term + name + is-a
|-
|For Categorical: Class 3 - value = meaning||Term + name + is-a
|-
|For Categorical: Class 4 - value = meaning||Term + name + is-a
|}

=SKOS files=
==SKOS file structure==
{| border="1" class="sortable"
!TD column!!SKOS
|-
|Crop||Used for setting up the namespace
|-
|Name of Trait||skos:prefLabel
|-
|Trait ID for modification, Blank for New||Local Name (URI) + rdf: type skos:concept
|-
|Description of Trait||skos:definition
|-
|Trait Class||rdf:type Skos:Concept + skos:broader
|-
|Language of submission (only in ISO 2 letter codes)||xml:lang of the literals. SKOS files are multilingual (if we have the info)
|-
|Name of submitting scientist||foaf:Person (not set so far but will be soon)
|-
|Institution||foaf:Organization (not set so far but will be soon)
|-
|Date of submission||dc:date (not set so far but will be soon)
|-
|Abbreviated name||skos:altLabel
|-
|Synonyms (separate by commas)||skos:altLabel
|-
|How is this trait routinely used||Not used
|-
|Name of method||skos:prefLabel
|-
|Method ID for modification, Blank for New||Local Name (URI) + rdf: type skos:concept
|-
|Describe how measured (method||skos:definition
|-
|Bibliographic Reference||Not set (dc: bibliographicCitation?)
|-
|Growth Stage||skos:related (not set so far)
|-
|Comments||skos:editorialNote
|-
|Scale ID for modification, Blank for New||Local Name (URI) + rdf: type skos:concept
|-
|Type of Measure (Continuous, Discrete or Categorical||Not used
|-
|For Continuous: units of measurement||skos:prefLabel
|-
|For Discrete: Name of scale or units of measurement||skos:prefLabel
|-
|For Categorical: Name of rating scale||skos:prefLabel
|-
|For Categorical: Class 1 - value = meaning||Local Name (URI) + rdf: type skos:concept
|-
|For Categorical: Class 2 - value = meaning ||Local Name (URI) + rdf: type skos:concept
|-
|For Categorical: Class 3 - value = meaning||Local Name (URI) + rdf: type skos:concept
|-
|For Categorical: Class 4 - value = meaning||Local Name (URI) + rdf: type skos:concept
|}

=List of Crops and IDs=
According to the project timeline, the crops that will be linked to the reference ontologies are:
{| border="1" class="sortable"
|-
! Crops
! Prefixes
|-
| Maize
| 322
|-
| Rice
| 320
|-
| Wheat
| 321 (traits) and 121 (anatomy)
|-
| Cassava
| 334
|-
| Cowpea
| 340
|-
| Chickpea
| 338
|-
| Potato
| 330
|-
| Sorghum
| 324
|-
| Soybean
| 336
|-
| Barley
| 323
|-
| Common Bean
| 335
|-
| Groundnut
| 337
|-
| Pearl Millet
| 327
|-
| Pigeon Pea
| 341
|-
| Musa
| 325 (traits) and 125 (anatomy)
|-
| Sweet Potato
| 331
|-
| Yam
| 333
|-
| Other crops ?????
|
|}

The trait ontologies start with 3XX whereas the anatomy ontologies start with 1XX.

Crop Ontology Pages

2015-05-29T13:39:41Z

Marieangelique.laporte: /* OBO file structure */

There are 3 ways of creating “ontologies” on the Crop Ontology website.
*First, one can choose to upload a Trait Dictionary in Excel. The TD is only used to store and load information about traits, thus it cannot be used for uploading ontologies that would belong to the other categories (Note, there are 5 sections on the CO website: General Germplasm Ontology, Phenotypes and Traits Ontology, Structural and Functional Genomic Ontology, Location and Environmental Ontology and Plant Anatomy & Development Ontology).
*OBO files can be uploaded as well. They can be used to create ontologies in any of the 5 sections.
*Finally, ontologies can be built from scratch using the website dedicated interface.

Once the files are uploaded or some terms are submitted using the web interface, the data are stored in a noSQL database (Google App Engine Datastore).
The ontologies can be downloaded in various formats: CSV, OBO, SKOS and JSON. The structures of the different formats are described in the following sections. Note that because there is no exact mapping between the different formats some compromises has been made. Not all the information is available in the different formats.

=Trait Template=
==Structure of the Trait Template V4==
So far, the Trait Template V4 is uploaded into the CO website. The Trait Template is used to gather information on traits along with their methods and scales of measurement. For each trait, some meta-information is added (5 first columns). An (unique) ID is created by the system for each trait, method and scale (several IDs are created when the scale is categorical). But for now, if two methods or scales are the same (seed length and leaf length are measured in centimeters), different IDs are created, which is far from being ideal or even ontologically correct.
The Trait Template V4 columns are:
*IBFieldbook
*Name of submitting scientist
*Institution
*Language of submission (only in ISO 2 letter codes)
*Date of submission
*Crop
*Name of Trait
*Abbreviated name
*Synonyms (separate by commas)
*Trait ID for modification, Blank for New
*Description of Trait
*How is this trait routinely used?
*Trait Class
*Method ID for modification, Blank for new
*Name of Method
*Describe how measured (method)
*Growth Stage
*Bibliographic Reference
*Comments
*Scale ID for modification, Blank for new
*Type of Measure (Continuous, Discrete or Categorical)
*For Continuous: units of measurement
*For Continuous: reporting units (if different from measurement)
*For Continuous: minimum
*For Continuous: maximum
*For Discrete: Name of scale or units of measurement
*For Categorical: Name of rating scale
*For Categorical: Class 1 - value = meaning
*For Categorical: Class 2 - value = meaning
*For Categorical: Class 3 - value = meaning
*For Categorical: Class 4 - value = meaning
*For Categorical: Class 5 - value = meaning

=OBO files=
==OBO file structure==
OBO files are created using the obo2owl library (which should sound familiar ;-)).
The main issue with the Trait Template is that because different IDs can be created for the same “thing” (e.g. the term “cm” will get different IDs if different traits are measured in cm), different obo terms can have the same name (but different IDs). That is a problem when our users tried to import the OBO files in a Chado database.
Consequently, I created a little script that created OBO files where all the names are unique in a given namespace. The script has not be inserted in the website yet but it will be soon. Example of an OBO files on Github.

{| border="1" class="sortable"
!TD column!!OBO element
|-
|Crop||Used for setting up the namespace
|-
|Name of Trait||name
|-
|Trait ID for modification, Blank for New||Term + id
|-
|Description of Trait||definition
|-
|Trait Class||Term +id + name + is-a
|-
|Language of submission (only in ISO 2 letter codes)||We have only English OBO files.
|-
|Name of submitting scientist||created_by
|-
|Institution||Not used
|-
|Date of submission||creation_date
|-
|Abbreviated name||synonym [EXACT]
|-
|Synonyms (separate by commas)||synonym [EXACT]
|-
|How is this trait routinely used||Not used
|-
|Name of method||name
|-
|Method ID for modification, Blank for New||Term + id + method_of
|-
|Describe how measured (method||definition
|-
|Bibliographic Reference||xref
|-
|Growth Stage||Not used
|-
|Comments||Not used
|-
|Scale ID for modification, Blank for New||Term + id + scale_of
|-
|Type of Measure (Continuous, Discrete or Categorical||Not used
|-
|For Continuous: units of measurement||name
|-
|For Discrete: Name of scale or units of measurement||name
|-
|For Categorical: Name of rating scale||name
|-
|For Categorical: Class 1 - value = meaning||Term + name + is-a
|-
|For Categorical: Class 2 - value = meaning ||Term + name + is-a
|-
|For Categorical: Class 3 - value = meaning||Term + name + is-a
|-
|For Categorical: Class 4 - value = meaning||Term + name + is-a
|}

=SKOS files=
==SKOS file structure==
{| border="1" class="sortable"
!TD column!!SKOS
|-
|Crop||Used for setting the namespace
|-
|Name of Trait||skos:prefLabel
|-
|Trait ID for modification, Blank for New||Local Name (URI) + rdf: type skos:concept
|-
|Description of Trait||skos:definition
|-
|Trait Class||rdf:type Skos:Concept + skos:broader
|-
|Language of submission (only in ISO 2 letter codes)||xml:lang of the literals. SKOS files are multilingual (if we have the info)
|-
|Name of submitting scientist||foaf:Person (not set so far but will be soon)
|-
|Institution||foaf:Organization (not set so far but will be soon)
|-
|Date of submission||dc:date (not set so far but will be soon)
|-
|Abbreviated name||skos:altLabel
|-
|Synonyms (separate by commas)||skos:altLabel
|-
|How is this trait routinely used||Not used
|-
|Name of method||skos:prefLabel
|-
|Method ID for modification, Blank for New||Local Name (URI) + rdf: type skos:concept
|-
|Describe how measured (method||skos:definition
|-
|Bibliographic Reference||Not set (dc: bibliographicCitation?)
|-
|Growth Stage||skos:related (not set so far)
|-
|Comments||skos:editorialNote
|-
|Scale ID for modification, Blank for New||Local Name (URI) + rdf: type skos:concept
|-
|Type of Measure (Continuous, Discrete or Categorical||Not used
|-
|For Continuous: units of measurement||skos:prefLabel
|-
|For Discrete: Name of scale or units of measurement||skos:prefLabel
|-
|For Categorical: Name of rating scale||skos:prefLabel
|-
|For Categorical: Class 1 - value = meaning||Local Name (URI) + rdf: type skos:concept
|-
|For Categorical: Class 2 - value = meaning ||Local Name (URI) + rdf: type skos:concept
|-
|For Categorical: Class 3 - value = meaning||Local Name (URI) + rdf: type skos:concept
|-
|For Categorical: Class 4 - value = meaning||Local Name (URI) + rdf: type skos:concept
|}

=List of Crops and IDs=
According to the project timeline, the crops that will be linked to the reference ontologies are:
{| border="1" class="sortable"
|-
! Crops
! Prefixes
|-
| Maize
| 322
|-
| Rice
| 320
|-
| Wheat
| 321 (traits) and 121 (anatomy)
|-
| Cassava
| 334
|-
| Cowpea
| 340
|-
| Chickpea
| 338
|-
| Potato
| 330
|-
| Sorghum
| 324
|-
| Soybean
| 336
|-
| Barley
| 323
|-
| Common Bean
| 335
|-
| Groundnut
| 337
|-
| Pearl Millet
| 327
|-
| Pigeon Pea
| 341
|-
| Musa
| 325 (traits) and 125 (anatomy)
|-
| Sweet Potato
| 331
|-
| Yam
| 333
|-
| Other crops ?????
|
|}

The trait ontologies start with 3XX whereas the anatomy ontologies start with 1XX.

Crop Ontology Pages

2015-05-29T13:38:39Z

Marieangelique.laporte: /* SKOS file structure */

There are 3 ways of creating “ontologies” on the Crop Ontology website.
*First, one can choose to upload a Trait Dictionary in Excel. The TD is only used to store and load information about traits, thus it cannot be used for uploading ontologies that would belong to the other categories (Note, there are 5 sections on the CO website: General Germplasm Ontology, Phenotypes and Traits Ontology, Structural and Functional Genomic Ontology, Location and Environmental Ontology and Plant Anatomy & Development Ontology).
*OBO files can be uploaded as well. They can be used to create ontologies in any of the 5 sections.
*Finally, ontologies can be built from scratch using the website dedicated interface.

Once the files are uploaded or some terms are submitted using the web interface, the data are stored in a noSQL database (Google App Engine Datastore).
The ontologies can be downloaded in various formats: CSV, OBO, SKOS and JSON. The structures of the different formats are described in the following sections. Note that because there is no exact mapping between the different formats some compromises has been made. Not all the information is available in the different formats.

=Trait Template=
==Structure of the Trait Template V4==
So far, the Trait Template V4 is uploaded into the CO website. The Trait Template is used to gather information on traits along with their methods and scales of measurement. For each trait, some meta-information is added (5 first columns). An (unique) ID is created by the system for each trait, method and scale (several IDs are created when the scale is categorical). But for now, if two methods or scales are the same (seed length and leaf length are measured in centimeters), different IDs are created, which is far from being ideal or even ontologically correct.
The Trait Template V4 columns are:
*IBFieldbook
*Name of submitting scientist
*Institution
*Language of submission (only in ISO 2 letter codes)
*Date of submission
*Crop
*Name of Trait
*Abbreviated name
*Synonyms (separate by commas)
*Trait ID for modification, Blank for New
*Description of Trait
*How is this trait routinely used?
*Trait Class
*Method ID for modification, Blank for new
*Name of Method
*Describe how measured (method)
*Growth Stage
*Bibliographic Reference
*Comments
*Scale ID for modification, Blank for new
*Type of Measure (Continuous, Discrete or Categorical)
*For Continuous: units of measurement
*For Continuous: reporting units (if different from measurement)
*For Continuous: minimum
*For Continuous: maximum
*For Discrete: Name of scale or units of measurement
*For Categorical: Name of rating scale
*For Categorical: Class 1 - value = meaning
*For Categorical: Class 2 - value = meaning
*For Categorical: Class 3 - value = meaning
*For Categorical: Class 4 - value = meaning
*For Categorical: Class 5 - value = meaning

=OBO files=
==OBO file structure==
OBO files are created using the obo2owl library (which should sound familiar ;-)).
The main issue with the Trait Template is that because different IDs can be created for the same “thing” (e.g. the term “cm” will get different IDs if different traits are measured in cm), different obo terms can have the same name (but different IDs). That is a problem when our users tried to import the OBO files in a Chado database.
Consequently, I created a little script that created OBO files where all the names are unique in a given namespace. The script has not be inserted in the website yet but it will be soon. Example of an OBO files on Github.

{| border="1" class="sortable"
!TD column!!OBO element
|-
|Crop||Used for setting the namespace
|-
|Name of Trait||name
|-
|Trait ID for modification, Blank for New||Term + id
|-
|Description of Trait||definition
|-
|Trait Class||Term +id + name + is-a
|-
|Language of submission (only in ISO 2 letter codes)||We have only English OBO files.
|-
|Name of submitting scientist||created_by
|-
|Institution||Not used
|-
|Date of submission||creation_date
|-
|Abbreviated name||synonym [EXACT]
|-
|Synonyms (separate by commas)||synonym [EXACT]
|-
|How is this trait routinely used||Not used
|-
|Name of method||name
|-
|Method ID for modification, Blank for New||Term + id + method_of
|-
|Describe how measured (method||definition
|-
|Bibliographic Reference||xref
|-
|Growth Stage||Not used
|-
|Comments||Not used
|-
|Scale ID for modification, Blank for New||Term + id + scale_of
|-
|Type of Measure (Continuous, Discrete or Categorical||Not used
|-
|For Continuous: units of measurement||name
|-
|For Discrete: Name of scale or units of measurement||name
|-
|For Categorical: Name of rating scale||name
|-
|For Categorical: Class 1 - value = meaning||Term + name + is-a
|-
|For Categorical: Class 2 - value = meaning ||Term + name + is-a
|-
|For Categorical: Class 3 - value = meaning||Term + name + is-a
|-
|For Categorical: Class 4 - value = meaning||Term + name + is-a
|}

=SKOS files=
==SKOS file structure==
{| border="1" class="sortable"
!TD column!!SKOS
|-
|Crop||Used for setting the namespace
|-
|Name of Trait||skos:prefLabel
|-
|Trait ID for modification, Blank for New||Local Name (URI) + rdf: type skos:concept
|-
|Description of Trait||skos:definition
|-
|Trait Class||rdf:type Skos:Concept + skos:broader
|-
|Language of submission (only in ISO 2 letter codes)||xml:lang of the literals. SKOS files are multilingual (if we have the info)
|-
|Name of submitting scientist||foaf:Person (not set so far but will be soon)
|-
|Institution||foaf:Organization (not set so far but will be soon)
|-
|Date of submission||dc:date (not set so far but will be soon)
|-
|Abbreviated name||skos:altLabel
|-
|Synonyms (separate by commas)||skos:altLabel
|-
|How is this trait routinely used||Not used
|-
|Name of method||skos:prefLabel
|-
|Method ID for modification, Blank for New||Local Name (URI) + rdf: type skos:concept
|-
|Describe how measured (method||skos:definition
|-
|Bibliographic Reference||Not set (dc: bibliographicCitation?)
|-
|Growth Stage||skos:related (not set so far)
|-
|Comments||skos:editorialNote
|-
|Scale ID for modification, Blank for New||Local Name (URI) + rdf: type skos:concept
|-
|Type of Measure (Continuous, Discrete or Categorical||Not used
|-
|For Continuous: units of measurement||skos:prefLabel
|-
|For Discrete: Name of scale or units of measurement||skos:prefLabel
|-
|For Categorical: Name of rating scale||skos:prefLabel
|-
|For Categorical: Class 1 - value = meaning||Local Name (URI) + rdf: type skos:concept
|-
|For Categorical: Class 2 - value = meaning ||Local Name (URI) + rdf: type skos:concept
|-
|For Categorical: Class 3 - value = meaning||Local Name (URI) + rdf: type skos:concept
|-
|For Categorical: Class 4 - value = meaning||Local Name (URI) + rdf: type skos:concept
|}

=List of Crops and IDs=
According to the project timeline, the crops that will be linked to the reference ontologies are:
{| border="1" class="sortable"
|-
! Crops
! Prefixes
|-
| Maize
| 322
|-
| Rice
| 320
|-
| Wheat
| 321 (traits) and 121 (anatomy)
|-
| Cassava
| 334
|-
| Cowpea
| 340
|-
| Chickpea
| 338
|-
| Potato
| 330
|-
| Sorghum
| 324
|-
| Soybean
| 336
|-
| Barley
| 323
|-
| Common Bean
| 335
|-
| Groundnut
| 337
|-
| Pearl Millet
| 327
|-
| Pigeon Pea
| 341
|-
| Musa
| 325 (traits) and 125 (anatomy)
|-
| Sweet Potato
| 331
|-
| Yam
| 333
|-
| Other crops ?????
|
|}

The trait ontologies start with 3XX whereas the anatomy ontologies start with 1XX.

Crop Ontology Pages

2015-05-29T13:37:13Z

Marieangelique.laporte: /* List of Crops and IDs */

There are 3 ways of creating “ontologies” on the Crop Ontology website.
*First, one can choose to upload a Trait Dictionary in Excel. The TD is only used to store and load information about traits, thus it cannot be used for uploading ontologies that would belong to the other categories (Note, there are 5 sections on the CO website: General Germplasm Ontology, Phenotypes and Traits Ontology, Structural and Functional Genomic Ontology, Location and Environmental Ontology and Plant Anatomy & Development Ontology).
*OBO files can be uploaded as well. They can be used to create ontologies in any of the 5 sections.
*Finally, ontologies can be built from scratch using the website dedicated interface.

Once the files are uploaded or some terms are submitted using the web interface, the data are stored in a noSQL database (Google App Engine Datastore).
The ontologies can be downloaded in various formats: CSV, OBO, SKOS and JSON. The structures of the different formats are described in the following sections. Note that because there is no exact mapping between the different formats some compromises has been made. Not all the information is available in the different formats.

=Trait Template=
==Structure of the Trait Template V4==
So far, the Trait Template V4 is uploaded into the CO website. The Trait Template is used to gather information on traits along with their methods and scales of measurement. For each trait, some meta-information is added (5 first columns). An (unique) ID is created by the system for each trait, method and scale (several IDs are created when the scale is categorical). But for now, if two methods or scales are the same (seed length and leaf length are measured in centimeters), different IDs are created, which is far from being ideal or even ontologically correct.
The Trait Template V4 columns are:
*IBFieldbook
*Name of submitting scientist
*Institution
*Language of submission (only in ISO 2 letter codes)
*Date of submission
*Crop
*Name of Trait
*Abbreviated name
*Synonyms (separate by commas)
*Trait ID for modification, Blank for New
*Description of Trait
*How is this trait routinely used?
*Trait Class
*Method ID for modification, Blank for new
*Name of Method
*Describe how measured (method)
*Growth Stage
*Bibliographic Reference
*Comments
*Scale ID for modification, Blank for new
*Type of Measure (Continuous, Discrete or Categorical)
*For Continuous: units of measurement
*For Continuous: reporting units (if different from measurement)
*For Continuous: minimum
*For Continuous: maximum
*For Discrete: Name of scale or units of measurement
*For Categorical: Name of rating scale
*For Categorical: Class 1 - value = meaning
*For Categorical: Class 2 - value = meaning
*For Categorical: Class 3 - value = meaning
*For Categorical: Class 4 - value = meaning
*For Categorical: Class 5 - value = meaning

=OBO files=
==OBO file structure==
OBO files are created using the obo2owl library (which should sound familiar ;-)).
The main issue with the Trait Template is that because different IDs can be created for the same “thing” (e.g. the term “cm” will get different IDs if different traits are measured in cm), different obo terms can have the same name (but different IDs). That is a problem when our users tried to import the OBO files in a Chado database.
Consequently, I created a little script that created OBO files where all the names are unique in a given namespace. The script has not be inserted in the website yet but it will be soon. Example of an OBO files on Github.

{| border="1" class="sortable"
!TD column!!OBO element
|-
|Crop||Used for setting the namespace
|-
|Name of Trait||name
|-
|Trait ID for modification, Blank for New||Term + id
|-
|Description of Trait||definition
|-
|Trait Class||Term +id + name + is-a
|-
|Language of submission (only in ISO 2 letter codes)||We have only English OBO files.
|-
|Name of submitting scientist||created_by
|-
|Institution||Not used
|-
|Date of submission||creation_date
|-
|Abbreviated name||synonym [EXACT]
|-
|Synonyms (separate by commas)||synonym [EXACT]
|-
|How is this trait routinely used||Not used
|-
|Name of method||name
|-
|Method ID for modification, Blank for New||Term + id + method_of
|-
|Describe how measured (method||definition
|-
|Bibliographic Reference||xref
|-
|Growth Stage||Not used
|-
|Comments||Not used
|-
|Scale ID for modification, Blank for New||Term + id + scale_of
|-
|Type of Measure (Continuous, Discrete or Categorical||Not used
|-
|For Continuous: units of measurement||name
|-
|For Discrete: Name of scale or units of measurement||name
|-
|For Categorical: Name of rating scale||name
|-
|For Categorical: Class 1 - value = meaning||Term + name + is-a
|-
|For Categorical: Class 2 - value = meaning ||Term + name + is-a
|-
|For Categorical: Class 3 - value = meaning||Term + name + is-a
|-
|For Categorical: Class 4 - value = meaning||Term + name + is-a
|}

=SKOS files=
==SKOS file structure==
{| border="1" class="sortable"
!TD column!!SKOS
|-
|Crop||Used for setting the namespace
|-
|Name of Trait||skos:prefLabel
|-
|Trait ID for modification, Blank for New||Local Name (URI) +
|-
|rdf: type skos:concept
|-
|Description of Trait||skos:definition
|-
|Trait Class||rdf:type Skos:Concept + skos:broader
|-
|Language of submission (only in ISO 2 letter codes)||xml:lang of the literals. SKOS files are multilingual (if we have the info)
|-
|Name of submitting scientist||foaf:Person (not set so far but will be soon)
|-
|Institution||foaf:Organization (not set so far but will be soon)
|-
|Date of submission||dc:date (not set so far but will be soon)
|-
|Abbreviated name||skos:altLabel
|-
|Synonyms (separate by commas)||skos:altLabel
|-
|How is this trait routinely used||Not used
|-
|Name of method||skos:prefLabel
|-
|Method ID for modification, Blank for New||Local Name (URI) +
|-
|rdf: type skos:concept
|-
|Describe how measured (method||skos:definition
|-
|Bibliographic Reference||Not set (dc: bibliographicCitation?)
|-
|Growth Stage||skos:related (not set so far)
|-
|Comments||skos:editorialNote
|-
|Scale ID for modification, Blank for New||Local Name (URI) +
|-
|rdf: type skos:concept
|-
|Type of Measure (Continuous, Discrete or Categorical||Not used
|-
|For Continuous: units of measurement||skos:prefLabel
|-
|For Discrete: Name of scale or units of measurement||skos:prefLabel
|-
|For Categorical: Name of rating scale||skos:prefLabel
|-
|For Categorical: Class 1 - value = meaning||Local Name (URI) +
|-
|rdf: type skos:concept
|-
|For Categorical: Class 2 - value = meaning ||Local Name (URI) +
|-
|rdf: type skos:concept
|-
|For Categorical: Class 3 - value = meaning||Local Name (URI) +
|-
|rdf: type skos:concept
|-
|For Categorical: Class 4 - value = meaning||Local Name (URI) +
|-
|rdf: type skos:concept
|}

=List of Crops and IDs=
According to the project timeline, the crops that will be linked to the reference ontologies are:
{| border="1" class="sortable"
|-
! Crops
! Prefixes
|-
| Maize
| 322
|-
| Rice
| 320
|-
| Wheat
| 321 (traits) and 121 (anatomy)
|-
| Cassava
| 334
|-
| Cowpea
| 340
|-
| Chickpea
| 338
|-
| Potato
| 330
|-
| Sorghum
| 324
|-
| Soybean
| 336
|-
| Barley
| 323
|-
| Common Bean
| 335
|-
| Groundnut
| 337
|-
| Pearl Millet
| 327
|-
| Pigeon Pea
| 341
|-
| Musa
| 325 (traits) and 125 (anatomy)
|-
| Sweet Potato
| 331
|-
| Yam
| 333
|-
| Other crops ?????
|
|}

The trait ontologies start with 3XX whereas the anatomy ontologies start with 1XX.

Crop Ontology Pages

2015-05-29T13:36:05Z

Marieangelique.laporte: /* SKOS file structure */

There are 3 ways of creating “ontologies” on the Crop Ontology website.
*First, one can choose to upload a Trait Dictionary in Excel. The TD is only used to store and load information about traits, thus it cannot be used for uploading ontologies that would belong to the other categories (Note, there are 5 sections on the CO website: General Germplasm Ontology, Phenotypes and Traits Ontology, Structural and Functional Genomic Ontology, Location and Environmental Ontology and Plant Anatomy & Development Ontology).
*OBO files can be uploaded as well. They can be used to create ontologies in any of the 5 sections.
*Finally, ontologies can be built from scratch using the website dedicated interface.

Once the files are uploaded or some terms are submitted using the web interface, the data are stored in a noSQL database (Google App Engine Datastore).
The ontologies can be downloaded in various formats: CSV, OBO, SKOS and JSON. The structures of the different formats are described in the following sections. Note that because there is no exact mapping between the different formats some compromises has been made. Not all the information is available in the different formats.

=Trait Template=
==Structure of the Trait Template V4==
So far, the Trait Template V4 is uploaded into the CO website. The Trait Template is used to gather information on traits along with their methods and scales of measurement. For each trait, some meta-information is added (5 first columns). An (unique) ID is created by the system for each trait, method and scale (several IDs are created when the scale is categorical). But for now, if two methods or scales are the same (seed length and leaf length are measured in centimeters), different IDs are created, which is far from being ideal or even ontologically correct.
The Trait Template V4 columns are:
*IBFieldbook
*Name of submitting scientist
*Institution
*Language of submission (only in ISO 2 letter codes)
*Date of submission
*Crop
*Name of Trait
*Abbreviated name
*Synonyms (separate by commas)
*Trait ID for modification, Blank for New
*Description of Trait
*How is this trait routinely used?
*Trait Class
*Method ID for modification, Blank for new
*Name of Method
*Describe how measured (method)
*Growth Stage
*Bibliographic Reference
*Comments
*Scale ID for modification, Blank for new
*Type of Measure (Continuous, Discrete or Categorical)
*For Continuous: units of measurement
*For Continuous: reporting units (if different from measurement)
*For Continuous: minimum
*For Continuous: maximum
*For Discrete: Name of scale or units of measurement
*For Categorical: Name of rating scale
*For Categorical: Class 1 - value = meaning
*For Categorical: Class 2 - value = meaning
*For Categorical: Class 3 - value = meaning
*For Categorical: Class 4 - value = meaning
*For Categorical: Class 5 - value = meaning

=OBO files=
==OBO file structure==
OBO files are created using the obo2owl library (which should sound familiar ;-)).
The main issue with the Trait Template is that because different IDs can be created for the same “thing” (e.g. the term “cm” will get different IDs if different traits are measured in cm), different obo terms can have the same name (but different IDs). That is a problem when our users tried to import the OBO files in a Chado database.
Consequently, I created a little script that created OBO files where all the names are unique in a given namespace. The script has not be inserted in the website yet but it will be soon. Example of an OBO files on Github.

{| border="1" class="sortable"
!TD column!!OBO element
|-
|Crop||Used for setting the namespace
|-
|Name of Trait||name
|-
|Trait ID for modification, Blank for New||Term + id
|-
|Description of Trait||definition
|-
|Trait Class||Term +id + name + is-a
|-
|Language of submission (only in ISO 2 letter codes)||We have only English OBO files.
|-
|Name of submitting scientist||created_by
|-
|Institution||Not used
|-
|Date of submission||creation_date
|-
|Abbreviated name||synonym [EXACT]
|-
|Synonyms (separate by commas)||synonym [EXACT]
|-
|How is this trait routinely used||Not used
|-
|Name of method||name
|-
|Method ID for modification, Blank for New||Term + id + method_of
|-
|Describe how measured (method||definition
|-
|Bibliographic Reference||xref
|-
|Growth Stage||Not used
|-
|Comments||Not used
|-
|Scale ID for modification, Blank for New||Term + id + scale_of
|-
|Type of Measure (Continuous, Discrete or Categorical||Not used
|-
|For Continuous: units of measurement||name
|-
|For Discrete: Name of scale or units of measurement||name
|-
|For Categorical: Name of rating scale||name
|-
|For Categorical: Class 1 - value = meaning||Term + name + is-a
|-
|For Categorical: Class 2 - value = meaning ||Term + name + is-a
|-
|For Categorical: Class 3 - value = meaning||Term + name + is-a
|-
|For Categorical: Class 4 - value = meaning||Term + name + is-a
|}

=SKOS files=
==SKOS file structure==
{| border="1" class="sortable"
!TD column!!SKOS
|-
|Crop||Used for setting the namespace
|-
|Name of Trait||skos:prefLabel
|-
|Trait ID for modification, Blank for New||Local Name (URI) +
|-
|rdf: type skos:concept
|-
|Description of Trait||skos:definition
|-
|Trait Class||rdf:type Skos:Concept + skos:broader
|-
|Language of submission (only in ISO 2 letter codes)||xml:lang of the literals. SKOS files are multilingual (if we have the info)
|-
|Name of submitting scientist||foaf:Person (not set so far but will be soon)
|-
|Institution||foaf:Organization (not set so far but will be soon)
|-
|Date of submission||dc:date (not set so far but will be soon)
|-
|Abbreviated name||skos:altLabel
|-
|Synonyms (separate by commas)||skos:altLabel
|-
|How is this trait routinely used||Not used
|-
|Name of method||skos:prefLabel
|-
|Method ID for modification, Blank for New||Local Name (URI) +
|-
|rdf: type skos:concept
|-
|Describe how measured (method||skos:definition
|-
|Bibliographic Reference||Not set (dc: bibliographicCitation?)
|-
|Growth Stage||skos:related (not set so far)
|-
|Comments||skos:editorialNote
|-
|Scale ID for modification, Blank for New||Local Name (URI) +
|-
|rdf: type skos:concept
|-
|Type of Measure (Continuous, Discrete or Categorical||Not used
|-
|For Continuous: units of measurement||skos:prefLabel
|-
|For Discrete: Name of scale or units of measurement||skos:prefLabel
|-
|For Categorical: Name of rating scale||skos:prefLabel
|-
|For Categorical: Class 1 - value = meaning||Local Name (URI) +
|-
|rdf: type skos:concept
|-
|For Categorical: Class 2 - value = meaning ||Local Name (URI) +
|-
|rdf: type skos:concept
|-
|For Categorical: Class 3 - value = meaning||Local Name (URI) +
|-
|rdf: type skos:concept
|-
|For Categorical: Class 4 - value = meaning||Local Name (URI) +
|-
|rdf: type skos:concept
|}

=List of Crops and IDs=
According to the project timeline, the crops that will be linked to the reference ontologies are:
{| class="wikitable"
|-
! Crops
! Prefixes
|-
| Maize
| 322
|-
| Rice
| 320
|-
| Wheat
| 321 (traits) and 121 (anatomy)
|-
| Cassava
| 334
|-
| Cowpea
| 340
|-
| Chickpea
| 338
|-
| Potato
| 330
|-
| Sorghum
| 324
|-
| Soybean
| 336
|-
| Barley
| 323
|-
| Common Bean
| 335
|-
| Groundnut
| 337
|-
| Pearl Millet
| 327
|-
| Pigeon Pea
| 341
|-
| Musa
| 325 (traits) and 125 (anatomy)
|-
| Sweet Potato
| 331
|-
| Yam
| 333
|-
| Other crops ?????
|
|}

The trait ontologies start with 3XX whereas the anatomy ontologies start with 1XX.

Crop Ontology Pages

2015-05-29T13:35:12Z

Marieangelique.laporte: /* OBO files */

Crop Ontology Pages

2015-05-29T13:28:47Z

Marieangelique.laporte: /* List of Crops and IDs */

Crop Ontology Pages

2015-05-29T13:14:38Z

Marieangelique.laporte:

Crop Ontology Pages

2015-05-29T13:12:04Z

Marieangelique.laporte:

Crop Ontology Pages

2015-05-29T13:05:08Z

Marieangelique.laporte: /* Structure of the Trait Template V4 */

you can type here....

=Trait Template=
==Structure of the Trait Template V4==
So far, the Trait Template V4 is uploaded into the CO website. The Trait Template is used to gather information on traits along with their methods and scales of measurement. For each trait, some meta-information is added (5 first columns). An (unique) ID is created by the system for each trait, method and scale (several IDs are created when the scale is categorical). But for now, if two methods or scales are the same (seed length and leaf length are measured in centimeters), different IDs are created, which is far from being ideal or even ontologically correct.
The Trait Template V4 columns are:
*IBFieldbook
*Name of submitting scientist
*Institution
*Language of submission (only in ISO 2 letter codes)
*Date of submission
*Crop
*Name of Trait
*Abbreviated name
*Synonyms (separate by commas)
*Trait ID for modification, Blank for New
*Description of Trait
*How is this trait routinely used?
*Trait Class
*Method ID for modification, Blank for new
*Name of Method
*Describe how measured (method)
*Growth Stage
*Bibliographic Reference
*Comments
*Scale ID for modification, Blank for new
*Type of Measure (Continuous, Discrete or Categorical)
*For Continuous: units of measurement
*For Continuous: reporting units (if different from measurement)
*For Continuous: minimum
*For Continuous: maximum
*For Discrete: Name of scale or units of measurement
*For Categorical: Name of rating scale
*For Categorical: Class 1 - value = meaning
*For Categorical: Class 2 - value = meaning
*For Categorical: Class 3 - value = meaning
*For Categorical: Class 4 - value = meaning
*For Categorical: Class 5 - value = meaning

Crop Ontology Pages

2015-05-28T10:18:16Z

Marieangelique.laporte: /* headings */

you can type here....

=Trait Template=
==Structure of the Trait Template V4==
So far, the Trait Template V4 is uploaded into the CO website. The Trait Template is used to gather information on traits along with their methods and scales of measurement. For each trait, some meta-information is added (5 first column). An (unique) ID is created by the system for each trait, method and scale (several IDs are created when the scale is categorical). But for now, if two methods or scales are the same (seed length and leaf length are measured in centimeters), different IDs are created, which is far from being ideal or even ontologically correct.
The Trait Template V4 columns are:
*IBFieldbook
*Name of submitting scientist
*Institution
*Language of submission (only in ISO 2 letter codes)
*Date of submission
*Crop
*Name of Trait
*Abbreviated name
*Synonyms (separate by commas)
*Trait ID for modification, Blank for New
*Description of Trait
*How is this trait routinely used?
*Trait Class
*Method ID for modification, Blank for new
*Name of Method
*Describe how measured (method)
*Growth Stage
*Bibliographic Reference
*Comments
*Scale ID for modification, Blank for new
*Type of Measure (Continuous, Discrete or Categorical)
*For Continuous: units of measurement
*For Continuous: reporting units (if different from measurement)
*For Continuous: minimum
*For Continuous: maximum
*For Discrete: Name of scale or units of measurement
*For Categorical: Name of rating scale
*For Categorical: Class 1 - value = meaning
*For Categorical: Class 2 - value = meaning
*For Categorical: Class 3 - value = meaning
*For Categorical: Class 4 - value = meaning
*For Categorical: Class 5 - value = meaning