The GCP Crop Ontology Team - GCP GRM, Sept. 2011
Crop Ontology Meeting Survey
Crop Ontology Agenda
GCP GRM 2011 - September
Sessions on Crop ontology, Trait dictionaries and Ontology curation/annotation tool
Objective of the sessions: To get the scientists interested in this technology and participating. This first meeting is to sensitize scientists to the problem and the tools and invite them to participate either on their own, or by submitting information to the Ontology Curators whom we will introduce.
Outputs:
1. report on the sessions
2. revisited for 2011 between the General Research Meeting and December
3. plans for 2012
4. identified scientists who are willing to contribute to the content of the ontology
5. identified curators for ontology on Sorghum, Chickpea, Cowpea and possibly for Beans and Groundnut
A series on sessions for the Crop ontology and Trait dictionaries will be organized during the GRM as follows:
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Time |
DAY 1 - Wednesday, 21st September |
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17:30-19:30 |
POSTER SESSION I |
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Poster 1 - Annotation and curation tool
Poster 2 - Cassava Ontology
Poster 3 - Musa Ontology |
All 3 posters related to ontologies will be presented on Day 1. |
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Time |
DAY 2 - Thursday, 22nd September |
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12:10-12:30 |
Plenary - Presentation on Ontology uses - Elizabeth Arnaud (according to GRM Draft Agenda) |
10’ presentation and 10’ questions |
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Objective: Overview of the Crop ontology principle as a support to data access, current content and progress made with additional traits, contribution to international initiatives, curation/annotation tool, issues/solutions and future plans |
with Rosemary and Luca
With the input of the curators of the crop specific ontologies |
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13:30-15:30 |
Parallel crop groups for wheat, rice, cassava, legumes, maize, sorghum |
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Objective: Introduce the crop specific curators and the ontology team, sensitize participants of the crop groups about the existence and content of the controlled vocabularies called Crop ontology, its purpose and the possible uses in ICIS fieldbook template. Explain the new possibility for the crop communities to actively contribute and identify the community partners who can contribute. Invite the participants to look at the online ontology and provide their comments online. |
Around 60 mns/group |
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Content
1. Presentation of the current content and uses of the crop specific ontology, current trait dictionaries, methods, scales
2. Demonstration of tools and tutorials - show what is available for their crops
3. Discussion on the material circulated by mail and the collaboration with other centers and partners for submitting new traits/methods/scales.
4. Practice of the tool and fill in the survey
5. What feedback workflow is needed from the crop community to the curator of the crop specific ontology and then to the global crop coordinator? What can be online?
6. Capture issues for the brainstorming session of Day 4 |
1 flipchart/one video projector |
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13:30-14:30 |
Maize
Convention Centre (Lobby Level) |
Rosemary, Tito, Luca |
Rice
Convention Centre (Lobby Level) |
Elizabeth, Milko, Mau, Nikki, Audrey |
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14:30-15:30 |
Legumes
Sapphire Ball Room 1 (-1) |
Elizabeth, Sam, Prasad, Milko, Audrey |
Wheat
Ruby Hall (2nd Floor) |
Rosemary, Tito, Luca |
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15:30-15:50 |
Coffee break |
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15:50-17:00 |
Parallel crop groups for wheat, rice, cassava, legumes, maize, sorghum (cont’d) |
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Cassava
Sapphire Ball Room 2 (-1) |
Elizabeth, Milko, Moshood |
Sorghum
Sapphire Ball Room 3 (-1) |
Rosemary, Praveen, Ibrahima, Luca, Audrey |
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17:00-17:30 |
Break |
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17:30 - 19:30 |
POSTER SESSION II |
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DAY 3 - Friday, 23rd September |
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9:00 – 12:30 |
Technical session at ICRISAT.
Objective: based on the feedback received in previous session and progress made in both the curation tool and the fieldbooks, discuss the technical implementation of the links to ICIS and workflow for the curators of the crop specific ontology – develop a draft workplan for end of 2011 and 2012
Remind curators to bring their laptops
1 video projector + 1 flipchart requested |
Meeting @ 07:45am in the lobby of the convention centre and departure @ 08:00am. Lunch organized.
Meeting rooms: 302 Seminar Hall + Classroom A |
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9:00 – 10:00
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Plenary session:
Discussion on workflow for curators.
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All CO team and Graham and Arllet’s team will attend |
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10:00 – 10:15
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Coffee Break |
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10:15 – 12:30 |
Parallel session:
I. Crop Ontology team
II. Data Management Team
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Elizabeth’s group
Arllet’s group |
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10:15 – 11:30
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For Crop Ontology team:
A. Linking CO tools to IB field book: CO team + Tito + Arllet
1. Presentation of structure and brainstorming
2. Is the representation of the methods and scale appropriate in the tool?
3. What workflow between the tool and with ICIS fieldbook template?
4. What preparation/ development is needed for the offline access with the standalone version?
5. What workflow/ exchange is needed with the crop databases?
6. Is it problematic to encode traits? How can we do this?
7. How do we structure Web services?
8. What services do they want?
9. What features/custom information do they want to share?
For Arllet team: Progress and plans for analysis and decision support tools for Integrated breeding - Candy (Clarissa, GCP) and William, IRRI, will run the session. |
Tito Sanchez, Arlett, Bakare, Mau, Nikki, Sam, Ibrahima, Rosemary, Luca, Milko, Elizabeth, Graham, Praveen, Prasad
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11:30 – 12:30 |
For CO team:
B. CO Workplan for 2011-2012
1. Draft workplan for end of 2011 and for 2012
2. Capture potential issues for the brainstorming session of Day 4
For Arllet team: Tutorial of uploading data from local to central ICIS databases. |
Arllet won’t be attending CO discussion. |
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13:30 – 14:30 |
Lunch at ICRISAT |
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p.m. |
Field visit at ICRISAT |
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DAY 4 - Saturday, 24th September |
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17:30-19:30 |
Session on Informatics Clinic |
Ruby Hall 2nd floor |
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Objective: hands on practice of the ontology, trait dictionaries, trait template where scientist can use their data sets and seat with the curator of the crop specific ontology. |
Whole team
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1. Test the tool using real data sets of the participants and load trait lists. understand the formats of the data
2. Demonstration of the use of OBO-Edit as necessary
3. Collect feedback on the tool and tutorials on the survey form |
6 LAPTOPS + internet |
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CO team meeting to wrap up and prepare a draft report after dinner |
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DAY 5 – Sunday, 25th September |
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14:00-14:15 |
Wrap-up comments T3: Crop information (G. McLaren) |
Convention Centre |
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ontology/ trait dictionaries included in the Theme 3: ‘Crop information brainstorming group’ |
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14:15-15:00 |
Meeting with curators to define 2011 work plan and activities |
Ruby Hall 2nd floor |
Crop Ontology Sessions Participants
CASSAVA
LEGUMES
MAIZE
RICE
SORGHUM
WHEAT
Posters & Abstracts
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3.5 & 3.6: Expansion of the crop ontology by adding cassava (3.5) and Musa (3.6) trait ontologies
Peter Arthur Kulakow,* Moshood Agba Bakare, Stephanie Channeliere,
Jean-Pierre Horry, Rosemary Shrestha and Elizabeth Arnaud
*International Institute of Tropical Agriculture, IITA, PMB 5320, Ibadan
NIGERIA
e-mail: p.kulakow@cgiar.org
The Crop Ontology describes traits, methods and scales of several
economically important plants (htt p://www.cropontology-curationtool.
org). Cassava (Manihot esculenta Crantz) and banana (Musa sp.) ontologies
were added to Crop Ontology in 2010. Simultaneously, the cassava team
is developing an ontology-driven cassava database called ICASS for
researchers to record and annotate measurements linked to genotypes with
defi ned pedigrees. The cassava crop ontology currently describes over 125
traits representing important trait groups (agronomic, biotic and abiotic
stress, morphological, physiological and quality traits).
These traits describe phenotypic variability for characteristics needed for
crop improvement. The cassava ontology will facilitate information sharing
and collaboration among researchers from CIAT, IITA, national programs
and other collaborators. The Crop Ontology also added the Musa trait
ontology to describe about 173 traits representing agronomic, biotic and
abiotic stress and morphology related trait groups. This ontology will be
useful for annotating phenotypic and genotypic data produced by banana
researchers at Bioversity, IITA and other Musa programs. Musa trait names
have been submitted to Plant Ontology with some already integrated while
others need discussion with experts. New ontology-based online curation
and annotation tools allow crop curators to provide standard protocols
explaining scale, scale value, scoring guidelines and growth stages for
scoring traits.
Related GCP project–G4010.06: Enhancement and implementation of
the crop ontology for data integration and data interoperability (PI: E
Arnaud, Bioversity) |
3.7: To contribute crop traits lists using the new online
Crop Ontology Curation and Annotation tool
Luca Matteis, Milko Skofic, Hector Sanchez, Rosemary
Shrestha, and Elizabeth Arnaud*
* Bioversity International;
e-mail: l.matt eis@cgiar.org; e.arnaud@cgiar.org
The Crop Ontology (http://cropontology.org/) provides validated
names, definitions and relationships for traits of cassava, chickpea,
maize, Musa, potato, rice, sorghum and wheat. These lists were
developed by Bioversity, CIMMYT, CIP, ICRISAT, IITA, IRRI.
The sources of breeders’ trait names were the International Crop
Information System (ICIS), the Bioversity key crop descriptors and
the Trait dictionaries developed by the GCP crop communities.
An online tool is now available (ht p://cropontology-curationtool.
org) for the crop communities to share trait lists, contribute new
trait names and download concepts for annotating data. The tool
allows users to display and print the lists. By using a login, curators
of crop trait lists can comment any term or add online attribute
information (e.g. photos). A full ontology can be directly uploaded
or created online using the current OBO upload service. The system
will support other standard formats like OWL. The ICIS teams will
synchronize their Trait Templates with the ontology using the web
service API. Any application can send to and receive data from the
Curation Tool using this API that provides the ability to create,
read, update and delete terms. The site is hosted on Google App
Engine and the versioned code is hosted on GitHub.
Related GCP project–G4011.01: Development, maintenance
and use of trait dictionaries and a Crop Ontology to facilitate
the annotation of phenotypic data by crop communities (PI:
Elizabeth Arnaud, Bioversity)
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Presentations
Videos
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 Updating... ĉ a.chaunac@cgxchange.org, Oct 10, 2011, 11:57 PM Ċ Elizabeth Arnaud, Oct 4, 2011, 6:51 AM Elizabeth Arnaud, Sep 25, 2011, 3:58 AM Elizabeth Arnaud, Sep 25, 2011, 3:56 AM Elizabeth Arnaud, Sep 25, 2011, 3:58 AM Elizabeth Arnaud, Sep 25, 2011, 3:51 AM ĉ Elizabeth Arnaud, Oct 4, 2011, 6:50 AM
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