H. GCP General Research Meeting (GRM), Hyderabad, September 21-25, 2011

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:

 

Time

DAY 1 - Wednesday, 21st September

 

17:30-19:30

POSTER SESSION I

 

 

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.

 

 

Time

DAY 2 - Thursday, 22nd September

 

 

12:10-12:30

Plenary - Presentation on Ontology uses - Elizabeth Arnaud (according to GRM Draft Agenda)

10’ presentation and 10’ questions

 

 

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

 

13:30-15:30

Parallel crop groups for wheat, rice, cassava, legumes, maize, sorghum

 

 

 

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

 

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

13:30-14:30

Maize

Convention Centre (Lobby Level)

Rosemary, Tito, Luca

Rice

Convention Centre (Lobby Level)

Elizabeth, Milko, Mau, Nikki, Audrey

14:30-15:30

Legumes

Sapphire Ball Room 1 (-1)

Elizabeth, Sam, Prasad, Milko, Audrey

Wheat

Ruby Hall (2nd Floor)

Rosemary, Tito, Luca

15:30-15:50

Coffee break

 

15:50-17:00

Parallel crop groups for wheat, rice, cassava, legumes, maize, sorghum (cont’d)

 

 

Cassava

Sapphire Ball Room 2 (-1)

Elizabeth, Milko, Moshood

Sorghum

Sapphire Ball Room 3 (-1)

Rosemary, Praveen, Ibrahima, Luca, Audrey

17:00-17:30

Break

 

17:30 - 19:30

POSTER SESSION II

 

 

 

DAY 3 - Friday, 23rd September

 

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

9:00 – 10:00

 

Plenary session:

Discussion on workflow for curators.

 

All CO team and Graham and Arllet’s team will attend

10:00 – 10:15

 

Coffee Break

 

10:15 – 12:30

Parallel session:

I.                 Crop Ontology team

II.               Data Management Team

 

Elizabeth’s group

Arllet’s group

10:15 – 11:30

 

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

 

 

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.

13:30 – 14:30

Lunch at ICRISAT

 

p.m.

Field visit at ICRISAT

 

 

 

DAY 4 - Saturday, 24th September

 

17:30-19:30

Session on Informatics Clinic

Ruby Hall 2nd floor

 

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

 

 

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

 

CO team meeting to wrap up and prepare a draft report after dinner

 

 

 

DAY 5 – Sunday, 25th September

 

14:00-14:15

Wrap-up comments T3: Crop information (G. McLaren)

Convention Centre

 

ontology/ trait dictionaries included in the Theme 3: ‘Crop information brainstorming group’

 

14:15-15:00

Meeting with curators to define 2011 work plan and activities

Ruby Hall 2nd floor

 


Crop Ontology Sessions Participants

 

CASSAVA

 

First Name

Last Name

Institution

Email

Larry

Butler

GCP

l.butler@cgiar.org

Chiedozie

Egesi

NRCRI

cegesi@yahoo.com

Morag

Ferguson

IITA

m.ferguson@cgiar.org

Geoffrey

Mkamilo

ARI Tanzania

geoffreymkamilo@yahoo.co.uk

Bakare

Moshood

IITA

m.bakare@cgiar.org

Emmanuel

Okogbenin

NRCRI

eokogbenin@yahoo.com

Anthony

Pariyo

NaCCRI-Uganda

tkakau@yahoo.co.uk

Elizabeth

Parkes

CSIR CRI Ghana

ey.parkes@yahoo.co.uk

Melissa

Reynolds

University of Pretoria

melissa.reynolds@fabi.up.ac.za

Harold

Roy-Macauley

CORAF/WECARD

h.roy-macauley@coraf.org

Tim

Setter

Cornell University

tls1@cornell.edu

Ruth

Thompson

CRI-Ghana

ginathompsongh@yahoo.com

 

LEGUMES

 

First Name

Last Name

Institution

Email

Steve

Beebe

CIAT

s.beebe@cgiar.org

A.

Bhanuprakash

ICRISAT

a.bhanuprakash@cgiar.org

Chellapilla

Bharadwaj

IARI

drchbharadwaj@gmail.com

Ousmane

Boukar

IITA Nigeria

o.boukar@cgiar.org

Rowland

Chirwa

CIAT Malawi

r.chirwa@cgiar.org

Issa

Drabo

INERA Burkina Faso

idrabo@yahoo.fr

Jeff

Ehiers

University of California Riverside

jeff.ehiers@ucr.edu

Issa

Faye

ISRA

issafaye2001@yahoo.fr

Asnake

Fikre

EIAR Ethiopia

fikreasnake@yahoo.com

Pooran

Gaur

ICRISAT Patancheru

p.gaur@cgiar.org

Pasupuleti

Janila

ICRISAT Patancheru

p.janila@cgiar.org

Mussa

Jarso

EIAR Ethiopia

mjarso@yahoo.com

Paul

Kimurto

Egerton University Kenya

kimurtopk@gmail.com

Lakshmanan

Krishnamurthy

ICRISAT

l.krishnamurthry@cgiar.org

Omari

M’ponda

ARI Nialendele

mpondaomari@hotmail.com

Godwill

Makunde

Crop Breeding Institute

mgodwill@hotmail.com

Teresa

Millan

University of Cordoba

teresa.millan@uco.es

Sam

Ofofile

IITA Nigeria

s.ofodile@cgiar.org

Pascal

Ojwang

KARI

pookwiri@yahoo.com

Halilou

Oumarou

ICRISAT Niger

h.oumarou@icrisatne.ne

Bodo

Raatz

CIAT

bodo.raatz@gmail.com

Abhishek

Rathore

ICRISAT

a.rathore@cgiar.org

Pasala

Ratnakumar

ICRISAT

p.ratnakumar@cgiar.org

Rachit

Saxena

ICRISAT

r.saxena@cgiar.org

Trushar

Shah

ICRISAT

tm.shah@cgiar.org

Mahendar

Thudi

ICRISAT

t.mahendar@cgiar.org

Jean-Baptiste

Tignegre

INERA Burkina Faso

racinetignegre@yahoo.com

Hari D.

Upadhyaya

ICRISAT

h.upadhyaya@cgiar.org

Vincent

Vadez

ICRISAT India

v.vadez@cgiar.org


MAIZE

 

First Name

Last Name

Institution

Email

Muhammad

Azrai

ICERI

azraimuh@yahoo.com

Jedidah

Danson

ACCI (University of KwazuluNatal)

dansonj@ukzn.ac.za

John

Derera

ACCI (University of KwazuluNatal)

dereraj@ukzn.ac.za

James

Ghetti

KARI

jgethi@wananchi.com

Samuel

Gudu

Moi University

samgudu2002@yahoo.com

Girish K.

Krishna

CIMMYT

g.krishna@cgiar.org

Dickson

Ligeyo

KARI

ligeyootieno@yahoo.com.uk

Thomas

Matonyei

Moi University

matonyei@yahoo.com

Jean-Marcel

Ribaut

GCP

j.ribaut@ciar.org

I.S.

Singh

Krishidan Seeds Pvt Ltd

indrasensingh@krishidhanseeds.com

Elliot

Tembo

Seed Co Limited

elliottembo@yahoo.com

Vedachalam

Vengadessan

CIMMYT

v.vengadessan@cgiar.org

Bindiganavile

Vivek

CIMMYT

b.vivek@cgiar.org


RICE

 

First Name

Last Name

Institution

Email

Nourollah

Ahmadi

CIRAD

nourollah.ahmadi@cirad.fr

Armin

Bhuiya

IRRI

arminbhuiya@gmail.com

Fousseyni

Cisse

IER

fousscisse@yahoo.fr

Ibnou

Dieng

Africa Rice

i.dieng@cgiar.org

William

Eusebio

IRRI

w.eusebio@cgiar.org

Drissa

Hema

INERA

djamihfr@yahoo.fr

Amelia

Henry

IRRI

a.henry@cgiar.org

Sigrid

Heuer

IRRI

s.heuer@cgiar.org

Glenn

Hyman

CIAT

g.hyman@cgiar.org

Boonrat

Jongdee

URRC

boonrat@brrd.mail.go.th

Honore

Kam

INERA

kamhonore@yahoo.fr

Arvind

Kumar

IRRI

a.kumar@cgiar.org

Hei

Leung

IRRI

h.leung@cgiar.org

Alhassan

Maji

NCRI

tswakoma@gmail.com

Nimai Prasad

Mandal

CRURSS (ICAR)

npmandal@hotmail.com

Graham

McLaren

GCP

g.mclaren@cgiar.org

Suhas

Nimbalkar

Atash Seeds Private Limited (groupe Limagrain)

suhas@atashseeds.net

Md. Sazzadur

Rahman

BRRI

s.rahman@irri.org

Jonaliza

Siangliw

RGDU

jsiangliw@gmail.com

Inthavong

Thavone

NAFRI

thavone.i@nafri.org.la

Theerajut

Toojinda

RGDU

toojindatheerajut@gmail.com

Ramaiah

Venuprasad

Africa Rice

r.venuprasad@cgiar.org

Khin Myo

Win

PhD student

Khinmyowin07@gmail.com

Guoyou

Ye

IRRI

g.ye@cgiar.org

 

SORGHUM

 

First Name

Last Name

Institution

Email

A.

Ashok Kumar

ICRISAT

a.ashokkumar@cgiar.org

Andrew

Borrell

University of Queensland

a.borrell@uq.edu.au

Sidi Bekaye

Coulibaly

IER Mali

scouliba@yahoo.com

N’deye Ndack

Diop

GCP

nn.diop@cgiar.org

Richard

Edema

Makerere University

redema12@yahoo.com

Theresa

Fulton

Cornell University

tf12@cornell.edu

Mamoutou

Kouressy

IER Mali

nanym63@gmail.com

Jurandir

Magalhaes

EMBRAPA

jurandir@cnpms.embrapa.br

Patrick

Okori

Makerere University

pokori@agric.mail.ac.ug

T.

PraveenReddy

ICRISAT

p.teegala@cgiar.org

Jean-Francois

Rami

CIRAD

rami@cirad.fr

Dramane

Sako

IER Mali

dramanesako@yahoo.fr

Ibrahima

Sissoko

ICRISAT Bamako

i.sissoko@icrisatml.org

Soumana

Souley

INRAN Niger

nsoumana@yahoo.com

Niaba

Teme

IER Mali

temaeniaba@yahoo.com

Eva

Weltzien

ICRISAT Mali

e.weltzien@icrisat.org

 

WHEAT

 

First Name

Last Name

Institution

Email

Tariq

Chattha

PBI, University of Sydney

tariq.chattha@sydney.edu.au

Mark

Dieters

University of Queensland

m.dieters@uq.edu.au

Fernanda

Dreccer

CSIRO

fernanda.dreccer@csiro.au

Delphine

Fleury

GCP

d.fleury@cgiar.org

P.K.

Gupta

CCS University

pkgupta36@gmail.com

Satish C.

Misra

ARI

scmisra@gmail.com

Bipwajit

Mondal

IARI

bipwagpb@gmail.com

Francis

Ogbonnaya

ICARDA

f.ogbonnaya@cgiar.org

Kumble Vinod

Prabhu

IARI

kvinodprabhu@rediffmail.com

Mark

Sawkins

Syngenta Seeds, France

mark.sawkins@syngenta.com

Manoj Kumas

Singh

NRCPB IARI

manoj@nscpb.org

Gyanendra P.

Singh

IARI

gyanendrapsingh@hotmail.com

John

Snape

John Innes Centre

john.snape@jic.ac.ujk

Yueqiang

Zhang

CAAS

zhangyqyhm@163.com

 


Posters & Abstracts
 

 

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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