Ontology Working Group Meetings- Jan 2015

Kick Off Meeting: Monday January 5th, 2015

Who: EA, LC and PJ Goal: Discuss the coordination between the NSF Planteome Project and the Crop Ontology.

1. Progress and Updates on the Crop Ontology (http://www.cropontology.org/)

• Annotation of phenotyping data through the IBP (https://www.integratedbreeding.net)
• Ontology manager on https://www.integratedbreeding.net/
• CO traits used to populate
• Agtrials (http://www.agtrials.org/) on CIAT another source
• Involvement of ICRISAT
• Genebank accessions- done at some centers e.g. CP
• Traits may be in common, but also there is variation between crops
• CO provides community-specific vocabularies for integration of data annotations

2. Ontology development and serving to users:

• With NSF's investment, they have certain requirements- need to minimize the duplication of efforts
• Centralized location for the ontology repositories- can be served to various portals as needed- such as the CO webpage the users are familiar with
• Need reliable system of versioning for the ontologies- Are the CO ones versioned currently?
• Reference ontologies need to be updated and expanded:
  • Core reference ontologies: PO, TO, GO, ENVO/EO, PATO, ChEBI
  • CO- species-specific vocabularies, ontologies
• CO has a tailored helpdesk for the users- needs to be maintained

• TO Development - could be opened to editing through Term Genie

3. Annotations and linking- vision of how the data is going to be shared

• SKOS format, OBO, move towards using OWL- at least in the reference ontologies
• Relations
• Need to be able to query across ontologies
• Need to create cross links between the crop-specific ontologies and the reference ones
• Design pilot project- pick a select group to focus on- will discuss further

4. Online resources web services, provide links to databases

• APIs can be set up as we move forward

5. Upcoming: Planteome-CO Coordination meeting at PAG Jan 12th

Crop Ontology and Planteome Project Meeting Monday Jan 12th @ PAG 2015

Moderator: Rex Nelson

1. Meeting Participants:

• Elizabeth Arnaud, Bioversity International*, CGIAR, France
• Laurel Cooper, Oregon State University, US
• Mathieu Rouard, Bioinformatics, Bioversity International*, CGIAR, France
• Graham McLaren, Integrated Breeding Platform, Canada
• Ruth Bastow, Global Plant Council, UK
• Cyril Pommier, Information System & Data integration, INRA*, France
• Pierre Larmande, Bioinformatics, IRD, France
• Rex Nelson, Soybase, USDA-ARS*, US
• Mary Shaeffer, MaizeGDB, USDA-ARS*, US
• Reinhard Simon, Bioinformatics, CIP*, CGIAR, Peru
• Ruaraidh Sackville Hamilton, Head of Genetic Resources Unit, IRRI*, CGIAR, Philippines
• Peter Kulakow, Cassava Breeding Prog., IITA, CGIAR , Nigeria
• Rebecca Berrigan, LeafNode Cie., IBP, New Zealand
• Drabo Inoussa, Institut National d’Etude, Burkina Faso
• Abhishek Rathore, Breeding Informatics Unit (BIU), ICRISAT, CGIAR, India
• Justin Elser, Oregon State University, US
• Justin Preece, Oregon State University, US

(* Institutions that have sent a letter of intent to Planteome for contributing to the ontology and annotations)

2. The International Crop Ontology (CO) project of the Integrated Breeding Platform

Elizabeth Arnaud

3. The NSF–funded Planteome project and Coordination with the CO:

Laurel Cooper: Introduction to the Planteome Project:

6.. Round table discussion on collaboration for ontology development and data annotations & key questions from partners:

Possible Use Cases: Alignment of CO with Ref Ontologies

• Maize (CIMMYT, USDA, Gramene) and Sorghum (ICRISAT)
• Rice (IRRI), Wheat (CIMMYT, INRA), Barley (ICARDA)
• Cassava (IITA), Potato (CIP), Sweet potato (CIP), Yam (IITA)
• Chickpea (ICRISAT), Cowpea (IITA), Soybean (IITA, USDA),
• Common bean (CIAT), Groundnut (ICRISAT), Pigeon pea (ICRISAT),
• Pearl Millet (ICRISAT), Musa (Bioversity) , and other crops

Comments from PJ- By email: Talking points on collaboration.

• Common database, data store and repository
• Trained and approved curators get read and write access to their data (ontologies and shared annotations)
• All the edits done on common site and files served by cROP. This includes CO and the reference ontologies.
• All the project data files and code to be served from GitHub
• iPlant will hots the live site and provide access via a website as well as via webservices. To be managed by cROP project. means less overhead on managing such resources
• Training for ontology editors for protege and Termgenie
• Training for data manager for integration in their annotation and database portals/tools.
• CO website will fetch the live stable ontologies released for integration from GitHub for integration in teh CO website. This site will be maintained as it is until we are ready to provide same services by integrating them in the Planteome website (from iPlant)
• Start by identifying crops with most data unless CGIAR center has a person who can work with us on a different crop that needs immediate attention ( we have limited hands and thus need help)
• All data and ontologies released in public domain under CC 3.0
• Everyone who contributes take a collective responsibility. We will make it visible on the project website.

4. Demonstration of the IRD Instance of the NCBO Bioportal Interface- Pierre Larmande, Bioinformatics, IRD, France

http://bioportal.lirmm.fr/ontologies

NCBO technology is domain independent and open source. The NCBO Bioportal virtual appliance is available for the community allowing to set up a local ontology repository and eventually customize it: http://www.bioontology.org/wiki/index.php/Category:NCBO_Virtual_Appliance

We have already set-up a local instance of BioPortal on a LIRMM server. It is a prototype that currently hosts French terminologies (for the SIFR project) and English plant related ontologies (around 15) aggregated for the IBC project and testing for INRA: http://bioportal.lirmm.fr. Crop related ontologies have been grouped under the CROP group. For instances:

· Visualize an ontology: http://bioportal.lirmm.fr/ontologies/CO-WTO/?p=classes&conceptid=root

· Search searches within all the crop ontologies: http://bioportal.lirmm.fr:8082/search?q=plant&apikey=aa5b0e2c-5a2e-4a01-b3a2-32cf024f3f27&ontologies=CO-BANANA,CO-CRO,CO-GO,CO-GMO,CO-MMO,CO-MCPO,CO-RTO,CO-WTO

· Annotates a piece of text with all the crop ontologies:

· Formalize, store and render mappings between ontologies of the portal (or between ontologies of the portal and the main NCBO BioPortal). For instance: http://bioportal.lirmm.fr:8082/mappings/http%3A%2F%2F193.49.110.102%3A8082%2Fmetadata%2Fmapping%2F3812940f027469be758257d7bc82388b173b2d35

This is a mapping (of type skos:exactMatch),uploaded to the portal through the API by user “jonquet” between Plant height in CO-WTO and plant height in PO.

All other features from BioPortal will be generically available for the LIRMM server: ontology versioning, UI widget, ontology metrics, ontology recommender service, projects listing, community feedback (comment, subscription to ontology changes), users management (and public or private access to ontologies). In addition 2 endpoints allow to automatically query the content of the portal:

· REST web service API: http://bioportal.lirmm.fr:8082/documentation

· SPARQL endpoint: http://bioportal.lirmm.fr:8081/test/

Indeed, the portal has fully embraced semantic web technologies and the ontologies will be stored in an RDF triple store

Planteome Ontology Working Group Meeting- Jan 22, 2015

Who: EA, LC and PJ Points of Discussion:

1. Planteome wiki set up

• will add EA and others on her team as needed..
• Will be closed, will have to login to access

2. Interaction with DivSeek.

• Ruth Bastow is on the board and is interested in coordinating between the projects. DivSeek is a partnership, advisory board role may create COI?

3. Scientific Advisory Board- will have info on the wiki- create page for Scientific Advisory Board

• Oversight, annual report, meeting in person or online
• advocates to community, users and funding agencies
• possibly representative from CG centers such as RH, PK

4. Prioritizing the CO vocabularies for cross referencing and curator training

• Rice- IRRI is shorthanded right now, possible person is Berta Miro- associated with IRRI (Ajay Kohli)
• Maize and wheat - CIMMYT- Rosemary; Project already underway with LC + Mary Schaeffer
  • WheatIS and WDIWG of the RDA- interested in using ontologies and setting standards
• Soybean- USDA Rex Nelson
• Potato - CIP Reinhard, Richard Finkers (also other solanaceae)

5. Planning is starting for Ontology Workshop in the Spring

• Owl training, etc
• more details TBA as they develop

6. Collaboration possibilities with PL, AV and CJ, from IRD in Montpellier

• CJ will be in Stanford this spring, has money for a postdoc for a year which will go away without a project.
• Southgreen platform, involvement with 3000 rice genomes project
• Semantic integration

To-do: create page for Scientific Advisory Board, Ontology Workshop