Pieces of the PuzzleSónia Dias
Bioversity International
Pieces of the Puzzle
Bioversity [email protected]
Joint PGR Secure/ECPGR workshop ‐ Conservation strategies for European crop wild relative and landrace diversity7–9 September 2011, Palanga, Lithuania
PURPOSE Pest andPest andPest and Pest and diseases diseases resistance, resistance,
AbioticAbiotic stresses stresses including droughtincluding droughtLink to Link to
Th fTh f
including drought,including drought,frost susceptibility frost susceptibility and other traits of and other traits of importance to importance to
breedersbreeders
characterization characterization data (data (phenomicphenomic, , genomic and genomic and transcriptomictranscriptomic)) The purpose of The purpose of
TIP is to provide TIP is to provide breeders with breeders with
information about information about
breedersbreederspp ))
where individual where individual traits can be traits can be
locatedlocatedAvailable Available
information of the information of the mentioned traits mentioned traits
Link toLink to thethe from existing from existing information sources information sources about gene bank about gene bank accessions or accessions or
Link to Link to the the CWR and LR CWR and LR inventoriesinventories
populationspopulationsSpecifically within Specifically within the project, the project,
information on information on resistance to sap resistance to sap feeding insects will feeding insects will be evaluated in WP1 be evaluated in WP1
OBJECTIVESO J C S•To produce a web‐based CWR and LR Trait Information Portal – TIP (Task 2.1)
Conceptualization of TIP
Identification of Information sources
TIP preliminary version ‐ beta version
Testing TIP ‐ silver version
Final version of TIP ‐Golden candidate
TIP infrastructure CRWIS/PLIS Testing with core data sets
Testing with all data sets available
Final web enabling
technical specifications
BrasEDB evaluationTesting with the other WP leaders
and
users requirements and data providers
survey
MedicagoDBpreliminary
testing with the other WP leaders
preliminary
Collaborating breeders
Revising of TIP todata types definition
Tools for data providers
EURISCO & GENESYS
National focal
preliminary testing with collaborating breeders
Revising of TIP to
Revising of TIP to ensure it meets the breeders’ demands
providers ‐intranet, upload system, data quality checks, data analysis
National focal points and project
partners
EMBL
Revising of TIP to ensure it meets the breeders’ demands
Tools for users –search,
download, mapping
EMBL
Some of the main sources of information identifiedSome of the main sources of information identified
EURISCOEURISCO
ECCDB ECCDB ‐‐AvenaAvena, , BetaBeta, ,
Crop Wild Crop Wild Relative Relative InformatiInformati
CWRISCWRIS––AEGROAEGRO––Population Population
CWRIS/PLIS CWRIS/PLIS &&GENESYSGENESYS
BrassicaBrassicaand and
MedicagoMedicagodatabasesdatabases
EMBLEMBLInformatiInformation System on System (CWRIS)(CWRIS)((PGRForumPGRForum))
Level Level Information Information System (PLIS)System (PLIS)
databasesdatabases (( ))
Users requirements and data providers survey Survey results
Plant breeders
‐ Survey results ‐
• Which are the CWR/LR of Medicago that bear specific traits (one ore more traits together)? Where are they maintained? Who is the contact person for information or seed samples? Are seed sample freely available?
• Where does the material originate What is the fenotype of the material (including photo's if possible) How to find material with specific traits (diseases, pests etc)
• Location of origin (country map) Phenotype (photo) Any self‐incompatibility (seed testing) Used in genetic studies
Use in plant improvement – other information type on the accession/population
• Location of origin (country, map) Phenotype (photo) Any self incompatibility (seed testing) Used in genetic studies (genetic maps available?) Availability of seeds
• Data about seed sample quantity and quality (germinability, purity) Uniformity and stability of the genotype Cross compatibility
B i dM di T it f i t t• Brassica‐ Disease resistance, insect resistance, drought tolerance, salt tolerance, stress tolerance, new morphological characters
• Medicago‐ origin (geographic, environment); ploidy; plant size; growth habit; dormancy; pest and pathogen i t fl l t i d fib t t h ti i d ti k
Brassica and Medicago – Traits of interest
resistances; flower colour; protein and fiber content; phenotipic and genetic markers
• It could be interesting to have the opportunity to receive and test a choice of the available genotypes, to see
Other ideas
characteristics and performances in the different areas; results could be returned and used to enrich the information on the portal
Ontologies for PGRSecure
A CWR ontology
gTriontology
• A CWR ontology• If needed work on the existing CWR Ontology defining the CWR inventory
• LR ontologygy• Ontology defining the LR inventory
• CROP ontologies –Trait ontology• Avena ontology• Beta ontology• Brassica ontology
d l• Medicago ontology
The goal is to:• Develop a controlled vocabulary (ontology) that describes Develop a controlled vocabulary (ontology) that describes the crops, themes, traits, anatomical and morphological the crops, themes, traits, anatomical and morphological structures and growth and developmental stages etcstructures and growth and developmental stages etcstructures and growth and developmental stages, etc. structures and growth and developmental stages, etc.
•• To establish a semantic framework for meaningful crossTo establish a semantic framework for meaningful cross‐‐To establish a semantic framework for meaningful crossTo establish a semantic framework for meaningful crossspecies queries across crops, inventories and traits species queries across crops, inventories and traits (genotyping and phenotype datasets). (genotyping and phenotype datasets).
•• Describe crops, CWR and LR structures and entities and the Describe crops, CWR and LR structures and entities and the relationships between themrelationships between themrelationships between them. relationships between them.
Examples :P l ti it it h l l t ti f• Population, site, unit, whole plant, portion of plant tissue, vascular system, seedling growth, plant growth, leaf development stages embryo development stages flowerstages, embryo development stages, flower development stages, etc.
Ontology Curation tool GCP SampleOntology Curation tool ‐ GCP Sample
Demo
http://www.cropontology‐curationtool.org/
Special resources available
Curation & Annotation tool CWR descriptors (PGRFORUM and CWR UNEP project CWR descriptors (PGRFORUM and CWR UNEP project LR descriptors (developed under the ECPGR network) CWR ontologyCWR ontology Trait ontology Plant ontology Ex situ platform Etc…
To complement the special resources available need to establish:
PGRSECURE Crop ontology group Avena Brassica Beta Medicago CWR LR Links to Trait ontology
What we proposeD ft TIP tDraft TIP concept
• Database - Mongo, Google, …• Upload system – CSV, Template
driven (customized template driven (customized template options).
• Annotation tool- Use GCP curation/annotation tool for developing PGRSECURE
lontologies.• Data views – data types• Web-enabled (internal and external Web-enabled, (internal and external
links).
Will TIP be a part of or linked to these? How?
EURISCO, l ifi ECCDB (i Arelevant crop specific ECCDB (i.e., Avena,
Beta, Brassica and Medicago databases) EMBLCrop Wild Relative Information System (CWRIS) (http://www pgrforum org/cwris/cwris asp)(http://www.pgrforum.org/cwris/cwris.asp) CWRIS–AEGRO–Population Level Information System (PLIS) GENESYS (http:/www.genesys‐pgr.org )
This system has firstly to serve you, the data provider, so it can efficiently serve the users. Think about this we need your ideas and thoughts on it.
i ?OUR questions?1. Who will be hosting the TIP?1. Who will be hosting the TIP?2. How do you see the links? Are they just re‐directing the
users to other sources? 3. Or are the links providing direct access to further
information?4 Is the proposed concept what you looking for?4. Is the proposed concept what you looking for?5. What features besides the indicated ones
would be needed (take into account the (data types provided)?
6. Which data types should be downloadable? On which formats?
7. What data sources are missing?8 What kind of access to analysis tools is8. What kind of access to analysis tools is
needed?
ConclusionConclusionConclusionConclusion
At the end of this workshop should have have an At the end of this workshop should have have an ppunderstanding on:understanding on:Data types to be used?Data types to be used?ypypFeatures envisaged ?Features envisaged ?Meaning and relation of the links ?Meaning and relation of the links ?Meaning and relation of the links ?Meaning and relation of the links ?Hosting of the TIP?Hosting of the TIP?TIP general concept endorsedTIP general concept endorsedTIP general concept endorsed TIP general concept endorsed Ontology groups establishedOntology groups established
Feedback and guidance on the TIPFeedback and guidance on the TIP