RDA Wheat Data Interoperability Cookbook and last developments
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The document outlines the goals and progress of a working group aimed at improving data interoperability in wheat science, focusing on creating a common framework for metadata, formats, and vocabularies. It details deliverables such as a survey report, a cookbook for data managers, and a library of linked vocabularies, while also addressing various challenges in data standardization and quality control. Future steps include refining guidelines, developing a semantic knowledge base, and enhancing metadata harmonization.
RDA Wheat Data Interoperability Cookbook and last developments
- 1. RDA Wheat Data Interoperability Cookbook and last developments 9th March 2015, San Diego
- 2. 2 The WDI working group in brief Endorsement: March 2014 Members: ~=30 members and 15 active members, Wheat scientists, data and metadata technologists The goal: contribute to the improvement of Wheat related data interoperability by Building a common interoperability framework (metadata, data formats and vocabularies) Providing guidelines for describing, representing and linking Wheat related data
- 3. 3 Deliverables A report of the survey of existing standards A cookbook intended for the Wheat data managers community, which provides them with guidelines on what data formats, metadata, vocabularies and ontologies they should use to describe, represent and link different types of Wheat data. A library of linked vocabularies and ontologies in machine readable formats with respect to the Linked Data standards. A prototype which showcases the gain of interoperability Initial plans
- 5. 5 Data type Data formats currently used Recommendations Standardized Tool specific Non standardized SNPs VCF BAM/SAM, BED, VARSCAN, VEP VCF files generated by using the survey sequences of IWGSC + metadata about VCF files to enrich the information about the SNPs. genome annotations Genbank Flat File, General Feature Format (GFF), EMBL GFF 3 + specifications with regard the description of specific columns Germplasms MPCD, ABCD, Darwin Core, Darwin Core Germplasm Grin Global tabulated MPCD Gene expression Many format standards laid out by repositories such as NCBI (GEO) and EBI Array Express Existing format standards laid out by the repositories such as NCBI (GEO) and EBI Array Express + ENA Physical maps GFF Cmap, fpc GFF3 Genetic maps Cmap, gnpmap GFF3 (to be confirmed) Phenotypes Drops, ped, isa- tab, ephesis tabulated Isa-tab
- 6. 6 Examples of use cases Title Searching for germplasm with specific traits Description Example of searching for germplasm with specific traits - tagged with ontology terms? Data types Germplasm Phenotype Challenges ● Metadata very important ~ standardized format ● Association of genes to traits, linked to germplasm, marker information ● Need for quality controls- how confident are you of the data source? ● Provenance of the germplasm- pedigree, ownership, ● Standard system for tracking germplasm, names Title Identification of wheat genes that control root growth Description Requires: Annotated genes (Gene Ontology, PFam, and other functional annotation) Data types Genomic annotations? - Gene location ? (IWGS-SS ID or MIPS HCS link) Challenges Mapping between wheat genes and orthologs from other species (deduce function by seq. similarity); Access to RNASeq data (genes that are not expressed in roots may be irrelevant) ; mapping of wheat genes and information on their function based on literature Title Query on trial data associated with varieties Data types Phenotypic data, GIS data, (wheat economy/production data) Description To search wheat varieties with distribution maps, production figures, performances in wheat mega environments, associated projects worldwide plus layers of climatic data on specific wheat production areas and disease prevention information. Challenges Phenotypic data should be linked to GIS data. Using keywords or ontology terms a system or a tool should be able to pull out such information from different websites/systems developed by wheat community.
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- 8. 8 Assess the level of visibility and interoperability of Wheat related vocabularies and ontologies Is the vocabulary/ontology updated regularly? What license and/or copyright is used? Is the vocabulary/ontology part of any ontology communities or listing services? Is the vocabulary/ontology used or implemented in any database/repository? Does the vocabulary/ontology interlink and/or map to other vocabularies and ontologies? Does the vocabulary/ontology Identify the domain covered by the ontologies and vocabularies Refine the cookbook Collect more interoperability use cases Collect some technical details Wheat related ontologies & vocabularies survey
- 9. 9 Wheat related ontologies & vocabularies survey
- 10. The Wheat related BioPortal allows one to search for terms across multiple ontologies, browse mappings between terms in different ontologies, receive recommendations on which ontologies are most relevant for a corpus, annotate text with terms from ontologies
- 11. 11 Next steps Metadata (harmonization, minimal metadata sets) Mappings Next workshop (summer 2015) Review and complete the recommendations Refine and complete the guidelines and the best practices Finalize the repository of Wheat related vocabularies Prototyping: a semantic knowledge base Integrate data from different data sources Provide smart search capabilities that leverage the vocabularies used against the metadata.
- 12. 12 Thank you!