Successfully reported this slideshow.
We use your LinkedIn profile and activity data to personalize ads and to show you more relevant ads. You can change your ad preferences anytime.

OSFair2017 Workshop | Bioschemas

87 views

Published on

Carole Goble presents the Bioschemas | OSFair2017 Workshop

Workshop title: How FAIR friendly is your data catalogue?

Workshop overview:
This workshop will build upon the work planned by the EOSCpilot data interoperability task and the BlueBridge workshop held on April 3 at the RDA meeting. We will investigate common mechanisms for interoperation of data catalogues that preserve established community standards, norms and resources, while simplifying the process of being/becoming FAIR. Can we have a simple interoperability architecture based on a common set of metadata types? What are the minimum metadata requirements to expose FAIR data to EOSC services and EOSC users?

DAY 3 - PARALLEL SESSION 6 & 7

Published in: Science
  • Be the first to comment

  • Be the first to like this

OSFair2017 Workshop | Bioschemas

  1. 1. Rafael Jimenez Norman Morrison ELIXIR Hub Hinxton Genome Campus Representing the Bioschemas.org Community carole.goble@manchester.ac.uk Carole Goble* Niall Beard* Alasdair Gray+ ELIXIR UK *The University of Manchester + Heriot-Watt University
  2. 2. The FAIR Guiding Principles for scientific data management and stewardship https://www.nature.com/articles/sdata201618 (2016) Catalogues Aggregators Search
  3. 3. Structured data markup for web pages Schema.org adds simple structured metadata markup to web pages & sitemaps for harvesting, search and summary snippet making. Search engines often highlight websites containing Schema.org Widespread commercial and open source infrastructure creates a low barrier to adoption
  4. 4. <div itemscope itemtype="http://schema.org/Recipe"> <h1 itemprop="name">Classic potato salad</h1> <div itemprop="nutrition” itemscope itemtype="http://schema.org/NutritionInformation"> Nutrition facts: <span itemprop="calories">144 kcal</span>, </div> Ingredients: - <span itemprop="recipeIngredient">800g small new potato</span> - <span itemprop="recipeIngredient">3 shallot</span> . . . Structured data markup for web pages RDFa JSON-LD Microdata With markup
  5. 5. From Potato Salad to Protein Annotation "taxon": "http://www.uniprot.org/taxonomy/9606", "alternateName": [ { "@language": "en", "@value": "ABL1_HUMAN" }, { "@language": "en", "@value": "Proto-oncogene c-Abl" } ], "description": { "@language": "en", "@value": "Non-receptor tyrosine-protein kinase that plays a role..." }, "identifier": "http://www.identifiers.org/uniprot/P00519", { "@context": "http://schema.org", "@type": "BiologicalEntity", "@id": "http://www.identifiers.org/uniprot/P00519 ", "biologicalType": "protein", "isMentionedIn": { "@type": "Dataset", "@id": "http://www.uniprot.org/news/2017/03/15/re lease" }, "associatedDisease": { "@type": "MedicalCondition", "@id": "http://www.omim.org/entry/608232", "name": "Leukemia, chronic myeloid (CML)", "code": { "@type": "MedicalCode", "code": "608232", "codingSystem": "OMIM" }, "sameAs": "http://www.uniprot.org/diseases/DI-03735" }, "biocoordinates": { "@type": "QuantitativeValue", "value": "1130" },
  6. 6. Bioschemas.org Data repository Data repository Training Resource Bioschemas Bioschemas Bioschemas Search engines Registries Data Aggregators Major datasets Smaller datasets• Standardised metadata • Feed bio registries and aggregators • Metadata publish and harvest without APIs or special feeds • Commodity • Off the Shelf tools • App eco-system A community initiative built on top of Schemas.org to improve Findability and Accessibility in Life Sciences • Rapid markup • Exposed to harvesting • Find
  7. 7. Bioschemas.org Data repository Data repository Training Resource Bioschemas Bioschemas Bioschemas Search engines Registries Data Aggregators A community initiative built on top of Schemas.org to improve Findability and Accessibility in Life Sciences
  8. 8. First specifications target: • Bio data infrastructure • Repositories • Datasets • Bio data types • Human beacons • Samples • Plant Phenotypes • Proteins … • Bio stuff • Training materials • Events • Laboratory protocols • Workflows andTools Life Sciences Bioschemas.org A community initiative built on top of Schemas.org to improve Findability and Accessibility in Life Sciences Tools!!! Specialist validators Data providers and consumers onboard Notably EMBL-EBI
  9. 9. Data Repository and Datasets Descriptions Information about repositories with consistent structured data Align overlapping registry efforts around certain metadata. Help with consistency of metadata collected by registries With: omicsDI Bioschemas.org
  10. 10. Restrictions Constraints Extensions Restrictions: the few concepts to minimally describe an entity Constraints: cardinalities, controlled vocabularies Extensions: new properties and new types, e.g. BiologicalEntity Bioschemas.org Adapts Schema.org
  11. 11. Bioschemas.org Who and How? First draft specs are out. ELIXIR Adoptors meeting , 2-4 Oct 201, EOSCpilot meeting, 4-5 Oct 2017 Hinxton Genome Campus, EMBL-EBI Sponsors Supporters Inclusion in Schema.org proposed for early 2018. Additional contributors include: Special thanks to: Dan Brickley, Schema.org & Google Inc Natash Noy, Google Inc Ian Fore, NIH

×