The Bioschemas community (http://bioschemas.org) is a loose collaboration formed by a wide range of life science resource providers and informaticians. The community is developing profiles over Schema.org to enable life science resources such as data about a specific protein, sample, or training event, to be more discoverable on the web. While the content of well-known resources such as Uniprot (for protein data) are easily discoverable, there is a long tail of specialist resources that would benefit from embedding Schema.org markup in a standardised approach.
The community have developed twelve profiles for specific types of life science resources (http://bioschemas.org/specifications/), with another six at an early draft stage. For each profile, a set of use cases have been identified. These typically focus on search, but several facilitate lightweight data exchange to support data aggregators such as Identifiers.org, FAIRsharing.org, and BioSamples. The next stage of the development of a profile consists of mapping the terms used in the use cases to existing properties in Schema.org and domain ontologies. The properties are then prioritised in order to support the use cases, with a minimal set of about six properties identified, along with a larger set of recommended and optional properties. For each property, an expected cardinality is defined and where appropriate, object values are specified from controlled vocabularies. Before a profile is finalised, it must first be demonstrated that resources can deploy the markup.
In this talk, we will outline the progress that has been made by the Bioschemas Community in a single year through three hackathon events. We will discuss the processes followed by the Bioschemas Community to foster collaboration, and highlight the benefits and drawbacks of using open Google documents and spreadsheets to support the community develop the profiles. We will conclude by summarising future opportunities and directions for the community.
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Bioschemas community: Developing profiles over Schema.org to make life sciences resources more findable
1. Alasdair J G Gray
Heriot-Watt University
Bioschemas Community
http://bioschemas.org/people/
Bioschemas Community:
Developing profiles over Schema.org
to make life sciences resources
more findable
2. 30 April 2018 #bioschemas 2
<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>
Schema.org: markup for web pages
RDFa
JSON-LD
Microdata
With markup
4. Bioschemas
• Schema.org for life sciences
–Introduce life sciences types
• Use case driven
–Finding data
–Presenting search results
–Metadata exchange
• Minimum properties – 6
• Link to domain ontologies
Specification on top of schema.org
Layer of constrains + documentation +
extensions Specification
Data model
Minimum information
Controlled vocabularies
Cardinality
Documentation
Examples
New (properties | types)
30 April 2018 #bioschemas 4
Machine interpretable
This example is with Microdata
Currently no rich search results
Would like something more like this
Define use case
Metadata crosswalk and mapping to schema.org
Metadata providers
Metadata registries
Standards defining metadata
Bioschemas specification
Define minimum properties based on “finding” use cases
Define cardinality and suggested controlled vocabularies
Test with existing entries
Adoption by data repositories and registries
Applications
Beacon
Data Catalog
Dataset
Event
Laboratory Protocol
Organization
Person
Phenotype
Protein
Protein Annotation
Protein Structure
Sample
Standard
Tool
Training Material