TeSS and Bioschemas

Niall Beard, Milo Thurston, Finn Bacall, Susanna-Assunta Sansone, Teresa Attwood, Carole Goble

FAIRDOM Webinar series2pm GMT - 19th January 2017

ELIXIR Platforms

+ Use Cases

ELIXIR: A (very) distributed infrastructure for Life science information

Institutions and organization providing training materials, courses, and eLearning

+ many, many, many more

Training discovery platform v0.0.1

Aka, Google it

Great discovery tool…

• If you know the specific name of the thing you’re looking for (e.g. ‘EuBIC Winter School’).

• Not so great if you just want to see what proteomics related events are available

The Long Tail of Training Resources

Number of websites

Volu

me

of m

ater

ials

Large institutions and repositories>30 training resourcesSignificant online presence

Smaller websites<30 training resourcesOften buried in search results

Quick TeSS Overview

• Aggregation and registration of training events and materials

• Tools to filter, search, and discover• Users can organize into packages and training workflows• Interlinking with other ELIXIR registries • ELIXIR Node ‘shop window’ view• https://tess.elixir-europe.org

TeSS Materials index page

Filter By:

Content ProviderScientific Topic ToolStandardsPoliciesTarget AudienceKeywordDifficulty LevelAuthorContributorLicenceELIXIR Node

Search for text and order results

Link to other resources (from ELIXIR registries and other)

Subscribe to calendar feeds

Embed in your sites using iAnn widget

Visual Workflows

• Developing workflows to represent typical data analyses.

• Attaching tools, training, and other resources to each stage.

Registry integration

• Associate TeSS resources with bio.tools and Biosharing.org resources.

• Search for all training materials about a specific tool, standard operating procedure, database etc.

• Tool-centric search

TeSS summary

• Aggregated training portal with functions:• Search and Filter

• Training workflows

• Subscription services

• iAnn events widgets

• Integration with bio.tools and biosharing.org

• ELIXIR node views

• Upcoming:• More curation tools

• Collaboration with BD2Ks training portal

• More integrations with other information services

Aggregation – Not a very API situation

Medium/Small sites - Manual entry

HTML scraper

• Difficult to write. • - Every site is unique• - Some have more treacherous HTML • Very susceptible to change• - Fixing is re-implementing. • - Build up of technical debt

http://cdn2.bigcommerce.com/server100/367cc/products/46401/images/183293/Super_Scraper__13402.1360690411.1280.1280.jpg?c=2

<p>Mon, 27 Feb 2017, 12:00 –</p>

Enter: Schema.org

Metadata modelie. Recipe type

<div itemscope itemtype="http://schema.org/Recipe">

<div itemprop="nutrition” itemscopeitemtype="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> . . .

<script type="application/ld+json">{ "@context": "http://schema.org", "@type": ”Recipe", "name": ”Potato Salad", “NutritionInformation”: {

"calories”: “144 kcal”, "recipeIngredient”: “800g small new potato”, "recipeIngredient”: “3 shallot”. . .

Tools to parse

Tools to parse

Mark up using schema.org – Google Markup Helper

Mark up using schema.org –Google Markup Helper

TeSS can then parse the schema.org structured data

Other ways

• By hand• By one of the many CMS extensions• Many online tools

What is Bioschemas• Developing schema.org

specifications to work for Life sciences

• Proposing amendments and new schemas to be able to describe Life science resources.

• Events and CreativeWork (materials). Also for tools, data, data repositories

Image: http://bioschemas.org/

Minimum informationControlled vocabularies

Cardinality

Data model

New properties

Bioschemas compliant

Bioschemas compliant

API

API

Special thanks to TeSS and Bioschemas’ collaborators, our guinea pigs, and community

TeSS TeamFinn BacallMilo ThurstonAleksandra NenadicSusanna-Assunta SansoneTeresa AttwoodCarole Goble+ Many more

Events/Training materials Bioschemas TeamRafael JiminezMartin CookPremysl VeselykAleksandra NenadicGabriella RusticiDominique Batista+ Many more

https://tess.elxir-europe.org and http://bioschemas.org