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ELIXIR TeSS And Bioschemas: An aggregated portal and an aggregation tool

Webinar by Niall Beard about the aggregated training platform TeSS, and the schema.org working group Bioschemas. The presentation describes the need for TeSS, many of it's features and a look into the difficulties aggregating ANY data online. We go on to the solution of using schema.org as a lightweight method for structuring data. This talk was for the FAIRDOM webinar series. A live recording of it can be found here>

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TeSS and Bioschemas
Niall Beard, Milo Thurston, Finn Bacall,
Susanna-Assunta Sansone, Teresa Attwood, Carole Goble
FAIRDOM Webinar series
2pm 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
Volumeofmaterials
Large institutions and repositories
>30 training resources
Significant online presence
Smaller websites
<30 training resources
Often 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 Provider
Scientific Topic
Tool
Standards
Policies
Target Audience
Keyword
Difficulty Level
Author
Contributor
Licence
ELIXIR 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/p
<p>Mon, 27 Feb 2017, 12:00 –</p>
Enter: Schema.org
Metadata model
ie. Recipe type
ELIXIR TeSS And Bioschemas: An aggregated portal and an aggregation tool
<div itemscope itemtype="http://schema.org/Recipe">
<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>
. . .
<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”
. . .
ELIXIR TeSS And Bioschemas: An aggregated portal and an aggregation tool
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 information
Controlled vocabula
Cardinality
Data model
New properties
Bioschemas
compliant
Bioschemas
compliant
API
API
Special thanks to TeSS and Bioschemas’
collaborators, our guinea pigs, and community
TeSS Team
Finn Bacall
Milo Thurston
Aleksandra Nenadic
Susanna-Assunta Sansone
Teresa Attwood
Carole Goble
+ Many more
Events/Training materials Bioschemas Team
Rafael Jiminez
Martin Cook
Premysl Veselyk
Aleksandra Nenadic
Gabriella Rustici
Dominique Batista
+ Many more
https://tess.elxir-europe.org and http://bioschemas.org

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ELIXIR TeSS And Bioschemas: An aggregated portal and an aggregation tool

  • 1. TeSS and Bioschemas Niall Beard, Milo Thurston, Finn Bacall, Susanna-Assunta Sansone, Teresa Attwood, Carole Goble FAIRDOM Webinar series 2pm GMT - 19th January 2017
  • 3. ELIXIR: A (very) distributed infrastructure for Life science information
  • 4. Institutions and organization providing training materials, courses, and eLearning + many, many, many more
  • 5. Training discovery platform v0.0.1 Aka, Google it
  • 6. 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
  • 7. The Long Tail of Training Resources Number of websites Volumeofmaterials Large institutions and repositories >30 training resources Significant online presence Smaller websites <30 training resources Often buried in search results
  • 8. 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
  • 9. TeSS Materials index page Filter By: Content Provider Scientific Topic Tool Standards Policies Target Audience Keyword Difficulty Level Author Contributor Licence ELIXIR Node Search for text and order results
  • 10. Link to other resources (from ELIXIR registries and other)
  • 12. Embed in your sites using iAnn widget
  • 13. Visual Workflows • Developing workflows to represent typical data analyses. • Attaching tools, training, and other resources to each stage.
  • 14. 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
  • 15. 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
  • 16. Aggregation – Not a very API situation
  • 18. 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/p <p>Mon, 27 Feb 2017, 12:00 –</p>
  • 22. <div itemscope itemtype="http://schema.org/Recipe"> <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> . . .
  • 23. <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” . . .
  • 27. Mark up using schema.org – Google Markup Helper
  • 28. Mark up using schema.org –Google Markup Helper
  • 29. TeSS can then parse the schema.org structured data
  • 30. Other ways •By hand •By one of the many CMS extensions •Many online tools
  • 31. 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/
  • 34. Special thanks to TeSS and Bioschemas’ collaborators, our guinea pigs, and community TeSS Team Finn Bacall Milo Thurston Aleksandra Nenadic Susanna-Assunta Sansone Teresa Attwood Carole Goble + Many more Events/Training materials Bioschemas Team Rafael Jiminez Martin Cook Premysl Veselyk Aleksandra Nenadic Gabriella Rustici Dominique Batista + Many more https://tess.elxir-europe.org and http://bioschemas.org

Editor's Notes

  1. ELIXIR is a pan-european infrastructure for life science information. Broadly, it’s goals are to comprising of 22 national nodes, plus a node for the EBI, and a special Hub node that aims to help connect and provide support for nodes. Like a spoke and hub system. Each node has many institutions associated with them, there are over 100 altogether which yield a complicated distributed architecture. Resources are being produced in each institution or across a selection of institutions in huge quantities. Tools, training, compute infrastructure, datasets etc. all exist on heterogenous collections of websites. Some in global repositories, some on country wide repositories, some on institutional, some on personal. There’s humongous diversity in the landscape these resources. ELIXIR hopes to aggregate and present uniformly distriibuted resources in order to improve their findability. The oft-cited FAIR Principles states guidelines for data stewardship should be Findable Accessible Interoperable and Reproducible. As such ELIXIR attempts to improve findabiity through discovery portals. And as you’ll see, certainly keep the AIR in mind. --0
  2. New providers and developments of old ones - each a unique challenge Proud to collect so many 500 Materials + 120 upcoming events + 4 thousand archived, looking forward to collecting more
  3. Distributed Research Infrastrtucture. Developing training opportunities across 20+ member nodes Collect and harmonize. Feture rich environment. Connected outwardly to complimentary projects. Promote ELIXIR nodes and keep access to data open to be utilized
  4. Once we have the data in TeSS we can implement novel and useful features. Subscription service for example. Plans to extend this to a subscription service – input twitter, email and other social media handles and receive notifcations as and when other events that meet your criteria appear.
  5. Navigational tools. Give context to training materials in real scientific processes. Agile dev so no complete, but we have a usable iteration. Hosting workshop in UK before March next year. Create content and review mechanism. Details to be announced. Implementation study for training workflows. Prioritised by training platform, waiting on tools platform. Led by Frederick Coppens from Belgium very capable guy
  6. Important to connect with other ELIXIR data with Biotools and Biosharing can improve usefulness of content
  7. Collection of schemas can be used to describe online objects
  8. Plugin to the Bioschemas spec development activities Driving events and training specifications. Prime example for other specifications. Slower going pathing the way but lots of good lessons for future implementations. Early on would write HTML scrapers if necessary. Now drawing a strong line under that. In last resort situations it will be put on the issue tracker with low priority. Development resources too expensive and maintenance is practically - repeat.