Building a resource sharing site with BioThings SDK and the CD2H Data Discovery Engine (part 3)

by Ginger Tsueng

Although there has been a proliferation of biological  datasets made available in recent years, often this information isn’t  machine readable, making it hard for things like Google Dataset Search to find and index them. In this series of blog posts, we’ll outline how  we are working to make datasets that our collaborators generate and  open data more findable, accessible, interoperable, and reusable, as  well as tools that we’ve developed to make it easier to share data. In this post we introduce the schema playground in the Data Discovery Engine and how to use it.

What is the Data Discovery Engine, and how can it help you leverage schemas?

The schema playground in the Data Discovery Engine allows you to  create a new schema (or data type) from existing schemas.  Schemas  generated with the Data Discovery Engine are so  that search engines will know how to interpret them, and they are  presented in an easy-to-use interface. (For more about schemas, check out our previous post)

When you first visit the schema playground in the Data Discovery  Engine, you’ll see that there are three ways to get started on creating  or using a schema.

schema playground screenshot

If you have worked with schemas before and are familiar with them–you  may prefer to just create them on your own.  In this case, you would  select the first option, ‘visualize schema’.  This option allows you to  visualize a pre-existing schema as long as the raw .json is available  online.  This includes .json schema files in repositories like GitHub.

The visualize schema function is handy for identifying errors in your  schema and will help check to ensure your schema is valid.  It includes  a built-in json schema validator, just like other json-schema  validators like the Json schema validator; only it will allow you easily visualize your schema AFTER your schema has been found to be valid.

That is, if you visualize a valid schema, you will be able to easily view the schema, related schemas, and properties.

On the complete other hand, if you don’t want anything to do with the  creation of a schema, you can try searching the schema registry (the  ‘search registry’ option) for a pre-existing schema to use.  Schemas  that are created and registered by other people to suit their specific  needs are included as well as all schemas from  Before you  go through the effort of creating a schema, we recommend that you search  the registry to see if one that suits your needs already exists and  save yourself the effort.  Using a pre-existing schema has the added  benefit of helping to standardize the use of that schema.

If you’re unable to find a schema that suits your needs, you can use  the middle option (‘create schema’) to create a new schema by  extending/manipulating a pre-existing schema.  In this case, you would  find a schema that most closely resembles what you need, and then extend  it to fit your needs.

schema playground screenshot

Note that some parts of the schema playground in the Data Discovery  Engine require a login to proceed.  The login requirements can be  satisfied using your github credentials.

Once you’ve successfully created a valid schema, you are encouraged  to register it.  When you register a schema, you share your schema  allowing other researchers with similar data to use your schema.  This  helps to improve metadata standardization, interoperability, findability, and reuse.

To share datasets on Ebola and Lassa Fever created by the Center for Viral Systems Biology, we developed a general biological Dataset schema using the Data Discovery Engine.  Working off of the Dataset  schema, we identified a small subset of properties that we thought are  essential to describe a dataset, and added properties that are unique to  infectious disease research, like infectiousAgent.  Working off of the  existing framework both saved us time and allows these  datasets to be compliant with data sharing projects like Google Dataset  Search.

Since this Dataset schema was registered and shared, when the  COVID-19 pandemic started, the team was able to quickly  adapt it to provide a standardized searchable interface of COVID-19  resources.  In addition to recycling the Dataset schema we already  developed, we identified a number of pre-existing schemas to adapt and  modify to cover additional resource types.  We expanded this NIAID  Dataset schema to also harmonize Analyses, Publications, Clinical  Trials, and Protocols from disparate sources.  Having these schemas  meant that the metadata for these resources could be parsed, normalized,  and made more findable for search engines.  The resulting schema can be used as the basis for other projects as well.

Now that we’ve invested so much time in creating standardized  metadata to describe datasets and other resources, the next step is to  easily access all this information. If you’re a researcher, sometimes  you’d prefer to access information in bulk–and for that you’d need an  Application Programmable Interface (or API).

Fortunately, for the team, the Wu and Su labs have a  lot of experience building APIs and already have a tool available for  spinning up RESTful APIs quickly: The BioThings Software Development Kit (SDK).  In the next post, we’ll describe how we used these tools to quickly create an API to access metadata on COVID-19 resources.