Sentient Solutions

Integrated, interdisciplinary science requires a new approach to managing data. Relational databases and even modern “federated” approaches to integration still dump data into boxes. In these systems, the format in which data is stored dictates how data gets accessed, used, and shared.

To help researchers ask questions that bridge disciplinary boundaries, IO Informatics has developed software that lets users think outside the boxes into which their organizations place data. The Sentient Suite puts the focus on the data itself—on the specific attributes and associations that make one piece of data unique and connect it to other types of data. The innovation is the intelligent multidimensional object (IMO), a portable database record.

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How It Works
A portable database record is analogous to the ubiquitous PDF. The portable document format takes the product of any application and, in a simple, post-processing step, converts the file into an “open” format that can be shared free of its original home application.

The PDF’s ability to preserve a document’s formatting and appearance outside of a single application has revolutionized the way information is published and disseminated. But when PDFs were introduced in the early 1990s, many were skeptical. The questions asked then are analogous to those that can be asked about IMO conversion:

  • Why would someone need to convert a file into a PDF?
  • What would be the advantage of viewing a document outside of its home application?
  • Don’t users want the full functionality of the home application when working with a file?

As many database providers have argued for years, users don’t care where data resides. They also don’t care about the data’s format. What they do care about is what the data means to their work and how it relates to other data.

Like a PDF, an IMO involves a conversion. But IMO conversion happens in a preprocessing step that transforms a specific data type into a freeform relational object. By pointing and clicking, users can create IMOs or specify subsets of data contained within IMOs that can in turn be linked to other IMOs. Like a Windows “Shortcut” (only much more sophisticated), IMOs point to data, defining and characterizing it from an individual user’s point of view or knowledge context. The original data remains intact, housed securely in the box into which it has been put. IMOs, however, can reside anywhere, be opened anywhere, and define anything—a single data value captured from a larger dataset, an entire spreadsheet, images and unstructured data, or the results of a search query.

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How IMOs Help Researchers
IMOs enable users to build and represent data relationships, or associations, at multiple levels of detail. Associations let researchers

  • Link data at project and document levels
  • Drill down to explore the fine-grained details and relationships within and across data
  • Define, model and search for real-world interactions indicated by specific data (such as reaction pathways, gene/protein function, or clinical events and observations)
  • Compare original data and information to external sources of knowledge about the same or similar data

Researchers build associations in Sentient through:

  • Attributes, which associate data according to its relationship or position within a predefined ontology, or area of interest. “This data looks like this and belongs in this area.”
  • Attachments, which associate data directly to other IMO level data and queries. “This data goes along with this data.”
  • Annotations, which associate data via links to analytical content subsets created by users. “I’ve analyzed this data, and I think this particular feature is interesting or important.”
  • Subset Linkages, which associate content subsets to other content subsets within IMOs. “I’ve analyzed this data, and I have found that the particular subset feature that I’ve noted here is explained by or influences something in this data over here.”
  • Queries, which identify and retrieve similar, covariant, manually or otherwise semantically associated objects. “I’m interested in all of the data related to this particular feature.”

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Sentient Suite: Making Semantics Work
Through associations, researchers endow data with meaning. Another term for parsing these connections between data is semantics. Many are championing open, semantic formats as the next stage in data management. But these semantic systems are proving difficult to implement even by knowledgeable IT staffs. Ultimately, users are the ones that must be able to create and interpret the connections between data. Without standards to support user-driven interpretations, meaning is lost.

IO Informatics is making semantics meaningful outside IT departments by providing a software environment that lets domain experts, rather than software programmers, create and compare connections between all the data sources relevant to their research. The Sentient Suite offers interactive tools, search capabilities, and security features that turn the basic distillation capabilities of the IMO into a usable, actionable service. With Sentient, users can point and click to build IMOs that describe data properties, such as nodes, edges, and pathways in data that were once accessible only to computer researchers. With Sentient, organizations can help researchers

  • Structure and define data relationships
  • Gain insights by viewing and querying these data relationships and contextualizing data within broader organizational knowledge
  • Comply with regulatory requirements through a secure, auditable framework
  • Accumulate valuable intellectual property—not just data, but researchers’ ideas about that data

Just as the PDF has not replaced but instead adds value to existing applications, Sentient and the fundamental IMO format do not disrupt or alter an organization’s existing data infrastructure. By “IMO-izing” data, users can turn any collection of databases and application files into a rich, fluid data pool—the Sentient iPool. An organization’s underlying data remains intact, safely stored in whichever box it resides. Sentient simply enables users to think outside of those boxes.

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