Leveraging Open Electronic Health Record Data and Environmental Exposures Data to Derive Insights Into Rare Pulmonary Disease.

Research on rare diseases has received increasing attention, in part due to the realized profitability of orphan drugs. Biomedical informatics holds promise in accelerating translational research on rare disease, yet challenges remain, including the lack of diagnostic codes for rare diseases and privacy concerns that prevent research access to electronic health records when few patients exist. The Integrated Clinical and Environmental Exposures Service (ICEES) provides regulatory-compliant open access to electronic health record data that have been integrated with environmental exposures data, as well as analytic tools to explore the integrated data.

A Biomedical Knowledge Graph System to Propose Mechanistic Hypotheses for Real-World Environmental Health Observations: Cohort Study and Informatics Application.

Background: Knowledge graphs are a common form of knowledge representation in biomedicine and many other fields. We developed an open biomedical knowledge graph-based system termed Reasoning Over Biomedical Objects linked in Knowledge Oriented Pathways (ROBOKOP). ROBOKOP consists of both a front-end user interface and a back-end knowledge graph.

Visualization Environment for Federated Knowledge Graphs: Development of an Interactive Biomedical Query Language and Web Application Interface.

Background: Efforts are underway to semantically integrate large biomedical knowledge graphs using common upper-level ontologies to federate graph-oriented application programming interfaces (APIs) to the data. However, federation poses several challenges, including query routing to appropriate knowledge sources, generation and evaluation of answer subsets, semantic merger of those answer subsets, and visualization and exploration of results.

Objective: We aimed to develop an interactive environment for query, visualization, and deep exploration of federated knowledge graphs.

Clinical Annotation Research Kit (CLARK): Computable Phenotyping Using Machine Learning.

Computable phenotypes are algorithms that translate clinical features into code that can be run against electronic health record (EHR) data to define patient cohorts. However, computable phenotypes that only make use of structured EHR data do not capture the full richness of a patient's medical record. While natural language processing (NLP) methods have shown success in extracting clinical features from text, the use of such tools has generally been limited to research groups with substantial NLP expertise.

ROBOKOP KG and KGB: Integrated Knowledge Graphs from Federated Sources.

A proliferation of data sources has led to the notional existence of an implicit Knowledge Graph (KG) that contains vast amounts of biological knowledge contributed by distributed Application Programming Interfaces (APIs). However, challenges arise when integrating data across multiple APIs due to incompatible semantic types, identifier schemes, and data formats. We present ROBOKOP KG ( http://robokopkg.

ROBOKOP: an abstraction layer and user interface for knowledge graphs to support question answering.

Summary: Knowledge graphs (KGs) are quickly becoming a common-place tool for storing relationships between entities from which higher-level reasoning can be conducted. KGs are typically stored in a graph-database format, and graph-database queries can be used to answer questions of interest that have been posed by users such as biomedical researchers. For simple queries, the inclusion of direct connections in the KG and the storage and analysis of query results are straightforward; however, for complex queries, these capabilities become exponentially more challenging with each increase in complexity of the query.

The impact of time on seizure prediction performance in the FSPEEG database.

We demonstrate evidence that high discriminability between preictal and interictal intracranial electroencephalogram (iEEG) recordings [1,2] of the Freiburg database (FSPEEG) may be due to the amount of time that occurred between recordings, as opposed to the underlying seizure state, i.e., preictal or interictal.

Moving Away From Error-Related Potentials to Achieve Spelling Correction in P300 Spellers.

P300 spellers can provide a means of communication for individuals with severe neuromuscular limitations. However, its use as an effective communication tool is reliant on high P300 classification accuracies ( > 70%) to account for error revisions. Error-related potentials (ErrP), which are changes in EEG potentials when a person is aware of or perceives erroneous behavior or feedback, have been proposed as inputs to drive corrective mechanisms that veto erroneous actions by BCI systems.

Projected accuracy metric for the P300 Speller.

The P300 Speller brain-computer interface (BCI) is a virtual keyboard that allows users to type without requiring neuromuscular control. P300 Speller research commonly aims to improve the system accuracy, which is typically estimated by spelling a small number of characters and calculating the percent spelled correctly. In this paper we introduce a new method for estimating the long-term ("projected") accuracy, which utilizes all available flash data and a probabilistic model of the Speller system to produce an estimate with lower variance and lower granularity than the standard measure.

Mandarin Chinese tone identification in cochlear implants: predictions from acoustic models.

It has been established that current cochlear implants do not supply adequate spectral information for perception of tonal languages. Comprehension of a tonal language, such as Mandarin Chinese, requires recognition of lexical tones. New strategies of cochlear stimulation such as variable stimulation rate and current steering may provide the means of delivering more spectral information and thus may provide the auditory fine-structure required for tone recognition.