Ontology of core data mining entities

In this article, we present OntoDM-core, an ontology of core data mining entities. OntoDM-core defines themost essential datamining entities in a three-layered ontological structure comprising of a specification, an implementation and an application layer. It provides a representational framework for the description of mining structured data, and in addition provides taxonomies of datasets, data mining tasks, generalizations, data mining algorithms and constraints, based on the type of data. OntoDM-core is designed to support a wide range of applications/use cases, such as semantic annotation of data mining algorithms, datasets and results; annotation of QSAR studies in the context of drug discovery investigations; and disambiguation of terms in text mining. The ontology has been thoroughly assessed following the practices in ontology engineering, is fully interoperable with many domain resources and is easy to extend

An Object-Oriented Approach to Knowledge Representation in a Biomedical Domain

An object-oriented approach has been applied to the different stages involved in developing a knowledge base about insulin metabolism. At an early stage the separation of terminological and assertional knowledge was made. The terminological component was developed by medical experts and represented in CORE. An object-oriented knowledge acquisition process was applied to the assertional knowledge. A frame description is proposed which includes features like states and events, inheritance and collaboration. States and events are formalized with qualitative calculus. The terminological knowledge was very useful in the development of the assertional component. It assisteed in understanding the problem domain, and in the implementation stage, it assisted in building good inheritance hierarchies

Tribally-Driven Participatory Research: State of the practice and potential strategies for the future

This paper discusses current practice of research with and by American Indian tribal governments in the United States. It begins with a brief overview of Community-Based Participatory Research and compares and contrasts its principles and methods with what this paper terms Tribally-Driven Participatory Research. The paper analyzes current challenges and offers concepts for continuing to improve the effectiveness of Tribally-Driven Participatory Research

Implementing a Portable Clinical NLP System with a Common Data Model - a Lisp Perspective

This paper presents a Lisp architecture for a portable NLP system, termed LAPNLP, for processing clinical notes. LAPNLP integrates multiple standard, customized and in-house developed NLP tools. Our system facilitates portability across different institutions and data systems by incorporating an enriched Common Data Model (CDM) to standardize necessary data elements. It utilizes UMLS to perform domain adaptation when integrating generic domain NLP tools. It also features stand-off annotations that are specified by positional reference to the original document. We built an interval tree based search engine to efficiently query and retrieve the stand-off annotations by specifying positional requirements. We also developed a utility to convert an inline annotation format to stand-off annotations to enable the reuse of clinical text datasets with inline annotations. We experimented with our system on several NLP facilitated tasks including computational phenotyping for lymphoma patients and semantic relation extraction for clinical notes. These experiments showcased the broader applicability and utility of LAPNLP.Comment: 6 pages, accepted by IEEE BIBM 2018 as regular pape

A Human Capital Approach to Reduce Health Disparities

Objective: To introduce a human capital approach to reduce health disparities in South Carolina by increasing the number and quality of trained minority professionals in public health practice and research. Methods: The conceptual basis and elements of Project EXPORT in South Carolina are described. Project EXPORT is a community based participatory research (CBPR) translational project designed to build human capital in public health practice and research. This project involves Claflin University (CU), a Historically Black College University (HBCU) and the African American community of Orangeburg, South Carolina to reduce health disparities, utilizing resources from the University of South Carolina (USC), a level 1 research institution to build expertise at a minority serving institution. The elements of Project EXPORT were created to advance the science base of disparities reduction, increase trained minority researchers, and engage the African American community at all stages of research. Conclusion: Building upon past collaborations between HBCU’s in South Carolina and USC, this project holds promise for a public health human capital approach to reduce health disparities

The development of non-coding RNA ontology

Identification of non-coding RNAs (ncRNAs) has been significantly improved over the past decade. On the other hand, semantic annotation of ncRNA data is facing critical challenges due to the lack of a comprehensive ontology to serve as common data elements and data exchange standards in the field. We developed the Non-Coding RNA Ontology (NCRO) to handle this situation. By providing a formally defined ncRNA controlled vocabulary, the NCRO aims to fill a specific and highly needed niche in semantic annotation of large amounts of ncRNA biological and clinical data

The Cognitive Atlas: Employing Interaction Design Processes to Facilitate Collaborative Ontology Creation

The Cognitive Atlas is a collaborative knowledge-building project that aims to develop an ontology that characterizes the current conceptual framework among researchers in cognitive science and neuroscience. The project objectives from the beginning focused on usability, simplicity, and utility for end users. Support for Semantic Web technologies was also a priority in order to support interoperability with other neuroscience projects and knowledge bases. Current off-the-shelf semantic web or semantic wiki technologies, however, do not often lend themselves to simple user interaction designs for non-technical researchers and practitioners; the abstract nature and complexity of these systems acts as point of friction for user interaction, inhibiting usability and utility. Instead, we take an alternate interaction design approach driven by user centered design processes rather than a base set of semantic technologies. This paper reviews the initial two rounds of design and development of the Cognitive Atlas system, including interactive design decisions and their implementation as guided by current industry practices for the development of complex interactive systems

A Hands-On, Active Learning Approach to Increasing Manufacturing Knowledge in Engineering Students

This paper describes a new learning module implemented as part of the senior capstone design course at Marquette University to teach engineering students about basic manufacturing processes, lean manufacturing principles, and design for manufacturability. The module includes several examples of active and student centered learning as part of an in-class assembly line simulation exercise. Students reflected on this experience, and suggested process improvements to save time, reduce cost and waste, and improve the assembly line process. They learned of the importance of manufacturing documentation, process design, and design for assembly. At the end of the module, students understood the importance of designing a product not only for the end user, but also for the assemblers and inspectors. Details of the module design and implementation will be presented along with comments from students

Bioinformatics advances in saliva diagnostics

There is a need recognized by the National Institute of Dental & Craniofacial Research and the National Cancer Institute to advance basic, translational and clinical saliva research. The goal of the Salivaomics Knowledge Base (SKB) is to create a data management system and web resource constructed to support human salivaomics research. To maximize the utility of the SKB for retrieval, integration and analysis of data, we have developed the Saliva Ontology and SDxMart. This article reviews the informatics advances in saliva diagnostics made possible by the Saliva Ontology and SDxMart