AIMC Topic: Biological Ontologies

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A Neuro-ontology for the neurological examination.

BMC medical informatics and decision making
BACKGROUND: The use of clinical data in electronic health records for machine-learning or data analytics depends on the conversion of free text into machine-readable codes. We have examined the feasibility of capturing the neurological examination as...

Training a Convolutional Neural Network with Terminology Summarization Data Improves SNOMED CT Enrichment.

AMIA ... Annual Symposium proceedings. AMIA Symposium
As a step toward learning to automatically insert new concepts into a large biomedical ontology, we are studying the easier problem of automatically verifying that an IS-A link should exist between a new child concept and an existing parent concept. ...

FHIR OWL: Transforming OWL ontologies into FHIR terminology resources.

AMIA ... Annual Symposium proceedings. AMIA Symposium
The FHIR specification provides a mechanism to access clinical terminologies using a standard API, and many existing terminologies, such as SNOMED CT, are well supported. However, in areas such as genomics, terminologies from other domains are starti...

Bootstrapping Adversarial Learning of Biomedical Ontology Alignments.

AMIA ... Annual Symposium proceedings. AMIA Symposium
Learning how to automatically align biomedical ontologies has been a long-standing goal, given their ever-growing content and the many applications that rely on them. Because the knowledge graphs underlying biomedical ontologies enable neural learnin...

genoDraw: A Web Tool for Developing Pedigree Diagrams Using the Standardized Human Pedigree Nomenclature Integrated with Biomedical Vocabularies.

AMIA ... Annual Symposium proceedings. AMIA Symposium
The integration of genetic information in current clinical routine has raised a need for tools to exploit family genetic knowledge. On the clinical side, an application for managing and visualizing pedigree diagrams could provide genetics specialists...

Towards an ontology of cognitive processes and their neural substrates: A structural equation modeling approach.

PloS one
A key challenge in the field of cognitive neuroscience is to identify discriminable cognitive functions, and then map these functions to brain activity. In the current study, we set out to explore the relationships between performance arising from di...

Searching for the Big Pictures.

Perspectives on psychological science : a journal of the Association for Psychological Science
My goal in searching for the big pictures is to discover novel ways of organizing information in psychology that will have both theoretical and practical significance. The first section lists my reasons for writing each of five articles. The second s...

Combining lexical and context features for automatic ontology extension.

Journal of biomedical semantics
BACKGROUND: Ontologies are widely used across biology and biomedicine for the annotation of databases. Ontology development is often a manual, time-consuming, and expensive process. Automatic or semi-automatic identification of classes that can be ad...

Evolving knowledge graph similarity for supervised learning in complex biomedical domains.

BMC bioinformatics
BACKGROUND: In recent years, biomedical ontologies have become important for describing existing biological knowledge in the form of knowledge graphs. Data mining approaches that work with knowledge graphs have been proposed, but they are based on ve...

DNA is not an ontologically distinctive developmental cause.

Studies in history and philosophy of biological and biomedical sciences
In this article I critically evaluate the thesis that DNA is an ontologically distinctive developmental cause. I shall critically analyse different versions of the latter thesis by taking into consideration concrete developmental cases. I shall argue...