NIDM-Experiment: A Controlled Vocabulary for Annotating Neuroscience-related Datasets
Presenting author:
Introduction:
Data annotation is important in the application of the FAIR[1] principles. NIDM-Experiment provides a rich set of defined terms that covers all aspects of neuroscience-related experiments. The goal of NIDM-Experiment is to provide an expandable basis set of terms that can be used by annotation tools.
Methods:
NIDM-Experiment was developed by referring to existing datasets and determining the terms needed to annotate them. New terms were only added if existing terms did not exist in existing Bioportal[2] ontologies or existing terms had incompatible definitions. NIDM-Experiment terms are available on Github[3]. We also created two term collections useful in the neuroscience domain, one for the BIDS standard[4] and one for DICOM[5].
NIDM-Experiment is hierarchical, meaning that terms are connected using the standard “is a” relationship. More general terms have been imported that provide the scaffolding upon with to build up new term domains and to provide semantic organizing principles. We have created two web interfaces to interact with NIDM-Experiment 1)a set of term-resolution web pages that can be used to provide a URL for each term, and 2)a web page that displays the term hierarchy in expandable form so that the relationships between terms and their organizing principles can be viewed.
Conclusions:
We have developed the NIDM-Experiment controlled vocabularies that can be used to annotate neuroscience-related datasets.
References
[1] FAIR. Available at: https://www.go-fair.org/fair-principles/
[2] Bioportal. Available at: https://bioportal.bioontology.org/
[3] NIDM-Experiment. Available at: https://github.com/incf-nidash/nidm-experiment
[4] BIDS. Available at: https://bids-specification.readthedocs.io/en/stable/
[5] DICOM Standard. Available at: https://www.dicomstandard.org/
Data annotation is important in the application of the FAIR[1] principles. NIDM-Experiment provides a rich set of defined terms that covers all aspects of neuroscience-related experiments. The goal of NIDM-Experiment is to provide an expandable basis set of terms that can be used by annotation tools.
Methods:
NIDM-Experiment was developed by referring to existing datasets and determining the terms needed to annotate them. New terms were only added if existing terms did not exist in existing Bioportal[2] ontologies or existing terms had incompatible definitions. NIDM-Experiment terms are available on Github[3]. We also created two term collections useful in the neuroscience domain, one for the BIDS standard[4] and one for DICOM[5].
NIDM-Experiment is hierarchical, meaning that terms are connected using the standard “is a” relationship. More general terms have been imported that provide the scaffolding upon with to build up new term domains and to provide semantic organizing principles. We have created two web interfaces to interact with NIDM-Experiment 1)a set of term-resolution web pages that can be used to provide a URL for each term, and 2)a web page that displays the term hierarchy in expandable form so that the relationships between terms and their organizing principles can be viewed.
Conclusions:
We have developed the NIDM-Experiment controlled vocabularies that can be used to annotate neuroscience-related datasets.
References
[1] FAIR. Available at: https://www.go-fair.org/fair-principles/
[2] Bioportal. Available at: https://bioportal.bioontology.org/
[3] NIDM-Experiment. Available at: https://github.com/incf-nidash/nidm-experiment
[4] BIDS. Available at: https://bids-specification.readthedocs.io/en/stable/
[5] DICOM Standard. Available at: https://www.dicomstandard.org/