Neuroimaging research contains information about experimental design, data acquisition, analysis, and results that are associated with study participants. The culmination and tracking of this information provides insight in to normal and diseased brain states with potential for translation to clinical applications. This document provides an overview of the NIDM Family of Documents that details a framework for data sharing in human brain imaging.
This document is part of the NIDM Family of Documents, a set of documents defining various aspects of neuroimaging research that are necessary to achieve the vision of interoperable interchange of information in heterogeneous environments such as the Web, research consortia, and laboratories. A list of current NIDM documents and the latest revision of this specification can be found in the NIDM specification index. These documents are listed below.
The NIDM Working Group encourages the implementation of the specifications overviewed in this document. Work on this document by the NIDM Working Group is ongoing, errors and suggestions may be reported in the NIDM issue tracker and these may be addressed in future revisions.
This document was published by the NIDM Working Group as a Working Draft. If you wish to make comments regarding this document, please report using the NIDM issue tracker. You can also ask questions at firstname.lastname@example.org. All comments are welcome.
This document provides a non-normative overview of the Neuroimaging Data Model (NIDM) Family of Documents and a roadmap to using them. Neuroimaging is a research discipline that uses imaging technologies to observe neurobiology at all levels of analysis, from molecules to organ systems (i.e., the brain). The focus of these documents is currently on human neuroimaging using Magnetic Resonance Imaging (MRI); however, the concepts described herein are intended to generalize to other modalities (e.g., PET, EEG). The goal of NIDM is to enable the wide publication and interchange of provenance information related to neuroimaging research to enable reproducible findings, which ranges from the experimental design and data acquisition of individual participant data to the analysis and results that produce scientific findings.
The design of NIDM stems from the need to address metadata-related barriers to data sharing [[!KEATORNI13]] that impact the reproducibility of scientific discoveries in neuroimaging, which is a focus of the NIDM Working Group. Provenance information is a key aspect of reproducibility, and the NIDM Family of Documents adopted the W3C PROV Working Group's approach to developing data sharing standards by extending the W3C PROV Recommendations. This approach embeds provenance as a fundamental data sharing primitive that captures the details of how a given dataset or analysis was produced. Summarizing, NIDM Working Group recommends that the metadata for a data sharing framework should support:
Figure 1 shows the organization of NIDM and how the specification documents relate to each other.
Underlying the NIDM Core is a conceptual data model called PROV ([[!prov-primer]], which defines a common vocabulary used to describe provenance. The PROV model is extended by the NIDM Core Vocabulary with terms that are used to describe neuroimaging research, and each term is designated as a PROV Entity, Activity, Agent, or Attribute. In the next layer, NIDM defines the Experiment ([[!nidm-experiment]]), Workflow ([[!nidm-workflow]]), and Results ([[!nidm-results]]) Components. Each of the Components in this layer provide additional constraints on PROV to define an arrangement of Entities, Activities, Agents, and Attributes using the NIDM Core Vocabulary, as well as terms specific to the given Component. The models defined in each Component are used to to construct a NIDM document with information within the Component's scope. The NIDM Dataset Descriptor ([[!nidm-dataset-descriptor]] provides a way to describe NIDM documents by adding metadata about the project, principle investigator, license, etc., as well as other important details (e.g., how NIDM documents can be merged together and provide a full study description). The NIDM NIQuery API ([[!nidm-niquery-api]] provides a way to access and query each of the NIDM Components, as well as validate their conformance to a given specification.
NIDM (currently) consists of 5 documents (including this one). In order to use NIDM you do not need to be familiar with every specification, but there are a few that will help you get started quickly depending on your usage. To help navigate NIDM, each document is broadly classified as being intended for a specific audience.
In the table below and Figure 1, we denote the type of each document as a Note or Component of NIDM.
|1||Users||Note||NIDM-Primer is the entry point to NIDM that offers an introduction to key concepts and examples of how NIDM is to be used.|
|2||Developers||Component||NIDM-Descriptor defines how to describe metadata about NIDM dataset documents and how to link NIDM components together appropriately.|
|3||Developers||Component||NIDM-Experiment defines how to describe metadata about an experiment, which includes a Project, Study, and Acquisitions of data from study participants.|
|4||Developers||Component||NIDM-Workflow defines how provenance information and metadata about an analysis is represented, with includes details about the computational environment and software versions used.|
|5||Developers||Component||NIDM-Results defines how to describe metadata about the results of a neuroimaging analysis.|
|6||Developers||Component||NIDM-NIQuery-API defines how to access metadata and provenance information from NIDM documents describing a neuroimaging analysis.|
All terms defined within NIDM are defined within the namespace http://incf.org/ns/nidash/nidm#. The prefix convention that is used is nidm. Thus, all of the terms defined in these specifications will be accessible at the same namespace for simplicity.
We would also like to refer the interested reader to complementary sources of information:
|Audience||Link||Description and link|
|Users||NIDASH page||Main INCF page for NIDASH Task Force, a child of the INCF Program on Standards for Data Sharing page.|
|Developers||NIDASH on Github||Organization hosting various code repositories of NIDASH projects, NIDM in particular.|
|Developers||NIDASH Google group||Wide distribution list for NIDASH activities|
|Modellers||NIDASH wiki||Overview of NIDASH activities; intended for both internal and external users.|
|Modellers||NIDM working group website||Site that hosts current information on the NIDM data model|
|Modellers||NIDASH Google Drive||Shared area for the INCF Neuroimaging task force (NIDASH) activities & NIDM development, including meeting agenda & minutes, specification, etc...|
|Allemail@example.com||NIDM mailing list|
This document has been produced by the NIDM Working Group, and its contents reflect extensive discussion within the Working Group as a whole.
Members of the NIDM Working Group at the time of publication of this document were: