About FAIR anatomical mapping

This is relevant for SPARC researchers.

You have access to curated anatomical terminology databases for comprehensive, FAIR (Findable, Accessible, Interoperable and Reusable) anatomical mapping specific to each organ and species of interest.

FAIR data is:

  • Findable: rich metadata with explicit data identifiers that are searchable in a registry or index
  • Accessible: open protocols with unique identifiers, metadata available even after data is not
  • Interoperable: represent knowledge with FAIR approved terminology
  • Reusable: sustainable metadata that complies with SPARC data sharing standards

 

These are databases that house vocabularies such as anatomical ontologies and reference atlas terminologies so that they can be used and managed by SPARC. Vocabularies from the anatomical terminology databases are used during mapping, segmentation and annotation to produce FAIR data that will carry through the MAP-CORE pipeline.

Make your SPARC data interoperable. Utilize the anatomical terminology lists while mapping your organ to ensure the names of the structures segmented are recognized by both humans and computers.

Vocabulary Services refers to the databases and infrastructure for serving and managing terminology for SPARC. The vocabulary services allow users to select from shared vocabularies for annotating their data and add new terms where necessary.

The FAIR Data Informatics lab (FDI) at the University of San Diego -part of the SPARC Data Curation team -is building each anatomical terminology list from vocabulary services using their SciGraph and Interlex platforms. SciGraph is a graph database that provides an API (programmatic interface) to the SPARC vocabularies; Interlex is a dynamic platform that allows SPARC users to edit and add terms. Once terms are approved by SPARC, they are added to SciGraph so they can be used by others.

SPARC Data Curation team.

The SPARC Data Curation team. Submit a new term by clicking the Request a new term button in the Contour Selection panel to launch the submission form on the SciCrunch website.

You’ll be able to initiate a dialog with the FAIR Data Informatics team by clicking the Request a new term button in the Contour Selection panel to launch the submission form on the SciCrunch website.

To request access to a particular atlas or have SPARC specific questions, communicate with the SPARC Data Curation team. Start a discussion in the #mapcore-support channel on the NIH SPARC #Slack.