FAIR Image Segmentation in MBF Bioscience Software

SPARC investigators have access to curated anatomical terminology databases in MBF Bioscience software for comprehensive, FAIR (Findable, Accessible, Interoperable and Reusable) anatomical mapping specific to each organ and species of interest.

What is FAIR data?

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

What are the anatomical terminology databases?

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.

What do I do with the anatomical terminology lists?

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.

What are Vocabulary Services?

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

Who curates the databases?

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 SPARC approves terms, they are added to SciGraph so others can use them.

Who curates the data we've created after using the database terminology?

The SPARC Data Curation team.

Who do I contact if I have a new term?

The SPARC Data Curation team. Submit a new term in MBF Bioscience software by clicking the REQUEST A NEW TERM button in the Contour Selection panel to launch the submission form on the SciCrunch website. The SPARC Anatomical Working Group (SAWG) will review the requested SPARC term submitted via the MBF Bioscience software. Refer to the SPARC term request sheet.

Who do I contact if I don't agree with the terminology?

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.