SPARC Anatomy Working Group

It is critical to the SPARC project that these terms lists be synched across the different contexts in which anatomical labels are applied. Towards that goal, we have gathered user requirements for annotation of data sets, images, flatmaps and models and created a set of term lists to make it easier for researchers to review and tools, e.g., MBF Biolucida, to use. Terms are extracted from existing ontologies whenever possible, primarily UBERON and FMA. UBERON, a cross species anatomical ontology, is the primary source of terms, but we also draw on FMA extensively for human terms as necessary. If the term does not exist in either ontology (UBERON or FMA) they are added to a tool built by UCSD for adding terms to ontologies called InterLex.

Below is a table containing all current anatomical term sets. They can be viewed as either a list in Google doc or a tree view in html. We posted them to Google Docs to make it easy for people to give feedback on individual terms by adding a comment. We also provide additional information on some of these term sets below.

Anatomy knowledge deals with the precise relationship between a human-readable anatomical term/label and the definition of that region (e.g. in the heart, community-wide consensus needs to be reached on the concept label/term “mitral valve” and the definition of what it is/what its boundaries are/over which range of organisms does homology of this structure hold). In addition, the identification (and, therefore, definition) of certain structures (e.g. subcellular) is dependent on a particular combination of preparing/staining/imaging/image processing techniques (i.e. a protocol). The navigation of such a wide combinatorial space of concepts, labels, definitions and protocols spawns a heterogeneity of approaches and, in consequence, opinions.

In this context, the SAWG provides community-supported leadership and arbitration on the accepted relationship between anatomical label and definition (and, by extension, the relationship between concepts - i.e. between a label-definition couplet and another).

In addition, part of this arbitration is to recommend and reconcile different topographical atlases that capture labelled regions within a coordinate system for some organ.

Another part of this arbitration is manifest via the term-request pipeline, in which a curator who has not found an appropriate label with which to annotate an image sub-region can submit a new term for global use within SPARC (and beyond).

1. Documentation for adding terms to the SPARC vocabularies.
   • SPARC has several methods for adding terms to the SPARC vocabularies, depending on the number of terms to be added. An overview of how to add to the SPARC vocabularies provides detailed instructions.
   • For internal or advanced users who are familiar with the process, you can access the InterLex webpage here.
2. SPARC vocabulary-building instructions
   • Slide presentation outlining the strategy and procedures for building the SPARC vocabularies are located here
     • We keep a master list of all terms that have been added to Interlex by SPARC researchers for annotation of data, flatmaps or models. Each of these terms are reviewed by a knowledge curator to determine whether or not the term may already exist (for example, it might be a synonym of an existing term) or whether it should be formally added to the SPARC vocabularies. The SAWG, comprised of SPARC researchers and outside experts, provides advice to the knowledge curators about vocabulary additions.
3. Adoption of InterLex terminology services (for developers)
   • Ontology documentation

4. Up-to-date term lists for annotation in MBF tools by species and organ,including nomenclatures derived from particular atlases (together with acknowledgment/contact details for leads responsible for each list);

   • Tabulization of peripheral organ parts
   • Atlas nomenclatures

   -see table above for CNS and peripheral nervous system structures.

5. Up-to-date listing of terms applied to SPARC1 metadata annotation
   • Term code
   • All Terms
6. Up-to-date listing of terms applied to flatmap metadata annotation
   • flatmap metadata annotation
7. Up-to-date listing of terms applied to ApiNATOMY metadata annotation google sheet
8. Up-to-date listing of terms applied to 3D scaffold metadata annotation
   • Coming soon…
9. Searchable full reference list of terms (drawn from UBERON/FMA/Nomina/atlases)
   • Coming soon…