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SAWG: SPARC Anatomical Working Group

About SAWG
Updated at: 05/26/2020

SPARC Anatomical Working Group (SAWG)

The Stimulating Peripheral Activity to Relieve Conditions (SPARC) effort is the result of National Institutes of Health’s (NIH) drive to map out the neural circuitry responsible for visceral control in higher vertebrates.

The SPARC Anatomy Working Group (SAWG) comprises anatomical experts who provide the necessary expertise and independent review of anatomical terminology used in SPARC. In particular, they provide relevant guidance and expertise for compiling and extending controlled lists of anatomy terms (cellular-, tissue- and gross-level) to standardize the annotation of SPARC products, including experimental data sets, 3D anatomical scaffolds and flat map schematics that display PNS circuitry.

The management of multimodal anatomical knowledge is one of the mainstays of Map Synthesis Core’s (MAP-Core) effort within SPARC. At the core of this effort is the curation of computable and Findable, Accessible, Interoperable, and Reusable (FAIR) knowledge for the inferencing of multiscale parts and connectivity route pathways in support of SPARC metadata discovery. It is critical to the success of the SPARC project that these anatomical terms be synched across the different contexts in which anatomical labels are applied. All SPARC vocabularies are themselves FAIR; that is, they can be interpreted by both humans and machines. So SPARC anatomical labels can be used by the SPARC system to effectively and efficiently search, display and, integrate (i.e., to relate two datasets to each other and across anatomical scales: cells to anatomical structures; molecules to cells and anatomy) and utilize SPARC data.

In support of FAIR, the overall strategy for SPARC is to build on anatomical ontologies already in use by the community. Because SPARC studies multiple species, our core anatomical ontology is UBERON, a pan-species anatomical ontology. When possible, we will annotate anatomical structures to UBERON terms. However, no anatomical ontology is complete, so we are supplementing UBERON with additional ontologies [FMA])http://sig.biostr.washington.edu/projects/fm/AboutFM.html) and EMAPA.

The SAWG provides community-supported leadership and arbitration on the accepted relationship between anatomical label and definition (and, by extension, the relationship). Parts of this arbitration are to:

  • Recommend and reconcile different topographical atlases that capture labeled regions within a coordinate system for some organ;
  • Moderate and review the SPARC Term Request pipeline to ensure that consistent terms are used amongst all SPARC data and external references. Currently, anatomical labels/terms are submitted via:
    • The team at MBF Biosciences. The MBF TissueMapper software draws on the SPARC vocabularies to annotate and segment 2D and 3D imaging data. If a term is not present in the SPARC vocabularies, anatomical terms are requested from MBF on behalf of SPARC investigators.
    • Modelers who are developing circuit diagrams of peripheral connectivity using the ApiNATOMY platform;
    • Engineers at the University of Auckland Bioengineering Institute (ABI) developing 3D scaffolds used for spatial registration of SPARC data;
    • Directly by SPARC investigators to align anatomical terms used in their SPARC datasets with other SPARC investigators.

SAWG Image1

Anatomical Term Request and Review Pipeline

SAWG Image 2

  1. Term(s) required by SPARC participants are submitted to the SAWG via 2 routes. Individual terms can be added directly to Interlex, the database used by SPARC to store and manage vocabularies; 2) A list of terms can be submitted via the SPARC Term Request Google Sheet. Along with the submitted terms, the requestor will also be asked to submit an email address for about terms. We have set up a dedicated portal where term requests are managed.

  2. All term requests are reviewed by the SAWG. These terms are either

  • Approved:

    • Terms and definitions will be added to the SPARC vocabularies
  • Edited:

    • The investigator or point of contact will be emailed to approve the edit.
  • Rejected:

    • The investigator or point of contact will be emailed to provide more information or
    • The investigator will be asked to use an alternative term
  1. All approved terms are incorporated into the formal ontology by SPARC knowledge engineers. At the recommendation of SAWG, some of these terms representing general anatomical structures are contributed back to community ontologies to enhance their coverage of CNS-PNS-Organ interactions.

The SAWG Term Request portal can be found here.

If there are any additional questions and/or concerns about this process, please contact us at sparc@scicrunch.zendesk.com

The SPARC Anatomy Working Group (SAWG) is responsible for the integrity of anatomical knowledge in SPARC. In particular, it provides the relevant guidance and expertise about:

  1. Defining and naming anatomical terms
  2. Maintaining ontologies of anatomical knowledge
  3. Compiling and curating computable knowledge about multiscale routes pathways

As part of this process, the SAWG is developing a term request pipeline so that any new terms required for the annotation of SPARC data or maps can be added to the SPARC vocabularies. All added terms are reviewed by the SAWG on a regular basis. Details about the SPARC vocabularies and the term request pipeline are available here.

More detailed information can be found at the SAWG Home Page.