In this section we will introduce the Maps interface for the ‘Functional Connectivity’ or FC flatmap.
The FC flatmap is a tool that provides the semantic description of all anatomical locations in the mammalian body along with the connectivity of networks that transfer information (neural connectivity) or mass flow (blood vessels and lymphatics) between these locations.
The anatomical locations are organised in a hierarchy that starts with the organ systems of the body including cardiorespiratory, digestive, musculo-skeletal, neural, endocrine, immune, male and female reproductive, integumentary (skin), naso-oral-pharyngeal, special sense organs, and urinary systems. Each of these systems contains organs, such as the esophagus, stomach, duodenum, pancreas, and others in the digestive system. These organs, in turn, contain ‘Functional Tissue Units’ or FTUs. FTUs are the primary anatomical unit (usually at a millimetre scale) where physiological function emerges from molecular and cellular biology. Examples of FTUs include the gastric cardia, gastric fundus, gastric body, pyloric antrum, and pyloric canal in stomach or nephron in the kidney, the lobule in the liver, the osteon in bone, the alveoli in the lungs, etc. Nearly every FTU is innervated by the autonomic nervous system, blood vessels, and lymphatics. The pathways present on the FC map represent the neuronal connections between the brainstem and the FTUs within each organ system. The various colours of these pathways represent different types of nerves (see the Controls section for information on the legend for these pathways).
The purpose of the FC map is primarily to capture the semantics and connectivity of the body’s anatomical and physiological organisation, and to provide an interface for building composite models. The information is provided by the SCKAN knowledgebase and is consistent with the ‘Anatomical Connectivity’ (AC) flatmap and the 3D whole-body models for each species. In the near future, it will provide a user interface to modeling studies that will be designed to address the integrative physiological function of the body.
When first loading the FC flatmap, all organ systems and connectivity are hidden. Users are able to use the systems legend (control G below) to select their systems of interest to make them visible. Connectivity relevant to the system(s) will also be displayed.
A. Search within display: This feature allows searching within the current map displayed.
B. Map controls: These icons manipulate the view of the map, toggle the map information and create a permalink of the current status of the map. Hover over each icon for more information.
C. Map sidebar: The arrow on the right hand side of the map interface opens the sidebar where datasets, maps, and scaffolds can be accessed. For more information refer to the How to use the sidebar in maps documentation.
D. Zoom controls: The map can be zoomed in and out with these controls. The right-most button allows a fit-to-window display. Note that zooming in/out can also be achieved by scrolling or with a pinch/spread gesture on a mouse trackpad.
E. Display settings: The display of the flatmap can be manipulated by clicking the computer icon. This prompts an interface that allows the user to change the background colour, the organs display and the outlines display.
F. Pathways: The latter part of the box in the lower left corner is a legend for the pathways on the FC flatmap. Interacting with the legend allows for triggering the display of desired pathways.
G. Systems: The upper part of the box in the lower left corner is a legend for controlling the display of the organ systems on the FC flatmap.
H. Beta tag: Note that the current state of the FC flatmap is under production. Hover over the beta tag for more information.
Moving around the FC map can be achieved with a single left-click and drag.
When hovering over any of the features in the FC map, a tooltip will be prompted that will provide information, as shown in Figure 2. See the Functional Connectivity Map section for more information on the features of the FC map.
Information about FTUs comes from external literature sources. Clicking on an FTU prompts the flatmap context card that allows access to this literature (not complete yet). For example, as illustrated in Figure 3, the Main bronchus FTU, present in the Pair of Lungs box in the Cardiorespiratory System has been annotated with a literature source that provides further information on bronchi.
Similarly, some pathways have been populated with an external literature source, as well as information relating to the origin, destination and components of the neuron connection. As shown in Figure 4, clicking on these pathways prompts the flatmap context card, and scrolling down reveals more information and the link to the literature source.
While hovering over pathways, a tooltip is prompted that provides information on the respective nerve, as shown in Figure 5. (Note: This information originates from SCKAN. For more information refer to the SPARC Connectivity Knowledge Base of the Autonomic Nervous System (SCKAN) documentation). There are often multiple pathways stacked upon each other. In these cases, the tooltip will provide information on all pathways present.
Updated 4 months ago