OBO-Edit:Experimental Graphviz Views

From GO Wiki
Jump to: navigation, search

This page shows some example screenshots of potential new displays in OBO-Edit. The idea is to nest boxes based on some relationship in order to communicate more information without the infamous hairball effect

Grouping by is_a

Containment in a box represents is_a

Note that this approach is only sensible on ontologies such as the FMA in which there is no is_a multiple parentage (otherwise the same terms would be placed in different boxes, which would be visually confusing)

Heart (FMA)

The heart and its systemic parts


Nuclear Chromosome (GO)

IMPORTANT NOTE: GO is_a graphs form a polyhierarchy, so we cannot uniquely contains nodes within boxes.

However, we can use a term's genus differentia definition as a grouping mechanism. A term with a computable G-D definition will only have one declared or core is_a parent.

Here we use CC genus differentia definitions. Note that these are incomplete -- "chromosome" lacks a G-D def, so it is an orphan as far as the visual spatial containment is concerned.


Grouping by start of development

Optic chiasm developmental lineage (ZFA)

The terms 'optic chiasm' and 'midbrain' are shown, overlaid onto boxes depending on when they come into existence (the start relation in ZFA).

Substages are shown nested inside their superstages (these are named things like pharyngula, segmentation, ...)

Note: there are some oddities with the drawing of this one; some reasoned links need filtered. E.g. everythings inferred to start at 'Unknown'

Follow the red lines from 'midbrain' down to see the developmental lineage


Grouping by parthood

This is perhaps more intuitive? The spatial arrangement of the boxes reflect actual spatial containment in the organism

Nucleus and ER (GO)

The parts of the nucleus and the ER are shown, with containment indicating the part_of relation.

One potential problem here is that outside-the-cell box could be taken to mean extracellular. In fact, outside the box just means that not all instances are part_of cell. Perhaps this would be clearer if there was a separate box shown for extracellular?


Mitosis (GO)


Brain Development (GO + Uberon XPs)

telencephalon and diencephalon development, linked to the relevant terms from uber-anatomy ontology. See: XP:biological_process_xp_anatomy

Both processual part_of and anatomical part_of are indicated via box containment


Nervous system (FBbt)


Brain (ZFA)