UPdate figure legend for view generation

[dosumis]

Minimal example:

Current text: Terms in ASCT+B tables are in red. Panel A shows the indirect relationship between 'descending loop of Henle' and 'nephron tubule' in Uberon. Panel B shows the direct subClassOf relationship between these two terms present in the Ubergraph redundant graph.

Draft replacement:

A simple example of view generation. The first panel depicts the relationship of the nephron tubule to subpart/types. The second shows an automatically generated view using only a subset of the terms in the first panel (those in red) as a seed. View generation build a minimal graph connecting all terms in the seed via some specified set of relationship types. In this case, we specified SUBCLASSOF and part_of relationships. Because all other terms in the seed are connected to 'nephron tubule' by a chain of SUBCLASSOF relationships, reasoning infers that they can all be directly connected via subClassOf. View generation takes into account all inferred relationship types (e.g. via property hierarchy or property chains (see figure ***)

Existing text:

Figure {renal_corpuscle}: Relationships between terms for the anatomy of the renal corpuscle in Uberon and HRA ontologies illustrating the vastly simplified view of CL and Uberon provided by the HRA ontology. Panel A: A schematic diagram showing the structure of the renal corpuscle. Panel B: A graph showing the relationship between terms under renal corpuscle in the HRA ontology - a highly simplified view of Uberon and the Cell Ontology, driven by the ASCT+B tables. Cell types are marked in cyan. Panel C: A cropped graph of relationships between terms for anatomical structures and cell types of the renal corpuscle in Uberon and CL (panel A). Terms from the ASCT+B Kidney table are marked in green. ~Modelling differences: Uberon includes the afferent and efferent arteriole as parts of the renal corpuscle, but not of the renal glomerulus. Both are also recorded as part of the kidney vasculature. The Kidney ASCT+B table doesn’t distinguish between glomerulus and corpuscle and includes the efferent and afferent arterioles only as part of the kidney vasculature.~. Comparing panels B and C, it is obvious that Uberon has much more complexity than the ASCT+B table. {TBA - SOME DETAILS ONCE WE HAVE FULL UBERON FIGURE TO VIEW}.

Dependent on https://github.com/hubmapconsortium/asctb-figures/issues/15

[dosumis]

New layout:

The extract/example from the full renal corpuscle figure can replace the minimal example above. Very rough draft of panels here. Order can change. Original Corpuscle image at https://atlas.kpmp.org/explorer/ - also here https://drive.google.com/drive/folders/1HdC_OuOOmp5WLaeYDZh9xKmBdPm-WSf9

[aleixpuigb]

Figure progress in Power Point

[dosumis]

I've been working on the legend. Here's the draft textL

View Generation for the renal corpuscle: Panel A shows a schematic of a renal corpuscle. Panel C shows a portion of the Uberon/CL ontology graph with terms for parts of the renal corpuscle in green. This illustrates the complexity of the Uberon graph compared to the needs of the HRA (many of the additional terms in Uberon are developmental and so not needed for an adult atlas. others are not applicable to humans (e.g. head kidney) or are grouping terms not needed by the HRA). Panel D shows a portion of that graph blown up, showing unused grouping terms such as "kidney afferent arteriole cell" Panel B shows the final view of the renal corpuscle generated from Uberon using terms from the ASCT+B table.

2 issues:

1. It would be better if the panel order followed an order that more logically fits the explanation in the legend. I think this means that C (complex ontology starting point) ->B; D (detail of complex ontology starting point) -> C; B - end result --> D. Hope we can make this fit.
2. I feel that the examples in D are not as strong as developmental examples - with are completely irrelevant to HRA. e.g. see pronephric and mesonephric terms here.
   Do you think we could find a view of the graph that would make this work?

[aleixpuigb]

New figure file: https://drive.google.com/file/d/175ZDcJbj-S2ZTid8AfX0Gz48pmBktqPf/view?usp=drive_link

[aleixpuigb]

Add a 5th panel with old panel D @aleixpuigb

[aleixpuigb]