Peter Midford and I recently attend the two-day Relations Ontology workshop in Denver, Colorado. The goal of the meeting was to further develop the Relations Ontology (RO) by moving relations from RO proposed (ontology for relations yet to be officially added to RO) to RO, and adding any new relations proposed by attendees. Impressively, almost all of the items on the original agenda were covered, and an ‘action list’ was produced to focus efforts subsequent to the meeting.
Phenoscape had several relations on the agenda, and Peter and I have summarized the discussion, definitions, and examples used.
On Monday afternoon, Wasila and Peter presented proposals for the following relations for the section organized by Suzi Lewis and Melissa Haendel on spatial relations:
Peter presented examples and definition for overlaps. Overlaps is particularly useful for Phenoscape so that we can represent a joint without having to create new terms for the parts of bones that participate in the joint. We can simply say, for example, that bone X overlaps joint XY. After brief discussion, it was decided that this relation will be added to RO with the proposed definition.
bone overlaps joint
axon overlaps axon tract
X overlaps Y =def. for every t and every x, if x instance_of X at t, then there is some instance y of Y at t such that (x overlaps y at t)
x overlaps y at t =def there is some z such that z is part_of x at t and z part_of y at t
Note that it can be the case that X overlaps Y as thus defined, even though Y does not overlaps
2. Attached_to and connected_to:
Wasila presented examples of these two relations and definitions given by the FMA (although the FMA definitions are reversed from how we use them in our use cases). There was discussion of whether or not it is useful to distinguish between fiat and bona fide boundaries, whether a single “connected” relation could suffice for all use cases, and whether a force-connected definition would be better to use. However, the overriding point was that biologists clearly make the distinction between attached and connected, and it was decided that attached_to and connected_to would be added to RO pending development of their formal definitions.
tooth attached_to bone
muscle attached_to bone
axon connected_to neuropil
3. Spatial Ontology
Wasila presented examples of how Phenoscape uses the Spatial Ontology, and much discussion centered on how to improve this relatively new and little used ontology. Some classes (e.g., anatomical region, anatomical surface) should be moved to CARO, and reference images would be helpful in providing examples for the different anatomical axes.
We presented a proposal for homology relations on Tuesday morning. Melissa started with a couple of background slides and Peter continued with a presentation of the definition we developed as a group on Monday night. That definition was revised again on Tuesday afternoon and the Tuesday afternoon revision can be found below. It, along with earlier revisions is available on the wiki page (http://www.bioontology.org/wiki/index.php/RO:Main_Page#Proposed_homologous_to_relation).
Directly_descends_from – This is currently defined as follows
Example: Child’s arm directly_descends_from parent’s arm
x1 directly_descends_from x2 iff there are y1, y2 such that:
- y1 is an organism
- x1 is an anatomical structure
- x1 part_of y1
- y2 is an organism
- x2 is an anatomical structure
- x2 part_of y2
- y2 is a parent of y1
- the genetic sequence that determined the morphology of x1 is partially a copy of the genetic sequence that determined the morphology of x2*.
* This clause still needs some work. Jim Balhoff added the following critique in discussion on the Phenoscape project list:
[Something that jumps out at me in the definition of directly_descends_from:
I would not say that genetic sequences “determine” any morphology. I would prefer something like “participates in the development of” the morphology of x1. Anyway, I don’t see genetic sequences as an absolutely necessary component of homology (although they would very often be an important component).]
Descends_from – This is currently defined as follows:
Example: My arm descends_from ancestral primate forelimb.
descends_from is the instance level relation which is the transitive closure over directly_descends_from:
A in B descends_from C in D:
For all A(a) -> exists b, d, c: B(b) & C(c) & D(d)
- a part_of b
- a descends_from c
- c part_of d
(Note – B must be a subclade of the clade descending* from D)
Homologous_to – Defined for classes of anatomical structures and clades
Example: Human arm homologous to robin wing.
A1 in B1 homologous_to A2 in B2 iff exists A3, B3:
- A1 in B1 descends_from A3 in B3 &
- A2 in B2 descends_from A3 in B3
(Note B1 and B2 must both be subclades of the clade descending* from D)
(*In the genealogical sense)
After presenting the definition, Peter presented a number of examples of character optimization – these included a schematic overview and a tree of bilateralians with a reconstruction that indicated that a heart was not present in the most recent common ancestor of bilateralians. There were also other examples that indicated different common ancestors and presence/absence of homology for traditional and Ecdysozoa/Lophotrochozoa-based phylogenies. The presentation finished with a discussion of the homology evidence codes and their use in Phenote.
We are uncertain of the need to include time (e.g., replace the atemporal usage of exists with temporally scoped exists and existed). Fabian suggested that just to be on the safe side we can include time – it’s not useful but it could stop some people complaining and it won’t affect the logic at all.
This definition mentions clades, avoiding the issue of whether taxa are individuals, classes or both.
We will be revisiting these definitions in the future.