cartilaginous radials

[wdahdul]

Classes for cartilaginous radials are needed. Also need radial element classes to group the bone radial classes (In uberon, 'radial' and its children are subclasses of 'endochondral bone').

Note, Uberon already has classes for cartilaginous pelvic radials ('pelvic radial cartilage and three children: 'pelvic radial 1 cartilage', pelvic radial 2 cartilage, pelvic radial 3 cartilage)

[cmungall]

Sounds like you're going to want to automate this so I added "tech" to the labels for this item.

Before heading down this route, this is definitely the way you want to go: a trad of classes for every element? (we might extend this to a quad to be consistent with how we've done things in tetrapods, with an additional pre-cartilage element). The other option is to consolidate on "element"

What is your timeline? I can help with automation but this may have to wait til 2nd week of Oct.

[wdahdul]

We (Paula, Alex, and I) think it's better to have the quad of classes for each element, otherwise we lose information on composition by having only a single 'element' for each class. Would be great if you could automate creating the classes, and second week of October is fine.
Thanks!

[cmungall]

Shall we treat the existing radial classes as elements?

[cmungall]

We would end up mapping the ZFA classes (which are bones) to elements, but I think this is fine

[wdahdul]

I think it's better to keep the existing radial classes as types of endochondral bone. For phenoscape, most of our exisitng annotations would refer to the bone class.

[wdahdul]

By the way, 'pelvic radial cartilage' and its children are already in uberon. Not sure if there are more cartilage classes though.

[cmungall]

OK, so this will prove a little harder to automate than I thought.

First, all the existing textual definitions would be moved to the new element class. The element should be treated as the primitive. The existing bone and new cartilage classes would have compositional defs of the form "A that is composed of {cartilage, bone tissue}". Would you agree? It means that people coming in from outside might first land on the bone term and be one step away from the more lovingly crafted element definition. However, this is the only way we can keep the approach scalable and maintainable, we can't be maintaining defs in 3 places at once.

Just want to be sure we're aware of the implications of going down this route. This would eventually apply to femur, etc as well.

[cmungall]

Just want to make sure we're on the same page; when you say:
"otherwise we lose information on composition by having only a single 'element' for each class."

it's not clear you would lose anything. You could have high level rules such that "(skeletal element and part_of some appendicular skeleton and part_of some Taxon:x) SubClassOf bone".

Even without this axiom, the only information you effectively lose is about the ossification state.

[wdahdul]

*all the existing textual definitions would be moved to the new element class.
Sounds fine to me. I think the genus-differentia format will cue the user to look at the parent class.

[wdahdul]

*You could have high level rules such that "(skeletal element and part_of some appendicular skeleton and part_of some Taxon:x) SubClassOf bone".
Even without this axiom, the only information you effectively lose is about the ossification state

I think adding taxon restrictions for element composition would require a lot of research, and there may not be sufficient information in the literature to adequately document this in Uberon. WIth the triad of element classes, it isn't difficult for curators to choose the appropriate class, given information in the paper they are curating.

[cmungall]

Ok, we'll have to be careful. 7 defs reference bones explicitly. So the
procedure will be: "clone" radials as elements. Manually check definitions
to ensure applicable at this level of generality. auto(?) rewrite defs for
existing terms whilst putting in owl equivalence axioms. Fill in gaps with
cartilage children. All the while being careful not to overwrite....

I will start with the cloning step.

On Fri, Nov 8, 2013 at 7:30 AM, wdahdul notifications@github.com wrote:

*all the existing textual definitions would be moved to the new element
class.
Sounds fine to me. I think the genus-differentia format will cue the user
to look at the parent class.

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Reply to this email directly or view it on GitHubhttps://github.com//issues/334#issuecomment-28070897
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[cmungall]

Some notes:

Not as straightforward as thought. For example, this was lifted from TAO when ext was created:

[Term]
id: TAO:0001589
name: propterygium
namespace: teleost_anatomy
def: "The propterygium is the lateralmost or anteriormost basal cartilage that originates from the pectoral fin endoskeletal disc. The bases of the pectoral lepidotrichium 1 plus the propterygium articulates with the scapula." [TAO:GA_TG]
comment: The cartilaginous propterygium may partially ossify and fuse to the base of the pectoral hemilepidotrichium 1 in teleosts, but remains as a separate element in non-teleostean fishes.
synonym: "pectoral propterygium" EXACT []
is_a: VSAO:0000145  ! endochondral bone
relationship: OBO_REL:part_of VSAO:0000153 ! pectoral fin skeleton
relationship: develops_from TAO:0001456 ! pectoral fin endoskeletal disc

The relationship says bone, but the text def says cartilage. There are no logical axioms telling us this is cartilage, so we must check using the text.

This has since been classified as a pect fin prox radial, hence its relevance here.

What do you want to be done with these? May be safest to obsolete?

[cmungall]

Committed fix to r4011 in phenoscape-ext. Requires review.

[cmungall]

still working on this. reconciling original cartilage radials:

• UBERON:2001538 ! pelvic radial cartilage [DEF: "Small cartilage that forms at the posterior edge of the basipterygium."]
• UBERON:2001540 ! pelvic radial 3 cartilage [DEF: "Small cartilage that forms at the posterior and medial edge of the basipterygium."]
• UBERON:2001541 ! pelvic radial 2 cartilage [DEF: "Small cartilage with a long posterior process and a shorter lateral one that forms at the posterior edge of the basipterygium, between radial cartilages 1 and 2."]
• UBERON:2001542 ! pelvic radial 1 cartilage [DEF: "Small cartilage that forms at the posterior and lateral edge of the basipterygium."]

is this all of them?

[cmungall]

@wdahdul - you'll have to do the pelvic radial {1,2,3} cartilage. Their relationship to the bones is not clear to me.

Can you also review basipterygium.

The rest follow a standard pattern. Take a look and confirm it's OK

Remember, look in the inferred hierarchy with Elk on

[cmungall]

Still to fix:

same_label_as   UBERON:2001539 ! basipterygium cartilage        UBERON:2200623 ! basipterygium cartilage        basipterygium cartilage label   label   5       1
same_label_as   UBERON:2000268 ! anal fin proximal radial bone  UBERON:2200268 ! anal fin proximal radial cartilage     basal radial of anal fin        exact   exact   0       1
same_label_as   UBERON:2000268 ! anal fin proximal radial bone  UBERON:2200268 ! anal fin proximal radial cartilage     proximal anal-fin radial        exact   exact   0       1
same_label_as   UBERON:2000271 ! radial bone    UBERON:2200271 ! radial cartilage       radials exact   exact   3       3
same_label_as   UBERON:2000623 ! basipterygium bone     UBERON:2200623 ! basipterygium cartilage        basipterygia    exact   exact   10      1
same_label_as   UBERON:2000623 ! basipterygium bone     UBERON:2200623 ! basipterygium cartilage        basiptrygium ischiatique        exact   exact   10      1
same_label_as   UBERON:2000623 ! basipterygium bone     UBERON:2200623 ! basipterygium cartilage        os pelvien      exact   exact   10      1
same_label_as   UBERON:2000623 ! basipterygium bone     UBERON:2200623 ! basipterygium cartilage        pelvic plate    exact   exact   10      1
same_label_as   UBERON:2000623 ! basipterygium bone     UBERON:2200623 ! basipterygium cartilage        pubic plate     exact   exact   10      1
same_label_as   UBERON:2000646 ! anal fin distal radial bone    UBERON:2200646 ! anal fin distal radial cartilage       distal anal fin radial  exact   exact   0       1
same_label_as   UBERON:2000947 ! dorsal fin proximal radial bone        UBERON:2200947 ! dorsal fin proximal radial cartilage   basal radial of dorsal fin      exact   exact   8       9
same_label_as   UBERON:2001586 ! pectoral fin radial bone       UBERON:2201586 ! pectoral fin radial cartilage  pectoral actinost       exact   exact   2       3
same_label_as   UBERON:2001613 ! dorsal fin middle radial bone  UBERON:2201613 ! dorsal fin middle radial cartilage     dorsal fin medial radial        exact   exact   0       1
same_label_as   UBERON:2001614 ! anal fin middle radial bone    UBERON:2201614 ! anal fin middle radial cartilage       anal fin medial radial  exact   exact   0       1
same_label_as   UBERON:2001614 ! anal fin middle radial bone    UBERON:2201614 ! anal fin middle radial cartilage       medial anal-fin radial  exact   exact   0       1
same_label_as   UBERON:2002026 ! pectoral fin proximal radial bone 1    UBERON:2202026 ! pectoral fin proximal radial cartilage 1       first pectoral basal radial     exact   exact   0       1
same_label_as   UBERON:2002027 ! pectoral fin proximal radial bone 2    UBERON:2202027 ! pectoral fin proximal radial cartilage 2       second pectoral basal radial    exact   exact   0       1
same_label_as   UBERON:2002028 ! pectoral fin proximal radial bone 3    UBERON:2202028 ! pectoral fin proximal radial cartilage 3       third pectoral basal radial     exact   exact   0       1
same_label_as   UBERON:2002029 ! pectoral fin proximal radial bone 4    UBERON:2202029 ! pectoral fin proximal radial cartilage 4       fourth pectoral basal radial    exact   exact   0       1
same_label_as   UBERON:2005225 ! median fin radial bone UBERON:2205225 ! median fin radial cartilage    actinophore     exact   exact   3       4
same_label_as   UBERON:2005225 ! median fin radial bone UBERON:2205225 ! median fin radial cartilage    actinoste       exact   exact   3       4
same_label_as   UBERON:2005225 ! median fin radial bone UBERON:2205225 ! median fin radial cartilage    axonoste        exact   exact   3       4
same_label_as   UBERON:2005225 ! median fin radial bone UBERON:2205225 ! median fin radial cartilage    ptrygiophore    exact   exact   3       4
same_label_as   UBERON:2005226 ! median fin proximal radial bone        UBERON:2205226 ! median fin proximal radial cartilage   basoste exact   exact   0       1
same_label_as   UBERON:2005226 ! median fin proximal radial bone        UBERON:2205226 ! median fin proximal radial cartilage   ptrygiophore proximal   exact   exact   0       1

[cmungall]

Done.

http://purl.obolibrary.org/obo/uberon/releases/2013-11-13/diffs

[wdahdul]

Thanks for this work, Chris! All looks fine. A few notes:

*we need the triad represented for propterygium, metapterygium, and mesopterygium. Can you add these? It's fine to obsolete 'propterygium' because it's been inconsistently used in our annotations.

• I added develops from relationship for basipterygium bone (dev from basipterygium cartilage).
• I still need to review pelvic radial {1,2,3} cartilage

[gouttegd]

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