transformation_of relations to add

[fbastian]

Here are some suggested transformation_of relations to add (or immediate_transformation_of, I let the choice to you), from @ANiknejad. Some might be debatable, let us know what you think. Note that it is fine for us if you decide to obsolete any of those "future" terms, rather than creating the relation.

UBERON:0002087 atrioventricular canal transformation_of: UBERON:0007279 presumptive atrioventricular canal UBERON:0000178 blood transformation_of: UBERON:0006596 presumptive blood UBERON:0000955 brain transformation_of: UBERON:0006238 future brain UBERON:0002081 cardiac atrium transformation_of: UBERON:0010227 future cardiac atrium UBERON:0002082 cardiac ventricle transformation_of: UBERON:0010226 future cardiac ventricle UBERON:0001017 central nervous system transformation_of: UBERON:3000469 presumptive central nervous system UBERON:0000924 ectoderm transformation_of: UBERON:0006601 presumptive ectoderm UBERON:0002165 endocardium transformation_of: UBERON:0007280 presumptive endocardium UBERON:0000925 endoderm transformation_of: UBERON:0006595 presumptive endoderm UBERON:0003079 floor plate transformation_of: UBERON:0007286 presumptive floor plate UBERON:0000045 ganglion transformation_of: UBERON:0003869 presumptive ganglion UBERON:0001299 glans penis transformation_of: UBERON:0013239 future glans penis UBERON:0002028 hindbrain transformation_of: UBERON:0007277 presumptive hindbrain UBERON:0003058 hypochord transformation_of: UBERON:0006599 presumptive hypochord UBERON:0002360 meninx transformation_of: UBERON:0007645 future meninx UBERON:0000926 mesoderm transformation_of: UBERON:0006603 presumptive mesoderm UBERON:0001891 midbrain transformation_of: UBERON:0009616 presumptive midbrain UBERON:0003052 midbrain-hindbrain boundary transformation_of: UBERON:0007281 presumptive midbrain hindbrain boundary UBERON:0001016 nervous system transformation_of: UBERON:3000477 presumptive nervous system UBERON:0003075 neural plate transformation_of: UBERON:0007284 presumptive neural plate UBERON:0003077 paraxial mesoderm transformation_of: UBERON:0007285 presumptive paraxial mesoderm UBERON:0001782 pigmented layer of retina transformation_of: UBERON:0005424 presumptive retinal pigmented epithelium UBERON:0002244 premaxilla transformation_of: UBERON:0011628 early premaxilla UBERON:0003059 presomitic mesoderm transformation_of: UBERON:0007282 presumptive segmental plate UBERON:0005721 pronephric mesoderm transformation_of: UBERON:0007297 presumptive pronephric mesoderm UBERON:0003902 retinal neural layer transformation_of: UBERON:0005425 presumptive neural retina UBERON:0002063 sinus venosus transformation_of: UBERON:0007278 presumptive sinus venosus UBERON:0001893 telencephalon transformation_of: UBERON:0014371 future telencephalon UBERON:0001675 trigeminal ganglion transformation_of: UBERON:0006304 future trigeminal ganglion UBERON:0003062 primitive knot transformation_of: UBERON:0007283 presumptive shield UBERON:0005110 metanephric nephron transformation_of: UBERON:0010535 primitive metanephric nephron UBERON:0001997 olfactory epithelium transformation_of: UBERON:2001431 primitive olfactory epithelium UBERON:0005297 testis sex cord transformation_of: UBERON:0010141 primitive sex cord of indifferent gonad UBERON:0001285 nephron transformation_of: UBERON:0010532 primitive nephron

[cmungall]

I think the developing kidney needs a bit of work in general.

For nephrons, I decided to forego the ZFA pattern (in which primitive nephrons are subtypes of nephrons) to go for the "future X" --> "X" pattern.

However we have a bit of confusion regarding progenitor vs primitive. Need to figure out what the difference is between these. cc @ybradford

[Term]
id: ZFA:0005587
name: nephron progenitor
namespace: zebrafish_anatomy
def: "Cluster of cells comprising a portion of tissue which gives rise to new mesonephric nephrons.  The cluster contains self-renewing stem cells." [ZFIN:ZDB-PUB-110131-33]
xref: ZFIN:ZDB-ANAT-110523-9
is_a: ZFA:0001477  ! portion of tissue
relationship: end ZFS:0000044 ! Adult
relationship: part_of ZFA:0000529 ! kidney
relationship: start ZFS:0000000 ! Unknown

[Term]
id: ZFA:0005584
name: developing mesonephric nephron
namespace: zebrafish_anatomy
def: "Anatomical cluster which give rise to mature mesonephric nephrons.  Zebrafish continously generate new mesonephric nephrons." [ZFA:curator]
xref: ZFIN:ZDB-ANAT-110523-6
is_a: ZFA:0005282  ! nephron
relationship: end ZFS:0000044 ! Adult
relationship: start ZFS:0000000 ! Unknown

[mellybelly]

I think they are the same, question is, is it a cluster or a tissue? I'd probably go with the former.

[ybradford]

I agree that progenitor and primitive are generally the same. Cluster seems like the correct type, but I'm not current on how it's described in the literature. I also like the "future X" --> "X" pattern. Let's put a ticket it to change this in ZFA.

I think they are the same, question is, is it a cluster or a tissue? I'd

probably go with the former.

Reply to this email directly or view it on GitHub: https://github.com/obophenotype/uberon/issues/438#issuecomment-41699533

[fbastian]

Question: when an entity has an immediate_transformation_of precursor, shouldn't we transfer all its developmentally_preceded_by relations to this precursor?

I am giving an example that I have handy: UBERON:0002363 "dura mater* immediate transformation of UBERON:0010115 "future dura mater", but also: develops_from UBERON:0007647 ectomeninx, has_developmental_contribution_from UBERON:0002342 neural crest. UBERON:0010115 "future dura mater" does not have these relations; should we understand that the future dura mater needs some contributions from ectomenynx and neural crest to reach its fully formed state? Or only the future dura mater received those contributions?

[cmungall]

I think these need to be examined on a case by case basis. The current situation is suboptimal, with different develops_from statements from different sources, some redundant, some - not exactly contradictory - but in need of alignment.

The situation is complicated here by the fact that in our current model the meninges are spatially disjoint from bone. Some sources treat the periosteal layer of the skull as being part of the dura mater.

This is reflected in the precursors - the ectomeninx develops into the dura mater proper (which remains unossified) and an outer superficial layer with chondrogenic/osteogenic properties (ISBN:9781607950325).

If we are to keep the stronger transformation relations (which I assume is preferable for bgee, and is in general cleaner) then the precursor and developed structure must "match up"

One option is to have two classes for the formed structure "DM proper" (aka meningeal layer of DM) which is part of "DM plus periosteam". NCIt makes this distinction.

[cmungall]

Actually, we already subdivide the DM in this way. So it seems the solution here is to merge ectomeninx with future DM. We should really be anchoring the future-X times temporally a bit more though

[cmungall]

It seems EHDAA2 makes a developmental distinction between 'primary meninx' and the future meningeal layers. Slicing things in 4D is hard enough already, I suggest we keep things simple and don't distinguish at this stage.

Here is an example

       po EHDAA2:0004661 ! meninges [ends_at: "CS20"] [starts_at: "CS11"]
        po EHDAA2:0004453 ! primary meninx ***  [ends_at: "CS20"] [starts_at: "CS14"]
         po EHDAA2:0000401 ! diencephalon primary meninx [ends_at: "CS18"] [starts_at: "CS16"]
          df EHDAA2:0000390 ! diencephalon primary meninx future arachnoid layer [ends_at: "CS18"] [starts_at: "CS18"]
          po EHDAA2:0000392 ! diencephalon primary meninx future dura mater [ends_at: "CS18"] [starts_at: "CS18"]
          po EHDAA2:0000394 ! diencephalon primary meninx future subarachnoid space [ends_at: "CS18"] [starts_at: "CS18"]
         po EHDAA2:0000773 ! hindbrain primary meninx [ends_at: "CS18"] [starts_at: "CS14"]
          df EHDAA2:0000691 ! hindbrain primary meninx future tentorium cerebelli [ends_at: "CS18"] [starts_at: "CS15"]
          df EHDAA2:0000751 ! hindbrain primary meninx future arachnoid layer [ends_at: "CS18"] [starts_at: "CS18"]
          df EHDAA2:0000753 ! hindbrain primary meninx future dura mater [ends_at: "CS18"] [starts_at: "CS18"]
          df EHDAA2:0000755 ! hindbrain primary meninx future subarachnoid space [ends_at: "CS18"] [starts_at: "CS18"]
         po EHDAA2:0001176 ! midbrain primary meninx [ends_at: "CS18"] [starts_at: "CS16"]
          df EHDAA2:0001166 ! midbrain primary meninx future arachnoid layer [ends_at: "CS18"] [starts_at: "CS18"]
          df EHDAA2:0001168 ! midbrain primary meninx future dura mater [ends_at: "CS18"] [starts_at: "CS18"]
          df EHDAA2:0001170 ! midbrain primary meninx future subarachnoid space [ends_at: "CS18"] [starts_at: "CS18"]
         po EHDAA2:0001993 ! telencephalon primary meninx [ends_at: "CS20"] [starts_at: "CS16"]
          df EHDAA2:0000608 ! future falx cerebri [ends_at: "CS20"] [starts_at: "CS17"]
          df EHDAA2:0001992 ! telencephalon pia mater [ends_at: "CS20"] [starts_at: "CS17"]

[JohnCork]

I can’t comment on the ontology but in humans (and I assume at least other mammals) the Dura mater in the skull has two layers, a periosteal layer and a meningeal layer. These can’t really be separated in the adult except at the sinuses where the meningeal layer extends into the cerebrum e.g. flax cerebri or tentorium.

To complicate things, the dura mater around the spinal cord does not have a periosteal layer.

John

Dr. John Cork, Associate Professor Computer Imaging Laboratory, MEB Rm 6226 Department of Cell Biology & Anatomy, LSU Health Sciences Center, 1901 Perdido St., Box P6-2 New Orleans, LA 70112

Tel. 504 568 7177 Fax. 504 568 4392

URL: http://virtualhumanembryo.lsuhsc.eduhttp://virtualhumanembryo.lsuhsc.edu/

There are only 10 types of people, those who understand binary and those who don't.

From: Chris Mungall [mailto:notifications@github.com] Sent: Tuesday, May 06, 2014 10:15 AM To: obophenotype/uberon Subject: Re: [uberon] transformation_of relations to add (#438)

I think these need to be examined on a case by case basis. The current situation is suboptimal, with different develops_from statements from different sources, some redundant, some - not exactly contradictory - but in need of alignment.

The situation is complicated here by the fact that in our current model the meninges are spatially disjoint from bone. Some sources treat the periosteal layer of the skull as being part of the dura mater.

This is reflected in the precursors - the ectomeninx develops into the dura mater proper (which remains unossified) and an outer superficial layer with chondrogenic/osteogenic properties (ISBN:9781607950325).

If we are to keep the stronger transformation relations (which I assume is preferable for bgee, and is in general cleaner) then the precursor and developed structure must "match up"

One option is to have two classes for the formed structure "DM proper" (aka meningeal layer of DM) which is part of "DM plus periosteam". NCIt makes this distinction.

— Reply to this email directly or view it on GitHubhttps://github.com/obophenotype/uberon/issues/438#issuecomment-42315570.

[cmungall]

Hi John,

this is what we currently have, does this make sense?

[Term]
id: UBERON:0010507
name: layer of dura mater
def: "The intracranial dura mater, consisting of two layers: the outer periosteal layer which normally always adheres to the periosteum of the bones of the cranial vault; and the inner meningeal layer which in most places is fused with the outer. The two layers separate to accommodate meningeal vessels and large venous (dural) sinuses. The meningeal layer is also involved in the formation of the various dural folds, such as the falx cerebri and tentorium cerebelli and is comparable to and continuous with the dural mater of the spinal cord. The cranial epidural space is then a potential space between the bone and the combined periosteum/periosteal layer of the dura mater realised only pathologically and is neither continuous with or comparable to the vertebral epidural space" [http://www.mondofacto.com/facts/dictionary?periosteal+layer+of+dura+mater] 
comment: Editors note: not clear whether this should be classified as part of cranial dura mater, as the division only makes sense in this area
is_a: UBERON:0004923 {source="FMA"} ! organ component layer
relationship: part_of UBERON:0002363 {source="FMA"} ! dura mater
xref: FMA:231545 ! layer of dura mater

[Term]
id: UBERON:0010505 ! periosteal dura mater
name: periosteal dura mater
def: "The outermost of the two layers of the cranial dura mater which normally always adheres to the periosteum of the bones of the cranial vault" [https://orcid.org/0000-0002-6601-2165]
synonym: "periosteal layer of dura mater" EXACT  [FMA:231547]
synonym: "outer periosteal layer of dura mater" EXACT  []
synonym: "periosteal dura" EXACT [FMA:231547]
synonym: "outer layer of dura mater" EXACT [FMA:231547]
is_a: UBERON:0010507 {source="FMA"} ! layer of dura mater
relationship: part_of UBERON:0002092 ! cranial dura mater
relationship: adjacent_to UBERON:0003129 ! skull
relationship: adjacent_to UBERON:0002515 ! periosteum
relationship: mutually_spatially_disjoint_with UBERON:0010506 ! meningeal dura mater
xref: FMA:231547 ! outer layer of dura mater
xref: ncithesaurus:Periosteal_Layer_of_the_Dura_Mater ! periosteal layer of the dura mater
xref: UMLS:C1518991 {source="ncithesaurus:Periosteal_Layer_of_the_Dura_Mater"}

[Term]
id: UBERON:0010506 ! meningeal dura mater
name: meningeal dura mater
def: "The inner layer of the dura mater surrounding the brain. It is mostly fused with the outer layer, the endocranium that is adherent to the inner aspect of the cranial bones. These two layers form the dura mater. The latter covers and protects the brain and the spinal cord." [ncithesaurus:Meningeal_Layer_of_the_Dura_Mater]
comment: Editors note: not clear whether this should be classified as part of cranial dura mater, as the division only makes sense in this area
synonym: "meningeal layer of dura mater" EXACT  [FMA:231549]
synonym: "meningeal dura" EXACT [FMA:231549]
synonym: "inner layer of dura mater" EXACT [FMA:231549]
is_a: UBERON:0010507 {source="FMA"} ! layer of dura mater
xref: FMA:231549 ! inner layer of dura mater
xref: ncithesaurus:Meningeal_Layer_of_the_Dura_Mater ! meningeal layer of the dura mater
xref: UMLS:C1513121 {source="ncithesaurus:Meningeal_Layer_of_the_Dura_Mater"}

[cmungall]

Frederic see what you think of the latest commit. There may be some slight conflation going on between clusters of layers and superclasses of layers (e.g. the leptomeninx - in FMA it's a superclass in others it's the mereological sum). In theory we could break these all out but this kind of division is infectious. Now we have quite a clean (overly simplified?) representation.

endomeninx --> leptomeninx (pia and/or atrachnoid) ectomeninx -> dura mater (periosteal and meningeal)

with the developmental relationships for the primitive meninx layers made more specific (head NC vs head paraxial mesoderm)

[fbastian]

It looks fine. (but I was just illustrating my point, my question was about reviewing terms with a transformation_of relation, but also other developmental relations, in general)

[cmungall]

Yes, we could do a report for all terms with redundant assertions of this type

[JohnCork]

Chris,

All of those defn’s look good. I think it is clear that the periosteal and meningeal layers are part_of the cranial dura mater which is a part_of the dura mater. The rest of the dura mater would then be the vertebral (spinal cord) dura mater which does not have the two layers.

John

Dr. John Cork, Associate Professor Computer Imaging Laboratory, MEB Rm 6226 Department of Cell Biology & Anatomy, LSU Health Sciences Center, 1901 Perdido St., Box P6-2 New Orleans, LA 70112

Tel. 504 568 7177 Fax. 504 568 4392

URL: http://virtualhumanembryo.lsuhsc.eduhttp://virtualhumanembryo.lsuhsc.edu/

There are only 10 types of people, those who understand binary and those who don't.

From: Chris Mungall [mailto:notifications@github.com] Sent: Tuesday, May 06, 2014 10:45 AM To: obophenotype/uberon Cc: Cork, Robert Subject: Re: [uberon] transformation_of relations to add (#438)

Hi John,

this is what we currently have, does this make sense?

[Term]

id: UBERON:0010507

name: layer of dura mater

def: "The intracranial dura mater, consisting of two layers: the outer periosteal layer which normally always adheres to the periosteum of the bones of the cranial vault; and the inner meningeal layer which in most places is fused with the outer. The two layers separate to accommodate meningeal vessels and large venous (dural) sinuses. The meningeal layer is also involved in the formation of the various dural folds, such as the falx cerebri and tentorium cerebelli and is comparable to and continuous with the dural mater of the spinal cord. The cranial epidural space is then a potential space between the bone and the combined periosteum/periosteal layer of the dura mater realised only pathologically and is neither continuous with or comparable to the vertebral epidural space" [http://www.mondofacto.com/facts/dictionary?periosteal+layer+of+dura+mater]

comment: Editors note: not clear whether this should be classified as part of cranial dura mater, as the division only makes sense in this area

is_a: UBERON:0004923 {source="FMA"} ! organ component layer

relationship: part_of UBERON:0002363 {source="FMA"} ! dura mater

xref: FMA:231545 ! layer of dura mater

[Term]

id: UBERON:0010505 ! periosteal dura mater

name: periosteal dura mater

def: "The outermost of the two layers of the cranial dura mater which normally always adheres to the periosteum of the bones of the cranial vault" [https://orcid.org/0000-0002-6601-2165]

synonym: "periosteal layer of dura mater" EXACT [FMA:231547]

synonym: "outer periosteal layer of dura mater" EXACT []

synonym: "periosteal dura" EXACT [FMA:231547]

synonym: "outer layer of dura mater" EXACT [FMA:231547]

is_a: UBERON:0010507 {source="FMA"} ! layer of dura mater

relationship: part_of UBERON:0002092 ! cranial dura mater

relationship: adjacent_to UBERON:0003129 ! skull

relationship: adjacent_to UBERON:0002515 ! periosteum

relationship: mutually_spatially_disjoint_with UBERON:0010506 ! meningeal dura mater

xref: FMA:231547 ! outer layer of dura mater

xref: ncithesaurus:Periosteal_Layer_of_the_Dura_Mater ! periosteal layer of the dura mater

xref: UMLS:C1518991 {source="ncithesaurus:Periosteal_Layer_of_the_Dura_Mater"}

[Term]

id: UBERON:0010506 ! meningeal dura mater

name: meningeal dura mater

def: "The inner layer of the dura mater surrounding the brain. It is mostly fused with the outer layer, the endocranium that is adherent to the inner aspect of the cranial bones. These two layers form the dura mater. The latter covers and protects the brain and the spinal cord." [ncithesaurus:Meningeal_Layer_of_the_Dura_Mater]

comment: Editors note: not clear whether this should be classified as part of cranial dura mater, as the division only makes sense in this area

synonym: "meningeal layer of dura mater" EXACT [FMA:231549]

synonym: "meningeal dura" EXACT [FMA:231549]

synonym: "inner layer of dura mater" EXACT [FMA:231549]

is_a: UBERON:0010507 {source="FMA"} ! layer of dura mater

xref: FMA:231549 ! inner layer of dura mater

xref: ncithesaurus:Meningeal_Layer_of_the_Dura_Mater ! meningeal layer of the dura mater

xref: UMLS:C1513121 {source="ncithesaurus:Meningeal_Layer_of_the_Dura_Mater"}

— Reply to this email directly or view it on GitHubhttps://github.com/obophenotype/uberon/issues/438#issuecomment-42319757.

[fbastian]

[Term]
id: UBERON:0000007
name: pituitary gland
...
relationship: develops_from UBERON:0034875 ! future pituitary gland

Shouldn't it be an immediate transformation of relation?

[ybradford]

I can't speak to whether or not all mature capillary networks are present in the 'pituitary gland' are also in the 'future pituitary gland'. Zebrafish are a bit different than human. If so then yes, but since I can't answer that I think develops_from is still correct.

[gouttegd]

WARNING: This issue has been automatically closed because it has not been updated in more than 3 years. Please re-open it if you still need this to be addressed addressed addressed – we are now getting some resources to deal with such issues.