obophenotype/human-developmental-anatomy-ontology

Ontology of human developmental anatomy

See: http://obofoundry.org/ontology/ehdaa2.html

human-developmental-anatomy-ontology's Issues

remove: CS03 isa anatomical group

this is incorrect

See: obophenotype/uberon#505

eyelid development axioms accidentally flipped

 / EHDAA2:0004546 ! zygote
  df EHDAA2:0000005 ! morula (2-16 cells)
   df EHDAA2:0000830 ! inner cell mass
    df EHDAA2:0000444 ! epiblast
     df EHDAA2:0000428 ! ectoderm
      df EHDAA2:0001248 ! neural ectoderm
       df EHDAA2:0000592 ! brain neural ectoderm
        df EHDAA2:0000665 ! prosencephalon neural fold
         df EHDAA2:0004428 ! future diencephalon D1 lateral wall
          df EHDAA2:0001315 ! optic (D1) neural crest
           df EHDAA2:0000485 ! eye mesenchyme
            df EHDAA2:0001016 ! lower eyelid epithelium *** 
            df EHDAA2:0002117 ! upper eyelid mesenchyme *** 
      df EHDAA2:0001968 ! surface ectoderm
       df EHDAA2:0001017 ! lower eyelid mesenchyme *** 
       df EHDAA2:0002116 ! upper eyelid epithelium *** 

Based on ISBN:0781772214 "Histology, Ross and Pawlina", I think that both epithelia should derive from the external ectoderm, and that the mesenchyme should develop from the eye mesenchyme

Fix broken ID EHDAA2:0001161416

[Term]
> id: EHDAA2:0001161416             it would be unique if it were id: EHDAA2:0001161
> name: pons sulcus limitans
> namespace: human_developmental_anatomy
> is_a: AEO:0000161 ! groove
> relationship: develops_from EHDAA2:0000638 ! future metencephalon sulcus limitans
> relationship: ends_at CS20 ! CS20
> relationship: located_in EHDAA2:0001159 ! pons lateral wall
> relationship: starts_at CS16 ! CS16

Anatomical surface oddities

you include CARO 'anatomical surface' and then add an AEO class with an identical definition but different name

• CARO:0000010 ! anatomical surface [DEF: "Non-material anatomical entity of two dimensions, that is demarcated by anatomical lines or points on the external or internal surfaces of anatomical structures."]
• AEO:0000192 ! anatomical surface feature [DEF: "Non-material anatomical entity of two dimensions, that is demarcated by anatomical lines or points on the external or internal surfaces of anatomical structures."]

these are connected via is_a

in addition, some structures such as foramen [DEF: "A hole in a tissue."] are connected to both

Create a release pipeline

Use standard OBO setup

Create OWL for export

Use Oort

is hepatic duct intrahepatic part always an arborising epithelium?

Superclasses:

   is_a CARO:0000043 ! simple tissue
     is_a CARO:0000066 ! epithelium
      is_a AEO:0000115 ! epithelial sac
       is_a AEO:0000117 ! arborising epithelial duct system
        is_a EHDAA2:0000743 ! hepatic duct intrahepatic part ***  [ends_at: "CS20"] [starts_at: "CS13"]

Is the is_a correct here?

Gives rise to:

                  df EHDAA2:0000941 ! left hepatic duct [ends_at: "CS20"] [starts_at: "CS14"]
                   df EHDAA2:0001002 ! liver left lobe parenchyma [ends_at: "CS20"] [starts_at: "CS14"]
                  df EHDAA2:0001727 ! right hepatic duct [ends_at: "CS20"] [starts_at: "CS14"]
                   df EHDAA2:0001007 ! liver right caudate lobe parenchyma [ends_at: "CS20"] [starts_at: "CS17"]
                   df EHDAA2:0001010 ! liver right lobe parenchyma [ends_at: "CS20"] [starts_at: "CS14"]
                   df EHDAA2:0001014 ! liver right quadrate lobe parenchyma [ends_at: "CS20"] [starts_at: "CS18"]
~

Is EHDAA2 intended for reasoning about non-epithelial layers of ducts? These would have different origins presumably. I think for Uberon we should read many EHDAA2 duct terms as being 'duct epithelium'. It might be an idea if EHDAA2 made this explicit in the label.

Original ticket:
obophenotype/uberon#654

EHDAA2:0001929 stomatodaeum

[Term]
id: EHDAA2:0001929
name: stomatodaeum
is_a: CARO:0000055  ! multi-tissue structure
relationship: ends_at CS11 ! CS11
relationship: located_in EHDAA2:0001326 ! oral region
relationship: starts_at CS09 ! CS09

This term has no children by any relation.

Loosely speaking, the stomatodeum is an invagination of ectoderm that develops into the mouth.

Modeling this precisely using strict EHDAA2 develops_from relations may be more difficult - the mouth includes many structures such as muscles and bones that may not be in the ectodermal lineage; also there may be some pharyngeal contribution, but the stomodeum may be conceived of as being anterior to the pharynx. The fact this is already classified as multi-tissue implies that in may have ectodermal and other components.

Add ends_at CS20 links back in

These were removed prematurely

cervical sclerotome lineage errors

This came from obophenotype/uberon#725

See image:

I think there are issues with C4 and axis

unlinked concepts for conceptus extraembryonic components

• EHDAA2:0000003 ! human conceptus extraembryonic component
• AEO:0000195 ! extraembryonic component

These should be linked but are not, see diagram

axis developmental relationships

is this correct?

[Term]
id: EHDAA2:0000162
name: axis cartilage condensation
namespace: human_developmental_anatomy
is_a: AEO:0000147 ! cartilagenous condensation
relationship: develops_from EHDAA2:0004002 ! vertebra C6 pre-cartilage condensation
relationship: ends_at CS20 ! CS20
relationship: part_of EHDAA2:0000240 ! cervical vertebral cartilage condensation group
relationship: starts_at CS17 ! CS17

See also:
obophenotype/uberon#316

Add obofoundry topic to repo metadata

The OBO Foundry has recently created a topics page at https://github.com/topics/obofoundry. It would be great if you could add the obofoundry topic to your repository, since it's currently listed as active in the OBO Foundry. If you're not sure how to do that, follow the instructions here. The main issue for this task is at OBOFoundry/OBOFoundry.github.io#1538 in case you want some more context or to join the larger discussion.

EHDAA2 is erroneously deprecating several terms from foreign ontologies

EHDAA2 contains several owl:deprecated assertions on terms outside of EHDAA2 scope, notably impacting Uberon, CL, FBbt (at least).

This is due to the use of alt_id tags in the OBO source, as here:

[Term]
id: CARO:0000000
name: anatomical entity
namespace: http://www.xspan.org/obo.owl#
alt_id: UBERON:0001062

This alt_id tag is interpreted by the OBO parser (at least the one in the OWL API) as a statement that UBERON:0001062 is deprecated and replaced by CARO:0000000. I suppose this was not the intention here, but either the editors didn’t know about the interpretation of the alt_id tag or maybe that tag was not interpreted that way back when EHDAA2 was still active.

Fix AEO fat tissue ID in AEO

Change AEO:000020 to AEO:0000493

Mike already did this for EHDAA2

groove in AEO

surely endoderm is not immaterial?

• CARO:0000007 ! immaterial anatomical entity
  • CARO:0000010 ! anatomical surface
    • AEO:0000161 ! groove
      • EHDAA2:0000009 ! 1st arch groove ectoderm
      • EHDAA2:0000046 ! 1st arch maxillary-mandibular groove ectoderm
      • EHDAA2:0000055 ! 2nd arch ectoderm
      • EHDAA2:0000061 ! 2nd arch endoderm
      • EHDAA2:0000072 ! 3rd arch ectoderm
      • EHDAA2:0000077 ! 3rd arch pouch endoderm
      • EHDAA2:0000195 ! interventricular sulcus
      • EHDAA2:0000250 ! lateral ventricle choroid fissure
      • EHDAA2:0000638 ! future metencephalon sulcus limitans
      • EHDAA2:0000653 ! future myelencephalon sulcus limitans
      • EHDAA2:0001100 ! medulla oblongata sulcus limitans
      • EHDAA2:0001161416 ! pons sulcus limitans
      • EHDAA2:0001265 ! spinal cord lateral wall sulcus limitans
      • EHDAA2:0001319 ! optic stalk fissure
      • EHDAA2:0001462 ! philtrum
      • EHDAA2:0001511 ! primitive groove
      • EHDAA2:0001945 ! myelencephalon sulcus limitans
      • EHDAA2:0004032 ! 4th arch ectoderm
      • EHDAA2:0004033 ! 4th arch endoderm
      • EHDAA2:0004073 ! laryngo-tracheal groove
      • EHDAA2:0004433 ! optic sulcus
      • EHDAA2:0004473 ! midbrain sulcus limitans

clavicle bone primordium

[Term]
id: EHDAA2:0000254
name: clavicle bone primordium
namespace: human_developmental_anatomy
is_a: AEO:0000085  ! membrane bone  *********
is_a: AEO:0000213  ! bone condensation
relationship: develops_from EHDAA2:0000179 ! body-wall mesenchyme
relationship: ends_at CS20 ! CS20
relationship: part_of EHDAA2:0001420 ! pectoral girdle
relationship: starts_at CS18 ! CS18

This is dubious, as a primordium is not yet a bone. Maybe AEO:0000085 ! membrane bone should be renamed "membrane element" if the goal is to have a class the groups all temporal stages of the bone.

(I know the clavicle is an interesting case with bone membrane and endochondral aspects, but the issue reported here is orthogonal to this)

Spotted by @wdahdul in obophenotype/uberon#401

rename EHDAA2:0001113 'mesenchyme'?

This is an odd class:

[Term]
id: EHDAA2:0001113
name: mesenchyme
is_a: CARO:0000054  ! anatomical group
relationship: develops_from EHDAA2:0001128 ! mesoderm
relationship: ends_at CS20 ! CS20
relationship: part_of EHDAA2:0000002 ! human embryo
relationship: starts_at CS07 ! CS07

Note the partonomy (embryo - not organism) and timing (CS7->)

Contrast with:

[Term]
id: AEO:0000145
name: mesenchymal tissue
def: "A group of not-yet-terminally-differentiatied cells that can pack in three dimensions." [AEO:JB]
is_a: CARO:0000043  ! simple tissue

The EHDAA2 class presumably refers to the mereological sum of all mesenchymal tissue in the embryo. It starts at CS07, but there is mesenchyme in the conceptus before this stage. (e.g. chorionic mesenchyme - which does not trace any kind of path up to EHDAA2 mesenchyme)

It has parts:

• df EHDAA2:0000830 ! inner cell mass
  • df EHDAA2:0000444 ! epiblast
    • df EHDAA2:0001128 ! mesoderm
      • df EHDAA2:0001113 ! mesenchyme
        • po EHDAA2:0000732 ! head mesenchyme
        • po EHDAA2:0001120 ! mesenchyme from somatopleure
        • po EHDAA2:0001122 ! mesenchyme from splanchnopleure
        • po EHDAA2:0002092 ! trunk and cervical mesenchyme

Perhaps this class should be renamed "entire embryonic mesenchyme"?

Consider using HsapDv IDs

EHDAA2 has stage classes like:

[Term]
id: CS01
name: CS01
namespace: carnegie_stage
is_a: CS:0  ! Carnegie stage

This is problematic for a couple of reasons. These are not well formed IDs because they lack ":"s. Unfortunately OboEdit is forgiving here but this causes downstream issues.

I would recommend using HsapDv here. Each class has more specific info, synonyms, definitions etc. If you are amenable I can swap these out.

Example:

[Term]
id: HsapDv:0000003
name: Carnegie stage 01
namespace: human_developmental_stage
def: "Embryonic stage defined by a fertilized oocyte and presence of pronuclei." [http://embryology.med.unsw.edu.au/wwwhuman/Stages/CStages.htm "adapted from"]
comment: Starts at day 1 post-fertilization, beginning of the first week.
is_a: HsapDv:0000000 ! human life cycle stage
relationship: part_of HsapDv:0000002 ! embryonic human stage
property_value: start_dpf "0.0" xsd:float
xref: XUO:0000130
xref: EHDAA2:CS01 ! CS01
synonym: "CS01" EXACT [EHDAA2:CS01]

For more info:
http://code.google.com/p/developmental-stage-ontologies/wiki/HsapDv

If you want access to the hsapdv ontology to contribute you'd be welcome.

incorrect isa link between heart associated veins and CS20

Term]
id: EHDAA2:0004523
name: heart associated veins
namespace: human_developmental_anatomy
is_a: CARO:0000054  ! anatomical group
****is_a: CS20  ! CS20
relationship: ends_at CS20 ! CS20
relationship: part_of EHDAA2:0004144 ! heart-associated blood vessels
relationship: part_of EHDAA2:0004543 ! body veins
relationship: starts_at CS09 ! CS09

typo: EHDAA2:0001291 ! olfactory cortx marginal layer

Should be cortex, not cortx