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obophenotype / uberon

An ontology of gross anatomy covering metazoa. Works in concert with https://github.com/obophenotype/cell-ontology
http://obophenotype.github.io/uberon/
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Review all anatomical lines #2215

Closed cmungall closed 2 years ago

cmungall commented 2 years ago

Extending #2214

I think many lines in uberon are not lines, causing cryptic incoherencies

Here is one strategy

First create explicit DPs for all line and boundary patterns

line connecting patterns

  1. anatomical line connecting two distinct structures: line connecting % to %
  2. anatomical line connecting two paralogous structures of the same type (must use QCR, outside EL++). inter-% line

these are true abstract lines and should never have cells, genes, etc in them

ANY class with line at end of label MUST conform to one of these

Example of violation:

id: UBERON:2007027
name: forebrain midbrain boundary neural keel
xref: ZFA:0007027
is_a: UBERON:0006800 ! anatomical line
relationship: develops_from UBERON:0009612 ! forebrain midbrain boundary neural plate
relationship: part_of UBERON:2007024 ! anterior neural keel

boundary patterns

these should be material

  1. X-Y boundary
  2. boundary, lacking clear logical def

IF a term has boundary in its label, it MUST conform to this

example of violation

id: UBERON:2001343
name: telencephalon diencephalon boundary
xref: ZFA:0001343
is_a: UBERON:0006800 ! anatomical line
relationship: part_of UBERON:0001890 ! forebrain

unsure what to do with

yaml

meghalithic commented 2 years ago

@cmungall are we going to discuss this at the next meeting? Maybe we could discuss midlines too?

shawntanzk commented 2 years ago

Look at uberon 2x terms that are under anatomical line and see which are actually lines and which arent

cmungall commented 2 years ago 

[Term]
id: UBERON:0000464 ! anatomical space
name: anatomical space
is_a: UBERON:0000466 ! immaterial anatomical entity
relationship: surrounded_by UBERON:0000061 ! anatomical structure

[Term]
id: UBERON:0002225 ! costal arch
name: costal arch
is_a: UBERON:0006800 {source="FMA"} ! anatomical line
relationship: part_of UBERON:0001443 ! chest
relationship: part_of UBERON:0002228 {source="MA"} ! rib

[Term]
id: UBERON:0004104 ! hairline
name: hairline
intersection_of: UBERON:0006800 ! anatomical line
intersection_of: connects UBERON:0000403 ! scalp
intersection_of: connects UBERON:0008200 ! forehead
relationship: only_in_taxon NCBITaxon:9606 ! Homo sapiens
relationship: part_of UBERON:0000033 ! head

[Term]
id: UBERON:0006800 ! anatomical line
name: anatomical line
is_a: UBERON:0000015 ! non-material anatomical boundary

[Term]
id: UBERON:0009038 ! sulcus ampullaris
name: sulcus ampullaris
is_a: UBERON:0006800 {source="FMA"} ! anatomical line
relationship: contributes_to_morphology_of UBERON:0001846 ! internal ear
relationship: part_of UBERON:0004043 {source="MA"} ! semicircular canal ampulla

[Term]
id: UBERON:0009612 ! forebrain midbrain boundary neural plate
name: forebrain midbrain boundary neural plate
is_a: UBERON:0006800 {source="ZFA"} ! anatomical line
relationship: develops_from UBERON:0007288 {source="ZFA"} ! presumptive forebrain midbrain boundary
relationship: part_of UBERON:0003056 {source="ZFA"} ! pre-chordal neural plate

[Term]
id: UBERON:0009848 ! zona limitans intrathalamica
name: zona limitans intrathalamica
intersection_of: UBERON:0006800 ! anatomical line
intersection_of: adjacent_to UBERON:0001900 ! ventral thalamus
intersection_of: adjacent_to UBERON:0004703 ! dorsal thalamus
relationship: part_of UBERON:0001897 {source="ZFA"} ! dorsal plus ventral thalamus

[Term]
id: UBERON:0010222 ! anatomical line between pupils
name: anatomical line between pupils
intersection_of: UBERON:0006800 ! anatomical line
intersection_of: connects UBERON:0010223 ! left pupil
intersection_of: connects UBERON:0010224 ! right pupil
relationship: part_of UBERON:0001456 ! face

[Term]
id: UBERON:0010231 ! anatomical line between outer ears
name: anatomical line between outer ears
intersection_of: UBERON:0006800 ! anatomical line
intersection_of: connects UBERON:0006616 ! right external ear
intersection_of: connects UBERON:0006617 ! left external ear

[Term]
id: UBERON:0011877 ! margin of tongue
name: margin of tongue
intersection_of: UBERON:0006800 ! anatomical line
intersection_of: connects UBERON:0007371 ! superior surface of tongue
intersection_of: connects UBERON:0007373 ! inferior surface of tongue
relationship: part_of UBERON:0001723 ! tongue

[Term]
id: UBERON:0011918 ! line of Schwalbe
name: line of Schwalbe
is_a: UBERON:0006800 {source="FMA"} ! anatomical line
relationship: contributes_to_morphology_of UBERON:0005969 ! eye trabecular meshwork
relationship: part_of UBERON:0000964 ! cornea
relationship: part_of UBERON:0005969 {source="MP"} ! eye trabecular meshwork

[Term]
id: UBERON:0012079 ! metapterygial axis
name: metapterygial axis
is_a: UBERON:0006800 ! anatomical line
relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata <vertebrates>
relationship: part_of UBERON:0000026 ! appendage

[Term]
id: UBERON:0012437 ! epithelial-mesenchymal boundary
name: epithelial-mesenchymal boundary
intersection_of: UBERON:0006800 ! anatomical line
intersection_of: adjacent_to UBERON:0000483 ! epithelium
intersection_of: adjacent_to UBERON:0003104 ! mesenchyme
relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa

[Term]
id: UBERON:0013445 ! pterygomaxillary fissure
name: pterygomaxillary fissure
is_a: UBERON:0006800 {source="FMA"} ! anatomical line
relationship: part_of UBERON:0003129 {source="Wikipedia"} ! skull

[Term]
id: UBERON:0013455 ! spheno-petrosal fissure
name: spheno-petrosal fissure
intersection_of: UBERON:0006800 ! anatomical line
intersection_of: connects UBERON:0001677 ! sphenoid bone
intersection_of: connects UBERON:0001694 ! petrous part of temporal bone
relationship: part_of UBERON:0003129 {source="Wikipedia"} ! skull

[Term]
id: UBERON:0013633 ! intertrochanteric crest
name: intertrochanteric crest
is_a: UBERON:0006800 ! anatomical line
relationship: connects UBERON:0002503 ! greater trochanter
relationship: connects UBERON:0002504 ! lesser trochanter
relationship: part_of UBERON:0004412 ! proximal epiphysis of femur

[Term]
id: UBERON:0013634 ! intertrochanteric line
name: intertrochanteric line
is_a: UBERON:0006800 {source="FMA"} ! anatomical line
relationship: part_of UBERON:0004412 ! proximal epiphysis of femur

[Term]
id: UBERON:0013670 ! midline of corpus cavernosum maxillaris
name: midline of corpus cavernosum maxillaris
is_a: UBERON:0006800 ! anatomical line
relationship: part_of UBERON:0013658 ! corpus cavernosum maxillaris

[Term]
id: UBERON:0013678 ! anatomical line between inner canthi
name: anatomical line between inner canthi
intersection_of: UBERON:0006800 ! anatomical line
intersection_of: connects UBERON:0013679 ! inner canthus of right eye
intersection_of: connects UBERON:0013680 ! inner canthus of left eye
intersection_of: part_of UBERON:0001456 ! face

[Term]
id: UBERON:0013692 ! inframammary fold
name: inframammary fold
is_a: UBERON:0006800 {source="FMA"} ! anatomical line
relationship: adjacent_to UBERON:0000310 ! breast
relationship: adjacent_to UBERON:0001443 ! chest
relationship: part_of UBERON:0002100 ! trunk

[Term]
id: UBERON:0013770 ! intermammary cleft
name: intermammary cleft
is_a: UBERON:0006800 {source="FMA"} ! anatomical line
relationship: only_in_taxon NCBITaxon:40674 ! Mammalia
relationship: part_of UBERON:0002100 ! trunk

[Term]
id: UBERON:0013771 ! line connecting laterally paired nipples
name: line connecting laterally paired nipples
intersection_of: UBERON:0006800 ! anatomical line
intersection_of: connects UBERON:0013772 ! left nipple
intersection_of: connects UBERON:0013773 ! right nipple
intersection_of: has_quality PATO:0001854 ! vertical
relationship: part_of UBERON:0002100 ! trunk

[Term]
id: UBERON:0014764 ! anatomical line along groove
name: anatomical line along groove
intersection_of: UBERON:0006800 ! anatomical line
intersection_of: in_superficial_part_of UBERON:0006846 ! surface groove

[Term]
id: UBERON:0015122 ! anatomical line between outer canthi
name: anatomical line between outer canthi
intersection_of: UBERON:0006800 ! anatomical line
intersection_of: connects UBERON:0015120 ! right outer canthus
intersection_of: connects UBERON:0015121 ! left outer canthus
intersection_of: part_of UBERON:0001456 ! face

[Term]
id: UBERON:0015854 ! interpedicular line
name: interpedicular line
intersection_of: UBERON:0006800 ! anatomical line
intersection_of: connects UBERON:0001078 {cardinality="2"} ! pedicle of vertebra
relationship: connects UBERON:0001078 ! pedicle of vertebra
relationship: part_of UBERON:0001130 ! vertebral column

[Term]
id: UBERON:0036013 ! intergluteal cleft
name: intergluteal cleft
intersection_of: UBERON:0006800 {exactly="2"} ! anatomical line
intersection_of: adjacent_to UBERON:0013691 {exactly="2"} ! buttock
relationship: adjacent_to UBERON:0013691 ! buttock
relationship: part_of UBERON:0001137 ! dorsum
relationship: part_of UBERON:0002355 ! pelvic region of trunk

[Term]
id: UBERON:2001343 ! telencephalon diencephalon boundary
name: telencephalon diencephalon boundary
is_a: UBERON:0006800 ! anatomical line
relationship: part_of UBERON:0001890 ! forebrain

[Term]
id: UBERON:2002051 ! scale circulus
name: scale circulus
is_a: UBERON:0006800 ! anatomical line
relationship: part_of UBERON:0007380 ! dermal scale

[Term]
id: UBERON:2007027 ! forebrain midbrain boundary neural keel
name: forebrain midbrain boundary neural keel
is_a: UBERON:0006800 ! anatomical line
relationship: develops_from UBERON:0009612 ! forebrain midbrain boundary neural plate
relationship: part_of UBERON:2007024 ! anterior neural keel

[Term]
id: UBERON:2007033 ! forebrain midbrain boundary neural rod
name: forebrain midbrain boundary neural rod
is_a: UBERON:0006800 ! anatomical line
relationship: develops_from UBERON:2007027 ! forebrain midbrain boundary neural keel
relationship: part_of UBERON:2007031 ! anterior neural rod

[Term]
id: UBERON:2007040 ! forebrain midbrain boundary neural tube
name: forebrain midbrain boundary neural tube
is_a: UBERON:0006800 ! anatomical line
relationship: develops_from UBERON:2007033 ! forebrain midbrain boundary neural rod
relationship: part_of UBERON:0003080 ! anterior neural tube

[Term]
id: UBERON:2007045 ! midbrain hindbrain boundary neural keel
name: midbrain hindbrain boundary neural keel
is_a: UBERON:0006800 ! anatomical line
relationship: develops_from UBERON:0009615 ! midbrain hindbrain boundary neural plate
relationship: part_of UBERON:0007135 ! neural keel

[Term]
id: UBERON:2007046 ! midbrain hindbrain boundary neural rod
name: midbrain hindbrain boundary neural rod
is_a: UBERON:0006800 ! anatomical line
relationship: develops_from UBERON:2007045 ! midbrain hindbrain boundary neural keel
relationship: part_of UBERON:0005068 ! neural rod

[Term]
id: UBERON:2007047 ! midbrain hindbrain boundary neural tube
name: midbrain hindbrain boundary neural tube
is_a: UBERON:0006800 ! anatomical line
relationship: develops_from UBERON:2007046 ! midbrain hindbrain boundary neural rod
relationship: part_of UBERON:0001049 ! neural tube

[Term]
id: UBERON:4200221 ! growth line
name: growth line
is_a: UBERON:0006800 ! anatomical line

[Term]
id: UBERON:7500036 ! line from caundal-sacral region of the vertebral column to the last vertebra
name: line from caundal-sacral region of the vertebral column to the last vertebra
intersection_of: UBERON:0006800 ! anatomical line
intersection_of: connects UBERON:0011271 ! caudal-sacral region of vertebral column
intersection_of: connects UBERON:7500035 ! tip of tail

[Term]
id: UBERON:7500037 ! line from helix of outer ear to intertragus incisure
name: line from helix of outer ear to intertragus incisure
intersection_of: UBERON:0006800 ! anatomical line
intersection_of: connects UBERON:0002488 ! helix of outer ear
intersection_of: connects UBERON:0036212 ! intertragic incisure

[Term]
id: UBERON:7500038 ! line from the distal-most end of the longest nail to the posterior-most part of the foot
name: line from the distal-most end of the longest nail to the posterior-most part of the foot
intersection_of: UBERON:0006800 ! anatomical line
intersection_of: connects UBERON:7500039 ! posterior of pes
intersection_of: connects UBERON:7500040 ! tip of nail

[Term]
id: UBERON:7500042 ! line from the distal-most end of the longest phalax of the foot to the posterior-most part of the foot
name: line from the distal-most end of the longest phalax of the foot to the posterior-most part of the foot
intersection_of: UBERON:0006800 ! anatomical line
intersection_of: connects UBERON:0009551 ! distal segment of digit
intersection_of: connects UBERON:7500039 ! posterior of pes

[Term]
id: UBERON:7500043 ! line from tip of nose to the caudal-sacral region of the vertebral column
name: line from tip of nose to the caudal-sacral region of the vertebral column
intersection_of: UBERON:0006800 ! anatomical line
intersection_of: connects UBERON:0011271 ! caudal-sacral region of vertebral column
intersection_of: connects UBERON:0012128 ! nose tip

[Term]
id: UBERON:7500044 ! line from tip of nose to the posterior-most part of the last caudal vertebra
name: line from tip of nose to the posterior-most part of the last caudal vertebra
intersection_of: UBERON:0006800 ! anatomical line
intersection_of: connects UBERON:0012128 ! nose tip
intersection_of: connects UBERON:7500035 ! tip of tail

[Term]
id: UBERON:7500045 ! line of medial condyle of femur to greater trochanter
name: line of medial condyle of femur to greater trochanter
intersection_of: UBERON:0006800 ! anatomical line
intersection_of: connects UBERON:7500033 ! distal-most point of medial condyle of femur
intersection_of: connects UBERON:7500049 ! proximal-most point of greater trochanter of femur

[Term]
id: UBERON:7500050 ! line of medial condyle of femur to head of femur
name: line of medial condyle of femur to head of femur
intersection_of: UBERON:0006800 ! anatomical line
intersection_of: connects UBERON:7500033 ! distal-most point of medial condyle of femur
intersection_of: connects UBERON:7500046 ! proximal-most point of head of femur

[Term]
id: UBERON:7500051 ! line from trochlea of humerus to proximal head of humerus
name: line from trochlea of humerus to proximal head of humerus
intersection_of: UBERON:0006800 ! anatomical line
intersection_of: connects UBERON:7500034 ! distal-most point of trochlea of humerus
intersection_of: connects UBERON:7500047 ! proximal-most point of head of humerus

[Term]
id: UBERON:7500060 ! line from trochlea of humerus to ventral tubercle of humerus
name: line from trochlea of humerus to ventral tubercle of humerus
intersection_of: UBERON:0006800 ! anatomical line
intersection_of: connects UBERON:7500034 ! distal-most point of trochlea of humerus
intersection_of: connects UBERON:7500048 ! proximal-most point of ventral tubercle of humerus
shawntanzk commented 2 years ago

non-abstract boundaries should use http://purl.obolibrary.org/obo/UBERON_0007651

shawntanzk commented 2 years ago

all uberon:2x except scale circulus should be changed to above