2016-09-07 release

Added glymphatic system. Created separate insect module.
2016-09-07 release image

This release of uberon has an interesting new class, for the glymphatic system. Comments welcome on this ticket

One of the major changes in this release was the ‘budding off’ of uberon to make a new insect module. This is analogous to the module created for phenoscape editors to edit highly specific vertebrate skeletal terms, described in:

Haendel, M. a, Balhoff, J. P., Bastian, F. B., Blackburn, D. C., Blake, J. a, Bradford, Y., … Mungall, C. J. (2014). Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon. Journal of Biomedical Semantics, 5(1), 21. doi:10.1186/2041-1480-5-21

This means that ontology editors can more easily add insect-specific terms, by editing this module independently. See: obophenotype/insect-anatomy-ontology

These ontologies are merged at the time of release. So for uberon users, this results in this release having an additional 235 insect-specific terms. But note these are filtered out in species-specific views, e.g. composite-metazoan.

For more details, see: issue 1262

Ontology Diff Report

  • Neuroanatomy
    • Added glymphatic system, see 1260 sbello
    • Added notes about modeling of meninges, see 1261
    • Fixes species labels from nifstd
  • Insect refactoring
    • splitting insect terms into new edit module 1262
    • obsoleting core uberon visceral musculature as it was not clear what was meant https://github.com/obophenotype/insect_neuroanatomy_ontology/issues/8
    • disambiguating cardiogenic mesoderm. See https://github.com/obophenotype/insect_neuroanatomy_ontology/issues/7
    • disambiguating spiracle
    • disambiguating egg
    • Adding missing xrefs for FBbts. See 1262
  • GO
    • taxon constraints for gallbladder, GOC:mr, https://github.com/geneontology/go-ontology/issues/12590
    • aligned GO with uberon
  • Design patterns
    • Created framework for DPs, 1257
    • aligning to endochondral pattern, 1257
    • phalanx cartilage syn

Original Ontology

  • IRI: http://purl.obolibrary.org/obo/uberon.owl
  • VersionIRI: http://purl.obolibrary.org/obo/uberon/releases/2016-08-12/uberon.owl

New Ontology

  • IRI: http://purl.obolibrary.org/obo/uberon.owl
  • VersionIRI: http://purl.obolibrary.org/obo/uberon/releases/2016-09-07/uberon.owl

Report for classes

Class objects lost from source: 0

Class objects new in target: 239

New Class : wing margin

New Class : synaptic neuropil block

New Class : embryonic/larval integumentary system

New Class : adult integumentary system

New Class : abdominal histoblast primordium

New Class : lymph gland primordium

New Class : circulatory system primordium

New Class : trunk mesoderm anlage

New Class : visual anlage

New Class : clypeo-labral anlage

New Class : visual anlage in statu nascendi

New Class : dorsal ectoderm anlage

New Class : ectoderm anlage

New Class : anlage in statu nascendi

New Class : chaeta

New Class : external sensory organ

New Class : adult external head

New Class : sternite

New Class : tergite

New Class : sclerite

New Class : Bolwig organ

New Class : adult somatic muscle

New Class : mesothoracic tergum

New Class : adult external mesothorax

New Class : dorsal mesothorax

New Class : tergum

New Class : adult external thorax

New Class : adult muscle system

New Class : basiproboscis

New Class : proboscis

New Class : clypeus

New Class : mouthpart

New Class : arista

New Class : meningeal branch of mandibular nerve

New Class : incisive duct

New Class : glymphatic system

New Class : dorsal imaginal precursor

New Class : Bolwig organ primordium

New Class : arista lateral

New Class : presumptive embryonic/larval tracheal system

New Class : ventral ectoderm

New Class : cardiogenic mesoderm

New Class : adult clypeo-labral anlage

New Class : ventral epidermis primordium

New Class : clypeo-labral primordium

New Class : dorsal epidermis primordium

New Class : adult clypeo-labral primordium

New Class : vein of vestibular aqueduct

New Class : sex comb

New Class : adult abdominal segment

New Class : adult abdomen

New Class : adult prothoracic segment

New Class : adult mesothoracic segment

New Class : adult thoracic segment

New Class : adult thorax

New Class : adult labral segment

New Class : adult antennal segment

New Class : adult procephalic segment

New Class : wing hair

New Class : adult tagma

New Class : adult head segment

New Class : insect adult segment

New Class : insect adult head

New Class : sensilla row

New Class : non-connected developing system

New Class : synaptic neuropil

New Class : synaptic neuropil domain

New Class : adult nervous system

New Class : adult central complex

New Class : supraesophageal ganglion

New Class : protocerebrum

New Class : adult brain

New Class : adult central nervous system

New Class : embryonic brain

New Class : presumptive embryonic/larval central nervous system

New Class : presumptive embryonic/larval nervous system

New Class : neurogenic region

New Class : visual primordium

New Class : embryonic/larval cuticle

New Class : third instar larval cuticle

New Class : trichome

New Class : prothoracic metatarsus

New Class : prothoracic leg

New Class : prothoracic tarsal segment

New Class : metatarsus

New Class : tarsal segment

New Class : trunk mesoderm derivative

New Class : visceral mesoderm derivative

New Class : adult external abdomen

New Class : male analia

New Class : female analia

New Class : analia

New Class : clypeo-labral anlage in statu nascendi

New Class : cephalic furrow

New Class : ventral furrow

New Class : dorsal appendage

New Class : abdominal segment 9

New Class : abdominal segment 8

New Class : insect abdominal segment

New Class : insect abdomen

New Class : metathoracic segment

New Class : mesothoracic segment

New Class : gnathal segment

New Class : insect thorax

New Class : labial segment

New Class : prothoracic segment

New Class : thoracic segment

New Class : trunk mesoderm

New Class : anterior ectoderm

New Class : dorsal ectoderm

New Class : mesoderm anlage

New Class : adult cerebral ganglion

New Class : embryonic optic lobe primordium

New Class : embryonic abdominal segment 9

New Class : embryonic abdominal segment 8

New Class : embryonic metathoracic segment

New Class : insect embryonic abdominal segment

New Class : insect embryonic abdomen

New Class : embryonic labial segment

New Class : embryonic thoracic segment

New Class : insect embryonic thorax

New Class : embryonic mesothoracic segment

New Class : embryonic prothoracic segment

New Class : embryonic antennal segment

New Class : embryonic gnathal segment

New Class : embryonic segment

New Class : embryonic procephalic segment

New Class : embryonic head segment

New Class : mesodermal crest of segment T3

New Class : mesodermal crest

New Class : embryonic tagma

New Class : visceral mesoderm

New Class : proneural cluster

New Class : labral segment

New Class : procephalic segment

New Class : antennal segment

New Class : germ layer derivative

New Class : tagma

New Class : head segment

New Class : ocular segment

New Class : embryonic/larval ocular segment sensillum

New Class : embryonic/larval sense organ

New Class : cephalopharyngeal skeleton

New Class : epipharyngeal sclerite

New Class : insect embryonic/larval digestive system

New Class : posterior dorsal histoblast nest abdominal

New Class : ventral ectoderm derivative

New Class : anterior ectoderm derivative

New Class : embryonic/larval protocerebrum

New Class : insect embryonic/larval brain

New Class : embryonic/larval central nervous system

New Class : insect embryonic/larval nervous system

New Class : presumptive prothoracic metatarsus

New Class : embryonic/larval lymph gland

  • embryonic/larval lymph gland has exact synonym embryonic/larval hematopoietic organ { database cross reference=FlyBase:FBrf0074444 }
  • embryonic/larval lymph gland id UBERON:6001668
  • embryonic/larval lymph gland label embryonic/larval lymph gland
  • embryonic/larval lymph gland has exact synonym hematopoietic organ
  • embryonic/larval lymph gland database cross reference FBbt:00001668
  • embryonic/larval lymph gland definition Hematopoietic organ of the larva, located along the dorsal vessel, behind the brain. It produces the plasmatocytes, crystal cells and lamellocytes which are released at the end of the larval instar and onset of metamorphosis. It is composed of 3 pairs of bilateral lobes: an anterior primary lobe, a posterior secondary lobe and the most posterior lobe (or multiple lobes), the tertiary lobe. Each lobe is separated by pericardial cells. In the late embryo, the lymph gland consists of a single pair of lobes (primary lobes) containing around 20 cells each that flank the dorsal vessel. By the second larval instar, the lymph gland is composed of two or three new pairs of posterior lobes, and the primary lobes have increased in size to contain around 200 cells. During the first and early second larval instars, the lymph gland comprises only the hematopoietic progenitor population. The lymph gland increases in size ten-fold by the late third instar, and at this stage the progenitor cells (prohemocytes) become restricted to the medial region (medullary zone) of the primary lobe and become quiescent. The differentiated hemocytes are found in the periphery (cortical zone) of the primary lobe and these cells proliferate extensively. The posterior signalling center is a group of about 30 cells at the posterior tip of the primary lobe that secretes several signalling molecules and functions as a stem-cell niche. The secondary and tertiary lobes contain prohemocytes, and rarely a differentiated cell. Lymph glands are eliminated at metamorphosis. { database cross reference=FlyBase:FBrf0031001 , database cross reference=FlyBase:FBrf0032406 , database cross reference=FlyBase:FBrf0074444 , database cross reference=FlyBase:FBrf0155787 , database cross reference=FlyBase:FBrf0162082 , database cross reference=FlyBase:FBrf0187467 }
  • embryonic/larval lymph gland SubClassOf multi-tissue structure

New Class : genital disc primordium

New Class : female genital disc primordium

New Class : male genital disc primordium

New Class : embryonic/larval circulatory system

New Class : ventral prothoracic disc primordium

New Class : ventral thoracic disc primordium

New Class : labial disc primordium

New Class : eye-antennal disc primordium

New Class : dorsal thoracic disc primordium

New Class : dorsal metathoracic disc primordium

New Class : dorsal mesothoracic disc primordium

New Class : imaginal disc primordium

New Class : embryonic imaginal precursor

New Class : presumptive arista

New Class : anterior dorsal histoblast nest abdominal

New Class : dorsal histoblast nest abdominal

New Class : histoblast nest

New Class : histoblast

New Class : prothoracic leg disc

New Class : genital disc

New Class : male genital disc

New Class : female genital disc

New Class : ventral thoracic disc

New Class : haltere disc

New Class : wing disc

New Class : dorsal thoracic disc

New Class : antennal disc

New Class : embryonic/larval imaginal precursor

New Class : labial disc

New Class : eye-antennal disc

New Class : clypeo-labral disc

New Class : larval abdominal segment 9

New Class : larval abdominal segment 8

New Class : larval abdomen

New Class : larval metathoracic segment

New Class : larval abdominal segment

New Class : larval labial segment

New Class : larval thoracic segment

New Class : larval thorax

New Class : larval mesothoracic segment

New Class : larval prothoracic segment

New Class : larval antennal segment

New Class : larval labral segment

New Class : larval gnathal segment

New Class : larval ocular segment

New Class : larval head

New Class : larval procephalic segment

New Class : larval head segment

New Class : larval tagma

New Class : larval segment

New Class : ring gland

New Class : anterior-posterior subdivision of organism

New Class : segment of leg

New Class : segment of antenna

New Class : adult protocerebrum

New Class : presumptive embryonic/larval system

New Class : insect integumentary specialisation

New Class : tagmatic subdivision of integument

New Class : insect region of integument

New Class : segmental subdivision of integument

New Class : embryonic/larval head sense organ

New Class : chorionic specialization

New Class : cuticular specialization

New Class : embryonic/larval sensillum

New Class : embryonic/larval head sensillum

New Class : internal sensillum

New Class : external sensillum

New Class : eo-type sensillum

New Class : centro-posterior medial synaptic neuropil domain

New Class : dorsal ectoderm derivative

New Class : trunk ectoderm

New Class : metatarsus of male prothoracic leg

New Class : abdominal histoblast anlage

New Class : stomatogastric nervous system

New Class : obsolete visceral muscle

New Class : spiracle

New Class : tracheal primordium

New Class : tracheal pit

New Class : imaginal precursor

New Class : internal sense organ

New Class : mesothoracic tergum primordium

New Class : pharate adult

New Class : segmental subdivision of organ system

New Class : endocrine system component

New Class : epithelial furrow

Changed Class objects: 108

Changes for: foramen magnum

Changes for: meninx

Changes for: sensory system

Changes for: dura mater

  • Added
    • + dura mater external ontology notes some ontologies consider dura mater part of the CNS, others dispute this and claim it surrounds it (e.g. http://dx.doi.org/10.1111/joa.12381)[https://github.com/obophenotype/uberon/issues/1261]

Changes for: vestibular aqueduct

Changes for: fused tarsal bones 2 and 3

Changes for: perirhinal cortex of primate of Burwell et al 1995

Changes for: fused carpal bones 2 and 3

Changes for: perivascular space

Changes for: intertrochanteric crest

  • Deleted
    • - intertrochanteric crest definition The intertrochanteric crest is a bony ridge located on the posterior side of the head of the femur, stretching obliquely downward and medially from the summit of the greater trochanter to the lesser trochanter. Together with the intertrochanteric line on the anterior side of the head, the crest mark the transition between of the neck of femur into the shaft of femur. An elevation between the middle and proximal third of the crest is known as the quadrate tubercle. The upper half of the crest forms the posterior border of the greater trochanter. The distal capsular attachment on the femur follows the shape of the irregular rim between the head and the neck. As a consequence, the capsule of the hip joint attaches in the region of the intertrochanteric line on the anterior side, but a finger away from the intertrochanteric crest on the posterior side of the head. { database cross reference=http://en.wikipedia.org/wiki/Intertrochanteric_crest }
  • Added
    • + intertrochanteric crest comment Together with the intertrochanteric line on the anterior side of the head, the crest mark the transition between of the neck of femur into the shaft of femur. An elevation between the middle and proximal third of the crest is known as the quadrate tubercle. The upper half of the crest forms the posterior border of the greater trochanter. The distal capsular attachment on the femur follows the shape of the irregular rim between the head and the neck. As a consequence, the capsule of the hip joint attaches in the region of the intertrochanteric line on the anterior side, but a finger away from the intertrochanteric crest on the posterior side of the head
    • + intertrochanteric crest definition The intertrochanteric crest is a bony ridge located on the posterior side of the head of the femur, stretching obliquely downward and medially from the summit of the greater trochanter to the lesser trochanter. { database cross reference=http://en.wikipedia.org/wiki/Intertrochanteric_crest }

Changes for: sesamoid cartilage

Changes for: intertrochanteric line

  • Deleted
    • - intertrochanteric line definition The intertrochanteric line (or spiral line of the femur) is a line located on the anterior side of the proximal end of the femur. The rough, variable ridge stretches between the lesser trochanter and the greater trochanter forming the base of the neck of the femur, roughly following the direction of the shaft of the femur. The iliofemoral ligament — the largest ligament of the human body — attaches above the line which also strengthen the capsule of the hip joint. The lower half, less prominent than the upper half, gives origin to the upper part of the Vastus medialis. Just like the intertrochanteric crest on the posterior side of the femural head, the intertrochanteric line mark the transition between the femural neck and shaft. The distal capsular attachment on the femur follows the shape of the irregular rim between the head and the neck. As a consequence, the capsule of the hip joint attaches in the region of the intertrochanteric line on the anterior side, but a finger away from the intertrochanteric crest on the posterior side of the head. The fibers of the ischiocapsular ligament attaches both on the joint capsule and to the intertrochanteric line. { database cross reference=http://en.wikipedia.org/wiki/Intertrochanteric_line }
  • Added

Changes for: distal tarsal bone 2

Changes for: distal tarsal bone 3

Changes for: calcaneus

Changes for: distal tarsal bone 1

Changes for: cervical vertebra cartilage element

Changes for: caudal vertebra cartilage element

Changes for: lumbar vertebra cartilage element

Changes for: thoracic vertebra cartilage element

Changes for: cerebrospinal fluid

Changes for: malleus cartilage element

Changes for: stapes cartilage element

Changes for: spiracle (sensu Vertebrata)

Changes for: femur cartilage element

Changes for: infra-orbital canal of maxilla

Changes for: anatomical group

Changes for: incisive foramen

Changes for: fused tarsal bones 1 and 2

Changes for: margin of tongue

Changes for: hindlimb intermedium bone

Changes for: dura mater lymph vessel

Changes for: sphenoid cartilage element

Changes for: anatomical row

Changes for: incus cartilage element

Changes for: shelled egg

Changes for: calcaneum cartilage element

Changes for: radius-ulna cartilage element

Changes for: obsolete visceral musculature

Changes for: sacral vertebra cartilage element

Changes for: alisphenoid cartilage element

Changes for: distal tarsal bone 4

Changes for: exoccipital cartilage element

Changes for: phalanx cartilage element

Changes for: iliac cartilage element

Changes for: pubic cartilage element

Changes for: obsolete brain of rodent

Changes for: obsolete telencephalon of rodent

Changes for: obsolete olfactory bulb main of rodent

Changes for: left lung associated mesenchyme

Changes for: right lung associated mesenchyme

Changes for: cardiogenic splanchnic mesoderm

Changes for: infra-orbital foramen of maxilla

Changes for: osseus cochlear canal

Changes for: facial nerve canal

Changes for: foramen for glossopharyngeal nerve

Changes for: humerus cartilage element

Changes for: ischial cartilage element

Changes for: basioccipital cartilage element

Changes for: scapula cartilage element

Changes for: rib cartilage element

Changes for: distal mesopodial endochondral element

Changes for: distal mesopodial cartilage element

Changes for: mental foramen

Changes for: foramen rotundum

Changes for: ectoderm-derived structure

Changes for: mesoderm-derived structure

Changes for: jugular foramen

Changes for: cartilaginous otic capsule

Changes for: alveolar canal

Changes for: carotid canal

Changes for: incisive canal

Changes for: mandibular canal

Changes for: distal tarsal bone 5 cartilage

Changes for: distal tarsal bone 4 endochondral element

Changes for: distal tarsal bone 4 cartilage

Changes for: distal tarsal bone 5 endochondral element

Changes for: distal tarsal bone 2 endochondral element

Changes for: distal tarsal bone 2 cartilage

Changes for: distal tarsal cartilage

Changes for: distal tarsal bone 1 endochondral element

Changes for: distal tarsal bone 1 cartilage

Changes for: distal tarsal bone 3 endochondral element

Changes for: distal tarsal bone 3 cartilage

Changes for: optic foramen

Changes for: proximal mesopodial cartilage element

Changes for: foramen spinosum of sphenoid bone

Changes for: orbitosphenoid cartilage element

Changes for: neural plate proneural cluster

Changes for: centrale cartilage

Changes for: proximal carpal endochondral element

Changes for: proximal carpal cartilage

Changes for: autopod cartilage

Changes for: distal carpal endochondral element

Changes for: distal carpal cartilage element

Changes for: distal carpal bone 5 endochondral element

Changes for: distal carpal bone 5 cartilage

Changes for: distal tarsal endochondral element

Changes for: distal carpal bone 4 endochondral element

Changes for: distal carpal bone 4 cartilage

Changes for: distal carpal bone 1 cartilage

Changes for: distal carpal bone 2 endochondral element

Changes for: distal carpal bone 2 cartilage

Changes for: proximal tarsal endochondral element

Changes for: proximal tarsal cartilage

Changes for: distal carpal bone 1 endochondral element

Changes for: distal carpal bone 3 endochondral element

Changes for: distal carpal bone 3 cartilage

Report for properties

ObjectProperty objects lost from source: 0

ObjectProperty objects new in target: 0

Changed ObjectProperty objects: 0

September 7, 2016 |

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