lepao.obo

format-version: 1.2
data-version: releases/2021-01-19
subsetdef: abnormal_slim ""
subsetdef: AISM:0000171 ""
subsetdef: attribute_slim ""
subsetdef: cell_quality ""
subsetdef: cumbo ""
subsetdef: developmental_classification ""
subsetdef: disposition_slim ""
subsetdef: early_development ""
subsetdef: efo_slim ""
subsetdef: emapa_ehdaa2 ""
subsetdef: functional_classification ""
subsetdef: goslim_aspergillus ""
subsetdef: goslim_candida ""
subsetdef: goslim_chembl ""
subsetdef: goslim_generic ""
subsetdef: goslim_metagenomics ""
subsetdef: goslim_pir ""
subsetdef: goslim_plant ""
subsetdef: goslim_pombe ""
subsetdef: goslim_yeast ""
subsetdef: grouping_class ""
subsetdef: inconsistent_with_fma ""
subsetdef: major_organ ""
subsetdef: mpath_slim ""
subsetdef: non_informative ""
subsetdef: organ_slim ""
subsetdef: pheno_slim ""
subsetdef: phenotype_rcn ""
subsetdef: relational_slim ""
subsetdef: ro-eco ""
subsetdef: RO:0002259 ""
subsetdef: scalar_slim ""
subsetdef: uberon_slim ""
subsetdef: ubprop:upper_level ""
subsetdef: upper_level ""
subsetdef: value_slim ""
subsetdef: vertebrate_core ""
ontology: lepao
property_value: dc-description "None" xsd:string
property_value: dc-title "lepidoptera anatomy ontology" xsd:string
property_value: dcterms-license https://creativecommons.org/licenses/unspecified
property_value: owl:versionInfo "2021-01-19" xsd:string

[Term]
id: AISM:00000000
name: root node

[Term]
id: AISM:0000002
name: articulation
def: "The anatomical cluster that is composed two articular surfaces that are adjacent to each other." []
is_a: AISM:0000174 ! region of cuticle
property_value: curator_notes "Articulations are `anatomical clusters`, collections of not direclty connected (continuous) sclerite surfaces that are adjacent to another sclerite. The cranio-mandibular articulation is the articular surface of the cranium and the adjacent articular surface of the mandible. The articular surfaces are sometimes located on the same sclerite." xsd:string {http://purl.org/dc/elements/1.1/contributor="imiko"}

[Term]
id: AISM:0000003
name: sclerite
def: "The region of the insect cuticle that is less flexible than the neighboring conjunctiva(e) (conjunctiva(e) that the sclerite is continuous with)." []
is_a: AISM:0000174 ! region of cuticle

[Term]
id: AISM:0000004
name: conjunctiva
def: "The region of the insect cuticle that is more flexible than the neighboring sclerite(s) (sclerite(s) that the conjunctiva is continuous with)." []
is_a: AISM:0000174 ! region of cuticle
relationship: continuous_with AISM:0000003 ! sclerite
property_value: curator_notes "Conjunctivae are more flexible and usually less thick than sclerties of the cuticle allowing the sclerites to move relative to each other.\nMicro-CT based methods cannot be used to accuirately to differentiate slcerites from conjunctiuvae. CLSM (the excitation wavelengths of sclerites and conjunctivae are different in response of 488 nm emission vawelength), histological sections or simple dissections need to be applied to define relative flexibility of the insect cuticle.\n\nIf a conjunctiva entirelly encircles a sclerites, than the `encircles` and `encircled by` object properties are used to link the sclerite and the conjunctiva even in cases in which the encircled sclerites or conjunctivae are part of an evagination allowing to model spatial relationship between appendage segments: the pedicel is encircled by the scapal-pedicel conjunctiva, which is encircled by the scape or the the coxa encircles the basal femoral conjunctiuva that encircels the femur." xsd:string

[Term]
id: AISM:0000005
name: cuticular depression
def: "The portion of the surface of the cuticle that is concave." []
is_a: AISM:0000174 ! region of cuticle
property_value: curator_notes "The surface of the cuticle in insects is the entire surface of an organism, and it is composed of flat, concave and convex regions. Concavities sometimes correspons with invaginations of the cuticle and the underlaying sinlge layer epidermis, somtimes correspond to a decreased cuticular thickness." xsd:string

[Term]
id: AISM:0000006
name: cuticular invagination
def: "The cuticular region that corresponds with an invagination of the single layer epidermis (epidermal fold). The cuticular invagination sometimes corresponds to a cuticular depression (concavity on the surface of the cuticle)." []
is_a: AISM:0000174 ! region of cuticle
relationship: bearer_of PATO:0001748 ! invaginated
relationship: RO:0002008 UBERON:0005157 ! coincident with epithelial fold

[Term]
id: AISM:0000007
name: elastic cuticle
is_a: AISM:0000174 ! region of cuticle
relationship: contains http://flybase.org/reports/FBgn0034157 ! resilin (fruit fly)

[Term]
id: AISM:0000008
name: cuticular protrusion
def: "The cuticular region that corresponds to a convex cuticular surface." [] {http://purl.org/dc/elements/1.1/contributor="imiko"}
is_a: AISM:0000174 ! region of cuticle
property_value: curator_notes "The surface of the cuticle in insects is the entire surface of an organism, and it is composed of flat, concave and convex regions. Convexities sometimes correspons with evaginations of the cuticle and the underlaying sinlge layer epidermis and sometimes correspond to an increased cuticular thickness.\"" xsd:string {http://purl.org/dc/elements/1.1/contributor="imiko"}

[Term]
id: AISM:0000013
name: evaginated
is_a: PATO:0001355 ! convex

[Term]
id: AISM:0000014
name: cranio-mandibular articulation
is_a: AISM:0000002 ! articulation

[Term]
id: AISM:0000015
name: cranio-cardinal articulation
is_a: AISM:0000002 ! articulation

[Term]
id: AISM:0000016
name: cranio-antennal articulation
def: "The articulation between the scape and the cranium." []
is_a: AISM:0000002 ! articulation
property_value: curator_notes "" xsd:string

[Term]
id: AISM:0000017
name: head-cervical articulation
is_a: AISM:0000002 ! articulation

[Term]
id: AISM:0000018
name: cardo
is_a: AISM:0000003 ! sclerite
relationship: continuous_with AISM:0000099 ! oral foraminal conjunctiva
relationship: continuous_with AISM:0000110 ! stipito-cardinal conjunctiva
relationship: proximal_to AISM:0000111 ! stipes

[Term]
id: AISM:0000019
name: cranium
is_a: AISM:0000003 ! sclerite
relationship: AISM:0000078 AISM:0000099 ! encircles oral foraminal conjunctiva
relationship: continuous_with AISM:0000098 ! neck membrane
relationship: has_part AISM:0000088 ! eye cuticle
relationship: surrounds UBERON:0000955 ! brain

[Term]
id: AISM:0000020
name: dorsal second axillary sclerite
is_a: AISM:0000003 ! sclerite

[Term]
id: AISM:0000021
name: first abdominal tergite
is_a: AISM:0000003 ! sclerite

[Term]
id: AISM:0000022
name: first axillary sclerite
is_a: AISM:0000003 ! sclerite

[Term]
id: AISM:0000023
name: galea
is_a: AISM:0000029 ! appendage

[Term]
id: AISM:0000024
name: labial palpus
is_a: AISM:0000029 ! appendage

[Term]
id: AISM:0000026
name: lacinia
is_a: AISM:0000029 ! appendage

[Term]
id: AISM:0000027
name: cuticular evagination
def: "The cuticular region that corresponds with an evagination of the cuticle and the single layer epidermis (epidermal fold). The cuticular evagination usually corresponds to a cuticular protrusion (convexity on the surface of the cuticle)." []
is_a: AISM:0000174 ! region of cuticle
relationship: bearer_of AISM:0000013 ! evaginated
relationship: RO:0002008 UBERON:0005157 ! coincident with epithelial fold

[Term]
id: AISM:0000028
name: solid cuticular protrusion
is_a: AISM:0000008 ! cuticular protrusion

[Term]
id: AISM:0000029
name: appendage
def: "The evagination of the cuticle that is musculated (connected to the body via muscles)." []
is_a: AISM:0000128 ! multicellular cuticular evagination
relationship: continuous_with UBERON:0001134 ! skeletal muscle tissue

[Term]
id: AISM:0000031
name: leg
is_a: AISM:0000029 ! appendage
relationship: posterior_to AISM:0000098 ! neck membrane

[Term]
id: AISM:0000032
name: antenna
is_a: AISM:0000029 ! appendage
relationship: AISM:0000079 AISM:0000112 ! encircled by basal antennal conjunctiva

[Term]
id: AISM:0000033
name: wing
is_a: AISM:0000029 ! appendage
relationship: bearer_of PATO:0000407 ! flat
relationship: contralateral_to AISM:0000033 {cardinality="1"} ! wing

[Term]
id: AISM:0000034
name: fore leg
is_a: AISM:0000031 ! leg
relationship: anterior_to AISM:0000035 ! mid leg

[Term]
id: AISM:0000035
name: mid leg
is_a: AISM:0000031 ! leg
relationship: anterior_to AISM:0000036 ! hind leg

[Term]
id: AISM:0000036
name: hind leg
is_a: AISM:0000031 ! leg

[Term]
id: AISM:0000037
name: fore wing
is_a: AISM:0000033 ! wing
relationship: continuous_with AISM:0000052 ! mesonotum

[Term]
id: AISM:0000038
name: hind wing
is_a: AISM:0000033 ! wing
relationship: continuous_with AISM:0000169 ! metanotum

[Term]
id: AISM:0000039
name: seta
is_a: AISM:0000003 ! sclerite
is_a: AISM:0000127 ! unicellular cuticular evagination
relationship: AISM:0000079 AISM:0000126 ! encircled by socket membrane
relationship: RO:0002008 CL:0000066 {cardinality="1"} ! coincident with epithelial cell

[Term]
id: AISM:0000040
name: spur {http://purl.obolibrary.org/obo/AISM_0000171="https://doi.org/10.1016/0020-7322(79)90013-8"}
def: "The multicellular evagination of the cuticle that corresponds to an epithelial fold, composed of a single sclerite that is encricled by a conjunctiva (moveable), and not musculated." [] {http://purl.org/dc/elements/1.1/contributor="imiko"}
is_a: AISM:0000003 ! sclerite
is_a: AISM:0000128 ! multicellular cuticular evagination
relationship: AISM:0000079 AISM:0000004 ! encircled by conjunctiva
property_value: curator_notes "The difference between an appendage and a spur is the lack of muscles attached to the spur, otherwise, the mandible would be also a spur. Spines are multicellular evaginations that are not encircled by conjunctivae. Moveable beetle horns are spurs while not moveable beetle horns are spines." xsd:string {http://purl.org/dc/elements/1.1/contributor="imiko"}

[Term]
id: AISM:0000041
name: scale
is_a: AISM:0000039 ! seta
relationship: bearer_of PATO:0002254 ! flattened

[Term]
id: AISM:0000042
name: labrum
is_a: AISM:0000029 ! appendage

[Term]
id: AISM:0000043
name: mandible
is_a: AISM:0000003 ! sclerite
is_a: AISM:0000029 ! appendage
relationship: AISM:0000079 AISM:0000099 ! encircled by oral foraminal conjunctiva
relationship: anterior_to AISM:0000044 ! maxilla
relationship: continuous_with AISM:0000082 ! cranio-mandibular muscle

[Term]
id: AISM:0000044
name: maxilla
is_a: AISM:0000029 ! appendage

[Term]
id: AISM:0000045
name: second valvifer
is_a: AISM:0000029 ! appendage

[Term]
id: AISM:0000046
name: second valvula
is_a: AISM:0000029 ! appendage

[Term]
id: AISM:0000047
name: pretarsus
is_a: AISM:0000029 ! appendage

[Term]
id: AISM:0000048
name: ligula
is_a: AISM:0000029 ! appendage

[Term]
id: AISM:0000049
name: glossa
is_a: AISM:0000029 ! appendage
relationship: part_of AISM:0000048 ! ligula

[Term]
id: AISM:0000050
name: paraglossa
is_a: AISM:0000029 ! appendage
relationship: part_of AISM:0000048 ! ligula

[Term]
id: AISM:0000051
name: maxillary palpus
is_a: AISM:0000029 ! appendage

[Term]
id: AISM:0000052
name: mesonotum
is_a: AISM:0000003 ! sclerite

[Term]
id: AISM:0000053
name: mesopectus
is_a: AISM:0000003 ! sclerite
relationship: continuous_with AISM:0000103 ! basal mesocoxal conjunctiva
relationship: has_part AISM:0000141 ! mesofurca

[Term]
id: AISM:0000054
name: mesotrochantin
is_a: AISM:0000003 ! sclerite

[Term]
id: AISM:0000055
name: protrochantin
is_a: AISM:0000003 ! sclerite

[Term]
id: AISM:0000056
name: metatrochantin
is_a: AISM:0000003 ! sclerite

[Term]
id: AISM:0000057
name: prementum
is_a: AISM:0000003 ! sclerite

[Term]
id: AISM:0000058
name: prepectus
is_a: AISM:0000003 ! sclerite

[Term]
id: AISM:0000059
name: pronotum
is_a: AISM:0000003 ! sclerite
relationship: continuous_with AISM:0000098 ! neck membrane
relationship: continuous_with AISM:0000121 ! pronoto-propleural conjunctiva
relationship: continuous_with AISM:0000145 ! procoxal muscle
relationship: continuous_with UBERON:0002376 ! cranial muscle
relationship: posterior_to AISM:0000098 ! neck membrane

[Term]
id: AISM:0000060
name: propeluron
is_a: AISM:0000003 ! sclerite
relationship: continuous_with AISM:0000106 ! basal procoxal conjunctiva
relationship: continuous_with AISM:0000121 ! pronoto-propleural conjunctiva
relationship: continuous_with AISM:0000145 ! procoxal muscle
relationship: continuous_with UBERON:0002376 ! cranial muscle

[Term]
id: AISM:0000061
name: prosternum
is_a: AISM:0000003 ! sclerite

[Term]
id: AISM:0000062
name: ring sclerite
is_a: AISM:0000003 ! sclerite

[Term]
id: AISM:0000063
name: appendage segment
is_a: AISM:0000062 ! ring sclerite
relationship: continuous_with UBERON:0001134 ! skeletal muscle tissue

[Term]
id: AISM:0000064
name: mesocoxa
is_a: AISM:0000077 ! coxa
relationship: AISM:0000078 AISM:0000124 ! encircles basal mesofemoral conjunctiva
relationship: AISM:0000079 AISM:0000103 ! encircled by basal mesocoxal conjunctiva

[Term]
id: AISM:0000065
name: metacoxa
is_a: AISM:0000077 ! coxa
relationship: AISM:0000078 AISM:0000125 ! encircles basal metafemoral conjunctiva
relationship: AISM:0000079 AISM:0000104 ! encircled by basal metacoxal conjunctiva

[Term]
id: AISM:0000066
name: procoxa
is_a: AISM:0000077 ! coxa
relationship: AISM:0000078 AISM:0000123 ! encircles basal profemoral conjunctiva
relationship: AISM:0000079 AISM:0000106 ! encircled by basal procoxal conjunctiva

[Term]
id: AISM:0000067
name: protibia
is_a: AISM:0000075 ! tibia

[Term]
id: AISM:0000068
name: mesotibia
is_a: AISM:0000075 ! tibia

[Term]
id: AISM:0000069
name: metatibia
is_a: AISM:0000075 ! tibia

[Term]
id: AISM:0000070
name: profemur
is_a: AISM:0000076 ! femur
relationship: AISM:0000079 AISM:0000123 ! encircled by basal profemoral conjunctiva

[Term]
id: AISM:0000071
name: mesofemur
is_a: AISM:0000076 ! femur
relationship: AISM:0000079 AISM:0000124 ! encircled by basal mesofemoral conjunctiva

[Term]
id: AISM:0000072
name: metafemur
is_a: AISM:0000076 ! femur
relationship: AISM:0000079 AISM:0000125 ! encircled by basal metafemoral conjunctiva

[Term]
id: AISM:0000073
name: mere
is_a: AISM:0000062 ! ring sclerite

[Term]
id: AISM:0000074
name: tarsomere
is_a: AISM:0000073 ! mere
relationship: AISM:0000079 AISM:0000075 ! encircled by tibia

[Term]
id: AISM:0000075
name: tibia
is_a: AISM:0000063 ! appendage segment
relationship: AISM:0000079 AISM:0000076 ! encircled by femur

[Term]
id: AISM:0000076
name: femur
is_a: AISM:0000063 ! appendage segment

[Term]
id: AISM:0000077
name: coxa
is_a: AISM:0000063 ! appendage segment

[Term]
id: AISM:0000080
name: cranial muscle
is_a: UBERON:0001134 ! skeletal muscle tissue
relationship: continuous_with UBERON:0003128 ! cranium

[Term]
id: AISM:0000081
name: cranio-antennal muscle
is_a: AISM:0000080 ! cranial muscle
relationship: continuous_with AISM:0000019 ! cranium
relationship: continuous_with AISM:0000032 ! antenna

[Term]
id: AISM:0000082
name: cranio-mandibular muscle
is_a: AISM:0000080 ! cranial muscle

[Term]
id: AISM:0000083
name: cranio-labial muscle
is_a: AISM:0000080 ! cranial muscle
relationship: continuous_with AISM:0000019 ! cranium
relationship: continuous_with AISM:0000087 ! labium

[Term]
id: AISM:0000084
name: cranio-labral muscle
is_a: AISM:0000080 ! cranial muscle
relationship: continuous_with AISM:0000042 ! labrum

[Term]
id: AISM:0000085
name: mesocoxal muscle
is_a: AISM:0000086 ! coxal muscle
relationship: continuous_with AISM:0000064 ! mesocoxa

[Term]
id: AISM:0000086
name: coxal muscle
comment: The skeletal muscle that inserts on the coxa. {http://purl.org/dc/elements/1.1/contributor="imiko"}
is_a: UBERON:0001134 ! skeletal muscle tissue
relationship: continuous_with AISM:0000077 ! coxa
property_value: curator_notes "All of the coxal muscles, except the second steranl-metacoxal muscle, are attached to the thorax." xsd:string {http://purl.org/dc/elements/1.1/contributor="imiko"}

[Term]
id: AISM:0000087
name: labium
is_a: AISM:0000029 ! appendage

[Term]
id: AISM:0000088
name: eye cuticle
is_a: AISM:0000007 ! elastic cuticle
relationship: bearer_of PATO:0000964 ! transparent
relationship: part_of AISM:0000019 ! cranium

[Term]
id: AISM:0000089
name: ligament
is_a: AISM:0000007 ! elastic cuticle
relationship: continuous_with AISM:0000003 ! sclerite
relationship: part_of AISM:0000004 ! conjunctiva

[Term]
id: AISM:0000090
name: tendon
def: "The usually cylindircal evagination of the ciuticle that is resilin rich and is continuous with skeletal muscles." [] {http://purl.org/dc/elements/1.1/contributor="imiko"}
is_a: AISM:0000006 ! cuticular invagination
is_a: AISM:0000007 ! elastic cuticle
relationship: continuous_with UBERON:0001134 ! skeletal muscle tissue
property_value: curator_notes "" xsd:string

[Term]
id: AISM:0000091
name: trachea
def: "\"The ivagination of the cuticle that is tubular and contains taenidia.\"" []
is_a: AISM:0000007 ! elastic cuticle
is_a: AISM:0000136 ! branching cuticular invagination
relationship: bearer_of PATO:0001873 ! cylindrical
relationship: has_part AISM:0000140 ! taenidium

[Term]
id: AISM:0000093
name: hypopharynx
is_a: AISM:0000004 ! conjunctiva

[Term]
id: AISM:0000094
name: mesopleuro-metapleural conjunctiva
is_a: AISM:0000004 ! conjunctiva

[Term]
id: AISM:0000095
name: mesopostnoto-mesonotal conjunctiva
is_a: AISM:0000004 ! conjunctiva

[Term]
id: AISM:0000096
name: mesosterno-mesopleural conjunctiva
is_a: AISM:0000004 ! conjunctiva

[Term]
id: AISM:0000097
name: metanoto-mesopostnotal conjunctiva
is_a: AISM:0000004 ! conjunctiva

[Term]
id: AISM:0000098
name: neck membrane
is_a: AISM:0000004 ! conjunctiva

[Term]
id: AISM:0000099
name: oral foraminal conjunctiva
is_a: AISM:0000004 ! conjunctiva

[Term]
id: AISM:0000100
name: pronoto-mesonotal conjunctiva
is_a: AISM:0000004 ! conjunctiva

[Term]
id: AISM:0000101
name: pronoto-mesopectal conjunctiva
is_a: AISM:0000004 ! conjunctiva

[Term]
id: AISM:0000102
name: ring conjunctiva
is_a: AISM:0000004 ! conjunctiva
relationship: AISM:0000078 AISM:0000003 ! encircles sclerite

[Term]
id: AISM:0000103
name: basal mesocoxal conjunctiva
def: "The basal conjunctiva of the mesoxoca." []
is_a: AISM:0000173 ! basal coxal conjunctiva

[Term]
id: AISM:0000104
name: basal metacoxal conjunctiva
is_a: AISM:0000173 ! basal coxal conjunctiva

[Term]
id: AISM:0000105
name: epipharynx
is_a: AISM:0000004 ! conjunctiva
relationship: continuous_with AISM:0000099 ! oral foraminal conjunctiva

[Term]
id: AISM:0000106
name: basal procoxal conjunctiva
is_a: AISM:0000173 ! basal coxal conjunctiva

[Term]
id: AISM:0000107
name: head
def: "The cuticular region that is anterior (distal) to the neck membrane (encircled by the neck membrane) and contains the antenna, the eyes, mouthparts and surrounds the brain." []
is_a: AISM:0000174 ! region of cuticle
relationship: AISM:0000079 AISM:0000098 ! encircled by neck membrane
relationship: distal_to AISM:0000098 ! neck membrane
relationship: has_part AISM:0000032 ! antenna
relationship: has_part UBERON:0003128 ! cranium
relationship: surrounds UBERON:0000955 ! brain
property_value: dc-description "" xsd:string

[Term]
id: AISM:0000108
name: thorax
def: "The region of cuticle that is connected to some muscles of the fore and hind legs and is posterior to the neck membrane and aterior to the first abdominal spiracle." [] {http://purl.org/dc/elements/1.1/contributor="imiko"}
is_a: AISM:0000174 ! region of cuticle
relationship: has_part AISM:0000031 ! leg
relationship: has_part AISM:0000085 ! mesocoxal muscle
relationship: has_part AISM:0000145 ! procoxal muscle
relationship: posterior_to AISM:0000098 ! neck membrane
property_value: curator_notes "The hind leg muscles sometimes attach to the second abdominal sternite. The abdominal sopiracles are different in their structure from tghe thoracic spiracles as they are opened and closed by two articulating sclerites that are moved by two sets of muscles whereas the thoracic spiracles are closed by only one occlusor muscle and opened by the flexibility of the distal tracheal region. The border between the thorax and the abdomen is sometimes marked by the anterior first abdmonial tergal conjunctiva. In Hymenoptera, the border between the abdomen and the thorax cannot be defined as the anterior first abdmonial tergal conjunctiva is absent, the sclerite that receives muscles from the metacoxa also contains the first abdominal spiracle." xsd:string {http://purl.org/dc/elements/1.1/contributor="imiko"}

[Term]
id: AISM:0000109
name: abdomen {http://purl.obolibrary.org/obo/AISM_0000171="Snodgrass, R.E., 1931. Morphology of the insect abdomen. Smithsonian Miscellaneous Collections.\n\nhttps://repository.si.edu/bitstream/handle/10088/23927/SMC_85_Snodgrass_1931_6_1-128.pdf"}
def: "The region of the cuticle that is posterior to the thorax." [] {http://purl.org/dc/elements/1.1/contributor="imiko"}
is_a: AISM:0000174 ! region of cuticle
relationship: posterior_to AISM:0000108 ! thorax
property_value: curator_notes "The thorax is defined based on local properties (e.g. attachment sites of coxal muscles) and therefore we can reference this class for the definition of the abdomen." xsd:string {http://purl.org/dc/elements/1.1/contributor="imiko"}

[Term]
id: AISM:0000110
name: stipito-cardinal conjunctiva
is_a: AISM:0000004 ! conjunctiva
relationship: continuous_with AISM:0000018 ! cardo

[Term]
id: AISM:0000111
name: stipes
is_a: AISM:0000003 ! sclerite
relationship: continuous_with AISM:0000110 ! stipito-cardinal conjunctiva
relationship: distal_to AISM:0000018 ! cardo

[Term]
id: AISM:0000112
name: basal antennal conjunctiva
def: "This conjunctiva encircle the base of the antenna (scape) and is encircled by the cranium as the antennal foramen." [] {http://purl.org/dc/elements/1.1/contributor="imiko"}
is_a: AISM:0000004 ! conjunctiva
relationship: AISM:0000078 AISM:0000113 ! encircles scape
relationship: continuous_with UBERON:0003128 ! cranium
property_value: curator_notes "" xsd:string

[Term]
id: AISM:0000113
name: scape
is_a: AISM:0000063 ! appendage segment
relationship: AISM:0000078 AISM:0000114 ! encircles scapal-pedicel conjunctiva
relationship: part_of AISM:0000032 ! antenna

[Term]
id: AISM:0000114
name: scapal-pedicel conjunctiva
is_a: AISM:0000004 ! conjunctiva

[Term]
id: AISM:0000115
name: pedicel
is_a: AISM:0000063 ! appendage segment
relationship: AISM:0000078 AISM:0000118 ! encircles pedicel-first flagellomere conjunctiva

[Term]
id: AISM:0000116
name: flagellomere
is_a: AISM:0000073 ! mere
relationship: part_of AISM:0000032 ! antenna

[Term]
id: AISM:0000117
name: first flagellomere
is_a: AISM:0000116 ! flagellomere

[Term]
id: AISM:0000118
name: pedicel-first flagellomere conjunctiva
is_a: AISM:0000004 ! conjunctiva
relationship: AISM:0000078 AISM:0000117 ! encircles first flagellomere

[Term]
id: AISM:0000119
name: metapleuron
is_a: AISM:0000003 ! sclerite
relationship: continuous_with AISM:0000104 ! basal metacoxal conjunctiva
relationship: part_of AISM:0000108 ! thorax

[Term]
id: AISM:0000120
name: pronoto-procoxal conjunctiva
is_a: AISM:0000004 ! conjunctiva

[Term]
id: AISM:0000121
name: pronoto-propleural conjunctiva
is_a: AISM:0000004 ! conjunctiva

[Term]
id: AISM:0000123
name: basal profemoral conjunctiva
is_a: AISM:0000004 ! conjunctiva

[Term]
id: AISM:0000124
name: basal mesofemoral conjunctiva
is_a: AISM:0000004 ! conjunctiva
relationship: AISM:0000078 AISM:0000071 ! encircles mesofemur
relationship: continuous_with AISM:0000064 ! mesocoxa

[Term]
id: AISM:0000125
name: basal metafemoral conjunctiva
is_a: AISM:0000004 ! conjunctiva

[Term]
id: AISM:0000126
name: socket membrane
is_a: AISM:0000004 ! conjunctiva
relationship: AISM:0000078 AISM:0000127 ! encircles unicellular cuticular evagination
relationship: RO:0002008 CL:0000066 {cardinality="1"} ! coincident with epithelial cell

[Term]
id: AISM:0000127
name: unicellular cuticular evagination
is_a: AISM:0000027 ! cuticular evagination
relationship: RO:0002008 CL:0000066 {cardinality="1"} ! coincident with epithelial cell

[Term]
id: AISM:0000128
name: multicellular cuticular evagination
is_a: AISM:0000027 ! cuticular evagination

[Term]
id: AISM:0000130
name: uniporous sensillum
is_a: AISM:0000127 ! unicellular cuticular evagination
relationship: has_part AISM:0000134 {cardinality="1"} ! exocrine gland duct

[Term]
id: AISM:0000131
name: multiporous sensillum
is_a: AISM:0000127 ! unicellular cuticular evagination
relationship: has_part AISM:0000134 {minCardinality="2"} ! exocrine gland duct

[Term]
id: AISM:0000132
name: placoid
is_a: AISM:0000133 ! multiporous plate
relationship: bearer_of PATO:0001154 ! elongated

[Term]
id: AISM:0000133
name: multiporous plate
is_a: AISM:0000131 ! multiporous sensillum
relationship: bearer_of PATO:0000407 ! flat

[Term]
id: AISM:0000134
name: exocrine gland duct
is_a: AISM:0000136 ! branching cuticular invagination
relationship: RO:0002008 CL:0000066 {cardinality="1"} ! coincident with epithelial cell

[Term]
id: AISM:0000135
name: spiracle
is_a: AISM:0000174 ! region of cuticle

[Term]
id: AISM:0000136
name: branching cuticular invagination
is_a: AISM:0000006 ! cuticular invagination
relationship: bearer_of PATO:0000402 ! branched

[Term]
id: AISM:0000137
name: malphigian tube
is_a: AISM:0000136 ! branching cuticular invagination

[Term]
id: AISM:0000138
name: apophysis
is_a: AISM:0000006 ! cuticular invagination

[Term]
id: AISM:0000140
name: taenidium
is_a: AISM:0000158 ! ridge
relationship: bearer_of PATO:0000404 ! coiled

[Term]
id: AISM:0000141
name: mesofurca
is_a: AISM:0000144 ! furca

[Term]
id: AISM:0000142
name: metafurca
is_a: AISM:0000144 ! furca

[Term]
id: AISM:0000143
name: profurca
is_a: AISM:0000144 ! furca

[Term]
id: AISM:0000144
name: furca
is_a: AISM:0000138 ! apophysis
relationship: part_of AISM:0000108 ! thorax
relationship: part_of BSPO:0000112 ! ventro-medial region

[Term]
id: AISM:0000145
name: procoxal muscle
is_a: AISM:0000086 ! coxal muscle
relationship: continuous_with AISM:0000066 ! procoxa

[Term]
id: AISM:0000146
name: metacoxal muscle
is_a: AISM:0000086 ! coxal muscle
relationship: continuous_with AISM:0000065 ! metacoxa

[Term]
id: AISM:0000147
name: femoral muscle
is_a: UBERON:0001134 ! skeletal muscle tissue
relationship: continuous_with AISM:0000076 ! femur

[Term]
id: AISM:0000148
name: tibial muscle
is_a: UBERON:0001134 ! skeletal muscle tissue

[Term]
id: AISM:0000149
name: muscle of the tarsal claw
def: "The skeletal muscle that inserts on the pretarsus." [] {http://purl.org/dc/elements/1.1/contributor="imiko"}
is_a: UBERON:0001134 ! skeletal muscle tissue
relationship: continuous_with AISM:0000047 ! pretarsus
property_value: curator_notes "There are usually two muscle bands of the pretarsal muscle, one is arising from the femur, the other from the tibia. The muscle usually inserts on a resilin rich basal sclerite of the pretarsus, the unguitractor plate." xsd:string {http://purl.org/dc/elements/1.1/contributor="imiko"}

[Term]
id: AISM:0000150
name: profemoral muscle
is_a: AISM:0000147 ! femoral muscle
relationship: continuous_with AISM:0000070 ! profemur

[Term]
id: AISM:0000151
name: mesofemoral muscle
is_a: AISM:0000147 ! femoral muscle
relationship: continuous_with AISM:0000071 ! mesofemur

[Term]
id: AISM:0000152
name: metafemoral muscle
is_a: AISM:0000147 ! femoral muscle
relationship: continuous_with AISM:0000072 ! metafemur

[Term]
id: AISM:0000153
name: protibial muscle
is_a: AISM:0000148 ! tibial muscle
relationship: continuous_with AISM:0000067 ! protibia

[Term]
id: AISM:0000154
name: mesotibial muscle
is_a: AISM:0000148 ! tibial muscle
relationship: continuous_with AISM:0000068 ! mesotibia

[Term]
id: AISM:0000155
name: metatibial muscle
is_a: AISM:0000148 ! tibial muscle
relationship: continuous_with AISM:0000069 ! metatibia

[Term]
id: AISM:0000156
name: fovea
def: "The cuticular depression that is circular." [] {http://purl.obolibrary.org/obo/IAO_0000232="imiko"}
is_a: AISM:0000005 ! cuticular depression
relationship: bearer_of PATO:0000411 ! circular

[Term]
id: AISM:0000157
name: impression
def: "The cuticular depression (concavity on the surface of the cuticle) that does not correspomnd to a cuticular invagination (epithelial fold). The cuticule is less thick at the site of a cuticular impression." [] {http://purl.org/dc/elements/1.1/contributor="imiko"}
is_a: AISM:0000005 ! cuticular depression

[Term]
id: AISM:0000158
name: ridge
def: "The invagination on a sclerite that is elongated." []
is_a: AISM:0000006 ! cuticular invagination
relationship: bearer_of PATO:0001154 ! elongated
relationship: part_of AISM:0000003 ! sclerite

[Term]
id: AISM:0000159
name: salivarium
is_a: AISM:0000160 ! pouch
relationship: continuous_with AISM:0000087 ! labium
relationship: continuous_with AISM:0000093 ! hypopharynx
relationship: continuous_with AISM:0000134 ! exocrine gland duct

[Term]
id: AISM:0000160
name: pouch
def: "The invagination of the cuticle that is largely membraneous." [] {http://purl.org/dc/elements/1.1/contributor="imiko"}
is_a: AISM:0000006 ! cuticular invagination
relationship: bearer_of AISM:0000004 ! conjunctiva
relationship: has_part BSPO:0000077 ! proximal region

[Term]
id: AISM:0000161
name: discrimenal lamella
def: "The ridge that is in the sagittal line of the ventral part thorax." []
is_a: AISM:0000158 ! ridge
relationship: RO:0002008 BSPO:0000417 ! coincident with sagittal plane

[Term]
id: AISM:0000162
name: sulcus
def: "The cuticular depression (concavity on cuticle surface) that corresponds with a ridge (an elongate cuticular invagination)." []
is_a: AISM:0000005 ! cuticular depression
relationship: RO:0002008 AISM:0000158 ! coincident with ridge

[Term]
id: AISM:0000163
name: discrimen
def: "The ridge that corresponds to the discrimenal lamella." []
is_a: AISM:0000162 ! sulcus

[Term]
id: AISM:0000165
name: mouthpart
is_a: AISM:0000174 ! region of cuticle
relationship: AISM:0000079 AISM:0000099 ! encircled by oral foraminal conjunctiva

[Term]
id: AISM:0000166
name: propleuro-procoxal artiulation
is_a: AISM:0000002 ! articulation

[Term]
id: AISM:0000167
name: articular surface
is_a: UBERON:0006984 ! anatomical surface
intersection_of: adjacent_to AISM:0000003 ! sclerite
intersection_of: part_of AISM:0000003 ! sclerite
relationship: adjacent_to AISM:0000003 ! sclerite
relationship: part_of AISM:0000003 ! sclerite

[Term]
id: AISM:0000168
name: salivary sclerite
is_a: AISM:0000003 ! sclerite
relationship: part_of AISM:0000159 ! salivarium

[Term]
id: AISM:0000169
name: metanotum
is_a: AISM:0000003 ! sclerite

[Term]
id: AISM:0000170
name: metapectus
is_a: AISM:0000003 ! sclerite

[Term]
id: AISM:0000172
name: apical tarsal conjunctiva
def: "The distalmost conjunctiva at the tarsus that encircles the pretarsus and encricled by the apicalmost tarsomere." []
is_a: AISM:0000004 ! conjunctiva
relationship: continuous_with AISM:0000047 ! pretarsus
property_value: curator_notes "" xsd:string

[Term]
id: AISM:0000173
name: basal coxal conjunctiva
def: "The conjunctiva that encircles the coxa and connects them to the ventral and lateral thoracic regions." [] {http://purl.org/dc/elements/1.1/contributor="imiko"}
is_a: AISM:0000004 ! conjunctiva
property_value: curator_notes "These conjunctivae can be used as stable reference points in insects that poseess legs, and can be used to define sclerites on the lateral side of the thorax." xsd:string

[Term]
id: AISM:0000174
name: region of cuticle
def: "The region of the insect integument that is part of the insect cuticle." []
is_a: UBERON:6007284 ! insect region of integument
relationship: part_of UBERON:0001001 ! chitin-based cuticle
property_value: curator_notes "The AISM focuses on anatomical structures that are part of the insect (chitinous) cuticle. These structures are acellular regions of the integument. Regions of the insect cuticle with different mechanical properties (i.e. increased and descresed flexinility, thickness and elasticity) are continuous with each other (e.g. sclerites are continuous with conjunctivae or resilin rich regions are continuou with regions with less resilin content)." xsd:string

[Term]
id: BSPO:0000070
name: anatomical region
namespace: spatial
def: "A 3D region in space without well-defined compartmental boundaries; for example, the dorsal region of an ectoderm." [BSPO:cjm]
comment: to be merged into CARO
xref: FBql:00005841

[Term]
id: BSPO:0000077
name: proximal region
namespace: spatial
def: "Anatomical region proximally located on the body or body part." [BSPO:wd]
xref: FBql:00005852
is_a: BSPO:0000070 ! anatomical region

[Term]
id: BSPO:0000080
name: dorso-lateral region
namespace: spatial
def: "Anatomical region that overlaps the dorsal and lateral regions of a body or body part." [BSPO:wd]
synonym: "dorsolateral region" EXACT []
xref: FBql:00005845
is_a: BSPO:0000070 ! anatomical region

[Term]
id: BSPO:0000112
name: ventro-medial region
namespace: spatial
def: "The region corresponding to the ventral region of the entity, towards the midline." [BSPO:wd]
synonym: "medioventral region" EXACT []
synonym: "ventromedial region" EXACT []
is_a: BSPO:0000070 ! anatomical region
created_by: Melissa  Haendel
creation_date: 2009-09-10T08:57:54Z

[Term]
id: BSPO:0000417
name: sagittal plane
namespace: spatial
def: "Anatomical plane that divides a bilateral body into left and right parts, not necessarily of even size." [BSPO:cjm, BSPO:DOS, BSPO:mah]
synonym: "left/right plane" EXACT []
synonym: "median plane" EXACT []
synonym: "sagittal section" EXACT []
xref: FMA:11361

[Term]
id: BSPO:0000671
name: anterior margin
namespace: spatial
def: "Anatomical margin that is located on the anterior side of a body or body part." [BSPO:wd]
is_a: BSPO:0000070 ! anatomical region

[Term]
id: BSPO:0000672
name: posterior margin
namespace: spatial
def: "Anatomical margin that is located on the posterior side of the body or body part." [BSPO:wd]
is_a: BSPO:0000070 ! anatomical region

[Term]
id: BSPO:0000677
name: proximal margin
namespace: spatial
def: "Anatomical margin that is located on the proximal region of the body or body part." [BSPO:wd]
is_a: BSPO:0000077 ! proximal region

[Term]
id: BSPO:0000678
name: distal margin
namespace: spatial
def: "Anatomical margin that is located on the distal side of the body or body part." [BSPO:wd]
is_a: BSPO:0000070 ! anatomical region

[Term]
id: BSPO:0000679
name: dorsal margin
namespace: spatial
def: "Anatomical margin that is located on the dorsal side of body or body part." [BSPO:wd]
is_a: BSPO:0000070 ! anatomical region

[Term]
id: BSPO:0000682
name: lateral margin
namespace: spatial
def: "Anatomical margin that is located on the lateral side of the body or body part." [BSPO:wd]
is_a: BSPO:0000070 ! anatomical region

[Term]
id: BSPO:0000683
name: medial margin
namespace: spatial
def: "Anatomical margin that is located on the medial side of the body or body part." [BSPO:wd]
is_a: BSPO:0000070 ! anatomical region

[Term]
id: BSPO:0000684
name: ventral margin
namespace: spatial
def: "Anatomical margin that is located on the ventral side of the body or body part." [BSPO:wd]
is_a: BSPO:0000070 ! anatomical region

[Term]
id: CL:0000066
name: epithelial cell
namespace: cell
def: "A cell that is usually found in a two-dimensional sheet with a free surface. The cell has a cytoskeleton that allows for tight cell to cell contact and for cell polarity where apical part is directed towards the lumen and the basal part to the basal lamina." [FB:ma, GOC:tfm, MESH:A11.436]
synonym: "epitheliocyte" EXACT []
xref: BTO:0000414
xref: CALOHA:TS-2026
xref: CARO:0000077
xref: FBbt:00000124
xref: FMA:66768
xref: WBbt:0003672

[Term]
id: LEPAO:00000000
name: root node

[Term]
id: PATO:0000402
name: branched
namespace: quality
def: "A branchiness quality inhering in a bearer by virtue of the bearer's having branches." [WordNet:WordNet]
subset: cell_quality
subset: mpath_slim
subset: value_slim
synonym: "ramified" EXACT []
synonym: "ramiform" EXACT []
property_value: RO:0002604 PATO:0000414

[Term]
id: PATO:0000404
name: coiled
namespace: quality
alt_id: PATO:0001363
def: "A shape quality inhering in a bearer by virtue of the bearer's being curled or wound (especially in concentric rings or spirals)." [WordNet:WordNet]
subset: cell_quality
subset: mpath_slim
subset: value_slim
synonym: "helical" RELATED []
synonym: "helicoid" RELATED []
synonym: "helicoidal" RELATED []
synonym: "helix-shaped" RELATED []
synonym: "spiral" EXACT []
property_value: RO:0002604 PATO:0000415

[Term]
id: PATO:0000407
name: flat
namespace: quality
def: "A quality inhering in a bearer by virtue of the bearer's having a horizontal surface without a slope, tilt, or curvature." [web:http\://www.merriam-webster.com/]
subset: cell_quality
subset: mpath_slim
subset: value_slim
synonym: "plate-like" RELATED []
is_a: PATO:0002254 ! flattened

[Term]
id: PATO:0000411
name: circular
namespace: quality
def: "A shape quality inhering in a bearer by virtue of the bearer's being such that every part of the surface or the circumference is equidistant from the center." [thefreedictionary.com:thefreedictionary.com]
subset: cell_quality
subset: mpath_slim
subset: value_slim
synonym: "round" RELATED []
synonym: "rounded" RELATED []

[Term]
id: PATO:0000591
name: increased thickness
namespace: quality
def: "A thickness which is relatively high." [PATOC:GVG]
subset: mpath_slim
subset: value_slim
synonym: "high thickness" EXACT []
synonym: "stout" EXACT []
synonym: "thick" RELATED []
synonym: "thickened" EXACT []
property_value: RO:0002604 PATO:0000592

[Term]
id: PATO:0000592
name: decreased thickness
namespace: quality
def: "A thickness which is relatively low." [PATOC:GVG]
subset: mpath_slim
subset: value_slim
synonym: "low thickness" EXACT []
synonym: "slender" RELATED []
synonym: "thin" RELATED []
property_value: RO:0002604 PATO:0000591

[Term]
id: PATO:0000964
name: transparent
namespace: quality
def: "A optical quality inhering in a bearer by virtue of the bearer's lacking opacity." [PATOC:GVG]
subset: mpath_slim
subset: value_slim
synonym: "clear" EXACT []
synonym: "hyaline" EXACT []
property_value: RO:0002604 PATO:0000963

[Term]
id: PATO:0001031
name: elasticity
namespace: quality
def: "A physical quality inhering in a bearer by virtue of the bearer's disposition to recover its size and shape after deformation in any way." [merriam-webster:merriam-webster]
subset: attribute_slim
subset: disposition_slim
subset: scalar_slim

[Term]
id: PATO:0001154
name: elongated
namespace: quality
def: "A quality inhering in a bearer by virtue of the bearer's length being notably higher than its width." [WordNet:WordNet]
subset: value_slim
property_value: RO:0002604 PATO:0002364

[Term]
id: PATO:0001171
name: elastic
namespace: quality
def: "An elasticity quality inhering in a bearer by virtue of the bearer's ability to recover its size and shape after deformation in any way." [merriam-webster:merriam-webster]
subset: disposition_slim
subset: mpath_slim
subset: value_slim
is_a: PATO:0001031 ! elasticity
property_value: RO:0002604 PATO:0001172

[Term]
id: PATO:0001355
name: convex
namespace: quality
def: "A shape quality that obtains by virtue of the bearer having inward facing edges; having a surface or boundary that curves or bulges outward, as the exterior of a sphere." [PATOC:GVG]
subset: cell_quality
subset: value_slim
property_value: RO:0002604 PATO:0001857

[Term]
id: PATO:0001369
name: raised
namespace: quality
def: "A shape quality inhering in a colony by virtue of the bearer's appearing above the medium surface with terraced edges." [PATOC:GVG]
subset: mpath_slim
subset: value_slim

[Term]
id: PATO:0001543
name: flexibility
namespace: quality
def: "A physical quality inhering in a bearer by virtue of the bearer's disposition to being turned, bowed, or twisted without breaking." [merriam-webster:merriam-webster]
subset: attribute_slim
subset: disposition_slim

[Term]
id: PATO:0001748
name: invaginated
namespace: quality
def: "A shape quality in which a portion of the outermost boundary of an entity folds in space such that a portion that was originally convex is now concave." [PATOC:GVG]
subset: cell_quality
subset: mpath_slim
subset: value_slim
is_a: PATO:0001857 ! concave

[Term]
id: PATO:0001857
name: concave
namespace: quality
def: "A shape quality in a bearer by virtue of the bearer's curving inward." [WordNet:WordNet]
subset: cell_quality
subset: value_slim
property_value: RO:0002604 PATO:0001355

[Term]
id: PATO:0001873
name: cylindrical
namespace: quality
alt_id: PATO:0001203
def: "A convex 3-D shape quality inhering in a bearer by virtue of the bearer's exhibiting a consistently-sized round cross section." [PATOC:MAH]
subset: cell_quality
subset: value_slim
synonym: "rod-like" EXACT []
synonym: "rod-shaped" EXACT []
synonym: "tubulate" NARROW []
relationship: has_cross_section PATO:0000411 ! circular

[Term]
id: PATO:0002254
name: flattened
namespace: quality
def: "A quality inhering in a bearer by virtue of the bearer's surface becoming more extended in a plane." [PATOC:CVS]
comment: Becoming flat but not necessarily completely flat.
subset: value_slim
synonym: "compressed" RELATED []
created_by: george
creation_date: 2010-08-16T03:59:34Z

[Term]
id: PATO:0002539
name: ring shaped
namespace: quality
def: "A shape quality inhering in a bearer by virtue of the bearer's having a shape like a ring (a circular shape enclosing a space)." [PATOC:WD]
subset: value_slim
synonym: "annular" EXACT []
synonym: "ring-shaped" EXACT []
created_by: wasila.dahdul
creation_date: 2014-08-12T12:01:56Z

[Term]
id: PR:Q9V7U0
name: pro-resilin (fruit fly)
namespace: protein
def: "A protein that is a translation product of the resilin gene in fruit fly." [PRO:DNx, UniProtKB:Q9V7U0]
comment: Category=organism-gene.
synonym: "CG15920" RELATED Gene-based [UniProtKB:Q9V7U0]
synonym: "fly-resilin" EXACT PRO-short-label [PRO:DNx]
synonym: "resilin" RELATED Gene-based [UniProtKB:Q9V7U0]
xref: UniProtKB:Q9V7U0
relationship: has_gene_template http://flybase.org/reports/FBgn0034157 ! resilin (fruit fly)

[Term]
id: UBERON:0000955
name: brain
namespace: uberon
def: "The brain is the center of the nervous system in all vertebrate, and most invertebrate, animals. Some primitive animals such as jellyfish and starfish have a decentralized nervous system without a brain, while sponges lack any nervous system at all. In vertebrates, the brain is located in the head, protected by the skull and close to the primary sensory apparatus of vision, hearing, balance, taste, and smell[WP]." [http://en.wikipedia.org/wiki/Brain, https://github.com/obophenotype/uberon/issues/300]
subset: cumbo
subset: efo_slim
subset: major_organ
subset: pheno_slim
subset: uberon_slim
subset: vertebrate_core
synonym: "encephalon" RELATED [BTO:0000142]
synonym: "suprasegmental levels of nervous system" RELATED [NeuroNames:21]
synonym: "suprasegmental structures" RELATED [NeuroNames:21]
synonym: "synganglion" RELATED []
synonym: "the brain" RELATED [NeuroNames:21]
xref: AAO:0010478
xref: ABA:Brain
xref: BAMS:Br
xref: BAMS:Brain
xref: BILA:0000135
xref: BIRNLEX:796
xref: BTO:0000142
xref: CALOHA:TS-0095
xref: DHBA:10155
xref: EFO:0000302
xref: EHDAA2:0000183
xref: EHDAA:2641
xref: EHDAA:6485
xref: EMAPA:16894
xref: EV:0100164
xref: FBbt:00005095
xref: FMA:50801
xref: GAID:571
xref: galen:Brain
xref: HBA:4005
xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=21
xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=21 {source="BIRNLEX:796"}
xref: http://en.wikipedia.org/wiki/Brain
xref: http://linkedlifedata.com/resource/umls/id/C0006104
xref: http://linkedlifedata.com/resource/umls/id/C1269537
xref: http://www.snomedbrowser.com/Codes/Details/258335003
xref: MA:0000168
xref: MAT:0000098
xref: MBA:8
xref: MBA:997
xref: MESH:D001921
xref: MIAA:0000098
xref: NCIT:C12439
xref: OpenCyc:Mx4rvVjT65wpEbGdrcN5Y29ycA
xref: PBA:3999
xref: TAO:0000008
xref: UMLS:C0006104 {source="ncithesaurus:Brain"}
xref: UMLS:C0006104 {source="BIRNLEX:796"}
xref: UMLS:C1269537 {source="BIRNLEX:796"}
xref: VHOG:0000157
xref: XAO:0000010
xref: ZFA:0000008
relationship: dc-contributor https://github.com/cmungall
relationship: has_boundary UBERON:0006984 ! anatomical surface
property_value: IAO:0000116 "requires review for applicability to invertebrate structures, e.g. synganglion" xsd:string
property_value: UBPROP:0000001 "Cavitated compound organ which is comprised of gray and white matter and surrounds the cerebral ventricular system.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000008", ontology="TAO", source="ZFIN:curator"}
property_value: UBPROP:0000001 "Part of the central nervous system situated within the cranium and composed of both nerve cell bodies and nerve fibers.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010478", ontology="AAO", source="AAO:BJB"}
property_value: UBPROP:0000001 "The part of the central nervous system contained within the cranium, comprising the forebrain, midbrain, hindbrain, and metencephalon. It is derived from the anterior part of the embryonic neural tube (or the encephalon). Does not include retina. (CUMBO)" xsd:string {source="Cumbo:terms"}
property_value: UBPROP:0000003 "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000157", ontology="VHOG", source="http://bgee.unil.ch/", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28, ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.165"}

[Term]
id: UBERON:0001001
name: chitin-based cuticle
namespace: uberon
alt_id: UBERON:FBbt_00004970
def: "A cuticular covering that is composed primarily of chitin. The main structural component of arthropod cuticle is a polysaccharide, chitin, composed of N-acetylglucosamine units, together with proteins and lipids[WP]." [http://en.wikipedia.org/wiki/Arthropod_exoskeleton, http://en.wikipedia.org/wiki/Cuticle#Invertebrate_zoology, https://orcid.org/0000-0002-6601-2165, https://sourceforge.net/tracker/index.php?func=detail&aid=3348965&group_id=36855&atid=440764]
subset: efo_slim
subset: uberon_slim
synonym: "arthropod cuticle" RELATED []
synonym: "arthropod exoskeleton" RELATED [http://en.wikipedia.org/wiki/Arthropod_exoskeleton]
synonym: "cuticle" NARROW [FBbt:00004970]
synonym: "exoskeleton" BROAD []
synonym: "insect cuticle" RELATED []
xref: Arthropod:exoskeleton
xref: EFO:0000944
xref: FBbt:00004970
xref: HAO:0000240
xref: MAT:0000150
xref: MIAA:0000150
xref: OpenCyc:Mx4rvVkBTJwpEbGdrcN5Y29ycA
property_value: IAO:0000116 "TODO - split from exoskeleton? Also: See above sf item to see if this belongs in GO" xsd:string

[Term]
id: UBERON:0001134
name: skeletal muscle tissue
namespace: uberon
def: "Muscle tissue that consists primarily of skeletal muscle fibers." [https://github.com/obophenotype/uberon/issues/324]
subset: pheno_slim
subset: uberon_slim
subset: vertebrate_core
synonym: "skeletal muscle" BROAD []
synonym: "skeletal muscle system" RELATED [BTO:0001103]
synonym: "somatic muscle" RELATED [BTO:0001103]
xref: EMAPA:32716
xref: FMA:14069
xref: http://en.wikipedia.org/wiki/Skeletal_striated_muscle
xref: http://linkedlifedata.com/resource/umls/id/C0242692
xref: http://www.snomedbrowser.com/Codes/Details/426215008
xref: MA:0002439
xref: NCIT:C13050
xref: UMLS:C0242692 {source="ncithesaurus:Skeletal_Muscle_Tissue"}
relationship: dc-contributor https://github.com/cmungall
relationship: dc-contributor https://github.com/dosumis
relationship: dc-contributor https://github.com/mellybelly
relationship: dc-contributor https://github.com/RDruzinsky
property_value: depicted:by Skeletal:muscle.jpg xsd:anyURI
property_value: IAO:0000116 "TODO - add skeletal muscle organ? See GO:0060538 skeletal muscle organ development. Todo - group FBbt:00005073 - somatic muscle." xsd:string
property_value: UBPROP:0000001 "Muscle, composed of long cylindrical, multinucleated cells that attaches to the skeleton via tendons.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005277", ontology="TAO", source="ZFIN:curator"}
property_value: UBPROP:0000001 "Tissue which consists of skeletal muscle fibers surrounded by endomysium. Examples: Skeletal muscle tissue of biceps, Skeletal muscle tissue of diaphragm[FMA]" xsd:string {external_class="FMA:14069", ontology="FMA"}
property_value: UBPROP:0000003 "This result implies the following views in terms of evolutionary differentiation: (1) Arthropod striated muscle and vertebrate skeletal and cardiac muscles share a common ancestor. In other words, they did not evolve independently (...) (5) The divergence of vertebrate skeletal and cardiac muscles/vertebrate smooth muscle and nonmuscle is at least before that of vertebrates/arthropods. In other words, emergence of skeletal and cardiac musle type tissues preceded the vertebrate/arthropod divergence (ca. 700 MYA).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000319", ontology="VHOG", source="http://bgee.unil.ch/", source="PMID:10368962 Oota S, Saitou N, Phylogenetic relationship of muscle tissues deduced from superimposition of gene trees. Mol Biol Evol (1999)"}

[Term]
id: UBERON:0002376
name: cranial muscle
namespace: uberon
alt_id: UBERON:0003899
def: "Any skeletal muscle that is part of the head region." [http://orcid.org/0000-0002-6601-2165]
comment: defined generically so could in theory encompass FBbt:00003260 'skeletal muscle of head', or the muscle of a starfish Aristotle's lantern, but we restrict this to craniates. Skeletal muscles of the head originate from the non-segmented head mesoderm (Noden, 1983; Wachtler et al., 1984)
subset: efo_slim
subset: uberon_slim
subset: vertebrate_core
synonym: "adult head muscle organ" NARROW [OBOL:automatic]
synonym: "cephalic muscle" EXACT [ZFA:0001652]
synonym: "cephalic musculature" EXACT []
synonym: "cranial muscle" RELATED [ZFA:0001652]
synonym: "head muscle" EXACT [MA:0000578]
synonym: "head muscle organ" EXACT [OBOL:automatic]
synonym: "head muscles" RELATED []
synonym: "muscle of head" EXACT [FMA:9616]
synonym: "muscle organ of adult head" EXACT [OBOL:automatic]
synonym: "muscle organ of head" EXACT [OBOL:automatic]
synonym: "musculus caput" EXACT []
xref: AAO:0000107
xref: BTO:0000021
xref: EFO:0003524
xref: EHDAA2:0000322
xref: EMAPA:18172
xref: FMA:9616
xref: http://www.snomedbrowser.com/Codes/Details/244718003
xref: MA:0000578
xref: ZFA:0001652
relationship: composed_primarily_of UBERON:0001134 ! skeletal muscle tissue
relationship: has_boundary UBERON:0006984 ! anatomical surface

[Term]
id: UBERON:0003128
name: cranium
namespace: uberon
def: "Upper portion of the skull that excludes the mandible (when present in the organism)." [http://en.wikipedia.org/wiki/Cranium_(anatomy), http://orcid.org/0000-0002-6601-2165]
subset: efo_slim
subset: pheno_slim
subset: uberon_slim
subset: vertebrate_core
synonym: "bones of cranium" EXACT [FMA:71325]
synonym: "calvarium" RELATED [BTO:0001328]
synonym: "epicranial plate" RELATED []
synonym: "ossa cranii" EXACT LATIN [FMA:71325, FMA:TA]
synonym: "set of bones of cranium" EXACT [FMA:71325]
synonym: "skeletal system of head" RELATED []
synonym: "skull minus mandible" EXACT []
synonym: "upper part of skull" EXACT []
xref: BTO:0001328
xref: Cranium:(anatomy)
xref: EFO:0000831
xref: EHDAA:6029
xref: EMAPA:17680
xref: FMA:71325
xref: http://www.snomedbrowser.com/Codes/Details/181889008
xref: MA:0000316
xref: MAT:0000340
xref: MIAA:0000340
xref: OpenCyc:Mx4rvVlEyJwpEbGdrcN5Y29ycA
xref: VHOG:0000334
property_value: UBPROP:0000007 "cranial" xsd:string
property_value: UBPROP:0000012 "the inclusion of the FMA class here is probably not quite correct, as this class includes as parts sutures, whereas this is not part of the bones of the cranium" xsd:string {external_ontology="FMA"}
property_value: UBPROP:0000013 "The term cranium can be ambiguous, in that it can refer to the neurocranium, or the neurocranium and the Facial skeleton" xsd:string {source="WP"}

[Term]
id: UBERON:0005157
name: epithelial fold
namespace: uberon
def: "An epithelial sheet bent on a linear axis." [GO:0060571]

[Term]
id: UBERON:0006984
name: anatomical surface
namespace: uberon
def: "A two dimensional anatomical structure that is the boundary between an anatomical structure and an anatomical substance, an anatomical space or the organism's environment. Examples include the surface of your skin, the surface of the lining of your gut; the surface of the endothelium of you aorta that is in contact with blood.n" [CARO:0001002]
comment: Old definition: 'Non-material anatomical entity of two dimensions, that is demarcated by anatomical lines or points on the external or internal surfaces of anatomical structures.' Note, in the new definition, the space referred to is not necessarily an anatomical space. It may be the outside of an organism.
subset: upper_level
xref: BILA:0000010
xref: CARO:0001002
xref: EHDAA2_RETIRED:0003192
xref: FMA:24137
xref: http://linkedlifedata.com/resource/umls/id/C1515977
xref: NCIT:C34022
xref: UMLS:C1515977 {source="ncithesaurus:Anatomic_Surface"}

[Term]
id: UBERON:0035159
name: entire surface of organism
namespace: uberon
def: "Anatomical surface, which is the external surface of the whole body. Examples: There is only one body surface." [FMA:61695]
synonym: "surface of body" EXACT [FMA:61695]
xref: FMA:61695
xref: http://linkedlifedata.com/resource/umls/id/C0489451
xref: http://www.snomedbrowser.com/Codes/Details/261060002
xref: NCIT:C29667
is_a: UBERON:0006984 ! anatomical surface

[Term]
id: UBERON:6007284
name: insect region of integument
namespace: uberon
def: "A region of cuticle and its underlying epidermis." [FBC:DOS]
xref: FBbt:00007284

[Term]
id: http://flybase.org/reports/FBgn0034157
name: resilin (fruit fly)
namespace: gene
def: "A protein coding gene resilin in fruit fly." [PRO:DNx]
comment: Category=external.

[Typedef]
id: AISM:0000011
name: lateral_to

[Typedef]
id: AISM:0000012
name: medial_to

[Typedef]
id: AISM:0000078
name: encircles
is_a: continuous_with ! continuous with
inverse_of: AISM:0000079 ! encircled by

[Typedef]
id: AISM:0000079
name: encircled by
is_a: continuous_with ! continuous with

[Typedef]
id: BFO:0000066
name: occurs in
def: "b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" []
comment: Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant
xref: BFO:0000066
property_value: IAO:0000111 "occurs in" xsd:string
property_value: IAO:0000118 "occurs_in" xsd:string
property_value: IAO:0000118 "unfolds in" xsd:string
property_value: IAO:0000118 "unfolds_in" xsd:string
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl
holds_over_chain: part_of BFO:0000066
inverse_of: BFO:0000067 ! contains process
transitive_over: part_of ! part_of

[Typedef]
id: BFO:0000067
name: contains process
def: "[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" []
comment: Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant
property_value: IAO:0000111 "site of" xsd:string
property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl

[Typedef]
id: IAO:0000136
name: is about
def: "A (currently) primitive relation that relates an information artifact to an entity." []
property_value: IAO:0000112 "This document is about information artifacts and their representations" xsd:string
property_value: IAO:0000116 "7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of \"mentions\" relation. Weaken the is_about relationship to be primitive. \n\nWe will try to build it back up by elaborating the various subproperties that are more precisely defined.\n\nSome currently missing phenomena that should be considered \"about\" are predications - \"The only person who knows the answer is sitting beside me\" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic." xsd:string
property_value: IAO:0000117 "person:Alan Ruttenberg" xsd:string
property_value: IAO:0000119 "Smith, Ceusters, Ruttenberg, 2000 years of philosophy" xsd:string

[Typedef]
id: IAO:0000219
name: denotes
def: "A primitive, instance-level, relation obtaining between an information content entity and some portion of reality. Denotation is what happens when someone creates an information content entity E in order to specifically refer to something. The only relation between E and the thing is that E can be used to 'pick out' the thing. This relation connects those two together. Freedictionary.com sense 3: To signify directly; refer to specifically" []
property_value: IAO:0000112 "A person's name denotes the person. A variable name in a computer program denotes some piece of memory. Lexically equivalent strings can denote different things, for instance \"Alan\" can denote different people. In each case of use, there is a case of the denotation relation obtaining, between \"Alan\" and the person that is being named." xsd:string
property_value: IAO:0000116 "2009-11-10 Alan Ruttenberg. Old definition said the following to emphasize the generic nature of this relation. We no longer have 'specifically denotes', which would have been primitive, so make this relation primitive.\ng denotes r =def \nr is a portion of reality\nthere is some c that is a concretization of g \nevery c that is a concretization of g specifically denotes r" xsd:string
property_value: IAO:0000117 "person:Alan Ruttenberg" xsd:string
property_value: IAO:0000119 "Conversations with Barry Smith, Werner Ceusters, Bjoern Peters, Michel Dumontier, Melanie Courtot, James Malone, Bill Hogan" xsd:string
is_a: IAO:0000136 ! is about
inverse_of: IAO:0000235 ! denoted by

[Typedef]
id: IAO:0000235
name: denoted by
def: "inverse of the relation 'denotes'" []
property_value: IAO:0000117 "Person: Jie Zheng, Chris Stoeckert, Mike Conlon" xsd:string
property_value: IAO:0000233 https://github.com/information-artifact-ontology/IAO/issues/206

[Typedef]
id: RO:0000052
name: inheres in
def: "a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence" []
property_value: IAO:0000111 "inheres in" xsd:string
property_value: IAO:0000112 "this fragility inheres in this vase" xsd:string
property_value: IAO:0000112 "this red color inheres in this apple" xsd:string
property_value: IAO:0000116 "A dependent inheres in its bearer at all times for which the dependent exists." xsd:string
property_value: IAO:0000118 "inheres_in" xsd:string
property_value: RO:0001900 RO:0001901
is_a: RO:0002314 ! inheres in part of
inverse_of: bearer_of ! bearer of

[Typedef]
id: RO:0000056
name: participates in
name: participates_in
def: "a relation between a continuant and a process, in which the continuant is somehow involved in the process" []
xref: RO:0000056
property_value: IAO:0000111 "participates in" xsd:string
property_value: IAO:0000112 "this blood clot participates in this blood coagulation" xsd:string
property_value: IAO:0000112 "this input material (or this output material) participates in this process" xsd:string
property_value: IAO:0000112 "this investigator participates in this investigation" xsd:string
property_value: IAO:0000118 "participates_in" xsd:string
inverse_of: RO:0000057 ! has participant

[Typedef]
id: RO:0000057
name: has participant
def: "a relation between a process and a continuant, in which the continuant is somehow involved in the process" []
property_value: http://purl.org/dc/elements/1.1/source http://www.obofoundry.org/ro/#OBO_REL:has_participant xsd:string
property_value: IAO:0000111 "has participant" xsd:string
property_value: IAO:0000112 "this blood coagulation has participant this blood clot" xsd:string
property_value: IAO:0000112 "this investigation has participant this investigator" xsd:string
property_value: IAO:0000112 "this process has participant this input material (or this output material)" xsd:string
property_value: IAO:0000116 "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time." xsd:string
property_value: IAO:0000118 "has_participant" xsd:string
holds_over_chain: has_part RO:0000057

[Typedef]
id: RO:0001018
name: contained in
subset: ro-eco
property_value: IAO:0000111 "contained in" xsd:string
property_value: IAO:0000116 "Containment is location not involving parthood, and arises only where some immaterial continuant is involved." xsd:string
property_value: IAO:0000116 "Containment obtains in each case between material and immaterial continuants, for instance: lung contained_in thoracic cavity; bladder contained_in pelvic cavity. Hence containment is not a transitive relation.    If c part_of c1 at t then we have also, by our definition and by the axioms of mereology applied to spatial regions, c located_in c1 at t. Thus, many examples of instance-level location relations for continuants are in fact cases of instance-level parthood. For material continuants location and parthood coincide. Containment is location not involving parthood, and arises only where some immaterial continuant is involved. To understand this relation, we first define overlap for continuants as follows:    c1 overlap c2 at t =def for some c, c part_of c1 at t and c part_of c2 at t. The containment relation on the instance level can then be defined (see definition):" xsd:string
property_value: IAO:0000116 "Intended meaning:\ndomain: material entity\nrange: spatial region or site (immaterial continuant)\n        " xsd:string
property_value: IAO:0000118 "contained_in" xsd:string
property_value: RO:0001900 RO:0001901
holds_over_chain: located_in part_of
inverse_of: contains ! contains

[Typedef]
id: RO:0002008
name: coincident with
def: "A relation that holds between two linear structures that are approximately parallel to each other for their entire length and where either the two structures are adjacent to each other or one is part of the other." []
comment: Example: if we define region of chromosome as any subdivision of a chromosome along its long axis, then we can define a region of chromosome that contains only gene x as 'chromosome region' that coincident_with some 'gene x', where the term gene X corresponds to a genomic sequence.
subset: ro-eco
property_value: IAO:0000116 "Note from NCEAS meeting: consider changing primary label" xsd:string
property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string
is_a: RO:0002323 ! mereotopologically related to

[Typedef]
id: RO:0002013
name: has regulatory component activity
def: "A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B." []
is_a: RO:0002017 ! has component activity
is_a: RO:0002334 ! regulated by
created_by: dos
creation_date: 2017-05-24T09:30:46Z

[Typedef]
id: RO:0002014
name: has negative regulatory component activity
def: "A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole.  More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B." []
comment: By convention GO molecular functions are classified by their effector function.  Internal regulatory functions are treated as components.  For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'.
is_a: RO:0002013 ! has regulatory component activity
is_a: RO:0002335 ! negatively regulated by
created_by: dos
creation_date: 2017-05-24T09:31:01Z

[Typedef]
id: RO:0002015
name: has positive regulatory component activity
def: "A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole.  More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B." []
comment: By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components.  So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'.
is_a: RO:0002013 ! has regulatory component activity
is_a: RO:0002336 ! positively regulated by
created_by: dos
creation_date: 2017-05-24T09:31:17Z

[Typedef]
id: RO:0002017
name: has component activity
comment: A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B.
is_a: RO:0002018 ! has component process
created_by: dos
creation_date: 2017-05-24T09:44:33Z

[Typedef]
id: RO:0002018
name: has component process
def: "w 'has process component' p if p and w are processes,  w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." []
is_a: RO:0002180 ! has component
created_by: dos
creation_date: 2017-05-24T09:49:21Z

[Typedef]
id: RO:0002022
name: directly regulated by
comment: Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2).  For example, if protein A has protein binding activity(P1) that targets protein B and this binding  regulates the kinase activity (P2) of protein B then P1 directly regulates P2. {xref="GOC:dos"}
is_a: RO:0002334 ! regulated by
inverse_of: RO:0002578 ! directly regulates
created_by: dos
creation_date: 2017-09-17T13:52:24Z

[Typedef]
id: RO:0002023
name: directly negatively regulated by
def: "Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2).  For example, if protein A has protein binding activity(P1) that targets protein B and this binding  negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1." [GOC:dos]
is_a: RO:0002022 ! directly regulated by
inverse_of: RO:0002630 ! directly negatively regulates
created_by: dos
creation_date: 2017-09-17T13:52:38Z

[Typedef]
id: RO:0002024
name: directly positively regulated by
def: "Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2).  For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1." [GOC:dos]
is_a: RO:0002022 ! directly regulated by
inverse_of: RO:0002629 ! directly positively regulates
created_by: dos
creation_date: 2017-09-17T13:52:47Z

[Typedef]
id: RO:0002025
name: has effector activity
def: "A 'has effector activity' B if A and B are GO molecular functions (GO_0003674),  A 'has component activity' B and B is the effector (output function) of B.  Each compound function has only one effector activity." [GOC:dos]
comment: This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations.
is_functional: true
is_a: RO:0002017 ! has component activity
is_a: RO:0002211 ! regulates
created_by: dos
creation_date: 2017-09-22T14:14:36Z

[Typedef]
id: RO:0002086
name: ends after
comment: X ends_after Y iff: end(Y) before_or_simultaneous_with end(X)
subset: ro-eco
property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string
is_transitive: true
is_a: RO:0002222 ! temporally related to

[Typedef]
id: RO:0002090
name: immediately precedes
comment: X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)
subset: ro-eco
property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string
property_value: IAO:0000118 "ends_at_start_of" xsd:string
property_value: IAO:0000118 "meets" xsd:string
property_value: RO:0002575 BFO:0000063
is_a: precedes ! precedes

[Typedef]
id: RO:0002162
name: in taxon
def: "x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed." []
comment: Connects a biological entity to its taxon of origin.
xref: RO:0002162
holds_over_chain: attaches_to RO:0002162
holds_over_chain: connected_to RO:0002162
holds_over_chain: connects RO:0002162
holds_over_chain: continuous_with RO:0002162
holds_over_chain: developmentally_induced_by RO:0002162
holds_over_chain: develops_from RO:0002162
holds_over_chain: existence_ends_during RO:0002162
holds_over_chain: existence_starts_during RO:0002162
holds_over_chain: has_developmental_contribution_from RO:0002162
holds_over_chain: has_part RO:0002162
holds_over_chain: has_potential_to_develop_into RO:0002162
holds_over_chain: part_of RO:0002162
holds_over_chain: produced_by RO:0002162
holds_over_chain: produces RO:0002162
holds_over_chain: RO:0002215 RO:0002162
is_a: RO:0002320 ! evolutionarily related to

[Typedef]
id: RO:0002163
name: spatially disjoint from
def: "A is spatially_disjoint_from B if and only if they have no parts in common" []
subset: ro-eco
property_value: curator_notes "Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy" xsd:string
property_value: http://xmlns.com/foaf/0.1/page https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern xsd:anyURI
property_value: IAO:0000116 "There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. " xsd:string
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552
property_value: RO:0001900 RO:0001901
is_a: RO:0002323 ! mereotopologically related to
expand_expression_to: "BFO_0000051 exactly 0 (BFO_0000050 some ?Y)" []

[Typedef]
id: RO:0002180
name: has component
name: has_component
def: "w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." []
subset: ro-eco
xref: RO:0002180
property_value: curator_notes "For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit." xsd:string
property_value: IAO:0000116 "The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity." xsd:string
property_value: RO:0001900 RO:0001901
property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:Componency
is_a: has_part ! has part

[Typedef]
id: RO:0002211
name: regulates
def: "process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2." []
xref: RO:0002211
property_value: curator_notes "Regulation precludes parthood; the regulatory process may not be within the regulated process." xsd:string
property_value: IAO:0000116 "We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit" xsd:string
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000117 "David Hill" xsd:string
property_value: IAO:0000117 "Tanya Berardini" xsd:string
property_value: IAO:0000119 "GO" xsd:string
property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
property_value: IAO:0000589 "regulates (processual)" xsd:string
property_value: IAO:0000600 "false" xsd:boolean
holds_over_chain: RO:0002578 RO:0002578
is_transitive: true
is_a: RO:0002411 ! causally upstream of
inverse_of: RO:0002334 ! regulated by
transitive_over: RO:0002025 ! has effector activity

[Typedef]
id: RO:0002212
name: negatively regulates
def: "Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2." []
xref: RO:0002212
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
property_value: IAO:0000589 "negatively regulates (process to process)" xsd:string
property_value: RO:0004050 RO:0002211
is_a: RO:0002211 ! regulates
is_a: RO:0002305 ! causally upstream of, negative effect
inverse_of: RO:0002335 ! negatively regulated by

[Typedef]
id: RO:0002213
name: positively regulates
def: "Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2." []
xref: RO:0002213
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
property_value: IAO:0000589 "positively regulates (process to process)" xsd:string
property_value: RO:0004049 RO:0002211
holds_over_chain: RO:0002212 RO:0002212
is_transitive: true
is_a: RO:0002211 ! regulates
is_a: RO:0002304 ! causally upstream of, positive effect
inverse_of: RO:0002336 ! positively regulated by

[Typedef]
id: RO:0002215
name: capable of
name: capable_of
def: "A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. " []
subset: ro-eco
xref: RO:0002215
property_value: curator_notes "For compatibility with BFO, this relation has a shortcut definition in which the expression \"capable of some P\" expands to \"bearer_of (some realized_by only P)\"." xsd:string
property_value: IAO:0000112 "mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)" xsd:string
property_value: IAO:0000112 "osteoclast SubClassOf 'capable of' some 'bone resorption'" xsd:string
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000118 "has function realized in" xsd:string
property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20123131
property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/21208450
is_a: RO:0002216 ! capable of part of
is_a: RO:0002328 ! functionally related to
expand_expression_to: "RO_0000053 some (RO_0000054 only ?Y)" []

[Typedef]
id: RO:0002216
name: capable of part of
def: "c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p." []
xref: RO:0002216
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000118 "has function in" xsd:string
property_value: seeAlso "defining-property-chains-involving-reflexivity"
holds_over_chain: RO:0002215 part_of {http://purl.obolibrary.org/obo/RO_0002582="true"}
is_a: RO:0002328 ! functionally related to
is_a: RO:0002500 ! causal agent in process
expand_expression_to: "RO_0000053 some (RO_0000054 only (BFO_0000050 some ?Y))" []

[Typedef]
id: RO:0002222
name: temporally related to
comment: A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.
subset: ro-eco
property_value: curator_notes "Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends." xsd:string
property_value: http://purl.org/dc/terms/source https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 xsd:anyURI
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000119 https://en.wikipedia.org/wiki/Allen%27s_interval_algebra

[Typedef]
id: RO:0002233
name: has input
def: "p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p." []
subset: ro-eco
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000118 "consumes" xsd:string
is_a: RO:0000057 ! has participant
inverse_of: RO:0002352 ! input of

[Typedef]
id: RO:0002258
name: developmentally preceded by
def: "Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p" []
comment: This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from
property_value: curator_notes "In general you should not use this relation to make assertions - use one of the more specific relations below this one" xsd:string
property_value: IAO:0000116 "false" xsd:boolean
property_value: IAO:0000117 "Chris Mungall" xsd:string
is_a: RO:0002324 ! developmentally related to
inverse_of: RO:0002286 ! developmentally succeeded by

[Typedef]
id: RO:0002263
name: acts upstream of
def: "c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes." []
property_value: IAO:0000112 "A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision." xsd:string
property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of
holds_over_chain: RO:0002327 RO:0002411
is_a: RO:0002264 ! acts upstream of or within

[Typedef]
id: RO:0002264
name: acts upstream of or within
def: "c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process." []
synonym: "affects" RELATED []
property_value: IAO:0000112 "A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway." xsd:string
property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within
holds_over_chain: RO:0002327 RO:0002418
is_a: RO:0002500 ! causal agent in process

[Typedef]
id: RO:0002286
name: developmentally succeeded by
def: "Inverse of developmentally preceded by" []
property_value: IAO:0000117 "Chris Mungall" xsd:string
is_a: RO:0002384 ! has developmental potential involving

[Typedef]
id: RO:0002304
name: causally upstream of, positive effect
comment: holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y
property_value: http://purl.org/dc/terms/creator "cjm" xsd:string
property_value: RO:0004049 RO:0002411
is_a: RO:0002411 ! causally upstream of
is_a: RO:0004047 ! causally upstream of or within, positive effect

[Typedef]
id: RO:0002305
name: causally upstream of, negative effect
comment: holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y
property_value: http://purl.org/dc/terms/creator "cjm" xsd:string
property_value: RO:0004050 RO:0002411
is_a: RO:0002411 ! causally upstream of
is_a: RO:0004046 ! causally upstream of or within, negative effect

[Typedef]
id: RO:0002314
name: inheres in part of
def: "q inheres in part of w if and only if there exists some p such that q inheres in p and p part of w." []
property_value: IAO:0000116 "Because part_of is transitive, inheres in is a sub-relation of inheres in part of" xsd:string
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205
property_value: RO:0001900 RO:0001901
property_value: seeAlso "defining-property-chains-involving-reflexivity"
holds_over_chain: RO:0000052 part_of {http://purl.obolibrary.org/obo/RO_0002582="true"}
is_a: RO:0002502 ! depends on
transitive_over: part_of ! part_of

[Typedef]
id: RO:0002320
name: evolutionarily related to
def: "A relationship that holds via some environmental process" []

[Typedef]
id: RO:0002323
name: mereotopologically related to
def: "A mereological relationship or a topological relationship" []
property_value: curator_notes "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships" xsd:string
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: RO:0001900 RO:0001901

[Typedef]
id: RO:0002324
name: developmentally related to
def: "A relationship that holds between entities participating in some developmental process (GO:0032502)" []
property_value: curator_notes "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development" xsd:string
property_value: IAO:0000117 "Chris Mungall" xsd:string

[Typedef]
id: RO:0002327
name: enables
property_value: curator_notes "This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized." xsd:string
property_value: curator_notes "This relation is currently used experimentally by the Gene Ontology Consortium. It may not be stable and may be obsoleted at some future time." xsd:string
property_value: IAO:0000112 "a particular instances of akt-2 enables some instance of protein kinase activity" xsd:string
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000118 "catalyzes" xsd:string
property_value: IAO:0000118 "executes" xsd:string
property_value: IAO:0000118 "has" xsd:string
property_value: IAO:0000118 "is catalyzing" xsd:string
property_value: IAO:0000118 "is executing" xsd:string
is_a: RO:0002215 ! capable_of
inverse_of: RO:0002333 ! enabled by
transitive_over: has_part ! has part
transitive_over: RO:0002017 ! has component activity

[Typedef]
id: RO:0002328
name: functionally related to
def: "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities." []
xref: RO:0002328
property_value: curator_notes "This is a grouping relation that collects relations used for the purpose of connecting structure and function" xsd:string
property_value: IAO:0000117 "Chris Mungall" xsd:string

[Typedef]
id: RO:0002329
name: part of structure that is capable of
def: "this relation holds between c and p when c is part of some c', and c' is capable of p." []
xref: RO:0002329
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000118 "false" xsd:boolean
holds_over_chain: part_of RO:0002215 {http://purl.obolibrary.org/obo/RO_0002581="true"}
is_a: RO:0002328 ! functionally related to

[Typedef]
id: RO:0002331
name: involved in
def: "c involved_in p if and only if c enables some process p', and p' is part of p" []
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000118 "actively involved in" xsd:string
property_value: IAO:0000118 "enables part of" xsd:string
property_value: seeAlso Involved:in
holds_over_chain: RO:0002327 part_of
is_a: RO:0000056 ! participates in
is_a: RO:0002431 ! involved in or involved in regulation of
transitive_over: part_of ! part_of

[Typedef]
id: RO:0002333
name: enabled by
def: "inverse of enables" []
property_value: IAO:0000117 "Chris Mungall" xsd:string
is_a: RO:0000057 ! has participant
is_a: RO:0002328 ! functionally related to

[Typedef]
id: RO:0002334
name: regulated by
def: "inverse of regulates" []
subset: RO:0002259
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000589 "regulated by (processual)" xsd:string
is_transitive: true
is_a: RO:0002427 ! causally downstream of or within

[Typedef]
id: RO:0002335
name: negatively regulated by
def: "inverse of negatively regulates" []
subset: RO:0002259
property_value: IAO:0000117 "Chris Mungall" xsd:string
is_a: RO:0002334 ! regulated by

[Typedef]
id: RO:0002336
name: positively regulated by
def: "inverse of positively regulates" []
subset: RO:0002259
property_value: IAO:0000117 "Chris Mungall" xsd:string
is_a: RO:0002334 ! regulated by

[Typedef]
id: RO:0002352
name: input of
def: "inverse of has input" []
subset: ro-eco
subset: RO:0002259
property_value: IAO:0000117 "Chris Mungall" xsd:string
is_a: RO:0000056 ! participates in
is_a: RO:0002328 ! functionally related to

[Typedef]
id: RO:0002379
name: spatially coextensive with
def: "x spatially_coextensive_with y if and inly if x and y have the same location" []
is_a: overlaps ! overlaps

[Typedef]
id: RO:0002384
name: has developmental potential involving
def: "x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction)." []
property_value: IAO:0000117 "Chris Mungall" xsd:string
is_a: RO:0002324 ! developmentally related to

[Typedef]
id: RO:0002388
name: has potential to directly develop into
def: "x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y" []
property_value: IAO:0000117 "Chris Mungall" xsd:string
is_a: has_potential_to_develop_into ! has potential to develop into

[Typedef]
id: RO:0002404
name: causally downstream of
def: "inverse of upstream of" []
property_value: IAO:0000117 "Chris Mungall" xsd:string
is_a: preceded_by ! preceded_by
is_a: RO:0002427 ! causally downstream of or within
inverse_of: RO:0002411 ! causally upstream of

[Typedef]
id: RO:0002405
name: immediately causally downstream of
property_value: IAO:0000117 "Chris Mungall" xsd:string
is_a: immediately_preceded_by ! immediately preceded by
is_a: RO:0002404 ! causally downstream of
inverse_of: RO:0002412 ! immediately causally upstream of

[Typedef]
id: RO:0002410
name: causally related to
def: "This relation groups causal relations between material entities and causal relations between processes" []
property_value: curator_notes "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string
property_value: IAO:0000116 "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." xsd:string
property_value: IAO:0000117 "Chris Mungall" xsd:string

[Typedef]
id: RO:0002411
name: causally upstream of
def: "p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain" []
property_value: IAO:0000117 "Chris Mungall" xsd:string
is_transitive: true
is_a: precedes ! precedes
is_a: RO:0002418 ! causally upstream of or within

[Typedef]
id: RO:0002412
name: immediately causally upstream of
def: "p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p  must be an input of q." []
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: RO:0002575 RO:0002411
is_a: RO:0002090 ! immediately precedes
is_a: RO:0002411 ! causally upstream of

[Typedef]
id: RO:0002418
name: causally upstream of or within
def: "p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q." []
synonym: "affects" RELATED []
property_value: IAO:0000116 "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" xsd:string
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000118 "influences (processual)" xsd:string
is_transitive: true
is_a: RO:0002501 ! causal relation between processes
inverse_of: RO:0002427 ! causally downstream of or within

[Typedef]
id: RO:0002427
name: causally downstream of or within
def: "inverse of causally upstream of or within" []
subset: RO:0002259
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
is_transitive: true
is_a: RO:0002501 ! causal relation between processes

[Typedef]
id: RO:0002428
name: involved in regulation of
def: "c involved in regulation of p if c is involved in some p' and p' regulates some p" []
property_value: IAO:0000117 "Chris Mungall" xsd:string
holds_over_chain: RO:0002327 RO:0002211
holds_over_chain: RO:0002331 RO:0002211
is_a: RO:0002263 ! acts upstream of
is_a: RO:0002431 ! involved in or involved in regulation of

[Typedef]
id: RO:0002429
name: involved in positive regulation of
def: "c involved in regulation of p if c is involved in some p' and p' positively regulates some p" []
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: RO:0004049 RO:0002428
holds_over_chain: RO:0002327 RO:0002213
holds_over_chain: RO:0002331 RO:0002213
is_a: RO:0002428 ! involved in regulation of

[Typedef]
id: RO:0002430
name: involved in negative regulation of
def: "c involved in regulation of p if c is involved in some p' and p' negatively regulates some p" []
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: RO:0004050 RO:0002428
holds_over_chain: RO:0002327 RO:0002212
holds_over_chain: RO:0002331 RO:0002212
is_a: RO:0002428 ! involved in regulation of

[Typedef]
id: RO:0002431
name: involved in or involved in regulation of
def: "c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p" []
property_value: IAO:0000116 "OWL does not allow defining object properties via a Union" xsd:string
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000118 "involved in or reguates" xsd:string
is_a: RO:0002264 ! acts upstream of or within
is_a: RO:0002328 ! functionally related to
is_a: RO:0002500 ! causal agent in process

[Typedef]
id: RO:0002432
name: is active in
def: "c executes activity in d if and only if c enables p and p occurs_in d.  Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure." [GOC:cjm, GOC:dos]
synonym: "enables activity in" EXACT []
property_value: IAO:0000112 "A protein that enables activity in a cytosol." xsd:string
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000118 "executes activity in" xsd:string
holds_over_chain: RO:0002327 BFO:0000066 {http://purl.obolibrary.org/obo/RO_0002581="true"}
is_a: overlaps ! overlaps
is_a: RO:0002328 ! functionally related to

[Typedef]
id: RO:0002434
name: interacts with
def: "A relationship that holds between two entities in which the processes executed by the two entities are causally connected." []
subset: ro-eco
synonym: "in pairwise interaction with" EXACT []
property_value: curator_notes "Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules." xsd:string
property_value: http://xmlns.com/foaf/0.1/page https://github.com/oborel/obo-relations/wiki/InteractionRelations xsd:anyURI
property_value: IAO:0000116 "Considering relabeling as 'pairwise interacts with'" xsd:anyURI
property_value: IAO:0000116 "This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact." xsd:string
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: seeAlso http://purl.obolibrary.org/obo/MI_0914 xsd:anyURI
is_symmetric: true

[Typedef]
id: RO:0002436
name: molecularly interacts with
def: "An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other." []
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000118 "binds" xsd:string
property_value: IAO:0000118 "molecularly binds with" xsd:string
property_value: seeAlso ECO:0000353
property_value: seeAlso http://purl.obolibrary.org/obo/MI_0915 xsd:anyURI
is_symmetric: true
is_a: RO:0002434 ! interacts with

[Typedef]
id: RO:0002447
name: phosphorylates
property_value: IAO:0000116 "Axiomatization to GO to be added later" xsd:string
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000118 "An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y." xsd:string
is_a: RO:0002436 ! molecularly interacts with

[Typedef]
id: RO:0002448
name: directly regulates activity of
def: "The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B.\n\nA and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B." []
synonym: "molecularly controls" EXACT []
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000117 "Vasundra Touré" xsd:string
is_a: RO:0002436 ! molecularly interacts with
is_a: RO:0011002 ! regulates activity of

[Typedef]
id: RO:0002449
name: directly negatively regulates activity of
def: "The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B." []
synonym: "molecularly decreases activity of" EXACT []
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000117 "Vasundra Touré" xsd:string
property_value: IAO:0000118 "directly inhibits" xsd:string
is_a: RO:0002448 ! directly regulates activity of

[Typedef]
id: RO:0002450
name: directly positively regulates activity of
def: "The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B." []
synonym: "molecularly increases activity of" EXACT []
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000117 "Vasundra Touré" xsd:string
property_value: IAO:0000118 "directly activates" xsd:string
is_a: RO:0002448 ! directly regulates activity of

[Typedef]
id: RO:0002464
name: helper property (not for use in curation)
property_value: curator_notes "This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning." xsd:string
property_value: IAO:0000117 "Chris Mungall" xsd:string

[Typedef]
id: RO:0002479
name: has part that occurs in
def: "p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c." []
subset: ro-eco
property_value: IAO:0000117 "Chris Mungall" xsd:string
holds_over_chain: has_part BFO:0000066 {http://purl.obolibrary.org/obo/RO_0002581="true"}

[Typedef]
id: RO:0002481
name: is kinase activity
property_value: IAO:0000117 "Chris Mungall" xsd:string
is_a: RO:0002564 ! molecular interaction relation helper property

[Typedef]
id: RO:0002500
name: causal agent in process
def: "A relationship between a material entity and a process where the material entity has some causal role that influences the process" []
property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
is_a: RO:0002595 ! causal relation between material entity and a process
inverse_of: RO:0002608 ! process has causal agent

[Typedef]
id: RO:0002501
name: causal relation between processes
def: "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q." []
property_value: curator_notes "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
is_a: RO:0002410 ! causally related to

[Typedef]
id: RO:0002502
name: depends on
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: seeAlso BFO:0000169

[Typedef]
id: RO:0002506
name: causal relation between entities
property_value: curator_notes "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string
property_value: IAO:0000116 "The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch" xsd:string
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
is_a: RO:0002410 ! causally related to

[Typedef]
id: RO:0002559
name: causally influenced by
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
property_value: IAO:0000589 "causally influenced by (entity-centric)" xsd:string
is_a: RO:0002506 ! causal relation between entities
inverse_of: RO:0002566 ! causally influences

[Typedef]
id: RO:0002563
name: interaction relation helper property
property_value: http://xmlns.com/foaf/0.1/page https://github.com/oborel/obo-relations/wiki/InteractionRelations xsd:anyURI
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:N-Ary_Relation_Pattern_%28OWL_2%29
is_a: RO:0002464 ! helper property (not for use in curation)

[Typedef]
id: RO:0002564
name: molecular interaction relation helper property
property_value: IAO:0000117 "Chris Mungall" xsd:string
is_a: RO:0002563 ! interaction relation helper property

[Typedef]
id: RO:0002566
name: causally influences
def: "The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size)." []
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000117 "Vasundra Touré" xsd:string
property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
property_value: IAO:0000589 "causally influences (entity-centric)" xsd:string
is_a: RO:0002506 ! causal relation between entities

[Typedef]
id: RO:0002578
name: directly regulates
def: "Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2).  For example, if protein A has protein binding activity(P1) that targets protein B and this binding  regulates the kinase activity (P2) of protein B then P1 directly regulates P2." []
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
property_value: IAO:0000589 "directly regulates (processual)" xsd:string
property_value: RO:0002575 RO:0002211
is_a: RO:0002211 ! regulates
is_a: RO:0002412 ! immediately causally upstream of

[Typedef]
id: RO:0002584
name: has part structure that is capable of
def: "s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p" []
property_value: IAO:0000112 "gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'" xsd:string
property_value: IAO:0000117 "Chris Mungall" xsd:string
holds_over_chain: has_part RO:0002215
is_a: RO:0002328 ! functionally related to
is_a: RO:0002595 ! causal relation between material entity and a process

[Typedef]
id: RO:0002595
name: causal relation between material entity and a process
def: "A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity." []
property_value: IAO:0000116 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
is_a: RO:0002410 ! causally related to

[Typedef]
id: RO:0002596
name: capable of regulating
def: "Holds between c and p if and only if c is capable of some activity a, and a regulates p." []
property_value: IAO:0000112 "pyrethroid -> growth" xsd:string
property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
holds_over_chain: RO:0002215 RO:0002211
is_a: RO:0002500 ! causal agent in process

[Typedef]
id: RO:0002597
name: capable of negatively regulating
def: "Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p." []
property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
holds_over_chain: RO:0002215 RO:0002212
is_a: RO:0002596 ! capable of regulating

[Typedef]
id: RO:0002598
name: capable of positively regulating
def: "Holds between c and p if and only if c is capable of some activity a, and a positively regulates p." []
property_value: IAO:0000112 "renin -> arteriolar smooth muscle contraction" xsd:string
property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
holds_over_chain: RO:0002215 RO:0002213
is_a: RO:0002596 ! capable of regulating

[Typedef]
id: RO:0002608
name: process has causal agent
def: "Inverse of 'causal agent in process'" []
property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
is_a: RO:0002410 ! causally related to

[Typedef]
id: RO:0002629
name: directly positively regulates
def: "Process(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2).  For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2." []
property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
property_value: IAO:0000589 "directly positively regulates (process to process)" xsd:string
property_value: RO:0004049 RO:0002578
is_a: RO:0002213 ! positively regulates
is_a: RO:0002578 ! directly regulates

[Typedef]
id: RO:0002630
name: directly negatively regulates
def: "Process(P1) directly negatively regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2).  For example, if protein A has protein binding activity(P1) that targets protein B and this binding  negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2." []
property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations
property_value: IAO:0000589 "directly negatively regulates (process to process)" xsd:string
property_value: RO:0004050 RO:0002578
is_a: RO:0002212 ! negatively regulates
is_a: RO:0002578 ! directly regulates

[Typedef]
id: RO:0004031
name: enables subfunction
def: "Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P." []
holds_over_chain: RO:0002327 has_part
is_a: RO:0002328 ! functionally related to
created_by: cjm
creation_date: 2018-01-25T23:20:13Z

[Typedef]
id: RO:0004032
name: acts upstream of or within, positive effect
property_value: RO:0004049 RO:0002264
property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within,_positive_effect
holds_over_chain: RO:0002327 RO:0004047
is_a: RO:0002264 ! acts upstream of or within
created_by: cjm
creation_date: 2018-01-26T23:49:30Z

[Typedef]
id: RO:0004033
name: acts upstream of or within, negative effect
property_value: RO:0004050 RO:0002264
holds_over_chain: RO:0002327 RO:0004046
is_a: RO:0002264 ! acts upstream of or within
created_by: cjm
creation_date: 2018-01-26T23:49:51Z

[Typedef]
id: RO:0004034
name: acts upstream of, positive effect
def: "c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive" []
property_value: RO:0004049 RO:0002263
property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of,_positive_effect
holds_over_chain: RO:0002327 RO:0002304
is_a: RO:0002263 ! acts upstream of
is_a: RO:0004032 ! acts upstream of or within, positive effect
created_by: cjm
creation_date: 2018-01-26T23:53:14Z

[Typedef]
id: RO:0004035
name: acts upstream of, negative effect
def: "c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative" []
property_value: RO:0004050 RO:0002263
property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of,_negative_effect
holds_over_chain: RO:0002327 RO:0002305
is_a: RO:0002263 ! acts upstream of
is_a: RO:0004033 ! acts upstream of or within, negative effect
created_by: cjm
creation_date: 2018-01-26T23:53:22Z

[Typedef]
id: RO:0004046
name: causally upstream of or within, negative effect
property_value: RO:0004050 RO:0002418
is_a: RO:0002418 ! causally upstream of or within
created_by: cjm
creation_date: 2018-03-13T23:55:05Z

[Typedef]
id: RO:0004047
name: causally upstream of or within, positive effect
property_value: RO:0004049 RO:0002418
is_a: RO:0002418 ! causally upstream of or within
created_by: cjm
creation_date: 2018-03-13T23:55:19Z

[Typedef]
id: RO:0011002
name: regulates activity of
def: "The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B." []
property_value: IAO:0000117 "Vasundra Touré" xsd:string
is_a: RO:0002566 ! causally influences

[Typedef]
id: adjacent_to
name: adjacent to
name: adjacent_to
namespace: spatial
namespace: uberon
def: "x adjacent to y if and only if x and y share a boundary." []
def: "x adjacent_to y iff: x and y share a boundary" []
xref: RO:0002220
property_value: IAO:0000112 "A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts." xsd:string {http://www.w3.org/2000/01/rdf-schema#seeAlso="issuecomment-218584934"}
property_value: IAO:0000112 "The epidermis layer of a vertebrate is adjacent to the dermis." xsd:string
property_value: IAO:0000112 "The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies." xsd:string
property_value: IAO:0000112 "The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used." xsd:string
property_value: IAO:0000116 "This relation acts as a join point with BSPO" xsd:string
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: RO:0001900 RO:0001901
is_symmetric: true
is_a: RO:0002163 ! spatially disjoint from

[Typedef]
id: anterior_to
name: anterior to
name: anterior_to
namespace: spatial
namespace: uberon
def: "x anterior to y iff x is further along the antero-posterior axis than y, towards the head. An antero-posterior axis is an axis that extends through an organism from head end to opposite end of body or tail." [BSPO:cjm]
def: "x anterior_to y iff x is further along the antero-posterior axis than y, towards the head. An antero-posterior axis is an axis that bisects an organism from head end to opposite end of body or tail: bearer" [http://orcid.org/0000-0002-6601-2165]
synonym: "rostral_to" EXACT []
xref: BSPO:0000096
property_value: seeAlso FBcv:0000039
property_value: seeAlso FBql:00005863
is_transitive: true
inverse_of: posterior_to ! posterior to
created_by: cjm
creation_date: 2009-07-31T02:15:46Z

[Typedef]
id: anteriorly_connected_to
name: anteriorly connected to
namespace: uberon
def: "x anteriorly_connected_to y iff the anterior part of x is connected to y. i.e. x connected_to y and x posterior_to y." [http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern]
is_a: connected_to ! connected to
is_a: posterior_to ! posterior to
is_a: transitively_anteriorly_connected_to ! transitively anteriorly connected to

[Typedef]
id: approximately_perpendicular_to
name: approximately perpendicular to
namespace: spatial
def: "Crosses at an angle that is 90 degrees, or close to 90 degrees. In any non-linear organism, the main axes are rarely perpendicular when taken through the organism as a whole." [BSPO:cjm]
xref: BSPO:0000104

[Typedef]
id: attaches_to
name: attaches_to
namespace: uberon
xref: RO:0002371
property_value: seeAlso FMA:85990
is_a: attaches_to_part_of ! attaches_to_part_of
is_a: connects ! connects

[Typedef]
id: attaches_to_part_of
name: attaches_to_part_of
namespace: uberon
xref: RO:0002177
equivalent_to_chain: attaches_to part_of ! part_of

[Typedef]
id: bearer_of
name: bearer of
namespace: uberon
def: "a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence" []
xref: RO:0000053
property_value: IAO:0000111 "bearer of" xsd:string
property_value: IAO:0000112 "this apple is bearer of this red color" xsd:string
property_value: IAO:0000112 "this vase is bearer of this fragility" xsd:string
property_value: IAO:0000116 "A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist." xsd:string
property_value: IAO:0000118 "bearer_of" xsd:string
property_value: IAO:0000118 "is bearer of" xsd:string
property_value: RO:0001900 RO:0001901

[Typedef]
id: boundary_of
name: 2D boundary of
name: boundary of
namespace: uberon
def: "a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity" []
xref: RO:0002000
property_value: IAO:0000112 "the surface of my skin is a 2D boundary of my body" xsd:string
property_value: IAO:0000116 "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." xsd:string
property_value: IAO:0000116 "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." xsd:string
property_value: IAO:0000118 "2D_boundary_of" xsd:string
property_value: IAO:0000118 "boundary of" xsd:string
property_value: IAO:0000118 "is 2D boundary of" xsd:string
property_value: IAO:0000118 "is boundary of" xsd:string
property_value: RO:0001900 RO:0001901
is_a: RO:0002323 ! mereotopologically related to
inverse_of: has_boundary ! has 2D boundary

[Typedef]
id: bounding_layer_of
name: bounding layer of
namespace: uberon
comment: A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane.
xref: RO:0002007
is_a: part_of ! part_of

[Typedef]
id: branching_part_of
name: branching_part_of
namespace: uberon
xref: RO:0002380
property_value: IAO:0000116 "we need to check if FMA branch_of implies part_of. the relation we intend to use here should - for example, see vestibulocochlear nerve" xsd:string
property_value: seeAlso FMA:85994
is_a: part_of ! part_of
inverse_of: has_branching_part ! has branching part

[Typedef]
id: channel_for
name: channel for
namespace: uberon
synonym: "carries" BROAD []

[Typedef]
id: channels_from
name: channels_from
namespace: uberon
is_transitive: true

[Typedef]
id: composed_primarily_of
name: composed primarily of
namespace: uberon
def: "x composed_primarily_of y iff: more than half of the mass of x is made from parts of y" []
xref: RO:0002473
is_a: has_part ! has part

[Typedef]
id: conduit_for
name: conduit for
namespace: uberon
def: "x is a conduit for y iff y passes through the lumen of x." []

[Typedef]
id: connected_to
name: connected to
namespace: uberon
def: "a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b" []
def: "Binary relationship: x connected_to y if and only if there exists some z such that z connects x and y in a ternary connected_to(x,y,z) relationship." [http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern]
comment: Connection does not imply overlaps.
xref: RO:0002170
property_value: seeAlso SIO:000652
is_a: RO:0002323 ! mereotopologically related to
is_a: transitively_connected_to ! transitively_connected to

[Typedef]
id: connects
name: connects
namespace: uberon
def: "Binary relationship: z connects x if and only if there exists some y such that z connects x and y in a ternary connected_to(x,y,z) relationship." [http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern]
xref: RO:0002176
property_value: IAO:0000116 "this is currently used for both structural relationships (such as between a valve and the chamber it connects) and abstract relationships (anatomical lines and the entities they connect)" xsd:string

[Typedef]
id: contains
name: contains
namespace: uberon
subset: ro-eco
xref: RO:0001019
property_value: IAO:0000111 "contains" xsd:string
property_value: RO:0001900 RO:0001901

[Typedef]
id: continuous_with
name: continuous with
name: continuous_with
namespace: uberon
def: "X continuous_with Y if and only if X and Y share a fiat boundary." []
xref: RO:0002150
property_value: curator_notes "The label for this relation was previously connected to. I relabeled this to \"continuous with\". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint)" xsd:string
property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string
property_value: IAO:0000118 "connected to" xsd:string
property_value: RO:0001900 RO:0001901
property_value: seeAlso FMA:85972 xsd:string
is_symmetric: true
is_a: RO:0002323 ! mereotopologically related to

[Typedef]
id: contralateral_to
name: contralateral to
namespace: spatial
def: "On the opposite side from. For example, the left arm is contralateral to the right arm (and the right leg)." [BSPO:cjm]
xref: BSPO:0000106
property_value: seeAlso FBql:00005851
is_symmetric: true
is_a: opposite_to ! opposite to

[Typedef]
id: contributes_to_morphology_of
name: contributes to morphology of
namespace: uberon
xref: RO:0002433

[Typedef]
id: curator_notes
name: curator note
name: curator notes
namespace: uberon
def: "An administrative note of use for a curator but of no use for a user" []
xref: IAO:0000232
property_value: IAO:0000111 "curator note" xsd:string
property_value: IAO:0000117 "PERSON:Alan Ruttenberg" xsd:string
property_value: isDefinedBy http://purl.obolibrary.org/obo/iao.owl
is_metadata_tag: true

[Typedef]
id: dc-contributor
name: contributor
namespace: uberon
xref: http://purl.org/dc/elements/1.1/contributor
is_metadata_tag: true

[Typedef]
id: dc-description
name: description
namespace: uberon
xref: http://purl.org/dc/elements/1.1/description
is_metadata_tag: true

[Typedef]
id: dc-title
name: title
namespace: uberon
xref: http://purl.org/dc/elements/1.1/title
is_metadata_tag: true

[Typedef]
id: dcterms-license
name: license
namespace: uberon
xref: http://purl.org/dc/terms/license
is_metadata_tag: true

[Typedef]
id: decreased_in_magnitude_relative_to
name: decreased_in_magnitude_relative_to
namespace: quality
def: "q1 decreased_in_magnitude_relative_to q2 if and only if magnitude(q1) < magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale." [PATOC:CJM]
comment: This relation is used to determine the 'directionality' of relative qualities such as 'decreased strength', relative to the parent type, 'strength'.
is_transitive: true
is_a: different_in_magnitude_relative_to ! different_in_magnitude_relative_to

[Typedef]
id: deep_to
name: deep_to
namespace: uberon
def: "Further away from the surface of the organism. Thus, the muscular layer is deep to the skin, but superficial to the intestines." [http://orcid.org/0000-0002-6601-2165]
xref: BSPO:0000107
is_transitive: true

[Typedef]
id: developmentally_contributes_to
name: developmentally contributes to
name: developmentally_contributes_to
namespace: uberon
def: "inverse of has developmental contribution from" []
subset: RO:0002259
xref: RO:0002255
property_value: IAO:0000117 "Chris Mungall" xsd:string
holds_over_chain: develops_into part_of
is_a: has_potential_to_developmentally_contribute_to ! has potential to developmentally contribute to
is_a: RO:0002286 ! developmentally succeeded by

[Typedef]
id: developmentally_induced_by
name: developmentally_induced_by
namespace: uberon
def: "t1 developmentally_induced_by t2 if there is a process of organ induction (GO:0001759) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor tissue type T to T', where T' develops_from T." [GO:0001759]
comment: sources for developmentally_induced_by relationships in Uberon: Developmental Biology, Gilbert, 8th edition, figure 6.5(F)
xref: RO:0002256

[Typedef]
id: developmentally_replaces
name: developmentally_replaces
namespace: uberon
xref: RO:0002285

[Typedef]
id: develops_from
name: develops from
name: develops_from
namespace: uberon
def: "x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y" []
comment: This is the transitive form of the develops from relation
xref: RO:0002202
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string
property_value: IAO:0000117 "Melissa Haendel" xsd:string
property_value: IAO:0000117 "Terry Meehan" xsd:string
holds_over_chain: part_of develops_from
is_transitive: true
is_a: has_developmental_contribution_from ! has developmental contribution from
is_a: RO:0002258 ! developmentally preceded by
inverse_of: develops_into ! develops_into
transitive_over: part_of ! part_of

[Typedef]
id: develops_into
name: develops into
name: develops_into
namespace: uberon
def: "inverse of develops from" []
subset: RO:0002259
xref: RO:0002203
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string
property_value: IAO:0000117 "Terry Meehan" xsd:string
is_transitive: true
is_a: has_potential_to_develop_into ! has potential to develop into
is_a: RO:0002286 ! developmentally succeeded by
is_a: RO:0002388 ! has potential to directly develop into

[Typedef]
id: different_in_magnitude_relative_to
name: different_in_magnitude_relative_to
namespace: quality
def: "q1 different_in_magnitude_relative_to q2 if and only if magnitude(q1) NOT =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale." [PATOC:CJM]

[Typedef]
id: distal_to
name: distal to
name: distal_to
namespace: spatial
namespace: uberon
def: "x distal to y iff x is further along the proximo-distal axis than y, towards the appendage tip. A proximo-distal axis extends from tip of an appendage (distal) to where it joins the body (proximal)." [BSPO:cjm]
def: "x distal_to y iff x is further along the proximo-distal axis than y, towards the appendage tip. A proximo-distal axis extends from tip of an appendage (distal) to where it joins the body (proximal)." [http://orcid.org/0000-0002-6601-2165]
xref: BSPO:0000097
property_value: seeAlso FBcv:0000040
property_value: seeAlso FBql:00005867
is_transitive: true
inverse_of: proximal_to ! proximal_to

[Typedef]
id: dorsal_to
name: dorsal to
name: dorsal_to
namespace: spatial
namespace: uberon
def: "x dorsal to y iff x is further along the dorso-ventral axis than y, towards the back. A dorso-ventral axis is an axis that extends through an organism from back (e.g. spinal column) to front (e.g. belly)." [BSPO:cjm]
def: "x dorsal_to y iff x is further along the dorso-ventral axis than y, towards the back. A dorso-ventral axis is an axis that bisects an organism from back (e.g. spinal column) to front (e.g. belly)." [http://orcid.org/0000-0002-6601-2165]
xref: BSPO:0000098
property_value: seeAlso FBcv:0000041
property_value: seeAlso FBql:00005865
is_transitive: true
inverse_of: ventral_to ! ventral_to

[Typedef]
id: drains
name: drains
namespace: uberon
comment: source: Wikipedia
synonym: "drains blood from" EXACT []
synonym: "drains from" EXACT []
xref: RO:0002179
is_a: connected_to ! connected to

[Typedef]
id: ends
name: ends
namespace: uberon
def: "Relation between occurrents, shares an end boundary with." [Allen:starts, https://orcid.org/0000-0002-6601-2165, ZFS:finishes]
synonym: "finishes" EXACT []
xref: RO:0002229
is_a: part_of ! part_of

[Typedef]
id: ends_with
name: ends with
namespace: uberon
xref: RO:0002230
is_transitive: true
is_a: has_part ! has part

[Typedef]
id: existence_ends_during
name: existence ends during
namespace: uberon
def: "Relation between continuant c and occurrent s, such that every instance of c ceases to exist during some s, if it does not die prematurely." [https://orcid.org/0000-0002-6601-2165]
synonym: "ceases_to_exist_during" EXACT []
xref: RO:0002492
is_a: existence_ends_during_or_before ! existence ends during or before
transitive_over: part_of ! part_of

[Typedef]
id: existence_ends_during_or_before
name: existence ends during or before
namespace: uberon
xref: RO:0002497
holds_over_chain: part_of existence_ends_during_or_before
transitive_over: part_of ! part_of
transitive_over: precedes ! precedes

[Typedef]
id: existence_ends_with
name: existence ends with
namespace: uberon
def: "Relation between continuant and occurrent, such that c ceases to exist at the end of p." [https://orcid.org/0000-0002-6601-2165]
xref: RO:0002493
is_a: existence_ends_during ! existence ends during

[Typedef]
id: existence_starts_and_ends_during
name: existence starts and ends during
namespace: uberon
xref: RO:0002491
is_a: existence_ends_during ! existence ends during
is_a: existence_starts_during ! existence starts during

[Typedef]
id: existence_starts_during
name: existence starts during
namespace: uberon
def: "Relation between continuant c and occurrent s, such that every instance of c comes into existing during some s." [https://orcid.org/0000-0002-6601-2165]
synonym: "begins_to_exist_during" EXACT []
xref: RO:0002488
is_a: existence_starts_during_or_after ! existence starts during or after
transitive_over: part_of ! part_of

[Typedef]
id: existence_starts_during_or_after
name: existence starts during or after
namespace: uberon
xref: RO:0002496
holds_over_chain: part_of existence_starts_during_or_after
transitive_over: part_of ! part_of
transitive_over: preceded_by ! preceded_by

[Typedef]
id: existence_starts_with
name: existence starts with
namespace: uberon
def: "Relation between continuant and occurrent, such that c comes into existence at the start of p." [https://orcid.org/0000-0002-6601-2165]
xref: RO:0002489
is_a: existence_starts_during ! existence starts during

[Typedef]
id: filtered_through
name: filtered through
namespace: uberon
def: "Relationship between a fluid and a material entity, where the fluid is the output of a realization of a filtration role that inheres in the material entity." []
comment: Relationship between a fluid and a filtration barrier, where the portion of fluid arises as a transformation of another portion of fluid on the other side of the barrier, with larger particles removed

[Typedef]
id: finishes_axis
name: finishes axis
namespace: spatial
comment: A directional axis can be divided by a plane. Following Allen Interval Algebra terminology we say that the side on which the axis initiates starts the axis, with the other side finishing the axis. If s finishes axis x, and x has end point p, then x overlaps p
xref: BSPO:0015001

[Typedef]
id: has_boundary
name: has 2D boundary
name: has boundary
namespace: uberon
def: "a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity" []
xref: RO:0002002
property_value: IAO:0000112 "my body has 2D boundary the surface of my skin" xsd:string
property_value: IAO:0000116 "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." xsd:string
property_value: IAO:0000116 "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." xsd:string
property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string
property_value: IAO:0000118 "has boundary" xsd:string
property_value: IAO:0000118 "has_2D_boundary" xsd:string
property_value: RO:0001900 RO:0001901
is_a: RO:0002323 ! mereotopologically related to

[Typedef]
id: has_branching_part
name: has branching part
namespace: uberon
xref: RO:0002569
is_transitive: true

[Typedef]
id: has_cross_section
name: has_cross_section
namespace: quality
def: "s3 has_cross_section s3 if and only if : there exists some 2d plane that intersects the bearer of s3, and the impression of s3 upon that plane has shape quality s2." [PATOC:CJM]
comment: Example: a spherical object has the quality of being spherical, and the spherical quality has_cross_section round.

[Typedef]
id: has_developmental_contribution_from
name: has developmental contribution from
namespace: uberon
def: "x has developmental contribution from y iff x has some part z such that z develops from y" []
xref: RO:0002254
property_value: IAO:0000112 "Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]" xsd:string
property_value: IAO:0000117 "Chris Mungall" xsd:string
holds_over_chain: has_part develops_from
is_transitive: true
is_a: RO:0002258 ! developmentally preceded by
inverse_of: developmentally_contributes_to ! developmentally contributes to

[Typedef]
id: has_gene_template
name: has_gene_template
namespace: protein
is_transitive: false

[Typedef]
id: has_member
name: has member
namespace: uberon
xref: RO:0002351
is_a: has_part ! has part

[Typedef]
id: has_muscle_insertion
name: has_muscle_insertion
namespace: uberon
def: "m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone." [http://en.wikipedia.org/wiki/Insertion_(anatomy)]
comment: The insertion is the point of attachment of a muscle that moves the most when the muscle shortens, or the most distal end of limb muscles
xref: RO:0002373
property_value: seeAlso dbpprop:insertion
is_a: attaches_to ! attaches_to

[Typedef]
id: has_part
name: has part
name: has_part
namespace: external
namespace: protein
namespace: quality
namespace: spatial
namespace: uberon
def: "a core relation that holds between a whole and its part" []
def: "Q1 has_part Q2 if and only if: every instance of Q1 is a quality_of an entity that has_quality some Q2." [PATOC:CJM]
comment: We use the has_part relation to relate complex qualities to more primitive ones. A complex quality is a collection of qualities. The complex quality cannot exist without the sub-qualities. For example, the quality 'swollen' necessarily comes with the qualities of 'protruding' and 'increased size'.
xref: BFO:0000051
property_value: IAO:0000111 "has part" xsd:string
property_value: IAO:0000112 "my body has part my brain (continuant parthood, two material entities)" xsd:string
property_value: IAO:0000112 "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)" xsd:string
property_value: IAO:0000112 "this year has part this day (occurrent parthood)" xsd:string
property_value: IAO:0000116 "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part." xsd:string
property_value: IAO:0000116 "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime" xsd:string
property_value: IAO:0000116 "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'." xsd:string
property_value: IAO:0000118 "has_part" xsd:string
property_value: RO:0001900 RO:0001901
is_transitive: true
is_a: overlaps ! overlaps

[Typedef]
id: has_potential_to_develop_into
name: has potential to develop into
namespace: uberon
def: "x has the potential to develop into y iff x develops into y or if x is capable of developing into y" []
xref: RO:0002387
property_value: IAO:0000117 "Chris Mungall" xsd:string
is_a: RO:0002384 ! has developmental potential involving

[Typedef]
id: has_potential_to_developmentally_contribute_to
name: has potential to developmentally contribute to
namespace: uberon
def: "x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y" []
xref: RO:0002385
property_value: IAO:0000117 "Chris Mungall" xsd:string
is_a: RO:0002384 ! has developmental potential involving

[Typedef]
id: has_quality
name: has_quality
namespace: protein
xref: RO:0000086
is_transitive: false

[Typedef]
id: has_skeleton
name: has skeleton
namespace: uberon
def: "A relation between a subdivision of an organism and the single subdivision of skeleton that provides structural support for that subdivision." [http://orcid.org/0000-0002-6601-2165]
synonym: "has sekeletal support" RELATED []
synonym: "has supporting framework" RELATED []
xref: RO:0002551
is_a: has_part ! has part
inverse_of: skeleton_of ! skeleton of

[Typedef]
id: immediate_transformation_of
name: immediate transformation of
namespace: uberon
synonym: "direct_transformation_of" EXACT [https://orcid.org/0000-0002-6601-2165]
synonym: "immediately transforms from" EXACT [SIO:000658]
xref: RO:0002495
property_value: seeAlso SIO:000658
is_a: transformation_of ! transformation of

[Typedef]
id: immediately_deep_to
name: immediately_deep_to
namespace: uberon
def: "This relation holds when both the deep_to and ajdacent_to relationship similarly hold." [http://orcid.org/0000-0002-6601-2165]
xref: BSPO:0001107
is_a: adjacent_to ! adjacent_to
is_a: deep_to ! deep_to

[Typedef]
id: immediately_preceded_by
name: immediately preceded by
name: immediately_preceded_by
namespace: uberon
def: "X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)" []
comment: X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)
synonym: "directly preceded by" EXACT []
synonym: "is directly preceded by" EXACT []
synonym: "is immediately preceded by" EXACT [SIO:000251]
synonym: "starts_at_end_of" EXACT []
xref: RO:0002087
property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string
property_value: IAO:0000118 "starts_at_end_of" xsd:string
property_value: seeAlso SIO:000251
property_value: UBPROP:0000001 "A non-transitive temporal relation in which one process immediately precedes another process, such that there is no interval of time between the two processes[SIO:000251]." xsd:string {source="SIO:000251"}
is_a: preceded_by ! preceded_by
inverse_of: RO:0002090 ! immediately precedes

[Typedef]
id: in_anterior_side_of
name: in_anterior_side_of
namespace: uberon
def: "X anterior_side_of Y <=> if Y is subdivided into two anterior and posterior portions, X is part_of the anterior portion." [BSPO:PATO_mtg_2009]
xref: BSPO:0000123
is_a: part_of ! part_of

[Typedef]
id: in_distal_side_of
name: in_distal_side_of
namespace: uberon
def: "X distal_side_of Y <=> if Y is subdivided into distal and proximal portions, X is part_of the distal portion." [BSPO:PATO_mtg_2009]
xref: BSPO:0000125
is_a: part_of ! part_of

[Typedef]
id: in_lateral_side_of
name: in_lateral_side_of
namespace: uberon
def: "X in_lateral_side_of Y <=> if X is in_left_side_of Y or X is in_right_side_of Y. X is often, but not always a paired structure" [https://orcid.org/0000-0002-6601-2165]
xref: BSPO:0000126
property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern xsd:anyURI
is_a: part_of ! part_of

[Typedef]
id: in_posterior_side_of
name: in_posterior_side_of
namespace: uberon
def: "X posterior_side_of Y <=> if Y is subdivided into two anterior and posterior portions, X is part_of the posterior portion." [BSPO:PATO_mtg_2009]
xref: BSPO:0000122
is_a: part_of ! part_of

[Typedef]
id: in_proximal_side_of
name: in_proximal_side_of
namespace: uberon
def: "X proximal_side_of Y <=> if Y is subdivided into distal and proximal portions, X is part_of the proximal portion." [BSPO:PATO_mtg_2009]
xref: BSPO:0000124
is_a: part_of ! part_of
inverse_of: in_distal_side_of ! in_distal_side_of

[Typedef]
id: increased_in_magnitude_relative_to
name: increased_in_magnitude_relative_to
namespace: quality
def: "q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale." [PATOC:CJM]
comment: This relation is used to determine the 'directionality' of relative qualities such as 'increased strength', relative to the parent type, 'strength'.
is_transitive: true
is_a: different_in_magnitude_relative_to ! different_in_magnitude_relative_to

[Typedef]
id: left_of
name: left of
namespace: spatial
def: "Closer to the left side of the organism. Example: The dorsal fin is right of the left pectoral fin, but is left of the right eye. On the type level: X left of Y <=> every instance x of X is left of some instance y of Y, and there exists some organism o such that x part of o and y part of o." [BSPO:cjm]
xref: BSPO:0000110
is_transitive: true
inverse_of: right_of ! right of

[Typedef]
id: located_in
name: located in
name: located_in
namespace: uberon
def: "a relation between two independent continuants, the target and the location, in which the target is entirely within the location" []
xref: RO:0001025
is_transitive: true
transitive_over: part_of ! part_of

[Typedef]
id: location_of
name: location of
name: location_of
namespace: uberon
def: "a relation between two independent continuants, the location and the target, in which the target is entirely within the location" []
xref: RO:0001015
is_transitive: true
inverse_of: located_in ! located in

[Typedef]
id: luminal_space_of
name: luminal space of
namespace: uberon
xref: RO:0002572
is_a: part_of ! part_of

[Typedef]
id: member_of
name: member of
namespace: uberon
xref: RO:0002350
is_a: part_of ! part_of
inverse_of: has_member ! has member

[Typedef]
id: only_in_taxon
name: only in taxon
name: only_in_taxon
namespace: protein
def: "S only_in_taxon T iff: S SubClassOf in_taxon only T" [http://www.ncbi.nlm.nih.gov/pubmed/20973947]
def: "U only_in_taxon T: U is a feature found in only in organisms of species of taxon T. The feature cannot be found in an organism of any species outside of (not subsumed by) that taxon. Down-propagates in U hierarchy, up-propagates in T hierarchy (species taxonomy). Implies applicable_to_taxon." [ROC:Waclaw]
def: "x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z." []
comment: Down-propagates. The original name for this in the paper is 'specific_to'. Applicable to genes because some genes are lost in sub-species (strains) of a species.
synonym: "never_outside_taxon" EXACT []
synonym: "specific_to" EXACT []
synonym: "specific_to_taxon" EXACT []
xref: RO:0002160
is_transitive: false
is_a: RO:0002162 ! in taxon

[Typedef]
id: opposite_to
name: opposite to
namespace: spatial
def: "Direcly opposite to. i.e. on the opposite side through the axis." [BSPO:cjm]
xref: BSPO:0000113

[Typedef]
id: orthogonal_to
name: orthogonal to
namespace: spatial
def: "crossing at right angles" [BSPO:cjm]
xref: BSPO:0015005

[Typedef]
id: output_of
name: output_of
namespace: protein
xref: RO:0002353
is_transitive: false

[Typedef]
id: overlaps
name: overlaps
namespace: spatial
def: "x overlaps y if and only if there exists some z such that x has part z and z part of y" []
def: "x overlaps y iff they have some part in common." [BSPO:cjm]
comment: "(forall (x y) (iff (overlaps x y) (exists (z) (and (part of z x) (part of z y)))))" CLIF []
subset: ro-eco
xref: RO:0002131
property_value: RO:0001900 RO:0001901
holds_over_chain: has_part overlaps
holds_over_chain: has_part part_of {http://purl.obolibrary.org/obo/RO_0002582="true"}
holds_over_chain: part_of part_of
is_a: RO:0002323 ! mereotopologically related to
transitive_over: part_of ! part_of
expand_expression_to: "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)" []

[Typedef]
id: parallel_to
name: parallel to
namespace: spatial
def: "x is parallel t y iff x and y are lines or planes which when extended indefinitely do not cross." [BSPO:curators]

[Typedef]
id: part_of
name: part of
name: part_of
namespace: external
namespace: protein
namespace: quality
namespace: spatial
namespace: uberon
def: "a core relation that holds between a part and its whole" []
xref: BFO:0000050
property_value: IAO:0000111 "is part of" xsd:string
property_value: IAO:0000112 "my brain is part of my body (continuant parthood, two material entities)" xsd:string
property_value: IAO:0000112 "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)" xsd:string
property_value: IAO:0000112 "this day is part of this year (occurrent parthood)" xsd:string
property_value: IAO:0000116 "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other." xsd:string
property_value: IAO:0000116 "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime" xsd:string
property_value: IAO:0000116 "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\n\nA continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'." xsd:string
property_value: IAO:0000118 "part_of" xsd:string
property_value: RO:0001900 RO:0001901
property_value: RO:0040042 BFO:0000017
property_value: seeAlso http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections
property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:PartOf
property_value: seeAlso http://www.obofoundry.org/ro/#OBO_REL:part_of xsd:string
is_transitive: true
is_a: overlaps ! overlaps
inverse_of: has_part ! has part

[Typedef]
id: passes_through
name: passes through
namespace: spatial
def: "Intersects at two points." [BSPO:cjm]
xref: BSPO:0015006

[Typedef]
id: posterior_to
name: posterior to
name: posterior_to
namespace: spatial
namespace: uberon
def: "x posterior to y iff x is further along the antero-posterior axis than y, towards the body/tail. An antero-posterior axis is an axis that extends through an organism from head end to opposite end of body or tail." [BSPO:cjm]
def: "x posterior_to y iff x is further along the antero-posterior axis than y, towards the body/tail. An antero-posterior axis is an axis that bisects an organism from head end to opposite end of body or tail." [http://orcid.org/0000-0002-6601-2165]
synonym: "caudal to" NARROW vertebrate []
synonym: "caudal_to" NARROW []
xref: BSPO:0000099
property_value: seeAlso FBcv:0000045
property_value: seeAlso FBql:00005864
is_transitive: true

[Typedef]
id: posteriorly_connected_to
name: posteriorly connected to
namespace: uberon
def: "x posteriorly_connected_to y iff the posterior part of x is connected to y. i.e. x connected_to y and x anterior_to y." [http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern]
is_a: anterior_to ! anterior_to
is_a: connected_to ! connected to

[Typedef]
id: preceded_by
name: preceded by
name: preceded_by
namespace: uberon
def: "x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." []
def: "X preceded_by Y iff: end(Y) before_or_simultaneous_with start(X)" []
subset: ro-eco
synonym: "is preceded by" EXACT [SIO:000249]
synonym: "takes place after" EXACT [Allen:precedes]
xref: BFO:0000062
property_value: http://purl.org/dc/elements/1.1/source http://www.obofoundry.org/ro/#OBO_REL:preceded_by xsd:string
property_value: IAO:0000111 "preceded by" xsd:string
property_value: IAO:0000116 "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C.    The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." xsd:string
property_value: IAO:0000118 "is preceded by" xsd:string
property_value: IAO:0000118 "preceded_by" xsd:string
holds_over_chain: part_of preceded_by
is_transitive: true
is_a: RO:0002086 ! ends after
inverse_of: precedes ! precedes

[Typedef]
id: precedes
name: precedes
namespace: uberon
def: "x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." []
subset: ro-eco
xref: BFO:0000063
property_value: IAO:0000111 "precedes" xsd:string
holds_over_chain: part_of precedes
is_transitive: true
is_a: RO:0002222 ! temporally related to

[Typedef]
id: produced_by
name: produced by
name: produced_by
namespace: uberon
def: "a produced_by b iff some process that occurs_in b has_output a." []
xref: RO:0003001

[Typedef]
id: produces
name: produces
namespace: uberon
def: "a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix." []
comment: Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue.
xref: RO:0003000
inverse_of: produced_by ! produced_by

[Typedef]
id: protects
name: protects
namespace: uberon

[Typedef]
id: proximal_to
name: proximal to
name: proximal_to
namespace: spatial
namespace: uberon
def: "x proximal to y iff x is closer to the point of attachment with the body than y." [BSPO:cjm]
def: "x proximal_to y iff x is closer to the point of attachment with the body than y." [http://orcid.org/0000-0002-6601-2165]
comment: The elbow is proximal to the hand, but distal to the shoulder.
xref: BSPO:0000100
property_value: seeAlso FBcv:0000047
property_value: seeAlso FBql:00005868
is_transitive: true

[Typedef]
id: proximalmost_part_of
name: proximalmost_part_of
namespace: uberon
def: "X proximalmost_part_of Y <=> X is part_of Y and X is adjacent_to the proximal boundary of Y" [https://orcid.org/0000-0002-6601-2165]
xref: BSPO:0001106
is_a: in_proximal_side_of ! in_proximal_side_of

[Typedef]
id: right_of
name: right of
namespace: spatial
def: "Closer to the right side of the organism. Example: The dorsal fin is right of the left pectoral fin, but is left of the right eye. On the type level: X left of Y <=> every instance x of X is right of some instance y of Y, and there exists some organism o such that x part of o and y part of o." [BSPO:cjm]
xref: BSPO:0000111
is_transitive: true

[Typedef]
id: similar_in_magnitude_relative_to
name: similar_in_magnitude_relative_to
namespace: quality
def: "q1 similar_in_magnitude_relative_to q2 if and only if magnitude(q1) =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale." [PATOC:CJM]

[Typedef]
id: skeleton_of
name: skeleton of
namespace: uberon
xref: RO:0002576
is_a: part_of ! part_of

[Typedef]
id: starts
name: starts
namespace: uberon
def: "Relation between occurrents, shares a start boundary with." [Allen:starts, https://orcid.org/0000-0002-6601-2165]
xref: RO:0002223
is_a: part_of ! part_of
inverse_of: starts_with ! starts with

[Typedef]
id: starts_axis
name: starts axis
namespace: spatial
comment: A directional axis can be divided by a plane. Following Allen Interval Algebra terminology we say that the side on which the axis initiates starts the axis, with the other side finishing the axis. . If s starts axis x, and x has start point p, then x overlaps p
xref: BSPO:0015007

[Typedef]
id: starts_with
name: starts with
namespace: uberon
xref: RO:0002224
is_transitive: true
is_a: has_part ! has part

[Typedef]
id: subdivision_of
name: subdivision of
namespace: uberon
comment: placeholder relation. X = 'subdivision of A' and subdivision_of some B means that X is the mereological sum of A and B

[Typedef]
id: superficial_to
name: superficial_to
namespace: uberon
def: "Near the outer surface of the organism. Thus, skin is superficial to the muscle layer." [http://orcid.org/0000-0002-6601-2165]
xref: BSPO:0000108

[Typedef]
id: surrounded_by
name: surrounded by
name: surrounded_by
namespace: uberon
def: "x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x" []
def: "x surrounded_by y iff: x is adjacent to y and for every region r adjacent to x, r overlaps y" [https://orcid.org/0000-0002-6601-2165]
xref: RO:0002219
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: RO:0001900 RO:0001901
is_a: adjacent_to ! adjacent_to
inverse_of: surrounds ! surrounds

[Typedef]
id: surrounds
name: surrounds
namespace: uberon
def: "inverse of surrounded by" []
def: "inverse of surrounded_by" [https://orcid.org/0000-0002-6601-2165]
subset: RO:0002259
xref: RO:0002221
property_value: IAO:0000117 "Chris Mungall" xsd:string
property_value: RO:0001900 RO:0001901
is_a: adjacent_to ! adjacent_to

[Typedef]
id: transformation_of
name: transformation of
namespace: uberon
synonym: "transforms from" EXACT [SIO:000657]
xref: RO:0002494
property_value: seeAlso SIO:000657
is_transitive: true
is_a: develops_from ! develops from

[Typedef]
id: transitively_anteriorly_connected_to
name: transitively anteriorly connected to
namespace: uberon
def: "." [http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern]
is_transitive: true

[Typedef]
id: transitively_connected_to
name: transitively_connected to
namespace: uberon
is_transitive: true

[Typedef]
id: tributary_of
name: tributary_of
namespace: uberon
synonym: "drains into" RELATED [dbpowl:drainsTo]
xref: RO:0002376

[Typedef]
id: ventral_to
name: ventral to
name: ventral_to
namespace: spatial
namespace: uberon
def: "x ventral to y iff x is further along the dorso-ventral axis than y, towards the front. A dorso-ventral axis is an axis that extends through an organism from back (e.g. spinal column) to front (e.g. belly)." [BSPO:cjm]
def: "x ventral_to y iff x is further along the dorso-ventral axis than y, towards the front. A dorso-ventral axis is an axis that bisects an organism from back (e.g. spinal column) to front (e.g. belly)." [http://orcid.org/0000-0002-6601-2165]
xref: BSPO:0000102
property_value: seeAlso FBcv:0000049
property_value: seeAlso FBql:00005866
is_transitive: true