diff --git a/src/ontology/efo-edit.owl b/src/ontology/efo-edit.owl index 0bf9dd41..5cbcbfd1 100644 --- a/src/ontology/efo-edit.owl +++ b/src/ontology/efo-edit.owl @@ -507913,7 +507913,7 @@ to hypernasality and abnormal speech reduction. - sequential division of tissue layers to expose (and isolate) organs and organ parts of a deceased animal or plant + Sequential division of tissue layers to expose (and isolate) organs and organ parts of a deceased human body. Dani Welter post-mortem dissection cadaver dissection @@ -752203,10 +752203,10 @@ Use: Orphanet_79452 Label: Milroy disease participates_in - preceded_by preceded_by - BFO:0000062 + preceded_by uberon + BFO:0000062 disjoint_from part_of, but this cannot be expressed in OWL2 takes place after preceded_by @@ -752227,10 +752227,10 @@ Use: Orphanet_79452 Label: Milroy disease Relation between continuant c and occurrent s, such that every instance of c comes into existing during some s. - existence_starts_during existence_starts_during - BFO:0000068 + existence_starts_during begins_to_exist_during + BFO:0000068 uberon existence_starts_during @@ -752246,8 +752246,8 @@ Use: Orphanet_79452 Label: Milroy disease BFO:0000069 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. uberon - existence_ends_during existence_ends_during + existence_ends_during ceases_to_exist_during @@ -752257,11 +752257,11 @@ Use: Orphanet_79452 Label: Milroy disease https://orcid.org/0000-0002-6601-2165 - 2009-07-31T02:15:46Z anterior_to anterior_to - BSPO:0000096 + 2009-07-31T02:15:46Z cjm + BSPO:0000096 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 uberon anterior_to @@ -752305,8 +752305,8 @@ Use: Orphanet_79452 Label: Milroy disease posterior_to BSPO:0000099 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. - posterior_to posterior_to + posterior_to caudal_to @@ -752320,8 +752320,8 @@ Use: Orphanet_79452 Label: Milroy disease proximal_to BSPO:0000100 uberon - x proximal_to y iff x is closer to the point of attachment with the body than y. proximal_to + x proximal_to y iff x is closer to the point of attachment with the body than y. @@ -752330,8 +752330,8 @@ Use: Orphanet_79452 Label: Milroy disease BSPO:cjm - ventral_to ventral_to + ventral_to 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). uberon BSPO:0000102 @@ -752346,9 +752346,9 @@ Use: Orphanet_79452 Label: Milroy disease deep_to uberon - deep_to deep_to Further away from the surface of the organism. Thus, the muscular layer is deep to the skin, but superficial to the intestines. + deep_to BSPO:0000107 @@ -752358,9 +752358,9 @@ Use: Orphanet_79452 Label: Milroy disease BSPO:cjm + superficial_to BSPO:0000108 superficial_to - superficial_to uberon superficial_to Near the outer surface of the organism. Thus, skin is superficial to the muscle layer. @@ -752373,12 +752373,12 @@ Use: Orphanet_79452 Label: Milroy disease uberon - in_left_side_of - in_left_side_of BSPO:0000120 + in_left_side_of + in_left_side_of http://purl.obolibrary.org/obo/uberon/references/reference_0000014 - in_left_side_of X in_left_side_of Y <=> if Y is subdivided into left and right portions, X is part_of the left portion. + in_left_side_of @@ -752388,9 +752388,9 @@ Use: Orphanet_79452 Label: Milroy disease uberon - in_right_side_of in_right_side_of BSPO:0000121 + in_right_side_of http://purl.obolibrary.org/obo/uberon/references/reference_0000014 X in_right_side_of Y <=> if Y is subdivided into left and right portions, X is part_of the right portion. in_right_side_of @@ -752406,8 +752406,8 @@ Use: Orphanet_79452 Label: Milroy disease X posterior_side_of Y <=> if Y is subdivided into two anterior and posterior portions, X is part_of the posterior portion. in_posterior_side_of BSPO:0000122 - in_posterior_side_of in_posterior_side_of + in_posterior_side_of @@ -752418,8 +752418,8 @@ Use: Orphanet_79452 Label: Milroy disease in_anterior_side_of uberon - in_anterior_side_of in_anterior_side_of + in_anterior_side_of BSPO:0000123 X anterior_side_of Y <=> if Y is subdivided into two anterior and posterior portions, X is part_of the anterior portion. @@ -752432,8 +752432,8 @@ Use: Orphanet_79452 Label: Milroy disease in_proximal_side_of uberon - in_proximal_side_of in_proximal_side_of + in_proximal_side_of X proximal_side_of Y <=> if Y is subdivided into distal and proximal portions, X is part_of the proximal portion. BSPO:0000124 @@ -752474,9 +752474,9 @@ Use: Orphanet_79452 Label: Milroy disease in_superficial_part_of - in_superficial_part_of in_superficial_part_of X superficial_part_of Y <=> if Y is subdivided into two superficial and deep portions, X is part_of the superficial portion. + in_superficial_part_of uberon BSPO:0001100 @@ -752490,8 +752490,8 @@ Use: Orphanet_79452 Label: Milroy disease in_deep_part_of BSPO:0001101 X superficial_part_of Y <=> if Y is subdivided into two superficial and deep portions, X is part_of the deep portion. - in_deep_part_of in_deep_part_of + in_deep_part_of uberon @@ -752502,11 +752502,11 @@ Use: Orphanet_79452 Label: Milroy disease proximalmost_part_of - BSPO:0001106 uberon + BSPO:0001106 proximalmost_part_of - proximalmost_part_of X proximalmost_part_of Y <=> X is part_of Y and X is adjacent_to the proximal boundary of Y + proximalmost_part_of @@ -752519,8 +752519,8 @@ Use: Orphanet_79452 Label: Milroy disease immediately_deep_to This relation holds when both the deep_to and ajdacent_to relationship similarly hold. uberon - immediately_deep_to immediately_deep_to + immediately_deep_to @@ -752530,8 +752530,8 @@ Use: Orphanet_79452 Label: Milroy disease BSPO:0001108 - distalmost_part_of distalmost_part_of + distalmost_part_of uberon distalmost_part_of X distalmost_part_of Y <=> X is part_of Y and X is adjacent_to the distal boundary of Y @@ -752543,8 +752543,8 @@ Use: Orphanet_79452 Label: Milroy disease https://orcid.org/0000-0002-6601-2165 - preaxialmost_part_of preaxialmost_part_of + preaxialmost_part_of BSPO:0001113 preaxialmost_part_of uberon @@ -752555,8 +752555,8 @@ Use: Orphanet_79452 Label: Milroy disease x preaxial_to y iff x is further along the preaxial-postaxial axis than y, towards the postaxial side. posterior_to (developmentally) uberon - postaxial_to postaxial_to + postaxial_to @@ -752571,27 +752571,27 @@ Use: Orphanet_79452 Label: Milroy disease MA:th - postaxialmost_part_of postaxialmost_part_of + postaxialmost_part_of BSPO:0001115 postaxialmost_part_of uberon - X intersects_median_plane of iff X crosses the midine plane of Y. intersects_midsagittal_plane_of + X intersects_median_plane of iff X crosses the midine plane of Y. intersects_midsagittal_plane_of BSPO:0005001 intersects_midsagittal_plane_of uberon - preaxial_to preaxial_to + preaxial_to x preaxial_to y iff x is further along the preaxial-postaxial axis than y, towards the front. BSPO:1000000 - lateral (radial) to anterior_to (developmentally) + lateral (radial) to preaxial_to medial (tibial) to uberon @@ -752621,8 +752621,8 @@ Use: Orphanet_79452 Label: Milroy disease uberon - relation between an artery and the structure is supplies with blood. supplies + relation between an artery and the structure is supplies with blood. FMA:86003 arterial supply of source: FMA @@ -752660,12 +752660,12 @@ Use: Orphanet_79452 Label: Milroy disease directly preceded by immediately_preceded_by is immediately preceded by - X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) starts_at_end_of + X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) http://semanticscience.org/resource/SIO_000251 is directly preceded by - 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]. uberon + 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]. immediately_preceded_by immediately_preceded_by @@ -752682,23 +752682,23 @@ Use: Orphanet_79452 Label: Milroy disease SIO:000251 - overlaps RO:0002131 + overlaps A overlaps B if they share some part in common. uberon overlaps overlaps - homologous_to homologous_to + homologous_to uberon homologous_to RO:0002158 - serially_homologous_to serially_homologous_to + serially_homologous_to RO:0002159 serially_homologous_to uberon @@ -752710,8 +752710,8 @@ Use: Orphanet_79452 Label: Milroy disease true uberon Class: <http://www.w3.org/2002/07/owl#Nothing> EquivalentTo: ?X and (RO_0002162 some ?Y) - never_in_taxon never_in_taxon + never_in_taxon true @@ -752732,8 +752732,8 @@ Use: Orphanet_79452 Label: Milroy disease uberon true S dubious_for_taxon T if it is probably the case that no instances of S can be found in any instance of T. - dubious_for_taxon dubious_for_taxon + dubious_for_taxon true @@ -752743,8 +752743,8 @@ Use: Orphanet_79452 Label: Milroy disease https://orcid.org/0000-0002-6601-2165 - develops_into develops_into + develops_into uberon RO:0002203 develops_into @@ -752768,8 +752768,8 @@ Use: Orphanet_79452 Label: Milroy disease x surrounded_by y iff: x is adjacent to y and for every region r adjacent to x, r overlaps y RO:0002219 uberon - surrounded_by surrounded_by + surrounded_by @@ -752782,15 +752782,15 @@ Use: Orphanet_79452 Label: Milroy disease RO:0002220 adjacent_to adjacent_to - x adjacent_to y iff: x and y share a boundary uberon + x adjacent_to y iff: x and y share a boundary RO:0002221 uberon inverse of surrounded_by - surrounds surrounds + surrounds surrounds @@ -752801,10 +752801,10 @@ Use: Orphanet_79452 Label: Milroy disease Relation between occurrents, shares a start boundary with. - starts starts - RO:0002224 uberon + RO:0002224 + starts starts @@ -752834,8 +752834,8 @@ Use: Orphanet_79452 Label: Milroy disease finishes uberon ends - finishes finishes + finishes RO:0002229 @@ -752883,8 +752883,8 @@ Use: Orphanet_79452 Label: Milroy disease uberon - developmentally_replaces developmentally_replaces + developmentally_replaces RO:0002285 developmentally_replaces @@ -752897,10 +752897,10 @@ Use: Orphanet_79452 Label: Milroy disease uberon - attaches_to attaches_to - uberon + attaches_to FMA:85990 + uberon attaches_to RO:0002371 @@ -752936,11 +752936,11 @@ Use: Orphanet_79452 Label: Milroy disease RO:0002374 - has_fused_element has_fused_element + has_fused_element uberon - has_fused_element x has_fused_element y iff: there exists some z : x has_part z, z homologous_to y, and y is a distinct element, the boundary between x and z is largely fiat + has_fused_element A single bone in one species may correspond to the fusion of two or more bones found as distinct elements in another. For example, tibiofibula has_fused_element tibia. A has_fused_element B does not imply that A has_part some B, rather than A has_part some B', where B' is not a subtype of B (because B is a distinct element but B' is a regional part) but has some evolutionary relationship to B. @@ -752951,9 +752951,9 @@ Use: Orphanet_79452 Label: Milroy disease produced_by + homology_notes homology_notes uberon - homology_notes This annotation property may be replaced with an annotation property from an external ontology such as IAO @@ -752974,16 +752974,16 @@ This annotation property may be replaced with an annotation property from an ext has_relational_adjective uberon UBPROP:0000007 - has_relational_adjective has_relational_adjective + has_relational_adjective Used to connect a class to an adjectival form of its label. For example, a class with label 'intestine' may have a relational adjective 'intestinal'. taxon_notes true + taxon_notes uberon taxon_notes - taxon_notes UBPROP:0000008 @@ -753056,8 +753056,8 @@ This annotation property may be replaced with an annotation property from an ext uberon FMA:85994 - branch_of branch_of + branch_of Source: FMA. Editor note: we need to check if FMA branch_of implies part_of. the relation we intend to use here should - for example, see vestibulocochlear nerve @@ -753067,8 +753067,8 @@ This annotation property may be replaced with an annotation property from an ext channel_for - channels_from channels_from + channels_from uberon @@ -753078,9 +753078,9 @@ This annotation property may be replaced with an annotation property from an ext 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. - uberon connects connects + uberon Editors note: 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) @@ -753104,20 +753104,20 @@ This annotation property may be replaced with an annotation property from an ext source: Wikipedia drains from - drains drains - uberon + drains drains blood from + uberon - enclosed_by enclosed_by + enclosed_by uberon x encloses y iff the convex hull formed by x contains all or the majority of y. - encloses encloses + encloses uberon @@ -753127,14 +753127,14 @@ This annotation property may be replaced with an annotation property from an ext https://orcid.org/0000-0002-6601-2165 - evolved_from evolved_from - uberon + evolved_from Status: experimental + uberon - evolved_multiple_times_in evolved_multiple_times_in + evolved_multiple_times_in Status: experimental uberon @@ -753165,8 +753165,8 @@ This annotation property may be replaced with an annotation property from an ext Relation between continuant and occurrent, such that c ceases to exist at the end of p. uberon - existence_ends_with existence_ends_with + existence_ends_with @@ -753205,8 +753205,8 @@ This annotation property may be replaced with an annotation property from an ext https://orcid.org/0000-0002-6601-2165 - existence_starts_or_ends_during existence_starts_or_ends_during + existence_starts_or_ends_during uberon @@ -753251,9 +753251,9 @@ This annotation property may be replaced with an annotation property from an ext dbprop:nerve + innervated_by http://code.google.com/p/obo-relations/issues/detail?id=6 innervated_by - innervated_by nerve supply FMA:85999 uberon @@ -753283,12 +753283,12 @@ This annotation property may be replaced with an annotation property from an ext applicable for taxon - present_in_taxon present_in_taxon + present_in_taxon true true - S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S uberon + S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S @@ -753321,8 +753321,8 @@ This annotation property may be replaced with an annotation property from an ext GOC:cjm - shares_no_parts_with true + shares_no_parts_with true uberon spatially_disjoint_from @@ -753338,8 +753338,8 @@ This annotation property may be replaced with an annotation property from an ext SO:cjm - start_of start_of + start_of uberon @@ -753351,8 +753351,8 @@ This annotation property may be replaced with an annotation property from an ext uberon transitively anteriorly connected to - transitively_anteriorly_connected_to . + transitively_anteriorly_connected_to @@ -753406,16 +753406,16 @@ This annotation property may be replaced with an annotation property from an ext http://semanticscience.org/resource/SIO_000008 has_quality uberon - has_quality has_quality + has_quality transformation_of transforms from - uberon transformation_of - http://semanticscience.org/resource/SIO_000657 + uberon transformation_of + http://semanticscience.org/resource/SIO_000657 @@ -753424,9 +753424,9 @@ This annotation property may be replaced with an annotation property from an ext SIO:000657 - immediate_transformation_of - http://semanticscience.org/resource/SIO_000658 immediate_transformation_of + http://semanticscience.org/resource/SIO_000658 + immediate_transformation_of immediately transforms from direct_transformation_of uberon