diff --git a/src/ontology/efo-edit.owl b/src/ontology/efo-edit.owl index 452f8066..bb3f9ce5 100644 --- a/src/ontology/efo-edit.owl +++ b/src/ontology/efo-edit.owl @@ -507075,6 +507075,20 @@ The procedure involves either a single lung transplant, bilateral sequential lun + + + + + The quantification of the amount of activated migroglia in the brain. + Elizabeth Lewis + true + PMID:30679421 + proportion of activated microglia + microglial activation measurement + + + + @@ -723417,10 +723431,10 @@ 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 @@ -723441,8 +723455,8 @@ 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 + existence_starts_during BFO:0000068 begins_to_exist_during uberon @@ -723455,13 +723469,13 @@ Use: Orphanet_79452 Label: Milroy disease https://orcid.org/0000-0002-6601-2165 - existence_ends_during todo - add full axioms to bfo - 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. + existence_ends_during 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 @@ -723471,13 +723485,13 @@ Use: Orphanet_79452 Label: Milroy disease https://orcid.org/0000-0002-6601-2165 - anterior_to 2009-07-31T02:15:46Z anterior_to - BSPO:0000096 + anterior_to cjm - uberon + 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 @@ -723490,8 +723504,8 @@ Use: Orphanet_79452 Label: Milroy disease 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). distal_to BSPO:0000097 - distal_to distal_to + distal_to uberon @@ -723516,11 +723530,11 @@ Use: Orphanet_79452 Label: Milroy disease uberon - posterior_to BSPO:0000099 + posterior_to 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 @@ -723533,9 +723547,9 @@ Use: Orphanet_79452 Label: Milroy disease proximal_to proximal_to BSPO:0000100 - x proximal_to y iff x is closer to the point of attachment with the body than y. proximal_to uberon + x proximal_to y iff x is closer to the point of attachment with the body than y. @@ -723572,9 +723586,9 @@ Use: Orphanet_79452 Label: Milroy disease BSPO:cjm + superficial_to superficial_to BSPO:0000108 - superficial_to uberon superficial_to Near the outer surface of the organism. Thus, skin is superficial to the muscle layer. @@ -723602,9 +723616,9 @@ 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 @@ -723646,8 +723660,8 @@ 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 @@ -723674,8 +723688,8 @@ Use: Orphanet_79452 Label: Milroy disease http://purl.obolibrary.org/obo/uberon/references/reference_0000014 uberon - in_lateral_side_of in_lateral_side_of + in_lateral_side_of 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 BSPO:0000126 in_lateral_side_of @@ -723689,8 +723703,8 @@ Use: Orphanet_79452 Label: Milroy disease 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 in_superficial_part_of + in_superficial_part_of uberon BSPO:0001100 @@ -723716,10 +723730,10 @@ Use: Orphanet_79452 Label: Milroy disease proximalmost_part_of - uberon BSPO:0001106 - proximalmost_part_of + uberon 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 @@ -723744,10 +723758,10 @@ Use: Orphanet_79452 Label: Milroy disease BSPO:0001108 - distalmost_part_of distalmost_part_of - uberon + distalmost_part_of distalmost_part_of + uberon X distalmost_part_of Y <=> X is part_of Y and X is adjacent_to the distal boundary of Y @@ -723785,23 +723799,23 @@ Use: Orphanet_79452 Label: Milroy disease MA:th - postaxialmost_part_of postaxialmost_part_of + postaxialmost_part_of BSPO:0001115 postaxialmost_part_of uberon + intersects_midsagittal_plane_of 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 anterior_to (developmentally) @@ -723930,8 +723944,8 @@ Use: Orphanet_79452 Label: Milroy disease SNOMEDCT:2579009 - SNOMEDCT:419583006 NCIt:C12946 + SNOMEDCT:419583006 GOC:tfm @@ -723942,9 +723956,9 @@ Use: Orphanet_79452 Label: Milroy disease FMA:85972 - continuous_with sourced from FMA continuous_with + continuous_with uberon continuous_with @@ -724025,8 +724039,8 @@ Use: Orphanet_79452 Label: Milroy disease ICD10:Q66 - NCIt:C26808 ICD10:N17 + NCIt:C26808 MedDRA:10013950 @@ -724045,8 +724059,8 @@ Use: Orphanet_79452 Label: Milroy disease ICD10:J93 - NCIt:C84475 DOID:9563 + NCIt:C84475 OMIM:613021 OMIM:613071 OMIM:211400 @@ -724056,8 +724070,8 @@ Use: Orphanet_79452 Label: Milroy disease DOID:11372 - NCIt:C34810 MedDRA:10027110 + NCIt:C34810 SNOMEDCT:33995003 @@ -724178,11 +724192,11 @@ Use: Orphanet_79452 Label: Milroy disease RO:0002082 is_equal_to - simultaneous_with coincides_with + simultaneous_with uberon - simultaneous_with simultaneous_with + simultaneous_with Relation between occurrents, shares start and end boundaries. @@ -724195,10 +724209,10 @@ Use: Orphanet_79452 Label: Milroy disease RO:0002087 directly preceded by - is immediately preceded by immediately_preceded_by - X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) + is immediately preceded by 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 uberon @@ -724219,23 +724233,23 @@ Use: Orphanet_79452 Label: Milroy disease SIO:000251 - RO:0002131 overlaps + RO:0002131 A overlaps B if they share some part in common. - overlaps 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 @@ -724267,8 +724281,8 @@ Use: Orphanet_79452 Label: Milroy disease this relation lacks a strong logical interpretation, but can be used in place of never_in_taxon where it is desirable to state that the definition of the class is too strict for the taxon under consideration, but placing a never_in_taxon link would result in a chain of inconsistencies that will take time to resolve. Example: metencephalon in teleost uberon - S dubious_for_taxon T if it is probably the case that no instances of S can be found in any instance of T. 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 true @@ -724280,8 +724294,8 @@ Use: Orphanet_79452 Label: Milroy disease https://orcid.org/0000-0002-6601-2165 - develops_into develops_into + develops_into uberon RO:0002203 develops_into @@ -724305,8 +724319,8 @@ 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 @@ -724319,8 +724333,8 @@ Use: Orphanet_79452 Label: Milroy disease RO:0002220 uberon x adjacent_to y iff: x and y share a boundary - adjacent_to adjacent_to + adjacent_to RO:0002221 @@ -724338,10 +724352,10 @@ Use: Orphanet_79452 Label: Milroy disease Relation between occurrents, shares a start boundary with. + starts starts - RO:0002224 uberon - starts + RO:0002224 starts @@ -724362,8 +724376,8 @@ Use: Orphanet_79452 Label: Milroy disease uberon develops_in develops_in - RO:0002226 This relation take from EHDAA2 - precise semantics yet to be defined + RO:0002226 develops_in @@ -724371,8 +724385,8 @@ Use: Orphanet_79452 Label: Milroy disease finishes uberon ends - finishes finishes + finishes RO:0002229 @@ -724398,8 +724412,8 @@ Use: Orphanet_79452 Label: Milroy disease RO:0002255 - developmentally_contributes_to developmentally_contributes_to + developmentally_contributes_to uberon developmentally_contributes_to @@ -724434,8 +724448,8 @@ Use: Orphanet_79452 Label: Milroy disease uberon - attaches_to attaches_to + attaches_to FMA:85990 uberon attaches_to @@ -724461,8 +724475,8 @@ Use: Orphanet_79452 Label: Milroy disease RO:0002373 has_muscle_insertion dbpprop:insertion - has_muscle_insertion has_muscle_insertion + has_muscle_insertion 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. @@ -724473,8 +724487,8 @@ 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 @@ -724488,9 +724502,9 @@ 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 @@ -724511,15 +724525,15 @@ 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'. true taxon_notes - taxon_notes taxon_notes + taxon_notes uberon UBPROP:0000008 @@ -724549,8 +724563,8 @@ This annotation property may be replaced with an annotation property from an ext FMA has terms like 'set of X'. In general we do not include set-of terms in uberon, but provide a mapping between the singular form and the FMA set term uberon - fma_set_term fma_set_term + fma_set_term true @@ -724572,8 +724586,8 @@ This annotation property may be replaced with an annotation property from an ext UBREL:0000002 - uberon composed_primarily_of + uberon x composed_primarily_of y iff: more than half of the mass of x is made from parts of y composed_primarily_of composed_primarily_of @@ -724593,8 +724607,8 @@ 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 @@ -724604,8 +724618,8 @@ This annotation property may be replaced with an annotation property from an ext channel_for - channels_from channels_from + channels_from uberon @@ -724616,8 +724630,8 @@ 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 + connects 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) @@ -724641,20 +724655,20 @@ This annotation property may be replaced with an annotation property from an ext source: Wikipedia drains from - drains drains + 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 @@ -724678,8 +724692,8 @@ This annotation property may be replaced with an annotation property from an ext uberon c existence_ends_at e iff c exists_at e and not ( exists e2 : c exists_at e2 and e before e2). - existence_ends_at existence_ends_at + existence_ends_at @@ -724690,8 +724704,8 @@ This annotation property may be replaced with an annotation property from an ext Relation between continuant c and occurrent s, such that every instance of c ceases to exist before s. uberon - existence_ends_before existence_ends_before + existence_ends_before @@ -724713,8 +724727,8 @@ This annotation property may be replaced with an annotation property from an ext Relation between continuant c and occurrent s, such that every instance of c comes into existing after some s has completed. - existence_starts_after existence_starts_after + existence_starts_after disjoint_from existence_starts_during (but this cannot be expressed in OWL2) uberon @@ -724730,8 +724744,8 @@ This annotation property may be replaced with an annotation property from an ext existence_starts_and_ends_during - existence_starts_at existence_starts_at + existence_starts_at uberon c existence_starts_at e iff c exists_at e and not ( exists e2 : c exists_at e2 and e2 before e) @@ -724742,8 +724756,8 @@ 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 @@ -724770,8 +724784,8 @@ This annotation property may be replaced with an annotation property from an ext dbpprop:antagonist - has_muscle_antagonist has_muscle_antagonist + has_muscle_antagonist uberon m1 has_muscle_antagonist m2 iff m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position. @@ -724783,13 +724797,13 @@ This annotation property may be replaced with an annotation property from an ext has_start - uberon has_start + uberon dbprop:nerve - http://code.google.com/p/obo-relations/issues/detail?id=6 innervated_by + http://code.google.com/p/obo-relations/issues/detail?id=6 innervated_by nerve supply FMA:85999 @@ -724803,8 +724817,8 @@ This annotation property may be replaced with an annotation property from an ext uberon - output_of output_of + output_of uberon @@ -724846,8 +724860,8 @@ This annotation property may be replaced with an annotation property from an ext UBERONREF:0000004 - site_of site_of + site_of C site_of P iff exists species S such that P occurs_in C for all members of S. Example: bursa of Fabricius site_of B-cell differentiation. uberon @@ -724862,8 +724876,8 @@ This annotation property may be replaced with an annotation property from an ext true true uberon - spatially_disjoint_from spatially_disjoint_from + spatially_disjoint_from Class: <http://www.w3.org/2002/07/owl#Nothing> EquivalentTo: (BFO_0000050 some ?X) and (BFO_0000050 some ?Y) A is spatially_disjoint_from B if they have no parts in common. non_overlapping_with @@ -724875,8 +724889,8 @@ This annotation property may be replaced with an annotation property from an ext SO:cjm - start_of start_of + start_of uberon @@ -724935,22 +724949,22 @@ This annotation property may be replaced with an annotation property from an ext Status: experimental uberon - homologous_in homologous_in + homologous_in true http://semanticscience.org/resource/SIO_000008 has_quality uberon - has_quality has_quality + has_quality transformation_of transforms from - uberon transformation_of + uberon transformation_of http://semanticscience.org/resource/SIO_000657 diff --git a/src/ontology/imports/hp_import.owl b/src/ontology/imports/hp_import.owl index b26bb85b..106fd2c9 100644 --- a/src/ontology/imports/hp_import.owl +++ b/src/ontology/imports/hp_import.owl @@ -43719,6 +43719,21 @@ Additionally, the headaches cannot attributed to another disorder. + + + + Increase in size of the left atrium. + 2017-08-13T21:38:04Z + peter + Fyler:3011 + Fyler:3020 + Enlarged heart left atrium + Left atrial enlargement + + + + diff --git a/src/ontology/imports/hp_terms.txt b/src/ontology/imports/hp_terms.txt index 09e96883..a45a89c0 100644 --- a/src/ontology/imports/hp_terms.txt +++ b/src/ontology/imports/hp_terms.txt @@ -1230,6 +1230,7 @@ http://purl.obolibrary.org/obo/HP_0031217 http://purl.obolibrary.org/obo/HP_0031273 http://purl.obolibrary.org/obo/HP_0031284 http://purl.obolibrary.org/obo/HP_0031292 +http://purl.obolibrary.org/obo/HP_0031295 http://purl.obolibrary.org/obo/HP_0031456 http://purl.obolibrary.org/obo/HP_0031458 http://purl.obolibrary.org/obo/HP_0031481 diff --git a/src/ontology/iri_dependencies/hp_terms.txt b/src/ontology/iri_dependencies/hp_terms.txt index 621944cb..12eaa105 100644 --- a/src/ontology/iri_dependencies/hp_terms.txt +++ b/src/ontology/iri_dependencies/hp_terms.txt @@ -1346,3 +1346,4 @@ http://purl.obolibrary.org/obo/HP_0001710 http://purl.obolibrary.org/obo/HP_0008994 http://purl.obolibrary.org/obo/HP_0003026 http://purl.obolibrary.org/obo/HP_0005387 +http://purl.obolibrary.org/obo/HP_0031295