From 35b5228f860caecd6bc54f43ce0e6be4dc5306fc Mon Sep 17 00:00:00 2001 From: hkir-dev Date: Mon, 14 Mar 2022 14:12:25 +0000 Subject: [PATCH 01/17] robot extract/merge should optionally inject provenance #893 --- docs/annotate.md | 19 +- docs/examples/edit3.owl | 19 + docs/examples/example2.owl | 1175 ++++ docs/examples/example2_defined_by.owl | 1333 ++++ docs/examples/example2_derived_by.owl | 5654 +++++++++++++++++ docs/examples/merged_defined_by.owl | 1248 ++++ docs/examples/merged_derived_by.owl | 818 +++ docs/merge.md | 17 + .../org/obolibrary/robot/AnnotateCommand.java | 50 + .../org/obolibrary/robot/MergeCommand.java | 15 +- .../org/obolibrary/robot/MergeOperation.java | 148 +- .../org/obolibrary/robot/OntologyHelper.java | 118 +- 12 files changed, 10607 insertions(+), 7 deletions(-) create mode 100644 docs/examples/edit3.owl create mode 100644 docs/examples/example2.owl create mode 100644 docs/examples/example2_defined_by.owl create mode 100644 docs/examples/example2_derived_by.owl create mode 100644 docs/examples/merged_defined_by.owl create mode 100644 docs/examples/merged_derived_by.owl diff --git a/docs/annotate.md b/docs/annotate.md index f52658ebb..2193d94f1 100644 --- a/docs/annotate.md +++ b/docs/annotate.md @@ -2,7 +2,7 @@ It's important to add metadata to an ontology before releasing it, and to update the ontology version IRI. -General annotations can be added one-by-one with `--anotation`, and the IRIs can be set with `--version-iri` and `--ontology-iri`. You can specify as many annotation flags as you'd like in one command: +General annotations can be added one-by-one with `--annotation`, and the IRIs can be set with `--version-iri` and `--ontology-iri`. You can specify as many annotation flags as you'd like in one command: robot annotate --input edit.owl \ --ontology-iri "https://github.com/ontodev/robot/examples/annotated.owl" \ @@ -38,6 +38,23 @@ This command can also remove all ontology annotations from your file with `--rem --annotation-file annotations.ttl \ --output results/annotated_2.owl + +## Annotating the Source + +It’s also possible to annotate the ontology axioms with the ontology IRI or version IRI. + + * `--annotate-derived-from true`: annotates all OWLAxioms with the source's version IRI if it exists, else with the ontology IRI, using `prov:wasDerivedFrom`. If the axiom already has an annotation using this property (`prov:wasDerivedFrom`), the existing annotation will be kept and no new annotation will be added. + + robot annotate --input example2.owl \ + --annotate-derived-from true + --output results/example2_derived_by.owl + + * `--annotate-defined-by true`: annotates all OWLEntities (class, data, annotation, object property and named individual declaration axioms) with the source's IRI using `rdfs:isDefinedBy`. If the term already has an annotation using this property (`rdfs:isDefinedBy`), the existing annotation will be kept and no new annotation will be added. + + robot annotate --input example2.owl \ + --annotate-defined-by true + --output results/example2_defined_by.owl + --- ## Error Messages diff --git a/docs/examples/edit3.owl b/docs/examples/edit3.owl new file mode 100644 index 000000000..1520d7ecc --- /dev/null +++ b/docs/examples/edit3.owl @@ -0,0 +1,19 @@ + + + + + + + + test + + + diff --git a/docs/examples/example2.owl b/docs/examples/example2.owl new file mode 100644 index 000000000..8ddd6a312 --- /dev/null +++ b/docs/examples/example2.owl @@ -0,0 +1,1175 @@ + + + + + Comment from annotations.ttl file. + + + + + + + + + + + + + + + definition + + + + + + + + + + + + + + IAO:0000116 + uberon + editor_note + true + editor_note + editor note + + + + + + + + + IAO:0000232 + uberon + curator_notes + true + curator_notes + curator notes + + + + + + + + An alternate textual definition for a class taken unmodified from an external source. This definition may have been used to derive a generalized definition for the new class. + UBPROP:0000001 + uberon + external_definition + true + external_definition + This annotation property may be replaced with an annotation property from an external ontology such as IAO + external_definition + + + + + + + + Notes on the homology status of this class. + UBPROP:0000003 + uberon + homology_notes + true + homology_notes + This annotation property may be replaced with an annotation property from an external ontology such as IAO + homology_notes + + + + + + + + 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'. + UBPROP:0000007 + uberon + has_relational_adjective + true + has_relational_adjective + has_relational_adjective + + + + + + + + Notes on the how instances of this class vary across species. + UBPROP:0000008 + uberon + taxon_notes + true + taxon_notes + taxon_notes + + + + + + + + Notes on the evolved function of instances of this class. + This annotation property may be replaced with an annotation property from an external ontology such as IAO + UBPROP:0000009 + uberon + function_notes + true + function_notes + function_notes + + + + + + + + Notes on how similar or equivalent classes are represented in other ontologies. + This annotation property may be replaced with an annotation property from an external ontology such as IAO + UBPROP:0000012 + uberon + external_ontology_notes + true + external_ontology_notes + external_ontology_notes + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + BFO:0000050 + uberon + part_of + part_of + part_of + + + + + + + + + X outer_layer_of Y iff: +. X :continuant that bearer_of some PATO:laminar +. X part_of Y +. exists Z :surface +. X has_boundary Z +. Z boundary_of Y + +has_boundary: http://purl.obolibrary.org/obo/RO_0002002 +boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + RO:0002007 + uberon + bounding_layer_of + bounding_layer_of + 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. + bounding layer of + + + + + + + + + + + + + + Material anatomical entity that has inherent 3D shape and is generated by coordinated expression of the organism's own genome. + + + AAO:0010825 + AEO:0000003 + BILA:0000003 + CARO:0000003 + EHDAA2:0003003 + EMAPA:0 + FBbt:00007001 + FMA:67135 + GAID:781 + HAO:0000003 + MA:0003000 + MESH:A13 + TAO:0000037 + TGMA:0001823 + VHOG:0001759 + WBbt:0000100 + XAO:0003000 + ZFA:0000037 + biological structure + uberon + UBERON:0000061 + + anatomical structure + + + + + + + + + + + + + + + + Anatomical structure that performs a specific function or group of functions [WP]. + Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions. + CARO does not include a generic 'organ' class, only simple and compound organ + + + + + + EFO:0000634 + EMAPA:35949 + ENVO:01000162 + FMA:67498 + MA:0003001 + OpenCyc:Mx4rv5XMb5wpEbGdrcN5Y29ycA + OpenCyc:Mx4rwP3iWpwpEbGdrcN5Y29ycA + UMLS:C0178784 + WBbt:0003760 + uberon + anatomical unit + body organ + element + UBERON:0000062 + + organ + + + + + + + + + + + + + + + Anatomical structure which has as its direct parts two or more types of tissue and is continuous with one or more anatomical structures likewise constituted by two or more portions of tissues distinct from those of their complement. Examples: osteon, cortical bone, neck of femur, bronchopulmonary segment, left lobe of liver, anterior right side of heart, interventricular branch of left coronary artery, right atrium, mitral valve, head of pancreas[FMA]. + + + + AAO:0011124 + EFO:0000635 + FMA:82472 + cardinal organ part + uberon + regional part of organ + UBERON:0000064 + + + + organ part + + + + + + + + + Anatomical entity that has mass. + AAO:0010264 + AEO:0000006 + BILA:0000006 + CARO:0000006 + EHDAA2:0003006 + FBbt:00007016 + FMA:67165 + HAO:0000006 + TAO:0001836 + TGMA:0001826 + VHOG:0001721 + uberon + UBERON:0000465 + + material anatomical entity + + + + + + + + + + + + + + + Anatomical group that is has as its parts distinct anatomical structures interconnected by anatomical structures at a lower level of granularity[CARO]. A group of organs that work together to perform a certain task [Wikipedia]. + system + + + + + + AAO:0000007 + AEO:0000011 + BILA:0000011 + BSA:0000049 + CALOHA:TS-2088 + CARO:0000011 + EHDAA2:0003011 + EHDAA:392 + EMAPA:16103 + EV:0100000 + FBbt:00004856 + FMA:7149 + HAO:0000011 + MA:0000003 + OpenCyc:Mx4rCWM0QCtDEdyAAADggVbxzQ + TAO:0001439 + TGMA:0001831 + UMLS:C0460002 + VHOG:0001725 + WBbt:0005746 + WBbt:0005763 + XAO:0003002 + ZFA:0001439 + galen:AnatomicalSystem + body system + organ system + uberon + UBERON:0000467 + + + anatomical system + + + + + + + + + + Anatomical structure that is an individual member of a species and consists of more than one cell. + TODO - split body and mc organism? body continues after death stage + organismal + + + + + AAO:0010026 + AEO:0000191 + BILA:0000012 + BSA:0000038 + BTO:0000042 + CARO:0000012 + EFO:0002906 + EHDAA2:0003103 + EHDAA2:0003191 + EHDAA:1 + EHDAA:9178 + EMAPA:25765 + EV:0100016 + FBbt:00000001 + FMA:256135 + HAO:0000012 + TADS:0000001 + TAO:0001094 + TGMA:0001832 + VHOG:0000671 + WBbt:0007833 + XAO:0003004 + ZFA:0001094 + galen:Organism + multi-cellular organism + organism + whole organism + animal + uberon + Koerper + body + whole body + UBERON:0000468 + + + + multicellular organism + + + + + + + + + Anatomical structure which is a subdivision of a whole organism, consisting of components of multiple anatomical systems, largely surrounded by a contiguous region of integument. + Reflects CARO2. todo - check the inclusion of FMA 'cardinal body part here', and check child terms for consistency + + + + + AAO:0010053 + AEO:0000032 + BILA:0000032 + CALOHA:TS-2084 + CARO:0000032 + EFO:0000808 + EHDAA2:0003032 + FBbt:00007009 + FMA:7153 + HAO:0000032 + MA:0002433 + MAT:0000293 + MESH:A01 + MIAA:0000293 + OpenCyc:Mx4rvViAHJwpEbGdrcN5Y29ycA + TAO:0001308 + TGMA:0001840 + UMLS:C0229962 + VHOG:0001758 + XAO:0003013 + ZFA:0001308 + galen:BodyPart + anatomic region + uberon + body part + body region + cardinal body part + UBERON:0000475 + + + + organism subdivision + + + + + + + + + Anatomical structure consisting of at least two non-overlapping organs, multi-tissue aggregates or portion of tissues or cells of different types that does not constitute an organism, organ, multi-tissue aggregate, or portion of tissue. + AAO:0010008 + AEO:0000054 + BILA:0000054 + CARO:0000054 + EHDAA2:0003054 + HAO:0000054 + TAO:0001512 + TGMA:0001846 + VHOG:0001724 + XAO:0003001 + ZFA:0001512 + uberon + UBERON:0000480 + + anatomical group + + + + + + + + + + + + + + + The subdivision of the vertebrate body between the thorax and pelvis. The ventral part of the abdomen contains the abdominal cavity and visceral organs. The dorsal part includes the abdominal section of the vertebral column. + Vertebrate specific. In arthropods 'abdomen' is the most distal section of the body which lies behind the thorax or cephalothorax. If need be we can introduce some grouping class + abdominal + + + BTO:0000020 + CALOHA:TS-0001 + EFO:0000968 + EMAPA:35102 + EV:0100011 + FMA:9577 + GAID:16 + MA:0000029 + MAT:0000298 + MESH:A01.047 + MIAA:0000298 + OpenCyc:Mx4rvVjgyZwpEbGdrcN5Y29ycA + galen:Abdomen + abdominopelvic region + abdominopelvis + uberon + adult abdomen + belly + celiac region + UBERON:0000916 + + + abdomen + + + + + + + + + Anatomical system that consists of the glands and parts of glands that produce endocrine secretions and help to integrate and control bodily metabolic activity. + Anatomical system containing glands which regulates bodily functions though the secretion of hormones.[AAO] + Multicellular organisms have complex endocrine systems, allowing responses to environmental stimuli, regulation of development, reproduction, and homeostasis. Nuclear receptors (NRs), a metazoan-specific family of ligand-activated transcription factors, play central roles in endocrine responses, as intermediates between signaling molecules and target genes. The NR family includes ligand-bound and orphan receptors, that is, receptors with no known ligand or for which there is no ligand Pocket. Understanding NR evolution has been further improved by comparison of several completed genomes, particularly those of deuterostomes and ecdysozoans. In contrast, evolution of NR ligands is still much debated. One hypothesis proposes that several independent gains and losses of ligand-binding ability in NRs occurred in protostomes and deuterostomes. A second hypothesis, pertaining to the NR3 subfamily (vertebrate steroid hormone receptors and estrogen related receptor), proposes that before the divergence of protostomes and deuterostomes, there was an ancestral steroid receptor (AncSR) that was ligand-activated and that orphan receptors secondarily lost the ability to bind a ligand. (...) Our analysis reveals that steroidogenesis has been independently elaborated in the 3 main bilaterian lineages (...).[well established][VHOG] + endocrine + + + + + AAO:0010279 + CALOHA:TS-1301 + EFO:0002969 + EHDAA2:0002224 + EMAPA:35306 + EV:0100128 + FBbt:00005068 + FMA:9668 + GAID:439 + MA:0000012 + MESH:A06 + TAO:0001158 + UMLS:C0014136 + VHOG:0000098 + XAO:0000158 + ZFA:0001158 + endocrine glandular system + endocrine system + systema endocrinum + uberon + UBERON:0000949 + + + + endocrine system + + + + + + + + + Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species. + + + + AAO:0010841 + AEO:0000000 + BILA:0000000 + CARO:0000000 + EHDAA2:0002229 + FBbt:10000000 + FBbt_root:00000000 + FMA:62955 + HAO:0000000 + MA:0000001 + TAO:0100000 + TGMA:0001822 + UMLS:C1515976 + XAO:0000000 + ZFA:0100000 + uberon + UBERON:0001062 + + anatomical entity + + + + + + + + + + + + + + + + + + + + Situated along the perimeter of the adrenal gland, the adrenal cortex mediates the stress response through the production of mineralocorticoids and glucocorticoids, including aldosterone and cortisol respectively. It is also a secondary site of androgen synthesis. [WP,unvetted]. + All craniates have groups of cells homologous to the mammalian adrenocortical and chromaffin tissues (medulla), but they are scattered in and near the kidneys in fishes. (...) The cortical and chromaffin tissues come together to form adrenal glands in tetrapods.[well established][VHOG] + Kardong states that mammals are the first to have distinct cortext and medulla, but this contradicts XAO + + + + + AAO:0011009 + BTO:0000045 + CALOHA:TS-0015 + EFO:0000237 + EMAPA:18427 + EV:0100136 + FMA:15632 + GAID:447 + MA:0000118 + MAT:0000494 + MESH:A06.407.071.140 + UMLS:C0001613 + VHOG:0001481 + XAO:0000165 + adrenal gland cortex + cortex (glandula suprarenalis) + cortex of adrenal gland + cortex of suprarenal gland + suprarenal cortex + uberon + cortex glandulae suprarenalis + suprarenal + UBERON:0001235 + + + adrenal cortex + + + + + + + + + + + + + + + + + Outermost layer of an organ[WP]. + cortical + this class is used more generically than in FMA, and includes e.g. cortex of hair + + EFO:0000383 + EHDAA:9344 + FMA:61109 + galen:Cortex + cortex + cortex of organ + uberon + UBERON:0001851 + + + cortex + + + + + + + + + + + + + + + Organism subdivision which is the part of the body posterior to the cervical region (or head, when cervical region not present) and anterior to the caudal region. Includes the sacrum when present. + Organism subdivision that is the part of the body posterior to the head and anterior to the tail.[AAO] + Organism subdivision which is the part of the body posterior to the head and anterior to the tail.[TAO] + + + + + AAO:0010339 + BILA:0000116 + BTO:0001493 + CALOHA:TS-1071 + EFO:0000966 + EMAPA:31857 + FMA:7181 + MA:0000004 + MAT:0000296 + MIAA:0000296 + OpenCyc:Mx4rvVkJjpwpEbGdrcN5Y29ycA + TAO:0001115 + UMLS:C0460005 + XAO:0000054 + XAO:0003025 + ZFA:0001115 + galen:Trunk + thoracolumbar region + torso + trunk region + uberon + Rumpf + UBERON:0002100 + + + + trunk + + + + + + + + + + + + + + + + + + + + + + + + + + Endocrine glands are glands of the endocrine system that secrete their products directly into the circulatory system rather than through a duct.[WP, modified]. + + + + + AEO:0000098 + BTO:0001488 + CALOHA:TS-1300 + EHDAA2:0003098 + EMAPA:35999 + FMA:9602 + GAID:335 + MA:0002563 + MESH:A06.407 + OpenCyc:Mx4rvbkiRZwpEbGdrcN5Y29ycA + UMLS:C0014133 + ductless gland + glandula endocrina + uberon + ductless gland + glandulae endocrinae + UBERON:0002368 + + + endocrine gland + + + + + + + + + + + + + + + + + + + + + + Either of a pair of complex endocrine organs near the anterior medial border of the kidney consisting of a mesodermal cortex that produces glucocorticoid, mineralocorticoid, and androgenic hormones and an ectodermal medulla that produces epinephrine and norepinephrine[BTO]. + Anatomical structure which is found on the surface of the kidney and secretes various hormones including epinephrine, norephinephrine, aldosterone, corticosterone, and cortisol.[AAO] + All craniates have groups of cells homologous to the mammalian adrenocortical and chromaffin tissues, but they are scattered in and near the kidneys in fishes. (...) The cortical and chromaffin tissues come together to form adrenal glands in tetrapods.[well established][VHOG] + The origin of the adrenal gland is still controversial. It is thought to share the same origin as the kidney and gonads, derived from coelomic epithelium of the urogenital ridge and/or the underlying mesenchyme (Keegan and Hammer, 2002; Morohashi, 1997). We follow Kardong and state homology at the level of the cortex and medulla rather than gland as a whole + suprarenal cortex manufactures corticosteroids; suprarenal medulla manufactures epinephrine and norepinephrine; suprarenal medulla receives preganglionic sympathetic innervation from the greater thoracic splanchnic n. + + + + + AAO:0010551 + BTO:0000047 + CALOHA:TS-0016 + EFO:0000238 + EMAPA:18426 + EV:0100135 + FMA:9604 + GAID:446 + MA:0000116 + MAT:0000071 + MESH:A06.407.071 + MIAA:0000071 + OpenCyc:Mx4rvXYiz5wpEbGdrcN5Y29ycA + UMLS:C0001625 + VHOG:0001141 + XAO:0000164 + galen:AdrenalGland + glandula adrenalis + glandula suprarenalis + uberon + adrenal + adrenal capsule + adrenal medulla cell + atrabiliary capsule + epinephric gland + epinephros + glandula suprarenalis + interrenal gland + suprarenal capsule + suprarenal gland + UBERON:0002369 + + + adrenal gland + + + + + + + + + + + + The abdominal segment of the torso. + + + EMAPA:35104 + FMA:259211 + MA:0000021 + uberon + abdomen/pelvis/perineum + lower body + lumbar region + UBERON:0002417 + abdominal segment of trunk + + + + + + + + + A gland is an organ in an animal's body that synthesizes a substance for release such as hormones or breast milk, often into the bloodstream (endocrine gland) or into cavities inside the body or its outer surface (exocrine gland). A gland is an organ specialised for secretion[GO]. + glandular + UBERON:MIAA_0000021 + + + + + AAO:0000212 + AEO:0000096 + BTO:0000522 + EFO:0000797 + EHDAA2:0003096 + EHDAA:2161 + EHDAA:4475 + EHDAA:6522 + EMAPA:18425 + FBbt:00100317 + FMA:86294 + HAO:0000375 + MA:0003038 + MAT:0000021 + MIAA:0000021 + OpenCyc:Mx4rwP3vyJwpEbGdrcN5Y29ycA + UMLS:C1285092 + WikipediaCategory:Glands + galen:Gland + uberon + Druese + glandula + UBERON:0002530 + + + gland + + + + + + + + + + + + + + + + This gland can either be a discrete structure located bilaterally above each kidney, or a cluster of cells in the head kidney that perform the functions of the adrenal gland. In either case, this organ consists of two cells types, aminergic chromaffin cells and steroidogenic cortical cells[GO] + keep this grouping class so long as it is required for GO + All craniates have groups of cells homologous to the mammalian adrenocortical and chromaffin tissues, but they are scattered in and near the kidneys in fishes. (...) The cortical and chromaffin tissues come together to form adrenal glands in tetrapods.[well established][VHOG] + VHOG:0001141 + adrenal gland - interrenal gland + adrenal gland/interrenal tissue + uberon + adrenal - interrenal gland + suprarenal gland - interrenal gland + UBERON:0006858 + + + adrenal/interrenal gland + + + + + + + + + + + + + + + + FMA:25054 + region of trunk + trunk subdivision + uberon + UBERON:0009569 + + subdivision of trunk + + + + + + + + + An anatomical structure that has more than one cell as a part. + CARO:0010000 + FBbt:00100313 + multicellular structure + uberon + UBERON:0010000 + + multicellular anatomical structure + + + + + + + + + + + + + + + A major subdivision of an organism that divides an organism along its main body axis (typically anterio-posterior axis). In vertebrates, this is based on the vertebral column. + Ideally this would be disjoint with analagous class for appendicular axes, but currently 'appendages' like antennae, horns cause a problem + axial subdivision of organism + uberon + body segment + main body segment + UBERON:0011676 + + subdivision of organism along main body axis + + + + + + + + + A principle subdivision of an organism that includes all structures along the primary axis, typically the anterior-posterior axis, from head to tail, including structures of the body proper where present (for example, ribs), but excluding appendages. + uberon + UBERON:0013701 + main body axis + + + + + + + + + + + + + + + The region of the organism associated with the visceral organs. + Cardinal body part, which consists of a maximal set of diverse subclasses of organ and organ part spatially associated with the vertebral column and ribcage. Examples: There is only one body proper[FMA:231424]. + AEO:0000103 + BTO:0001489 + FMA:231424 + uberon + body + whole body + UBERON:0013702 + + body proper + + + + + dummy individal 1 + + + + + + + + + + + dummy individal 2 + + + + dummy individal 3 + + + + + + + + + + dummy individal 4 + + + + + + + + diff --git a/docs/examples/example2_defined_by.owl b/docs/examples/example2_defined_by.owl new file mode 100644 index 000000000..52e58e7a5 --- /dev/null +++ b/docs/examples/example2_defined_by.owl @@ -0,0 +1,1333 @@ + + + + + Comment from annotations.ttl file. + + + + + + + + + + + + + + definition + + + + + + + + + + + + + + IAO:0000116 + uberon + editor_note + true + editor_note + + editor note + + + + + + + + IAO:0000232 + uberon + curator_notes + true + curator_notes + + curator notes + + + + + + + + An alternate textual definition for a class taken unmodified from an external source. This definition may have been used to derive a generalized definition for the new class. + UBPROP:0000001 + uberon + external_definition + true + external_definition + This annotation property may be replaced with an annotation property from an external ontology such as IAO + + external_definition + + + + + + + + Notes on the homology status of this class. + UBPROP:0000003 + uberon + homology_notes + true + homology_notes + This annotation property may be replaced with an annotation property from an external ontology such as IAO + + homology_notes + + + + + + + + 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'. + UBPROP:0000007 + uberon + has_relational_adjective + true + has_relational_adjective + + has_relational_adjective + + + + + + + + Notes on the how instances of this class vary across species. + UBPROP:0000008 + uberon + taxon_notes + true + taxon_notes + + taxon_notes + + + + + + + + Notes on the evolved function of instances of this class. + This annotation property may be replaced with an annotation property from an external ontology such as IAO + UBPROP:0000009 + uberon + function_notes + true + function_notes + + function_notes + + + + + + + + Notes on how similar or equivalent classes are represented in other ontologies. + This annotation property may be replaced with an annotation property from an external ontology such as IAO + UBPROP:0000012 + uberon + external_ontology_notes + true + external_ontology_notes + + external_ontology_notes + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + BFO:0000050 + uberon + part_of + part_of + + part_of + + + + + + + + + X outer_layer_of Y iff: +. X :continuant that bearer_of some PATO:laminar +. X part_of Y +. exists Z :surface +. X has_boundary Z +. Z boundary_of Y + +has_boundary: http://purl.obolibrary.org/obo/RO_0002002 +boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + RO:0002007 + uberon + bounding_layer_of + bounding_layer_of + 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. + + bounding layer of + + + + + + + + + + + + + + Material anatomical entity that has inherent 3D shape and is generated by coordinated expression of the organism's own genome. + + + AAO:0010825 + AEO:0000003 + BILA:0000003 + CARO:0000003 + EHDAA2:0003003 + EMAPA:0 + FBbt:00007001 + FMA:67135 + GAID:781 + HAO:0000003 + MA:0003000 + MESH:A13 + TAO:0000037 + TGMA:0001823 + VHOG:0001759 + WBbt:0000100 + XAO:0003000 + ZFA:0000037 + biological structure + uberon + UBERON:0000061 + + + anatomical structure + + + + + + + + + + + + + + + Anatomical structure that performs a specific function or group of functions [WP]. + Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions. + CARO does not include a generic 'organ' class, only simple and compound organ + + + + + + EFO:0000634 + EMAPA:35949 + ENVO:01000162 + FMA:67498 + MA:0003001 + OpenCyc:Mx4rv5XMb5wpEbGdrcN5Y29ycA + OpenCyc:Mx4rwP3iWpwpEbGdrcN5Y29ycA + UMLS:C0178784 + WBbt:0003760 + uberon + anatomical unit + body organ + element + UBERON:0000062 + + + organ + + + + + + + + + + + + + + + Anatomical structure which has as its direct parts two or more types of tissue and is continuous with one or more anatomical structures likewise constituted by two or more portions of tissues distinct from those of their complement. Examples: osteon, cortical bone, neck of femur, bronchopulmonary segment, left lobe of liver, anterior right side of heart, interventricular branch of left coronary artery, right atrium, mitral valve, head of pancreas[FMA]. + + + + AAO:0011124 + EFO:0000635 + FMA:82472 + cardinal organ part + uberon + regional part of organ + UBERON:0000064 + + + + + organ part + + + + + + + + + Anatomical entity that has mass. + AAO:0010264 + AEO:0000006 + BILA:0000006 + CARO:0000006 + EHDAA2:0003006 + FBbt:00007016 + FMA:67165 + HAO:0000006 + TAO:0001836 + TGMA:0001826 + VHOG:0001721 + uberon + UBERON:0000465 + + + material anatomical entity + + + + + + + + + + + + + + + Anatomical group that is has as its parts distinct anatomical structures interconnected by anatomical structures at a lower level of granularity[CARO]. A group of organs that work together to perform a certain task [Wikipedia]. + system + + + + + + AAO:0000007 + AEO:0000011 + BILA:0000011 + BSA:0000049 + CALOHA:TS-2088 + CARO:0000011 + EHDAA2:0003011 + EHDAA:392 + EMAPA:16103 + EV:0100000 + FBbt:00004856 + FMA:7149 + HAO:0000011 + MA:0000003 + OpenCyc:Mx4rCWM0QCtDEdyAAADggVbxzQ + TAO:0001439 + TGMA:0001831 + UMLS:C0460002 + VHOG:0001725 + WBbt:0005746 + WBbt:0005763 + XAO:0003002 + ZFA:0001439 + galen:AnatomicalSystem + body system + organ system + uberon + UBERON:0000467 + + + + anatomical system + + + + + + + + + + Anatomical structure that is an individual member of a species and consists of more than one cell. + TODO - split body and mc organism? body continues after death stage + organismal + + + + + AAO:0010026 + AEO:0000191 + BILA:0000012 + BSA:0000038 + BTO:0000042 + CARO:0000012 + EFO:0002906 + EHDAA2:0003103 + EHDAA2:0003191 + EHDAA:1 + EHDAA:9178 + EMAPA:25765 + EV:0100016 + FBbt:00000001 + FMA:256135 + HAO:0000012 + TADS:0000001 + TAO:0001094 + TGMA:0001832 + VHOG:0000671 + WBbt:0007833 + XAO:0003004 + ZFA:0001094 + galen:Organism + multi-cellular organism + organism + whole organism + animal + uberon + Koerper + body + whole body + UBERON:0000468 + + + + + multicellular organism + + + + + + + + + Anatomical structure which is a subdivision of a whole organism, consisting of components of multiple anatomical systems, largely surrounded by a contiguous region of integument. + Reflects CARO2. todo - check the inclusion of FMA 'cardinal body part here', and check child terms for consistency + + + + + AAO:0010053 + AEO:0000032 + BILA:0000032 + CALOHA:TS-2084 + CARO:0000032 + EFO:0000808 + EHDAA2:0003032 + FBbt:00007009 + FMA:7153 + HAO:0000032 + MA:0002433 + MAT:0000293 + MESH:A01 + MIAA:0000293 + OpenCyc:Mx4rvViAHJwpEbGdrcN5Y29ycA + TAO:0001308 + TGMA:0001840 + UMLS:C0229962 + VHOG:0001758 + XAO:0003013 + ZFA:0001308 + galen:BodyPart + anatomic region + uberon + body part + body region + cardinal body part + UBERON:0000475 + + + + + organism subdivision + + + + + + + + + Anatomical structure consisting of at least two non-overlapping organs, multi-tissue aggregates or portion of tissues or cells of different types that does not constitute an organism, organ, multi-tissue aggregate, or portion of tissue. + AAO:0010008 + AEO:0000054 + BILA:0000054 + CARO:0000054 + EHDAA2:0003054 + HAO:0000054 + TAO:0001512 + TGMA:0001846 + VHOG:0001724 + XAO:0003001 + ZFA:0001512 + uberon + UBERON:0000480 + + + anatomical group + + + + + + + + + + + + + + + The subdivision of the vertebrate body between the thorax and pelvis. The ventral part of the abdomen contains the abdominal cavity and visceral organs. The dorsal part includes the abdominal section of the vertebral column. + Vertebrate specific. In arthropods 'abdomen' is the most distal section of the body which lies behind the thorax or cephalothorax. If need be we can introduce some grouping class + abdominal + + + BTO:0000020 + CALOHA:TS-0001 + EFO:0000968 + EMAPA:35102 + EV:0100011 + FMA:9577 + GAID:16 + MA:0000029 + MAT:0000298 + MESH:A01.047 + MIAA:0000298 + OpenCyc:Mx4rvVjgyZwpEbGdrcN5Y29ycA + galen:Abdomen + abdominopelvic region + abdominopelvis + uberon + adult abdomen + belly + celiac region + UBERON:0000916 + + + + abdomen + + + + + + + + + Anatomical system that consists of the glands and parts of glands that produce endocrine secretions and help to integrate and control bodily metabolic activity. + Anatomical system containing glands which regulates bodily functions though the secretion of hormones.[AAO] + Multicellular organisms have complex endocrine systems, allowing responses to environmental stimuli, regulation of development, reproduction, and homeostasis. Nuclear receptors (NRs), a metazoan-specific family of ligand-activated transcription factors, play central roles in endocrine responses, as intermediates between signaling molecules and target genes. The NR family includes ligand-bound and orphan receptors, that is, receptors with no known ligand or for which there is no ligand Pocket. Understanding NR evolution has been further improved by comparison of several completed genomes, particularly those of deuterostomes and ecdysozoans. In contrast, evolution of NR ligands is still much debated. One hypothesis proposes that several independent gains and losses of ligand-binding ability in NRs occurred in protostomes and deuterostomes. A second hypothesis, pertaining to the NR3 subfamily (vertebrate steroid hormone receptors and estrogen related receptor), proposes that before the divergence of protostomes and deuterostomes, there was an ancestral steroid receptor (AncSR) that was ligand-activated and that orphan receptors secondarily lost the ability to bind a ligand. (...) Our analysis reveals that steroidogenesis has been independently elaborated in the 3 main bilaterian lineages (...).[well established][VHOG] + endocrine + + + + + AAO:0010279 + CALOHA:TS-1301 + EFO:0002969 + EHDAA2:0002224 + EMAPA:35306 + EV:0100128 + FBbt:00005068 + FMA:9668 + GAID:439 + MA:0000012 + MESH:A06 + TAO:0001158 + UMLS:C0014136 + VHOG:0000098 + XAO:0000158 + ZFA:0001158 + endocrine glandular system + endocrine system + systema endocrinum + uberon + UBERON:0000949 + + + + + endocrine system + + + + + + + + + Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species. + + + + AAO:0010841 + AEO:0000000 + BILA:0000000 + CARO:0000000 + EHDAA2:0002229 + FBbt:10000000 + FBbt_root:00000000 + FMA:62955 + HAO:0000000 + MA:0000001 + TAO:0100000 + TGMA:0001822 + UMLS:C1515976 + XAO:0000000 + ZFA:0100000 + uberon + UBERON:0001062 + + + anatomical entity + + + + + + + + + + + + + + + + + + + + Situated along the perimeter of the adrenal gland, the adrenal cortex mediates the stress response through the production of mineralocorticoids and glucocorticoids, including aldosterone and cortisol respectively. It is also a secondary site of androgen synthesis. [WP,unvetted]. + All craniates have groups of cells homologous to the mammalian adrenocortical and chromaffin tissues (medulla), but they are scattered in and near the kidneys in fishes. (...) The cortical and chromaffin tissues come together to form adrenal glands in tetrapods.[well established][VHOG] + Kardong states that mammals are the first to have distinct cortext and medulla, but this contradicts XAO + + + + + AAO:0011009 + BTO:0000045 + CALOHA:TS-0015 + EFO:0000237 + EMAPA:18427 + EV:0100136 + FMA:15632 + GAID:447 + MA:0000118 + MAT:0000494 + MESH:A06.407.071.140 + UMLS:C0001613 + VHOG:0001481 + XAO:0000165 + adrenal gland cortex + cortex (glandula suprarenalis) + cortex of adrenal gland + cortex of suprarenal gland + suprarenal cortex + uberon + cortex glandulae suprarenalis + suprarenal + UBERON:0001235 + + + + adrenal cortex + + + + + + + + + + + + + + + + + Outermost layer of an organ[WP]. + cortical + this class is used more generically than in FMA, and includes e.g. cortex of hair + + EFO:0000383 + EHDAA:9344 + FMA:61109 + galen:Cortex + cortex + cortex of organ + uberon + UBERON:0001851 + + + + cortex + + + + + + + + + + + + + + + Organism subdivision which is the part of the body posterior to the cervical region (or head, when cervical region not present) and anterior to the caudal region. Includes the sacrum when present. + Organism subdivision that is the part of the body posterior to the head and anterior to the tail.[AAO] + Organism subdivision which is the part of the body posterior to the head and anterior to the tail.[TAO] + + + + + AAO:0010339 + BILA:0000116 + BTO:0001493 + CALOHA:TS-1071 + EFO:0000966 + EMAPA:31857 + FMA:7181 + MA:0000004 + MAT:0000296 + MIAA:0000296 + OpenCyc:Mx4rvVkJjpwpEbGdrcN5Y29ycA + TAO:0001115 + UMLS:C0460005 + XAO:0000054 + XAO:0003025 + ZFA:0001115 + galen:Trunk + thoracolumbar region + torso + trunk region + uberon + Rumpf + UBERON:0002100 + + + + + trunk + + + + + + + + + + + + + + + + + + + + + + + + + + Endocrine glands are glands of the endocrine system that secrete their products directly into the circulatory system rather than through a duct.[WP, modified]. + + + + + AEO:0000098 + BTO:0001488 + CALOHA:TS-1300 + EHDAA2:0003098 + EMAPA:35999 + FMA:9602 + GAID:335 + MA:0002563 + MESH:A06.407 + OpenCyc:Mx4rvbkiRZwpEbGdrcN5Y29ycA + UMLS:C0014133 + ductless gland + glandula endocrina + uberon + ductless gland + glandulae endocrinae + UBERON:0002368 + + + + endocrine gland + + + + + + + + + + + + + + + + + + + + + + Either of a pair of complex endocrine organs near the anterior medial border of the kidney consisting of a mesodermal cortex that produces glucocorticoid, mineralocorticoid, and androgenic hormones and an ectodermal medulla that produces epinephrine and norepinephrine[BTO]. + Anatomical structure which is found on the surface of the kidney and secretes various hormones including epinephrine, norephinephrine, aldosterone, corticosterone, and cortisol.[AAO] + All craniates have groups of cells homologous to the mammalian adrenocortical and chromaffin tissues, but they are scattered in and near the kidneys in fishes. (...) The cortical and chromaffin tissues come together to form adrenal glands in tetrapods.[well established][VHOG] + The origin of the adrenal gland is still controversial. It is thought to share the same origin as the kidney and gonads, derived from coelomic epithelium of the urogenital ridge and/or the underlying mesenchyme (Keegan and Hammer, 2002; Morohashi, 1997). We follow Kardong and state homology at the level of the cortex and medulla rather than gland as a whole + suprarenal cortex manufactures corticosteroids; suprarenal medulla manufactures epinephrine and norepinephrine; suprarenal medulla receives preganglionic sympathetic innervation from the greater thoracic splanchnic n. + + + + + AAO:0010551 + BTO:0000047 + CALOHA:TS-0016 + EFO:0000238 + EMAPA:18426 + EV:0100135 + FMA:9604 + GAID:446 + MA:0000116 + MAT:0000071 + MESH:A06.407.071 + MIAA:0000071 + OpenCyc:Mx4rvXYiz5wpEbGdrcN5Y29ycA + UMLS:C0001625 + VHOG:0001141 + XAO:0000164 + galen:AdrenalGland + glandula adrenalis + glandula suprarenalis + uberon + adrenal + adrenal capsule + adrenal medulla cell + atrabiliary capsule + epinephric gland + epinephros + glandula suprarenalis + interrenal gland + suprarenal capsule + suprarenal gland + UBERON:0002369 + + + + adrenal gland + + + + + + + + + + + + The abdominal segment of the torso. + + + EMAPA:35104 + FMA:259211 + MA:0000021 + uberon + abdomen/pelvis/perineum + lower body + lumbar region + UBERON:0002417 + + abdominal segment of trunk + + + + + + + + + A gland is an organ in an animal's body that synthesizes a substance for release such as hormones or breast milk, often into the bloodstream (endocrine gland) or into cavities inside the body or its outer surface (exocrine gland). A gland is an organ specialised for secretion[GO]. + glandular + UBERON:MIAA_0000021 + + + + + AAO:0000212 + AEO:0000096 + BTO:0000522 + EFO:0000797 + EHDAA2:0003096 + EHDAA:2161 + EHDAA:4475 + EHDAA:6522 + EMAPA:18425 + FBbt:00100317 + FMA:86294 + HAO:0000375 + MA:0003038 + MAT:0000021 + MIAA:0000021 + OpenCyc:Mx4rwP3vyJwpEbGdrcN5Y29ycA + UMLS:C1285092 + WikipediaCategory:Glands + galen:Gland + uberon + Druese + glandula + UBERON:0002530 + + + + gland + + + + + + + + + + + + + + + + This gland can either be a discrete structure located bilaterally above each kidney, or a cluster of cells in the head kidney that perform the functions of the adrenal gland. In either case, this organ consists of two cells types, aminergic chromaffin cells and steroidogenic cortical cells[GO] + keep this grouping class so long as it is required for GO + All craniates have groups of cells homologous to the mammalian adrenocortical and chromaffin tissues, but they are scattered in and near the kidneys in fishes. (...) The cortical and chromaffin tissues come together to form adrenal glands in tetrapods.[well established][VHOG] + VHOG:0001141 + adrenal gland - interrenal gland + adrenal gland/interrenal tissue + uberon + adrenal - interrenal gland + suprarenal gland - interrenal gland + UBERON:0006858 + + + + adrenal/interrenal gland + + + + + + + + + + + + + + + + FMA:25054 + region of trunk + trunk subdivision + uberon + UBERON:0009569 + + + subdivision of trunk + + + + + + + + + An anatomical structure that has more than one cell as a part. + CARO:0010000 + FBbt:00100313 + multicellular structure + uberon + UBERON:0010000 + + + multicellular anatomical structure + + + + + + + + + + + + + + + A major subdivision of an organism that divides an organism along its main body axis (typically anterio-posterior axis). In vertebrates, this is based on the vertebral column. + Ideally this would be disjoint with analagous class for appendicular axes, but currently 'appendages' like antennae, horns cause a problem + axial subdivision of organism + uberon + body segment + main body segment + UBERON:0011676 + + + subdivision of organism along main body axis + + + + + + + + + A principle subdivision of an organism that includes all structures along the primary axis, typically the anterior-posterior axis, from head to tail, including structures of the body proper where present (for example, ribs), but excluding appendages. + uberon + UBERON:0013701 + + main body axis + + + + + + + + + + + + + + + The region of the organism associated with the visceral organs. + Cardinal body part, which consists of a maximal set of diverse subclasses of organ and organ part spatially associated with the vertebral column and ribcage. Examples: There is only one body proper[FMA:231424]. + AEO:0000103 + BTO:0001489 + FMA:231424 + uberon + body + whole body + UBERON:0013702 + + + body proper + + + + + + + + + + + + + + + + + + + + + + dummy individal 1 + + + + + + + + + + + + + + + dummy individal 2 + + + + + + + + + dummy individal 3 + + + + + + + + + + + + + + + dummy individal 4 + + + + + + + diff --git a/docs/examples/example2_derived_by.owl b/docs/examples/example2_derived_by.owl new file mode 100644 index 000000000..de79486d7 --- /dev/null +++ b/docs/examples/example2_derived_by.owl @@ -0,0 +1,5654 @@ + + + + + Comment from annotations.ttl file. + + + + + + + + + + + + + definition + + + + + + + + + + + definition + + + + + + + + + IAO:0000116 + uberon + editor_note + true + editor_note + + editor note + + + + + editor note + + + + + + + + + + + + IAO:0000116 + + + + + + uberon + + + + + + editor_note + + + + + + true + + + + + + editor_note + + + + + + + + + + + + + + + IAO:0000232 + uberon + curator_notes + true + curator_notes + curator notes + + + + + + + + + + + IAO:0000232 + + + + + + uberon + + + + + + curator_notes + + + + + + true + + + + + + curator_notes + + + + + + curator notes + + + + + + + + + An alternate textual definition for a class taken unmodified from an external source. This definition may have been used to derive a generalized definition for the new class. + UBPROP:0000001 + uberon + external_definition + true + external_definition + This annotation property may be replaced with an annotation property from an external ontology such as IAO + external_definition + + + + + + + + + + + An alternate textual definition for a class taken unmodified from an external source. This definition may have been used to derive a generalized definition for the new class. + + + + + + UBPROP:0000001 + + + + + + uberon + + + + + + external_definition + + + + + + true + + + + + + external_definition + + + + + + This annotation property may be replaced with an annotation property from an external ontology such as IAO + + + + + + external_definition + + + + + + + + + Notes on the homology status of this class. + UBPROP:0000003 + uberon + homology_notes + true + homology_notes + This annotation property may be replaced with an annotation property from an external ontology such as IAO + homology_notes + + + + + + + + + + + Notes on the homology status of this class. + + + + + + UBPROP:0000003 + + + + + + uberon + + + + + + homology_notes + + + + + + true + + + + + + homology_notes + + + + + + This annotation property may be replaced with an annotation property from an external ontology such as IAO + + + + + + homology_notes + + + + + + + + + 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'. + UBPROP:0000007 + uberon + has_relational_adjective + true + 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'. + + + + + + UBPROP:0000007 + + + + + + uberon + + + + + + has_relational_adjective + + + + + + true + + + + + + has_relational_adjective + + + + + + has_relational_adjective + + + + + + + + + Notes on the how instances of this class vary across species. + UBPROP:0000008 + uberon + taxon_notes + true + taxon_notes + taxon_notes + + + + + + + + + + + Notes on the how instances of this class vary across species. + + + + + + UBPROP:0000008 + + + + + + uberon + + + + + + taxon_notes + + + + + + true + + + + + + taxon_notes + + + + + + taxon_notes + + + + + + + + + Notes on the evolved function of instances of this class. + This annotation property may be replaced with an annotation property from an external ontology such as IAO + UBPROP:0000009 + uberon + function_notes + true + function_notes + function_notes + + + + + + + + + + + Notes on the evolved function of instances of this class. + + + + + + This annotation property may be replaced with an annotation property from an external ontology such as IAO + + + + + + UBPROP:0000009 + + + + + + uberon + + + + + + function_notes + + + + + + true + + + + + + function_notes + + + + + + function_notes + + + + + + + + + Notes on how similar or equivalent classes are represented in other ontologies. + This annotation property may be replaced with an annotation property from an external ontology such as IAO + UBPROP:0000012 + uberon + external_ontology_notes + true + external_ontology_notes + external_ontology_notes + + + + + + + + + + + Notes on how similar or equivalent classes are represented in other ontologies. + + + + + + This annotation property may be replaced with an annotation property from an external ontology such as IAO + + + + + + UBPROP:0000012 + + + + + + uberon + + + + + + external_ontology_notes + + + + + + true + + + + + + external_ontology_notes + + + + + + external_ontology_notes + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + BFO:0000050 + uberon + part_of + part_of + part_of + + + + + + + + + + + + + + + + + BFO:0000050 + + + + + + uberon + + + + + + part_of + + + + + + part_of + + + + + + part_of + + + + + + + + + + X outer_layer_of Y iff: +. X :continuant that bearer_of some PATO:laminar +. X part_of Y +. exists Z :surface +. X has_boundary Z +. Z boundary_of Y + +has_boundary: http://purl.obolibrary.org/obo/RO_0002002 +boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + RO:0002007 + uberon + bounding_layer_of + bounding_layer_of + 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. + bounding layer of + + + + + + + + + + + + + + + + + X outer_layer_of Y iff: +. X :continuant that bearer_of some PATO:laminar +. X part_of Y +. exists Z :surface +. X has_boundary Z +. Z boundary_of Y + +has_boundary: http://purl.obolibrary.org/obo/RO_0002002 +boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + + + + + + RO:0002007 + + + + + + uberon + + + + + + bounding_layer_of + + + + + + bounding_layer_of + + + + + + 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. + + + + + + bounding layer of + + + + + + + + + + + + + + + Material anatomical entity that has inherent 3D shape and is generated by coordinated expression of the organism's own genome. + + + AAO:0010825 + AEO:0000003 + BILA:0000003 + CARO:0000003 + EHDAA2:0003003 + EMAPA:0 + FBbt:00007001 + FMA:67135 + GAID:781 + HAO:0000003 + MA:0003000 + MESH:A13 + TAO:0000037 + TGMA:0001823 + VHOG:0001759 + WBbt:0000100 + XAO:0003000 + ZFA:0000037 + biological structure + uberon + UBERON:0000061 + + + anatomical structure + + + + + + + + + + + Material anatomical entity that has inherent 3D shape and is generated by coordinated expression of the organism's own genome. + + + + + + + + + + + + + + + + + + AAO:0010825 + + + + + + AEO:0000003 + + + + + + BILA:0000003 + + + + + + CARO:0000003 + + + + + + EHDAA2:0003003 + + + + + + EMAPA:0 + + + + + + FBbt:00007001 + + + + + + FMA:67135 + + + + + + GAID:781 + + + + + + HAO:0000003 + + + + + + MA:0003000 + + + + + + MESH:A13 + + + + + + TAO:0000037 + + + + + + TGMA:0001823 + + + + + + VHOG:0001759 + + + + + + WBbt:0000100 + + + + + + XAO:0003000 + + + + + + ZFA:0000037 + + + + + + biological structure + + + + + + uberon + + + + + + UBERON:0000061 + + + + + + + + + + + + + + + + + + anatomical structure + + + + + + + + + + + + + + + + + + + + + + Anatomical structure that performs a specific function or group of functions [WP]. + Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions. + CARO does not include a generic 'organ' class, only simple and compound organ + + + + + + EFO:0000634 + EMAPA:35949 + ENVO:01000162 + FMA:67498 + MA:0003001 + OpenCyc:Mx4rv5XMb5wpEbGdrcN5Y29ycA + OpenCyc:Mx4rwP3iWpwpEbGdrcN5Y29ycA + UMLS:C0178784 + WBbt:0003760 + uberon + anatomical unit + body organ + element + UBERON:0000062 + + organ + + + + + + + + + + + + + + + + + + + + + + + + + + + + Anatomical structure that performs a specific function or group of functions [WP]. + + + + + + Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions. + + + + + + CARO does not include a generic 'organ' class, only simple and compound organ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + EFO:0000634 + + + + + + EMAPA:35949 + + + + + + ENVO:01000162 + + + + + + FMA:67498 + + + + + + MA:0003001 + + + + + + OpenCyc:Mx4rv5XMb5wpEbGdrcN5Y29ycA + + + + + + OpenCyc:Mx4rwP3iWpwpEbGdrcN5Y29ycA + + + + + + UMLS:C0178784 + + + + + + WBbt:0003760 + + + + + + uberon + + + + + + anatomical unit + + + + + + body organ + + + + + + element + + + + + + UBERON:0000062 + + + + + + + + + + + + organ + + + + + + + + + + + + + + + + Anatomical structure which has as its direct parts two or more types of tissue and is continuous with one or more anatomical structures likewise constituted by two or more portions of tissues distinct from those of their complement. Examples: osteon, cortical bone, neck of femur, bronchopulmonary segment, left lobe of liver, anterior right side of heart, interventricular branch of left coronary artery, right atrium, mitral valve, head of pancreas[FMA]. + + + + AAO:0011124 + EFO:0000635 + FMA:82472 + cardinal organ part + uberon + regional part of organ + UBERON:0000064 + + + + organ part + + + + + + + + + + + + + + + + + + + + + + + + + + + + Anatomical structure which has as its direct parts two or more types of tissue and is continuous with one or more anatomical structures likewise constituted by two or more portions of tissues distinct from those of their complement. Examples: osteon, cortical bone, neck of femur, bronchopulmonary segment, left lobe of liver, anterior right side of heart, interventricular branch of left coronary artery, right atrium, mitral valve, head of pancreas[FMA]. + + + + + + + + + + + + + + + + + + + + + + + + AAO:0011124 + + + + + + EFO:0000635 + + + + + + FMA:82472 + + + + + + cardinal organ part + + + + + + uberon + + + + + + regional part of organ + + + + + + UBERON:0000064 + + + + + + + + + + + + + + + + + + + + + + + + organ part + + + + + + + + + + Anatomical entity that has mass. + AAO:0010264 + AEO:0000006 + BILA:0000006 + CARO:0000006 + EHDAA2:0003006 + FBbt:00007016 + FMA:67165 + HAO:0000006 + TAO:0001836 + TGMA:0001826 + VHOG:0001721 + uberon + UBERON:0000465 + + material anatomical entity + + + + + + + + + + + + + + + + + Anatomical entity that has mass. + + + + + + AAO:0010264 + + + + + + AEO:0000006 + + + + + + BILA:0000006 + + + + + + CARO:0000006 + + + + + + EHDAA2:0003006 + + + + + + FBbt:00007016 + + + + + + FMA:67165 + + + + + + HAO:0000006 + + + + + + TAO:0001836 + + + + + + TGMA:0001826 + + + + + + VHOG:0001721 + + + + + + uberon + + + + + + UBERON:0000465 + + + + + + + + + + + + material anatomical entity + + + + + + + + + + + + + + + + Anatomical group that is has as its parts distinct anatomical structures interconnected by anatomical structures at a lower level of granularity[CARO]. A group of organs that work together to perform a certain task [Wikipedia]. + system + + + + + + AAO:0000007 + AEO:0000011 + BILA:0000011 + BSA:0000049 + CALOHA:TS-2088 + CARO:0000011 + EHDAA2:0003011 + EHDAA:392 + EMAPA:16103 + EV:0100000 + FBbt:00004856 + FMA:7149 + HAO:0000011 + MA:0000003 + OpenCyc:Mx4rCWM0QCtDEdyAAADggVbxzQ + TAO:0001439 + TGMA:0001831 + UMLS:C0460002 + VHOG:0001725 + WBbt:0005746 + WBbt:0005763 + XAO:0003002 + ZFA:0001439 + galen:AnatomicalSystem + body system + organ system + uberon + UBERON:0000467 + + + anatomical system + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Anatomical group that is has as its parts distinct anatomical structures interconnected by anatomical structures at a lower level of granularity[CARO]. A group of organs that work together to perform a certain task [Wikipedia]. + + + + + + system + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + AAO:0000007 + + + + + + AEO:0000011 + + + + + + BILA:0000011 + + + + + + BSA:0000049 + + + + + + CALOHA:TS-2088 + + + + + + CARO:0000011 + + + + + + EHDAA2:0003011 + + + + + + EHDAA:392 + + + + + + EMAPA:16103 + + + + + + EV:0100000 + + + + + + FBbt:00004856 + + + + + + FMA:7149 + + + + + + HAO:0000011 + + + + + + MA:0000003 + + + + + + OpenCyc:Mx4rCWM0QCtDEdyAAADggVbxzQ + + + + + + TAO:0001439 + + + + + + TGMA:0001831 + + + + + + UMLS:C0460002 + + + + + + VHOG:0001725 + + + + + + WBbt:0005746 + + + + + + WBbt:0005763 + + + + + + XAO:0003002 + + + + + + ZFA:0001439 + + + + + + galen:AnatomicalSystem + + + + + + body system + + + + + + organ system + + + + + + uberon + + + + + + UBERON:0000467 + + + + + + + + + + + + + + + + + + anatomical system + + + + + + + + + + + + + + + + Anatomical structure that is an individual member of a species and consists of more than one cell. + TODO - split body and mc organism? body continues after death stage + organismal + + + + + AAO:0010026 + AEO:0000191 + BILA:0000012 + BSA:0000038 + BTO:0000042 + CARO:0000012 + EFO:0002906 + EHDAA2:0003103 + EHDAA2:0003191 + EHDAA:1 + EHDAA:9178 + EMAPA:25765 + EV:0100016 + FBbt:00000001 + FMA:256135 + HAO:0000012 + TADS:0000001 + TAO:0001094 + TGMA:0001832 + VHOG:0000671 + WBbt:0007833 + XAO:0003004 + ZFA:0001094 + galen:Organism + multi-cellular organism + organism + whole organism + animal + uberon + Koerper + body + whole body + UBERON:0000468 + + + + multicellular organism + + + + + + + + + + + + + + + + + Anatomical structure that is an individual member of a species and consists of more than one cell. + + + + + + TODO - split body and mc organism? body continues after death stage + + + + + + organismal + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + AAO:0010026 + + + + + + AEO:0000191 + + + + + + BILA:0000012 + + + + + + BSA:0000038 + + + + + + BTO:0000042 + + + + + + CARO:0000012 + + + + + + EFO:0002906 + + + + + + EHDAA2:0003103 + + + + + + EHDAA2:0003191 + + + + + + EHDAA:1 + + + + + + EHDAA:9178 + + + + + + EMAPA:25765 + + + + + + EV:0100016 + + + + + + FBbt:00000001 + + + + + + FMA:256135 + + + + + + HAO:0000012 + + + + + + TADS:0000001 + + + + + + TAO:0001094 + + + + + + TGMA:0001832 + + + + + + VHOG:0000671 + + + + + + WBbt:0007833 + + + + + + XAO:0003004 + + + + + + ZFA:0001094 + + + + + + galen:Organism + + + + + + multi-cellular organism + + + + + + organism + + + + + + whole organism + + + + + + animal + + + + + + uberon + + + + + + Koerper + + + + + + body + + + + + + whole body + + + + + + UBERON:0000468 + + + + + + + + + + + + + + + + + + + + + + + + multicellular organism + + + + + + + + + + Anatomical structure which is a subdivision of a whole organism, consisting of components of multiple anatomical systems, largely surrounded by a contiguous region of integument. + Reflects CARO2. todo - check the inclusion of FMA 'cardinal body part here', and check child terms for consistency + + + + + AAO:0010053 + AEO:0000032 + BILA:0000032 + CALOHA:TS-2084 + CARO:0000032 + EFO:0000808 + EHDAA2:0003032 + FBbt:00007009 + FMA:7153 + HAO:0000032 + MA:0002433 + MAT:0000293 + MESH:A01 + MIAA:0000293 + OpenCyc:Mx4rvViAHJwpEbGdrcN5Y29ycA + TAO:0001308 + TGMA:0001840 + UMLS:C0229962 + VHOG:0001758 + XAO:0003013 + ZFA:0001308 + galen:BodyPart + anatomic region + uberon + body part + body region + cardinal body part + UBERON:0000475 + + + + organism subdivision + + + + + + + + + + + + + + + + + Anatomical structure which is a subdivision of a whole organism, consisting of components of multiple anatomical systems, largely surrounded by a contiguous region of integument. + + + + + + Reflects CARO2. todo - check the inclusion of FMA 'cardinal body part here', and check child terms for consistency + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + AAO:0010053 + + + + + + AEO:0000032 + + + + + + BILA:0000032 + + + + + + CALOHA:TS-2084 + + + + + + CARO:0000032 + + + + + + EFO:0000808 + + + + + + EHDAA2:0003032 + + + + + + FBbt:00007009 + + + + + + FMA:7153 + + + + + + HAO:0000032 + + + + + + MA:0002433 + + + + + + MAT:0000293 + + + + + + MESH:A01 + + + + + + MIAA:0000293 + + + + + + OpenCyc:Mx4rvViAHJwpEbGdrcN5Y29ycA + + + + + + TAO:0001308 + + + + + + TGMA:0001840 + + + + + + UMLS:C0229962 + + + + + + VHOG:0001758 + + + + + + XAO:0003013 + + + + + + ZFA:0001308 + + + + + + galen:BodyPart + + + + + + anatomic region + + + + + + uberon + + + + + + body part + + + + + + body region + + + + + + cardinal body part + + + + + + UBERON:0000475 + + + + + + + + + + + + + + + + + + + + + + + + organism subdivision + + + + + + + + + + Anatomical structure consisting of at least two non-overlapping organs, multi-tissue aggregates or portion of tissues or cells of different types that does not constitute an organism, organ, multi-tissue aggregate, or portion of tissue. + AAO:0010008 + AEO:0000054 + BILA:0000054 + CARO:0000054 + EHDAA2:0003054 + HAO:0000054 + TAO:0001512 + TGMA:0001846 + VHOG:0001724 + XAO:0003001 + ZFA:0001512 + uberon + UBERON:0000480 + + anatomical group + + + + + + + + + + + + + + + + + Anatomical structure consisting of at least two non-overlapping organs, multi-tissue aggregates or portion of tissues or cells of different types that does not constitute an organism, organ, multi-tissue aggregate, or portion of tissue. + + + + + + AAO:0010008 + + + + + + AEO:0000054 + + + + + + BILA:0000054 + + + + + + CARO:0000054 + + + + + + EHDAA2:0003054 + + + + + + HAO:0000054 + + + + + + TAO:0001512 + + + + + + TGMA:0001846 + + + + + + VHOG:0001724 + + + + + + XAO:0003001 + + + + + + ZFA:0001512 + + + + + + uberon + + + + + + UBERON:0000480 + + + + + + + + + + + + anatomical group + + + + + + + + + + + + + + + + The subdivision of the vertebrate body between the thorax and pelvis. The ventral part of the abdomen contains the abdominal cavity and visceral organs. The dorsal part includes the abdominal section of the vertebral column. + Vertebrate specific. In arthropods 'abdomen' is the most distal section of the body which lies behind the thorax or cephalothorax. If need be we can introduce some grouping class + abdominal + + + BTO:0000020 + CALOHA:TS-0001 + EFO:0000968 + EMAPA:35102 + EV:0100011 + FMA:9577 + GAID:16 + MA:0000029 + MAT:0000298 + MESH:A01.047 + MIAA:0000298 + OpenCyc:Mx4rvVjgyZwpEbGdrcN5Y29ycA + galen:Abdomen + abdominopelvic region + abdominopelvis + uberon + adult abdomen + belly + celiac region + UBERON:0000916 + + + abdomen + + + + + + + + + + + + + + + + + + + + + + + + + + + + The subdivision of the vertebrate body between the thorax and pelvis. The ventral part of the abdomen contains the abdominal cavity and visceral organs. The dorsal part includes the abdominal section of the vertebral column. + + + + + + Vertebrate specific. In arthropods 'abdomen' is the most distal section of the body which lies behind the thorax or cephalothorax. If need be we can introduce some grouping class + + + + + + abdominal + + + + + + + + + + + + + + + + + + BTO:0000020 + + + + + + CALOHA:TS-0001 + + + + + + EFO:0000968 + + + + + + EMAPA:35102 + + + + + + EV:0100011 + + + + + + FMA:9577 + + + + + + GAID:16 + + + + + + MA:0000029 + + + + + + MAT:0000298 + + + + + + MESH:A01.047 + + + + + + MIAA:0000298 + + + + + + OpenCyc:Mx4rvVjgyZwpEbGdrcN5Y29ycA + + + + + + galen:Abdomen + + + + + + abdominopelvic region + + + + + + abdominopelvis + + + + + + uberon + + + + + + adult abdomen + + + + + + belly + + + + + + celiac region + + + + + + UBERON:0000916 + + + + + + + + + + + + + + + + + + abdomen + + + + + + + + + + Anatomical system that consists of the glands and parts of glands that produce endocrine secretions and help to integrate and control bodily metabolic activity. + Anatomical system containing glands which regulates bodily functions though the secretion of hormones.[AAO] + Multicellular organisms have complex endocrine systems, allowing responses to environmental stimuli, regulation of development, reproduction, and homeostasis. Nuclear receptors (NRs), a metazoan-specific family of ligand-activated transcription factors, play central roles in endocrine responses, as intermediates between signaling molecules and target genes. The NR family includes ligand-bound and orphan receptors, that is, receptors with no known ligand or for which there is no ligand Pocket. Understanding NR evolution has been further improved by comparison of several completed genomes, particularly those of deuterostomes and ecdysozoans. In contrast, evolution of NR ligands is still much debated. One hypothesis proposes that several independent gains and losses of ligand-binding ability in NRs occurred in protostomes and deuterostomes. A second hypothesis, pertaining to the NR3 subfamily (vertebrate steroid hormone receptors and estrogen related receptor), proposes that before the divergence of protostomes and deuterostomes, there was an ancestral steroid receptor (AncSR) that was ligand-activated and that orphan receptors secondarily lost the ability to bind a ligand. (...) Our analysis reveals that steroidogenesis has been independently elaborated in the 3 main bilaterian lineages (...).[well established][VHOG] + endocrine + + + + + AAO:0010279 + CALOHA:TS-1301 + EFO:0002969 + EHDAA2:0002224 + EMAPA:35306 + EV:0100128 + FBbt:00005068 + FMA:9668 + GAID:439 + MA:0000012 + MESH:A06 + TAO:0001158 + UMLS:C0014136 + VHOG:0000098 + XAO:0000158 + ZFA:0001158 + endocrine glandular system + endocrine system + systema endocrinum + uberon + UBERON:0000949 + + + + endocrine system + + + + + + + + + + + + + + + + + Anatomical system that consists of the glands and parts of glands that produce endocrine secretions and help to integrate and control bodily metabolic activity. + + + + + + Anatomical system containing glands which regulates bodily functions though the secretion of hormones.[AAO] + + + + + + Multicellular organisms have complex endocrine systems, allowing responses to environmental stimuli, regulation of development, reproduction, and homeostasis. Nuclear receptors (NRs), a metazoan-specific family of ligand-activated transcription factors, play central roles in endocrine responses, as intermediates between signaling molecules and target genes. The NR family includes ligand-bound and orphan receptors, that is, receptors with no known ligand or for which there is no ligand Pocket. Understanding NR evolution has been further improved by comparison of several completed genomes, particularly those of deuterostomes and ecdysozoans. In contrast, evolution of NR ligands is still much debated. One hypothesis proposes that several independent gains and losses of ligand-binding ability in NRs occurred in protostomes and deuterostomes. A second hypothesis, pertaining to the NR3 subfamily (vertebrate steroid hormone receptors and estrogen related receptor), proposes that before the divergence of protostomes and deuterostomes, there was an ancestral steroid receptor (AncSR) that was ligand-activated and that orphan receptors secondarily lost the ability to bind a ligand. (...) Our analysis reveals that steroidogenesis has been independently elaborated in the 3 main bilaterian lineages (...).[well established][VHOG] + + + + + + endocrine + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + AAO:0010279 + + + + + + CALOHA:TS-1301 + + + + + + EFO:0002969 + + + + + + EHDAA2:0002224 + + + + + + EMAPA:35306 + + + + + + EV:0100128 + + + + + + FBbt:00005068 + + + + + + FMA:9668 + + + + + + GAID:439 + + + + + + MA:0000012 + + + + + + MESH:A06 + + + + + + TAO:0001158 + + + + + + UMLS:C0014136 + + + + + + VHOG:0000098 + + + + + + XAO:0000158 + + + + + + ZFA:0001158 + + + + + + endocrine glandular system + + + + + + endocrine system + + + + + + systema endocrinum + + + + + + uberon + + + + + + UBERON:0000949 + + + + + + + + + + + + + + + + + + + + + + + + endocrine system + + + + + + + + + + Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species. + + + + AAO:0010841 + AEO:0000000 + BILA:0000000 + CARO:0000000 + EHDAA2:0002229 + FBbt:10000000 + FBbt_root:00000000 + FMA:62955 + HAO:0000000 + MA:0000001 + TAO:0100000 + TGMA:0001822 + UMLS:C1515976 + XAO:0000000 + ZFA:0100000 + uberon + UBERON:0001062 + + anatomical entity + + + + + + + + + + + + + + + + + Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species. + + + + + + + + + + + + + + + + + + + + + + + + AAO:0010841 + + + + + + AEO:0000000 + + + + + + BILA:0000000 + + + + + + CARO:0000000 + + + + + + EHDAA2:0002229 + + + + + + FBbt:10000000 + + + + + + FBbt_root:00000000 + + + + + + FMA:62955 + + + + + + HAO:0000000 + + + + + + MA:0000001 + + + + + + TAO:0100000 + + + + + + TGMA:0001822 + + + + + + UMLS:C1515976 + + + + + + XAO:0000000 + + + + + + ZFA:0100000 + + + + + + uberon + + + + + + UBERON:0001062 + + + + + + + + + + + + anatomical entity + + + + + + + + + + + + + + + + + + + + + Situated along the perimeter of the adrenal gland, the adrenal cortex mediates the stress response through the production of mineralocorticoids and glucocorticoids, including aldosterone and cortisol respectively. It is also a secondary site of androgen synthesis. [WP,unvetted]. + All craniates have groups of cells homologous to the mammalian adrenocortical and chromaffin tissues (medulla), but they are scattered in and near the kidneys in fishes. (...) The cortical and chromaffin tissues come together to form adrenal glands in tetrapods.[well established][VHOG] + Kardong states that mammals are the first to have distinct cortext and medulla, but this contradicts XAO + + + + + AAO:0011009 + BTO:0000045 + CALOHA:TS-0015 + EFO:0000237 + EMAPA:18427 + EV:0100136 + FMA:15632 + GAID:447 + MA:0000118 + MAT:0000494 + MESH:A06.407.071.140 + UMLS:C0001613 + VHOG:0001481 + XAO:0000165 + adrenal gland cortex + cortex (glandula suprarenalis) + cortex of adrenal gland + cortex of suprarenal gland + suprarenal cortex + uberon + cortex glandulae suprarenalis + suprarenal + UBERON:0001235 + + + adrenal cortex + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Situated along the perimeter of the adrenal gland, the adrenal cortex mediates the stress response through the production of mineralocorticoids and glucocorticoids, including aldosterone and cortisol respectively. It is also a secondary site of androgen synthesis. [WP,unvetted]. + + + + + + All craniates have groups of cells homologous to the mammalian adrenocortical and chromaffin tissues (medulla), but they are scattered in and near the kidneys in fishes. (...) The cortical and chromaffin tissues come together to form adrenal glands in tetrapods.[well established][VHOG] + + + + + + Kardong states that mammals are the first to have distinct cortext and medulla, but this contradicts XAO + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + AAO:0011009 + + + + + + BTO:0000045 + + + + + + CALOHA:TS-0015 + + + + + + EFO:0000237 + + + + + + EMAPA:18427 + + + + + + EV:0100136 + + + + + + FMA:15632 + + + + + + GAID:447 + + + + + + MA:0000118 + + + + + + MAT:0000494 + + + + + + MESH:A06.407.071.140 + + + + + + UMLS:C0001613 + + + + + + VHOG:0001481 + + + + + + XAO:0000165 + + + + + + adrenal gland cortex + + + + + + cortex (glandula suprarenalis) + + + + + + cortex of adrenal gland + + + + + + cortex of suprarenal gland + + + + + + suprarenal cortex + + + + + + uberon + + + + + + cortex glandulae suprarenalis + + + + + + suprarenal + + + + + + UBERON:0001235 + + + + + + + + + + + + + + + + + + adrenal cortex + + + + + + + + + + + + + + + + + + + + + + + + + + + + Outermost layer of an organ[WP]. + cortical + this class is used more generically than in FMA, and includes e.g. cortex of hair + + EFO:0000383 + EHDAA:9344 + FMA:61109 + galen:Cortex + cortex + cortex of organ + uberon + UBERON:0001851 + + + cortex + + + + + + + + + + + + + + + + + + + + + + + + + + + + Outermost layer of an organ[WP]. + + + + + + cortical + + + + + + this class is used more generically than in FMA, and includes e.g. cortex of hair + + + + + + + + + + + + EFO:0000383 + + + + + + EHDAA:9344 + + + + + + FMA:61109 + + + + + + galen:Cortex + + + + + + cortex + + + + + + cortex of organ + + + + + + uberon + + + + + + UBERON:0001851 + + + + + + + + + + + + + + + + + + cortex + + + + + + + + + + + + + + + + Organism subdivision which is the part of the body posterior to the cervical region (or head, when cervical region not present) and anterior to the caudal region. Includes the sacrum when present. + Organism subdivision that is the part of the body posterior to the head and anterior to the tail.[AAO] + Organism subdivision which is the part of the body posterior to the head and anterior to the tail.[TAO] + + + + + AAO:0010339 + BILA:0000116 + BTO:0001493 + CALOHA:TS-1071 + EFO:0000966 + EMAPA:31857 + FMA:7181 + MA:0000004 + MAT:0000296 + MIAA:0000296 + OpenCyc:Mx4rvVkJjpwpEbGdrcN5Y29ycA + TAO:0001115 + UMLS:C0460005 + XAO:0000054 + XAO:0003025 + ZFA:0001115 + galen:Trunk + thoracolumbar region + torso + trunk region + uberon + Rumpf + UBERON:0002100 + + + + trunk + + + + + + + + + + + + + + + + + + + + + + + + + + + + Organism subdivision which is the part of the body posterior to the cervical region (or head, when cervical region not present) and anterior to the caudal region. Includes the sacrum when present. + + + + + + Organism subdivision that is the part of the body posterior to the head and anterior to the tail.[AAO] + + + + + + Organism subdivision which is the part of the body posterior to the head and anterior to the tail.[TAO] + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + AAO:0010339 + + + + + + BILA:0000116 + + + + + + BTO:0001493 + + + + + + CALOHA:TS-1071 + + + + + + EFO:0000966 + + + + + + EMAPA:31857 + + + + + + FMA:7181 + + + + + + MA:0000004 + + + + + + MAT:0000296 + + + + + + MIAA:0000296 + + + + + + OpenCyc:Mx4rvVkJjpwpEbGdrcN5Y29ycA + + + + + + TAO:0001115 + + + + + + UMLS:C0460005 + + + + + + XAO:0000054 + + + + + + XAO:0003025 + + + + + + ZFA:0001115 + + + + + + galen:Trunk + + + + + + thoracolumbar region + + + + + + torso + + + + + + trunk region + + + + + + uberon + + + + + + Rumpf + + + + + + UBERON:0002100 + + + + + + + + + + + + + + + + + + + + + + + + trunk + + + + + + + + + + + + + + + + + + + + + + + + + + + Endocrine glands are glands of the endocrine system that secrete their products directly into the circulatory system rather than through a duct.[WP, modified]. + + + + + AEO:0000098 + BTO:0001488 + CALOHA:TS-1300 + EHDAA2:0003098 + EMAPA:35999 + FMA:9602 + GAID:335 + MA:0002563 + MESH:A06.407 + OpenCyc:Mx4rvbkiRZwpEbGdrcN5Y29ycA + UMLS:C0014133 + ductless gland + glandula endocrina + uberon + ductless gland + glandulae endocrinae + UBERON:0002368 + + + endocrine gland + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Endocrine glands are glands of the endocrine system that secrete their products directly into the circulatory system rather than through a duct.[WP, modified]. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + AEO:0000098 + + + + + + BTO:0001488 + + + + + + CALOHA:TS-1300 + + + + + + EHDAA2:0003098 + + + + + + EMAPA:35999 + + + + + + FMA:9602 + + + + + + GAID:335 + + + + + + MA:0002563 + + + + + + MESH:A06.407 + + + + + + OpenCyc:Mx4rvbkiRZwpEbGdrcN5Y29ycA + + + + + + UMLS:C0014133 + + + + + + ductless gland + + + + + + glandula endocrina + + + + + + uberon + + + + + + ductless gland + + + + + + glandulae endocrinae + + + + + + UBERON:0002368 + + + + + + + + + + + + + + + + + + endocrine gland + + + + + + + + + + + + + + + + + + + + + + + + + + + + Either of a pair of complex endocrine organs near the anterior medial border of the kidney consisting of a mesodermal cortex that produces glucocorticoid, mineralocorticoid, and androgenic hormones and an ectodermal medulla that produces epinephrine and norepinephrine[BTO]. + Anatomical structure which is found on the surface of the kidney and secretes various hormones including epinephrine, norephinephrine, aldosterone, corticosterone, and cortisol.[AAO] + All craniates have groups of cells homologous to the mammalian adrenocortical and chromaffin tissues, but they are scattered in and near the kidneys in fishes. (...) The cortical and chromaffin tissues come together to form adrenal glands in tetrapods.[well established][VHOG] + The origin of the adrenal gland is still controversial. It is thought to share the same origin as the kidney and gonads, derived from coelomic epithelium of the urogenital ridge and/or the underlying mesenchyme (Keegan and Hammer, 2002; Morohashi, 1997). We follow Kardong and state homology at the level of the cortex and medulla rather than gland as a whole + suprarenal cortex manufactures corticosteroids; suprarenal medulla manufactures epinephrine and norepinephrine; suprarenal medulla receives preganglionic sympathetic innervation from the greater thoracic splanchnic n. + + + + + AAO:0010551 + BTO:0000047 + CALOHA:TS-0016 + EFO:0000238 + EMAPA:18426 + EV:0100135 + FMA:9604 + GAID:446 + MA:0000116 + MAT:0000071 + MESH:A06.407.071 + MIAA:0000071 + OpenCyc:Mx4rvXYiz5wpEbGdrcN5Y29ycA + UMLS:C0001625 + VHOG:0001141 + XAO:0000164 + galen:AdrenalGland + glandula adrenalis + glandula suprarenalis + uberon + adrenal + adrenal capsule + adrenal medulla cell + atrabiliary capsule + epinephric gland + epinephros + glandula suprarenalis + interrenal gland + suprarenal capsule + suprarenal gland + UBERON:0002369 + + + adrenal gland + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Either of a pair of complex endocrine organs near the anterior medial border of the kidney consisting of a mesodermal cortex that produces glucocorticoid, mineralocorticoid, and androgenic hormones and an ectodermal medulla that produces epinephrine and norepinephrine[BTO]. + + + + + + Anatomical structure which is found on the surface of the kidney and secretes various hormones including epinephrine, norephinephrine, aldosterone, corticosterone, and cortisol.[AAO] + + + + + + All craniates have groups of cells homologous to the mammalian adrenocortical and chromaffin tissues, but they are scattered in and near the kidneys in fishes. (...) The cortical and chromaffin tissues come together to form adrenal glands in tetrapods.[well established][VHOG] + + + + + + The origin of the adrenal gland is still controversial. It is thought to share the same origin as the kidney and gonads, derived from coelomic epithelium of the urogenital ridge and/or the underlying mesenchyme (Keegan and Hammer, 2002; Morohashi, 1997). We follow Kardong and state homology at the level of the cortex and medulla rather than gland as a whole + + + + + + suprarenal cortex manufactures corticosteroids; suprarenal medulla manufactures epinephrine and norepinephrine; suprarenal medulla receives preganglionic sympathetic innervation from the greater thoracic splanchnic n. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + AAO:0010551 + + + + + + BTO:0000047 + + + + + + CALOHA:TS-0016 + + + + + + EFO:0000238 + + + + + + EMAPA:18426 + + + + + + EV:0100135 + + + + + + FMA:9604 + + + + + + GAID:446 + + + + + + MA:0000116 + + + + + + MAT:0000071 + + + + + + MESH:A06.407.071 + + + + + + MIAA:0000071 + + + + + + OpenCyc:Mx4rvXYiz5wpEbGdrcN5Y29ycA + + + + + + UMLS:C0001625 + + + + + + VHOG:0001141 + + + + + + XAO:0000164 + + + + + + galen:AdrenalGland + + + + + + glandula adrenalis + + + + + + glandula suprarenalis + + + + + + uberon + + + + + + adrenal + + + + + + adrenal capsule + + + + + + adrenal medulla cell + + + + + + atrabiliary capsule + + + + + + epinephric gland + + + + + + epinephros + + + + + + glandula suprarenalis + + + + + + interrenal gland + + + + + + suprarenal capsule + + + + + + suprarenal gland + + + + + + UBERON:0002369 + + + + + + + + + + + + + + + + + + adrenal gland + + + + + + + + + + + + + + + + + + + + + + + The abdominal segment of the torso. + + + EMAPA:35104 + FMA:259211 + MA:0000021 + uberon + abdomen/pelvis/perineum + lower body + lumbar region + UBERON:0002417 + abdominal segment of trunk + + + + + + + + + + + + + + + + + + + + + + + The abdominal segment of the torso. + + + + + + + + + + + + + + + + + + EMAPA:35104 + + + + + + FMA:259211 + + + + + + MA:0000021 + + + + + + uberon + + + + + + abdomen/pelvis/perineum + + + + + + lower body + + + + + + lumbar region + + + + + + UBERON:0002417 + + + + + + abdominal segment of trunk + + + + + + + + + + A gland is an organ in an animal's body that synthesizes a substance for release such as hormones or breast milk, often into the bloodstream (endocrine gland) or into cavities inside the body or its outer surface (exocrine gland). A gland is an organ specialised for secretion[GO]. + glandular + UBERON:MIAA_0000021 + + + + + AAO:0000212 + AEO:0000096 + BTO:0000522 + EFO:0000797 + EHDAA2:0003096 + EHDAA:2161 + EHDAA:4475 + EHDAA:6522 + EMAPA:18425 + FBbt:00100317 + FMA:86294 + HAO:0000375 + MA:0003038 + MAT:0000021 + MIAA:0000021 + OpenCyc:Mx4rwP3vyJwpEbGdrcN5Y29ycA + UMLS:C1285092 + WikipediaCategory:Glands + galen:Gland + uberon + Druese + glandula + UBERON:0002530 + + + gland + + + + + + + + + + + + + + + + + + A gland is an organ in an animal's body that synthesizes a substance for release such as hormones or breast milk, often into the bloodstream (endocrine gland) or into cavities inside the body or its outer surface (exocrine gland). A gland is an organ specialised for secretion[GO]. + + + + + + glandular + + + + + + UBERON:MIAA_0000021 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + AAO:0000212 + + + + + + AEO:0000096 + + + + + + BTO:0000522 + + + + + + EFO:0000797 + + + + + + EHDAA2:0003096 + + + + + + EHDAA:2161 + + + + + + EHDAA:4475 + + + + + + EHDAA:6522 + + + + + + EMAPA:18425 + + + + + + FBbt:00100317 + + + + + + FMA:86294 + + + + + + HAO:0000375 + + + + + + MA:0003038 + + + + + + MAT:0000021 + + + + + + MIAA:0000021 + + + + + + OpenCyc:Mx4rwP3vyJwpEbGdrcN5Y29ycA + + + + + + UMLS:C1285092 + + + + + + WikipediaCategory:Glands + + + + + + galen:Gland + + + + + + uberon + + + + + + Druese + + + + + + glandula + + + + + + UBERON:0002530 + + + + + + + + + + + + + + + + + + gland + + + + + + + + + + + + + + + + + + + + + + This gland can either be a discrete structure located bilaterally above each kidney, or a cluster of cells in the head kidney that perform the functions of the adrenal gland. In either case, this organ consists of two cells types, aminergic chromaffin cells and steroidogenic cortical cells[GO] + keep this grouping class so long as it is required for GO + All craniates have groups of cells homologous to the mammalian adrenocortical and chromaffin tissues, but they are scattered in and near the kidneys in fishes. (...) The cortical and chromaffin tissues come together to form adrenal glands in tetrapods.[well established][VHOG] + VHOG:0001141 + adrenal gland - interrenal gland + adrenal gland/interrenal tissue + uberon + adrenal - interrenal gland + suprarenal gland - interrenal gland + UBERON:0006858 + + + adrenal/interrenal gland + + + + + + + + + + + + + + + + + + + + + + + + + + + + This gland can either be a discrete structure located bilaterally above each kidney, or a cluster of cells in the head kidney that perform the functions of the adrenal gland. In either case, this organ consists of two cells types, aminergic chromaffin cells and steroidogenic cortical cells[GO] + + + + + + keep this grouping class so long as it is required for GO + + + + + + All craniates have groups of cells homologous to the mammalian adrenocortical and chromaffin tissues, but they are scattered in and near the kidneys in fishes. (...) The cortical and chromaffin tissues come together to form adrenal glands in tetrapods.[well established][VHOG] + + + + + + VHOG:0001141 + + + + + + adrenal gland - interrenal gland + + + + + + adrenal gland/interrenal tissue + + + + + + uberon + + + + + + adrenal - interrenal gland + + + + + + suprarenal gland - interrenal gland + + + + + + UBERON:0006858 + + + + + + + + + + + + + + + + + + adrenal/interrenal gland + + + + + + + + + + + + + + + + + FMA:25054 + region of trunk + trunk subdivision + uberon + UBERON:0009569 + + subdivision of trunk + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + FMA:25054 + + + + + + region of trunk + + + + + + trunk subdivision + + + + + + uberon + + + + + + UBERON:0009569 + + + + + + + + + + + + subdivision of trunk + + + + + + + + + + An anatomical structure that has more than one cell as a part. + CARO:0010000 + FBbt:00100313 + multicellular structure + uberon + UBERON:0010000 + + multicellular anatomical structure + + + + + + + + + + + + + + + + + An anatomical structure that has more than one cell as a part. + + + + + + CARO:0010000 + + + + + + FBbt:00100313 + + + + + + multicellular structure + + + + + + uberon + + + + + + UBERON:0010000 + + + + + + + + + + + + multicellular anatomical structure + + + + + + + + + + + + + + + + A major subdivision of an organism that divides an organism along its main body axis (typically anterio-posterior axis). In vertebrates, this is based on the vertebral column. + Ideally this would be disjoint with analagous class for appendicular axes, but currently 'appendages' like antennae, horns cause a problem + axial subdivision of organism + uberon + body segment + main body segment + UBERON:0011676 + + subdivision of organism along main body axis + + + + + + + + + + + + + + + + + + + + + + + + + + + + A major subdivision of an organism that divides an organism along its main body axis (typically anterio-posterior axis). In vertebrates, this is based on the vertebral column. + + + + + + Ideally this would be disjoint with analagous class for appendicular axes, but currently 'appendages' like antennae, horns cause a problem + + + + + + axial subdivision of organism + + + + + + uberon + + + + + + body segment + + + + + + main body segment + + + + + + UBERON:0011676 + + + + + + + + + + + + subdivision of organism along main body axis + + + + + + + + + + A principle subdivision of an organism that includes all structures along the primary axis, typically the anterior-posterior axis, from head to tail, including structures of the body proper where present (for example, ribs), but excluding appendages. + uberon + UBERON:0013701 + main body axis + + + + + + + + + + + + + + + + + A principle subdivision of an organism that includes all structures along the primary axis, typically the anterior-posterior axis, from head to tail, including structures of the body proper where present (for example, ribs), but excluding appendages. + + + + + + uberon + + + + + + UBERON:0013701 + + + + + + main body axis + + + + + + + + + + + + + + + + The region of the organism associated with the visceral organs. + Cardinal body part, which consists of a maximal set of diverse subclasses of organ and organ part spatially associated with the vertebral column and ribcage. Examples: There is only one body proper[FMA:231424]. + AEO:0000103 + BTO:0001489 + FMA:231424 + uberon + body + whole body + UBERON:0013702 + + body proper + + + + + + + + + + + + + + + + + + + + + + + + + + + + The region of the organism associated with the visceral organs. + + + + + + Cardinal body part, which consists of a maximal set of diverse subclasses of organ and organ part spatially associated with the vertebral column and ribcage. Examples: There is only one body proper[FMA:231424]. + + + + + + AEO:0000103 + + + + + + BTO:0001489 + + + + + + FMA:231424 + + + + + + uberon + + + + + + body + + + + + + whole body + + + + + + UBERON:0013702 + + + + + + + + + + + + body proper + + + + + + + + + + + + + + + dummy individal 1 + + + + + + + + + + + + + + + + + dummy individal 1 + + + + + + + + + + dummy individal 2 + + + + + + + + + + + + + + + + + dummy individal 2 + + + + + + + + + dummy individal 3 + + + + + + + + + + + dummy individal 3 + + + + + + + + + dummy individal 4 + + + + + + + + + + + dummy individal 4 + + + + + + + + diff --git a/docs/examples/merged_defined_by.owl b/docs/examples/merged_defined_by.owl new file mode 100644 index 000000000..c870f41af --- /dev/null +++ b/docs/examples/merged_defined_by.owl @@ -0,0 +1,1248 @@ + + + + + + + + + + + + + + + + definition + + + + + + + + IAO:0000116 + uberon + editor_note + true + editor_note + + editor note + + + + + + + + IAO:0000232 + uberon + curator_notes + true + curator_notes + + curator notes + + + + + + + + An alternate textual definition for a class taken unmodified from an external source. This definition may have been used to derive a generalized definition for the new class. + UBPROP:0000001 + uberon + external_definition + true + external_definition + This annotation property may be replaced with an annotation property from an external ontology such as IAO + + external_definition + + + + + + + + Notes on the homology status of this class. + UBPROP:0000003 + uberon + homology_notes + true + homology_notes + This annotation property may be replaced with an annotation property from an external ontology such as IAO + + homology_notes + + + + + + + + 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'. + UBPROP:0000007 + uberon + has_relational_adjective + true + has_relational_adjective + + has_relational_adjective + + + + + + + + Notes on the how instances of this class vary across species. + UBPROP:0000008 + uberon + taxon_notes + true + taxon_notes + + taxon_notes + + + + + + + + Notes on the evolved function of instances of this class. + This annotation property may be replaced with an annotation property from an external ontology such as IAO + UBPROP:0000009 + uberon + function_notes + true + function_notes + + function_notes + + + + + + + + Notes on how similar or equivalent classes are represented in other ontologies. + This annotation property may be replaced with an annotation property from an external ontology such as IAO + UBPROP:0000012 + uberon + external_ontology_notes + true + external_ontology_notes + + external_ontology_notes + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + BFO:0000050 + uberon + part_of + part_of + + part_of + + + + + + + + + X outer_layer_of Y iff: +. X :continuant that bearer_of some PATO:laminar +. X part_of Y +. exists Z :surface +. X has_boundary Z +. Z boundary_of Y + +has_boundary: http://purl.obolibrary.org/obo/RO_0002002 +boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + RO:0002007 + uberon + bounding_layer_of + bounding_layer_of + 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. + + bounding layer of + + + + + + + + + + + + + + Material anatomical entity that has inherent 3D shape and is generated by coordinated expression of the organism's own genome. + + + AAO:0010825 + AEO:0000003 + BILA:0000003 + CARO:0000003 + EHDAA2:0003003 + EMAPA:0 + FBbt:00007001 + FMA:67135 + GAID:781 + HAO:0000003 + MA:0003000 + MESH:A13 + TAO:0000037 + TGMA:0001823 + VHOG:0001759 + WBbt:0000100 + XAO:0003000 + ZFA:0000037 + biological structure + uberon + UBERON:0000061 + + + anatomical structure + + + + + + + + + + + + + + + Anatomical structure that performs a specific function or group of functions [WP]. + Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions. + CARO does not include a generic 'organ' class, only simple and compound organ + + + + + + EFO:0000634 + EMAPA:35949 + ENVO:01000162 + FMA:67498 + MA:0003001 + OpenCyc:Mx4rv5XMb5wpEbGdrcN5Y29ycA + OpenCyc:Mx4rwP3iWpwpEbGdrcN5Y29ycA + UMLS:C0178784 + WBbt:0003760 + uberon + anatomical unit + body organ + element + UBERON:0000062 + + + organ + + + + + + + + + + + + + + + Anatomical structure which has as its direct parts two or more types of tissue and is continuous with one or more anatomical structures likewise constituted by two or more portions of tissues distinct from those of their complement. Examples: osteon, cortical bone, neck of femur, bronchopulmonary segment, left lobe of liver, anterior right side of heart, interventricular branch of left coronary artery, right atrium, mitral valve, head of pancreas[FMA]. + + + + AAO:0011124 + EFO:0000635 + FMA:82472 + cardinal organ part + uberon + regional part of organ + UBERON:0000064 + + + + + organ part + + + + + + + + + Anatomical entity that has mass. + AAO:0010264 + AEO:0000006 + BILA:0000006 + CARO:0000006 + EHDAA2:0003006 + FBbt:00007016 + FMA:67165 + HAO:0000006 + TAO:0001836 + TGMA:0001826 + VHOG:0001721 + uberon + UBERON:0000465 + + + material anatomical entity + + + + + + + + + + + + + + + Anatomical group that is has as its parts distinct anatomical structures interconnected by anatomical structures at a lower level of granularity[CARO]. A group of organs that work together to perform a certain task [Wikipedia]. + system + + + + + + AAO:0000007 + AEO:0000011 + BILA:0000011 + BSA:0000049 + CALOHA:TS-2088 + CARO:0000011 + EHDAA2:0003011 + EHDAA:392 + EMAPA:16103 + EV:0100000 + FBbt:00004856 + FMA:7149 + HAO:0000011 + MA:0000003 + OpenCyc:Mx4rCWM0QCtDEdyAAADggVbxzQ + TAO:0001439 + TGMA:0001831 + UMLS:C0460002 + VHOG:0001725 + WBbt:0005746 + WBbt:0005763 + XAO:0003002 + ZFA:0001439 + galen:AnatomicalSystem + body system + organ system + uberon + UBERON:0000467 + + + + anatomical system + + + + + + + + + + Anatomical structure that is an individual member of a species and consists of more than one cell. + TODO - split body and mc organism? body continues after death stage + organismal + + + + + AAO:0010026 + AEO:0000191 + BILA:0000012 + BSA:0000038 + BTO:0000042 + CARO:0000012 + EFO:0002906 + EHDAA2:0003103 + EHDAA2:0003191 + EHDAA:1 + EHDAA:9178 + EMAPA:25765 + EV:0100016 + FBbt:00000001 + FMA:256135 + HAO:0000012 + TADS:0000001 + TAO:0001094 + TGMA:0001832 + VHOG:0000671 + WBbt:0007833 + XAO:0003004 + ZFA:0001094 + galen:Organism + multi-cellular organism + organism + whole organism + animal + uberon + Koerper + body + whole body + UBERON:0000468 + + + + + multicellular organism + + + + + + + + + Anatomical structure which is a subdivision of a whole organism, consisting of components of multiple anatomical systems, largely surrounded by a contiguous region of integument. + Reflects CARO2. todo - check the inclusion of FMA 'cardinal body part here', and check child terms for consistency + + + + + AAO:0010053 + AEO:0000032 + BILA:0000032 + CALOHA:TS-2084 + CARO:0000032 + EFO:0000808 + EHDAA2:0003032 + FBbt:00007009 + FMA:7153 + HAO:0000032 + MA:0002433 + MAT:0000293 + MESH:A01 + MIAA:0000293 + OpenCyc:Mx4rvViAHJwpEbGdrcN5Y29ycA + TAO:0001308 + TGMA:0001840 + UMLS:C0229962 + VHOG:0001758 + XAO:0003013 + ZFA:0001308 + galen:BodyPart + anatomic region + uberon + body part + body region + cardinal body part + UBERON:0000475 + + + + + organism subdivision + + + + + + + + + Anatomical structure consisting of at least two non-overlapping organs, multi-tissue aggregates or portion of tissues or cells of different types that does not constitute an organism, organ, multi-tissue aggregate, or portion of tissue. + AAO:0010008 + AEO:0000054 + BILA:0000054 + CARO:0000054 + EHDAA2:0003054 + HAO:0000054 + TAO:0001512 + TGMA:0001846 + VHOG:0001724 + XAO:0003001 + ZFA:0001512 + uberon + UBERON:0000480 + + + anatomical group + + + + + + + + + + + + + + + The subdivision of the vertebrate body between the thorax and pelvis. The ventral part of the abdomen contains the abdominal cavity and visceral organs. The dorsal part includes the abdominal section of the vertebral column. + Vertebrate specific. In arthropods 'abdomen' is the most distal section of the body which lies behind the thorax or cephalothorax. If need be we can introduce some grouping class + abdominal + + + BTO:0000020 + CALOHA:TS-0001 + EFO:0000968 + EMAPA:35102 + EV:0100011 + FMA:9577 + GAID:16 + MA:0000029 + MAT:0000298 + MESH:A01.047 + MIAA:0000298 + OpenCyc:Mx4rvVjgyZwpEbGdrcN5Y29ycA + galen:Abdomen + abdominopelvic region + abdominopelvis + uberon + adult abdomen + belly + celiac region + UBERON:0000916 + + + + abdomen + + + + + + + + + Anatomical system that consists of the glands and parts of glands that produce endocrine secretions and help to integrate and control bodily metabolic activity. + Anatomical system containing glands which regulates bodily functions though the secretion of hormones.[AAO] + Multicellular organisms have complex endocrine systems, allowing responses to environmental stimuli, regulation of development, reproduction, and homeostasis. Nuclear receptors (NRs), a metazoan-specific family of ligand-activated transcription factors, play central roles in endocrine responses, as intermediates between signaling molecules and target genes. The NR family includes ligand-bound and orphan receptors, that is, receptors with no known ligand or for which there is no ligand Pocket. Understanding NR evolution has been further improved by comparison of several completed genomes, particularly those of deuterostomes and ecdysozoans. In contrast, evolution of NR ligands is still much debated. One hypothesis proposes that several independent gains and losses of ligand-binding ability in NRs occurred in protostomes and deuterostomes. A second hypothesis, pertaining to the NR3 subfamily (vertebrate steroid hormone receptors and estrogen related receptor), proposes that before the divergence of protostomes and deuterostomes, there was an ancestral steroid receptor (AncSR) that was ligand-activated and that orphan receptors secondarily lost the ability to bind a ligand. (...) Our analysis reveals that steroidogenesis has been independently elaborated in the 3 main bilaterian lineages (...).[well established][VHOG] + endocrine + + + + + AAO:0010279 + CALOHA:TS-1301 + EFO:0002969 + EHDAA2:0002224 + EMAPA:35306 + EV:0100128 + FBbt:00005068 + FMA:9668 + GAID:439 + MA:0000012 + MESH:A06 + TAO:0001158 + UMLS:C0014136 + VHOG:0000098 + XAO:0000158 + ZFA:0001158 + endocrine glandular system + endocrine system + systema endocrinum + uberon + UBERON:0000949 + + + + + endocrine system + + + + + + + + Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species. + + + + AAO:0010841 + AEO:0000000 + BILA:0000000 + CARO:0000000 + EHDAA2:0002229 + FBbt:10000000 + FBbt_root:00000000 + FMA:62955 + HAO:0000000 + MA:0000001 + TAO:0100000 + TGMA:0001822 + UMLS:C1515976 + XAO:0000000 + ZFA:0100000 + uberon + UBERON:0001062 + + + anatomical entity + + + + + + + + + + + + + + + + + + + + Situated along the perimeter of the adrenal gland, the adrenal cortex mediates the stress response through the production of mineralocorticoids and glucocorticoids, including aldosterone and cortisol respectively. It is also a secondary site of androgen synthesis. [WP,unvetted]. + All craniates have groups of cells homologous to the mammalian adrenocortical and chromaffin tissues (medulla), but they are scattered in and near the kidneys in fishes. (...) The cortical and chromaffin tissues come together to form adrenal glands in tetrapods.[well established][VHOG] + Kardong states that mammals are the first to have distinct cortext and medulla, but this contradicts XAO + + + + + AAO:0011009 + BTO:0000045 + CALOHA:TS-0015 + EFO:0000237 + EMAPA:18427 + EV:0100136 + FMA:15632 + GAID:447 + MA:0000118 + MAT:0000494 + MESH:A06.407.071.140 + UMLS:C0001613 + VHOG:0001481 + XAO:0000165 + adrenal gland cortex + cortex (glandula suprarenalis) + cortex of adrenal gland + cortex of suprarenal gland + suprarenal cortex + uberon + cortex glandulae suprarenalis + suprarenal + UBERON:0001235 + + + + adrenal cortex + + + + + + + + + + + + + + + + + Outermost layer of an organ[WP]. + cortical + this class is used more generically than in FMA, and includes e.g. cortex of hair + + EFO:0000383 + EHDAA:9344 + FMA:61109 + galen:Cortex + cortex + cortex of organ + uberon + UBERON:0001851 + + + + cortex + + + + + + + + + + + + + + + Organism subdivision which is the part of the body posterior to the cervical region (or head, when cervical region not present) and anterior to the caudal region. Includes the sacrum when present. + Organism subdivision that is the part of the body posterior to the head and anterior to the tail.[AAO] + Organism subdivision which is the part of the body posterior to the head and anterior to the tail.[TAO] + + + + + AAO:0010339 + BILA:0000116 + BTO:0001493 + CALOHA:TS-1071 + EFO:0000966 + EMAPA:31857 + FMA:7181 + MA:0000004 + MAT:0000296 + MIAA:0000296 + OpenCyc:Mx4rvVkJjpwpEbGdrcN5Y29ycA + TAO:0001115 + UMLS:C0460005 + XAO:0000054 + XAO:0003025 + ZFA:0001115 + galen:Trunk + thoracolumbar region + torso + trunk region + uberon + Rumpf + UBERON:0002100 + + + + + trunk + + + + + + + + + + + + + + + + + + + + + + + + + + Endocrine glands are glands of the endocrine system that secrete their products directly into the circulatory system rather than through a duct.[WP, modified]. + + + + + AEO:0000098 + BTO:0001488 + CALOHA:TS-1300 + EHDAA2:0003098 + EMAPA:35999 + FMA:9602 + GAID:335 + MA:0002563 + MESH:A06.407 + OpenCyc:Mx4rvbkiRZwpEbGdrcN5Y29ycA + UMLS:C0014133 + ductless gland + glandula endocrina + uberon + ductless gland + glandulae endocrinae + UBERON:0002368 + + + + endocrine gland + + + + + + + + + + + + + + + + + + + + + + Either of a pair of complex endocrine organs near the anterior medial border of the kidney consisting of a mesodermal cortex that produces glucocorticoid, mineralocorticoid, and androgenic hormones and an ectodermal medulla that produces epinephrine and norepinephrine[BTO]. + Anatomical structure which is found on the surface of the kidney and secretes various hormones including epinephrine, norephinephrine, aldosterone, corticosterone, and cortisol.[AAO] + All craniates have groups of cells homologous to the mammalian adrenocortical and chromaffin tissues, but they are scattered in and near the kidneys in fishes. (...) The cortical and chromaffin tissues come together to form adrenal glands in tetrapods.[well established][VHOG] + The origin of the adrenal gland is still controversial. It is thought to share the same origin as the kidney and gonads, derived from coelomic epithelium of the urogenital ridge and/or the underlying mesenchyme (Keegan and Hammer, 2002; Morohashi, 1997). We follow Kardong and state homology at the level of the cortex and medulla rather than gland as a whole + suprarenal cortex manufactures corticosteroids; suprarenal medulla manufactures epinephrine and norepinephrine; suprarenal medulla receives preganglionic sympathetic innervation from the greater thoracic splanchnic n. + + + + + AAO:0010551 + BTO:0000047 + CALOHA:TS-0016 + EFO:0000238 + EMAPA:18426 + EV:0100135 + FMA:9604 + GAID:446 + MA:0000116 + MAT:0000071 + MESH:A06.407.071 + MIAA:0000071 + OpenCyc:Mx4rvXYiz5wpEbGdrcN5Y29ycA + UMLS:C0001625 + VHOG:0001141 + XAO:0000164 + galen:AdrenalGland + glandula adrenalis + glandula suprarenalis + uberon + adrenal + adrenal capsule + adrenal medulla cell + atrabiliary capsule + epinephric gland + epinephros + glandula suprarenalis + interrenal gland + suprarenal capsule + suprarenal gland + UBERON:0002369 + + + + adrenal gland + + + + + + + + + + + + The abdominal segment of the torso. + + + EMAPA:35104 + FMA:259211 + MA:0000021 + uberon + abdomen/pelvis/perineum + lower body + lumbar region + UBERON:0002417 + + abdominal segment of trunk + + + + + + + + + A gland is an organ in an animal's body that synthesizes a substance for release such as hormones or breast milk, often into the bloodstream (endocrine gland) or into cavities inside the body or its outer surface (exocrine gland). A gland is an organ specialised for secretion[GO]. + glandular + UBERON:MIAA_0000021 + + + + + AAO:0000212 + AEO:0000096 + BTO:0000522 + EFO:0000797 + EHDAA2:0003096 + EHDAA:2161 + EHDAA:4475 + EHDAA:6522 + EMAPA:18425 + FBbt:00100317 + FMA:86294 + HAO:0000375 + MA:0003038 + MAT:0000021 + MIAA:0000021 + OpenCyc:Mx4rwP3vyJwpEbGdrcN5Y29ycA + UMLS:C1285092 + WikipediaCategory:Glands + galen:Gland + uberon + Druese + glandula + UBERON:0002530 + + + + gland + + + + + + + + + + + + + + + + This gland can either be a discrete structure located bilaterally above each kidney, or a cluster of cells in the head kidney that perform the functions of the adrenal gland. In either case, this organ consists of two cells types, aminergic chromaffin cells and steroidogenic cortical cells[GO] + keep this grouping class so long as it is required for GO + All craniates have groups of cells homologous to the mammalian adrenocortical and chromaffin tissues, but they are scattered in and near the kidneys in fishes. (...) The cortical and chromaffin tissues come together to form adrenal glands in tetrapods.[well established][VHOG] + VHOG:0001141 + adrenal gland - interrenal gland + adrenal gland/interrenal tissue + uberon + adrenal - interrenal gland + suprarenal gland - interrenal gland + UBERON:0006858 + + + + adrenal/interrenal gland + + + + + + + + + + + + + + + + FMA:25054 + region of trunk + trunk subdivision + uberon + UBERON:0009569 + + + subdivision of trunk + + + + + + + + + An anatomical structure that has more than one cell as a part. + CARO:0010000 + FBbt:00100313 + multicellular structure + uberon + UBERON:0010000 + + + multicellular anatomical structure + + + + + + + + + + + + + + + A major subdivision of an organism that divides an organism along its main body axis (typically anterio-posterior axis). In vertebrates, this is based on the vertebral column. + Ideally this would be disjoint with analagous class for appendicular axes, but currently 'appendages' like antennae, horns cause a problem + axial subdivision of organism + uberon + body segment + main body segment + UBERON:0011676 + + + subdivision of organism along main body axis + + + + + + + + + A principle subdivision of an organism that includes all structures along the primary axis, typically the anterior-posterior axis, from head to tail, including structures of the body proper where present (for example, ribs), but excluding appendages. + uberon + UBERON:0013701 + + main body axis + + + + + + + + + + + + + + + The region of the organism associated with the visceral organs. + Cardinal body part, which consists of a maximal set of diverse subclasses of organ and organ part spatially associated with the vertebral column and ribcage. Examples: There is only one body proper[FMA:231424]. + AEO:0000103 + BTO:0001489 + FMA:231424 + uberon + body + whole body + UBERON:0013702 + + + body proper + + + + + + + + + test + + + + + + + diff --git a/docs/examples/merged_derived_by.owl b/docs/examples/merged_derived_by.owl new file mode 100644 index 000000000..53737ca55 --- /dev/null +++ b/docs/examples/merged_derived_by.owl @@ -0,0 +1,818 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + cellular_component + + + + + + + + + + + cellular_component + + + + + + + + + + intracellular + + + + + intracellular + + + + + + + + + + + + + + + + + + + + + + cell + + + + + + + + + + + + + + + + + cell + + + + + + + + + + nucleus + + + + + + + + + + + + + + + + + nucleus + + + + + + + + + + mitochondrion + + + + + + + + + + + + + + + + + mitochondrion + + + + + + + + + + membrane-enclosed lumen + + + + + + + + + + + + + + + + + membrane-enclosed lumen + + + + + + + + + + + + + + + + + nuclear lumen + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + nuclear lumen + + + + + + + + + + organelle + + + + + + + + + + + + + + + + + organelle + + + + + + + + + + membrane-bounded organelle + + + + + + + + + + + + + + + + + membrane-bounded organelle + + + + + + + + + + + + + + + + + intracellular organelle + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + intracellular organelle + + + + + + + + + + + intracellular membrane-bounded organelle + + + + + + + + + + + + + + + + + + + + + + + intracellular membrane-bounded organelle + + + + + + + + + + + + + + + + + organelle lumen + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + organelle lumen + + + + + + + + + + + + + + + + organelle part + + + + + + + + + + + + + + + + + + + + + + + + + + + + organelle part + + + + + + + + + + + + + + + + intracellular part + + + + + + + + + + + + + + + + + + + + + + + + + + + + intracellular part + + + + + + + + + + + + + + + + nuclear part + + + + + + + + + + + + + + + + + + + + + + + + + + + + nuclear part + + + + + + + + + + + + + + + + + + + + + + + + + + + + + intracellular organelle part + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + intracellular organelle part + + + + + + + + + + + + + + + + cell part + + + + + + + + + + + + + + + + + + + + + + + + + + + + cell part + + + + + + + + + + + + + + + + + intracellular organelle lumen + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + intracellular organelle lumen + + + + + + + + diff --git a/docs/merge.md b/docs/merge.md index 8ef7c8dff..b27efebed 100644 --- a/docs/merge.md +++ b/docs/merge.md @@ -29,3 +29,20 @@ By adding `--collapse-import-closure false`, the imports will not be merged in a The `--include-annotations` option is, by default, `false`. This refers to the ontology annotations, and when merging, these are typically ignored and the output will only include the ontology annotations from the *first* input. If you would like to merge the ontology annotations from several inputs, add `--include-annotations true`. + +### Provenance Annotations + +It’s also possible to annotate the imported or merged ontology axioms with the source ontology or version IRI. + + * `--annotate-derived-from true`: annotates all OWLAxioms with the source's version IRI if it exists, else with the ontology IRI, using `prov:wasDerivedFrom`. If the axiom already has an annotation using this property (`prov:wasDerivedFrom`), the existing annotation will be kept and no new annotation will be added. + + robot merge --catalog catalog.xml \ + --input imports-nucleus.owl \ + --annotate-derived-from true \ + --output results/merged_derived_by.owl + + * `--annotate-defined-by true`: annotates all OWLEntities (class, data, annotation, object property and named individual declaration axioms) with the source's IRI using `rdfs:isDefinedBy`. If the term already has an annotation using this property (`rdfs:isDefinedBy`), the existing annotation will be kept and no new annotation will be added. + + robot merge --input edit.owl --input edit3.owl \ + --annotate-defined-by true \ + --output results/merged_defined_by.owl diff --git a/robot-command/src/main/java/org/obolibrary/robot/AnnotateCommand.java b/robot-command/src/main/java/org/obolibrary/robot/AnnotateCommand.java index 9e8242b46..0a7b94725 100644 --- a/robot-command/src/main/java/org/obolibrary/robot/AnnotateCommand.java +++ b/robot-command/src/main/java/org/obolibrary/robot/AnnotateCommand.java @@ -6,7 +6,11 @@ import org.apache.commons.cli.Option; import org.apache.commons.cli.Options; import org.semanticweb.owlapi.model.IRI; +import org.semanticweb.owlapi.model.OWLAnnotationProperty; +import org.semanticweb.owlapi.model.OWLAxiom; +import org.semanticweb.owlapi.model.OWLEntity; import org.semanticweb.owlapi.model.OWLOntology; +import org.semanticweb.owlapi.vocab.PROVVocabulary; import org.slf4j.Logger; import org.slf4j.LoggerFactory; @@ -61,6 +65,17 @@ public AnnotateCommand() { o.addOption("i", "input", true, "convert ontology from a file"); o.addOption("I", "input-iri", true, "convert ontology from an IRI"); o.addOption("o", "output", true, "save ontology to a file"); + o.addOption( + "f", + "annotate-derived-from", + true, + "if true, annotate all axioms in the ontology with the ontology version IRI"); + o.addOption( + "d", + "annotate-defined-by", + true, + "if true, annotate all entities in the ontology with the ontology IRI"); + options = o; // Annotate with a property and plain literal - expects 2 args @@ -273,6 +288,41 @@ public CommandState execute(CommandState state, String[] args) throws Exception OntologyHelper.setOntologyIRI(ontology, ontologyIRI, versionIRI); } + // Annotate all axioms with version IRI + boolean derivedFrom = CommandLineHelper.getBooleanValue(line, "annotate-derived-from", false); + if (derivedFrom) { + hasAnnotation = true; + IRI provenanceIRI = + ontology + .getOntologyID() + .getVersionIRI() + .or(ontology.getOntologyID().getOntologyIRI().orNull()); + if (provenanceIRI != null) { + OWLAnnotationProperty annotationProp = + ontology + .getOWLOntologyManager() + .getOWLDataFactory() + .getOWLAnnotationProperty(PROVVocabulary.WAS_DERIVED_FROM.getIRI()); + for (OWLAxiom axiom : ontology.getAxioms()) { + OntologyHelper.addAxiomAnnotation(ontology, axiom, annotationProp, provenanceIRI, false); + } + } + } + + // Annotate all axioms with ontology IRI + boolean definedBy = CommandLineHelper.getBooleanValue(line, "annotate-defined-by", false); + if (definedBy) { + hasAnnotation = true; + IRI ontIRI = ontology.getOntologyID().getOntologyIRI().orNull(); + if (ontIRI != null) { + OWLAnnotationProperty rdfsIsDefinedBy = + ontology.getOWLOntologyManager().getOWLDataFactory().getRDFSIsDefinedBy(); + for (OWLEntity owlEntity : ontology.getSignature()) { + OntologyHelper.addEntityAnnotation(ontology, owlEntity, rdfsIsDefinedBy, ontIRI, false); + } + } + } + // Validate that annotations were provided if (!hasAnnotation) { throw new IllegalArgumentException(missingAnnotationError); diff --git a/robot-command/src/main/java/org/obolibrary/robot/MergeCommand.java b/robot-command/src/main/java/org/obolibrary/robot/MergeCommand.java index dd24d0c1a..e37a54520 100644 --- a/robot-command/src/main/java/org/obolibrary/robot/MergeCommand.java +++ b/robot-command/src/main/java/org/obolibrary/robot/MergeCommand.java @@ -30,6 +30,16 @@ public MergeCommand() { o.addOption( "c", "collapse-import-closure", true, "if true, the imports closure will be merged"); o.addOption("a", "include-annotations", true, "if true, ontology annotations will be merged"); + o.addOption( + "f", + "annotate-derived-from", + true, + "if true, annotate all axioms in the ontology with the ontology version IRI"); + o.addOption( + "d", + "annotate-defined-by", + true, + "if true, annotate all entities in the ontology with the ontology IRI"); options = o; } @@ -117,8 +127,11 @@ public CommandState execute(CommandState state, String[] args) throws Exception CommandLineHelper.getBooleanValue(line, "collapse-import-closure", true); boolean includeAnnotations = CommandLineHelper.getBooleanValue(line, "include-annotations", false); + boolean derivedFrom = CommandLineHelper.getBooleanValue(line, "annotate-derived-from", false); + boolean definedBy = CommandLineHelper.getBooleanValue(line, "annotate-defined-by", false); OWLOntology outputOntology = - MergeOperation.merge(inputOntologies, includeAnnotations, collapseImportClosure); + MergeOperation.merge( + inputOntologies, includeAnnotations, collapseImportClosure, definedBy, derivedFrom); CommandLineHelper.maybeSaveOutput(line, outputOntology); diff --git a/robot-core/src/main/java/org/obolibrary/robot/MergeOperation.java b/robot-core/src/main/java/org/obolibrary/robot/MergeOperation.java index 573a9cf40..9c79ff9d3 100644 --- a/robot-core/src/main/java/org/obolibrary/robot/MergeOperation.java +++ b/robot-core/src/main/java/org/obolibrary/robot/MergeOperation.java @@ -1,8 +1,23 @@ package org.obolibrary.robot; -import java.util.*; -import org.semanticweb.owlapi.model.*; +import java.util.ArrayList; +import java.util.HashMap; +import java.util.List; +import java.util.Map; +import java.util.Set; +import org.semanticweb.owlapi.model.AddImport; +import org.semanticweb.owlapi.model.IRI; +import org.semanticweb.owlapi.model.OWLAnnotation; +import org.semanticweb.owlapi.model.OWLAnnotationProperty; +import org.semanticweb.owlapi.model.OWLAxiom; +import org.semanticweb.owlapi.model.OWLDataFactory; +import org.semanticweb.owlapi.model.OWLEntity; +import org.semanticweb.owlapi.model.OWLImportsDeclaration; +import org.semanticweb.owlapi.model.OWLOntology; +import org.semanticweb.owlapi.model.OWLOntologyManager; +import org.semanticweb.owlapi.model.RemoveImport; import org.semanticweb.owlapi.model.parameters.Imports; +import org.semanticweb.owlapi.vocab.PROVVocabulary; import org.slf4j.Logger; import org.slf4j.LoggerFactory; @@ -56,8 +71,33 @@ public static OWLOntology merge(List ontologies) { */ public static OWLOntology merge( List ontologies, boolean includeAnnotations, boolean collapseImportsClosure) { + return merge(ontologies, includeAnnotations, collapseImportsClosure, false, false); + } + + /** + * Given one or more ontologies, add all their axioms first ontology, and return the first + * ontology. Option to include ontology annotations and collapse import closure. + * + *

We use a list instead of a set because OWLAPI judges identity simply by the ontology IRI, + * even if two ontologies have different axioms. + * + * @param ontologies the list of ontologies to merge + * @param includeAnnotations if true, ontology annotations should be merged; annotations on + * imports are not merged + * @param collapseImportsClosure if true, imports closure from all ontologies included + * @param definedBy if true, annotate all entities in the ontology with the ontology IRI + * @param derivedFrom if true, annotate all axioms in the ontology with the ontology version IRI + * @return the first ontology + */ + public static OWLOntology merge( + List ontologies, + boolean includeAnnotations, + boolean collapseImportsClosure, + boolean definedBy, + boolean derivedFrom) { OWLOntology ontology = ontologies.get(0); - mergeInto(ontologies, ontology, includeAnnotations, collapseImportsClosure); + mergeInto( + ontologies, ontology, includeAnnotations, collapseImportsClosure, definedBy, derivedFrom); return ontology; } @@ -177,8 +217,32 @@ public static void mergeInto( OWLOntology targetOntology, boolean includeAnnotations, boolean collapseImportsClosure) { + mergeInto(ontologies, targetOntology, includeAnnotations, collapseImportsClosure, false, false); + } + + /** + * Given a list of ontologies and a target ontology, add all the axioms from the listed ontologies + * and their import closure into the target ontology. The target ontology is not itself merged, so + * any of its imports remain distinct, unless collapsing imports closure. + * + * @param ontologies the list of ontologies to merge + * @param targetOntology the ontology to merge axioms into + * @param includeAnnotations true if ontology annotations should be merged; annotations on imports + * are not merged + * @param collapseImportsClosure true if imports closure from all ontologies included + * @param definedBy if true, annotate all entities in the ontology with the ontology IRI + * @param derivedFrom if true, annotate all axioms in the ontology with the ontology version IRI + */ + public static void mergeInto( + List ontologies, + OWLOntology targetOntology, + boolean includeAnnotations, + boolean collapseImportsClosure, + boolean definedBy, + boolean derivedFrom) { for (OWLOntology ontology : ontologies) { if (collapseImportsClosure) { + annotateProvenanceOfImports(ontology, targetOntology, definedBy, derivedFrom); // Merge the ontologies with imports included targetOntology .getOWLOntologyManager() @@ -192,6 +256,12 @@ public static void mergeInto( // Continue without removing imports continue; } + if (definedBy) { + annotateWithOntologyIRI(ontology, targetOntology, Imports.EXCLUDED); + } + if (derivedFrom) { + annotateWithVersionIRI(ontology, targetOntology, Imports.EXCLUDED); + } targetOntology .getOWLOntologyManager() .addAxioms(targetOntology, ontology.getAxioms(Imports.EXCLUDED)); @@ -215,6 +285,78 @@ public static void mergeInto( } } + /** + * Annotates provenance of all axioms through considering imports. + * + * @param ontology the ontology to merge + * @param targetOntology the ontology to merge axioms into + * @param definedBy if true, annotate all entities in the ontology with the ontology IRI + * @param derivedFrom if true, annotate all axioms in the ontology with the ontology version IRI + */ + private static void annotateProvenanceOfImports( + OWLOntology ontology, OWLOntology targetOntology, boolean definedBy, boolean derivedFrom) { + if (definedBy) { + for (OWLOntology importedOnt : ontology.getImports()) { + annotateWithOntologyIRI(importedOnt, ontology, Imports.EXCLUDED); + } + annotateWithOntologyIRI(ontology, targetOntology, Imports.EXCLUDED); + } + if (derivedFrom) { + for (OWLOntology importedOnt : ontology.getImports()) { + annotateWithVersionIRI(importedOnt, ontology, Imports.EXCLUDED); + } + annotateWithVersionIRI(ontology, targetOntology, Imports.EXCLUDED); + } + } + + /** + * Annotates all axioms in the ontology with the ontology version IRI if defined,annotates with + * the ontology IRI otherwise. + * + * @param sourceOntology the ontology to annotate its all axioms. + * @param targetOntology the ontology to add annotation + * @param includeImportsClosure if INCLUDED, the imports closure is included. + */ + private static void annotateWithVersionIRI( + OWLOntology sourceOntology, OWLOntology targetOntology, Imports includeImportsClosure) { + IRI provenanceIRI = + sourceOntology + .getOntologyID() + .getVersionIRI() + .or(sourceOntology.getOntologyID().getOntologyIRI().orNull()); + if (provenanceIRI != null) { + OWLAnnotationProperty annotationProp = + targetOntology + .getOWLOntologyManager() + .getOWLDataFactory() + .getOWLAnnotationProperty(PROVVocabulary.WAS_DERIVED_FROM.getIRI()); + for (OWLAxiom axiom : sourceOntology.getAxioms(includeImportsClosure)) { + OntologyHelper.addAxiomAnnotation( + targetOntology, axiom, annotationProp, provenanceIRI, false); + } + } + } + + /** + * Annotate all entities in the ontology with the ontology IRI. + * + * @param sourceOntology the ontology to annotate its entities + * @param targetOntology the ontology to add annotation + * @param includeImportsClosure if INCLUDED, the imports closure is included. + */ + private static void annotateWithOntologyIRI( + OWLOntology sourceOntology, OWLOntology targetOntology, Imports includeImportsClosure) { + IRI ontIRI = sourceOntology.getOntologyID().getOntologyIRI().orNull(); + if (ontIRI != null) { + OWLAnnotationProperty rdfsIsDefinedBy = + targetOntology.getOWLOntologyManager().getOWLDataFactory().getRDFSIsDefinedBy(); + for (OWLEntity owlEntity : sourceOntology.getSignature(includeImportsClosure)) { + OntologyHelper.addEntityAnnotation( + targetOntology, owlEntity, rdfsIsDefinedBy, ontIRI, false); + } + } + } + /** * Given an ontology, remove the import statements. * diff --git a/robot-core/src/main/java/org/obolibrary/robot/OntologyHelper.java b/robot-core/src/main/java/org/obolibrary/robot/OntologyHelper.java index bb287158a..73e8b07a3 100644 --- a/robot-core/src/main/java/org/obolibrary/robot/OntologyHelper.java +++ b/robot-core/src/main/java/org/obolibrary/robot/OntologyHelper.java @@ -2,14 +2,63 @@ import com.google.common.base.Optional; import java.io.StringWriter; -import java.util.*; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.Collections; +import java.util.HashMap; +import java.util.HashSet; +import java.util.List; +import java.util.Map; +import java.util.Set; import java.util.function.Function; import org.obolibrary.robot.checks.InvalidReferenceChecker; import org.obolibrary.robot.export.RendererType; import org.obolibrary.robot.providers.QuotedAnnotationValueShortFormProvider; import org.semanticweb.owlapi.apibinding.OWLManager; import org.semanticweb.owlapi.manchestersyntax.renderer.ManchesterOWLSyntaxObjectRenderer; -import org.semanticweb.owlapi.model.*; +import org.semanticweb.owlapi.model.AddAxiom; +import org.semanticweb.owlapi.model.AddOntologyAnnotation; +import org.semanticweb.owlapi.model.AxiomType; +import org.semanticweb.owlapi.model.IRI; +import org.semanticweb.owlapi.model.OWLAnnotation; +import org.semanticweb.owlapi.model.OWLAnnotationAssertionAxiom; +import org.semanticweb.owlapi.model.OWLAnnotationProperty; +import org.semanticweb.owlapi.model.OWLAnnotationSubject; +import org.semanticweb.owlapi.model.OWLAnnotationValue; +import org.semanticweb.owlapi.model.OWLAxiom; +import org.semanticweb.owlapi.model.OWLClass; +import org.semanticweb.owlapi.model.OWLClassAssertionAxiom; +import org.semanticweb.owlapi.model.OWLClassExpression; +import org.semanticweb.owlapi.model.OWLDataFactory; +import org.semanticweb.owlapi.model.OWLDataProperty; +import org.semanticweb.owlapi.model.OWLDataPropertyExpression; +import org.semanticweb.owlapi.model.OWLDatatype; +import org.semanticweb.owlapi.model.OWLDisjointUnionAxiom; +import org.semanticweb.owlapi.model.OWLEntity; +import org.semanticweb.owlapi.model.OWLEquivalentDataPropertiesAxiom; +import org.semanticweb.owlapi.model.OWLHasKeyAxiom; +import org.semanticweb.owlapi.model.OWLImportsDeclaration; +import org.semanticweb.owlapi.model.OWLLiteral; +import org.semanticweb.owlapi.model.OWLNamedObject; +import org.semanticweb.owlapi.model.OWLNaryClassAxiom; +import org.semanticweb.owlapi.model.OWLNaryIndividualAxiom; +import org.semanticweb.owlapi.model.OWLNaryPropertyAxiom; +import org.semanticweb.owlapi.model.OWLNegativeObjectPropertyAssertionAxiom; +import org.semanticweb.owlapi.model.OWLObject; +import org.semanticweb.owlapi.model.OWLObjectProperty; +import org.semanticweb.owlapi.model.OWLObjectPropertyAssertionAxiom; +import org.semanticweb.owlapi.model.OWLObjectPropertyAxiom; +import org.semanticweb.owlapi.model.OWLObjectPropertyExpression; +import org.semanticweb.owlapi.model.OWLOntology; +import org.semanticweb.owlapi.model.OWLOntologyCreationException; +import org.semanticweb.owlapi.model.OWLOntologyID; +import org.semanticweb.owlapi.model.OWLOntologyManager; +import org.semanticweb.owlapi.model.OWLSameIndividualAxiom; +import org.semanticweb.owlapi.model.OWLSubClassOfAxiom; +import org.semanticweb.owlapi.model.OWLUnaryPropertyAxiom; +import org.semanticweb.owlapi.model.RemoveImport; +import org.semanticweb.owlapi.model.RemoveOntologyAnnotation; +import org.semanticweb.owlapi.model.SetOntologyID; import org.semanticweb.owlapi.model.parameters.Imports; import org.semanticweb.owlapi.model.parameters.OntologyCopy; import org.semanticweb.owlapi.search.EntitySearcher; @@ -50,6 +99,71 @@ public class OntologyHelper { private static final String nullIRIError = NS + "NULL IRI ERROR import ontology does not have an IRI"; + /** + * Given an ontology, an entity, annotates the entity with the given annotation in the ontology. + * + * @param ontology the ontology to modify + * @param owlEntity the entity to annotate + * @param property annotation property + * @param value the IRI or literal value to add + * @param overload when false: if the entity already has an annotation with the given property, + * doesn't add the annotation. When true, adds the annotation anyway. + */ + public static void addEntityAnnotation( + OWLOntology ontology, + OWLEntity owlEntity, + OWLAnnotationProperty property, + OWLAnnotationValue value, + boolean overload) { + OWLAnnotationAssertionAxiom existingAnnotation = + EntitySearcher.getAnnotationAssertionAxioms(owlEntity.getIRI(), ontology).stream() + .filter(a -> a.getProperty().getIRI().equals(property.getIRI())) + .findFirst() + .orElse(null); + if (overload || existingAnnotation == null) { + OWLOntologyManager manager = ontology.getOWLOntologyManager(); + OWLDataFactory factory = manager.getOWLDataFactory(); + OWLAnnotation annotation = factory.getOWLAnnotation(property, value); + OWLAxiom ax = factory.getOWLAnnotationAssertionAxiom(owlEntity.getIRI(), annotation); + manager.applyChange(new AddAxiom(ontology, ax)); + } + } + + /** + * Given an ontology, an axiom, and a set of annotations, annotate the axiom with the annotations + * in the ontology. + * + *

Note that as axioms are immutable, the axiom is removed and replaced with a new one. + * + * @param ontology the ontology to modify + * @param axiom the axiom to annotate + * @param property annotation property to add + * @param value the IRI or literal value to add + * @param overload when false: if the axiom already has an annotation with the given propertyIRI, + * doesn't add the annotation. When true, adds the annotation anyway. + */ + public static void addAxiomAnnotation( + OWLOntology ontology, + OWLAxiom axiom, + OWLAnnotationProperty property, + OWLAnnotationValue value, + boolean overload) { + OWLAnnotation existingAnnotation = + axiom.getAnnotations().stream() + .filter(a -> a.getProperty().getIRI().equals(property.getIRI())) + .findFirst() + .orElse(null); + if (overload || existingAnnotation == null) { + OWLOntologyManager manager = ontology.getOWLOntologyManager(); + OWLDataFactory factory = manager.getOWLDataFactory(); + OWLAnnotation annotation = factory.getOWLAnnotation(property, value); + + OWLAxiom newAxiom = axiom.getAnnotatedAxiom(new HashSet<>(Arrays.asList(annotation))); + manager.removeAxiom(ontology, axiom); + manager.addAxiom(ontology, newAxiom); + } + } + /** * Given an ontology, an axiom, a property IRI, and a value string, add an annotation to this * ontology with that property and value. From 0183532e5f25491137747ce7808e93c8cea19523 Mon Sep 17 00:00:00 2001 From: hkir-dev Date: Mon, 14 Mar 2022 14:23:55 +0000 Subject: [PATCH 02/17] fix comment #893 --- .../src/main/java/org/obolibrary/robot/AnnotateCommand.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/robot-command/src/main/java/org/obolibrary/robot/AnnotateCommand.java b/robot-command/src/main/java/org/obolibrary/robot/AnnotateCommand.java index 0a7b94725..72e1ddf12 100644 --- a/robot-command/src/main/java/org/obolibrary/robot/AnnotateCommand.java +++ b/robot-command/src/main/java/org/obolibrary/robot/AnnotateCommand.java @@ -309,7 +309,7 @@ public CommandState execute(CommandState state, String[] args) throws Exception } } - // Annotate all axioms with ontology IRI + // Annotate all entities with ontology IRI boolean definedBy = CommandLineHelper.getBooleanValue(line, "annotate-defined-by", false); if (definedBy) { hasAnnotation = true; From 1e00dbf63825ca06851ff136059f1d6caa7e09c1 Mon Sep 17 00:00:00 2001 From: hkir-dev Date: Mon, 14 Mar 2022 14:34:47 +0000 Subject: [PATCH 03/17] fixing imports #893 --- .../org/obolibrary/robot/OntologyHelper.java | 53 +------------------ 1 file changed, 2 insertions(+), 51 deletions(-) diff --git a/robot-core/src/main/java/org/obolibrary/robot/OntologyHelper.java b/robot-core/src/main/java/org/obolibrary/robot/OntologyHelper.java index 73e8b07a3..d67c5bea2 100644 --- a/robot-core/src/main/java/org/obolibrary/robot/OntologyHelper.java +++ b/robot-core/src/main/java/org/obolibrary/robot/OntologyHelper.java @@ -2,63 +2,14 @@ import com.google.common.base.Optional; import java.io.StringWriter; -import java.util.ArrayList; -import java.util.Arrays; -import java.util.Collections; -import java.util.HashMap; -import java.util.HashSet; -import java.util.List; -import java.util.Map; -import java.util.Set; +import java.util.*; import java.util.function.Function; import org.obolibrary.robot.checks.InvalidReferenceChecker; import org.obolibrary.robot.export.RendererType; import org.obolibrary.robot.providers.QuotedAnnotationValueShortFormProvider; import org.semanticweb.owlapi.apibinding.OWLManager; import org.semanticweb.owlapi.manchestersyntax.renderer.ManchesterOWLSyntaxObjectRenderer; -import org.semanticweb.owlapi.model.AddAxiom; -import org.semanticweb.owlapi.model.AddOntologyAnnotation; -import org.semanticweb.owlapi.model.AxiomType; -import org.semanticweb.owlapi.model.IRI; -import org.semanticweb.owlapi.model.OWLAnnotation; -import org.semanticweb.owlapi.model.OWLAnnotationAssertionAxiom; -import org.semanticweb.owlapi.model.OWLAnnotationProperty; -import org.semanticweb.owlapi.model.OWLAnnotationSubject; -import org.semanticweb.owlapi.model.OWLAnnotationValue; -import org.semanticweb.owlapi.model.OWLAxiom; -import org.semanticweb.owlapi.model.OWLClass; -import org.semanticweb.owlapi.model.OWLClassAssertionAxiom; -import org.semanticweb.owlapi.model.OWLClassExpression; -import org.semanticweb.owlapi.model.OWLDataFactory; -import org.semanticweb.owlapi.model.OWLDataProperty; -import org.semanticweb.owlapi.model.OWLDataPropertyExpression; -import org.semanticweb.owlapi.model.OWLDatatype; -import org.semanticweb.owlapi.model.OWLDisjointUnionAxiom; -import org.semanticweb.owlapi.model.OWLEntity; -import org.semanticweb.owlapi.model.OWLEquivalentDataPropertiesAxiom; -import org.semanticweb.owlapi.model.OWLHasKeyAxiom; -import org.semanticweb.owlapi.model.OWLImportsDeclaration; -import org.semanticweb.owlapi.model.OWLLiteral; -import org.semanticweb.owlapi.model.OWLNamedObject; -import org.semanticweb.owlapi.model.OWLNaryClassAxiom; -import org.semanticweb.owlapi.model.OWLNaryIndividualAxiom; -import org.semanticweb.owlapi.model.OWLNaryPropertyAxiom; -import org.semanticweb.owlapi.model.OWLNegativeObjectPropertyAssertionAxiom; -import org.semanticweb.owlapi.model.OWLObject; -import org.semanticweb.owlapi.model.OWLObjectProperty; -import org.semanticweb.owlapi.model.OWLObjectPropertyAssertionAxiom; -import org.semanticweb.owlapi.model.OWLObjectPropertyAxiom; -import org.semanticweb.owlapi.model.OWLObjectPropertyExpression; -import org.semanticweb.owlapi.model.OWLOntology; -import org.semanticweb.owlapi.model.OWLOntologyCreationException; -import org.semanticweb.owlapi.model.OWLOntologyID; -import org.semanticweb.owlapi.model.OWLOntologyManager; -import org.semanticweb.owlapi.model.OWLSameIndividualAxiom; -import org.semanticweb.owlapi.model.OWLSubClassOfAxiom; -import org.semanticweb.owlapi.model.OWLUnaryPropertyAxiom; -import org.semanticweb.owlapi.model.RemoveImport; -import org.semanticweb.owlapi.model.RemoveOntologyAnnotation; -import org.semanticweb.owlapi.model.SetOntologyID; +import org.semanticweb.owlapi.model.*; import org.semanticweb.owlapi.model.parameters.Imports; import org.semanticweb.owlapi.model.parameters.OntologyCopy; import org.semanticweb.owlapi.search.EntitySearcher; From b4e9a66587defc75f3c5119b57e879b04245aaf0 Mon Sep 17 00:00:00 2001 From: hkir-dev Date: Mon, 14 Mar 2022 14:41:04 +0000 Subject: [PATCH 04/17] change log updated #893 --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 31b437b0d..30be36440 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -7,6 +7,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ## [Unreleased] - Sort [`report`] violations by rule name within level [#955] +- [`extract`] and [`merge`] should optionally inject provenance [#893] ## [1.8.3] - 2021-12-16 From 6320f25dd833fc1d29eb190e283426b9055e2e60 Mon Sep 17 00:00:00 2001 From: hkir-dev Date: Mon, 14 Mar 2022 15:08:43 +0000 Subject: [PATCH 05/17] fix change log #893 --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 30be36440..85c976e72 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -295,6 +295,7 @@ First official release of ROBOT! [`template`]: http://robot.obolibrary.org/template [`validate`]: http://robot.obolibrary.org/validate +[#893]: https://github.com/ontodev/robot/issues/893 [#955]: https://github.com/ontodev/robot/pull/955 [#953]: https://github.com/ontodev/robot/pull/953 [#951]: https://github.com/ontodev/robot/pull/951 From 7744bb55a5c03bff65baa8f6e88998b18ff3da0f Mon Sep 17 00:00:00 2001 From: hkir-dev Date: Mon, 14 Mar 2022 15:16:45 +0000 Subject: [PATCH 06/17] renamed edit3.owl to merge.owl since it was causing random failures due in --inputs "edit*.owl" command #893 --- docs/examples/{edit3.owl => merge.owl} | 0 docs/merge.md | 2 +- 2 files changed, 1 insertion(+), 1 deletion(-) rename docs/examples/{edit3.owl => merge.owl} (100%) diff --git a/docs/examples/edit3.owl b/docs/examples/merge.owl similarity index 100% rename from docs/examples/edit3.owl rename to docs/examples/merge.owl diff --git a/docs/merge.md b/docs/merge.md index b27efebed..fe843d64f 100644 --- a/docs/merge.md +++ b/docs/merge.md @@ -43,6 +43,6 @@ It’s also possible to annotate the imported or merged ontology axioms with the * `--annotate-defined-by true`: annotates all OWLEntities (class, data, annotation, object property and named individual declaration axioms) with the source's IRI using `rdfs:isDefinedBy`. If the term already has an annotation using this property (`rdfs:isDefinedBy`), the existing annotation will be kept and no new annotation will be added. - robot merge --input edit.owl --input edit3.owl \ + robot merge --input edit.owl --input merge.owl \ --annotate-defined-by true \ --output results/merged_defined_by.owl From a4fed9c940943ceafb163461b9ecc86abd6c7fe2 Mon Sep 17 00:00:00 2001 From: hkir-dev Date: Mon, 14 Mar 2022 19:41:34 +0000 Subject: [PATCH 07/17] PR #977 review fixes --- docs/annotate.md | 6 +++--- .../{example2_derived_by.owl => example2_derived_from.owl} | 0 .../{merged_derived_by.owl => merged_derived_from.owl} | 0 docs/merge.md | 6 +++--- 4 files changed, 6 insertions(+), 6 deletions(-) rename docs/examples/{example2_derived_by.owl => example2_derived_from.owl} (100%) rename docs/examples/{merged_derived_by.owl => merged_derived_from.owl} (100%) diff --git a/docs/annotate.md b/docs/annotate.md index 2193d94f1..c75e1d4be 100644 --- a/docs/annotate.md +++ b/docs/annotate.md @@ -43,13 +43,13 @@ This command can also remove all ontology annotations from your file with `--rem It’s also possible to annotate the ontology axioms with the ontology IRI or version IRI. - * `--annotate-derived-from true`: annotates all OWLAxioms with the source's version IRI if it exists, else with the ontology IRI, using `prov:wasDerivedFrom`. If the axiom already has an annotation using this property (`prov:wasDerivedFrom`), the existing annotation will be kept and no new annotation will be added. + * `--annotate-derived-from true`: annotates all axioms with the source's version IRI if it exists, else with the ontology IRI, using `prov:wasDerivedFrom`. If the axiom already has an annotation using this property (`prov:wasDerivedFrom`), the existing annotation will be kept and no new annotation will be added. robot annotate --input example2.owl \ --annotate-derived-from true - --output results/example2_derived_by.owl + --output results/example2_derived_from.owl - * `--annotate-defined-by true`: annotates all OWLEntities (class, data, annotation, object property and named individual declaration axioms) with the source's IRI using `rdfs:isDefinedBy`. If the term already has an annotation using this property (`rdfs:isDefinedBy`), the existing annotation will be kept and no new annotation will be added. + * `--annotate-defined-by true`: annotates all entities (class, data, annotation, object property and named individual declaration axioms) with the source's IRI using `rdfs:isDefinedBy`. If the term already has an annotation using this property (`rdfs:isDefinedBy`), the existing annotation will be kept and no new annotation will be added. robot annotate --input example2.owl \ --annotate-defined-by true diff --git a/docs/examples/example2_derived_by.owl b/docs/examples/example2_derived_from.owl similarity index 100% rename from docs/examples/example2_derived_by.owl rename to docs/examples/example2_derived_from.owl diff --git a/docs/examples/merged_derived_by.owl b/docs/examples/merged_derived_from.owl similarity index 100% rename from docs/examples/merged_derived_by.owl rename to docs/examples/merged_derived_from.owl diff --git a/docs/merge.md b/docs/merge.md index fe843d64f..1713b10aa 100644 --- a/docs/merge.md +++ b/docs/merge.md @@ -34,14 +34,14 @@ If you would like to merge the ontology annotations from several inputs, add `-- It’s also possible to annotate the imported or merged ontology axioms with the source ontology or version IRI. - * `--annotate-derived-from true`: annotates all OWLAxioms with the source's version IRI if it exists, else with the ontology IRI, using `prov:wasDerivedFrom`. If the axiom already has an annotation using this property (`prov:wasDerivedFrom`), the existing annotation will be kept and no new annotation will be added. + * `--annotate-derived-from true`: annotates all axioms with the source's version IRI if it exists, else with the ontology IRI, using `prov:wasDerivedFrom`. If the axiom already has an annotation using this property (`prov:wasDerivedFrom`), the existing annotation will be kept and no new annotation will be added. robot merge --catalog catalog.xml \ --input imports-nucleus.owl \ --annotate-derived-from true \ - --output results/merged_derived_by.owl + --output results/merged_derived_from.owl - * `--annotate-defined-by true`: annotates all OWLEntities (class, data, annotation, object property and named individual declaration axioms) with the source's IRI using `rdfs:isDefinedBy`. If the term already has an annotation using this property (`rdfs:isDefinedBy`), the existing annotation will be kept and no new annotation will be added. + * `--annotate-defined-by true`: annotates all entities (class, data, annotation, object property and named individual declaration axioms) with the source's IRI using `rdfs:isDefinedBy`. If the term already has an annotation using this property (`rdfs:isDefinedBy`), the existing annotation will be kept and no new annotation will be added. robot merge --input edit.owl --input merge.owl \ --annotate-defined-by true \ From f77493af347ed8370fc4e43f1eb9d03166197ad4 Mon Sep 17 00:00:00 2001 From: hkir-dev Date: Wed, 6 Apr 2022 10:42:47 +0100 Subject: [PATCH 08/17] #977 example files simplified --- docs/examples/example2.owl | 964 +--- docs/examples/example2_defined_by.owl | 1068 +---- docs/examples/example2_derived_from.owl | 5518 +---------------------- docs/examples/merged_defined_by.owl | 1088 +---- docs/merge.md | 2 +- 5 files changed, 225 insertions(+), 8415 deletions(-) diff --git a/docs/examples/example2.owl b/docs/examples/example2.owl index 8ddd6a312..8b83bfe64 100644 --- a/docs/examples/example2.owl +++ b/docs/examples/example2.owl @@ -71,163 +71,10 @@ - - - - An alternate textual definition for a class taken unmodified from an external source. This definition may have been used to derive a generalized definition for the new class. - UBPROP:0000001 - uberon - external_definition - true - external_definition - This annotation property may be replaced with an annotation property from an external ontology such as IAO - external_definition - - - - - - - - Notes on the homology status of this class. - UBPROP:0000003 - uberon - homology_notes - true - homology_notes - This annotation property may be replaced with an annotation property from an external ontology such as IAO - homology_notes - - - - - - - - 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'. - UBPROP:0000007 - uberon - has_relational_adjective - true - has_relational_adjective - has_relational_adjective - - - - - - - - Notes on the how instances of this class vary across species. - UBPROP:0000008 - uberon - taxon_notes - true - taxon_notes - taxon_notes - - - - - - - - Notes on the evolved function of instances of this class. - This annotation property may be replaced with an annotation property from an external ontology such as IAO - UBPROP:0000009 - uberon - function_notes - true - function_notes - function_notes - - - - - - - - Notes on how similar or equivalent classes are represented in other ontologies. - This annotation property may be replaced with an annotation property from an external ontology such as IAO - UBPROP:0000012 - uberon - external_ontology_notes - true - external_ontology_notes - external_ontology_notes - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - @@ -252,30 +99,7 @@ part_of part_of - - - - - - - - X outer_layer_of Y iff: -. X :continuant that bearer_of some PATO:laminar -. X part_of Y -. exists Z :surface -. X has_boundary Z -. Z boundary_of Y - -has_boundary: http://purl.obolibrary.org/obo/RO_0002002 -boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - RO:0002007 - uberon - bounding_layer_of - bounding_layer_of - 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. - bounding layer of - - + - - - - - - - - - - Anatomical structure which has as its direct parts two or more types of tissue and is continuous with one or more anatomical structures likewise constituted by two or more portions of tissues distinct from those of their complement. Examples: osteon, cortical bone, neck of femur, bronchopulmonary segment, left lobe of liver, anterior right side of heart, interventricular branch of left coronary artery, right atrium, mitral valve, head of pancreas[FMA]. - - - - AAO:0011124 - EFO:0000635 - FMA:82472 - cardinal organ part - uberon - regional part of organ - UBERON:0000064 - - - - organ part - - - - - - - - - Anatomical entity that has mass. - AAO:0010264 - AEO:0000006 - BILA:0000006 - CARO:0000006 - EHDAA2:0003006 - FBbt:00007016 - FMA:67165 - HAO:0000006 - TAO:0001836 - TGMA:0001826 - VHOG:0001721 - uberon - UBERON:0000465 - - material anatomical entity - - - - - - - - - - - - - - - Anatomical group that is has as its parts distinct anatomical structures interconnected by anatomical structures at a lower level of granularity[CARO]. A group of organs that work together to perform a certain task [Wikipedia]. - system - - - - - - AAO:0000007 - AEO:0000011 - BILA:0000011 - BSA:0000049 - CALOHA:TS-2088 - CARO:0000011 - EHDAA2:0003011 - EHDAA:392 - EMAPA:16103 - EV:0100000 - FBbt:00004856 - FMA:7149 - HAO:0000011 - MA:0000003 - OpenCyc:Mx4rCWM0QCtDEdyAAADggVbxzQ - TAO:0001439 - TGMA:0001831 - UMLS:C0460002 - VHOG:0001725 - WBbt:0005746 - WBbt:0005763 - XAO:0003002 - ZFA:0001439 - galen:AnatomicalSystem - body system - organ system - uberon - UBERON:0000467 - - - anatomical system - - - - - - - - - - Anatomical structure that is an individual member of a species and consists of more than one cell. - TODO - split body and mc organism? body continues after death stage - organismal - - - - - AAO:0010026 - AEO:0000191 - BILA:0000012 - BSA:0000038 - BTO:0000042 - CARO:0000012 - EFO:0002906 - EHDAA2:0003103 - EHDAA2:0003191 - EHDAA:1 - EHDAA:9178 - EMAPA:25765 - EV:0100016 - FBbt:00000001 - FMA:256135 - HAO:0000012 - TADS:0000001 - TAO:0001094 - TGMA:0001832 - VHOG:0000671 - WBbt:0007833 - XAO:0003004 - ZFA:0001094 - galen:Organism - multi-cellular organism - organism - whole organism - animal - uberon - Koerper - body - whole body - UBERON:0000468 - - - - multicellular organism - - - - - - - - - Anatomical structure which is a subdivision of a whole organism, consisting of components of multiple anatomical systems, largely surrounded by a contiguous region of integument. - Reflects CARO2. todo - check the inclusion of FMA 'cardinal body part here', and check child terms for consistency - - - - - AAO:0010053 - AEO:0000032 - BILA:0000032 - CALOHA:TS-2084 - CARO:0000032 - EFO:0000808 - EHDAA2:0003032 - FBbt:00007009 - FMA:7153 - HAO:0000032 - MA:0002433 - MAT:0000293 - MESH:A01 - MIAA:0000293 - OpenCyc:Mx4rvViAHJwpEbGdrcN5Y29ycA - TAO:0001308 - TGMA:0001840 - UMLS:C0229962 - VHOG:0001758 - XAO:0003013 - ZFA:0001308 - galen:BodyPart - anatomic region - uberon - body part - body region - cardinal body part - UBERON:0000475 - - - - organism subdivision - - - - - - - - - Anatomical structure consisting of at least two non-overlapping organs, multi-tissue aggregates or portion of tissues or cells of different types that does not constitute an organism, organ, multi-tissue aggregate, or portion of tissue. - AAO:0010008 - AEO:0000054 - BILA:0000054 - CARO:0000054 - EHDAA2:0003054 - HAO:0000054 - TAO:0001512 - TGMA:0001846 - VHOG:0001724 - XAO:0003001 - ZFA:0001512 - uberon - UBERON:0000480 - - anatomical group - - - - - - - - - - - - - - - The subdivision of the vertebrate body between the thorax and pelvis. The ventral part of the abdomen contains the abdominal cavity and visceral organs. The dorsal part includes the abdominal section of the vertebral column. - Vertebrate specific. In arthropods 'abdomen' is the most distal section of the body which lies behind the thorax or cephalothorax. If need be we can introduce some grouping class - abdominal - - - BTO:0000020 - CALOHA:TS-0001 - EFO:0000968 - EMAPA:35102 - EV:0100011 - FMA:9577 - GAID:16 - MA:0000029 - MAT:0000298 - MESH:A01.047 - MIAA:0000298 - OpenCyc:Mx4rvVjgyZwpEbGdrcN5Y29ycA - galen:Abdomen - abdominopelvic region - abdominopelvis - uberon - adult abdomen - belly - celiac region - UBERON:0000916 - - - abdomen - - - - - - - - - Anatomical system that consists of the glands and parts of glands that produce endocrine secretions and help to integrate and control bodily metabolic activity. - Anatomical system containing glands which regulates bodily functions though the secretion of hormones.[AAO] - Multicellular organisms have complex endocrine systems, allowing responses to environmental stimuli, regulation of development, reproduction, and homeostasis. Nuclear receptors (NRs), a metazoan-specific family of ligand-activated transcription factors, play central roles in endocrine responses, as intermediates between signaling molecules and target genes. The NR family includes ligand-bound and orphan receptors, that is, receptors with no known ligand or for which there is no ligand Pocket. Understanding NR evolution has been further improved by comparison of several completed genomes, particularly those of deuterostomes and ecdysozoans. In contrast, evolution of NR ligands is still much debated. One hypothesis proposes that several independent gains and losses of ligand-binding ability in NRs occurred in protostomes and deuterostomes. A second hypothesis, pertaining to the NR3 subfamily (vertebrate steroid hormone receptors and estrogen related receptor), proposes that before the divergence of protostomes and deuterostomes, there was an ancestral steroid receptor (AncSR) that was ligand-activated and that orphan receptors secondarily lost the ability to bind a ligand. (...) Our analysis reveals that steroidogenesis has been independently elaborated in the 3 main bilaterian lineages (...).[well established][VHOG] - endocrine - - - - - AAO:0010279 - CALOHA:TS-1301 - EFO:0002969 - EHDAA2:0002224 - EMAPA:35306 - EV:0100128 - FBbt:00005068 - FMA:9668 - GAID:439 - MA:0000012 - MESH:A06 - TAO:0001158 - UMLS:C0014136 - VHOG:0000098 - XAO:0000158 - ZFA:0001158 - endocrine glandular system - endocrine system - systema endocrinum - uberon - UBERON:0000949 - - - - endocrine system - - - - - - - - - Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species. - - - - AAO:0010841 - AEO:0000000 - BILA:0000000 - CARO:0000000 - EHDAA2:0002229 - FBbt:10000000 - FBbt_root:00000000 - FMA:62955 - HAO:0000000 - MA:0000001 - TAO:0100000 - TGMA:0001822 - UMLS:C1515976 - XAO:0000000 - ZFA:0100000 - uberon - UBERON:0001062 - - anatomical entity - - - - - - - - - - - - - - - - - - - - Situated along the perimeter of the adrenal gland, the adrenal cortex mediates the stress response through the production of mineralocorticoids and glucocorticoids, including aldosterone and cortisol respectively. It is also a secondary site of androgen synthesis. [WP,unvetted]. - All craniates have groups of cells homologous to the mammalian adrenocortical and chromaffin tissues (medulla), but they are scattered in and near the kidneys in fishes. (...) The cortical and chromaffin tissues come together to form adrenal glands in tetrapods.[well established][VHOG] - Kardong states that mammals are the first to have distinct cortext and medulla, but this contradicts XAO - - - - - AAO:0011009 - BTO:0000045 - CALOHA:TS-0015 - EFO:0000237 - EMAPA:18427 - EV:0100136 - FMA:15632 - GAID:447 - MA:0000118 - MAT:0000494 - MESH:A06.407.071.140 - UMLS:C0001613 - VHOG:0001481 - XAO:0000165 - adrenal gland cortex - cortex (glandula suprarenalis) - cortex of adrenal gland - cortex of suprarenal gland - suprarenal cortex - uberon - cortex glandulae suprarenalis - suprarenal - UBERON:0001235 - - - adrenal cortex - - - - - - - - - - - - - - - - - Outermost layer of an organ[WP]. - cortical - this class is used more generically than in FMA, and includes e.g. cortex of hair - - EFO:0000383 - EHDAA:9344 - FMA:61109 - galen:Cortex - cortex - cortex of organ - uberon - UBERON:0001851 - - - cortex - - - - - - - - - - - - - - - Organism subdivision which is the part of the body posterior to the cervical region (or head, when cervical region not present) and anterior to the caudal region. Includes the sacrum when present. - Organism subdivision that is the part of the body posterior to the head and anterior to the tail.[AAO] - Organism subdivision which is the part of the body posterior to the head and anterior to the tail.[TAO] - - - - - AAO:0010339 - BILA:0000116 - BTO:0001493 - CALOHA:TS-1071 - EFO:0000966 - EMAPA:31857 - FMA:7181 - MA:0000004 - MAT:0000296 - MIAA:0000296 - OpenCyc:Mx4rvVkJjpwpEbGdrcN5Y29ycA - TAO:0001115 - UMLS:C0460005 - XAO:0000054 - XAO:0003025 - ZFA:0001115 - galen:Trunk - thoracolumbar region - torso - trunk region - uberon - Rumpf - UBERON:0002100 - - - - trunk - - - - - - - - - - - - - - - - - - - - - - - - - - Endocrine glands are glands of the endocrine system that secrete their products directly into the circulatory system rather than through a duct.[WP, modified]. - - - - - AEO:0000098 - BTO:0001488 - CALOHA:TS-1300 - EHDAA2:0003098 - EMAPA:35999 - FMA:9602 - GAID:335 - MA:0002563 - MESH:A06.407 - OpenCyc:Mx4rvbkiRZwpEbGdrcN5Y29ycA - UMLS:C0014133 - ductless gland - glandula endocrina - uberon - ductless gland - glandulae endocrinae - UBERON:0002368 - - - endocrine gland - - - - - - - - - - - - - - - - - - - - - - Either of a pair of complex endocrine organs near the anterior medial border of the kidney consisting of a mesodermal cortex that produces glucocorticoid, mineralocorticoid, and androgenic hormones and an ectodermal medulla that produces epinephrine and norepinephrine[BTO]. - Anatomical structure which is found on the surface of the kidney and secretes various hormones including epinephrine, norephinephrine, aldosterone, corticosterone, and cortisol.[AAO] - All craniates have groups of cells homologous to the mammalian adrenocortical and chromaffin tissues, but they are scattered in and near the kidneys in fishes. (...) The cortical and chromaffin tissues come together to form adrenal glands in tetrapods.[well established][VHOG] - The origin of the adrenal gland is still controversial. It is thought to share the same origin as the kidney and gonads, derived from coelomic epithelium of the urogenital ridge and/or the underlying mesenchyme (Keegan and Hammer, 2002; Morohashi, 1997). We follow Kardong and state homology at the level of the cortex and medulla rather than gland as a whole - suprarenal cortex manufactures corticosteroids; suprarenal medulla manufactures epinephrine and norepinephrine; suprarenal medulla receives preganglionic sympathetic innervation from the greater thoracic splanchnic n. - - - - - AAO:0010551 - BTO:0000047 - CALOHA:TS-0016 - EFO:0000238 - EMAPA:18426 - EV:0100135 - FMA:9604 - GAID:446 - MA:0000116 - MAT:0000071 - MESH:A06.407.071 - MIAA:0000071 - OpenCyc:Mx4rvXYiz5wpEbGdrcN5Y29ycA - UMLS:C0001625 - VHOG:0001141 - XAO:0000164 - galen:AdrenalGland - glandula adrenalis - glandula suprarenalis - uberon - adrenal - adrenal capsule - adrenal medulla cell - atrabiliary capsule - epinephric gland - epinephros - glandula suprarenalis - interrenal gland - suprarenal capsule - suprarenal gland - UBERON:0002369 - - - adrenal gland - - - - - - - - - - - - The abdominal segment of the torso. - - - EMAPA:35104 - FMA:259211 - MA:0000021 - uberon - abdomen/pelvis/perineum - lower body - lumbar region - UBERON:0002417 - abdominal segment of trunk - - - - - - - - - A gland is an organ in an animal's body that synthesizes a substance for release such as hormones or breast milk, often into the bloodstream (endocrine gland) or into cavities inside the body or its outer surface (exocrine gland). A gland is an organ specialised for secretion[GO]. - glandular - UBERON:MIAA_0000021 - - - - - AAO:0000212 - AEO:0000096 - BTO:0000522 - EFO:0000797 - EHDAA2:0003096 - EHDAA:2161 - EHDAA:4475 - EHDAA:6522 - EMAPA:18425 - FBbt:00100317 - FMA:86294 - HAO:0000375 - MA:0003038 - MAT:0000021 - MIAA:0000021 - OpenCyc:Mx4rwP3vyJwpEbGdrcN5Y29ycA - UMLS:C1285092 - WikipediaCategory:Glands - galen:Gland - uberon - Druese - glandula - UBERON:0002530 - - - gland - - - - - - - - - - - - - - - - This gland can either be a discrete structure located bilaterally above each kidney, or a cluster of cells in the head kidney that perform the functions of the adrenal gland. In either case, this organ consists of two cells types, aminergic chromaffin cells and steroidogenic cortical cells[GO] - keep this grouping class so long as it is required for GO - All craniates have groups of cells homologous to the mammalian adrenocortical and chromaffin tissues, but they are scattered in and near the kidneys in fishes. (...) The cortical and chromaffin tissues come together to form adrenal glands in tetrapods.[well established][VHOG] - VHOG:0001141 - adrenal gland - interrenal gland - adrenal gland/interrenal tissue - uberon - adrenal - interrenal gland - suprarenal gland - interrenal gland - UBERON:0006858 - - - adrenal/interrenal gland - - - - - - - - - - - - - - - - FMA:25054 - region of trunk - trunk subdivision - uberon - UBERON:0009569 - - subdivision of trunk - - - - - - - - - An anatomical structure that has more than one cell as a part. - CARO:0010000 - FBbt:00100313 - multicellular structure - uberon - UBERON:0010000 - - multicellular anatomical structure - - - - - - - - - - - - - - - A major subdivision of an organism that divides an organism along its main body axis (typically anterio-posterior axis). In vertebrates, this is based on the vertebral column. - Ideally this would be disjoint with analagous class for appendicular axes, but currently 'appendages' like antennae, horns cause a problem - axial subdivision of organism - uberon - body segment - main body segment - UBERON:0011676 - - subdivision of organism along main body axis - - - - - - - - - A principle subdivision of an organism that includes all structures along the primary axis, typically the anterior-posterior axis, from head to tail, including structures of the body proper where present (for example, ribs), but excluding appendages. - uberon - UBERON:0013701 - main body axis - - - - - - - - - - - - - - - The region of the organism associated with the visceral organs. - Cardinal body part, which consists of a maximal set of diverse subclasses of organ and organ part spatially associated with the vertebral column and ribcage. Examples: There is only one body proper[FMA:231424]. - AEO:0000103 - BTO:0001489 - FMA:231424 - uberon - body - whole body - UBERON:0013702 - - body proper - - dummy individal 1 @@ -1167,6 +215,16 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 dummy individal 4 + + dummy individal 5 + + + + + + + + diff --git a/docs/examples/example2_defined_by.owl b/docs/examples/example2_defined_by.owl index 52e58e7a5..542b1cf69 100644 --- a/docs/examples/example2_defined_by.owl +++ b/docs/examples/example2_defined_by.owl @@ -6,7 +6,6 @@ xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:xml="http://www.w3.org/XML/1998/namespace" xmlns:xsd="http://www.w3.org/2001/XMLSchema#" - xmlns:foaf="http://xmlns.com/foaf/0.1/" xmlns:prov="http://www.w3.org/ns/prov#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> @@ -46,11 +45,7 @@ - IAO:0000116 uberon - editor_note - true - editor_note editor note @@ -60,111 +55,13 @@ - IAO:0000232 uberon - curator_notes - true - curator_notes curator notes - - - - An alternate textual definition for a class taken unmodified from an external source. This definition may have been used to derive a generalized definition for the new class. - UBPROP:0000001 - uberon - external_definition - true - external_definition - This annotation property may be replaced with an annotation property from an external ontology such as IAO - - external_definition - - - - - - - - Notes on the homology status of this class. - UBPROP:0000003 - uberon - homology_notes - true - homology_notes - This annotation property may be replaced with an annotation property from an external ontology such as IAO - - homology_notes - - - - - - - - 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'. - UBPROP:0000007 - uberon - has_relational_adjective - true - has_relational_adjective - - has_relational_adjective - - - - - - - - Notes on the how instances of this class vary across species. - UBPROP:0000008 - uberon - taxon_notes - true - taxon_notes - - taxon_notes - - - - - - - - Notes on the evolved function of instances of this class. - This annotation property may be replaced with an annotation property from an external ontology such as IAO - UBPROP:0000009 - uberon - function_notes - true - function_notes - - function_notes - - - - - - - - Notes on how similar or equivalent classes are represented in other ontologies. - This annotation property may be replaced with an annotation property from an external ontology such as IAO - UBPROP:0000012 - uberon - external_ontology_notes - true - external_ontology_notes - - external_ontology_notes - - - - @@ -173,38 +70,6 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - @@ -213,46 +78,6 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - @@ -277,14 +102,6 @@ - - - - - - - - @@ -293,14 +110,6 @@ - - - - - - - - - - - - - - - @@ -343,40 +144,12 @@ - BFO:0000050 - uberon - part_of - part_of part_of - - - - - X outer_layer_of Y iff: -. X :continuant that bearer_of some PATO:laminar -. X part_of Y -. exists Z :surface -. X has_boundary Z -. Z boundary_of Y - -has_boundary: http://purl.obolibrary.org/obo/RO_0002002 -boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - RO:0002007 - uberon - bounding_layer_of - bounding_layer_of - 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. - - bounding layer of - - - - - - - - - - - - - - Anatomical structure which has as its direct parts two or more types of tissue and is continuous with one or more anatomical structures likewise constituted by two or more portions of tissues distinct from those of their complement. Examples: osteon, cortical bone, neck of femur, bronchopulmonary segment, left lobe of liver, anterior right side of heart, interventricular branch of left coronary artery, right atrium, mitral valve, head of pancreas[FMA]. - - - - AAO:0011124 - EFO:0000635 - FMA:82472 - cardinal organ part - uberon - regional part of organ - UBERON:0000064 - - - - - organ part - - - - - - Anatomical entity that has mass. - AAO:0010264 - AEO:0000006 - BILA:0000006 - CARO:0000006 - EHDAA2:0003006 - FBbt:00007016 - FMA:67165 - HAO:0000006 - TAO:0001836 - TGMA:0001826 - VHOG:0001721 - uberon - UBERON:0000465 - - material anatomical entity @@ -520,663 +198,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - - - - - - - - Anatomical group that is has as its parts distinct anatomical structures interconnected by anatomical structures at a lower level of granularity[CARO]. A group of organs that work together to perform a certain task [Wikipedia]. - system - - - - - - AAO:0000007 - AEO:0000011 - BILA:0000011 - BSA:0000049 - CALOHA:TS-2088 - CARO:0000011 - EHDAA2:0003011 - EHDAA:392 - EMAPA:16103 - EV:0100000 - FBbt:00004856 - FMA:7149 - HAO:0000011 - MA:0000003 - OpenCyc:Mx4rCWM0QCtDEdyAAADggVbxzQ - TAO:0001439 - TGMA:0001831 - UMLS:C0460002 - VHOG:0001725 - WBbt:0005746 - WBbt:0005763 - XAO:0003002 - ZFA:0001439 - galen:AnatomicalSystem - body system - organ system - uberon - UBERON:0000467 - - - - anatomical system - - - - - - - - - - Anatomical structure that is an individual member of a species and consists of more than one cell. - TODO - split body and mc organism? body continues after death stage - organismal - - - - - AAO:0010026 - AEO:0000191 - BILA:0000012 - BSA:0000038 - BTO:0000042 - CARO:0000012 - EFO:0002906 - EHDAA2:0003103 - EHDAA2:0003191 - EHDAA:1 - EHDAA:9178 - EMAPA:25765 - EV:0100016 - FBbt:00000001 - FMA:256135 - HAO:0000012 - TADS:0000001 - TAO:0001094 - TGMA:0001832 - VHOG:0000671 - WBbt:0007833 - XAO:0003004 - ZFA:0001094 - galen:Organism - multi-cellular organism - organism - whole organism - animal - uberon - Koerper - body - whole body - UBERON:0000468 - - - - - multicellular organism - - - - - - - - - Anatomical structure which is a subdivision of a whole organism, consisting of components of multiple anatomical systems, largely surrounded by a contiguous region of integument. - Reflects CARO2. todo - check the inclusion of FMA 'cardinal body part here', and check child terms for consistency - - - - - AAO:0010053 - AEO:0000032 - BILA:0000032 - CALOHA:TS-2084 - CARO:0000032 - EFO:0000808 - EHDAA2:0003032 - FBbt:00007009 - FMA:7153 - HAO:0000032 - MA:0002433 - MAT:0000293 - MESH:A01 - MIAA:0000293 - OpenCyc:Mx4rvViAHJwpEbGdrcN5Y29ycA - TAO:0001308 - TGMA:0001840 - UMLS:C0229962 - VHOG:0001758 - XAO:0003013 - ZFA:0001308 - galen:BodyPart - anatomic region - uberon - body part - body region - cardinal body part - UBERON:0000475 - - - - - organism subdivision - - - - - - - - - Anatomical structure consisting of at least two non-overlapping organs, multi-tissue aggregates or portion of tissues or cells of different types that does not constitute an organism, organ, multi-tissue aggregate, or portion of tissue. - AAO:0010008 - AEO:0000054 - BILA:0000054 - CARO:0000054 - EHDAA2:0003054 - HAO:0000054 - TAO:0001512 - TGMA:0001846 - VHOG:0001724 - XAO:0003001 - ZFA:0001512 - uberon - UBERON:0000480 - - - anatomical group - - - - - - - - - - - - - - - The subdivision of the vertebrate body between the thorax and pelvis. The ventral part of the abdomen contains the abdominal cavity and visceral organs. The dorsal part includes the abdominal section of the vertebral column. - Vertebrate specific. In arthropods 'abdomen' is the most distal section of the body which lies behind the thorax or cephalothorax. If need be we can introduce some grouping class - abdominal - - - BTO:0000020 - CALOHA:TS-0001 - EFO:0000968 - EMAPA:35102 - EV:0100011 - FMA:9577 - GAID:16 - MA:0000029 - MAT:0000298 - MESH:A01.047 - MIAA:0000298 - OpenCyc:Mx4rvVjgyZwpEbGdrcN5Y29ycA - galen:Abdomen - abdominopelvic region - abdominopelvis - uberon - adult abdomen - belly - celiac region - UBERON:0000916 - - - - abdomen - - - - - - - - - Anatomical system that consists of the glands and parts of glands that produce endocrine secretions and help to integrate and control bodily metabolic activity. - Anatomical system containing glands which regulates bodily functions though the secretion of hormones.[AAO] - Multicellular organisms have complex endocrine systems, allowing responses to environmental stimuli, regulation of development, reproduction, and homeostasis. Nuclear receptors (NRs), a metazoan-specific family of ligand-activated transcription factors, play central roles in endocrine responses, as intermediates between signaling molecules and target genes. The NR family includes ligand-bound and orphan receptors, that is, receptors with no known ligand or for which there is no ligand Pocket. Understanding NR evolution has been further improved by comparison of several completed genomes, particularly those of deuterostomes and ecdysozoans. In contrast, evolution of NR ligands is still much debated. One hypothesis proposes that several independent gains and losses of ligand-binding ability in NRs occurred in protostomes and deuterostomes. A second hypothesis, pertaining to the NR3 subfamily (vertebrate steroid hormone receptors and estrogen related receptor), proposes that before the divergence of protostomes and deuterostomes, there was an ancestral steroid receptor (AncSR) that was ligand-activated and that orphan receptors secondarily lost the ability to bind a ligand. (...) Our analysis reveals that steroidogenesis has been independently elaborated in the 3 main bilaterian lineages (...).[well established][VHOG] - endocrine - - - - - AAO:0010279 - CALOHA:TS-1301 - EFO:0002969 - EHDAA2:0002224 - EMAPA:35306 - EV:0100128 - FBbt:00005068 - FMA:9668 - GAID:439 - MA:0000012 - MESH:A06 - TAO:0001158 - UMLS:C0014136 - VHOG:0000098 - XAO:0000158 - ZFA:0001158 - endocrine glandular system - endocrine system - systema endocrinum - uberon - UBERON:0000949 - - - - - endocrine system - - - - - - - - - Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species. - - - - AAO:0010841 - AEO:0000000 - BILA:0000000 - CARO:0000000 - EHDAA2:0002229 - FBbt:10000000 - FBbt_root:00000000 - FMA:62955 - HAO:0000000 - MA:0000001 - TAO:0100000 - TGMA:0001822 - UMLS:C1515976 - XAO:0000000 - ZFA:0100000 - uberon - UBERON:0001062 - - - anatomical entity - - - - - - - - - - - - - - - - - - - - Situated along the perimeter of the adrenal gland, the adrenal cortex mediates the stress response through the production of mineralocorticoids and glucocorticoids, including aldosterone and cortisol respectively. It is also a secondary site of androgen synthesis. [WP,unvetted]. - All craniates have groups of cells homologous to the mammalian adrenocortical and chromaffin tissues (medulla), but they are scattered in and near the kidneys in fishes. (...) The cortical and chromaffin tissues come together to form adrenal glands in tetrapods.[well established][VHOG] - Kardong states that mammals are the first to have distinct cortext and medulla, but this contradicts XAO - - - - - AAO:0011009 - BTO:0000045 - CALOHA:TS-0015 - EFO:0000237 - EMAPA:18427 - EV:0100136 - FMA:15632 - GAID:447 - MA:0000118 - MAT:0000494 - MESH:A06.407.071.140 - UMLS:C0001613 - VHOG:0001481 - XAO:0000165 - adrenal gland cortex - cortex (glandula suprarenalis) - cortex of adrenal gland - cortex of suprarenal gland - suprarenal cortex - uberon - cortex glandulae suprarenalis - suprarenal - UBERON:0001235 - - - - adrenal cortex - - - - - - - - - - - - - - - - - Outermost layer of an organ[WP]. - cortical - this class is used more generically than in FMA, and includes e.g. cortex of hair - - EFO:0000383 - EHDAA:9344 - FMA:61109 - galen:Cortex - cortex - cortex of organ - uberon - UBERON:0001851 - - - - cortex - - - - - - - - - - - - - - - Organism subdivision which is the part of the body posterior to the cervical region (or head, when cervical region not present) and anterior to the caudal region. Includes the sacrum when present. - Organism subdivision that is the part of the body posterior to the head and anterior to the tail.[AAO] - Organism subdivision which is the part of the body posterior to the head and anterior to the tail.[TAO] - - - - - AAO:0010339 - BILA:0000116 - BTO:0001493 - CALOHA:TS-1071 - EFO:0000966 - EMAPA:31857 - FMA:7181 - MA:0000004 - MAT:0000296 - MIAA:0000296 - OpenCyc:Mx4rvVkJjpwpEbGdrcN5Y29ycA - TAO:0001115 - UMLS:C0460005 - XAO:0000054 - XAO:0003025 - ZFA:0001115 - galen:Trunk - thoracolumbar region - torso - trunk region - uberon - Rumpf - UBERON:0002100 - - - - - trunk - - - - - - - - - - - - - - - - - - - - - - - - - - Endocrine glands are glands of the endocrine system that secrete their products directly into the circulatory system rather than through a duct.[WP, modified]. - - - - - AEO:0000098 - BTO:0001488 - CALOHA:TS-1300 - EHDAA2:0003098 - EMAPA:35999 - FMA:9602 - GAID:335 - MA:0002563 - MESH:A06.407 - OpenCyc:Mx4rvbkiRZwpEbGdrcN5Y29ycA - UMLS:C0014133 - ductless gland - glandula endocrina - uberon - ductless gland - glandulae endocrinae - UBERON:0002368 - - - - endocrine gland - - - - - - - - - - - - - - - - - - - - - - Either of a pair of complex endocrine organs near the anterior medial border of the kidney consisting of a mesodermal cortex that produces glucocorticoid, mineralocorticoid, and androgenic hormones and an ectodermal medulla that produces epinephrine and norepinephrine[BTO]. - Anatomical structure which is found on the surface of the kidney and secretes various hormones including epinephrine, norephinephrine, aldosterone, corticosterone, and cortisol.[AAO] - All craniates have groups of cells homologous to the mammalian adrenocortical and chromaffin tissues, but they are scattered in and near the kidneys in fishes. (...) The cortical and chromaffin tissues come together to form adrenal glands in tetrapods.[well established][VHOG] - The origin of the adrenal gland is still controversial. It is thought to share the same origin as the kidney and gonads, derived from coelomic epithelium of the urogenital ridge and/or the underlying mesenchyme (Keegan and Hammer, 2002; Morohashi, 1997). We follow Kardong and state homology at the level of the cortex and medulla rather than gland as a whole - suprarenal cortex manufactures corticosteroids; suprarenal medulla manufactures epinephrine and norepinephrine; suprarenal medulla receives preganglionic sympathetic innervation from the greater thoracic splanchnic n. - - - - - AAO:0010551 - BTO:0000047 - CALOHA:TS-0016 - EFO:0000238 - EMAPA:18426 - EV:0100135 - FMA:9604 - GAID:446 - MA:0000116 - MAT:0000071 - MESH:A06.407.071 - MIAA:0000071 - OpenCyc:Mx4rvXYiz5wpEbGdrcN5Y29ycA - UMLS:C0001625 - VHOG:0001141 - XAO:0000164 - galen:AdrenalGland - glandula adrenalis - glandula suprarenalis - uberon - adrenal - adrenal capsule - adrenal medulla cell - atrabiliary capsule - epinephric gland - epinephros - glandula suprarenalis - interrenal gland - suprarenal capsule - suprarenal gland - UBERON:0002369 - - - adrenal gland - - - - - - - - - - - - The abdominal segment of the torso. - - - EMAPA:35104 - FMA:259211 - MA:0000021 - uberon - abdomen/pelvis/perineum - lower body - lumbar region - UBERON:0002417 - - abdominal segment of trunk - - - - - - - - - A gland is an organ in an animal's body that synthesizes a substance for release such as hormones or breast milk, often into the bloodstream (endocrine gland) or into cavities inside the body or its outer surface (exocrine gland). A gland is an organ specialised for secretion[GO]. - glandular - UBERON:MIAA_0000021 - - - - - AAO:0000212 - AEO:0000096 - BTO:0000522 - EFO:0000797 - EHDAA2:0003096 - EHDAA:2161 - EHDAA:4475 - EHDAA:6522 - EMAPA:18425 - FBbt:00100317 - FMA:86294 - HAO:0000375 - MA:0003038 - MAT:0000021 - MIAA:0000021 - OpenCyc:Mx4rwP3vyJwpEbGdrcN5Y29ycA - UMLS:C1285092 - WikipediaCategory:Glands - galen:Gland - uberon - Druese - glandula - UBERON:0002530 - - - - gland - - - - - - - - - - - - - - - - This gland can either be a discrete structure located bilaterally above each kidney, or a cluster of cells in the head kidney that perform the functions of the adrenal gland. In either case, this organ consists of two cells types, aminergic chromaffin cells and steroidogenic cortical cells[GO] - keep this grouping class so long as it is required for GO - All craniates have groups of cells homologous to the mammalian adrenocortical and chromaffin tissues, but they are scattered in and near the kidneys in fishes. (...) The cortical and chromaffin tissues come together to form adrenal glands in tetrapods.[well established][VHOG] - VHOG:0001141 - adrenal gland - interrenal gland - adrenal gland/interrenal tissue - uberon - adrenal - interrenal gland - suprarenal gland - interrenal gland - UBERON:0006858 - - - - adrenal/interrenal gland - - - - - - - - - - - - - - - - FMA:25054 - region of trunk - trunk subdivision - uberon - UBERON:0009569 - - - subdivision of trunk @@ -1184,91 +206,11 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - - An anatomical structure that has more than one cell as a part. - CARO:0010000 - FBbt:00100313 - multicellular structure - uberon - UBERON:0010000 - - - multicellular anatomical structure - - - - - - - - - - - - - - - A major subdivision of an organism that divides an organism along its main body axis (typically anterio-posterior axis). In vertebrates, this is based on the vertebral column. - Ideally this would be disjoint with analagous class for appendicular axes, but currently 'appendages' like antennae, horns cause a problem - axial subdivision of organism - uberon - body segment - main body segment - UBERON:0011676 - - subdivision of organism along main body axis - - - - - A principle subdivision of an organism that includes all structures along the primary axis, typically the anterior-posterior axis, from head to tail, including structures of the body proper where present (for example, ribs), but excluding appendages. - uberon - UBERON:0013701 - - main body axis - - - - - - - - - - - - - - - The region of the organism associated with the visceral organs. - Cardinal body part, which consists of a maximal set of diverse subclasses of organ and organ part spatially associated with the vertebral column and ribcage. Examples: There is only one body proper[FMA:231424]. - AEO:0000103 - BTO:0001489 - FMA:231424 - uberon - body - whole body - UBERON:0013702 - - - body proper - - - - - - - - - - - - + + + + dummy individal 5 + - diff --git a/docs/examples/example2_derived_from.owl b/docs/examples/example2_derived_from.owl index de79486d7..7230cadb2 100644 --- a/docs/examples/example2_derived_from.owl +++ b/docs/examples/example2_derived_from.owl @@ -6,7 +6,6 @@ xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:xml="http://www.w3.org/XML/1998/namespace" xmlns:xsd="http://www.w3.org/2001/XMLSchema#" - xmlns:foaf="http://xmlns.com/foaf/0.1/" xmlns:prov="http://www.w3.org/ns/prov#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> @@ -51,5499 +50,239 @@ - IAO:0000116 uberon - editor_note - true - editor_note editor note - - editor note - - - - - - - - - - - - IAO:0000116 - - - - - - uberon - - - - - - editor_note - - - - - - true - - - - - - editor_note - - - - - - - - - - - - - - - IAO:0000232 - uberon - curator_notes - true - curator_notes - curator notes - - - - - - - - - - - IAO:0000232 - - - - - - uberon - - - - - - curator_notes - - - - - - true - - - - - - curator_notes - - - - - - curator notes - - - - - - - - - An alternate textual definition for a class taken unmodified from an external source. This definition may have been used to derive a generalized definition for the new class. - UBPROP:0000001 - uberon - external_definition - true - external_definition - This annotation property may be replaced with an annotation property from an external ontology such as IAO - external_definition - - - - - - - - - - - An alternate textual definition for a class taken unmodified from an external source. This definition may have been used to derive a generalized definition for the new class. - - - - - - UBPROP:0000001 - - - - - - uberon - - - - - - external_definition - - - - - - true - - - - - - external_definition - - - - - - This annotation property may be replaced with an annotation property from an external ontology such as IAO - - - - - - external_definition - - - - - - - - - Notes on the homology status of this class. - UBPROP:0000003 - uberon - homology_notes - true - homology_notes - This annotation property may be replaced with an annotation property from an external ontology such as IAO - homology_notes - - - - - - - - - - - Notes on the homology status of this class. - - - - - - UBPROP:0000003 - - - - - - uberon - - - - - - homology_notes - - - - - - true - - - - - - homology_notes - - - - - - This annotation property may be replaced with an annotation property from an external ontology such as IAO - - - - - - homology_notes - - - - - - - - - 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'. - UBPROP:0000007 - uberon - has_relational_adjective - true - 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'. - - - - - - UBPROP:0000007 - - - - - - uberon - - - - - - has_relational_adjective - - - - - - true - - - - - - has_relational_adjective - - - - - - has_relational_adjective - - - - - - - - - Notes on the how instances of this class vary across species. - UBPROP:0000008 - uberon - taxon_notes - true - taxon_notes - taxon_notes - - - - - - - - - - - Notes on the how instances of this class vary across species. - - - - - - UBPROP:0000008 - - - - - - uberon - - - - - - taxon_notes - - - - - - true - - - - - - taxon_notes - - - - - - taxon_notes - - - - - - - - - Notes on the evolved function of instances of this class. - This annotation property may be replaced with an annotation property from an external ontology such as IAO - UBPROP:0000009 - uberon - function_notes - true - function_notes - function_notes - - - - - - - - - - - Notes on the evolved function of instances of this class. - - - - - - This annotation property may be replaced with an annotation property from an external ontology such as IAO - - - - - - UBPROP:0000009 - - - - - - uberon - - - - - - function_notes - - - - - - true - - - - - - function_notes - - - - - - function_notes - - - - - - - - - Notes on how similar or equivalent classes are represented in other ontologies. - This annotation property may be replaced with an annotation property from an external ontology such as IAO - UBPROP:0000012 - uberon - external_ontology_notes - true - external_ontology_notes - external_ontology_notes - - - - - - - - - - - Notes on how similar or equivalent classes are represented in other ontologies. - - - - - - This annotation property may be replaced with an annotation property from an external ontology such as IAO - - - - - - UBPROP:0000012 - - - - - - uberon - - - - - - external_ontology_notes - - - - - - true - - - - - - external_ontology_notes - - - - - - external_ontology_notes - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - BFO:0000050 - uberon - part_of - part_of - part_of - - - - - - - - - - - - - - - - - BFO:0000050 - - - - - - uberon - - - - - - part_of - - - - - - part_of - - - - - - part_of - - - - - - - - - - X outer_layer_of Y iff: -. X :continuant that bearer_of some PATO:laminar -. X part_of Y -. exists Z :surface -. X has_boundary Z -. Z boundary_of Y - -has_boundary: http://purl.obolibrary.org/obo/RO_0002002 -boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - RO:0002007 - uberon - bounding_layer_of - bounding_layer_of - 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. - bounding layer of - - - - - - - - - - - - - - - - - X outer_layer_of Y iff: -. X :continuant that bearer_of some PATO:laminar -. X part_of Y -. exists Z :surface -. X has_boundary Z -. Z boundary_of Y - -has_boundary: http://purl.obolibrary.org/obo/RO_0002002 -boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - - - - - - RO:0002007 - - - - - - uberon - - - - - - bounding_layer_of - - - - - - bounding_layer_of - - - - - - 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. - - - - - - bounding layer of - - - - - - - - - - - - - - - Material anatomical entity that has inherent 3D shape and is generated by coordinated expression of the organism's own genome. - - - AAO:0010825 - AEO:0000003 - BILA:0000003 - CARO:0000003 - EHDAA2:0003003 - EMAPA:0 - FBbt:00007001 - FMA:67135 - GAID:781 - HAO:0000003 - MA:0003000 - MESH:A13 - TAO:0000037 - TGMA:0001823 - VHOG:0001759 - WBbt:0000100 - XAO:0003000 - ZFA:0000037 - biological structure - uberon - UBERON:0000061 - - - anatomical structure - - - - - - - - - - - Material anatomical entity that has inherent 3D shape and is generated by coordinated expression of the organism's own genome. - - - - - - - - - - - - - - - - - - AAO:0010825 - - - - - - AEO:0000003 - - - - - - BILA:0000003 - - - - - - CARO:0000003 - - - - - - EHDAA2:0003003 - - - - - - EMAPA:0 - - - - - - FBbt:00007001 - - - - - - FMA:67135 - - - - - - GAID:781 - - - - - - HAO:0000003 - - - - - - MA:0003000 - - - - - - MESH:A13 - - - - - - TAO:0000037 - - - - - - TGMA:0001823 - - - - - - VHOG:0001759 - - - - - - WBbt:0000100 - - - - - - XAO:0003000 - - - - - - ZFA:0000037 - - - - - - biological structure - - - - - - uberon - - - - - - UBERON:0000061 - - - - - - - - - - - - - - - - - - anatomical structure - - - - - - - - - - - - - - - - - - - - - - Anatomical structure that performs a specific function or group of functions [WP]. - Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions. - CARO does not include a generic 'organ' class, only simple and compound organ - - - - - - EFO:0000634 - EMAPA:35949 - ENVO:01000162 - FMA:67498 - MA:0003001 - OpenCyc:Mx4rv5XMb5wpEbGdrcN5Y29ycA - OpenCyc:Mx4rwP3iWpwpEbGdrcN5Y29ycA - UMLS:C0178784 - WBbt:0003760 - uberon - anatomical unit - body organ - element - UBERON:0000062 - - organ - - - - - - - - - - - - - - - - - - - - - - - - - - - - Anatomical structure that performs a specific function or group of functions [WP]. - - - - - - Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions. - - - - - - CARO does not include a generic 'organ' class, only simple and compound organ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - EFO:0000634 - - - - - - EMAPA:35949 - - - - - - ENVO:01000162 - - - - - - FMA:67498 - - - - - - MA:0003001 - - - - - - OpenCyc:Mx4rv5XMb5wpEbGdrcN5Y29ycA - - - - - - OpenCyc:Mx4rwP3iWpwpEbGdrcN5Y29ycA - - - - - - UMLS:C0178784 - - - - - - WBbt:0003760 - - - - - - uberon - - - - - - anatomical unit - - - - - - body organ - - - - - - element - - - - - - UBERON:0000062 - - - - - - - - - - - - organ - - - - - - - - - - - - - - - - Anatomical structure which has as its direct parts two or more types of tissue and is continuous with one or more anatomical structures likewise constituted by two or more portions of tissues distinct from those of their complement. Examples: osteon, cortical bone, neck of femur, bronchopulmonary segment, left lobe of liver, anterior right side of heart, interventricular branch of left coronary artery, right atrium, mitral valve, head of pancreas[FMA]. - - - - AAO:0011124 - EFO:0000635 - FMA:82472 - cardinal organ part - uberon - regional part of organ - UBERON:0000064 - - - - organ part - - - - - - - - - - - - - - - - - - - - - - - - - - - - Anatomical structure which has as its direct parts two or more types of tissue and is continuous with one or more anatomical structures likewise constituted by two or more portions of tissues distinct from those of their complement. Examples: osteon, cortical bone, neck of femur, bronchopulmonary segment, left lobe of liver, anterior right side of heart, interventricular branch of left coronary artery, right atrium, mitral valve, head of pancreas[FMA]. - - - - - - - - - - - - - - - - - - - - - - - - AAO:0011124 - - - - - - EFO:0000635 - - - - - - FMA:82472 - - - - - - cardinal organ part - - - - - - uberon - - - - - - regional part of organ - - - - - - UBERON:0000064 - - - - - - - - - - - - - - - - - - - - - - - - organ part - - - - - - - - - - Anatomical entity that has mass. - AAO:0010264 - AEO:0000006 - BILA:0000006 - CARO:0000006 - EHDAA2:0003006 - FBbt:00007016 - FMA:67165 - HAO:0000006 - TAO:0001836 - TGMA:0001826 - VHOG:0001721 - uberon - UBERON:0000465 - - material anatomical entity - - - - - - - - - - - - - - - - - Anatomical entity that has mass. - - - - - - AAO:0010264 - - - - - - AEO:0000006 - - - - - - BILA:0000006 - - - - - - CARO:0000006 - - - - - - EHDAA2:0003006 - - - - - - FBbt:00007016 - - - - - - FMA:67165 - - - - - - HAO:0000006 - - - - - - TAO:0001836 - - - - - - TGMA:0001826 - - - - - - VHOG:0001721 - - - - - - uberon - - - - - - UBERON:0000465 - - - - - - - - - - - - material anatomical entity - - - - - - - - - - - - - - - - Anatomical group that is has as its parts distinct anatomical structures interconnected by anatomical structures at a lower level of granularity[CARO]. A group of organs that work together to perform a certain task [Wikipedia]. - system - - - - - - AAO:0000007 - AEO:0000011 - BILA:0000011 - BSA:0000049 - CALOHA:TS-2088 - CARO:0000011 - EHDAA2:0003011 - EHDAA:392 - EMAPA:16103 - EV:0100000 - FBbt:00004856 - FMA:7149 - HAO:0000011 - MA:0000003 - OpenCyc:Mx4rCWM0QCtDEdyAAADggVbxzQ - TAO:0001439 - TGMA:0001831 - UMLS:C0460002 - VHOG:0001725 - WBbt:0005746 - WBbt:0005763 - XAO:0003002 - ZFA:0001439 - galen:AnatomicalSystem - body system - organ system - uberon - UBERON:0000467 - - - anatomical system - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Anatomical group that is has as its parts distinct anatomical structures interconnected by anatomical structures at a lower level of granularity[CARO]. A group of organs that work together to perform a certain task [Wikipedia]. - - - - - - system - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAO:0000007 - - - - - - AEO:0000011 - - - - - - BILA:0000011 - - - - - - BSA:0000049 - - - - - - CALOHA:TS-2088 - - - - - - CARO:0000011 - - - - - - EHDAA2:0003011 - - - - - - EHDAA:392 - - - - - - EMAPA:16103 - - - - - - EV:0100000 - - - - - - FBbt:00004856 - - - - - - FMA:7149 - - - - - - HAO:0000011 - - - - - - MA:0000003 - - - - - - OpenCyc:Mx4rCWM0QCtDEdyAAADggVbxzQ - - - - - - TAO:0001439 - - - - - - TGMA:0001831 - - - - - - UMLS:C0460002 - - - - - - VHOG:0001725 - - - - - - WBbt:0005746 - - - - - - WBbt:0005763 - - - - - - XAO:0003002 - - - - - - ZFA:0001439 - - - - - - galen:AnatomicalSystem - - - - - - body system - - - - - - organ system - - - - - - uberon - - - - - - UBERON:0000467 - - - - - - - - - - - - - - - - - - anatomical system - - - - - - - - - - - - - - - - Anatomical structure that is an individual member of a species and consists of more than one cell. - TODO - split body and mc organism? body continues after death stage - organismal - - - - - AAO:0010026 - AEO:0000191 - BILA:0000012 - BSA:0000038 - BTO:0000042 - CARO:0000012 - EFO:0002906 - EHDAA2:0003103 - EHDAA2:0003191 - EHDAA:1 - EHDAA:9178 - EMAPA:25765 - EV:0100016 - FBbt:00000001 - FMA:256135 - HAO:0000012 - TADS:0000001 - TAO:0001094 - TGMA:0001832 - VHOG:0000671 - WBbt:0007833 - XAO:0003004 - ZFA:0001094 - galen:Organism - multi-cellular organism - organism - whole organism - animal - uberon - Koerper - body - whole body - UBERON:0000468 - - - - multicellular organism - - - - - - - - - - - - - - - - - Anatomical structure that is an individual member of a species and consists of more than one cell. - - - - - - TODO - split body and mc organism? body continues after death stage - - - - - - organismal - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAO:0010026 - - - - - - AEO:0000191 - - - - - - BILA:0000012 - - - - - - BSA:0000038 - - - - - - BTO:0000042 - - - - - - CARO:0000012 - - - - - - EFO:0002906 - - - - - - EHDAA2:0003103 - - - - - - EHDAA2:0003191 - - - - - - EHDAA:1 - - - - - - EHDAA:9178 - - - - - - EMAPA:25765 - - - - - - EV:0100016 - - - - - - FBbt:00000001 - - - - - - FMA:256135 - - - - - - HAO:0000012 - - - - - - TADS:0000001 - - - - - - TAO:0001094 - - - - - - TGMA:0001832 - - - - - - VHOG:0000671 - - - - - - WBbt:0007833 - - - - - - XAO:0003004 - - - - - - ZFA:0001094 - - - - - - galen:Organism - - - - - - multi-cellular organism - - - - - - organism - - - - - - whole organism - - - - - - animal - - - - - - uberon - - - - - - Koerper - - - - - - body - - - - - - whole body - - - - - - UBERON:0000468 - - - - - - - - - - - - - - - - - - - - - - - - multicellular organism - - - - - - - - - - Anatomical structure which is a subdivision of a whole organism, consisting of components of multiple anatomical systems, largely surrounded by a contiguous region of integument. - Reflects CARO2. todo - check the inclusion of FMA 'cardinal body part here', and check child terms for consistency - - - - - AAO:0010053 - AEO:0000032 - BILA:0000032 - CALOHA:TS-2084 - CARO:0000032 - EFO:0000808 - EHDAA2:0003032 - FBbt:00007009 - FMA:7153 - HAO:0000032 - MA:0002433 - MAT:0000293 - MESH:A01 - MIAA:0000293 - OpenCyc:Mx4rvViAHJwpEbGdrcN5Y29ycA - TAO:0001308 - TGMA:0001840 - UMLS:C0229962 - VHOG:0001758 - XAO:0003013 - ZFA:0001308 - galen:BodyPart - anatomic region - uberon - body part - body region - cardinal body part - UBERON:0000475 - - - - organism subdivision - - - - - - - - - - - - - - - - - Anatomical structure which is a subdivision of a whole organism, consisting of components of multiple anatomical systems, largely surrounded by a contiguous region of integument. - - - - - - Reflects CARO2. todo - check the inclusion of FMA 'cardinal body part here', and check child terms for consistency - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAO:0010053 - - - - - - AEO:0000032 - - - - - - BILA:0000032 - - - - - - CALOHA:TS-2084 - - - - - - CARO:0000032 - - - - - - EFO:0000808 - - - - - - EHDAA2:0003032 - - - - - - FBbt:00007009 - - - - - - FMA:7153 - - - - - - HAO:0000032 - - - - - - MA:0002433 - - - - - - MAT:0000293 - - - - - - MESH:A01 - - - - - - MIAA:0000293 - - - - - - OpenCyc:Mx4rvViAHJwpEbGdrcN5Y29ycA - - - - - - TAO:0001308 - - - - - - TGMA:0001840 - - - - - - UMLS:C0229962 - - - - - - VHOG:0001758 - - - - - - XAO:0003013 - - - - - - ZFA:0001308 - - - - - - galen:BodyPart - - - - - - anatomic region - - - - - - uberon - - - - - - body part - - - - - - body region - - - - - - cardinal body part - - - - - - UBERON:0000475 - - - - - - - - - - - - - - - - - - - - - - - - organism subdivision - - - - - - - - - - Anatomical structure consisting of at least two non-overlapping organs, multi-tissue aggregates or portion of tissues or cells of different types that does not constitute an organism, organ, multi-tissue aggregate, or portion of tissue. - AAO:0010008 - AEO:0000054 - BILA:0000054 - CARO:0000054 - EHDAA2:0003054 - HAO:0000054 - TAO:0001512 - TGMA:0001846 - VHOG:0001724 - XAO:0003001 - ZFA:0001512 - uberon - UBERON:0000480 - - anatomical group - - - - - - - - - - - - - - - - - Anatomical structure consisting of at least two non-overlapping organs, multi-tissue aggregates or portion of tissues or cells of different types that does not constitute an organism, organ, multi-tissue aggregate, or portion of tissue. - - - - - - AAO:0010008 - - - - - - AEO:0000054 - - - - - - BILA:0000054 - - - - - - CARO:0000054 - - - - - - EHDAA2:0003054 - - - - - - HAO:0000054 - - - - - - TAO:0001512 - - - - - - TGMA:0001846 - - - - - - VHOG:0001724 - - - - - - XAO:0003001 - - - - - - ZFA:0001512 - - - - - - uberon - - - - - - UBERON:0000480 - - - - - - - - - - - - anatomical group - - - - - - - - - - - - - - - - The subdivision of the vertebrate body between the thorax and pelvis. The ventral part of the abdomen contains the abdominal cavity and visceral organs. The dorsal part includes the abdominal section of the vertebral column. - Vertebrate specific. In arthropods 'abdomen' is the most distal section of the body which lies behind the thorax or cephalothorax. If need be we can introduce some grouping class - abdominal - - - BTO:0000020 - CALOHA:TS-0001 - EFO:0000968 - EMAPA:35102 - EV:0100011 - FMA:9577 - GAID:16 - MA:0000029 - MAT:0000298 - MESH:A01.047 - MIAA:0000298 - OpenCyc:Mx4rvVjgyZwpEbGdrcN5Y29ycA - galen:Abdomen - abdominopelvic region - abdominopelvis - uberon - adult abdomen - belly - celiac region - UBERON:0000916 - - - abdomen - - - - - - - - - - - - - - - - - - - - - - - - - - - - The subdivision of the vertebrate body between the thorax and pelvis. The ventral part of the abdomen contains the abdominal cavity and visceral organs. The dorsal part includes the abdominal section of the vertebral column. - - - - - - Vertebrate specific. In arthropods 'abdomen' is the most distal section of the body which lies behind the thorax or cephalothorax. If need be we can introduce some grouping class - - - - - - abdominal - - - - - - - - - - - - - - - - - - BTO:0000020 - - - - - - CALOHA:TS-0001 - - - - - - EFO:0000968 - - - - - - EMAPA:35102 - - - - - - EV:0100011 - - - - - - FMA:9577 - - - - - - GAID:16 - - - - - - MA:0000029 - - - - - - MAT:0000298 - - - - - - MESH:A01.047 - - - - - - MIAA:0000298 - - - - - - OpenCyc:Mx4rvVjgyZwpEbGdrcN5Y29ycA - - - - - - galen:Abdomen - - - - - - abdominopelvic region - - - - - - abdominopelvis - - - - - - uberon - - - - - - adult abdomen - - - - - - belly - - - - - - celiac region - - - - - - UBERON:0000916 - - - - - - - - - - - - - - - - - - abdomen - - - - - - - - - - Anatomical system that consists of the glands and parts of glands that produce endocrine secretions and help to integrate and control bodily metabolic activity. - Anatomical system containing glands which regulates bodily functions though the secretion of hormones.[AAO] - Multicellular organisms have complex endocrine systems, allowing responses to environmental stimuli, regulation of development, reproduction, and homeostasis. Nuclear receptors (NRs), a metazoan-specific family of ligand-activated transcription factors, play central roles in endocrine responses, as intermediates between signaling molecules and target genes. The NR family includes ligand-bound and orphan receptors, that is, receptors with no known ligand or for which there is no ligand Pocket. Understanding NR evolution has been further improved by comparison of several completed genomes, particularly those of deuterostomes and ecdysozoans. In contrast, evolution of NR ligands is still much debated. One hypothesis proposes that several independent gains and losses of ligand-binding ability in NRs occurred in protostomes and deuterostomes. A second hypothesis, pertaining to the NR3 subfamily (vertebrate steroid hormone receptors and estrogen related receptor), proposes that before the divergence of protostomes and deuterostomes, there was an ancestral steroid receptor (AncSR) that was ligand-activated and that orphan receptors secondarily lost the ability to bind a ligand. (...) Our analysis reveals that steroidogenesis has been independently elaborated in the 3 main bilaterian lineages (...).[well established][VHOG] - endocrine - - - - - AAO:0010279 - CALOHA:TS-1301 - EFO:0002969 - EHDAA2:0002224 - EMAPA:35306 - EV:0100128 - FBbt:00005068 - FMA:9668 - GAID:439 - MA:0000012 - MESH:A06 - TAO:0001158 - UMLS:C0014136 - VHOG:0000098 - XAO:0000158 - ZFA:0001158 - endocrine glandular system - endocrine system - systema endocrinum - uberon - UBERON:0000949 - - - - endocrine system - - - - - - - - - - - - - - - - - Anatomical system that consists of the glands and parts of glands that produce endocrine secretions and help to integrate and control bodily metabolic activity. - - - - - - Anatomical system containing glands which regulates bodily functions though the secretion of hormones.[AAO] - - - - - - Multicellular organisms have complex endocrine systems, allowing responses to environmental stimuli, regulation of development, reproduction, and homeostasis. Nuclear receptors (NRs), a metazoan-specific family of ligand-activated transcription factors, play central roles in endocrine responses, as intermediates between signaling molecules and target genes. The NR family includes ligand-bound and orphan receptors, that is, receptors with no known ligand or for which there is no ligand Pocket. Understanding NR evolution has been further improved by comparison of several completed genomes, particularly those of deuterostomes and ecdysozoans. In contrast, evolution of NR ligands is still much debated. One hypothesis proposes that several independent gains and losses of ligand-binding ability in NRs occurred in protostomes and deuterostomes. A second hypothesis, pertaining to the NR3 subfamily (vertebrate steroid hormone receptors and estrogen related receptor), proposes that before the divergence of protostomes and deuterostomes, there was an ancestral steroid receptor (AncSR) that was ligand-activated and that orphan receptors secondarily lost the ability to bind a ligand. (...) Our analysis reveals that steroidogenesis has been independently elaborated in the 3 main bilaterian lineages (...).[well established][VHOG] - - - - - - endocrine - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAO:0010279 - - - - - - CALOHA:TS-1301 - - - - - - EFO:0002969 - - - - - - EHDAA2:0002224 - - - - - - EMAPA:35306 - - - - - - EV:0100128 - - - - - - FBbt:00005068 - - - - - - FMA:9668 - - - - - - GAID:439 - - - - - - MA:0000012 - - - - - - MESH:A06 - - - - - - TAO:0001158 - - - - - - UMLS:C0014136 - - - - - - VHOG:0000098 - - - - - - XAO:0000158 - - - - - - ZFA:0001158 - - - - - - endocrine glandular system - - - - - - endocrine system - - - - - - systema endocrinum - - - - - - uberon - - - - - - UBERON:0000949 - - - - - - - - - - - - - - - - - - - - - - - - endocrine system - - - - - - - - - - Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species. - - - - AAO:0010841 - AEO:0000000 - BILA:0000000 - CARO:0000000 - EHDAA2:0002229 - FBbt:10000000 - FBbt_root:00000000 - FMA:62955 - HAO:0000000 - MA:0000001 - TAO:0100000 - TGMA:0001822 - UMLS:C1515976 - XAO:0000000 - ZFA:0100000 - uberon - UBERON:0001062 - - anatomical entity - - - - - - - - - - - - - - - - - Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species. - - - - - - - - - - - - - - - - - - - - - - - - AAO:0010841 - - - - - - AEO:0000000 - - - - - - BILA:0000000 - - - - - - CARO:0000000 - - - - - - EHDAA2:0002229 - - - - - - FBbt:10000000 - - - - - - FBbt_root:00000000 - - - - - - FMA:62955 - - - - - - HAO:0000000 - - - - - - MA:0000001 - - - - - - TAO:0100000 - - - - - - TGMA:0001822 - - - - - - UMLS:C1515976 - - - - - - XAO:0000000 - - - - - - ZFA:0100000 - - - - - - uberon - - - - - - UBERON:0001062 - - - - - - - - - - - - anatomical entity - - - - - - - - - - - - - - - - - - - - - Situated along the perimeter of the adrenal gland, the adrenal cortex mediates the stress response through the production of mineralocorticoids and glucocorticoids, including aldosterone and cortisol respectively. It is also a secondary site of androgen synthesis. [WP,unvetted]. - All craniates have groups of cells homologous to the mammalian adrenocortical and chromaffin tissues (medulla), but they are scattered in and near the kidneys in fishes. (...) The cortical and chromaffin tissues come together to form adrenal glands in tetrapods.[well established][VHOG] - Kardong states that mammals are the first to have distinct cortext and medulla, but this contradicts XAO - - - - - AAO:0011009 - BTO:0000045 - CALOHA:TS-0015 - EFO:0000237 - EMAPA:18427 - EV:0100136 - FMA:15632 - GAID:447 - MA:0000118 - MAT:0000494 - MESH:A06.407.071.140 - UMLS:C0001613 - VHOG:0001481 - XAO:0000165 - adrenal gland cortex - cortex (glandula suprarenalis) - cortex of adrenal gland - cortex of suprarenal gland - suprarenal cortex - uberon - cortex glandulae suprarenalis - suprarenal - UBERON:0001235 - - - adrenal cortex - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Situated along the perimeter of the adrenal gland, the adrenal cortex mediates the stress response through the production of mineralocorticoids and glucocorticoids, including aldosterone and cortisol respectively. It is also a secondary site of androgen synthesis. [WP,unvetted]. - - - - - - All craniates have groups of cells homologous to the mammalian adrenocortical and chromaffin tissues (medulla), but they are scattered in and near the kidneys in fishes. (...) The cortical and chromaffin tissues come together to form adrenal glands in tetrapods.[well established][VHOG] - - - - - - Kardong states that mammals are the first to have distinct cortext and medulla, but this contradicts XAO - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAO:0011009 - - - - - - BTO:0000045 - - - - - - CALOHA:TS-0015 - - - - - - EFO:0000237 - - - - - - EMAPA:18427 - - - - - - EV:0100136 - - - - - - FMA:15632 - - - - - - GAID:447 - - - - - - MA:0000118 - - - - - - MAT:0000494 - - - - - - MESH:A06.407.071.140 - - - - - - UMLS:C0001613 - - - - - - VHOG:0001481 - - - - - - XAO:0000165 - - - - - - adrenal gland cortex - - - - - - cortex (glandula suprarenalis) - - - - - - cortex of adrenal gland - - - - - - cortex of suprarenal gland - - - - - - suprarenal cortex - - - - - - uberon - - - - - - cortex glandulae suprarenalis - - - - - - suprarenal - - - - - - UBERON:0001235 - - - - - - - - - - - - - - - - - - adrenal cortex - - - - - - - - - - - - - - - - - - - - - - - - - - - - Outermost layer of an organ[WP]. - cortical - this class is used more generically than in FMA, and includes e.g. cortex of hair - - EFO:0000383 - EHDAA:9344 - FMA:61109 - galen:Cortex - cortex - cortex of organ - uberon - UBERON:0001851 - - - cortex - - - - - - - - - - - - - - - - - - - - - - - - - - - - Outermost layer of an organ[WP]. - - - - - - cortical - - - - - - this class is used more generically than in FMA, and includes e.g. cortex of hair - - - - - - - - - - - - EFO:0000383 - - - - - - EHDAA:9344 - - - - - - FMA:61109 - - - - - - galen:Cortex - - - - - - cortex - - - - - - cortex of organ - - - - - - uberon - - - - - - UBERON:0001851 - - - - - - - - - - - - - - - - - - cortex - - - - - - - - - - - - - - - - Organism subdivision which is the part of the body posterior to the cervical region (or head, when cervical region not present) and anterior to the caudal region. Includes the sacrum when present. - Organism subdivision that is the part of the body posterior to the head and anterior to the tail.[AAO] - Organism subdivision which is the part of the body posterior to the head and anterior to the tail.[TAO] - - - - - AAO:0010339 - BILA:0000116 - BTO:0001493 - CALOHA:TS-1071 - EFO:0000966 - EMAPA:31857 - FMA:7181 - MA:0000004 - MAT:0000296 - MIAA:0000296 - OpenCyc:Mx4rvVkJjpwpEbGdrcN5Y29ycA - TAO:0001115 - UMLS:C0460005 - XAO:0000054 - XAO:0003025 - ZFA:0001115 - galen:Trunk - thoracolumbar region - torso - trunk region - uberon - Rumpf - UBERON:0002100 - - - - trunk - - - - - - - - - - - - - - - - - - - - - - - - - - - - Organism subdivision which is the part of the body posterior to the cervical region (or head, when cervical region not present) and anterior to the caudal region. Includes the sacrum when present. - - - - - - Organism subdivision that is the part of the body posterior to the head and anterior to the tail.[AAO] - - - - - - Organism subdivision which is the part of the body posterior to the head and anterior to the tail.[TAO] - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAO:0010339 - - - - - - BILA:0000116 - - - - - - BTO:0001493 - - - - - - CALOHA:TS-1071 - - - - - - EFO:0000966 - - - - - - EMAPA:31857 - - - - - - FMA:7181 - - - - - - MA:0000004 - - - - - - MAT:0000296 - - - - - - MIAA:0000296 - - - - - - OpenCyc:Mx4rvVkJjpwpEbGdrcN5Y29ycA - - - - - - TAO:0001115 - - - - - - UMLS:C0460005 - - - - - - XAO:0000054 - - - - - - XAO:0003025 - - - - - - ZFA:0001115 - - - - - - galen:Trunk - - - - - - thoracolumbar region - - - - - - torso - - - - - - trunk region - - - - - - uberon - - - - - - Rumpf - - - - - - UBERON:0002100 - - - - - - - - - - - - - - - - - - - - - - - - trunk - - - - - - - - - - - - - - - - - - - - - - - - - - - Endocrine glands are glands of the endocrine system that secrete their products directly into the circulatory system rather than through a duct.[WP, modified]. - - - - - AEO:0000098 - BTO:0001488 - CALOHA:TS-1300 - EHDAA2:0003098 - EMAPA:35999 - FMA:9602 - GAID:335 - MA:0002563 - MESH:A06.407 - OpenCyc:Mx4rvbkiRZwpEbGdrcN5Y29ycA - UMLS:C0014133 - ductless gland - glandula endocrina - uberon - ductless gland - glandulae endocrinae - UBERON:0002368 - - - endocrine gland - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Endocrine glands are glands of the endocrine system that secrete their products directly into the circulatory system rather than through a duct.[WP, modified]. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AEO:0000098 - - - - - - BTO:0001488 - - - - - - CALOHA:TS-1300 - - - - - - EHDAA2:0003098 - - - - - - EMAPA:35999 - - - - - - FMA:9602 - - - - - - GAID:335 - - - - - - MA:0002563 - - - - - - MESH:A06.407 - - - - - - OpenCyc:Mx4rvbkiRZwpEbGdrcN5Y29ycA - - - - - - UMLS:C0014133 - - - - - - ductless gland - - - - - - glandula endocrina - - - - - - uberon - - - - - - ductless gland - - - - - - glandulae endocrinae - - - - - - UBERON:0002368 - - - - - - - - - - - - - - - - - - endocrine gland - - - - - - - - - - - - - - - - - - - - - - - - - - - - Either of a pair of complex endocrine organs near the anterior medial border of the kidney consisting of a mesodermal cortex that produces glucocorticoid, mineralocorticoid, and androgenic hormones and an ectodermal medulla that produces epinephrine and norepinephrine[BTO]. - Anatomical structure which is found on the surface of the kidney and secretes various hormones including epinephrine, norephinephrine, aldosterone, corticosterone, and cortisol.[AAO] - All craniates have groups of cells homologous to the mammalian adrenocortical and chromaffin tissues, but they are scattered in and near the kidneys in fishes. (...) The cortical and chromaffin tissues come together to form adrenal glands in tetrapods.[well established][VHOG] - The origin of the adrenal gland is still controversial. It is thought to share the same origin as the kidney and gonads, derived from coelomic epithelium of the urogenital ridge and/or the underlying mesenchyme (Keegan and Hammer, 2002; Morohashi, 1997). We follow Kardong and state homology at the level of the cortex and medulla rather than gland as a whole - suprarenal cortex manufactures corticosteroids; suprarenal medulla manufactures epinephrine and norepinephrine; suprarenal medulla receives preganglionic sympathetic innervation from the greater thoracic splanchnic n. - - - - - AAO:0010551 - BTO:0000047 - CALOHA:TS-0016 - EFO:0000238 - EMAPA:18426 - EV:0100135 - FMA:9604 - GAID:446 - MA:0000116 - MAT:0000071 - MESH:A06.407.071 - MIAA:0000071 - OpenCyc:Mx4rvXYiz5wpEbGdrcN5Y29ycA - UMLS:C0001625 - VHOG:0001141 - XAO:0000164 - galen:AdrenalGland - glandula adrenalis - glandula suprarenalis - uberon - adrenal - adrenal capsule - adrenal medulla cell - atrabiliary capsule - epinephric gland - epinephros - glandula suprarenalis - interrenal gland - suprarenal capsule - suprarenal gland - UBERON:0002369 - - - adrenal gland - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Either of a pair of complex endocrine organs near the anterior medial border of the kidney consisting of a mesodermal cortex that produces glucocorticoid, mineralocorticoid, and androgenic hormones and an ectodermal medulla that produces epinephrine and norepinephrine[BTO]. - - - - - - Anatomical structure which is found on the surface of the kidney and secretes various hormones including epinephrine, norephinephrine, aldosterone, corticosterone, and cortisol.[AAO] - - - - - - All craniates have groups of cells homologous to the mammalian adrenocortical and chromaffin tissues, but they are scattered in and near the kidneys in fishes. (...) The cortical and chromaffin tissues come together to form adrenal glands in tetrapods.[well established][VHOG] - - - - - - The origin of the adrenal gland is still controversial. It is thought to share the same origin as the kidney and gonads, derived from coelomic epithelium of the urogenital ridge and/or the underlying mesenchyme (Keegan and Hammer, 2002; Morohashi, 1997). We follow Kardong and state homology at the level of the cortex and medulla rather than gland as a whole - - - - - - suprarenal cortex manufactures corticosteroids; suprarenal medulla manufactures epinephrine and norepinephrine; suprarenal medulla receives preganglionic sympathetic innervation from the greater thoracic splanchnic n. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAO:0010551 - - - - - - BTO:0000047 - - - - - - CALOHA:TS-0016 - - - - - - EFO:0000238 - - - - - - EMAPA:18426 - - - - - - EV:0100135 - - - - - - FMA:9604 - - - - - - GAID:446 - - - - - - MA:0000116 - - - - - - MAT:0000071 - - - - - - MESH:A06.407.071 - - - - - - MIAA:0000071 - - - - - - OpenCyc:Mx4rvXYiz5wpEbGdrcN5Y29ycA - - - - - - UMLS:C0001625 - - - - - - VHOG:0001141 - - - - - - XAO:0000164 - - - - - - galen:AdrenalGland - - - - - - glandula adrenalis - - - - - - glandula suprarenalis - - - - - - uberon - - - - - - adrenal - - - - - - adrenal capsule - - - - - - adrenal medulla cell - - - - - - atrabiliary capsule - - - - - - epinephric gland - - - - - - epinephros - - - - - - glandula suprarenalis - - - - - - interrenal gland - - - - - - suprarenal capsule - - - - - - suprarenal gland - - - - - - UBERON:0002369 - - - - - - - - - - - - - - - - - - adrenal gland - - - - - - - - - - - - - - - - - - - - - - - The abdominal segment of the torso. - - - EMAPA:35104 - FMA:259211 - MA:0000021 - uberon - abdomen/pelvis/perineum - lower body - lumbar region - UBERON:0002417 - abdominal segment of trunk - - - - - - - - - - - - - - - - - - - - - - - The abdominal segment of the torso. - - - - - - - - - - - - - - - - - - EMAPA:35104 - - - - - - FMA:259211 - - - - - - MA:0000021 - - - - - - uberon - - - - - - abdomen/pelvis/perineum - - - - - - lower body - - - - - - lumbar region - - - - - - UBERON:0002417 - - - - - - abdominal segment of trunk - - - - - - - - - - A gland is an organ in an animal's body that synthesizes a substance for release such as hormones or breast milk, often into the bloodstream (endocrine gland) or into cavities inside the body or its outer surface (exocrine gland). A gland is an organ specialised for secretion[GO]. - glandular - UBERON:MIAA_0000021 - - - - - AAO:0000212 - AEO:0000096 - BTO:0000522 - EFO:0000797 - EHDAA2:0003096 - EHDAA:2161 - EHDAA:4475 - EHDAA:6522 - EMAPA:18425 - FBbt:00100317 - FMA:86294 - HAO:0000375 - MA:0003038 - MAT:0000021 - MIAA:0000021 - OpenCyc:Mx4rwP3vyJwpEbGdrcN5Y29ycA - UMLS:C1285092 - WikipediaCategory:Glands - galen:Gland - uberon - Druese - glandula - UBERON:0002530 - - - gland - - - - - - - - - - - - - - - - - - A gland is an organ in an animal's body that synthesizes a substance for release such as hormones or breast milk, often into the bloodstream (endocrine gland) or into cavities inside the body or its outer surface (exocrine gland). A gland is an organ specialised for secretion[GO]. - - - - - - glandular - - - - - - UBERON:MIAA_0000021 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAO:0000212 - - - - - - AEO:0000096 - - - - - - BTO:0000522 - - - - - - EFO:0000797 - - - - - - EHDAA2:0003096 - - - - - - EHDAA:2161 - - - - - - EHDAA:4475 - - - - - - EHDAA:6522 - - - - - - EMAPA:18425 - - - - - - FBbt:00100317 - - - - - - FMA:86294 - - - - - - HAO:0000375 - - - - - - MA:0003038 - - - - - - MAT:0000021 - - - - - - MIAA:0000021 - - - - - - OpenCyc:Mx4rwP3vyJwpEbGdrcN5Y29ycA - - - - - - UMLS:C1285092 - - - - - - WikipediaCategory:Glands - - - - - - galen:Gland - - - - - - uberon - - - - - - Druese - - - - - - glandula - - - - - - UBERON:0002530 - - - - - - - - - - - - - - - - - - gland - - - - - - - - - - - - - - - - - - - - - - This gland can either be a discrete structure located bilaterally above each kidney, or a cluster of cells in the head kidney that perform the functions of the adrenal gland. In either case, this organ consists of two cells types, aminergic chromaffin cells and steroidogenic cortical cells[GO] - keep this grouping class so long as it is required for GO - All craniates have groups of cells homologous to the mammalian adrenocortical and chromaffin tissues, but they are scattered in and near the kidneys in fishes. (...) The cortical and chromaffin tissues come together to form adrenal glands in tetrapods.[well established][VHOG] - VHOG:0001141 - adrenal gland - interrenal gland - adrenal gland/interrenal tissue - uberon - adrenal - interrenal gland - suprarenal gland - interrenal gland - UBERON:0006858 - - - adrenal/interrenal gland - - - - - - - - - - - - - - - - - - - - - - - - - - - - This gland can either be a discrete structure located bilaterally above each kidney, or a cluster of cells in the head kidney that perform the functions of the adrenal gland. In either case, this organ consists of two cells types, aminergic chromaffin cells and steroidogenic cortical cells[GO] - - - - - - keep this grouping class so long as it is required for GO - - - - - - All craniates have groups of cells homologous to the mammalian adrenocortical and chromaffin tissues, but they are scattered in and near the kidneys in fishes. (...) The cortical and chromaffin tissues come together to form adrenal glands in tetrapods.[well established][VHOG] - - - - - - VHOG:0001141 - - - - - - adrenal gland - interrenal gland - - - - - - adrenal gland/interrenal tissue - - - - - - uberon - - - - - - adrenal - interrenal gland - - - - - - suprarenal gland - interrenal gland - - - - - - UBERON:0006858 - - - - - - - - - - - - - - - - - - adrenal/interrenal gland - - - - - - - - - - - - - - - - - FMA:25054 - region of trunk - trunk subdivision - uberon - UBERON:0009569 - - subdivision of trunk - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - FMA:25054 - - - - - - region of trunk - - - - - - trunk subdivision + + - + uberon - - - UBERON:0009569 - - - - - - + + + - + - subdivision of trunk + editor note - + - - - An anatomical structure that has more than one cell as a part. - CARO:0010000 - FBbt:00100313 - multicellular structure + uberon - UBERON:0010000 - - multicellular anatomical structure - + curator notes + - + - - - - - - - - - - - - - An anatomical structure that has more than one cell as a part. - - - - - - CARO:0010000 - - - - - - FBbt:00100313 - - - - - - multicellular structure + - + uberon - - - UBERON:0010000 - - - - - - - - - - + - multicellular anatomical structure + curator notes - + - - - - - - - - - A major subdivision of an organism that divides an organism along its main body axis (typically anterio-posterior axis). In vertebrates, this is based on the vertebral column. - Ideally this would be disjoint with analagous class for appendicular axes, but currently 'appendages' like antennae, horns cause a problem - axial subdivision of organism - uberon - body segment - main body segment - UBERON:0011676 - - subdivision of organism along main body axis - + - + - - - - - - - - - - - - - - - - - - - - - - - - A major subdivision of an organism that divides an organism along its main body axis (typically anterio-posterior axis). In vertebrates, this is based on the vertebral column. - - - - - - Ideally this would be disjoint with analagous class for appendicular axes, but currently 'appendages' like antennae, horns cause a problem - - - - - - axial subdivision of organism - - - - - - uberon - - - - - - body segment + + + + + + + + + + + + + - - - main body segment + + + + + + + + + + + + + + + + part_of + - - - UBERON:0011676 + + + - - - + + + - + - subdivision of organism along main body axis + part_of - + + + + - - - A principle subdivision of an organism that includes all structures along the primary axis, typically the anterior-posterior axis, from head to tail, including structures of the body proper where present (for example, ribs), but excluding appendages. - uberon - UBERON:0013701 - main body axis + + + + + + anatomical structure - + - + - - - - - - - A principle subdivision of an organism that includes all structures along the primary axis, typically the anterior-posterior axis, from head to tail, including structures of the body proper where present (for example, ribs), but excluding appendages. - - - - - - uberon + - - - UBERON:0013701 + + + - + - main body axis + anatomical structure - + - - + + - + - The region of the organism associated with the visceral organs. - Cardinal body part, which consists of a maximal set of diverse subclasses of organ and organ part spatially associated with the vertebral column and ribcage. Examples: There is only one body proper[FMA:231424]. - AEO:0000103 - BTO:0001489 - FMA:231424 - uberon - body - whole body - UBERON:0013702 - - body proper + organ - + - + - + - + - + - - - The region of the organism associated with the visceral organs. - - - - - - Cardinal body part, which consists of a maximal set of diverse subclasses of organ and organ part spatially associated with the vertebral column and ribcage. Examples: There is only one body proper[FMA:231424]. - - - - - - AEO:0000103 - - - - - - BTO:0001489 - - - - - - FMA:231424 - - - - - - uberon - - - - - - body - - - - - - whole body - - - - - - UBERON:0013702 - - - - - - - - - - + - body proper + organ + + + + + + + + + + + + + + + + + + + + + dummy individal 5 + + + + + + + + + + + dummy individal 5 + + - diff --git a/docs/examples/merged_defined_by.owl b/docs/examples/merged_defined_by.owl index c870f41af..d988d4fa2 100644 --- a/docs/examples/merged_defined_by.owl +++ b/docs/examples/merged_defined_by.owl @@ -6,10 +6,13 @@ xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:xml="http://www.w3.org/XML/1998/namespace" xmlns:xsd="http://www.w3.org/2001/XMLSchema#" - xmlns:foaf="http://xmlns.com/foaf/0.1/" + xmlns:prov="http://www.w3.org/ns/prov#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + + + Comment from annotations.ttl file. + @@ -30,18 +33,20 @@ definition + + + + + + - IAO:0000116 uberon - editor_note - true - editor_note - + editor note @@ -50,111 +55,13 @@ - IAO:0000232 uberon - curator_notes - true - curator_notes curator notes - - - - An alternate textual definition for a class taken unmodified from an external source. This definition may have been used to derive a generalized definition for the new class. - UBPROP:0000001 - uberon - external_definition - true - external_definition - This annotation property may be replaced with an annotation property from an external ontology such as IAO - - external_definition - - - - - - - - Notes on the homology status of this class. - UBPROP:0000003 - uberon - homology_notes - true - homology_notes - This annotation property may be replaced with an annotation property from an external ontology such as IAO - - homology_notes - - - - - - - - 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'. - UBPROP:0000007 - uberon - has_relational_adjective - true - has_relational_adjective - - has_relational_adjective - - - - - - - - Notes on the how instances of this class vary across species. - UBPROP:0000008 - uberon - taxon_notes - true - taxon_notes - - taxon_notes - - - - - - - - Notes on the evolved function of instances of this class. - This annotation property may be replaced with an annotation property from an external ontology such as IAO - UBPROP:0000009 - uberon - function_notes - true - function_notes - - function_notes - - - - - - - - Notes on how similar or equivalent classes are represented in other ontologies. - This annotation property may be replaced with an annotation property from an external ontology such as IAO - UBPROP:0000012 - uberon - external_ontology_notes - true - external_ontology_notes - - external_ontology_notes - - - - @@ -163,38 +70,6 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - @@ -203,46 +78,6 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - @@ -251,25 +86,25 @@ - + - + - + - + - + - + @@ -286,14 +121,6 @@ - - - - - - - - @@ -317,40 +144,12 @@ - BFO:0000050 - uberon - part_of - part_of part_of - - - - - X outer_layer_of Y iff: -. X :continuant that bearer_of some PATO:laminar -. X part_of Y -. exists Z :surface -. X has_boundary Z -. Z boundary_of Y - -has_boundary: http://purl.obolibrary.org/obo/RO_0002002 -boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - RO:0002007 - uberon - bounding_layer_of - bounding_layer_of - 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. - - bounding layer of - - - - - - - - - - - - - - Anatomical structure which has as its direct parts two or more types of tissue and is continuous with one or more anatomical structures likewise constituted by two or more portions of tissues distinct from those of their complement. Examples: osteon, cortical bone, neck of femur, bronchopulmonary segment, left lobe of liver, anterior right side of heart, interventricular branch of left coronary artery, right atrium, mitral valve, head of pancreas[FMA]. - - - - AAO:0011124 - EFO:0000635 - FMA:82472 - cardinal organ part - uberon - regional part of organ - UBERON:0000064 - - - - - organ part - - - - - - Anatomical entity that has mass. - AAO:0010264 - AEO:0000006 - BILA:0000006 - CARO:0000006 - EHDAA2:0003006 - FBbt:00007016 - FMA:67165 - HAO:0000006 - TAO:0001836 - TGMA:0001826 - VHOG:0001721 - uberon - UBERON:0000465 - - material anatomical entity @@ -494,755 +198,95 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - - - - - - - - Anatomical group that is has as its parts distinct anatomical structures interconnected by anatomical structures at a lower level of granularity[CARO]. A group of organs that work together to perform a certain task [Wikipedia]. - system - - - - - - AAO:0000007 - AEO:0000011 - BILA:0000011 - BSA:0000049 - CALOHA:TS-2088 - CARO:0000011 - EHDAA2:0003011 - EHDAA:392 - EMAPA:16103 - EV:0100000 - FBbt:00004856 - FMA:7149 - HAO:0000011 - MA:0000003 - OpenCyc:Mx4rCWM0QCtDEdyAAADggVbxzQ - TAO:0001439 - TGMA:0001831 - UMLS:C0460002 - VHOG:0001725 - WBbt:0005746 - WBbt:0005763 - XAO:0003002 - ZFA:0001439 - galen:AnatomicalSystem - body system - organ system - uberon - UBERON:0000467 - - - anatomical system - - - - - - Anatomical structure that is an individual member of a species and consists of more than one cell. - TODO - split body and mc organism? body continues after death stage - organismal - - - - - AAO:0010026 - AEO:0000191 - BILA:0000012 - BSA:0000038 - BTO:0000042 - CARO:0000012 - EFO:0002906 - EHDAA2:0003103 - EHDAA2:0003191 - EHDAA:1 - EHDAA:9178 - EMAPA:25765 - EV:0100016 - FBbt:00000001 - FMA:256135 - HAO:0000012 - TADS:0000001 - TAO:0001094 - TGMA:0001832 - VHOG:0000671 - WBbt:0007833 - XAO:0003004 - ZFA:0001094 - galen:Organism - multi-cellular organism - organism - whole organism - animal - uberon - Koerper - body - whole body - UBERON:0000468 - - - - - multicellular organism - - - - - - - - - Anatomical structure which is a subdivision of a whole organism, consisting of components of multiple anatomical systems, largely surrounded by a contiguous region of integument. - Reflects CARO2. todo - check the inclusion of FMA 'cardinal body part here', and check child terms for consistency - - - - - AAO:0010053 - AEO:0000032 - BILA:0000032 - CALOHA:TS-2084 - CARO:0000032 - EFO:0000808 - EHDAA2:0003032 - FBbt:00007009 - FMA:7153 - HAO:0000032 - MA:0002433 - MAT:0000293 - MESH:A01 - MIAA:0000293 - OpenCyc:Mx4rvViAHJwpEbGdrcN5Y29ycA - TAO:0001308 - TGMA:0001840 - UMLS:C0229962 - VHOG:0001758 - XAO:0003013 - ZFA:0001308 - galen:BodyPart - anatomic region - uberon - body part - body region - cardinal body part - UBERON:0000475 - - - - - organism subdivision - - - - - - - - - Anatomical structure consisting of at least two non-overlapping organs, multi-tissue aggregates or portion of tissues or cells of different types that does not constitute an organism, organ, multi-tissue aggregate, or portion of tissue. - AAO:0010008 - AEO:0000054 - BILA:0000054 - CARO:0000054 - EHDAA2:0003054 - HAO:0000054 - TAO:0001512 - TGMA:0001846 - VHOG:0001724 - XAO:0003001 - ZFA:0001512 - uberon - UBERON:0000480 - - - anatomical group - - - - - - - - - - - - - - - The subdivision of the vertebrate body between the thorax and pelvis. The ventral part of the abdomen contains the abdominal cavity and visceral organs. The dorsal part includes the abdominal section of the vertebral column. - Vertebrate specific. In arthropods 'abdomen' is the most distal section of the body which lies behind the thorax or cephalothorax. If need be we can introduce some grouping class - abdominal - - - BTO:0000020 - CALOHA:TS-0001 - EFO:0000968 - EMAPA:35102 - EV:0100011 - FMA:9577 - GAID:16 - MA:0000029 - MAT:0000298 - MESH:A01.047 - MIAA:0000298 - OpenCyc:Mx4rvVjgyZwpEbGdrcN5Y29ycA - galen:Abdomen - abdominopelvic region - abdominopelvis - uberon - adult abdomen - belly - celiac region - UBERON:0000916 - - - - abdomen - - - - - - - - - Anatomical system that consists of the glands and parts of glands that produce endocrine secretions and help to integrate and control bodily metabolic activity. - Anatomical system containing glands which regulates bodily functions though the secretion of hormones.[AAO] - Multicellular organisms have complex endocrine systems, allowing responses to environmental stimuli, regulation of development, reproduction, and homeostasis. Nuclear receptors (NRs), a metazoan-specific family of ligand-activated transcription factors, play central roles in endocrine responses, as intermediates between signaling molecules and target genes. The NR family includes ligand-bound and orphan receptors, that is, receptors with no known ligand or for which there is no ligand Pocket. Understanding NR evolution has been further improved by comparison of several completed genomes, particularly those of deuterostomes and ecdysozoans. In contrast, evolution of NR ligands is still much debated. One hypothesis proposes that several independent gains and losses of ligand-binding ability in NRs occurred in protostomes and deuterostomes. A second hypothesis, pertaining to the NR3 subfamily (vertebrate steroid hormone receptors and estrogen related receptor), proposes that before the divergence of protostomes and deuterostomes, there was an ancestral steroid receptor (AncSR) that was ligand-activated and that orphan receptors secondarily lost the ability to bind a ligand. (...) Our analysis reveals that steroidogenesis has been independently elaborated in the 3 main bilaterian lineages (...).[well established][VHOG] - endocrine - - - - - AAO:0010279 - CALOHA:TS-1301 - EFO:0002969 - EHDAA2:0002224 - EMAPA:35306 - EV:0100128 - FBbt:00005068 - FMA:9668 - GAID:439 - MA:0000012 - MESH:A06 - TAO:0001158 - UMLS:C0014136 - VHOG:0000098 - XAO:0000158 - ZFA:0001158 - endocrine glandular system - endocrine system - systema endocrinum - uberon - UBERON:0000949 - - - - - endocrine system - - - - - - - - Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species. - - - - AAO:0010841 - AEO:0000000 - BILA:0000000 - CARO:0000000 - EHDAA2:0002229 - FBbt:10000000 - FBbt_root:00000000 - FMA:62955 - HAO:0000000 - MA:0000001 - TAO:0100000 - TGMA:0001822 - UMLS:C1515976 - XAO:0000000 - ZFA:0100000 - uberon - UBERON:0001062 - - - anatomical entity - - - - - - - - - - - - - - - - - - - - Situated along the perimeter of the adrenal gland, the adrenal cortex mediates the stress response through the production of mineralocorticoids and glucocorticoids, including aldosterone and cortisol respectively. It is also a secondary site of androgen synthesis. [WP,unvetted]. - All craniates have groups of cells homologous to the mammalian adrenocortical and chromaffin tissues (medulla), but they are scattered in and near the kidneys in fishes. (...) The cortical and chromaffin tissues come together to form adrenal glands in tetrapods.[well established][VHOG] - Kardong states that mammals are the first to have distinct cortext and medulla, but this contradicts XAO - - - - - AAO:0011009 - BTO:0000045 - CALOHA:TS-0015 - EFO:0000237 - EMAPA:18427 - EV:0100136 - FMA:15632 - GAID:447 - MA:0000118 - MAT:0000494 - MESH:A06.407.071.140 - UMLS:C0001613 - VHOG:0001481 - XAO:0000165 - adrenal gland cortex - cortex (glandula suprarenalis) - cortex of adrenal gland - cortex of suprarenal gland - suprarenal cortex - uberon - cortex glandulae suprarenalis - suprarenal - UBERON:0001235 - - - - adrenal cortex - - - - - - - - - - - - - - - - - Outermost layer of an organ[WP]. - cortical - this class is used more generically than in FMA, and includes e.g. cortex of hair - - EFO:0000383 - EHDAA:9344 - FMA:61109 - galen:Cortex - cortex - cortex of organ - uberon - UBERON:0001851 - - - - cortex - - - - - - - - - - - - - - - Organism subdivision which is the part of the body posterior to the cervical region (or head, when cervical region not present) and anterior to the caudal region. Includes the sacrum when present. - Organism subdivision that is the part of the body posterior to the head and anterior to the tail.[AAO] - Organism subdivision which is the part of the body posterior to the head and anterior to the tail.[TAO] - - - - - AAO:0010339 - BILA:0000116 - BTO:0001493 - CALOHA:TS-1071 - EFO:0000966 - EMAPA:31857 - FMA:7181 - MA:0000004 - MAT:0000296 - MIAA:0000296 - OpenCyc:Mx4rvVkJjpwpEbGdrcN5Y29ycA - TAO:0001115 - UMLS:C0460005 - XAO:0000054 - XAO:0003025 - ZFA:0001115 - galen:Trunk - thoracolumbar region - torso - trunk region - uberon - Rumpf - UBERON:0002100 - - - - - trunk - - - - - - - - - - - - - - - - - - - - - - - - - - Endocrine glands are glands of the endocrine system that secrete their products directly into the circulatory system rather than through a duct.[WP, modified]. - - - - - AEO:0000098 - BTO:0001488 - CALOHA:TS-1300 - EHDAA2:0003098 - EMAPA:35999 - FMA:9602 - GAID:335 - MA:0002563 - MESH:A06.407 - OpenCyc:Mx4rvbkiRZwpEbGdrcN5Y29ycA - UMLS:C0014133 - ductless gland - glandula endocrina - uberon - ductless gland - glandulae endocrinae - UBERON:0002368 - - - - endocrine gland - - - - - - + - - - - - - - - - - - - - - - Either of a pair of complex endocrine organs near the anterior medial border of the kidney consisting of a mesodermal cortex that produces glucocorticoid, mineralocorticoid, and androgenic hormones and an ectodermal medulla that produces epinephrine and norepinephrine[BTO]. - Anatomical structure which is found on the surface of the kidney and secretes various hormones including epinephrine, norephinephrine, aldosterone, corticosterone, and cortisol.[AAO] - All craniates have groups of cells homologous to the mammalian adrenocortical and chromaffin tissues, but they are scattered in and near the kidneys in fishes. (...) The cortical and chromaffin tissues come together to form adrenal glands in tetrapods.[well established][VHOG] - The origin of the adrenal gland is still controversial. It is thought to share the same origin as the kidney and gonads, derived from coelomic epithelium of the urogenital ridge and/or the underlying mesenchyme (Keegan and Hammer, 2002; Morohashi, 1997). We follow Kardong and state homology at the level of the cortex and medulla rather than gland as a whole - suprarenal cortex manufactures corticosteroids; suprarenal medulla manufactures epinephrine and norepinephrine; suprarenal medulla receives preganglionic sympathetic innervation from the greater thoracic splanchnic n. - - - - - AAO:0010551 - BTO:0000047 - CALOHA:TS-0016 - EFO:0000238 - EMAPA:18426 - EV:0100135 - FMA:9604 - GAID:446 - MA:0000116 - MAT:0000071 - MESH:A06.407.071 - MIAA:0000071 - OpenCyc:Mx4rvXYiz5wpEbGdrcN5Y29ycA - UMLS:C0001625 - VHOG:0001141 - XAO:0000164 - galen:AdrenalGland - glandula adrenalis - glandula suprarenalis - uberon - adrenal - adrenal capsule - adrenal medulla cell - atrabiliary capsule - epinephric gland - epinephros - glandula suprarenalis - interrenal gland - suprarenal capsule - suprarenal gland - UBERON:0002369 - - + - adrenal gland - - - - - - - - The abdominal segment of the torso. - - - EMAPA:35104 - FMA:259211 - MA:0000021 - uberon - abdomen/pelvis/perineum - lower body - lumbar region - UBERON:0002417 - - abdominal segment of trunk - - - + - - - - - A gland is an organ in an animal's body that synthesizes a substance for release such as hormones or breast milk, often into the bloodstream (endocrine gland) or into cavities inside the body or its outer surface (exocrine gland). A gland is an organ specialised for secretion[GO]. - glandular - UBERON:MIAA_0000021 - - - - - AAO:0000212 - AEO:0000096 - BTO:0000522 - EFO:0000797 - EHDAA2:0003096 - EHDAA:2161 - EHDAA:4475 - EHDAA:6522 - EMAPA:18425 - FBbt:00100317 - FMA:86294 - HAO:0000375 - MA:0003038 - MAT:0000021 - MIAA:0000021 - OpenCyc:Mx4rwP3vyJwpEbGdrcN5Y29ycA - UMLS:C1285092 - WikipediaCategory:Glands - galen:Gland - uberon - Druese - glandula - UBERON:0002530 - - - - gland - + + + test - + - - - - - - - - - This gland can either be a discrete structure located bilaterally above each kidney, or a cluster of cells in the head kidney that perform the functions of the adrenal gland. In either case, this organ consists of two cells types, aminergic chromaffin cells and steroidogenic cortical cells[GO] - keep this grouping class so long as it is required for GO - All craniates have groups of cells homologous to the mammalian adrenocortical and chromaffin tissues, but they are scattered in and near the kidneys in fishes. (...) The cortical and chromaffin tissues come together to form adrenal glands in tetrapods.[well established][VHOG] - VHOG:0001141 - adrenal gland - interrenal gland - adrenal gland/interrenal tissue - uberon - adrenal - interrenal gland - suprarenal gland - interrenal gland - UBERON:0006858 - - - - adrenal/interrenal gland - - + - - - - - - - - - - FMA:25054 - region of trunk - trunk subdivision - uberon - UBERON:0009569 - - - subdivision of trunk - + + + dummy individal 1 + + + + + + + - + - - - An anatomical structure that has more than one cell as a part. - CARO:0010000 - FBbt:00100313 - multicellular structure - uberon - UBERON:0010000 - - - multicellular anatomical structure - + + + dummy individal 2 + - + - - - - - - - - - A major subdivision of an organism that divides an organism along its main body axis (typically anterio-posterior axis). In vertebrates, this is based on the vertebral column. - Ideally this would be disjoint with analagous class for appendicular axes, but currently 'appendages' like antennae, horns cause a problem - axial subdivision of organism - uberon - body segment - main body segment - UBERON:0011676 - + - subdivision of organism along main body axis - + dummy individal 3 + + + + + + + - + - - - A principle subdivision of an organism that includes all structures along the primary axis, typically the anterior-posterior axis, from head to tail, including structures of the body proper where present (for example, ribs), but excluding appendages. - uberon - UBERON:0013701 + - main body axis - + dummy individal 4 + - + - - - - - - - - - The region of the organism associated with the visceral organs. - Cardinal body part, which consists of a maximal set of diverse subclasses of organ and organ part spatially associated with the vertebral column and ribcage. Examples: There is only one body proper[FMA:231424]. - AEO:0000103 - BTO:0001489 - FMA:231424 - uberon - body - whole body - UBERON:0013702 - + - body proper - - - - - - - - - test - + dummy individal 5 + - diff --git a/docs/merge.md b/docs/merge.md index 1713b10aa..b8d1a80c8 100644 --- a/docs/merge.md +++ b/docs/merge.md @@ -43,6 +43,6 @@ It’s also possible to annotate the imported or merged ontology axioms with the * `--annotate-defined-by true`: annotates all entities (class, data, annotation, object property and named individual declaration axioms) with the source's IRI using `rdfs:isDefinedBy`. If the term already has an annotation using this property (`rdfs:isDefinedBy`), the existing annotation will be kept and no new annotation will be added. - robot merge --input edit.owl --input merge.owl \ + robot merge --input example2.owl --input merge.owl \ --annotate-defined-by true \ --output results/merged_defined_by.owl From 6db54a22bf28d1af6f2605c05418583793d2224d Mon Sep 17 00:00:00 2001 From: hkir-dev Date: Wed, 6 Apr 2022 10:45:35 +0100 Subject: [PATCH 09/17] #977 resolve conflict --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 85c976e72..067388c5f 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -296,6 +296,7 @@ First official release of ROBOT! [`validate`]: http://robot.obolibrary.org/validate [#893]: https://github.com/ontodev/robot/issues/893 +[#979]: https://github.com/ontodev/robot/pull/979 [#955]: https://github.com/ontodev/robot/pull/955 [#953]: https://github.com/ontodev/robot/pull/953 [#951]: https://github.com/ontodev/robot/pull/951 From 492630647e98fe386c0ebd7aaaf9e5acb52ba512 Mon Sep 17 00:00:00 2001 From: hkir-dev Date: Wed, 6 Apr 2022 11:15:18 +0100 Subject: [PATCH 10/17] #977 example2.owl file simplified --- docs/examples/example2.owl | 60 -------------------------------------- 1 file changed, 60 deletions(-) diff --git a/docs/examples/example2.owl b/docs/examples/example2.owl index 8b83bfe64..ab178ff1c 100644 --- a/docs/examples/example2.owl +++ b/docs/examples/example2.owl @@ -47,11 +47,7 @@ - IAO:0000116 uberon - editor_note - true - editor_note editor note @@ -61,11 +57,7 @@ - IAO:0000232 uberon - curator_notes - true - curator_notes curator notes @@ -93,10 +85,6 @@ - BFO:0000050 - uberon - part_of - part_of part_of @@ -117,31 +105,6 @@ - Material anatomical entity that has inherent 3D shape and is generated by coordinated expression of the organism's own genome. - - - AAO:0010825 - AEO:0000003 - BILA:0000003 - CARO:0000003 - EHDAA2:0003003 - EMAPA:0 - FBbt:00007001 - FMA:67135 - GAID:781 - HAO:0000003 - MA:0003000 - MESH:A13 - TAO:0000037 - TGMA:0001823 - VHOG:0001759 - WBbt:0000100 - XAO:0003000 - ZFA:0000037 - biological structure - uberon - UBERON:0000061 - anatomical structure @@ -158,29 +121,6 @@ - Anatomical structure that performs a specific function or group of functions [WP]. - Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions. - CARO does not include a generic 'organ' class, only simple and compound organ - - - - - - EFO:0000634 - EMAPA:35949 - ENVO:01000162 - FMA:67498 - MA:0003001 - OpenCyc:Mx4rv5XMb5wpEbGdrcN5Y29ycA - OpenCyc:Mx4rwP3iWpwpEbGdrcN5Y29ycA - UMLS:C0178784 - WBbt:0003760 - uberon - anatomical unit - body organ - element - UBERON:0000062 - organ From 4a45ceac9376b570c88e64e3f3b579a6c05d0bac Mon Sep 17 00:00:00 2001 From: hkir-dev Date: Thu, 7 Apr 2022 08:21:09 +0100 Subject: [PATCH 11/17] point changelog to the PR --- CHANGELOG.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 49daff812..6a2e2b865 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -9,7 +9,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Changed - Sort [`report`] violations by rule name within level [#955] -- [`extract`] and [`merge`] should optionally inject provenance [#893] +- [`extract`] and [`merge`] should optionally inject provenance [#977] ### Fixed - Fix subClassOf cycles in related object selection [#979] @@ -300,7 +300,7 @@ First official release of ROBOT! [`template`]: http://robot.obolibrary.org/template [`validate`]: http://robot.obolibrary.org/validate -[#893]: https://github.com/ontodev/robot/issues/893 +[#977]: https://github.com/ontodev/robot/pull/977 [#979]: https://github.com/ontodev/robot/pull/979 [#955]: https://github.com/ontodev/robot/pull/955 [#953]: https://github.com/ontodev/robot/pull/953 From 3ca329481348c4f3a6e0c204253807f138da0373 Mon Sep 17 00:00:00 2001 From: "James A. Overton" Date: Thu, 9 Jun 2022 13:21:58 -0400 Subject: [PATCH 12/17] Fix missing linebreak in new examples/tests --- docs/annotate.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/docs/annotate.md b/docs/annotate.md index c75e1d4be..8863dd6c9 100644 --- a/docs/annotate.md +++ b/docs/annotate.md @@ -46,13 +46,13 @@ It’s also possible to annotate the ontology axioms with the ontology IRI or ve * `--annotate-derived-from true`: annotates all axioms with the source's version IRI if it exists, else with the ontology IRI, using `prov:wasDerivedFrom`. If the axiom already has an annotation using this property (`prov:wasDerivedFrom`), the existing annotation will be kept and no new annotation will be added. robot annotate --input example2.owl \ - --annotate-derived-from true + --annotate-derived-from true \ --output results/example2_derived_from.owl - + * `--annotate-defined-by true`: annotates all entities (class, data, annotation, object property and named individual declaration axioms) with the source's IRI using `rdfs:isDefinedBy`. If the term already has an annotation using this property (`rdfs:isDefinedBy`), the existing annotation will be kept and no new annotation will be added. robot annotate --input example2.owl \ - --annotate-defined-by true + --annotate-defined-by true \ --output results/example2_defined_by.owl --- From b9d9767592e59045b68cbab30df179bce2df6ba8 Mon Sep 17 00:00:00 2001 From: Nico Matentzoglu Date: Fri, 10 Jun 2022 11:20:18 +0300 Subject: [PATCH 13/17] Update OntologyHelper.java --- .../main/java/org/obolibrary/robot/OntologyHelper.java | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) diff --git a/robot-core/src/main/java/org/obolibrary/robot/OntologyHelper.java b/robot-core/src/main/java/org/obolibrary/robot/OntologyHelper.java index d67c5bea2..4c023a4a2 100644 --- a/robot-core/src/main/java/org/obolibrary/robot/OntologyHelper.java +++ b/robot-core/src/main/java/org/obolibrary/robot/OntologyHelper.java @@ -66,11 +66,14 @@ public static void addEntityAnnotation( OWLAnnotationProperty property, OWLAnnotationValue value, boolean overload) { - OWLAnnotationAssertionAxiom existingAnnotation = + OWLAnnotationAssertionAxiom existingAnnotation = null; + if (!overload) { + existingAnnotation = EntitySearcher.getAnnotationAssertionAxioms(owlEntity.getIRI(), ontology).stream() .filter(a -> a.getProperty().getIRI().equals(property.getIRI())) .findFirst() .orElse(null); + } if (overload || existingAnnotation == null) { OWLOntologyManager manager = ontology.getOWLOntologyManager(); OWLDataFactory factory = manager.getOWLDataFactory(); @@ -99,11 +102,14 @@ public static void addAxiomAnnotation( OWLAnnotationProperty property, OWLAnnotationValue value, boolean overload) { - OWLAnnotation existingAnnotation = + OWLAnnotationAssertionAxiom existingAnnotation = null; + if (!overload) { + existingAnnotation = axiom.getAnnotations().stream() .filter(a -> a.getProperty().getIRI().equals(property.getIRI())) .findFirst() .orElse(null); + } if (overload || existingAnnotation == null) { OWLOntologyManager manager = ontology.getOWLOntologyManager(); OWLDataFactory factory = manager.getOWLDataFactory(); From 907fe6c0bcf5b9c0532f949bf604ef9a869071f1 Mon Sep 17 00:00:00 2001 From: Nico Matentzoglu Date: Fri, 10 Jun 2022 11:24:18 +0300 Subject: [PATCH 14/17] Copy/paste error --- .../src/main/java/org/obolibrary/robot/OntologyHelper.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/robot-core/src/main/java/org/obolibrary/robot/OntologyHelper.java b/robot-core/src/main/java/org/obolibrary/robot/OntologyHelper.java index 4c023a4a2..d2540102b 100644 --- a/robot-core/src/main/java/org/obolibrary/robot/OntologyHelper.java +++ b/robot-core/src/main/java/org/obolibrary/robot/OntologyHelper.java @@ -102,7 +102,7 @@ public static void addAxiomAnnotation( OWLAnnotationProperty property, OWLAnnotationValue value, boolean overload) { - OWLAnnotationAssertionAxiom existingAnnotation = null; + OWLAnnotation existingAnnotation = null; if (!overload) { existingAnnotation = axiom.getAnnotations().stream() From 34155be5210fb780bb56312f5913c9e4d1dea418 Mon Sep 17 00:00:00 2001 From: hkir-dev Date: Wed, 29 Jun 2022 14:10:16 +0100 Subject: [PATCH 15/17] PR #977 removed duplicate axioms --- .../org/obolibrary/robot/MergeOperation.java | 22 ++++- .../org/obolibrary/robot/OntologyHelper.java | 18 ++-- .../obolibrary/robot/MergeOperationTest.java | 64 +++++++++++++ .../src/test/resources/simple_defined_by.owl | 82 +++++++++++++++++ .../test/resources/simple_derived_from.owl | 91 +++++++++++++++++++ 5 files changed, 263 insertions(+), 14 deletions(-) create mode 100644 robot-core/src/test/resources/simple_defined_by.owl create mode 100644 robot-core/src/test/resources/simple_derived_from.owl diff --git a/robot-core/src/main/java/org/obolibrary/robot/MergeOperation.java b/robot-core/src/main/java/org/obolibrary/robot/MergeOperation.java index 9c79ff9d3..92d1a13a4 100644 --- a/robot-core/src/main/java/org/obolibrary/robot/MergeOperation.java +++ b/robot-core/src/main/java/org/obolibrary/robot/MergeOperation.java @@ -11,6 +11,7 @@ import org.semanticweb.owlapi.model.OWLAnnotationProperty; import org.semanticweb.owlapi.model.OWLAxiom; import org.semanticweb.owlapi.model.OWLDataFactory; +import org.semanticweb.owlapi.model.OWLDeclarationAxiom; import org.semanticweb.owlapi.model.OWLEntity; import org.semanticweb.owlapi.model.OWLImportsDeclaration; import org.semanticweb.owlapi.model.OWLOntology; @@ -325,14 +326,25 @@ private static void annotateWithVersionIRI( .getVersionIRI() .or(sourceOntology.getOntologyID().getOntologyIRI().orNull()); if (provenanceIRI != null) { + OWLOntologyManager manager = targetOntology.getOWLOntologyManager(); OWLAnnotationProperty annotationProp = - targetOntology - .getOWLOntologyManager() + manager .getOWLDataFactory() .getOWLAnnotationProperty(PROVVocabulary.WAS_DERIVED_FROM.getIRI()); - for (OWLAxiom axiom : sourceOntology.getAxioms(includeImportsClosure)) { - OntologyHelper.addAxiomAnnotation( - targetOntology, axiom, annotationProp, provenanceIRI, false); + OWLDeclarationAxiom provenancePropDeclaration = + manager.getOWLDataFactory().getOWLDeclarationAxiom(annotationProp); + + Set sourceAxioms = sourceOntology.getAxioms(includeImportsClosure); + for (OWLAxiom axiom : sourceAxioms) { + if (!axiom.equals(provenancePropDeclaration)) { + OntologyHelper.addAxiomAnnotation( + targetOntology, axiom, annotationProp, provenanceIRI, false); + } + } + + manager.addAxiom(targetOntology, provenancePropDeclaration); + if (sourceOntology != targetOntology) { + sourceOntology.getOWLOntologyManager().removeAxioms(sourceOntology, sourceAxioms); } } } diff --git a/robot-core/src/main/java/org/obolibrary/robot/OntologyHelper.java b/robot-core/src/main/java/org/obolibrary/robot/OntologyHelper.java index d2540102b..770a02c27 100644 --- a/robot-core/src/main/java/org/obolibrary/robot/OntologyHelper.java +++ b/robot-core/src/main/java/org/obolibrary/robot/OntologyHelper.java @@ -69,10 +69,10 @@ public static void addEntityAnnotation( OWLAnnotationAssertionAxiom existingAnnotation = null; if (!overload) { existingAnnotation = - EntitySearcher.getAnnotationAssertionAxioms(owlEntity.getIRI(), ontology).stream() - .filter(a -> a.getProperty().getIRI().equals(property.getIRI())) - .findFirst() - .orElse(null); + EntitySearcher.getAnnotationAssertionAxioms(owlEntity.getIRI(), ontology).stream() + .filter(a -> a.getProperty().getIRI().equals(property.getIRI())) + .findFirst() + .orElse(null); } if (overload || existingAnnotation == null) { OWLOntologyManager manager = ontology.getOWLOntologyManager(); @@ -105,10 +105,10 @@ public static void addAxiomAnnotation( OWLAnnotation existingAnnotation = null; if (!overload) { existingAnnotation = - axiom.getAnnotations().stream() - .filter(a -> a.getProperty().getIRI().equals(property.getIRI())) - .findFirst() - .orElse(null); + axiom.getAnnotations().stream() + .filter(a -> a.getProperty().getIRI().equals(property.getIRI())) + .findFirst() + .orElse(null); } if (overload || existingAnnotation == null) { OWLOntologyManager manager = ontology.getOWLOntologyManager(); @@ -116,8 +116,8 @@ public static void addAxiomAnnotation( OWLAnnotation annotation = factory.getOWLAnnotation(property, value); OWLAxiom newAxiom = axiom.getAnnotatedAxiom(new HashSet<>(Arrays.asList(annotation))); - manager.removeAxiom(ontology, axiom); manager.addAxiom(ontology, newAxiom); + manager.removeAxiom(ontology, axiom); } } diff --git a/robot-core/src/test/java/org/obolibrary/robot/MergeOperationTest.java b/robot-core/src/test/java/org/obolibrary/robot/MergeOperationTest.java index 7164fd542..ffbaed40d 100644 --- a/robot-core/src/test/java/org/obolibrary/robot/MergeOperationTest.java +++ b/robot-core/src/test/java/org/obolibrary/robot/MergeOperationTest.java @@ -1,6 +1,9 @@ package org.obolibrary.robot; +import static org.junit.Assert.assertEquals; + import java.io.IOException; +import java.net.URISyntaxException; import java.util.ArrayList; import java.util.List; import org.junit.Test; @@ -35,4 +38,65 @@ public void testMergeTwo() throws IOException { OWLOntology merged = MergeOperation.merge(ontologies); assertIdentical("/simple_parts.owl", merged); } + + /** + * Test merging a single ontology without imports and annotating with derived from provenance. + * Expect old axioms are cleaned and a new provenance property is declared. + * + * @throws IOException on file problem + */ + @Test + public void testMergeDerivedFrom() throws IOException { + OWLOntology simple = loadOntology("/simple.owl"); + List ontologies = new ArrayList<>(); + ontologies.add(simple); + + assertEquals(5, simple.getAxiomCount()); + OWLOntology merged = MergeOperation.merge(ontologies, false, false, false, true); + + assertEquals(6, merged.getAxiomCount()); + // old axioms should be cleaned + OWLOntology expected = loadOntology("/simple_derived_from.owl"); + assertEquals(6, expected.getAxiomCount()); + assertIdentical(expected, merged); + } + + /** + * Test merging a single ontology with imports and annotating with derived from provenance. Expect + * imported axioms are merged without redundancy. + * + * @throws IOException on file problem + * @throws URISyntaxException + */ + @Test + public void testMergeImportDerivedFrom() throws IOException, URISyntaxException { + OWLOntology simple = loadOntologyWithCatalog("/import_test.owl"); + List ontologies = new ArrayList<>(); + ontologies.add(simple); + + assertEquals(0, simple.getAxiomCount()); + + OWLOntology merged = MergeOperation.merge(ontologies, false, true, false, true); + assertEquals(6, merged.getAxiomCount()); + } + + /** + * Test merging a single ontology without imports and annotating with defined by provenance. + * + * @throws IOException on file problem + */ + @Test + public void testMergeTwoDefinedBy() throws IOException { + OWLOntology simple = loadOntology("/simple.owl"); + List ontologies = new ArrayList<>(); + ontologies.add(simple); + + assertEquals(5, simple.getAxiomCount()); + OWLOntology merged = MergeOperation.merge(ontologies, false, false, true, false); + + assertEquals(9, merged.getAxiomCount()); + OWLOntology expected = loadOntology("/simple_defined_by.owl"); + assertEquals(9, expected.getAxiomCount()); + assertIdentical(expected, merged); + } } diff --git a/robot-core/src/test/resources/simple_defined_by.owl b/robot-core/src/test/resources/simple_defined_by.owl new file mode 100644 index 000000000..890c1075d --- /dev/null +++ b/robot-core/src/test/resources/simple_defined_by.owl @@ -0,0 +1,82 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Test 1 + test one + + + + + + + + + + + + + + + diff --git a/robot-core/src/test/resources/simple_derived_from.owl b/robot-core/src/test/resources/simple_derived_from.owl new file mode 100644 index 000000000..6be15e0ed --- /dev/null +++ b/robot-core/src/test/resources/simple_derived_from.owl @@ -0,0 +1,91 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + Test 1 + test one + + + + + + + + + + + Test 1 + + + + + + test one + + + + + + + + + + + + + + + + + + + + + + + + + + + + From dd71d5482a6913c40436fb0a57d38a7582b13b65 Mon Sep 17 00:00:00 2001 From: hkir-dev Date: Wed, 29 Jun 2022 14:28:35 +0100 Subject: [PATCH 16/17] PR #977 renamed unit test --- .../src/test/java/org/obolibrary/robot/MergeOperationTest.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/robot-core/src/test/java/org/obolibrary/robot/MergeOperationTest.java b/robot-core/src/test/java/org/obolibrary/robot/MergeOperationTest.java index ffbaed40d..ae5728e85 100644 --- a/robot-core/src/test/java/org/obolibrary/robot/MergeOperationTest.java +++ b/robot-core/src/test/java/org/obolibrary/robot/MergeOperationTest.java @@ -86,7 +86,7 @@ public void testMergeImportDerivedFrom() throws IOException, URISyntaxException * @throws IOException on file problem */ @Test - public void testMergeTwoDefinedBy() throws IOException { + public void testMergeDefinedBy() throws IOException { OWLOntology simple = loadOntology("/simple.owl"); List ontologies = new ArrayList<>(); ontologies.add(simple); From 9969376f94a7eb39ea69315731f1bf008e86d59e Mon Sep 17 00:00:00 2001 From: hkir-dev Date: Wed, 29 Jun 2022 14:33:30 +0100 Subject: [PATCH 17/17] PR #977 improve merge import unit test --- .../test/java/org/obolibrary/robot/MergeOperationTest.java | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/robot-core/src/test/java/org/obolibrary/robot/MergeOperationTest.java b/robot-core/src/test/java/org/obolibrary/robot/MergeOperationTest.java index ae5728e85..a5fe42ca8 100644 --- a/robot-core/src/test/java/org/obolibrary/robot/MergeOperationTest.java +++ b/robot-core/src/test/java/org/obolibrary/robot/MergeOperationTest.java @@ -1,12 +1,14 @@ package org.obolibrary.robot; import static org.junit.Assert.assertEquals; +import static org.junit.Assert.assertTrue; import java.io.IOException; import java.net.URISyntaxException; import java.util.ArrayList; import java.util.List; import org.junit.Test; +import org.semanticweb.owlapi.model.OWLAxiom; import org.semanticweb.owlapi.model.OWLOntology; /** Tests for MergeOperation. */ @@ -78,6 +80,11 @@ public void testMergeImportDerivedFrom() throws IOException, URISyntaxException OWLOntology merged = MergeOperation.merge(ontologies, false, true, false, true); assertEquals(6, merged.getAxiomCount()); + + OWLOntology expected = loadOntology("/simple_derived_from.owl"); + for (OWLAxiom axiom : expected.getAxioms()) { + assertTrue(merged.containsAxiom(axiom)); + } } /**