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Created April 24, 2025 03:05
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trace.json
{
"id": "msg_01MUhMFswt344QGvVaDs5Cv4",
"type": "message",
"role": "assistant",
"model": "claude-3-7-sonnet-20250219",
"content": [
{
"type": "text",
"text": "Let me help fix issue 3003. I'll first check what the issue is about."
},
{
"type": "tool_use",
"id": "toolu_01Xuvyt6hbxHYxezVB7am95Z",
"name": "Bash",
"input": {
"command": "gh issue view 3003"
}
}
],
"stop_reason": "tool_use",
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"usage": {
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}
}
{
"role": "user",
"content": [
{
"type": "tool_result",
"content": "title:\treview definition of cardiac septum and its child terms\nstate:\tOPEN\nauthor:\tsbello\nlabels:\tStale, textual definition\ncomments:\t1\nassignees:\tnicolevasilevsky\nprojects:\t\nmilestone:\t\nnumber:\t3003\n--\n**Uberon term**\r\ncardiac septum (UBERON:0002099)\r\n\r\ncurrent definition is too narrow for the child terms \r\n\r\nThe definition is \"The thin membranous structure between the two heart atria or the thick muscular structure between the two heart ventricles\" but child terms include septa between the atria and ventricles and outflow tract septa.\r\n\r\n**Suggested revision of textual definition**\r\nRevised definition assuming the child terms are correct (that is this term is intended to cover all septa between parts of the heart not just those between the atria or ventricles)\r\n\r\n\"The thin membranous structure between parts of the heart, including the atria, ventricles, and outflow tract.\"",
"tool_use_id": "toolu_01Xuvyt6hbxHYxezVB7am95Z"
}
]
}
{
"id": "msg_01FCgfBpC1DSEnbMedyiNi7h",
"type": "message",
"role": "assistant",
"model": "claude-3-7-sonnet-20250219",
"content": [
{
"type": "text",
"text": "Let me check out the cardiac septum term and its child terms to understand the issue better."
},
{
"type": "tool_use",
"id": "toolu_015TojffyZvNTbkbsSgGo2PJ",
"name": "Bash",
"input": {
"command": "obo-grep.pl -r 'id: UBERON:0002099' src/ontology/uberon-edit.obo"
}
}
],
"stop_reason": "tool_use",
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{
"role": "user",
"content": [
{
"type": "tool_result",
"content": "format-version: 1.2\nsubsetdef: added_for_HCA \"Classes tagged with this subset property were added upon request from the Human Cell Atlas (HCA).\"\nsubsetdef: common_anatomy \"Terms applicable across life, not restricted to Metazoa\"\nsubsetdef: cumbo \"CUMBO\"\nsubsetdef: cyclostome_subset \"cyclostome structures\"\nsubsetdef: defined_by_cytoarchitecture \"brain region defined by cyto-architecture\"\nsubsetdef: defined_by_ordinal_series \"classes that are defined by relative position counting from first in a series of elements along an axis in an individual organism rather than by strict homology\"\nsubsetdef: developmental_classification \"developmental_classification\"\nsubsetdef: dubious_grouping \"Indicates that subclasses in AOs may be inappropriately linked\"\nsubsetdef: early_development \"A class that represents an early developmental structure, like a blastocyst. This part of the ontology is undergoing review to remove inappropriate grouping classes.\"\nsubsetdef: efo_slim \"EFO slim\"\nsubsetdef: emapa_ehdaa2 \"derived from the union of EHDAA2 and EMAPA - still to be checked\"\nsubsetdef: feed_aligned \"subset of classes that have logical defs text defs and synonyms aligned with FEED\"\nsubsetdef: functional_classification \"functional_classification\"\nsubsetdef: grouping_class \"Subset consisting of classes creating for grouping purposes\"\nsubsetdef: homology_grouping \"A grouping class that depends on an assumption of homology between subclasses\"\nsubsetdef: human_reference_atlas \"\"\nsubsetdef: inconsistent_with_fma \"classes that have some inconsistency with FMA\"\nsubsetdef: location_grouping \"\"\nsubsetdef: major_organ \"somewhat fuzzy grouping for analysis purposes, currently composed of something like: liver, heart, skeletal, kidney, bladder, brain, skin, mouth, esophagus, stomach, small intestine, large intestines, trachea nose, lungs, brain, spinal cord, peripheral nerves, kidneys, ureters, bladder, urethra, gonads\"\nsubsetdef: metazoa_core \"core classes typically found across metazoa. one purpose is to create a rough set of terms that could be used to start a new metazoan AO. Note this subset is not yet fully fleshed out\"\nsubsetdef: non_informative \"abstract class brought in to group ontology classes but not informative\"\nsubsetdef: organ_slim \"organs, excluding individual muscles and skeletal elements\"\nsubsetdef: pheno_slim \"Phenotype slim\"\nsubsetdef: phenotype_rcn \"A subset specifically created for the 2012 Phenotype RCN meeting. Includes some human-specific terms that may eventually be removed when they are adequately represented with part of relationships in FMA\"\nsubsetdef: uberon_slim \"Uberon slim - subset that excludes obscure terms and deep compositional terms\"\nsubsetdef: unverified_taxonomic_grouping \"Indicates that the class encompasses classes from other AOs that have not been verified\"\nsubsetdef: upper_level \"abstract upper-level terms not directly useful for analysis\"\nsubsetdef: vertebrate_core \"core classes typically found across vertebrates. one purpose is to create a rough set of terms that could be used to start a new vertebrate AO\"\nsynonymtypedef: BRAIN_NAME_ABV \"brain name abbreviations (drosophila)\"\nsynonymtypedef: COMPARATIVE_PREFERRED \"preferred term in the context of comparative anatomy\"\nsynonymtypedef: DEPRECATED \"A historic synonym, no longer encouraged\"\nsynonymtypedef: DEVELOPMENTAL \"developmental term\"\nsynonymtypedef: HOMOLOGY \"a synonym made on the basis of a possibly homologous structure in another species\"\nsynonymtypedef: HUMAN_PREFERRED \"preferred term when talking about an instance of this class in Homo sapiens\"\nsynonymtypedef: INCONSISTENT \"indicates that a synonym is used in an inconsistent or confusing way, typically between species\"\nsynonymtypedef: MISSPELLING \"a mis-spelling that is in common use and thus recorded\"\nsynonymtypedef: NON_AMNIOTE \"synonym that is inappropriate for amniotes\"\nsynonymtypedef: NON_MAMMAL \"synonym that is inappropriate for mammals\"\nsynonymtypedef: OMO:0003000 \"abbreviation\"\nsynonymtypedef: OMO:0003002 \"dubious synonym\"\nsynonymtypedef: OMO:0003004 \"plural form\"\nsynonymtypedef: OMO:0003011 \"latin term\"\nsynonymtypedef: PENDING_REVIEW \"expert consultation and attribution required\"\nsynonymtypedef: SENSU \"taxonomic disambiguation\"\nsynonymtypedef: SYSTEMATIC \"a systematic synonym used as the base name for design patterns\"\ndefault-namespace: uberon\ntreat-xrefs-as-equivalent: AEO\ntreat-xrefs-as-equivalent: BILA\ntreat-xrefs-as-equivalent: BSPO\ntreat-xrefs-as-equivalent: CARO\ntreat-xrefs-as-equivalent: GO\ntreat-xrefs-as-equivalent: OG\ntreat-xrefs-as-equivalent: VSAO\ntreat-xrefs-as-is_a: BFO\ntreat-xrefs-as-is_a: VHOG\nremark: Aurelie Comte, Bill Bug, Catherine Leroy, Duncan Davidson and Trish Whetzel are also contributors. However their ORCIDs were not found.\nimport: http://purl.obolibrary.org/obo/uberon/components/disjoint_union_over.owl\nimport: http://purl.obolibrary.org/obo/uberon/components/hra_depiction_3d_images.owl\nimport: http://purl.obolibrary.org/obo/uberon/components/hra_subset.owl\nimport: http://purl.obolibrary.org/obo/uberon/components/in-subset.owl\nimport: http://purl.obolibrary.org/obo/uberon/components/mappings.owl\nimport: http://purl.obolibrary.org/obo/uberon/components/vasculature_class.owl\nimport: http://purl.obolibrary.org/obo/uberon/imports/merged_import.owl\nimport: http://purl.obolibrary.org/obo/uberon/imports/orcidio_import.owl\nimport: http://purl.obolibrary.org/obo/uberon/patterns/definitions.owl\nontology: uberon/core\nproperty_value: dc-contributor https://github.com/orgs/pato-ontology/teams/pato-community\nproperty_value: dc-contributor https://orcid.org/0000-0001-5889-4463\nproperty_value: dc-contributor https://orcid.org/0000-0001-7433-0086\nproperty_value: dc-contributor https://orcid.org/0000-0001-7476-6306\nproperty_value: dc-contributor https://orcid.org/0000-0001-7920-5321\nproperty_value: dc-contributor https://orcid.org/0000-0001-7958-3701\nproperty_value: dc-contributor https://orcid.org/0000-0001-8682-8754\nproperty_value: dc-contributor https://orcid.org/0000-0001-9107-0714\nproperty_value: dc-contributor https://orcid.org/0000-0001-9990-8331\nproperty_value: dc-contributor https://orcid.org/0000-0002-0819-0473\nproperty_value: dc-contributor https://orcid.org/0000-0002-0956-8634\nproperty_value: dc-contributor https://orcid.org/0000-0002-1112-5832\nproperty_value: dc-contributor https://orcid.org/0000-0002-1572-1316\nproperty_value: dc-contributor https://orcid.org/0000-0002-1604-3078\nproperty_value: dc-contributor https://orcid.org/0000-0002-1615-2899\nproperty_value: dc-contributor https://orcid.org/0000-0002-2061-091X\nproperty_value: dc-contributor https://orcid.org/0000-0002-2244-7917\nproperty_value: dc-contributor https://orcid.org/0000-0002-3437-3329\nproperty_value: dc-contributor https://orcid.org/0000-0002-3467-2636\nproperty_value: dc-contributor https://orcid.org/0000-0002-3734-1859\nproperty_value: dc-contributor https://orcid.org/0000-0002-5111-7263\nproperty_value: dc-contributor https://orcid.org/0000-0002-6490-7723\nproperty_value: dc-contributor https://orcid.org/0000-0002-7073-9172\nproperty_value: dc-contributor https://orcid.org/0000-0002-8406-3871\nproperty_value: dc-contributor https://orcid.org/0000-0002-8455-3213\nproperty_value: dc-contributor https://orcid.org/0000-0002-8688-6599\nproperty_value: dc-contributor https://orcid.org/0000-0002-9415-5104\nproperty_value: dc-contributor https://orcid.org/0000-0002-9818-3030\nproperty_value: dc-contributor https://orcid.org/0000-0002-9900-7880\nproperty_value: dc-contributor https://orcid.org/0000-0003-1980-3228\nproperty_value: dc-contributor https://orcid.org/0000-0003-2105-2283\nproperty_value: dc-contributor https://orcid.org/0000-0003-2338-2550\nproperty_value: dc-contributor https://orcid.org/0000-0003-3691-0324\nproperty_value: dc-contributor https://orcid.org/0000-0003-4423-4370\nproperty_value: dc-contributor https://www.wikidata.org/wiki/Q11695472\nproperty_value: dc-contributor https://www.wikidata.org/wiki/Q23809253\nproperty_value: dc-contributor https://www.wikidata.org/wiki/Q4964264\nproperty_value: dc-contributor https://www.wikidata.org/wiki/Q54985720\nproperty_value: dc-contributor https://www.wikidata.org/wiki/Q6983890\nproperty_value: dc-contributor https://www.wikidata.org/wiki/Q7650732\nproperty_value: dc-contributor https://www.wikidata.org/wiki/Q85793053\nproperty_value: dc-creator https://orcid.org/0000-0001-5839-6798\nproperty_value: dc-creator https://orcid.org/0000-0001-7972-3866\nproperty_value: dc-creator https://orcid.org/0000-0001-9114-8737\nproperty_value: dc-creator https://orcid.org/0000-0002-1810-9886\nproperty_value: dc-creator https://orcid.org/0000-0002-6601-2165\nproperty_value: dc-creator https://orcid.org/0000-0002-7356-1779\nproperty_value: dc-creator https://orcid.org/0000-0002-9611-1279\nproperty_value: dc-creator https://orcid.org/0000-0003-3162-7490\nproperty_value: dc-creator https://orcid.org/0000-0003-3308-6245\nproperty_value: dc-description \"Uberon is an integrated cross-species anatomy ontology representing a variety of entities classified according to traditional anatomical criteria such as structure, function and developmental lineage. The ontology includes comprehensive relationships to taxon-specific anatomical ontologies, allowing integration of functional, phenotype and expression data.\" xsd:string\nproperty_value: dc-publisher \"http://uberon.org\" xsd:anyURI\nproperty_value: dc-source \"aggregates AAO from 13:04:2012\" xsd:string\nproperty_value: dc-source \"aggregates TAO from 09:08:2012\" xsd:string\nproperty_value: dc-source \"aggregates VSAO from 16:07:2012\" xsd:string\nproperty_value: dc-source http://braininfo.rprc.washington.edu/\nproperty_value: dc-source http://dbpedia.org\nproperty_value: dc-source http://en.wikipedia.org/wiki/\nproperty_value: dc-source http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-GrossAnatomy.owl\nproperty_value: dc-source http://palaeos.com\nproperty_value: dc-source http://pons.incf.org/wiki/Common_Upper_Mammalian_Brain_Ontology_%28Cumbo%29\nproperty_value: dc-source http://purl.obolibrary.org/obo/aao.owl\nproperty_value: dc-source http://purl.obolibrary.org/obo/aba.owl\nproperty_value: dc-source http://purl.obolibrary.org/obo/aeo.owl\nproperty_value: dc-source http://purl.obolibrary.org/obo/bila.owl\nproperty_value: dc-source http://purl.obolibrary.org/obo/bto.owl\nproperty_value: dc-source http://purl.obolibrary.org/obo/caro.owl\nproperty_value: dc-source http://purl.obolibrary.org/obo/cl.owl\nproperty_value: dc-source http://purl.obolibrary.org/obo/ehdaa2.owl\nproperty_value: dc-source http://purl.obolibrary.org/obo/emapa.owl\nproperty_value: dc-source http://purl.obolibrary.org/obo/fbbt.owl\nproperty_value: dc-source http://purl.obolibrary.org/obo/fma.owl\nproperty_value: dc-source http://purl.obolibrary.org/obo/go.owl\nproperty_value: dc-source http://purl.obolibrary.org/obo/hp.owl\nproperty_value: dc-source http://purl.obolibrary.org/obo/ma.owl\nproperty_value: dc-source http://purl.obolibrary.org/obo/mp.owl\nproperty_value: dc-source http://purl.obolibrary.org/obo/tao.owl\nproperty_value: dc-source http://purl.obolibrary.org/obo/vhog.owl\nproperty_value: dc-source http://purl.obolibrary.org/obo/vsao.owl\nproperty_value: dc-source http://purl.obolibrary.org/obo/wbbt.owl\nproperty_value: dc-source http://purl.obolibrary.org/obo/xao.owl\nproperty_value: dc-source http://purl.obolibrary.org/obo/zfa.owl\nproperty_value: dc-source http://uri.neuinfo.org/nif/nifstd\nproperty_value: dc-source \"http://wiki.phenotypercn.org/wg/phenotypercn/index.php?title=Neural_Crest_Workshop\" xsd:anyURI\nproperty_value: dc-source \"http://wiki.phenotypercn.org/wiki/August_2012_Notes\" xsd:anyURI\nproperty_value: dc-source http://www.brain-map.org\nproperty_value: dc-source http://www.e-lico.eu/public/kupo/kupo.owl\nproperty_value: dc-source http://www.ebi.ac.uk/efo/efo.owl\nproperty_value: dc-source \"https://docs.google.com/document/d/16JZOuH9sh_a8uIXA4cqg0Q1H6MV5yCj3-rhuKsZoV_U/edit\" xsd:anyURI\nproperty_value: dc-source \"https://docs.google.com/document/d/1cPWBqrl_Qy7XHEWFqtR_PgQX61yRkgGuLaiDpnEXxkE/edit\" xsd:anyURI\nproperty_value: dc-source \"https://docs.google.com/document/d/1MnUgispgGfNQoezYzWzzGTnkAnI0gzRnJIwdip6MMtw/edit\" xsd:anyURI\nproperty_value: dc-source \"https://docs.google.com/document/d/1r9kNPpFYGdu0SpJDLyFAVQczBlG0wAZCBMd18gG3Ot8/edit#\" xsd:anyURI\nproperty_value: dc-source \"https://docs.google.com/spreadsheet/ccc?key=0Aj8NJdyb-leqdDM0R3hTVTRHRExDVjRCSkZEbDc5N1E#gid=0\" xsd:anyURI\nproperty_value: dc-source \"ISBN:0030229073 Invertebrate Zoology, Barnes\" xsd:string\nproperty_value: dc-source \"ISBN:0073040584 Vertebrates, Kardong\" xsd:string\nproperty_value: dc-source \"ISBN:0123813611 Comparative Anatomy and Histology: A Mouse and Human Atlas, Treuting and Dintzis\" xsd:string\nproperty_value: dc-source \"ISBN:0226313379 Fins into Limbs: Evolution, Development, and Transformation, Hall\" xsd:string\nproperty_value: dc-source \"ISBN:0443065837 Human embryology, Larsen\" xsd:string\nproperty_value: dc-source \"ISBN:0471888893 Comparative Vertebrate Neuroanatomy: Evolution and Adaptation by Butler and Hodos\" xsd:string\nproperty_value: dc-source \"ISBN:0683400088 Stedman's Medical Dictionary\" xsd:string\nproperty_value: dc-source \"ISBN:1588900649 Color Atlas and Textbook of Human Anatomy: Nervous system and sensory organs By Werner Kahle, Michael Frotscher\" xsd:string\nproperty_value: dc-source \"ISBN:1588903958 Principles and practice of pediatric neurosurgery By A. Leland Albright, P. David Adelson, Ian F. Pollack\" xsd:string\nproperty_value: dc-source \"ISBN:1607950324 Craniofacial Embryogenetics & Development, 2nd edition, Sperber\" xsd:string\nproperty_value: dc-source \"ISBN:978-0-12-369548-2 Principles of Developmental Genetics, Sally A Moody\" xsd:string\nproperty_value: dc-source \"ISBN:9780120749034 The laboratory rat\" xsd:string\nproperty_value: dc-source \"ISBN:9780397517251 Surgical anatomy of the hand and upper extremity. By James R. Doyle and Michael J. Botte\" xsd:string\nproperty_value: dc-source \"ISBN:9780674021839 The Tree of Life - Guillaume Lecointre, Herve Le Guyader\" xsd:string\nproperty_value: dc-source \"ISBN:9780878932504 Developmental Biology\" xsd:string\nproperty_value: dc-source \"MESH\" xsd:string\nproperty_value: dc-source \"PMID:11433360 Placental development: lessons from mouse mutants\" xsd:string\nproperty_value: dc-source \"PMID:16417468 Forgotten and novel aspects in pancreas development, Pieler and Chen\" xsd:string\nproperty_value: dc-title \"Uber-anatomy ontology\" xsd:string\nproperty_value: dcterms-isReferencedBy \"http://genomebiology.com/2012/13/1/R5\" xsd:anyURI\nproperty_value: dcterms-isReferencedBy \"http://www.ncbi.nlm.nih.gov/pubmed/22293552\" xsd:anyURI\nproperty_value: dcterms-license http://creativecommons.org/licenses/by/3.0/\nproperty_value: doap-bug-database \"https://github.com/obophenotype/uberon/issues/\" xsd:anyURI\nproperty_value: doap-GitRepository \"https://github.com/cmungall/uberon/\" xsd:anyURI\nproperty_value: doap-mailing-list \"https://lists.sourceforge.net/lists/listinfo/obo-anatomy\" xsd:anyURI\nproperty_value: doap-SVNRepository \"https://obo.svn.sourceforge.net/svnroot/obo/uberon/\" xsd:anyURI\nproperty_value: foaf-homepage \"http://uberon.org\" xsd:anyURI\nproperty_value: has_ontology_root_term UBERON:0000104\nproperty_value: has_ontology_root_term UBERON:0001062\ntreat-xrefs-as-has-subclass: EHDAA\ntreat-xrefs-as-has-subclass: EV\ntreat-xrefs-as-has-subclass: NCIT\ntreat-xrefs-as-has-subclass: OGES\ntreat-xrefs-as-has-subclass: SCTID\ntreat-xrefs-as-reverse-genus-differentia: AAO part_of NCBITaxon:8292\ntreat-xrefs-as-reverse-genus-differentia: DHBA part_of NCBITaxon:9606\ntreat-xrefs-as-reverse-genus-differentia: EHDAA2 part_of NCBITaxon:9606\ntreat-xrefs-as-reverse-genus-differentia: EMAPA part_of NCBITaxon:10090\ntreat-xrefs-as-reverse-genus-differentia: FBdv part_of NCBITaxon:7227\ntreat-xrefs-as-reverse-genus-differentia: FMA part_of NCBITaxon:9606\ntreat-xrefs-as-reverse-genus-differentia: HAO part_of NCBITaxon:7399\ntreat-xrefs-as-reverse-genus-differentia: HBA part_of NCBITaxon:9606\ntreat-xrefs-as-reverse-genus-differentia: KUPO part_of NCBITaxon:9606\ntreat-xrefs-as-reverse-genus-differentia: MA part_of NCBITaxon:10090\ntreat-xrefs-as-reverse-genus-differentia: MFO part_of NCBITaxon:8089\ntreat-xrefs-as-reverse-genus-differentia: PBA part_of NCBITaxon:9443\ntreat-xrefs-as-reverse-genus-differentia: SPD part_of NCBITaxon:6893\ntreat-xrefs-as-reverse-genus-differentia: TADS part_of NCBITaxon:6939\ntreat-xrefs-as-reverse-genus-differentia: TAO part_of NCBITaxon:32443\ntreat-xrefs-as-reverse-genus-differentia: TGMA part_of NCBITaxon:44484\ntreat-xrefs-as-reverse-genus-differentia: WBbt part_of NCBITaxon:6237\ntreat-xrefs-as-reverse-genus-differentia: WBls part_of NCBITaxon:6237\ntreat-xrefs-as-reverse-genus-differentia: XAO part_of NCBITaxon:8353\ntreat-xrefs-as-reverse-genus-differentia: ZFA part_of NCBITaxon:7954\ntreat-xrefs-as-reverse-genus-differentia: ZFS part_of NCBITaxon:7954\n\n[Term]\nid: UBERON:0002099\nname: cardiac septum\ndef: \"The thin membranous structure between the two heart atria or the thick muscular structure between the two heart ventricles.\" [MESH:A07.541.459]\nsubset: pheno_slim\nsubset: uberon_slim\nsynonym: \"cardiac septa\" EXACT OMO:0003004 []\nsynonym: \"heart septa\" EXACT OMO:0003004 []\nsynonym: \"heart septum\" EXACT []\nsynonym: \"septum of heart\" EXACT []\nsynonym: \"spiral septa\" RELATED OMO:0003004 [XAO:0004141]\nxref: EMAPA:35400\nxref: FMA:7180\nxref: GAID:562\nxref: MA:0000083\nxref: MESH:D006346\nxref: NCIT:C49485\nxref: SCTID:362014000\nxref: UMLS:C0018819 {source=\"ncithesaurus:Heart_Septum\"}\nis_a: UBERON:0003037 ! septum\nintersection_of: UBERON:0003037 ! septum\nintersection_of: part_of UBERON:0000948 ! heart\nrelationship: adjacent_to UBERON:0004151 ! cardiac chamber\nrelationship: contributes_to_morphology_of UBERON:0000948 ! heart\nrelationship: part_of UBERON:0000948 ! heart\nproperty_value: external_ontology_notes \"in GO, septum morphogenesis is part of cardiac chamber morphogenesis; need to add axioms to infer this\" xsd:string {external_ontology=\"GO\"}\nproperty_value: taxon_notes \"'Terrestrial vertebrates have divided hearts in which septae separate the oxygenated and deoxygenated blood within the pulmonary and systemic circulations'\" xsd:string",
"tool_use_id": "toolu_015TojffyZvNTbkbsSgGo2PJ"
}
]
}
{
"id": "msg_01RrESanFCidm5iHejfuqd7E",
"type": "message",
"role": "assistant",
"model": "claude-3-7-sonnet-20250219",
"content": [
{
"type": "text",
"text": "Let me check the child terms of cardiac septum to understand what needs to be included in the updated definition."
},
{
"type": "tool_use",
"id": "toolu_01M4oSQSrio71gSujFXMEzAi",
"name": "Bash",
"input": {
"command": "obo-grep.pl -r 'relationship: is_a UBERON:0002099' src/ontology/uberon-edit.obo"
}
}
],
"stop_reason": "tool_use",
"stop_sequence": null,
"usage": {
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"cache_read_input_tokens": 31011,
"output_tokens": 110
}
}
{
"role": "user",
"content": [
{
"type": "tool_result",
"content": "format-version: 1.2\nsubsetdef: added_for_HCA \"Classes tagged with this subset property were added upon request from the Human Cell Atlas (HCA).\"\nsubsetdef: common_anatomy \"Terms applicable across life, not restricted to Metazoa\"\nsubsetdef: cumbo \"CUMBO\"\nsubsetdef: cyclostome_subset \"cyclostome structures\"\nsubsetdef: defined_by_cytoarchitecture \"brain region defined by cyto-architecture\"\nsubsetdef: defined_by_ordinal_series \"classes that are defined by relative position counting from first in a series of elements along an axis in an individual organism rather than by strict homology\"\nsubsetdef: developmental_classification \"developmental_classification\"\nsubsetdef: dubious_grouping \"Indicates that subclasses in AOs may be inappropriately linked\"\nsubsetdef: early_development \"A class that represents an early developmental structure, like a blastocyst. This part of the ontology is undergoing review to remove inappropriate grouping classes.\"\nsubsetdef: efo_slim \"EFO slim\"\nsubsetdef: emapa_ehdaa2 \"derived from the union of EHDAA2 and EMAPA - still to be checked\"\nsubsetdef: feed_aligned \"subset of classes that have logical defs text defs and synonyms aligned with FEED\"\nsubsetdef: functional_classification \"functional_classification\"\nsubsetdef: grouping_class \"Subset consisting of classes creating for grouping purposes\"\nsubsetdef: homology_grouping \"A grouping class that depends on an assumption of homology between subclasses\"\nsubsetdef: human_reference_atlas \"\"\nsubsetdef: inconsistent_with_fma \"classes that have some inconsistency with FMA\"\nsubsetdef: location_grouping \"\"\nsubsetdef: major_organ \"somewhat fuzzy grouping for analysis purposes, currently composed of something like: liver, heart, skeletal, kidney, bladder, brain, skin, mouth, esophagus, stomach, small intestine, large intestines, trachea nose, lungs, brain, spinal cord, peripheral nerves, kidneys, ureters, bladder, urethra, gonads\"\nsubsetdef: metazoa_core \"core classes typically found across metazoa. one purpose is to create a rough set of terms that could be used to start a new metazoan AO. Note this subset is not yet fully fleshed out\"\nsubsetdef: non_informative \"abstract class brought in to group ontology classes but not informative\"\nsubsetdef: organ_slim \"organs, excluding individual muscles and skeletal elements\"\nsubsetdef: pheno_slim \"Phenotype slim\"\nsubsetdef: phenotype_rcn \"A subset specifically created for the 2012 Phenotype RCN meeting. Includes some human-specific terms that may eventually be removed when they are adequately represented with part of relationships in FMA\"\nsubsetdef: uberon_slim \"Uberon slim - subset that excludes obscure terms and deep compositional terms\"\nsubsetdef: unverified_taxonomic_grouping \"Indicates that the class encompasses classes from other AOs that have not been verified\"\nsubsetdef: upper_level \"abstract upper-level terms not directly useful for analysis\"\nsubsetdef: vertebrate_core \"core classes typically found across vertebrates. one purpose is to create a rough set of terms that could be used to start a new vertebrate AO\"\nsynonymtypedef: BRAIN_NAME_ABV \"brain name abbreviations (drosophila)\"\nsynonymtypedef: COMPARATIVE_PREFERRED \"preferred term in the context of comparative anatomy\"\nsynonymtypedef: DEPRECATED \"A historic synonym, no longer encouraged\"\nsynonymtypedef: DEVELOPMENTAL \"developmental term\"\nsynonymtypedef: HOMOLOGY \"a synonym made on the basis of a possibly homologous structure in another species\"\nsynonymtypedef: HUMAN_PREFERRED \"preferred term when talking about an instance of this class in Homo sapiens\"\nsynonymtypedef: INCONSISTENT \"indicates that a synonym is used in an inconsistent or confusing way, typically between species\"\nsynonymtypedef: MISSPELLING \"a mis-spelling that is in common use and thus recorded\"\nsynonymtypedef: NON_AMNIOTE \"synonym that is inappropriate for amniotes\"\nsynonymtypedef: NON_MAMMAL \"synonym that is inappropriate for mammals\"\nsynonymtypedef: OMO:0003000 \"abbreviation\"\nsynonymtypedef: OMO:0003002 \"dubious synonym\"\nsynonymtypedef: OMO:0003004 \"plural form\"\nsynonymtypedef: OMO:0003011 \"latin term\"\nsynonymtypedef: PENDING_REVIEW \"expert consultation and attribution required\"\nsynonymtypedef: SENSU \"taxonomic disambiguation\"\nsynonymtypedef: SYSTEMATIC \"a systematic synonym used as the base name for design patterns\"\ndefault-namespace: uberon\ntreat-xrefs-as-equivalent: AEO\ntreat-xrefs-as-equivalent: BILA\ntreat-xrefs-as-equivalent: BSPO\ntreat-xrefs-as-equivalent: CARO\ntreat-xrefs-as-equivalent: GO\ntreat-xrefs-as-equivalent: OG\ntreat-xrefs-as-equivalent: VSAO\ntreat-xrefs-as-is_a: BFO\ntreat-xrefs-as-is_a: VHOG\nremark: Aurelie Comte, Bill Bug, Catherine Leroy, Duncan Davidson and Trish Whetzel are also contributors. However their ORCIDs were not found.\nimport: http://purl.obolibrary.org/obo/uberon/components/disjoint_union_over.owl\nimport: http://purl.obolibrary.org/obo/uberon/components/hra_depiction_3d_images.owl\nimport: http://purl.obolibrary.org/obo/uberon/components/hra_subset.owl\nimport: http://purl.obolibrary.org/obo/uberon/components/in-subset.owl\nimport: http://purl.obolibrary.org/obo/uberon/components/mappings.owl\nimport: http://purl.obolibrary.org/obo/uberon/components/vasculature_class.owl\nimport: http://purl.obolibrary.org/obo/uberon/imports/merged_import.owl\nimport: http://purl.obolibrary.org/obo/uberon/imports/orcidio_import.owl\nimport: http://purl.obolibrary.org/obo/uberon/patterns/definitions.owl\nontology: uberon/core\nproperty_value: dc-contributor https://github.com/orgs/pato-ontology/teams/pato-community\nproperty_value: dc-contributor https://orcid.org/0000-0001-5889-4463\nproperty_value: dc-contributor https://orcid.org/0000-0001-7433-0086\nproperty_value: dc-contributor https://orcid.org/0000-0001-7476-6306\nproperty_value: dc-contributor https://orcid.org/0000-0001-7920-5321\nproperty_value: dc-contributor https://orcid.org/0000-0001-7958-3701\nproperty_value: dc-contributor https://orcid.org/0000-0001-8682-8754\nproperty_value: dc-contributor https://orcid.org/0000-0001-9107-0714\nproperty_value: dc-contributor https://orcid.org/0000-0001-9990-8331\nproperty_value: dc-contributor https://orcid.org/0000-0002-0819-0473\nproperty_value: dc-contributor https://orcid.org/0000-0002-0956-8634\nproperty_value: dc-contributor https://orcid.org/0000-0002-1112-5832\nproperty_value: dc-contributor https://orcid.org/0000-0002-1572-1316\nproperty_value: dc-contributor https://orcid.org/0000-0002-1604-3078\nproperty_value: dc-contributor https://orcid.org/0000-0002-1615-2899\nproperty_value: dc-contributor https://orcid.org/0000-0002-2061-091X\nproperty_value: dc-contributor https://orcid.org/0000-0002-2244-7917\nproperty_value: dc-contributor https://orcid.org/0000-0002-3437-3329\nproperty_value: dc-contributor https://orcid.org/0000-0002-3467-2636\nproperty_value: dc-contributor https://orcid.org/0000-0002-3734-1859\nproperty_value: dc-contributor https://orcid.org/0000-0002-5111-7263\nproperty_value: dc-contributor https://orcid.org/0000-0002-6490-7723\nproperty_value: dc-contributor https://orcid.org/0000-0002-7073-9172\nproperty_value: dc-contributor https://orcid.org/0000-0002-8406-3871\nproperty_value: dc-contributor https://orcid.org/0000-0002-8455-3213\nproperty_value: dc-contributor https://orcid.org/0000-0002-8688-6599\nproperty_value: dc-contributor https://orcid.org/0000-0002-9415-5104\nproperty_value: dc-contributor https://orcid.org/0000-0002-9818-3030\nproperty_value: dc-contributor https://orcid.org/0000-0002-9900-7880\nproperty_value: dc-contributor https://orcid.org/0000-0003-1980-3228\nproperty_value: dc-contributor https://orcid.org/0000-0003-2105-2283\nproperty_value: dc-contributor https://orcid.org/0000-0003-2338-2550\nproperty_value: dc-contributor https://orcid.org/0000-0003-3691-0324\nproperty_value: dc-contributor https://orcid.org/0000-0003-4423-4370\nproperty_value: dc-contributor https://www.wikidata.org/wiki/Q11695472\nproperty_value: dc-contributor https://www.wikidata.org/wiki/Q23809253\nproperty_value: dc-contributor https://www.wikidata.org/wiki/Q4964264\nproperty_value: dc-contributor https://www.wikidata.org/wiki/Q54985720\nproperty_value: dc-contributor https://www.wikidata.org/wiki/Q6983890\nproperty_value: dc-contributor https://www.wikidata.org/wiki/Q7650732\nproperty_value: dc-contributor https://www.wikidata.org/wiki/Q85793053\nproperty_value: dc-creator https://orcid.org/0000-0001-5839-6798\nproperty_value: dc-creator https://orcid.org/0000-0001-7972-3866\nproperty_value: dc-creator https://orcid.org/0000-0001-9114-8737\nproperty_value: dc-creator https://orcid.org/0000-0002-1810-9886\nproperty_value: dc-creator https://orcid.org/0000-0002-6601-2165\nproperty_value: dc-creator https://orcid.org/0000-0002-7356-1779\nproperty_value: dc-creator https://orcid.org/0000-0002-9611-1279\nproperty_value: dc-creator https://orcid.org/0000-0003-3162-7490\nproperty_value: dc-creator https://orcid.org/0000-0003-3308-6245\nproperty_value: dc-description \"Uberon is an integrated cross-species anatomy ontology representing a variety of entities classified according to traditional anatomical criteria such as structure, function and developmental lineage. The ontology includes comprehensive relationships to taxon-specific anatomical ontologies, allowing integration of functional, phenotype and expression data.\" xsd:string\nproperty_value: dc-publisher \"http://uberon.org\" xsd:anyURI\nproperty_value: dc-source \"aggregates AAO from 13:04:2012\" xsd:string\nproperty_value: dc-source \"aggregates TAO from 09:08:2012\" xsd:string\nproperty_value: dc-source \"aggregates VSAO from 16:07:2012\" xsd:string\nproperty_value: dc-source http://braininfo.rprc.washington.edu/\nproperty_value: dc-source http://dbpedia.org\nproperty_value: dc-source http://en.wikipedia.org/wiki/\nproperty_value: dc-source http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-GrossAnatomy.owl\nproperty_value: dc-source http://palaeos.com\nproperty_value: dc-source http://pons.incf.org/wiki/Common_Upper_Mammalian_Brain_Ontology_%28Cumbo%29\nproperty_value: dc-source http://purl.obolibrary.org/obo/aao.owl\nproperty_value: dc-source http://purl.obolibrary.org/obo/aba.owl\nproperty_value: dc-source http://purl.obolibrary.org/obo/aeo.owl\nproperty_value: dc-source http://purl.obolibrary.org/obo/bila.owl\nproperty_value: dc-source http://purl.obolibrary.org/obo/bto.owl\nproperty_value: dc-source http://purl.obolibrary.org/obo/caro.owl\nproperty_value: dc-source http://purl.obolibrary.org/obo/cl.owl\nproperty_value: dc-source http://purl.obolibrary.org/obo/ehdaa2.owl\nproperty_value: dc-source http://purl.obolibrary.org/obo/emapa.owl\nproperty_value: dc-source http://purl.obolibrary.org/obo/fbbt.owl\nproperty_value: dc-source http://purl.obolibrary.org/obo/fma.owl\nproperty_value: dc-source http://purl.obolibrary.org/obo/go.owl\nproperty_value: dc-source http://purl.obolibrary.org/obo/hp.owl\nproperty_value: dc-source http://purl.obolibrary.org/obo/ma.owl\nproperty_value: dc-source http://purl.obolibrary.org/obo/mp.owl\nproperty_value: dc-source http://purl.obolibrary.org/obo/tao.owl\nproperty_value: dc-source http://purl.obolibrary.org/obo/vhog.owl\nproperty_value: dc-source http://purl.obolibrary.org/obo/vsao.owl\nproperty_value: dc-source http://purl.obolibrary.org/obo/wbbt.owl\nproperty_value: dc-source http://purl.obolibrary.org/obo/xao.owl\nproperty_value: dc-source http://purl.obolibrary.org/obo/zfa.owl\nproperty_value: dc-source http://uri.neuinfo.org/nif/nifstd\nproperty_value: dc-source \"http://wiki.phenotypercn.org/wg/phenotypercn/index.php?title=Neural_Crest_Workshop\" xsd:anyURI\nproperty_value: dc-source \"http://wiki.phenotypercn.org/wiki/August_2012_Notes\" xsd:anyURI\nproperty_value: dc-source http://www.brain-map.org\nproperty_value: dc-source http://www.e-lico.eu/public/kupo/kupo.owl\nproperty_value: dc-source http://www.ebi.ac.uk/efo/efo.owl\nproperty_value: dc-source \"https://docs.google.com/document/d/16JZOuH9sh_a8uIXA4cqg0Q1H6MV5yCj3-rhuKsZoV_U/edit\" xsd:anyURI\nproperty_value: dc-source \"https://docs.google.com/document/d/1cPWBqrl_Qy7XHEWFqtR_PgQX61yRkgGuLaiDpnEXxkE/edit\" xsd:anyURI\nproperty_value: dc-source \"https://docs.google.com/document/d/1MnUgispgGfNQoezYzWzzGTnkAnI0gzRnJIwdip6MMtw/edit\" xsd:anyURI\nproperty_value: dc-source \"https://docs.google.com/document/d/1r9kNPpFYGdu0SpJDLyFAVQczBlG0wAZCBMd18gG3Ot8/edit#\" xsd:anyURI\nproperty_value: dc-source \"https://docs.google.com/spreadsheet/ccc?key=0Aj8NJdyb-leqdDM0R3hTVTRHRExDVjRCSkZEbDc5N1E#gid=0\" xsd:anyURI\nproperty_value: dc-source \"ISBN:0030229073 Invertebrate Zoology, Barnes\" xsd:string\nproperty_value: dc-source \"ISBN:0073040584 Vertebrates, Kardong\" xsd:string\nproperty_value: dc-source \"ISBN:0123813611 Comparative Anatomy and Histology: A Mouse and Human Atlas, Treuting and Dintzis\" xsd:string\nproperty_value: dc-source \"ISBN:0226313379 Fins into Limbs: Evolution, Development, and Transformation, Hall\" xsd:string\nproperty_value: dc-source \"ISBN:0443065837 Human embryology, Larsen\" xsd:string\nproperty_value: dc-source \"ISBN:0471888893 Comparative Vertebrate Neuroanatomy: Evolution and Adaptation by Butler and Hodos\" xsd:string\nproperty_value: dc-source \"ISBN:0683400088 Stedman's Medical Dictionary\" xsd:string\nproperty_value: dc-source \"ISBN:1588900649 Color Atlas and Textbook of Human Anatomy: Nervous system and sensory organs By Werner Kahle, Michael Frotscher\" xsd:string\nproperty_value: dc-source \"ISBN:1588903958 Principles and practice of pediatric neurosurgery By A. Leland Albright, P. David Adelson, Ian F. Pollack\" xsd:string\nproperty_value: dc-source \"ISBN:1607950324 Craniofacial Embryogenetics & Development, 2nd edition, Sperber\" xsd:string\nproperty_value: dc-source \"ISBN:978-0-12-369548-2 Principles of Developmental Genetics, Sally A Moody\" xsd:string\nproperty_value: dc-source \"ISBN:9780120749034 The laboratory rat\" xsd:string\nproperty_value: dc-source \"ISBN:9780397517251 Surgical anatomy of the hand and upper extremity. By James R. Doyle and Michael J. Botte\" xsd:string\nproperty_value: dc-source \"ISBN:9780674021839 The Tree of Life - Guillaume Lecointre, Herve Le Guyader\" xsd:string\nproperty_value: dc-source \"ISBN:9780878932504 Developmental Biology\" xsd:string\nproperty_value: dc-source \"MESH\" xsd:string\nproperty_value: dc-source \"PMID:11433360 Placental development: lessons from mouse mutants\" xsd:string\nproperty_value: dc-source \"PMID:16417468 Forgotten and novel aspects in pancreas development, Pieler and Chen\" xsd:string\nproperty_value: dc-title \"Uber-anatomy ontology\" xsd:string\nproperty_value: dcterms-isReferencedBy \"http://genomebiology.com/2012/13/1/R5\" xsd:anyURI\nproperty_value: dcterms-isReferencedBy \"http://www.ncbi.nlm.nih.gov/pubmed/22293552\" xsd:anyURI\nproperty_value: dcterms-license http://creativecommons.org/licenses/by/3.0/\nproperty_value: doap-bug-database \"https://github.com/obophenotype/uberon/issues/\" xsd:anyURI\nproperty_value: doap-GitRepository \"https://github.com/cmungall/uberon/\" xsd:anyURI\nproperty_value: doap-mailing-list \"https://lists.sourceforge.net/lists/listinfo/obo-anatomy\" xsd:anyURI\nproperty_value: doap-SVNRepository \"https://obo.svn.sourceforge.net/svnroot/obo/uberon/\" xsd:anyURI\nproperty_value: foaf-homepage \"http://uberon.org\" xsd:anyURI\nproperty_value: has_ontology_root_term UBERON:0000104\nproperty_value: has_ontology_root_term UBERON:0001062\ntreat-xrefs-as-has-subclass: EHDAA\ntreat-xrefs-as-has-subclass: EV\ntreat-xrefs-as-has-subclass: NCIT\ntreat-xrefs-as-has-subclass: OGES\ntreat-xrefs-as-has-subclass: SCTID\ntreat-xrefs-as-reverse-genus-differentia: AAO part_of NCBITaxon:8292\ntreat-xrefs-as-reverse-genus-differentia: DHBA part_of NCBITaxon:9606\ntreat-xrefs-as-reverse-genus-differentia: EHDAA2 part_of NCBITaxon:9606\ntreat-xrefs-as-reverse-genus-differentia: EMAPA part_of NCBITaxon:10090\ntreat-xrefs-as-reverse-genus-differentia: FBdv part_of NCBITaxon:7227\ntreat-xrefs-as-reverse-genus-differentia: FMA part_of NCBITaxon:9606\ntreat-xrefs-as-reverse-genus-differentia: HAO part_of NCBITaxon:7399\ntreat-xrefs-as-reverse-genus-differentia: HBA part_of NCBITaxon:9606\ntreat-xrefs-as-reverse-genus-differentia: KUPO part_of NCBITaxon:9606\ntreat-xrefs-as-reverse-genus-differentia: MA part_of NCBITaxon:10090\ntreat-xrefs-as-reverse-genus-differentia: MFO part_of NCBITaxon:8089\ntreat-xrefs-as-reverse-genus-differentia: PBA part_of NCBITaxon:9443\ntreat-xrefs-as-reverse-genus-differentia: SPD part_of NCBITaxon:6893\ntreat-xrefs-as-reverse-genus-differentia: TADS part_of NCBITaxon:6939\ntreat-xrefs-as-reverse-genus-differentia: TAO part_of NCBITaxon:32443\ntreat-xrefs-as-reverse-genus-differentia: TGMA part_of NCBITaxon:44484\ntreat-xrefs-as-reverse-genus-differentia: WBbt part_of NCBITaxon:6237\ntreat-xrefs-as-reverse-genus-differentia: WBls part_of NCBITaxon:6237\ntreat-xrefs-as-reverse-genus-differentia: XAO part_of NCBITaxon:8353\ntreat-xrefs-as-reverse-genus-differentia: ZFA part_of NCBITaxon:7954\ntreat-xrefs-as-reverse-genus-differentia: ZFS part_of NCBITaxon:7954",
"tool_use_id": "toolu_01M4oSQSrio71gSujFXMEzAi"
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"text": "Let me use a different approach to check all child terms of cardiac septum:"
},
{
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"content": "Found 15 files\n/Users/cjm/repos/uberon/uberon.obo\n/Users/cjm/repos/uberon/src/ontology/uberon-edit-reasoned-tagged-filtered.obo\n/Users/cjm/repos/uberon/src/ontology/uberon-edit-reasoned-tagged.obo\n/Users/cjm/repos/uberon/src/ontology/uberon-edit-reasoned.obo\n/Users/cjm/repos/uberon/composite-vertebrate.obo\n/Users/cjm/repos/uberon/composite-metazoan.obo\n/Users/cjm/repos/uberon/composite-metazoan-basic.obo\n/Users/cjm/repos/uberon/bridge/uberon-bridge-to-ncit.obo\n/Users/cjm/repos/uberon/bridge/uberon-bridge-to-sctid.obo\n/Users/cjm/repos/uberon/src/ontology/taxmods/uberon-taxmod-amniote.obo\n/Users/cjm/repos/uberon/subsets/uberon-with-isa-for-FMA-MA-ZFA.obo\n/Users/cjm/repos/uberon/uberon-taxmod-amniote.obo\n/Users/cjm/repos/uberon/uberon-with-isa.obo\n/Users/cjm/repos/uberon/subsets/aves-basic.obo\n/Users/cjm/repos/uberon/musculoskeletal.obo",
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{
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"type": "message",
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"content": [
{
"type": "text",
"text": "Let me check the main uberon-edit.obo file for all cardiac septum child terms:"
},
{
"type": "tool_use",
"id": "toolu_018ZziHCqaexWVVDvmWZHqqY",
"name": "Bash",
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"command": "obo-grep.pl -r 'is_a: UBERON:0002099' src/ontology/uberon-edit.obo"
}
}
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"content": "format-version: 1.2\nsubsetdef: added_for_HCA \"Classes tagged with this subset property were added upon request from the Human Cell Atlas (HCA).\"\nsubsetdef: common_anatomy \"Terms applicable across life, not restricted to Metazoa\"\nsubsetdef: cumbo \"CUMBO\"\nsubsetdef: cyclostome_subset \"cyclostome structures\"\nsubsetdef: defined_by_cytoarchitecture \"brain region defined by cyto-architecture\"\nsubsetdef: defined_by_ordinal_series \"classes that are defined by relative position counting from first in a series of elements along an axis in an individual organism rather than by strict homology\"\nsubsetdef: developmental_classification \"developmental_classification\"\nsubsetdef: dubious_grouping \"Indicates that subclasses in AOs may be inappropriately linked\"\nsubsetdef: early_development \"A class that represents an early developmental structure, like a blastocyst. This part of the ontology is undergoing review to remove inappropriate grouping classes.\"\nsubsetdef: efo_slim \"EFO slim\"\nsubsetdef: emapa_ehdaa2 \"derived from the union of EHDAA2 and EMAPA - still to be checked\"\nsubsetdef: feed_aligned \"subset of classes that have logical defs text defs and synonyms aligned with FEED\"\nsubsetdef: functional_classification \"functional_classification\"\nsubsetdef: grouping_class \"Subset consisting of classes creating for grouping purposes\"\nsubsetdef: homology_grouping \"A grouping class that depends on an assumption of homology between subclasses\"\nsubsetdef: human_reference_atlas \"\"\nsubsetdef: inconsistent_with_fma \"classes that have some inconsistency with FMA\"\nsubsetdef: location_grouping \"\"\nsubsetdef: major_organ \"somewhat fuzzy grouping for analysis purposes, currently composed of something like: liver, heart, skeletal, kidney, bladder, brain, skin, mouth, esophagus, stomach, small intestine, large intestines, trachea nose, lungs, brain, spinal cord, peripheral nerves, kidneys, ureters, bladder, urethra, gonads\"\nsubsetdef: metazoa_core \"core classes typically found across metazoa. one purpose is to create a rough set of terms that could be used to start a new metazoan AO. Note this subset is not yet fully fleshed out\"\nsubsetdef: non_informative \"abstract class brought in to group ontology classes but not informative\"\nsubsetdef: organ_slim \"organs, excluding individual muscles and skeletal elements\"\nsubsetdef: pheno_slim \"Phenotype slim\"\nsubsetdef: phenotype_rcn \"A subset specifically created for the 2012 Phenotype RCN meeting. Includes some human-specific terms that may eventually be removed when they are adequately represented with part of relationships in FMA\"\nsubsetdef: uberon_slim \"Uberon slim - subset that excludes obscure terms and deep compositional terms\"\nsubsetdef: unverified_taxonomic_grouping \"Indicates that the class encompasses classes from other AOs that have not been verified\"\nsubsetdef: upper_level \"abstract upper-level terms not directly useful for analysis\"\nsubsetdef: vertebrate_core \"core classes typically found across vertebrates. one purpose is to create a rough set of terms that could be used to start a new vertebrate AO\"\nsynonymtypedef: BRAIN_NAME_ABV \"brain name abbreviations (drosophila)\"\nsynonymtypedef: COMPARATIVE_PREFERRED \"preferred term in the context of comparative anatomy\"\nsynonymtypedef: DEPRECATED \"A historic synonym, no longer encouraged\"\nsynonymtypedef: DEVELOPMENTAL \"developmental term\"\nsynonymtypedef: HOMOLOGY \"a synonym made on the basis of a possibly homologous structure in another species\"\nsynonymtypedef: HUMAN_PREFERRED \"preferred term when talking about an instance of this class in Homo sapiens\"\nsynonymtypedef: INCONSISTENT \"indicates that a synonym is used in an inconsistent or confusing way, typically between species\"\nsynonymtypedef: MISSPELLING \"a mis-spelling that is in common use and thus recorded\"\nsynonymtypedef: NON_AMNIOTE \"synonym that is inappropriate for amniotes\"\nsynonymtypedef: NON_MAMMAL \"synonym that is inappropriate for mammals\"\nsynonymtypedef: OMO:0003000 \"abbreviation\"\nsynonymtypedef: OMO:0003002 \"dubious synonym\"\nsynonymtypedef: OMO:0003004 \"plural form\"\nsynonymtypedef: OMO:0003011 \"latin term\"\nsynonymtypedef: PENDING_REVIEW \"expert consultation and attribution required\"\nsynonymtypedef: SENSU \"taxonomic disambiguation\"\nsynonymtypedef: SYSTEMATIC \"a systematic synonym used as the base name for design patterns\"\ndefault-namespace: uberon\ntreat-xrefs-as-equivalent: AEO\ntreat-xrefs-as-equivalent: BILA\ntreat-xrefs-as-equivalent: BSPO\ntreat-xrefs-as-equivalent: CARO\ntreat-xrefs-as-equivalent: GO\ntreat-xrefs-as-equivalent: OG\ntreat-xrefs-as-equivalent: VSAO\ntreat-xrefs-as-is_a: BFO\ntreat-xrefs-as-is_a: VHOG\nremark: Aurelie Comte, Bill Bug, Catherine Leroy, Duncan Davidson and Trish Whetzel are also contributors. However their ORCIDs were not found.\nimport: http://purl.obolibrary.org/obo/uberon/components/disjoint_union_over.owl\nimport: http://purl.obolibrary.org/obo/uberon/components/hra_depiction_3d_images.owl\nimport: http://purl.obolibrary.org/obo/uberon/components/hra_subset.owl\nimport: http://purl.obolibrary.org/obo/uberon/components/in-subset.owl\nimport: http://purl.obolibrary.org/obo/uberon/components/mappings.owl\nimport: http://purl.obolibrary.org/obo/uberon/components/vasculature_class.owl\nimport: http://purl.obolibrary.org/obo/uberon/imports/merged_import.owl\nimport: http://purl.obolibrary.org/obo/uberon/imports/orcidio_import.owl\nimport: http://purl.obolibrary.org/obo/uberon/patterns/definitions.owl\nontology: uberon/core\nproperty_value: dc-contributor https://github.com/orgs/pato-ontology/teams/pato-community\nproperty_value: dc-contributor https://orcid.org/0000-0001-5889-4463\nproperty_value: dc-contributor https://orcid.org/0000-0001-7433-0086\nproperty_value: dc-contributor https://orcid.org/0000-0001-7476-6306\nproperty_value: dc-contributor https://orcid.org/0000-0001-7920-5321\nproperty_value: dc-contributor https://orcid.org/0000-0001-7958-3701\nproperty_value: dc-contributor https://orcid.org/0000-0001-8682-8754\nproperty_value: dc-contributor https://orcid.org/0000-0001-9107-0714\nproperty_value: dc-contributor https://orcid.org/0000-0001-9990-8331\nproperty_value: dc-contributor https://orcid.org/0000-0002-0819-0473\nproperty_value: dc-contributor https://orcid.org/0000-0002-0956-8634\nproperty_value: dc-contributor https://orcid.org/0000-0002-1112-5832\nproperty_value: dc-contributor https://orcid.org/0000-0002-1572-1316\nproperty_value: dc-contributor https://orcid.org/0000-0002-1604-3078\nproperty_value: dc-contributor https://orcid.org/0000-0002-1615-2899\nproperty_value: dc-contributor https://orcid.org/0000-0002-2061-091X\nproperty_value: dc-contributor https://orcid.org/0000-0002-2244-7917\nproperty_value: dc-contributor https://orcid.org/0000-0002-3437-3329\nproperty_value: dc-contributor https://orcid.org/0000-0002-3467-2636\nproperty_value: dc-contributor https://orcid.org/0000-0002-3734-1859\nproperty_value: dc-contributor https://orcid.org/0000-0002-5111-7263\nproperty_value: dc-contributor https://orcid.org/0000-0002-6490-7723\nproperty_value: dc-contributor https://orcid.org/0000-0002-7073-9172\nproperty_value: dc-contributor https://orcid.org/0000-0002-8406-3871\nproperty_value: dc-contributor https://orcid.org/0000-0002-8455-3213\nproperty_value: dc-contributor https://orcid.org/0000-0002-8688-6599\nproperty_value: dc-contributor https://orcid.org/0000-0002-9415-5104\nproperty_value: dc-contributor https://orcid.org/0000-0002-9818-3030\nproperty_value: dc-contributor https://orcid.org/0000-0002-9900-7880\nproperty_value: dc-contributor https://orcid.org/0000-0003-1980-3228\nproperty_value: dc-contributor https://orcid.org/0000-0003-2105-2283\nproperty_value: dc-contributor https://orcid.org/0000-0003-2338-2550\nproperty_value: dc-contributor https://orcid.org/0000-0003-3691-0324\nproperty_value: dc-contributor https://orcid.org/0000-0003-4423-4370\nproperty_value: dc-contributor https://www.wikidata.org/wiki/Q11695472\nproperty_value: dc-contributor https://www.wikidata.org/wiki/Q23809253\nproperty_value: dc-contributor https://www.wikidata.org/wiki/Q4964264\nproperty_value: dc-contributor https://www.wikidata.org/wiki/Q54985720\nproperty_value: dc-contributor https://www.wikidata.org/wiki/Q6983890\nproperty_value: dc-contributor https://www.wikidata.org/wiki/Q7650732\nproperty_value: dc-contributor https://www.wikidata.org/wiki/Q85793053\nproperty_value: dc-creator https://orcid.org/0000-0001-5839-6798\nproperty_value: dc-creator https://orcid.org/0000-0001-7972-3866\nproperty_value: dc-creator https://orcid.org/0000-0001-9114-8737\nproperty_value: dc-creator https://orcid.org/0000-0002-1810-9886\nproperty_value: dc-creator https://orcid.org/0000-0002-6601-2165\nproperty_value: dc-creator https://orcid.org/0000-0002-7356-1779\nproperty_value: dc-creator https://orcid.org/0000-0002-9611-1279\nproperty_value: dc-creator https://orcid.org/0000-0003-3162-7490\nproperty_value: dc-creator https://orcid.org/0000-0003-3308-6245\nproperty_value: dc-description \"Uberon is an integrated cross-species anatomy ontology representing a variety of entities classified according to traditional anatomical criteria such as structure, function and developmental lineage. The ontology includes comprehensive relationships to taxon-specific anatomical ontologies, allowing integration of functional, phenotype and expression data.\" xsd:string\nproperty_value: dc-publisher \"http://uberon.org\" xsd:anyURI\nproperty_value: dc-source \"aggregates AAO from 13:04:2012\" xsd:string\nproperty_value: dc-source \"aggregates TAO from 09:08:2012\" xsd:string\nproperty_value: dc-source \"aggregates VSAO from 16:07:2012\" xsd:string\nproperty_value: dc-source http://braininfo.rprc.washington.edu/\nproperty_value: dc-source http://dbpedia.org\nproperty_value: dc-source http://en.wikipedia.org/wiki/\nproperty_value: dc-source http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-GrossAnatomy.owl\nproperty_value: dc-source http://palaeos.com\nproperty_value: dc-source http://pons.incf.org/wiki/Common_Upper_Mammalian_Brain_Ontology_%28Cumbo%29\nproperty_value: dc-source http://purl.obolibrary.org/obo/aao.owl\nproperty_value: dc-source http://purl.obolibrary.org/obo/aba.owl\nproperty_value: dc-source http://purl.obolibrary.org/obo/aeo.owl\nproperty_value: dc-source http://purl.obolibrary.org/obo/bila.owl\nproperty_value: dc-source http://purl.obolibrary.org/obo/bto.owl\nproperty_value: dc-source http://purl.obolibrary.org/obo/caro.owl\nproperty_value: dc-source http://purl.obolibrary.org/obo/cl.owl\nproperty_value: dc-source http://purl.obolibrary.org/obo/ehdaa2.owl\nproperty_value: dc-source http://purl.obolibrary.org/obo/emapa.owl\nproperty_value: dc-source http://purl.obolibrary.org/obo/fbbt.owl\nproperty_value: dc-source http://purl.obolibrary.org/obo/fma.owl\nproperty_value: dc-source http://purl.obolibrary.org/obo/go.owl\nproperty_value: dc-source http://purl.obolibrary.org/obo/hp.owl\nproperty_value: dc-source http://purl.obolibrary.org/obo/ma.owl\nproperty_value: dc-source http://purl.obolibrary.org/obo/mp.owl\nproperty_value: dc-source http://purl.obolibrary.org/obo/tao.owl\nproperty_value: dc-source http://purl.obolibrary.org/obo/vhog.owl\nproperty_value: dc-source http://purl.obolibrary.org/obo/vsao.owl\nproperty_value: dc-source http://purl.obolibrary.org/obo/wbbt.owl\nproperty_value: dc-source http://purl.obolibrary.org/obo/xao.owl\nproperty_value: dc-source http://purl.obolibrary.org/obo/zfa.owl\nproperty_value: dc-source http://uri.neuinfo.org/nif/nifstd\nproperty_value: dc-source \"http://wiki.phenotypercn.org/wg/phenotypercn/index.php?title=Neural_Crest_Workshop\" xsd:anyURI\nproperty_value: dc-source \"http://wiki.phenotypercn.org/wiki/August_2012_Notes\" xsd:anyURI\nproperty_value: dc-source http://www.brain-map.org\nproperty_value: dc-source http://www.e-lico.eu/public/kupo/kupo.owl\nproperty_value: dc-source http://www.ebi.ac.uk/efo/efo.owl\nproperty_value: dc-source \"https://docs.google.com/document/d/16JZOuH9sh_a8uIXA4cqg0Q1H6MV5yCj3-rhuKsZoV_U/edit\" xsd:anyURI\nproperty_value: dc-source \"https://docs.google.com/document/d/1cPWBqrl_Qy7XHEWFqtR_PgQX61yRkgGuLaiDpnEXxkE/edit\" xsd:anyURI\nproperty_value: dc-source \"https://docs.google.com/document/d/1MnUgispgGfNQoezYzWzzGTnkAnI0gzRnJIwdip6MMtw/edit\" xsd:anyURI\nproperty_value: dc-source \"https://docs.google.com/document/d/1r9kNPpFYGdu0SpJDLyFAVQczBlG0wAZCBMd18gG3Ot8/edit#\" xsd:anyURI\nproperty_value: dc-source \"https://docs.google.com/spreadsheet/ccc?key=0Aj8NJdyb-leqdDM0R3hTVTRHRExDVjRCSkZEbDc5N1E#gid=0\" xsd:anyURI\nproperty_value: dc-source \"ISBN:0030229073 Invertebrate Zoology, Barnes\" xsd:string\nproperty_value: dc-source \"ISBN:0073040584 Vertebrates, Kardong\" xsd:string\nproperty_value: dc-source \"ISBN:0123813611 Comparative Anatomy and Histology: A Mouse and Human Atlas, Treuting and Dintzis\" xsd:string\nproperty_value: dc-source \"ISBN:0226313379 Fins into Limbs: Evolution, Development, and Transformation, Hall\" xsd:string\nproperty_value: dc-source \"ISBN:0443065837 Human embryology, Larsen\" xsd:string\nproperty_value: dc-source \"ISBN:0471888893 Comparative Vertebrate Neuroanatomy: Evolution and Adaptation by Butler and Hodos\" xsd:string\nproperty_value: dc-source \"ISBN:0683400088 Stedman's Medical Dictionary\" xsd:string\nproperty_value: dc-source \"ISBN:1588900649 Color Atlas and Textbook of Human Anatomy: Nervous system and sensory organs By Werner Kahle, Michael Frotscher\" xsd:string\nproperty_value: dc-source \"ISBN:1588903958 Principles and practice of pediatric neurosurgery By A. Leland Albright, P. David Adelson, Ian F. Pollack\" xsd:string\nproperty_value: dc-source \"ISBN:1607950324 Craniofacial Embryogenetics & Development, 2nd edition, Sperber\" xsd:string\nproperty_value: dc-source \"ISBN:978-0-12-369548-2 Principles of Developmental Genetics, Sally A Moody\" xsd:string\nproperty_value: dc-source \"ISBN:9780120749034 The laboratory rat\" xsd:string\nproperty_value: dc-source \"ISBN:9780397517251 Surgical anatomy of the hand and upper extremity. By James R. Doyle and Michael J. Botte\" xsd:string\nproperty_value: dc-source \"ISBN:9780674021839 The Tree of Life - Guillaume Lecointre, Herve Le Guyader\" xsd:string\nproperty_value: dc-source \"ISBN:9780878932504 Developmental Biology\" xsd:string\nproperty_value: dc-source \"MESH\" xsd:string\nproperty_value: dc-source \"PMID:11433360 Placental development: lessons from mouse mutants\" xsd:string\nproperty_value: dc-source \"PMID:16417468 Forgotten and novel aspects in pancreas development, Pieler and Chen\" xsd:string\nproperty_value: dc-title \"Uber-anatomy ontology\" xsd:string\nproperty_value: dcterms-isReferencedBy \"http://genomebiology.com/2012/13/1/R5\" xsd:anyURI\nproperty_value: dcterms-isReferencedBy \"http://www.ncbi.nlm.nih.gov/pubmed/22293552\" xsd:anyURI\nproperty_value: dcterms-license http://creativecommons.org/licenses/by/3.0/\nproperty_value: doap-bug-database \"https://github.com/obophenotype/uberon/issues/\" xsd:anyURI\nproperty_value: doap-GitRepository \"https://github.com/cmungall/uberon/\" xsd:anyURI\nproperty_value: doap-mailing-list \"https://lists.sourceforge.net/lists/listinfo/obo-anatomy\" xsd:anyURI\nproperty_value: doap-SVNRepository \"https://obo.svn.sourceforge.net/svnroot/obo/uberon/\" xsd:anyURI\nproperty_value: foaf-homepage \"http://uberon.org\" xsd:anyURI\nproperty_value: has_ontology_root_term UBERON:0000104\nproperty_value: has_ontology_root_term UBERON:0001062\ntreat-xrefs-as-has-subclass: EHDAA\ntreat-xrefs-as-has-subclass: EV\ntreat-xrefs-as-has-subclass: NCIT\ntreat-xrefs-as-has-subclass: OGES\ntreat-xrefs-as-has-subclass: SCTID\ntreat-xrefs-as-reverse-genus-differentia: AAO part_of NCBITaxon:8292\ntreat-xrefs-as-reverse-genus-differentia: DHBA part_of NCBITaxon:9606\ntreat-xrefs-as-reverse-genus-differentia: EHDAA2 part_of NCBITaxon:9606\ntreat-xrefs-as-reverse-genus-differentia: EMAPA part_of NCBITaxon:10090\ntreat-xrefs-as-reverse-genus-differentia: FBdv part_of NCBITaxon:7227\ntreat-xrefs-as-reverse-genus-differentia: FMA part_of NCBITaxon:9606\ntreat-xrefs-as-reverse-genus-differentia: HAO part_of NCBITaxon:7399\ntreat-xrefs-as-reverse-genus-differentia: HBA part_of NCBITaxon:9606\ntreat-xrefs-as-reverse-genus-differentia: KUPO part_of NCBITaxon:9606\ntreat-xrefs-as-reverse-genus-differentia: MA part_of NCBITaxon:10090\ntreat-xrefs-as-reverse-genus-differentia: MFO part_of NCBITaxon:8089\ntreat-xrefs-as-reverse-genus-differentia: PBA part_of NCBITaxon:9443\ntreat-xrefs-as-reverse-genus-differentia: SPD part_of NCBITaxon:6893\ntreat-xrefs-as-reverse-genus-differentia: TADS part_of NCBITaxon:6939\ntreat-xrefs-as-reverse-genus-differentia: TAO part_of NCBITaxon:32443\ntreat-xrefs-as-reverse-genus-differentia: TGMA part_of NCBITaxon:44484\ntreat-xrefs-as-reverse-genus-differentia: WBbt part_of NCBITaxon:6237\ntreat-xrefs-as-reverse-genus-differentia: WBls part_of NCBITaxon:6237\ntreat-xrefs-as-reverse-genus-differentia: XAO part_of NCBITaxon:8353\ntreat-xrefs-as-reverse-genus-differentia: ZFA part_of NCBITaxon:7954\ntreat-xrefs-as-reverse-genus-differentia: ZFS part_of NCBITaxon:7954",
"tool_use_id": "toolu_018ZziHCqaexWVVDvmWZHqqY"
}
]
}
{
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"type": "message",
"role": "assistant",
"model": "claude-3-7-sonnet-20250219",
"content": [
{
"type": "text",
"text": "Let me try another approach to find the child terms of cardiac septum:"
},
{
"type": "tool_use",
"id": "toolu_01QfLEREgbjpXLPNi7JW8rxe",
"name": "dispatch_agent",
"input": {
"prompt": "Find all child terms of cardiac septum (UBERON:0002099) in the uberon-edit.obo file. Look for terms that have \"is_a: UBERON:0002099\" in their definition. For each child term found, provide the term ID, term name, and definition."
}
}
],
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}
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{
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"content": [
{
"type": "tool_result",
"content": "Cannot read properties of undefined (reading 'filename')",
"is_error": true,
"tool_use_id": "toolu_01QfLEREgbjpXLPNi7JW8rxe"
}
]
}
{
"id": "msg_01Fs8bABHu5b25Y56b3R4U49",
"type": "message",
"role": "assistant",
"model": "claude-3-7-sonnet-20250219",
"content": [
{
"type": "text",
"text": "Let me try using the GlobTool to help find relevant files more efficiently:"
},
{
"type": "tool_use",
"id": "toolu_0125xQh5ATphdMNcJTwQhxMi",
"name": "GlobTool",
"input": {
"pattern": "**/*uberon*.obo"
}
}
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{
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{
"type": "tool_result",
"content": "/Users/cjm/repos/uberon/attic/uberon_disjoint_from_strict.obo\n/Users/cjm/repos/uberon/experimental/zebrafish_anatomy_xp_uberon.obo\n/Users/cjm/repos/uberon/experimental/uberon_xp.obo\n/Users/cjm/repos/uberon/experimental/uberon_CL.obo\n/Users/cjm/repos/uberon/experimental/mouse_anatomy_xp_uberon.obo\n/Users/cjm/repos/uberon/experimental/hog_xp_uberon.obo\n/Users/cjm/repos/uberon/experimental/fma_xp_uberon.obo\n/Users/cjm/repos/uberon/uberon-with-isa.obo\n/Users/cjm/repos/uberon/uberon-simple-rel.obo\n/Users/cjm/repos/uberon/uberon-taxmod-amniote.obo\n/Users/cjm/repos/uberon/subsets/uberon-with-isa-for-FMA-MA-ZFA.obo\n/Users/cjm/repos/uberon/src/ontology/taxmods/uberon-taxmod-amniote.obo\n/Users/cjm/repos/uberon/bridge/uberon-ext-bridge-to-zfa.obo\n/Users/cjm/repos/uberon/bridge/uberon-bridge-to-zfs.obo\n/Users/cjm/repos/uberon/bridge/uberon-bridge-to-zfa.obo\n/Users/cjm/repos/uberon/bridge/uberon-bridge-to-xao.obo\n/Users/cjm/repos/uberon/bridge/uberon-bridge-to-wbls.obo\n/Users/cjm/repos/uberon/bridge/uberon-bridge-to-wbbt.obo\n/Users/cjm/repos/uberon/bridge/uberon-bridge-to-vsao.obo\n/Users/cjm/repos/uberon/bridge/uberon-bridge-to-vhog.obo\n/Users/cjm/repos/uberon/bridge/uberon-bridge-to-vao.obo\n/Users/cjm/repos/uberon/bridge/uberon-bridge-to-tgma.obo\n/Users/cjm/repos/uberon/bridge/uberon-bridge-to-tao.obo\n/Users/cjm/repos/uberon/bridge/uberon-bridge-to-tads.obo\n/Users/cjm/repos/uberon/bridge/uberon-bridge-to-spd.obo\n/Users/cjm/repos/uberon/bridge/uberon-bridge-to-sctid.obo\n/Users/cjm/repos/uberon/bridge/uberon-bridge-to-pba.obo\n/Users/cjm/repos/uberon/bridge/uberon-bridge-to-olatdv.obo\n/Users/cjm/repos/uberon/bridge/uberon-bridge-to-oges.obo\n/Users/cjm/repos/uberon/bridge/uberon-bridge-to-og.obo\n/Users/cjm/repos/uberon/bridge/uberon-bridge-to-nifstd.obo\n/Users/cjm/repos/uberon/bridge/uberon-bridge-to-ncit.obo\n/Users/cjm/repos/uberon/bridge/uberon-bridge-to-mfo.obo\n/Users/cjm/repos/uberon/bridge/uberon-bridge-to-mmusdv.obo\n/Users/cjm/repos/uberon/bridge/uberon-bridge-to-mba.obo\n/Users/cjm/repos/uberon/bridge/uberon-bridge-to-ma.obo\n/Users/cjm/repos/uberon/bridge/uberon-bridge-to-hsapdv.obo\n/Users/cjm/repos/uberon/bridge/uberon-bridge-to-hba.obo\n/Users/cjm/repos/uberon/bridge/uberon-bridge-to-hao.obo\n/Users/cjm/repos/uberon/bridge/uberon-bridge-to-go.obo\n/Users/cjm/repos/uberon/bridge/uberon-bridge-to-fma.obo\n/Users/cjm/repos/uberon/bridge/uberon-bridge-to-fbdv.obo\n/Users/cjm/repos/uberon/bridge/uberon-bridge-to-fbbt.obo\n/Users/cjm/repos/uberon/bridge/uberon-bridge-to-ev.obo\n/Users/cjm/repos/uberon/bridge/uberon-bridge-to-emapa.obo\n/Users/cjm/repos/uberon/bridge/uberon-bridge-to-emap.obo\n/Users/cjm/repos/uberon/bridge/uberon-bridge-to-ehdaa2.obo\n/Users/cjm/repos/uberon/bridge/uberon-bridge-to-ehdaa.obo\n/Users/cjm/repos/uberon/bridge/uberon-bridge-to-efo.obo\n/Users/cjm/repos/uberon/bridge/uberon-bridge-to-dmba.obo\n/Users/cjm/repos/uberon/bridge/uberon-bridge-to-dhba.obo\n/Users/cjm/repos/uberon/bridge/uberon-bridge-to-caro.obo\n/Users/cjm/repos/uberon/bridge/uberon-bridge-to-bsd.obo\n/Users/cjm/repos/uberon/bridge/uberon-bridge-to-bspo.obo\n/Users/cjm/repos/uberon/bridge/uberon-bridge-to-bila.obo\n/Users/cjm/repos/uberon/bridge/uberon-bridge-to-bfo.obo\n/Users/cjm/repos/uberon/bridge/uberon-bridge-to-aeo.obo\n/Users/cjm/repos/uberon/bridge/uberon-bridge-to-aba.obo\n/Users/cjm/repos/uberon/bridge/uberon-bridge-to-aao.obo\n/Users/cjm/repos/uberon/bridge/hdr-uberon-ext-bridge-to-zfa.obo\n/Users/cjm/repos/uberon/bridge/hdr-uberon-bridge-to-zfa.obo\n/Users/cjm/repos/uberon/bridge/hdr-uberon-bridge-to-xao.obo\n/Users/cjm/repos/uberon/bridge/hdr-uberon-bridge-to-vsao.obo\n/Users/cjm/repos/uberon/bridge/hdr-uberon-bridge-to-vhog.obo\n/Users/cjm/repos/uberon/bridge/hdr-uberon-bridge-to-tao.obo\n/Users/cjm/repos/uberon/bridge/hdr-uberon-bridge-to-sctid.obo\n/Users/cjm/repos/uberon/bridge/hdr-uberon-bridge-to-ma.obo\n/Users/cjm/repos/uberon/bridge/hdr-uberon-bridge-to-fma.obo\n/Users/cjm/repos/uberon/bridge/hdr-uberon-bridge-to-fbbt.obo\n/Users/cjm/repos/uberon/bridge/hdr-uberon-bridge-to-emapa.obo\n/Users/cjm/repos/uberon/bridge/hdr-uberon-bridge-to-ehdaa2.obo\n/Users/cjm/repos/uberon/bridge/hdr-uberon-bridge-to-aao.obo\n/Users/cjm/repos/uberon/src/ontology/uberon-edit-reasoned.obo\n/Users/cjm/repos/uberon/src/ontology/uberon-edit-reasoned-tagged.obo\n/Users/cjm/repos/uberon/src/ontology/uberon-edit-reasoned-tagged-filtered.obo\n/Users/cjm/repos/uberon/uberon.obo\n/Users/cjm/repos/uberon/terms/UBERON_0000002.obo\n/Users/cjm/repos/uberon/terms/UBERON_0000451.obo\n/Users/cjm/repos/uberon/terms/UBERON_0002616.obo\n/Users/cjm/repos/uberon/src/ontology/uberon-edit.obo\n/Users/cjm/repos/uberon/terms/UBERON_0002099.obo\n/Users/cjm/repos/uberon/terms/UBERON_0002085.obo\n/Users/cjm/repos/uberon/terms/UBERON_0004142.obo\n/Users/cjm/repos/uberon/terms/UBERON_0005989.obo\n/Users/cjm/repos/uberon/terms/UBERON_0015224.obo\n/Users/cjm/repos/uberon/terms/UBERON_0015225.obo\n/Users/cjm/repos/uberon/terms/UBERON_0015226.obo\n/Users/cjm/repos/uberon/terms/UBERON_0002094.obo",
"tool_use_id": "toolu_0125xQh5ATphdMNcJTwQhxMi"
}
]
}
{
"id": "msg_01JZzvNQ5epojFV7MHNuDYc3",
"type": "message",
"role": "assistant",
"model": "claude-3-7-sonnet-20250219",
"content": [
{
"type": "text",
"text": "Let me try a better approach using Bash to find child terms:"
},
{
"type": "tool_use",
"id": "toolu_01RqFum2REydrszDs1sBprLg",
"name": "Bash",
"input": {
"command": "obo-checkout.pl src/ontology/uberon-edit.obo UBERON:0002099"
}
}
],
"stop_reason": "tool_use",
"stop_sequence": null,
"usage": {
"input_tokens": 6,
"cache_creation_input_tokens": 2499,
"cache_read_input_tokens": 50730,
"output_tokens": 92
}
}
{
"role": "user",
"content": [
{
"type": "tool_result",
"content": "Reading src/ontology/uberon-edit.obo\nChecking out UBERON:0002099",
"tool_use_id": "toolu_01RqFum2REydrszDs1sBprLg"
}
]
}
{
"id": "msg_01SCoc4keCimrkZV2R19bzQq",
"type": "message",
"role": "assistant",
"model": "claude-3-7-sonnet-20250219",
"content": [
{
"type": "text",
"text": "Let me look at what got checked out and examine the cardiac septum term first:"
},
{
"type": "tool_use",
"id": "toolu_01B9KuQSvyKPnLuYiYoVYaNr",
"name": "View",
"input": {
"file_path": "/Users/cjm/repos/uberon/terms/UBERON_0002099.obo"
}
}
],
"stop_reason": "tool_use",
"stop_sequence": null,
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"cache_read_input_tokens": 53229,
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}
}
{
"role": "user",
"content": [
{
"type": "tool_result",
"content": " 1\t[Term]\n 2\tid: UBERON:0002099\n 3\tname: cardiac septum\n 4\tdef: \"The thin membranous structure between the two heart atria or the thick muscular structure between the two heart ventricles.\" [MESH:A07.541.459]\n 5\tsubset: pheno_slim\n 6\tsubset: uberon_slim\n 7\tsynonym: \"cardiac septa\" EXACT OMO:0003004 []\n 8\tsynonym: \"heart septa\" EXACT OMO:0003004 []\n 9\tsynonym: \"heart septum\" EXACT []\n 10\tsynonym: \"septum of heart\" EXACT []\n 11\tsynonym: \"spiral septa\" RELATED OMO:0003004 [XAO:0004141]\n 12\txref: EMAPA:35400\n 13\txref: FMA:7180\n 14\txref: GAID:562\n 15\txref: MA:0000083\n 16\txref: MESH:D006346\n 17\txref: NCIT:C49485\n 18\txref: SCTID:362014000\n 19\txref: UMLS:C0018819 {source=\"ncithesaurus:Heart_Septum\"}\n 20\tis_a: UBERON:0003037 ! septum\n 21\tintersection_of: UBERON:0003037 ! septum\n 22\tintersection_of: part_of UBERON:0000948 ! heart\n 23\trelationship: adjacent_to UBERON:0004151 ! cardiac chamber\n 24\trelationship: contributes_to_morphology_of UBERON:0000948 ! heart\n 25\trelationship: part_of UBERON:0000948 ! heart\n 26\tproperty_value: external_ontology_notes \"in GO, septum morphogenesis is part of cardiac chamber morphogenesis; need to add axioms to infer this\" xsd:string {external_ontology=\"GO\"}\n 27\tproperty_value: taxon_notes \"'Terrestrial vertebrates have divided hearts in which septae separate the oxygenated and deoxygenated blood within the pulmonary and systemic circulations'\" xsd:string\n 28\t\n 29\t",
"tool_use_id": "toolu_01B9KuQSvyKPnLuYiYoVYaNr"
}
]
}
{
"id": "msg_01W6RaRsc4M9KpCiNneJqDr1",
"type": "message",
"role": "assistant",
"model": "claude-3-7-sonnet-20250219",
"content": [
{
"type": "text",
"text": "Now let me search for terms with a relationship to cardiac septum to understand what needs to be included in the updated definition:"
},
{
"type": "tool_use",
"id": "toolu_01F71diQd5Jf3nH6mM9zFEfw",
"name": "Bash",
"input": {
"command": "grep -A5 \"is_a: UBERON:0002099\" src/ontology/uberon-edit.obo | grep \"^id\\|^name\\|^def:\""
}
}
],
"stop_reason": "tool_use",
"stop_sequence": null,
"usage": {
"input_tokens": 6,
"cache_creation_input_tokens": 660,
"cache_read_input_tokens": 53356,
"output_tokens": 122
}
}
{
"role": "user",
"content": [
{
"type": "tool_result",
"content": "Error",
"is_error": true,
"tool_use_id": "toolu_01F71diQd5Jf3nH6mM9zFEfw"
}
]
}
{
"id": "msg_019wipewtYgrU899Doa9KqqG",
"type": "message",
"role": "assistant",
"model": "claude-3-7-sonnet-20250219",
"content": [
{
"type": "text",
"text": "Let me use a better approach to find the child terms of cardiac septum:"
},
{
"type": "tool_use",
"id": "toolu_01TocwF1US3q8VBQPtj8eFHc",
"name": "GrepTool",
"input": {
"pattern": "is_a: UBERON:0002099",
"path": "/Users/cjm/repos/uberon/src/ontology/uberon-edit.obo"
}
}
],
"stop_reason": "tool_use",
"stop_sequence": null,
"usage": {
"input_tokens": 7,
"cache_creation_input_tokens": 141,
"cache_read_input_tokens": 54016,
"output_tokens": 122
}
}
{
"role": "user",
"content": [
{
"type": "tool_result",
"content": "No files found",
"tool_use_id": "toolu_01TocwF1US3q8VBQPtj8eFHc"
}
]
}
{
"id": "msg_01Wcnny5RdJmBsoUs2WhzS45",
"type": "message",
"role": "assistant",
"model": "claude-3-7-sonnet-20250219",
"content": [
{
"type": "text",
"text": "Let me try a different approach to find child terms:"
},
{
"type": "tool_use",
"id": "toolu_01YadGvWR6TSTEfTfGkZDpbo",
"name": "Bash",
"input": {
"command": "grep -n \"is_a: UBERON:0002099\" /Users/cjm/repos/uberon/src/ontology/uberon-edit.obo"
}
}
],
"stop_reason": "tool_use",
"stop_sequence": null,
"usage": {
"input_tokens": 6,
"cache_creation_input_tokens": 137,
"cache_read_input_tokens": 54157,
"output_tokens": 104
}
}
{
"role": "user",
"content": [
{
"type": "tool_result",
"content": "Error",
"is_error": true,
"tool_use_id": "toolu_01YadGvWR6TSTEfTfGkZDpbo"
}
]
}
{
"id": "msg_01TdN6c4Mo53pimZDLbW8umv",
"type": "message",
"role": "assistant",
"model": "claude-3-7-sonnet-20250219",
"content": [
{
"type": "text",
"text": "Let me take a more systematic approach to find the child terms:"
},
{
"type": "tool_use",
"id": "toolu_01CQzGRTNdjRqLZsoQVz7sE1",
"name": "Bash",
"input": {
"command": "cd /Users/cjm/repos/uberon && grep -B 20 -A 3 \"is_a: UBERON:0002099\" uberon.obo | grep -E \"^id:|^name:|^def:\""
}
}
],
"stop_reason": "tool_use",
"stop_sequence": null,
"usage": {
"input_tokens": 7,
"cache_creation_input_tokens": 123,
"cache_read_input_tokens": 54294,
"output_tokens": 122
}
}
{
"role": "user",
"content": [
{
"type": "tool_result",
"content": "name: interatrial septum\ndef: \"A cardiac septum that divides the left and right atria of the heart.\" [http://orcid.org/0000-0002-6601-2165]\nid: UBERON:0004142\nname: outflow tract septum\ndef: \"The outflow tract septum is a partition in the outflow tract.\" [GO:0003148]\nid: UBERON:0005989\nname: atrioventricular septum\ndef: \"The wall of the heart that separates the right atrium and left ventricle; and is located just above the septal cusp of the tricuspid valve.\" [MP:0010592]\nid: UBERON:0015225\nname: atrial foramen intermedium\ndef: \"An anatomical conduit that is part of a atrial septum intermedium.\" [OBOL:automatic]\nid: UBERON:0015226\nname: bulbar spiral septum",
"tool_use_id": "toolu_01CQzGRTNdjRqLZsoQVz7sE1"
}
]
}
{
"id": "msg_01XVEudemJw5sgEWaibgYPBi",
"type": "message",
"role": "assistant",
"model": "claude-3-7-sonnet-20250219",
"content": [
{
"type": "text",
"text": "I can now see some of the child terms. Let me search for a few of these to get their definitions:"
},
{
"type": "tool_use",
"id": "toolu_011GNVcVk2J9uLetghtYE6Wq",
"name": "GrepTool",
"input": {
"pattern": "bulbar spiral septum",
"path": "/Users/cjm/repos/uberon/uberon.obo"
}
}
],
"stop_reason": "tool_use",
"stop_sequence": null,
"usage": {
"input_tokens": 6,
"cache_creation_input_tokens": 359,
"cache_read_input_tokens": 54417,
"output_tokens": 116
}
}
{
"role": "user",
"content": [
{
"type": "tool_result",
"content": "Found 1 file\n/Users/cjm/repos/uberon/uberon.obo",
"tool_use_id": "toolu_011GNVcVk2J9uLetghtYE6Wq"
}
]
}
{
"id": "msg_01S7tSebCd1VQaoMZBo4EHuN",
"type": "message",
"role": "assistant",
"model": "claude-3-7-sonnet-20250219",
"content": [
{
"type": "tool_use",
"id": "toolu_01EbWQHaAp9KaxKyptS1XS3t",
"name": "Bash",
"input": {
"command": "cd /Users/cjm/repos/uberon && grep -A 10 \"id: UBERON:0015226\" uberon.obo"
}
}
],
"stop_reason": "tool_use",
"stop_sequence": null,
"usage": {
"input_tokens": 6,
"cache_creation_input_tokens": 150,
"cache_read_input_tokens": 54776,
"output_tokens": 87
}
}
{
"role": "user",
"content": [
{
"type": "tool_result",
"content": "id: UBERON:0015226\nname: bulbar spiral septum\nsubset: human_subset\nsubset: mouse_subset\nxref: SCTID:361469006\nis_a: UBERON:0002099 ! cardiac septum\nrelationship: part_of UBERON:0000948 ! heart\n\n[Term]\nid: UBERON:0015227\nname: peristaltic circulatory vessel",
"tool_use_id": "toolu_01EbWQHaAp9KaxKyptS1XS3t"
}
]
}
{
"id": "msg_01CKau7y95fK7SV5bDLdKJ1Z",
"type": "message",
"role": "assistant",
"model": "claude-3-7-sonnet-20250219",
"content": [
{
"type": "text",
"text": "Let me check for information about the interventricular septum and other key types of cardiac septa:"
},
{
"type": "tool_use",
"id": "toolu_01C2q9C37g2C9iERXiyc22FA",
"name": "GrepTool",
"input": {
"pattern": "interventricular septum",
"path": "/Users/cjm/repos/uberon/uberon.obo"
}
}
],
"stop_reason": "tool_use",
"stop_sequence": null,
"usage": {
"input_tokens": 6,
"cache_creation_input_tokens": 197,
"cache_read_input_tokens": 54926,
"output_tokens": 114
}
}
{
"role": "user",
"content": [
{
"type": "tool_result",
"content": "Found 1 file\n/Users/cjm/repos/uberon/uberon.obo",
"tool_use_id": "toolu_01C2q9C37g2C9iERXiyc22FA"
}
]
}
{
"id": "msg_01DbVsz8LGxJ9CsRj4nANyxs",
"type": "message",
"role": "assistant",
"model": "claude-3-7-sonnet-20250219",
"content": [
{
"type": "tool_use",
"id": "toolu_01FtBB6qHyh2y9bTXHygSm9Z",
"name": "Bash",
"input": {
"command": "cd /Users/cjm/repos/uberon && grep -B 3 -A 15 \"name: interventricular septum\" uberon.obo"
}
}
],
"stop_reason": "tool_use",
"stop_sequence": null,
"usage": {
"input_tokens": 6,
"cache_creation_input_tokens": 148,
"cache_read_input_tokens": 55123,
"output_tokens": 90
}
}
{
"role": "user",
"content": [
{
"type": "tool_result",
"content": "[Term]\nid: UBERON:0002094\nname: interventricular septum\ndef: \"Cardiac septum which separates the right ventricle from the left ventricle.[FMA].\" [FMA:7133]\nsubset: efo_slim\nsubset: human_reference_atlas\nsubset: human_subset\nsubset: mouse_subset\nsubset: pheno_slim\nsubset: uberon_slim\nsynonym: \"heart interventricular septum\" EXACT [MA:0000085]\nsynonym: \"heart ventricular septum\" EXACT [MA:0000085]\nsynonym: \"interventricular septum of heart\" RELATED [BTO:0002483]\nsynonym: \"interventriculare cordis\" RELATED [BTO:0002483]\nsynonym: \"intraventricular septum\" RELATED [Wikipedia:Interventricular_septum]\nsynonym: \"s. interventriculare cordis\" RELATED OMO:0003011 [Wikipedia:Interventricular_septum]\nsynonym: \"septum inferius\" RELATED [Wikipedia:Interventricular_septum]\nsynonym: \"septum membranaceum\" RELATED [Wikipedia:Interventricular_septum]\n--\n\n[Term]\nid: UBERON:0004666\nname: interventricular septum membranous part\nalt_id: UBERON:0004143\ndef: \"The membranous portion of the wall between the two lower chambers of the heart.\" [MP:0008823]\nsubset: human_subset\nsubset: mouse_subset\nsubset: pheno_slim\nsynonym: \"cardiac ventricular membranous septum\" EXACT [http://orcid.org/0000-0002-6601-2165]\nsynonym: \"membranous interventricular septum\" EXACT [FMA:7135]\nsynonym: \"membranous interventricular septum\" RELATED [MA:0002939]\nsynonym: \"membranous part interventricular septum\" EXACT [VHOG:0000927]\nsynonym: \"membranous part of interventricular septum\" EXACT [FMA:7135]\nsynonym: \"membranous portion of interventricular septum\" EXACT [FMA:7135]\nsynonym: \"membranous septum\" BROAD [GO:0003149]\nsynonym: \"pars membranacea (septi interventricularis)\" EXACT [FMA:7135]\nsynonym: \"pars membranacea septi interventricularis\" EXACT OMO:0003011 [FMA:7135, FMA:TA]\nsynonym: \"ventricle membranous septum\" BROAD [VT:0000018]\n--\n\n[Term]\nid: UBERON:0004667\nname: interventricular septum muscular part\nalt_id: UBERON:0004144\ndef: \"The muscular portion of the wall between the two lower chambers of the heart.\" [http://orcid.org/0000-0002-6601-2165, Wikipedia:Interventricular_septum#Portions]\nsubset: human_subset\nsubset: mouse_subset\nsubset: pheno_slim\nsynonym: \"cardiac ventricular muscular septum\" EXACT [http://orcid.org/0000-0002-6601-2165]\nsynonym: \"muscular interventricular septum\" EXACT [FMA:7134]\nsynonym: \"muscular interventricular septum\" RELATED [MA:0002940]\nsynonym: \"muscular part interventricular septum\" EXACT []\nsynonym: \"muscular part of interventricular septum\" EXACT [FMA:7134]\nsynonym: \"muscular septum\" BROAD [GO:0003150]\nsynonym: \"pars muscularis (septi interventricularis)\" EXACT [FMA:7134]\nsynonym: \"pars muscularis septi interventricularis\" EXACT OMO:0003011 [FMA:7134, FMA:TA]\nsynonym: \"septum membranaceum\" EXACT OMO:0003011 []\nsynonym: \"ventricular muscular septum\" EXACT []\n--\n\n[Term]\nid: UBERON:0005243\nname: interventricular septum endocardium\ndef: \"An endocardium that is part of a interventricular septum [Automatically generated definition].\" [OBOL:automatic]\nsubset: human_subset\nsubset: mouse_subset\nsynonym: \"endocardium of interventricular septum\" EXACT [FMA:83584]\nsynonym: \"interventricular septum endocardial tissue\" RELATED [VHOG:0000615]\nxref: EHDAA2:0000886\nxref: EHDAA2:0000887\nxref: FMA:83584\nxref: VHOG:0000615\nis_a: UBERON:0002165 ! endocardium\nintersection_of: UBERON:0002165 ! endocardium\nintersection_of: part_of UBERON:0002094 ! interventricular septum\nrelationship: part_of UBERON:0002094 ! interventricular septum\nproperty_value: editor_note \"TODO - split?\" xsd:string",
"tool_use_id": "toolu_01FtBB6qHyh2y9bTXHygSm9Z"
}
]
}
{
"id": "msg_01MaNdgzSdxDE49asDFBw7iy",
"type": "message",
"role": "assistant",
"model": "claude-3-7-sonnet-20250219",
"content": [
{
"type": "text",
"text": "Now let me check for the interatrial septum:"
},
{
"type": "tool_use",
"id": "toolu_01ETE21dziqX6ufDRaUZ79i6",
"name": "Bash",
"input": {
"command": "cd /Users/cjm/repos/uberon && grep -B 3 -A 15 \"name: interatrial septum\" uberon.obo"
}
}
],
"stop_reason": "tool_use",
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"usage": {
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"cache_read_input_tokens": 55271,
"output_tokens": 103
}
}
{
"role": "user",
"content": [
{
"type": "tool_result",
"content": "[Term]\nid: UBERON:0002085\nname: interatrial septum\ndef: \"A cardiac septum that divides the left and right atria of the heart.\" [http://orcid.org/0000-0002-6601-2165]\nsubset: human_subset\nsubset: mouse_subset\nsubset: pheno_slim\nsubset: uberon_slim\nsynonym: \"atrial septum\" EXACT []\nsynonym: \"atrium septum\" EXACT []\nsynonym: \"interatrial septal wall\" EXACT []\nxref: EHDAA2:0000838\nxref: EHDAA:1896\nxref: EMAPA:17011\nxref: FMA:7108\nxref: galen:InteratrialSeptum\nxref: MA:0000084\nxref: NCIT:C32818",
"tool_use_id": "toolu_01ETE21dziqX6ufDRaUZ79i6"
}
]
}
{
"id": "msg_01677R9CD261WCoBJJ5sX7iS",
"type": "message",
"role": "assistant",
"model": "claude-3-7-sonnet-20250219",
"content": [
{
"type": "text",
"text": "Let me also check what other relevant cardiac septum types might exist:"
},
{
"type": "tool_use",
"id": "toolu_01AQQC1ctkiye7KdA4cuUBPf",
"name": "GrepTool",
"input": {
"pattern": "atrioventricular septum",
"path": "/Users/cjm/repos/uberon/uberon.obo"
}
}
],
"stop_reason": "tool_use",
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"usage": {
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}
}
{
"role": "user",
"content": [
{
"type": "tool_result",
"content": "Found 1 file\n/Users/cjm/repos/uberon/uberon.obo",
"tool_use_id": "toolu_01AQQC1ctkiye7KdA4cuUBPf"
}
]
}
{
"id": "msg_01HEZjYPLLbC1WsjVoBzBvMg",
"type": "message",
"role": "assistant",
"model": "claude-3-7-sonnet-20250219",
"content": [
{
"type": "tool_use",
"id": "toolu_01WfauqyiH34yoeBu2FMdCK5",
"name": "Bash",
"input": {
"command": "cd /Users/cjm/repos/uberon && grep -B 3 -A 15 \"id: UBERON:0005989\" uberon.obo"
}
}
],
"stop_reason": "tool_use",
"stop_sequence": null,
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}
}
{
"role": "user",
"content": [
{
"type": "tool_result",
"content": "relationship: part_of UBERON:0004124 {source=\"ZFA\"} ! myocardium trabecular layer\n\n[Term]\nid: UBERON:0005989\nname: atrioventricular septum\ndef: \"The wall of the heart that separates the right atrium and left ventricle; and is located just above the septal cusp of the tricuspid valve.\" [MP:0010592]\nsubset: human_subset\nsubset: mouse_subset\nsubset: pheno_slim\nsynonym: \"membranous atrioventricular septum\" EXACT [FMA:7136]\nxref: EMAPA:37431 {source=\"MA:th\"}\nxref: FMA:7136\nxref: SCTID:280151006\nxref: Wikipedia:Atrioventricular_septum\nis_a: UBERON:0002099 ! cardiac septum\nis_a: UBERON:0010313 ! neural crest-derived structure\nintersection_of: UBERON:0002099 ! cardiac septum\nintersection_of: adjacent_to UBERON:0002078 ! right cardiac atrium\nintersection_of: adjacent_to UBERON:0002084 ! heart left ventricle",
"tool_use_id": "toolu_01WfauqyiH34yoeBu2FMdCK5"
}
]
}
{
"id": "msg_01FainA1X6QkhYuYrNAP6xvw",
"type": "message",
"role": "assistant",
"model": "claude-3-7-sonnet-20250219",
"content": [
{
"type": "text",
"text": "Let me check the outflow tract septum:"
},
{
"type": "tool_use",
"id": "toolu_01Fjp1r1gixzZ2NiLcPaMUHv",
"name": "Bash",
"input": {
"command": "cd /Users/cjm/repos/uberon && grep -B 3 -A 15 \"id: UBERON:0004142\" uberon.obo"
}
}
],
"stop_reason": "tool_use",
"stop_sequence": null,
"usage": {
"input_tokens": 6,
"cache_creation_input_tokens": 399,
"cache_read_input_tokens": 57082,
"output_tokens": 103
}
}
{
"role": "user",
"content": [
{
"type": "tool_result",
"content": "property_value: external_definition \"the paired, longitudinal, endothelial-lined channels formed from the cardiogenic mesoderm in embryonic development; angiogenic cell clusters (aka angioblastic cords) located in a horse-shoe shape configuration in the cardiogenic plate coalesce to form the right and left endocardial heart tubes which then fuse in cephalo-caudal direction to form a single primitive heart tube.\" xsd:string {source=\"MP:0012700\"}\n\n[Term]\nid: UBERON:0004142\nname: outflow tract septum\ndef: \"The outflow tract septum is a partition in the outflow tract.\" [GO:0003148]\nsubset: human_subset\nsubset: mouse_subset\nxref: XAO:0004141\nis_a: UBERON:0002099 ! cardiac septum\nintersection_of: UBERON:0002099 ! cardiac septum\nintersection_of: part_of UBERON:0004145 ! outflow tract\nrelationship: part_of UBERON:0004145 ! outflow tract\n\n[Term]\nid: UBERON:0004145\nname: outflow tract\ndef: \"The outflow tract is the portion of the heart through which blood flows into the arteries.\" [GO:0003151]\nsubset: human_subset",
"tool_use_id": "toolu_01Fjp1r1gixzZ2NiLcPaMUHv"
}
]
}
{
"id": "msg_01YDa1ruoJ43khC3tdNhkYLk",
"type": "message",
"role": "assistant",
"model": "claude-3-7-sonnet-20250219",
"content": [
{
"type": "text",
"text": "Based on all this information, I can now update the definition for cardiac septum. Let me check out the term:"
},
{
"type": "tool_use",
"id": "toolu_012AAHReyvbD6ovFHi6rqZb5",
"name": "Bash",
"input": {
"command": "obo-checkout.pl src/ontology/uberon-edit.obo UBERON:0002099"
}
}
],
"stop_reason": "tool_use",
"stop_sequence": null,
"usage": {
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}
}
{
"role": "user",
"content": [
{
"type": "tool_result",
"content": "Reading src/ontology/uberon-edit.obo\nChecking out UBERON:0002099",
"tool_use_id": "toolu_012AAHReyvbD6ovFHi6rqZb5"
}
]
}
{
"id": "msg_011urNAGmN1H3wQJeyVinDU7",
"type": "message",
"role": "assistant",
"model": "claude-3-7-sonnet-20250219",
"content": [
{
"type": "text",
"text": "Now I'll update the definition to include all the types of septa:"
},
{
"type": "tool_use",
"id": "toolu_01MxXow9kpMefutMZ4kWDp58",
"name": "Edit",
"input": {
"file_path": "/Users/cjm/repos/uberon/terms/UBERON_0002099.obo",
"old_string": "def: \"The thin membranous structure between the two heart atria or the thick muscular structure between the two heart ventricles.\" [MESH:A07.541.459]",
"new_string": "def: \"The thin membranous structure between parts of the heart, including the atria, ventricles, and outflow tract.\" [MESH:A07.541.459]"
}
}
],
"stop_reason": "tool_use",
"stop_sequence": null,
"usage": {
"input_tokens": 6,
"cache_creation_input_tokens": 137,
"cache_read_input_tokens": 57906,
"output_tokens": 209
}
}
{
"role": "user",
"content": [
{
"type": "tool_result",
"content": "File has been modified since read, either by the user or by a linter. Read it again before attempting to write it.",
"is_error": true,
"tool_use_id": "toolu_01MxXow9kpMefutMZ4kWDp58"
}
]
}
{
"id": "msg_01BwymqCGx1i3xNNWb4iaqJ6",
"type": "message",
"role": "assistant",
"model": "claude-3-7-sonnet-20250219",
"content": [
{
"type": "text",
"text": "Let me retry:"
},
{
"type": "tool_use",
"id": "toolu_019BRUXXA1eBXArbSEigRxvS",
"name": "View",
"input": {
"file_path": "/Users/cjm/repos/uberon/terms/UBERON_0002099.obo"
}
}
],
"stop_reason": "tool_use",
"stop_sequence": null,
"usage": {
"input_tokens": 7,
"cache_creation_input_tokens": 252,
"cache_read_input_tokens": 58043,
"output_tokens": 82
}
}
{
"role": "user",
"content": [
{
"type": "tool_result",
"content": " 1\t[Term]\n 2\tid: UBERON:0002099\n 3\tname: cardiac septum\n 4\tdef: \"The thin membranous structure between the two heart atria or the thick muscular structure between the two heart ventricles.\" [MESH:A07.541.459]\n 5\tsubset: pheno_slim\n 6\tsubset: uberon_slim\n 7\tsynonym: \"cardiac septa\" EXACT OMO:0003004 []\n 8\tsynonym: \"heart septa\" EXACT OMO:0003004 []\n 9\tsynonym: \"heart septum\" EXACT []\n 10\tsynonym: \"septum of heart\" EXACT []\n 11\tsynonym: \"spiral septa\" RELATED OMO:0003004 [XAO:0004141]\n 12\txref: EMAPA:35400\n 13\txref: FMA:7180\n 14\txref: GAID:562\n 15\txref: MA:0000083\n 16\txref: MESH:D006346\n 17\txref: NCIT:C49485\n 18\txref: SCTID:362014000\n 19\txref: UMLS:C0018819 {source=\"ncithesaurus:Heart_Septum\"}\n 20\tis_a: UBERON:0003037 ! septum\n 21\tintersection_of: UBERON:0003037 ! septum\n 22\tintersection_of: part_of UBERON:0000948 ! heart\n 23\trelationship: adjacent_to UBERON:0004151 ! cardiac chamber\n 24\trelationship: contributes_to_morphology_of UBERON:0000948 ! heart\n 25\trelationship: part_of UBERON:0000948 ! heart\n 26\tproperty_value: external_ontology_notes \"in GO, septum morphogenesis is part of cardiac chamber morphogenesis; need to add axioms to infer this\" xsd:string {external_ontology=\"GO\"}\n 27\tproperty_value: taxon_notes \"'Terrestrial vertebrates have divided hearts in which septae separate the oxygenated and deoxygenated blood within the pulmonary and systemic circulations'\" xsd:string\n 28\t\n 29\t",
"tool_use_id": "toolu_019BRUXXA1eBXArbSEigRxvS"
}
]
}
{
"id": "msg_011Ei4odNf2BLV9dZwD2RYWg",
"type": "message",
"role": "assistant",
"model": "claude-3-7-sonnet-20250219",
"content": [
{
"type": "text",
"text": "Now I'll update the definition:"
},
{
"type": "tool_use",
"id": "toolu_015d2xMsR8edtL9iK4yLqC9V",
"name": "Edit",
"input": {
"file_path": "/Users/cjm/repos/uberon/terms/UBERON_0002099.obo",
"old_string": "def: \"The thin membranous structure between the two heart atria or the thick muscular structure between the two heart ventricles.\" [MESH:A07.541.459]",
"new_string": "def: \"The thin membranous structure between parts of the heart, including the atria, ventricles, and outflow tract.\" [MESH:A07.541.459]"
}
}
],
"stop_reason": "tool_use",
"stop_sequence": null,
"usage": {
"input_tokens": 6,
"cache_creation_input_tokens": 648,
"cache_read_input_tokens": 58295,
"output_tokens": 201
}
}
{
"role": "user",
"content": [
{
"type": "tool_result",
"content": "The file /Users/cjm/repos/uberon/terms/UBERON_0002099.obo has been updated. Here's the result of running `cat -n` on a snippet of the edited file:\n 1\t[Term]\n 2\tid: UBERON:0002099\n 3\tname: cardiac septum\n 4\tdef: \"The thin membranous structure between parts of the heart, including the atria, ventricles, and outflow tract.\" [MESH:A07.541.459]\n 5\tsubset: pheno_slim\n 6\tsubset: uberon_slim\n 7\tsynonym: \"cardiac septa\" EXACT OMO:0003004 []\n 8\tsynonym: \"heart septa\" EXACT OMO:0003004 []\n 9\tsynonym: \"heart septum\" EXACT []",
"tool_use_id": "toolu_015d2xMsR8edtL9iK4yLqC9V"
}
]
}
{
"id": "msg_013EbfmZkPP4mjoZBPj5Kbqv",
"type": "message",
"role": "assistant",
"model": "claude-3-7-sonnet-20250219",
"content": [
{
"type": "text",
"text": "Now I'll check it back in:"
},
{
"type": "tool_use",
"id": "toolu_01M41xJJtR7tm773sm9Zp9s7",
"name": "Bash",
"input": {
"command": "obo-checkin.pl src/ontology/uberon-edit.obo UBERON:0002099"
}
}
],
"stop_reason": "tool_use",
"stop_sequence": null,
"usage": {
"input_tokens": 6,
"cache_creation_input_tokens": 412,
"cache_read_input_tokens": 58943,
"output_tokens": 87
}
}
{
"role": "user",
"content": [
{
"type": "tool_result",
"content": "",
"tool_use_id": "toolu_01M41xJJtR7tm773sm9Zp9s7"
}
]
}
{
"id": "msg_016fChsnqMnrGKGftJQ3tLec",
"type": "message",
"role": "assistant",
"model": "claude-3-7-sonnet-20250219",
"content": [
{
"type": "text",
"text": "Now let's create a branch for this fix:"
},
{
"type": "tool_use",
"id": "toolu_0192v1gLTKWR6CB6ZSzyMpPx",
"name": "Bash",
"input": {
"command": "git checkout -b issue-3003"
}
}
],
"stop_reason": "tool_use",
"stop_sequence": null,
"usage": {
"input_tokens": 7,
"cache_creation_input_tokens": 111,
"cache_read_input_tokens": 59355,
"output_tokens": 71
}
}
{
"role": "user",
"content": [
{
"type": "tool_result",
"content": "Switched to a new branch 'issue-3003'",
"tool_use_id": "toolu_0192v1gLTKWR6CB6ZSzyMpPx"
}
]
}
{
"id": "msg_019RZGfGReuA2aBZoKDe6QhX",
"type": "message",
"role": "assistant",
"model": "claude-3-7-sonnet-20250219",
"content": [
{
"type": "text",
"text": "Let's add and commit the change:"
},
{
"type": "tool_use",
"id": "toolu_01Ew96RfbunFCJK9eyhKUX9X",
"name": "Bash",
"input": {
"command": "git add src/ontology/uberon-edit.obo"
}
}
],
"stop_reason": "tool_use",
"stop_sequence": null,
"usage": {
"input_tokens": 6,
"cache_creation_input_tokens": 96,
"cache_read_input_tokens": 59466,
"output_tokens": 75
}
}
{
"role": "user",
"content": [
{
"type": "tool_result",
"content": "",
"tool_use_id": "toolu_01Ew96RfbunFCJK9eyhKUX9X"
}
]
}
{
"id": "msg_01TvbfmypNt56P1CiJzJ3E3e",
"type": "message",
"role": "assistant",
"model": "claude-3-7-sonnet-20250219",
"content": [
{
"type": "tool_use",
"id": "toolu_01Jscm81CMimk8FAmCwuuThm",
"name": "Bash",
"input": {
"command": "git commit -m \"Fix issue #3003: Updated cardiac septum definition to include all heart partitions\n\nThe definition for cardiac septum (UBERON:0002099) was too narrow, only including septa between atria or ventricles. Updated to include all septa between parts of the heart, including the atria, ventricles, and outflow tract, which better encompasses all child terms.\" --signoff"
}
}
],
"stop_reason": "tool_use",
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"usage": {
"input_tokens": 7,
"cache_creation_input_tokens": 99,
"cache_read_input_tokens": 59562,
"output_tokens": 142
}
}
{
"role": "user",
"content": [
{
"type": "tool_result",
"content": "[issue-3003 21ab6ba63] Fix issue #3003: Updated cardiac septum definition to include all heart partitions\n 1 file changed, 1 insertion(+), 1 deletion(-)",
"tool_use_id": "toolu_01Jscm81CMimk8FAmCwuuThm"
}
]
}
{
"id": "msg_016pKRHy9abMa5wy8G8mkwAR",
"type": "message",
"role": "assistant",
"model": "claude-3-7-sonnet-20250219",
"content": [
{
"type": "text",
"text": "Now let's create a pull request:"
},
{
"type": "tool_use",
"id": "toolu_0119vGHdjEKRqyVZhiTPAsqt",
"name": "Bash",
"input": {
"command": "gh pr create --title \"Fix issue #3003: Updated cardiac septum definition\" --body \"## Summary\n- Updated definition of cardiac septum (UBERON:0002099) to include all septa between parts of the heart, specifically including the outflow tract and better accommodating all child terms\n- The previous definition was too narrow and only mentioned atria and ventricles, but child terms include atrioventricular septum and outflow tract septum\n\nFixes #3003\n\nSigned-off-by: @dragon-ai-agent\" --web"
}
}
],
"stop_reason": "tool_use",
"stop_sequence": null,
"usage": {
"input_tokens": 5,
"cache_creation_input_tokens": 202,
"cache_read_input_tokens": 59661,
"output_tokens": 184
}
}
{
"role": "user",
"content": [
{
"type": "tool_result",
"content": "Warning: 254 uncommitted changes\naborted: you must first push the current branch to a remote, or use the --head flag",
"is_error": true,
"tool_use_id": "toolu_0119vGHdjEKRqyVZhiTPAsqt"
}
]
}
{
"id": "msg_011Qm8JqVFMWn4yVQeFSFmCM",
"type": "message",
"role": "assistant",
"model": "claude-3-7-sonnet-20250219",
"content": [
{
"type": "text",
"text": "Let's push the branch first:"
},
{
"type": "tool_use",
"id": "toolu_01LK5c4suuyZSNHP5xApbWPh",
"name": "Bash",
"input": {
"command": "git push -u origin issue-3003"
}
}
],
"stop_reason": "tool_use",
"stop_sequence": null,
"usage": {
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"content": "branch 'issue-3003' set up to track 'origin/issue-3003'.\nremote: \nremote: Create a pull request for 'issue-3003' on GitHub by visiting: \nremote: https://github.com/obophenotype/uberon/pull/new/issue-3003 \nremote: \nTo github.com:obophenotype/uberon.git\n * [new branch] issue-3003 -> issue-3003",
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"command": "gh pr create --title \"Fix issue #3003: Updated cardiac septum definition\" --body \"## Summary\n- Updated definition of cardiac septum (UBERON:0002099) to include all septa between parts of the heart, specifically including the outflow tract and better accommodating all child terms\n- The previous definition was too narrow and only mentioned atria and ventricles, but child terms include atrioventricular septum and outflow tract septum\n\nFixes #3003\n\nSigned-off-by: @dragon-ai-agent\""
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"content": "https://github.com/obophenotype/uberon/pull/3511\nWarning: 254 uncommitted changes",
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"text": "I've successfully:\n1. Updated the definition of cardiac septum (UBERON:0002099) to include all septa between parts of the heart\n2. Created a branch and committed the change\n3. Created a pull request that fixes issue #3003\n\nThe PR is now available at: https://github.com/obophenotype/uberon/pull/3511"
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