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is_mcq_subject_qnode() in trapi.py made more tolerant of set_interpretation annotation on secondary query nodes. Release 0.1.0 also has partial implementation (incomplete) supporting a Docker Compose managed local semsim server (but keeps the default mode as external Monarch API semsimian calls for now).
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‎CHANGELOG.md

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# Change Log
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## 0.1.0
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- Constraints relaxed for the filtering of Query Node specification of set_interpretation such that incomplete nodes (which may be specified as a part of multistep MCQ) generate a warning but are ignored (they don't now raise an exception).
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- minor release includes partial implementation (including SEMSIMIAN related environment variables, including a new SEMSIMIAN_MODE flag to tag two distinct layers of SemSimian access: server and (indirect) Monarch)
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## 0.0.12
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- Input Query Graph list of nodes more robustly checked for constrain of having one and only one well-formed MCQ node with a set_interpretation directive

‎DEVELOPER_README.md

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1. Run the unit test suite to ensure that nothing fails. Iterate to fix failures (in the code or in terms of revised unit tests to reflect fresh code designs)
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2. Document release changes in the **CHANGELOG.md**
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3. Update the **`[Tool Poetry]version =`** field in the **pyprojects.yaml**, e.g. "0.0.12"
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3. Update the **`[Tool Poetry]version =`** field in the **pyprojects.yaml**, e.g. "0.1.0"
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4. Run **`poetry update`** (preferably, within a **`poetry shell`**)
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5. The project pip **requirements.txt** file snapshot of dependencies should also be updated at this point (type **`$ poetry export --output requirements.txt`**, assuming that the [proper poetry export plugin is installed](https://python-poetry.org/docs/pre-commit-hooks#poetry-export)). This may facilitate module deployment within environments that prefer to use pip rather than poetry to manage their deployments.
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6. Commit or pull request merge all files (including the **poetry.lock** file) to the local **main** branch.
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7. Add the equivalent Git **tag** to **main**. This should be the Semantic Version string from step 4 with an added 'v' prefix, e.g. "v0.0.9".
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7. Add the equivalent Git **tag** to **main**. This should be the Semantic Version string from step 4 with an added 'v' prefix, e.g. "v0.1.0".
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8. Push **main** to remote.
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9. Check if Git Actions for testing and documentation complete successfully.
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10. Create a Git package release using the same release tag, e.g. "v0.0.9".

‎README.md

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# SemSimian backend API for 'development' environment
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# (see the '.env-template' file for possible alternat
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# parameters for a 'production' deployment)
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SEMSIMIAN_MODE="monarch"
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SEMSIMIAN_SCHEME="http://"
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SEMSIMIAN_HOST="api-v3.monarchinitiative.org"
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SEMSIMIAN_PORT="" # default is HTTP port '80'

‎mmcq/examples/sample_monarch_semsian_output.json

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{
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"subject": {
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"id": "MONDO:0008807",
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"category": "biolink:Disease",
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"name": "obsolete apnea, central sleep",
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"full_name": null,
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"deprecated": true,
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"description": null,
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"xref": [
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"OMIM:107640",
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"OMIM:207720"
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],
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"provided_by": "phenio_nodes",
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"in_taxon": null,
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"in_taxon_label": null,
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"symbol": null,
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"synonym": [
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"apnea, central sleep",
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"sleep apnea",
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"lethal central"
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],
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"uri": "http://purl.obolibrary.org/obo/MONDO_0008807",
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"iri": null,
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"namespace": "MONDO",
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"has_phenotype": [
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"HP:0001699",
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"HP:0010535"
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],
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"has_phenotype_label": [
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"Sudden death",
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"Sleep apnea"
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],
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"has_phenotype_closure": [
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"GO:0050896",
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"UBERON:0001004",
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"HP:0002360",
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"UPHENO:0002433",
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"HP:0002795",
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"UBERON:0010000",
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"UPHENO:0049587",
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"UPHENO:0002536",
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"HP:0010535",
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"UBERON:0001062",
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"GO:0030431",
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"NBO:0000313",
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"UBERON:0000061",
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"BFO:0000003",
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"HP:0011446",
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"BFO:0000001",
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"UPHENO:0082875",
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"HP:0002104",
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"HP:0000708",
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"UPHENO:0075696",
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"UPHENO:0001002",
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"UPHENO:0001003",
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"UBERON:0001016",
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"HP:0002086",
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"UPHENO:0001001",
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"HP:0012638",
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"BFO:0000020",
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"HP:0000118",
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"PATO:0000001",
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"HP:0002793",
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"HP:0025142",
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"UPHENO:0002448",
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"UPHENO:0004536",
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"UPHENO:0034024",
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"UBERON:0000465",
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"UPHENO:0004523",
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"UPHENO:0001005",
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"GO:0007610",
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"UPHENO:0049586",
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"BFO:0000002",
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"GO:0032501",
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"BFO:0000004",
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"HP:0001699",
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"UBERON:0000467",
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"HP:0000707",
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"UPHENO:0079826",
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"HP:0000001",
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"UPHENO:0002332",
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"UBERON:0000468",
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"GO:0008150",
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"GO:0007585",
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"UPHENO:0049622",
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"BFO:0000040",
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"UPHENO:0080585",
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"BFO:0000015",
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"UPHENO:0078461"
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],
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"has_phenotype_closure_label": [
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"anatomical structure",
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"abnormal biological_process",
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"multicellular organism",
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"response to stimulus",
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"Abnormality of the respiratory system",
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"multicellular organismal process",
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"multicellular anatomical structure",
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"Abnormality of the nervous system",
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"biological_process",
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"abnormal response to stimulus",
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"material entity",
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"absent respiratory gaseous exchange by respiratory system",
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"abnormal nervous system",
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"Abnormality of mental function",
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"occurrent",
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"phenotype by ontology source",
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"abnormal behavior",
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"Sudden death",
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"abnormality of nervous system physiology",
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"continuant",
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"Constitutional symptom",
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"Abnormal pattern of respiration",
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"nervous system",
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"All",
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"Phenotypic abnormality",
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"entity",
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"Sleep apnea",
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"specifically dependent continuant",
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"abnormal phenotype by ontology source",
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"phenotype",
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"quality",
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"behavior process",
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"independent continuant",
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"abnormal respiratory system",
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"sleep",
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"Abnormal respiratory system physiology",
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"material anatomical entity",
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"anatomical system",
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"anatomical entity",
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"respiratory gaseous exchange by respiratory system",
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"Sleep disturbance",
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"Apnea",
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"process",
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"Atypical behavior",
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"abnormal behavior process",
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"behavior",
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"abnormality of anatomical entity physiology",
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"respiratory system",
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"abnormal anatomical entity",
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"absent biological_process",
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"Abnormal nervous system physiology",
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"abnormality of respiratory system physiology"
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],
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"has_phenotype_count": 2
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},
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"score": 13.190702260828903,
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"similarity": {
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"subject_termset": {
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"HP:0001699": {
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"id": "HP:0001699",
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"label": "Sudden death"
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},
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"HP:0010535": {
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"id": "HP:0010535",
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"label": "Sleep apnea"
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}
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},
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"object_termset": {
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"HP:0002104": {
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"id": "HP:0002104",
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"label": "Apnea"
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},
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"HP:0012378": {
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"id": "HP:0012378",
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"label": "Fatigue"
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}
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},
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"subject_best_matches": {
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"HP:0001699": {
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"match_source": "HP:0001699",
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"match_source_label": "Sudden death",
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"match_target": "HP:0012378",
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"match_target_label": "Fatigue",
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"score": 11.35921975446769,
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"match_subsumer": null,
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"match_subsumer_label": null,
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"similarity": {
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"subject_id": "HP:0001699",
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"subject_label": null,
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"subject_source": null,
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"object_id": "HP:0012378",
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"object_label": null,
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"object_source": null,
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"ancestor_id": "HP:0025142",
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"ancestor_label": "Constitutional symptom",
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"ancestor_source": null,
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"object_information_content": null,
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"subject_information_content": null,
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"ancestor_information_content": 11.35921975446769,
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"jaccard_similarity": 0.8461538461538461,
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"cosine_similarity": null,
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"dice_similarity": null,
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"phenodigm_score": 3.100265711926896
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},
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"score_metric": "ancestor_information_content"
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},
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"HP:0010535": {
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"match_source": "HP:0010535",
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"match_source_label": "Sleep apnea",
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"match_target": "HP:0002104",
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"match_target_label": "Apnea",
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"score": 15.022184767190119,
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"match_subsumer": null,
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"match_subsumer_label": null,
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"similarity": {
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"subject_id": "HP:0010535",
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"subject_label": null,
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"subject_source": null,
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"object_id": "HP:0002104",
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"object_label": null,
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"object_source": null,
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"ancestor_id": "HP:0002104",
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"ancestor_label": "Apnea",
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"ancestor_source": null,
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"object_information_content": null,
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"subject_information_content": null,
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"ancestor_information_content": 15.022184767190119,
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"jaccard_similarity": 0.6285714285714286,
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"cosine_similarity": null,
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"dice_similarity": null,
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"phenodigm_score": 3.072867738672891
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},
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"score_metric": "ancestor_information_content"
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}
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},
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"object_best_matches": {
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"HP:0002104": {
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"match_source": "HP:0002104",
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"match_source_label": "Apnea",
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"match_target": "HP:0010535",
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"match_target_label": "Sleep apnea",
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"score": 15.022184767190119,
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"match_subsumer": null,
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"match_subsumer_label": null,
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"similarity": {
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"subject_id": "HP:0002104",
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"subject_label": null,
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"subject_source": null,
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"object_id": "HP:0010535",
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"object_label": null,
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"object_source": null,
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"ancestor_id": "HP:0002104",
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"ancestor_label": "Apnea",
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"ancestor_source": null,
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"object_information_content": null,
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"subject_information_content": null,
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"ancestor_information_content": 15.022184767190119,
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"jaccard_similarity": 0.6285714285714286,
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"cosine_similarity": null,
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"dice_similarity": null,
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"phenodigm_score": 3.072867738672891
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},
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"score_metric": "ancestor_information_content"
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},
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"HP:0012378": {
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"match_source": "HP:0012378",
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"match_source_label": "Fatigue",
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"match_target": "HP:0001699",
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"match_target_label": "Sudden death",
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"score": 11.35921975446769,
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"match_subsumer": null,
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"match_subsumer_label": null,
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"similarity": {
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"subject_id": "HP:0012378",
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"subject_label": null,
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"subject_source": null,
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"object_id": "HP:0001699",
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"object_label": null,
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"object_source": null,
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"ancestor_id": "HP:0025142",
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"ancestor_label": "Constitutional symptom",
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"ancestor_source": null,
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"object_information_content": null,
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"subject_information_content": null,
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"ancestor_information_content": 11.35921975446769,
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"jaccard_similarity": 0.8461538461538461,
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"cosine_similarity": null,
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"dice_similarity": null,
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"phenodigm_score": 3.100265711926896
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},
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"score_metric": "ancestor_information_content"
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}
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},
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"average_score": 13.190702260828903,
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"best_score": 15.022184767190119,
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"metric": "AncestorInformationContent"
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}
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}

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