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“Agent” }, “contributionDate”: { “date”: “2017/6/29”, “description”: “Date on which this evidence was provided” }, “contributionRole”: { “@id”: “https://obofoundry.org/sepio/0000156”, “id”: “SEPIO:0000516”, “type”: “ContributoryRole”, “label”: “curator role” } } ], “evidenceLine”: [ { “@id”: “https://erepo.genome.network/evidence-repo/api/interpretation/CA377482283/MONDO:0017623/001/el/1840/1597/1599”, “id”: “CG-PCER-VARINT:CA377482283/MONDO:0017623/001/1840/1597/1599”, “type”: “EvidenceLine”, “evidenceItem”: [ { “@id”: “CG-PCER:curatorInference/CA377482283/MONDO:0017623/001/ci/CA377482283/MONDO:0017623/001.002”, “id”: “CA377482283/MONDO:0017623/001/ci/CA377482283/MONDO:0017623/001.002”, “type”: “InfFromBkgrndSciKnow”, “contribution”: [ { “type”: “Contribution”, “agent”: { “@id”: “https://erepo.genome.network/evidence-repo/api//agent/Jessica_Mester_153376223213854”, “id”: “CG-PCER-AGENT:Jessica_Mester_153376223213854”, “type”: “Agent” }, “contributionDate”: { “date”: “2017/6/29”, “description”: “Date on which this evidence was provided” }, “contributionRole”: { “@id”: “https://obofoundry.org/sepio/0000156”, “id”: “SEPIO:0000516”, “type”: “ContributoryRole”, “label”: “curator role” } } ] } ] } ] } ] }, { “@id”: “https://erepo.genome.network/evidence-repo/api/interpretation/CA377482283/MONDO:0017623/001/el/1840/1579”, “id”: “CG-PCER-VARINT:CA377482283/MONDO:0017623/001/1840/1579”, “type”: “EvidenceLine”, “evidenceStrength”: { “@id”: “https://obofoundry.org/sepio/SEPIO:0000327”, “id”: “SEPIO:0000327”, “label”: “Benign Supporting” }, “evidenceItem”: [ { “@id”: “https://erepo.genome.network/evidence-repo/api/interpretation/CA377482283/MONDO:0017623/001/ei/1841/1580”, “id”: “CG-PCER-VARINT:CA377482283/MONDO:0017623/001/1841/1580”, “type”: “CriterionAssessment”, “criterion”: { “@id”: “https://obofoundry.org/sepio/clingen/SEPIO-CG:99047”, “id”: “SEPIO-CG:99047”, “type”: “Criterion”, “label”: “BP5”, “defaultStrength”: { “@id”: “https://obofoundry.org/sepio/SEPIO:0000327”, “id”: “SEPIO:0000327”, “label”: “Benign Supporting” } }, “statementOutcome”: { “@id”: “SEPIO:0000224”, “label”: “Not Met” }, “contribution”: [ { “type”: “Contribution”, “agent”: { “@id”: “https://erepo.genome.network/evidence-repo/api//agent/Jessica_Mester_153376223213854”, “id”: “CG-PCER-AGENT:Jessica_Mester_153376223213854”, “type”: “Agent” }, “contributionDate”: { “date”: “2017/6/27”, “description”: “Date on which this evidence was provided” }, “contributionRole”: { “@id”: “https://obofoundry.org/sepio/0000156”, “id”: “SEPIO:0000516”, “type”: “ContributoryRole”, “label”: “curator role” } } ], “evidenceLine”: [ { “@id”: “https://erepo.genome.network/evidence-repo/api/interpretation/CA377482283/MONDO:0017623/001/el/1840/1579/1581”, “id”: “CG-PCER-VARINT:CA377482283/MONDO:0017623/001/1840/1579/1581”, “type”: “EvidenceLine”, “evidenceItem”: [ { “@id”: “CG-PCER:curatorInference/CA377482283/MONDO:0017623/001/ci/CA377482283/MONDO:0017623/001.002”, “id”: “CA377482283/MONDO:0017623/001/ci/CA377482283/MONDO:0017623/001.002”, “type”: “InfFromBkgrndSciKnow”, “contribution”: [ { “type”: “Contribution”, “agent”: { “@id”: “https://erepo.genome.network/evidence-repo/api//agent/Jessica_Mester_153376223213854”, “id”: “CG-PCER-AGENT:Jessica_Mester_153376223213854”, “type”: “Agent” }, “contributionDate”: { “date”: “2017/6/27”, “description”: “Date on which this evidence was provided” }, “contributionRole”: { “@id”: “https://obofoundry.org/sepio/0000156”, “id”: “SEPIO:0000516”, “type”: “ContributoryRole”, “label”: “curator role” } } ] } ] } ] } ] } ] } ] } ] } } } }, “summary”: “GetFullSEPIOInterpretation”, “description”: "Get the full Scientific Evidence and Provenance Information Ontology (SEPIO) compliant JSON-LD document containing interpretation data for an allele-condition (condition id is namespaced) pair under a specific guideline of interest. \n\nThe hierarchically structured document will include:\n1. Variant information and condition/syndrome info that the variant is known to be associated with as well as Outcome that conveys whether a variant is pathogenic, likely pathogenic, benign, etc for a given genetic condition.\n2. Evidence Lines pertaining to various intermediate outcome(s) that are further supported by ACMG tags backed by one or more evidences that could be in the form of published articles or some other type of evidence. In case of tag less assertions, the intermediate outcome(s) will be supported directly by evidence sources.\n3. Agent/Contributor info conveying which agent contributed to what evidence along with the date of evidence supplied. ", “parameters”: [ { “$ref”: “#/parameters/caid” }, { “$ref”: “#/parameters/disease” }, { “$ref”: “#/parameters/did” }, { “$ref”: “#/parameters/gid” } ], “tags”: [ “INTERPRETATIONS” ] }, “parameters”: [ { “name”: “caid”, “in”: “path”, “type”: “string”, “required”: true }, { “name”: “disease”, “in”: “path”, “type”: “string”, “required”: true }, { “name”: “did”, “in”: “path”, “type”: “string”, “required”: true }, { “name”: “gid”, “in”: “path”, “type”: “string”, “required”: true } ] }, “/interpretation/{gid-or-uuid}”: { “put”: { “responses”: { “200”: { “description”: “”, “schema”: { “$ref”: “#/definitions/success-resp” } } }, “summary”: “AddInterpretation”, “description”: “Upload an entire SEPIO interpretation document.”, “security”: [ { “Redmine API Key”: [] } ], “parameters”: [ { “$ref”: “#/parameters/upload-type” }, { “$ref”: “#/parameters/gid-or-uuid” }, { “$ref”: “#/parameters/data-sepio-param” } ], “tags”: [ “INTERPRETATIONS” ] }, “get”: { “responses”: { “200”: { “description”: “”, “schema”: { “type”: “object”, “properties”: {} }, “examples”: { “application/json”: { “@id”: “https://erepo.genome.network/evidence-repo/api/interpretation/CA377482283/MONDO:0017623/001”, “id”: “CG-PCER-VARINT:CA377482283/MONDO:0017623/001”, “type”: “VariantInterpretation”, “@context”: “https://erepo.genome.network/pcer/api/context”, “variant”: { “@id”: “https://reg.genome.network/allele/CA377482283”, “id”: “CAR:CA377482283”, “type”: “CanonicalAllele” }, “condition”: { “@id”: “https://www.omim.org”, “id”: “OMIM:”, “type”: “Disease”, “label”: “PTEN hamartoma tumor syndrome” }, “outcome”: { “@id”: “https://loinc.org/LA6668-3”, “id”: “LN:LA6668-3”, “type”: “Significance”, “label”: “Pathogenic”, “description”: “Final assertion for the variant as generated by the reasoner software.” }, “assertionMethod”: { “@id”: “https://obofoundry.org/sepio/0000193”, “id”: “AssertMeth331”, “type”: “AssertionMethod”, “version”: “1.0”, “description”: “ACMG ISV guidelines 2015”, “url”: “https://www.acmg.net/docs/Standards_Guidelines_for_the_Interpretation_of_Sequence_Variants.pdf”, “scoringAlgorithm”: { “description”: “This is the description of how the weighting of the satisfied criterion are typically evaluated to arrive at a specific clinical significance.”, “id”: “SEPIO-CG:99300” } }, “agent”: { “@id”: “https://data.bioontology.org/ontologies/PROVO/classes/SoftwareAgent”, “id”: “PROVO:SoftwareAgent”, “type”: “SoftwareAgent”, “description”: “Final Assertion generated by reasoner software.” }, “evidenceLine”: [ { “@id”: “https://erepo.genome.network/evidence-repo/api/interpretation/CA377482283/MONDO:0017623/001/el/1840”, “id”: “CG-PCER-VARINT:CA377482283/MONDO:0017623/001/1840”, “type”: “EvidenceLine”, “evidenceItem”: [ { “@id”: “https://erepo.genome.network/evidence-repo/api/interpretation/CA377482283/MONDO:0017623/001/ei/1841”, “id”: “CG-PCER-VARINT:CA377482283/MONDO:0017623/001/1841”, “type”: “CriterionAssessment”, “variant”: { “@id”: “https://reg.genome.network/allele/CA377482283”, “id”: “CAR:CA377482283”, “type”: “CanonicalAllele” }, “outcome”: { “@id”: “https://loinc.org/LA6668-3”, “id”: “LN:LA6668-3”, “type”: “Significance”, “label”: “Pathogenic”, “description”: “Final assertion for the variant as generated by the reasoner software.” }, “assertionMethod”: { “@id”: “https://obofoundry.org/sepio/0000193”, “id”: “AssertMeth331”, “type”: “AssertionMethod”, “version”: “1.0”, “description”: “ACMG ISV guidelines 2015”, “url”: “https://www.acmg.net/docs/Standards_Guidelines_for_the_Interpretation_of_Sequence_Variants.pdf”, “scoringAlgorithm”: { “description”: “This is the description of how the weighting of the satisfied criterion are typically evaluated to arrive at a specific clinical significance.”, “id”: “SEPIO-CG:99300” } }, “agent”: { “@id”: “https://data.bioontology.org/ontologies/PROVO/classes/SoftwareAgent”, “id”: “PROVO:SoftwareAgent”, “type”: “SoftwareAgent”, “description”: “Intermediate Assertion generated by reasoner software using tags applied by different agents.” }, “evidenceLine”: [ { “@id”: “https://erepo.genome.network/evidence-repo/api/interpretation/CA377482283/MONDO:0017623/001/el/1840/1702”, “id”: “CG-PCER-VARINT:CA377482283/MONDO:0017623/001/1840/1702”, “type”: “EvidenceLine”, “evidenceStrength”: { “@id”: “https://obofoundry.org/sepio/SEPIO:0000328”, “id”: “SEPIO:0000328”, “label”: “Benign Strong” }, “evidenceItem”: [ { “@id”: “https://erepo.genome.network/evidence-repo/api/interpretation/CA377482283/MONDO:0017623/001/ei/1841/1703”, “id”: “CG-PCER-VARINT:CA377482283/MONDO:0017623/001/1841/1703”, “type”: “CriterionAssessment”, “criterion”: { “@id”: “https://obofoundry.org/sepio/clingen/SEPIO-CG:99040”, “id”: “SEPIO-CG:99040”, “type”: “Criterion”, “label”: “BS2”, “defaultStrength”: { “@id”: “https://obofoundry.org/sepio/SEPIO:0000328”, “id”: “SEPIO:0000328”, “label”: “Benign Strong” } }, “statementOutcome”: { “@id”: “SEPIO:0000224”, “label”: “Not Met” }, “contribution”: [ { “type”: “Contribution”, “agent”: { “@id”: “https://erepo.genome.network/evidence-repo/api//agent/Jessica_Mester_153376223213854”, “id”: “CG-PCER-AGENT:Jessica_Mester_153376223213854”, “type”: “Agent” }, “contributionDate”: { “date”: “2017/6/27”, “description”: “Date on which this evidence was provided” }, “contributionRole”: { “@id”: “https://obofoundry.org/sepio/0000156”, “id”: “SEPIO:0000516”, “type”: “ContributoryRole”, “label”: “curator role” } } ], “evidenceLine”: [ { “@id”: “https://erepo.genome.network/evidence-repo/api/interpretation/CA377482283/MONDO:0017623/001/el/1840/1702/1704”, “id”: “CG-PCER-VARINT:CA377482283/MONDO:0017623/001/1840/1702/1704”, “type”: “EvidenceLine”, “evidenceItem”: [ { “@id”: “CG-PCER:curatorInference/CA377482283/MONDO:0017623/001/ci/CA377482283/MONDO:0017623/001.002”, “id”: “CA377482283/MONDO:0017623/001/ci/CA377482283/MONDO:0017623/001.002”, “type”: “InfFromBkgrndSciKnow”, “contribution”: [ { “type”: “Contribution”, “agent”: { “@id”: “https://erepo.genome.network/evidence-repo/api//agent/Jessica_Mester_153376223213854”, “id”: “CG-PCER-AGENT:Jessica_Mester_153376223213854”, “type”: “Agent” }, “contributionDate”: { “date”: “2017/6/27”, “description”: “Date on which this evidence was provided” }, “contributionRole”: { “@id”: “https://obofoundry.org/sepio/0000156”, “id”: “SEPIO:0000516”, “type”: “ContributoryRole”, “label”: “curator role” } } ] } ] } ] } ] }, { “@id”: “https://erepo.genome.network/evidence-repo/api/interpretation/CA377482283/MONDO:0017623/001/el/1840/1804”, “id”: “CG-PCER-VARINT:CA377482283/MONDO:0017623/001/1840/1804”, “type”: “EvidenceLine”, “evidenceStrength”: { “@id”: “https://obofoundry.org/sepio/SEPIO:0000328”, “id”: “SEPIO:0000328”, “label”: “Benign Strong” }, “evidenceItem”: [ { “@id”: “https://erepo.genome.network/evidence-repo/api/interpretation/CA377482283/MONDO:0017623/001/ei/1841/1805”, “id”: “CG-PCER-VARINT:CA377482283/MONDO:0017623/001/1841/1805”, “type”: “CriterionAssessment”, “criterion”: { “@id”: “https://obofoundry.org/sepio/clingen/SEPIO-CG:99039”, “id”: “SEPIO-CG:99039”, “type”: “Criterion”, “label”: “BS1”, “defaultStrength”: { “@id”: “https://obofoundry.org/sepio/SEPIO:0000328”, “id”: “SEPIO:0000328”, “label”: “Benign Strong” } }, “statementOutcome”: { “@id”: “SEPIO:0000224”, “label”: “Not Met” }, “contribution”: [ { “type”: “Contribution”, “agent”: { “@id”: “https://erepo.genome.network/evidence-repo/api//agent/Jessica_Mester_153376223213854”, “id”: “CG-PCER-AGENT:Jessica_Mester_153376223213854”, “type”: “Agent” }, “contributionDate”: { “date”: “2017/6/27”, “description”: “Date on which this evidence was provided” }, “contributionRole”: { “@id”: “https://obofoundry.org/sepio/0000156”, “id”: “SEPIO:0000516”, “type”: “ContributoryRole”, “label”: “curator role” } } ], “evidenceLine”: [ { “@id”: “https://erepo.genome.network/evidence-repo/api/interpretation/CA377482283/MONDO:0017623/001/el/1840/1804/1806”, “id”: “CG-PCER-VARINT:CA377482283/MONDO:0017623/001/1840/1804/1806”, “type”: “EvidenceLine”, “evidenceItem”: [ { “@id”: “CG-PCER:curatorInference/CA377482283/MONDO:0017623/001/ci/CA377482283/MONDO:0017623/001.002”, “id”: “CA377482283/MONDO:0017623/001/ci/CA377482283/MONDO:0017623/001.002”, “type”: “InfFromBkgrndSciKnow”, “contribution”: [ { “type”: “Contribution”, “agent”: { “@id”: “https://erepo.genome.network/evidence-repo/api//agent/Jessica_Mester_153376223213854”, “id”: “CG-PCER-AGENT:Jessica_Mester_153376223213854”, “type”: “Agent” }, “contributionDate”: { “date”: “2017/6/27”, “description”: “Date on which this evidence was provided” }, “contributionRole”: { “@id”: “https://obofoundry.org/sepio/0000156”, “id”: “SEPIO:0000516”, “type”: “ContributoryRole”, “label”: “curator role” } } ] } ] } ] } ] }, { “@id”: “https://erepo.genome.network/evidence-repo/api/interpretation/CA377482283/MONDO:0017623/001/el/1840/1768”, “id”: “CG-PCER-VARINT:CA377482283/MONDO:0017623/001/1840/1768”, “type”: “EvidenceLine”, “evidenceStrength”: { “@id”: “https://obofoundry.org/sepio/SEPIO:0000328”, “id”: “SEPIO:0000328”, “label”: “Benign Strong” }, “evidenceItem”: [ { “@id”: “https://erepo.genome.network/evidence-repo/api/interpretation/CA377482283/MONDO:0017623/001/ei/1841/1769”, “id”: “CG-PCER-VARINT:CA377482283/MONDO:0017623/001/1841/1769”, “type”: “CriterionAssessment”, “criterion”: { “@id”: “https://obofoundry.org/sepio/clingen/SEPIO-CG:99042”, “id”: “SEPIO-CG:99042”, “type”: “Criterion”, “label”: “BS4”, “defaultStrength”: { “@id”: “https://obofoundry.org/sepio/SEPIO:0000328”, “id”: “SEPIO:0000328”, “label”: “Benign Strong” } }, “statementOutcome”: { “@id”: “SEPIO:0000224”, “label”: “Not Met” }, “contribution”: [ { “type”: “Contribution”, “agent”: { “@id”: “https://erepo.genome.network/evidence-repo/api//agent/Jessica_Mester_153376223213854”, “id”: “CG-PCER-AGENT:Jessica_Mester_153376223213854”, “type”: “Agent” }, “contributionDate”: { “date”: “2017/6/27”, “description”: “Date on which this evidence was provided” }, “contributionRole”: { “@id”: “https://obofoundry.org/sepio/0000156”, “id”: “SEPIO:0000516”, “type”: “ContributoryRole”, “label”: “curator role” } } ], “evidenceLine”: [ { “@id”: “https://erepo.genome.network/evidence-repo/api/interpretation/CA377482283/MONDO:0017623/001/el/1840/1768/1770”, “id”: “CG-PCER-VARINT:CA377482283/MONDO:0017623/001/1840/1768/1770”, “type”: “EvidenceLine”, “evidenceItem”: [ { “@id”: “CG-PCER:curatorInference/CA377482283/MONDO:0017623/001/ci/CA377482283/MONDO:0017623/001.002”, “id”: “CA377482283/MONDO:0017623/001/ci/CA377482283/MONDO:0017623/001.002”, “type”: “InfFromBkgrndSciKnow”, “contribution”: [ { “type”: “Contribution”, “agent”: { “@id”: “https://erepo.genome.network/evidence-repo/api//agent/Jessica_Mester_153376223213854”, “id”: “CG-PCER-AGENT:Jessica_Mester_153376223213854”, “type”: “Agent” }, “contributionDate”: { “date”: “2017/6/27”, “description”: “Date on which this evidence was provided” }, “contributionRole”: { “@id”: “https://obofoundry.org/sepio/0000156”, “id”: “SEPIO:0000516”, “type”: “ContributoryRole”, “label”: “curator role” } } ] } ] } ] } ] }, { “@id”: “https://erepo.genome.network/evidence-repo/api/interpretation/CA377482283/MONDO:0017623/001/el/1840/1588”, “id”: “CG-PCER-VARINT:CA377482283/MONDO:0017623/001/1840/1588”, “type”: “EvidenceLine”, “evidenceStrength”: { “@id”: “https://obofoundry.org/sepio/SEPIO:0000328”, “id”: “SEPIO:0000328”, “label”: “Benign Strong” }, “evidenceItem”: [ { “@id”: “https://erepo.genome.network/evidence-repo/api/interpretation/CA377482283/MONDO:0017623/001/ei/1841/1589”, “id”: “CG-PCER-VARINT:CA377482283/MONDO:0017623/001/1841/1589”, “type”: “CriterionAssessment”, “criterion”: { “@id”: “https://obofoundry.org/sepio/clingen/SEPIO-CG:99041”, “id”: “SEPIO-CG:99041”, “type”: “Criterion”, “label”: “BS3”, “defaultStrength”: { “@id”: “https://obofoundry.org/sepio/SEPIO:0000328”, “id”: “SEPIO:0000328”, “label”: “Benign Strong” } }, “statementOutcome”: { “@id”: “SEPIO:0000224”, “label”: “Not Met” }, “contribution”: [ { “type”: “Contribution”, “agent”: { “@id”: “https://erepo.genome.network/evidence-repo/api//agent/Jessica_Mester_153376223213854”, “id”: “CG-PCER-AGENT:Jessica_Mester_153376223213854”, “type”: “Agent” }, “contributionDate”: { “date”: “2017/6/27”, “description”: “Date on which this evidence was provided” }, “contributionRole”: { “@id”: “https://obofoundry.org/sepio/0000156”, “id”: “SEPIO:0000516”, “type”: “ContributoryRole”, “label”: “curator role” } } ], “evidenceLine”: [ { “@id”: “https://erepo.genome.network/evidence-repo/api/interpretation/CA377482283/MONDO:0017623/001/el/1840/1588/1590”, “id”: “CG-PCER-VARINT:CA377482283/MONDO:0017623/001/1840/1588/1590”, “type”: “EvidenceLine”, “evidenceItem”: [ { “@id”: “CG-PCER:curatorInference/CA377482283/MONDO:0017623/001/ci/EV000000009”, “id”: “CA377482283/MONDO:0017623/001/ci/EV000000009”, “type”: “CuratorInference”, “traceableAuthorStatement”: 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“https://erepo.genome.network/evidence-repo/api/interpretation/CA377482283/MONDO:0017623/001/el/1840/1684/1686”, “id”: “CG-PCER-VARINT:CA377482283/MONDO:0017623/001/1840/1684/1686”, “type”: “EvidenceLine”, “evidenceItem”: [ { “@id”: “CG-PCER:curatorInference/CA377482283/MONDO:0017623/001/ci/CA377482283/MONDO:0017623/001.002”, “id”: “CA377482283/MONDO:0017623/001/ci/CA377482283/MONDO:0017623/001.002”, “type”: “InfFromBkgrndSciKnow”, “contribution”: [ { “type”: “Contribution”, “agent”: { “@id”: “https://erepo.genome.network/evidence-repo/api//agent/Jessica_Mester_153376223213854”, “id”: “CG-PCER-AGENT:Jessica_Mester_153376223213854”, “type”: “Agent” }, “contributionDate”: { “date”: “2017/6/27”, “description”: “Date on which this evidence was provided” }, “contributionRole”: { “@id”: “https://obofoundry.org/sepio/0000156”, “id”: “SEPIO:0000516”, “type”: “ContributoryRole”, “label”: “curator role” }, “comments”: “BP4/PP3 not being applied for PTEN missense variants” } ] } ] } ] } ] }, { 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“https://erepo.genome.network/evidence-repo/api//agent/Jessica_Mester_153376223213854”, “id”: “CG-PCER-AGENT:Jessica_Mester_153376223213854”, “type”: “Agent” }, “contributionDate”: { “date”: “2017/6/27”, “description”: “Date on which this evidence was provided” }, “contributionRole”: { “@id”: “https://obofoundry.org/sepio/0000156”, “id”: “SEPIO:0000516”, “type”: “ContributoryRole”, “label”: “curator role” } } ], “evidenceLine”: [ { “@id”: “https://erepo.genome.network/evidence-repo/api/interpretation/CA377482283/MONDO:0017623/001/el/1840/1726/1728”, “id”: “CG-PCER-VARINT:CA377482283/MONDO:0017623/001/1840/1726/1728”, “type”: “EvidenceLine”, “evidenceItem”: [ { “@id”: “CG-PCER:curatorInference/CA377482283/MONDO:0017623/001/ci/CA377482283/MONDO:0017623/001.002”, “id”: “CA377482283/MONDO:0017623/001/ci/CA377482283/MONDO:0017623/001.002”, “type”: “InfFromBkgrndSciKnow”, “contribution”: [ { “type”: “Contribution”, “agent”: { “@id”: “https://erepo.genome.network/evidence-repo/api//agent/Jessica_Mester_153376223213854”, “id”: “CG-PCER-AGENT:Jessica_Mester_153376223213854”, “type”: “Agent” }, “contributionDate”: { “date”: “2017/6/27”, “description”: “Date on which this evidence was provided” }, “contributionRole”: { “@id”: “https://obofoundry.org/sepio/0000156”, “id”: “SEPIO:0000516”, “type”: “ContributoryRole”, “label”: “curator role” } } ] } ] } ] } ] }, { “@id”: “https://erepo.genome.network/evidence-repo/api/interpretation/CA377482283/MONDO:0017623/001/el/1840/1756”, “id”: “CG-PCER-VARINT:CA377482283/MONDO:0017623/001/1840/1756”, “type”: “EvidenceLine”, “evidenceStrength”: { “@id”: “https://obofoundry.org/sepio/SEPIO:0000327”, “id”: “SEPIO:0000327”, “label”: “Benign Supporting” }, “evidenceItem”: [ { “@id”: “https://erepo.genome.network/evidence-repo/api/interpretation/CA377482283/MONDO:0017623/001/ei/1841/1757”, “id”: “CG-PCER-VARINT:CA377482283/MONDO:0017623/001/1841/1757”, “type”: “CriterionAssessment”, “criterion”: { “@id”: “https://obofoundry.org/sepio/clingen/SEPIO-CG:99048”, “id”: “SEPIO-CG:99048”, “type”: “Criterion”, “label”: “BP6”, “defaultStrength”: { “@id”: “https://obofoundry.org/sepio/SEPIO:0000327”, “id”: “SEPIO:0000327”, “label”: “Benign Supporting” } }, “statementOutcome”: { “@id”: “SEPIO:0000224”, “label”: “Not Met” }, “contribution”: [ { “type”: “Contribution”, “agent”: { “@id”: “https://erepo.genome.network/evidence-repo/api//agent/Jessica_Mester_153376223213854”, “id”: “CG-PCER-AGENT:Jessica_Mester_153376223213854”, “type”: “Agent” }, “contributionDate”: { “date”: “2017/6/27”, “description”: “Date on which this evidence was provided” }, “contributionRole”: { “@id”: “https://obofoundry.org/sepio/0000156”, “id”: “SEPIO:0000516”, “type”: “ContributoryRole”, “label”: “curator role” } } ], “evidenceLine”: [ { “@id”: “https://erepo.genome.network/evidence-repo/api/interpretation/CA377482283/MONDO:0017623/001/el/1840/1756/1758”, “id”: “CG-PCER-VARINT:CA377482283/MONDO:0017623/001/1840/1756/1758”, “type”: “EvidenceLine”, “evidenceItem”: [ { “@id”: “CG-PCER:curatorInference/CA377482283/MONDO:0017623/001/ci/CA377482283/MONDO:0017623/001.002”, “id”: “CA377482283/MONDO:0017623/001/ci/CA377482283/MONDO:0017623/001.002”, “type”: “InfFromBkgrndSciKnow”, “contribution”: [ { “type”: “Contribution”, “agent”: { “@id”: “https://erepo.genome.network/evidence-repo/api//agent/Jessica_Mester_153376223213854”, “id”: “CG-PCER-AGENT:Jessica_Mester_153376223213854”, “type”: “Agent” }, “contributionDate”: { “date”: “2017/6/27”, “description”: “Date on which this evidence was provided” }, “contributionRole”: { “@id”: “https://obofoundry.org/sepio/0000156”, “id”: “SEPIO:0000516”, “type”: “ContributoryRole”, “label”: “curator role” }, “comments”: “Criteria aren’t being used by PTEN variant curation group.” } ] } ] } ] } ] }, { “@id”: “https://erepo.genome.network/evidence-repo/api/interpretation/CA377482283/MONDO:0017623/001/el/1840/1597”, “id”: “CG-PCER-VARINT:CA377482283/MONDO:0017623/001/1840/1597”, “type”: “EvidenceLine”, “evidenceStrength”: { “@id”: “https://obofoundry.org/sepio/SEPIO:0000327”, “id”: “SEPIO:0000327”, “label”: “Benign Supporting” }, “evidenceItem”: [ { “@id”: “https://erepo.genome.network/evidence-repo/api/interpretation/CA377482283/MONDO:0017623/001/ei/1841/1598”, “id”: “CG-PCER-VARINT:CA377482283/MONDO:0017623/001/1841/1598”, “type”: “CriterionAssessment”, “criterion”: { “@id”: “https://obofoundry.org/sepio/clingen/SEPIO-CG:99044”, “id”: “SEPIO-CG:99044”, “type”: “Criterion”, “label”: “BP2”, “defaultStrength”: { “@id”: “https://obofoundry.org/sepio/SEPIO:0000327”, “id”: “SEPIO:0000327”, “label”: “Benign Supporting” } }, “statementOutcome”: { “@id”: “SEPIO:0000224”, “label”: “Not Met” }, “contribution”: [ { “type”: “Contribution”, “agent”: { “@id”: “https://erepo.genome.network/evidence-repo/api//agent/Jessica_Mester_153376223213854”, “id”: “CG-PCER-AGENT:Jessica_Mester_153376223213854”, “type”: “Agent” }, “contributionDate”: { “date”: “2017/6/29”, “description”: “Date on which this evidence was provided” }, “contributionRole”: { “@id”: “https://obofoundry.org/sepio/0000156”, “id”: “SEPIO:0000516”, “type”: “ContributoryRole”, “label”: “curator role” } } ], “evidenceLine”: [ { “@id”: “https://erepo.genome.network/evidence-repo/api/interpretation/CA377482283/MONDO:0017623/001/el/1840/1597/1599”, “id”: “CG-PCER-VARINT:CA377482283/MONDO:0017623/001/1840/1597/1599”, “type”: “EvidenceLine”, “evidenceItem”: [ { “@id”: “CG-PCER:curatorInference/CA377482283/MONDO:0017623/001/ci/CA377482283/MONDO:0017623/001.002”, “id”: “CA377482283/MONDO:0017623/001/ci/CA377482283/MONDO:0017623/001.002”, “type”: “InfFromBkgrndSciKnow”, “contribution”: [ { “type”: “Contribution”, “agent”: { “@id”: “https://erepo.genome.network/evidence-repo/api//agent/Jessica_Mester_153376223213854”, “id”: “CG-PCER-AGENT:Jessica_Mester_153376223213854”, “type”: “Agent” }, “contributionDate”: { “date”: “2017/6/29”, “description”: “Date on which this evidence was provided” }, “contributionRole”: { “@id”: “https://obofoundry.org/sepio/0000156”, “id”: “SEPIO:0000516”, “type”: “ContributoryRole”, “label”: “curator role” } } ] } ] } ] } ] }, { “@id”: “https://erepo.genome.network/evidence-repo/api/interpretation/CA377482283/MONDO:0017623/001/el/1840/1579”, “id”: “CG-PCER-VARINT:CA377482283/MONDO:0017623/001/1840/1579”, “type”: “EvidenceLine”, “evidenceStrength”: { “@id”: “https://obofoundry.org/sepio/SEPIO:0000327”, “id”: “SEPIO:0000327”, “label”: “Benign Supporting” }, “evidenceItem”: [ { “@id”: “https://erepo.genome.network/evidence-repo/api/interpretation/CA377482283/MONDO:0017623/001/ei/1841/1580”, “id”: “CG-PCER-VARINT:CA377482283/MONDO:0017623/001/1841/1580”, “type”: “CriterionAssessment”, “criterion”: { “@id”: “https://obofoundry.org/sepio/clingen/SEPIO-CG:99047”, “id”: “SEPIO-CG:99047”, “type”: “Criterion”, “label”: “BP5”, “defaultStrength”: { “@id”: “https://obofoundry.org/sepio/SEPIO:0000327”, “id”: “SEPIO:0000327”, “label”: “Benign Supporting” } }, “statementOutcome”: { “@id”: “SEPIO:0000224”, “label”: “Not Met” }, “contribution”: [ { “type”: “Contribution”, “agent”: { “@id”: “https://erepo.genome.network/evidence-repo/api//agent/Jessica_Mester_153376223213854”, “id”: “CG-PCER-AGENT:Jessica_Mester_153376223213854”, “type”: “Agent” }, “contributionDate”: { “date”: “2017/6/27”, “description”: “Date on which this evidence was provided” }, “contributionRole”: { “@id”: “https://obofoundry.org/sepio/0000156”, “id”: “SEPIO:0000516”, “type”: “ContributoryRole”, “label”: “curator role” } } ], “evidenceLine”: [ { “@id”: “https://erepo.genome.network/evidence-repo/api/interpretation/CA377482283/MONDO:0017623/001/el/1840/1579/1581”, “id”: “CG-PCER-VARINT:CA377482283/MONDO:0017623/001/1840/1579/1581”, “type”: “EvidenceLine”, “evidenceItem”: [ { “@id”: “CG-PCER:curatorInference/CA377482283/MONDO:0017623/001/ci/CA377482283/MONDO:0017623/001.002”, “id”: “CA377482283/MONDO:0017623/001/ci/CA377482283/MONDO:0017623/001.002”, “type”: “InfFromBkgrndSciKnow”, “contribution”: [ { “type”: “Contribution”, “agent”: { “@id”: “https://erepo.genome.network/evidence-repo/api//agent/Jessica_Mester_153376223213854”, “id”: “CG-PCER-AGENT:Jessica_Mester_153376223213854”, “type”: “Agent” }, “contributionDate”: { “date”: “2017/6/27”, “description”: “Date on which this evidence was provided” }, “contributionRole”: { “@id”: “https://obofoundry.org/sepio/0000156”, “id”: “SEPIO:0000516”, “type”: “ContributoryRole”, “label”: “curator role” } } ] } ] } ] } ] } ] } ] } ] } } } }, “summary”: “GetFullSEPIOInterpretationByVCIID”, “description”: "Get the full Scientific Evidence and Provenance Information Ontology (SEPIO) compliant JSON-LD document containing interpretation data for an allele-condition (condition id is namespaced) pair under a specific guideline of interest. The retrieval will be by the ID which was provided by the ClinGen VCI group when the interpretation was first uploaded.\n\nThe hierarchically structured document will include:\n1. Variant information and condition/syndrome info that the variant is known to be associated with as well as Outcome that conveys whether a variant is pathogenic, likely pathogenic, benign, etc for a given genetic condition.\n2. Evidence Lines pertaining to various intermediate outcome(s) that are further supported by ACMG tags backed by one or more evidences that could be in the form of published articles or some other type of evidence. In case of tag less assertions, the intermediate outcome(s) will be supported directly by evidence sources.\n3. Agent/Contributor info conveying which agent contributed to what evidence along with the date of evidence supplied. ", “tags”: [ “INTERPRETATIONS” ], “parameters”: [ { “$ref”: “#/parameters/gid-or-uuid” } ] } }, “/interpretations”: { “get”: { “responses”: { “200”: { “description”: “”, “schema”: { “type”: “object”, “properties”: { “@context”: { “type”: “string”, “format”: “uri” }, “variantInterpretations”: { “type”: “array”, “items”: { “$ref”: “#/definitions/variant-interpretation-model-in-search-resp” } } } }, “examples”: {} } }, “summary”: “SearchInterpretations”, “description”: “Search end point for the repository. Accepts one or more of the supported query fields.”, “parameters”: [ { “$ref”: “#/parameters/gene-query” }, { “$ref”: “#/parameters/condition-query” }, { “$ref”: “#/parameters/hgvs-query” }, { “$ref”: “#/parameters/assertion-query” }, { “$ref”: “#/parameters/caid-query” }, { “$ref”: “#/parameters/match-logic-query” }, { “$ref”: “#/parameters/match-mode-query” }, { “$ref”: “#/parameters/match-limit-query” }, { “$ref”: “#/parameters/match-skip-query” } ], “tags”: [ “INTERPRETATIONS” ] } }, “/guideline/{gid}”: { “get”: { “responses”: { “200”: { “description”: “”, “schema”: { “type”: “object”, “properties”: { “@context”: { “type”: “string” }, “@id”: { “type”: “string” }, “@type”: { “type”: “string” }, “label”: { “type”: “string” }, “description”: { “type”: “string” }, “url”: { “type”: “string” }, “assertionMethod”: { “type”: “object”, “properties”: { “type”: { “type”: “string” }, “url”: { “type”: “string” }, “version”: { “type”: “string” }, “description”: { “type”: “string” } } }, “evidenceCodes”: { “type”: “array”, “items”: { “type”: “object”, “properties”: { “@id”: { “type”: “string” }, “label”: { “type”: “string” }, “description”: { “type”: “string” }, “evidenceStrength”: { “$ref”: “#/definitions/evidenceStrengthInGuideline” }, “comment”: { “type”: “string” } } } }, “rules”: { “type”: “array”, “items”: { “type”: “object”, “properties”: { “@id”: { “type”: “string” }, “inference”: { “type”: “string” }, “comment”: { “type”: “string” }, “isSatisfiedBy”: { “type”: “array”, “items”: { “anyOf”: [ { “properties”: { “@id”: { “type”: “string” }, “conditionSet”: { “type”: “array”, “items”: { “type”: “object”, “properties”: { “@id”: { “type”: “string” }, “evidenceStrength”: { “$ref”: “#/definitions/evidenceStrengthInGuideline” }, “occurence”: { “type”: “string” } } } } } } ], “type”: “object” } } } } }, “metaRules”: { “type”: “array”, “items”: { “type”: “object”, “properties”: { “@id”: { “type”: “string” }, “comment”: { “type”: “string” }, “metaInference”: { “type”: “string” }, “description”: { “type”: “string” }, “uniqueInferences”: { “type”: “array”, “items”: { “type”: “string” } } } } } } }, “examples”: { “application/json”: { “@context”: “https://erepo.genome.network/evrepo/api/context/guideline”, “@id”: “https://erepo.genome.network/evrepo/api/guideline/GN002”, “@type”: “Guideline”, “label”: “MYH7-associated inherited cardiomyopathies - adapted from ACMG/AMP”, “description”: “Adaptation and validation of the ACMG/AMP variant classification framework for MYH7-associated inherited cardiomyopathies: recommendations by ClinGen’s Inherited Cardiomyopathy Expert Panel”, “url”: “https://www.nature.com/articles/gim2017218#t1”, “assertionMethod”: { “@type”: “AssertionMethod”, “url”: “https://www.clinicalgenome.org/site/assets/files/8832/clingen_cmp_acmg_specifications_v1.pdf”, “version”: “1.0”, “@id”: “:am1", “description”: “MYH7-associated inherited cardiomyopathies - adapted from ACMG/AMP” }, “evidenceCodes”: [ { “@id”: “https://erepo.genome.network/evrepo/api/guideline/GN002/evcode/BA1”, “label”: “BA1”, “description”: “Allele frequency is >= 0.1% based on the filtering allele frequency (FAF) in ExAC”, “evidenceStrength”: { “@id”: ":ec1”, “label”: “Benign Stand Alone” }, “comment”: "Only a couple of evidence codes have been included for modeling. Remove comment property in final version. " }, { “@id”: “https://erepo.genome.network/evrepo/api/guideline/GN002/evcode/PS4_Moderate”, “label”: “PS4-Moderate”, “description”: “Variant identified in >=6 probands with consistent phenotypes”, “evidenceStrength”: { “@id”: “:ec2", “label”: “Pathogenic Moderate” } } ], “rules”: [ { “@id”: ":r1”, “inference”: “Pathogenic”, “comment”: “Only a few rules have been included for modeling. Remove comment property in final version. isSatisfiedBy contains all the possible conditionSets that can yield a Pathogenic inference.”, “isSatisfiedBy”: [ { “@id”: “:ao1", “conditionSet”: [ { “@id”: ":sb1”, “evidenceStrength”: { “@id”: “:ec3", “label”: “Pathogenic Very Strong” }, “occurrence”: “==1” }, { “@id”: ":sb2”, “evidenceStrength”: { “@id”: “:ec4", “label”: “Pathogenic Strong” }, “occurrence”: “>=1” } ] }, { “@id”: ":ao2”, “conditionSet”: [ { “@id”: “:sb1", “evidenceStrength”: { “label”: “Pathogenic Very Strong” }, “occurrence”: “==1” }, { “@id”: ":sb3”, “evidenceStrength”: { “label”: “Pathogenic Moderate”, “@id”: “:ec2" }, “occurrence”: “>=2” } ] } ] } ], “metaRules”: [ { “@id”: ":mr1”, “comment”: “Only a few of the metarules are shown in this example. Remove comment prop in final version.”, “metaInference”: “Uncertain Significance - Insufficient Evidence”, “description”: “Given set of evidence are not sufficient to make any assertions.”, “uniqueInferences”: [] }, { “@id”: “:mr2", “metaInference”: “Pathogenic”, “description”: “As the rules only suggest one assertion that is Pathogenic, the final assertion is Pathogenic”, “uniqueInferences”: [ “Pathogenic” ] }, { “@id”: ":mr3”, “metaInference”: “Benign - Stand Alone”, “description”: “”, “uniqueInferences”: [ “Pathogenic”, “Benign”, “Benign - Stand Alone” ] } ] } } } }, “summary”: “GetGuideline”, “description”: “Get the full representation for a specific guideline”, “parameters”: [ { “$ref”: “#/parameters/gid” } ], “tags”: [ “GUIDELINES” ], “operationId”: “getGuideline” }, “parameters”: [ { “name”: “gid”, “in”: “path”, “type”: “string”, “required”: true } ] }, “/context”: { “get”: { “responses”: { “200”: { “description”: “”, “schema”: { “type”: “object”, “properties”: {} }, “examples”: { “application/json”: { “@context”: { “IGSR-population-type”: “https://www.internationalgenome.org/category/population/”, “ascertainment”: { “@type”: “@id”, “@id”: “SEPIO:0000255” }, “totalOfAllelePosConditionNegIndividuals”: { “@type”: “@id”, “@id”: “SEPIO:0000291” }, “disease”: { “@type”: “@id”, “@id”: “BFO:0000051” }, “Agent”: { “@id”: “PROV:agent” }, “hemizygousAlleleIndividualCount”: { “@type”: “@id”, “@id”: “SEPIO:0000299” }, “UserLabel”: { “@id”: “SEPIO-CG:03500” }, “LocusSpecificity”: { “@id”: “SEPIO:0000348” }, “AlleleFunctionalAssayMethod”: { “@id”: “SEPIO-CG:55110” }, “individual”: { “@type”: “@id”, “@id”: “SEPIO:0000280” }, “mechanism”: { “@type”: “@id”, “@id”: “SEPIO:0000197” }, “RegionType”: { “@id”: “SEPIO:0000243” }, “InfFromBkgrndSciKnowManAsser”: { “@id”: “ECO:0000306” }, “transcript”: { “@type”: “@id”, “@id”: “SEPIO:0000283” }, “totalOfUntestedConditionNegIndividuals”: { “@type”: “@id”, “@id”: “SEPIO:0000294” }, “MESH”: “https://meshb.nlm.nih.gov/”, “allele”: { “@type”: “@id”, “@id”: “SEPIO:0000275” }, “consequence”: { “@type”: “@id”, “@id”: “SEPIO:0000197” }, “penetrance”: { “@type”: “@id”, “@id”: “SEPIO:0000197” }, “ConditionMechanismStrength”: { “@id”: “SEPIO:0000354” }, “BenignMissenseVariationRateOutcome”: { “@id”: “SEPIO:0000349” }, “LRG”: “https://www.lrg-sequence.org/”, “GeneticVariation”: { “@id”: “https://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C17248” }, “prediction”: { “@type”: “@id”, “@id”: “SEPIO:0000168” }, “traceableAuthorStatement”: { “@type”: “@id”, “@id”: “ECO:0000033” }, “modeOfInheritance”: { “@type”: “@id”, “@id”: “cg-attributes:modeOfInheritance” }, “ModeOfInheritance”: { “@id”: “SEPIO-CG:55105” }, “evidenceItem”: { “@type”: “@id”, “@id”: “SEPIO:0000084” }, “GENO”: “https://obofoundry.org/geno/”, “IAO”: “https://purl.obolibrary.org/obo/IAO_”, “base”: “https://datamodel.clinicalgenome.org/types/”, “index”: { “@type”: “@id”, “@id”: “cg-attributes:index” }, “individualHasCondition”: { “@type”: “@id”, “@id”: “SEPIO:0000197” }, “CG-PCER-TAGCAT”: “CG-PCER:tagcat/”, “phenotypePositiveAlleleNegative”: { “@type”: “@id”, “@id”: “SEPIO:0000290” }, “DomainEntity”: { “@id”: “SEPIO-CG:03000” }, “InSilicoPrediction”: { “@id”: “SEPIO:0000249” }, “contributionRole”: { “@type”: “@id”, “@id”: “BFO:0000055” }, “contextualAllele”: { “@type”: “@id”, “@id”: “SEPIO:0000275” }, “MONDO”: “https://api.monarchinitiative.org/api/bioentity/phenotype/MONDO:”, “assayType”: { “@type”: “@id”, “@id”: “SEPIO:0000255” }, “VariantInterpretation”: { “@id”: “SEPIO:0000190” }, “inconsistentSegregationCount”: { “@type”: “@id”, “@id”: “SEPIO:0000315” }, “MEDGEN”: “https://www.ncbi.nlm.nih.gov/medgen/”, “ConditionMechanism”: { “@id”: “SEPIO:0000228” }, “searchTags”: “cg-attributes:searchTags”, “prevelance”: { “@type”: “@id”, “@id”: “SEPIO:0000310” }, “scoringAlgorithm”: { “@type”: “@id”, “@id”: “BFO:0000051” }, “BenignMissenseVariationRate”: { “@id”: “SEPIO:0000246” }, “InfBasedOnIndClinicalExp”: { “@id”: “ECO:0006018” }, “BROAD-population-type”: “https://broadinstitute.org/populations/”, “ScoringAlgorithm”: { “@id”: “SEPIO:0000224” }, “score”: { “@type”: “@id”, “@id”: “SEPIO:0000168” }, “Conservation”: { “@id”: “SEPIO-CG:55122” }, “Phase”: { “@id”: “SEPIO:0000344” }, “criterion”: { “@type”: “@id”, “@id”: “SEPIO:0000041” }, “EvidenceLine”: { “@id”: “SEPIO:0000002” }, “variant”: { “@type”: “@id”, “@id”: “SEPIO:0000275” }, “ReferenceSequence”: { “@id”: “GENO:0000017” }, “CG-PCER”: “https://erepo.genome.network/evrepo/api/”, “canonicalAllele”: { “@type”: “@id”, “@id”: “SEPIO:0000275” }, “CG-PCER-GUIDE”: “CG-PCER:guideline/”, “MolecularConsequence”: { “@id”: “SEPIO-CG:55102” }, “minimum”: { “@type”: “@id”, “@id”: “SEPIO:0000312” }, “image”: { “@type”: “@id”, “@id”: “cg-attributes:image” }, “CanonicalAllele”: { “@id”: “GENO:0000890” }, “phenotypePositiveAllelePositive”: { “@type”: “@id”, “@id”: “SEPIO:0000292” }, “CaseControl”: { “@id”: “SEPIO:0000242” }, “MONAPI”: “https://api.monarchinitiative.org/api/bioentity/phenotype/”, “ContextualAllele”: { “@id”: “GENO:0000891” }, “Penetrance”: { “@id”: “SEPIO-CG:55113” }, “FamilySegregation”: { “@id”: “SEPIO:0000247” }, “description”: “cg-attributes:description”, “tagCategory”: { “@type”: “@id”, “@id”: “Cg-CER-TAGCAT:000” }, “RegionAlleles”: { “@id”: “SEPIO:0000244” }, “informationId”: { “@type”: “@id”, “@id”: “cg-attributes:informationId” }, “familySegregation”: { “@type”: “@id”, “@id”: “SEPIO:0000287” }, “homozygousAlleleIndividualCount”: { “@type”: “@id”, “@id”: “SEPIO:0000301” }, “Criterion”: { “@id”: “SEPIO:0000192” }, “genotypeValues”: “SEPIO:0000317”, “gene”: { “@type”: “@id”, “@id”: “SEPIO:0000278” }, “HGNC”: “https://www.genenames.org/”, “conceptType”: “DC:description”, “ECO”: “https://purl.obolibrary.org/obo/ECO_”, “alleleCount”: { “@type”: “@id”, “@id”: “SEPIO:0000296” }, “mechanismConfidence”: { “@type”: “@id”, “@id”: “SEPIO:0000167” }, “value”: { “@type”: “@id”, “@id”: “SEPIO:0000197” }, “accession”: “cg-attributes:accession”, “annotation”: { “@type”: “@id”, “@id”: “SEPIO:0000197” }, “Orphanet”: “https://www.orpha.net/”, “ConditionStatus”: { “@id”: “SEPIO-CG:55124” }, “IdentifierSystem”: { “@id”: “SEPIO:0000374” }, “cg-types”: “https://datamodel.clinicalgenome.org/types/”, “type”: “@type”, “familyHasCondition”: { “@type”: “@id”, “@id”: “SEPIO:0000197” }, “IndividualGenotype”: { “@id”: “SEPIO:0000245” }, “version”: “PAV:version”, “phenotypeNegativeAlleleNegative”: { “@type”: “@id”, “@id”: “SEPIO:0000289” }, “InconsistentSegregationObserved”: { “@id”: “SEPIO-CG:55125” }, “Population”: { “@id”: “SEPIO-CG:55111” }, “oid”: “RDFS:label”, “evidenceStrength”: { “@type”: “@id”, “@id”: “SEPIO:0000132” }, “HP”: “https://human-phenotype-ontology.github.io/”, “Gene”: { “@id”: “SO:0000704” }, “id”: “@id”, “label”: “cg-attributes:label”, “population”: { “@type”: “@id”, “@id”: “SEPIO:0000277” }, “affectedValues”: “SEPIO:0000313”, “phenotypeNegativeAllelePositive”: { “@type”: “@id”, “@id”: “SEPIO:0000291” }, “ENSEMBL”: “https://www.ensembl.org/”, “FinalAssertion”: { “@id”: “CG-PCER:FinalAssertion” }, “NullAllele”: { “@id”: “SEPIO:0000274” }, “LN”: “https://loinc.org/”, “Contribution”: { “@id”: “SEPIO:0000158” }, “confidenceIntervalUpper”: { “@type”: “@id”, “@id”: “SEPIO:0000307” }, “totalOfAlleleNegConditionPosIndividuals”: { “@type”: “@id”, “@id”: “SEPIO:0000290” }, “Statement”: { “@id”: “SEPIO:0000174” }, “SequenceLocation”: { “@id”: “GENO:0000815” }, “AlleleConservationScore”: { “@id”: “SEPIO:0000369” }, “Genotype”: { “@id”: “cg-types:Genotype” }, “OBI”: “https://purl.obolibrary.org/obo/OBI_”, “AlleleMolecularConsequence”: { “@id”: “SEPIO:0000229” }, “RegionAllelesOutcome”: { “@id”: “cg-types:RegionAllelesOutcome” }, “AlleleInheritance”: { “@id”: “SEPIO-CG:55119” }, “url”: “ERO:0000480”, “CLINVAR”: “https://www.ncbi.nlm.nih.gov/clinvar/variation/”, “alleleName”: “RDFS:label”, “EvidenceLineStrength”: { “@id”: “SEPIO:0000353” }, “region”: { “@type”: “@id”, “@id”: “SEPIO:0000279” }, “Example”: { “@id”: “cg-types:Example” }, “totalOfAllelePosConditionPosIndividuals”: { “@type”: “@id”, “@id”: “SEPIO:0000292” }, “columns”: “SEPIO:0000316”, “algorithm”: “SEPIO:0000130”, “CAR”: “https://reg.genome.network/allele/”, “iri”: “cg-attributes:iri”, “name”: “RDFS:label”, “LocusHeterogeneity”: { “@id”: “SEPIO:0000250” }, “condition”: { “@type”: “@id”, “@id”: “SEPIO:0000276” }, “Disease”: { “@id”: “SEPIO-CG:55116” }, “CriterionEvaluation”: { “@id”: “SEPIO:0000347” }, “DOID”: “https://api.monarchinitiative.org/api/bioentity/phenotype/DOID:”, “PUBMED”: “https://www.ncbi.nlm.nih.gov/pubmed/”, “proband”: { “@type”: “@id”, “@id”: “SEPIO:0000281” }, “concept”: { “@type”: “@id”, “@id”: “cg-attributes:concept” }, “medianCoverage”: { “@type”: “@id”, “@id”: “SEPIO:0000303” }, “IntermediateAssertion”: { “@id”: “CG-PCER:intermediateAssertion” }, “evidenceLine”: { “@type”: “@id”, “@id”: “SEPIO:0000006” }, “source”: “DC:source”, “Prediction”: { “@id”: “SEPIO:0000345” }, “userLabel”: { “@type”: “@id”, “@id”: “cg-attributes:userLabel” }, “Individual”: { “@id”: “foaf:Person” }, “Ascertainment”: { “@id”: “SEPIO-CG:55120” }, “Significance”: { “@id”: “SEPIO:0000371” }, “FamilyCondition”: { “@id”: “SEPIO:0000239” }, “CG-PCER-EVITEM”: “CG-PCER:evidenceItem/”, “ContributoryRole”: { “@id”: “SEPIO-CG:55118” }, “conceptListExtensibility”: { “@type”: “@id”, “@id”: “DC:identifier” }, “IndividualAlleleInheritance”: { “@id”: “SEPIO:0000240” }, “alleleFrequency”: { “@type”: “@id”, “@id”: “SEPIO:0000297” }, “individualCount”: { “@type”: “@id”, “@id”: “SEPIO:0000302” }, “Phenotype”: { “@id”: “SEPIO-CG:55117” }, “CG-PCER-COND”: “CG-PCER:condition/”, “start”: { “@type”: “@id”, “@id”: “GENO:000894” }, “SEPIO”: “https://obofoundry.org/sepio/”, “produces”: { “@type”: “@id”, “@id”: “RO:0003000” }, “AggregateSegregation”: { “@id”: “SEPIO:0000248” }, “AlleleConservation”: { “@id”: “SEPIO:0000253” }, “preferredCtxAllele”: { “@type”: “@id”, “@id”: “SEPIO:0000256” }, “CG-PCER-CI”: “CG-PCER:curatorInference/”, “defaultStrength”: { “@type”: “@id”, “@id”: “SEPIO:0000196” }, “InSilicoPredictionScore”: { “@id”: “SEPIO:0000368” }, “alleleNumber”: { “@type”: “@id”, “@id”: “SEPIO:0000298” }, “totalOfFamiliesWithInconsistentSegregations”: { “@type”: “@id”, “@id”: “SEPIO:0000293” }, “agent”: { “@type”: “@id”, “@id”: “SEPIO:0000017” }, “ConditionPenetrance”: { “@id”: “SEPIO:0000252” }, “prefix”: “cg-attributes:prefix”, “GeneticCondition”: { “@id”: “SEPIO:0000219” }, “CG-PCER-VARINT”: “CG-PCER:interpretation/”, “stop”: { “@type”: “@id”, “@id”: “GENO:000895” }, “InfFromBkgrndSciKnow”: { “@id”: “ECO:0000001” }, “AllelicState”: { “@id”: “SEPIO:0000338” }, “AlleleFunctionalImpact”: { “@id”: “SEPIO:0000241” }, “phenotype”: { “@type”: “@id”, “@id”: “BFO:0000051” }, “CuratorInference”: { “@id”: “ECO:000205” }, “zygosity”: { “@type”: “@id”, “@id”: “cg-attributes:zygosity” }, “CG-PCER-AGENT”: “CG-PCER:agent/”, “alleleInheritance”: { “@type”: “@id”, “@id”: “SEPIO:0000197” }, “confidenceLevel”: { “@type”: “@id”, “@id”: “SEPIO:0000308” }, “Haplotype”: { “@id”: “cg-types:Haplotype” }, “specificity”: { “@type”: “@id”, “@id”: “SEPIO:0000197” }, “maximum”: { “@type”: “@id”, “@id”: “SEPIO:0000311” }, “RegionAnnotation”: { “@id”: “SEPIO:0000343” }, “totalOfAlleleNegConditionNegIndividuals”: { “@type”: “@id”, “@id”: “SEPIO:0000289” }, “Mechanism”: { “@id”: “SEPIO-CG:55107” }, “IndividualCondition”: { “@id”: “SEPIO:0000238” }, “ValueSet”: { “@id”: “SEPIO-CG:02000” }, “ESP-population-type”: “https://evs.gs.washington.edu/EVS/”, “haplotype”: { “@type”: “@id”, “@id”: “cg-attributes:haplotype” }, “OMIM”: “https://api.monarchinitiative.org/api/bioentity/phenotype/OMIM:”, “CalculatorEvidenceRepository”: { “@id”: “CG-PCER:calculatorEvRepo” }, “geneSymbol”: “ERO:0000574”, “ValueSetConceptListExtensibility”: { “@id”: “SEPIO:0000363” }, “assertionMethod”: { “@type”: “@id”, “@id”: “SEPIO:0000041” }, “REFSEQ”: “https://www.ncbi.nlm.nih.gov/nuccore/”, “controlGroupFrequency”: { “@type”: “@id”, “@id”: “SEPIO:0000305” }, “caseGroupFrequency”: { “@type”: “@id”, “@id”: “SEPIO:0000304” }, “NCIT”: “https://purl.bioontology.org/ontology/NCIT”, “SEPIO-CG”: “https://obofoundry.org/sepio/clingen/”, “NullAlleleOutcome”: { “@id”: “SEPIO-CG:55126” }, “relatedCanonicalAllele”: { “@type”: “@id”, “@id”: “SEPIO:0000285” }, “PROVO”: “https://data.bioontology.org/ontologies/PROVO/classes/”, “heterozygousAlleleIndividualCount”: { “@type”: “@id”, “@id”: “SEPIO:0000300” }, “pedigree”: “SEPIO:0000318”, “RO”: “https://obofoundry.org/ro/”, “resultDescription”: “DC:description”, “AlleleFrequency”: { “@id”: “SEPIO:0000227” }, “genotype”: { “@type”: “@id”, “@id”: “cg-attributes:genotype” }, “parentalConfirmation”: { “@type”: “@id”, “@id”: “SEPIO:0000167” }, “legacyNames”: “IAO:0000118”, “oddsRatio”: { “@type”: “@id”, “@id”: “SEPIO:0000309” }, “outcome”: { “@type”: “@id”, “@id”: “SEPIO:0000197” }, “Family”: { “@id”: “PCO:0000032” }, “ConditionPrevelance”: { “@id”: “SEPIO:0000251” }, “totalOfUntestedConditionPosIndividuals”: { “@type”: “@id”, “@id”: “SEPIO:0000295” }, “family”: { “@type”: “@id”, “@id”: “SEPIO:0000282” }, “CG-PCER-EVLN”: “CG-PCER:evidenceLine/”, “AssertionMethod”: { “@id”: “SEPIO:0000193” }, “cg-attributes”: “https://datamodel.clinicalgenome.org/attributes/”, “ParentalConfirmation”: { “@id”: “SEPIO-CG:55123” }, “conservationType”: { “@type”: “@id”, “@id”: “SEPIO:0000197” }, “comments”: “DC:description”, “totalNumberOfSegregations”: { “@type”: “@id”, “@id”: “SEPIO:0000288” }, “confidenceIntervalLower”: { “@type”: “@id”, “@id”: “SEPIO:0000306” }, “SO”: “https://sequenceontology.org/”, “CriterionAssessment”: { “@id”: “SEPIO:0000191” }, “HGVS”: “https://www.hgvs.org/mutnomen/”, “sourceIdentifierSystems”: { “@type”: “@id”, “@id”: “DC:description” }, “qualifier”: “SEPIO:0000346”, “DBSNP”: “https://www.ncbi.nlm.nih.gov/projects/SNP/”, “TagCategory”: { “@id”: “CG-PCER-TAGCAT:01” }, “inconsistentSegregationsObserved”: { “@type”: “@id”, “@id”: “SEPIO:0000314” }, “predictionType”: { “@type”: “@id”, “@id”: “SEPIO:0000255” }, “referenceSequence”: { “@type”: “@id”, “@id”: “FALDO:reference” }, “contribution”: { “@type”: “@id”, “@id”: “SEPIO:0000159” }, “author”: “cg-attributes:author”, “producedBy”: { “@type”: “@id”, “@id”: “RO:0003001” }, “contributionDate”: { “@type”: “@id”, “@id”: “SEPIO:0000163” } } } } } }, “summary”: “GetFullContext”, “description”: “Retrieve the full context.json file”, “tags”: [ “CONTEXT” ] } }, “/context/light”: { “get”: { “responses”: { “200”: { “description”: “”, “schema”: { “type”: “object”, “properties”: {} }, “examples”: { “application/json”: { “@context”: { “outcome”: { “@id”: “SEPIO:0000197”, “@type”: “@id” }, “CAR”: “https://reg.genome.network/allele/”, “SEPIO”: “https://obofoundry.org/sepio/”, “evidenceLinks”: { “@container”: “@set”, “@id”: “ECO:0000033” }, “guidelines”: { “@container”: “@set”, “@id”: “SEPIO:0000041” }, “gene”: { “@id”: “SEPIO:0000278”, “@type”: “@id” }, “label”: “cg-attributes:label”, “variantInterpretations”: { “@container”: “@set”, “@id”: “SEPIO:0000190” }, “evidenceCodes”: { “@container”: “@set”, “@id”: “SEPIO:0000192” }, “GENO”: “http://obofoundry.org/geno/”, “LN”: “http://loinc.org/”, “caid”: { “@id”: “CanonicalAllele”, “@type”: “@id” }, “cg-attributes”: “http://datamodel.clinicalgenome.org/attributes/”, “condition”: { “@id”: “SEPIO:0000276” }, “CanonicalAllele”: { “@id”: “GENO:0000890” }, “agents”: { “@container”: “@set”, “@id”: “SEPIO:0000017” }, “OMIM”: “https://www.omim.org/” } } } } }, “summary”: “GetLightContext”, “description”: “Get the compact version of the context file. This is used by some of the specific api paths.”, “tags”: [ “CONTEXT” ] } }, “/context/guideline”: { “get”: { “responses”: { “200”: { “description”: “”, “schema”: { “type”: “object”, “properties”: {} }, “examples”: { “application/json”: { “@context”: { “Guideline”: { “@id”: “https://health-lifesci.schema.org/guideline” }, “schema”: “https://schema.org/”, “label”: { “@id”: “https://www.w3.org/2000/01/rdf-schema#label” }, “id”: “@id”, “type”: “@type”, “assertionMethod”: { “@id”: “http://purl.obolibrary.org/obo/ECO_0000218” }, “AssertionMethod”: { “@id”: “http://purl.obolibrary.org/obo/ECO_0000217” }, “evidenceCodes”: { “@id”: “http://purl.obolibrary.org/obo/ECO_0000000”, “@container”: “@set” }, “evidenceStrength”: { “@id”: “https://health-lifesci.schema.org/MedicalEvidenceLevel” }, “rules”: { “@container”: “@set” }, “metaRules”: { “@container”: “@set” }, “isSatisfiedBy”: { “@container”: “@set”, “@id”: “http://purl.obolibrary.org/obo/ECO_0000501” }, “inference”: { “@id”: “http://purl.obolibrary.org/obo/ECO_0000203” }, “metaInference”: { “@id”: “http://purl.obolibrary.org/obo/ECO_0000361” }, “uniqueAssertions”: { “@container”: “@set”, “@id”: “http://purl.obolibrary.org/obo/ECO_0000203” }, “conditionSet”: { “@container”: “@set”, “@id”: “http://purl.obolibrary.org/obo/ECO_0000000” } } } } } }, “summary”: "GetGuidelineContext ", “tags”: [ “CONTEXT” ] } }, “/guideline/{gid}/classify”: { “get”: { “responses”: { “200”: { “description”: “”, “schema”: { “type”: “object”, “properties”: {} }, “examples”: { “application/json”: { “@context”: { “assertion”: “http://purl.obolibrary.org/obo/ECO_0000203” }, “assertion”: { “@id”: “_:a1”, “label”: “Pathogenic” } } } } }, “summary”: “ClassifyVariant”, “tags”: [ “GUIDELINES” ], “parameters”: [ { “$ref”: “#/parameters/gid” }, { “$ref”: “#/parameters/data-classify” } ], “description”: “Generate a live classification/interpretation under a specific guideline. The idea is to simply take in a list of evidence-codes that fall under a guideline and generate a classification/interpretation by running the reasoning engine. You can get the list of available evidence-codes for a guideline from the path GetGuideline (See the label field under evidenceCodes). \n\nFor evidence-codes with strength adjustment, you can either provide an underscore or a hyphen. For example both PM1-Strong and PM1_Strong are acceptable.\n\nNo data will be stored” }, “parameters”: [ { “name”: “gid”, “in”: “path”, “type”: “string”, “required”: true } ] } }, “host”: “erepo.genome.network”, “basePath”: “/evrepo/api”, “schemes”: [ “http”, “https” ], “consumes”: [ “application/json” ], “produces”: [ “application/json” ], “securityDefinitions”: { “Redmine API Key”: { “type”: “apiKey”, “in”: “query”, “name”: “key”, “description”: “Select API requests require a Redmine API key, typically because they are write-operations.\n* Even with the API key, there can be restrictive permissions that constrain the request to sensible authorized individuals or Sites.” } }, “parameters”: { “caid”: { “name”: “caid”, “in”: “path”, “type”: “string”, “required”: true, “description”: “Canonical Allele identifier” }, “disease”: { “in”: “path”, “type”: “string”, “required”: true, “name”: “disease”, “description”: “Disease namespace.”, “default”: “OMIM”, “enum”: [ “OMIM”, “MONDO”, “DO” ] }, “did”: { “name”: “did”, “in”: “path”, “type”: “string”, “required”: true, “description”: “The id of the disease. Usually numeric.” }, “gid”: { “in”: “path”, “type”: “string”, “required”: true, “name”: “gid”, “default”: “001”, “description”: “The guideline id.” }, “gene-query”: { “in”: “query”, “type”: “string”, “name”: “gene”, “description”: “HUGO gene name you want to search by.” }, “condition-query”: { “in”: “query”, “type”: “string”, “name”: “condition”, “description”: “name of the condition you want to search by.” }, “hgvs-query”: { “in”: “query”, “type”: “string”, “name”: “hgvs”, “description”: “hgvs expression you want to search by.” }, “assertion-query”: { “in”: “query”, “type”: “string”, “name”: “assertion”, “description”: “assertion you want to search by. Eg. Pathogenic” }, “caid-query”: { “in”: “query”, “type”: “string”, “name”: “caid”, “description”: "Canonical Allele identifier you want to search by. " }, “match-logic-query”: { “name”: “matchLogic”, “in”: “query”, “type”: “string”, “default”: “and”, “enum”: [ “and”, “or” ] }, “match-mode-query”: { “name”: “matchMode”, “in”: “query”, “type”: “string”, “default”: “keyword”, “enum”: [ “keyword”, “prefix” ] }, “match-limit-query”: { “name”: “matchLimit”, “in”: “query”, “type”: “string”, “description”: "Controls the size of the search response. " }, “match-skip-query”: { “name”: “matchSkip”, “in”: “query”, “type”: “string”, “description”: “Skip these many from the beginning when returning a search response. Used in paginating response” }, “upload-type”: { “in”: “query”, “type”: “string”, “name”: “type”, “default”: “vci”, “description”: "Data format for the interpretation document. ", “enum”: [ “vci”, “sepio” ] }, “gid-or-uuid”: { “in”: “path”, “type”: “string”, “required”: true, “description”: “Path param allowing either gid or VCI ID/UUID. When doing a PUT use gid, When doing a GET, use VCI ID”, “name”: “gid-or-uuid” }, “data-sepio-param”: { “in”: “formData”, “type”: “string”, “description”: “The full JSON SEPIO interpretation document generated by the ClinGen Data-Ex.”, “name”: “data” }, “data-classify”: { “in”: “formData”, “type”: “string”, “name”: “data”, “default”: “{ “evidenceCodes”: [“PS1”, “PS2”, “PVS1”] }”, “description”: "The payload should contain a list of evidence codes that passed the MET criteria. " } }, “responses”: {}, “definitions”: { “success-resp”: { “type”: “object”, “properties”: { “success”: { “type”: “string” }, “status”: { “type”: “integer” } }, “title”: “SuccessResp” }, “guidelines-model”: { “type”: “array”, “title”: “Guidelines”, “items”: { “$ref”: “#/definitions/guideline-model” } }, “guideline-model”: { “type”: “object”, “title”: “Guideline”, “properties”: { “@id”: { “type”: “string”, “format”: “uri” }, “label”: { “type”: “string” } }, “required”: [ “@id”, “label” ] }, “variant-interpretation-model-in-search-resp”: { “type”: “object”, “title”: “VariantInterpretationInSearchResp”, “properties”: { “hgvs”: { “type”: “array”, “items”: { “type”: “string” } }, “caid”: { “type”: “string” }, “guidelines”: { “type”: “array”, “items”: { “$ref”: “#/definitions/guideline-in-search-resp-model” } }, “gene”: { “type”: “object”, “properties”: { “NCBI_ID”: { “type”: “string” }, “label”: { “type”: “string” } }, “required”: [ “NCBI_ID”, “label” ] }, “@id”: { “type”: “string”, “format”: “uri” }, “evidenceLinks”: { “type”: “array”, “items”: { “$ref”: “#/definitions/evidence-link-insearch-resp” } }, “condition”: { “type”: “object”, “properties”: { “@id”: { “type”: “string” }, “label”: { “type”: “string” } }, “required”: [ “@id”, “label” ] }, “variationId”: { “type”: “string” } }, “required”: [ “hgvs”, “caid” ] }, “guideline-in-search-resp-model”: { “type”: “object”, “title”: “GuidelinesInSearchResp”, “properties”: { “agents”: { “type”: “array”, “items”: { “type”: “object”, “properties”: { “evidenceCodes”: { “type”: “array”, “items”: {} }, “outcome”: { “type”: “object”, “properties”: { “@id”: { “type”: “string” }, “label”: { “type”: “string” } } }, “@id”: { “type”: “string” }, “affiliation”: { “type”: “string” }, “label”: { “type”: “string” } } } }, “outcome”: { “type”: “object”, “properties”: { “@id”: { “type”: “string” }, “label”: { “type”: “string” } } }, “@id”: { “type”: “string” }, “label”: { “type”: “string” } } }, “evidence-link-insearch-resp”: { “type”: “object”, “title”: “EvidenceLinkInSearchResp”, “properties”: { “@id”: { “type”: “string”, “format”: “uri” } } }, “evidenceStrengthInGuideline”: { “type”: “object”, “title”: “EvidenceStrengthInGuideline”, “properties”: { “label”: { “type”: “string” }, “@id”: { “type”: “string” } } } }, “tags”: [ { “name”: “INTERPRETATIONS” }, { “name”: “GUIDELINES” }, { “name”: “CONTEXT” } ] }