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korikuzma/gist:4385ef29ef76b956c73bdf84f922f5ad

Last active June 26, 2024 17:47
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Example of oncogenicitySubmission where citation gives error when including both db/id and url records (excluded other fields for brevity). In this example, it can be processed by ClinVar but errors out.
Raw
gistfile1.json
{
"assertionCriteria": {
"db": "PubMed",
"id": "36063163"
},
"oncogenicitySubmission": [
{
"citation": [
{
"db": "PubMed",
"id": "16338952"
},
{
"db": "PubMed",
"id": "16338952"
},
{
"db": "PubMed",
"id": "19381019"
},
{
"db": "PubMed",
"id": "23786770"
},
{
"db": "PubMed",
"id": "31316618"
},
{
"db": "PubMed",
"id": "17384684"
},
{
"db": "PubMed",
"id": "25606676"
},
{
"db": "PubMed",
"id": "19749790"
},
{
"url": "https://civicdb.org/links/evidence/7306"
},
{
"url": "https://civicdb.org/links/evidence/4871"
},
{
"url": "https://civicdb.org/links/evidence/8853"
},
{
"url": "https://civicdb.org/links/evidence/10386"
},
{
"url": "https://civicdb.org/links/evidence/7941"
},
{
"url": "https://civicdb.org/links/evidence/8642"
},
{
"url": "https://civicdb.org/links/evidence/8811"
},
{
"url": "https://civicdb.org/links/evidence/8854"
},
{
"url": "https://civicdb.org/links/evidence/8855"
}
]
}
]
}
@korikuzma
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Author

This gave me the following error:

{
    "errors": [
        {
            "input": [
                {
                    "field": "ClinicalSignificance.citation",
                    "value": "PubMed:16338952;PubMed:16338952;PubMed:19381019;PubMed:23786770;PubMed:31316618;PubMed:17384684;PubMed:25606676;PubMed:19749790;https://civicdb.org/links/evidence/7306;https://civicdb.org/links/evidence/4871;https://civicdb.org/links/evidence/8853;https://civicdb.org/links/evidence/10386;https://civicdb.org/links/evidence/7941;https://civicdb.org/links/evidence/8642;https://civicdb.org/links/evidence/8811;https://civicdb.org/links/evidence/8854;https://civicdb.org/links/evidence/8855"
                }
            ],
            "output": {
                "errors": [
                    {
                        "userMessage": "PubMed:16338952;PubMed:16338952;PubMed:19381019;PubMed:23786770;PubMed:31316618;PubMed:17384684;PubMed:25606676;PubMed:19749790;https://civicdb.org/links/evidence/7306;https://civicdb.org/links/evidence/4871;https://civicdb.org/links/evidence/8853;https://civicdb.org/links/evidence/10386;https://civicdb.org/links/evidence/7941;https://civicdb.org/links/evidence/8642;https://civicdb.org/links/evidence/8811;https://civicdb.org/links/evidence/8854;https://civicdb.org/links/evidence/8855 is an invalid citation. Please check both the name of the database and the identifier from that database"
                    }
                ]
            }
        },
        {
            "input": [
                {
                    "field": "ClinicalSignificance.citation",
                    "value": "PubMed:16338952;PubMed:16338952;PubMed:19381019;PubMed:23786770;PubMed:31316618;PubMed:17384684;PubMed:25606676;PubMed:19749790;https://civicdb.org/links/evidence/7306;https://civicdb.org/links/evidence/4871;https://civicdb.org/links/evidence/8853;https://civicdb.org/links/evidence/10386;https://civicdb.org/links/evidence/7941;https://civicdb.org/links/evidence/8642;https://civicdb.org/links/evidence/8811;https://civicdb.org/links/evidence/8854;https://civicdb.org/links/evidence/8855"
                }
            ],
            "output": {
                "errors": [
                    {
                        "userMessage": "PubMed:16338952;PubMed:16338952;PubMed:19381019;PubMed:23786770;PubMed:31316618;PubMed:17384684;PubMed:25606676;PubMed:19749790;https://civicdb.org/links/evidence/7306;https://civicdb.org/links/evidence/4871;https://civicdb.org/links/evidence/8853;https://civicdb.org/links/evidence/10386;https://civicdb.org/links/evidence/7941;https://civicdb.org/links/evidence/8642;https://civicdb.org/links/evidence/8811;https://civicdb.org/links/evidence/8854;https://civicdb.org/links/evidence/8855 is an invalid citation. Please check both the name of the database and the identifier from that database"
                    }
                ]
            }
        },
        {
            "input": [
                {
                    "field": "ClinicalSignificance.citation",
                    "value": "PubMed:16338952;PubMed:16338952;PubMed:19381019;PubMed:23786770;PubMed:31316618;PubMed:17384684;PubMed:25606676;PubMed:19749790;https://civicdb.org/links/evidence/7306;https://civicdb.org/links/evidence/4871;https://civicdb.org/links/evidence/8853;https://civicdb.org/links/evidence/10386;https://civicdb.org/links/evidence/7941;https://civicdb.org/links/evidence/8642;https://civicdb.org/links/evidence/8811;https://civicdb.org/links/evidence/8854;https://civicdb.org/links/evidence/8855"
                }
            ],
            "output": {
                "errors": [
                    {
                        "userMessage": "PubMed:16338952;PubMed:16338952;PubMed:19381019;PubMed:23786770;PubMed:31316618;PubMed:17384684;PubMed:25606676;PubMed:19749790;https://civicdb.org/links/evidence/7306;https://civicdb.org/links/evidence/4871;https://civicdb.org/links/evidence/8853;https://civicdb.org/links/evidence/10386;https://civicdb.org/links/evidence/7941;https://civicdb.org/links/evidence/8642;https://civicdb.org/links/evidence/8811;https://civicdb.org/links/evidence/8854;https://civicdb.org/links/evidence/8855 is an invalid citation. Please check both the name of the database and the identifier from that database"
                    }
                ]
            }
        },
        {
            "input": [
                {
                    "field": "ClinicalSignificance.citation",
                    "value": "PubMed:16338952;PubMed:16338952;PubMed:19381019;PubMed:23786770;PubMed:31316618;PubMed:17384684;PubMed:25606676;PubMed:19749790;https://civicdb.org/links/evidence/7306;https://civicdb.org/links/evidence/4871;https://civicdb.org/links/evidence/8853;https://civicdb.org/links/evidence/10386;https://civicdb.org/links/evidence/7941;https://civicdb.org/links/evidence/8642;https://civicdb.org/links/evidence/8811;https://civicdb.org/links/evidence/8854;https://civicdb.org/links/evidence/8855"
                }
            ],
            "output": {
                "errors": [
                    {
                        "userMessage": "PubMed:16338952;PubMed:16338952;PubMed:19381019;PubMed:23786770;PubMed:31316618;PubMed:17384684;PubMed:25606676;PubMed:19749790;https://civicdb.org/links/evidence/7306;https://civicdb.org/links/evidence/4871;https://civicdb.org/links/evidence/8853;https://civicdb.org/links/evidence/10386;https://civicdb.org/links/evidence/7941;https://civicdb.org/links/evidence/8642;https://civicdb.org/links/evidence/8811;https://civicdb.org/links/evidence/8854;https://civicdb.org/links/evidence/8855 is an invalid citation. Please check both the name of the database and the identifier from that database"
                    }
                ]
            }
        },
        {
            "input": [
                {
                    "field": "ClinicalSignificance.citation",
                    "value": "PubMed:16338952;PubMed:16338952;PubMed:19381019;PubMed:23786770;PubMed:31316618;PubMed:17384684;PubMed:25606676;PubMed:19749790;https://civicdb.org/links/evidence/7306;https://civicdb.org/links/evidence/4871;https://civicdb.org/links/evidence/8853;https://civicdb.org/links/evidence/10386;https://civicdb.org/links/evidence/7941;https://civicdb.org/links/evidence/8642;https://civicdb.org/links/evidence/8811;https://civicdb.org/links/evidence/8854;https://civicdb.org/links/evidence/8855"
                }
            ],
            "output": {
                "errors": [
                    {
                        "userMessage": "PubMed:16338952;PubMed:16338952;PubMed:19381019;PubMed:23786770;PubMed:31316618;PubMed:17384684;PubMed:25606676;PubMed:19749790;https://civicdb.org/links/evidence/7306;https://civicdb.org/links/evidence/4871;https://civicdb.org/links/evidence/8853;https://civicdb.org/links/evidence/10386;https://civicdb.org/links/evidence/7941;https://civicdb.org/links/evidence/8642;https://civicdb.org/links/evidence/8811;https://civicdb.org/links/evidence/8854;https://civicdb.org/links/evidence/8855 is an invalid citation. Please check both the name of the database and the identifier from that database"
                    }
                ]
            }
        },
        {
            "input": [
                {
                    "field": "ClinicalSignificance.citation",
                    "value": "PubMed:16338952;PubMed:16338952;PubMed:19381019;PubMed:23786770;PubMed:31316618;PubMed:17384684;PubMed:25606676;PubMed:19749790;https://civicdb.org/links/evidence/7306;https://civicdb.org/links/evidence/4871;https://civicdb.org/links/evidence/8853;https://civicdb.org/links/evidence/10386;https://civicdb.org/links/evidence/7941;https://civicdb.org/links/evidence/8642;https://civicdb.org/links/evidence/8811;https://civicdb.org/links/evidence/8854;https://civicdb.org/links/evidence/8855"
                }
            ],
            "output": {
                "errors": [
                    {
                        "userMessage": "PubMed:16338952;PubMed:16338952;PubMed:19381019;PubMed:23786770;PubMed:31316618;PubMed:17384684;PubMed:25606676;PubMed:19749790;https://civicdb.org/links/evidence/7306;https://civicdb.org/links/evidence/4871;https://civicdb.org/links/evidence/8853;https://civicdb.org/links/evidence/10386;https://civicdb.org/links/evidence/7941;https://civicdb.org/links/evidence/8642;https://civicdb.org/links/evidence/8811;https://civicdb.org/links/evidence/8854;https://civicdb.org/links/evidence/8855 is an invalid citation. Please check both the name of the database and the identifier from that database"
                    }
                ]
            }
        },
        {
            "input": [
                {
                    "field": "ClinicalSignificance.citation",
                    "value": "PubMed:16338952;PubMed:16338952;PubMed:19381019;PubMed:23786770;PubMed:31316618;PubMed:17384684;PubMed:25606676;PubMed:19749790;https://civicdb.org/links/evidence/7306;https://civicdb.org/links/evidence/4871;https://civicdb.org/links/evidence/8853;https://civicdb.org/links/evidence/10386;https://civicdb.org/links/evidence/7941;https://civicdb.org/links/evidence/8642;https://civicdb.org/links/evidence/8811;https://civicdb.org/links/evidence/8854;https://civicdb.org/links/evidence/8855"
                }
            ],
            "output": {
                "errors": [
                    {
                        "userMessage": "PubMed:16338952;PubMed:16338952;PubMed:19381019;PubMed:23786770;PubMed:31316618;PubMed:17384684;PubMed:25606676;PubMed:19749790;https://civicdb.org/links/evidence/7306;https://civicdb.org/links/evidence/4871;https://civicdb.org/links/evidence/8853;https://civicdb.org/links/evidence/10386;https://civicdb.org/links/evidence/7941;https://civicdb.org/links/evidence/8642;https://civicdb.org/links/evidence/8811;https://civicdb.org/links/evidence/8854;https://civicdb.org/links/evidence/8855 is an invalid citation. Please check both the name of the database and the identifier from that database"
                    }
                ]
            }
        },
        {
            "input": [
                {
                    "field": "ClinicalSignificance.citation",
                    "value": "PubMed:16338952;PubMed:16338952;PubMed:19381019;PubMed:23786770;PubMed:31316618;PubMed:17384684;PubMed:25606676;PubMed:19749790;https://civicdb.org/links/evidence/7306;https://civicdb.org/links/evidence/4871;https://civicdb.org/links/evidence/8853;https://civicdb.org/links/evidence/10386;https://civicdb.org/links/evidence/7941;https://civicdb.org/links/evidence/8642;https://civicdb.org/links/evidence/8811;https://civicdb.org/links/evidence/8854;https://civicdb.org/links/evidence/8855"
                }
            ],
            "output": {
                "errors": [
                    {
                        "userMessage": "PubMed:16338952;PubMed:16338952;PubMed:19381019;PubMed:23786770;PubMed:31316618;PubMed:17384684;PubMed:25606676;PubMed:19749790;https://civicdb.org/links/evidence/7306;https://civicdb.org/links/evidence/4871;https://civicdb.org/links/evidence/8853;https://civicdb.org/links/evidence/10386;https://civicdb.org/links/evidence/7941;https://civicdb.org/links/evidence/8642;https://civicdb.org/links/evidence/8811;https://civicdb.org/links/evidence/8854;https://civicdb.org/links/evidence/8855 is an invalid citation. Please check both the name of the database and the identifier from that database"
                    }
                ]
            }
        },
        {
            "input": [
                {
                    "field": "ClinicalSignificance.citation",
                    "value": "PubMed:16338952;PubMed:16338952;PubMed:19381019;PubMed:23786770;PubMed:31316618;PubMed:17384684;PubMed:25606676;PubMed:19749790;https://civicdb.org/links/evidence/7306;https://civicdb.org/links/evidence/4871;https://civicdb.org/links/evidence/8853;https://civicdb.org/links/evidence/10386;https://civicdb.org/links/evidence/7941;https://civicdb.org/links/evidence/8642;https://civicdb.org/links/evidence/8811;https://civicdb.org/links/evidence/8854;https://civicdb.org/links/evidence/8855"
                }
            ],
            "output": {
                "errors": [
                    {
                        "userMessage": "PubMed:16338952;PubMed:16338952;PubMed:19381019;PubMed:23786770;PubMed:31316618;PubMed:17384684;PubMed:25606676;PubMed:19749790;https://civicdb.org/links/evidence/7306;https://civicdb.org/links/evidence/4871;https://civicdb.org/links/evidence/8853;https://civicdb.org/links/evidence/10386;https://civicdb.org/links/evidence/7941;https://civicdb.org/links/evidence/8642;https://civicdb.org/links/evidence/8811;https://civicdb.org/links/evidence/8854;https://civicdb.org/links/evidence/8855 is an invalid citation. Please check both the name of the database and the identifier from that database"
                    }
                ]
            }
        }
    ]
}

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