Create JSON file for example IDs

[ReneRanzinger]

Create a JSON file that contains for each type of data:

• Motif
• Glycan
• Protein
• Site
• Biomarker
• Publication

A list of test cases for the presence/absence of each type of information. This also includes special cases. For example:

• Glycosylation sites with notes
• Glycans with ranges on proteins
• ...

[rykahsay]

generated/misc/id_examples.json

{
    "basic":[
        {"recordtype":"protein", "idlist":["P14210"]},
        {"recordtype":"glycan", "idlist":["G17689DH"]},
        {"recordtype":"motif", "idlist":["GGM.000001"]},
        {"recordtype":"biomarker", "idlist":["AA4686-1"]},
        {"recordtype":"publication", "idlist":["10731668"]}
    ],
    "high_volume":[
        {"recordtype":"protein", "section":"glycosylation", "idlist":["P14210"]}
    ],
    "glycosylation_sites_with_notes":[
        {"recordtype":"site", "idlist":[""]},
        {"recordtype":"protein", "idlist":[""]}
    ],
    "glycans_with_ranges_on_protein":[
                {"recordtype":"glycan", "idlist":[""]}
        ]
}

[ubhuiyan]

Current Version: (https://data.glygen.org/ln2data/releases/data/current/misc/id_examples.json) By Release: (https://data.glygen.org/ln2data/releases/data/v-2.6.1/misc/id_examples.json)

[katewarner]

@ReneRanzinger @sujeetvkulkarni We've created a draft for the json file, and added some additional fields as well that you may like for checking. Please let us know what you think and if you would like any fields removed and/or added.

File location: /data/projects/glygen/generated/misc/id_examples.json

{
    "basic":[
        {"recordtype":"protein", "idlist":["P14210"]},
        {"recordtype":"glycan", "idlist":["G17689DH"]},
        {"recordtype":"motif", "idlist":["GGM.000001"]},
        {"recordtype":"biomarker", "idlist":["AA4686-1"]},
        {"recordtype":"publication", "idlist":["10731668"]}
    ],
    "high_volume":[
        {"recordtype":"protein", "section":"glycosylation", "idlist":["P14210"]}
    ],
    "glycosylation_sites_with_notes":[
        {"recordtype":"site", "idlist":["Q08554-1.165.165"]},
        {"recordtype":"protein", "idlist":["Q14247-1"]}
    ],
    "glycans_with_ranges_on_protein":[
        {"recordtype":"glycan", "idlist":["G57321FI"]}
    ], 
    "proteins_with_multiple_pdb_structures":[
        {"recordtype":"protein", "idlist":["Q01484-4"]}
    ],
    "isoforms.sequence.sequence":[
        {"recordtype":"protein", "idlist":["A0A8V1A9P1-1"]} 
    ], 
    "expression_tissue.tissue.name":[
        {"recordtype":"protein", "idlist":["Q92731-1"]}
    ],
    "site_annotation.annotation":[
        {"recordtype":"protein", "idlist":["Q553E3-1"]}
    ],  
    "snv.disease.synonyms.id":[
        {"recordtype":"protein", "idlist":["Q92731-1"]}
    ],
    "tool_support.gnome_glygen_oglycans":[
        {"recordtype":"glycan", "idlist":["G97100OV"]}
    ],
    "tool_support.sandbox":[
    {"recordtype":"glycan", "idlist":["G97100OV"]}
    ], 
    "tool_support.gnome":[
    {"recordtype":"glycan", "idlist":["G97100OV"]}
    ], 
    "species.name":[
        {"recordtype":"glycan", "idlist":["G97100OV"]},
        {"recordtype":"protein", "idlist":["A0A8V1A9P1-1"]},
        {"recordtype":"publication", "idlist":["pubmed.35142393"]}
    ],
    "enzyme_evidence_id":[
        {"recordtype":"glycan", "idlist":["G97100OV"]}
    ],
    "enzyme.evidence.database":[
        {"recordtype":"glycan", "idlist":["G97100OV"]}
    ],
    "publication.evidence.database":[
        {"recordtype":"motif", "idlist":["GGM.000096"]},
        {"recordtype":"protein", "idlist":["Q553E3-1"]}
    ],
    "residues.name":[
        {"recordtype":"motif", "idlist":["GGM.000096"]},
        {"recordtype":"glycan", "idlist":["G97100OV"]}
    ],
    "biomarkers.biomarker_id'":[
        {"recordtype":"motif", "idlist":["GGM.000024"]},
        {"recordtype":"protein", "idlist":["P46937-1"]},
        {"recordtype":"glycan", "idlist":["G10256JP"]}
    ],
    "species.evidence.id":[
        {"recordtype":"publication", "idlist":["pubmed.35142393"]},
        {"recordtype":"protein", "idlist":["A0A8V1A9P1-1"]},
        {"recordtype":"glycan", "idlist":["G97100OV"]}
    ],
    "glycosylation.type":[
        {"recordtype":"publication", "idlist":["pubmed.37350405"]},
        {"recordtype":"protein", "idlist":["F1RQW9-1"]}
    ]
}

[sujeetvkulkarni]

Added labels examples, informative. Which can be used to retrieve these tickets in future.