ENTRY.md

BMRB Entry JSON format

To convert from NMR-STAR to JSON format the minimal amount of data needed to reconstruct a BMRB entry is converted to dictionaries and lists in JSON format in a hierarchical approach that attempts to mimic that which exists in the NMR-STAR format. If you are using the PyNMR-STAR python library that we have released there are fromJSON() and toJSON() methods available for entries, saveframes, and loops that allow you to convert into and read from JSON format.

This page will allow you to view a full entry interactively.

If you need a reminder on the format of NMR-STAR - which the JSON is created from - please see the NMR-STAR viewer page for the same entry. As an aside, the STAR-viewer page linked here is using the API to load the data which it displays in NMR-STAR format.

Entry

Here is the structure of one entry in JSON format:

{
    "bmrb_id": "bmrb_id",
    "saveframes": ["..."]
}

The ... above contains all of the entry's saveframes in JSON format:

Saveframe

{
    "category": "saveframe_category",
    "tag_prefix": "_Entry",
    "name": "saveframe_name",
    "tags": [["tag1", "value1"], ["tag2", "value2"], ["etc.", "etc."]],
    "loops": ["..."]
}

Again - the ... above contains the saveframes' loops in JSON format:

Loop

{
    "category": "_Entry_author",
    "tags": ["tag1", "tag2", "etc."],
    "data": [
        ["row", 1, "data"],
        ["row", 2, "data"],
        ["etc", 3, "data"]
    ]
}

Note that "tags" key corresponds to the column names in the loop.

Example entry

Here is an example of entry 15000 in JSON format, but with all but the first saveframe removed.

{
    "bmrb_id": "15000",
    "saveframes": [
    {
        "category": "entry_information",
        "tag_prefix": "_Entry",
        "name": "entry_information",
        "tags": [
            ["Sf_category", "entry_information"],
            ["Sf_framecode", "entry_information"],
            ["ID", "15000" ],
            ["Title", "Solution structure of chicken villin headpiece subdomain containing a fluorinated side chain in the core\n"],
            ["Type", "macromolecule"],
            ["Version_type", "original"],
            ["Submission_date", "2006-09-07"],
            ["Accession_date", "2006-09-07"],
            ["Last_release_date", "."],
            ["Original_release_date", "."],
            ["Origination", "author"],
            ["NMR_STAR_version", "3.1.1.61"],
            ["Original_NMR_STAR_version", "."],
            ["Experimental_method", "NMR"],
            ["Experimental_method_subtype", "solution"],
            ["Details", "."],
            ["BMRB_internal_directory_name", "."]
        ],
        "loops": [
            {
                "category": "_Entry_author",
                "data": [
                  ["1", "Claudia", "Cornilescu", ".", "C.", ".", "15000"],
                  ["2", "Gabriel", "Cornilescu", ".", ".", ".", "15000"],
                  ["3", "Erik", "Hadley", ".", "B.", ".", "15000"],
                  ["4", "Samuel", "Gellman", ".", "H.", ".", "15000"],
                  ["5", "John", "Markley", ".", "L.", ".", "15000"]
                ],
                "tags": ["Ordinal", "Given_name", "Family_name", "First_initial", "Middle_initials", "Family_title", "Entry_ID"]
              },
              {
                "category": "_SG_project",
                "data": [
                  ["1", "not applicable", "not applicable", ".", "15000"]
                ],
                "tags": ["SG_project_ID", "Project_name", "Full_name_of_center", "Initial_of_center", "Entry_ID"]
              },
              {
                "category": "_Struct_keywords",
                "data": [
                  ["chicken villin headpiece", ".", "15000"],
                  ["fluorinated Phe", ".", "15000"],
                  ["VHP", ".", "15000"]
                ],
                "tags": ["Keywords", "Text", "Entry_ID"]
              },
              {
                "category": "_Data_set",
                "data": [
                  ["assigned_chemical_shifts", "1", "15000"]
                ],
                "tags": ["Type", "Count", "Entry_ID"]
              },
              {
                "category": "_Datum",
                "data": [
                  ["13C chemical shifts", "77", "15000" ],
                  ["15N chemical shifts", "40", "15000"],
                  ["1H chemical shifts", "223", "15000"]
                ],
                "tags": ["Type", "Count", "Entry_ID"]
              },
              {
                "category": "_Release",
                "data": [
                  ["2", ".", ".", "2008-07-17", "2006-09-06", "update", "BMRB", "complete entry citation", "15000"],
                  ["1", ".", ".", "2006-10-20", "2006-09-06", "original", "author", "original release", "15000"]
                ],
                "tags": ["Release_number", "Format_type", "Format_version", "Date", "Submission_date", "Type", "Author", "Detail", "Entry_ID"]
              },
              {
                "category": "_Related_entries",
                "data": [
                    ["PDB", "2JM0", "BMRB Entry Tracking System", "15000"]
                ],
                "tags": ["Database_name", "Database_accession_code", "Relationship", "Entry_ID"]
              }
        ]
        },
        "More saveframes would go here..."
    ]
}