[{"data":1,"prerenderedAt":411},["ShallowReactive",2],{"navigation":3,"\u002Ftechnical-details\u002Fmetadata-model":44,"\u002Ftechnical-details\u002Fmetadata-model-surround":406},[4,8,30],{"title":5,"path":6,"stem":7},"TREAT-NMD Core Datasets","\u002F","0.index",{"title":9,"icon":10,"path":11,"stem":12,"children":13,"page":29},"Introduction","i-lucide-book-open","\u002Fintroduction","1.introduction",[14,19,24],{"title":15,"path":16,"stem":17,"icon":18},"About","\u002Fintroduction\u002Fabout","1.introduction\u002F1.about","i-lucide-house",{"title":20,"path":21,"stem":22,"icon":23},"Item","\u002Fintroduction\u002Fitems","1.introduction\u002F2.items","i-lucide-download",{"title":25,"path":26,"stem":27,"icon":28},"Records","\u002Fintroduction\u002Frecords","1.introduction\u002F3.records","i-lucide-sliders",false,{"title":31,"icon":32,"path":33,"stem":34,"children":35,"page":29},"Technical details","i-lucide-cog","\u002Ftechnical-details","2.technical-details",[36,40],{"title":37,"path":38,"stem":39},"Metadata model","\u002Ftechnical-details\u002Fmetadata-model","2.technical-details\u002F1.metadata-model",{"title":41,"path":42,"stem":43},"Data model","\u002Ftechnical-details\u002Fdata-model","2.technical-details\u002F2.data-model",{"id":45,"title":37,"body":46,"description":399,"extension":400,"links":401,"meta":402,"navigation":403,"path":38,"seo":404,"stem":39,"__hash__":405},"docs\u002F2.technical-details\u002F1.metadata-model.md",{"type":47,"value":48,"toc":377},"minimark",[49,53,79,84,91,100,104,107,114,117,123,126,136,160,165,175,182,191,197,210,219,229,263,266,292,296,300,327,337,344,348,363,367],[50,51,37],"h1",{"id":52},"metadata-model",[54,55,56,57,64,65,72,73,78],"p",{},"The TREAT-NMD Core Datasets are described on a ",[58,59,63],"a",{"href":60,"rel":61},"https:\u002F\u002Fdatasets.treat-nmd.org\u002F",[62],"nofollow","dedicated web app",". The content of this website is completely defined in the JSON file ",[58,66,68],{"href":67},"\u002Flibrary.json",[69,70,71],"code",{},"library.json",". This structure of this file, which should serve as source for any tools operating on data in the TREAT-NMD data model, is described in the following. Note that this document only contains the technical and imlementation details that are not described in the ",[58,74,77],{"href":75,"rel":76},"https:\u002F\u002Fdatasets.treat-nmd.org\u002Fintroduction",[62],"general introduction"," to the datasets, so please read that document first.",[80,81,83],"h2",{"id":82},"overview","Overview",[54,85,86,87,90],{},"The following UML diagram shows an overview of the conceptual model of the dataset specifaction. In the JSON file, relations between the objects are implemented using references to the ",[69,88,89],{},"id"," properties.",[54,92,93],{},[58,94,96],{"href":95},"\u002Fmetadata.png",[97,98],"img",{"alt":99,"src":95},"Metadata UML model",[80,101,103],{"id":102},"classes","Classes",[54,105,106],{},"In the following, the classes are described on more detail, although the JSON objects may contain further properties than mentioned here.",[108,109,111],"h3",{"id":110},"dataset",[69,112,113],{},"Dataset",[54,115,116],{},"This class describes a disease-specific dataset, e.g. SMA, DMD or LGMD. Since the core datasets should be harmonized as much as possible, all items are defined in a shared library and the datasets contain references to the shared items.",[108,118,120],{"id":119},"datasetgroup",[69,121,122],{},"DatasetGroup",[54,124,125],{},"Each component in a dataset belongs to one group. The groups determine how the components are presented; e.g. the specification website contains one page per group. The groups have no further semantic significance.",[108,127,129,132,133],{"id":128},"itemreference-and-record",[69,130,131],{},"ItemReference"," and ",[69,134,135],{},"Record",[54,137,138,139,141,142,145,146,148,149,152,153,155,156,159],{},"Items are included in a disease-specific dataset through an ",[69,140,131],{}," object. This can be either directly through an instance of ",[69,143,144],{},"IndividualItemReference",", or through a ",[69,147,135],{}," which in turn contains a ",[69,150,151],{},"RecordItemReference",". Individual item references and records are contained in an ordered list in a ",[69,154,122],{},", which is modeled through the ",[69,157,158],{},"Component"," interface.",[108,161,163],{"id":162},"item",[69,164,20],{},[54,166,167,168,171,172,174],{},"This class defines the semantics of an item. Every item has one of eight possible item types. In the UML diagram, single selection and multiple selection items are represented as ",[69,169,170],{},"OptionItem","; all other items are represented by the ",[69,173,20],{}," class for simplicity, as they do not contain further properties or relations.",[54,176,177,178,181],{},"Every item belongs to an instance of ",[69,179,180],{},"Category",". Similar to dataset groups, categories group related items for convenience and have no semantic relevance. Currently, the item library is not displayed on the specification website, therefore the categories are only visible in the editor.",[108,183,185,132,188],{"id":184},"option-and-optionreference",[69,186,187],{},"Option",[69,189,190],{},"OptionReference",[54,192,193,194,196],{},"Single selection and multiple selection items have a fixed list of possible values. The semantics of each possible value is defined in an instance of ",[69,195,187],{},". Options are shared among items to ensure that semantics and mappings do not have to be repeated.",[54,198,199,200,202,203,206,207,209],{},"The inclusion of an option in an item is defined through an ordered list of ",[69,201,190],{}," instances. By default, the ID of the option is used as item value, but this can overriden through the ",[69,204,205],{},"value"," property of ",[69,208,190],{},".",[108,211,213,132,216],{"id":212},"concept-and-ontology",[69,214,215],{},"Concept",[69,217,218],{},"Ontology",[54,220,221,222,224,225,228],{},"Items and options can be mapped to terms in ontologies using IRIs. This is modeled using the ",[69,223,215],{}," class. The property ",[69,226,227],{},"type"," defines the role of the mapping:",[230,231,232,239,245,251,257],"ul",{},[233,234,235,238],"li",{},[69,236,237],{},"Value",": Concepts of this type define the main meaning of the item or option. For many items and options, this will be the only concept.",[233,240,241,244],{},[69,242,243],{},"Negative",": When an item or option has a positive as well as a negative interpretation, for instance \"the individual is able to walk\" and \"the individual is unable to walk\", a concept of this type can be added in addition to the main value to map the opposite meaning.",[233,246,247,250],{},[69,248,249],{},"Specification",": This type of concept defines how a value is obtained, for example a description of a motor function test.",[233,252,253,256],{},[69,254,255],{},"Unit",": A concept with this role defines the unit of a measurement, e.g. \"kilogram\". Although mostly items will have this kind of concept, it may also apply to options, e.g. when a value can be provided in multiple different units.",[233,258,259,262],{},[69,260,261],{},"BaseIri",": This type is used when instead of a full IRI, a base IRI is provided which is prepended to a value of a restricted text item to form a full IRI.",[54,264,265],{},"Every item and option can have multiple concepts, but at most one of each role.",[54,267,268,269,272,273,276,277,280,281,284,285,287,288,291],{},"The ",[69,270,271],{},"term"," property of a concept does not contain a full IRI, but only the last part, e.g. ",[69,274,275],{},"0001324"," of the HPO term ",[69,278,279],{},"http:\u002F\u002Fpurl.obolibrary.org\u002Fobo\u002FHP_0001324",". The base IRI, e.g. ",[69,282,283],{},"http:\u002F\u002Fpurl.obolibrary.org\u002Fobo\u002FHP_"," for HPO, is defined in an ",[69,286,218],{}," object. This object also defines a prefix such as ",[69,289,290],{},"HP"," which is used to display terms.",[80,293,295],{"id":294},"tools","Tools",[108,297,299],{"id":298},"editor","Editor",[54,301,302,303,309,310,315,316,322,323,326],{},"The file ",[58,304,306],{"href":305},"\u002Feditor.txt",[69,307,308],{},"editor.html"," contains a basic editor for the JSON file based on ",[58,311,314],{"href":312,"rel":313},"https:\u002F\u002Fgithub.com\u002Fjson-editor\u002Fjson-editor",[62],"JSON editor",". It is configured through the JSON schema in ",[58,317,319],{"href":318},"\u002Fschema.json",[69,320,321],{},"schema.json",". The editor needs to read the JSON and schema files in the same directory. When opening the local HTML file with a browser (please rename the file above to end in ",[69,324,325],{},".html"," if you download it), this is normally disallowed for security reasons. Therefore, open with Chrome or Chromium like this:",[328,329,334],"pre",{"className":330,"code":332,"language":333},[331],"language-text","chromium --allow-file-access-from-files editor.html\n","text",[69,335,332],{"__ignoreMap":336},"",[54,338,339,340,343],{},"In Firefox, the setting ",[69,341,342],{},"security.fileuri.strict_origin_policy"," can be set to false.",[108,345,347],{"id":346},"zod-schema","Zod schema",[54,349,302,350,356,357,362],{},[58,351,353],{"href":352},"\u002Fschema.ts",[69,354,355],{},"schema.ts"," contains schema definitions based on ",[58,358,361],{"href":359,"rel":360},"https:\u002F\u002Fzod.dev\u002F",[62],"Zod",". It can be used to partially validate the JSON file; however a number of constraints as well as referential integrity are not checked.",[108,364,366],{"id":365},"typescript-model","TypeScript model",[54,368,369,370,376],{},"Based on the Zod schema, the file ",[58,371,373],{"href":372},"\u002Flibrary.ts",[69,374,375],{},"library.ts"," contains classes that perform further validation on the JSON data and enable using the data.",{"title":336,"searchDepth":378,"depth":379,"links":380},1,2,[381,382,394],{"id":82,"depth":379,"text":83},{"id":102,"depth":379,"text":103,"children":383},[384,386,387,389,390,392],{"id":110,"depth":385,"text":113},3,{"id":119,"depth":385,"text":122},{"id":128,"depth":385,"text":388},"ItemReference and Record",{"id":162,"depth":385,"text":20},{"id":184,"depth":385,"text":391},"Option and OptionReference",{"id":212,"depth":385,"text":393},"Concept and Ontology",{"id":294,"depth":379,"text":295,"children":395},[396,397,398],{"id":298,"depth":385,"text":299},{"id":346,"depth":385,"text":347},{"id":365,"depth":385,"text":366},"The TREAT-NMD Core Datasets are described on a dedicated web app. The content of this website is completely defined in the JSON file library.json. This structure of this file, which should serve as source for any tools operating on data in the TREAT-NMD data model, is described in the following. Note that this document only contains the technical and imlementation details that are not described in the general introduction to the datasets, so please read that document first.","md",null,{},true,{"title":37,"description":399},"iGhvTROM3BpFTAq-qYMNn8chEL5-8DYzxglrQ_LYEv4",[407,409],{"title":25,"path":26,"stem":27,"description":408,"icon":28,"children":-1},"Information about different types of records, which group related items",{"title":41,"path":42,"stem":43,"description":410,"children":-1},"To understand the data model, please first consult the general introduction on the specification website and the technical description of the metadata model.",1782940343511]