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This is a test . This is a test . This is a test . 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Loader to ensure that it is available before initialisation (so that we + // Loader to ensure that it is available before initialization (so that we // can calculate the dimensions of SVG Text elements accurately) const fontLoadPromise = new Promise((resolve, reject) => { WebFont.load({ @@ -63,29 +63,49 @@ $(async () => { await fontLoadPromise; - // ------------- - // Basic example - // ------------- - const $basicContainer = $("#basicContainer"); - const basicTag = TAG.tag({ - // The `container` parameter can take either the ID of the main element or - // the main element itself (as either a jQuery or native object) - container: $basicContainer, - - // The initial data to load. - // Different formats might expect different types for `data`: - // E.g., the "odin" format expects the annotations as an - // (already-parsed) Object, while the "brat" format expects them as a raw - // String. - // See the full documentation for details. - data: require("../data/test-odin.json"), - format: "odin", - - // Overrides for default options - options: { - showTopArgLabels: true - } - }); + + /** + * Initialize TAG instance for the given element ID and data file + * NOTE: elemId should be in form of "#id-name-here" + * + */ + function loadTagForElem(elemId, annoData, dataFormat) { + console.log(elemId); + console.log(dataFormat); + const $elem = $(elemId); + TAG.tag({ + // The `container` parameter can take either the ID of the main element or + // the main element itself (as either a jQuery or native object) + container: $elem, + + // The initial data to load. + // Different formats might expect different types for `data`: + // E.g., the "odin" format expects the annotations as an + // (already-parsed) Object, while the "brat" format expects them as a raw + // String. + // See the full documentation for details. + data: annoData, + format: dataFormat, + + // Overrides for default options + options: { + showTopArgLabels: true, + compactRows: true, + bottomLinkCategory: "universal-enhanced" + } + }); + } + + // Demo examples + // NOTE: require can't load data dynamically (ex. (require(filePath)) + const ex1Data = require("../data/ex1.json"); + loadTagForElem("#ex1", ex1Data, "odin"); + const ex2Data = require("../data/ex2.json"); + loadTagForElem("#ex2", ex2Data, "odin"); + const ex3Data = require("../data/ex3.json"); + loadTagForElem("#ex3", ex3Data, "odin"); + const ex4Data = require("../data/ex2.json"); + loadTagForElem("#ex4", ex4Data, "odin") // ------------------- // Advanced/UI example @@ -95,9 +115,9 @@ $(async () => { container: $uiContainer }); - // Data can be loaded after initialisation using the `.loadData()` function, + // Data can be loaded after initialization using the `.loadData()` function, // or from a remote URL via the asynchronous `.loadUrlAsync()` function. - await uiTag.loadUrlAsync("data/sentence-1-odin.json", "odin"); + await uiTag.loadUrlAsync("data/ex1.json", "odin"); // -------------------------------------------------------------------------- @@ -536,8 +556,7 @@ $(async () => { // Debug window._ = require("lodash"); - window.basicTag = basicTag; window.uiTag = uiTag; window.editor = editor; window.yaml = require("js-yaml"); -}); \ No newline at end of file +}); diff --git a/demo/taxonomy.yml b/demo/taxonomy.yml index 44971bb..ea08118 100644 --- a/demo/taxonomy.yml +++ b/demo/taxonomy.yml @@ -1,102 +1,32 @@ -- Alias -- ModificationTrigger -- Site -- Context: +- Sentence: + - XP: + - VerbPhrase + - PrepPhrase + - WhPhrase + # NOTE: these are converted in an action to create Concepts + - NounPhrase + +- Entity: + - Concept: + - Crop + - Symptom + - Stressor: + - AbioticStressor + - BioticStressor: + - BacterialStressor + - FungalStressor + - InsectStressor + - NematodeStressor + - ViralStressor - Species - - CellLine - - Organ - - CellType - - Cellular_component - - TissueType - - ContextDirection - - ContextLocation - - ContextPossessive -- Modification: - - PTM - - Mutant: - - GenericMutant - - SubstitutionMutant - - DeletionMutant - - DuplicationMutant - - InsertionMutant - - FrameshiftMutant - - EventSite - - Negation -- PossibleController: - - Event: - - SimpleEvent: - - Binding - - Generic_event - - Translocation - - Amount: - - IncreaseAmount: - - Transcription - - DecreaseAmount - - AdditionEvent: - - Acetylation - - Farnesylation - - Glycosylation - - Hydrolysis - - Hydroxylation - - Methylation - - Phosphorylation: - - AutoPhosphorylation - - Ribosylation - - Sumoylation - - Ubiquitination - - RemovalEvent: - - Deacetylation - - Defarnesylation - - Deglycosylation - - Dehydrolysis - - Dehydroxylation - - Demethylation - - Dephosphorylation - - Deribosylation - - Desumoylation - - Deubiquitination - - ComplexEvent: - - Regulation: - - Positive_regulation - - Negative_regulation - - ActivationEvent: - - Positive_activation - - Negative_activation - - Entity: - # Any BioEntity may appear as the controlled in an Activation - - BioEntity: - - BioProcess # ex. "apoptosis" - - BioChemicalEntity: - - Generic_entity - - Simple_chemical - - Equivalable: #TODO: Better name - - Family - - MacroMolecule: - - Protein - - Gene_or_gene_product - - Complex - - GENE -# a preliminary taxonomy for assembly (precedence relations) -- Precedence: - # for pairs that are directly (immediately) connected - # difficult to know from odin rules alone, but not impossible - - DirectConnection - # for pairs that are indirectly (not immediately) connected - - IndirectConnection - # Between-sentence precedence - - BetweenSentence: - - TimexAfter - - TimexBefore - - SentenceInitialEvent - - InterAfter - - InterBefore - # tense and aspect detection - - TAM: - - Aux - - Tense: - - PastTense - - PresentTense - - FutureTense - - Aspect: - - Perfective - - Progressive + +- Event: + - Causal: + - Increase + - Decrease + - Correlation + - SameAs + +- Coref +- Avoid: + - PossibleTrigger