[Target Identification] Export results

mzueva commented 12 months ago

Background Three approaches shall be supported for target identification export:

every table shall be exported as a separate csv file
overall target identification reports shall be exported as a multi-sheet excel file
overall target identification reports shall be as static html page

AlfiyaRF commented 11 months ago

For the static html page the server need to generate data in following format:

{
  name: string,
  interest: [{
    id: string,
    name: string,
    species: string,
    description?: string,
  }],
  translational: [{
    id: string,
    name: string,
    species: string,
    description?: string,
  }],
  totalCounts: {
    knownDrugs?: {
      drugs?: number;
      records?: number;
    },
    diseases?: number,
    sequences?: {
      dnas?: number,
      mrnas?: number,
      proteins?: number,
    },
    genomics?: number,
    structures?: number,
    publications?: number,
  },
  knownDrugs: [
    {
      source: "OPEN_TARGETS",
      data: [{
        target: string,
        drug: {
          value: string,
          link?: string,
        },
        type?: string
        mechanism?: string,
        action?: string,
        disease?: {
          value: string,
          link?: string,
        },
        phase?: string,
        status?: string,
        source?: {
          value: string,
          link?: string,
        }
      }],
    },
    {
      source: "DGIDB",
      data: [{
        target: string,
        drug: {
          value: string,
          link?: string,
        },
        interactionSource?: string,
        interactionType:? string,
      }],
    },
    {
      source: "PHARMGKB",
      data: [{
        target: string,
        drug: {
          value: string,
          link?: string,
        },
        source?: string,
      }],
    },
  ],
  associatedDiseases: [
    {
      source: "OPEN_TARGETS",
      data: [{
        target: string,
        disease: {
          value: string,
          link?: string,
        },
        overallScore?: number,
        geneticAssociation?: number,
        somaticMutations?: number,
        drugs?: number,
        pathwaysSystems?: number,
        textMining?: number,
        animalModels?: number,
        RNAExpression?: number,
      }],
    },
    {
      source: "PHARMGKB",
      data: [{
        target: string,
        disease: {
          value: string,
          link?: string,
        },
      }],
    },
  ],
  sequences: [
    {
      gene: {
        id: string,
        name: string,
        species: string,
      },
      reference?: {
        value: string,
        link?: string,
      },
      data: [{
        target: string,
        transcript?: {
          value: string,
          link?: string,
        },
        mrnaLength?: number,
        protein?: {
          value: string,
          link?: string,
        }
        proteinLength?: number,
        proteinName?: string,
      }]
    }
  ],
  comparativeGenomics: [{
    target: string,
    species: string,
    homologyType: string,
    homologue?: {
      value: string,
      link?: string,
    },
    homologyGroup?: string,
    protein?: string,
    aa?: number,
  }],
  structures: [
    {
      source: 'PROTEIN_DATA_BANK',
      data: [{
        id: {
          value: string,
          link?: string,
        },
        name: string,
        method?: string,
        source?: string,
        resolution?: number,
        chains?: string,
      }]
    },
    {
      source: 'LOCAL_FILES',
      data: [{
        id: {
          value: string,
          link?: string,
        },
        name: string,
        owner: string,
      }]
    },
  ],
  publications: [{
    title: {
      name: 'string',
      link: 'string',
    },
    authors?: string[],
    date?: 'string'
  }]
}