index.tsx

import { MetaNode } from '@/spec/metanode'
import { GeneSet } from '@/components/core/set'
import { MetGeneStudyTable } from '@/components/MW/metgene_study_table'
import { metgene_icon, additional_info_icon, gene_icon, set_icon } from '@/icons'
import { MetGeneSummary } from '@/components/MW/metgene_summary'

// A unique name for your resolver is used here
export const MetGeneStudies = MetaNode('MetGeneStudies')
  // Human readble descriptors about this node should go here
  .meta({
    label: 'MetGENE Studies',
    description: 'Extract Metabolomics studies for the gene from MetGENE',
    icon: [metgene_icon],
    external: true,
  })


  // This should be a mapping from argument name to argument type
  //  the types are previously defined Meta Node Data Types
  .inputs({ summary: MetGeneSummary })
  // This should be a single Meta Node Data Type
  .output(MetGeneStudyTable)
  // The resolve function uses the inputs and returns output
  //  both in the shape prescribed by the data type codecs
  .resolve(async (props) => {
    const species_id = "hsa"
    const geneID_type = "SYMBOL_OR_ALIAS"

    const gene_ID = props.inputs.summary.gene
    const vtf = "json"
    const req = await fetch(`https://bdcw.org/MetGENE/rest/studies/species/${species_id}/GeneIDType/${geneID_type}/GeneInfoStr/${gene_ID}/anatomy/NA/disease/NA/phenotype/NA/viewType/${vtf}`)
    const res = await req.json()



    return  res
  })
  .story(props => ({
    abstract: `${props.inputs?.summary?.gene ? props.inputs.summary.gene : 'The gene'} was then searched in the Metabolomics Workbench\\ref{The Metabolomics Workbench, https://www.metabolomicsworkbench.org/} to identify relevant studies related to the gene.`,
    introduction: `MetGENE is a information retrieval tool that connects a gene or a set of genes to metabolomic studies in the Metabolomic Workbench. It uses a knowledge based approach where the gene is connected to pathways it regulates, followed by reactions within the pathways and metabolites particicpating in the reactions. The metabolites are connected to studies in Metabolomics Workbench.`,
    methods: `Given a gene, MetGENE provides REST API to extract information regarding all the studies in the MW by obtaining first the pathways where the gene participates and the reactions within the pathways, followed by the metabolites participating in the reaction and the corresponding metbolomics studies in which the metabolite is measured. e.g.  for human species (hsa), with anatomy blood and disease diabetes,\\ref{https://bdcw.org/MetGENE/rest/studies/species/hsa/GeneIDType/SYMBOL/GeneInfoStr/HK1/anatomy/blood/disease/diabetes/phenotype/NA/viewType/json}, returns the KEGG Compound IDS, KEGG Reaction names as well as KEGG Reaction equations for the corresponding gene in the form of a JSON output.`,
    legend: `The results are displayed in a table containing KEGG Compound IDs, RefMet names, and Study IDs. Each entry is hyperlinked: KEGG Compound IDs link to the corresponding compound information page on the KEGG website, RefMet names link to the RefMet information on the Metabolomics Workbench (MW) website, and Study IDs link to the relevant study information on the MW website.`,
  }))
  .build()

export const MetGeneStudiesGeneSet = MetaNode('MetGeneStudiesGeneSet')
  // Human readble descriptors about this node should go here
  .meta({
    label: 'MetGENE Studies with Gene Set',
    description: 'Compute the MetGENE studies function for a gene set',
    tags: {
      Service: { 'MetGENE': 1 },
    },
    icon: [gene_icon, set_icon, additional_info_icon],
    external: true,
  })


  // This should be a mapping from argument name to argument type
  //  the types are previously defined Meta Node Data Types
  .inputs({ geneset: GeneSet })
  // This should be a single Meta Node Data Type
  .output(MetGeneStudyTable)
  // The resolve function uses the inputs and returns output
  //  both in the shape prescribed by the data type codecs
  .resolve(async (props) => {
    const species_id = "hsa"
    const geneID_type = "SYMBOL_OR_ALIAS"

    const gene_ID = props.inputs.geneset.set.join(",");
    const vtf = "json"
    const req = await fetch(`https://bdcw.org/MetGENE/rest/studies/species/${species_id}/GeneIDType/${geneID_type}/GeneInfoStr/${gene_ID}/anatomy/NA/disease/NA/phenotype/NA/viewType/${vtf}`)
    const res = await req.json()



    return  res
  })
  .story(props => ({
    abstract: `The gene set was then searched in the Metabolomics Workbench\\ref{The Metabolomics Workbench, https://www.metabolomicsworkbench.org/} to identify relevant studies related to the genes.`,
    methods: `MetGENE provides a REST API that allows users to extract detailed information about studies in the Metabolomics Workbench (MW) based on a given gene set. The process involves identifying pathways in which the genes participate, the reactions within those pathways, the metabolites involved in these reactions, and finally, the metabolomics studies that measure these metabolites. For example, for the human species (hsa) with the anatomy specified as blood, disease as diabetes, and a gene set including genes like HK1 and RPE, the API\\ref{https://bdcw.org/MetGENE/rest/studies/species/hsa/GeneIDType/SYMBOL/GeneInfoStr/HK1,RPE/anatomy/blood/disease/diabetes/phenotype/NA/viewType/json} provides a JSON output that includes the KEGG Compound ID, MW RefMet name, and MW Study IDs for the corresponding genes. The KEGG Compound ID links to detailed compound information on the KEGG website, the RefMet Name links to RefMet details on the MW website, and the study IDs link to specific study information on the MW website.`,
    legend: `The results table includes KEGG compound IDs for metabolites involved in all reactions corresponding to the gene set. These IDs are hyperlinked to their respective KEGG compound information pages. Additionally, the table lists their corresponding RefMet names, which are hyperlinked to the relevant pages on the Metabolomics Workbench (MW) website, along with MW Study IDs that link to the specific study information pages on the MW site.`,
  }))
  .build()