R/20_WIKIPATHWAYS.R

In tidymass/massdatabase: Play with databases about mass spectrometry

#' Retrieve Available Organisms from WikiPathways
#'
#' This function queries WikiPathways to obtain a list of organisms for which pathways are available.
#'
#' @return A character vector of organism names available in the WikiPathways database.
#' @export
#' @examples
#' request_wikipathway_organisms_info()

request_wikipathway_organisms_info <-
  function() {
    result <- rjson::fromJSON(file = "https://www.wikipathways.org/json/listOrganisms.json")
    return(result$organisms)
  }

#' Retrieve Pathway Information for a Specific Organism
#'
#' This function fetches all available pathways from WikiPathways for a specified organism.
#'
#' @param organism A character string specifying the organism name. Default is "Homo sapiens".
#' @return A data frame containing pathway information, including pathway names, IDs, and species.
#' @export
#' @examples
#' request_wikipathway_info("Homo sapiens")

request_wikipathway_info <-
  function(organism = "Homo sapiens") {
    organism <-
      match.arg(organism, choices = wikipathway_organisms_info)
    result <-
      rjson::fromJSON(file = "https://www.wikipathways.org/json/listPathways.json")

    result <- result$organisms %>%
      purrr::map_dfr(~ .x$pathways)

    if (organism != "") {
      result <- dplyr::filter(result, species == organism)
    }
    if (nrow(result) == 0) {
      message("No resultults")
      return(NULL)
    }
    return(result)
  }


#' Retrieve Detailed Pathway Data from WikiPathways
#'
#' This function fetches detailed information about a specific pathway from WikiPathways using its pathway ID.
#'
#' @param pathway_id A character string specifying the WikiPathways ID (e.g., "WP5293").
#' @return A list containing:
#'   \itemize{
#'     \item \code{pathway_info} - Metadata about the pathway.
#'     \item \code{pathway_description} - A description of the pathway.
#'     \item \code{node_info} - A data frame containing gene/metabolite nodes.
#'     \item \code{edge_info} - A data frame containing interaction edges.
#'   }
#' @export
#' @examples
#' data = request_wikipathway("WP5293")
#' data$pathway_info

request_wikipathway <-
  function(pathway_id = "WP5293") {
    url <-
      paste0(
        "https://www.wikipathways.org/wikipathways-assets/pathways/",
        pathway_id,
        "/",
        pathway_id,
        ".gpml"
      )

    # Read the XML file
    result <-
      tryCatch(
        expr = xml2::read_xml(url),
        error = function(e) {
          message("Error: ", e)
          return(NULL)
        }
      )

    # Extract pathway information
    pathway_name <- xml2::xml_attr(result, "Name")
    data_source <- xml2::xml_attr(result, "Data-Source")
    version <- xml2::xml_attr(result, "Version")
    author <- xml2::xml_attr(result, "Author")
    last_modified <- xml2::xml_attr(result, "Last-Modified")
    organism <- xml2::xml_attr(result, "Organism")

    # Print pathway information
    pathway_info <- list(
      Name = pathway_name,
      DataSource = data_source,
      Version = version,
      Author = author,
      LastModified = last_modified,
      Organism = organism
    )

    # Extract pathway description
    pathway_description <-
      xml2::xml_find_all(result, ".//d1:Comment", ns = xml2::xml_ns(result))

    # Get the text content of each comment
    pathway_description <-
      xml2::xml_text(pathway_description)

    if (length(pathway_description) > 1) {
      pathway_description <-
        pathway_description[1]
    }

    # Extract BiopaxRef elements
    biopax_refs <-
      xml2::xml_find_all(result, ".//d1:BiopaxRef", ns = xml2::xml_ns(result))

    # Get the text content of each BiopaxRef
    biopax_ref_texts <-
      xml2::xml_text(biopax_refs)

    # Extract all DataNode elements
    datanodes <-
      xml2::xml_find_all(result, ".//d1:DataNode", ns = xml2::xml_ns(result))

    # Extract Xref elements within DataNodes
    xref_nodes <- xml2::xml_find_all(datanodes, ".//d1:Xref", ns = xml2::xml_ns(result))

    # Extract TextLabel, GraphId, and Type attributes
    node_info <- data.frame(
      TextLabel = xml2::xml_attr(datanodes, "TextLabel"),
      GraphId = xml2::xml_attr(datanodes, "GraphId"),
      Type = xml2::xml_attr(datanodes, "Type"),
      Database = xml2::xml_attr(xref_nodes, "Database"),
      ID = xml2::xml_attr(xref_nodes, "ID"),
      stringsAsFactors = FALSE
    )


    # # Extract all Graphics elements inside DataNodes
    # graphics_nodes <-
    #   xml2::xml_find_all(result, ".//d1:DataNode/d1:Graphics", ns = xml2::xml_ns(result))
    #
    # # Extract positions (CenterX, CenterY)
    # graphics_info <-
    #   data.frame(
    #   GraphId = xml2::xml_attr(
    #     xml2::xml_find_all(result, ".//d1:DataNode", ns = xml2::xml_ns(result)),
    #     "GraphId"
    #   ),
    #   CenterX = as.numeric(xml2::xml_attr(graphics_nodes, "CenterX")),
    #   CenterY = as.numeric(xml2::xml_attr(graphics_nodes, "CenterY")),
    #   stringsAsFactors = FALSE
    # )


    # Extract all Interaction elements
    interactions <-
      xml2::xml_find_all(result, ".//d1:Interaction", ns = xml2::xml_ns(result))

    # Extract GraphId and references to connecting nodes
    edge_info <-
      data.frame(
        GraphId = xml2::xml_attr(interactions, "GraphId"),
        Points = sapply(interactions, function(inter) {
          points <- xml2::xml_find_all(inter, ".//d1:Point", ns = xml2::xml_ns(result))
          paste(xml2::xml_attr(points, "GraphRef"), collapse = " -> ")
        }),
        stringsAsFactors = FALSE
      )


    return_result <-
      list(
        pathway_info = pathway_info,
        pathway_description = pathway_description,
        node_info = node_info,
        edge_info = edge_info
      )
    return(return_result)
  }



wikipathway_organisms_info <-
  c(
    "Anopheles gambiae",
    "Arabidopsis thaliana",
    "Bacillus subtilis",
    "Bos taurus",
    "Caenorhabditis elegans",
    "Canis familiaris",
    "Caulobacter vibrioides",
    "Danio rerio",
    "Drosophila melanogaster",
    "Equus caballus",
    "Escherichia coli",
    "Gallus gallus",
    "Gibberella zeae",
    "Homo sapiens" ,
    "Hordeum vulgare",
    "Mus musculus",
    "Mycobacterium tuberculosis",
    "Oryza sativa",
    "Pan troglodytes" ,
    "Plasmodium falciparum",
    "Populus trichocarpa",
    "Rattus norvegicus",
    "Saccharomyces cerevisiae",
    "Solanum lycopersicum",
    "Sus scrofa",
    "Vitis vinifera",
    "Zea mays"
  )