In MRCIEU/epigraphdb-r: Interface Package for the 'EpiGraphDB' Platform

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

This RMarkdown document demonstrates how key elements from the github notebook for the meta functionalities can be achieved using the R package. For detailed explanations of the case study please refer to the notebook on github.

Here we show the following aspects of the EpiGraphDB platform, and how to use the API to get the information:

Metadata: meta nodes and meta edges, and the overall schema.
Search for a specific node under the meta node.
Cypher: how to query the database directly using Neo4j Cypher

For detailed documentation on the API endpoints please visit:

The Swagger interface: https://api.epigraphdb.org
The sections regarding API endpoints on the documentation site: https://docs.epigraphdb.org/api/api-endpoints/

library("magrittr")
library("dplyr")
library("purrr")
library("igraph")
library("epigraphdb")

Metadata

Here we query for the metadata information using the endpoint GET /meta/schema, which will be used for downstream processing.

endpoint <- "/meta/schema"
params <- list(
  graphviz = FALSE,
  plot = FALSE
)
metadata <- query_epigraphdb(
  route = endpoint, params = params, mode = "raw"
)

metadata %>% str(2)

Meta nodes

We can extract the specific meta node information as a dataframe from the metadata.

meta_node_df <- metadata %>%
  pluck("nodes") %>%
  {
    names <- names(.)
    transpose(.) %>%
      as_tibble() %>%
      mutate(meta_node = names) %>%
      # Hide properties column which does not display well
      select(meta_node, count) %>%
      # We also need to flatten count
      mutate(count = flatten_int(count))
  }

meta_node_df %>%
  arrange(meta_node) %>%
  mutate(count = format(count, big.mark = ","))

Meta relationships and connections

We can also extract the meta relationship (edge) information, and the connections.

meta_rel_df <- metadata %>%
  pluck("edges") %>%
  {
    names <- names(.)
    transpose(.) %>%
      as_tibble() %>%
      mutate(meta_rel = names) %>%
      mutate(count = flatten_int(count)) %>%
      select(meta_rel, count)
  } %>%
  inner_join(
    metadata %>% pluck("connections") %>%
      {
        transpose(.) %>%
          as_tibble() %>%
          mutate(meta_rel = flatten_chr(rel)) %>%
          mutate_at(vars(from_node, to_node), flatten_chr) %>%
          select(meta_rel, from_node, to_node)
      }
  )

meta_rel_df %>%
  arrange(from_node, to_node) %>%
  mutate(count = format(count, big.mark = ","))

Search for specific node

Users can use the explorer on the Web UI to search for a specific node by:

fuzzy matching by "name" field.
exact matching by "ID" field if you know the its ID (e.g. the ID to a GWAS from IEU GWAS Database).

Here we show how these are done at the API level using Gwas nodes as an example.

First we need to know what the "ID" and "name" fields are for the meta nodes using GET /meta/nodes/id-name-schema:

endpoint <- "/meta/nodes/id-name-schema"
meta_node_fields <- query_epigraphdb(
  route = endpoint, params = NULL, mode = "raw"
)
meta_node_fields

Fuzzy matching

Here we search for nodes can contain "body mass index" in their traits.

name <- "body mass index"

endpoint <- "/meta/nodes/Gwas/search"
params <- list(name = name)

results <- query_epigraphdb(
  route = endpoint, params = params, mode = "table"
)
results

Exact matching

Similarly, we can exact match a specific node by its ID.

id <- "ieu-a-2"

endpoint <- "/meta/nodes/Gwas/search"
params <- list(id = id)

results <- query_epigraphdb(
  route = endpoint, params = params, mode = "table"
)
results

Cypher (advanced)

Advanced users that are familiar with Neo4j Cypher can query the database using Cypher directly.

query <- "
    MATCH (exposure:Gwas)-[mr:MR]->(outcome:Gwas)
    WHERE exposure.trait = 'Body mass index'
    RETURN exposure, outcome, mr LIMIT 2
"

endpoint <- "/cypher"
params <- list(query = query)

# NOTE this is a POST request
results <- query_epigraphdb(
  route = endpoint, params = params, method = "POST",
  mode = "table"
)
results