In Sage-Bionetworks/porTools: Sage portal curation tools

knitr::opts_chunk$set(echo = TRUE)
library(dccvalidator)
library(dplyr)
library(easyPubMed)
library(readr)
library(reticulate)
synapseclient <- reticulate::import("synapseclient")
syntab <- reticulate::import("synapseclient.table")
syn <- synapseclient$Synapse()
syn$login()

Query Pubmed and store data as file annotations

The schema for these steps is pubmedId, grants and study. Theses functions take a list of PubmedIds and queries the site to pull down title, abstract, authors, journal name, year and DOI. Theses annotations are visible in the PEC Portal - Publications View. See the Explore Publications module for a visual of how this data is surfaced on the portal.

tribble(~pubmedId, ~grants, ~study,
        "24057217", "R21MH103877", c("study1,study2")
        )

Import the list of Pubmed Ids and define the Synapse parentId where the file entities will be stored with the Pubmed-relevant annotations.

parent <- "syn22235314"
pmids <- readr::read_tsv(syn$get("syn22080024")$path, 
                         col_types = readr::cols(.default = "c"))

Run the code

Any character vector can be passed to query_list_pmids. This function wraps several functions: - query Pubmed - create an entity name from first author, journal, year and Id - abbreviates the author names by first initial, last name - creates one row per PubmedId

dat <- query_list_pmids(pmids$pubmedId)

I am keeping an eye out for weird edge cases. These (hacky) steps clean some missing values and remove extraneous characters.

dat$title <- gsub("<i>|</i>", "", dat$title)
dat$authors <- gsub("NA", "", dat$authors)
dat$entity_name <- gsub("NA ", "", dat$entity_name)
dat$journal <- remove_unacceptable_characters(dat$journal)
dat$entity_name <- remove_unacceptable_characters(dat$entity_name)

set_up_multiannotations parses comma-separated lists to be stored correctly in Synapse as multi-value annotations. Then, study and grant annotations are joined to the Pubmed queries.

pmids <- set_up_multiannotations(pmids, "study")
pmids <- set_up_multiannotations(pmids, "grants")

mapping <- dplyr::right_join(pmids, dat, by = c("pubmedId" = "pmid"))
mapping <- dplyr::rename(mapping, DOI = doi)

The final data is transposed so that it can be iterated over by purrr and stored in Synapse.

list <- purrr::transpose(mapping)
store_as_annotations(parent = "syn22235314", list)

Sage-Bionetworks/porTools documentation built on Nov. 24, 2024, 10:22 a.m.