rif
R client for the Neuroscience Information Framework APIs.
- API docs at https://neuinfo.org/about/webservices
Auth
You now need an API key to use the NIF API. Steps:
- Go to https://www.neuinfo.org/
- If you don't have an account yet, register for an account.
- Log in
- Go to https://www.neuinfo.org/account/developer - you'll need to
enter your password again
- Create an API key
- Store your API key ideally as an environment variable in
.Renviron
or similar. Or, you can save as an R option. (see ?Startup for help on
env vars and R options). You can also pass in your API key to each function
but that's not ideal.
Installation
CRAN version
install.packages("rif")development version
install.packages("devtools")
devtools::install_github("ropensci/rif")Load rif
library('rif')Summary
out <- rif_summary("cellular")
head(out$result$federationSummary$results)#> parentCategory category db indexable
#> 1 Output Type Data or Model Barres Brain RNA-Seq ExpressionData
#> 2 Category Expression Barres Brain RNA-Seq ExpressionData
#> 3 Category Gene Barres Brain RNA-Seq ExpressionData
#> 4 Category Cell Barres Brain RNA-Seq ExpressionData
#> 5 Category Molecule PubMed Health Drug
#> 6 Output Type Information PubMed Health Drug
#> nifId count totalCount snippets
#> 1 scr_013736-2 9 22458 NULL
#> 2 scr_013736-2 9 22458 NULL
#> 3 scr_013736-2 9 22458 NULL
#> 4 scr_013736-2 9 22458 NULL
#> 5 nlx_32805-3 2 19179 NULL
#> 6 nlx_32805-3 2 19179 NULL
#> summaryString
#> 1 Barres Brain RNA-Seq: ExpressionData (9)[]
#> 2 Barres Brain RNA-Seq: ExpressionData (9)[]
#> 3 Barres Brain RNA-Seq: ExpressionData (9)[]
#> 4 Barres Brain RNA-Seq: ExpressionData (9)[]
#> 5 PubMed Health: Drug (2)[]
#> 6 PubMed Health: Drug (2)[]Query
List NIF query categories
rif_query_categories()#> [1] "anatomy" "antibody" "catalognumber"
#> [4] "cell" "coordinate" "disease"
#> [7] "environment" "fulltext" "function"
#> [10] "gene" "genetargetreagent" "genomiclocus"
#> [13] "genomiclocusvariant" "genotype" "identifier"
#> [16] "interaction" "interactiontype" "moleculardomain"
#> [19] "molecule" "organism" "pathway"
#> [22] "phenotype" "protocol" "publication"
#> [25] "quality" "resource" "sequence"
#> [28] "sequencefeature" "specimen" "stage"
#> [31] "strain" "subcellularanatomy"Vocabulary
Search for vocabulary terms
vocabulary_search("cell", limit = 3)#> uuid term id category
#> 1 c2aad6c6-a2b8-4818-b2c8-5271dd5f431c cell NEMO_9559000 cell
#> 2 439b50ba-d1a6-4b4c-bbfd-d1d61d74ba69 cell GO_0005623 cell
#> 3 8ddd9932-4e66-4a25-84af-237c0784cef4 On cell nifext_32 Cell
#> provider inferred acronym abbreviation synonyms definition
#> 1 NIFSTD FALSE FALSE FALSE NA NA
#> 2 NIFSTD FALSE FALSE FALSE NA NA
#> 3 NIFSTD FALSE FALSE FALSE NA NALexical
Break up text into various things
text <- "Lorem ipsum inceptos dolor nisi torquent porttitor donec, blandit scelerisque
mattis cras quis mi, aliquam sagittis. Convallis placerat commodo imperdiet varius nunc
tempus urna vitae ultrices tristique eu mi ornare velit donec, posuere laoreet pretium
vitae porta augue porta feugiat in sapien egestas. Quam odio nullam pulvinar litora
curabitur amet lacus sociosqu gravida ligula molestie dui netus fusce bibendum
scelerisque, dictum malesuada proin elit etiam aliquam, mattis euismod donec nisl facilisis."
text <- gsub("\n", "", text)Sentences
lexical_sentences(text)#> $sentence
#> [1] "Lorem ipsum inceptos dolor nisi torquent porttitor donec, blandit scelerisquemattis cras quis mi, aliquam sagittis."
#> [2] "Convallis placerat commodo imperdiet varius nunctempus urna vitae ultrices tristique eu mi ornare velit donec, posuere laoreet pretiumvitae porta augue porta feugiat in sapien egestas."
#> [3] "Quam odio nullam pulvinar litoracurabitur amet lacus sociosqu gravida ligula molestie dui netus fusce bibendumscelerisque, dictum malesuada proin elit etiam aliquam, mattis euismod donec nisl facilisis."Chunks
head(lexical_chunks(text))#> token start end
#> 1 Lorem ipsum inceptos 0 20
#> 2 dolor nisi torquent porttitor donec 21 56
#> 3 blandit scelerisquemattis 58 83
#> 4 cras 84 88
#> 5 quis mi 89 96
#> 6 aliquam sagittis 98 114Entities
head(lexical_entities(text))#> token start end
#> 1 Lorem ipsum inceptos dolor 0 26
#> 2 torquent porttitor donec 32 56
#> 3 blandit scelerisquemattis 58 83
#> 4 cras 84 88
#> 5 quis mi 89 96
#> 6 aliquam sagittis . 98 115Literature
Search
library("dplyr")
out <- literature_search(query = "cellular", count = 5)
out$result$publications %>%
select(pmid, journal, year)#> # A tibble: 5 x 3
#> pmid
#> * <chr>
#> 1 12944235
#> 2 27417120
#> 3 8789268
#> 4 2987169
#> 5 15088773
#> # ... with 2 more variables: journal <chr>, year <int>Get retractions
out <- literature_retractions()
out[1:20]#> [1] "12768027" "11167165" "22576713" "17973093" "10050223" "21613570"
#> [7] "12438313" "22364277" "26214776" "10784445" "17519423" "21177250"
#> [13] "23745088" "26009721" "1824564" "15260988" "20656892" "1400454"
#> [19] "12200953" "22893106"Then get info on some articles
arts <- literature_pmid(pmid = out[1:2])
lapply(arts, "[[", "title")#> [[1]]
#> [1] "Basic residues of the helix six domain of influenza virus M1 involved in nuclear translocation of M1 can be replaced by PTAP and YPDL late assembly domain motifs."
#>
#> [[2]]
#> [1] "Point-of-care (POC) testing of lactate in the intensive care patient. Accuracy, reliability, and costs of different measurement systems."Data
Search for data
out <- federation_search("cellular")
out$query#> $clauses
#> category property query expansion id quoted require forbid
#> 1 NA NA cellular NULL NA FALSE FALSE FALSE
#>
#> $operator
#> [1] "AND"head(out$result$results)#> parentCategory category db indexable
#> 1 Category Expression Barres Brain RNA-Seq ExpressionData
#> 2 Category Gene Barres Brain RNA-Seq ExpressionData
#> 3 Category Cell Barres Brain RNA-Seq ExpressionData
#> 4 Output Type Data or Model Barres Brain RNA-Seq ExpressionData
#> 5 Category Molecule PubMed Health Drug
#> 6 Output Type Information PubMed Health Drug
#> nifId count totalCount snippets
#> 1 scr_013736-2 9 22458 NULL
#> 2 scr_013736-2 9 22458 NULL
#> 3 scr_013736-2 9 22458 NULL
#> 4 scr_013736-2 9 22458 NULL
#> 5 nlx_32805-3 2 19179 NULL
#> 6 nlx_32805-3 2 19179 NULL
#> summaryString
#> 1 Barres Brain RNA-Seq: ExpressionData (9)[]
#> 2 Barres Brain RNA-Seq: ExpressionData (9)[]
#> 3 Barres Brain RNA-Seq: ExpressionData (9)[]
#> 4 Barres Brain RNA-Seq: ExpressionData (9)[]
#> 5 PubMed Health: Drug (2)[]
#> 6 PubMed Health: Drug (2)[]Get some data
out <- federation_data(id = "nlx_152871-2")
out$result$result#> # A tibble: 20 x 12
#> Gene
#> <chr>
#> 1 tyrosine hydroxylase
#> 2 maternally expressed 3
#> 3 G protein-coupled receptor 37
#> 4 TANK-binding kinase 1
#> 5 zinc finger, ZZ domain containing 3
#> 6 deleted in azoospermia-like
#> 7 forkhead box A2
#> 8 phospholipase A2, group IIF
#> 9 homeobox C5
#> 10 GATA binding protein 4
#> 11 sal-like 4 (Drosophila)
#> 12 nitric oxide synthase 1, neuronal
#> 13 RIKEN cDNA C130073F10 gene
#> 14 choline acetyltransferase
#> 15 cystatin 12
#> 16 ash1 (absent, small, or homeotic)-like (Drosophila)
#> 17 neurogenic differentiation 4
#> 18 developing brain homeobox 2
#> 19 zinc finger and SCAN domain containing 22
#> 20 Nanog homeobox
#> # ... with 11 more variables: Anatomical.Component <chr>,
#> # Assay.Type <chr>, Theiler.Stage <chr>, Tissue <chr>,
#> # Expression.Strength <chr>, Expression.Pattern <chr>,
#> # Expression.Pattern.Location <chr>, Authors <chr>, Notes <chr>,
#> # v_uuid <chr>, Source <chr>Meta
- Please report any issues or bugs.
- License: MIT
- Get citation information for
rifin R doingcitation(package = 'rif') - Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.