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
.Renvironor similar. Or, you can save as an R option. (see?Startupfor 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("remotes")
remotes::install_github("ropensci/rif")Load rif
library('rif')Summary
out <- rif_summary("cellular")
head(out$result$federationSummary$results)#> parentCategory category db indexable nifId
#> 1 Output Type Data or Model Barres Brain RNA-Seq ExpressionData scr_013736-2
#> 2 Category Gene Barres Brain RNA-Seq ExpressionData scr_013736-2
#> 3 Category Cell Barres Brain RNA-Seq ExpressionData scr_013736-2
#> 4 Category Expression Barres Brain RNA-Seq ExpressionData scr_013736-2
#> 5 Output Type Information PubMed Health Drug nlx_32805-3
#> 6 Category Molecule PubMed Health Drug nlx_32805-3
#> count totalCount snippets summaryString
#> 1 9 22458 NULL Barres Brain RNA-Seq: ExpressionData (9)[]
#> 2 9 22458 NULL Barres Brain RNA-Seq: ExpressionData (9)[]
#> 3 9 22458 NULL Barres Brain RNA-Seq: ExpressionData (9)[]
#> 4 9 22458 NULL Barres Brain RNA-Seq: ExpressionData (9)[]
#> 5 2 20110 NULL PubMed Health: Drug (2)[]
#> 6 2 20110 NULL 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 provider
#> 1 c2aad6c6-a2b8-4818-b2c8-5271dd5f431c cell NEMO_9559000 cell NIFSTD
#> 2 439b50ba-d1a6-4b4c-bbfd-d1d61d74ba69 cell GO_0005623 cell NIFSTD
#> 3 8ddd9932-4e66-4a25-84af-237c0784cef4 On cell nifext_32 Cell NIFSTD
#> inferred acronym abbreviation synonyms definition
#> 1 FALSE FALSE FALSE NA NA
#> 2 FALSE FALSE FALSE NA NA
#> 3 FALSE FALSE FALSE NA NA
Lexical
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)#> $sentence
#> [1] "Lorem ipsum inceptos dolor nisi torquent porttitor donec, blandit scelerisquemattis cras quis mi, aliquam sagittis."
#> [2] "Convallis placerat commodo imperdiet varius nunctempus urna vitae ultrices tristique eu mi ornare velit donec, posuere laoreet pretiumvitae porta augue porta feugiat in sapien egestas."
#> [3] "Quam odio nullam pulvinar litoracurabitur amet lacus sociosqu gravida ligula molestie dui netus fusce bibendumscelerisque, dictum malesuada proin elit etiam aliquam, mattis euismod donec nisl facilisis."
Chunks
head(lexical_chunks(text))#> token start end
#> 1 Lorem ipsum inceptos 0 20
#> 2 dolor nisi torquent porttitor donec 21 56
#> 3 blandit scelerisquemattis 58 83
#> 4 cras 84 88
#> 5 quis mi 89 96
#> 6 aliquam sagittis 98 114
Entities
head(lexical_entities(text))#> token start end
#> 1 Lorem ipsum inceptos dolor 0 26
#> 2 torquent porttitor donec 32 56
#> 3 blandit scelerisquemattis 58 83
#> 4 cras 84 88
#> 5 quis mi 89 96
#> 6 aliquam sagittis . 98 115
Literature
Search
library("dplyr")
out <- literature_search(query = "cellular", count = 5)
out$result$publications %>%
select(pmid, journal, year)#> # A tibble: 5 x 3
#> pmid journal year
#> <chr> <chr> <int>
#> 1 27417120 BioEssays : news and reviews in molecular, cellular and develo… 2017
#> 2 12944235 Cytotherapy 2003
#> 3 31084436 Cellular reprogramming 2020
#> 4 30785345 American journal of physiology. Lung cellular and molecular ph… 2019
#> 5 31687085 Oxidative medicine and cellular longevity 2020
Get retractions
out <- literature_retractions()
out[1:20]#> [1] "30065046" "12768027" "11167165" "23439334" "21613570" "12438313"
#> [7] "26214776" "17519423" "23745088" "24145124" "26009721" "1824564"
#> [13] "25497757" "20656892" "12200953" "18252834" "26339438" "18444895"
#> [19] "20175642" "23782032"
Then get info on some articles
arts <- literature_pmid(pmid = out[1:2])
lapply(arts, "[[", "title")#> [[1]]
#> [1] "OST1 Activation by the Brassinosteroid-Regulated Kinase CDG1-LIKE1 in Stomatal Closure."
#>
#> [[2]]
#> [1] "Basic residues of the helix six domain of influenza virus M1 involved in nuclear translocation of M1 can be replaced by PTAP and YPDL late assembly domain motifs."
Data
Search for data
out <- federation_search("cellular")
out$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$results)#> parentCategory category db indexable nifId
#> 1 Category Gene Barres Brain RNA-Seq ExpressionData scr_013736-2
#> 2 Output Type Data or Model Barres Brain RNA-Seq ExpressionData scr_013736-2
#> 3 Category Cell Barres Brain RNA-Seq ExpressionData scr_013736-2
#> 4 Category Expression Barres Brain RNA-Seq ExpressionData scr_013736-2
#> 5 Output Type Information PubMed Health Drug nlx_32805-3
#> 6 Category Molecule PubMed Health Drug nlx_32805-3
#> count totalCount snippets summaryString
#> 1 9 22458 NULL Barres Brain RNA-Seq: ExpressionData (9)[]
#> 2 9 22458 NULL Barres Brain RNA-Seq: ExpressionData (9)[]
#> 3 9 22458 NULL Barres Brain RNA-Seq: ExpressionData (9)[]
#> 4 9 22458 NULL Barres Brain RNA-Seq: ExpressionData (9)[]
#> 5 2 20110 NULL PubMed Health: Drug (2)[]
#> 6 2 20110 NULL PubMed Health: Drug (2)[]
Get some data
out <- federation_data(id = "nlx_152871-2")
out$result$result#> # A tibble: 20 x 12
#> Gene Anatomical.Comp… Assay.Type Theiler.Stage Tissue Expression.Stre…
#> <chr> <chr> <chr> <chr> <chr> <chr>
#> 1 tyro… nerve of bladder IHC (Immu… TS28 bladd… strong
#> 2 mate… urogenital mese… ISH (In S… TS20 urina… unspecified
#> 3 G pr… ovary ISH (In S… TS23 Not p… unspecified
#> 4 TANK… testis ISH (In S… TS23 Not p… unspecified
#> 5 zinc… ureter ISH (In S… TS23 Not p… unspecified
#> 6 dele… ovary ISH (In S… TS27 ovary strong
#> 7 fork… urinary system ISH (In S… TS25 Not p… moderate
#> 8 phos… pelvis ISH (In S… TS26 metan… strong
#> 9 home… testis ISH (In S… TS22 testis moderate
#> 10 GATA… ovary ISH (In S… TS23 Not p… unspecified
#> 11 sal-… testis ISH (In S… TS23 Not p… unspecified
#> 12 nitr… nerve of bladder IHC (Immu… TS26 bladd… strong
#> 13 RIKE… metanephros ISH (In S… TS26 metan… weak
#> 14 chol… pelvic ganglion TG (trans… TS22 pelvi… strong
#> 15 cyst… oviduct ISH (In S… TS27 ovary moderate
#> 16 ash1… ureter ISH (In S… TS23 Not p… unspecified
#> 17 neur… ureter ISH (In S… TS23 Not p… unspecified
#> 18 deve… testis ISH (In S… TS23 Not p… unspecified
#> 19 zinc… bladder ISH (In S… TS23 Not p… unspecified
#> 20 Nano… ureter ISH (In S… TS23 Not p… unspecified
#> # … with 6 more variables: 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.
