R client for the Neuroscience Information Framework APIs.
- API docs at http://nif-services.neuinfo.org/servicesv1/
- Various clients at http://nif-services.neuinfo.org/servicesv1/downloads.html
Install development version from GitHub (not on CRAN yet)
install.packages("devtools")
devtools::install_github("ropensci/rif")Load rif
library('rif')out <- rif_summary("cellular")
head(out$result$federationSummary$results)#> parentCategory category db indexable
#> 1 System Level Molecule PeptideAtlas MassSpec
#> 2 Type of Data Phenotype IMPC KnockoutPhenotypes
#> 3 Type of Data Cell line Coriell Cell Repositories NIGMS
#> 4 System Level Cell Coriell Cell Repositories NIGMS
#> 5 Type of Data Expression GEO MicroarrayExperiment
#> 6 Type of Data Microarray GEO MicroarrayExperiment
#> nifId count totalCount snippets
#> 1 nif-0000-03266-2 4 76 NULL
#> 2 nlx_151660-1 2 11373 NULL
#> 3 nif-0000-00182-2 11 9854 NULL
#> 4 nif-0000-00182-2 11 9854 NULL
#> 5 nif-0000-00142-1 4340 68725 NULL
#> 6 nif-0000-00142-1 4340 68725 NULL
#> summaryString
#> 1 PeptideAtlas: MassSpec (4)[]
#> 2 IMPC: KnockoutPhenotypes (2)[]
#> 3 Coriell Cell Repositories: NIGMS (11)[]
#> 4 Coriell Cell Repositories: NIGMS (11)[]
#> 5 GEO: MicroarrayExperiment (4340)[]
#> 6 GEO: MicroarrayExperiment (4340)[]
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"
Search for vocabulary terms
vocabulary_search("cell", limit = 3)#> uuid term id category
#> 1 1bbad62f-b412-41a4-9018-e1ffd5c4b335 cell NEMO_9559000 cell
#> 2 69ca235c-b002-48d1-b0e5-6af148397f26 cell GO_0005623 cell
#> 3 3dab9b07-6a44-4822-b5cf-34dab10db8f7 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 NA
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)lexical_sentences(text)#> $sentence
#> [1] "Lorem ipsum inceptos dolor nisi torquent porttitor donec, blandit scelerisquemattis cras quis mi, aliquam sagittis."
#> [2] "Convallis placerat commodo imperdiet varius nunctempus urna vitae ultrices tristique eu mi ornare velit donec, posuere laoreet pretiumvitae porta augue porta feugiat in sapien egestas."
#> [3] "Quam odio nullam pulvinar litoracurabitur amet lacus sociosqu gravida ligula molestie dui netus fusce bibendumscelerisque, dictum malesuada proin elit etiam aliquam, mattis euismod donec nisl facilisis."
head(lexical_chunks(text))#> token start end
#> 1 Lorem ipsum inceptos 0 20
#> 2 dolor nisi torquent porttitor donec 21 56
#> 3 blandit scelerisquemattis 58 83
#> 4 cras 84 88
#> 5 quis mi 89 96
#> 6 aliquam sagittis 98 114
head(lexical_entities(text))#> token start end
#> 1 Lorem ipsum inceptos dolor 0 26
#> 2 torquent porttitor donec 32 56
#> 3 blandit scelerisquemattis 58 83
#> 4 cras 84 88
#> 5 quis mi 89 96
#> 6 aliquam sagittis . 98 115
Search
library("dplyr")
out <- literature_search(query = "cellular", count = 5)
out$result$publications %>%
select(pmid, journal, year)#> Source: local data frame [5 x 3]
#>
#> pmid
#> 1 12944235
#> 2 8789268
#> 3 2987169
#> 4 15088773
#> 5 22482413
#> Variables not shown: journal (chr), year (int)
Get retractions
out <- literature_retractions()
out[1:20]#> [1] "21386829" "16519442" "23675629" "15968000" "16934686" "10318977"
#> [7] "16373573" "22360771" "9593639" "11108151" "19723695" "18410446"
#> [13] "23551690" "17251587" "22992046" "12554767" "11146662" "8909298"
#> [19] "9503219" "11006278"
Then get info on some articles
arts <- literature_pmid(pmid = out[1:2])
lapply(arts, "[[", "title")#> [[1]]
#> [1] "Lamellar gels and spontaneous vesicles in catanionic surfactant mixtures."
#>
#> [[2]]
#> [1] "Molecular pathways underlying IBD-associated colorectal neoplasia: therapeutic implications."
Search for data
out <- federation_search("cellular")
out$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$results)#> parentCategory category db indexable
#> 1 System Level Molecule PeptideAtlas MassSpec
#> 2 Type of Data Phenotype IMPC KnockoutPhenotypes
#> 3 Type of Data Cell line Coriell Cell Repositories NIGMS
#> 4 System Level Cell Coriell Cell Repositories NIGMS
#> 5 Type of Data Expression GEO MicroarrayExperiment
#> 6 Type of Data Microarray GEO MicroarrayExperiment
#> nifId count totalCount snippets
#> 1 nif-0000-03266-2 4 76 NULL
#> 2 nlx_151660-1 2 11373 NULL
#> 3 nif-0000-00182-2 11 9854 NULL
#> 4 nif-0000-00182-2 11 9854 NULL
#> 5 nif-0000-00142-1 4340 68725 NULL
#> 6 nif-0000-00142-1 4340 68725 NULL
#> summaryString
#> 1 PeptideAtlas: MassSpec (4)[]
#> 2 IMPC: KnockoutPhenotypes (2)[]
#> 3 Coriell Cell Repositories: NIGMS (11)[]
#> 4 Coriell Cell Repositories: NIGMS (11)[]
#> 5 GEO: MicroarrayExperiment (4340)[]
#> 6 GEO: MicroarrayExperiment (4340)[]
Get some data
out <- federation_data(id = "nlx_152871-2")
out$result$result#> Source: local data frame [20 x 11]
#>
#> Gene
#> 1 nuclear receptor subfamily 1, group H, member 4
#> 2 scratch homolog 1, zinc finger protein (Drosophila)
#> 3 myogenic factor 5
#> 4 ALX homeobox 1
#> 5 frizzled homolog 6 (Drosophila)
#> 6 homeobox A3
#> 7 cadherin 11
#> 8 interleukin-1 receptor-associated kinase 1
#> 9 tumor necrosis factor receptor superfamily, member 18
#> 10 four and a half LIM domains 4
#> 11 folate receptor 1 (adult)
#> 12 syndecan 3
#> 13 fibroblast growth factor receptor 2
#> 14 IKAROS family zinc finger 2
#> 15 guanylate cyclase 1, soluble, alpha 3
#> 16 estrogen receptor 1 (alpha)
#> 17 transmembrane protein 184a
#> 18 developmental pluripotency associated 4
#> 19 mesenchyme homeobox 2
#> 20 POU domain, class 2, transcription factor 2
#> Variables not shown: 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), Source (chr)
- 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.
