Nothing
In rif: Client for 'Neuroscience' Information Framework 'APIs'
Introduction to the rif package
rif is an R wrapper for the Neuroscience Information Framework (NIF) APIs.
- API docs at https://neuinfo.org/about/webservices
Install
Stable rif version from CRAN
install.packages("rif")
Or, the development version from Github
devtools::install_github("ropensci/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 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
literature_search(query = "cellular", count = 5)
#> $result
#> $result$publications
#> # A tibble: 5 x 18
#> pmid pmcid
#> * <chr> <lgl>
#> 1 12944235 NA
#> 2 27417120 NA
#> 3 8789268 NA
#> 4 2987169 NA
#> 5 15088773 NA
#> # ... with 16 more variables: title <chr>, authors <list>,
#> # grantIds <list>, grantAgencies <list>, retractions <list>,
#> # journal <chr>, journalShort <chr>, day <int>, month <int>, year <int>,
#> # meshHeadings <list>, hasAbstract <lgl>, score <dbl>, snippets <list>,
#> # abstract <chr>, affiliation <list>
#>
#> $result$facets
#> list()
#>
#> $result$debugInfo
#> [1] "title_exact:cellular^20.0 grantId:cellular^20.0 journal:cellular meshHeading:cellular^7.0 author:cellular^3.0 pmcid_search:cellular^10.0 year_search:cellular^10.0 abstract:cellular^5.0 pmid_search:cellular^10.0 title:cellular^10.0 abstract_exact:cellular^10.0"
#>
#> $result$resultCount
#> [1] 816438
#>
#> $result$offset
#> [1] 0
#>
#>
#> $query
#> $query$clauses
#> category property query expansion id quoted require forbid
#> 1 NA NA cellular NULL NA FALSE FALSE FALSE
#>
#> $query$operator
#> [1] "AND"
#>
#>
#> $messages
#> list()
Get retractions
out <- literature_retractions()
out[1:20]
#> [1] "12768027" "11167165" "22576713" "17973093" "10050223" "21613570"
#> [7] "12438313" "22364277" "26214776" "10784445" "17519423" "21177250"
#> [13] "23745088" "26009721" "1824564" "15260988" "20656892" "1400454"
#> [19] "12200953" "22893106"
Then get info on some articles
arts <- literature_pmid(pmid = out[1:2])
lapply(arts, "[[", "title")
#> [[1]]
#> [1] "Basic residues of the helix six domain of influenza virus M1 involved in nuclear translocation of M1 can be replaced by PTAP and YPDL late assembly domain motifs."
#>
#> [[2]]
#> [1] "Point-of-care (POC) testing of lactate in the intensive care patient. Accuracy, reliability, and costs of different measurement systems."
Data
Search for data
out <- federation_search("cellular")
out$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$results)
#> parentCategory category db indexable
#> 1 Category Expression Barres Brain RNA-Seq ExpressionData
#> 2 Output Type Data or Model Barres Brain RNA-Seq ExpressionData
#> 3 Category Cell Barres Brain RNA-Seq ExpressionData
#> 4 Category Gene Barres Brain RNA-Seq ExpressionData
#> 5 Output Type Information PubMed Health Drug
#> 6 Category Molecule PubMed Health Drug
#> nifId count totalCount snippets
#> 1 scr_013736-2 9 22458 NULL
#> 2 scr_013736-2 9 22458 NULL
#> 3 scr_013736-2 9 22458 NULL
#> 4 scr_013736-2 9 22458 NULL
#> 5 nlx_32805-3 2 19179 NULL
#> 6 nlx_32805-3 2 19179 NULL
#> summaryString
#> 1 Barres Brain RNA-Seq: ExpressionData (9)[]
#> 2 Barres Brain RNA-Seq: ExpressionData (9)[]
#> 3 Barres Brain RNA-Seq: ExpressionData (9)[]
#> 4 Barres Brain RNA-Seq: ExpressionData (9)[]
#> 5 PubMed Health: Drug (2)[]
#> 6 PubMed Health: Drug (2)[]
Get some data
out <- federation_data(id = "nlx_152871-2")
out$result$result
#> # A tibble: 20 x 12
#> Gene
#> <chr>
#> 1 tyrosine hydroxylase
#> 2 maternally expressed 3
#> 3 G protein-coupled receptor 37
#> 4 TANK-binding kinase 1
#> 5 zinc finger, ZZ domain containing 3
#> 6 deleted in azoospermia-like
#> 7 forkhead box A2
#> 8 phospholipase A2, group IIF
#> 9 homeobox C5
#> 10 GATA binding protein 4
#> 11 sal-like 4 (Drosophila)
#> 12 nitric oxide synthase 1, neuronal
#> 13 RIKEN cDNA C130073F10 gene
#> 14 choline acetyltransferase
#> 15 cystatin 12
#> 16 ash1 (absent, small, or homeotic)-like (Drosophila)
#> 17 neurogenic differentiation 4
#> 18 developing brain homeobox 2
#> 19 zinc finger and SCAN domain containing 22
#> 20 Nanog homeobox
#> # ... with 11 more variables: Anatomical.Component <chr>,
#> # Assay.Type <chr>, Theiler.Stage <chr>, Tissue <chr>,
#> # Expression.Strength <chr>, Expression.Pattern <chr>,
#> # Expression.Pattern.Location <chr>, Authors <chr>, Notes <chr>,
#> # v_uuid <chr>, Source <chr>
Try the rif package in your browser
Any scripts or data that you put into this service are public.
rif documentation built on May 2, 2019, 5:54 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Introduction to the rif package
rif is an R wrapper for the Neuroscience Information Framework (NIF) APIs.
- API docs at https://neuinfo.org/about/webservices
Install
Stable rif version from CRAN
install.packages("rif")
Or, the development version from Github
devtools::install_github("ropensci/rif")
library("rif")
Summary
out <- rif_summary("cellular") head(out$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 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
literature_search(query = "cellular", count = 5) #> $result #> $result$publications #> # A tibble: 5 x 18 #> pmid pmcid #> * <chr> <lgl> #> 1 12944235 NA #> 2 27417120 NA #> 3 8789268 NA #> 4 2987169 NA #> 5 15088773 NA #> # ... with 16 more variables: title <chr>, authors <list>, #> # grantIds <list>, grantAgencies <list>, retractions <list>, #> # journal <chr>, journalShort <chr>, day <int>, month <int>, year <int>, #> # meshHeadings <list>, hasAbstract <lgl>, score <dbl>, snippets <list>, #> # abstract <chr>, affiliation <list> #> #> $result$facets #> list() #> #> $result$debugInfo #> [1] "title_exact:cellular^20.0 grantId:cellular^20.0 journal:cellular meshHeading:cellular^7.0 author:cellular^3.0 pmcid_search:cellular^10.0 year_search:cellular^10.0 abstract:cellular^5.0 pmid_search:cellular^10.0 title:cellular^10.0 abstract_exact:cellular^10.0" #> #> $result$resultCount #> [1] 816438 #> #> $result$offset #> [1] 0 #> #> #> $query #> $query$clauses #> category property query expansion id quoted require forbid #> 1 NA NA cellular NULL NA FALSE FALSE FALSE #> #> $query$operator #> [1] "AND" #> #> #> $messages #> list()
Get retractions
out <- literature_retractions() out[1:20] #> [1] "12768027" "11167165" "22576713" "17973093" "10050223" "21613570" #> [7] "12438313" "22364277" "26214776" "10784445" "17519423" "21177250" #> [13] "23745088" "26009721" "1824564" "15260988" "20656892" "1400454" #> [19] "12200953" "22893106"
Then get info on some articles
arts <- literature_pmid(pmid = out[1:2]) lapply(arts, "[[", "title") #> [[1]] #> [1] "Basic residues of the helix six domain of influenza virus M1 involved in nuclear translocation of M1 can be replaced by PTAP and YPDL late assembly domain motifs." #> #> [[2]] #> [1] "Point-of-care (POC) testing of lactate in the intensive care patient. Accuracy, reliability, and costs of different measurement systems."
Data
Search for data
out <- federation_search("cellular") out$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$results) #> parentCategory category db indexable #> 1 Category Expression Barres Brain RNA-Seq ExpressionData #> 2 Output Type Data or Model Barres Brain RNA-Seq ExpressionData #> 3 Category Cell Barres Brain RNA-Seq ExpressionData #> 4 Category Gene Barres Brain RNA-Seq ExpressionData #> 5 Output Type Information PubMed Health Drug #> 6 Category Molecule PubMed Health Drug #> nifId count totalCount snippets #> 1 scr_013736-2 9 22458 NULL #> 2 scr_013736-2 9 22458 NULL #> 3 scr_013736-2 9 22458 NULL #> 4 scr_013736-2 9 22458 NULL #> 5 nlx_32805-3 2 19179 NULL #> 6 nlx_32805-3 2 19179 NULL #> summaryString #> 1 Barres Brain RNA-Seq: ExpressionData (9)[] #> 2 Barres Brain RNA-Seq: ExpressionData (9)[] #> 3 Barres Brain RNA-Seq: ExpressionData (9)[] #> 4 Barres Brain RNA-Seq: ExpressionData (9)[] #> 5 PubMed Health: Drug (2)[] #> 6 PubMed Health: Drug (2)[]
Get some data
out <- federation_data(id = "nlx_152871-2") out$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>
Try the rif package in your browser
Any scripts or data that you put into this service are public.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.