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README.md

Project Status: Active – The project has reached a stable, usable state and is being actively developed. Build Status Build status cran checks codecov.io rstudio mirror downloads cran version

oai is an R client to work with OAI-PMH (Open Archives Initiative Protocol for Metadata Harvesting) services, a protocol developed by the Open Archives Initiative (https://en.wikipedia.org/wiki/Open_Archives_Initiative). OAI-PMH uses XML data format transported over HTTP.

OAI-PMH Info:

oai is built on xml2 and httr. In addition, we give back data.frame's whenever possible to make data comprehension, manipulation, and visualization easier. We also have functions to fetch a large directory of OAI-PMH services - it isn't exhaustive, but does contain a lot.

OAI-PMH instead of paging with e.g., page and per_page parameters, uses (optionally) resumptionTokens, optionally with an expiration date. These tokens can be used to continue on to the next chunk of data, if the first request did not get to the end. Often, OAI-PMH services limit each request to 50 records, but this may vary by provider, I don't know for sure. The API of this package is such that we while loop for you internally until we get all records. We may in the future expose e.g., a limit parameter so you can say how many records you want, but we haven't done this yet.

Install

Install from CRAN

install.packages("oai")

Development version

devtools::install_github("ropensci/oai")
library("oai")

Identify

id("http://oai.datacite.org/oai")
#>   repositoryName                      baseURL protocolVersion
#> 1       DataCite https://oai.datacite.org/oai             2.0
#>             adminEmail    earliestDatestamp deletedRecord          granularity
#> 1 support@datacite.org 2011-01-01T00:00:00Z    persistent YYYY-MM-DDThh:mm:ssZ
#>   compression compression.1                                    description
#> 1        gzip       deflate oaioai.datacite.org:oai:oai.datacite.org:12425

ListIdentifiers

list_identifiers(from = '2018-05-01T', until = '2018-06-01T')
#> # A tibble: 249 x 5
#>    identifier          datestamp     setSpec             setSpec.1     setSpec.2
#>    <chr>               <chr>         <chr>               <chr>         <chr>    
#>  1 cf7fbc99-de82-41a5… 2018-05-31T1… installation:791e3… dataset_type… country:…
#>  2 09d5405e-ca86-45f2… 2018-05-30T1… installation:804b8… dataset_type… country:…
#>  3 4b64d1f2-31c2-40c9… 2018-05-30T1… installation:804b8… dataset_type… country:…
#>  4 884378d6-d591-4760… 2018-05-29T1… installation:a1650… dataset_type… country:…
#>  5 772de164-541d-4db6… 2018-05-22T1… installation:68845… dataset_type… country:…
#>  6 9d022797-7aa4-40f4… 2018-05-18T1… installation:73ebc… dataset_type… country:…
#>  7 18799ce9-1a66-40fc… 2018-05-14T1… installation:d1b0a… dataset_type… country:…
#>  8 7e91aacb-c994-41ee… 2018-05-21T1… installation:d5b61… dataset_type… country:…
#>  9 79f51633-b5e8-47c5… 2018-05-11T0… installation:68845… dataset_type… country:…
#> 10 56c48715-9f8b-445a… 2018-05-15T1… installation:73ebc… dataset_type… country:…
#> # … with 239 more rows

Count Identifiers

count_identifiers()
#>                            url   count
#> 1 http://export.arxiv.org/oai2 1586724

ListRecords

list_records(from = '2018-05-01T', until = '2018-05-15T')
#> # A tibble: 44 x 26
#>    identifier datestamp setSpec setSpec.1 setSpec.2 title publisher identifier.1
#>    <chr>      <chr>     <chr>   <chr>     <chr>     <chr> <chr>     <chr>       
#>  1 18799ce9-… 2018-05-… instal… dataset_… country:… Bird… Sokoine … https://www…
#>  2 79f51633-… 2018-05-… instal… dataset_… country:… Impl… Aïgos SAS https://www…
#>  3 f83746ee-… 2018-05-… instal… dataset_… country:… NDFF… Dutch Na… https://www…
#>  4 a3533a61-… 2018-05-… instal… dataset_… country:… EDP … EDP - En… https://www…
#>  5 ba9b66a3-… 2018-05-… instal… dataset_… country:… Ende… Sokoine … https://www…
#>  6 78b696d9-… 2018-05-… instal… dataset_… country:… Ende… Sokoine … https://www…
#>  7 c791b255-… 2018-05-… instal… dataset_… country:… Ende… Sokoine … https://www…
#>  8 b929ccda-… 2018-05-… instal… dataset_… country:… List… Sokoine … https://www…
#>  9 da285c2a-… 2018-05-… instal… dataset_… country:… Moni… Corporac… https://www…
#> 10 87372877-… 2018-05-… instal… dataset_… country:… Moni… Corporac… https://www…
#> # … with 34 more rows, and 18 more variables: subject <chr>, source <chr>,
#> #   description <chr>, description.1 <chr>, type <chr>, creator <chr>,
#> #   date <chr>, language <chr>, coverage <chr>, coverage.1 <chr>, format <chr>,
#> #   source.1 <chr>, subject.1 <chr>, coverage.2 <chr>, creator.1 <chr>,
#> #   description.2 <chr>, creator.2 <chr>, subject.2 <chr>

GetRecords

ids <- c("87832186-00ea-44dd-a6bf-c2896c4d09b4", "d981c07d-bc43-40a2-be1f-e786e25106ac")
get_records(ids)
#> $`87832186-00ea-44dd-a6bf-c2896c4d09b4`
#> $`87832186-00ea-44dd-a6bf-c2896c4d09b4`$header
#> # A tibble: 1 x 3
#>   identifier              datestamp      setSpec                                
#>   <chr>                   <chr>          <chr>                                  
#> 1 87832186-00ea-44dd-a6b… 2018-06-29T12… installation:729a7375-b120-4e4f-bb81-a…
#> 
#> $`87832186-00ea-44dd-a6bf-c2896c4d09b4`$metadata
#> # A tibble: 0 x 0
#> 
#> 
#> $`d981c07d-bc43-40a2-be1f-e786e25106ac`
#> $`d981c07d-bc43-40a2-be1f-e786e25106ac`$header
#> # A tibble: 1 x 3
#>   identifier              datestamp      setSpec                                
#>   <chr>                   <chr>          <chr>                                  
#> 1 d981c07d-bc43-40a2-be1… 2018-01-21T21… installation:804b8dd0-07ac-4a30-bf92-3…
#> 
#> $`d981c07d-bc43-40a2-be1f-e786e25106ac`$metadata
#> # A tibble: 1 x 12
#>   title publisher identifier subject source description type  creator date 
#>   <chr> <chr>     <chr>      <chr>   <chr>  <chr>       <chr> <chr>   <chr>
#> 1 Pece… Institut… https://w… peces,… http:… Caracteriz… Data… Fernan… 2018…
#> # … with 3 more variables: language <chr>, coverage <chr>, format <chr>

List MetadataFormats

list_metadataformats(id = "87832186-00ea-44dd-a6bf-c2896c4d09b4")
#> $`87832186-00ea-44dd-a6bf-c2896c4d09b4`
#>   metadataPrefix                                                   schema
#> 1         oai_dc           http://www.openarchives.org/OAI/2.0/oai_dc.xsd
#> 2            eml http://rs.gbif.org/schema/eml-gbif-profile/1.0.2/eml.xsd
#>                             metadataNamespace
#> 1 http://www.openarchives.org/OAI/2.0/oai_dc/
#> 2          eml://ecoinformatics.org/eml-2.1.1

List Sets

list_sets("http://api.gbif.org/v1/oai-pmh/registry")
#> # A tibble: 582 x 2
#>    setSpec                     setName         
#>    <chr>                       <chr>           
#>  1 dataset_type                per dataset type
#>  2 dataset_type:OCCURRENCE     occurrence      
#>  3 dataset_type:CHECKLIST      checklist       
#>  4 dataset_type:METADATA       metadata        
#>  5 dataset_type:SAMPLING_EVENT sampling_event  
#>  6 country                     per country     
#>  7 country:AD                  Andorra         
#>  8 country:AO                  Angola          
#>  9 country:AR                  Argentina       
#> 10 country:AT                  Austria         
#> # … with 572 more rows

Examples of other OAI providers

Biodiversity Heritage Library

Identify

id("http://www.biodiversitylibrary.org/oai")
#>                                 repositoryName
#> 1 Biodiversity Heritage Library OAI Repository
#>                                   baseURL protocolVersion
#> 1 https://www.biodiversitylibrary.org/oai             2.0
#>                    adminEmail earliestDatestamp deletedRecord granularity
#> 1 oai@biodiversitylibrary.org        2006-01-01            no  YYYY-MM-DD
#>                                                        description
#> 1 oaibiodiversitylibrary.org:oai:biodiversitylibrary.org:item/1000

Get records

get_records(c("oai:biodiversitylibrary.org:item/7", "oai:biodiversitylibrary.org:item/9"),
            url = "http://www.biodiversitylibrary.org/oai")
#> $`oai:biodiversitylibrary.org:item/7`
#> $`oai:biodiversitylibrary.org:item/7`$header
#> # A tibble: 1 x 3
#>   identifier                         datestamp            setSpec
#>   <chr>                              <chr>                <chr>  
#> 1 oai:biodiversitylibrary.org:item/7 2016-07-13T09:13:41Z item   
#> 
#> $`oai:biodiversitylibrary.org:item/7`$metadata
#> # A tibble: 1 x 11
#>   title creator subject description publisher contributor date  type  identifier
#>   <chr> <chr>   <chr>   <chr>       <chr>     <chr>       <chr> <chr> <chr>     
#> 1 Die … Fleisc… Bogor;… pt.5:v.1 (… Leiden :… Missouri B… 1900  text… https://w…
#> # … with 2 more variables: language <chr>, rights <chr>
#> 
#> 
#> $`oai:biodiversitylibrary.org:item/9`
#> $`oai:biodiversitylibrary.org:item/9`$header
#> # A tibble: 1 x 3
#>   identifier                         datestamp            setSpec
#>   <chr>                              <chr>                <chr>  
#> 1 oai:biodiversitylibrary.org:item/9 2016-07-13T09:13:41Z item   
#> 
#> $`oai:biodiversitylibrary.org:item/9`$metadata
#> # A tibble: 1 x 11
#>   title creator subject description publisher contributor date  type  identifier
#>   <chr> <chr>   <chr>   <chr>       <chr>     <chr>       <chr> <chr> <chr>     
#> 1 Die … Fleisc… Bogor;… pt.5:v.3 (… Leiden :… Missouri B… 1906  text… https://w…
#> # … with 2 more variables: language <chr>, rights <chr>

Acknowledgements

Michal Bojanowski thanks National Science Centre for support through grant 2012/07/D/HS6/01971.

Meta

  • Please report any issues or bugs.
  • License: MIT
  • Get citation information for oai in R doing citation(package = 'oai')
  • 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.

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