oai package - RDocumentation

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:

Wikipedia (https://en.wikipedia.org/wiki/Open_Archives_Initiative_Protocol_for_Metadata_Harvesting)
OAI V2 specification (http://www.openarchives.org/OAI/openarchivesprotocol.html)

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 MDS https://oai.datacite.org/oai             2.0
#>             adminEmail    earliestDatestamp deletedRecord
#> 1 support@datacite.org 2011-01-01T00:00:00Z    persistent
#>            granularity compression compression.1
#> 1 YYYY-MM-DDThh:mm:ssZ        gzip       deflate
#>                                      description
#> 1 oaioai.datacite.org:oai:oai.datacite.org:12425

ListIdentifiers

list_identifiers(from = '2018-05-01T', until = '2018-06-01T')
#> # A tibble: 255 x 5
#>    identifier        datestamp    setSpec            setSpec.1    setSpec.2
#>    <chr>             <chr>        <chr>              <chr>        <chr>
#>  1 cf7fbc99-de82-41… 2018-05-31T… installation:791e… dataset_typ… country:…
#>  2 cf7d6c01-309b-45… 2018-05-30T… installation:394c… dataset_typ… country:…
#>  3 cca13f2c-0d2c-4c… 2018-05-30T… installation:394c… dataset_typ… country:…
#>  4 09d5405e-ca86-45… 2018-05-30T… installation:804b… dataset_typ… country:…
#>  5 4b64d1f2-31c2-40… 2018-05-30T… installation:804b… dataset_typ… country:…
#>  6 884378d6-d591-47… 2018-05-29T… installation:a165… dataset_typ… country:…
#>  7 a0b06e2e-287a-46… 2018-05-31T… installation:4c5f… dataset_typ… country:…
#>  8 772de164-541d-4d… 2018-05-22T… installation:6884… dataset_typ… country:…
#>  9 f1a4ce9a-97cd-4d… 2018-05-21T… installation:394c… dataset_typ… country:…
#> 10 9d022797-7aa4-40… 2018-05-18T… installation:73eb… dataset_typ… country:…
#> # … with 245 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
#>    <chr>      <chr>     <chr>   <chr>     <chr>     <chr> <chr>
#>  1 18799ce9-… 2018-05-… instal… dataset_… country:… Bird… Sokoine …
#>  2 79f51633-… 2018-05-… instal… dataset_… country:… Impl… Aïgos SAS
#>  3 f83746ee-… 2018-05-… instal… dataset_… country:… NDFF… Dutch Na…
#>  4 a3533a61-… 2018-05-… instal… dataset_… country:… EDP … EDP - En…
#>  5 ba9b66a3-… 2018-05-… instal… dataset_… country:… Ende… Sokoine …
#>  6 78b696d9-… 2018-05-… instal… dataset_… country:… Ende… Sokoine …
#>  7 c791b255-… 2018-05-… instal… dataset_… country:… Ende… Sokoine …
#>  8 b929ccda-… 2018-05-… instal… dataset_… country:… List… Sokoine …
#>  9 da285c2a-… 2018-05-… instal… dataset_… country:… Moni… Corporac…
#> 10 87372877-… 2018-05-… instal… dataset_… country:… Moni… Corporac…
#> # … with 34 more rows, and 19 more variables: identifier.1 <chr>,
#> #   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-a6… 2018-06-29T12… installation:729a7375-b120-4e4f-bb…
#>
#> $`87832186-00ea-44dd-a6bf-c2896c4d09b4`$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-be… 2018-01-21T21… installation:804b8dd0-07ac-4a30-bf…
#>
#> $`d981c07d-bc43-40a2-be1f-e786e25106ac`$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: 572 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 562 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
#>   <chr> <chr>   <chr>   <chr>       <chr>     <chr>       <chr> <chr>
#> 1 Die … Fleisc… Bogor;… pt.5:v.1 (… Leiden :… Missouri B… 1900… text…
#> # … with 3 more variables: identifier <chr>, 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
#>   <chr> <chr>   <chr>   <chr>       <chr>     <chr>       <chr> <chr>
#> 1 Die … Fleisc… Bogor;… pt.5:v.3 (… Leiden :… Missouri B… 1906… text…
#> # … with 3 more variables: identifier <chr>, language <chr>, rights <chr>

Acknowledgements

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

Install

Identify

ListIdentifiers

Count Identifiers

ListRecords

GetRecords

List MetadataFormats

List Sets

Examples of other OAI providers

Biodiversity Heritage Library

Acknowledgements

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Functions in oai (0.3.0)