oai: General Purpose ‘Oai-PMH’ Services Client
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 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:12425ListIdentifiers
list_identifiers(from = '2018-05-01T', until = '2018-06-01T')
#> # A tibble: 75 × 5
#> identifier datestamp setSpec setSp…¹ setSp…²
#> <chr> <chr> <chr> <chr> <chr>
#> 1 4b64d1f2-31c2-40c9-80aa-bb7ddb424684 2018-05-30T13:5… instal… datase… countr…
#> 2 884378d6-d591-4760-bb70-7b4851784d96 2018-05-29T19:1… instal… datase… countr…
#> 3 18799ce9-1a66-40fc-ad18-5ac54cd3417b 2018-05-14T12:1… instal… datase… countr…
#> 4 7e91aacb-c994-41ee-a7b7-bd23c02cd5bf 2018-05-21T10:5… instal… datase… countr…
#> 5 f83746ee-4cf2-4e60-a720-dd508b559794 2018-05-08T09:4… instal… datase… countr…
#> 6 a3533a61-6f88-443e-89ae-37611ea88267 2018-05-08T13:5… instal… datase… countr…
#> 7 ba9b66a3-2d11-4193-922e-ace4d5909239 2018-05-05T23:5… instal… datase… countr…
#> 8 78b696d9-8f0d-41ab-9c23-1c3547da411d 2018-05-05T23:0… instal… datase… countr…
#> 9 c791b255-a184-4600-b828-ef9d4092a212 2018-05-05T14:2… instal… datase… countr…
#> 10 b929ccda-03b1-4166-9e5b-34588339d61d 2018-05-09T02:5… instal… datase… countr…
#> # … with 65 more rows, and abbreviated variable names ¹setSpec.1, ²setSpec.2Count Identifiers
count_identifiers()
#> url count
#> 1 http://export.arxiv.org/oai2 2158148ListRecords
list_records(from = '2018-05-01T', until = '2018-05-15T')
#> # A tibble: 41 × 26
#> identi…¹ dates…² setSpec setSp…³ setSp…⁴ title publi…⁵ ident…⁶ subject source
#> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
#> 1 18799ce… 2018-0… instal… datase… countr… Bird… Sokoin… https:… Occurr… ""
#> 2 f83746e… 2018-0… instal… datase… countr… NDFF… Dutch … https:… Metada… "http…
#> 3 a3533a6… 2018-0… instal… datase… countr… EDP … EDP - … https:… Occurr… ""
#> 4 ba9b66a… 2018-0… instal… datase… countr… Ende… Sokoin… https:… Occurr… ""
#> 5 78b696d… 2018-0… instal… datase… countr… Ende… Sokoin… https:… Occurr… ""
#> 6 c791b25… 2018-0… instal… datase… countr… Ende… Sokoin… https:… Occurr… ""
#> 7 b929ccd… 2018-0… instal… datase… countr… List… Sokoin… https:… Occurr… ""
#> 8 da285c2… 2018-0… instal… datase… countr… Moni… Corpor… https:… seguim… ""
#> 9 8737287… 2018-0… instal… datase… countr… Moni… Corpor… https:… seguim… ""
#> 10 ed7d4c2… 2018-0… instal… datase… countr… Samo… Minist… https:… Occurr… ""
#> # … with 31 more rows, 16 more variables: 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>, creator.1 <chr>, coverage.2 <chr>, description.2 <chr>,
#> # creator.2 <chr>, subject.2 <chr>, and abbreviated variable names
#> # ¹identifier, ²datestamp, ³setSpec.1, ⁴setSpec.2, ⁵publisher, ⁶identifier.1GetRecords
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 × 3
#> identifier datestamp setSpec
#> <chr> <chr> <chr>
#> 1 87832186-00ea-44dd-a6bf-c2896c4d09b4 2018-06-29T12:08:17Z installation:729a73…
#>
#> $`87832186-00ea-44dd-a6bf-c2896c4d09b4`$metadata
#> # A tibble: 0 × 0
#>
#>
#> $`d981c07d-bc43-40a2-be1f-e786e25106ac`
#> $`d981c07d-bc43-40a2-be1f-e786e25106ac`$header
#> # A tibble: 1 × 3
#> identifier datestamp setSpec
#> <chr> <chr> <chr>
#> 1 d981c07d-bc43-40a2-be1f-e786e25106ac 2021-09-28T13:58:57Z installation:804b8d…
#>
#> $`d981c07d-bc43-40a2-be1f-e786e25106ac`$metadata
#> # A tibble: 1 × 12
#> title publi…¹ ident…² subject source descr…³ type creator date langu…⁴
#> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
#> 1 Peces de l… Instit… https:… Occurr… http:… Caract… Data… Fernan… 2021… es
#> # … with 2 more variables: coverage <chr>, format <chr>, and abbreviated
#> # variable names ¹publisher, ²identifier, ³description, ⁴languageList 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-2.1.1List Sets
list_sets("http://api.gbif.org/v1/oai-pmh/registry")
#> # A tibble: 621 × 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:AM Armenia
#> 9 country:AO Angola
#> 10 country:AQ Antarctica
#> # … with 611 more rowsExamples 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/1000Get 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 × 3
#> identifier datestamp setSpec
#> <chr> <chr> <chr>
#> 1 oai:biodiversitylibrary.org:item/7 2016-01-26T06:05:19Z item
#>
#> $`oai:biodiversitylibrary.org:item/7`$metadata
#> # A tibble: 1 × 11
#> title creator subject descr…¹ publi…² contr…³ type ident…⁴ langu…⁵ relat…⁶
#> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
#> 1 Die Mus… Fleisc… Bogor;… pt.5:v… Leiden… Missou… text… https:… Dutch https:…
#> # … with 1 more variable: rights <chr>, and abbreviated variable names
#> # ¹description, ²publisher, ³contributor, ⁴identifier, ⁵language, ⁶relation
#>
#>
#> $`oai:biodiversitylibrary.org:item/9`
#> $`oai:biodiversitylibrary.org:item/9`$header
#> # A tibble: 1 × 3
#> identifier datestamp setSpec
#> <chr> <chr> <chr>
#> 1 oai:biodiversitylibrary.org:item/9 2016-01-26T06:05:19Z item
#>
#> $`oai:biodiversitylibrary.org:item/9`$metadata
#> # A tibble: 1 × 11
#> title creator subject descr…¹ publi…² contr…³ type ident…⁴ langu…⁵ relat…⁶
#> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
#> 1 Die Mus… Fleisc… Bogor;… pt.5:v… Leiden… Missou… text… https:… Dutch https:…
#> # … with 1 more variable: rights <chr>, and abbreviated variable names
#> # ¹description, ²publisher, ³contributor, ⁴identifier, ⁵language, ⁶relationAcknowledgements
Michał 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
oaiin R doingcitation(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.