General Purpose 'Oai-PMH' Services Client

A general purpose client to work with any 'OAI-PMH' (Open Archives Initiative Protocol for 'Metadata' Harvesting) service. The 'OAI-PMH' protocol is described at < http://www.openarchives.org/OAI/openarchivesprotocol.html>. Functions are provided to work with the 'OAI-PMH' verbs: 'GetRecord', 'Identify', 'ListIdentifiers', 'ListMetadataFormats', 'ListRecords', and 'ListSets'.

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. 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 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 http://oai.datacite.org/oai             2.0
#>           adminEmail    earliestDatestamp deletedRecord
#> 1 [email protected] 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 = '2011-05-01T', until = '2011-09-01T')
#> # A tibble: 889 × 6
#>                    identifier            datestamp setSpec setSpec.1
#>                         <chr>                <chr>   <chr>     <chr>
#> 1  oai:oai.datacite.org:32153 2011-06-08T08:57:11Z     TIB  TIB.WDCC
#> 2  oai:oai.datacite.org:32200 2011-06-20T08:12:41Z     TIB TIB.DAGST
#> 3  oai:oai.datacite.org:32220 2011-06-28T14:11:08Z     TIB TIB.DAGST
#> 4  oai:oai.datacite.org:32241 2011-06-30T13:24:45Z     TIB TIB.DAGST
#> 5  oai:oai.datacite.org:32255 2011-07-01T12:09:24Z     TIB TIB.DAGST
#> 6  oai:oai.datacite.org:32282 2011-07-05T09:08:10Z     TIB TIB.DAGST
#> 7  oai:oai.datacite.org:32309 2011-07-06T12:30:54Z     TIB TIB.DAGST
#> 8  oai:oai.datacite.org:32310 2011-07-06T12:42:32Z     TIB TIB.DAGST
#> 9  oai:oai.datacite.org:32325 2011-07-07T11:17:46Z     TIB TIB.DAGST
#> 10 oai:oai.datacite.org:32326 2011-07-07T11:18:47Z     TIB TIB.DAGST
#> # ... with 879 more rows, and 2 more variables: setSpec.2 <chr>,
#> #   setSpec.3 <chr>

Count Identifiers

count_identifiers()
#>                           url   count
#> 1 http://oai.datacite.org/oai 8333894

ListRecords

list_records(from = '2011-05-01T', until = '2011-08-15T')
#> # A tibble: 109 × 44
#>                    identifier            datestamp setSpec setSpec.1
#>                         <chr>                <chr>   <chr>     <chr>
#> 1  oai:oai.datacite.org:32153 2011-06-08T08:57:11Z     TIB  TIB.WDCC
#> 2  oai:oai.datacite.org:32200 2011-06-20T08:12:41Z     TIB TIB.DAGST
#> 3  oai:oai.datacite.org:32220 2011-06-28T14:11:08Z     TIB TIB.DAGST
#> 4  oai:oai.datacite.org:32241 2011-06-30T13:24:45Z     TIB TIB.DAGST
#> 5  oai:oai.datacite.org:32255 2011-07-01T12:09:24Z     TIB TIB.DAGST
#> 6  oai:oai.datacite.org:32282 2011-07-05T09:08:10Z     TIB TIB.DAGST
#> 7  oai:oai.datacite.org:32309 2011-07-06T12:30:54Z     TIB TIB.DAGST
#> 8  oai:oai.datacite.org:32310 2011-07-06T12:42:32Z     TIB TIB.DAGST
#> 9  oai:oai.datacite.org:32325 2011-07-07T11:17:46Z     TIB TIB.DAGST
#> 10 oai:oai.datacite.org:32326 2011-07-07T11:18:47Z     TIB TIB.DAGST
#> # ... with 99 more rows, and 40 more variables: title <chr>,
#> #   creator <chr>, creator.1 <chr>, creator.2 <chr>, creator.3 <chr>,
#> #   creator.4 <chr>, creator.5 <chr>, creator.6 <chr>, creator.7 <chr>,
#> #   publisher <chr>, date <chr>, identifier.2 <chr>, identifier.1 <chr>,
#> #   subject <chr>, description <chr>, description.1 <chr>,
#> #   contributor <chr>, language <chr>, type <chr>, type.1 <chr>,
#> #   format <chr>, format.1 <chr>, rights <chr>, subject.1 <chr>,
#> #   relation <chr>, subject.2 <chr>, subject.3 <chr>, subject.4 <chr>,
#> #   setSpec.2 <chr>, setSpec.3 <chr>, format.2 <chr>, subject.5 <chr>,
#> #   subject.6 <chr>, subject.7 <chr>, description.2 <chr>,
#> #   description.3 <chr>, description.4 <chr>, description.5 <chr>,
#> #   title.1 <chr>, contributor.1 <chr>

GetRecords

get_records(c("oai:oai.datacite.org:32255", "oai:oai.datacite.org:32325"))
#> # A tibble: 2 × 23
#>                   identifier            datestamp setSpec setSpec.1
#>                        <chr>                <chr>   <chr>     <chr>
#> 1 oai:oai.datacite.org:32255 2011-07-01T12:09:24Z     TIB TIB.DAGST
#> 2 oai:oai.datacite.org:32325 2011-07-07T11:17:46Z     TIB TIB.DAGST
#> # ... with 19 more variables: title <chr>, creator <chr>, creator.1 <chr>,
#> #   creator.2 <chr>, creator.3 <chr>, publisher <chr>, date <chr>,
#> #   identifier.1 <chr>, subject <chr>, subject.1 <chr>, description <chr>,
#> #   description.1 <chr>, contributor <chr>, language <chr>, type <chr>,
#> #   type.1 <chr>, format <chr>, format.1 <chr>, rights <chr>

List MetadataFormats

list_metadataformats(id = "oai:oai.datacite.org:32348")
#> $`oai:oai.datacite.org:32348`
#>   metadataPrefix
#> 1         oai_dc
#> 2       datacite
#> 3   oai_datacite
#>                                                        schema
#> 1              http://www.openarchives.org/OAI/2.0/oai_dc.xsd
#> 2 http://schema.datacite.org/meta/nonexistant/nonexistant.xsd
#> 3              http://schema.datacite.org/oai/oai-1.0/oai.xsd
#>                             metadataNamespace
#> 1 http://www.openarchives.org/OAI/2.0/oai_dc/
#> 2      http://datacite.org/schema/nonexistant
#> 3     http://schema.datacite.org/oai/oai-1.0/

List Sets

list_sets("http://oai.datacite.org/oai")
#> # A tibble: 1,651 × 2
#>                     setSpec
#>                       <chr>
#> 1                REFQUALITY
#> 2                      ANDS
#> 3           ANDS.REFQUALITY
#> 4             ANDS.CENTRE-1
#> 5  ANDS.CENTRE-1.REFQUALITY
#> 6             ANDS.CENTRE-2
#> 7  ANDS.CENTRE-2.REFQUALITY
#> 8             ANDS.CENTRE-3
#> 9  ANDS.CENTRE-3.REFQUALITY
#> 10            ANDS.CENTRE-5
#> # ... with 1,641 more rows, and 1 more variables: setName <chr>

Examples of other OAI providers

Global Biodiversity Information Facility

Identify

id("http://api.gbif.org/v1/oai-pmh/registry")
#>   repositoryName                                 baseURL protocolVersion
#> 1  GBIF Registry http://api.gbif.org/v1/oai-pmh/registry             2.0
#>     adminEmail    earliestDatestamp deletedRecord          granularity
#> 1 [email protected] 2007-01-01T00:00:01Z    persistent YYYY-MM-DDThh:mm:ssZ
#>                                                                                                                                                                                                                                                                                                                    description
#> 1 GBIF RegistryGlobal Biodiversity Information Facility Secretariat\n\t\tThe GBIF Registry — the entities that make up the GBIF network.\n\t\tThis OAI-PMH service exposes Datasets, organized into sets of country, installation and resource type.\n\t\tFor more information, see http://www.gbif.org/developer/registry\n\t

Get records

get_records(c("816f4734-6b49-41ab-8a1d-1b21e6b5486d", "95e3042f-f48d-4a04-8251-f755bebeced6"),
            url = "http://api.gbif.org/v1/oai-pmh/registry")
#> # A tibble: 2 × 28
#>                             identifier            datestamp
#>                                  <chr>                <chr>
#> 1 816f4734-6b49-41ab-8a1d-1b21e6b5486d 2016-01-28T15:36:07Z
#> 2 95e3042f-f48d-4a04-8251-f755bebeced6 2016-08-30T13:43:31Z
#> # ... with 26 more variables: setSpec <chr>, setSpec.1 <chr>,
#> #   setSpec.2 <chr>, title <chr>, publisher <chr>, identifier.1 <chr>,
#> #   source <chr>, description <chr>, description.1 <chr>, type <chr>,
#> #   language <chr>, format <chr>, source.1 <chr>, subject <chr>,
#> #   subject.1 <chr>, subject.2 <chr>, subject.3 <chr>, subject.4 <chr>,
#> #   subject.5 <chr>, description.2 <chr>, creator <chr>, creator.1 <chr>,
#> #   date <chr>, coverage <chr>, coverage.1 <chr>, coverage.2 <chr>

Biodiversity Heritage Library

Identify

id("http://www.biodiversitylibrary.org/oai")
#>                                 repositoryName
#> 1 Biodiversity Heritage Library OAI Repository
#>                                  baseURL protocolVersion
#> 1 http://www.biodiversitylibrary.org/oai             2.0
#>                    adminEmail earliestDatestamp deletedRecord granularity
#> 1 [email protected]        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")
#> # A tibble: 2 × 17
#>                           identifier            datestamp setSpec
#>                                <chr>                <chr>   <chr>
#> 1 oai:biodiversitylibrary.org:item/7 2016-07-13T08:13:41Z    item
#> 2 oai:biodiversitylibrary.org:item/9 2016-07-13T08:13:41Z    item
#> # ... with 14 more variables: title <chr>, creator <chr>, subject <chr>,
#> #   subject.1 <chr>, subject.2 <chr>, description <chr>, publisher <chr>,
#> #   contributor <chr>, date <chr>, type <chr>, type.1 <chr>,
#> #   identifier.1 <chr>, language <chr>, rights <chr>

News

oai 0.2.2

NEW FEATURES

Added new parsers in get_records() specific to different OAI prefixes. Currently has parsers for oai_dc and oai_datacite. For prefixes we don't have parsers for we return raw XML so you can parse it yourself. (#45)

MINOR IMPROVEMENTS

Replace xml2::xml_find_one() with xml2::xml_find_first() (#39)
Update URLs in DESCRIPTION file (#43)
Using tibble now for compact data.frame instead of internal methods for the same (#44)
as parameter in get_records() now has options parsed or raw, which replaces df list, or raw

oai 0.2.0

NEW FEATURES

A set of new functions for dealing with larger data results: dump_raw_to_txt(), dump_to_rds(), and dump_raw_to_db(). They can be used with oai functions list_identifiers(), list_sets(), and list_records() (#9) (#15) (#21) thanks @mbojan

MINOR IMPROVEMENTS

Sped up some tests (#19)
Better description of OAI protocol in the DESCRIPTION file (#28)
Commented about where some internal functions come from (#31)
Import plyr for rbind.fill() (#32)
Including now some examples using OAI-PMH with GBIF and BHL (#33)
Better error handling! (#10) (#12) (#22) (#27) thanks @mbojan

BUG FIXES

Fixed bug where list_identifiers() threw error when no result was found (#13)
Dealing better with bad inputs to as parameter - stop with informative message now instead of failing without anything returned (#34)