Scholarly metadata from R
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Metadata! Metadata is very cool. It’s super hot right now – everybody is talking about it. Okay, maybe not everyone, but it’s an important part of archiving scholarly work.
We are working on a repo on GitHub rmetadata to be a one stop shop for querying metadata from around the web. Various repos on GitHub we have started – rpmc, rdatacite, rdryad, rpensoft, rhindawi – will at least in part be folded into rmetadata.
As a start we are writing functions to hit any metadata services that use the OAI-PMH: “Open Archives Initiative Protocol for Metadata Harvesting” framework. OAI-PMH has six methods (or verbs as they are called) for data harvesting that are the same across different metadata providers:
GetRecordIdentifyListIdentifiersListMetadataFormatsListRecordsListSets
OAI-PMH provides an updating list of data providers, which we can easily use to get the base URLs for their data. Then we just use one of the six above methods to query their metadata.
Let’s install rmetadata first.
install_github("rmetadata", "ropensci")
library(rmetadata)
The most basic thing you can do with OAI-PMH is identify the data provider, getting their basic information. The Identify verb.
# one provider
md_identify(provider = "datacite")
repositoryName baseURL protocolVersion
1 DataCite MDS http://oai.datacite.org/oai 2.0
adminEmail earliestDatestamp deletedRecord
1 [email protected] 2011-01-01T00:00:00Z no
granularity compression compression.1
1 YYYY-MM-DDThh:mm:ssZ gzip deflate
description
1 oai, oai.datacite.org, :, oai:oai.datacite.org:12425, http://www.openarchives.org/OAI/2.0/oai-identifier http://www.openarchives.org/OAI/2.0/oai-identifier.xsd
# many providers
md_identify(provider = c("datacite", "pensoft"))
repositoryName baseURL protocolVersion
1 DataCite MDS http://oai.datacite.org/oai 2.0
2 Pensoft Publishers http://oai.pensoft.eu 2.0
adminEmail earliestDatestamp deletedRecord
1 [email protected] 2011-01-01T00:00:00Z no
2 NULL 2008-07-04 no
granularity compression compression.1
1 YYYY-MM-DDThh:mm:ssZ gzip deflate
2 YYYY-MM-DD NULL NULL
description
1 oai, oai.datacite.org, :, oai:oai.datacite.org:12425, http://www.openarchives.org/OAI/2.0/oai-identifier http://www.openarchives.org/OAI/2.0/oai-identifier.xsd
2 NULL
# no match for one, two matches for other
md_identify(provider = c("harvard", "journal"))
$harvard
x
1 no match found
$journal
repo_name
1 Hrcak - Portal of scientific journals of Croatia
2 International journal of Power Electronics Engineering
# let's pick one from the second
md_identify(provider = "Hrcak")
repositoryName
1 Hrcak - Portal of scientific journals of Croatia
baseURL protocolVersion adminEmail
1 http://hrcak.srce.hr/oai/ 2.0 [email protected]
earliestDatestamp deletedRecord granularity
1 2005-12-01 no YYYY-MM-DD
description
1 oai, hrcak.srce.hr, :, oai:hrcak.srce.hr:anIdentifier, http://www.openarchives.org/OAI/2.0/oai-identifier http://www.openarchives.org/OAI/2.0/oai-identifier.xsd
There are a variety of metadata formats, depending on the data provider – list them with the ListMetadataFormats verb.
# List metadata formats for a provider
md_listmetadataformats(provider = "dryad")
metadataPrefix
1 oai_dc
2 rdf
3 ore
4 mets
schema
1 http://www.openarchives.org/OAI/2.0/oai_dc.xsd
2 http://www.openarchives.org/OAI/2.0/rdf.xsd
3 http://tweety.lanl.gov/public/schemas/2008-06/atom-tron.sch
4 http://www.loc.gov/standards/mets/mets.xsd
metadataNamespace
1 http://www.openarchives.org/OAI/2.0/oai_dc/
2 http://www.openarchives.org/OAI/2.0/rdf/
3 http://www.w3.org/2005/Atom
4 http://www.loc.gov/METS/
# List metadata formats for a specific identifier for a provider
md_listmetadataformats(provider = "pensoft", identifier = "10.3897/zookeys.1.10")
identifier metadataPrefix
1 10.3897/zookeys.1.10 oai_dc
2 10.3897/zookeys.1.10 mods
schema
1 http://www.openarchives.org/OAI/2.0/oai_dc.xsd
2 http://www.loc.gov/standards/mods/v3/mods-3-1.xsd
metadataNamespace
1 http://www.openarchives.org/OAI/2.0/oai_dc/
2 http://www.loc.gov/mods/v3
The ListRecords verb is used to harvest records from a repository
head(md_listrecords(provider = "datacite")[[1]][, 2:4])
identifier datestamp setSpec
1 oai:oai.datacite.org:32153 2011-06-08T08:57:11Z TIB
2 oai:oai.datacite.org:32200 2011-06-20T08:11:08Z TIB
3 oai:oai.datacite.org:32220 2011-06-28T14:11:08Z TIB
4 oai:oai.datacite.org:32241 2011-06-30T13:24:45Z TIB
5 oai:oai.datacite.org:32255 2011-07-01T12:09:24Z TIB
6 oai:oai.datacite.org:32282 2011-07-05T09:08:10Z TIB
ListIdentifiers is an abbreviated form of ListRecords, retrieving only headers rather than records.
# Single provider
md_listidentifiers(provider = "datacite", set = "REFQUALITY")[[1]][1:10]
[1] "oai:oai.datacite.org:32426" "oai:oai.datacite.org:32152"
[3] "oai:oai.datacite.org:25453" "oai:oai.datacite.org:25452"
[5] "oai:oai.datacite.org:25451" "oai:oai.datacite.org:25450"
[7] "oai:oai.datacite.org:25449" "oai:oai.datacite.org:25407"
[9] "oai:oai.datacite.org:48328" "oai:oai.datacite.org:48439"
md_listidentifiers(provider = "dryad", from = "2012-07-15")[[1]][1:10]
[1] "oai:datadryad.org:10255/dryad.9106"
[2] "oai:datadryad.org:10255/dryad.33780"
[3] "oai:datadryad.org:10255/dryad.33901"
[4] "oai:datadryad.org:10255/dryad.33902"
[5] "oai:datadryad.org:10255/dryad.34472"
[6] "oai:datadryad.org:10255/dryad.34558"
[7] "oai:datadryad.org:10255/dryad.39975"
[8] "oai:datadryad.org:10255/dryad.35065"
[9] "oai:datadryad.org:10255/dryad.35081"
[10] "oai:datadryad.org:10255/dryad.35082"
# Many providers
out <- md_listidentifiers(provider = c("datacite", "pensoft"), from = "2012-08-21")
llply(out, function(x) x[1:10]) # display just a few of them
[[1]]
[1] "oai:oai.datacite.org:1099317" "oai:oai.datacite.org:1099572"
[3] "oai:oai.datacite.org:1099824" "oai:oai.datacite.org:1099695"
[5] "oai:oai.datacite.org:1088239" "oai:oai.datacite.org:1088122"
[7] "oai:oai.datacite.org:1088190" "oai:oai.datacite.org:1175749"
[9] "oai:oai.datacite.org:1175288" "oai:oai.datacite.org:1115603"
[[2]]
[1] "10.3897/phytokeys.16.2884" "10.3897/phytokeys.16.3602"
[3] "10.3897/phytokeys.16.3186" "10.3897/zookeys.216.3407"
[5] "10.3897/zookeys.216.3332" "10.3897/zookeys.216.3224"
[7] "10.3897/zookeys.216.3769" "10.3897/zookeys.216.3360"
[9] "10.3897/zookeys.216.3646" "10.3897/neobiota.14.3140"
With ListSets you can retrieve the set structure of a repository.
# arXiv, returns a data.frame
head(md_listsets(provider = "arXiv")[[1]])
setName setSpec
1 Computer Science cs
2 Mathematics math
3 Nonlinear Sciences nlin
4 Physics physics
5 Astrophysics physics:astro-ph
6 Condensed Matter physics:cond-mat
# many providers, returns a list
md_listsets(provider = c("pensoft", "arXiv"))
[[1]]
setName setSpec
1 ZooKeys zookeys
2 BioRisk biorisk
3 PhytoKeys phytokeys
4 NeoBiota neobiota
5 Journal of Hymenoptera Research jhr
6 International Journal of Myriapodology ijm
7 Comparative Cytogenetics compcytogen
8 Subterranean Biology subtbiol
9 Nature Conservation natureconservation
10 MycoKeys mycokeys
[[2]]
setName setSpec
1 Computer Science cs
2 Mathematics math
3 Nonlinear Sciences nlin
4 Physics physics
5 Astrophysics physics:astro-ph
6 Condensed Matter physics:cond-mat
7 General Relativity and Quantum Cosmology physics:gr-qc
8 High Energy Physics - Experiment physics:hep-ex
9 High Energy Physics - Lattice physics:hep-lat
10 High Energy Physics - Phenomenology physics:hep-ph
11 High Energy Physics - Theory physics:hep-th
12 Mathematical Physics physics:math-ph
13 Nuclear Experiment physics:nucl-ex
14 Nuclear Theory physics:nucl-th
15 Physics (Other) physics:physics
16 Quantum Physics physics:quant-ph
17 Quantitative Biology q-bio
18 Quantitative Finance q-fin
19 Statistics stat
Retrieve an individual metadata record from a repository using the GetRecord verb.
# Single provider, one identifier
md_getrecord(provider = "pensoft", identifier = "10.3897/zookeys.1.10")
identifier datestamp
1 10.3897/zookeys.1.10 2008-07-04
dc.title
1 A new candidate for a Gondwanaland distribution in the Zodariidae (Araneae): Australutica in Africa
dc.creator dc.subject dc.subject.1 dc.subject.2 dc.subject.3
1 Jocqué,Rudy new species Gondwanaland Soutpansberg Araneae
dc.source
1 ZooKeys 1: 59-66
dc.description
1 Two new species of Australutica Jocqué, 1995, a genus formerly only known from Australia, are described from South Africa: A. africana n. sp. from Soutpansberg and A. normanlarseni n. sp. from the Cape Peninsula. The taxonomic position of the new species is discussed and a key to the species of Australutica is provided.
dc.publisher dc.date dc.type dc.format
1 Pensoft Publishers 2008 Research Article text/html
dc.identifier
1 http://dx.doi.org/10.3897/zookeys.1.10
dc.identifier.1 dc.language
1 http://www.pensoft.net/journals/zookeys/article/10/ en
dc..attrs
1 http://www.openarchives.org/OAI/2.0/oai_dc/ http://www.openarchives.org/OAI/2.0/oai_dc.xsd
# Single provider, multiple identifiers
md_getrecord(provider = "pensoft", identifier = c("10.3897/zookeys.1.10", "10.3897/zookeys.4.57"))
identifier datestamp
1 10.3897/zookeys.1.10 2008-07-04
2 10.3897/zookeys.4.57 2008-12-17
dc.title
1 A new candidate for a Gondwanaland distribution in the Zodariidae (Araneae): Australutica in Africa
2 Studies of Tiger Beetles. CLXXVIII. A new Lophyra (Lophyra) from Somaliland (Coleoptera, Cicindelidae)
dc.creator dc.subject dc.subject.1 dc.subject.2 dc.subject.3
1 Jocqué,Rudy new species Gondwanaland Soutpansberg Araneae
2 Cassola,Fabio Tiger Beetles Cicindelidae Lophyra Somaliland
dc.source
1 ZooKeys 1: 59-66
2 ZooKeys 4: 65-69
dc.description
1 Two new species of Australutica Jocqué, 1995, a genus formerly only known from Australia, are described from South Africa: A. africana n. sp. from Soutpansberg and A. normanlarseni n. sp. from the Cape Peninsula. The taxonomic position of the new species is discussed and a key to the species of Australutica is provided.
2 A new tiger beetle species, Lophyra (Lophyra) praetermissa n. sp. (Coleoptera, Cicindelidae), obviously a close relative of L. (L.) histrio (Tschitschérine, 1903), is described from the environs of Erigavo, Somaliland (northern Somalia). Its discovery thus brings up to 73 the number of the species of this genus presently known worldwide (39 species of which - 29 from Africa - belong to the typonominal subgenus).
dc.publisher dc.date dc.type dc.format
1 Pensoft Publishers 2008 Research Article text/html
2 Pensoft Publishers 2008 Research Article text/html
dc.identifier
1 http://dx.doi.org/10.3897/zookeys.1.10
2 http://dx.doi.org/10.3897/zookeys.4.57
dc.identifier.1 dc.language
1 http://www.pensoft.net/journals/zookeys/article/10/ en
2 http://www.pensoft.net/journals/zookeys/article/57/ en
dc..attrs
1 http://www.openarchives.org/OAI/2.0/oai_dc/ http://www.openarchives.org/OAI/2.0/oai_dc.xsd
2 http://www.openarchives.org/OAI/2.0/oai_dc/ http://www.openarchives.org/OAI/2.0/oai_dc.xsd
Cool, so I hope people find this post and package useful. Let me know what you think in comments below, or if you have code specific comments or additions, go to the GitHub repo for rmetadata. In a upcoming post I will show an example of what you can do with rmetadata in terms of an actual research question.
Get the .Rmd file used to create this post at my github account - or .md file.
Written in Markdown, with help from knitr, and nice knitr highlighting/etc. in in RStudio.
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