mDIS User Documentation

DOI Metadata Formats and Metadata Catalogs at GFZ Potsdam

Querying OAI-PMH endpoints to study Metadata Formats at https://doidb.wdc-terra.org/oaip (opens new window) endpoint, (NOT the igsnoaip/oai endpoint).

Note

The following does not have to do much with mDIS in particular. It is still useful background knowledge for anyone who intends to work with IGSNs, the International Generic Sample Number.

From DOIs to IGSNs - resolve a DOI, get lots of IGSNs.
IGSN Endpoint - send queries to GFZ's /igsnoaip Endpoint for read-only access.

Exploring the Metadata Formats of GFZ's WDC-Terra

Resolving a DOI to various metadata formats

This article explores the DOI infrastructure.
By resolving DOIs we will study 3 different DOI metadata formats.

For "IGSN metadata formats", see equivalent article for IGSN service.

As such, this article provides some background knowledge about a likely long-term use of mDIS.

The WDC-Terra site for DOIs

The www.wdc-terra.org (opens new window) website is hosted by GFZ Potsdam, Germany. The domain www.wdc-terra.org has been abandoned, and the successor is https://dataservices.gfz-potsdam.de (opens new window).

Exploratory queries

The GFZ Dataservices page lists a lot of DOIs and IGSNs on a humanreadable web-page.
That page is https://dataservices.gfz-potsdam.de (opens new window).
For developers, API access is also possible.
That API Endpoint is here: https://doidb.wdc-terra.org/oaip.

Walkthrough

The following codesnippets demonstrate a drill-down into WDC-Terra, in order to learn more about DOIs. All code is Shellscript (Bash).

Examples:

5 Metadata Formats

3 of 5 are important

# 1) find all metadata Formats in WDC-Terra
url_doi="https://doidb.wdc-terra.org/oaip/oai?"
url_mdf="verb=ListMetadataFormats"
curl -ksL "${url_doi}${url_mdf}" | xmllint --format -  |   xidel -s -e "//metadataPrefix"
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will return the following (# comments illustrate key characteristics)

dif               # archaic format; less often supported
oai_datacite      # more verbose, finegrained, fewer XML namespaces used
iso19139          # extremely verbose, elements in "gmd:" namespace
oai_dc            # more compact, many elements in "dc:" namespace
datacite          # marked as 'nonexistant' - do not use (yet)! Work in progress?
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So there are 5 Metadata formats: dif, oai_datacite, iso19139 oai_dc, and datacite.
We will focus on oai_dc(the most compact), oai_datacite, and iso19139 (the most verbose).

Clients can gather detailed records about repository datasets in each of these formats.
See below for details.

Detailed exploratory queries

Find "Sets" (Catalogs) in WDC-Terra.

These are independent DOI catalogs, from different source organizations (registrants).

url_doi="https://doidb.wdc-terra.org/oaip/oai?"
url_sets="verb=ListSets"

curl -ksL "${url_doi}${url_sets}" | xmllint --format - | head 
# curl -ksL "${url_doi}${url_sets}" | xmllint --format - | tail
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This returns this xml:

<?xml version="1.0" encoding="UTF-8"?>
<?xml-stylesheet type="text/xsl" href="xsl/oaitohtml.xsl"?>
<OAI-PMH xmlns="http://www.openarchives.org/OAI/2.0/" 
  xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" 
  xsi:schemaLocation="http://www.openarchives.org/OAI/2.0/ http://www.openarchives.org/OAI/2.0/OAI-PMH.xsd">
  <responseDate>2022-07-21T10:06:49Z</responseDate>
  <request verb="ListSets">http://doidb.wdc-terra.org/oaip/oai</request>
  <ListSets>
    <set>
      <setSpec>REFQUALITY</setSpec>
      <setName>Reference quality citations only.</setName>
    </set>
    <!-- and many more <set>s ...-->
    <set>
      <setSpec>DOIDB.WSM.REFQUALITY</setSpec>
      <setName>WDS World Stress Map (reference quality citations only)</setName>
    </set>
    <resumptionToken expirationDate="2022-07-21T11:09:20Z" completeListSize="47" cursor="0"/>
  </ListSets>
</OAI-PMH>
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We want the names of all datasets/catalogs in the repository:

url_doi="https://doidb.wdc-terra.org/oaip/oai?"
url_sets="verb=ListSets"

curl -ksL "${url_doi}${url_sets}" \
  | xmllint --format -  \
  | xidel -s -e "[//setSpec, //setName]" \
  | jq -cr '. | transpose| .[] | @csv' \
  | perl -ple 's/DOIDB\.//g' \
  | grep -v only \
  | csvlook -l -H
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There are quite a few "Sets" in WDC-Terra. Here is the text-content of the <setSpec> and <setName> Elements.

# SetSpec Metadata Catalog
1 DOIDB DOI Database (total)
2 ARBODAT ArboDat 2016
3 CRC1211 CRC1211DB CRC 1211 Database
4 DEKORP DEKORP - German Continental Seismic Reflection Program
5 ENMAP EnMAP
6 FID FID GEO
7 GEOFON GEOFON Seismic Events
8 GFZ GFZ German Research Centre for Geosciences
9 GIPP GIPP Geophysical Instrument Pool Potsdam
10 ICGEM ICGEM International Centre for Global Earth Models
11 IGETS IGETS International Geodynamics and Earth Tide Service
12 INTERMAG INTERMAGNET
13 ISDC ISDC Information System and Data Center
14 ISG ISG International Service for the Geoid
15 PIK PIK Potsdam Institute for Climate Impact Research
16 RIESGOS Riesgos
17 SDDB SDDB Scientific Drilling Database
18 SEISNET GEOFON Seismic Networks
19 SFB806 SFB806 and CRC806-Database
20 TERENO TERENO
21 TR32DB TR32DB CRC/Transregio 32 Database
22 TRR228 TRR228DB CRC/Transregio 228 Database
23 WSM WDS World Stress Map

An (older) GUI based interface to this result is also available externally (opens new window).

Now we want the number of records in each Set.

url_doi="https://doidb.wdc-terra.org/oaip/oai?"
url_sets="verb=ListSets"
# use these in ""perl -anF, ..." command;
last_20_years=$(date +"%Y-%m-%d" -d "20 years ago")
url_params="&from=${last_20_years}&metadataPrefix=oai_dc&set="
url_records="https://doidb.wdc-terra.org//oaip/oai?verb=ListRecords"

curl -ksL "${url_doi}${url_sets}"     \
  | xmllint --format -   \
  | xidel -s -e "[//setSpec, //setName]"  \
  | jq -cr '. | transpose| .[] | @csv'    \
  | grep -vi refquality  \
  | perl -ple 's/"//g' \
  | perl -anF, -E "\$F[1]=~ s/\\s+\$//;\$cmd= qq(sleep 5 && curl -ksL  \"${url_records}${url_params}\$F[0]\"| xidel -s -e \"concat(\\\\\"\$F[0],\$F[1], \\\\\", //resumptionToken/\@completeListSize)\"); system(\$cmd)" \
  | perl -ple 's/DOIDB\.//g' \
  > "./doidb-sets-completeListSize.csv"
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The second perl command generates a bunch of shell commands, one for each set. You could replace the system() function call with a say() call to see what is going on.

Resulting output (doidb-sets-completeListSize.csv formatted with csvlook), as of July 2022:

# SetSpec Sets / Metadata Catalogs Count
1 DOIDB DOI Database (total) 7535
2 ARBODAT ArboDat 2016 169
3 ARBODAT ArboDat2016 169
4 CRC1211 CRC1211DB CRC 1211 Database 50
5 DEKORP DEKORP - German Continental Seismic Reflection Program 28
6 ENMAP EnMAP 19
7 FID FID GEO 167
8 GEOFON GEOFON Seismic Events 5.559
9 GFZ GFZ German Research Centre for Geosciences 451
10 GIPP GIPP Geophysical Instrument Pool Potsdam 41
11 ICGEM ICGEM International Centre for Global Earth Models 38
12 IGETS IGETS International Geodynamics and Earth Tide Service 22
13 INTERMAG INTERMAGNET 6
14 ISDC ISDC Information System and Data Center 31
15 ISG ISG International Service for the Geoid 53
16 PIK PIK Potsdam Institute for Climate Impact Research 58
17 RIESGOS Riesgos 11
18 SDDB SDDB Scientific Drilling Database 354
19 SEISNET GEOFON Seismic Networks 109
20 SFB806 SFB806 and CRC806-Database 80
21 TERENO TERENO 133
22 TR32DB TR32DB CRC/Transregio 32 Database 115
23 TRR228 TRR228DB CRC/Transregio 228 Database 17
24 WSM WDS World Stress Map 24

Catalog GFZ seems to be the only one that grows, by ~10 records per week - the approximate number of new GFZ Publications per week.

And now we want the number of records in each Set per year, from 2010-2022 (the current year at the time of writing). Then we will plot a barchart for each Set/Catalog.

See extra analysis file for more details, [written in R Markdown format](analysis file.

The 2010-2022 timeseries 2 largest catalogs (GEOFON, GFZ) and of the total DOI count, look like this:

timeseries of GFZ DOI counts
Count of DOIs registered by GFZ Dataservices, by year

The plot above shows 2 major GFZ-Sets, or catalogs:

  • (1) DOIs of GEOFON earthquakes (2013-2015)
  • (2) DOI counts of GFZ Publications
  • as a fraction of the total (DOIDB)

The 20 smaller catalogs look like this:

timeseries of DOI counts in smaller GFZ catalogs
Count of DOIs registered by GFZ Dataservices, by year, in the smaller GFZ metadata catalogs

The plot above shows 3 classes of activity for the GFZ catalogs:

  • red color: catalogs with larger activity, "bursty", in the past
  • green: medium count of DOIS registered
  • blue: recent catalogs with smaller activity, or abandoned catalogs.

Explore SDDB Scientific Drilling Database

Let's study the SDDB, for example.
Select "SDDB" via Query-String: set=DOIDB.SDDB.

# DOIDB.SDDB is the setSpec of SDDB Scientific Drilling Database
url_setspec="https://doidb.wdc-terra.org//oaip/oai?verb=ListIdentifiers"
url_params="&metadataPrefix=oai_dc&&set=DOIDB.SDDB&from=2017-01-01"

curl -ksL "${url_setspec}${url_params}" \
  |   xmllint --format -  \
  | xidel -s -e "[//header/datestamp, //header/identifier]" \
  | jq -cr '. | transpose| .[] | @csv'  \
  | perl -plE "s/:+\d\dZ//" \
  | csvlook -S -H -l

# (the "perl" command just shortens the date-strings.)
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This returns a list of registration dates and oai-Identifiers for datasets in the SDDB.:

# Date Identifier
1 2017-01-16 11:33:00 oai:doidb.wdc-terra.org:6244
2 2017-03-11 11:43:00 oai:doidb.wdc-terra.org:896
3 2017-03-11 11:44:00 oai:doidb.wdc-terra.org:897
4 2017-10-15 10:54:00 oai:doidb.wdc-terra.org:6323
5 2017-10-15 10:54:00 oai:doidb.wdc-terra.org:6324
6 2019-05-21 17:40:00 oai:doidb.wdc-terra.org:6674
7 2019-05-21 17:41:00 oai:doidb.wdc-terra.org:6099
8 2020-02-27 09:49:00 oai:doidb.wdc-terra.org:6814
9 2020-09-26 12:52:00 oai:doidb.wdc-terra.org:6309
10 2020-10-01 07:20:00 oai:doidb.wdc-terra.org:871
11 2020-10-01 07:22:00 oai:doidb.wdc-terra.org:875
12 2020-10-01 07:23:00 oai:doidb.wdc-terra.org:877
13 2021-08-13 15:49:00 oai:doidb.wdc-terra.org:1036
14 2021-08-13 21:01:00 oai:doidb.wdc-terra.org:34
15 2021-08-16 10:42:00 oai:doidb.wdc-terra.org:35
16 2021-08-18 11:49:00 oai:doidb.wdc-terra.org:115
17 2021-08-27 11:02:00 oai:doidb.wdc-terra.org:6329
18 2021-09-30 10:42:00 oai:doidb.wdc-terra.org:7197
19 2022-05-13 11:45:00 oai:doidb.wdc-terra.org:54

Q: What are the Date and Identifier columns exactly?

  • oai:doidb.wdc-terra.org:54: OAI seems to assign its own oai: prefix, the suffix number seem to be another id column.
  • Registration-Update-Dates are probably given in the Date column,because the ids are no longer sorted/in sequential order.

(So SDDB did not return anything intersting and recent for us. Also, no IGSNs to be seen in this response.)

Focused query

GetRecord Verb/Call

Return a complete record for a single dataset, using the above (oai:...) identifier to get an XML response.

# Return a complete record for a single dataset, selected from the above results
url_doi='https://doidb.wdc-terra.org/oaip/oai?'
url_verb='verb=GetRecord&identifier=oai:doidb.wdc-terra.org:7373'
url_mdfmt='&metadataPrefix=oai_dc'

curl -ksL "${url_doi}${url_verb}${url_mdfmt}"   \
  | xmllint --format -
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Metadata format/prefix oai_dc returns a relatively "short" <GetRecord> XML:

<?xml version="1.0" encoding="UTF-8"?>
<?xml-stylesheet type="text/xsl" href="xsl/oaitohtml.xsl"?>
<OAI-PMH xmlns="http://www.openarchives.org/OAI/2.0/" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.openarchives.org/OAI/2.0/ http://www.openarchives.org/OAI/2.0/OAI-PMH.xsd">
  <responseDate>2022-07-15T18:49:55Z</responseDate>
  <request verb="GetRecord" metadataPrefix="oai_dc" identifier="oai:doidb.wdc-terra.org:7373">http://doidb.wdc-terra.org/oaip/oai</request>
  <GetRecord>
    <record>
      <header>
        <identifier>oai:doidb.wdc-terra.org:7373</identifier>
        <datestamp>2022-05-19T07:08:29Z</datestamp>
        <setSpec>DOIDB</setSpec>
        <setSpec>DOIDB.FID</setSpec>
      </header>
      <metadata>
        <oai_dc:dc xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:oai_dc="http://www.openarchives.org/OAI/2.0/oai_dc/" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.openarchives.org/OAI/2.0/oai_dc/ http://www.openarchives.org/OAI/2.0/oai_dc.xsd">
          <dc:title>Catalog of start and end times of lava fountaining episodes from 2 May to 14 June 2021 during the Fagradalsfjall eruption</dc:title>
          <dc:creator>Eibl, Eva P. S.</dc:creator>
          <dc:creator>Gnauck, Undine </dc:creator>
          <dc:creator>Hamzaliyev, Shaig </dc:creator>
          <dc:creator>Hersir, Gylfi Páll </dc:creator>
          <dc:creator>Gudnason, Egill Árni </dc:creator>
          <dc:creator>Pétursson, Fridgeir </dc:creator>
          <dc:publisher>GFZ Data Services</dc:publisher>
          <dc:date>2022</dc:date>
          <dc:identifier>http://dx.doi.org/10.5880/fidgeo.2022.010</dc:identifier>
          <dc:identifier>doi:10.5880/fidgeo.2022.010</dc:identifier>
          <dc:relation>doi:10.21203/rs.3.rs-1453738/v1</dc:relation>
          <dc:relation>doi:10.14470/4S7576570845</dc:relation>
          <dc:subject>eruption catalogue</dc:subject>
          <dc:subject>Iceland</dc:subject>
          <dc:subject>seismology</dc:subject>
          <dc:subject>volcanic tremor</dc:subject>
          <dc:subject>lava fountaining</dc:subject>
          <dc:subject>EARTH SCIENCE &gt; SOLID EARTH &gt; GEOMORPHIC LANDFORMS/PROCESSES &gt; TECTONIC LANDFORMS &gt; GEYSER</dc:subject>
          <dc:subject>EARTH SCIENCE &gt; SOLID EARTH &gt; TECTONICS &gt; EARTHQUAKES</dc:subject>
          <dc:subject>EARTH SCIENCE &gt; SOLID EARTH &gt; TECTONICS &gt; EARTHQUAKES &gt; EARTHQUAKE OCCURRENCES</dc:subject>
          <dc:subject>EARTH SCIENCE &gt; SOLID EARTH &gt; TECTONICS &gt; VOLCANIC ACTIVITY</dc:subject>
          <dc:subject>In Situ Land-based Platforms &gt; GEOPHYSICAL STATIONS/NETWORKS</dc:subject>
          <dc:description>Abstract</dc:description>
          <dc:description>The Fagradalsfjall eruption from 19 March to 18 September 2021 featured lava fountaining episodes from 2 May to 14 June. These episodes were recorded as tremor pulses on our broadband seismic station NUPH (Nanometrics Trillium Compact 120s) at 5.5 km southeast of the active vent.    
We used the seismic data bandpass filtered between 1 and 4 Hz to mark the start and end of 7058 tremor pulses. The catalog hence comprises 14116 markers, that are statistically further evaluated in Eibl et al. (in review). From 2 May to 14 June, several changes in pulse duration and repose time were found and used to subdivide this time interval into 6 periods with characteristic pulse pattern. We find exponentially decreasing pulse durations, coexisting short and long pulses and stable pulse durations superimposed by gradually increasing or suddenly decreasing repose times. We discuss the findings in the context of an evolving shallow-conduit container, the crater geometries, partial collapses from the crater rim and the amount of accumulating outgassed magma in Eibl et al. (in review). This data publications releases the catalog of 14116 tremor pulses /lava fountaining episodes.   </dc:description>
          <dc:description>Methods</dc:description>
          <dc:description>We installed a Trillium Compact 120 s seismometer (Nanometrics) as station NUPH (9F seismic network) at the southeast corner of Núpshlídarháls 5.5 km southeast of the eruptive site in Geldingadalir, Iceland. The instrument stood on a concrete base slab shielded from wind and rain using a bucket partly covered by rocks. The instrument was powered using batteries from 16 March, solar panels from 24 March and a wind generator at 10 m distance from 6 April 2021. Data were sampled at 200 Hz, they were stored on a Datacube and regularly downloaded. We used a compass to align the instrument to geographic north.   </dc:description>
          <dc:contributor>Eibl, Eva P. S.</dc:contributor>
          <dc:contributor>Eibl, Eva P. S.</dc:contributor>
          <dc:contributor>Gnauck, Undine </dc:contributor>
          <dc:contributor>Hamzaliyev, Shaig </dc:contributor>
          <dc:contributor>Hersir, Gylfi Páll </dc:contributor>
          <dc:contributor>Gudnason, Egill Árni </dc:contributor>
          <dc:contributor>Pétursson, Fridgeir </dc:contributor>
          <dc:contributor>Eibl, Eva P. S.</dc:contributor>
          <dc:type>Dataset</dc:type>
          <dc:type>Dataset</dc:type>
          <dc:rights>CC BY 4.0</dc:rights>
          <dc:rights>http://creativecommons.org/licenses/by/4.0/</dc:rights>
          <dc:coverage>Location of seismometer (Nanometrics) as station NUPH (9F seismic network)</dc:coverage>
          <dc:coverage>-22.1 -22.4 63.8 63.9</dc:coverage>
        </oai_dc:dc>
      </metadata>
    </record>
  </GetRecord>
</OAI-PMH>
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There is quite some repetition in some elements. Line 10 and 11 in the <header> indicate that the dataset is available in the Sets DOIDB, DOIDB.FID.

Metadata formats

Query a single record, return in various formats:

Querystring-Parameter metadataPrefix determines the Reponse Format:

This seems to be similar to HTTP content negotiation, but instead of sending
Accept: application/json headers, the client must send all info in HTTP Querystring Parameters such as:

  • verb=GetRecord&metadataPrefix=oai_dc&identifer=... ).
url_doi="https://doidb.wdc-terra.org/oaip/oai?verb=GetRecord&identifier=oai:doidb.wdc-terra.org:7373"
url_doi_oai="&metadataPrefix=oai_dc"
url_doi_oai_datacite="&metadataPrefix=oai_datacite"
url_doi_iso19139="&metadataPrefix=iso19139"
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Three metadata formats are supported.
Just count the number of lines in the responses:

curl -ksL "${url_doi}${url_doi_oai}"          | xmllint --format - | wc -l # 62
curl -ksL "${url_doi}${url_doi_oai_datacite}" | xmllint --format - | wc -l # 167
curl -ksL "${url_doi}${url_doi_iso19139}"     | xmllint --format - | wc -l # 445
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This returns xml responses which are 62, 167, and 445 lines long, respectively. This represents 23, 50, and 110 XML elements in each response.

# oai oai_datacite iso19139
1 OAI-PMH OAI-PMH OAI-PMH
2 responseDate responseDate responseDate
3 request request request
4 GetRecord GetRecord GetRecord
5 record record record
6 header header header
7 identifier identifier identifier
8 datestamp datestamp datestamp
9 setSpec setSpec setSpec
10 metadata metadata metadata
11 oai_dc:dc oai_datacite gmd:MD_Metadata
12 dc:title isReferenceQuality gmd:fileIdentifier
13 dc:creator schemaVersion gco:CharacterString
14 dc:publisher datacentreSymbol gmd:language
15 dc:date payload gmd:LanguageCode
16 dc:identifier resource gmd:characterSet
17 dc:relation creators gmd:MD_CharacterSetCode
18 dc:subject creator gmd:hierarchyLevel
19 dc:description creatorName gmd:MD_ScopeCode
20 dc:contributor givenName gmd:hierarchyLevelName
21 dc:type familyName gmd:contact
22 dc:rights nameIdentifier gmd:CI_ResponsibleParty
23 dc:coverage affiliation gmd:organisationName
24 titles gmd:contactInfo
25 title gmd:CI_Contact
26 publisher gmd:address
27 publicationYear gmd:CI_Address
28 subjects gmd:electronicMailAddress
29 subject gmd:onlineResource
30 contributors gmd:CI_OnlineResource
31 contributor gmd:linkage
32 contributorName gmd:URL
33 resourceType gmd:name
34 relatedIdentifiers gmd:description
35 relatedIdentifier gmd:role
36 sizes gmd:CI_RoleCode
37 formats gmd:dateStamp
38 rightsList gco:Date
39 rights gmd:referenceSystemInfo
40 descriptions gmd:MD_ReferenceSystem
41 description gmd:referenceSystemIdentifier
42 br gmd:RS_Identifier
43 geoLocations gmd:code
44 geoLocation gmd:identificationInfo
45 geoLocationPlace gmd:MD_DataIdentification
46 geoLocationBox gmd:citation
47 westBoundLongitude gmd:CI_Citation
48 eastBoundLongitude gmd:title
49 southBoundLatitude gmd:date
50 northBoundLatitude gmd:CI_Date
51 gmd:dateType
52 gmd:CI_DateTypeCode
53 gmd:identifier
54 gmd:MD_Identifier
55 gmd:citedResponsibleParty
56 gmd:individualName
57 gmd:abstract
58 gmd:pointOfContact
59 gmd:descriptiveKeywords
60 gmd:MD_Keywords
61 gmd:keyword
62 gmd:thesaurusName
63 gmd:resourceConstraints
64 gmd:MD_Constraints
65 gmd:useLimitation
66 gmd:MD_LegalConstraints
67 gmd:accessConstraints
68 gmd:MD_RestrictionCode
69 gmd:otherConstraints
70 gmd:MD_SecurityConstraints
71 gmd:classification
72 gmd:MD_ClassificationCode
73 gmd:aggregationInfo
74 gmd:MD_AggregateInformation
75 gmd:aggregateDataSetIdentifier
76 gmd:codeSpace
77 gmd:associationType
78 gmd:DS_AssociationTypeCode
79 gmd:topicCategory
80 gmd:MD_TopicCategoryCode
81 gmd:extent
82 gmd:EX_Extent
83 gmd:geographicElement
84 gmd:EX_GeographicBoundingBox
85 gmd:westBoundLongitude
86 gco:Decimal
87 gmd:eastBoundLongitude
88 gmd:southBoundLatitude
89 gmd:northBoundLatitude
90 gmd:temporalElement
91 gmd:EX_TemporalExtent
92 gml:TimePeriod
93 gml:beginPosition
94 gml:endPosition
95 gmd:distributionInfo
96 gmd:MD_Distribution
97 gmd:transferOptions
98 gmd:MD_DigitalTransferOptions
99 gmd:onLine
100 gmd:protocol
101 gmd:function
102 gmd:CI_OnLineFunctionCode
103 gmd:dataQualityInfo
104 gmd:DQ_DataQuality
105 gmd:scope
106 gmd:DQ_Scope
107 gmd:level
108 gmd:lineage
109 gmd:LI_Lineage
110 gmd:statement

Q: However do the records contain almost the same information?
A: This is what a records in the iso19139 Metadata Format Looks like:

Commandline Query:

url_doi='https://doidb.wdc-terra.org/oaip/oai?'
url_verb='verb=GetRecord&identifier=oai:doidb.wdc-terra.org:7373'
url_mdfmt='&metadataPrefix=iso19139'

curl -ksL "${url_doi}${url_verb}${url_mdfmt}"  \
  |  xidel -s -e "[(/)[1]//name(), (/)[1]//normalize-space()]" \
  | jq -r '. | transpose| .[] | @csv'  \
  | grep -v '"",""'     \
  | csvlook -H -l
1
2
3
4
5
6
7
8
9

Result - example for a full iso19139 record, flattened:

# Column name Value
1
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4 responseDate 2022-07-24T11:55:12Z
5 2022-07-24T11:55:12Z
6 request http://doidb.wdc-terra.org/oaip/oai
7 http://doidb.wdc-terra.org/oaip/oai
8 GetRecord (see below)
9 record (see below)
10 header oai:doidb.wdc-terra.org:73732022-05-19T07:08:29ZDOIDBDOIDB.FID
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71 gmd:MD_DataIdentification Catalog of start and end times of lava fountaining episodes from 2 May to 14 June 2021 during the Fagradalsfjall eruption 2022-05-19 revision doi:10.5880/fidgeo.2022.010 Eibl, Eva P. S. Institute of Geosciences, University of Potsdam, Potsdam, Germany author Gnauck, Undine Institute of Geosciences, University of Potsdam, Potsdam, Germany author Hamzaliyev, Shaig Institute of Geosciences, University of Potsdam, Potsdam, Germany author Hersir, Gylfi Páll retired, formerly: Iceland GeoSurvey (ÍSOR), Reykjavik, Iceland author Gudnason, Egill Árni Iceland GeoSurvey (ÍSOR), Reykjavik, Iceland author Pétursson, Fridgeir Iceland GeoSurvey (ÍSOR), Reykjavik, Iceland author GFZ Data Services publisher The Fagradalsfjall eruption from 19 March to 18 September 2021 featured lava fountaining episodes from 2 May to 14 June. These episodes were recorded as tremor pulses on our broadband seismic station NUPH (Nanometrics Trillium Compact 120s) at 5.5 km southeast of the active vent. We used the seismic data bandpass filtered between 1 and 4 Hz to mark the start and end of 7058 tremor pulses. The catalog hence comprises 14116 markers, that are statistically further evaluated in Eibl et al. (in review). From 2 May to 14 June, several changes in pulse duration and repose time were found and used to subdivide this time interval into 6 periods with characteristic pulse pattern. We find exponentially decreasing pulse durations, coexisting short and long pulses and stable pulse durations superimposed by gradually increasing or suddenly decreasing repose times. We discuss the findings in the context of an evolving shallow-conduit container, the crater geometries, partial collapses from the crater rim and the amount of accumulating outgassed magma in Eibl et al. (in review). This data publications releases the catalog of 14116 tremor pulses /lava fountaining episodes. Eibl, Eva P. S. Institute of Geosciences, University of Potsdam, Potsdam, Germany eva.eibl@uni-potsdam.de pointOfContact eruption catalogue Iceland seismology volcanic tremor lava fountaining EARTH SCIENCE > SOLID EARTH > GEOMORPHIC LANDFORMS/PROCESSES > TECTONIC LANDFORMS > GEYSER EARTH SCIENCE > SOLID EARTH > TECTONICS > EARTHQUAKES EARTH SCIENCE > SOLID EARTH > TECTONICS > EARTHQUAKES > EARTHQUAKE OCCURRENCES EARTH SCIENCE > SOLID EARTH > TECTONICS > VOLCANIC ACTIVITY NASA/GCMD Earth Science Keywords publication In Situ Land-based Platforms > GEOPHYSICAL STATIONS/NETWORKS GCMD Platforms publication CC BY 4.0 CC BY 4.0 10.21203/rs.3.rs-1453738/v1 DOI IsSupplementTo 10.14470/4S7576570845 DOI IsDerivedFrom eng geoscientificInformation Location of seismometer (Nanometrics) as station NUPH (9F seismic network) -22.1 -22.4 63.8 63.9 2021-05-02 2021-06-14
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73 gmd:CI_Citation Catalog of start and end times of lava fountaining episodes from 2 May to 14 June 2021 during the Fagradalsfjall eruption 2022-05-19 revision doi:10.5880/fidgeo.2022.010 Eibl, Eva P. S. Institute of Geosciences, University of Potsdam, Potsdam, Germany author Gnauck, Undine Institute of Geosciences, University of Potsdam, Potsdam, Germany author Hamzaliyev, Shaig Institute of Geosciences, University of Potsdam, Potsdam, Germany author Hersir, Gylfi Páll retired, formerly: Iceland GeoSurvey (ÍSOR), Reykjavik, Iceland author Gudnason, Egill Árni Iceland GeoSurvey (ÍSOR), Reykjavik, Iceland author Pétursson, Fridgeir Iceland GeoSurvey (ÍSOR), Reykjavik, Iceland author GFZ Data Services publisher
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75 gco:CharacterString Catalog of start and end times of lava fountaining episodes from 2 May to 14 June 2021 during the Fagradalsfjall eruption
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164 gmd:abstract The Fagradalsfjall eruption from 19 March to 18 September 2021 featured lava fountaining episodes from 2 May to 14 June. These episodes were recorded as tremor pulses on our broadband seismic station NUPH (Nanometrics Trillium Compact 120s) at 5.5 km southeast of the active vent. We used the seismic data bandpass filtered between 1 and 4 Hz to mark the start and end of 7058 tremor pulses. The catalog hence comprises 14116 markers, that are statistically further evaluated in Eibl et al. (in review). From 2 May to 14 June, several changes in pulse duration and repose time were found and used to subdivide this time interval into 6 periods with characteristic pulse pattern. We find exponentially decreasing pulse durations, coexisting short and long pulses and stable pulse durations superimposed by gradually increasing or suddenly decreasing repose times. We discuss the findings in the context of an evolving shallow-conduit container, the crater geometries, partial collapses from the crater rim and the amount of accumulating outgassed magma in Eibl et al. (in review). This data publications releases the catalog of 14116 tremor pulses /lava fountaining episodes.
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340 information
341 gmd:dataQualityInfo We installed a Trillium Compact 120 s seismometer (Nanometrics) as station NUPH (9F seismic network) at the southeast corner of Núpshlídarháls 5.5 km southeast of the eruptive site in Geldingadalir, Iceland. The instrument stood on a concrete base slab shielded from wind and rain using a bucket partly covered by rocks. The instrument was powered using batteries from 16 March, solar panels from 24 March and a wind generator at 10 m distance from 6 April 2021. Data were sampled at 200 Hz, they were stored on a Datacube and regularly downloaded. We used a compass to align the instrument to geographic north.
342 gmd:DQ_DataQuality We installed a Trillium Compact 120 s seismometer (Nanometrics) as station NUPH (9F seismic network) at the southeast corner of Núpshlídarháls 5.5 km southeast of the eruptive site in Geldingadalir, Iceland. The instrument stood on a concrete base slab shielded from wind and rain using a bucket partly covered by rocks. The instrument was powered using batteries from 16 March, solar panels from 24 March and a wind generator at 10 m distance from 6 April 2021. Data were sampled at 200 Hz, they were stored on a Datacube and regularly downloaded. We used a compass to align the instrument to geographic north.
343 gmd:scope
344 gmd:DQ_Scope
345 gmd:level
346 gmd:MD_ScopeCode
347 gmd:lineage We installed a Trillium Compact 120 s seismometer (Nanometrics) as station NUPH (9F seismic network) at the southeast corner of Núpshlídarháls 5.5 km southeast of the eruptive site in Geldingadalir, Iceland. The instrument stood on a concrete base slab shielded from wind and rain using a bucket partly covered by rocks. The instrument was powered using batteries from 16 March, solar panels from 24 March and a wind generator at 10 m distance from 6 April 2021. Data were sampled at 200 Hz, they were stored on a Datacube and regularly downloaded. We used a compass to align the instrument to geographic north.
348 gmd:LI_Lineage We installed a Trillium Compact 120 s seismometer (Nanometrics) as station NUPH (9F seismic network) at the southeast corner of Núpshlídarháls 5.5 km southeast of the eruptive site in Geldingadalir, Iceland. The instrument stood on a concrete base slab shielded from wind and rain using a bucket partly covered by rocks. The instrument was powered using batteries from 16 March, solar panels from 24 March and a wind generator at 10 m distance from 6 April 2021. Data were sampled at 200 Hz, they were stored on a Datacube and regularly downloaded. We used a compass to align the instrument to geographic north.
349 gmd:statement We installed a Trillium Compact 120 s seismometer (Nanometrics) as station NUPH (9F seismic network) at the southeast corner of Núpshlídarháls 5.5 km southeast of the eruptive site in Geldingadalir, Iceland. The instrument stood on a concrete base slab shielded from wind and rain using a bucket partly covered by rocks. The instrument was powered using batteries from 16 March, solar panels from 24 March and a wind generator at 10 m distance from 6 April 2021. Data were sampled at 200 Hz, they were stored on a Datacube and regularly downloaded. We used a compass to align the instrument to geographic north.
350 gco:CharacterString We installed a Trillium Compact 120 s seismometer (Nanometrics) as station NUPH (9F seismic network) at the southeast corner of Núpshlídarháls 5.5 km southeast of the eruptive site in Geldingadalir, Iceland. The instrument stood on a concrete base slab shielded from wind and rain using a bucket partly covered by rocks. The instrument was powered using batteries from 16 March, solar panels from 24 March and a wind generator at 10 m distance from 6 April 2021. Data were sampled at 200 Hz, they were stored on a Datacube and regularly downloaded. We used a compass to align the instrument to geographic north.
351 We installed a Trillium Compact 120 s seismometer (Nanometrics) as station NUPH (9F seismic network) at the southeast corner of Núpshlídarháls 5.5 km southeast of the eruptive site in Geldingadalir, Iceland. The instrument stood on a concrete base slab shielded from wind and rain using a bucket partly covered by rocks. The instrument was powered using batteries from 16 March, solar panels from 24 March and a wind generator at 10 m distance from 6 April 2021. Data were sampled at 200 Hz, they were stored on a Datacube and regularly downloaded. We used a compass to align the instrument to geographic north.

Query 5:

Get only first record, whitespace trimmed, multiline

# Get only first record, whitespace trimmed, multiline
curl -ksL  "${url_records}${url_params}"   | xidel -s -e "(//record)[1]"
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2

(result not shown on purpose)

Same as beforem but this time get only 3 selected elements from first record, single line

# Get only selected elements from first record, single line
curl -ksL  "${url_records}${url_params}"   | xidel -s -e "[(//dc:title)[1], (//dc:identifier)[1], (//dc:creator)[1]]"
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2

(result not shown on purpose, see Query 6 below, shows HTML instead of XML)

Query 6:

(Q6) format output as html fragment (1 link per line)

# (6) format output as html fragment (1 link per line)
curl -ksL  "${url_records}${url_params}" \
  | xidel -s -e "[//dc:title[1], //dc:identifier[1], //dc:creator[1]]" \
  | jq -r '. | transpose| .[] | @tsv' \
  | perl -nl -E '@F = split /\t/;say qq(<a href="$F[1]"><code>$F[1]</code></a> - $F[0] - <i>$F[2]</i>)' \
  | tail -3 \
  | csvlook  -H -l -t
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6
7
# Dataset (Query 5, 6)
1 http://dx.doi.org/10.5880/hA-ArboDat_AK17 - AK17 Archäobotanische Funde des römischen Bestattungsplatzes des 2. Jh. AD von Karben-Okarben (Wetteraukreis, Hessen) - Kreuz, Angela
2 http://dx.doi.org/10.5880/hA-ArboDat_AK184 - AK184 Archäobotanische Funde der frühneolithischen ältestbandkeramischen Siedlung Bad Camberg Würges (Limburg-Weilburg, Hessen) - Wiethold, Julian
3 http://dx.doi.org/10.5880/hA-ArboDat_AK187 - AK187 Archäobotanische Funde der römerzeitlich-germanischen und frühmittelalterlichen karolingischen Siedlung Usingen (Hochtaunuskreis, Hessen) - Kreuz, Angela
Query 7:

These are the elements available in the XML record:

curl -ksL "${url_records}${url_params}" |   xidel -s -e "distinct-values(//*/name())"
1
OAI-PMH, responseDate, request, ListRecords, record, 
header, identifier, datestamp,setSpec, metadata, 
oai_dc:dc
dc:title
dc:creator
dc:publisher
dc:date
dc:identifier
dc:relation
dc:subject
dc:description
dc:contributor
dc:type
dc:rights
dc:coverage
dc:language
dc:format
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17

The elements with the dc: prefix describe the classic Dublin-Core metadata set. Note that it only contains the author of the dataset but not the institution, which is not in the XML record.

The End.

Note: Some examples use the powerful xidel (opens new window), a little-known command-line tool for XML querying. It is free software.