. Opening Up the Natural History Heritage IfTVjcD UP! for Europeana 1 V * Г.£Г D25 - DELIVERABLE СЗ.2.2 Project Acronym: Grant Agreement No: Project Title: OpenUp! 270890 Opening up the Natural History Heritage for Europeana D25 / СЗ.2.2 Domain specific vocabularies for EUROPEANA - final Concept for inclusion of domain specific metadata vocabularies and contribution to improving access to scientific information via EDM Revision: Version 1.1 Authors (in alphabetical order): Benda Odo AIT Forschungsgesellschaft mbH Höller Astrid AIT Forschungsgesellschaft mbH Koch Gerda AIT Forschungsgesellschaft mbH Koch Walter AIT Forschungsgesellschaft mbH Project co-funded by the European Commission within the 1СГ Policy Support Programme Dissemination Level Ρ Public x C Confidential, only for members of the consortium and the Commission Services AIT, 2014 D25 / СЗ.2.2 version 1.1 p.l
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. Opening Up the Natural History Heritage IfTVjcD UP! for Europeana 1V * Г.£Г
D25 - DELIVERABLE СЗ.2.2
Project Acronym:
Grant Agreement No:
Project Title:
OpenUp!
270890
Opening up the Natural History Heritage for Europeana
D25 / СЗ.2.2 Domain specific vocabularies for EUROPEANA - final
Concept for inclusion of domain specific metadata vocabularies and contribution to improving access to scientific information via EDM
Revision: Version 1.1
Authors (in alphabetical order):
Benda Odo AIT Forschungsgesellschaft mbH
Höller Astrid AIT Forschungsgesellschaft mbH
Koch Gerda AIT Forschungsgesellschaft mbH
Koch Walter AIT Forschungsgesellschaft mbH
Project co-funded by the European Commission within the 1СГ Policy Support Programme
Dissemination Level
Ρ Public x
C Confidential, only for members of the consortium and the Commission Services
AIT, 2014 D25 / СЗ.2.2 version 1.1 p.l
•^3 <ňf Opening Up the Natural History Heritage |£Tpc ρ
! for Europeana ' UPi
Revision History
Revision Date Author Organisation Description
Draft 0.1 2014-01-27 A. Höller AIT Concept and Draft
Version 0.2 0. Benda, Α. Höller, W. Koch, G. Koch
AIT Including comments
Version 1.0 2014-01-28 G. Koch AIT Finalisation of Version 1
Version 1.1 2014-01-29 Coordination Team (P.Böttinger, Α. Michel)
BGBM Minor Editing
Statement of Originality
This deliverable contains original unpublished work except where clearly indicated otherwise. Acknowledgement of previously published material and of the work of others has been made through appropriate citation, quotation or both.
Distribution
Recipient Date Version Accepted YES/NO
TMG 29.1.2014 1.0 YES
Project Coordinator 29.1.2014 1.1 YES
AIT, 2014 D25 / C3.2.2 version 1.1
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. Opening Up the Natural History Heritage IfTr UP! for Europeana ¡V'J
Table of Contents
1 DESCRIPTION OF WORK 4
2 COMMON NAMES VOCABULARY SERVICE 5
2.1 Extension of Pentaho Transformation and its Parameters 5
•Λ UP! ^ Opening Up the Natural History Heritage ICTP*ÎP
for Europeana '«ΊΓ3Γ
1 DESCRIPTION OF WORK
Based on the analysis of EDM and various domain specific vocabularies a concept for inclusion of metadata vocabularies and metadata enrichment was worked out. For this purpose existing tools for building and deploying semantic knowledge representations were evaluated.
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Stylesheet
Europeana bibliographic
information *om BHL
«wastMct» Ontology Servteea
Figure 1 Ingesting records into Europeana (technical components)
The contextual classes of EDM support the modelling of semantic enrichment and allow to present information that is distinct from the actually provided cultural heritage object as giving additional details on eg. the common names of the depicted natural heritage object data, or the link to the place of gathering. Usually the values of the properties of these classes are taken from controlled vocabularies and thesauri in form of identifiers that link to further information to the vocabulary term (eg. the longitude/latitude of the place of finding, the various common names etc.) The enrichment processes in OpenUp! fulfil the tasks to provide the values of the properties of the EDM contextual classes edm:Place and skos:Concept, and OpenUpl enriches the data by linking to an object type vocabulary (edm:hasType) and to external bibliographic information from the Biodiversity Heritage Library (dc:relation).
AIT, 2014 D25 / C3.2.2 version 1.1
UP! v Opening Up the Natural History Heritage ICTPQP for Europeana r iSr
In this document the used services and results are presented.
2 COMMON NAMES VOCABULARY SERVICE
A style sheet is used in order to set the rules for displaying the mapped vocabulary information (see Figure 2).
This stylesheet defines that the vocabulary information is added to a record via the metadata field dasubject. For each abcd:FullScientificNameString the vocabulary is searched for an appropriate common name. When one is found it is added to the metadata as a value of dc:subject.
Because Europeana does not display the skos:note that carries the references to the vocabulary sources so far in the portal OpenUp! added the to the common names web service the skos:editorialNote field that displays a link to the vocabulary information. The skos:editorialNote is added as final dasubject field to the object description.
<xsl:tf tc,t- contavns(., 'http;//'} or contains(., 'http«://')"> «de:subject»
<xsl:value-of select=".* /> </đc:subject>
</xsl:lf> </xsl:for-each>
Figure 2 EDM Stylesheet
2.1 Extension of Pentaho Transformation and its Parameters
The transformation of the OpenUp metadata from the ABCD format into the ESE/EDM format is done with the Pentaho Kettle PDI tool. In order to generate the metadata suitable for Europeana's EDM format the ESE transformation routine is extended with the Ontology data. This is done by using the Ontology Data Gateway's REST service in the transformation program (see Figure 3).
AIT, 2014 D25 / C3.2.2 version 1.1
- iQi^ Opening Up the Natural History Heritage UP! for Europeana ICTPSP
Figure 3 Extended Pentaho Transformation with REST service (marked red)
AIT, 2014 D25 / C3.2.2 version 1.1 P· 6
Λ, . I_.^ř Opening Up the Natural History Heritage 1ГТпсr> UP! for Europeana 'V |Г-?К
2.1.1 Extension 1: Voc URI? The first step called "Voc URI?" is a Filter Rows step. If there is a vocabulary URI the data is forwarded to step two "Add NS". Otherwise it is directly sent to "Get Units from XML" (compare Figure 3). Figure 4 shows the configuration of this step with its condition.
Step name |уое uri?)
Send 'true' data to step: [д^ NS * ~ Y
Send 'false' data to step: units from XML j rj
The condition:
, % Iv&cabulftry_łervlce_uri Į [STARTS WITH |
{String^
[ OK ļ Cancel I
Figure 4 The Filter Rows step "Voc URI?"
2.1.2 Extension 2: Add NS When there is a vocabulary URI the data is sent to the second step "Add NS" (add namespace). This "Replace in String" step replaces <biocase:response with <biocase:response xmlns:dc=httD://purl.ora/dc/elements/1.1/and adds the namespace (see Figure 6).
Step name [AddNS
Fields string * # In stream field Out stream field useRegEx Search Replace Wtth Replace with field
1 abcdXML N <biocase:response <biocase:responsexmlns:dc="http://purl.org/dc/elements/1.1/"
Figure 5 Step 2: Adding а namespace
2.1.3 Extension 3: Voc Service The "Rest clienť step named "Voc Service" accesses the Ontology Service (see Figure 6) and is defined with the variable URL ${vocabulary_service_uri} which is represented in the Transformation Parameters (see Figure 7, Parameter number 18 with URL http://aitll7:8080/Vocabularv/rest/~Mapping/NHMW common name/perform ).
. Opening Up the Natural History Heritage l£Tpçp UP! for Europeana
Step name ļvoc Service!
.Authentication! SSL1 Headers] Parameter^!
Settings
URL [ş{vocabulary_service_uri}
Accept URL from field? Г)
URL fteld name [Г , ΖΞΞ3ΞΞΖΞΙΞΖ2^ HTTP method Ipqjţ
Get Method from field π
Method fieidname ļ~
Body field ¡abcdXML
Application type XML
Į T •
!β"*Ϊ^ Output fields
Result fieldname abcdXMLwithVoc
HTTP status code fieldname
Response time (milliseconds) fieldname .]* Ύ
ok
Figure 6 Pentaho Ontology Service access
Job entry name: [j.i Blocase_HarvestJo_ESE
Job specification ( Advanced ļ Logging settings | Argument /ЯНВЯЯ&Ч^ Pass aü parameter values down to the sub-job y
A * Parameter Stream column name •Š
f
1 ANALYSE J M G_DS N !
? CLEAR_DłR5 γ 3 USE_JMG_DS N
lillil RESTRICTED N 5 collectlonjiame CLDBIS:MFN:GERMANY c basejdlr /opt/ħft 7 dataset_narne Glo&łS - Global Butterfly Information System (GloBIS) S dataset_uď<ň_key not4fHJddl-573M77 9 imageTable
Ηβΐβ kng_data5et_name 11 lmg_dataset_uddljcey 12 Job ${lnternaUob.Name} 13 idzebra_dir /var/www/oal-provider-edm/zebra/openup 14 DUPLICATE^HANDLINC F ' " IS PUBLISH Y 16 DROPJ5_SHOWN_BY N 17 SAVEFILES Y 18 voca buta ry_s ervi ce_urí httpV/3ftl17;SOeo/Vocabułary/rest/-^pp1ng/NHMW_common_narne/pefform
DUPLICATEJMGHANDLINC A EDM Y
21 hít_db hlt
в* п&шУ
Figure 7 Pentaho Parameters
AIT, 2014 D25 / C3.2.2 version 1.1 p. 8
Oy» ^ A*. / . ģe4t^ Opening Up the Natural History Heritage IfToC D UP! for Europeana JfeJUSöT
2.1.4 Extension 4: use abed + voc Finally the forth step "use abed + voc" is a "Select Values" step which is executed in order to select other needed fields. As can be seen in Figure 8 the field abcdXMLwithVoc is renamed to abcdXML.
10 vocabula ry_servlce_urt 11 duplicate_lmg_handllng U coUectlon_name 13 abcdXMLwithVoc
Rename to Length Precision
abcdXML
include unspecified fields, ordered by name
Figure 8 Renaming "abcdXMLwithVoc" to "abcdXML"
2.2 Transformation result
Figure 9 shows the butterfly Papilio machaon Linnaeus, 1758. The sample record for this specimen is shown in Figure 10. As can be seen the record includes many subjects with common names in different languages.
Figure 9 Papilio machaon Linnaeus, 1758
AIT, 2014 D25 / C3.2.2 version 1.1
'fc, • iijí^ Opening Up the Natural History Heritage ICTP^P Ur! for Europeana JTäJr
<dc : identif ier>MfN - Global Butterfly Information System (GloBIS) - 10325</dc : identifier> <dc : title>Papilio machaon Linnaeus, 17SB</dc : title> <dc : description>Current type depository: MFNB, Berlin (1 [m], syn type) // Cited type material: // Other remarks:</dc : description> <dc:description>Syntype(s)</dc:description> <dc : date>1903 (identification)</dc : date> <dc: relation>http://www.biodiversityiibrary.org /name/Papilio_machaon_Linnaeus%2C_17S8</dc : relation> <dc : source>Global Butterfly Information System (GloBIS)</dc: source> <dc : sub j ect>flutura bajrake</dc : sub j ect> <dc : sub j ect>Koninginnenpage</dc : sub j ect> <dc : sub j ect>makaonfjãril</dc : sub j ect> <dc : sub j ect>Svalehale</dc : sub j ect> <dc : sub j ect>svaiestjert</dc : sub j ect> <dc : sub j ect>Swallowtail</dc : sub j ect> <dc: subject>MaxaoH</dc: subject> <dc : sub j ect>Artemisia Swatlowtail</dc : sub j ect> <dc : sub j ectXľommon Yellow SwallowtaiK/dc : sub j ect> <dc : sub j ect>Old World Swallowtail</dc : sub j ect> <dc : sub j ect>Ritariperhonen</dc : sub j ect> <dc: subject>Le Grand Porte-queue</dc : sub j ect> <dc : sub j ect>Schwalbenschwanz</dc : sub j ect> <dc : sub j ect>Paz królowej</dc : sub j ect> <dc : sub j ect>Makaon</dc : sub j ect> <dc : subj ect>Makaonfjaril</dc : sub j act> <dc: subj ect>Riddarfjäril</dc : subj ect> <dc : subj ect>ritariperhonen</dc : subj ect> <dc: subj ect>Koninginnepage</dc : sub ject> <dc : subj ect>fecskefarkű iepke</dc : subj ect> <dc : subj ect>Fecskefarkú piHe</dc : subj ect> <dc : subject>http://openup.nhm-wien.ac.at/commonNames/references/scientificName /1549</dc:subj ect> <dc : type>Preserved Specimen</dc : type> <dcterms:spatial>Japan</dcterms:spatial> <dcterms : temporalX/dcterms : fcemporal> <edm:hasType rdf:resource="http://rs.tdwg.org/dwc/dwctype/PraservedSpecimen"> </edm:hasType> <edm: type>IMAGE</edni: type>
</edm:ProvidedCHO>
Figure 10 Record with description of the object
The stylesheet defines that the vocabulary information is added to a record via the metadata fields dc:subject. For each abcd:FullScientificNameString the vocabulary is searched for an appropriate common name. When one is found it is added to the metadata as a value of dasubject. In addition, the source of the .common name with its reference link is added to the final dasubject metadata field (see Figure 10).
In Europeana the record with the subjects looks like shown in Figure 11.
http:;7www.btodlv»fs)ty(torary.or3/naine/Papílio_machaon_Unnaeus%2C_175S; http'Wrs.ttiwgorg/äwc'dwctype'PreservffdSpednro Source: Globe) Butterfly Information System (GloBIS) Duta providen GloBIS I Museum für Naturkunde Berlin Provider Open Upi Providing country: Germany
Auto-generated tags »
What »
Where »
Figure 11 Europeana record with Subjects
3 BIODIVERSITY HERITAGE LIBRARY
The stylesheet also defines that for each scientific name the BHL API "bibliography by URL" is evoked and a link to the BHL bibliography is added in the dc:relation metadata field.
Description : Sį current type depository: MFNB, Beriłn U Cited type materiat Type: [m] In coll. Staudinser (Zoolog. Museum, Bertin) U Other remarks: Description: ¡Ü Hoiotype
Identffler: (Д щд - Global Butterfly Information System (GloBIS) - 8515 Source : (^Global Buüerfly Intormaïon System (GloBiS)
Relation : [į t Spatial Coverage : Hį Japan
Has Type: Sį htlpZ/rsMivgorgtevc/dVfcJype/PreservedSpeämen Europeana Type: [į |mage
Figure 14 Record with dc:relation
When clicking on http://www.biodiversitvlibrarv.org/name/Luehdorfia japónica Leech%2C 1889 (28. Jan. 2014.) the following information can be seen (see Figure 15).
Figure 15 Bibliographie information concerning Luehdorfia japónica Leech, 1889
When clicking on one of the result sets (Page # for example the first one) the bibliographic source is shown in detail (see Figure 16).
BHL About BHL Help Biodiversity Heritage Library
y/Fwrnt Search
Figure 16 Bibliographic source in detail
AIT, 2014 D25 / C3.2.2 version 1.1 p. 13
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. Opening Up the Natural History Heritage IfToCD UP! for Europeana 'Ь1ЩГ
In Europeana the relation looks like shown in Figure 17.
Luehdorfia japónica Leech, 1889 ! β«*.·!.»*»·. I
Ш Description: Current type depository MFNB, Berlin // Cited type material; ; TW» | Type; [m] in col Slaudiriger (Zoolog. Museum, Bertin)// Other remarks.; ļ Luetxtoma japonka Leech 1889 (1) ι Hototype what |
View item at GloBIS / Museum für Naturku nde Berlin Ef
klentffler: MfN - Global Butterfly Information System (GloBIS) - 8515 RetatJon: ПШННШШШШШдИШНШЙШ httpY/rs tdwg org/dwc/dwctype/PreservedSpecimen
Source: Global Butterfly Information System (GloBIS) Osta provider. GloBIS / Museum fflr Naturkunde Berlin Provider Openllpl
Share Providing country: Germany
\S(7 Cite on Wikipedia Auto-generated tags '
tà Translate details
Select language
Powered by Mlcrosoit®Translator
Figure 17 The BHL-service in Europeana
4 GEONAMES and DWC Type vocabulary
When a raw record contains geographic coordinates the http://www.eeonames.org/maps/google %7BLatitudeDecimal%7D %7BLongitudeDecimal%7D.html service is used. In the stylesheet the service is mapped to edm:Place. (see Figure 18).
<xsl:lf test="LongtţudeOecU»l andLatttud«Decimal and eotCtongltudeoeclnaWe1 and LatttudeOeclnaX«'»')"> <«fn: Place rdf:about=*http;//wwM,BHBHB-org/naps/gDogl«_ÎLatlti)d»Oeclna'l}_[Longltut}eDeclnal} .HtnV»
Ranunculus trichophyllus Chalx Detcription: Hydrobotanische Exkursion ins Wiener Becken unter der Leitung von UnivProíDr. Georg Janauer. Contributor: Gili,C (collector), C. Gidi & G. Janauer (identifier)
Source: University of Vienna, Institute for Botany - Herbarium WU Data provider University of Vienna, Institute for Botany - Herbarium WU Provider OpenUpl
Providing country: Austria
Auto-generated lags *
What·
Where * Place Term: http7/www geonames org/maps/google_47 7208333327 16 0672222216 html
Geo Space: 47.720833, 16.067223
Search also for
Titte Ranunculus tnchophyJfus Chaix (52)
Who Gilts,C (cołfeclor) (1140) C Girti & G Janauef (identifier) (14)
What Preserved Specimen (1170381) Water buttercup (5)
Provider UnPYersüy of Vienna Instituie for Botan y-Herbarium WU (26174) OpenUpí (1520441)
Figure 20 Europeana record with "Geographic coverage"and "Place Term"information
AIT, 2014 D25 / C3.2.2 version 1.1 p. 15
Ол jè-—
. .q·''' Opening Up the Natural History Herltage 1£Ţr UP! for Europeana ™».1
Who Gift Ľ (Cü#CCtïW>(1l33) c Gđa β G tóflauer (identifier) (14)
What FreseivedSpeílnxífl (B&43fl1) Wat e f butte'eup (5)
Provider Ореяир! (1240571)
Relation: http://www biodìvereitylibrary org/nama/Ranud http://re.tdwg org/dwc/dwctype/PreservadSpsdmen Link tO DaľWÍn СОГе Vocabulary Source: University of Vienna, Institute fori kny - Hert
Provider: OpenUp! J L Providing couoffîr riinjnn
Auto-genera tec
What * Concept Term Concept Label
! Term Name: preservedšpedmen
Identifier:
Deflnłoon:
Comment:
Type of Term:
Member Of:
Verston:
Refines:
Deta is:
http://rs.tdwg.org/dwc/dwctYpc/PresefvedSpedmen
A resource describing a preserved specimen.
For discussion see ö
http://www.w3.Org/2000/01/rdf-schema#Ctass
http://rs.tdwg.org/dwc/terms/DwCType
PreservedSpedmen-2011-10-16
PreservgdSoedmen
Figure 22 Europeana record with Link to Darwin Core Type vocabulary
2 http://rs.tdwg.org/dwc/dwctvpe/ 28 Jan 2014.
AIT, 2014 D25 / C3.2.2 version 1.1
. Opening Up the Natural History Heritage UP. for Europeana
5 LIST OF FIGURES
Figure 1 Ingesting records into Europeana (technical components) 4
Figure 2 EDM Stylesheet 5
Figure 3 Extended Pentaho Transformation with REST service (marked red) 6
Figure 4 The Filter Rows step "Voc URI?" 7
Figure 5 Step 2: Adding a namespace 7
Figure 6 Pentaho Ontology Service access 8
Figure 7 Pentaho Parameters 8
Figure 8 Renaming "abcdXMLwithVoc" to "abcdXML" 9
Figure 9 Papilio machaon Linnaeus, 1758 9
Figure 10 Record with description of the object 10
Figure 11 Europeana record with Subjects 11
Figure 12 Mapping dc:relation 11
Figure 13 Luehdorfia japónica Leech, 1889 12
Figure 14 Record with dc: relation 12
Figure 15 Bibliographic information concerning Luehdorfia japónica Leech, 1889 13
Figure 16 Bibliographic source in detail 13
Figure 17 The BHL-service in Europeana 14
Figure 18 Stylesheet containing geonames information 14
Figure 19 The specimen Ranunculus trichophyllus Chaix 15
Figure 20 Europeana record with "Geographic coverage" and "Place Term" information 15