Difference between revisions of "CETAF Specimen Preview Profile (CSPP)"

Latest revision as of 18:02, 30 January 2023

The CSPP is a minimal set of agreed (RDF) collection metadata elements implemented consistently across CETAF organisations (see minutes of the Geneva meeting of the ISTC stable identifier initiative). The purpose of CSPP is to provide a stable resource enabling preview functions in specimen portals. The CSPP is not meant to be comprehensive, which means that Linked Open (collection) Data implementations of CETAF institutions will usually provide much richer metadata with additional RDF-elements.

CSPP Elements

CSPP element	Mandatory	RDF resource URI	Notes
title	yes	http://purl.org/dc/terms/title	Mandatory. Collection may decide themselves on the content of the title element. This could usually be a scientific name (with or without authorship), but it could also contain additional information on collectors and projects for example.
kindOfMaterial	no	http://purl.org/dc/terms/type	The nature of the specimen. Example: herbarium sheet, fossil, conserved in alcohol
scientificNameCurrent	no	http://rs.tdwg.org/dwc/terms/scientificName	The latest full scientific name, with authorship and date information if known.
family	no	http://rs.tdwg.org/dwc/terms/family	The full scientific name of the family in which the taxon is classified.
scientifcNameOriginal	no	http://rs.tdwg.org/dwc/terms/previousIdentifications	The original name appearing on the specimen.
collectorNumber	no	http://rs.tdwg.org/dwc/terms/fieldNumber	An identifier given to the Occurrence at the time it was recorded. Often serves as a link between field notes and an Occurrence record, such as a specimen collector’s number.
collectorName	no	http://rs.tdwg.org/dwc/terms/recordedBy	A list (concatenated and separated) of names of people, groups, or organizations responsible for recording the original Occurrence. The primary collector or observer, especially one who applies a personal identifier (recordNumber), should be listed first.
webscaledImageLink	no	http://rs.tdwg.org/dwc/terms/associatedMedia	Link to “nice” webscaled image.
latitude	no	http://rs.tdwg.org/dwc/terms/decimalLatitude	The geographic latitude (WGS84, in decimal degrees, using the spatial reference system given in geodeticDatum) of the geographic center of a Location. Positive values are north of the Equator, negative values are south of it. Legal values lie between -90 and 90, inclusive.
longitude	no	http://rs.tdwg.org/dwc/terms/decimalLongitude	The geographic longitude (WGS84, in decimal degrees, using the spatial reference system given in geodeticDatum) of the geographic center of a Location. Positive values are east of the Greenwich Meridian, negative values are west of it. Legal values lie between -180 and 180, inclusive.
isoCountry	no	http://rs.tdwg.org/dwc/terms/countryCode	The standard (ISO 3166-1 alpha-2) code for the country in which the specimen has been collected. Recommended best practice is to use ISO 3166-1-alpha-2 country codes.
collectionDate	no	http://purl.org/dc/terms/created	(ISO) date of the gathering event.
sourceLink	no	http://purl.org/dc/terms/publisher	URI to a web page with information about the institution/collection/owner responsible for publishing the specimen.

CSPP-compliant RDF-documents

An example with all recommended elements would look like this:

<?xml version="1.0" encoding="utf-8"?>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
    xmlns:dwc="http://rs.tdwg.org/dwc/terms/"
    xmlns:dc="http://purl.org/dc/terms/">

  <!-- Because this very RDF document got to by a redirect (HTTP response code 303 (=See Other)) this is only metadata about the document, the CETAF-ID is comming later below -->
  <rdf:Description rdf:about="http://herbarium.bgbm.org/data/rdf/B100068798">
    <!-- relate RDF document to the CETAF-ID (rdf:Description below) -->
    <dc:subject rdf:resource="http://herbarium.bgbm.org/object/B100068798"/>
    <!-- the date time this very RDF file was created -->
    <dc:created>2019-11-11T15:41:25+01:00</dc:created>
  </rdf:Description>

  <!--This is metadata about this specimen and the originally requested CETAF-ID -->
  <rdf:Description rdf:about="http://herbarium.bgbm.org/object/B100068798">
    <!--   CSPP element: title (mandatory)  -->
    <dc:title>Erysimum salangense Polatschek &amp; Rech.f.</dc:title>
    <!--   CSPP element: collectionDate   -->
    <dc:created>1967-07-14</dc:created>
    <!--   CSPP element: kindOfMaterial   -->
    <dc:type>Specimen</dc:type>
    <!--   CSPP element: sourceLink   -->
    <dc:publisher rdf:resource="https://www.bgbm.org" />
    <!--   CSPP elements: scientificNameCurrent, scientifcNameOriginal, family  -->
    <dwc:scientificName>Erysimum salangense Polatschek &amp; Rech.f.</dwc:scientificName>
    <dwc:previousIdentifications>Erysimum salangense Polatschek &amp; Rech.f.</dwc:previousIdentifications>
    <dwc:family>CRUCIFERAE</dwc:family>
    <!--   CSPP element: isoCountry   -->
    <dwc:countryCode>AF</dwc:countryCode>
    <!--   CSPP element: longitude   -->
    <dwc:decimalLongitude rdf:datatype="http://www.w3.org/2001/XMLSchema#decimal">69.033332824707</dwc:decimalLongitude>
    <!--   CSPP element: latitude   -->
    <dwc:decimalLatitude rdf:datatype="http://www.w3.org/2001/XMLSchema#decimal">35.366664886475</dwc:decimalLatitude>
    <!--   CSPP element: collectorName   -->
    <dwc:recordedBy>Rechinger,K.H.</dwc:recordedBy>
    <!--   CSPP element: collectorNumber   -->
    <dwc:fieldNumber>37047</dwc:fieldNumber>
    <!--   CSPP element: webscaledImageLink   -->
    <dwc:associatedMedia rdf:resource="http://ww2.bgbm.org/herbarium/images/B/10/00/68/79/B_10_0068798.jpg"/>
  </rdf:Description>
</rdf:RDF>

A more complex RDF—including other data sources and image data—is the example for the CETAF-ID http://herbarium.bgbm.org/object/B100068798 and it can contain the following:

<?xml version="1.0" encoding="utf-8"?>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
    xmlns:dwc="http://rs.tdwg.org/dwc/terms/"
    xmlns:dwciri="http://rs.tdwg.org/dwc/iri/"
    xmlns:dc="http://purl.org/dc/terms/"
    xmlns:owl="http://www.w3.org/2002/07/owl#">

  <!--This is metadata about this very RDF document (got to by redirect via HTTP response code 303 (=See Other)) -->
  <rdf:Description rdf:about="http://herbarium.bgbm.org/data/rdf/B100068798">
    <!-- relate RDF document to the CETAF-ID (rdf:Description below) -->
    <dc:subject rdf:resource="http://herbarium.bgbm.org/object/B100068798"/>
    <!-- the date time this very RDF file was created -->
    <dc:created>2019-11-11T15:41:25+01:00</dc:created>
  </rdf:Description>

  <!--This is metadata about this specimen and the originally requested CETAF-ID -->
  <rdf:Description rdf:about="http://herbarium.bgbm.org/object/B100068798">
    <!--   CSPP element: title (mandatory)  -->
    <dc:title>Erysimum salangense Polatschek &amp; Rech.f.</dc:title>
    <dc:description>A herbarium specimen of Erysimum salangense Polatschek &amp; Rech.f. collected by Rechinger,K.H.</dc:description>
    <dc:creator>Rechinger, K.H.</dc:creator>
    <!--   CSPP element: collectionDate   -->
    <dc:created>1967-07-14</dc:created>
    <!--   CSPP element: kindOfMaterial   -->
    <dc:type>Specimen</dc:type>
    <!--   CSPP element: sourceLink   -->
    <dc:publisher rdf:resource="https://www.bgbm.org" />
    <dwc:materialSampleID>http://herbarium.bgbm.org/object/B100068798</dwc:materialSampleID>
    <dwc:basisOfRecord>PreservedSpecimen</dwc:basisOfRecord>
    <dwc:collectionCode>B</dwc:collectionCode>
    <dwc:catalogNumber>B 10 0068798</dwc:catalogNumber>
    <!--   CSPP element: scientificNameCurrent   -->
    <dwc:scientificName>Erysimum salangense Polatschek &amp; Rech.f.</dwc:scientificName>
    <!--   CSPP element: scientifcNameOriginal   -->
    <dwc:previousIdentifications>Erysimum salangense Polatschek &amp; Rech.f.</dwc:previousIdentifications>
    <dwc:family>CRUCIFERAE</dwc:family>
    <dwc:genus>Erysimum</dwc:genus>
    <dwc:specificEpithet>salangense</dwc:specificEpithet>
    <dwc:country>Afghanistan</dwc:country>
    <!--   CSPP element: isoCountry   -->
    <dwc:countryCode>AF</dwc:countryCode>
    <dwc:locality>
      Afghanistan: NE-Afghanistan, Kathagan. Sar-i Hauz, in declivibus borealibus jugi Salang. substr. granit. Alt.: 2600 m. 14.07.1967, Leg.: K. H. Rechinger 37047.
    </dwc:locality>
    <!--   CSPP element: longitude   -->
    <dwc:decimalLongitude rdf:datatype="http://www.w3.org/2001/XMLSchema#decimal">69.033332824707</dwc:decimalLongitude>
    <!--   CSPP element: latitude   -->
    <dwc:decimalLatitude rdf:datatype="http://www.w3.org/2001/XMLSchema#decimal">35.366664886475</dwc:decimalLatitude>
    <dwc:eventDate>1967-07-14</dwc:eventDate>
    <dwc:recordNumber>37047</dwc:recordNumber>

    <!--   CSPP element: collectorName   -->
    <dwc:recordedBy>Rechinger,K.H.</dwc:recordedBy>
    <dwciri:recordedBy rdf:resource="http://www.wikidata.org/entity/Q78738"/><!--  Internationalized Resource Identifier (IRI) of recordedBy   -->
    <!--   CSPP element: collectorNumber   -->
    <dwc:fieldNumber>37047</dwc:fieldNumber>    

    <!--   CSPP element: webscaledImageLink   -->
    <dwc:associatedMedia rdf:resource="http://ww2.bgbm.org/herbarium/images/B/10/00/68/79/B_10_0068798.jpg"/>

    <!-- Experimental: add a relation to media data as iiif (see https://iiif.io) -->
    <dc:relation>
      <rdf:Description rdf:about="http://herbarium.bgbm.org/iiif/B100068798">
        <dc:identifier rdf:resource="http://herbarium.bgbm.org/iiif/B100068798"/>
        <dc:type rdf:resource="http://iiif.io/api/presentation/3#Manifest"/>
        <dc:subject rdf:resource="http://herbarium.bgbm.org/object/B100068798"/>
        <dc:format>application/ld+json</dc:format>
        <dc:description xml:lang="en">A IIIF resource for this specimen.</dc:description>
          <dc:created/>
        </rdf:Description>
    </dc:relation>
  </rdf:Description>

  <rdf:Description rdf:about="http://www.wikidata.org/entity/Q78738"><!-- further detail above dwciri:recordedBy -->
    <owl:sameAs rdf:resource="http://purl.oclc.org/net/edu.harvard.huh/guid/uuid/d5fea488-5786-4106-af90-396ef452c3aa"/>
    <owl:sameAs rdf:resource="https://viaf.org/viaf/100383596/"/>
  </rdf:Description>
</rdf:RDF>

Note that …

rdf:Description first describes the very RDF resource (got to by redirect) and it relates to the requested CETAF-ID by dc:subject
all the following rdf:Description elaborate the CSPP-details and more related properties to this species data (images, other same data objects etc.)
Other Data: for instance dwciri:recordedBy points to a WikiData IRI resource
-  this is further described by another rdf:Description which in itself points via owl:sameAs to other resources to be equal as the WikiData resource (this illustrates perhaps better read in TriG format)
- note that the whole dwciri namespace is intended for use with non-literal objects and the dwciri:recordedBy here has the same meaning as dwc:recordedBy and can be repeatable as well but points to an IRI-reference object instead of being a literal string value.
Media: besides the “nice” webscaled image (dwc:associatedMedia) …
- … there is also one dc:relation defined again in a rdf:Description with details for software clients that understand triple i-f (iiif—International Image Interoperability Framework https://iiif.io)
- … there could also be further dc:relation after the first one if it needs to, containing other relations

Additional recommended data terms

Data Term	RDF resource URI	Notes
`dwc:institutionCode`	http://rs.tdwg.org/dwc/terms/institutionCode	The name (or acronym) in use by the institution having custody of the object(s) or information referred to in the record. Examples: MVZ, BGBM, CLO, UCMP
`dwc:institutionID`	http://rs.tdwg.org/dwc/terms/institutionID	An identifier for the institution having custody of the object(s) or information referred to in the record. Examples: the ROR ID like `https://ror.org/00bv4cx53` (here for BGBM)
`dwc:basisOfRecord`	http://rs.tdwg.org/dwc/terms/basisOfRecord	The specific nature of the data record. Comments: Recommended best practice is to use the standard label of one of the Darwin Core classes. Examples: PreservedSpecimen or FossilSpecimen
`dwciri:recordedBy`	http://rs.tdwg.org/dwc/iri/recordedBy	A person, group, or organization responsible for recording the original Occurrence. (Note that terms in the `dwciri` namespace are intended to be used in RDF with non-literal objects). Example: `<dwciri:recordedBy rdf:resource="http://www.wikidata.org/entity/Q78738"/>`—this is the IRI-notation equivalent to the string notation of `<dwc:recordedBy>Rechinger, K.H.</dwc:recordedBy>`

Conversion into other formats (help for development)

For the purpose of developping the meta data eventually into RDF you can checked your RDF online by https://www.w3.org/RDF/Validator/ or use the command line tools of Apache Jena (jena.apache.org) which provide useful commands to parse, check and convert from one format to another—this can also help for readability.

RDF to TriG Format (CLI: trig) — See TriG Documentation (www.w3.org). This format can be read like sentences with a final dot marking the end of the statements; additional elements are separated by semicolon. (toggle on the right to see hidden content)

To convert it use in CLI

turtle --output=trig B100068798-Wiki-Example.rdf > B100068798-Wiki-Example.rdf.trig 2> B100068798-Wiki-Example.rdf.error.log

If you want to generate RDF from TriG back or have developed your meta data in TriG and want to generate RDF, use

trig --output=rdf/xml B100068798-Wiki-Example.rdf.trig

The RDF from above converted into TriG format looks (of course without line numbers) like the following (yellow indicates lines that are related):

 1 @prefix rdf:  <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
 2 @prefix dwc:  <http://rs.tdwg.org/dwc/terms/> .
 3 @prefix dwciri:  <http://rs.tdwg.org/dwc/iri/> .
 4 @prefix dc:  <http://purl.org/dc/terms/> .
 5 @prefix owl:  <http://www.w3.org/2002/07/owl#> .
 6 
 7 <http://herbarium.bgbm.org/data/rdf/B100068798>
 8         dc:subject  <http://herbarium.bgbm.org/object/B100068798> ;
 9         dc:created  "2019-11-11T15:41:25+01:00" .
10 
11 <http://herbarium.bgbm.org/object/B100068798>
12         dc:title                     "Erysimum salangense Polatschek & Rech.f." ;
13         dc:description               "A herbarium specimen of Erysimum salangense Polatschek & Rech.f. collected by Rechinger,K.H." ;
14         dc:creator                   "Rechinger, K.H." ;
15         dc:created                   "1967-07-14" ;
16         dc:type                      "Specimen" ;
17         dc:publisher                 <https://www.bgbm.org> ;
18         dwc:materialSampleID         "http://herbarium.bgbm.org/object/B100068798" ;
19         dwc:basisOfRecord            "Specimen" ;
20         dwc:collectionCode           "B" ;
21         dwc:catalogNumber            "B 10 0068798" ;
22         dwc:scientificName           "Erysimum salangense Polatschek & Rech.f." ;
23         dwc:previousIdentifications  "Erysimum salangense Polatschek & Rech.f." ;
24         dwc:family                   "CRUCIFERAE" ;
25         dwc:genus                    "Erysimum" ;
26         dwc:specificEpithet          "salangense" ;
27         dwc:country                  "Afghanistan" ;
28         dwc:countryCode              "AF" ;
29         dwc:locality                 "\n      Afghanistan: NE-Afghanistan, Kathagan. Sar-i Hauz, in declivibus borealibus jugi Salang. substr. granit. Alt.: 2600 m. 14.07.1967, Leg.: K. H. Rechinger 37047.\n    " ;
30         dwc:decimalLongitude         69.033332824707 ;
31         dwc:decimalLatitude          35.366664886475 ;
32         dwc:eventDate                "1967-07-14" ;
33         dwc:recordNumber             "37047" ;
34         dwc:recordedBy               "Rechinger,K.H." ;
35         dwc:fieldNumber              "37047" ;
36         dwciri:recordedBy            <http://www.wikidata.org/entity/Q78738> ;
37         dwc:associatedMedia          <http://ww2.bgbm.org/herbarium/images/B/10/00/68/79/B_10_0068798.jpg> ;
38         dc:relation                  <http://herbarium.bgbm.org/iiif/B100068798> .
39 
40 <http://herbarium.bgbm.org/iiif/B100068798>
41         dc:identifier   <http://herbarium.bgbm.org/iiif/B100068798> ;
42         dc:type         <http://iiif.io/api/presentation/3#Manifest> ;
43         dc:subject      <http://herbarium.bgbm.org/object/B100068798> ;
44         dc:format       "application/ld+json" ;
45         dc:description  "A IIIF resource for this specimen."@en ;
46         dc:created      "" .
47 
48 <http://www.wikidata.org/entity/Q78738>
49         owl:sameAs  <http://purl.oclc.org/net/edu.harvard.huh/guid/uuid/d5fea488-5786-4106-af90-396ef452c3aa> ;
50         owl:sameAs  <https://viaf.org/viaf/100383596/> .

RDF to Simple Triples (CLI: rdfparse) — See Documentation of Simple Triples of Turtle format (www.w3.org). This step converts or resolves RDF into subject—predicate—object. (toggle on the right to see hidden content)

The RDF-example provided above can be checked using turtle B100068798-Wiki-Example.rdf

<http://herbarium.bgbm.org/data/rdf/B100068798> <http://purl.org/dc/terms/subject> <http://herbarium.bgbm.org/object/B100068798> .
<http://herbarium.bgbm.org/data/rdf/B100068798> <http://purl.org/dc/terms/created> "2019-11-11T15:41:25+01:00" .
<http://herbarium.bgbm.org/object/B100068798> <http://purl.org/dc/terms/title> "Erysimum salangense Polatschek & Rech.f." .
<http://herbarium.bgbm.org/object/B100068798> <http://purl.org/dc/terms/description> "A herbarium specimen of Erysimum salangense Polatschek & Rech.f. collected by Rechinger,K.H." .
<http://herbarium.bgbm.org/object/B100068798> <http://purl.org/dc/terms/creator> "Rechinger, K.H." .
<http://herbarium.bgbm.org/object/B100068798> <http://purl.org/dc/terms/created> "1967-07-14" .
<http://herbarium.bgbm.org/object/B100068798> <http://purl.org/dc/terms/type> "Specimen" .
<http://herbarium.bgbm.org/object/B100068798> <http://purl.org/dc/terms/publisher> <https://www.bgbm.org> .
<http://herbarium.bgbm.org/object/B100068798> <http://rs.tdwg.org/dwc/terms/materialSampleID> "http://herbarium.bgbm.org/object/B100068798" .
<http://herbarium.bgbm.org/object/B100068798> <http://rs.tdwg.org/dwc/terms/basisOfRecord> "Specimen" .
<http://herbarium.bgbm.org/object/B100068798> <http://rs.tdwg.org/dwc/terms/collectionCode> "B" .
<http://herbarium.bgbm.org/object/B100068798> <http://rs.tdwg.org/dwc/terms/catalogNumber> "B 10 0068798" .
<http://herbarium.bgbm.org/object/B100068798> <http://rs.tdwg.org/dwc/terms/scientificName> "Erysimum salangense Polatschek & Rech.f." .
<http://herbarium.bgbm.org/object/B100068798> <http://rs.tdwg.org/dwc/terms/previousIdentifications> "Erysimum salangense Polatschek & Rech.f." .
<http://herbarium.bgbm.org/object/B100068798> <http://rs.tdwg.org/dwc/terms/family> "CRUCIFERAE" .
<http://herbarium.bgbm.org/object/B100068798> <http://rs.tdwg.org/dwc/terms/genus> "Erysimum" .
<http://herbarium.bgbm.org/object/B100068798> <http://rs.tdwg.org/dwc/terms/specificEpithet> "salangense" .
<http://herbarium.bgbm.org/object/B100068798> <http://rs.tdwg.org/dwc/terms/country> "Afghanistan" .
<http://herbarium.bgbm.org/object/B100068798> <http://rs.tdwg.org/dwc/terms/countryCode> "AF" .
<http://herbarium.bgbm.org/object/B100068798> <http://rs.tdwg.org/dwc/terms/locality> "\n      Afghanistan: NE-Afghanistan, Kathagan. Sar-i Hauz, in declivibus borealibus jugi Salang. substr. granit. Alt.: 2600 m. 14.07.1967, Leg.: K. H. Rechinger 37047.\n    " .
<http://herbarium.bgbm.org/object/B100068798> <http://rs.tdwg.org/dwc/terms/decimalLongitude> "69.033332824707"^^<http://www.w3.org/2001/XMLSchema#decimal> .
<http://herbarium.bgbm.org/object/B100068798> <http://rs.tdwg.org/dwc/terms/decimalLatitude> "35.366664886475"^^<http://www.w3.org/2001/XMLSchema#decimal> .
<http://herbarium.bgbm.org/object/B100068798> <http://rs.tdwg.org/dwc/terms/eventDate> "1967-07-14" .
<http://herbarium.bgbm.org/object/B100068798> <http://rs.tdwg.org/dwc/terms/recordNumber> "37047" .
<http://herbarium.bgbm.org/object/B100068798> <http://rs.tdwg.org/dwc/terms/recordedBy> "Rechinger,K.H." .
<http://herbarium.bgbm.org/object/B100068798> <http://rs.tdwg.org/dwc/terms/fieldNumber> "37047" .
<http://herbarium.bgbm.org/object/B100068798> <http://rs.tdwg.org/dwc/iri/recordedBy> <http://www.wikidata.org/entity/Q78738> .
<http://herbarium.bgbm.org/object/B100068798> <http://rs.tdwg.org/dwc/terms/associatedMedia> <http://ww2.bgbm.org/herbarium/images/B/10/00/68/79/B_10_0068798.jpg> .
<http://herbarium.bgbm.org/object/B100068798> <http://purl.org/dc/terms/relation> <http://herbarium.bgbm.org/iiif/B100068798> .
<http://herbarium.bgbm.org/iiif/B100068798> <http://purl.org/dc/terms/identifier> <http://herbarium.bgbm.org/iiif/B100068798> .
<http://herbarium.bgbm.org/iiif/B100068798> <http://purl.org/dc/terms/type> <http://iiif.io/api/presentation/3#Manifest> .
<http://herbarium.bgbm.org/iiif/B100068798> <http://purl.org/dc/terms/subject> <http://herbarium.bgbm.org/object/B100068798> .
<http://herbarium.bgbm.org/iiif/B100068798> <http://purl.org/dc/terms/format> "application/ld+json" .
<http://herbarium.bgbm.org/iiif/B100068798> <http://purl.org/dc/terms/description> "A IIIF resource for this specimen."@en .
<http://herbarium.bgbm.org/iiif/B100068798> <http://purl.org/dc/terms/created> "" .
<http://www.wikidata.org/entity/Q78738> <http://www.w3.org/2002/07/owl/sameAs> <http://purl.oclc.org/net/edu.harvard.huh/guid/uuid/d5fea488-5786-4106-af90-396ef452c3aa> .
<http://www.wikidata.org/entity/Q78738> <http://www.w3.org/2002/07/owl/sameAs> <https://viaf.org/viaf/100383596/> .

Further Questions and Discussion

Difference between revisions of "CETAF Specimen Preview Profile (CSPP)"

Latest revision as of 18:02, 30 January 2023

Contents

CSPP Elements

CSPP-compliant RDF-documents

Additional recommended data terms

Conversion into other formats (help for development)

Further Questions and Discussion

Navigation menu

Personal tools

Namespaces

Variants

Views

More

Search

Navigation

Tools