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From:
Éamonn Ó Tuama [GBIF] <[log in to unmask]>
Reply To:
Global Information System on PGRFA <[log in to unmask]>
Date:
Wed, 11 Mar 2015 10:03:50 +0100
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Dear All,

 

Reading through the requirements, a few items stand out for me.

 

I would encourage GLIS to adopt RDF for the metadata from the start as that
will avoid the restrictions often encountered with XML schema based models
(e.g., ISO 19139, EML). I think the approach promoted by Dublin Core for
extensible metadata application profiles [1] is worth investigating. RDF
should allow you to make relations explicit in the metadata. The use of RDF
should also encourage re-use of existing vocabularies thus promoting
interoperability and the GLIS can benefit from ongoing work in TDWG and
elsewhere, highlighted by Dag, to provide a solid foundation to biodiversity
informatics through ontology development.

 

I agree that a key function of the metadata will be to contain the mappings
to related identifiers so that already existing identifiers are preserved.

 

Best regards,

Éamonn

 

[1] http://dublincore.org/documents/2009/05/18/profile-guidelines/

 

From: Global Information System on PGRFA
[mailto:[log in to unmask]] On Behalf Of Dag Endresen
Sent: 10 March 2015 22:02
To: [log in to unmask]
Subject: Fw: Week 3 - MCPD to DWC mapping - the DwC germplasm extension

 

Dear all,

Francisco has encouraged me to share the mapping table  between the MCPD [1]
and the Darwin Core standard [2] as input to the discussions for week 3 on
metadata. When this mapping was developed [3], we started with the Darwin
Core and created an extension to include the descriptors from the MCPD not
already covered by terms established in the Darwin Core. The mapping has
later developed into a SKOS vocabulary of terms [4]. An overview of this
mapping (Germplasm Vocabulary) was also presented at the ECPGR Information
and documentation network meeting last year [5] (see slide number 27).

 


MCPD to DWC mapping


MCPD

DWC


 

dwc.datasetID


 

dwc.occurrenceID


INSTCODE

dwc.institutionCode


ACCENUMB

dwc.catalogNumber


COLLNUMB

dwc.recordNumber


COLLCODE

g.collectingInstituteID


COLLNAME

dwc.recordedBy


COLLINSTADDRESS

dwc.recordedBy


COLLMISSID

dwc.collectionCode


GENUS

dwc.genus


SPECIES

dwc.specificEpithet


SPAUTHOR

dwc.scientificNameAuthorship


SUBTAXA

dwc.infraspecificEpithet, dwc.taxonRank


SUBTAUTHOR

dwc.scientificNameAuthorship


CROPNAME

dwc.vernacularName


ACCENAME

g.breedingIdentifier 


ACQDATE

g.acquisitionDate 


ORIGCTY

dwc.countryCode


COLLSITE

dwc.locality


DECLATITUDE

dwc.decimalLatitude


LATITUDE

dwc.verbatimLatitude


DECLONGITUDE

dwc.decimalLongitude


LONGITUDE

dwc.verbatimLongitude


COORDUNCERT

dwc.coordinateUncertaintyInMeters


COORDDATUM

dwc.geodetic.Datum


GEOREFMETH

dwc.georeferenceSources


ELEVATION

dwc.minimumElevationinMeters


COLLDATE

dwc.eventDate


BREDCODE

g.breederInstituteID 


BREDNAME

g.breedingInstitute


SAMPSTAT

g.biologicalStatus 


ANCEST

g.ancestralData, g.purdyPedigree


COLLSRC

g.acquisitionSource


DONORCODE

g.donorInstituteID


DONORNAME

g.donorInstitute


DONORNUMB

g.donorsIdentifier


OTHERNUMB

dwc.otherCatalogNumbers


DUPLSITE

g.safetyDuplicationInstituteID


DUPLINSTNAME

g.safetyDuplicationInstitute


STORAGE

g.storageCondition


MLSSTAT

g.mlsStatus


REMARKS

dwc.occurrenceRemarks

		

Extensions


Term

Description


dwc.relatedResourceID

Allow for definition f any relation type between the current entity and
another entity


dwc.relationshipOfResource


dwc.relationshipRemarks


dwc.relationshipAccordingTo


dwc.relationshipEstablishedDate


dc.references

Allows for additional targets to be associated to the Entity for multiple
resolution

 

 

I would also like to highlight two other recent developments that I find
particular relevant to the discussion for metadata this week. The first
activity is championed by Ramona Walls and seeks to develop and ontological
anchoring for the Darwin Core terminology [6,7] for specimens such as the
genebank accessions, PGRFA. The second activity is the development
championed by Steve Baskauf of an ontology for describing relationships
between Darwin Core entities [8] and an RDF guide for Darwin Core [9].

 

Best regards

Dag Endresen

[1] Alercia A., S. Diulgheroff, and M. Mackay (2012). FAO/Bioversity
Multi-crop passport descriptors v.2 [MCPD v.2]. Food and Agriculture
Organization of the United Nations (FAO), and Bioversity International,
Rome, Italy. 11 pp. Available at
[http://www.bioversityinternational.org/index.php?id=19&user_bioversitypubli
cations_pi1%5BshowUid%5D=6901]

[2] Wieczorek J, Bloom D, Guralnick R, Blum S, Döring M, Giovanni R,
Robertson T, Vieglais D. (2012). Darwin Core: An Evolving
Community-Developed Biodiversity Data Standard. PLoS ONE 7:e29715.
[http://doi.org/10.1371/journal.pone.0029715]

[3] Endresen DTF and Knüpffer H (2012). The Darwin Core extension for
genebanks opens up new opportunities for sharing genebank datasets.
Biodiversity Informatics 8:12-29. [http://doi.org/10.17161/bi.v8i1.4095]

[4] Germplasm vocabulary [http://terms.tdwg.org/wiki/Germplasm]
[https://code.google.com/p/darwincore-germplasm/]

[5]
http://www.slideshare.net/DagEndresen/european-agrobidioversity-ecpgr-networ
k-meeting-on-eurisco-central-crop-databases-and-users-prague-may-2014

[6] Walls R, Deck J, Guralnick R, et al. (2014). Semantics in Support of
Biodiversity Knowledge Discovery: An Introduction to the Biological
Collections Ontology and Related Ontologies. PLoS ONE 9(3):e89606.
[http://doi.org/10.1371/journal.pone.0089606]

[7] http://biocodecommons.org/

[8] Baskauf SJ, & Webb CO (2014). Darwin-SW: Darwin Core-based terms for
expressing biodiversity data as RDF. Semantic web [#995-2206].
[http://www.semantic-web-journal.net/system/files/swj995.pdf]

[9] Baskauf SJ, Wieczorek J, Deck J, Webb CO (2014). An RDF guide for the
Darwin Core standard. Semantic web [#636-1846]
[http://www.semantic-web-journal.net/system/files/swj635.pdf] 

 

 

-----------------------------

From: Lopez, Francisco (AGDT) <[log in to unmask]>
Sent: 10 March 2015 16:56
To: Dag Endresen
Subject: Week 3 - MCPD to DWC mapping - the DwC germplasm extension 

 

Dear Dag,

                I think that it is very relevant, for the discussions of
week 3 we started today, that we show this mapping table with all the
participants (DwC germplasm extension).  As it is very much based on your
work,  I think that it is more appropriate for you to circulate it.  Unless
you prefer we do it. 

 

Thank you.

Regards,

Francisco

 

 

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