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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