I second Éamonn's suggestion to work closely with existing standards organization, especially TDWG,  GSC (Genomics Standards Consortium), and OBO Foundry (http://www.obofoundry.org/). Please do not invent another standard or a new ontology in a silo!

Ramona

------------------------------------------------------
Ramona L. Walls, Ph.D.
Scientific Analyst, The iPlant Collaborative, University of Arizona
Research Associate, Bio5 Institute, University of Arizona
Laboratory Research Associate, New York Botanical Garden

On Wed, Mar 11, 2015 at 2:03 AM, Éamonn Ó Tuama [GBIF] <[log in to unmask]> wrote:

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_bioversitypublications_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-network-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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