Dear colleagues,

Using MCPD descriptors is a good starting point. In my opinion, the
OTHERNUMB descriptor is a very important one. From the EURISCO experiences I
know that also in well-organised genebanks accessions numbers may change
more often than we would like. Also taxonomic information is changing from
time to time. So any other number (e.g. internal DB identifier, sample ID of
a donor etc.) which is available would be a great help.

Best regards,
Stephan

> -----Original Message-----
> From: Global Information System on PGRFA [mailto:GLIS-PGRFA-
> [log in to unmask]] On Behalf Of Alercia, Adriana (Bioversity)
> Sent: Thursday, March 12, 2015 3:25 PM
> To: [log in to unmask]
> Subject: Re: Week 3 - MCPD to DWC mapping - the DwC germplasm
> extension
> 
> Dear Marco, Francisco and colleagues,
> 
> I agree with proposals below and would add that the concepts:
> INSTCODE:ACCENUMB but also GENUS/SPECIES mostly provide an
> acceptable key to the germplasm accessions and what is of outmost
> importance are available data of any genebank.
> 
> 
> 
> Those identifiers listed below are fine. Regarding the ‘kernel’ Marco is
> referring to, in addition to the descriptors above, I would agree on
including:
> Accession name, Donor institute code, Common crop name, Ancestral data
> (this could help in tracing back its origin) and Acquisition date.
> 
> 
> 
> With regards to ‘collecting’ descriptors, yes, I believe that COLLNUMBER
> (original sample identifier, valuable when searching duplicates among
> germplasm collections), ORIGCTY (Country of origin); and COLLDATE
> (optional?), are useful descriptors along with OTHERNUM.
> 
> 
> 
> Information on the BREDCODE and SAMPSTAT could be important too.
> 
> 
> 
> Finally, it is important to also consider ‘data availability’ for the
‘priority’
> (kernel)  descriptors identified. From a practical point of view, out of
the 28
> MCPD descriptors that are being used since 1997, maybe only the half have
> ‘data’ in  available platforms, the rest is empty. I agree on defining a
small set
> before and later build on that.
> 
> Best,
> 
> Adriana
> 
> 
> 
> From: Global Information System on PGRFA [mailto:GLIS-PGRFA-
> [log in to unmask]] On Behalf Of Lopez, Francisco (AGDT)
> Sent: Thursday, March 12, 2015 11:12 AM
> To: [log in to unmask]
> Subject: Week 3 - MCPD to DWC mapping - the DwC germplasm extension
> 
> 
> 
> Dear Marco,
> 
>                               I would like add MLSSTAT to this list of
initial set of fields to be
> associated with the global identifier to know whether the material is the
> Multilateral System or not.
> 
> 
> 
> I also think that DONORCODE and DONORNUMBER as well as OTHERNUMB
> (eg. collecting number in GRIN-Global) could be also very useful to find
out
> potential duplicates and for the Global system to facilitate relationships
when
> the material is transferred.
> 
> 
> 
> Following on the discussions we had in the previous weeks, I also support
the
> inclusion of SAMPSTAT in the list.
> 
> 
> 
> Thank you.
> 
> Regards,
> 
> Francisco
> 
> 
> 
> From: Global Information System on PGRFA [mailto:GLIS-PGRFA-
> [log in to unmask]] On Behalf Of Marsella Marco
> Sent: 12 March 2015 10:13
> To: [log in to unmask]
> Subject: Re: Week 3 - MCPD to DWC mapping - the DwC germplasm
> extension
> 
> 
> 
> Dear colleagues,
> 
> as an attempt to keep the discussion on very practical terms, I would like
to
> follow-up on Dag’s message below. Trying for a moment not to focus too
> much on the specific ontology, can we compile a short list of “kernel”
fields
> that:
> 
> 
> 
> - are readily available to users who will be registering PGRFA in GLIS,
e.g.
> genebanks
> 
> - can be used to discriminate two different PGRFA
> 
> - convey enough information to the querying user or application
> 
> - can be marked as mandatory to register a new PGRFA in GLIS
> 
> 
> 
> My initial proposal would be, using MCPD terminology:
> 
> 
> 
> INSTCODE
> 
> ACCENUMB
> 
> GENUS
> 
> SPECIES
> 
> SPAUTHOR
> 
> SUBTAXA
> 
> SUBAUTHOR
> 
> 
> 
> I would also include CROPNAME but, without referencing a controlled
> vocabulary, it cannot be used as key field given the wide variations in
> common crop names we are already experiencing in Easy-SMTA. It can very
> well be an optional field instead, although it would be great to have it
> translated…
> 
> 
> 
> What about the collection information? Would they be useful to
discriminate
> two different PGRFA coming from the same institute? Isn’t the Accession
> Number enough?
> 
> 
> 
> Do we add SAMPSTAT?
> 
> 
> 
> Once we define this “kernel” description, we can extend it as we se fit
with
> optional fields.
> 
> 
> 
> Best regards
> 
> 
> 
> M
> 
> 
> 
> 
> 
> 	On 10 Mar 2015, at 22:02, Dag Endresen
> <[log in to unmask]> wrote:
> 
> 
> 
> 	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_bioversityp
> ublications_pi1%5BshowUid%5D=6901
> <http://www.bioversityinternational.org/index.php?id=19&user_bioversityp
> ublications_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
> <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
> <http://doi.org/10.17161/bi.v8i1.4095> ]
> 
> 	[4] Germplasm vocabulary [http://terms.tdwg.org/wiki/Germplasm]
> [https://code.google.com/p/darwincore-germplasm/
> <http://terms.tdwg.org/wiki/Germplasm%5d%20%5bhttps:/code.google.co
> m/p/darwincore-germplasm/> ]
> 
> 	[5] http://www.slideshare.net/DagEndresen/european-
> agrobidioversity-ecpgr-network-meeting-on-eurisco-central-crop-
> databases-and-users-prague-may-2014
> <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
> <http://doi.org/10.1371/journal.pone.0089606> ]
> 
> 	[7] http://biocodecommons.org/ <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
> <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
> <http://www.semantic-web-journal.net/system/files/swj635.pdf> ]
> 
> 
> 
> 
> 
> 	-----------------------------
> 
> 	From: Lopez, Francisco (AGDT) <[log in to unmask]
> <mailto:[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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> 
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> 
> 
> 
> 
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