Dear colleagues,
As we are approaching the end of the first week I would like to comment on the issue of “entity” and “accession number”. We may want to clearly indicate that. (B) The Treaty community already dealt with this issue during the process for the development Standard Material Transfer Agreement (SMTA) and the document refers more generically, following the text of the Treaty, to “PGRFA” for which the definition is included in paragraph 2 of the SMTA.
“Plant Genetic Resources for Food and Agriculture” any material of plant origin, including reproductive and vegetative propagating material, containing functional units of heredity of actual or potential value for food and agriculture.
You and Dag have already indicated, under the discussion on “#9 Compatibility” that we are not referring only to accession numbers, but also to other entities, and have provided as an additional example “collecting number”, which I think that it should be reflected also under #9.
I think that there is a wide consensus, as advanced by Axel, on the issue that PUIDs do not replace accession numbers (ACCENUM) and that we should not try to re-define what it is already a well-known management concept. At the same time there is agreement on the need to associate accession numbers, when available, to the entity.
The #3 opacity requirement does not affect at all #9 compatibility as the accession number can be associated through the metadata. It helps to prevent human mistakes on one side, and to make the formulation of PUIDs independent from other data associated (which could be subject to change).
Thank you.
Regards,
Francisco
From: Global Information System on PGRFA [mailto:[log in to unmask]] On Behalf Of Alercia, Adriana (Bioversity)
Sent: 27 February 2015 17:51
To: [log in to unmask]
Subject: Re: W1 -Task Force on Permanent Unique Identifiers: Requirements
Few Additional comments.
Agree with Axel and Barnabas regarding ‘accession numbers’.
- With regards to #1 – Uniqueness and #9 Compatibility: Dave comment about the need to clarify the nature of the entity. “Accession” is a management and not a biological concept and should be treated as such. It is an ‘entry’ in a genebank, and constitutes the ‘unit of management at the Genebank’ (RS Hamilton, 2002) -whatever its composition- held in storage for conservation or use. The FAO/Bioversity list of Multi-Crop Passport Descriptors defines the Accession number as: the unique identifier for accessions within a genebank, and is assigned when a sample is entered into the genebank collection. This standard was the result of consultations with more than 100 scientists worldwide, and is accepted and used at the global level since decades.
- Not sure if #3 Opacity agrees with #9 Compatibility. Nevertheless, #3 is irrelevant to me too.
Best,
Adriana
From: Global Information System on PGRFA [mailto:[log in to unmask]] On Behalf Of Dag Endresen
Sent: Thursday, February 26, 2015 9:03 AM
To: [log in to unmask]
Subject: Re: W1 -Task Force on Permanent Unique Identifiers: Requirements
Hi Axel,
#3 Opacity: I will stress the importance of the opacity best practice for PUID name strings. How about reformulation as: "No information on the entity should be inferrable from the PUID name string alone"? See eg. GBIF (2011) [1] (page 9).
#9 Compatibility: I agree that naming accession number as local identifier is an unfortunate and bad wording. How about "traditional identifier" or perhaps "verbatim identifier"? I fully agree that keeping the accession numbers as the most common identifiers in communication between humans remains the most pragmatic option!
#13 Acquisition costs: There will anyway be costs for maintaining any PUID system. The interesting question is rather the most cost effective solution, where the costs saved are higher than the investments. If more costly investments in acquisition of eg. DOIs result in much higher cost-savings in operation of the GLIS, then these investments are justified!
#14 Acceptance by publishers: Perhaps use the accession number in the body text of the manuscript and include the PUID in the reference list for each accession - possibly using a PUID for the dataset or collection if the number of accessions are too large?
I am also concerned with the risk of setting new PUIDs for everything. Whenever there is a n existing and good-enough PUID for any given thing, best practice is (generally) to use this existing PUID and not generate any new PUID.
"each thing has one and only one identifier
each identifier refers to one and only one thing" (Coyle, 20016)
Coyle, Karen. (2006, July). Identifiers: Unique, persistent, global. The Journal of Academic Librarianship, 32(4), 428- 431.
INSTCODE + ACCENUMB
Your pragmatic suggestion to use the WIEWS institution codes pluss the accession number as the PUID (?) is in fact already a very common approach for many datasets published in GBIF - and a recommendation of the Darwin Core standard [2]. The format used is urn:catalog:INSTCODE:[Collection code:]ACCENUMB (collection code is a code for the sub-collection of material conserved at the institute) and often called a Darwin Core Triplett. However, this approach has well-known and documented problems (Guralnick et al. 2014) [3].
[1] http://www.gbif.org/resource/80575
[2] http://rs.tdwg.org/dwc/terms/#occurrenceID
[3] http://doi.org/10.1371/journal.pone.0114069
Best regards
Dag
From: Global Information System on PGRFA <[log in to unmask]> on behalf of Diederichsen, Axel <[log in to unmask]>
Sent: 26 February 2015 06:12
To: [log in to unmask]
Subject: Re: W1 -Task Force on Permanent Unique Identifiers: Requirements
Dear Colleagues,
In the attached I inserted a few comments.
As I see the PUI from the ongoing discussions, this concept will, if accepted in the broad sense, grow exponentially at rate that ridicules the snowball effect. If all things listed in the initial e-mail (genebank accessions, fragments of them, seed lots, selections, gene sequences, individuals, publications…) will receive a PUI this will not help the cause of the GLIS but create a global and eventually cosmic catalogue of everything. The GlIS has not this purpose. I think we need to restrict this and perhaps need to focus more on what we want to achieve, and not so much on what machines can all do. I would suggest a very pragmatic approach. The old FAO WEWS system had unique institution codes, which could be followed by the accession identifier in the respective institution. That could serve as a PUI and restrict this concept to genebank accessions to start with.
As this suggestion may be too simplistic, I in any case need to strongly advice not to strive replacing the genebank accession numbers, which have a different nature but very useful purpose. I also strictly oppose to degrade in wording an accession number of an organized genebank to a local identifier. It is a well accepted and useful identifier of a usually living entity that can be heterogeneous, changes over time, ages, dies, mutates and needs for sure a lot of care. I saw some wording in that suggest accession numbers are outdated.
Best regards,
Axel Diederichsen
From: Global Information System on PGRFA [mailto:[log in to unmask]] On Behalf Of Dag Endresen
Sent: Wednesday, February 25, 2015 11:56 AM
To: [log in to unmask]
Subject: Re: W1 -Task Force on Permanent Unique Identifiers: Requirements
Regarding #21 Identification of fragments, I agree with the concern raised by Eugene and Stephan. My understanding of what could be an example of a fragment (of an accession entity) might be seeds of an accession from a given harvest year (I have seen this thing to be called a batch). And if there is a need to identify such "fragment"-things, a clean opaque PUID for such things would generally be preferred compared to to appending codes to the accession-level PUID identifier string. Perhaps there are other use cases, but in general I agree with these concerns.
Dag
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