Dear Colleagues,
I have been stuck in a hospital bed for the last week, so I have been unable to actively participate in this very stimulating discussion. I hope to be back home tomorrow for week 2.
Anyway, I would just like to clarify our position about the two points raised by Ramona and others.
Firstly, our first and most urgent need is to assign PUIDs to PGRFA as defined by the SMTA and quoted by Francisco. However, we should take into account that the scope of GLIS is *likely* to expand to other entities such as those mentioned by Ramona. This should advise us to prefer a PUID scheme that can be used across very diverse entity types.
About the second concern, on one side GLIS will have to accept entity registration from organizations using any kind of identifier (just to name a few: Accession Numbers, LSIDs, UUIDs, PURLs etc.). It is then obvious that we need to assign to those entities a new PUID. Of course, and this has always been very clearly stated, we will accommodate (in the PUIDS metadata) any existing identifier already assigned to the same entity. In other words, access to GLIS entities will be possible by using our own PUID or through any other identifier associated to that entity. The only difference, in the latter case, being that the resolution might produce two or more results because, for instance, the identifier used as key is not globally unique.
I hope this clarifies the issues.
I would like to thank you all for the very insightful comments and the time you are dedicating to this discussion.
M
Sent from my iPhone
> On 01 Mar 2015, at 03:39, Ramona Walls <[log in to unmask]> wrote:
>
> Dear Colleagues,
>
> Attached is the latest version of the Word doc with my comments inserted. As an overall comment, my greatest concern is the lack of clarity about what will be identified with these PUIDs. The paragraph quoted by Fransisco:
>
> "“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."
>
> sounds very clearly like the PUIDs will be limited to material entities, which would primarily be specimens. However, reading the document "cogis1w3.pdf" gave the distinct impression that PGRFA PUIDs could apply to about anything, including gene sequences or other bits of information associated with specimens, or even processes that PGRFAs take part in or relations between them. I think an additional requirment specifying what types of entities the PUIDs can be applied to would be helpful. Although I am comforted by Fransisco's comment
>
> "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. "
>
> I would prefer to see it spelled out more explicitly in the documentation.
>
> After that, my major concerns is that new identifiers not be issued for things that already have identifiers, A resoluition system should be able to resolved some kinds of exisitng identifiers, even if they don't meet every criterion listed here (although obviously uniqueness would be essential).
>
> 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 Fri, Feb 27, 2015 at 12:16 PM, Lopez, Francisco (AGDT) <[log in to unmask]> wrote:
>> 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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> <W1_PUID_Requirements_DE_DFM_AA1_RW.docx>
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