[Taxacom] Showing the importance of natural history collections
and the networks they are building
Roderic Page
Roderic.Page at glasgow.ac.uk
Fri Apr 25 10:56:43 CDT 2014
2014
Hi Quentin,
Put DOIs on the things that you want to cite or otherwise refer to. Should specimen have DOIs? Yes, absolutely (some already do). That way we can refer to the specimen when we put sequences in GenBank, images in Morphbank, and list it in material examined.
DOIs can also be digital things (e.g., an article which only exists online). We could also have DOIs for sets of things (e.g., a particular set of records that form a data set).
Yes, there will be a lot of of DOIs. But, hey, there are a gazillion URLs out there and we seem OK with that.
Regards
Rod
On 25 Apr 2014, at 08:17, Quentin Groom <quentin.groom at br.fgov.be> wrote:
> Hi All,
> do the DOIs (or other identifiers) allocated to specimens refer to the
> physical object or the database entry describing them?
> I would have thought it was the former, in which case versions are
> rather irrelevent. I tend to agree with Rod, that versioning is not that
> important. Where it is an issue it can often be resolved by comaring
> publication dates and version time stamps.
> Observations are more tricky as there is only a virtual representation
> of the observation. In this case, I don't see any reason why there
> should not be a new DOI for each version. In the end there will be an
> awful lot of DOIs around!
> Regards
> Quentin
>
> On 24/04/2014 22:17, Roderic Page wrote:
>> Hi Rich,
>>
>> I have two standard responses to this question:
>>
>> 1. Who cares about versions? No, really - we keep worrying about this, but does anybody actually take versions into account? For example, GenBank has versioned DNA sequences and I have never seen anyone cite a sequence accession number AND version. So, to a first approximation, I don?t think this is the issue people make it out to be. Anyone every seen a versioned link to a Wikipedia page?
>>
>> 2.OK, so you really, really, care about versions. Then I think one answer is to provide a DOI for the data e.g., 10.1234/data (which you can think of as either all the versions, or the latest version), and a DOI for each version (e.g., 10.1234/data.v1, 10.1234/data.v2). If, like most folks, you couldn?t care less (?just give me the latest version please?) then you?d use the DOI for the data (10.1234/data) that resolves to the latest version. If you care about the version (e.g., reproducibility is your thing) then use the DOI for the particular version (e.g., 10.1234/data.v1).
>>
>> There are examples of versioned DOIs in the wild. For example, http://dx.doi.org/10.12688/f1000research.2-92.v1 is a versioned DOI. CrossRef supports versions through Crossmark http://www.crossref.org/crossmark/i to handle things like errata, retractions, etc.
>>
>> Regards
>>
>> Rod
>>
>> P.S. For the sake of all our sanity, let us never speak of LSID metadata vs data ;)
>>
>> On 24 Apr 2014, at 20:50, Richard Pyle <deepreef at bishopmuseum.org> wrote:
>>
>>> Agreed! I forgot to mention that the archived snapshot documents in our
>>> planned system would be assigned persistent identifiers (most likely DOIs).
>>>
>>> However, this raises another issue that I have not seen adequately addressed
>>> in any of these discussions about identifiers for datasets (including DOIs):
>>>
>>> Is there an expectation that the object represented by an identifier remains
>>> static? In the case of traditional publications, this seems to be the case.
>>> When I dereference a DOI, I get a digital document (or a landing page for a
>>> digital document). In my mind, that DOI identifies the conceptual object
>>> (i.e., the published work as an abstract entity, not any particular digital
>>> manifestation/instantiation of the published work, such as a particular PDF
>>> file on a particular hard drive somewhere). But in the case of
>>> "traditional" publications (including electronic publications, and as
>>> opposed to datasets), the content of the object is expected to remain static
>>> over time. A hundred years from now, when I (more likely my grandchildren)
>>> dereference a DOI, they will get the same information content (at least at a
>>> human-perception level, if not a bit-identical data file) that I get today.
>>>
>>> Now, I know lots of people (particularly Rod) like to say we should assign
>>> DOIs to "datasets". That's fine, and totally within scope of what DOIs were
>>> intended for. But is it implicit that a DOI assigned to a dataset is
>>> actually assigned to a *snapshot* of that dataset at a particular moment in
>>> time? Or is the DOI representing the conceptual notion of the dataset,
>>> which changes in content over time?
>>>
>>> So, I could assign a single DOI to the Bishop Museum fish collection
>>> dataset, representing the "conceptual" notion of the Bishop Museum fish
>>> collection dataset. Tomorrow the content is likely to be different from
>>> what it is now. To me, this seems to border on useless. One of the critical
>>> issues of citing databases that comes up again and again is to include the
>>> date on which the dataset was accessed (see my previous post). Is that date
>>> part of the permanent DOI metadata? If so, there may be hundreds of DOIs
>>> issued for the Bishop Museum fish collection dataset, each one representing
>>> a particular moment in time for which someone wishes to be able to cite the
>>> dataset content.
>>>
>>> Glancing over through the DOI specification, it seems to me that there is an
>>> implicit assumption that the document identified by a DOI is static in
>>> content. But I haven't read it thoroughly, and am by no means an expert.
>>>
>>> So, my question to Rod (and anyone else) is: if we assign an identifier
>>> such as a DOI to a dataset, is there an expectation that the dataset
>>> indicated by the identifier is static? Or, might it be dynamic? In the
>>> parlance of LSID-speak, what is implicitly the "data", vs. the "metadata"?
>>>
>>> Aloha,
>>> Rich
>>>
>>>
>>>
>>>> -----Original Message-----
>>>> From: taxacom-bounces at mailman.nhm.ku.edu [mailto:taxacom-
>>>> bounces at mailman.nhm.ku.edu] On Behalf Of Roderic Page
>>>> Sent: Thursday, April 24, 2014 9:19 AM
>>>> To: Taxacom at mailman.nhm.ku.edu
>>>> Subject: Re: [Taxacom] Showing the importance of natural history
>>> collections
>>>> and the networks they are building
>>>>
>>>> Surely we can learn from past mistakes and do this properly. Citations are
>>>> meaningless unless they are counted, and the way to do this efficiently is
>>>> with identifiers such as DOIs, not developing some arbitrary way of citing
>>>> databases or datasets. Mint DOIs for collections, mint DOIs for datasets
>>> (GBIF
>>>> is heading down this route), make data a first class citizen by making it
>>> trivially
>>>> easy to cite. Don't moan about people not citing data if you haven't made
>>> it
>>>> easy for them to do so. If you value your data, make it easy to cite -
>>> give it a
>>>> DOI.
>>>>
>>>> Regards
>>>>
>>>> Rod
>>>>
>>>> Sent from my iPhone
>>>>
>>>>> On 24 Apr 2014, at 19:34, "Richard Pyle" <deepreef at bishopmuseum.org>
>>>> wrote:
>>>>> Hi Mary,
>>>>>
>>>>> I have LONG supported this notion. One of the problems, though, is
>>>>> that very few databases allow future users to see what the database
>>>>> contained on the date on which it was accessed. In an ideal world,
>>>>> all online databases would include a parameter "asOfDate" or something
>>>>> similar, where users can pass in a particular date and see what the
>>>>> database consisted of as of that date. For some systems (which
>>>>> maintain robust edit logs or "audit trails", or maintain explicit
>>>>> versioning), it would be possible to do this; but for many systems it
>>> would
>>>> not.
>>>>> Recognizing this issue, about ten years ago we conceived of a system
>>>>> where users of our online databases could select an option to
>>>>> "publish" a full snapshot of the query results they examined. The
>>>>> idea would be for a user to construct a query of the database and get
>>>>> a result-set back, then upon deciding that this result-set is the one
>>>>> to be cited, there would be a button that "published" the result set
>>>>> as an XML file (which could be represented as a styled PDF or
>>>>> converted to Excel, complete with its own title, authorship [jointly
>>>>> the person constructing the query, and the database owner], full data
>>>>> set, and its own "references" section that cited the original sources
>>>>> of the data). This XML file would then be permanently archived for
>>>>> future access, and would be the digital object cited in the work for
>>> which it
>>>> was generated.
>>>>> We never followed through with the development of that concept (budget
>>>>> issues, different priorities, etc.); but there may yet be some value
>>>>> in doing it. For example, perhaps there could be an automated system
>>>>> that allowed users of online databases to snap-shot result-sets
>>>>> directly into a publication venue such as the Biodiversity Data Journal.
>>>>>
>>>>> Speaking of that journal, we are planning to publish a regional
>>>>> checklist (fishes of the Northwestern Hawaiian Islands) in BDJ that
>>>>> changes the way such regional checklists are created. Basically, we
>>>>> build an evidence-based checklist of occurrence records for
>>>>> within-scope taxa at within-scope region, and store this in a
>>>>> database. The checklist is annotated and curated by the authors, who
>>>>> vet all the data, flag dubious records, confirm taxonomic
>>>>> identifications, etc. The checklist is then published in a highly
>>>>> structured form (ala BDJ), with a link back to the database. The link
>>>>> would then go to a page that displays everything as it appeared in the
>>>>> published version, as well as all data that were altered or added
>>>>> since the moment of publication. The "vetted" (published) records
>>>>> would be formatted clearly to distinguish from all the un-vetted,
>>>>> "raw" data that became available following the publication. That way
>>>>> people who come to that website could see the full content of what was
>>>>> published, *AND* all of the new information that has become available
>>>>> since the time it was published. Eventually, when there is enough new
>>>>> information, it would be vetted again and a new-snapshot generated and
>>>>> published (in the form of a "revised" checklist, or new-records paper,
>>>>> or whatever). The idea is to be able to clearly show the full dataset
>>>>> as it was snapshot-published, and also give acces to up-to-the-moment
>>>>> additional data; thus avoiding the current problem with regional
>>> checklists,
>>>> which is that they become obsolete the moment they are published.
>>>>> In any case, I fully support the idea of more consistent and
>>>>> deliberate citation of online data systems in the "references" section
>>>>> of publications, and I'd like to see us move even beyond that to a
>>>>> standard system that allows people to immediately compare what was
>>>>> available at the time the dataset was cited to what is currently in the
>>>> dataset now.
>>>>> Aloha,
>>>>> Rich
>>>>>
>>>>>> -----Original Message-----
>>>>>> From: taxacom-bounces at mailman.nhm.ku.edu [mailto:taxacom-
>>>>>> bounces at mailman.nhm.ku.edu] On Behalf Of Mary Barkworth
>>>>>> Sent: Thursday, April 24, 2014 6:49 AM
>>>>>> To: (Taxacom at mailman.nhm.ku.edu)
>>>>>> Subject: [Taxacom] Showing the importance of natural history
>>>>>> collections
>>>>> and
>>>>>> the networks they are building
>>>>>>
>>>>>> The other day I reviewed a paper that stated it drew information from
>>>>>> lots
>>>>> of
>>>>>> databases and networks but to find out which one had to go to the
>>>> authors'
>>>>>> web site and click on a pull-down list. That started me thinking of
>>>>>> how to
>>>>> get
>>>>>> more recognition for collections, databases, and networks.
>>>>>> Suggestion: Collections, databases, and networks that contributed
>>>>>> significantly to development of any paper, poster, pamphlet, report
>>> etc.
>>>>>> should be cited in the references section (the old "Literature cited"
>>>>> section).
>>>>>> We should do this ourselves, ask other authors to do so when
>>>>>> reviewing papers, and promote the idea at meetings we go to in which
>>>>>> people make use of collections data - whether of environmental
>>>>>> consultants,
>>>>> politicians, or
>>>>>> ecologists. Having collections and networks (and floras consulted
>>>>>> too)
>>>>> listed
>>>>>> in the reference section would mean that publishers will start
>>>>>> marking
>>>>> them
>>>>>> up and search engines may find them, all of which would, I suspect,
>>>>>> make
>>>>> it
>>>>>> easier to show how fundamental collections and networks are to
>>>>>> today's research. Below I have some suggested formats for networks
>>>> that I use.
>>>>>> 1. SEINet Network. 2014+. Provider of records from over 60 US
>>>>> herbaria.
>>>>>> Accessed via http://ngpherbaria.org<http://ngpherbaria.org/>, 23
>>>>>> April
>>>>> 2014.
>>>>>> 2. NGPHerbaria.org. 2014+. Portal to records from over 60 US
>>>>> herbaria.
>>>>>> Accessed via http://ngpherbaria.org<http://ngpherbaria.org/>, 23
>>>>>> April
>>>>> 2014.
>>>>>> 3. Intermountainbiota.org. 2014+. For records to herbaria of Utah
>>>>> State
>>>>>> University's campuses. Accessed via
>>>>>> http<http://ngpherbaria.org/>://intermountainbiota.org<http://ngpherb
>>>>>> ari
>>>>>> a.org/>, 23 April 2014.
>>>>>> 4. BHSC. 2014+. Records from the herbarium of Black Hills State
>>>>> University.
>>>>>> Accessed via http://swbiodiversity.org/, 23 April 2014
>>>>>> 5. Intermountain Herbarium. 2014+. Records from the herbarium of
>>>>> Utah
>>>>>> State University, Logan Campus. Accessed via https://www.idigbio.org/
>>>>>> 23 April 2014 Logically, one could also ask to see herbaria from
>>>>>> which one borrowed specimens listed in the References cited rather
>>>>>> than (or in addition to) acknowledgments.
>>>>>> I am a plant person. I would think that the same approach would serve
>>>>> other
>>>>>> natural history collections and networks but perhaps not.
>>>>>> Comments welcome.
>>>>>> Mary
>>>>>>
>>>>>> _______________________________________________
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>>>>>> The Taxacom Archive back to 1992 may be searched at:
>>>>>> http://taxacom.markmail.org
>>>>>>
>>>>>> Celebrating 27 years of Taxacom in 2014.
>>>>>
>>>>> _______________________________________________
>>>>> Taxacom Mailing List
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>>>>>
>>>>> Celebrating 27 years of Taxacom in 2014.
>>>> _______________________________________________
>>>> Taxacom Mailing List
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>>>>
>>>> Celebrating 27 years of Taxacom in 2014.
>> ---------------------------------------------------------
>> Roderic Page
>> Professor of Taxonomy
>> Institute of Biodiversity, Animal Health and Comparative Medicine
>> College of Medical, Veterinary and Life Sciences
>> Graham Kerr Building
>> University of Glasgow
>> Glasgow G12 8QQ, UK
>>
>> Email: r.page at bio.gla.ac.uk
>> Tel: +44 141 330 4778
>> Fax: +44 141 330 2792
>> Skype: rdmpage
>> Facebook: http://www.facebook.com/rdmpage
>> LinkedIn: http://uk.linkedin.com/in/rdmpage
>> Twitter: http://twitter.com/rdmpage
>> Blog: http://en.wikipedia.org/wiki/Roderic_D._M._Page
>> Citations: http://scholar.google.co.uk/citations?hl=en&user=4Z5WABAAAAAJ
>> ORCID: http://orcid.org/0000-0002-7101-9767
>>
>>
>> _______________________________________________
>> Taxacom Mailing List
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>> http://mailman.nhm.ku.edu/mailman/listinfo/taxacom
>> The Taxacom Archive back to 1992 may be searched at: http://taxacom.markmail.org
>>
>> Celebrating 27 years of Taxacom in 2014.
>>
>>
>>
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>>
>
> --
> Dr. Quentin Groom
> (Botany and Information Technology)
>
> Botanic Garden, Meise
> Domein van Bouchout
> B-1860 Meise
> Belgium
>
> ORCID: 0000-0002-0596-5376
>
> Landline; +32 (0) 226 009 20 ext. 364
> FAX: +32 (0) 226 009 45
>
> E-mail: quentin.groom at br.fgov.be
> Skype name: qgroom
> Website: www.botanicgarden.be
>
>
> _______________________________________________
> Taxacom Mailing List
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> http://mailman.nhm.ku.edu/mailman/listinfo/taxacom
> The Taxacom Archive back to 1992 may be searched at: http://taxacom.markmail.org
>
> Celebrating 27 years of Taxacom in 2014.
---------------------------------------------------------
Roderic Page
Professor of Taxonomy
Institute of Biodiversity, Animal Health and Comparative Medicine
College of Medical, Veterinary and Life Sciences
Graham Kerr Building
University of Glasgow
Glasgow G12 8QQ, UK
Email: r.page at bio.gla.ac.uk
Tel: +44 141 330 4778
Fax: +44 141 330 2792
Skype: rdmpage
Facebook: http://www.facebook.com/rdmpage
LinkedIn: http://uk.linkedin.com/in/rdmpage
Twitter: http://twitter.com/rdmpage
Blog: http://en.wikipedia.org/wiki/Roderic_D._M._Page
Citations: http://scholar.google.co.uk/citations?hl=en&user=4Z5WABAAAAAJ
ORCID: http://orcid.org/0000-0002-7101-9767
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