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[Taxacom] Showing the importance of natural history collections and the networks they are building

Roderic Page Roderic.Page at glasgow.ac.uk
Thu Apr 24 15:03:04 CDT 2014 

Hi Mary,

I think there are  bunch of issues here. I don?t think that citing collections directly is terribly useful, certainly not for users. It?s like citing a journal publisher. I think it is more useful to cite data (e.g., the set of n specimens I used). This would then be something that somebody else could retrieve (using the DOI) and, for example, try to repeat your analysis.

The DOIs can provide useful information for the collection that issues them. For example, DataCite publishes statistics by ?Datacentre?. We can see that the Barcode of Life has some 30,000 DOIs, and you can get month access statistics (see http://stats.datacite.org/?fqÚtacentre_facet%3A%22CISTI.BOLD+-+Biodiversity+Institute+of+Ontario%22&#tab-resolution-report ). I suspect this is the sort of data collections would like access to if they want to measure the impact they are having).

I am not a fan of simply relying on search engines to find citations. This doesn?t happen automagically, publishers follow certain conventions to ensure Google finds their publications. But more importantly, having identifiers such as DOIs enables another level of services. For example, CrossRef have created a searchable database of millions of papers http://search.crossref.org. If you have an ORCID http://orcid.org which uniquely identifies you, you can ?claim? your publications. ORCIDs can be used to identify other contributions (such as writing reviews of papers). Imagine extending this to other contributions, such as listing taxonomic that you described, or specimens you have identified.

I think there is a lot we can learnt from looking at what the publishing industry has been doing in the last 10-20 years, They have worked out many of the issues that face data publishers (which is what collections are in the digital age), and we can avoid a lot of heartache (and wasted effort) by learning from their experience.

Regards

Rod

On 24 Apr 2014, at 20:33, Mary Barkworth <Mary.Barkworth at usu.edu> wrote:

> It is not the data - it is the collection/network. But I shall look into DOIs. 
> 
> 
> 
> 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 1:19 PM
> 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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>>> 
>>> Celebrating 27 years of Taxacom in 2014.
>> 
>> 
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>> 
>> Celebrating 27 years of Taxacom in 2014.
> 
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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
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