[tdwg-content] delimiter characters for concatenated IDs
jdeck at berkeley.edu
Tue May 6 08:28:28 CEST 2014
The biggest appeal to me of the linked data framework is connecting data
across domains... you have bio-, geo-, eco-, -omic, and not to mention all
their various media representations. Hard to believe that DOIs solve all
of these needs (just wait till someone wants to assign DOIs to Loci from
NextGen sequencing, or delving into transcriptomics with this). I'd hope
that GUID services could provide high level consistent metadata (such as
the Datacite metadata, but maybe just a bit more like type), and provide a
clear articulation of the service that stands behind the identifiers, no
matter what you're dealing with.
As far as delivering more specific RDF, I'm more inclined to think along
the lines of your last sentence: " But maybe that's just a function of
where the data provider choses to redirect RDF requests" and let the
providers themselves describe it.
On Mon, May 5, 2014 at 5:42 PM, Steve Baskauf
<steve.baskauf at vanderbilt.edu>wrote:
> I'm a big fan of not reinventing the wheel, and as such find the idea of
> using DOIs appealing. I think they pretty much follow all of the "rules"
> set out in the TDWG GUID Applicability Standard. They also play nicely in
> the Linked Data universe in their HTTP URI form, i.e. they redirect to HTML
> or RDF depending on the request header.
> But I have a question for someone who understands how DOIs work better
> than I do. The HTML representation seems to arise by redirection to
> whatever is the current web page for the resource. You can see this by
> pasting this DOI for a specimen into a browser:
> http://dx.doi.org/10.7299/X7VQ32SJ which redirects to
> http://arctos.database.museum/guid/UAM:Ento:230092 when HTML is requested
> by a client. However, when the client requests RDF, one gets redirected to
> a DataCite metadata page: http://data.datacite.org/10.7299/X7VQ32SJ .
> Can the creator of the DOI redirect to any desired URI for the RDF?
> The resulting RDF metadata doesn't have any of the kind useful information
> about the specimen that you get on the web page but rather looks like what
> you would expect for a publication (creator, publisher, date, etc.):
> "Derek S. Sikes" ;
> "2004" ;
> "10.7299/X7VQ32SJ" ;
> "University of Alaska Museum" ;
> "UAM:Ento:230092 - Grylloblatta campodeiformis" ;
> "info:doi/10.7299/X7VQ32SJ" , "doi:10.7299/X7VQ32SJ" .
> Can one control what kinds of metadata are provided in "DataCite's
> metadata"? Assuming that we get our act together and adopt an RDF guide
> for Darwin Core, it would be nice for the RDF metadata to look more like
> the description of a specimen and less like the description of a book. But
> maybe that's just a function of where the data provider choses to redirect
> RDF requests.
> John Deck wrote:
> +1 on DOIs, and on ARKS (see:
> https://wiki.ucop.edu/display/Curation/ARK ), and also i'll mention
> IGSN:'s (see http://www.geosamples.org/) IGSN: is rapidly gaining
> traction for geo-samples. I don't know of anyone using them for
> bio-samples but they offer many features that we've been asking for as
> well. What our community considers a sample (or observation) is diverse
> enough that multiple ID systems are probably inevitable and perhaps even
> Whatever the ID system, the data providers (museums, field researchers,
> labs, etc..) must adopt that identifier and use it whenever linking to
> downstream sequence, image, and sub-sampling repository agencies. This is
> great to say this in theory but difficult to do in reality because the
> decision to adopt long term and stable identifiers is often an
> institutional one, and the technology is still new and argued about, in
> particular, on this fine list. Further, those agencies that receive data
> associated with a GUID must honor that source GUID when passing to
> consumers and other aggregators, who must also have some level of
> confidence in the source GUIDs as well. Thus, a primary issue that we're
> confronted with here is trust.
> Having Hilmar's hackathon support several possible GUID schemes (each
> with their own long term persistence strategy), and sponsored by a well
> known global institution affiliated with biodiversity informatics that
> could offer technical guidance to data providers, good name branding, and
> the nuts and bolts expertise to demonstrate good shepherding of source
> GUIDs through a data aggregation chain would be ideal. I nominate GBIF :)
> John Deck
> On Mon, May 5, 2014 at 1:09 PM, Roderic Page <r.page at bio.gla.ac.uk> wrote:
>> Hi Markus,
>> I have three use cases that
>> 1. Linking sequences in GenBank to voucher specimens. Lots of voucher
>> specimens are listed in GenBank but not linked to digital records for those
>> specimens. These links are useful in two directions, one is to link GBIF to
>> genomic data, the second is to enhance data in both databases, see
>> http://iphylo.blogspot.co.uk/2012/02/linking-gbif-and-genbank.html(e.g., by adding missing georeferencing that is available in one database
>> but not the other).
>> 2. Linking to specimens cited in the literature. I've done some work on
>> this in BioStor, see
>> http://iphylo.blogspot.co.uk/2012/02/linking-gbif-and-biodiversity-heritage.html One immediate benefit of this is that GBIF could display the scientific
>> literature associated with a specimen, so we get access to the evidence
>> supporting identification, georeferencing, etc.
>> 3. Citation metrics for collections, see
>> http://iphylo.blogspot.co.uk/2012/02/gbif-specimens-in-biostor-who-are-top.htmlBased on citation sod specimens in the literature, and in databases such as
>> GenBank (i.e., basically combining 1 + 2 above) we can demonstrate the
>> value of a collection.
>> All of these use cases depend on GBIF occurenceIds remaining stable, I
>> have often ranted on iPHylo when this doesn't happen:
>> On 5 May 2014, at 20:51, Markus Döring <mdoering at gbif.org> wrote:
>> Hi Rod,
>> I agree GBIF has troubles to keep identifiers stable for *some*
>> records, but in general we do a much better job than the original
>> publishers in the first place. We try hard to keep GBIF ids stable even if
>> publishers change collection codes, registered datasets twice or do other
>> things to break a simple automated way of mapping source records to
>> existing GBIF ids. Also the stable identifier in GBIF never has been the
>> URL, but it is the local GBIF integer alone. The GBIF services that consume
>> those ids have changed over the years, but its pretty trivial to adjust if
>> you use the GBIF ids instead of the URLs. If there is a clear need to have
>> stable URLs instead I am sure we can get that working easily.
>> The two real issues for GBIF are a) duplicates and b) records with
>> varying local identifiers of any sort (triplet, occurrenceID or whatever
>> When it comes to the varying source identifiers I always liked the idea
>> of flagging those records and datasets as unstable, so it is obvious to
>> users. This is not a 100% safe, but most terrible datasets change all of
>> their ids and that is easily detectable.
>> Also with a service like that it would become more obvious to publishers
>> how important stable source ids are.
>> Before jumping on DOIs as the next big thing I would really like to
>> understand what needs the community has around specimen ids.
>> Gabi clearly has a very real use case, are there others we know about?
>> On 05 May 2014, at 21:05, Roderic Page <r.page at bio.gla.ac.uk> wrote:
>> Hi Hilmar,
>> I'm not arguing that we shouldn't build a resolver (I have one that I
>> use, Rich has mentioned he's got one, Markus has one at GBIF, etc.).
>> Nor do I think we should wait for institutional and social commitment
>> (because then we'd never get anything done).
>> But I do think it would be useful to think it through. For example,
>> it's easy to create a URL for a specimen. Easy peasy. OK, how do I discover
>> that URL? How do I discover these for all specimens? Sounds like I need a
>> centralised discover service like you'e described.
>> How do I handle changes in those URLs? I built a specimen code to GBIF
>> resolver for BioStor so that I could link to specimens, GBIF changed lots
>> of those URLs, all my work was undone, boy does GBIF suck sometimes. For
>> example, if I map codes to URLs, I need to handle cases when they change.
>> If URLs can change, is there a way to defend against that (this is one
>> reason for DOIs, or other methods of indirection, such as PURLs).
>> If providers change, will the URLs change? Is there a way to defend
>> against that (again, DOIs handle this nicely by virtue of (a) indirection,
>> and (b) lack of branding).
>> How can I encourage people to use the specimen service? What can I do
>> to make them think it will persist? Can I convince academic publishers to
>> trust it enough to link to it in articles? What's the pitch to Pensoft, to
>> Magnolai Press, to Springer and Elsevier?
>> Is there some way to make the service itself become trusted? For
>> example if I look at a journal and see that it has DOIs issued by CrossRef,
>> I take that journal more seriously than if it's just got simple URLs. I
>> know that papers in that journal will be linked into the citation network,
>> I also know that there is a backup plan if the journal goes under (because
>> you need that to have DOIs in CrossRef). Likewise, I think Figshare got a
>> big boost when it stared minting DOIs (wow, a DOI, I know DOIs, you mean I
>> can now cite stuff I've uploaded there?).
>> How can museums and herbaria be persuaded to keep their identifiers
>> stable? What incentives can we provide (e.g., citation metrics for
>> collections)? What system would enable us to do this? What about tracing
>> funding (e.g., the NSF paid for these n papers, and they cite these y
>> specimens, from these z collections, so science paid for by the NSF
>> requires these collections to exist).
>> I guess I'm arguing that we should think all this through, because a
>> specimen code to specimen URL is a small piece of the puzzle. Now, I'm
>> desperately trying not to simply say what I think is blindingly obvious
>> here (put DOIs on specimens, add metadata to specimen and specimen citation
>> services, and we are done), but I think if we sit back and look at where we
>> want to be, this is exactly what we need (or something functionally
>> equivalent). Until we see the bigger picture, we will be stuck in amateur
>> Take a look at:
>> Isn't this the kind of stuff we'd like to do? If so, let's work out
>> what's needed and make it happen.
>> In short, I think we constantly solve an immediate problem in the
>> quickest way we know how, without thinking it through. I'd argue that if we
>> think about the bigger picture (what do we want to be able to, what are the
>> questions we want to be able to ask) then things become clearer. This is
>> independent of getting everyone's agreement (but it would help if we made
>> their agreement seem a no brainer by providing solutions to things that
>> cause them pain).
>> On 5 May 2014, at 19:14, Hilmar Lapp <hlapp at nescent.org> wrote:
>> On Mon, May 5, 2014 at 1:29 PM, Roderic Page <r.page at bio.gla.ac.uk>wrote:
>>> Contrary to Hilmar, there is more to this than simply a quick hackathon.
>>> Yes, a service that takes metadata and returns one or more identifiers is a
>>> good idea and easy to create (there will often be more than one because
>>> museum codes are not unique). But who maintains this service? Who maintains
>>> the identifiers? Who do I complain to if they break? How do we ensure that
>>> they persist when, say, a museum closes down, moves its collection, changes
>>> it's web technology? Who provides the tools that add value to the
>>> identifiers? (there's no point having them if they are not useful)
>> Jonathan Rees pointed this out to me too off-list. Just for the record,
>> this isn't contrary but fully in line with what I was saying (or trying to
>> say). Yes, I didn't elaborate that part, assuming, perhaps rather
>> erroneously, that all this goes without saying, but I did mention that one
>> part of this becoming a real solution has to be an institution with an
>> in-scope cyberinfrastructure mandate that going in would make a commitment
>> to sustain the resolver, including working with partners on the above slew
>> of questions. The institution I gave was iDigBio; perhaps for some reason
>> that would not be a good choice, but whether they are or not wasn't my
>> I will add one point to this, though. It seems to me that by continuing
>> to argue that we can't go ahead with building a resolver that works (as far
>> as technical requirements are concerned) before we haven't first fully
>> addressed the institutional and social long-term sustainability commitment
>> problem, we are and have been making this one big hairy problem that we
>> can't make any practical pragmatic headway about, rather than breaking it
>> down into parts, some of which (namely the primarily technical ones) are
>> actually fairly straightforward to solve. As a result, to this day we don't
>> have some solution that even though it's not very sustainable yet, at least
>> proves to everyone how critical it is, and that the community can rally
>> behind. Perhaps that's naïve, but I do think that once there's a solution
>> the community rallies behind, ways to sustain it will be found.
>> Hilmar Lapp -:- informatics.nescent.org/wiki -:- lappland.io
>> tdwg-content mailing list
>> tdwg-content at lists.tdwg.org
> John Deck
> (541) 321-0689
> Steven J. Baskauf, Ph.D., Senior Lecturer
> Vanderbilt University Dept. of Biological Sciences
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