Duplicate DOIs for the same article: alias DOIs, who knew?

As part of a project to map taxonomic citations to bibliographic identifiers I'm tackling strings like this (from the ION record urn:lsid:organismnames.com:name:1405511 for Pseudomyrmex crudelis):

<tdwg_co:PublishedIn>
Systematics, biogeography and host plant associations of the Pseudomyrmex viduus group (Hymenoptera: Formicidae), Triplaris- and Tachigali-inhabiting ants. Zoological Journal of the Linnean Society, 126(4), August 1999: 451-540. 516 [Zoological Record Volume 136]
</tdwg_co:PublishedIn>

I parse the string into its components (e.g., journal, volume, issue, pagination) and use scripts to locate identifiers such as DOIs. I regard DOIs as the gold standard for bibliographic identifiers. The are (usually) unique, and CrossRef provides some really useful services to support them (DOIs now also support linked data if you are in to that sort of thing). Occasionally there are problems, such as duplicate DOIs when material moves from a publisher's site to, say, JSTOR. And some publishers are really, really bad at releasing DOIs that don't resolve. For example, Taylor & Francis Online have at least 18,000 DOIs for the Annals and Magazine of Natural History that don't resolve (e.g., doi:10.1080/00222933809512318 for this paper).

Sometimes my automated scripts for finding DOIs fail and I have to resort to Googling. To my surprise, I found two versions of the paper "Systematics, biogeography and host plant associations of the Pseudomyrmex viduus group (Hymenoptera: Formicidae), Triplaris- and Tachigali-inhabiting ants", each with a different DOI:

• doi:10.1006/zjls.1998.0158 at Science Direct
• doi:10.1111/j.1096-3642.1999.tb00157.x at Wiley

Now, this isn't supposed to happen. Interestingly, if you resolve doi:10.1006/zjls.1998.0158, either on the web or using CrossRef's OpenURL resolver, you get the page/metadata for doi:10.1111/j.1096-3642.1999.tb00157.x.

To see what was going on I fired up my local installation of Tony Hammnd's OpenHandle tool (see http://bioguid.info/openhandle/) and entered the Elsevier DOI (10.1006/zjls.1998.0158) and got this:

{
    "comment" : "OpenHandle (JSON) - see http://code.google.com/p/openhandle/" ,
    "handle" : "hdl:10.1006/zjls.1998.0158" ,
    "handleStatus" : {
        "code" : "1" ,
        "message" : "SUCCESS"
    } ,
    "handleValues" : [
        {
            "index" : "100" ,
            "type" : "HS_ADMIN" ,
         "data" : {
                "adminRef" : "hdl:10.1006/zjls.1998.0158?index=100" ,
                "adminPermission" : "111111110111"
            } ,
            "permission" : "1110" ,
            "ttl" : "+86400" ,
            "timestamp" : "Thu Apr 13 19:09:03 BST 2000" ,
            "reference"  : []
        } ,
        {
            "index" : "1" ,
            "type" : "URL" ,
            "data" : "http://linkinghub.elsevier.com/retrieve/pii/S0024408298901583" ,
            "permission" : "1110" ,
            "ttl" : "+86400" ,
            "timestamp" : "Tue Aug 12 16:43:12 BST 2003" ,
            "reference"  : []
        } ,
        {
            "index" : "700050" ,
            "type" : "700050" ,
            "data" : "20030811104844000" ,
            "permission" : "1110" ,
            "ttl" : "+86400" ,
            "timestamp" : "Tue Aug 12 16:43:16 BST 2003" ,
            "reference"  : []
        } ,
        {
            "index" : "1970" ,
            "type" : "HS_ALIAS" ,
            "data" : "10.1111/j.1096-3642.1999.tb00157.x" ,
            "permission" : "1110" ,
            "ttl" : "+86400" ,
            "timestamp" : "Mon Aug 25 21:06:50 BST 2008" ,
            "reference"  : []
        }
    ]
}

The interesting bit is the "HS_ALIAS" at the bottom. I'd not come across this before, although it's in the spec (RFC 3651) for all to see (yeah, but who reads those?). The handle system that underlies DOIs has mechanism to support aliases, so that a DOI that originally pointed to a web page (say, for an article) can be redirected to point to another DOI. In this case, the Elsevier DOI redirects to the Wiley DOI ("10.1111/j.1096-3642.1999.tb00157.x" in the HS_ALIAS section), so the user ends up at Wiley's page for this article, not Elsevier's. This provides a way to accommodate changes in article ownership, without requiring an existing publisher to reuse the previous publisher's DOI.

In one sense this seems to defeat the point of DOIs, namely that they are effectively opaque identifiers that any publisher should be able to host. Perhaps in this case the issue is that the DOI prefix ("10.1006" and "10.1111" for Elsevier and Wiley, respectively) corresponds to a publisher, and when something goes wrong with a DOI it's easier to identify who is responsible based on this prefix, rather than the individual DOI.

In any event, next time I come across a duplicate DOI I'll need to check whether it is an alias of another DOI before launching into another rant about the (occasional) failings of DOIs.

Mendeley mangles my references: phantom documents and the problem of duplicate references

One issue I'm running into with Mendeley is that it can create spurious documents, mangling my references in the process. This appears to be due to some over-zealous attempts to de-duplicate documents. Duplicate documents is the number one problem faced by Mendeley, and has been discussed in some detail by Duncan Hull in his post How many unique papers are there in Mendeley?. Duncan focussed on the case where the same article may appear multiple times in Mendeley's database, which will inflate estimates of how many distinct references the database contains. It also has implications for metrics derived from the Mendeley, such as those displayed by ReaderMeter.

In this post I discuss the reverse problem, combining two or more distinct references into one. I've been uploading large collections of references based on harvesting metadata for journal articles. Although the metadata isn't perfect, it's usually pretty good, and in many cases linked to Open Access content in BioStor. References that I upload appear in public groups listed on my profile, such as the group Proceedings of the Entomological Society of Washington.

Reverse engineering Mendeley
In the absence of a good description by Mendeley of how their tools work, we have to try and figure it out ourselves. If you click on a refernece that has been recently added to Mendeley you get a URL that looks like this: http://www.mendeley.com/c/3708087012/g/584201/magalhaes-2008-a-new-species-of-kingsleya-from-the-yanomami-indians-area-in-the-upper-rio-orinoco-venezuela-crustacea-decapoda-brachyura-pseudothelphusidae/ where 584201 is the group id, 3708087012 is the "remoteId" of the document (this is what it's called in the SQLite database that underlies the desktop client), and the rest of the URL is the article title, minus stop words.

After a while (perhaps a day or so) Mendeley gets around to trying to merge the references I've added with those it already knows about, and the URLs lose the group and remoteId and look like this: http://www.mendeley.com/research/review-genus-saemundssonia-timmerman-phthiraptera-philopteridae-alcidae-aves-charadriiformes-including-new-species-new-host/ . Let's call this document the "canonical document" (this document also has a UUID, which is what the Mendeley API uses to retrieve the document). Once the document gets one of these URLs Mendeley will also display how many people are "reading" that document, and whether anyone has tagged it.

But that's not my paper!
The problem is that sometimes (and more often than I'd like) the canonical document bears little relation to the document I uploaded. For example, here is a paper that I uploaded to the group Proceedings of the Entomological Society of Washington:

Review of the genus Saemundssonia Timmermann (Phthiraptera: Philopteridae) from the Alcidae (Aves: Charadriiformes), including a new species and new host records by Roger D Price, Ricardo L Palma, Dale H Clayton, Proceedings of the Entomological Society of Washington, 105(4):915-924 (2003).

You can see the actual paper in BioStor: http://biostor.org/reference/57185. To see the paper in the Mendeley group, browse it using the tag Phthiraptera:

Note the 2, indicating that two people (including myself) have this paper in their library. The URL for this paper is http://www.mendeley.com/research/review-genus-saemundssonia-timmerman-phthiraptera-philopteridae-alcidae-aves-charadriiformes-including-new-species-new-host/, but this is not the paper I added!.

What Mendeley displays for this URL is this:

Not only is this not the paper I added, there is no such paper! There is a paper entitled "A new genus and a new species of Daladerini (Hemiptera: Heteroptera: Coreidae) from Madagascar", but that is by Harry Brailovsky, not Clayton and Price (you can see this paper in BioStor as http://biostor.org/reference/55669). The BioStor link for the phantom paper displayed by Mendeley, http://biostor.org/reference/55761, is for a third paper "A review of ground beetle species (Coleoptera: Carabidae) of Minnesota, United States : New records and range extensions". The table below shows the original details for the paper, the details for the "canonical paper" created by Mendeley, and the details for two papers that have some of the bibliographic details in common with this non-existent paper (highlighted in bold).

Field	Original paper	Mendeley
Title	Review of the genus Saemundssonia Timmermann (Phthiraptera: Philopteridae) from the Alcidae (Aves: Charadriiformes), including a new species and new host records	A new genus and a new species of Daladerini (Hemiptera: Heteroptera: Coreidae) from Madagascar	A new genus and a new species of Daladerini (Hemiptera: Heteroptera: Coreidae) from Madagascar	A review of ground beetle species (Coleoptera: Carabidae) of Minnesota, United States : New records and range extensions
Author(s)	Roger D Price, Ricardo L Palma, Dale H Clayton	DH Clayton, RD Price	Harry Brailovsky
Volume	105	105	104	107
Pages	915-924	915-924	111-118	917-940
BioStor	57185	55761	55669	55761

As you can see it's a bit of a mess. Now, finding and merging duplicates is a hard problem (see doi:10.1145/1141753.1141817 for some background), but I'm struggling to see why these documents were considered to be duplicates.

What I'd like to see
I'm a big fan of Mendeley, so I'd like to see this problem fixed. What I'd really like to see is the following:

1. Mendeley publish a description of how their de-duplication algorithms work


2. Mendeley describe the series of steps a document goes through as they process it (if nothing else, so that users can make sense of the multiple URLs a document may get over it's lifetime in Mendeley).


3. For each canonical reference Mendeley shows the the set of documents that have been merged to create that canonical reference, and display some measure of their confidence that the match is genuine.


4. Mendeley enables users to provide feedback on a canonical document (e.g., a button by each document in the set that enables the user to say "yes this is a match" or "no, this isn't a match").

Perhaps what would be useful is if Mendeley (or the community) assemble a test collection of documents which contains duplicates, together with a set of the canonical documents this collection actually contains, and use this to evaluate alternative algorithms for finding duplicates. Let's make this a "challenge" with prizes! In many ways I'd be much more impressed by a duplication challenge than the DataTEL challenge, especially as it seems clear that Mendeley readership data is too sparse to generate useful recommendations (see Mendeley Data vs. Netflix Data).