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February 11, 2010

Does a CrossRef DOI identify a "work?"

Tony's recent thread on making DOIs play nicely in a linked data world has raised an issue I've meant to discuss here for some time- a lot of the thread is predicated on the idea that CrossRef DOIs are applied at the abstract "work" level. Indeed, that it what it currently says in our guidelines. Unfortunately, this is a case where theory, practice and documentation all diverge.

When the CrossRef linking system was developed it was focused primarily on facilitating persistent linking amongst journals and conference proceedings. The system was quickly adapted to handle books and more recently to handle working papers, technical reports, standards and “components”- a catchall term used to refer to everything from individual article images to database records.

In practice the content outside of the core journals and conference proceedings has accounted for relatively low volume. However, we expect that over the next few years this will change and that books and databases will increasingly drive the future growth in CrossRef’s citation linking services. Interestingly, these content types all share characteristics that make them substantially different from the journals and conference proceedings that we have hitherto focused on.

Both books and databases introduce new challenges to technology and policies of our citation linking service. The challenges revolved around two areas:

  • Structure: Both books and databases can have complex structures and the publishers of this content are likely to require granular identification of these content substructures along with a mechanism for documenting the relationship between these substructures (e.g. this section is part of this chapter which is part of this monograph which is part of this series)
  • Versioning: Unlike typical journals and conference proceedings, books and database records sometimes change over time.


When confronted with the issues of structure and versioning publishers are often tempted to take shortcuts and decide to simply assign DOIs at the highest level structure and to the “work” instead of a particular “manifestation” or version of that work. Indeed, section 5.5 of CrossRef's DOI Name Information and Guidelines recommends this. But this approach could have a negative impact on the integrity of the scholarly citation record that CrossRef is attempting to maintain.

Fundamentally, CrossRef DOIs are aimed at providing a persistent online citation infrastructure for scholarly and professional publishers. Consequently, decisions about where to apply CrossRef DOIs should be guided by common expectations about the way in which citations work. Citations are typically used to credit ideas or provide evidence. A reader follows a citation in order to obtain more detail or to verify that an author is accurately representing the item cited. A rule of thumb is that a reader has a reasonable expectation that when they follow a citation, they will be taken to what the author saw when creating the citation. Any divergent behavior could result in the reader concluding that the author was misrepresenting the item cited. A further implication of this is that any changes to content that are likely to effect the crediting or interpretation of the content should result in that changed content getting a new CrossRef DOI.

Typically, this means that CrossRef DOIs should be probably assigned at the expression level and different expressions should be assigned different CrossRef DOIs. This is because assigning a CrossRef DOI at the higher "work" level is generally not granular enough to guarantee that a reader following the citation will see what the author saw when creating the citation. For example, one translation of a work might be substantially different from another translation of the same work. Similarly a draft version of a work might be substantially different from the final published version of the work. In each case, resolving a citation to a different expression of the work than the expression that was originally cited might result in the reader interpreting the content differently than the citing author.

In general, different "equivalent manifestations" of the same work can safely be assigned the same CrossRef DOI. So, for instance, the HTML formatted version an article and the PDF formatted version of an article can almost always be assigned the same CrossRef DOI. Any differences between the two are unlikely to affect the crediting of, or reader's interpretation of, the work. But sometimes it is even possible that different manifestations of an expression will differ enough to merit different CrossRef DOIs. For instance, a semantically enhanced version of an article might require new crediting (e.g. the parties responsible for adding the semantic information) and the resulting semantic enhancement may conceivably alter the reader's interpretation of the article.

Unfortunately, there is no hard and fast rule about where and when to assign new CrossRef DOIs. Instead there is only a guideline, namely:

"Assign new CrossRef DOIs to content in a way that will ensure that a reader following the citation will see something as close to what the original author cited as is possible."

The implications of this to publishers are important, especially when they are assigning DOIs to protean content types. For instance, it may mean that:

  • Book publishers should be expected to keep old editions of books available for link resolution purposes.
  • Publishers of content that can change rapidly (e.g. by the second) should provide facilities for creating frozen, archived snapshots of content for citation purposes.
  • All publishers of protean content should issue guidelines instructing researchers on when it is appropriate to cite a work, manifestation or version.

CrossRef needs to actively consider these issues as publishers start assigning CrossRef DOIs to more dynamic types of content. Minimally, we should be able to provide publishers with recommendations on how to make dynamic content citable. We may even want to consider enshrining certain types of behavior in our terms and conditions so as to ensure the future integrity of the scholarly citation record.

In short, we need to update our guidelines.

December 13, 2009

A Christmas Reading List... with DOIs

Was outraged (outraged, I tell you) that one of my favorite online comics, PhD, didn't include DOIs in their recent bibliography of Christmas-related citations.. So I've compiled them below.

We care about these things so that you don't have to. Bet you will sleep better at night knowing this.

Or perhaps not...

A Christmas Reading List... with DOIs.

Citation:  Biggs, R, Douglas, A, Macfarlane, R, Dacie, J, Pitney, W, Merskey, C & O'Brien, J, 1952, 'Christmas Disease', BMJ, vol. 2, no. 4799, pp. 1378-1382.
CrossRef DOI:  http://dx.doi.org/10.1136/bmj.2.4799.1378

Title:  More Than a Labor of Love: Gender Roles and Christmas Gift Shopping
Citation:  Fischer, E & Arnold, S, 1990, 'More Than a Labor of Love: Gender Roles and Christmas Gift Shopping', Journal of Consumer Research, vol. 17, no. 3, p. 333.
CrossRef DOI:  http://dx.doi.org/10.1086/208561

Title:  Looking at Christmas trees in the nucleolus
Citation:  Scheer, U, Xia, B, Merkert, H & Weisenberger, D, 1997, 'Looking at Christmas trees in the nucleolus', Chromosoma, vol. 105, no. 7-8, pp. 470-480.
CrossRef DOI:  http://dx.doi.org/10.1007/s004120050209

Title:  The Vela glitch of Christmas 1988
Citation:  McCulloch, P, Hamilton, P, McConnell, D & King, E, 1990, 'The Vela glitch of Christmas 1988', Nature, vol. 346, no. 6287, pp. 822-824.
CrossRef DOI:  http://dx.doi.org/10.1038/346822a0

Title:  Cardiac Mortality Is Higher Around Christmas and New Year's Than at Any Other Time: The Holidays as a Risk Factor for Death
Citation:  Phillips, D, 2004, 'Cardiac Mortality Is Higher Around Christmas and New Year's Than at Any Other Time: The Holidays as a Risk Factor for Death', Circulation, vol. 110, no. 25, pp. 3781-3788.
CrossRef DOI:  http://dx.doi.org/10.1161/01.CIR.0000151424.02045.F7

Title:  Red Crabs in Rain Forest, Christmas Island: Biotic Resistance to Invasion by an Exotic Snail
Citation:  Lake, P & O'Dowd, D, 1991, 'Red Crabs in Rain Forest, Christmas Island: Biotic Resistance to Invasion by an Exotic Snail', Oikos, vol. 62, no. 1, p. 25.
CrossRef DOI:  http://dx.doi.org/10.2307/3545442

Title:  The Carvedilol Hibernation Reversible Ischaemia Trial, Marker of Success (CHRISTMAS) study Methodology of a randomised, placebo controlled, multicentre study of carvedilol in hibernation and heart failure
Citation:  Pennell, D, 2000, 'The Carvedilol Hibernation Reversible Ischaemia Trial, Marker of Success (CHRISTMAS) study Methodology of a randomised, placebo controlled, multicentre study of carvedilol in hibernation and heart failure', International Journal of Cardiology, vol. 72, no. 3, pp. 265-274.
CrossRef DOI:  http://dx.doi.org/10.1016/S0167-5273(99)00198-9

March 20, 2009

Citation Typing Ontology

I was happy to read David Shotton's recent Learned Publishing article, Semantic Publishing: The Coming Revolution in scientific journal publishing, and see that he and his team have drafted a Citation Typing Ontology.*

Anybody who has seen me speak at conferences knows that I often like to proselytize about the concept of the "typed link", a notion that hypertext pioneer, Randy Trigg, discussed extensively in his 1983 Ph.D. thesis.. Basically, Trigg points out something that should be fairly obvious- a citation (i.e. "a link") is not always a "vote" in favor of the thing being cited.

In fact, there are all sorts of reasons that an author might want to cite something. They might be elaborating on the item cited, they might be critiquing the item cited, they might even be trying to refute the item cited (For an exhaustive and entertaining survey of the use and abuse of citations in the humanities, Anthony Grafton's, The Footnote: A Curious History, is a rich source of examples)

Unfortunately, the naive assumption that a citation is tantamount to a vote of confidence has become inshrined in everything from the way in which we measure scholarly reputation, to the way in which we fund universities and the way in which search engines rank their results. The distorting affect of this assumption is profound. If nothing else, it leads to a perverse situation in which people will often discuss books, articles, and blog postings that they disagree with without actually citing the relevant content, just so that they can avoid inadvertently conferring "wuffie" on the item being discussed. This can't be right.

Having said that, there has been a half-hearted attempt to introduce a gross level of link typology with the introduction of the "nofollow" link attribute- an initiative started by Google in order to try to address the increasing problem of "Spamdexing". But this is a pretty ham-fisted form of link typing- particularly in the way it is implemented by the Wikipedia where CrossRef DOI links to formally published scholarly literature have a "nofollow" attribute attached to them but, inexplicably, items with a PMID are not so hobbled (view the HTML source of this page, for example). Essentially, this means that, the Wikipedia is a black-hole of reputation. That is, it absorbs reputation (through links too the Wikipedia), but it doesn't let reputation back out again. Hell, I feel dirty for even linking to it here ;-).

Anyway, scholarly publishers should certainly read Shotton's article because it is full of good, and practical ideas about what can can be done with today's technology in order to help us move beyond the "digital incunabula" that the industry is currently churning out. The sample semantic article that Shotton's team created is inspirational and I particularly encourage people to look at the source file for the ontology-enhanced bibliography which reveals just how much more useful metadata can be associated with the humble citation.

And now I wonder whether CiteULike, Connotea, 2Collab or Zotero will consider adding support for the CItation Typing Ontology into their respective services?


* Disclosure:

a) I am on the editorial board of Learned Publishing
b) CrossRef has consulted with David Shotton on the subject of semantically enhancing journal articles

February 19, 2009

An interview about "Author IDs"

Over the past few months there seems to have been a sharp upturn in general interest around implementing an "author identifier" system for the scholarly community. This, in turn, has meant that more people have been getting in touch with us about our nascent "Contributor ID" project. The other day, after seeing my comments in the above thread, Martin Fenner asked if he could interview me about the issue of author identifiers for his blog on Nature Networks, Gobbledygook. I agreed and he posted the interview the other day.

I warn you ahead of time, I did ramble on a bit and the interview is long. There is a lot of stuff at the beginning about the DOI and it might seem off-topic, but I do think that there is a lot that we can learn from our DOI experiences which would apply to any author identifier. Just be thankful I didn't start talking about the privacy issues that will inevitably arise from any author identifier system. If I had, the interview would have probably gone on for another six pages ;-).

Anyway, as most of our membership knows, we have a pilot project underway to explore what it would take to launch a "CrossRef Contributor ID" system. We still haven't concluded whether it makes sense for us to do it, but one thing is clear from the recent discussions we've had and that is that, if we don't do it, somebody else almost certainly will.

January 19, 2009

CURIE Syntax 1.0

The W3C has recently (Jan. 16) released CURIE Syntax 1.0 as a Candidate Recommendation and is inviting implementations.

(Note that I made a fuller post here on CURIEs and erroneously confused the Editor's Draft (Oct. 23, '08) as being a Candidate Recommendation. Well, at least it's got there now.)

January 17, 2009

Standard InChI Defined

IUPAC has just released the final version (1.02) of its InChI software, which generates Standard InChIs and Standard InChIKeys. (InChI is the IUPAC International Chemical Identifier.)

The Standard InChI "removes options for properties such as tautomerism and stereoconfiguration", so that a molecule will always generate the same stable identifier - a unique InChI - which facilitates "interoperability/compatibility between large databases/web searching and information exchange". Note also that any "shortcomings in Standard InChI may be addressed using non-Standard InChI (currently obtainable using InChI version 1.02beta)".

On a practical level this means that the 27-character length InChIKeys (a hashed form of the InChI), with the following generic form

AAAAAAAAAAAAAA-BBBBBBBBFV-P
can now be readily and reliably generated and will start to be used in search indexing and linking applications.

December 03, 2008

CURIEs - A Cure for URIs

A quick straw poll of a few folks at London Online yesterday revealed that they had not heard of CURIE's. And there was I thinking that most everybody must have heard of them by now. :) So anyway here's something brief by way of explanation.

CURIE stands for Compact URI and does the signal job or rendering long and difficult to read URI strings into something more manageable. (URIs do have the particular gift of being "human transcribable" but in practice their length and the actual characters used in the URI strings tend to muddy things for the reader.) So given that the Web is built upon a bedrock of URIs, anything that then makes URIs easier to handle is going to be an important contributor to our overall ease of interaction with the Web.

(Continues)

Continue reading "CURIEs - A Cure for URIs" »

July 28, 2008

Five Years

Oh wow! A rather remarkable plea here from Dan Brickley on the public-lod mailing list which calls for the registrant of the dbpedia.org DNS entry to top it up with another 5+ years worth of clocktime. Some quotes:

"The idea of such a cool RDF namespace having only 6 months left on the DNS registration gives me the worries."

"If you could add another 5-10 years to the DNS registration I'd sleep easier at night."

"Let me stress I'm not suggesting that this domain is actually at risk. Just that the not-at-risk-ness isn't readily evident from a quick look in the DNS."

"Those in the know are probably confident this is all in hand, but as the SW gets bigger I suspect we ought to establish practices such as "vocabularies that seek global adoption should always have 5+ years on their DNS registries"."

Yes, and maybe those cool URIs should have kite marks, too. ;)

(Btw, for those who may not already know the maximum length of time that any DNS name may be leased out in a single registration is 10 years, see the FAQ put out by ICANN.)

So, pity the poor user of a given semantic web application who may not know what the expectancy is behind the nodes in an RDF graph of assertions. Shifting sands, indeed.

May 23, 2008

Tombstone

So, the big guns have decided that XRI is out. In a message from the TAG yesterday, variously noted as being "categorical" (Andy Powell, eFoundations) and a "proclamation" (Edd Dumbill, XML.com), the co-chairs (Tim Berners-Lee and Stuart Williams) had this to say:

"We are not satisfied that XRIs provide functionality not readily available from http: URIs. Accordingly the TAG recommends against taking the XRI specifications forward, or supporting the use of XRIs as identifiers in other specifications."
Alas, poor XRI. But what might this also mean for other URI schemes (note the reference above to "http: URIs)? Well, the message starts out with this:
"In The Architecture of the World Wide Web [1] the TAG sets out the reasons why http: URIs are the foundation of the value proposition for the Web, and should be used for naming on the Web. "
Now I'm not sure that this is quite what AWWW actually says. I don't find it to be that insistent that "http" URIs ... should be used for naming on the Web" but I would need to read it more carefully. Certainly, "http: URIs" fit the bill and are top of the class. But there is also a general recognition that other schemes than "http:" do exist.

Interesting times anyway with a "winner takes all" approach to identification. I wonder what this all means for DOI.

April 15, 2008

NIH Mandate and PMCIDs

The NIH Public Access Policy says "When citing their NIH-funded articles in NIH applications, proposals or progress reports, authors must include the PubMed Central reference number for each article" and the FAQ provides some examples of this:

Examples:

Varmus H, Klausner R, Zerhouni E, Acharya T, Daar A, Singer P. 2003. PUBLIC HEALTH: Grand Challenges in Global Health. Science 302(5644): 398-399. PMCID: 243493

Zerhouni, EA. (2003) A New Vision for the National Institutes of Health. Journal of Biomedicine and Biotechnology (3), 159-160. PMCID: 400215

It's interesting to note that on PMC itself both the PMCID and DOI are included - but the DOI isn't linked. Two things occur to me - 1) should CrossRef map DOIs to PMCIDs and vice versa and make PMCIDs available in it's query interfaces and 2) shouldn't publishers ask that the PMC copy of the article link back to the publisher version? It would be very easy with the DOI.

February 22, 2008

ISO/CD 26324 (DOI)

Following on from my previous post about prism:doi I didn't mention, or reference, the ongoing ISO work on DOI, Indeed I hadn't realized that the DOI site now has a status update on the ISO work:

"The DOI® System is currently being standardised through ISO. It is expected that the process will be finalised during 2008. In December 2007 the Working Group for this project approved a final draft as a Committee Draft (standard for voting) which is now being processed by ISO. Copies of the Committee Draft (SC9N475) and an accompanying explanatory document detailing issues dealt with during the standards process (SC9N474) are provided here for information.


Committee Draft 26324 is subject to ISO's copyright and is for information only to those interested in the project; it may not be re-distributed. This is currently undergoing the formal ISO voting process; the deadline for comments on CD 26324 from TC46/SC9's national bodies is April 25, 2008: please contact your national member of ISO TC46/SC9 if you would like it contribute to comments on this draft standard. Other documents for the ISO DOI Working Group are available on a DOI Project Register."


January 14, 2008

BISG Paper on Identifying Digital Book Content

BISG and BIC have published a discussion paper called "The identification of digital book content" - http://www.bisg.org/docs/DigitalIdentifiers_07Jan08.pdf. The paper discusses ISBN, ISTC and DOI amongst other things and makes a series of recommendations which basically say to consider applying DOI, ISBN and ISTC to digital book content. The paper highlights in a positive way that DOI and ISBN are different but can work together (the idea of the "actionable ISBN" and aiding discovery of content). However, it doesn't go into much depth on any of the issues or really explain how all these identifiers would work together and the critical role that metadata plays.

Nevertheless it's great that the paper has been put forward as a discussion document - CrossRef plans to respond and be part of the ongoing discussion in this area.

December 14, 2007

Zotero and the IA

Dan Cohen at Zotero reports (Zotero and the Internet Archive Join Forces) on a very interesting tie up that will allow researchers using Zotero to deposit content in the Internet Archive and have OCR done on scanned material for free under a two year Mellon grant. Each piece of content will be given a "permanent URI that includes a time and date stamp in addition to the URL" ( would Handle or DOI add value here?) and be part of Zotero Commons (things can also be kept private within a group).

Zotero Commons is related to but different from Nature Precedings and WebCite in that it's intended focus is on public domain stuff on researchers hard drives rather than someone else's material or website that is cited (WebCite) or preprints, datasets, technical reports that are given at least an initial screening (Nature Precedings).

October 17, 2007

DCMI Identifiers Community

Another DCMI invitation. And a list. Lovely.

See this message (copied below) from Douglas Campbell, National Library of New Zealand, to the dc-general mailing list.

(Continues)

Continue reading "DCMI Identifiers Community" »

October 15, 2007

NLM Blog Citation Guidelines

I've just returned from Frankfurt Book fair and noticed that there has been some recent popular interest in the The NLM Style Guide for Authors, Editors and Publishers recommendations concerning citing blogs.

Which reminds me of an issue that has periodically been raised here at CrossRef- should we be doing something to try and provide a service for reliably citing more ephemeral content such as blogs, wikis, etc.?

Continue reading "NLM Blog Citation Guidelines" »

October 02, 2007

InChIKey

The InChI (International Chemical Identifier from IUPAC) has been blogged earlier here. RSC have especially taken this on board in their Project Prospect and now routinely syndicate InChI identifiers in their RSS feeds as blogged here.

As reported variously last month (see here for one such review) IUPAC have now released a new (1.02beta) version of their software which allows hashed versions (fixed length 25-character) of the InChI, so-called InChIKey's, to be generated which are much more search engine friendly. Compare a regular InChI identifier:

InChI=1/C49H70N14O11/c1-26(2)39(61-42(67)33(12-8-18-55
-49(52)53)57-41(66)32(50)23-38(51)65)45(70)58-34(20-29-1
4-16-31(64)17-15-29)43(68)62-40(27(3)4)46(71)59-35(22-30
-24-54-25-56-30)47(72)63-19-9-13-37(63)44(69)60-36(48(7
3)74)21-28-10-6-5-7-11-28/h5-7,10-11,14-17,24-27,32-3
7,39-40,64H,8-9,12-13,18-23,50H2,1-4H3,(H2,51,65)(H,54,56
)(H,57,66)(H,58,70)(H,59,71)(H,60,69)(H,61,67)(H,62,68)(H,73,74)
(H4,52,53,55)/f/h56-62,73H,51-53H2

with its InChIKey counterpart:

InChIKey=JYPVVOOBQVVUQV-UHFFFAOYAR

That's some saving.

Oh No, Not You Again!

Oh dear. Yesterday's post "Using ISO URNs" was way off the mark. I don't know. I thought that walk after lunch had cleared my mind. But apparently not. I guess I was fixing on eyeballing the result in RDF/N3 rather than the logic to arrive at that result.

(Continues.)

Continue reading "Oh No, Not You Again!" »

October 01, 2007

Using ISO URNs

(Update - 2007.10.02: Just realized that there were some serious flaws in the post below regarding publication and form of namespace URIs which I've now addressed in a subsequent post here.)

By way of experimenting with a use case for ISO URNs, below is a listing of the document metadata for an arbitrary PDF. (You can judge for yourselves whether the metadata disclosed here is sufficient to describe the document.) Here, the metadata is taken from the information dictionary and from the document metadata stream (XMP packet).

The metadata is expressed in RDF/N3. That may not be a surprise for the XMP packet which is serialized in RDF/XML, as it's just a hop, skip and a jump to render it as RDF/N3 with properties taken from schema whose namespaces are identified by URI. What may be more unusual is to see the document information dictionary metadata (the "normal" metadata in a PDF) rendered as RDF/N3 since the information dictionary is not nodelled on RDF, not expressed in XML, and not namespaced. Here, in addition to the trusty HTTP URI scheme, I've made use of two particular URI schemes: "iso:" URN namespaces, and "data:" URIs.

(Continues.)

Continue reading "Using ISO URNs" »

Whole Lotta ID

ISO has registered with the IANA a URN namespace identifier ("iso:") for ISO persistent resources. From the Internet-Draft:

"This URN NID is intended for use for the identification of persistent resources published by the ISO standards body (including documents, document metadata, extracted resources such as standard schemata and standard value sets, and other resources)."

The toplevel grammar rules (ABNF) give some indication of scope:

NSS     = std-nss
std-nss = "std:" docidentifier *supplement *docelement [addition]

Just wanted to quote here one of the funkier examples cited in the document:

urn:iso:std:iso:9999:-1:ed-1:v1-amd1.v1:en,fr:amd:2:v2:en:clause:3.1,a.2-b.9
 
"refers to (sub)clauses 3.1 and A.2 to B.9 in the corrected version of Amendment 2, in English, which amends the document comprising the 1st version of edition 1 of ISO 9999-1 incorporating the 1st version of Amendment 1, in English/French (bilingual document)"
Wow! That's some ID. That's something else.

As far as DOI is concerned there is nothing obvious to be learned. It is interesting to see such a level of granularity supported though. And since all these documents issue from a central publisher they can be prescriptive about the identifier syntax. Something which cannot be mandated for the many CrossRef publishers with their own commercial arrangements. Hence DOI is generally agnostic about suffix strings.

Seems to be a little confusion about the registration though. The NID was approved Jan. 15, '07 by the IESG and the IANA Registry of URN Namespaces (last updated Aug. 22, '07) lists the namespace "iso" with the provisional (unnumbered) RFC labelled "RFC-goodwin-iso-urn-01.txt" (being the -01 draft). However, the IETF I-D Tracker reports this status for draft-goodwin-iso-urn, which shows that a new I-D (an -02 draft) was submitted in Sept. 7, '07:

"A Uniform Resource Name (URN) Namespace for the International Organization for Standardization (ISO), draft-goodwin-iso-urn-02.txt"

July 28, 2007

URI Template Republished

Well, it all went very quiet for a while but glad to see that the URI Template Internet-Draft has just been republished:

"A New Internet-Draft is available from the on-line Internet-Drafts
directories.

Title : URI Template
Author(s) : J. Gregorio, et al.
Filename : draft-gregorio-uritemplate-01.txt
Pages : 9
Date : 2007-7-23

URI Templates are strings that can be transformed into URIs after
embedded variables are substituted. This document defines the
syntax and processing of URI Templates.

A URL for this Internet-Draft is:

http://www.ietf.org/internet-drafts/draft-gregorio-uritemplate-01.txt"

URI templates should be a very useful publishing tool. Templates are already used by technologies such as OpenSearch - see here.

July 12, 2007

PURL Redux

Seems that there's life in the old dog yet. :~) See this post about PURL from Thom Hickey, OCLC, This extract:

OCLC has contracted with Zepheira to reimplement the PURL code which has become a bit out of date over the years. The new code will be in written in Java and released under the Apache 2.0 license.