Implementation of TaxPub, an NLM DTD Extension for Domain-specific Markup in Taxonomy, from the Experience of a Biodiversity Publisher
Penev, Lyubomir
Catapano, Terence
Agosti, Donat
Georgiev, Teodor
Sautter, Guido
Pavel Stoev,
TaxPub was created as an XML extension to the general JATS to provide domain-specific markup for prospective publishing in the area of biological systematics. The core idea of the schema is to delimit descriptions of taxa, or treatments, within an article, and to use these individual portions of information for various purposes. TaxPub was developed in a close cooperation between the author (Terence Catapano), a community interested in such markup (Plazi), the NLM JATS group and a journal publisher (Pensoft). Since July 2009, TaxPub has been routinely implemented in the everyday publishing practice of Pensoft, to provide: (1) Semantically enhanced, domain-specific XML versions of articles for archiving in PubMedCentral (PMC); (2) Visualization of taxon treatments on PMC; (3) Export of taxon treatments to various aggregators, such as Encyclopedia of Life, Plazi Treatment Repository, and the Wiki Species-ID.net.
 Good morning. All right. So I am here to talk about the implementation of tax pub, which is an extension to the NLM DTB Jats that me and a team of other people developed a few years ago. I'd like to point out, which is what is obvious, this presentation in the paper is the product of several mines distributed across the world. Coming from different domains as well, it's the Amaliburian Gita Sauder is a computer scientist, Pavel Theodor and Lubo work for PennSoft, scientific publisher. And this distribution of talent and work will be evident in the rather rocky nature of the presentation, which I apologize for in advance. But here we go. So yeah, we're going to focus on what we've done with, or what really PennSoft and Lubo has done with the tax pub extension over the past several years. The focus will be on what we're calling semantic tagging and enhancements. In other words, bringing out the items of interest inside of the scientific literature, in this case, tax nomad literature. And then once having done that, the dissemination of this data from the literature to various external aggregators. And then we'll talk briefly about what we want to do with tax pub in the future. OK, so to start off, I'll give some background on Plesi. Plesi is kind of a weird organization. Donat, Auguste and I, Donat is a scientist. He's a mermicologist. Studies ants. He's a taxonomist. We met on a project, an NSF-funded project a few years ago. The project then did, and we didn't stop working. We found the work to be very interesting. So we founded a company, or organization in Switzerland. We have members in Switzerland, Germany, the US. In fact, another Plesi member, Bob Morris, is here in the audience. And Iran, where Donat happens to live right now. We are, I like this term, a research-based think tank. That's the term that Donat came up with. I kind of accept that. You could think of it as an indie scientific label, almost. We have a very DIY approach to doing our work. And we definitely have the mission to promote open access. I mean, that is the major goal. We do this in four different areas. We have a lawyer on board who advocates, and argues, in the way lawyers can about open access. I and Edo, a few other people, work on technical solutions, such as taxpub. We maintain what we call a treatment repository, which is simply a electronic repository where treatments, which I will describe later, are deposited so that they can be accessed directly and cited using stable URLs. And of course, people form advocacy for open access. Recently, we founded a GMBH in Switzerland, which, from my understanding, is something like a limited liability company. So it's a commercial entity. A small, medium-sized employer owned by Blase, the organization, the Varain, our association, to perform actual commercial services, such as document conversion and consultation. We receive funding from public donors, from private donors. And recently, we've been involved into European Union grants that have just been funded. And yes, and we have clients all over the world. All right, so the context for this work is three or four fold. First is the global diverse biodiversity crisis, that we are in the midst of one of the greatest die-offs in history. And it certainly is a crisis. It's been well known for about 20 years, at least. But there are very few systems and tools to measure and document what is going on. There's a scientific aspect to this that we estimate that there's about 1.8 million species that have been described that we know about. And it's estimated there's something like 8 million more that we don't know about, or that haven't been described, and may in fact be dying, if we're becoming extinct, as we speak. The identification of these species takes place within scientific publications. The naming of new species is governed by codes. I'm sure many of you know this already. There's ICZN, the International Co-Frisiological Nomeclature, ICBN, International Co-Frize and Biological Nomeclature. These codes require publication of descriptions of species in actually up until very recently, paper publications. Just very recently, I think ICBN, the Biological Nomeclature Code, has a lot of publishing in electronic documents. Unfortunately, they specifically said PDF, which is unfortunate that they got that specific. But it is a major leap forward to actually accept the electronic publication. And there's obviously a lot of activity in this area. There's 17,000 species described every year, new species described every year, and about 100,000 redistrictions of existing species. So there's a tremendous amount of content locked up in the literature and coming out at an increasing rate. And however, the challenge here is that it's fragmented over about 2,500 taxonomic journals and books. So it's difficult to access. So that open access is really the key. An open access in both sense of the term. You need to have open free access to this literature. And the content itself needs to be open in the sense of being able to be accessible directly so you can take a great advantage of the rich content that is in there. And so yes, this is the solution we hope is open access and both senses, semantically enhanced publications. Which one of the goals that this does not slide that he's mentioning here is that we really want to, through electronic publication, accelerate the publication process so that descriptions do not take that long to get out and that the data from the descriptions don't take that long to get out. And that the names are registered, new names of species are registered in these developing registries quickly. And we hope the tax pub has helped in that regard. You've already seen that slide. Slipped in there twice. I apologize. OK, so background of tax pub. Tax pub is a very small extension to the blue publishing DTD. As Jeff mentioned, I gave presentation on this and there's a paper available describing it online. There's the URL. The focus of tax pub is on treatments. What I've been talking about this treatments are, think of them as species descriptions. These are very formal descriptions of a newly named organism or a renamed organism. The treatments are, again, highly formal. They're easily identified and they often are separated off from the publication in which they're in. So they're kind of independent entities and have a very important part in the nomenclature process because you have to point to previous treatments if you're renaming species. I hope I'm getting this right. But there's an interlocking set of references between treatments in the naming process. So they're very significant document objects. Another legal point that we've tried to go out and lemmon make is that treatments being statements of fact and not creative works, at least in the Swiss intellectual property regime, do not qualify for copyright. So that we're trying to advance the idea that publishers and should acknowledge that the treatments should be allowed to be free of copyright. The rest of the article, fine. But the treatment itself is of such a nature that it's not copyrightable. And I am not going to argue this point. I'm not a lawyer, nor do I want to be in any life. But that is a contention of ours. And believe it or not, we've had traction from publishers on this. They accept the idea of letting treatments float on their own and be cited and available on their own. So the treatments contain basically two parts. One is the nomenclature section, which is a heading. Think of it as a heading that says what the name of the species is and its status and the fuel. And who's the author of the taxons, things like that. And then there's various treatment sections. We don't even bother to name what they are. We punt out to the type attribute to do that. And then there's some domain-specific elements we added for inline content. Taxon names, created an element for that. Material citation, which basically references to specimens, but could be references to any sort of material that is used to describe a species. And then the weakest component of taxpub currently, this element, descriptive statement, which is an attempt to somehow mark up the phrases that are used to describe the anatomy or morphological features of a taxon. There we go. OK, so here's a sample. Sorry, I shouldn't actually look at this. It marked up treatment. Very simple. You have your outer treatment. Whoops. Treatment element. Then you have a required. The only required element there is a nomenclature element. The nomenclature element contains a name. The name contains the name part, which is the genus name. And this is by the CLEO. I believe. And then the name of the species, Mizzanzi. This is a paristhoid wasp, I believe. Then there's an identifier. This is a zoo bank identifier for this species. And there's another identifier, which comes from a different system. There's the taxon authority. In other words, the people who were responsible for the naming of the species, and the status species, no more new species, essentially, is what that means. So you can see the way in what taxbugs try to do here. Put in some of our own elements to bring out the important taxonomic features, but also using whenever necessary generic NLM or JATS elements like object ID to do the rest. And this is just an example of a section of a treatment. This is the section that discusses the materials and the specimens that were used to name the species. We have an element called material citation that bundles together or delineates one particular specimen. In this case, it's marked up fairly granularly to point out different facets of that citation that this is a holotype, that its location is this King's South Museum in Saudi Arabia. And then there's a collecting event, which is where this specimen was actually collected from. And it was collected in Saudi Arabia, in this particular province, et cetera. And then, again, using a generic NLM element named content, rather than putting all of this elements for things like latitude, longitude, altitude, all this, we sort of advise our users to just use existing vocabularies to provide the semantics and use the name content element to do the actual structural delineation. So here, there's a perfectly adequate term in the Dub Darwin core vocabulary of the coordinates that can serve to supply semantics for the latitude and longitude of this specimen is collected. So, tax pub, I don't really have much else to say about what's changed since 2010. Don't take that as an example of our laziness, but frankly, as a success, that it's been fairly stable. It's worked. And we haven't received much demand from our primary user, PENSOFT, to change it much. One of the things, though, that we did have to do was introduce the notorious x element. I'm not sure all of you are familiar with x. x is an element that gives you a lot of wiggle room. It's there to tag anything, all this interstitial stuff, that doesn't really have, I like to think, shouldn't really be there, but is. And the publishers don't want to take out. And so I conceded this, that they want to put a semicolon between to the tax on status and the tax on authority. So I added x to the content model. We're all happy about it. It's fine. However, this signals a trend that I also had wanted to avoid. Tax pub is really designed with an eye towards new literature. Our hope was that, this is kind of a strategic goal, to shift the work on markup of taxonomic literature from retrospective markup to prospective markup. Because we have those 8 million other species that have not yet to be described sitting out there. And we have 1.8 million that have been. So we'd like to focus on the 8 million that are going to be described. And also hopefully describe them in a way that's structured and granular, that will open up the data to reuse. However, there's a persistent urge to markup the legacy literature and a surprising amount of money behind that urge to do it. So this enables me to use this term, reunification, which I just had to use because it's when do you ever get a chance. So one of the things that we're probably going to do a tax bump, if I shouldn't say probably, is a goal is to have and make an extension not just to the blue TTB but to the green TTB so that we can address the legacy literature as well. There is interest in, for instance, marking up existing floras. And we definitely need to loosen it up more in order to address those types of publications. And we have, there's been interest from other journals to adopt TaxPub, the European Journal Taxonomy. Just last week, we signed a very modest contract, POSY did with them, to consult on seeing how to get their workflow to be based around TaxPub. We'll see how that goes. I'm optimistic. And then the journals you tax, which is one of the major taxonomic journals in the world. The Encyclopedia of Life, which is an organization attempting to create basically a web page for every species on Earth, I guess anywhere. I don't think they're going to limit themselves to the Earth if we find anything else. They're offering us a contract to help Zutaxa also adopt a TaxPub into their workflow. So that they can, and their desires so that they can get the data that's currently locked up in PDFs, which is what Zutaxa produces, to pull out a lot of that data and put it into their species pages in Encyclopedia of Life. And then another major area is development. The enhancement of this description of the morphological features of the organisms. The existing markup we have is really just a first attempt that isn't that successful. No one uses it, I should say. And so there was a proposal to address that. Briefly show this. First thing I want to point out is that those of you who aren't familiar with these type of descriptive data or descriptive language. This is nasty stuff to mark up because it's a combination of very formal language, but also natural language that's tough to mark up in such a way that it can get into databases or get represented even, say, in RDF. So when you get phrases like extremely rarely yellow, often shallily joined around the node, these are, it's kind of fuzzy stuff, hard to mark up. Glabrous or weakly hear her suits. So you have this wonderful combination of terms like labrous and her suits, which means something very specific, but with these words like weakly. So this proposal is to introduce a few elements that basically are saying, this is a categorical element, is saying, well, here's a, I believe what you can call it, a categorical character. It's something that something is, the stem color is what's being referred to here. And luckily there is a plant ontology that we can point to to say what category of feature that we're talking about. And then it has a state. So the stem color is greenish, and believe it or not, there is a non-tall ontology term for greenish out there somewhere. And so for the categorical things you have that, and then you can also address the quantitative features, like just measurements. And here you have the stipule width, which is 3.10 millimeters. So we'll be testing this, and hopefully we can, you know, this might serve to be a lightweight, but yet effective way to address these types of, this type of language. OK. And to wrap up on tax, there's been some challenges. We maintain the code on source forage, which is cumbersome, for a variety of reasons. I'd like to move it to something better. I'm thinking maybe GitHub, I'm not sure yet. But then that's the technical maintenance, or the infrastructure. But the other maintenance, the sort of governance and administrative maintenance, is also very challenging. I mean, plosy, we're all, this is all volunteer effort. We all have other jobs. I'm a librarian. Don't know, it's a diplomatic spouse living in Tehran. He's got a lot of things to take care of. And we do actually have some funding now, but we're not a wash in funding. There's nothing really paying for tax prep development. But it is supported under plosy. And to the extent that plosy is getting these grants and funding, we can hopefully direct some of the funds that way. And then I mentioned this in my talk two years ago, and it still remains, I think, the greatest challenge. When I first created tax prep, I naively focused on the scheme, or the extension. And that's the easy part. Especially because Jats was made in such a way, designed very well to enable extension. It's very doable. But that is the easy part. And that's not the sum total of what an extension or a DTD or a standard or whatever you want to call it is. The documentation is really critical to explaining what stuff is, what you're doing, how to use it. And the documentation infrastructure is not that great. Right now, we use these comments in the extension with some ad hoc markup that is used by, I believe, a Perl script that NCBI has to generate the online HTML documentation. And it's a cumbersome process, as I mentioned, to put it there. And then I've got to send it to Kim. And she runs the conversion. And I get these files back, and I got to post them somewhere. I'm looking for a better way to do that. We also maintain the documentation on a Wiki called Species ID, which is another Palsy project, which actually I've recently found out has been moved to. Anyway, here's the, I'll pick up that for a second. So here is the documentation. Just like the ordinary JET documentation, except we have our elements mixed in. And I should point out also, while probably been noticing, that there's a namespace prefix for the tax put elements. This was, we decided to keep the extension in its own namespace, just to distinguish it better and prevent name clashes with the general blue DTD. So we have this nice documentation that periodically gets generated when I get around to it. And then the documentation is also on this Wiki maintained by GBIFF, the Global Biodiversity Information Facility, which I just found out, is maintaining a collection of vocabularies in the domain. So I'm very happy to see that it's on this GBIFF Wiki. And the value here is that people can come in and add examples and work more collaboratively on the documentation. So I'm going to shift gears to the other side of this presentation. And this is the side I have less authority to speak about, so bear with me. The primary author, Luba Pennev, is the owner, or the president's, imagine of Pensop, a scientific publisher. And Zuki's is their major journal publishing taxonic literature for zoological taxonic literature. As you can see, it's founded almost 20, over 20 years ago. Zuki's, the journal, was launched four years ago. It's a completely open access journal, taxonomy. It's been very productive and successful in the last four years. They're very forward looking and want to take advantage of all the new technologies they can. So they register any new names in Zubank, which is a global registry of zoological names, and then supply data to Encyclopedia of Life, the Pwazi, our dream repository, and Species ID, which is a wiki for species descriptions. I'm a librarian, and I know most of these things, but not all of them. But they're cross-draft members of the issue DOIs. ISI, I guess, is calculating their impact factor and doing their reverse indexing. They're in scopus, blah, blah, blah, blah, blah. I want blah, blah, blah of this one, the PubMed Central. This is one of our, I think, our proudest achievements is that Zuki's actually became, I believe, the first taxonomic journal to enter PubMed Central. And that's, again, an achievement we're very proud of. And then he has the PENSOF journal system, which is next in L-based workflow that drives all this stuff. And it's very productive, as you'll see by this chart. There's been a nice upward trend with a mysterious dip in 2010. But the pages and the articles are coming out, and people are publishing with Zuki's, and they've been very active in these four years. OK, I'll do my best with this. But this is a nice chart, laying out the landscape here. So, I mean, basically with the taxon literature, as I mentioned earlier, you have your perspective publishing and your historical literature. For historical literature, there's other schemas, Taxon X, which is another schema that I'm co-author of, and Taxon O'Litt. And Closie has an editor that helps to mark up the stuff. There's also these systems, scratch pads, and things like that, where that data goes. And then there's perspective publishing that goes through PENSOF's markup tool, blah, blah, blah, peer review, automated submission. The things are very automated. But I think the major emphasis here is that the data, when it's all brought together in this format, the data is going all sorts of places, playing lots of roles in different areas. And there is this feedback also to these other systems as well, for stages, submission, peer review, publication, dissemination, and each with their own challenges. As you can see. All right, so here's a nice slide showing. Here's a, basically here you have a treatment. This is what it looks like in print, sections of it at least. So you have your nomenclature section, and that data goes to Zoo Bank, which is a red pick in the registry of Zoo and Logical Nomenclature. The references go to the Biodiversity Heritage Library. Here's that description, the more morphological description area with these wonderful terms like, you know, to lace or I brownish yellow and, you know, publish one. It's a fusive lack along a lateral margin and all that stuff. That data goes to ELL, goes into their species pages, into species ID, which is a wiki, which does essentially the same thing, and the entire treatment goes to our plazios treatmen repository. Images go to ELL alongside the descriptions and into the species pages. And images also go to Morph Bank, which is a database from images of specimens plus metadata. Very large and important resource in this area. And then the occurrence data, which is where the material is collected, goes into Gepeth Global Biodiversity Information Facility. And when it's done right, all this that long stuff becomes mappable on Google Earth or other resources. So here, again, the goal is to be open in both senses, open access in the legal sense, but also open in the sense that the data is open and able to be manipulated and reused widely. OK, so this is a run through what PENSOFT has done in terms of displaying these articles. So there's some semantic enhancements as we were calling them. Right up here, I'll point out, there's these tabs that allow you to highlight in the article the treatments, the tax on names, citations, localities, et cetera. So this will, yeah. So if you click on localities, you get a list of the tax of the described in the article, and they're plotted out for you. So this is where this parasite wasp has been collected from. What's going on with the key here? There we go. So you have a key to species, which I haven't really talked about. Key is a diagnostic tool. It's a way if you have an animal or something in front of you, you follow these sets of instructions to figure out what it is. So here, it mentions a figure, and the figure, of course, is linked to, and that, I suppose, is linked to, this might probably has gone to Morph Bank also. Then you have a citation, a Sharki 2007, and you get the citation, and this happens to be in Zutaxa. But if you follow this footnote, it might link to it. Zutaxa doesn't issue DOIs, so I'm not sure. Here you have a mention of a taxon. In fact, this is a very large, high-ranking taxon, Hymenoptera. And click on that, and you can get different explanations of what Hymenoptera is. In this case, it's PENSOFT has a thing called taxon profile, which is a page that aggregates information about organisms. This is PENSOFT's profile of Hymenoptera. Hymenoptera are ants and rocks and bees, and you can see they're very widespread, probably in this room. Sure, there's an ant somewhere in here, nearby. And then here's another one, Solonium. Plant, I believe. And here you find, you can follow references to Solonium in the biodiversity heritage library. They're all over the place. And so you choose Solonium abalotum, and there you go. You go to a publication about them in the BNDHL. And so that's one, that's basically what you get when you go to PENSOFT and you read one of their articles. Another thing I should publish point out, it was back there, which is mentioned yesterday, that is not showing it. There is a link right to the side. You can get the XML. We PENSOFT post the XML alongside the PDF. It's very easy to get to. So it's not something that, as a publisher, they're hiding. It's right out there. So anyone can grab the XML and do what they want with it. So as I mentioned, Zookiz has been archived in PubMed Central very happily. And the scripted sections go to EOL. So that has extracted out of these materials, examin sections, and goes to EOL. Whoops. Whoa. Hold on. Wow. Sorry. Now I have three minutes. Four. Four minutes. Almost there. Is there some sort of electronic hook that pulls the presentation off? OK. And there's a species space, which is particularly ugly bug, I think. Really long antennas. And then the material treatments, the isolated treatments go to our plaudite treatment repository. We have something like over 10,000 treatments of different organisms now that are referable directly. And you can get XML for them. And then, oh yeah, this is an interesting paper. In this paper, the authors simultaneously published to the journal and to a wiki at the same time. So here's the actual article, as you'd see it on the keys, but there's a link to the entry in the wiki. And there you go. All the data, as it's mentioned here, is derived from the article. So this simultaneous publication, this allows the collaborative work on the species as well as having an official peer reviewed article. And this isn't just to show the key, the species has been added to the wiki. Data is also provided to wiki species and wiki immediate commons. There's a wiki species page. With the commons, all these kind of scary little pictures of bugs. That's another gross one. I don't know what that is. And note here the abstract PDF or link to. So you can get to the article for this from the wiki species page. OK, so I'm going to speed this up. Yes, we want more symmetric web enhancements. So PENSOF is working on a tool to help authors create collaboratively, write these taxonomic articles that will involve community based peer review. And then PENSOF is very much interested in data journals. So publishing, publications that include data, in this case these are in the term small data, of all sorts. Collaborative offering tool, web interface to help you structure, to help you create the article. And of course, there's commenters. You've got collaborators, commenters, involved in publication process. So here's where you would add your treatment information at the high level, then you've got a subsection, fill in your content. And then this is my favorite part of the presentation. So OK, so then why is it? I'm over time now, but I think I have five minutes. OK, so we have in this case, I'm an optorist. He's captioning off B, goes to his lab, finds, he's curious about it, writes up his little treatment, gets in up with all of them. And this is the peer review process, a wonderful depiction. Then lo and behold, the article is published in a PDF format, great. But there's this underlying data that we all want. And this is my favorite part of the presentation, because I don't know what this means. My theory is that that is a cross over a grave, and that the paper is dead, or the book is dead. And then as I said to Wendell earlier, we want to roll away the stone to reveal the data that's underneath the publication, and then share the primary data to enable reuse of content. So there you go. Yeah, and then here's some quick facts about the data journal, no upper limit of managed size. It's very important. Previously, the amount of data that you could publish in the taxonomic article is very limited, and it was very frustrating to authors. Collaboration, collaboration, community, all that's important, standard compliance, JATS, DOM-Accord, DOM-Accord, et cetera, and code compliance, this will be done in such a way that it will be compliant to the various codes. Lots of stuff goes into the manuscript. It all gets structured, and it goes places. Because of the structuring of the data. And then it goes places and comes back. Lessons learned. Yeah, specificity of domains, a challenge. Market for Currents data is a very big challenge, all that long collecting information. There's other information, but locality is very difficult to identify and mark up if you're not getting the original data, lowering the cost of efficiency of the market process. This point cannot be overstated. It's likely that you're not going to. It's hard to get authors to provide data, provide them articles that format you want. And so you have to either give them incentives or tools, but also probably recognize that you're going to be spending time in the editorial process to do this. And this last point is it can't be overstated. The small taxonomy of publishers, the 2,500 journals, are very, very small scale on storage, huge stream budgets, and very firm in their habits. So not changing. It may not be turning a super tanker, but sometimes it's hard to even turn a dinghy if all you know is to rope over it. OK, I think that's it. Yes. Final point, not easy, exciting. Possible throw up on access. And then, yes, donuts claim that this is the only way. Donuts, I think, very strong and accurate claim that really this is really the only way to go for the missing species that we don't know about on Earth. All right. There you go. Thanks. OK, we have time for one or two questions. Just a comment. I'd like to congratulate you and you, Beau, and everybody else involved. I think this is exactly a brilliant example of what a journal should be about. And you've done it in a particular area. Everybody else now needs to do it in their particular areas. It's fabulous work. I couldn't agree more. Thank you. All right. All right. Good, well, thank you very much.
 Good morning.  All right.  So I am here to talk about the implementation of tax pub,  which is an extension to the NLM DTB Jats that  me and a team of other people developed a few years ago.  I'd like to point out, which is what is obvious,  this presentation in the paper is the product of several mines  distributed across the world.  Coming from different domains as well,  it's the Amaliburian Gita Sauder is a computer scientist,  Pavel Theodor and Lubo work for PennSoft,  scientific publisher.  And this distribution of talent and work  will be evident in the rather rocky nature  of the presentation, which I apologize for in advance.  But here we go.  So yeah, we're going to focus on what we've done with,  or what really PennSoft and Lubo has done with the tax  pub extension over the past several years.  The focus will be on what we're calling  semantic tagging and enhancements.  In other words, bringing out the items of interest  inside of the scientific literature, in this case,  tax nomad literature.  And then once having done that, the dissemination  of this data from the literature to various external  aggregators.  And then we'll talk briefly about what  we want to do with tax pub in the future.  OK, so to start off, I'll give some background on Plesi.  Plesi is kind of a weird organization.  Donat, Auguste and I, Donat is a scientist.  He's a mermicologist.  Studies ants.  He's a taxonomist.  We met on a project, an NSF-funded project a few years  ago.  The project then did, and we didn't stop working.  We found the work to be very interesting.  So we founded a company, or organization in Switzerland.  We have members in Switzerland, Germany, the US.  In fact, another Plesi member, Bob Morris,  is here in the audience.  And Iran, where Donat happens to live right now.  We are, I like this term, a research-based think tank.  That's the term that Donat came up with.  I kind of accept that.  You could think of it as an indie scientific label, almost.  We have a very DIY approach to doing our work.  And we definitely have the mission  to promote open access.  I mean, that is the major goal.  We do this in four different areas.  We have a lawyer on board who advocates, and argues,  in the way lawyers can about open access.  I and Edo, a few other people, work  on technical solutions, such as taxpub.  We maintain what we call a treatment repository, which  is simply a electronic repository where  treatments, which I will describe later, are deposited  so that they can be accessed directly and cited using  stable URLs.  And of course, people form advocacy for open access.  Recently, we founded a GMBH in Switzerland, which,  from my understanding, is something like a limited  liability company.  So it's a commercial entity.  A small, medium-sized employer owned by Blase,  the organization, the Varain, our association,  to perform actual commercial services, such as document  conversion and consultation.  We receive funding from public donors, from private donors.  And recently, we've been involved into European Union  grants that have just been funded.  And yes, and we have clients all over the world.  All right, so the context for this work is three or four  fold.  First is the global diverse biodiversity crisis,  that we are in the midst of one of the greatest die-offs  in history.  And it certainly is a crisis.  It's been well known for about 20 years, at least.  But there are very few systems and tools to measure and  document what is going on.  There's a scientific aspect to this that we estimate that  there's about 1.8 million species that have been  described that we know about.  And it's estimated there's something like 8 million more  that we don't know about, or that haven't been described,  and may in fact be dying, if we're becoming extinct,  as we speak.  The identification of these species takes place within  scientific publications.  The naming of new species is governed by codes.  I'm sure many of you know this already.  There's ICZN, the International Co-Frisiological  Nomeclature, ICBN, International Co-Frize  and Biological Nomeclature.  These codes require publication of descriptions of  species in actually up until very recently, paper  publications.  Just very recently, I think ICBN, the Biological  Nomeclature Code, has a lot of publishing in electronic  documents.  Unfortunately, they specifically said PDF, which is  unfortunate that they got that specific.  But it is a major leap forward to actually accept the  electronic publication.  And there's obviously a lot of activity in this area.  There's 17,000 species described every year, new  species described every year, and about 100,000  redistrictions of existing species.  So there's a tremendous amount of content locked up in the  literature and coming out at an increasing rate.  And however, the challenge here is that it's fragmented over  about 2,500 taxonomic journals and books.  So it's difficult to access.  So that open access is really the key.  An open access in both sense of the term.  You need to have open free access to this literature.  And the content itself needs to be open in the sense of  being able to be accessible directly so you can take a  great advantage of the rich content that is in there.  And so yes, this is the solution we hope is open access  and both senses, semantically enhanced publications.  Which one of the goals that this does not slide that he's  mentioning here is that we really want to, through  electronic publication, accelerate the  publication process so that descriptions do not take that  long to get out and that the data from the descriptions  don't take that long to get out.  And that the names are registered, new names of  species are registered in these developing registries  quickly.  And we hope the tax pub has helped in that regard.  You've already seen that slide.  Slipped in there twice.  I apologize.  OK, so background of tax pub.  Tax pub is a very small extension to the blue  publishing DTD.  As Jeff mentioned, I gave presentation on this and there's  a paper available describing it online.  There's the URL.  The focus of tax pub is on treatments.  What I've been talking about this treatments are, think of  them as species descriptions.  These are very formal descriptions of a newly named  organism or a renamed organism.  The treatments are, again, highly formal.  They're easily identified and they often are separated  off from the publication in which they're in.  So they're kind of independent entities and have a very  important part in the nomenclature process because  you have to point to previous treatments if you're  renaming species.  I hope I'm getting this right.  But there's an interlocking set of references between  treatments in the naming process.  So they're very significant document objects.  Another legal point that we've tried to go out and  lemmon make is that treatments being statements of fact and  not creative works, at least in the Swiss intellectual  property regime, do not qualify for copyright.  So that we're trying to advance the idea that publishers  and should acknowledge that the treatments should be allowed  to be free of copyright.  The rest of the article, fine.  But the treatment itself is of such a nature that it's not  copyrightable.  And I am not going to argue this point.  I'm not a lawyer, nor do I want to be in any life.  But that is a contention of ours.  And believe it or not, we've had traction from publishers  on this.  They accept the idea of letting treatments float on their  own and be cited and available on their own.  So the treatments contain basically two parts.  One is the nomenclature section, which is a heading.  Think of it as a heading that says what the name of the  species is and its status and the fuel.  And who's the author of the taxons, things like that.  And then there's various treatment sections.  We don't even bother to name what they are.  We punt out to the type attribute to do that.  And then there's some domain-specific elements we  added for inline content.  Taxon names, created an element for that.  Material citation, which basically references to  specimens, but could be references to any sort of  material that is used to describe a species.  And then the weakest component of taxpub currently, this  element, descriptive statement, which is an attempt to  somehow mark up the phrases that are used to describe the  anatomy or morphological features of a taxon.  There we go.  OK, so here's a sample.  Sorry, I shouldn't actually look at this.  It marked up treatment.  Very simple.  You have your outer treatment.  Whoops.  Treatment element.  Then you have a required.  The only required element there is a nomenclature element.  The nomenclature element contains a name.  The name contains the name part, which is the genus name.  And this is by the CLEO.  I believe.  And then the name of the species, Mizzanzi.  This is a paristhoid wasp, I believe.  Then there's an identifier.  This is a zoo bank identifier for this species.  And there's another identifier, which comes from a  different system.  There's the taxon authority.  In other words, the people who were responsible for the  naming of the species, and the status species, no more new  species, essentially, is what that means.  So you can see the way in what taxbugs  try to do here.  Put in some of our own elements to bring out the  important taxonomic features, but also using whenever  necessary generic NLM or JATS elements like  object ID to do the rest.  And this is just an example of a section of a treatment.  This is the section that discusses the materials and  the specimens that were used to name the species.  We have an element called material citation that  bundles together or delineates one particular specimen.  In this case, it's marked up fairly granularly to point  out different facets of that citation that this is a  holotype, that its location is this King's  South Museum in Saudi Arabia.  And then there's a collecting event, which is where this  specimen was actually collected from.  And it was collected in Saudi Arabia, in this particular  province, et cetera.  And then, again, using a generic NLM  element named content, rather than putting all of this  elements for things like latitude, longitude,  altitude, all this, we sort of advise our users to just use  existing vocabularies to provide the semantics and use  the name content element to do the actual  structural delineation.  So here, there's a perfectly adequate term in the  Dub Darwin core vocabulary of the coordinates that can  serve to supply semantics for the latitude and longitude of  this specimen is collected.  So, tax pub, I don't really have much else to say about  what's changed since 2010.  Don't take that as an example of our laziness, but frankly,  as a success, that it's been fairly stable.  It's worked.  And we haven't received much demand from our primary user,  PENSOFT, to change it much.  One of the things, though, that we did have to do was  introduce the notorious x element.  I'm not sure all of you are familiar with x.  x is an element that gives you a lot of wiggle room.  It's there to tag anything, all this interstitial stuff, that  doesn't really have, I like to think, shouldn't really be  there, but is.  And the publishers don't want to take out.  And so I conceded this, that they want to put a semicolon  between to the tax on status and the tax on authority.  So I added x to the content model.  We're all happy about it.  It's fine.  However, this signals a trend that I also had wanted to  avoid.  Tax pub is really designed with an eye towards  new literature.  Our hope was that, this is kind of a strategic goal, to  shift the work on markup of taxonomic literature from  retrospective markup to prospective markup.  Because we have those 8 million other species that have not  yet to be described sitting out there.  And we have 1.8 million that have been.  So we'd like to focus on the 8 million that are going to be  described.  And also hopefully describe them in a way that's  structured and granular, that will open up the data to  reuse.  However, there's a persistent urge to markup the legacy  literature and a surprising amount of money behind that  urge to do it.  So this enables me to use this term, reunification, which I  just had to use because it's when do you ever get a chance.  So one of the things that we're probably going to do a tax  bump, if I shouldn't say probably, is a goal is to  have and make an extension not just to the blue TTB but to  the green TTB so that we can address the legacy literature  as well.  There is interest in, for instance, marking up existing  floras.  And we definitely need to loosen it up more in order to  address those types of publications.  And we have, there's been interest from other journals  to adopt TaxPub, the European Journal Taxonomy.  Just last week, we signed a very modest contract,  POSY did with them, to consult on seeing how to get their  workflow to be based around TaxPub.  We'll see how that goes.  I'm optimistic.  And then the journals you tax, which is one of the major  taxonomic journals in the world.  The Encyclopedia of Life, which is an organization  attempting to create basically a web page for every species on  Earth, I guess anywhere.  I don't think they're going to limit themselves to the Earth  if we find anything else.  They're offering us a contract to help Zutaxa also adopt a  TaxPub into their workflow.  So that they can, and their desires so that they can get  the data that's currently locked up in PDFs, which is what  Zutaxa produces, to pull out a lot of that data and put it  into their species pages in Encyclopedia of Life.  And then another major area is development.  The enhancement of this description of the morphological  features of the organisms.  The existing markup we have is really just a first attempt  that isn't that successful.  No one uses it, I should say.  And so there was a proposal to address that.  Briefly show this.  First thing I want to point out is that those of you who  aren't familiar with these type of descriptive data or  descriptive language.  This is nasty stuff to mark up because it's a combination of  very formal language, but also natural language that's tough  to mark up in such a way that it can get into databases or  get represented even, say, in RDF.  So when you get phrases like extremely rarely yellow,  often shallily joined around the node, these are,  it's kind of fuzzy stuff, hard to mark up.  Glabrous or weakly hear her suits.  So you have this wonderful combination of terms like  labrous and her suits, which means something very  specific, but with these words like weakly.  So this proposal is to introduce a few elements  that basically are saying, this is a categorical element,  is saying, well, here's a, I believe what you can call it,  a categorical character.  It's something that something is, the stem color is what's  being referred to here.  And luckily there is a plant ontology that we can point to  to say what category of feature that we're talking about.  And then it has a state.  So the stem color is greenish, and believe it or not,  there is a non-tall ontology term for greenish out  there somewhere.  And so for the categorical things you have that, and  then you can also address the quantitative features, like  just measurements.  And here you have the stipule width, which is 3.10  millimeters.  So we'll be testing this, and hopefully we can,  you know, this might serve to be a lightweight, but yet  effective way to address these types of, this type of  language.  OK.  And to wrap up on tax, there's been some challenges.  We maintain the code on source forage, which is cumbersome,  for a variety of reasons.  I'd like to move it to something better.  I'm thinking maybe GitHub, I'm not sure yet.  But then that's the technical maintenance, or the  infrastructure.  But the other maintenance, the sort of governance and  administrative maintenance, is also very challenging.  I mean, plosy, we're all, this is all volunteer effort.  We all have other jobs.  I'm a librarian.  Don't know, it's a diplomatic spouse living in Tehran.  He's got a lot of things to take care of.  And we do actually have some funding now, but we're not a  wash in funding.  There's nothing really paying for tax prep development.  But it is supported under plosy.  And to the extent that plosy is getting these grants and  funding, we can hopefully direct some of the funds that  way.  And then I mentioned this in my talk two years ago, and it  still remains, I think, the greatest challenge.  When I first created tax prep, I naively focused on the  scheme, or the extension.  And that's the easy part.  Especially because Jats was made in such a way, designed  very well to enable extension.  It's very doable.  But that is the easy part.  And that's not the sum total of what an extension or a DTD or  a standard or whatever you want to call it is.  The documentation is really critical to explaining what  stuff is, what you're doing, how to use it.  And the documentation infrastructure is not that  great.  Right now, we use these comments in the extension with some  ad hoc markup that is used by, I believe, a  Perl script that NCBI has to generate the online HTML  documentation.  And it's a cumbersome process, as I mentioned, to put it  there.  And then I've got to send it to Kim.  And she runs the conversion.  And I get these files back, and I got to post them somewhere.  I'm looking for a better way to do that.  We also maintain the documentation on a Wiki called  Species ID, which is another Palsy project, which  actually I've recently found out has been moved to.  Anyway, here's the, I'll pick up that for a second.  So here is the documentation.  Just like the ordinary JET documentation, except we have  our elements mixed in.  And I should point out also, while probably been noticing,  that there's a namespace prefix for the  tax put elements.  This was, we decided to keep the extension in its own  namespace, just to distinguish it better and prevent  name clashes with the general blue DTD.  So we have this nice documentation that periodically  gets generated when I get around to it.  And then the documentation is also on this Wiki maintained  by GBIFF, the Global Biodiversity Information  Facility, which I just found out, is maintaining a  collection of vocabularies in the domain.  So I'm very happy to see that it's on this GBIFF Wiki.  And the value here is that people can come in and add  examples and work more collaboratively on the  documentation.  So I'm going to shift gears to the other side of this  presentation.  And this is the side I have less authority to speak  about, so bear with me.  The primary author, Luba Pennev, is the owner,  or the president's, imagine of Pensop, a scientific  publisher.  And Zuki's is their major journal publishing taxonic  literature for zoological taxonic literature.  As you can see, it's founded almost 20, over 20 years  ago.  Zuki's, the journal, was launched four years ago.  It's a completely open access journal, taxonomy.  It's been very productive and successful in the last four  years.  They're very forward looking and want to take advantage of  all the new technologies they can.  So they register any new names in Zubank, which is a  global registry of zoological names, and then supply  data to Encyclopedia of Life, the Pwazi, our dream  repository, and Species ID, which is a wiki for  species descriptions.  I'm a librarian, and I know most of these things, but not  all of them.  But they're cross-draft members of the issue DOIs.  ISI, I guess, is calculating their impact factor and  doing their reverse indexing.  They're in scopus, blah, blah, blah, blah, blah.  I want blah, blah, blah of this one, the PubMed Central.  This is one of our, I think, our proudest achievements is  that Zuki's actually became, I believe, the first taxonomic  journal to enter PubMed Central.  And that's, again, an achievement we're very proud of.  And then he has the PENSOF journal system, which is  next in L-based workflow that drives all this stuff.  And it's very productive, as you'll see by this chart.  There's been a nice upward trend with a mysterious dip in  2010.  But the pages and the articles are coming out, and people  are publishing with Zuki's, and they've been very active  in these four years.  OK, I'll do my best with this.  But this is a nice chart, laying out the landscape here.  So, I mean, basically with the taxon literature, as I  mentioned earlier, you have your perspective publishing and  your historical literature.  For historical literature, there's other schemas,  Taxon X, which is another schema that I'm co-author of,  and Taxon O'Litt.  And Closie has an editor that helps to mark up the stuff.  There's also these systems, scratch pads, and things like  that, where that data goes.  And then there's perspective publishing that goes through  PENSOF's markup tool, blah, blah, blah, peer review,  automated submission.  The things are very automated.  But I think the major emphasis here is that the data, when  it's all brought together in this format, the data is  going all sorts of places, playing lots of roles in  different areas.  And there is this feedback also to these other systems as  well, for stages, submission, peer review, publication,  dissemination, and each with their own challenges.  As you can see.  All right, so here's a nice slide showing.  Here's a, basically here you have a treatment.  This is what it looks like in print, sections of it at least.  So you have your nomenclature section, and that data goes  to Zoo Bank, which is a red pick in the registry of Zoo  and Logical Nomenclature.  The references go to the Biodiversity Heritage Library.  Here's that description, the more morphological  description area with these wonderful terms like, you know,  to lace or I brownish yellow and, you know,  publish one.  It's a fusive lack along a lateral margin and all that stuff.  That data goes to ELL, goes into their species pages,  into species ID, which is a wiki, which does essentially  the same thing, and the entire treatment goes to our  plazios treatmen repository.  Images go to ELL alongside the descriptions and into the  species pages.  And images also go to Morph Bank, which is a database  from images of specimens plus metadata.  Very large and important resource in this area.  And then the occurrence data, which is where the material  is collected, goes into Gepeth Global Biodiversity  Information Facility.  And when it's done right, all this that long stuff becomes  mappable on Google Earth or other resources.  So here, again, the goal is to be open in both senses, open  access in the legal sense, but also open in the sense that  the data is open and able to be manipulated and reused  widely.  OK, so this is a run through what PENSOFT has done in  terms of displaying these articles.  So there's some semantic enhancements as we were  calling them.  Right up here, I'll point out, there's these tabs that allow  you to highlight in the article the treatments, the tax  on names, citations, localities, et cetera.  So this will, yeah.  So if you click on localities, you get a list of the tax of  the described in the article, and they're plotted out for  you.  So this is where this parasite wasp has been collected  from.  What's going on with the key here?  There we go.  So you have a key to species, which I haven't really talked  about.  Key is a diagnostic tool.  It's a way if you have an animal or something in front of  you, you follow these sets of instructions to figure out  what it is.  So here, it mentions a figure, and the figure, of course,  is linked to, and that, I suppose, is linked to, this  might probably has gone to Morph Bank also.  Then you have a citation, a Sharki 2007, and you get the  citation, and this happens to be in Zutaxa.  But if you follow this footnote, it might link to it.  Zutaxa doesn't issue DOIs, so I'm not sure.  Here you have a mention of a taxon.  In fact, this is a very large, high-ranking taxon,  Hymenoptera.  And click on that, and you can get different explanations of  what Hymenoptera is.  In this case, it's PENSOFT has a thing called taxon profile,  which is a page that aggregates information about  organisms.  This is PENSOFT's profile of Hymenoptera.  Hymenoptera are ants and rocks and bees, and you can see  they're very widespread, probably in this room.  Sure, there's an ant somewhere in here, nearby.  And then here's another one, Solonium.  Plant, I believe.  And here you find, you can follow references to Solonium  in the biodiversity heritage library.  They're all over the place.  And so you choose Solonium abalotum, and there you go.  You go to a publication about them in the BNDHL.  And so that's one, that's basically what you get when  you go to PENSOFT and you read one of their articles.  Another thing I should publish point out, it was back there,  which is mentioned yesterday, that is not showing it.  There is a link right to the side.  You can get the XML.  We PENSOFT post the XML alongside the PDF.  It's very easy to get to.  So it's not something that, as a publisher, they're hiding.  It's right out there.  So anyone can grab the XML and do what they want with it.  So as I mentioned, Zookiz has been archived in PubMed  Central very happily.  And the scripted sections go to EOL.  So that has extracted out of these materials, examin  sections, and goes to EOL.  Whoops.  Whoa.  Hold on.  Wow.  Sorry.  Now I have three minutes.  Four.  Four minutes.  Almost there.  Is there some sort of electronic hook that pulls the  presentation off?  OK.  And there's a species space, which is particularly ugly  bug, I think.  Really long antennas.  And then the material treatments, the isolated  treatments go to our plaudite treatment repository.  We have something like over 10,000 treatments of  different organisms now that are referable directly.  And you can get XML for them.  And then, oh yeah, this is an interesting paper.  In this paper, the authors simultaneously published to the  journal and to a wiki at the same time.  So here's the actual article, as you'd see it on the  keys, but there's a link to the entry in the wiki.  And there you go.  All the data, as it's mentioned here, is derived  from the article.  So this simultaneous publication, this allows the  collaborative work on the species as well as having an  official peer reviewed article.  And this isn't just to show the key, the species has been  added to the wiki.  Data is also provided to wiki species and wiki  immediate commons.  There's a wiki species page.  With the commons, all these kind of scary little  pictures of bugs.  That's another gross one.  I don't know what that is.  And note here the abstract PDF or link to.  So you can get to the article for this from the wiki  species page.  OK, so I'm going to speed this up.  Yes, we want more symmetric web enhancements.  So PENSOF is working on a tool to help authors create  collaboratively, write these taxonomic articles that will  involve community based peer review.  And then PENSOF is very much interested in data journals.  So publishing, publications that include data, in this case  these are in the term small data, of all sorts.  Collaborative offering tool, web interface to help you  structure, to help you create the article.  And of course, there's commenters.  You've got collaborators, commenters, involved in  publication process.  So here's where you would add your treatment information  at the high level, then you've got a subsection,  fill in your content.  And then this is my favorite part of the presentation.  So OK, so then why is it?  I'm over time now, but I think I have five minutes.  OK, so we have in this case, I'm an optorist.  He's captioning off B, goes to his lab, finds, he's curious  about it, writes up his little treatment, gets in  up with all of them.  And this is the peer review process, a wonderful depiction.  Then lo and behold, the article is published in a PDF  format, great.  But there's this underlying data that we all want.  And this is my favorite part of the presentation, because I  don't know what this means.  My theory is that that is a cross over a grave, and that  the paper is dead, or the book is dead.  And then as I said to Wendell earlier, we want to roll  away the stone to reveal the data that's  underneath the publication, and then share the primary data  to enable reuse of content.  So there you go.  Yeah, and then here's some quick facts about the data  journal, no upper limit of managed size.  It's very important.  Previously, the amount of data that you could publish in  the taxonomic article is very limited, and it was very  frustrating to authors.  Collaboration, collaboration, community, all that's  important, standard compliance, JATS,  DOM-Accord, DOM-Accord, et cetera, and code compliance,  this will be done in such a way that it will be compliant to  the various codes.  Lots of stuff goes into the manuscript.  It all gets structured, and it goes places.  Because of the structuring of the data.  And then it goes places and comes back.  Lessons learned.  Yeah, specificity of domains, a challenge.  Market for Currents data is a very big challenge, all that  long collecting information.  There's other information, but locality is very difficult to  identify and mark up if you're not getting the original data,  lowering the cost of efficiency of the market process.  This point cannot be overstated.  It's likely that you're not going to.  It's hard to get authors to provide data, provide them  articles that format you want.  And so you have to either give them incentives or tools,  but also probably recognize that you're going to be  spending time in the editorial process to do this.  And this last point is it can't be overstated.  The small taxonomy of publishers, the 2,500 journals,  are very, very small scale on storage, huge stream budgets,  and very firm in their habits.  So not changing.  It may not be turning a super tanker, but sometimes it's  hard to even turn a dinghy if all you know is to  rope over it.  OK, I think that's it.  Yes.  Final point, not easy, exciting.  Possible throw up on access.  And then, yes, donuts claim that this is the only way.  Donuts, I think, very strong and accurate claim that  really this is really the only way to go for the missing  species that we don't know about on Earth.  All right.  There you go.  Thanks.  OK, we have time for one or two questions.  Just a comment.  I'd like to congratulate you and you, Beau, and everybody  else involved.  I think this is exactly a brilliant example of what a  journal should be about.  And you've done it in a particular area.  Everybody else now needs to do it in their particular areas.  It's fabulous work.  I couldn't agree more.  Thank you.  All right.  All right.  Good, well, thank you very much.
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Good morning. All right. So I am here to talk about the implementation of tax pub, which is an extension to the NLM DTB Jats that me and a team of other people developed a few years ago. I'd like to point out, which is what is obvious, this presentation in the paper is the product of several mines distributed across the world. Coming from different domains as well, it's the Amaliburian Gita Sauder is a computer scientist, Pavel Theodor and Lubo work for PennSoft, scientific publisher. And this distribution of talent and work will be evident in the rather rocky nature of the presentation, which I apologize for in advance. But here we go. So yeah, we're going to focus on what we've done with, or what really PennSoft and Lubo has done with the tax pub extension over the past several years. The focus will be on what we're calling semantic tagging and enhancements. In other words, bringing out the items of interest inside of the scientific literature, in this case, tax nomad literature. And then once having done that, the dissemination of this data from the literature to various external aggregators. And then we'll talk briefly about what we want to do with tax pub in the future. OK, so to start off, I'll give some background on Plesi. Plesi is kind of a weird organization. Donat, Auguste and I, Donat is a scientist. He's a mermicologist. Studies ants. He's a taxonomist. We met on a project, an NSF-funded project a few years ago. The project then did, and we didn't stop working. We found the work to be very interesting. So we founded a company, or organization in Switzerland. We have members in Switzerland, Germany, the US. In fact, another Plesi member, Bob Morris, is here in the audience. And Iran, where Donat happens to live right now. We are, I like this term, a research-based think tank. That's the term that Donat came up with. I kind of accept that. You could think of it as an indie scientific label, almost. We have a very DIY approach to doing our work. And we definitely have the mission to promote open access. I mean, that is the major goal. We do this in four different areas. We have a lawyer on board who advocates, and argues, in the way lawyers can about open access. I and Edo, a few other people, work on technical solutions, such as taxpub. We maintain what we call a treatment repository, which is simply a electronic repository where treatments, which I will describe later, are deposited so that they can be accessed directly and cited using stable URLs. And of course, people form advocacy for open access. Recently, we founded a GMBH in Switzerland, which, from my understanding, is something like a limited liability company. So it's a commercial entity. A small, medium-sized employer owned by Blase, the organization, the Varain, our association, to perform actual commercial services, such as document conversion and consultation. We receive funding from public donors, from private donors. And recently, we've been involved into European Union grants that have just been funded. And yes, and we have clients all over the world. All right, so the context for this work is three or four fold. First is the global diverse biodiversity crisis, that we are in the midst of one of the greatest die-offs in history. And it certainly is a crisis. It's been well known for about 20 years, at least. But there are very few systems and tools to measure and document what is going on. There's a scientific aspect to this that we estimate that there's about 1.8 million species that have been described that we know about. And it's estimated there's something like 8 million more that we don't know about, or that haven't been described, and may in fact be dying, if we're becoming extinct, as we speak. The identification of these species takes place within scientific publications. The naming of new species is governed by codes. I'm sure many of you know this already. There's ICZN, the International Co-Frisiological Nomeclature, ICBN, International Co-Frize and Biological Nomeclature. These codes require publication of descriptions of species in actually up until very recently, paper publications. Just very recently, I think ICBN, the Biological Nomeclature Code, has a lot of publishing in electronic documents. Unfortunately, they specifically said PDF, which is unfortunate that they got that specific. But it is a major leap forward to actually accept the electronic publication. And there's obviously a lot of activity in this area. There's 17,000 species described every year, new species described every year, and about 100,000 redistrictions of existing species. So there's a tremendous amount of content locked up in the literature and coming out at an increasing rate. And however, the challenge here is that it's fragmented over about 2,500 taxonomic journals and books. So it's difficult to access. So that open access is really the key. An open access in both sense of the term. You need to have open free access to this literature. And the content itself needs to be open in the sense of being able to be accessible directly so you can take a great advantage of the rich content that is in there. And so yes, this is the solution we hope is open access and both senses, semantically enhanced publications. Which one of the goals that this does not slide that he's mentioning here is that we really want to, through electronic publication, accelerate the publication process so that descriptions do not take that long to get out and that the data from the descriptions don't take that long to get out. And that the names are registered, new names of species are registered in these developing registries quickly. And we hope the tax pub has helped in that regard. You've already seen that slide. Slipped in there twice. I apologize. OK, so background of tax pub. Tax pub is a very small extension to the blue publishing DTD. As Jeff mentioned, I gave presentation on this and there's a paper available describing it online. There's the URL. The focus of tax pub is on treatments. What I've been talking about this treatments are, think of them as species descriptions. These are very formal descriptions of a newly named organism or a renamed organism. The treatments are, again, highly formal. They're easily identified and they often are separated off from the publication in which they're in. So they're kind of independent entities and have a very important part in the nomenclature process because you have to point to previous treatments if you're renaming species. I hope I'm getting this right. But there's an interlocking set of references between treatments in the naming process. So they're very significant document objects. Another legal point that we've tried to go out and lemmon make is that treatments being statements of fact and not creative works, at least in the Swiss intellectual property regime, do not qualify for copyright. So that we're trying to advance the idea that publishers and should acknowledge that the treatments should be allowed to be free of copyright. The rest of the article, fine. But the treatment itself is of such a nature that it's not copyrightable. And I am not going to argue this point. I'm not a lawyer, nor do I want to be in any life. But that is a contention of ours. And believe it or not, we've had traction from publishers on this. They accept the idea of letting treatments float on their own and be cited and available on their own. So the treatments contain basically two parts. One is the nomenclature section, which is a heading. Think of it as a heading that says what the name of the species is and its status and the fuel. And who's the author of the taxons, things like that. And then there's various treatment sections. We don't even bother to name what they are. We punt out to the type attribute to do that. And then there's some domain-specific elements we added for inline content. Taxon names, created an element for that. Material citation, which basically references to specimens, but could be references to any sort of material that is used to describe a species. And then the weakest component of taxpub currently, this element, descriptive statement, which is an attempt to somehow mark up the phrases that are used to describe the anatomy or morphological features of a taxon. There we go. OK, so here's a sample. Sorry, I shouldn't actually look at this. It marked up treatment. Very simple. You have your outer treatment. Whoops. Treatment element. Then you have a required. The only required element there is a nomenclature element. The nomenclature element contains a name. The name contains the name part, which is the genus name. And this is by the CLEO. I believe. And then the name of the species, Mizzanzi. This is a paristhoid wasp, I believe. Then there's an identifier. This is a zoo bank identifier for this species. And there's another identifier, which comes from a different system. There's the taxon authority. In other words, the people who were responsible for the naming of the species, and the status species, no more new species, essentially, is what that means. So you can see the way in what taxbugs try to do here. Put in some of our own elements to bring out the important taxonomic features, but also using whenever necessary generic NLM or JATS elements like object ID to do the rest. And this is just an example of a section of a treatment. This is the section that discusses the materials and the specimens that were used to name the species. We have an element called material citation that bundles together or delineates one particular specimen. In this case, it's marked up fairly granularly to point out different facets of that citation that this is a holotype, that its location is this King's South Museum in Saudi Arabia. And then there's a collecting event, which is where this specimen was actually collected from. And it was collected in Saudi Arabia, in this particular province, et cetera. And then, again, using a generic NLM element named content, rather than putting all of this elements for things like latitude, longitude, altitude, all this, we sort of advise our users to just use existing vocabularies to provide the semantics and use the name content element to do the actual structural delineation. So here, there's a perfectly adequate term in the Dub Darwin core vocabulary of the coordinates that can serve to supply semantics for the latitude and longitude of this specimen is collected. So, tax pub, I don't really have much else to say about what's changed since 2010. Don't take that as an example of our laziness, but frankly, as a success, that it's been fairly stable. It's worked. And we haven't received much demand from our primary user, PENSOFT, to change it much. One of the things, though, that we did have to do was introduce the notorious x element. I'm not sure all of you are familiar with x. x is an element that gives you a lot of wiggle room. It's there to tag anything, all this interstitial stuff, that doesn't really have, I like to think, shouldn't really be there, but is. And the publishers don't want to take out. And so I conceded this, that they want to put a semicolon between to the tax on status and the tax on authority. So I added x to the content model. We're all happy about it. It's fine. However, this signals a trend that I also had wanted to avoid. Tax pub is really designed with an eye towards new literature. Our hope was that, this is kind of a strategic goal, to shift the work on markup of taxonomic literature from retrospective markup to prospective markup. Because we have those 8 million other species that have not yet to be described sitting out there. And we have 1.8 million that have been. So we'd like to focus on the 8 million that are going to be described. And also hopefully describe them in a way that's structured and granular, that will open up the data to reuse. However, there's a persistent urge to markup the legacy literature and a surprising amount of money behind that urge to do it. So this enables me to use this term, reunification, which I just had to use because it's when do you ever get a chance. So one of the things that we're probably going to do a tax bump, if I shouldn't say probably, is a goal is to have and make an extension not just to the blue TTB but to the green TTB so that we can address the legacy literature as well. There is interest in, for instance, marking up existing floras. And we definitely need to loosen it up more in order to address those types of publications. And we have, there's been interest from other journals to adopt TaxPub, the European Journal Taxonomy. Just last week, we signed a very modest contract, POSY did with them, to consult on seeing how to get their workflow to be based around TaxPub. We'll see how that goes. I'm optimistic. And then the journals you tax, which is one of the major taxonomic journals in the world. The Encyclopedia of Life, which is an organization attempting to create basically a web page for every species on Earth, I guess anywhere. I don't think they're going to limit themselves to the Earth if we find anything else. They're offering us a contract to help Zutaxa also adopt a TaxPub into their workflow. So that they can, and their desires so that they can get the data that's currently locked up in PDFs, which is what Zutaxa produces, to pull out a lot of that data and put it into their species pages in Encyclopedia of Life. And then another major area is development. The enhancement of this description of the morphological features of the organisms. The existing markup we have is really just a first attempt that isn't that successful. No one uses it, I should say. And so there was a proposal to address that. Briefly show this. First thing I want to point out is that those of you who aren't familiar with these type of descriptive data or descriptive language. This is nasty stuff to mark up because it's a combination of very formal language, but also natural language that's tough to mark up in such a way that it can get into databases or get represented even, say, in RDF. So when you get phrases like extremely rarely yellow, often shallily joined around the node, these are, it's kind of fuzzy stuff, hard to mark up. Glabrous or weakly hear her suits. So you have this wonderful combination of terms like labrous and her suits, which means something very specific, but with these words like weakly. So this proposal is to introduce a few elements that basically are saying, this is a categorical element, is saying, well, here's a, I believe what you can call it, a categorical character. It's something that something is, the stem color is what's being referred to here. And luckily there is a plant ontology that we can point to to say what category of feature that we're talking about. And then it has a state. So the stem color is greenish, and believe it or not, there is a non-tall ontology term for greenish out there somewhere. And so for the categorical things you have that, and then you can also address the quantitative features, like just measurements. And here you have the stipule width, which is 3.10 millimeters. So we'll be testing this, and hopefully we can, you know, this might serve to be a lightweight, but yet effective way to address these types of, this type of language. OK. And to wrap up on tax, there's been some challenges. We maintain the code on source forage, which is cumbersome, for a variety of reasons. I'd like to move it to something better. I'm thinking maybe GitHub, I'm not sure yet. But then that's the technical maintenance, or the infrastructure. But the other maintenance, the sort of governance and administrative maintenance, is also very challenging. I mean, plosy, we're all, this is all volunteer effort. We all have other jobs. I'm a librarian. Don't know, it's a diplomatic spouse living in Tehran. He's got a lot of things to take care of. And we do actually have some funding now, but we're not a wash in funding. There's nothing really paying for tax prep development. But it is supported under plosy. And to the extent that plosy is getting these grants and funding, we can hopefully direct some of the funds that way. And then I mentioned this in my talk two years ago, and it still remains, I think, the greatest challenge. When I first created tax prep, I naively focused on the scheme, or the extension. And that's the easy part. Especially because Jats was made in such a way, designed very well to enable extension. It's very doable. But that is the easy part. And that's not the sum total of what an extension or a DTD or a standard or whatever you want to call it is. The documentation is really critical to explaining what stuff is, what you're doing, how to use it. And the documentation infrastructure is not that great. Right now, we use these comments in the extension with some ad hoc markup that is used by, I believe, a Perl script that NCBI has to generate the online HTML documentation. And it's a cumbersome process, as I mentioned, to put it there. And then I've got to send it to Kim. And she runs the conversion. And I get these files back, and I got to post them somewhere. I'm looking for a better way to do that. We also maintain the documentation on a Wiki called Species ID, which is another Palsy project, which actually I've recently found out has been moved to. Anyway, here's the, I'll pick up that for a second. So here is the documentation. Just like the ordinary JET documentation, except we have our elements mixed in. And I should point out also, while probably been noticing, that there's a namespace prefix for the tax put elements. This was, we decided to keep the extension in its own namespace, just to distinguish it better and prevent name clashes with the general blue DTD. So we have this nice documentation that periodically gets generated when I get around to it. And then the documentation is also on this Wiki maintained by GBIFF, the Global Biodiversity Information Facility, which I just found out, is maintaining a collection of vocabularies in the domain. So I'm very happy to see that it's on this GBIFF Wiki. And the value here is that people can come in and add examples and work more collaboratively on the documentation. So I'm going to shift gears to the other side of this presentation. And this is the side I have less authority to speak about, so bear with me. The primary author, Luba Pennev, is the owner, or the president's, imagine of Pensop, a scientific publisher. And Zuki's is their major journal publishing taxonic literature for zoological taxonic literature. As you can see, it's founded almost 20, over 20 years ago. Zuki's, the journal, was launched four years ago. It's a completely open access journal, taxonomy. It's been very productive and successful in the last four years. They're very forward looking and want to take advantage of all the new technologies they can. So they register any new names in Zubank, which is a global registry of zoological names, and then supply data to Encyclopedia of Life, the Pwazi, our dream repository, and Species ID, which is a wiki for species descriptions. I'm a librarian, and I know most of these things, but not all of them. But they're cross-draft members of the issue DOIs. ISI, I guess, is calculating their impact factor and doing their reverse indexing. They're in scopus, blah, blah, blah, blah, blah. I want blah, blah, blah of this one, the PubMed Central. This is one of our, I think, our proudest achievements is that Zuki's actually became, I believe, the first taxonomic journal to enter PubMed Central. And that's, again, an achievement we're very proud of. And then he has the PENSOF journal system, which is next in L-based workflow that drives all this stuff. And it's very productive, as you'll see by this chart. There's been a nice upward trend with a mysterious dip in 2010. But the pages and the articles are coming out, and people are publishing with Zuki's, and they've been very active in these four years. OK, I'll do my best with this. But this is a nice chart, laying out the landscape here. So, I mean, basically with the taxon literature, as I mentioned earlier, you have your perspective publishing and your historical literature. For historical literature, there's other schemas, Taxon X, which is another schema that I'm co-author of, and Taxon O'Litt. And Closie has an editor that helps to mark up the stuff. There's also these systems, scratch pads, and things like that, where that data goes. And then there's perspective publishing that goes through PENSOF's markup tool, blah, blah, blah, peer review, automated submission. The things are very automated. But I think the major emphasis here is that the data, when it's all brought together in this format, the data is going all sorts of places, playing lots of roles in different areas. And there is this feedback also to these other systems as well, for stages, submission, peer review, publication, dissemination, and each with their own challenges. As you can see. All right, so here's a nice slide showing. Here's a, basically here you have a treatment. This is what it looks like in print, sections of it at least. So you have your nomenclature section, and that data goes to Zoo Bank, which is a red pick in the registry of Zoo and Logical Nomenclature. The references go to the Biodiversity Heritage Library. Here's that description, the more morphological description area with these wonderful terms like, you know, to lace or I brownish yellow and, you know, publish one. It's a fusive lack along a lateral margin and all that stuff. That data goes to ELL, goes into their species pages, into species ID, which is a wiki, which does essentially the same thing, and the entire treatment goes to our plazios treatmen repository. Images go to ELL alongside the descriptions and into the species pages. And images also go to Morph Bank, which is a database from images of specimens plus metadata. Very large and important resource in this area. And then the occurrence data, which is where the material is collected, goes into Gepeth Global Biodiversity Information Facility. And when it's done right, all this that long stuff becomes mappable on Google Earth or other resources. So here, again, the goal is to be open in both senses, open access in the legal sense, but also open in the sense that the data is open and able to be manipulated and reused widely. OK, so this is a run through what PENSOFT has done in terms of displaying these articles. So there's some semantic enhancements as we were calling them. Right up here, I'll point out, there's these tabs that allow you to highlight in the article the treatments, the tax on names, citations, localities, et cetera. So this will, yeah. So if you click on localities, you get a list of the tax of the described in the article, and they're plotted out for you. So this is where this parasite wasp has been collected from. What's going on with the key here? There we go. So you have a key to species, which I haven't really talked about. Key is a diagnostic tool. It's a way if you have an animal or something in front of you, you follow these sets of instructions to figure out what it is. So here, it mentions a figure, and the figure, of course, is linked to, and that, I suppose, is linked to, this might probably has gone to Morph Bank also. Then you have a citation, a Sharki 2007, and you get the citation, and this happens to be in Zutaxa. But if you follow this footnote, it might link to it. Zutaxa doesn't issue DOIs, so I'm not sure. Here you have a mention of a taxon. In fact, this is a very large, high-ranking taxon, Hymenoptera. And click on that, and you can get different explanations of what Hymenoptera is. In this case, it's PENSOFT has a thing called taxon profile, which is a page that aggregates information about organisms. This is PENSOFT's profile of Hymenoptera. Hymenoptera are ants and rocks and bees, and you can see they're very widespread, probably in this room. Sure, there's an ant somewhere in here, nearby. And then here's another one, Solonium. Plant, I believe. And here you find, you can follow references to Solonium in the biodiversity heritage library. They're all over the place. And so you choose Solonium abalotum, and there you go. You go to a publication about them in the BNDHL. And so that's one, that's basically what you get when you go to PENSOFT and you read one of their articles. Another thing I should publish point out, it was back there, which is mentioned yesterday, that is not showing it. There is a link right to the side. You can get the XML. We PENSOFT post the XML alongside the PDF. It's very easy to get to. So it's not something that, as a publisher, they're hiding. It's right out there. So anyone can grab the XML and do what they want with it. So as I mentioned, Zookiz has been archived in PubMed Central very happily. And the scripted sections go to EOL. So that has extracted out of these materials, examin sections, and goes to EOL. Whoops. Whoa. Hold on. Wow. Sorry. Now I have three minutes. Four. Four minutes. Almost there. Is there some sort of electronic hook that pulls the presentation off? OK. And there's a species space, which is particularly ugly bug, I think. Really long antennas. And then the material treatments, the isolated treatments go to our plaudite treatment repository. We have something like over 10,000 treatments of different organisms now that are referable directly. And you can get XML for them. And then, oh yeah, this is an interesting paper. In this paper, the authors simultaneously published to the journal and to a wiki at the same time. So here's the actual article, as you'd see it on the keys, but there's a link to the entry in the wiki. And there you go. All the data, as it's mentioned here, is derived from the article. So this simultaneous publication, this allows the collaborative work on the species as well as having an official peer reviewed article. And this isn't just to show the key, the species has been added to the wiki. Data is also provided to wiki species and wiki immediate commons. There's a wiki species page. With the commons, all these kind of scary little pictures of bugs. That's another gross one. I don't know what that is. And note here the abstract PDF or link to. So you can get to the article for this from the wiki species page. OK, so I'm going to speed this up. Yes, we want more symmetric web enhancements. So PENSOF is working on a tool to help authors create collaboratively, write these taxonomic articles that will involve community based peer review. And then PENSOF is very much interested in data journals. So publishing, publications that include data, in this case these are in the term small data, of all sorts. Collaborative offering tool, web interface to help you structure, to help you create the article. And of course, there's commenters. You've got collaborators, commenters, involved in publication process. So here's where you would add your treatment information at the high level, then you've got a subsection, fill in your content. And then this is my favorite part of the presentation. So OK, so then why is it? I'm over time now, but I think I have five minutes. OK, so we have in this case, I'm an optorist. He's captioning off B, goes to his lab, finds, he's curious about it, writes up his little treatment, gets in up with all of them. And this is the peer review process, a wonderful depiction. Then lo and behold, the article is published in a PDF format, great. But there's this underlying data that we all want. And this is my favorite part of the presentation, because I don't know what this means. My theory is that that is a cross over a grave, and that the paper is dead, or the book is dead. And then as I said to Wendell earlier, we want to roll away the stone to reveal the data that's underneath the publication, and then share the primary data to enable reuse of content. So there you go. Yeah, and then here's some quick facts about the data journal, no upper limit of managed size. It's very important. Previously, the amount of data that you could publish in the taxonomic article is very limited, and it was very frustrating to authors. Collaboration, collaboration, community, all that's important, standard compliance, JATS, DOM-Accord, DOM-Accord, et cetera, and code compliance, this will be done in such a way that it will be compliant to the various codes. Lots of stuff goes into the manuscript. It all gets structured, and it goes places. Because of the structuring of the data. And then it goes places and comes back. Lessons learned. Yeah, specificity of domains, a challenge. Market for Currents data is a very big challenge, all that long collecting information. There's other information, but locality is very difficult to identify and mark up if you're not getting the original data, lowering the cost of efficiency of the market process. This point cannot be overstated. It's likely that you're not going to. It's hard to get authors to provide data, provide them articles that format you want. And so you have to either give them incentives or tools, but also probably recognize that you're going to be spending time in the editorial process to do this. And this last point is it can't be overstated. The small taxonomy of publishers, the 2,500 journals, are very, very small scale on storage, huge stream budgets, and very firm in their habits. So not changing. It may not be turning a super tanker, but sometimes it's hard to even turn a dinghy if all you know is to rope over it. OK, I think that's it. Yes. Final point, not easy, exciting. Possible throw up on access. And then, yes, donuts claim that this is the only way. Donuts, I think, very strong and accurate claim that really this is really the only way to go for the missing species that we don't know about on Earth. All right. There you go. Thanks. OK, we have time for one or two questions. Just a comment. I'd like to congratulate you and you, Beau, and everybody else involved. I think this is exactly a brilliant example of what a journal should be about. And you've done it in a particular area. Everybody else now needs to do it in their particular areas. It's fabulous work. I couldn't agree more. Thank you. All right. All right. Good, well, thank you very much.
extension to the NLM DTB Jats that me and a team literature to various external aggregators. And perform actual commercial services, such as descriptions of species in actually up until very has a lot of publishing in electronic documents. accept the idea of letting treatments float on and the fuel. And who's the author of the taxons, names, created an element for that. Material whenever necessary generic NLM or JATS elements to just use existing vocabularies to provide the between to the tax on status and the tax on markup to prospective markup. Because we have their species pages in Encyclopedia of Life. And then another major area is development. The was made in such a way, designed very well to great. Right now, we use these comments in the publisher. And Zuki's is their major journal article the treatments, the tax on names, this parasite wasp has been collected from. articles that will involve community based peer