Ready for Boot Camp?

September 1, 2014  
Posted in Access Insights, News, Taxonomy

Maybe you are a pro at taxonomies, or maybe it is time for a refresher. This year’s Taxonomy Boot Camp offers something for everyone. The theme at the November 4-5 event in Washington D.C. is “Organizing the Future: Taxonomies Leading the Way?Register by October 3, 2014 and receive an early bird discount.

The keynote speaker opening this year’s workshop is Patrick Lambe from Straits Knowledge Bangkok University with his topic: From Cataloguers to Designers: A New Role for Taxonomists in Knowledge Graphs, Machine Classification, and Search Based Applications.

The first day of Taxonomy Boot Camp features a track just for you. On November 4th, you can hear from our own Eric Ziecker, taxonomist, editor, and information consultant, as he shares how to stay current with taxonomy-related research and implementation in his session – Taxonomy: Resources & Revelations.

Melody K. Smith

Sponsored by Access Innovations, the world leader in indexing and making content findable.

Data Harmony® v.3.9 Named 2014 Trend-Setting Product by KMWorld

August 25, 2014  
Posted in Access Insights, Featured

Access Innovations, Inc., the industry leader in data organization and innovator of the Data Harmony® software suite, is pleased to announce that KMWorld has selected Data Harmony 3.9 for their Trend-Setting Products list for 2014.

“We enhance and enlarge the Data Harmony offerings every year. This year the suite has increased to 14 modules. It is vitally important to stay at the forefront of knowledge management. With Data Harmony v.3.9, we have delivered the most integrated, flexible, and streamlined user-friendly semantic enrichment software on the market,” notes Marjorie Hlava, president of Access Innovations, Inc. “We will continue developing new and innovative ways to analyze, enhance, and access data to increase findability and distribution options for our customers.”

The proven, patented Data Harmony software is the knowledge management solution to index information resources and, in 2014, pushed farther into the future with the inclusion of Inline Tagging, which automatically finds and labels text strings, and Smart Submit, a module that greatly streamlines the author submission process. With these in place, Data Harmony offers a richer, more advanced, and friendlier customer experience.

The Trend-Setting Product awards from KMWorld began in 2003. More than 650 offerings from vendors were assessed by KMWorld’s judging panel, which consists of editorial colleagues, analysts, system integrators, vendors themselves, line-of-business managers, and users. All products selected demonstrate clearly identifiable technology breakthroughs that serve vendors’ full spectrum of constituencies, especially their customers.

“Data Harmony was selected by the panel because it demonstrates thoughtful, well-reasoned innovation and execution for the most important constituency of them all: the customers,” explained Hugh McKellar, editor-in-chief of KMWorld Magazine.

Data Harmony v.3.9 is available through the cloud, a hosted SaaS version, or an enterprise version hosted on a client’s server. More information about Data Harmony and the 14 software modules is available at


About Access Innovations, Inc. –,,

Access Innovations has extensive experience with Internet technology applications, master data management, content-aware database creation, thesaurus/taxonomy creation, and semantic integration. Access Innovations’ Data Harmony software includes machine aided indexing, thesaurus management, an XML Intranet System (XIS), and metadata extraction for content creation developed to meet production environment needs. Data Harmony is used by publishers, governments, and corporate clients throughout the world. Access Innovations: changing search to found since 1978.

About KMWorld –

KMWorld ( is the leading information provider serving the Knowledge Management systems market and covers the latest in Content, Document and KnowledgeManagement, informing more than 40,000 subscribers about the components and processes – and subsequent success stories – that together offer solutions for improving business performance. KMWorld is a publishing unit of Information Today, Inc. (

A Taxonomy for Contributor Role Metadata

August 21, 2014  
Posted in Access Insights, News, Taxonomy

We’ve written before about how taxonomies can provide the material for metadata (especially subject matter terms) describing information resources. One taxonomy currently under development has the potential to standardize how authors and other contributors are described in a resource’s metadata. The development group is led by Amy Brand (VP Academic & Research Relations and VP North America for Digital Science) and Liz Allen (Head of Evaluation for the Wellcome Trust).

An article published yesterday in the Scholarly Kitchen on the contributor role taxonomy includes an interview with Dr. Brand, who described the active involvement of scholarly publishers, institutions, and others in the development group:

“The contributorship effort has been highly collaborative from the start. We are working closely with the Wellcome Trust evaluation team, and have some financial support from Wellcome as well. Publishers including Nature, Elsevier, PLOS, AAAS, and APS have been involved at various stages in the project. We also had some help early on from Access Innovations. And individuals from several institutions, including Cornell, Harvard, MIT, Columbia, NIH and NSF have been engaged as well. We are currently collaborating with both CASRAI (the Consortia Advancing Standards in Research Administration Information) and NISO in the development of the taxonomy.”

Access Innovations is proud to have been involved in this effort and we look forward to future collaborations along the way.

Melody K. Smith

Sponsored by Data Harmony, a unit of Access Innovations, the world leader in indexing and making content findable.

Taxonomy in the Pipeline, Part 2: The Need for Quick Publishing

August 18, 2014  
Posted in Access Insights, Featured, Taxonomy

Regardless of discipline, there’s one thing that connects most academics I’ve encountered: the desire to keep practicing their respective fields. They’ve spent years cultivating their expertise and want to make a difference in their field. But in order for that to happen, they all share the same obstacle: tenure.

Increasingly, universities are favoring adjunct jobs over tenured professorships. When one looks at it from a business perspective, as administrations with budgets are bound to, it isn’t hard to see why that happened.  They get to pay less for the same work (though maybe not the same quality of work) and they retain power over the adjunct’s job security.

Whether one agrees with that policy, it makes a certain kind of sense from that side of the pipeline. The system isn’t exactly ideal for the academics in adjunct positions, though, whose lack of job security means that, year after year, the potential of finding a new job (another adjunct position, likely) weighs heavily on their minds. Nobody can do great work under that kind of pressure.

Finally, they do get that tenure-track position. Initially, it might seem like the hard part is over, but it’s only just begun. Convincing a university administration to offer a position is one thing; it’s a whole different story when it comes to the thing that most fuels a university’s engine: publication.

It’s inviting to think high-mindedly about higher education, but a professor’s value is based far more on their academic prestige and contributions to the field, at least at the administrative level, than the professor’s skills as an instructor. These contributions are marked by the quantity of articles published in academic journals and by the prestige of those journals. There really is no other road to tenure.

It’s a cutthroat game and professors are playing for keeps…they have to. There aren’t more total jobs on the academic market; the tenured positions are replaced by adjunct ones at the first available opportunity. Those with tenure hold onto to the privilege for dear life, and rarely does a seat open up at the table.

It’s a simple equation then, once they do find a seat, why the institution would demand publication. The institution wants prestige, which they get through having a prestigious faculty that publishes in renowned journals. They select for it, because it’s a bottom-line situation for them; a well-respected faculty means a higher class of student, which means a higher rate of tuition and a better result at the end of the fiscal year.

This is why it’s vital for the journal itself to make sure that what is printed on their pages meets their academic standards. Enter the peer review process. While it was designed to uphold academic rigor (and often succeeds at that purpose), it has the consequence of acting as a gatekeeper for those seeking tenure. That consequence may not have been intentional, but it has become a growing issue.

Submitted articles, certainly, must be vetted for accuracy and content, but they also must be filtered so they get into the right hands for peer review. This process takes time—always has—but it has grown even slower in recent years. With fewer tenured positions, there are fewer people available to review articles. The number of articles hasn’t necessarily changed, though, so those available are now busier than ever and, unfortunately, less attentive on top of it.

The trouble is that those on the tenure track only have so much time before their window closes. It can take months and even years for an article to slog through the pipeline, often preventing viable candidates from receiving tenure for the simple and fixable issue of delay. This inefficiency does a grave disservice to the very people the system was designed to help.

Without wholesale change in university administration mentality, the issue will not fix itself, so it must be addressed from a new angle. By identifying and analyzing the metadata present in a given article submission, it becomes clear where the submission comes from and who it should go to, which can help to streamline the process and make it easier on both the author and the peer reviewer, which will subsequently speed up the publishing process.

Data Harmony software is able to take care of this quickly and easily with the Smart Submit module. Using the article metadata in conjunction with a taxonomy, Smart Submit automatically identifies the subject areas covered in a submitted article. With that information, and with a properly designed management system,  a publisher can find qualified peer reviewers for the submission and ensure that reviewers don’t get overwhelmed with submissions. A lighter workload means that more time and care can be taken with a given submission, making for a better work environment and, potentially, a smoother path through the pipeline.

Academic publishing is a two-way street. Publishers need authors to write articles to populate their journals. Authors need journals to publish their research, which furthers their career and their field. When the two sides work together, that’s when a field of study can really flourish.

Why set up these barriers? It should be difficult to get published in a prestigious journal because academic rigor demands it, not because of an inefficient system that doesn’t help either side of the system. Smart Submit won’t solve all the problems an author might face in getting published, but getting the submission and review parts of the process streamlined and more transparent will make the process less frustrating for users and, ideally, speed up an arduous process that often hinders, when it should be an avenue for fresh voices to be heard.

Daryl Loomis
Access Innovations

Taxonomy in the Pipeline, Part 1: Introduction

August 11, 2014  
Posted in Access Insights, Featured, metadata, Taxonomy

It can be tempting to look at a taxonomy and only see it in terms of the search results generated from it. That part of it is very important, no doubt, but taxonomies have far-reaching tendrils that extend deep into many industries, especially publishing. They work subtly and are often invisible to the end user, but the effects can be extraordinarily powerful.

Colossal_octopus_by_Pierre_Denys_de_MontfortDrawing by Pierre Dénys de Montfort, 1801,

Taxonomies interact with and enrich the publication pipeline in so many ways. This is especially apparent in the world of academic publishing, but the principles can be applied throughout the industry.

With the explosion of electronic content, the use of metadata has become increasingly important. Hunting down print records from an archive by hand is simply unacceptable today; documents get lost, forcing the unnecessary duplication of work. This is even more frustrating with electronic content because, in theory, the conversion to digital was supposed to streamline the retrieval process.

It hasn’t really worked out so smoothly. This isn’t simply about finding something with a search function; inefficiencies gum up the works at every stage, costing companies valuable time that could be more effectively used elsewhere. In fact, studies have shown that people in publishing spend up to 35% of their time hunting down information. That’s simply too much time.

Access Innovations’ Data Harmony software products can help clean up the mess, both literally and figuratively. With applications at every stage, from submission to publication, the software suite is specifically designed to improve accuracy and efficiency, from the writer submitting the work to the publisher putting it in a journal, to the end user who needs to access it.

We will examine these ideas in a nine-part series to see just how integral taxonomies are to publishers. Some features will specifically address how Data Harmony works to improve data, while some will be more general. The following topics will be covered:

  • THE NEED FOR QUICK PUBLISHING: Academics publishing papers in journals—crucial for tenure—often face months and even years of waiting, sometimes so long that the tenure window passes. How does Data Harmony, specifically Smart Submit, streamline the submission process?
  • SEMANTIC ENRICHMENT: The capture of metadata is key to meaningful analysis of content. The resulting metadata allows a user to view content in unique ways to draw previously invisible patterns that dramatically improve the accuracy of content retrieval and enable analytics.
  • BY THE NUMBERS: We look at the real cost of slow turnaround in academic publishing—it doesn’t just affect the writer. There is a real cost to publishers when their systems are inefficient.
  • INLINE TAGGING—WHEN YOU STILL CAN’T FIND IT: Data Harmony’s constant refinement has now led to inline tagging solutions that allow users to easily zoom in on and identify concepts in a full text document.
  • FINGERS IN MANY POTS—FROM SUBMISSION TO PUBLICATION: From Smart Submit to precision search results at the end, Data Harmony has a hand in making each piece of the workflow production pipeline smoother, easier, and more accessible.
  • FEEDBACK LOOPS FOR TRULY ACCURATE INDEXING: One of the more interesting aspects of Data Harmony indexing solutions is how they enable constant checking of content extraction effectiveness, so that it becomes ever more accurate with each new piece of added content.
  • THE FUTURE—REAL-TIME ANALYSIS OF THE CHANGES IN PUBLISHING: The explosion of content being housed online instead of in print brings up some interesting speculative issues about the future of journal publication.

The series will close with an installment that will demonstrate, on a broader level, that high-quality metadata and accurate taxonomy-based indexing streamline and enrich the publication process. Today’s technology gives publishers the opportunity to enhance the way their journals are compiled and disseminated to the public. However, many publishers have not yet taken advantage of that opportunity. This makes for a frustrating search experience for the end user that, most importantly, does not precisely deliver the content they require.

Ultimately, that end user experience is most crucial, but in order for a system to really work, it requires improved efficiency at every level. Certainly, good semantic enrichment software such as Data Harmony can help with that, but changes in mentality are also required. That doesn’t happen overnight, but the faster that publishers can start to implement new methods of looking at their data and making their content available, the faster that users throughout the pipeline will get true satisfaction from their results.

When the author is satisfied and the publisher is satisfied, the end user wins. That builds trust in your client base, which translates into revenue. That revenue allows the publisher to offer improved and diversified products, leading to a broader user base that is assured of a reliable content offering, which once again, leads to even more revenue. This kind of cycle drives industry to improve upon itself, and good semantic enrichment software such as Data Harmony can facilitate that process.

Daryl Loomis
Access Innovations

Data Harmony Version 3.9 Shines a Spotlight On Inline Tagging Web-based Service Extension

August 4, 2014  
Posted in Access Insights, Featured, Taxonomy

Access Innovations, Inc. is pleased to announce that the Data Harmony software line now includes inline tagging capability, beginning with Version 3.9, released earlier this year.

Inline Tagging Feature In Data Harmony 3.9 Installations Employing inline tags, the TestMAI screen in the MAIstro™  module now displays matching content in a highlighted font when a Data Harmony user runs M.A.I.™ (Machine Aided Indexer), putting the focus on indexing concepts as they appear in the input text. XML elements are applied in the text at the exact location where a word or phrase triggered a term suggestion from the controlled vocabulary (taxonomy or thesaurus).

Inline tagging keeps the context in view when M.A.I. makes a subject indexing match, and generates a statistical summary showing the list of matched terms. This provides a look at the operation of term-matching rules and improves the user’s experience during rule base testing and refinement.

Inline Tagging As a Software Product The Inline Tagging extension module is available as a Data Harmony web-based service, with configuration options for integrating M.A.I. into the user interface of a content management system.

“For Version 3.9, we added inline tagging for MAIstro and M.A.I. installations, as Data Harmony customers are seeing now when they run TestMAI on their data,” remarked Marjorie M. K. Hlava, President of Access Innovations, Inc. “And, we packaged Inline Tagging as a software module to be integrated with an organization’s content management program, in the interface.

The Inline Tagging extension puts M.A.I.’s indexing precision within the reach of users, users who may be requesting more Web functionality! Often, the first step to offering more interactivity at document level is the precise placement of inline subject tags… this step is accomplished through a thoughtful configuration of the Inline Tagging extension.”

“The Inline Tagging extension inserts an XML ‘wrapper element’ around matched words; it locates concepts from your vocabulary inside full-text documents,” explains Bob Kasenchak, Production Manager at Access Innovations. “The XML wrapper can be configured so your interface displays related information when a user points their cursor at the match. Or, the interface can display a link for the user to visit. But that’s not all… an IT department can deploy inline text tags to make search and retrieval in a large document collection more precise and context-sensitive.”

Implementation Ideas for Inline Tagging Web-based Service Extension:

  •  As a search engine tool to boost document search results
  • To turn up the volume of social media postings
  • To create a better, more searchable index of an XML database
  • To foster increased user interaction opportunities with documents

How the Inline Tagging Extension Works, Simplified Implementations of the Inline Tagging extension module are based on an organization’s controlled vocabulary and accompanying rule base, stored in a Data Harmony installation. The Inline Tagging API can retrieve any element from the vocabulary term record in order to offer relevant information alongside matched content, and it handles this ‘on the fly.’ This makes it convenient for a Web developer to implement customized functions for a content management system. Driven by data already stored in the term records, with Web-based services configured for the CMS interface, Inline Tagging gives users immediate access to supplemental information about the relevant controlled vocabulary terms, and any related concepts.

About Access Innovations, Inc. –,,

Access Innovations has extensive experience with Internet technology applications, master data management, database creation, content-aware thesaurus/taxonomy creation, and semantic integration. Access Innovations’ Data Harmony software includes machine aided indexing, thesaurus management, an XML Intranet System (XIS), and metadata extraction for content creation developed to meet production environment needs.  Data Harmony is used by publishers, governments, and corporate clients throughout the world. Access Innovations has been changing search to found since 1978.

Buzzwords, Bling, and Being Snowed

July 28, 2014  
Posted in Access Insights, Featured, Taxonomy


breathofsnow / / CC BY-ND 3.0

I recently had the opportunity to see webinars featuring a couple of software systems for taxonomy construction/management and content categorization. The systems were both impressive and, if I didn’t have 20 years in the business, I would have been totally awed … and snowed. It’s easy to be overwhelmed by a slick appearance and professional presentation.

Early in my career, I was overwhelmed and confused by the terminology—its abundance, multiplicity, and ambiguity. Each software company used different words, all very catchy, developed by a creative marketing department. I didn’t get whether they were talking about different concepts or the same in different verbal wrappers. Cutting through the terminology to identify key software features and functions can be tough. Yet that’s just what must be done for an informed buying decision.

One of the buzzwords I came across in these recent webinars was “content-driven” (or “data-driven”) to describe a taxonomy. To my amazement, this was described as a “trend” in taxonomy construction by the presenter for the company “with over 15 years of experience.” Apparently it was intended as a strike at a “top-down” approach to pulling together terms for a taxonomy based on an abstract, authoritative view of a domain. The top-down approach was described as more complex than necessary and including nodes not reflecting your content.

However, the discussion ignored the equally familiar and long established counterpart to top-down. This is the “bottom-up” approach, drawing terms directly from the documents to be categorized, i.e., content-driven. Here’s a link to a brief description of the strategies written in 1996 by Jessica Milstead.

In most cases, building a taxonomy or thesaurus requires a hybrid approach, with the overall organization based on a top-down approach for navigation and the bulk of terms reflecting the preferred terms for concepts in the domain and drawn from the actual documents. The strategies are most often used in balance, with the taxonomist providing a logical “top” structure into which the content-linked terms can fit.

The software on display generated a list of candidate terms, offering words and phrases from the content as terms. But this was just a starting point in taxonomy construction. Time for the taxonomist to add the value of organization through hierarchical, associative, and equivalence relationships.

Ah, “relationships” takes me to semantics, another buzzword that sounds very impressive and truly represents the power of taxonomies. The key thing to remember is that semantics in a taxonomy starts with the hierarchical, associative, and equivalence relationships. (Actually, a taxonomy with all those features is more accurately called a thesaurus). Organizing terms in a hierarchy of broader and narrower concepts—from general to specific—and recognizing synonymous alternative expressions and internal conceptual links all add semantic richness to terms by providing context based on the meanings of words. These are features built into a well-developed taxonomy, providing pivot points from one term to another through logical semantic associations. Applied as metadata to content items, the taxonomy terms provide semantic enrichment.

Another slick webinar focused on semantic enrichment with an artfully designed but effective presentation. As jaded as I have become, I was duly impressed by the appealing motifs, the jazzy colors, the graphics in motion, and the requisite buzzwords in the opening. This is the part you show to the CIO, CTO, etc., the one with final budget authority. We are still talking about semantically enriching content with metadata from a domain-specific taxonomy. You say, “This is just what I need!”

Several modules were described. One extracts words and phrases as key topics for a taxonomy-ish product, called by a name not found in the ANSI/NISO Z39.19 standard for taxonomy construction. Another is for human taxonomy building from scratch, if the ready-built domain taxonomies are not a good fit. Others serve categorizing/indexing/tagging/annotating content (chose your favorite expression), also known as applying taxonomy terms as metadata or … semantically enriching the content.

I must admit I was impressed, but not snowed. I’m an editor, not in marketing or in an art department. I knew what this was all about because this is basic taxonomy and indexing work that I do daily, using software that delivers these functions. I know that slick is cool to look at, but it comes at a price.


“Gee, thanks for the spin in your Ferrari, but I was hoping for a Chevy pricetag and Honda/Volvo/Subaru reliability.”

civicPhoto by Ahmad Mukhlis, / CC BY-SA 3.0

I also know that essential functions are available in products much more accessible to organizations on a budget.

If you are interested in software for taxonomy creation, management, and application, don’t get snowed by the buzzwords and bling. Know the basics of taxonomy construction and implementation, and use that knowledge as a starting point when comparing software. Know the functions you need to perform and avoid slick but unnecessary frills, as alluring as they may be. Know if the product will work with other systems and whether you’ll need a high-priced mechanic or an editor to do the work. When you hear about trends, consider established history and experience. Data Harmony software from Access Innovations was developed for a demanding production setting, starting in 1995 and continually improving over the years. It may be eclipsed on the slick presentation front, but the software has proven it’s up to the job. Just ask any of our satisfied customers. Contact us; we’d be happy to give you the list.

Alice Redmond-Neal, Senior Taxonomist
Access Innovations

Trees, Fractals, and Taxonomies

July 21, 2014  
Posted in Access Insights, Featured, Taxonomy

Dragon_treesImage by Solkoll,

If you look at a branch of a typical deciduous tree, you can see that it looks like a smaller tree. Likewise, that branch branches off into smaller branches that look like even smaller trees.

This characteristic of trees is an example of what mathematicians, biologists, and systems scientists call self-similarity. Self-similar systems repeat their basic geometry at smaller and smaller scales, creating multiple miniatures of themselves at different scales. In general, natural and mathematical systems in which self-similarity results in complex and detailed patterns are referred to as fractal systems.

Many natural phenomena are or can be fractal:



Photo of a 12-sided snowflake by Becky Ramotowski,

ocean waves,


Painting by Katsushika Hokusai,
/CC BY-NC-ND 3.0

and even broccoli.


Photo by Jon Sullivan,

Trees are loosely fractal. While the trunks don’t keep replicating, the branches do. As the Fractal Explorer observes:

If you don’t know anything about fractals a tree might seem as a very random object. No patterns, no rules. But if you know something about fractals and look closer you can see that basically a tree is a trunk with trees on it. That is a basic pattern that every tree follows.

Taxonomies are often described as taxonomic trees, or as having a tree-like structure. To carry the analogy further, we often refer to the progressively more specific and more numerous hierarchical subdivisions in a taxonomy as branches. The overall domain of a taxonomy, while sometimes referred to as its root, might also be viewed as its trunk.

So this begs the question: Are taxonomies fractal? As it turns out, several authors have written articles on the fractal nature of biological genus-and-species taxonomies. These articles discuss the branching characteristics of these taxonomies, the same branching characteristics that we see in taxonomies outside the realm of biological species categorization. They also discuss the mathematical tendencies of the proportions of the various branches, tendencies that could perhaps be a natural result of the degree to which things in a group need to be different before we find it appropriate to give them different names.

In recent years, interdisciplinary scientists such as Christophe Eloy have been studying the natural forces that make trees grow the way they do, and how their growth patterns might make them resilient in windstorms. Interestingly enough, these scientists have been inspired, in part, by an observation that another person with an interdisciplinary approach, Leonardo da Vinci, made 500 years ago.

As Joe Palca explains in “The Wisdom Of Trees (Leonardo Da Vinci Knew It)”:

Leonardo noticed that when trees branch, smaller branches have a precise, mathematical relationship to the branch from which they sprang. Many people have verified Leonardo’s rule, as it’s known, but no one had a good explanation for it. …

Leonardo’s rule is fairly simple, but stating it mathematically is a bit, well, complicated. Eloy did his best:

“When a mother branch branches in two daughter branches, the diameters are such that the surface areas of the two daughter branches, when they sum up, is equal to the area of the mother branch.”

Translation: The surface areas of the two daughter branches add up to the surface area of the mother branch.

Here’s another explanation, from Esther Inglis-Arkell’s article “Scientists Still Puzzled by a Fractal Discovered 500 Years Ago”, that might be more intuitive:

Strip the leaves off of the average tree, soak the whole thing in water until it gets mushy, bundle the branches up together, and you’ll get what looks like one long trunk. That’s what Leonardo Da Vinci said in the fifteen hundreds. If a tree trunk splits off into three main branches, each of the branches will be one third the size of the trunk. When each of those branches splits into three again, making nine branches on the second ‘tier’ of the tree, each of these second tier branches will be one ninth the side of the trunk. As the branches grow and split, they will always be a particular fraction of the size of the trunk, and adding together all the fractional bits of each ‘tier’ of branches will always add up to ‘one trunk.’ This isn’t the case in all trees, but the majority hold to this pattern.

Can we gain a new perspective on taxonomies from all this? I think the lesson might have to do with scope, specificity, and detail. According to da Vinci’s observation, tree branches uniformly become ever thinner until they taper off, yet their total bulk at most levels of the tree will be approximately the same. So, in a taxonomy that grows naturally, we might expect that the terms at any given depth might be at approximately the same level of specificity. At the same time, their individual scopes at any given depth will add up to a sum total that will ideally (I think) cover the same scope as the top level of terms. As with trees branches tapering off, though, this will be less true as the taxonomy branches naturally taper off and end at the most specific levels.

Inglis-Arkell sums up with some interesting observations about the beauty of branches:

This pattern of growth has a mathematical, as well as physical, beauty. Trees are natural fractals, patterns that repeat smaller and smaller copies of themselves. Each tree branch, from the trunk to the tips, is a copy of the one that came before it. Branches split off from the highest tip the same way they do from the trunk, and set of branches splits off at the same angle to each other. Physics, math, and biology come together to create the simplest and most efficient growth pattern. It just took Leonardo Da Vinci to first notice it, the big show-off.

 Barbara Gilles, Taxonomist
Access Innovations

Thesaurus evolution – a case study in “Synthetic biology”

July 14, 2014  
Posted in Access Insights, Featured, Taxonomy

The following post, by Rachel Drysdale, originally appeared in PLOS BLOGS on April 8, 2014.

Science does not stand still and neither does the PLOS thesaurus. With more than 10,700 Subject Area terms, we use the thesaurus to index our articles and provide useful links to related papers, enhanced search functions, and, for PLOS ONE (more than 90 articles published every day!), customizable Subject Area-based email alerts and Subject Area landing pages.

Sometimes we decide to renovate a sector of the thesaurus to better reflect the make-up of the PLOS corpus. For example, we’ve long had a Subject Area term for “Synthetic biology,” sitting beneath “Biology and life sciences.” We even have a healthy Synthetic Biology Collection. However, the Subject Area term “Synthetic biology” was being applied to only a handful of articles despite the fact that many more PLOS articles were about synthetic biology and should ideally have been indexed accordingly. Why was this?

Part of the explanation is that ‘synthetic biology’ is not a phrase that is frequently used in natural language. So whereas an article about hypertension may use the word ‘hypertension’ 26 times within the text, an article about synthetic biology might state ‘synthetic biology’ rarely, if at all. This poses a challenge to the Machine Aided Indexing process which assigns Subject Areas to articles based on the frequency of matches in the text.

The way around this is to introduce a level of abstraction to the rulebase that governs the Machine Aided Indexing. The base rules are very literal: “if I see ‘synthetic biology’ in the text I’m going to use the ‘Synthetic biology’ Subject Area term.” But there are additional words and phrases that are diagnostic of synthetic biology topics, such as “biobricks” and “Registry of Standard Biological Parts.” Adding rules for these terms – for example “if I see ‘Registry of Standard Biological Parts’ in the text I’m going to use ‘Synthetic biology’” – increases the frequency of indexing to “Synthetic biology” and thus the retrieval of relevant articles in our searches.

A second factor is to do with the hierarchical structure of the thesaurus – an especially important factor given that our search functionality is designed to utilize this hierarchy. For example, a Subject search for “Vascular medicine,” beneath which Hypertension sits, retrieves articles indexed specifically with Hypertension, even if they have not been explicitly tagged with “Vascular medicine.” In earlier versions of the PLOS thesaurus “Synthetic biology” had no narrower terms, and this was doing it no favours with regard to how useful it was for retrieving relevant articles. We therefore reviewed essays about synthetic biology, scope descriptions from relevant institutional and departmental web sites, and proceedings from synthetic biology conferences, all in light of the content of our articles, and introduced new, narrower terms to sit beneath our existing “Synthetic biology” where that made sense.  So we went from having the single “Synthetic biology” term to the new structure of 30 terms in one renovation.  Here is what we have now:


Much of the evolution of the PLOS thesaurus is gradual, as for example when we realised that “puma” can be used as an abbreviation for “p53 upregulated modulator of apoptosis” as well as a kind of big cat, or learned that asteroids can be starfish. Dealing with these indexing missteps requires small-scale changes to specific rules. But sometimes the change needs to be more radical. Our new “Synthetic biology” sector was implemented in Ambra 2.9.12 (released March 26th, 2014). Where previously only a handful of articles was indexed with “Synthetic biology,” now a Subject search across all PLOS journals retrieves over 400 “Synthetic biology” articles – much more fitting for this important and developing field.

For more about the work PLOS is doing with Synthetic biology see “An Invitation to Contribute to the Second Life of the Synthetic Biology Collection.”

Access Innovations, Inc. Now Accepting Presentation Abstracts for the Eleventh Annual Data Harmony Users Group Meeting

July 7, 2014  
Posted in Access Insights, Featured, Taxonomy

Access Innovations, Inc. is pleased to announce the Call for Presentations for the 2015 Data Harmony Users Group (DHUG) meeting. The annual DHUG meeting is held every February at Access Innovations company headquarters in Albuquerque, New Mexico. DHUG 2015 is the eleventh annual meeting and will focus on leveraging of taxonomies and tagged data, techniques for integrating tagged data flows into production cycles, and inventive ways to improve the user experience.

The theme for the meeting, “Beyond Subject Metadata, or, So you have a Taxonomy!… now what?” urges Data Harmony users to ask questions such as the following:

  • What do I do now that my content is tagged?
  • How do I integrate that tagged content into my workflow or production cycle?
  • How can I get my newly-tagged content in front of my users?
  • How can I improve the search experience for my users who want to access these information assets?
  • Are there other features I can add based on the metadata tagging now in place?
  • What other implementations can I set up to capitalize on content objects organized around my taxonomy?

For the first time, Data Harmony users can now submit presentation proposals using the company’s Smart Submit software extension module, at The system is a full working implementation of the module and demonstrates how easy it is to use. The deadline for inclusion in the preliminary program is September 20, 2014.

In the DHUG 2015 implementation of Smart Submit, the first screen includes fields for entering such information as title, creator (author or presenter, usually a DHUG member), abstract, contact information, and a brief biography of the presenter. Optionally, the user may choose to upload a PDF or Microsoft Word file. There are also some fields customized for the meeting organizer, such as on what day of the week a presenter would prefer to be scheduled, and how long his/her presentation will be.

In the second screen, Smart Submit uses Data Harmony’s M.A.I.(TM) (Machine Aided Indexer) software module to display  suggested indexing terms from the Access Innovations thesaurus to characterize the presentation. M.A.I. bases its automated indexing assistance on the text in the title, the abstract, and any PDF or Microsoft Word document that was uploaded via the first screen. The presenter chooses to retain or remove each of the suggested terms and may add additional terms from the thesaurus. The system also allows for searching the thesaurus and adding terms from the search results view.

“This is an exciting addition to the DHUG meeting planning process,” remarked Heather Kotula, Marketing Coordinator for Access Innovations. “We made it a priority to showcase our own software this year. Using Smart Submit to collect presentation proposals is going to make my job of organizing the meeting easier, faster, more complete, and more accurate.”

DHUG registration includes breakfast, lunch, and breaks with refreshments for all five days of the meeting, February 16th-20th, 2015. A networking reception will be held Monday evening at the University/Midtown Hampton Inn. On Tuesday evening, dinner will be provided for all attendees at a unique Albuquerque attraction. The University/Midtown Hampton Inn is the primary DHUG meeting hotel, offering a $79 nightly rate for members.

For more information about DHUG 2015, please visit

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