Trees, Fractals, and Taxonomies

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

Dragon_treesImage by Solkoll,
en.wikipedia.org/wiki/Patterns_in_nature#mediaviewer/File:Dragon_trees.jpg

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:

snowflakes,

12armSnowflake2004UTbr

Photo of a 12-sided snowflake by Becky Ramotowski,
www.srh.noaa.gov/abq/?n=features_snowflake

ocean waves,

Mount-Fuji-Seen-Below-a-Wave-at-Kanagawa

Painting by Katsushika Hokusai,
www.katsushikahokusai.org/Mount-Fuji-Seen-Below-a-Wave-at-Kanagawa.html
/CC BY-NC-ND 3.0

and even broccoli.

640px-Fractal_Broccoli

Photo by Jon Sullivan,
en.wikipedia.org/wiki/Romanesco_broccoli#mediaviewer/File:Fractal_Broccoli.jpg

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

Taxonomies Can Level the Playing Field

July 21, 2014  
Posted in indexing, metadata, News, search, semantic, Taxonomy

We already know that metadata and metatagging enable findability in search-based applications, but what happens when there are diverse formats? Search Content Management brought this thought to our attention in their article, “Metadata tagging and the innovation behind search-based applications.”

When we are looking for information within an ever-widening array of technologies, from mobile devices to the cloud – where does the search technology come in? A search-based application can query a variety of structures and return the results of the query in a single, unified view. This is powerful because it encompasses all types of content.

This is where a solid taxonomy comes into play, as it can provide consistency for tags that don’t quite line up with one another. Indexing metadata against this taxonomy results in solid and comprehensive search results. Access Innovations is one of a very small number of companies able to help its clients generate ANSI/ISO/W3C-compliant taxonomies.

Melody K. Smith

Sponsored by Access Innovations, the world leader in thesaurus, ontology, and taxonomy creation and metadata application.

The Value of a Taxonomy Tool

July 18, 2014  
Posted in indexing, News, Taxonomy

TEMIS has launched Luxid 7, the seventh generation of its flagship semantic content enrichment platform. Luxid 7 promises a beefed up scalable and robust semantic enrichment pipeline and includes a dedicated ontology management tool. Broadway World Geeks brought this to our attention in their article, “TEMIS Integrates Ontology Management and Semantic Enrichment in Luxid’ 7.”

When building a taxonomy or ontology, you want that model to be available across the enterprise and not tied to one single program. All of this is done to make it a dynamic and comprehensive system with outstanding search results. Access Innovations provides Search Harmony to allow that same taxonomy/ontology to be used on the user search side to leverage the tagging of the documents and further enhance search results. A user can easily change the configuration of the ontology/thesaurus/taxonomy through our administrative module so the data model retains integrity by matching the guidelines of the standards while modifications are made to the user needs. This easily integrated feature is critical to quality, progressive search results.

Melody K. Smith

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

Standards and Taxonomies – Match Made in Heaven

July 17, 2014  
Posted in News, Standards, Taxonomy

A recent study revealed that an open standard for fixed-income reference data would better coordinate taxonomies, even with the Enterprise Data Management (EDM) Council’s Financial Industry Business Ontology (FIBO). Waters Technology brought this news to our attention in their article, “Study Recommends Open Standard For Taxonomies.”

Standards create consistency and in taxonomies, that is key for success. The common language and classification from the beginning result in fast and thorough results.

Proper indexing against a strong standards-based taxonomy increases the findability of data. Access Innovations is one of a very small number of companies able to help its clients generate ANSI/ISO/W3C-compliant taxonomies.

Melody K. Smith

Sponsored by Access Innovations, the world leader in thesaurus, ontology, and taxonomy creation and metadata application.

 

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:

synbio_crop

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 Author Submit software extension module, at http://www.dataharmony.com/dhug/submissions. 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 Author 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, Author 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 Author 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 http://www.dataharmony.com/dhug/dhug2015.

Focusing on Accuracy

July 4, 2014  
Posted in News, search, Taxonomy

Smartlogic recently released Semaphore 3.7 with assurance that this release provides even more accuracy in the massively improved information extraction capabilities. Digital Journal brought this news to our attention in their article, “Smartlogic Releases Semaphore 3.7 With Major Improvements to Its SharePoint integration.”

Semaphore 3.7 offers some new features, including improved functionality for SharePoint 2013 and 2010, better metadata ability for the Google Search Appliance, and improvements in handling of large models in Ontology Manager, as well as others.

Semantic technology continues to grow and expand in its uses, at Smartlogic and elsewhere. Access Innovations, developer of the M.A.I. machine-assisted indexing system, has continued to expand its coding, tagging, and indexing capabilities.

Melody K. Smith

Sponsored by Access Innovations, the world leader in thesaurus, ontology, and taxonomy creation and metadata application.

Finding Your Content

July 2, 2014  
Posted in News, Taxonomy

Atypon has released Literatum 14.1 for professional and scholarly publishers. Literatum powers the websites of over 200 professional and scholarly publishers, including many of the most prestigious publishers in the world. This interesting news came from Knowledgespeak in their article, “Atypon unveils Literatum 14.1.

This being the first of multiple releases scheduled for 2014, Literatum 14.1 adds dozens of new features such as taxonomy management capabilities.

Access to data is important. It can be achieved by creating strong taxonomies. Proper indexing against a strong standards-based taxonomy increases the findability of data. Access Innovations is one of a very small number of companies able to help its clients generate ANSI/ISO/W3C-compliant taxonomies.

Melody K. Smith

Sponsored by Access Innovations, the world leader in thesaurus, ontology, and taxonomy creation and metadata application.

The Value of Search

July 1, 2014  
Posted in News, search, Taxonomy

Concept Searching and information governance are often seen together in articles and white papers. It is a popular topic, but a complicated one as well. Search is a key component of information governance and therein lies our interest on the topic. Digital Journal brought this news to us in their article, “Concept Searching’s Intelligent Search Solves Information Governance Challenges Article Published.”

Martin Garland, President of Concept Searching, commented, “Search is no longer a nice to have, but is one of the most critical tools used by all users within an organization. Most search engines do not accommodate the way in which different users search, therefore information cannot be found. Now, issues such as potential security breaches and non-compliance are exposed during the search process. Search must be included in a solid information governance plan, and gains in productivity, better decision making, and risk reduction are all quantifiable business benefits that can be achieved immediately.”

It is important to remember the value of a solid taxonomy and its role in the search process. How the content is classified impacts how successful making your content findable becomes.

Melody K. Smith

Sponsored by Access Innovations, the world leader in thesaurus, ontology, and taxonomy creation and metadata application.

Smoothing the Way

July 1, 2014  
Posted in indexing, metadata, News, Taxonomy

Cambridge Semantics has released Anzo Smart Data Integration (ASDI) software to help enterprises rapidly understand and integrate information assets. This new software is designed to reduce integration timeframes and costs by a factor of 10. KM World brought this interesting information to our attention in their article, “Easing data migration.”

ASDI uses common, conceptual business models to automate traditional data integration tasks, eliminating the need for hand-coding and direct data exchanges between teams.

Comprehensive search is important for any document management system, which is why data integration success is so important. Proper indexing against a strong standards-based taxonomy increases the findability of data. Access Innovations is one of a very small number of companies able to help its clients generate ANSI/ISO/W3C-compliant taxonomies.

Melody K. Smith

Sponsored by Access Innovations, the world leader in thesaurus, ontology, and taxonomy creation and metadata application.

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