I'm sorry.

It seems that this thing has become my forum for school related quandaries. Whether that interests you or not....is probably up to you. Anywho, this semester is gonna be rather interesting. The biology classes I'm taking seem to be rather unorthodox in their teaching method. I'm taking a plant taxonomy class which is actually really cool cause I like plants. The professor is really knowledgeable, but not quite all there sometimes (as most science professors are). So for our first project we need to go out into the field and find 5 or so plants that we are gonna have to identify and turn in.

I already know where I'm gonna go to do this. There's a park around the corner from the apartment, so there should be no shortage of foliage for finding. I hope there's a little league game going on or somethin while I'm rooting around for my specimens so parents can watch me lurking around in the under brush picking flowers.

Why?

Frankly, because it would be amusing. It'll be a little social experiment while I'm doin my homework. As long as the social experiment doesn't turn out to look like I'm a pedophile...

Maybe its not such a good idea after all...

Jon

The disease is caused by a parasite - a multicellular microorganism. Not just a simple bacteria, the malaria plasmodium is a complex critter that still remains quite mysterious. It is very hard to work with in the laboratory: it doesn't culture well and the risks involved are immense.

The discovery of a non-infectious relative (albeit, rather distant) by Australian researchers is exciting news for many.

Paydirt hasn't quite been hit as far as medical research. However the fun isn't just for medicos, but the evolutionary biologists as well.

Chromera velia is clearly related to Plasmodium parasites, but rather than being a blood-borne obligate parasite of mammals and insects that rarely sees light of day, it is a plankton-like photosynthesising obligate symbiont of corals.

These long-lost cousins are so very different, it could almost make the ghost script of the next Wil Farrell comedy (or not, besides its been done before).

Can they really be from the same origin?

The evidence is convincing.

For more information, take a read of a great interview (it says so in the title) with the scientists responsible for the discovery, as well as the University of Sydney press release.

Image: Copyright University of Sydney. Use only for non-commercial and educational purposes with attribution.

Digital Libraries

In practice, digital libraries are often viewed as an extension of traditional library collections. They usually contain digitized materials from the library’s paper or analog collections, and are often drawn from rare books collections, special collections, archives, or otherwise highlight the particular strengths of a given library. Digital library collections have focused on these types of materials because digital formats are an ideal access medium for items too fragile to withstand repeated handling, materials too rare to circulate, and formats awkward to handle and manipulate in the original, such as large maps. When appropriate standards are used for digitizing, structuring, and describing these materials, digital libraries can be considered analogous to other preservation reformatting and distribution processes, such as microfilm. The digital library concept can be expanded to include materials in any digital format, including sound, video, multi-media, “born-digital” (resources that were originally created in an electronic environment), data sets, computer programs, and licensed content such as e-books and art images purchased from vendors.

Digital library collections are most often stored in Digital Asset Management Systems (DAMS), which are specialized storage and retrieval systems that support digital formats and metadata. Metadata for digital collections is typically repurposed from existing records in library catalogs (when they exist) or is created by library personnel, much as other library materials are cataloged. The proliferation of digital libraries has inspired a parallel proliferation of metadata standards that are used not only describe the digital content, but also provide its structure and enable its management (Read more about metadata). Some storage and delivery systems offer opportunities for enhanced functionality such as full-text searching and image manipulation, allowing users to interact with library resources in ways not previously possible. The UNH Library currently uses DigiTool as our DAMS.

Continues at UNH Library Newsletter

An ontology is concerned with the categorization of things.  A "thing" can be just about anything -- a person, a company, a particular news story, a video, an application, or a web page.  Ontology is a broad concept and subsumes taxonomy and folksonomy. Google Search delivers relevant results because it leverages a massive corpus ontological information about web sites and entities.  PageRank is but one device in the search arsenal that infers ontological information about both the classification and quality of a page.

A taxonomy is a more formal construct concerned with the ordering of things, usually in a hierarchical structure.  Yahoo's Directory is a taxonomic organization of the web, for example.  The Open Directory Project (DMOZ) is also a taxonomic organization of the web, but rather than leveraging a group of internal "surfers" as Yahoo! did, DMOZ is an open source directory.  

In the early days of tagging, the term folksonomy emerged to describe a non-hierarchical ordering of things through collaborative input.  For example, when a user tags a photo in Flickr, she is creating an informal taxonomy.  These tags are aggregated to help consumers find photos -- either by "tag surfing" or by making search more precise as a result of better meta-data.

Who needs philosophy?

Let's review some of the big wins over the past decade on the consumer internet.

Yahoo!  

Started with a directory built by web surfers.  Employed a chief taxonomist to overlook the organization of the directory.

Google 

As the amount of data on the web grew exponentially, taxonomies will too structured to keep up -- a more flexible ontology was required.  Google replaced the directory (a taxonomy) with search (a less formal ontology).

Facebook

Social networks are ontologies.  When you search for a name (e.g., Joe Smith) on Google, you get the NBA player.  When you search for Joe Smith on Facebook, you are far more likely to find the Joe you are looking for.  When search for Joe Smith on Flickr, you get the photo of this man.  The Joe Smith tag on Flickr is text.  When you tag a photo on Facebook, you are encouraged to highlight objects (usually a face) and then select a name from your friends list.  The value of the tag "Joe Smith" tag on Facebook is far more valuable than the "Joe Smith" tag on Flickr because it has more information embedded in the tag.

And don't forget that the Internet is the ultimate taxonomy -- DNS is a system that maps human-readable names (e.g., http://laserlike.com/) to an IP address (http://76.74.254.123/, which is the IP address for Wordpress).

 Opportunities.

If you can invent something that improves the information about a big class of things on the web, you can have a massive impact.  

For example, there really isn't a dominant ontology for organizations.  We have tickers for the ~10,000 public companies in the United States.  What about the other 8MM businesses in the US?  Nonprofits and clubs?  And the rest of the world?  There are firms who have tried to create some of this information (e.g., Hoovers, Crunchbase, VentureWire).   Once you have a solid ontology for this type of thing (ideally with some sort of namespace), you can pivot around it to create massive value.  You could munge together the social graph with the organizational namespace for a definitive guide of who belongs to which organizations.  How about the automated inclusion of hypertext links (ala Yahoo! Shortcuts) in every bit of text on the web linking to that organizational namespace?  And clustering groups of organizations for the purposes of discovery and analysis?

How about a location-based namespace?  You have some of this today with addresses and zip codes.  But what if you could take the GPS coordinates of every fixed object on the planet and append a human-readable name (like DNS does with IP addresses)?  And not only based on horizontal location, but also including vertical location (e.g., the 30th floor of the Bank of America building in SF)?  Perhaps you append a location code to an URL (e.g., bankofamerica.com/sf/555-30)?

In shopping, certain categories like music and books have formal ontologies (e.g., ISBN codes).  But most categories lack universal codes (or SKUs), requiring every retail and online site to create their own ontology -- a pair of Levis 501 Jeans may have the code Levi501_2008 at one retailer and LS12345 at another.  Ebay has employed a very loose ontology due to the fact that they continuously have sellers adding and subtracting products from inventory.  This makes finding a product and comparing prices far more laborious than is ideal.

These are simply examples that come to mind as I type.  Any other ideas about categories that would benefit from improved classification?

"I had thought it would be rather nice to call it Mindarus ebayi," said Dr Harrington.

"Unfortunately using flippant names to describe new species is rather frowned upon these days."

Call me old-fashioned, but I think more new species should have flippant names.

For all users of a Digital Asset Management solution, the true value of the system is proportional to the richness of the metadata and its underlying structure. Without the proper metadata, a media asset is merely a file. So it is critical that a Digital Asset Management system enable the modeling of metadata to fit business processes and content workflows. Further, to properly define, manage and evolve your metadata, the Digital Asset Management system should provide tools that maximize flexibility and control of metadata configurations.

With the latest release of Artesia DAM 6.8 in December of 2007, metadata configuration has become much simpler with the introduction of an industry unique Flex-based Metadata Configuration Tool. This drag-and-drop tool allows business analysts, rather than database administrators or IT personnel, to model and configure asset metadata. With a graphical interface that allows metadata configuration to be accomplished in minutes not hours, the effort of deploying and maintaining the Digital Asset Management system is greatly reduced. When metadata models have been defined and developed, it is only takes a few simple steps to move that configuration from a staging system to the production Digital Asset Management system.

Artesia

I'll be supporting Paul's morphological studies in the taxonomically troublesome wasp genus Heterospilus with molecular genetic data, but be warned. There are several hundred species yet to be named in the genus, and who knows what sort of nomenclatural mischief awaits.

At the heart of this project was Digital Asset Management (DAM), a rapidly growing area as more multimedia content is being distributed online, particularly for marketing purposes. The inherent problem with digital assets is the potentially large amount of information about what a piece of content is but the lack of information describing what that content is about. Unlike other content, which may contain text or be located with surrounding textual context, digital assets do not typically contain text, especially any which is structured for discovery by search engines. Any textual and searchable elements must be associated to digital assets through the use of metadata. Metadata describing what the content is, including attributes like video length, number of pixels, and file size, can be associated to the content and is often automatically attributed through business rules.

What the asset is about, however, is not inherent. It must be associated to the content either manually or automatically by loading the content once business rules have been thought out and established.

This can be established for single format assets, but things get a little more complicated when content can be assembled from “pieces” which may or may not share common values once reassembled into something new. In other words, what an asset is about may change once it is combined with other elements to form a new and unique asset.

An additional challenge with digital assets is versioning. Digital assets are frequently large and high-resolution, requiring a lot of storage space and management as versions are created and retained. Since digital assets are expensive and time-consuming to create, reuse and repurposing is common, leading to multiple versions and formats of a single beginning asset.

Though not the single answer to the challenges of DAM, a controlled vocabulary of descriptive terms used in association with common metadata attributes can help to manage the versions and combinations of assets from creation to reuse to final storage or disposition. Since there is no, or very little, textual context for digital assets, the descriptive vocabulary can be tailored to fit existing assets and those to be created, creating uniformity in description and a basis for honing search for asset location.

Tagging assets with terms from a controlled vocabulary provides the descriptive metadata used for tracking and locating assets. Some of the takeaways from a recent DAM project address the above challenges and how taxonomy values would assist with DAM.

Asset aboutness

The most difficult aspect is how to index what a digital asset is about. Stock photo companies, such as Getty Images, have indexers with established rules and controlled vocabularies in order to provide searchable context for images. The same can be done in any organization but requires an established controlled vocabulary to use for tagging and training of subject matter experts who do the indexing and tagging of content. The SMEs should have common guidelines about controlled vocabulary application to assets to provide consistency.

What we found in our project was multiple and potentially far-flung asset creators uploading assets and tagging with no rules and no controlled vocabulary. Centralized tagging provides the most control over application of terms, but decentralized tagging can be streamlined by creating fixed dropdown values for content tagging or centralized review and retagging of submitted assets.

Asset assembly

Another challenge is the “parts is parts” nature of digital assets. Unlike assembling text from multiple sources, assembling multiple assets into a new and unique creation which itself will be versioned, tracked, and stored can lead to a disconnect between the tagging of the parts and the tagging of the whole. Retaining metadata for the individual assets within an assemblage retains the original context, but an additional round of tagging should be applied to the final product to capture the change in function. For example, we encountered assets which had been created in parts for reuse but were all fused into a final 30-second commercial. Those individual elements could be reused in other contexts. Both the elements and the combined whole should have applied terms.

Asset versioning

Asset versioning is really a function of the tools used to track and store digital assets. However, applying controlled vocabulary terms early in the asset creation process will also assist with locating individual versions of assets as the content changes. For example, the first draft of an asset should have applied to it the necessary core metadata elements such as date of creation and author. Additionally, the content and context of what the asset is about should also be tagged. As the message of the asset changes in subsequent versions, so too will the terms describing what the asset is about. This retagging will help to clarify and track changes to assets over time.

Controlled vocabulary is just one aspect of managing digital assets, but if done in conjunction with a DAM project, the tracking of assets can be managed before volume and versioning issues cost more time and money to fix later down the line.

The olive-backed forest robin (Stiphrornis pyrrholaemus) . . .

Image: Science Daily

The bird has been named as the olive-backed forest robin for its distinctive olive back and rump. The average adult is about 11.5 centimetres long and weighs about 18 grams. The birds have a white dot in front of each eye. The male has a bright orange throat and breast, a yellow belly and a black head. The female has the same colours but appears dull when compared to the male.

Though the bird was first observed by scientists from the Smithsonian Institution in 2001 in the south-western part of Gabon, it has been officially recognised as a new species only now after scientists collected more specimens and compared their DNA to those of the other known forest robins.

While we keep hearing of species becoming extinct or getting endangered at an alarming rate, this discovery would definitely bring cheer to the hearts of ornithologists and other nature lovers!

Search engine optimization (SEO) has become one of the most important tools in helping us taxonomists get hard data that is meaningful and fight against the inclusion of terms that are too cute, ambiguous or otherwise detract from the findability of content.

I recently read an old blog post (from way back in 06 - which is unfortunately unsigned) on the links between SEO and taxonomies. This post describes how important it is to get your site to fall in line with the terminology popular in the major search engines to boost search engine rankings. The author explains how the taxonomy helps determine context for the indexing spiders - your site taxonomy is like a higher-order outline of what it is your site is about, regardless of how many keywords you shove into the metatags (and search engines are smart to most keyword spamming and other subterfuge).

Site taxonomy becomes search engine taxonomy through the regular indexing of 150 million pages of site text each day...Search engines use the keywords that top-level sites employ to develop their own methodology for site classification... And, if your site taxonomy dovetails with the search engine taxonomy, you’ll be accurately indexed and may, in fact, see a significant increase in SE-driven traffic because your site is where it should be when SE users query.

Lots of marketing folks - and don't get me wrong, I love marketers - like to come up with campaigns that introduce "new and improved" labels for things to try to drum up interest and buzz. This is fine, cause that's their job: to be creative and come up with catchy new ways to sell people the same products. Except that when you stray too far from industry standard terms in the online world, you are actually doing yourself a larger disservice by confusing users and reducing your site's search engine results.

I sometimes find it hard to come up with compelling (enough) theoretical arguments on why it's bad practice to do this ... so I prefer hard data. And SEO keyword analysis in conjunction with competitive analysis is the best kind of data to prove this point.

I always include some level of competitive analysis anytime I create a new taxonomy for use in a customer-facing website, as well as process changes to existing ones. While you certainly don't want to have a carbon-copy taxonomy of your main competitors', I can't emphasize how important it is to be at least aware of the trends out there so that you can make informed decisions about when to stray from the norm. The reality is that users don't come to your site only - they surf, they shop, they read. So as the industry converges around specific terms, so do users - AND so do search engines.

So, if the rest of the world calls it an MP3 player and you choose to call it a music blaster or a digital music projection device (hokey example, but you get my point), not only will your customers have to think harder to find your product once on your website, they won't even see it when searching for iPod in Google. I always recommend checking at least 3 competitor websites and 2 other sources - such as review sites, or wikipedia - to use as indicators of popular language.

SEO keyword analysis is a great way to prove this alongside competitive analysis. SEO tools are easy enough to find - the SEO Book Keyword Tool is my favourite - and use. Simply pop in that fancy new term people want to include and show them the dearth of searches (if it is the case). These tools also help you determine if a term has a different meaning in search engine taxonomies based on the related terms it pulls up. For example, a customer recently asked me to add a new label in the taxonomy based on what the stores were going to call the product in their marketing campaign, but with a little research I found out that the term referred to a completely different type of product in the online world, given the search results and keyword analysis. I might have had to argue longer had I not had those statistics to show and back up my case, but the stakeholder quickly understood my point and agreed to diverge for the e-commerce experience.

If you are involved in managing your company's site navigation or taxonomy, I strongly recommend if you haven't already, boning up on key SEO concepts and tools to bolster not only your site's performance but your ability to combat against bad taxonomy. A great start is our recent 60 minute webinar on taxonomy and SEO (featuring one of our consultants, Jeff Carr), or this list of 21 SEO tips.

Equivalent (Synonyms: "International Business Machines = IBM")

Hierarchical (Parent/Child : "Computer Manufacturers => IBM")

Associative (Concept/Concept: "Software Group - Software")

Heather Hedden's presentation on taxonomy powered discovery for a recent Boston KM Forum contained an interesting set of examples for how to organize the last type of conceptually related term sets.

Process and agent: Programming - Programmers
Process and instrument: Skiing - Skis
Process and counter-agent: Infections - Antibiotics
Action and property: Environmental cleanup - Pollution
Action and target: Auto repair - Automobiles
Cause and effect: Hurricanes - Flooding
Object and property: Plastics - Elasticity
Raw material and product: Timber - Wood products
Discipline and practitioner: Physics - Physicists
Discipline and object: Literature - Books

Associative relationships are the mechanism behind a search interface that presents related content to a user. "You might also be interested in..."  By building out these kinds of conceptual relationships, it's possible to anticipate what a user wants (if we know who they are and something about what they are doing).

This is also one way to turn a taxonomy into an ontology.  An ontology is simply a set of terms and term relationships that represents a body of knowledge.  For the life sciences industry, this might include biochemical pathways, genes, mechanism of action, generic names of drugs, chemical compounds and so on.  For the insurance industry it might mean products, risks, regions, policies, claims processes, etc. 

Developing the associative relationships between terms allows users to locate the information needed for a task.  If I am a researcher, I might want to find current antibiotics in development for an infectious agent.  If a claims processor I might want to know contributing factors to an accident. 

These types of relationships require human judgement to be applied to your content, your users and your processes.  What is important? What related information could help someone make a decision? 

The advantage of mapping these semantically is that content in multiple systems can then be related and the relationships can be changed quickly without having to reorganize the actual content at the repository level.

While some local academics tried to hush up the very negative local reactions to this latest episode of scientific imperialism (it's no surprise that they would do so, given their dependence on academic networks owned and controlled within the dominant seats of Western power), Barbadians are clearly right to be critical.

What kind of world is it where one people gets to name the world for the rest of the world?

What kind of world is it where words from one particular, dead, European language are granted exclusive dominance in the name of "science"?

The answer: it's a 2008 world, hardly different from a 1492 world.

So name that scientist!

Hattip failblog.

I'm running this through my head, but you would have to be insanely overworked/tired/whacked out on pixie dust to make this mix up - and need someone else to point out your mistake...

But really it doesn't answer my question of how physically big these animals are. I mean if toad is truly toad-sized then why do they think he's a washerwoman...A toad is smaller than the size of my hand and I believe even the smallest of washerwoman would probably come up to at least my knee. (And don't even think about bringing up the phrase "willing suspension of disbelief"--I don't think even Coleridge could have held off from these plot discrepancies).

And now to a little chastisement...an excuse of "I want to read fun books" is not an acceptable excuse for delaying the end of The Wind and the Willows. I wanted to read fun books too, but I sucked it up and read, what I like to call, "The Book that Fun Forgot" and finished. And need I remind you that you picked this book? So put fun by the wayside, and finish this book!

And no amount of truly hilarious Toad and Badger puns will change my mind.

Your Stalwart Twin,

Jon

Folksonomy is a term I've come across recently in a couple of articles and on my company's blog. To begin with, taxonomy is the science of classification - that's my understanding. The way in which content creators/librarians/administrators, etc... create categories to classify information.

Folksonomy is play on the word taxonomy. Its how "folks", normal people like you and me and the general web community can add our own labels known as "tags" to information. A good example is Youtube, Del.ico.us and Flickr and blogs. When you upload information or media, each of these allows the user to apply our own "tags" to create our own categories to search. For example when I finish writing this post on this blog, I have the option of creatiing new tags which allow others and myself to find it when the search function is used. It also will put it in a category allowing others to see it. So I'll add tags like "taxonomy", "folksonomy", "metadata", etc...

A classical example of a taxonomy is dewey decimal system used for books in libraries. It is a system to classify the hundreds of millions of books, so that users can find books. Folksonomies differ because the user can add their own labels, effectively creating our own kind of dewey decimal system.

The strength of folksnomies is that it allows more users to create labels (tags or if your really nerdy - "metadata") and is more useful in a system where there are even more information to categorise. In the past, taxonomies were restricted to administrators like librarians or authors (content creators). But now, with the explosion of information, videos, pictures, websites being uploaded and shared on the internet - folksnomies has had its greatest use. It allows scalability - it can grow with the more users and more information that is shared.

I've actually being using tags for a while - for my own blogs. It is an easy to keep track of everything and to search for posts. Because I know in my mind what kind of tags I would use.

The second strength of tags is that users are better equipped to label their own information because they are more engaged with the content and have a deeper interaction with it. For example, if I read an article that I like and add it to the social bookmarking site "Del.ico.us" (now www.delicous.com), I will add in labels about what I feel the article is about. I would have read the article, thought about it, etc.. and put related tags opposed to a search engine that uses web crawlers that would scan for the keywords in the article.

However, this is also a weakness of folksonomy because the user is biased as to what that article is about - different users can potentially put vastly different labels. Further, users can use the same labels for different things. As this paper mentions, the tag ANT can refer to "Actor Network Theory" but also "Apache ANT" a programming language. So folksnomies is not without its problems.

One of the interesting things I found with Delicous is that when you are about to save a link and add in your tags, it will actually recommend tags that other people have put on there. I look at them and think "ok, that sounds alright" and you can click on those links - that is one way to help users add labels and create consistency across tagging. I can also add in my own tags as well and ignore the recommended ones.

Folksonomies allow users to create new terms and to start creating paths for finding things. It also can introduce you to new information or media, because you can click on a category or tag and discover what other people have posted up under the same tag.

And to clarify, metadata is the search terms or tags you put into a page, allowing web crawlers to find your information. It is important when putting in the terms for metadata to think of all the various terms a user might type in to find something - for example if you have a company webpage about soccer, you also want to use the term "football" which is what the rest of the world calls it. So the page wont get rejected if people dont type in soccer.

I'm out like folksonomies,

Matt.

Recognize.

You guys came through in a big way and let me know that I basically did the right thing on that whole "shrew-ossum" thing, with some potential room for improvement.  Story of my life, right?

So anyhow, I'm over 50 posts, and that feels good.  What else?  Oh yeah!  Today I officially set a new record for "Weirdest Search Terms" that brought someone to the FIC/LMC.  Someone punched "taxonomy debrazza" into their Google machine...

Wait for it...

And ended up here!  Ha!  Add "taxonomy debrazza" to the growing list of search terms, previously discussed here, for which I enjoy Page 1 status on the Google. 

I hope that the person looking for more information on the taxonomic classification of Debrazza's monkeys left satisfied, but something tells me that that isn't likely.   What's really funny is that those two words didn't even show up in the same post.  The first term, "taxonomy", appeared in a post titled Massive Missive, about how kids and adults are different.  A topic that I will be revisiting very soon.  The second term, "debrazza", is from a post about a trip to the zoo with my best girl.  Something that went unmentioned in that post is the trip to Comotown she forced on me.  I rode rides designed for 8-year olds.  So we'll be talking about that some more as well, probably in the same post.  Maybe it'll go something like this,

Kids like to ride rides designed for kids.  Adult men do not.  The reasons are simple.  You see, the human shin is not designed to take high-velocity impacts from the pedals of the Skyglider.  It's just not one of the things that God or Darwin were looking out for.  Them-a culpa.  You'll notice that the height requirement for that particularly vicious contraption states that those over 51 inches tall are free to go unaccompanied.  What happens when a 72 inch tall man is accompanied by a girlfriend with a sadistic commitment to youthful fun?

The management of Comotown is silent on this topic.  Shame on you Comotown.

So you have that to look forward to.

Getting back to that person who was probably writing a paper about monkeys for a summer college class that they would rather not be taking, I'm sorry. 

And you're welcome.

You're welcome to come back to the FIC/LMC anytime!  Just don't get on my case if I don't give you any info that you can plagiarize for your summer survey of primate taxonomy.

And finally, if you're wondering why in the hell I titled this post what I did, it's because I am getting tired of "McCain is old" jokes.  It's not that he isn't old, because good God is he ever old.  I just think it's time to broaden the scope of our mockery a little bit.  I know you're reading this Conan, let's step it up a little, yeah?