@BioDivLib SXSW Interactive session, vote now!! #sxswLAM

VOTE NOW for the Biodiversity Heritage Library SXSW Internactive session: "Will Sea Monkeys Survive the Zombie Apocalypse?"

It's that time of year again, the SXSW Panel picker, this year, Chris Freeland and I have a session proposal called "Will Sea Monkeys Survive the Zombie Apocalypse?".

We're happy this year to again be part of the SXSWlam (librar*, archiv*, museum*) gang of incredibly great and cool people (I'm looking at @DetailMatters and @Audrey_renee). More info at SXSWLam.info.

Sounds a bit high concept, but the idea is all about organism names as they appear in nomenclatural taxonomy and the Biodiversity Heritage Library.

Here are more details:

Description
Will Sea Monkeys Survive the Zombie Apocalypse? It’s this, and other important questions from the world of biodiversity that at first glance might seem odd, but it’s only through the proper naming of organisms that we can understand both their current place in the ecosystem, as well as their past and future.

Questions Answered

1. Will Sea Monkeys survive the Zombie apocalypse? Or, how does taxonomic nomenclature affect how humans interact with the rest of the earth's biota? Zombies eat humans (e.g. primates), sea monkey are crustaceans. So, will sea monkeys survive the apocalypse or is common name nomenclature destiny?
2. How to find organism names in 40 million pages of text? The Biodiversity Heritage Library is the world's largest repository of computational bioinformatic text data. What purposes, outside of systematic taxonomy can it serve?
3. The importance of names in biodiversity literature. Taxonomy has been systematically naming organisms for over 250 years. Only by knowing the names of organisms can we know where they were in the past and how their ecosystems have changed.
4. You say Physeter macrocephelus, I say Physeter catadon; the problem of syonyms. Taxonomists change and reclassify the names of organisms on a frightfully regular basis (some studies show it to be upwards of 10% of names change every year. How can a legacy project, such at the Biodiversity Heritage Library work in this environment?
5. What is the Biodiversity Heritage Library (BHL) and how can it help you survive the Zombie Apocalypse? With over 40 million pages of taxonomic literature available online in a fully open manner, we are just scratching the surface of how BHL can be used. The latest projects including data mining the content for illustrations that can be used in a variety of humanities projects.

Tags

• names, library, taxonomy

Meta

• Event
• Interactive
• Format
• Dual
• Category
• Science and Space Exploration
• Level
• Intermediate

Speakers

• Chris Freeland Washington University/Biodiversity Heritage Library
• Martin Kalfatovic, Smithsonian Libraries/Biodiversity Heritage Library

Organizer

• Martin Kalfatovic Smithsonian Libraries

Additional Supporting Materials

• BHL From Local to Global
• BHL

@BioDivLibrary @ #SXSW

I've been handing out BHL buttons and talking up BHL at SXSW. Getting a very good response from people. The BHL Button has got to meet a number of friends from the social media and tech world. There it is with Android on the left, below a slide show of some BHL adventures in Austin.

BHL bunch

STL. DCA. RIC. And Maryland

Spinning the BHL travel globe ...

Taking another spin of the globe for the Biodiversity Heritage Library. Give it a big spin and see where we're gonna land!

Sometimes less is more (when it comes to data)

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Originally uploaded by martin_kalfatovic

In a project I work on (the Biodiversity Heritage Library), we always say “BHL is important because it’s a complete (planned at least) of a type of data (biodiv lit)”. Generally speaking, we don’t data to support this assumption, but a firm called Infochimps is designing metrics and data analysis that can quantify this assumption; here’s an interesting post by Eric Hellman (on his "Go to Hellman" blog which you should all ready by the way) about scaling data value, Eric has a longer/fuller discussion, but the key point in relation to BHL  is the following:

Kromer has noticed that the price (or perhaps cost) of a partial data set follows a non-monotonic curve (see graphic). Small amounts of data are essentially free, but a peak value is reached when portions of the data set are extracted from the full data set.

Kromer has noticed that the price (or perhaps cost) of a partial data set follows a non-monotonic curve (see graphic). Small amounts of data are essentially free, but a peak value is reached when portions of the data set are extracted from the full data set. If we were discussing book metadata, for example, peak value might accrue for a set of the 100,000 top selling books.

There's much less value, according to Kromer, in having a large incomplete chunk of a data set. Data for 10,000,000 books, for example, would have less value than the 100,000 book data set, because it's not complete. Complete data sets become extremely expensive because of the logistics involved, and because of the value of having the complete set.

In the BHL context, substitute “Google” for 10m books and “BHL” for 100k books. The BHL data set, acquired at a higher unit cost than the Google data set, is of more “value” because of the coherency of the data (operations on a small, coherent set of data will return greater value than on large incoherent data sets). So, the current ~85,000 BHL volumes online could be of more value than the entire Google Books set.

Where have all the dodos gone?

Where have all the dodos gone?

Dead as a dodo ... you've heard that phrase before, but is the dodo really gone? Is it really extinct?

Well, is our good friend, Raphus cucullatus, aka Didus ineptus, really gone? If so, how would you know, statistically speaking that is?

When I was in Canberra recently, I learned a little bit more about just what it means to be extinct, and it's not quite as clear-cut as you may think.

While attending some meetings for the Biodiversity Heritage Library (specifically, the kick-off meeting for the BHL-Australia project), a colleague, knowing my fondness for dodos, gave me a copy of Decision Point (a monthly magazine of the Applied Environmental Decision Analysis research hub.

In this April 2010 issue was a great article by Tracy Rout, "Dead as a Dodo?" that gave some very interesting statistical models of how scientists can determine if a species is, indeed, extinct.

By using a number of quantifiable metrics (e.g. confirmed sightings, time since last confirmed sighting, commonality of sighting, etc.), the statistical probability that a given species is extinct can be calculated and assigned a value. For the dodo, the likelihood of finding one (outside of my blogposts and avatars of course!) is a tiny 3.07 x 10^-6.

Why is this important? Well, for some species with a high probability of extinction, there's not really much value in this calculation). But for other species, where there is still a statistical possibility of being extant, a range of other financial and environmental management factors come into play.

For instance, if it was known that the ivory billed woodpecker might still be alive, actions could be taken to preserve the habitat and investigate locating the survivors (sadly, the statistical probability of the ivory bill still being extant is a minimal 1.78 x 10 ^-13 - actually lower than the dodo because there were more historic sightings of the ivory bill than of dodos).

So, though there isn't much hope for the dodo or the ivory billed woodpecker, there are still surprises, the so-called "Lazarus Species", thought to be extinct, and in probability extinct, but which rise from the ultimate exit. Rout and his co-authors point out the yellow-spotted bell frog as an example (and don't forget one of my favorite species, the coelacanth).

For more, see the full article:
Rout, TM, D Heinze & M McCarthy (2010). Optimal allocation of conservation resources to species that may be extinct. Conservation Biology. DOI: 10.111/j.1523-1739.2010.01461.x

Huntsman spider (Delena cancerides)

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Originally uploaded by martin_kalfatovic

Shortly after the American group from BHL-US arrived in Canberra for the BHL-Au meeting, the group all noticed that we had an eight legged visitor from the world of Biodiversity at the meeting. The 5-6 inch Huntsman hung around on the curtains for the rest of the meeting. Waving legs at appropriate times duing the meeting, I think that we have full buy-in for the Global BHL from the arachnids at least.

(Gate crasher at BHL-Au meeting: Delena cancerides. Learn more about the Hunstman spider in the EOL: www.eol.org/pages/1207262?image_id=3236892).

Presentation for the National Library of Australia

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Originally uploaded by martin_kalfatovic

While in Canberra, I was asked to give a presentation on the Biodiversity Heritage Library at the National Library of Australia. Here it is:

An Introduction to the Biodiversity Heritage Library. Martin R. Kalfatovic. BHL Australian Node Meeting: National Library of Australia. 4 June 2010. Canberra, Australia.

An Introduction to the Biodiversity Heritage Library

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An Anatomy of a Mass Scanning Project: The Biodiversity Heritage Library

Presentation for the Medical Heritage Library meeting, Rochester, MN.

An Anatomy of a Mass Scanning Project: The Biodiversity Heritage Library. Martin R. Kalfatovic. The Medical Heritage Library Meeting. Rochester, MN. 28 April 2010

An Anatomy of a Mass Scanning Project: The Biodiversity Heritage Library

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BHL presentation for St. Patrick's Day @ SIL

Here's a preview of the Biodiversity Heritage Library update I'm giving at the SI Libraries' staff meeting.

The majority of the images are from Gemeinnüzzige Naturgeschichte des Thierreichs : darinn die merkwürdigsten und nüzlichsten Thiere in systematischer Ordnung beschrieben und alle Geschlechter in Abbildungen nach der Natur vorgestellet werden / ausgefertigt von D. Georg Heinrich Borowski ...
Publication info: Berlin ;bei Gottlieb August Lange,1780-1789, but there are a few thrown in from other sources (e.g. Haeckel’s work, Kunstformen der Natur).

The Biodiversity Heritage Library: Smithsonian Libraries Staff Update

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Presentation at XXVIII Congresso Brasileiro de Zoologia, Belém, Brasil

At the conclusion of the Workshop Coleção de Obras Raras Essencial, I travelled from São Paulo to the northen city of Belém to attend the XXVIII Congresso Brasileiro de Zoologia. Belém was founded in the 17th century and served as a major trading port and capital of the rubber boom of the 19th century. A key gateway to Amazonia, Belém is a fascinating place with an abundance of exotic fruits and freshwater fish.

At the Congress, I presented on the Biodiversity Heritage Library. The Congress was attended by over 2,500 zoologists from around Brasil and the world. My session. which focused on various aspects of scientific literature. My fellow presenters were: Abel Packer, Director of BIREME and Hussam Zaher, Director of the Museum of Zoology, São Paulo. Our session was introducted by Dr. Nilson Gabas, director of the Museu Paraense Emilio Goeldi (in Belém). There was also a presentation by Bráulio Dias, Director of the National Biodiversity Program, Ministry of Environment.

Here's my talk:

Building a Global Library of Taxonomic Literature. XXVIII Congresso Brasileiro de Zoologia. 9 February 2010. Belém, Brazil.

Building a Global Library of Taxonomic Literature

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Workshop Coleção de Obras Raras Essencial, more slides

Here's some quick slides I gave at the Workshop Coleção de Obras Raras Essencial. 3-5 February 2010. São Paulo, Brazil, to explain file format specifications ...

File Format Specifications

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Yet another BHL presentation

I'm in San Francisco to attend the "Internet Archive Leaders' Forum" and also their "Making Books Apparent" meeting. Also doing some other assorted Biodiversity Heritage Library and Smithsonian Library work and visits.

Our BHL group had a very good meeting yesterday followed up by an Internet Archive hosted dinner for out of towners at the St. Francis Yacht Club.

Today the Internet Archive meetings start to be followed tonight by a large press reception at the new Internet Archive headquarters (didn't know they were moving?). Yes, after all these years, IA will be leaving the Presidio for new digs. Where are they and what does it  look like? I'll let Internet search hounds figure that out for themselves, the rest of you can wait to find out later tonight (hint: as one Internet Archiver told me, "we've finally found a building that looks like our logo").

Here my presentation that will occur later today:

“Yet Another BHL Presentation”: The Biodiversity Heritage Library

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Metadata passing in the night: Librarians, taxonomists, and the BHL project

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Originally uploaded by martin_kalfatovic

In a recent post on iPhylo, Rod Page comments on the Biodiversity Heritage Library:

The more I look at BHL the more I think the resource is (a) wonderfully useful and (b) hampered by some dodgy metadata.

I'll gleefully embrace item (a) and and greet (b) with a a mournful shrug of the shoulders that says, "yes, I'm so sorry, we in the library field have failed our users in this regards."

Page goes on to document known metadata problems in the BHL, including this one:

Another issue is that of duplicates. Searching for publications on Rana grahamii, I found items 41040 and 45847. Although one item is treated as a book, and the other as a volume of the journal Records of the Indian Museum, these are the same thing.

You would think that after 200 years or so, librarians would know the difference between a monograph and a serial? Well, of course we do, but the problem is too often, instead of adhering to standards that meet the common goal of access, libraries have cataloged materials to meet their local users' needs, or to provide access at varying degrees of granularity to meet local standards. This wasn't a problem when all metadata was local, but one we've started to move into large scale, collaborative metadata mashups (such as is the BHL), all those individual aberrations from the standards (as well as the typos, non-standard rule application, etc.) have led not exactly to the "train-wreck" that the Google Book Project is faced with, but maybe something worse, a failure to serve the needs of a key user community of the BHL - taxonomists.

---

In 2003, my colleagues Tom Garnett  and Suzanne Pilsk (Smithsonian Libraries), Anna Weitzman (Smithsonian/Botany Department) and Chris Lyal (Natural History Museum, London), began work on the digitization of the Biologia Centrali-Americana. After working with Anna and Chris for a few months (through numerous meetings in a windowless conference room - Chris on speakerphone), it dawned on the library side of the group that for a 150 plus years, we'd been providing our users with great metadata, the only trouble was, it was nearly useless to them and the jobs they were trying to do. When we would say "author" we meant the author of a bibliographic work; when they said author they meant the describer of a taxon (e.g. Homo sapiens L. - the L is the author, Linnaeus). Library metadata didn't cover this; Library of Congress Subject Headings (LCSH) might be applied, but were far to broad or general (Frogs -- North America). We were breaking Ranganathan's Law #4 of Library Science: Save the Time of the User.

Of course, part of the problem was we really weren't talking to our users. At the same time that many of the great library thinkers were working (Cutter, Dewey, Ranganathan, Bowker, Poole, etc. - I'm stretching the timeline here, I know!), there were similar life science indexing projects. Charles Davies Sherborn was compiling the Index Animalium (an index to known animal species described 1758 to 1850). Sherborn lists described species as follows:

cucullatus Struthio, Linnaeus, Syst. Nat., ed. 10, 1758, 155.—[Didus ineptus, ed. 12.]

(note since this is a species index, the name is given species/genus, not the usual genus/species, fyi, this is the dodo, later reclassed as R. cucullatus). Note how bibliographic citation is done: Linnaeus, Syst. Nat., ed 10, 1758. Could you find that a library catalog? Unlikely, taxonomists and librarians were (and are) using totally different rules to describe bibliographic things. Every taxonomist knows that Syst. Nat. is Systema Naturae, but rarely capture all the common abbreviations used in taxonomic literature (of course, taxonomist, being human - mostly at least - they do don't always follow their own rules assiduously, make typos, or just plain whack errors; Sherborn is often very inconsistent in his citations, e.g. sometimes referencing the publications of the United States Exploring Expedition by the individual volume authors and sometimes under Charles Wilkes, commander of the Expedition).

The BHL project has been a great experiment in bringing together librarians, informaticians, taxonomists, and computer scientists. It's great to be in yet another roomful (YAR) of librarians/scientists and hash out these problems. The really great thing is that now were talking to each other, not going our own ways, tending our own gardens, but actually working together to solve these problems and build great projects.

BHL presentation at National Agriculture Library

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Originally uploaded by martin_kalfatovic

Smithsonian Institution Libraries staff members Martin Kalfatovic and Suzanne Pilsk gave a presentation on BHL to staff from the National Agriculture Library, the USDA Agriculture Research Service, the NASA Goddard Space Flight Center, and others.

• The Biodiversity Heritage Library. Martin R. Kalfatovic and Suzanne C. Pilsk. National Agriculture Library: Issues and Answers Seminar. January 30, 2008. Beltsville, MD.