ChrisFreeland.com

Made it to Sydney!

2008-10-10T08:17:00.001-07:00

Sydeny Opera House, originally uploaded by chrisfreeland2002.

Feeling great, having a wonderful time. Walked around the Opera House, harbour, & Royal Botanic Garden, then crashed from the jet lag! Sydney is great, except I don't know how to order things. I'll explain later. But, word is good - we're here, we're loving it, we're safe!

Chris

Status of biodiversity services

2008-10-08T06:20:00.000-07:00

The brilliant Rod Page has created a monitoring service for bioinformatics web sites & services (like DiGIR) after he ran into uptime issues with databases at Smithsonian & other large institutions. Check it out at:
http://bioguid.info/status/

His rationale, posted to the Taxacom listserv:
http://mailman.nhm.ku.edu/pipermail/taxacom/2008-October/027827.html

Additional information about Rod's thoughts here, on Twitter:
http://twitter.com/rdmpage
(Tweets as documentation. A first!)

I applaud this idea. As I Twittered (Tweeted?) back to Rod, he has "created an incentive chart for bioinformatics services, like in sales." A little competition is good among peers, and this is the first time I've seen a visual overview of how my servers & sites are doing compared with others in my field. I'm sure this was Rod's goal and he nailed it.

Now, how do we ensure that the service monitor is up?

Riley, In Memoriam

2008-10-07T17:40:00.001-07:00

Riley 2, originally uploaded by chrisfreeland2002.

The Right Rev. Chris Freeland

2008-10-06T05:25:00.001-07:00

Rev. Freeland, Chris & Emily Hoskins, originally uploaded by chrisfreeland2002.

So in addition to running technology projects and writing a cooking blog I also marry people. Chris and Emily are neighbors of ours, and great friends. I offered my services in jest at a dinner party more than a year ago and they took me up on the spot. They held the wedding at my place of employment (Missouri Botanical Garden), which was very cool for me, and absolutely beautiful. The whole event, from processional to last dance, was traditional, yet unconventional, and totally unique - just like Chris & Emily. I was honored & thrilled to play a part in their day.

And maybe someday my partner of more than 10 years and I will be able to do the same. Sure, we can go to California or Massachusetts, but that would carry no legal benefit as we live in Missouri. Someday.

Tennessee v. John T. Scopes Trial: John Thomas Scopes

2008-09-29T19:08:00.001-07:00

Tennessee v. John T. Scopes Trial: John Thomas Scopes, originally uploaded by Smithsonian Institution.

See that guy up there? He's my hero. He taught what he believed to be true, in spite of the social pressures against doing just that. He is John Scopes, the teacher at the center of our country's first (but unfortunately not last) assault on science and evolution.

The Smithsonian Institution has just posted rarely seen pictures from "The Scopes Monkey Trial." From Wikipedia:

John Scopes, a high school teacher, was charged on May 5, 1925 with teaching evolution from a chapter in a textbook which showed ideas developed from those set out in Charles Darwin's book On the Origin of Species. The trial pitted two of the preeminent legal minds of the time against one another. Three-time presidential candidate, Congressman and former Secretary of State William Jennings Bryan headed up the prosecution, while prominent trial attorney Clarence Darrow spoke for the defense.

I'm so glad that the Smithsonian (and their fabulous Library) has made these pictures widely available through Flickr. I'd like to think our country is past this assault on reason, but I'm afraid that's simplistic thinking. Kudos to the Smithsonian for making these historical documents available in an unbiased and documentary fashion through an emerging social network. This is a model that all museums and libraries should follow.

Death by PowerPoint

2008-09-25T05:58:00.000-07:00

Death by PowerPoint

View SlideShare presentation or Upload your own. (tags: powerpoint ppt)

This should come bundled with PowerPoint. Throw out the Help docs and just put this in. Or, you have to click through every slide before you can use PowerPoint, like an activation or something.

It's just such good information for presenters. This presentation I gave last year is probably the closest to that ideal:

Plays Well with Others, or What I’ve learned as a data provider in an interoperable world.

View SlideShare presentation or Upload your own. (tags: mcn bhl)

Plays well with others, or What I’ve learned as a data provider in an interoperable world. Museum Computer Network Annual Conference, Chicago, IL. 2007.

Report on the United States and Mexican Boundary Survey

2008-09-23T20:05:00.000-07:00

http://books.google.com/books?id=5dx3MqsSdCgC

New EOL Flickr group

2008-09-18T05:12:00.001-07:00

Stellar Sea Lion, originally uploaded by polly.snodgrass.

The Encyclopedia of Life has opened a new Flickr group as a way of bringing images into their site at www.eol.org. They are using machine tags to describe the taxonomic classification of the species in the photo, as in these tags applied to the image above:

taxonomy:kingdom=Animalia
taxonomy:phylum=Chordata
taxonomy:class=Mammalia
taxonomy:order=Carnivora
taxonomy:family=Otariidae
taxonomy:genus=Eumetopias
taxonomy:species=E. jubatus
taxonomy:binomial=Eumetopias jubatus
taxonomy:trinomial=Eumetopias jubatus otariinae
taxonomy:common=Stellar sea lion
geo:lat=60°7'N geo:lat=60°7'N
geo:lon=149°27'W geo:lon=149°27'W

Nice photo, good metadata. But will this information be vetted? How can I trust Flickr user polly.snodgrass' opinion? She may well be the world's foremost expert on Eumetopias, but those credentials aren't anywhere on her profile...little is, in fact, which makes me assume this is a facade account for the EOL'ers trying things out. No worries, I do the same (here for plant images, here for book images). If not, all apologies, Polly. Great photos!
Update 9/29/08: Polly is a real person!

Don't get me wrong, I applaud the integration of Flickr and its enormous, enthusiastic community into EOL - very, very smart move. But the anonymity with which accounts can be created gives me pause. Who will vet these photos, if anyone? I accept that when I go to Flickr and search for a species I might get bogus results - if I find a photo I'm going to do a comparison search on Google Images or try to find a specialist image database to confirm that the image is, in fact, for the species in question. However, I think I want more from EOL. I want to go to EOL and have a reasonable measure of confidence that an image they put on the Stellar Sea Lion page is actually a Stellar Sea Lion.

One other issue is the ability as a Flickr user to add tags to photos that allow it (rather, photos the photographer has allowed to be tagged). For instance, I just tagged that lovely Stellar Sea Lion image with my favorite species, taxonomy:binomial=Zea mays:

http://www.flickr.com/photos/30576522@N03/tags/taxonomy%3Abinomial%3Dzeamays/

In case Polly gets wise to this absolutely, completely wrong tag I applied to her photo, I grabbed a screen shot showing my inappropriate tagging.

If the information in these tags is treated as truth, how long before that sea lion image shows up on the EOL page for Zea mays?

I expect the EOL developers are turning this kind of vetting back onto the community of users, or enthusiasts around a particular species, to notify or comment on factually wrong or inappropriate images (egads...who will be the first to post a raunchy pic tagged taxonomy:binomial=Homo sapiens??). I worry how well that approach will work.

Sure, the pages for Great White Shark or Giraffe will probably have an active community of editors and will be able to easily weed out these "sea lions as corn" kinds of errors. But what about the little critter without a community? Who's going to vet the images and their validity when some prankster uploads a picture of one obscure species and tags it as another? Maybe that won't happen, but this scenario is certainly one that any scholarly repository faces (like EOL and our own Tropicos) when considering incorporating Flickr or Google images to augment their own vetted content. How do you harness the crowd and still keep it authoritative?

Chris Freeland
cfreeland27@gmail.com

2008-09-09T13:04:00.000-07:00

Terms used in my cooking blog, Countrypolitan Cooking, courtesy of Wordle.

John McCain: "The Mavrick"

2008-09-05T05:06:00.001-07:00

Teach an illiterate adult to read, originally uploaded by chrisfreeland2002.

This sign cracked me up during John McCain's speech at last night's Republican National Convention. It was shown just a few seconds after John McCain's charge to "Teach an illiterate adult to read."

Other people thought this was funny, too...check out the Mavrick group on Flickr!

So, it had to be done. John McCain: The Mavrick

Chris Freeland, Hutsonville High Class of '76 Vice President

2008-08-19T22:34:00.001-07:00

1976, originally uploaded by chrisfreeland2002.

Thanks, yearbookyourself.com!

Brent Fry & me

2008-08-18T05:11:00.001-07:00

(l-r) Brent Fry & me, originally uploaded by chrisfreeland2002.

Brent A. Fry

August 12, 1975 - June 27, 2008

Visit his tribute on YouTube
Obituary
Brent's MySpace page

Home Sweet Trailer

2008-07-25T05:25:00.001-07:00

Home Sweet Trailer, originally uploaded by chrisfreeland2002.

This is the trailer I lived in when I was 6mos. to 3 yrs. old. We built a house on the site the summer of my 3rd birthday and someone came and drove the trailer away. It was odd to watch the only place you knew as 'home' leaving you behind.

Plate 38

2008-06-20T05:02:00.001-07:00

Plate 38, originally uploaded by botanicus_mbg.

From Flickr:
Illustration from Köhler's Medizinal-Pflanzen in naturgetreuen Abbildungen mit kurz erläuterndem Texte : online at the Biodiversity Heritage Library.

View page in book.

Publication Details:

Gera-Untermhaus :Fr. Eugen Köhler,[1883-1914]

Authors:

Brandt, Wilhelm, b. 1879.

Gürke, M. 1854-1911.

Köhler, F. E.

Pabst, G. d. 1911.

Schellenberg, G. b. 1882.

Vogtherr, Max.

Scientific Names:

Papaver

Common Names:

poppy

Usage:

Contributor:

Missouri Botanical Garden

Tech Honesty

2008-06-09T18:52:00.001-07:00

Tech Honesty, originally uploaded by chrisfreeland2002.

We have no idea what we are doing today!
Actually, we just installed a new ticketing system that we are still learning. Thanks for bearing with us, the view is worth it!

I'm not sure whether to applaud the folks who made this sign for their honesty or cringe that it was created in the first place. Why do ticketing/POS implementations so frequently stumble out of the gate??

BHL Technology Overview

2008-05-21T14:05:00.001-07:00

2008-05-06-dscn3681, originally uploaded by martin_kalfatovic.

Biodiversity Heritage Library (BHL) Technology Overview. Chris Freeland. Smithsonian Institution Office of the Chief Information Officer. May 6, 2008.

Paper published on geocoding LCSH

2008-03-25T05:50:00.000-07:00

The paper we submitted to The Code4Lib Journal was published March 24, 2008:

Abstract:

Reusing metadata generated through years of cataloging practice is a natural and pragmatic way of leveraging an institution’s investment in describing its resources. Using Library of Congress Subject Headings (LCSH), the Biodiversity Heritage Library generates new interfaces for browsing and navigating books in a digital library. LCSH are grouped into tag clouds and plotted on interactive maps using methods available within the Google Maps Application Programming Interface (API). Code examples are included, and issues related to these interfaces and the underlying LCSH data are examined.

By Chris Freeland, Martin Kalfatovic, Jay Paige, and Marc Crozier

http://journal.code4lib.org/articles/52

Literature citations supporting Jaws

2008-03-04T04:48:00.001-08:00

Or, What the heck are Great white sharks doing in the vicinity of New York City??

Since I'm the tech lead for the Biodiversity Heritage Library, I get to review a good sampling of our digitized content as I'm testing out new functionality. It never fails to amaze me the interesting things I stumble across, and yesterday's discovery was no different.

I was checking out language on our Developer Tools section and clicked on the example link to view the discovered bibliography for Carcharodon carcharias, the Great white shark:
http://www.biodiversitylibrary.org/name/Carcharodon_carcharias

About halfway down the list a title caught my eye:
"Fishes of the vicinity of New York city"
http://www.biodiversitylibrary.org/page/1634152

Great white shark + Fishes of the vicinity of New York city = Yikes!!

Naturally, I was intrigued, so I viewed the page on which Carcharodon carcharias had been found. It had this entry:

14. Carcharodon carcharias (Linn.) White Shark. "Man-eater."
Accidental in summer. June to July 14, 1916.

The book was published in 1918, and here the author, John Nichols, is documenting an occurrence of a Great white shark - a "Man-eater" - in the New York area during the summer of 1916.

That rang a bell - it made me think of some show I'd seen on Shark Week or the History Channel about historic shark attacks. So, I Googled "great white shark 1916 new york" and got this as the first result:

Jersey Shore shark attacks of 1916 - Wikipedia, the free encyclopedia

It wasn't until I glanced over the content that it clicked - this is the true story that inspired Jaws. Jaws!! I was born a month after it came out, so I literally grew up in the wake of that film and its impact on popular culture. It defined the summer blockbuster, made a star out of Steven Spielberg, and yet also did something not so good - it further perpetuated the myth of the Great white shark as a merciless killer...a myth that grew into legend with the real life occurrence of a Great white shark in the vicinity of New York city in the summer of 1916; an event that was documented in Nichol's book.

As I read through the article in more detail I realized there were several mentions of Nichols giving his professional opinion, as an ichthyologist from the nearby American Museum of Natural History, about this rare and unusual (and unfortunately deadly) occurrence. Being a WikiCitizen, I wanted to put my knowledge of this digitized book into the Wikipedia article since it documents this sensational event within a scholarly publication. I added the title to "Further Reading" and updated the "Revising science" section to include a reference to Nichols' documentation of the occurrence. Within 2 hours my addition had been further refined. You can see that another WikiCitizen and I are wrangling over some phrasing, but regardless, I've made my contribution. I've helped - hurrah!

My point here is not to keep perpetuating the myth of the Great white shark as a "Man-eater," because hopefully by now that myth has been debunked and everyone knows that Great white sharks are just perfectly streamlined predators at the top of their game - if you put up a cage in my natural habitat, led me to it with food, then poked me with a stick I might try to bite your arm off, too. No, my point is to illustrate but one of many events where science and pop culture overlap, and how efforts like the Biodiversity Heritage Library can help illuminate them.

This factual event was widely reported in the popular press and was a big sensational story of its time. It also made its way into scholarly publications, like Nichols' biological survey. Using tools we've developed for BHL, I was able to identify some unusual results in the discovered bibliography for Carcharodon carcharias that made me connect stories I'd heard before in a new way and motivated me to learn more on a particular topic. Further, observing this unusual result got me to contribute this tiny, tiny bit of information to the wider universe of knowledge that is Wikipedia and the greater internet.

And that, I think, is really, really cool.

An aside: Once the Encyclopedia of Life allows user contributions, I'll be sure to muss up that page as well with this tiny, tiny bit of information. By the way, it's great to see our bibliography in EOL, including the Nichols reference!

Another aside: That text was copied directly from the OCR text, showing that in some cases the OCR can be quite good for historic materials (this book was published by the American Museum of Natural History in 1918).

The Encyclopedia of Life, No Bookshelf Required

2008-02-26T05:27:00.000-08:00

Science

The Encyclopedia of Life, No Bookshelf Required

By CARL ZIMMER

Published: February 26, 2008

Scientists are writing the Book of All Species on the Web, in the hopes it will be useful to scientists and nonscientists alike.

The Biodiversity Heritage Library is mentioned in the article as "scanning millions of pages of scientific literature, which computers are text-mining to add more information to species pages."