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Connecting Content 

January 18, 2013

Kendra Hay, Information Connections – Guest blogger

For the past four months, I have had the pleasure of working with the California Academy of Sciences as Information Connections Research Intern on Connecting Content—a project to digitize field books and natural history collections from seven partnering institutions, generate metadata for each, and link these digitized collections to published work in a variety of ways. My primary task has been to review scanned journals and letters for taxa names, conduct research to verify the scientific name of those taxa identified, and enter said names into the Biodiversity Heritage Library (BHL) catalog. In doing so, I sought to identify idiosyncrasies found in the various types of materials, standardize notation methods for each identified, and create a workflow for future interns and volunteers.

To date, I have worked on E.W. Gifford’s Galapagos Bird journals from 1905 and 1906 (California Academy of Sciences), the John Torrey correspondence from the 1830s-50s (New York Botanical Garden), the journals of Walter Deane from 1882 and 1891 (Harvard University Herbaria), the George Engelmann papers from the 1850s, 1860s and 1880s (Missouri Botanical Garden), and the Warren Manning correspondence from 1894-98 (Harvard University Ernst Mayer Library). Altogether, I have reviewed 2,049 pages and identified over 10,200 taxa and common names.

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As a graduate student studying in the field of Library and Information Science, I found this project of particular interest. Establishing context between library and other collections or ‘connecting content’ is the wave of the future; librarians and archivists, like so many other professionals, must begin to grapple with this challenge. This project has been an amazing opportunity to explore how the partner institutions are beginning to approach these questions, and I look forward to seeing the new connections that the project generates.

- Kendra Hay


May 1, 2012

Rollo Beck Galapagos Expedition Journal Now Accessible Online

Excerpt from the Rollo Beck Galapagos expedition journal

Excerpt from the Rollo Beck Galapagos expedition journal.

The California Academy of Sciences Library is pleased to announce that The Rollo Beck Galapagos Expedition Journal is now accessible online via the Biodiversity Heritage Library.  The Beck field notes are the first test submission to the Connecting Content field note scanning project. Their successful inclusion into BHL marks many months of planning, effort, and collaboration between the Academy staff and our amazing partner institutions.

The Connecting Content project, made possible by an IMLS National Leadership Grant, involves digitizing field notebooks and natural history specimen collections, making the results available free for open access, and testing methods to create links between the items. This is the first step in an effort to create linked digital item-level access to archival resources, published literature, and biological data. This project has come together through the combined efforts of multiple institutions and with rigorous planning about how best to create and disseminate content that is discoverable, enduring, and openly accessible.

Rollo H. Beck was the leader of the 1905-06 expedition, and his style of field note taking provided a broader overview and unique perspective of the expedition, which differed from the very specific specimen-collecting notes of the other members of the team. The field notes are quite fragile and much care was needed to scan each page on our flatbed photo scanner. A highlight for those doing the scanning was finding the page that describes the first news of the 1906 earthquake that destroyed much of San Francisco and nearly all of the Academy of Science’s collections. The specimens that the expedition brought back from the Galapagos formed the core of the new Academy.

After digitization, we had to package the materials for submission to the Internet Archive and ingest into BHL by creating a MARC (MAchine- Readable Cataloguing) record for each item. (We’d like to recognize and send a HUGE thank-you to the amazing and incredibly bright cataloguers who have toiled over this effort! Michelle Abeln at Missouri Botanical Gardens, Lisa Studier at New York Botanical Gardens, Chris Robson at Harvard University Herbaria, and our own Stella Tang here at the California Academy of Sciences, we couldn’t do this without you!) These records are then combined with a spreadsheet containing page-level metadata, and the corresponding digital files of the scanned pages are submitted to the Internet Archive, and ultimately into the Biodiversity Heritage Library.

We are now in the process of preparing several other field notebooks and our digitized specimens for our pilot scanning project, and have invited our partner institutions to begin the process of uploading their field notes in preparation for ingest into the Biodiversity Heritage Library. After the materials are scanned, input into our database, cataloged, exported, and delivered via BHL, we will use the extrapolate metadata to experiment with mash-ups and make connections between names, dates, localities, and other contextual information, published materials, and specimen data. We hope you enjoy our first submission and keep checking back often for news and progress!

-Yolanda Bustos and Kelly Jensen


Filed under: Digitization,Fieldnotes — ybustos @ 12:19 pm

September 9, 2011

Connecting Content Goes on Tour

Although my Information Connections Research at the Smithsonian formally concluded at the beginning of August, that is when the real excitement began as I took Connecting Content on the road and presented the project and my particular work on it to a variety of different audiences.

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First up was the hometown show, a brown bag lunch at the Smithsonian National Museum of Natural History. This was no warm up though, as the event had been announced Museum-wide, and the attendance was high enough to warrant the use of two conference rooms in the Natural History Library. As this audience was a strongly scientific one, I focused my discussion on how the archival processes central to Connecting Content seek to make primary source biodiversity materials more broadly accessible and richly connected to supporting information. I fielded several excellent questions from the extremely intelligent audience that really helped me clarify and further conceptualize the project. It was a great finale to a great summer working with Field Book Project Manager Carolyn Sheffield and Botany Department Collections Manager Rusty Russell.

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Next on my itinerary was another familiar setting, the American Museum of Natural History Research Library in New York, where I was an intern on their Archive Project for the first half of 2011. Their Archive Project consists of a Cataloging Hidden Collections component and a Preservation Risk Assessment Survey component that work together to enhance archival control and accessibility to their wonderful collections. Here the audience consisted of Research Library staff and current interns, and I placed Connecting Content in the framework of their on-going Archive Project and we had a really active back-and-forth discussion about implementing plans in natural history archives and the various successes and challenges that all of our projects face.

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My final destination, at least thus far, in discussing the research I conducted in Washington this summer on behalf of the California Academy of Sciences, was the Society of American Archivists National Conference, dubbed Archives 360 this year, in Chicago. I represented Connecting Content at the SAA Research Forum, a day long event in which practitioners report on archival research projects that are currently in process. Though I was a touch froggy by this point, a microphone on the podium saved the day, and I greatly enjoyed the opportunity to deliver a 30-minute platform presentation. It was very interesting to shift to a general archives audience as opposed to a sceintific audience or natural history archives audience, and I made sure to thoroughly and clearly explain the technical and scientific facets of the project. I was also able to meet California Academy of Sciences Library Archivist Danielle Castronovo, and we had a very nice time discussing the different possibilities for this exciting project moving forward, while enjoying some SAA-provided ice cream bars. An appropriate end for an appropriately weary throat after a mid-late August tour of speaking engagements.

I very much enjoyed having the opportunity to represent Connecting Content and report on my Information Connections Research.

– Richard T. Fischer, Information Connections Research Intern



Filed under: Fieldnotes,Interns — Christina Fidler @ 10:04 am

August 16, 2011

Connecting Content visits NightLife

This blog post was originally posted at From the Stacks: the Academy Library blog on July 21, 2011

Thursday night, July 14, was the Academy’s ‘Crafty’ themed NightLife which featured an array of booths from Bizarre Bazaar selling hand-made items from local artists. The Library and Archives had a chance to discuss Connecting Content, an IMLS grant-funded project, and to talk about collection theory, both historically and within contemporary situations. Of course, our visitors were enacting their own ‘collecting’ by selecting objects and purchasing them from the Bizarre Bazaar booths, perhaps adding these objects to what could be considered a collection at home on their walls, in their drawers, or even choosing to wear them.

There were two parts of this display. First, a table was set up next to the Project Lab that displayed Ole Worm’s (1588-1654) book Museum Wormianum, showing his “cabinet of curiosities” in Copenhagen, finches from the Galapagos Islands often referred to as “Darwin’s finches,” and a photograph of the 1905-06 Academy of Science Galapagos expedition team. Visitors approached this display and were given glimpses into why these people collected their specimens, with Project Manager Daina Dickman available to provide additional information. The second part to this display was the Collections Scanning Intern Stephanie Stewart-Bailey with a desk drawer full of ‘curiosities’ on loan from the Naturalist Center. She wandered around the museum floor having conversations with visitors and playing a guessing game of “what do you think this object is?” Through this display Stephanie hoped to introduce the idea to visitors that collecting occurs first due to curiosity.

This game fostered the idea that collectors found these animals and other such specimens, curious. The second step after noticing something was curious was to draw out further knowledge from them. Stephanie then showed the visitors the table with the Library and Archives display of examples of historic natural history collections.

By participating in NightLife, the Library and Archive’s Connecting Content project was shown directly to the public, initiating participatory discussions with visitors over collection theory and how some projects at the California Academy of Sciences deal with both historic and contemporary collecting methods.

–Stephanie Stewart-Bailey


Filed under: Fieldnotes,Interns,Specimens — ddickman @ 11:08 am

Connecting Content, Information Connections Research Update

This blog post was originally posted at From the Stacks: the Academy Library blog on July 18, 2011

Greetings from the nation’s capital! I have been working on the California Academy of Sciences Connecting Content project as the Information Connections Research Intern, based at the Smithsonian Institution National Museum of Natural History. I have been conducting research for the past six weeks into the information connections between archival scientific field books, digitized scientific publications, and natural history specimen collections. I’d like to introduce the nature of the research I’m doing and report on some of my findings.

Field books containing specimen data and observations, publications resulting from formalized post-expedition research, and natural history specimen collection databases comprise an information relationship with multiple points of entry. The connective thread may be followed in any number of directions depending upon how the sources are cross-referenced. For example, a specimen number (“CAS 3156”) in a CAS Collection Database could be searched in JSTOR to see if it has been cited in a publication. Assuming it has been cited, one could proceed to search the collector’s field notebooks, to see if the same specimen is recorded in the field.

Galapagos Penguins. Gerald and Buff Corsi © California Academy of Sciences

I have discovered that beginning with the field book itself, surveying its format and contents for geographical location, dates, and presence of specimen numbers, followed by searching the relevant author or curator in JSTOR or the Biodiversity Heritage Library (BHL) quickly narrows down whether there is a direct link between a scientific publication and an expedition field book. If such a link exists, then searching the relevant natural history specimen collection database for holdings which can be verified as the same specimens described in the original field book is the next step.

Of the different types of matches between these sources that arise through this research methodology, the three of greatest interest to the research goals of the project are the direct three-way match, the indirect three-way match, and the ambiguous possible three-way match. A direct three-way match describes an information relationship in which collected specimens are recorded with numbers in a field book, those same numbers, along with the same locations and dates, are cited in a digitized publication, and an institutional specimen collection database includes the same specimens, citing the original field book number.

To illustrate how that works, here is a selection from a yet to be digitized field book created by the 1905-06 Galápagos Expedition ornithologist, Gifford: “December 8 1905, Duncan (Pinzon) Island: Spheniscus mendiculus [1646]. I shot one in the forenoon which was swimming and diving about the little cove…”. The date, location and a specimen number are given in this primary collecting document. After a search of the BHL, a publication authored by Gifford titled The Birds of the Galapagos Islands describes the following encounter in his section on Spheniscus mendiculus, or Galápagos penguin, as having occurred on December 8 1905:

Giffords Publication

The specimen number has a prefix CAS, referring to its number in the California Academy of Sciences Ornithology Collections. One of the frequent complications in my information connections research is keeping track of individual collector numbering systems and the numbering systems of the institutions that later accession the specimens. Luckily, the collection databases at times do an excellent job of preserving the original collector specimen number along with its number in the scope of all CAS bird specimens.

CAS Ornithology Collections Screen Shot Gifford

Since Giffords’ number 1646 is traceable with geographic and location verification from the field book, to a publication, to a collection database, it represents the information relationship I have termed a direct three-way match. As you may guess, things do not often line up quite this nicely, and the indirect three-way matches, ambiguous possible matches, and nil matches are much more frequent occurrences. However, that the life of a collecting event on an expedition over 100 years ago is traceable via modern technological tools is an exciting development in the use of primary sources in the sciences, and as more of these field books are cataloged and digitized this rich connective information will be integrated smoothly into biodiversity research.

- Richard Fischer, Information Connections Research Intern


Filed under: Fieldnotes,Interns — ddickman @ 11:06 am

Galapagos Islands 1905-1906 Digitization Project Update: Imaging Finch Specimens

This blog post was originally posted at From the Stacks: the Academy Library blog on May 12, 2011

I am almost at the end of my 16-week internship at the Academy Library, and I am excited to have started imaging finch specimens. This is part of the Connecting Content project, which has been made possible with grant funding from the Institute of Museum and Library Services. This project involves digitizing and providing access to expedition field notes and avian specimens from a 1905-1906 expedition to the Galapagos Islands. At the end of the project the finch specimen images will be available through the Encyclopedia of Life.

During the first few months of the project I worked on digitizing the expedition field notes while we prepared for imaging the finches. A lot of planning and experimenting had to be done before we could begin, and I learned a lot along the way.

The finch collection from this expedition consists of over 4,000 specimens; this includes numerous species collected from many of the islands in the Galapagos Archipelago. Before beginning this project, the project staff had to figure out how we would select the 1,000 specimens that will be imaged as our sample from this collection.

Through our selection process we want to provide researchers and users with a balanced and deep collection, so we are imaging a proportional sample of each species, including an equal sampling of male and female specimens, from every island where they were collected.

One of the goals of this project is to provide researchers with the ability to view these images online and conduct research remotely, so it was important that we considered image quality, camera angles, and image uniformity. After discussions with staff scientists and researchers we are taking six images of each specimen, from different points of view. This includes shots of the ventral (belly), dorsal (back), lateral (side), and head/beak of the finches, as well as the front and back sides of the collection tags. The collection tags are important as they contain information such as the genus, species, collection date, specimen number, and the island where they were collected.

The bird specimens must be handled carefully. Although they are quite rigid, some parts of them may break or come off with rough or excessive handling, particularly their feathers and legs. Each specimen is gently placed on a uniform background with a ruler and a color bar before the photograph is taken. The color bar allows us, as well as the user, to gauge color representation and accuracy.

The camera that we are using for this part of the project is a Canon E05 5D with a 50mm lens. It creates highly detailed and crisp images. One can zoom in and view incredible detail, including individual strands of feathers, and even dandruff particles. The camera is attached to a custom-built mount, and is affectionately known as “the Big Kahuna.” This equipment was provided by Academy curator of Herpetology Bob Drewes. You can read about his ongoing work teaching about and studying the incredible biodiversity of Sao Tome and Principe on his blog.

It has been fun and a great learning experience to work on this project. Although my internship is coming to an end in a couple of weeks, I am certain you will be hearing more about the progress of this exciting project from the staff and other interns over the next couple of years.

Josh Roselle


Filed under: Digitization,Fieldnotes,Interns,Specimens — ddickman @ 11:02 am

Connecting Content: Galapagos Islands 1905-1906 Expedition Field Notes Digitization, Project Update

This blog post was originally posted at From the Stacks: the Academy Library blog on March 24, 2011

Since my last blog post I have finished scanning the field notes of Alban Stewart, the expedition botanist, and I have moved on to Washington Ochsner’s geology field notes. The pages are unbound and very brittle, so I have to be quite gentle with them and handle them as little as possible.

During the year the expedition was in the Galapagos, the scientists went to several islands multiple times. It seems that after the expedition these notes were reordered by island, so I check closely while scanning to make sure that the pages are not out of place.

Ochsner’s geology journal is divided into four sections:

The first, and largest section, is comprised of notes and general observations. It describes geological formations, strata, and rock composition. In this section he often describes a formation or an island’s origin, and explains how it may relate to other islands in the Galapagos chain. This section also contains interesting figures and maps to help visualize the descriptions. The maps and figures show rock strata and geological formations— such as lakes, cliffs, craters, and volcanic formations—with numbers or alpha-notations connecting features to the notes. These have been some of my favorite parts of the notes. I enjoy cartography, particularly old maps, and it is fascinating to read through Ochsner’s notes and connect them to his drawings.

Ochsner called the second section “occasional ideas.” These seem to be general thoughts that did not fit in with the notes on specific islands. It also contains citations for literature related to his observations.

The third section is a rock specimen catalog. This section contains a list of rock specimens Ochsner, and other members of the expedition, collected on the various islands. He assigned the specimens a unique catalog number and also a number relating to where they were found.

The final section consists of photograph metadata. This is descriptive information that corresponds to images taken during the expedition.

I am almost finished digitizing Ochsner’s field notes, and, after receiving further training with the imaging hardware and software, I will probably begin taking high resolution digital images of finch specimens. It should be lots of fun!

Josh Roselle


Filed under: Digitization,Fieldnotes,Interns — ddickman @ 10:59 am

July 22, 2011

Connecting Content: 1905-1906 Galapagos Expedition Field Notes

This blog post was originally posted at From the Stacks: the Academy Library blog on March 11, 2011

The California Academy of Sciences was recently awarded a National Leadership Grant from the Institute of Museum and Library Services for a project called Connecting Content. This pilot project involves digitizing and providing access to expedition field notes and avian specimens from a 1905-1906 expedition to the Galapagos Islands, and I get to create the digital images! At the end of the project we will make the field notes available through the Biodiversity Heritage Library and specimen images available through the Encyclopedia of Life.

josh_inside_lab

Besides the scientific and research value of this collection, it is also one of the Academy’s oldest collections. While the expedition was in the Galapagos the 1906 Earthquake devastated San Francisco and destroyed the old Academy building along with many collections. The Galapagos expedition’s field notes and specimens became part of the foundation materials for the new Academy.

I have begun scanning the field notes of Alban Stewart, the expedition botanist. The notes are divided into three sections. In the first section Stewart tracked plant species he encountered and recorded them using a numbering system, and he provided brief notes about them.

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The second section is composed of his journal. In the journal Stewart describes in greater detail the various species and locations of plants found on the many islands of the Galapagos Archipelago. Stewart would survey an area and describe species he found and note any particulars of their surroundings, including if they were abundant or scarce. Stewart’s journal traces the biodiversity of the flora in relation to other islands and continental regions. In his notes he often mentions other regions where these plants grow, and whether or not a species can be found on other islands in the chain.

The final section is a chart of air and water temperature readings. I was surprised to find that the water and air temperature readings were often very similar.

I am working in the project lab on the first floor, across from the rainforest dome. It is a high-tech lab where visitors can walk by and view ongoing projects and research being conducted live. It has been kind of fun to scan, view, and process the images on three large computer screens while visitors can peer in through the glass. We set up a display with some related artifacts from the expedition—such as a pith helmet, some of the field notes, an old camera, and an expedition group photograph—for visitors to view as well so that they can get an idea of what we are doing. A few special tours have come through the lab and it has been great to interact with them and explain the project, why it is important, and what we hope to accomplish. It is quite rare in the archive world to have this much engagement with the public, so I am hopeful we can help demystify archives a little and show people what we are doing to make important primary materials more accessible.

josh_outside_lab


– Josh Roselle


Filed under: Digitization,Fieldnotes,Interns — ddickman @ 11:40 am

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