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Connecting Content 

September 13, 2013

Bird specimen photos take flight

Over the past two years, the California Academy of Sciences has been selecting and photographing a selection of finch specimens collected during the Academy’s 1905-1906 Galapagos expedition as part of Connecting Content grant. The Institute for Museum and Library Services funded grant aims to digitize field books and related specimens and allow for the creation of dynamic linkages between these interconnected materials.

We began our project by digitizing the field books created during the expedition which provided a rich picture of collecting on the Galapagos Islands. These accounts allowed us to look inside the personal experiences of the men who for a year and a day lived aboard ship collecting the specimens that now form the core of our scientific collections.  The field books illuminate the fine details of the specimens beyond what the collection tags could capture. These records indicate valuable information such as what the weather was like or the way in which specimens were caught. But the field books were only part of the picture.

After collection, all of the specimens from this expedition were retained by the California Academy of Sciences for study. The finch skins are a heavily used and popular collection, as they represent the species described by Darwin. This collection is not available for loan, not only due to our ongoing research on natural selection, but also because efforts to preserve and support the endemic species of the Galapagos have ended collecting on the islands. This project aimed to provide a look into the specimen collections and provide researchers worldwide with images to use for study and reference.

The California Academy of Sciences is home to 7401 finch specimens collected during  the 1905-1906 expedition, and providing digital access required significant planning. To do this work, we (the Academy’s Library and Archives) teamed up with the Ornithology and Mammalogy department to select a representative sample of over 750 specimens. The selection process was careful and deliberate. Since time and resources were both in short supply, we had to ensure that the specimens photographed for this project showed a representative sample of the diverse traits and characteristics of the birds in our collection. Ornithology researcher Ore Carmi and Collections Intern Logan Kahle took to the task, laboriously opening drawers and making careful observations not only about aesthetic qualities of the birds but also their age, molt, and the season in which they were collected.

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Ore Carmi and Logan Kahle select finches from the 1905-1906 expedition to the Galapagos Islands.

After representative examples of the collection were selected, the finches were photographed in the California Academy of Sciences’ Project Lab, which is a space on the museum’s public floor that allows visitors to see the work we do behind the scenes at the Academy. We are lucky enough to have access to The Big Kahuna, a custom-built digital macro imaging system that allows us to take extraordinarily close-up shots of specimens without sacrificing resolution or depth of field. Our skilled digital imaging assistants took six photographs of each specimen: lateral, ventral, dorsal, and head views, as well as both sides of each collection tag.

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Digital Production Assistant, Kelly Jensen photographing a specimen.

These images were then sent through a quality assurance process to make sure that the images were clear, with the relevant information in focus, and that all of the photos were a consistent quality and size. Once all the images went through the QA process and were normalized, they were then sent to join more than 122,800 vetted photos of animals on CalPhotos, which shares images with the Encyclopedia of Life. This process allows diverse users all over the globe to have access to our collections.

We are excited to share 4,763 new photographs of Galapagos finch specimenswith you and we look forward to continuing to look for new ways to provide improved access to the collections.


Filed under: Uncategorized — ybustos @ 4:37 pm

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


June 7, 2012

Ria D’Aversa, Creating Partnerships through Digitization- Guest blogger

Here at California Academy of Sciences I work on the Global Plants Initiative (GPI) project in the Botany department. Like Connecting Content, it aims to provide scientific resources and materials to the public through an online platform. In the instance of GPI the materials are botanical type specimens, which are, simply put, the specimen cited by the author of any new botanical species. These specimens offer essential information including plant type and description, collecting location, and nomenclatural evolutions. The plant specimens are photographed in the Botany department. The images are then sent to our partner organization JSTOR, who uploads the information to the project page (http://plants.jstor.org). These efforts provide distant researchers, students, and amateur botanists a more accessible opportunity to study plants and botanical history. Many people can now focus on their areas of botanical interest from their home computer instead of traveling to the Academy for research.

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(CAS0003527) Isotype of Scalesia stewartii Riley

At the GPI conference this year I highlighted Connecting Content’s efforts to digitize field collections and field notes of the botanist Alban Stewart from the Academy’s 1905-06 Galapagos expedition. The Botany department holds many important botanical collections from the Galapagos expeditions, including the pivotal 1905-06 journey. In the future I would like to use the ancillary materials (field notes, correspondence, photographs, and drawings) from the Academy archives for the GPI project in collaboration with Connecting Content. It would be a significant intersection between the Botany department and library collections, which would hopefully provide the public with additional resources to dissect and learn from.

Telanthera nudicaulis, Hook. Holotype collected by Col. Alban Stewart on the CAS expedition to the Galapagos Islands, 1905-1906.

(CAS0000313) Holotype of Alternanthera filifolia subsp. glauca J. T. Howell

Research institutions are moving quickly toward new media with most providing their collections online. Both Connecting Content and GPI illustrate how we are establishing partnerships with other institutions in order to provide and promote the best research materials for future scientific study.

-Ria D’Aversa


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

March 15, 2012

Rachel Sargent, CC Intern – Guest blogger

I came into my museum studies program with an interest in digitizing collections.  I had volunteered on a project photographing butterflies, which introduced me to the possibilities of improving collections access while preserving fragile specimens.  Throughout my classes, sections on digital access always piqued my interest, so when I heard about the opportunity with Connecting Content, I jumped on it.  Connecting Content is a unique and exciting project and, it turns out, exactly the kind of project I’m advocating for with my Master’s thesis.

I’ve been investigating online access to digital collections specifically with natural history museums in mind.  It turns out, most natural history museums don’t do much to make their digitized collections findable by the average person.  Even high profile natural history museums present their digital collections through keyword searches that can be difficult to use, sometimes even for research experts.  This is interesting for two reasons: one, natural history museums do want to encourage interest in natural history.  Two, art museums have been making browsing of their collections websites creative, accessible, and even entertaining for years.  My research is focused on applying user interface strategies from art museum collections websites to natural history collections websites.

So where does Connecting Content fit into all this?  It’s at the forefront of what I hope is a trend towards creative and multidisciplinary collections web presences that seek to engage all types of visitors, not just researchers.  By attempting to virtually re-unite specimens with field journals and published literature, Connecting Content will provide a more complete picture of the process of natural history  research to everyone and a unique window into an exciting field for the general public.  Connecting Content is a pilot study and with a little luck more and more innovative projects like this one will be coming to a natural history museum near you.


Filed under: Uncategorized — Christina Fidler @ 10:03 am

January 23, 2012

Rachel Sargent – Connecting Content Fall intern

The California Academy of Sciences brought in Rachel Sargent as the Fall intern for the IMLS Connecting Content grant.  Rachel graduated from the University of Vermont with a BA in Biology and is now enrolled in the John F. Kennedy University Museum Studies Program.  Her work experience includes managing the neurobiology and microscopy lab at Harvard University and volunteering at the Harvard Museum of Comparative Zoology where she participated in a project digitizing butterfly specimens.  In addition to the Connecting Content grant, Rachel is also volunteering in the California Academy of Sciences Ornithology and Mammalogy Department.

Rachel has spent much of the Fall assisting in the development of the technical specifications for the Connecting Content specimen photography.  She has also scanned the Rollo Beck field notebook.  She is now hard at work photographing the Connecting Content finch specimens.  You can see Rachel in action in the California Academy of Sciences Project Lab, located on the West side of the museum public floor.

Rachel in the Ornithology and Mammalogy collection room.

Rachel in the Ornithology and Mammalogy collection room.


Filed under: Uncategorized — Christina Fidler @ 5:47 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

Welcome to Richard and Stephanie, our summer Connecting Content interns

This blog post was originally posted at From the Stacks: the Academy Library blog on June 13, 2011

We are very excited to welcome the new Summer Connecting Content interns to the California Academy of Sciences. Although we are sad to see our Fall intern Josh Roselle leave, he has produced a great foundation for our incoming interns to build on.

Our Information Connections intern is Richard Fischer. Although his internship is with the California Academy of Sciences he will be working at our partner site, the Smithsonian Institution National Museum of Natural History in Washington, D.C. and will be focused on establishing appropriate connections between digitized field books, natural history specimens and the published literature in the Biodiversity Heritage Library

Richard Fischer graduated from the Queens College Graduate School of Library and Information Studies, City University of New York, in May 2011 with a Master of Library Science degree and a Certificate in Archives and Preservation of Cultural Materials. While working on his degree, Richard interned at the Louis Armstrong House Museum Archives, the New-York Historical Society Library Manuscript Division, and the American Museum of Natural History Research Library Special Collections and Archives. He was a Queens College Libraries Special Collections Fellow for the 2010-2011 academic year. Richard holds a BA in English from Rutgers University.

Our Collections Scanning intern is Stephanie Stewart Bailey. She will be working at the California Academy of Sciences and focusing on digitizing fieldnotes and specimens from the 1906/06 Galapagos exhibition for our pilot project.

Stephanie is an interdisciplinary artist pursuing a master’s thesis in museum studies, integrating art with science. Interested in the reuse of museum space through the representation of the physical human body, she strives to make museums accessible to everyone by the means of artistic installations and spaces like the Project Lab at the Academy of Sciences. By holding an internship with the Connecting Content team, she hopes to make connections with dedicated science professionals to further investigate the natural world with hands on experience. She is also excited to investigate possible educational strategies by interpreting this project for the public, through the glass wall of the Project Lab.
With a fascination for the natural world, Stephanie collects specimen from birds to insects and fossils, to incorporate in her artistic process. She holds a BFA from the School of the Art Institute of Chicago in photography and performance art and has worked at the Smithsonian and Göteborg Natural History Museums, and at the International Museum of Surgical Science, Chicago. She is currently a Museum Studies Graduate Student from the University of Gothenburg, Sweden. You can see some of her recent thesis work in natural history museums at http://thebodyappropriate.tumblr.com/

Daina Dickman, Project Manager


Filed under: Interns — ddickman @ 11:04 am
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