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Connecting Content 

June 17, 2014

The California Academy of Sciences Archives is proud to announce that we have digitized five field books from the collection of botanist and former California Academy of Sciences Curator of Botany, John Thomas Howell.

In a cooperative effort to publish primary sources, the California Academy of Sciences Archives has completed the digitization of five additional field books as a part of Connecting Content, a National Leadership Grant funded by the Institute for Museum and Library Services.  Field books record the time, date, location, and circumstances under which a specimen was collected. These detailed notes are used by researchers to retrace the steps of an expedition, understand the methodology behind a collecting trip, and confirm the details of a specific encounter.

 

Connecting Content sought to create contextual links between field books, research specimens, and published literature. In our first round of scanning, we digitized content from field books created by the esteemed researchers Alban Stewart, Rollo Beck, Edward W Gifford, FX Williams, Joseph Hunter, Joseph Slevin, and Washington Henry Oschner during the Academy’s 1905-06 expedition to the Galapagos Islands. These scanned volumes can be found at the Internet Archive and the Biodiversity Heritage Library.

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Rollo Beck photographing a Booby on the Academy’s expedition to the Galapagos Islands circa 1905-1906. Beck documented his collecting activities in the field books, which we have recently published on BHL.
C.A.S. Lantern Slide No. 1084. © California Academy of Sciences

 

We also photographed a representative selection of bird specimens collected during this expedition, and published them online at CalPhotos and the Encyclopedia of Life. Similarly, our partners at the Harvard University Herbaria, The Missouri Botanical Garden, The Museum of Comparative Zoology at Harvard University, The New York Botanical Garden, and the Smithsonian Institution digitized field books and unpublished primary source materials, related specimens, and published texts.

 

In the interest of broadening our digitized collection to better represent our local holdings, we hired a brave and over-qualified intern called Justin Wasterlain to digitize five field books from former Academy Curator of Botany, John Thomas Howell. He was also tasked with the shared duty of painstakingly teasing out taxonomic names from field book entries on BHL. I asked him to write a bit about his experience:

 

Since late January, I’ve had the opportunity to work as an intern for the Connecting Content grant project digitizing the field notes of Mr. Howell. As of writing this, we have digitized five volumes spanning from August 1936 until May 1943. Within these books, there are entries for over 5,240 species he collected mostly within the Bay Area and Northern California. Sounds like a lot, right? It’s only a drop in the bucket. The Academy archives hold and additional 64 notebooks of his field notes spanning the collecting years of 1923 through 1984. And this is only one of a multitude of field books created by pioneers of scientific exploration and held by the California Academy of Sciences!

John Howell conducting field work, 1932.
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© California Academy of Sciences

 

The process of digitizing these books began with scanning them in the Library’s Corsi Digital Lab. As the notebooks were in good condition, not particularly fragile, and created to lay relatively flat, we were able to use a flatbed scanner as opposed to a cradle scanner. Anyone who has made a photocopy will be familiar with that process. But imagine doing so with a delicate, unique historical document. It can be a bit nerve racking at first. Which is good because it forces you to be extremely cautious and precise.

Once scanned, the file is checked to make sure all the basic metadata is appropriate (at this stage, that’s just to say that the file size, name, and type are all what they need to be). If there are any adjustments that need to be made to the image like a closer crop or the like, these were performed in Adobe Photoshop. From there, its final form is stored on the Academy’s servers as a high quality tiff file.

 

After all the books were scanned and saved on the computer, we uploaded the files to Macaw. Macaw is a metadata collection tool developed by the Smithsonian Institution Libraries. For our purposes, it allows us to add page level metadata to the entirety of the books. This includes things like the orientation of the page (verso/recto), the content of the page (cover, blank, text), the date of the work, etc.  After page level metadata  has been added to the scanned images, Macaw allows us to push the complete digital volume to the Internet Archives and the Biodiversity Heritage Library, where the digitized volumes can be accessed and enjoyed the world over. By uploading the content we have scanned into the Internet Archives and Biodiversity Heritage Library (BHL), it allows far greater access to the material for researchers and the general public than what the physical object allows. Were you to perform a search for “John Thomas Howell botanical collecting notebook” in BHL, there it is- accessible to anyone with a connection to the internet.

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Click to enlarge.
Excerpt from Howell field notebook, volume 37, page 104.

 

This is only half the process though. In order to make the content searchable, we have labouriously transcribed and verified the scientific names found within the volumes through BHL’s administrative portal. This will make the material searchable and allow for cross referencing the other content within BHL. Moreover, the content is now available for others in the wider science world to use for various projects or applications we don’t even know about yet. They may not either at this point. But by digitizing this material and making it searchable, its use is only limited by imagination.

 

Handwritten volumes are challenging and time consuming  to transcribe. Keep in mind these notebooks were handwritten out in the field under less than ideal conditions. Worse yet, a scientist’s cursive handwriting is often unclear; Howell’s penmanship could only be described as “maddeningly squiggly.” Ds look like Hs which look like Ts which are interchangeable with Js. Thankfully there are a number of authoritative taxonomic databases which we check each name against. Ubio, Encyclopedia of Life, and GBIF were constant resources during this process. Particularly uBio which powers the Biodiversity Heritage Library’s taxonomic name search and  allows you to type in a few letters of a word and see results that match that beginning. If it comes up blank, you can quickly realize that big swoopy capital Q, is actually a really a sloppy I. This transcription is a slow process of deciphering, verifying, and double checking. -JW

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Excerpt from Howell botanical collecting notebook, volume 37, page 104, as viewed on BHL.
Every name in the field notes must be transcribed and verified by an actual person!

 

We would like to extend a huge thank-you to Justin for diligently spending many hours in front of a computer confirming that he was looking at Erigeron and not Eriogonum or vice versa. I estimate it took us on average at least two minutes per entry and sometimes (although very rarely) as many as ten minutes to pull and verify an individual specimen name from the field books. Given the number of entries in this selection, this means that the process of making these five field books searchable took over 175 hours of labor. This points to the research problem of improving Optical Character Recognition software and what we might be able to accomplish until technology is able to read and understand the intricacies of human penmanship. Luckily, our peers at the Smithsonian Transcription Center and BHL’s Purposeful Gaming project are looking at these problems and working towards viable solutions to help make more field books and primary source materials searchable now and in the future.

 

We hope you’ll join us again in August when we announce what we have built with this test bed of enhanced field notes.. Are you excited that we are making more primary source material available? Let us know in the comments below and we’ll be sure to keep you informed about future contributions.

-Yolanda Bustos, Connecting Content Project Manager


Filed under: Connecting Content,Digitization,Fieldnotes,Interns,Metadata — ybustos @ 12:12 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

August 16, 2011

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.

stewart_mss448_0223_copy

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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