Month: September 2016

Situating Chemistry: Creating a Database of 18th-c. Chemists

*This post is the first section of a talk I gave at the 7th International Conference of the European Society for the History of Science.

In 1756, fifty-nine students attended William Cullen’s (1710-1790) chemistry course at the University of Edinburgh. Amongst them was George Fordyce (1736-1802) of Aberdeen who would go on to earn his medical degree from Edinburgh and become a lecturer of chemistry and medicine in London. He also wrote a book called the Elements of Agriculture and Vegetation that includes diagrams of his interpretation of Cullen’s teachings on the chemical attractions of particles. Although there is no monograph length biography of Fordyce, he has entries in the Dictionary of National Biography and the Dictionary of Scientific Biography and is a relatively well-documented individual.

Page 83 of George Fordyce's Elements of Agriculture including diagrams of chemical particles

George Fordyce’s 1783 diagram of chemical particles

The other fifty-eight attendees of the course are less known. We know from Cullen’s notes that Robert Cumming was from Edinburgh, that John Richardson was from Northumberland, and that Henry Dunston was from some unspecified part of England. More surprisingly, at least two of the attendees were from Virginia—Thomas Clayton and James Taylor—and one was from Antigua—Christopher Hodge. Clayton, Fordyce, and eight other students would go on to earn their MDs from Edinburgh.

In designing the prosopographical part of the Situating Chemistry database, John Perkins and I wanted to ensure that we could capture structured, machine-readable data on someone like George Fordyce, or for that matter William Cullen. Additionally, we also wanted to be able to create records for people like Henry Dunston, for whom we had only a name and relationships of interest, in this case that he was a student in Cullen’s chemistry course, in Edinburgh, in 1756, with these other people, and he was from England.

Within Situating Chemistry, we assembled the structured data fields for collecting information about people with the assumption that a researcher would more often than not have incomplete data. The only required field is the title of the record. The fields to record dates of birth and death can be partially filled out when only a year or year and month are known. They can also be marked approximate to indicate ambiguity in the historical record.

Screen shot of the Situating Chemistry Database depicting the fields available for recording data about a person

The database was developed for the ‘Situating Chemistry, 1760-1840’ research group and funded in part by a grant from the Netherlands Organisation for Scientific Research, so we built it to accommodate the variety of different research projects being conducted by the research group. John Perkins has spent a great deal of time studying probate records to collect information about the relationships, business practices, personal belongings and wealth of French apothecaries and chemical manufacturers. In my research, I have focused instead on networks of education tracking the courses taken and taught in and around universities and the note sets related to those courses. Both of us are interested in the chemical substances and processes studied by our individuals as well as their correspondence.

The record for any individual can be linked to other individuals in several different ways. In addition to familial relations, we also have structured fields to collect information on instructor-student relationships and correspondents. There is also a somewhat generic person-to-person connection field that offers a list of relationships that can be expanded if and when needed. We designed the database such that every individual is the subject of their own record. A field denoting that a person was active in chemistry is automatically checked for every new record, but can be deactivated for familial relations, business partners, and others who are of interest but were not actively ‘doing’ chemistry even in the broadest definition.

In addition to linking a person to other individuals within the system, a person can also be linked to many other kinds of data. The database was initially conceived of as a way to catalogue sites of chemistry. We thus started the database with a table to collect information on apothecary shops, lecture halls, pharmaceutical manufactories, bleach fields, labs, etc. For a given site, the latitude and longitude of the site along with a modern address can be recorded along with information about the ownership and financial history of the site, the chemical activities associated with it, the organizational history, related images, documents, sources, etc. For each individual in the system, we display the sites that they owned and operated and also those additional sites that they were associated with.

After developing tables for the sites and people involved in chemistry, we developed further tables for chemical substances collections, courses, documents, events, images, letters, objects, organizations, primary and secondary sources, processes and techniques of chemistry, and archival and museum repositories. A person can be connected to any of these record types with an extensible series of extensible subject-predicate-object. For example a given individual could be a member of an organization or might have studied a particular chemical substance or been a practitioner of a particular process or technique of chemistry. Every record, whether it be for a person or any other type of data, can and should be sourced by linking it to primary and/or secondary sources. For the system as a whole then, we have tables for more than a dozen types of information and hundreds of structured data fields, all strung together into a relational web of information.

In its first conception, the Situating Chemistry database was thought of as a single table for sites with about a dozen fields. However, this variety of tables and fields grew organically through discussion of the research questions and practices that we, as historians of chemistry, conduct. The goal for the project was not to publish a completed set of sites or records, but rather to facilitate active research. A researcher could enter the data that they were collecting for a research project to organize and analyze the information, and they could take the database with them into the archives to continue to collect information. Researchers can access their records and add new records to Situating Chemistry from a laptop, tablet, or even a phone.

To accommodate both offline note-taking and the rapid upload of external data sets, the database has also been designed so that users can upload CSV files (excel-type tables). Any data in the system can in turn be downloaded as a CSV or in other structured formats including XML, RDF, and JSON. Because Situating Chemistry was designed as a research tool rather than a data-publication, the goal of the database is to allow users to both enter and access whatever fields and records sets they consider interesting. Several visualizations including tables, graphs, and a timeline are built into the system. The user can also extract whatever structured data they want to pull from the system, so that she can also generate her own visualizations using tools like Tableau or programming languages like Python and R.

Recap of the 3rd Digital Humanities Day at OU

Today I attended the 3rd Digital Humanities Day at OU. Below I’ve identified a couple of the emergent themes and given my thoughts. Below that, I included notes on each talk.

Making as a Means of Authority and Inclusion in the Digital Humanities

Many of the talks touched on the idea of faculty and students as makers. Bob Pavlik introduced this theme in the first talk with his discussion of students using digital-material design to make architectural models and structures. Adam Croom returned to the theme with his focus on promoting the infrastructure for students to Create and own their own digital domains.

In the keynote talk, Julia Flanders returned to the idea of making with a discussion of researchers as builders within the digital humanities. There is an ongoing debate in the digital humanities of whether one needs to be a coder or a maker in order to be counted as a digital humanist. Are the researchers who work with coders to design projects somehow outside the group of digital humanists? Are coders and it workers with little training in the humanities included in the group of digital humanists when they work on such projects? What is at stake with this debate over inclusion and technical credit? How does gender, class, and politics play into authority and credit within making, digital humanities, and academics more broadly.

Suzanne Moon opened the commentary on Flanders’ paper which was wonderful for me in that she taught me history of technology and technology dissemination, the fields through which I understand and interpret Flanders’ questions. The history of technology is a field built to answer the types of questions that Flanders is raising and that currently permeate not only digital humanities but educational technology and computing research as well. I think there’s a lot of room for work in applying history of technology to modern debates over both research and educational technology.

Born-Digital Publication & New Humanities Research

A second theme that permeated almost all of the talks was the ways in which digital publication not only changes and increases knowledge dissemination but also how it fundamentally changes the types of questions asked and means of answering those questions. This was the central point in Nick Bauch’s presentation on his Enchanting the Desert project. Nick presented his own research as an example of the different and new types of questions that can be asked and presented with digital tools and should be valued equally with traditional monograph publications.

Catherine Kelly’s discussion of the differences in editing a born-digital journal, Common-Places, with a traditional journal, the Journal of the Early Republic, really brought the affordances of the digital age to the forefront.

Though not explicitly a point of conversation today, part of the appeal for me in digital publication is the open sharing of knowledge and the production of open educational resources. Why we as academics have accepted the idea that we should hand over copyrights for the work we produce to for-profit publishing houses is beyond me. There is no personal gain in this system, and the public is impoverished by having to pay to access our work that has been locked away for the benefit of an unnecessary middleman.

The unthinking bias against digital products as opposed to print products also bothers me. Both Nick Bauch’s work and Catherine Kelly’s journals are peer-reviewed with all of the rigor of traditional academic monographs and journals. They both convey information just as well if not better than their analog antecedents. Why Nick’s work would ever be weighed less than a monograph or a digital journal weighed less than its paper counterpart is entirely beyond me. Today’s workshop shows that the academic world is moving beyond these traditional biases, but I think there is still a long way to go in revising tenure requirements and research expectations.


Bob Pavlik, Assistant Professor in the Division of Architecture, “Digital Fabrication in Architecture: Computational Ideation and the Conflict of Matter.”

The initial talk for the day was given by Bob Pavlik, who talked about how the digital opens and enables a new aesthetic in architecture as exemplified by beautiful designs of the Zaha Hadid Architectural firm.

Photograph of the Heydar Aliyev Centre in Baku, Azerbaijan

While computer code and CAD led to a period of formalism in architecture, Pavlik shifted our attention to the integration of digital design as part of a system with the study of materials. His students use both CAD design and material study to design and design and build new architecture. Even in the introductory surveys, students work with digital architecture to create forms and then test those forms with materials in both the digital and physical realms. This talk opened one of the major themes of the day: students as makers.

Diana Folsom, Director of Digital Collections at the Gilcrease Museum, “Adding Art into the Humanities: Combining and Shaping Data at the Gilcrease Museum.”

In the second talk, Diana Folsom discussed the efforts of museums generally and the Gilcrease Museum more specifically to catch up to the digital cataloguing practices of the library world. Museums face interpretive challenges in categorizing and tagging their objects to help make unique objects discoverable in broader contexts.

Photograph of the sculpture of a Native American man shooting a bow that stands in front of the Gilcrease Museum in Tulsa, OK

The Gilcrease is working with outside experts to review and add data to their system. Linked Open Data from the Getty and other major international museums provides information about the artists featured and connects the collections at the Gilcrease with the broader world. Additionally, non-expert tagging collected from visitors to the museum and website create a non-jargon, non-academic taxonomy. This provides both a search tool for other users and an insight in public interest, use, and understandings of museum collections.

Nick Bauch, Assistant Professor in the Department of Geography & Environmental Sustainability at OU, “Design and Digital Publishing: Representing Theoretical Advances in the Geohumanities.”

Nick Bauch (twitter) has recently completed work on a spacial-narrative project called Enchanting the Desert, a born-digital, interactive web application. Rather than being an addendum to a print book, the web site is the primary research product for his project on cultural geography of the Grand Canyon.

Henry Peabody's photo, "Down Granite Gorge, from Grand View Trail" (1899)

Bauch used his project as an example of the ongoing shift from print books to born-digital publications. In his work with the Stanford University Press, Bauch is using his own work (and his career) to advocate for equal recognition of digital projects with the traditional academic monograph. Enchanting the Desert has approximately the same number of words as a monograph, and can be easily compared to a book. But the production of it enables and indeed requires a different form of research and analysis than the traditional monograph.

Valuing this project and similar projects with the same weight as a traditional monograph opens up new research questions, visual argumentation, and public outreach. These are questions that we, as academics, have struggled with, and it is a solution that many academics are still uncomfortable with. Bauch’s work though demonstrates the rigor and richness of such work and fit well with the broader discussion of digital publication that carried through the day.

June Abbas, Professor of Library & Information Studies at OU, “How I learned to Love Classical Studies: Information Behavior Studies and Digital Humanities,”

After a coffee break, the second panel started off with a talk by June Abbas, Professor of Library & Information Studies here at OU. In “How I learned to Love Classical Studies: Information Behavior Studies and Digital Humanities,” she talked about her work on the Digital Latin Library. As co-PIs with Sam Huskie (associate professor in classics) and Chris Weaver (associate professor in computer science), Abbas and the team are working to digitize critical editions of Latin texts and conceptualize the digital representation of the traditional critical apparatus.

Abbas conducted interviews of the participants in the Digital Latin Library project. In depth interviews and task demonstrations with everyone from her co-PIs to the PhD candidates working on the project and the high-school instructors using it helped Abbas to map the current UI and UX and work to iteratively design improvements. Using Dedooce, she coded and analyzed these interviews to study the information seeking behaviors of each user and collective user groups. In this way, the study is not just about UI and UX but gets at what type of information the users are seeking and thus what types of questions the researchers might ask and data they might present.

Abbas’ work is a great demonstration of how we can think about, study, and improve UI and UX during project development. Again, this fits with the broader themes of the day in that we can think about digital research and publication to improve both our current projects and better understand the user in digital humanities. The very act of producing born-digital research products can encourage the development of new questions and the integration of users into digital humanities projects.

Catherine Kelly, L.R. Brammer Jr. Presidential Professor in the Department of History at OU & editor for the Journal of the Early Republic, “From Print to Digital and Back Again: Adventures in Editing.”

Catherine Kelly contrasted her work editing Common-Place and Journal of the Early Republic. Common-Place is a born digital journal that from its start tried to integrate music, images, reader comments and interactives into an academic journal. In editing Common-Place, Kelly and her co-editors quickly realized that great writing was still key, but that their use of technologies and integration of media could help to amplify the audience of a traditional academic journal.

Screen shot of Common-Place.org

In working with the more traditional Journal of the Early Republic, Kelly has sought to provide educational content related to the traditional academic pieces submitted by researchers. Integrating these two pieces in the online space extends and enhances each. She is drawing on the traditional strengths of the JER and using digital tools to broaden the audience of academic research and enhancing the depth and insight of online educational resources.

As part of the second panel, Kelly’s talk was moderated by Suzanne Moon, the editor of Technology and Culture. As Moon and the Society for the History of Technology think about how T&C will adapt to the digital space, Kelly’s experiences serves as great guide. Digital publication does not simply mean moving the print publication onto the web, but rather using the affordances of the digital realm to enhance the publication and open new pathways for research and engagement.

Adam Croom, Director of Digital Learning, Center for Teaching Excellence at OU, “Indie EdTech and the Digital Humanities.”

Adam Croom’s presentation focused on the integration of digital humanities into our teaching practices. Using an autobiographical narrative, Croom talked about how he developed his teaching philosophy. He started by having students reflectively blog about their experiences. That perspective as a humanist led to his push for a Domain of One’s Own Project here at OU and ultimately OU Create.

In Croom’s current course, he continues to use reflective blogging as the core of the class, and he is also using student choice through challenge banks to encourage students to engage with the skills they want and to develop towards they goals that they have.

Croom’s presentation was ostensibly focused on the development of his courses, but he was using that experience to argue for a broader understanding of Digital Humanities that not only includes but can at times prioritize Digital Pedagogy. In a conference that tends to focus on research, he was trying to draw the room back towards our dual roles of researchers and teachers. These two aspects should be balanced and can be should be integrated to enable and encourage students to participate with us in research and/in the digital humanities.

Both in our individual pedagogy and in the infrastructure we provide, we need to provide digital space for our faculty, staff, and students where we can integrate our research, our pedagogy, and our personal lives.

Mary Larson, Associate Dean for Special Collections, Oklahoma State University, “What You Do with a Million Oral Histories (with apologies to Stephen Ramsay).”

Mary Larson‘s presentation on oral history and the digital humanities cast oral histories as a potential data set. Drawing of Stephen Ramsay’s famous essay on distant reading of texts, Larson argued for applying semantic and corpus analysis of oral history data sets. Larson used AntConc to study interviews from the Oklahoma Women and the Dust Bowl archive, and found common themes about the positive memories, the omissions,  and the common challenges of women who suffered through the Dust Bowl. The women fondly remembered their school days and their youths. The word husband on the other hand was far less common than many other familial terms.

The distant reading of such a corpus indicated sociological patterns that had been overlooked in any single history or even prosopographical study. As with all distant reading, the indications have to be followed up and studied, but the point is that distant reading affords a different set of questions than have existed before. These affordances have been recognized in the study of high literature and popular publications, but they have not been recognized or at least broadly used in the study of oral history.

Keynote: Julia Flanders, Professor of the Practice in English, Northeastern University; Director, Women Writers Project; & Editor-in-Chief, Digital Humanities Quarterly, “Building Otherwise: Gender, Race, and Difference in the Digital Humanities.”

Julia Flanders started off by reminding us that there are no purely technological systems or technological design issues. The technology is part of a system that includes the human designers and users who determine cultural meaning and informational interpretation. Flanders’ focused our attention on the idea of digital humanities as a system that unites research and praxis. She then asked, “How do race, gender, and other forms of otherance operate? Does it matter where we look for them? Do we have alternatives?”

Flanders continued from these questions by delving into prior talks by Moya Bailey, Miriam Posner, and others that focused on the politics of the digital humanities stack. The tools borrowed from the business world, login authorizations, data entry interfaces, etc. carry with them socio-cultural baggage. The Cartesian maps promoted by Google Earth and used in countless research projects (including my situatingchemistry.org) carry colonial & imperial connotations and too often (especially in the case of my site because of our Eurocentric focus) reinforce colonial rhetoric.

Flanders’ point was that the very technologies and research projects are born from and reinforce an ideologically problematic tradition. The question raised is what can we do about this?

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