Sense of Humerus

Emily Streetman: Anthropology Doctoral Student

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Database brainstorm

Let’s suss this idea out in blog post format, shall we? The database my lab is currently working with for a bioarchaeology project has a very limited number of queries that do not currently function, possibly due to my user error, but even when functioning, the situation is less than ideal. One complete and one nearly complete dissertation have been written using this collection, and each author had to create her own database after entering all of her data in the lab’s database.

At face value, it seems a simple task, since so much data has been collected, for me to ask: How many adults were aged using the fourth rib (a standard method)? I would have to manually pull out and search 200-some adult folders containing 20 pages each and tally the ones who have this bit of data.

I would like to improve this system. The in-progress dissertation author just told me that she’d like to link excavation notes, digital copies of data sheets, and photographic images for each set of remains in this skeletal collection. This is a great idea. Assuming that some volunteer or intern-sourced manpower could be dedicated to data entry, here are some things I’d like researchers to be able to do with the data collected from 400-some medieval skeletons.

[Before the archaeologists in the room start asking about the associated material culture, we don’t have it, but excavation notes should mention its presence, so it can be included in the database. These Christian burials are largely devoid of grave goods, but there were a handful of jewelry items and a few extant pieces of shroud in the cemeteries.]

Input for each individual: pdfs of excavation notes, location of grave on cemetery schematic, pdfs of data entry sheets (with data re-coded or tagged?, to allow search by sex or age group), images and xrays of pathologies (tagged with limited number of disease or symptom tags to allow search for all, say, crania with cribra orbitalia), data collected by, data collected on date, cemetery, skeleton number.

Audience: this is to be an internal organizational system, with access limited at the discretion of the lab director. This would ostensibly include graduate and undergraduate students who have received permission to collect data or perform analysis on the collection.

Back end: volunteers and interns would input the data, using either a scanning xerox machine or a plate scanner and manual data entry.

Front end: the audience is not, in general, technologically inclined and is most familiar with SPSS and Excel to organize data and run statistics. Furthermore, these are the programs that will likely be used for analysis of New Database data, so I would like findings to be exportable. E.g., export the age/sex profile data of all adult females. I always picture these sorts of filters as similar to when I shop at Best Buy online. I’m looking for (male/female/either) (adult/subadult) (age range:0—–20 sliding scale) (with:right and left femurs).

How can I do this? Omeka and Kora are both database scaffoldings, but I’ve heard a variety of reviews about both and I don’t remember which is which.


Additional note: It might be possible to use one of the pre-existing excel sheets as a base for this.


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My experience as a JPAC visiting scientist

In June 2012, I visited the Joint POW/MIA Accounting Command Central Identification Laboratory (JPAC/CIL) at Hickam Joint Base in Honolulu, Hawaii. Despite the lengthy name, you might guess from the “POW/MIA” part of it that their mission is to identify and bring home all unaccounted-for American military servicemembers. It’s the single largest employer of forensic anthropologists in the country, trailed by the New York City Office of the Medical Examiner. You might not know that there are thousands of unaccounted-for American service members from conflicts in the 20th century. What you should know is that the team at JPAC works daily to find Americans’ remains, identify them, and send them home to family members who have lived in limbo for decades.

Photo by Flickr user Beverly & Pack

As a visiting scientist, I was there to work on a specific project. In this case, a two-pronged look at the patella (kneecap) as a uniquely identifying bone. Previous research* by Dr. Carl N. Stephan, the JPAC/CIL anthropologist who sponsored my visit, has looked at the clavicle in a similar way. The clavicle and cervical vertebrae 3-7 is a great locus to start, because all service members had to be screened for tuberculosis in the mid-20th century, so archives are filled with radiographic (x-ray) and photo-fleuroscopic films waiting to be matched to unidentified remains.

The first part of the patella research continues a series of validation studies that show how good forensic anthropologists are at determining a match – does this Person’s medical record match the John Doe in front of you?

The second part is more quantitative. Following Stephan et al. 2011a, we used a NextEngine scanner (3D-imager) to digitize the patella, processed the surface images with Meshlab, derived 15 outlines from each scan, generated Elliptical Fourier coefficients for each using Shape v.1.3.We compared these outlines with outlines derived from radiographs of the same patella in situ and analyzed the results with new code in R. (For a post on my experiences as a novice coding in R, click here.) . The results of both parts of the study have been submitted to the 2013 Annual Meeting of the American Academy of Forensic Sciences.

Overall, I had a great time at JPAC/CIL. Being on a military base was a new experience for me, and this was really only the second lab of which I’ve gotten to see the inner workings. Many of the employees from the CIL participate in the Scientific Working Group for Forensic Anthropology (SWGANTH) along with my advisor, Todd Fenton, so there’s a lot of overlap in the way we do things. However, in addition to lab work, CIL employees also go into the field (mostly in Southeast Asia, but with some European missions) to do recoveries. It’s this that seems to make or break newbies – so I’m interested in getting a taste of it by applying to the Forensic Science Academy, a semester-long program offered by JPAC/CIL that includes a 30-day field mission to Vietnam. Wish me luck!


*Stephan CN, Emanovsky PD, and Tyrrell AJ. 2011a. The use of clavicle boundary outlines to identify skeletal remains of US personnel recovered from past conflicts: results of initial tests. In: Lestrell PE, editor. Proceedings of the First International Symposium of Biological Shape Analysis. 2009 Jun 3–5. Tsukuba, Ibaraki, Japan. Singapore: World Scientific Publishing.

Stephan CN, Winburn AP, Christensen AF, and Tyrrell AJ. 2011b. Skeletal Identification by Radiographic Comparison: Blind Tests of a Morphoscopic Method Using Antemortem Chest Radiographs. Journal of Forensic Sciences 56:320–332.