Jekyll2026-09-29T00:59:01+00:00https://baskauf.github.io/feed.xmlSteve BaskaufProfessional website Enabling ecological survey data integration2025-12-05T13:00:00+00:002025-12-05T13:00:00+00:00https://baskauf.github.io/2025/12/05/ecographyOur paper describing the Humboldt Extension to Darwin Core has been published in Ecography. The Humboldt Extension adds 55 terms that enrich the Darwin Core, providing the terms needed to capture and share multiple types of biodiversity survey data. The paper illustrates the benefits of implementing the Humboldt Extension with three case studies and demonstrates how richer data can be used in research, modelling, and to inform decision-making.

The full citation is:

Sica, Y.V., Hochachka, W.M., Stevenson, R.D., Ingenloff, K., Zermoglio, P.F., Wieczorek, J., Gan, Y.M., Schigel, D., Kachian, Z.R., Baskauf, S., Brenton, P., Kazem, A.J.N., Jetz, W. and Guralnick, R. 2025. Enabling ecological survey data integration with the Humboldt Extension to Darwin Core. Ecography e08223. https://doi.org/10.1002/ecog.08223

]]>Steve BaskaufBiological survey and monitoring data publishing guide2025-10-15T17:00:00+00:002025-10-15T17:00:00+00:00https://baskauf.github.io/2025/10/15/eco-guideMy coauthors and I have published a guide to help people understand how to use the new Humboldt Extension for Biological Inventories of the Darwin Core standard. The guide includes diagrams and detailed information about how to structure the data to capture the hierarchical structure typically found in monitoring projects.

The guide is freely available under a Creative Commons Attribution (CC BY) license as a web page and in PDF format at https://docs.gbif.org/guide-publishing-survey-data/en/

The full citation is:

Ingenloff K, Svenningsen C, Earl C, Shimabukuro PHF, Sica Y, Gan Y-M, Kachian ZR, Brenton P, Hochachka W, Wieczorek J, Stevenson R, Kazem A, Baskauf S, Zermoglio PF, Bloom D, Rodrigues A, Gamboa Martínez J & Schigel D. Guide for publishing biological survey and monitoring data to GBIF. GBIF Secretariat: Copenhagen. https://doi.org/10.35035/doc-ynvs-eh84

]]>Steve BaskaufOpen Science recipes published2025-06-25T18:00:00+00:002025-06-25T18:00:00+00:00https://baskauf.github.io/2025/06/25/recipesMy colleage from the Vanderbilt Libraries’ Digital Lab, Shenmeng Xu, an I have published two chapters in the ACRL’s 2025 Open Science Cookbook. The Cookbook is a lighthearted take on technical topics where instructions are given in “recipe” format to teach beginners new tech skills.

Chapter 15, in the “Outreach” section is “Increasing Visibility and Discoverability of Electronic Theses and Dissertations Using Linked Open Data: A Simple Process for Uploading Metadata to Wikidata and is based on what we learned from a project we carried out a few years ago to upload all theses and dissertations from the Vanderbilt Institutional Repository to Wikidata, the free knowledge graph open for anyone to contribute. It features the VanderBot script that has been used to make over 53,000 contributions to Wikidata. You can view the chapter here.

Chapter 22, in the “Collaborations and Partnerships” section is entitled “Bibliometric Fusion: An Open Science Collaborative Project on Research Collaboration Network Mapping”. It is based on a project that Shenmeng and I did with researchers in the Vanderbilt Department of Otolaryngology to try to understand patterns of publication collaboration among otolaryngologists. The results were presented at the Triological Society Combined Sections Meeting in 2024 (1) and the project is being described in a manuscript that is in preparation. You can view the chapter here.

(1) Vivek, L., E. Clark, S.J. Baskauf, S. Xu, L. Gao, K. Nguyen, M. Goldin, K. Prasad, A. Miller, M.C. Topf, and A. Gelbard. 2024. Network Analysis of American Otolaryngologists. Triological Society Combined Sections Meeting, West Palm Beach, FL. January 26, 2024.

]]>Steve BaskaufFavorite winners of Nebula Award for Best Novel2025-03-31T18:00:00+00:002025-03-31T18:00:00+00:00https://baskauf.github.io/2025/03/31/nebulaIn March 2025, I finished reading all 60 of the winners of the the Nebula Award for Best Science Fiction or Fantasy novel. Many of my favorites were also winners of the Hugo Award, so I wrote a follow-up blog post to my earlier post about my favorite Hugo winners, focusing on favorites that weren’t already discussed in the Hugo post.

I am of the opinion that the overall quality of science fiction from the 1950’s and early 1960’s was generally terrible, so since the Nebula Award didn’t start until 1966, I was spared from reading as many awful books as I did when I read the Hugo winners (which went back to 1953). Nevertheless, there were a couple books that rated being on my list of least favorite Nebula winners, also included in the post.

Read the blog post

To see all reviews that I wrote on the Nebula winners, visit my GoodReads books.

For more about my favorite Hugo winners, see this earlier news item.

]]>Steve BaskaufFavorite winners of Hugo Award for Best Novel2025-02-16T21:00:00+00:002025-02-16T21:00:00+00:00https://baskauf.github.io/2025/02/16/hugoIn May 2023, I finished reading all 71 of the winners of the the Hugo Award for Best Science Fiction or Fantasy novel. There were some fantastic books on that list and some real duds.

I decided it would be fun to write a blog post listing my favorites with a brief description of why I liked them. In the post, I list other five-star books from the list, as well as my list of the worst books to win the award. (Some of them were really awful!)

I’m currently close to finishing all of the Nebula Award winners, so expect some comments about them soon!

Read the blog post

To see all reviews that I wrote on the Hugo winners, visit my GoodReads books.

]]>Steve BaskaufHumboldt Extension for Ecological Inventories Published2024-03-19T21:00:00+00:002024-03-19T21:00:00+00:00https://baskauf.github.io/2024/03/19/humboldtThe Humboldt Extension for Ecological Inventories is a new metadata vocabulary that extends the Darwin Core Standard to make it possible to describe the inventories and sampling events that are used to collect organism occurrence data. This is the largest extension to Darwin Core since the original vocabulary was ratified in 2009 and it represents over three years of work by the Humboldt Extension Task Group. This group of international experts met weekly over that time period to develop the vocabulary, carry out implementation testing, and publish the vocabulary and associated documentation.

The launch of the Humboldt Extension has been greeted with considerable interest by the ecological community, which has previously struggled to publish this type of data. Early adopters will include the Atlas of Living Australia, eBird, and the Field Museum in Chicago.

The landing page for the extension is at https://eco.tdwg.org/.

Full citation: Yanina V. Sica, Kate Ingenloff, Paula Zermoglio, Yi-Ming Gan, Peter Brenton, John Wieczorek, Wesley M. Hochachka, Zachary R. Kachian, Robert D. Stevenson, Anahita J. N. Kazem, Dmitry Schigel, Steven J. Baskauf, Tomomi Suwa, Robert Guralnick, Ramona L. Walls, Walter Jetz. 2024. Humboldt Extension Vocabulary List of Terms. Biodiversity Information Standards (TDWG). http://rs.tdwg.org/dwc/doc/eco/

Image at top of page: Fig. 5 from the Humboldt Extension for Ecological Inventories User Guide.

Image at side: Fig. 7 from the Humboldt Extension for Ecological Inventories User Guide.

]]>Steve BaskaufCamtrap DP paper published2023-12-10T08:00:00+00:002023-12-10T08:00:00+00:00https://baskauf.github.io/2023/12/10/camtrap-dpCamera trapping is an increasingly important method used by ecologists for monitoring animals in the wild. Camera trap data has previously been difficult to publish by conventional means, since the data includes many related images or videos that must be associated with the occurrence data. The new Camtrap DP standard provides a way to package camera trap data based on the open Frictionless Data Package specification. Camtrap DP datasets can be easily exchanged or published to the Global Biodiversity Information Facility (GBIF) where the included occurrence data will be integrated with biodiversity data collected by other means.

Publication of our paper describing version 1.0 of the standard is the first step in the process of further development by the camera trapping community, and adoption of the standard under the auspices of the Biodiversity Information Standards (TDWG) organization.

Full citation: Jakub W. Bubnicki, Ben Norton, Steven J. Baskauf, Tom Bruce, Francesca Cagnacci, Jim Casaer, Marcin Churski, Joris P.G.M. Cromsigt, Simone Dal Farra, Christian Fiderer, Tavis D. Forrester, Heidi Hendry, Marco Heurich, Tim R. Hofmeester, Patrick A. Jansen, Roland Kays, Dries P.J. Kuijper, Yorick Liefting, John D.C. Linnell, Matthew S Luskin, Christopher Mann, Tanja Milotic, Peggy Newman, Jürgen Niedballa, Damiano Oldoni, Federico Ossi, Tim Robertson, Francesco Rovero, Marcus Rowcliffe, Lorenzo Seidenari, Izabela Stachowicz, Dan Stowell, Mathias W. Tobler, John Wieczorek, Fridolin Zimmermann, Peter Desmet. 2023. Camtrap DP: An open standard for the FAIR exchange and archiving of camera trap data. Remote Sensing in Ecology and Conservation. 2023. https://doi.org/10.1002/rse2.374

Image at top of page: Camera trap image of white-lipped peccaries (Tayassu pecari) 2013-07-29T08:42:12-03:00 at Foles, Ilha do Cardoso, Cananéia County, São Paulo, Brazil. -25.160643° latitude,-47.933229° longitude. Photo courtesy of Maria Luísa Jorge. http://bioimages.vanderbilt.edu/jorgem/rec13_1771. Available under a CC BY 4.0 license.

Image at side: Image from Fig. 1 of Bubnicki et al. 2023. Camtrap DP: an open standard for the FAIR exchange and archiving of camera trap data. Remote Sensing in Ecology and Conservation. https://doi.org/10.1002/rse2.374. Available under a CC BY-NC 4.0 license.

]]>Steve BaskaufNine hundred images added to Wikimedia Commons from ACT2023-11-21T12:00:00+00:002023-11-21T12:00:00+00:00https://baskauf.github.io/2023/11/21/actCharlotte Lew and I have been working for some time to improve access to images in the Art in the Christian Tradition database by linking descriptive metadata in Wikidata to the corresponding artwork images in Wikimedia Commons. In the first part of the project, we were primarily cleaning up and linking Wikidata metadata to images that were already in Commons.

In the most recent phase of the project, we have been working out a workflow for uploading images from the database to Commons. The first batch that we’ve uploaded are over 900 images that were taken by Anne Richardson (formerly of the Vanderbilt Divinity Library) and Jim Womack (retired art teacher at Montgomery Bell Academy) on various trips to Europe. These images are primarily of cathedral artwork and early Christian art, although there are also some images that are illustrations of the Macklin Bible, one of the holdings of the Vanderbilt Libraries’ Special Collections that was a gift to Vanderbilt University from John J. and Anne Czura.

To view the recently uploaded images, you can search Commons for the category “Art in the Christian Tradition”.

Image at top of page: Chartres Cathedral; Apostles Paul, John, James the Major, James the Minor, Bartholomew; right embrasure jamb figures, central portal, south transept. ACT ID: 26342 and Wikidata Q ID: Q122959379. Image © Jim Womack and Anne Richardson via Wikimedia Commons and available under a CC BY-SA 4.0 license.

Image at side: Jesus the Good Shepherd.ACT ID: 51560 and Wikidata Q ID: Q122960188. Image © Jim Womack and Anne Richardson via Wikimedia Commons and available under a CC BY-SA 4.0 license.

]]>Steve BaskaufBuilding an Omeka website on AWS2023-08-06T16:30:00+00:002023-08-06T16:30:00+00:00https://baskauf.github.io/2023/08/06/omekaI recently finished building an Omeka digital collection for images from the files of Bassett Associates, a landscape architectural firm that operated for over 60 years in Lima, Ohio. This award-winning firm, which disbanded in 2017, was well known for its zoological design work and also did ground-breaking work in incorporating storm water retention as part of landscape site design.

During the process of building the site, I figured out how to use Amazon Web Services (AWS) to implement all of the features of a production Omeka Classic instance. I describe what I learned in a blog post and have also published detailed instructions that should allow someone with patience and moderate command line skills to replicate what I’ve done.

Operating Omeka on AWS is quite affordable. Including the EC2 cloud server, S3 file storage, and a custom domain name, the total cost to operate the site is about US$10 per month.

To view the completed site, visit https://bassettassociates.org/archive/.

Image at top of page: James H. Bassett, “African Plains,” Bassett Associates Archive, accessed August 6, 2023, https://bassettassociates.org/archive/items/show/415. Available under a CC BY 4.0 license.

Image at side: James H. Bassett, “Okapi,” Bassett Associates Archive, accessed August 6, 2023, https://bassettassociates.org/archive/items/show/337. Available under a CC BY 4.0 license.

]]>Steve BaskaufPublication of subjectPart and subjectOrientation controlled vocabularies2023-05-09T09:30:00+00:002023-05-09T09:30:00+00:00https://baskauf.github.io/2023/05/09/viewsOn 26 April 2023 the Executive Committee of Biodiversity Information Standards (TDWG) ratified two new controlled vocabularies to become a part of the Audiovisual Core standard. This marks the culmination of hundreds of hours of work on my part over many years.

In the early 2000’s, Bruce Kirchoff and I had extensive discussions on how living plants should be photographed so that their important features could be recorded. As a result, we developed “views” (standardized orientations for particular parts of the plants) that were important for capturing this information. In 2008, we published “Digital plant images as specimens: toward standards for photographing living plants.” (Vulpina 7:16-30) to share this work with the biodiversity informatics community.

Although these views were “standardizedized”, they weren’t officially part of any actual standard. In the 2010’s I became involved with TDWG in various capacities, but notably as the review manager for the new Audubon Core Multimedia Resources Metadata schema (now known as “Audiovisual Core” or “AC”). After that standard was adopted in 2013, a maintenance group was formed for it and I served as the convener. The stage was then set to develop an actual international standard for views by establishing controlled vocabularies for the two terms in AC that describe the viewing orientation relative to a particular part of an organism: ac:subjecPart and ac:subjectOrientation. In 2018, I wrote the charter and recruited members for a Views Controlled Vocabularies Task Group.

Over the next several years, the Task Group met regularly to collect use cases, establish requirements, write the vocabularies, and oversee implementation testing. I am particularly grateful to Task Group core members Jennifer C. Girón Duque of the Natural Science Research Laboratory, Museum of Texas Tech University and Matthew Nielsen of the University of Oulu in Finland who kept the momentum going in the later stages of the work. The details of our work is described in our published implementation experience report (https://doi.org/10.3897/biss.7.94188). The end product included:

To learn more about these controlled vocabularies and how they can be used, see the subjectPart and subjectOrientation Controlled Vocabularies User Guide.

Insect image from Fig. 3.D. of https://doi.org/10.3897/BDJ.8.e55474

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