All posts tagged with technical-team

William Ulate Rodríguez, past Biodiversity Heritage Library (BHL) Technical Director, died in St. Louis on September 20, 2023. William was a father, a friend, a colleague, and a passionate advocate of using the tools of bioinformatics to better understand life on our planet.

William’s friends and colleagues share their fond memories of his life and work.

In 2023, BHL’s Technical Team dedicated significant efforts to improve our data ecosystem, now comprising 61+ million pages of biodiversity literature. Last year’s Technical Priorities underscored BHL’s steadfast commitment to data quality by focusing on both upstream and downstream data flows. Notable milestones include delivering refined taxonomic data to researchers, implementing interface improvements based on user feedback, and forging data pipelines for existing and new downstream data consumers. 

For BHL, 2022 was a year to focus on critical upgrades for the BHL platform to ensure the sustainability of our services for our global users. Although BHL’s basic technical infrastructure remains the same, consisting of years of refinement, knowledge, and reliability, a few updates were definitely in order. Most of these upgrades were “behind-the-scenes” work and would not be noticeable to a majority of our users. However, keeping up with these important enhancements is a crucial component of any technology project.

BHL has deployed a new taxonomic name finding tool to improve the speed and accuracy of identifying names throughout its 58+ million pages.

BHL is now usingGlobal Names Architecture’s (GNA) gnfinder tool to locate taxonomic names in the BHL corpus. Prior to this deployment, BHL’s name finding services were based on an index of scientific names created by GNA developers six years ago by parsing every page in BHL one by one. This took 45 days to accomplish, and the cost of repeating this process made updating or improving the index infeasible.

The gnfinder tool uses fast, scalable programming languages to significantly reduce computational time. Using Open Source applications in Go and Scala, the tool detects candidate scientific names and compares them to millions of scientific name-strings aggregated by GNA for verification. The new process decreases the time needed for name detection and name verification from 35 days to 5 hours and from 7 days to 12 hours, respectively. As a result, the entire BHL corpus can now be indexed in less than a day, compared to the 45 days needed for the previous index. Additionally, by significantly reducing computational time, implementing iterative improvements to the index is now achievable.

The Global Names Project held a workshop on 17-19 June 2019 on the Campus of the University of Illinois at Urbana-Champaign. The workshop was titled Scientific names indexing and data mobilization of Biodiversity Heritage Library using tools from Global Names project and was hosted by the Species File Group at the  Illinois Natural History Survey. Eighteen people attended representing a variety of organizations interested in BHL content: Global Names Architecture, iDigBio, TaxonWorks, UIUC Species File Group, the Illinois Library, Encyclopedia of Life, the DINA Project, the Catalogue of Life, GBIF, Species File Group Argentina, the HathiTrust Research Center, and Global Biotic Interactions.

HTTPS? What does it mean? HTTP is the language that your browser uses to communicate to BHL and the S stands for Secure, encrypted, unreadable, or at least much, much harder to read.The web is moving to encrypted connections across the board. In 2014 Google announced that their page rank algorithm that decides the order of your google.com search results will now rank insecure pages slightly lower than secure pages. From security to rankings, encrypted connections are better for everyone.