ALBERT

Description: [1]  Antarctic Intermediate Water (AAIW) and Subantarctic Mode Water (SAMW) are the main conduits for the supply of dissolved silicon (silicic acid) from the deep Southern Ocean to the low latitude surface ocean, and therefore have an important control on low latitude diatom productivity. Enhanced supply of silicic acid by AAIW (and SAMW) during glacial periods may have enabled tropical diatoms to outcompete carbonate-producing phytoplankton, decreasing the relative export of inorganic to organic carbon to the deep ocean and lowering atmospheric p CO 2 . This mechanism is known as the ‘Silicic Acid Leakage Hypothesis’ (SALH). Here we present records of neodymium and silicon isotopes from the western tropical Atlantic that provide the first direct evidence of increased silicic acid leakage from the Southern Ocean to the tropical Atlantic within AAIW during glacial Marine Isotope Stage (MIS) 4 (~60–70 ka). This leakage was approximately coeval with enhanced diatom export in the NW Atlantic and across the eastern equatorial Atlantic and provides support for the SALH as a contributor to CO 2 drawdown during full glacial development.

Description: Advances in biodiversity genomic sequencing will increasingly depend on the availability of DNA samples—and their quantifiable metadata—preserved in large institutional biorepositories that are discoverable to the scientific community. Improvements in sequencing technology constantly provide longer reads, such that longer fragment length, higher molecular weight, and overall “genome-quality” DNA (gDNA) will be desirable. Ideally, biorepositories should publish numerical scale measurements of DNA quality useful to the user community. However, the most widely used technique to evaluate DNA quality, the classic agarose gel, has yet to be quantified. Here we propose a simple and economical method using open source image analysis software to make gDNA gel images quantifiable, and propose percentage of gDNA “greater thanXkb” as a standard of comparison, whereXis a band from any widely used DNA ladder with desirably large band sizes. We employ two metadata standards (“DNA Threshold” and “Percent above Threshold”) introduced as part of the Global Genome Biodiversity Network (GGBN) Darwin Core extension. We illustrate the method using the traditionally usedHindIII ladder and the 9,416 base-pair (bp) band as a standard. We also present data, for two taxa, a vertebrate (fish) and an invertebrate (crab), on how gDNA quality varies with seven tissue preservation methods, time since death, preservation method (i.e. buffers vs. cold temperatures), and storage temperature of various buffers over time. Our results suggest that putting tissue into a buffer prior to freezing may be better than directly into ultra-cold conditions.

Description: Omic BON is a thematic Biodiversity Observation Network under the Group on Earth Observations Biodiversity Observation Network (GEO BON), focused on coordinating the observation of biomolecules in organisms and the environment. Our founding partners include representatives from national, regional, and global observing systems; standards organizations; and data and sample management infrastructures. By coordinating observing strategies, methods, and data flows, Omic BON will facilitate the co-creation of a global omics meta-observatory to generate actionable knowledge. Here, we present key elements of Omic BON's founding charter and first activities.

Description: “If names be not correct, language is not in accordance with the truth of things. If language be not in accordance with the truth of things, affairs cannot be carried on to success.” - Confucius, Analects, Book XIII, Chapter 3, verses 4-7, translated by James Legge Two workshops (hereafter described as “workshops”) were held in 2012, which brought together domain experts from genomic and biodiversity informatics, information modeling and biology, to clarify concepts and terms at the intersection of these domains. These workshops grew out of efforts sponsored by the NSF funded Resource Coordination Network (RCN) project for GSC [1] (RCN4GSC, hosted at UCSD, with John Wooley as PI) to reconcile terms from the Darwin Core (DwC) [2] vocabulary and with those in the MIxS family of checklists (Minimum Information about Any Type of Sequence) [3]. The original RCN4GSC meetings were able to align many terms between DwC and MIxS, finding both common and complementary terms. However, deciding exactly what constitutes the concept of a sample, a specimen, and an occurrence [4] to satisfy the needs of all use cases proved difficult, especially given the wide variety of sampling strategies employed within and between communities. Further, participants in the initial RCN4GSC workshops needed additional guidance on how to relate these entities to processes that act upon them and the environments in which organisms live. These issues provided the motivation for the workshops described below. The two workshops drew largely from experiences of the Basic Formal Ontology (BFO) [5] and were led by Barry Smith, State University of New York at Buffalo. We chose to interact with Smith based on his successful interactions with the GSC in developing the Environment Ontology (EnvO) [6] and also, on the ability of BFO to unite previously disconnected ontologies in the medical domain [7]. The first workshop addressed term definitions in biodiversity informatics, working within the BFO framework, while the second workshop developed a prototype Bio-Collections Ontology, dealing with samples and processes acting on samples. Concurrent with these workshops were two ongoing efforts involving data acquisition, visualization, and analysis that rely on a solid conceptual understanding of samples, specimens, and occurrences. These implementations are included in this report to show practical applications of term clarification. Finally, this report provides a discussion of some of the next steps discussed during the workshops.

Description: For the last 15 years, Biodiversity Information Standards (TDWG) has recognized two competing standards for organism occurrence data, ABCD (Access to Biological Collections Data; Holetschek et al. 2012) and DarwinCore (Wieczorek et al. 2012). These two representations emerged from contrasting strategies for mobilizing information about organism occurrences (also commonly called species occurrence data). ABCD was capable of representing details of more kinds of information, but was necessarily more complicated. DarwinCore, on the other hand, was simpler but more limited in its ability to represent data of different kinds and formats. TDWG endorsed both standards because the different projects and communities that generated them remained dedicated to their different strategies and tool sets, and the Global Biodiversity Information Facility (GBIF) developed the ability to integrate data published in either standard. Since their inceptions, DarwinCore and ABCD have become more similar. DarwinCore has gotten more complicated through the addition of terms and has begun to assign terms to classes. ABCD is now expressed in RDF (Resource Description Framework), potentially enabling re-use of terms with alternative structures among classes. At the same time, methodologies for conceptual modeling and representing complex scientific data have continued to evolve. In particular, a suite of modeling and data representation methods related to linked data and the semantic web, i.e., RDF, SKOS (Simple Knowledge Organization System), and OWL (web Ontology Language), promise to make it easier for us to reconcile shared concepts among different representations or schemas. A mapping between ABCD 2.1 and DarwinCore has existed since before 2005.*1 ABCD 3.0 and DarwinCore are both now represented in RDF. In addition, the BioCollections Ontology (BCO) covers many of the shared concepts and is derived from the Basic Formal Ontology (BFO), an upper level ontology that has oriented many other biomedical ontologies. Reconciling ABCD and DarwinCore through alignment with BCO (in the OBO Foundry; Smith et al. 2007) would better connect TDWG standards to other domains in biology. We appreciate that many working scientists and data managers perceive ontologies as overly complicated. To mitigate the steep learning curve associated with ontologies, we expect to create simpler application profiles or schemas to guide and serve narrower communities of practice within the wider biodiversity domain. We also plan to integrate the current work of the Taxonomic Names and Concepts Interest Group and thereby eliminate the redundancy between DarwinCore and Taxonomic Concepts Transfer Schema (TCS; Kennedy et al. 2006). At the time of this writing, we have only agreements from the authors (i.e., conveners of relevant TDWG Interest Groups and other key stakeholders) to collaborate in pursuit of these common goals. In this presentation we will give a more detailed description of our objectives and products, the methods we are using to achieve them, and our progress to date.

Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Lewin, H. A., Richards, S., Lieberman Aiden, E., Allende, M. L., Archibald, J. M., Bálint, M., Barker, K. B., Baumgartner, B., Belov, K., Bertorelle, G., Blaxter, Mark L., Cai, J., Caperello, N. D., Carlson, K., Castilla-Rubio, J. C., Chaw, S-M., Chen, L., Childers, A. K., Coddington, J. A., Conde, D. A., Corominas, M., Crandall, K. A., Crawford, A. J., DiPalma, F., Durbin, R., Ebenezer, T. E., Edwards, S. V., Fedrigo, O., Flicek, P., Formenti, G., Gibbs, R. A., Gilbert, M. Thomas P., Goldstein, M. M., Graves, J. M., Greely, H. T., Grigoriev, I. V., Hackett, K. J., Hall, N., Haussler, D., Helgen, K. M., Hogg, C. J., Isobe, S., Jakobsen, K. S., Janke, A., Jarvis, E. D., Johnson, W. E., Jones, S. J. M., Karlsson, E. K., Kersey, P. J., Kim, J-H., Kress, W. J., Kuraku, S., Lawniczak, M. K. N., Leebens-Mack, J. H., Li, X., Lindblad-Toh, K., Liu, X., Lopez, J. V., Marques-Bonet, T., Mazard, S., Mazet, J. A. K., Mazzoni, C. J., Myers, E. W., O’Neill, R. J., Paez, S., Park, H., Robinson, G. E., Roquet, C., Ryder, O. A., Sabir, J. S. M., Shaffer, H. B., Shank, T. M., Sherkow, J. S., Soltis, P. S., Tang, B., Tedersoo, L., Uliano-Silva, M., Wang, K., Wei, X., Wetzer, R., Wilson, J. L., Xu, X., Yang, H., Yoder, A. D., Zhang, G. The Earth BioGenome Project 2020: starting the clock. Proceedings of the National Academy of Sciences of the United States of America, 119(4), (2022): e2115635118, https://doi.org/10.1073/pnas.2115635118.

Description: November 2020 marked 2 y since the launch of the Earth BioGenome Project (EBP), which aims to sequence all known eukaryotic species in a 10-y timeframe. Since then, significant progress has been made across all aspects of the EBP roadmap, as outlined in the 2018 article describing the project’s goals, strategies, and challenges (1). The launch phase has ended and the clock has started on reaching the EBP’s major milestones. This Special Feature explores the many facets of the EBP, including a review of progress, a description of major scientific goals, exemplar projects, ethical legal and social issues, and applications of biodiversity genomics. In this Introduction, we summarize the current status of the EBP, held virtually October 5 to 9, 2020, including recent updates through February 2021. References to the nine Perspective articles included in this Special Feature are cited to guide the reader toward deeper understanding of the goals and challenges facing the EBP.