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1. Scientific Cooperation: Supporting Circumpolar Permafrost Monitoring and Data Sharing

   https://doi.org/10.3390/land10060590  

   Bouffard, Troy J. ; Uryupova, Ekaterina ; Dodds, Klaus ; Romanovsky, Vladimir E. ; Bennett, Alec P. ; Streletskiy, Dmitry ( June 2021 , Land)

   null (Ed.)

   While the world continues to work toward an understanding and projections of climate change impacts, the Arctic increasingly becomes a critical component as a bellwether region. Scientific cooperation is a well-supported narrative and theme in general, but in reality, presents many challenges and counter-productive difficulties. Moreover, data sharing specifically represents one of the more critical cooperation requirements, as part of the “scientific method [which] allows for verification of results and extending research from prior results”. One of the important pieces of the climate change puzzle is permafrost. In general, observational data on permafrost characteristics are limited. Currently, most permafrost data remain fragmented and restricted to national authorities, including scientific institutes. The preponderance of permafrost data is not available openly—important datasets reside in various government or university labs, where they remain largely unknown or where access restrictions prevent effective use. Although highly authoritative, separate data efforts involving creation and management result in a very incomplete picture of the state of permafrost as well as what to possibly anticipate. While nations maintain excellent individual permafrost research programs, a lack of shared research—especially data—significantly reduces effectiveness of understanding permafrost overall. Different nations resource and employ various approaches to studying permafrost, including the growing complexity of scientific modeling. Some are more effective than others and some achieve different purposes than others. Whereas it is not possible for a nation to effectively conduct the variety of modeling and research needed to comprehensively understand impacts to permafrost, a global community can. In some ways, separate scientific communities are not necessarily concerned about sharing data—their work is secured. However, decision and policy makers, especially on the international stage, struggle to understand how best to anticipate and prepare for changes, and thus support for scientific recommendations during policy development. To date, there is a lack of research exploring the need to share circumpolar permafrost data. This article will explore the global data systems on permafrost, which remain sporadic, rarely updated, and with almost nothing about the subsea permafrost publicly available. The authors suggest that the global permafrost monitoring system should be real time (within technical and reasonable possibility), often updated and with open access to the data (general way of representing data required). Additionally, it will require robust co-ordination in terms of accessibility, funding, and protocols to avoid either duplication and/or information sharing. Following a brief background, this article will offer three supporting themes, (1) the current state of permafrost data, (2) rationale and methods to share data, and (3) implications for global and national interests. 

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2. Terrestrial Parasite Tracker indexed biotic interactions and review summary

   https://doi.org/10.5281/zenodo.6761707  

   Poelen, Jorrit H. ; Seltmann, Katja C. ; Campbell, Mariel ; Orlofske, Sarah A. ; Light, Jessica E. ; Tucker, Erika M. ; Demboski, John R ; McElrath, Tommy ; Grinter, Christopher C ; Diaz-Bastin, Rachel ; et al ( January 2022 , Zenodo)

   PLEASE CONTACT AUTHORS IF YOU CONTRIBUTE AND WOULD LIKE TO BE LISTED AS A CO-AUTHOR. (this message will be removed some time weeks/months after the first publication)

   Terrestrial Parasite Tracker indexed biotic interactions and review summary.

   The Terrestrial Parasite Tracker (TPT) project began in 2019 and is funded by the National Science foundation to mobilize data from vector and ectoparasite collections to data aggregators (e.g., iDigBio, GBIF) to help build a comprehensive picture of arthropod host-association evolution, distributions, and the ecological interactions of disease vectors which will assist scientists, educators, land managers, and policy makers. Arthropod parasites often are important to human and wildlife health and safety as vectors of pathogens, and it is critical to digitize these specimens so that they, and their biotic interaction data, will be available to help understand and predict the spread of human and wildlife disease.

   This data publication contains versioned TPT associated datasets and related data products that were tracked, reviewed and indexed by Global Biotic Interactions (GloBI) and associated tools. GloBI provides open access to finding species interaction data (e.g., predator-prey, pollinator-plant, pathogen-host, parasite-host) by combining existing open datasets using open source software.

   If you have questions or comments about this publication, please open an issue at https://github.com/ParasiteTracker/tpt-reporting or contact the authors by email.

   Funding:
   The creation of this archive was made possible by the National Science Foundation award "Collaborative Research: Digitization TCN: Digitizing collections to trace parasite-host associations and predict the spread of vector-borne disease," Award numbers DBI:1901932 and DBI:1901926

   References:
   Jorrit H. Poelen, James D. Simons and Chris J. Mungall. (2014). Global Biotic Interactions: An open infrastructure to share and analyze species-interaction datasets. Ecological Informatics. https://doi.org/10.1016/j.ecoinf.2014.08.005.

   GloBI Data Review Report

   Datasets under review:
    - University of Michigan Museum of Zoology Insect Division. Full Database Export 2020-11-20 provided by Erika Tucker and Barry Oconner. accessed via https://github.com/EMTuckerLabUMMZ/ummzi/archive/6731357a377e9c2748fc931faa2ff3dc0ce3ea7a.zip on 2022-06-24T14:02:48.801Z
    - Academy of Natural Sciences Entomology Collection for the Parasite Tracker Project accessed via https://github.com/globalbioticinteractions/ansp-para/archive/5e6592ad09ec89ba7958266ad71ec9d5d21d1a44.zip on 2022-06-24T14:04:22.091Z
    - Bernice Pauahi Bishop Museum, J. Linsley Gressitt Center for Research in Entomology accessed via https://github.com/globalbioticinteractions/bpbm-ent/archive/c085398dddd36f8a1169b9cf57de2a572229341b.zip on 2022-06-24T14:04:37.692Z
    - Texas A&M University, Biodiversity Teaching and Research Collections accessed via https://github.com/globalbioticinteractions/brtc-para/archive/f0a718145b05ed484c4d88947ff712d5f6395446.zip on 2022-06-24T14:06:40.154Z
    - Brigham Young University Arthropod Museum accessed via https://github.com/globalbioticinteractions/byu-byuc/archive/4a609ac6a9a03425e2720b6cdebca6438488f029.zip on 2022-06-24T14:06:51.420Z
    - California Academy of Sciences Entomology accessed via https://github.com/globalbioticinteractions/cas-ent/archive/562aea232ec74ab615f771239451e57b057dc7c0.zip on 2022-06-24T14:07:16.371Z
    - Clemson University Arthropod Collection accessed via https://github.com/globalbioticinteractions/cu-cuac/archive/6cdcbbaa4f7cec8e1eac705be3a999bc5259e00f.zip on 2022-06-24T14:07:40.925Z
    - Denver Museum of Nature and Science (DMNS) Parasite specimens (DMNS:Para) accessed via https://github.com/globalbioticinteractions/dmns-para/archive/a037beb816226eb8196533489ee5f98a6dfda452.zip on 2022-06-24T14:08:00.730Z
    - Field Museum of Natural History IPT accessed via https://github.com/globalbioticinteractions/fmnh/archive/6bfc1b7e46140e93f5561c4e837826204adb3c2f.zip on 2022-06-24T14:18:51.995Z
    - Illinois Natural History Survey Insect Collection accessed via https://github.com/globalbioticinteractions/inhs-insects/archive/38692496f590577074c7cecf8ea37f85d0594ae1.zip on 2022-06-24T14:19:37.563Z
    - UMSP / University of Minnesota / University of Minnesota Insect Collection accessed via https://github.com/globalbioticinteractions/min-umsp/archive/3f1b9d32f947dcb80b9aaab50523e097f0e8776e.zip on 2022-06-24T14:20:27.232Z
    - Milwaukee Public Museum Biological Collections Data Portal accessed via https://github.com/globalbioticinteractions/mpm/archive/9f44e99c49ec5aba3f8592cfced07c38d3223dcd.zip on 2022-06-24T14:20:46.185Z
    - Museum for Southern Biology (MSB) Parasite Collection accessed via https://github.com/globalbioticinteractions/msb-para/archive/178a0b7aa0a8e14b3fe953e770703fe331eadacc.zip on 2022-06-24T15:16:07.223Z
    - The Albert J. Cook Arthropod Research Collection accessed via https://github.com/globalbioticinteractions/msu-msuc/archive/38960906380443bd8108c9e44aeff4590d8d0b50.zip on 2022-06-24T16:09:40.702Z
    - Ohio State University Acarology Laboratory accessed via https://github.com/globalbioticinteractions/osal-ar/archive/876269d66a6a94175dbb6b9a604897f8032b93dd.zip on 2022-06-24T16:10:00.281Z
    - Frost Entomological Museum, Pennsylvania State University accessed via https://github.com/globalbioticinteractions/psuc-ento/archive/30b1f96619a6e9f10da18b42fb93ff22cc4f72e2.zip on 2022-06-24T16:10:07.741Z
    - Purdue Entomological Research Collection accessed via https://github.com/globalbioticinteractions/pu-perc/archive/e0909a7ca0a8df5effccb288ba64b28141e388ba.zip on 2022-06-24T16:10:26.654Z
    - Texas A&M University Insect Collection accessed via https://github.com/globalbioticinteractions/tamuic-ent/archive/f261a8c192021408da67c39626a4aac56e3bac41.zip on 2022-06-24T16:10:58.496Z
    - University of California Santa Barbara Invertebrate Zoology Collection accessed via https://github.com/globalbioticinteractions/ucsb-izc/archive/825678ad02df93f6d4469f9d8b7cc30151b9aa45.zip on 2022-06-24T16:12:29.854Z
    - University of Hawaii Insect Museum accessed via https://github.com/globalbioticinteractions/uhim/archive/53fa790309e48f25685e41ded78ce6a51bafde76.zip on 2022-06-24T16:12:41.408Z
    - University of New Hampshire Collection of Insects and other Arthropods UNHC-UNHC accessed via https://github.com/globalbioticinteractions/unhc/archive/f72575a72edda8a4e6126de79b4681b25593d434.zip on 2022-06-24T16:12:59.500Z
    - Scott L. Gardner and Gabor R. Racz (2021). University of Nebraska State Museum - Parasitology. Harold W. Manter Laboratory of Parasitology. University of Nebraska State Museum. accessed via https://github.com/globalbioticinteractions/unl-nsm/archive/6bcd8aec22e4309b7f4e8be1afe8191d391e73c6.zip on 2022-06-24T16:13:06.914Z
    - Data were obtained from specimens belonging to the United States National Museum of Natural History (USNM), Smithsonian Institution, Washington DC and digitized by the Walter Reed Biosystematics Unit (WRBU). accessed via https://github.com/globalbioticinteractions/usnmentflea/archive/ce5cb1ed2bbc13ee10062b6f75a158fd465ce9bb.zip on 2022-06-24T16:13:38.013Z
    - US National Museum of Natural History Ixodes Records accessed via https://github.com/globalbioticinteractions/usnm-ixodes/archive/c5fcd5f34ce412002783544afb628a33db7f47a6.zip on 2022-06-24T16:13:45.666Z
    - Price Institute of Parasite Research, School of Biological Sciences, University of Utah accessed via https://github.com/globalbioticinteractions/utah-piper/archive/43da8db550b5776c1e3d17803831c696fe9b8285.zip on 2022-06-24T16:13:54.724Z
    - University of Wisconsin Stevens Point, Stephen J. Taft Parasitological Collection accessed via https://github.com/globalbioticinteractions/uwsp-para/archive/f9d0d52cd671731c7f002325e84187979bca4a5b.zip on 2022-06-24T16:14:04.745Z
    - Giraldo-Calderón, G. I., Emrich, S. J., MacCallum, R. M., Maslen, G., Dialynas, E., Topalis, P., … Lawson, D. (2015). VectorBase: an updated bioinformatics resource for invertebrate vectors and other organisms related with human diseases. Nucleic acids research, 43(Database issue), D707–D713. doi:10.1093/nar/gku1117. accessed via https://github.com/globalbioticinteractions/vectorbase/archive/00d6285cd4e9f4edd18cb2778624ab31b34b23b8.zip on 2022-06-24T16:14:11.965Z
    - WIRC / University of Wisconsin Madison WIS-IH / Wisconsin Insect Research Collection accessed via https://github.com/globalbioticinteractions/wis-ih-wirc/archive/34162b86c0ade4b493471543231ae017cc84816e.zip on 2022-06-24T16:14:29.743Z
    - Yale University Peabody Museum Collections Data Portal accessed via https://github.com/globalbioticinteractions/yale-peabody/archive/43be869f17749d71d26fc820c8bd931d6149fe8e.zip on 2022-06-24T16:23:29.289Z

   Generated on:
   2022-06-24

   by:
   GloBI's Elton 0.12.4 
   (see https://github.com/globalbioticinteractions/elton).

   Note that all files ending with .tsv are files formatted 
   as UTF8 encoded tab-separated values files.

   https://www.iana.org/assignments/media-types/text/tab-separated-values

   
   Included in this review archive are:

   README:
     This file.

   review_summary.tsv:
     Summary across all reviewed collections of total number of distinct review comments.

   review_summary_by_collection.tsv:
     Summary by reviewed collection of total number of distinct review comments.

   indexed_interactions_by_collection.tsv: 
     Summary of number of indexed interaction records by institutionCode and collectionCode.

   review_comments.tsv.gz:
     All review comments by collection.

   indexed_interactions_full.tsv.gz:
     All indexed interactions for all reviewed collections.

   indexed_interactions_simple.tsv.gz:
     All indexed interactions for all reviewed collections selecting only sourceInstitutionCode, sourceCollectionCode, sourceCatalogNumber, sourceTaxonName, interactionTypeName and targetTaxonName.

   datasets_under_review.tsv:
     Details on the datasets under review.

   elton.jar: 
     Program used to update datasets and generate the review reports and associated indexed interactions.

   datasets.zip:
     Source datasets used by elton.jar in process of executing the generate_report.sh script.

   generate_report.sh:
     Program used to generate the report

   generate_report.log:
     Log file generated as part of running the generate_report.sh script
    

    

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3. Making Parasite-Host Associations Visible using Global Biotic Interactions

   https://doi.org/10.3897/biss.4.58985  

   Seltmann, Katja ; Poelen, Jorrit ; Sullivan, Kathryn ; Zaspel, Jennifer ( October 2020 , Biodiversity Information Science and Standards)

   null (Ed.)

   A wealth of information about how parasites interact with their hosts already exists in collections, scientific publications, specialized databases, and grey literature. The US National Science Foundation-funded Terrestrial Parasite Tracker Thematic Collection Network (TPT) project began in 2019 to help build a comprehensive picture of arthropod ectoparasites including the evolution of these parasite-host biotic associations, distributions, and the ecological interactions of disease vectors. TPT is a network of biodiversity collections whose data can assist scientists, educators, land managers, and policymakers to better understand the complex relationship between hosts and parasites including emergent properties that may explain the causes and frequency of human and wildlife pathogens. TPT member collections make their association information easier to access via Global Biotic Interactions (GloBI, Poelen et al. 2014), which is periodically archived through Zenodo to track progress in the TPT project. TPT leverages GloBI's ability to index biotic associations from specimen occurrence records that come from existing management systems (e.g., Arctos, Symbiota, EMu, Excel, MS Access) to avoid having to completely rework existing, or build new, cyber-infrastructures before collections can share data. TPT-affiliated collection managers use collection-specific translation tables to connect their verbatim (or original) terms used to describe associations (e.g., "ex", "found on", "host") to their interpreted, machine-readable terms in the OBO Relations Ontology (RO). These interpreted terms enable searches across previously siloed association record sets, while the original verbatim values remain accessible to help retain provenance and allow for interpretation improvements. TPT is an ambitious project, with the goal to database label data from over 1.2 million specimens of arthropod parasites of vertebrates coming from 22 collections across North America. In the first year of the project, the TPT collections created over 73,700 new records and 41,984 images. In addition, 17 TPT data providers and three other collaborators shared datasets that are now indexed by GloBI, visible on the TPT GloBI project page. These datasets came from collection specimen occurrence records and literature sources. Two TPT data archives that capture and preserve the changes in the data coming from TPT to GloBI were published through Zenodo (Poelen et al. 2020a, Poelen et al. 2020b). The archives document the changes in how data are shared by collections including the biotic association data format and quantity of data captured. The Poelen et al. 2020b report included all TPT collections and biotic interactions from Arctos collections in VertNet and the Symbiota Collection of Arthropods Network (SCAN). The total number of interactions included in this report was 376,671 records (500,000 interactions is the overall goal for TPT). In addition, close coordination with TPT collection data managers including many one-on-one conversations, a workshop, and a webinar (Sullivan et al. 2020) was conducted to help guide the data capture of biotic associations. GloBI is an effective tool to help integrate biotic association data coming from occurrence records into an openly accessible, global, linked view of existing species interaction records. The results gleaned from the TPT workshop and Zenodo data archives demonstrate that minimizing changes to existing workflows allow for custom interpretation of collection-specific interaction terms. In addition, including collection data managers in the development of the interaction term vocabularies is an important part of the process that may improve data sharing and the overall downstream data quality. 

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4. Wildfire effects on aquatic chemistry (Yukon Kuskokwim Delta, Alaska), 2015-2019

   https://doi.org/10.18739/A2K35MF90  

   Zolkos, Scott ; MacDonald, Erin ; Hung, Jacqueline ; Schade, John ; Ludwig, Sarah ; Mann, Paul ; Treharne, Rachael ; Natali, Susan ( January 2022 , NSF Arctic Data Center)

   Data from this study originate from the NSF (National Science Foundation) Polaris Project. The Polaris Project integrates scientific research in the Arctic-boreal region with education and outreach, with a primary focus on engaging and inspiring the next generation of scientists. The overarching scientific issue that drives the Polaris Project is the vulnerability and fate of ancient carbon stored in perennially frozen ground, permafrost. Although extensive permafrost thaw is expected to occur across the northern permafrost region this century, large uncertainties remain in the timing, magnitude, and form of carbon that will be released. Participants of the Polaris Project conducted field research in the Yukon-Kuskokwim Delta (YKD), collaborating to make fundamental scientific discoveries related to the transformation and fate of thawed permafrost carbon, and implications for global climate. This data set includes aquatic chemistry data from expeditions to the YKD during 2015–2019. Parameters measured include water temperature, pH, dissolved oxygen, conductivity, dissolved organic and inorganic carbon, nitrogen species, phosphorous, greenhouse gases, stables isotopes of carbon and water, optical properties of water, and fluxes of methane and carbon dioxide made in the field. These data were compiled and underwent quality assurance / quality control specifically for the scientific objectives of the manuscript published by Zolkos et al. (2022). Consequently, this dataset contains a modified version of Polaris Project YKD aquatic chemistry data previously published for 2015–2016 (http://doi.org/10.18739/A22804Z8M) and 2017 (http://doi.org/10.18739/A23775V7T). Data from 2018–2019 were not previously published. Therefore, users interested in the original datasets for 2015–2017 are encouraged to access them via the provided links, while users interested in the data and metadata specific to the associated manuscript by Zolkos et al. are encouraged to use this companion dataset. 

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5. Addressing Urgent Questions for PFAS in the 21st Century

   https://doi.org/10.1021/acs.est.1c03386  

   Ng, Carla ; Cousins, Ian T. ; DeWitt, Jamie C. ; Glüge, Juliane ; Goldenman, Gretta ; Herzke, Dorte ; Lohmann, Rainer ; Miller, Mark ; Patton, Sharyle ; Scheringer, Martin ; et al ( September 2021 , Environmental Science & Technology)

   Despite decades of research on per- and polyfluoroalkyl substances (PFAS), fundamental obstacles remain to addressing worldwide contamination by these chemicals and their associated impacts on environmental quality and health. Here, we propose six urgent questions relevant to science, technology, and policy that must be tackled to address the “PFAS problem”: (1) What are the global production volumes of PFAS, and where are PFAS used? (2) Where are the unknown PFAS hotspots in the environment? (3) How can we make measuring PFAS globally accessible? (4) How can we safely manage PFAS-containing waste? (5) How do we understand and describe the health effects of PFAS exposure? (6) Who pays the costs of PFAS contamination? The importance of each question and barriers to progress are briefly described, and several potential paths forward are proposed. Given the diversity of PFAS and their uses, the extreme persistence of most PFAS, the striking ongoing lack of fundamental information, and the inequity of the health and environmental impacts from PFAS contamination, there is a need for scientific and regulatory communities to work together, with cooperation from PFAS-related industries, to fill in critical data gaps and protect human health and the environment. 

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