Alphabet Soup and Advocacy: a penseive approach Quick
Alphabet Soup and Advocacy: a penseive approach Quick overview of some acronyms, projects, software, etc. affiliated with natural history collections data use and digitization initiatives @SPNHC2017 NHC Biodiversity Informatics 101 Deborah Paul - iDigBio and Shelley James Royal Botanic Gardens Sydney Sunday 18 June 2017 iDigBio is funded by a grant from the National Science Foundations Advancing Digitization of Biodiversity Collections Program. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation. An acronym rich environment (ARE) 2 Advocating for Collections NSCA Wash DC-based community supporting collections, staff, and research activities. Membership in the NSC Alliance links you to a network of institutions, scientists and other professionals in North America through which you can share news, information and common concerns - and help shape the future of our community. AIBS providing peer-reviewed, vetted information about the biology field and
profession takes action to build the capacity and the leadership of the community to address matters of common concern. 3 From NIBA to the ADBC A diverse group of scientists created the vision of a Networked Integrated Biocollections Alliance (NIBA) to mobilize collections data, increase biodiversity informatics collections skills and knowledge capacity, foster research and educational use of collections data, develop a robust cyber and software infrastructure to support this work, Proposed such to the National Science Foundation (NSF) NIBA Strategic Plan NIBA Implementation Plan Resulted in the program Advancing the Digitization of Biological Collections (ADBC) 4 Biodiversity Collections Network (BCoN) (formerly NIBA) a 5-year NSF funded Research Coordinated Network (RCN) Develop a coordinated, large-scale effort to digitize the nations biological collections, and all that this entails. http://bcon.aibs.org/
5 Issus coleoptratus Advancing the Digitization of Biological Collections iDigBio, thats Integrated Digitized Biocollections Credit: Malcolm Burrows to develop an integrated national infrastructure and resource for digitization of existing biodiversity collections in the U.S. iDigBio Thematic Collection Networks (TCNs) A network of collaborative institutions Digitize around a particular research theme. charged with defining and delineating subprojects for technology development or content generation; identifying deliverable goals, metrics for assessment, and specific needs for community support; providing technical support; and strengthening communications and outreach to other collections Partners to Existing Networks (PENs) must increase the number of specimens digitized in the ongoing project and fill gaps not addressed by the specimens in the existing TCN. 6 iDigBio the home uniting biocollections (HUB) Sustainability, digitization, facilitating research and
educational use of collections data, cyberinfrastructure, Advanced Computing and Information Science (ACIS) CyberInfrastructure Community Implementing the cyberinfrastructure for iDigBio Research Community Planet-wide collaborative 4-day event to engage the public, including students, to transcribe collections data and meet scientists Digitization Community n WeDigBio tio ra ist in
Collections coming to life in 3-D, classroom applications, collaboration with TCNs, ASU m Ad Libraries of Life (a free app) Education & Outreach Community The FOSSIL Project Engaging amateur fossil clubs and societies as downstream users of digitized data 7 Thematic Collections Networks (TCNs) and Partners to Existing Networks (PENs) 1 1 1 TCN: network of institutions strategically digitizing information for a particular research theme, such as impacts of climate change or biota of a region.
The Cretaceous World 4 2 The Mid-Atlantic Megalopolis 2 2 4 8 Digitization Collection Management Software Data Mobilization TDWG Biodiversity Information Standards (tdwg) dwc - Darwin Core ac - Audubon Core IPT Integrated Publishing Toolkit
(from GBIF) Kurator and Akka GEOLocate DAMS ABBYY GUID, UUID, ARK, IGSN Arctos Symbiota Specify Axiell EMu collectionspace Community Building SPNHC GRBio SCNet ECN Working Groups: DROID, GWG, (more about these next slide) 9
VISION E&O DIGITIZATION Working and Interest Groups (wg) Developing Robust Object to Image to Data (DROID1,2,3,4) International Whole-Drawer Digitization Interest Group (WDD) Fluid-preserved Arthropod and Microscopic Slide Imaging Interest Group Paleo Digitization Working Group (PaleoDigi) North American Network of Small Herbaria Working Group (NANSH) Biodiversity Informatics Management (BIM) Working Group Georeferencing Working Group (GWG) Symbiota Working Group (SWG) Augmenting OCR (aOCR) Outlier Detection and Documentation by Collectors Working Group (ODD
Collectors) Education & Outreach (E&O) Augmented Reality Public Education/Outreach Working Group (ARPEO) User Engagement for Public Participation in Digitization (CitSciEngage) Interoperability for Public Participation in Digitization (CitSciInterop) Cyberinfrastructure (CYWG) Data Management Interest Group (DMI) 10 Data aggregation and Data use EoL BHL NEON CyVerse (iPlant)
GBIF iDigBio VertNet BISON USVH ALA, DigiVol Canadensys SiBBr CONABIO (Mexico) CRIA (Brazil) and SpeciesLink
Lifemapper Phylolink (was Phylojive) Carto (aka CartoDB) QGIS API tools riDigBio, rGBIF, rVertNet, ePandda Python R, Rstudio, ROpenSci MySQL, SQL, SQLite GitHub Architectur e Aggregating Specimen Data Research tools and resources Implementation Biodiversity Data Mobilization and
Use 11 Data aggregation and Data use Biodiversity Data Mobilization and Use Aggregating Specimen Data EoL - Encyclopedia of Life BHL Biodiversity Heritage Library NEON National Ecological Observatory Network CyVerse (iPlant) - facilitating scientific research in the cloud GBIF Global Biodiversity Information Facility
iDigBio VertNet Vertebrate data portal, Data Mobilization and cleaning services BISON Biodiversity Serving our Nation GBIF North American Node USVH United States Virtual Herbarium CSIRO, ALA, DigiVol Atlas of Living Australia Canadensys - unlocking specimen information held by Canadian university-based biological collections SiBBr Brazilian Biodiversity Information System or Sistema de Informao sobre a Biodiversidade Brasileira) CONABIO (Mexico) CRIA (Brazil) and SpeciesLink 12 Education, Outreach, Inreach AIM-UP! Advancing Integration of Museums into Undergraduate Programs; exploring the use of collections data in undergraduate education Notes from Nature Crowdsourcing collections transcription, creating communities WeDigBio Worldwide 4-day collaborative crowdsourcing transcription event Libraries-of-Life Using the magic of specimens in 3-D to engage the public and students specimen-based research, iDigBio + TCNs + ASU
The FOSSIL Project Engaging US fossil clubs in using digitized fossil data iNaturalist observation app, connecting scientists and the general public ePandda Enhancing Paleontological and Neontological Data Discovery API, connecting scientific literature with specimens Data Carpentry & Software Carpentry (DC and SwC) Biodiversity informatics skills for graduate students and researchers. Focus on tidy data, fit for reproducible research. DC novices, SwC for self-taught programmers in the sciences. 13 Publishing Pensoft ARPHA Writing Tool (AWT): Authoring, Reviewing, Publishing, Hosting and Archiving DataCite, DOI Find, share and reuse, cite data, connect and get credit Mendeley Free reference manager; organize papers, read & annotate your PDFs, collaborate in private or open groups, and securely access your research from everywhere. ORCiD Open Researcher and Contributor ID
DataONE Data Observation Network for Earth (DataONE) data repository and data management best practices Data Dryad Curated resource making the data underlying scientific publications discoverable, freely reusable, and citable general-purpose home for a wide diversity of datatypes Figshare online digital repository where researchers can preserve and share their research outputs, including figures, datasets, images, and videos. Open data 14 Got more? idigbio.org/wiki facebook.com/iDigBio twitter.com/iDigBio vimeo.com/iDigBio idigbio.org/rss-feed.xml idigbio.org/events-calendar/export.ics iDigBio is funded by a grant from the National Science Foundations Advancing Digitization of Biodiversity Collections Program. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.
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