demo

Examples:

Invertnet

Drawer 5 image tilt

Diptera_Agromyzidae_Paraphytomyza_Phytomyza_5342



Philip Anders - Biological Informatician - Illinois Natural History Survey

This email address is being protected from spambots. You need JavaScript enabled to view it.

http://wwx.inhs.illinois.edu/directory/show/anders2

Presentation:

    Invertnet short history

InvertNet: A new paradigm for digital access to invertebrate collections

InvertNet, one of the three Thematic Collection Networks (TCNs) funded in the first round of the U.S. National Science Foundation's Advancing Digitization of Biological Collections (ADBC) program, is tasked with providing digital access to ~60 million specimens housed in 22 arthropod (primarily insect) collections at institutions distributed throughout the upper midwestern USA. The traditional workflow for insect collection digitization involves manually keying information from specimen labels into a database and attaching a unique identifier label to each specimen. This remains the dominant paradigm, despite some recent attempts to automate various steps in the process using more advanced technologies. InvertNet aims to develop improved semi-automated, high-throughput workflows for digitizing and providing access to invertebrate collections that balance the need for speed and cost-effectiveness with long-term preservation of specimens and accuracy of data capture. The proposed workflows build on recent methods for digitizing and providing access to high-quality images of multiple specimens (e.g., entire drawers of pinned insects) simultaneously.(ref. https://experts.illinois.edu/en/publications/invertnet-a-new-paradigm-for-digital-access-to-invertebrate-colle)


    BugEye -> lets take some pictures

 Digitization portals ->

        Demo - http://www.invertnet.org/demo
        What is the purpose?
            Provide basic information, specimen/occurrence data
            Catalog #'s,Taxon, collector, determination, dates, locality, habitat, associated species
            Media files, images
            Visual maps
            *Comments, *annotations, *linked resources
            *quick access
            *auto agents, rss
        *How to encourage these better?

      INHS data portal examples:
        Insects of Braidwood Dunes and Savanna (Custom)
          http://wwx.inhs.illinois.edu/collections/data/braidwood/

        Wild Plants of the Prairie State (Custom)
          http://wwx.inhs.illinois.edu/data/plantdb/

        Illinois Natural History Survey Collections (Symbiota)
            Amphibians & Reptiles, Annelids, Birds, Crustaceans, Fish, Fossils,
            Fungi, Insects, Mammals, Mollusks, Plants
            http://biocoll.inhs.illinois.edu

        Mycology Collections data Portal (Symbiota)
            http://mycoportal.org/portal/index.php

        Consortium of Midwest Herbaria (Symbiota)
            http://midwestherbaria.org/portal/

        Illinois Natural History Survey: Insect Collection (Custom)
            http://inhsinsectcollection.speciesfile.org/InsectCollection.aspx

        Therevid PEET Database (FileMaker)
            http://wwn.inhs.illinois.edu/research/therevidphp/

        Orthoptera Species File Online (speciesfile.org)
            http://orthoptera.speciesfile.org/HomePage/Orthoptera/HomePage.aspx

      How do you find what your looking for? using the web?
      Networking with technology


 Reference notes:

== iDigBio (ref. https://www.idigbio.org/)
  Welcome to Integrated Digitized Biocollections (iDigBio), the National Resource for Advancing Digitization of Biodiversity Collections (ADBC) funded by the National Science Foundation. Through ADBC, data and images for millions of biological specimens are being made available in electronic format for the research community, government agencies, students, educators, and the general public.

== Specify (ref. http://www.sustain.specifysoftware.org/)
  Capabilities. With your collection database loaded on a tablet computer offering a gesture-based interface anyone can master in seconds, Specify Insight will mobilize your research data, and create opportunities for education and outreach engagement. Utilize your taxonomic and geographic data on the iPad to showcase your science to a more inclusive group of researchers and students. Let stakeholders personally experience the diversity and uniqueness of your collection on their iPads. Extend your collection’s data reach to students in classrooms and to informal science education activities. And for your own curatorial and research uses, you can take your collection data anywhere you go.
  Specify Insight links to web images sources of Flickr, FishBase, and to your own collection’s specimen images served though the Specify Attachment Server. With wireless internet, available web images automatically appear as thumbnails for each mapped species, and pressing on thumbnails brings up a full-sized copy.
  Insight also presents summary statistics of your collection, showing collection growth through time, and the top families and countries in your database. Insight’s map display shows specimen counts by continent, country, and for the U.S., by state.
  Collecting localities are represented as pins on iPad maps. Pressing on a pin shows detailed locality information, and swiping across the data panel at the top of the Insight display shows each Collection Object (lot or specimen) from the highlighted locality. Distribution maps can be filtered further by species with the right side pull-down taxon menu.
  Multiple collection databases can be downloaded and explored on an iPad running Insight. Specify database managers can provide access to the iPad copy of their data by offering Insight Cloud Server logins to other iPad users. Multiple collections from the same institution can be loaded onto an iPad as well as databases from multiple institutions.

  Ten Research Uses of Collection Data on an iPad:

    Verify your georeferences and geography data with the Insight map interface.
    Browse and verify your taxonomic determinations with the taxon tree browser.
    Identify taxonomic and geographic gaps in your collection for development and expedition planning.
    Locate well-collected localities to document collection geographical strengths.
    Take your iPad into the collection gallery for inventory and to verify IDs and data on specimen labels.
    Take your collection data into the field to review existing vouchers and collecting priorities in situ.
    Take your collection data home, to the coffee shop, to bed! You are not a 9-5 scientist after all, why not utilize all of those unexpected snippets of idle time to review your collection information?
    Un-tether! Take your collection data to places without a wire, Wi-Fi or cellular data services.
    Take your collection data on the road to meetings, workshops, to provide copies to your colleagues.
    Load up your iPad with multiple collections from your institution or from multiple institutions to compare taxonomic strengths and distribution patterns across collections.
    Education. The iPad is an intuitive platform to integrate your biological collection information for formal and informal science curricula. K-12 teachers and students alike will find its interface easy to use, fun, and a rich, informative representation of your biodiversity holdings. By making your iPad credentials publicly available, anyone with an iPad2+ can install Specify Insight and download your collection data to peruse and appreciate your holdings.
    Stakeholders. What is the probability that your Director, Dean, Provost, President, or Minister of Science would ever sit down and keystroke a query into a workstation to explore your collection? Would they find searching a specimen database and staring at data forms about as engaging as watching paint dry?
    Not any longer! Sidle up to those suits and slip a copy of Specify Insight and your collection data onto their iPads and let them experience the ease of exploring your collection with simple finger swipes and presses. In a few seconds, impress your stakeholders with the geographical breadth, regional strength, and historical legacy of your holdings.
    Try Specify Insight. To evaluate Insight now, download a copy from the Apple Store. Then use the account credentials below to log into the Specify Insight Cloud Server and download the sample databases from the Ichthyology Collection at the University of Kansas.
    With Specify Insight running on an iPad, log in with:
    Username: This email address is being protected from spambots. You need JavaScript enabled to view it.
    Password: insight
    Specify Insight on the iPad will bring the science and data of biological collections to new audiences by mobilizing specimen information and images away from research desktops and museum galleries, and by providing an easy, gesture-based interface for biodiversity data visualization and exploration.

== Symbiota (ref. http://http://symbiota.org/docs/)
Built-in OCR/NLP and georeferencing tools
Powerful data/products management tools
Facilitates data mobilization to iDigBio, GBIF
Download entire biodiversity datasets in 2-3 clicks
Map georeferenced specimen records in 2-3 clicks
High-resolution images and species profile pages
Create collaborative regional taxon checklists
Interactive, region-sensitive identification keys
"Name that species" educational game
Flash Card Quiz educational game

A core goal of Symbiota is to offer a platform for documenting biodiversity occurrences based on
specimens and observations, by providing modular tools to share, visualize and synthesize biodiversity
data for question-driven research (e.g. via checklists and interactive keys). Creating robust, multifunctional
biodiversity software and data processing workflows, as well as curating data relationships for
flexible management and on-line publication, are each goals capable of overwhelming the IT resources of
an individual collection. A central premise of Symbiota is that through a collaborative partnership of
biodiversity informaticians and collection research communities, higher quality and more publicly useful
biodiversity portals can be built, rather than the old model of often highly customized stand-alone
databases at an individual institution. Symbiota's open source software development framework promotes
use-driven code innovation and tool creation. All of this allows collection scientists to concentrate their
efforts on the curation of high-quality datasets.

The Symbiota Working Group (SWG) provides an active user help forum and strategic community support.

http://symbiota.org/docs/wp-content/uploads/Symbiota_Primer_2017.pdf

List of Known Symbiota Portals (Updated February, 2016)
  Portal Name & Theme Portal Web Address (URL)
  Consortium of North American Lichen Herbaria http://lichenportal.org/portal/index.php
  Arctic Lichen Flora http://lichenportal.org/arctic/index.php
  Consortium of North American Bryophyte Herbaria http://bryophyteportal.org/portal/
  Frullania Collaborative Research Network http://bryophyteportal.org/frullania/
  Macroalgal Consortium Herbarium Portal http://macroalgae.org/portal/index.php
  MyCoPortal http://mycoportal.org/portal/index.php
  Smithsonian Tropical Research Institute Portal (STRI) http://stricollections.org/portal/
  Aquatic Invasives http://greatlakesinvasives.org/portal/index.php
  Consortium of Midwest Herbaria http://midwestherbaria.org/portal/index.php
  SEINet (Original Portal – Plants) http://swbiodiversity.org/seinet/index.php
  Intermountain Region Herbarium Network (IRHN) http://intermountainbiota.org/portal/index.php
  SouthEast Regional Network of Expertise and Collections
  (SERNEC) http://sernecportal.org/portal/
  North American Network of Small Herbaria http://nansh.org/portal/index.php
  Northern Great Plains Herbaria http://ngpherbaria.org/portal/index.php
  New Mexico Biodiversity Portal http://swbiodiversity.unm.edu/
  Consortium of Northeastern Herbaria (CNH) http://portal.neherbaria.org/portal/
  Madrean Archipelago Biodiversity Assessment (MABA) Flora http://madrean.org/symbflora/projects/index.php
  Madrean Archipelago Biodiversity Assessment (MABA) Fauna http://madrean.org/symbfauna/projects/index.php
  Herbario Virtual Austral Americano http://herbariovaa.org/
  CoTRAM – Cooperative Taxonomic Resource for Amer.
  Myrtaceae http://cotram.org/
  InvertEBase Data Portal http://invertebase.org/portal/index.php
  Symbiota Collections of Arthropods Network (SCAN) http://symbiota4.acis.ufl.edu/scan/portal/index.php
  Neotropical Entomology http://symbiota.org/neotrop/entomology/index.php
  Neotropical Flora http://symbiota.org/neotrop/plantae/index.php
  Monarch (California Academy of Sciences) http://monarch.calacademy.org/
  The Lundell Plant Diversity Portal http://prc-symbiota.tacc.utexas.edu/index.php
  Virtual Flora of Wisconsin http://symbiota.botany.wisc.edu
  Red de Herbarios del Noroeste de México http://herbanwmex.net/portal/index.php
  University of Colorado Herbarium https://botanydb.colorado.edu/
  Open Herbarium http://openherbarium.org/index.php
  Consortium of Pacific Herbaria http://www.pacificherbaria.org/

Example checklists (Symbiota):        
  http://invertebase.org/portal/checklists/checklist.php?dynclid=6571
  http://invertebase.org/portal/taxa/index.php?taxauthid=1&taxon=HELICODISCIDAE&cl=

=== TaxonWorks (ref. http://taxonworks.org/)
  TaxonWorks is part of your research data pipeline.
  Flow data in via batch loaders, wrappers on external providers, scripts, the TaxonWorks JSON API, and an ever improving optimized user interface.
  Adapt core data with many customizable annotations that optionally reference external standards.
  Improve your data with a wealth of non-constraining validators.
  Export an ever growing number of formats directly to your analysis tools, manuscript-ready documents, and global archives.

  Describe taxa, specimens, and anatomy
      A wide range of metadata to describe life.
    Free text notes and descriptions
      Cite figure and annotate them. Compare, clone, and copy from your own templates
    Biological relationships (example: host parasites)
    Sequences
      Manage curated DNA sequences. Annotate them with protocols, and other sequence related metadata (e.g. extract and specimen, primers, or query sequences)
    Phylogenetic matrices
      Create or import traditional qualitative or quantitative phylogenetic matrices.
      Annotate characters with notes, images, tags, and confidence levels.
    Anatomical reference systems
      Create controlled vocabularies describing the morphology of your organisms, with tools to facilitate the transformation of these vocabularies into formal structures like OWL ontologies.
      Use these systems to annotate, query, and organize your data by anatomy.
    Manuscript and datasets export
      Summarize data into taxonomic descriptions (e.g. nomenclatural history, descriptions, material examined sections) ready for publication.
      Export CSV, DWCA, Nexus, and many other data formats.
    Keys
      Create dichotomous and multi-entry keys.
    Advanced anatomical interfaces
      Describe anatomical features using graphical interfaces.
      Drag, drop, and slide to measure, characterize, and qualify observations.
    Landmark metadata
      Create landmark data and tie it to anatomical ontologies for future use and organization.
  Specimens and collecting events
      The best descriptions are those tied directly to specimens and collections.
      Capture these data at the personal or institutional level.
    Digitaztion workflows
      Capture detail for collecting events and specimens with features like customizable, fine grained attributes, lockable values, and varying levels of form complexity.
      Built in OCR and image processing.
    Integrated GIS
      Search and return specimen data spatially.
      Create georeferences of any shape. Also wraps geolocate.
    Loan handling
      Manage personal or institutional loans
  Nomenclature
      Curate all levels of nomenclature with specific reference to the governing codes of nomenclature, plants and animals are covered.
      Rich coverage of nomenclatural rules are included to ensure adequate metadata are provided.
    Catalog exports
      Summarize nomenclatural data in print and machine readable formats.
        DWC checklist
          Export basic nomenclatural data as a Darwin Core Checklist.
        Catalog of Life
          Export basic nomenclatural data to the Catalog of Life format.
        ITIS
          Export basic nomenclatural data to the format used by ITIS.
    Validation
      Use well over a hundred non-constraining validations to ensure data meet plant, animal, and bacterial codes of nomenclature.
  Import, annotate, and export
      Handle data at all stages of the scientific pipeline. Batch load, annotated and refine, export via files or API.
    Cite everything
      Tie *all* your data to references that you can import from BibTeX.
    Media and references
      Load references, images, and other supporting documents. Link them as citations, depictions, or supporting data to all of the core data classes.
    Data attributes, alternative value, notes
      Add your own attributes that optionally reference external controlled vocabularies. Provide translations, abbreviations, misspellings for existing records.
  Rich support for collaborating developers
      An open-source code base with a community that facilitates new collaborators and a long-term development process.
    JSON serving API
      Work with the TaxonWorks back end through a token-based JSON serving API. Develop in your favorite framework, and integrate natively, or as a standalone tool.
    Unit tests
      TaxonWorks has hundreds of unit tests. Test minimize the likelihood of new features breaking existing functionality.
      They clarify intent, and when included in new code, make new code acceptance straightforward.
    Support
      A growing group of developers supporting developers on Gitter, Github, and other channels.


=== Others

Emu/Axiell - https://emu.kesoftware.com/