Giddens ecn2013
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This document discusses solutions for digitizing scientific collections and making data available online. It outlines services for optimizing image capture, processing label images, creating collection portals, developing interactive maps, and providing technical support. It also summarizes techniques for digitization including optical character recognition, machine learning, crowdsourcing, and human verification. Web portal features are shown including taxonomy browsing, custom checklists, specimen details, and interactive mapping of occurrence data.
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The Expanding Access to Biodiversity Literature project is thanks to the generosity of one of the IMLS Leadership Grant. The project is dedicated to getting more content into the Biodiversity Heritage Library and will significantly increase online access to biodiversity material by positioning BHL as an on-ramp for biodiversity content providers that would like to contribute to the national digital library infrastructure through the Digital Public Library of America (DPLA). The grant proposes to address challenges facing content providers—including insufficient amounts of content, indexing of scientific names, and metadata creation—and make necessary digital infrastructure enhancements by creating an innovative model for open access to data and to support collaboration among these institutions. If you are interested in gaining more information about the project please let us know.
The workflows for the ingest of digital objects into a repository/digital li...
Different workflows for the ingestion of different types of digital objects into a library catalog/digital library
The workflows for the ingest of digital objects into a repository/digital l...
The document discusses best practices and considerations for developing workflows for ingesting digital objects into repositories and digital libraries. It covers key aspects of ingest workflows including standards, quality assurance procedures, metadata, tools and software. Example ingest workflows are provided using systems like Archivematica, DSpace and DataVerse to illustrate the ingest process.
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Council on Botanical and Horticultural Libraries 2016 Presentation
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Giddens ecn2013
- 1. Getting collection data, maps, and images online via open source and commercial solutions Michael Giddens
- 2. Software developer with a focus in biodiversity informatics. Follow me @silverbiology
- 3. What we do • Design workflows and software to optimize image capture • Analyze & Process label images • Create portals for entomological and scientific collections • Develop interactive maps to tell stories about data • Provide support and technical advice for NSF projects
- 4. Digitization & Data Capture • • • • • • • Seconds count 28,800 seconds in an 8 work day 100k @ 30 seconds = 34.7 days 100k @ 29 seconds = 33.5 days … 100k @ 15 seconds = 17.3 days Humans are not robots
- 5. Solutions • • • • • • Look at every action as a micro task Find tasks to fill any wait time Stick to a single workflow Filename conventions are important Stick with image sizes and formats needed Renaming filenames using scanners or data entry e.g. SilverImage • Backup Images!!!
- 6. Things we learned • Make sure your lighting environment does not change • Dragon dictation is not accurate enough for number or scientific words • Manually renaming files is slow • Some student workers do not care as much as you do about your collection • People get burned out
- 7. Data Processing • • • • Optical Character Recognition Engines Machine Learning Crowd Sourcing Human in the Middle
- 8. Optical Character Recognition Engines • Free – Tesseract • Commercial – OmniPage – Abbyy • Services – www.silverbiology.com • Font Training • No handwriting solution on market
- 9. Machine Learning • • • • • Data Dictionaries Conditional logic / Decision Trees Past data to predict future data Label / Word Boundaries Orientation
- 10. Crowd Sourcing Notes From Nature • http://www.notesfromnature.org Ornithological from Natural History Museum Calbug – Essig Museum Collections
- 11. ALA Volunteer Program • http://volunteer.ala.org.au
- 12. Human In The Middle • • • • • • Rotating Images Tagging Areas Metadata tagging Identifying False Positives Verification Steps Bulk Validation
- 13. Web Portals • • • • In-House Specify 6 Portal Symbiota SilverCollection – California Academy of Sciences – Angelo State Natural History Museum – Louisiana State Arthropod Museum – Kansas State University Entomology Dept. – Mississippi Entomological Museum – NLBIF
- 14. Explore / Browse • • • • • • • • Taxonomy Taxonomy (Filtered) Family Genus Type Status Regions Collectors Custom
- 18. Images
- 19. Specimen Details
- 20. Reports
- 21. Interactive Maps
- 22. • Online service to Map, Analyze and Build applications with your data • Simple to use • Easily create distribution maps, heat maps, and category maps • Access to full geospatial query engine • Visualizing ecological models • Works well with lots of data
- 23. GBIF - 350 Million Records http://www.gbif.org/occurrence
- 24. Visualizing two months in the life of seagull Eric Blog on Lifewatch by Peter Desmet
- 26. Interactive Map Modes Density Maps Polygons Grids
- 27. Useful Tools Provided By the Global Biodiversity Information Facility http://tools.gbif.org • • • • • • • Darwin Core Archive Assistant Darwin Core Archive Validator Higher Taxonomy Services Name Finder Name Parser GBIF API Services Integrated Publishing Toolkit (IPT)
- 28. Global Names Architecture http://www.gloablnames.org • Global Names Recognition and Discovery • Global Names Index
Editor's Notes
- Crash Course - Hope that you learn some technical stuff today and some places you can reach out for help.
- Close to 20 years of programming experience with 9 years focused directly in informatics to help make things better.
- Background with herbaria building equipment and software to capture specimen images. 1st year at ECN
- Hodges number vs scientific names
- Crash Course - Hope that you learn some technical stuff today and some places you can reach out for help.