@conference {2417, title = {Accelerating Digitization of Biodiversity Research Specimens Through Online Public Participation}, booktitle = {SPNHC 2015}, year = {2015}, keywords = {EF-1115210, Presentation, SPNHC2015}, author = {Ellwood, Elizabeth R. and Dunckel, Betty A. and Flemons, Paul and Guralnick, Robert P. and Nelson, Gil and Paul, Deborah L. and Riccardi, Greg and Rios, Nelson and Seltmann, Katja C. and Mast, Austin R.} } @conference {1621, title = {Accelerating Digitization of Biodiversity Research Specimens through Online Public Participation}, booktitle = {Botany 2014}, year = {2014}, keywords = {EF-1115210}, url = {http://www.2014.botanyconference.org/engine/search/index.php?func=detail\&aid=692}, author = {Elizabeth R. Ellwood and Betty Dunckel and Paul Flemons and Robert Guralnick and Nelson, Gil and Greg Newman and Paul, Deborah L. and Greg Riccardi and Nelson E. Rios and Katja Seltmann and Austin R. Mast} } @article {2066, title = {Biocode Field Information Management System}, year = {2015}, keywords = {Field to Database}, url = {https://docs.google.com/file/d/0B6UQCyNEE7qEd1RzMGp4ZFdweUU/edit?usp=drive_web}, author = {John Deck} } @conference {804, title = {Biodiversity Information Standards (TDWG) 2013 Symposium Talk: NEON{\textquoteright}s collections program: Developing a collaborative network of museums and a resource in support of biodiversity research}, booktitle = {TDWG 2013 Annual Conference}, year = {2013}, month = {10/2013}, publisher = {Biodiversity Information Standards (TDWG) Conference 2013}, organization = {Biodiversity Information Standards (TDWG) Conference 2013}, address = {Florence, Italy}, keywords = {Biodiversity Information Standards, collaboration, NEON, Sustainability, TDWG}, url = {https://mbgserv18.mobot.org/ocs/index.php/tdwg/2013/paper/view/410}, author = {Michael Denslow} } @article {2198, title = {Citizen science: A symbiotic future for research and education using biological collections}, year = {2015}, keywords = {Small Collections Symposium SPNHC 2015, SPNHC 2015}, url = {https://www.idigbio.org/wiki/images/4/43/Meineke_spnhc.pdf}, author = {Emily Meineke and Steven D. Frank and Robert Dunn} } @article {1274, title = {Collections-From Local to Global- Building Strength in an Interconnected Digital World}, year = {2014}, keywords = {Collections for the 21st Century Symposium}, url = {https://www.idigbio.org/wiki/images/c/cd/Daly-iDigBio_Mon_1630_Daly_local_to_global-vf.pdf}, author = {Joanne Daly} } @article {2255, title = {Connecting your data to the outside world }, year = {2015}, keywords = {ASM 2015}, url = {https://www.idigbio.org/wiki/images/3/33/Dunnum_ASM_2015_Idigbio_talk.pdf}, author = {Jonathan L. Dunnum} } @article {235, title = {Darwin Core: An Evolving Community-Developed Biodiversity Data Standard}, journal = {PLoS One}, volume = {7}, year = {2012}, month = {01/2012}, chapter = {e29715}, abstract = {Biodiversity data derive from myriad sources stored in various formats on many distinct hardware and software platforms. An essential step towards understanding global patterns of biodiversity is to provide a standardized view of these heterogeneous data sources to improve interoperability. Fundamental to this advance are definitions of common terms. This paper describes the evolution and development of Darwin Core, a data standard for publishing and integrating biodiversity information. We focus on the categories of terms that define the standard, differences between simple and relational Darwin Core, how the standard has been implemented, and the community processes that are essential for maintenance and growth of the standard. We present case-study extensions of the Darwin Core into new research communities, including metagenomics and genetic resources. We close by showing how Darwin Core records are integrated to create new knowledge products documenting species distributions and changes due to environmental perturbations.}, keywords = {Darwin Core, Data Standards, metagenomics}, doi = {10.1371/journal.pone.0029715}, url = {http://www.plosone.org/article/info\%3Adoi\%2F10.1371\%2Fjournal.pone.0029715}, author = {John Wieczorek}, editor = {David Bloom and Robert Guralnick and Stan Blum and Markus D{\"o}ring and Renato Giovanni and Tim Robertson and David Vieglais} } @article {1100, title = {Darwin Core Terms: A quick reference guide}, year = {2009}, month = {2013-10-22}, abstract = {This document is a quick reference for all recommended Darwin Core terms. For complete historical term information, including version changes and pre-standard terms, see [HISTORY]. For a comparative table of elements from pre-standard versions of Darwin Core to the current terms in the standard, see [VERSIONS]. }, keywords = {iDigBio Georeferencing Workshop Group (GWG), iDigBio GWG TTT 2}, url = {http://rs.tdwg.org/dwc/terms/}, author = {Darwin Core Task Group and John Wieczorek and Markus D{\"o}ring and Renato Giovanni and Tim Robertson and Dave Vieglais} } @article {1200, title = {DATA BASING SPECIMENS IN THE PAPUA NEW GUINE NATION HERBARIUM{\textendash}LAE}, year = {2014}, keywords = {Biological Collections Digitization in the Pacific}, url = {https://www.idigbio.org/wiki/images/9/95/LAE_HERBARIUM_-_PAPUA_NEW_GUINEA.pdf}, author = {Kipiro Damas} } @article {1990, title = {Digitization at the NCSU Insect Museum and the Frost Entomological Museum}, year = {2015}, keywords = {Digitizing Dried Insects Digitization Workshop}, url = {https://www.idigbio.org/wiki/images/6/6b/DeansDigitizationDriedInsects2013.pdf}, author = {Andy Deans} } @article {1167, title = {Digitizing in Guide to Trees of Papua New Guinea }, year = {2014}, keywords = {Biological Collections Digitization in the Pacific}, url = {https://www.idigbio.org/wiki/images/e/e9/Guide_to_trees_of_Papua_New_Guinea.pdf}, author = {Kipiro Damas and Barry Conn} } @article {1064, title = {FOSSIL- A national network of amateur and professional paleontologists in the U.S.}, year = {2014}, keywords = {NAPC Symposium}, url = {http://vimeo.com/album/2740344/video/87100158}, author = {Bruce MacFadden and Kent Crippen and Betty Dunckel and Shari Ellis and Austin Hendy and Katherine Hendy and Claudia Grant} } @article {1057, title = {FOSSIL- A national network of amateur and professional paleontologists in the U.S.}, year = {2014}, keywords = {NAPC Symposium}, url = {https://www.idigbio.org/sites/default/files/workshop-presentations/napc-2014/Mon-4.00-MacFadden.pdf}, author = {Bruce MacFadden and Kent Crippen and Betty Dunckel and Shari Ellis and Austin Hendy and Katherine Hendy and Claudia Grant} } @article {1007, title = {Fossil Insect Collaborative Digitization Project:Our E\&O Activities}, year = {2014}, keywords = {iDigBio Education and Outreach Workshop}, url = {https://www.idigbio.org/sites/default/files/workshop-presentations/eoworkshop/Byrd\%20EandO\%20workshop.pdf}, author = {Christina Byrd and Alton Dooley} } @article {1702, title = {Getting an insect collection ready for digitization at the Illinois Natural History Survey{\textquoteright}s InvertNet project }, year = {2014}, keywords = {Leveraging Digitization}, url = {https://www.idigbio.org/wiki/images/b/b6/Dmitriev_2014_Invertnet.pdf}, author = {Dmitry Dmitriev} } @article {1194, title = {Getting Collections Ready for Digitization: Fishes and a Tale of Two Bar Codes }, year = {2014}, keywords = {Biological Collections Digitization in the Pacific}, url = {https://www.idigbio.org/wiki/images/7/7d/Donaldson_IDigBio_Fishes_nov_26_10_min.pdf}, author = {Terry Donaldson} } @conference {2537, title = {A global survey of natural history collections}, booktitle = {Society for the Preservation of Natural History Collections 31st Annual Meeting}, year = {2016}, month = {06/2016}, address = {Berlin, Germany}, author = {Paul, Deborah L. and Masinde, Siro and Shari Ellis and Leonard Krishtalka and Barbara M. Thiers and Ganglo, Jean and Dalcin, Eduardo and Nakae, Masanori} } @article {898, title = {Hand Sanitizer Macro-Photography}, year = {2013}, keywords = {Fluid preserved Invertebrate and Microscopic Slide Imaging Workshop}, url = {https://www.idigbio.org/wiki/images/d/d7/Hand_sanitizer_Droege.pdf}, author = {Sam Droege} } @article {692, title = {Herbarium data in support of biodiversity research: Opportunities and Challenges}, year = {2013}, keywords = {SPNHC, SPNHC 2013}, url = {https://www.idigbio.org/sites/default/files/workshop-presentations/spnhc2013/Denslow-HerbUseiDigBio2013.pdf}, author = {Michael Denslow} } @article {1068, title = {Herbarium data in support of biodiversity research: Opportunities and Challenges}, year = {2013}, keywords = {SPNHC, SPNHC 2013}, url = {http://vimeo.com/74491702}, author = {Michael Denslow} } @article {1478, title = {The iCollection model for digitising small collections of natural history}, year = {2014}, abstract = {Modern curation requires digitisation in order to preserve the specimens by reducing the amount of handling and to mobilise and make the data available efficiently. iCollections has digitised 125,000 British Lepidoptera, 15,000 British flowering plants, 8,000 Psyllids and 12,000 beetles in nearly 18 months, and it is, among other projects, piloting the mass digitisation of all collection at the NHM. iCollections aims to mobilise and disseminate through biodiversity informatics portals the data associated with the specimens, and to assign a unique identifier to each specimen. Small natural history collections contribute to increase scientific knowledge applicable to societal needs and interests in the same way as large collections do. In order to test the work flow and pipelines involved, collections of different size of particular interest to NHM researchers have been used; these comprised a variety of specimens on pins, slides,and herbarium sheets. Having achieved a balanced compromise between the need of speed and cost-effectiveness, the work flow adaptation to small collections is proposed and possible solutions for achieving a robust data management system are suggested }, keywords = {Small Collections Symposium SPNHC 2014}, url = {https://www.idigbio.org/wiki/images/9/93/SPNCHlynscript.pdf}, author = {Lyndsey Douglas and Elisa Cane and Peter Wing and Joanna Durant and Gerardo Mazzetta and Flavia Toloni} } @article {367, title = {iDigBio Augmenting OCR Workshop: OCR within the digitisation workflow at RBGE}, year = {2012}, abstract = {Haston, Elspeth et al. Assistant Curator: Digitisation, Royal Botanic Garden Edinburgh (RBGE) Edinburgh, Scotland. OCR within the digitisation workflow at RBGE }, keywords = {iDigBio Augmenting OCR Workshop}, url = {https://www.idigbio.org/sites/default/files/workshop-presentations/aocr-wgw/Haston_OCR within the digitisation workflow at RBGE.pptx}, author = {Elspeth Haston and Hannah Atkins and Rob Cubey and Robyn Drinkwater and David Harris and Katherine O{\textquoteright}Donnell and Martin Pullan} } @article {287, title = {iDigBio Botany 2012 Symposium: Introducing ApplePie: A botanical annotation network powered by Filtered Push}, year = {2012}, abstract = {This presentation was given by James Macklin, Lei Dou, James Hanken, Maureen Kelley, David Lowery, Bertram Ludaescher, Paul Morris, and Robert Morris at the iDigBio Botany 2012 Symposium.}, keywords = {iDigBio Botany 2012 Symposium}, url = {https://www.idigbio.org/sites/default/files/workshop-presentations/botany2012/symposium/Macklin_Botany2012_final.ppt}, author = {James Macklin and Lei Dou and James Hanken and Maureen Kelley and David Lowery and Bertram Ludaescher and Paul Morris and Robert Morris} } @article {283, title = {iDigBio Botany 2012 Symposium: Mobilizing New England Vascular Plant Specimen Data to Track Environmental Changes}, year = {2012}, abstract = {This presentation was given by Patrick Sweeney, David Barrington, Charles Davis, Michael Donoghue, Erika Edwards, David Foster, Paul Morris, Chris Neefus, Richard Primack, Karen Searcy, Binil Starly, and Janet Sullivan at the iDigBio Botany 2012 Symposium.}, keywords = {iDigBio Botany 2012 Symposium}, url = {https://www.idigbio.org/sites/default/files/workshop-presentations/botany2012/symposium/Sweeney_Botany2012_iDigBio.pdf}, author = {Patrick Sweeney and David Barrington and Charles Davis and Michael Donoghue and Erika Edwards and David Foster and Paul Morris and Chris Neefus and Richard Primack and Karen Searcy and Binil Starly and Janet Sullivan} } @article {265, title = {iDigBio Botany 2012 Workshop: "Databasing and digitization of a smaller herbarium at a smaller institution: it CAN be done and funded, too"}, year = {2012}, abstract = {This presentation was given by Rebecca W. Dolan at the iDigBio Botany 2012 Workshop.}, keywords = {iDigBio Botany 2012 Workshop}, url = {https://www.idigbio.org/sites/default/files/workshop-presentations/botany2012/workshop/DOLAN.IdigBio.pptx}, author = {Rebecca W. Dolan} } @article {267, title = {iDigBio Botany 2012 Workshop: SWITCH (SouthWest Idaho: The Comprehensive Herbarium)}, year = {2012}, abstract = {This presentation was given by Alexa DiNicola, Don Mansfield, and James Smith at the iDigBio Botany 2012 Workshop.}, keywords = {iDigBio Botany 2012 Workshop}, url = {https://www.idigbio.org/sites/default/files/workshop-presentations/botany2012/workshop/DINICOLA_Talk.pptx}, author = {Alexa DiNicola and Don Mansfield and James Smith} } @article {447, title = {iDigBio Paleocollections Workshop 2012: Small is beautiful: how databasing small collections can enhance the research and outreach missions of larger university collections and museums}, year = {2012}, keywords = {iDigBio Paleocollections Workshop 2012}, url = {https://www.idigbio.org/sites/default/files/videos/slides/iDigBioDeVore.pptx}, author = {Melanie DeVore} } @article {341, title = {iDigBio Public Participation in Digitization of Biodiversity Specimens Workshop: Notes from Nature: a scalable citizen science platform for transcribing records from natural history collections. }, year = {2012}, abstract = {Denslow, Michael. Appalachian State Univ. Notes from Nature: a scalable citizen science platform for transcribing records from natural history collections. }, keywords = {Public Participation in Digitization of Biodiversity Specimens Workshop}, url = {https://www.idigbio.org/sites/default/files/workshop-presentations/ppws-2012/Denslow_NFNiDigBio2012v3.pptx}, author = {Michael Denslow} } @article {487, title = {IDigBio Summit II: InvertNet: An Integrative Platform for Research on Environmental Change, Species Discovery and Identification}, year = {2012}, keywords = {IDigBio Summit II}, url = {https://www.idigbio.org/sites/default/files/workshop-presentations/summit2/Dietrich_idigbio_summitII.invertnet.final.pptx}, author = {Chris Dietrich and Omar Sobh} } @article {392, title = {iDigBio Summit: TCN Overview, {\textquotedblleft}InvertNet{\textquotedblright}}, year = {2011}, keywords = {iDigBio 2011 Summit}, url = {https://www.idigbio.org/videos/idigbio-summit-TCN-Dietrich-Sobh-30NOV2011.mp4}, author = {Chris Dietrich} } @article {393, title = {iDigBio Summit: TCN Overview, {\textquotedblleft}InvertNet{\textquotedblright}}, year = {2011}, keywords = {iDigBio 2011 Summit}, url = {https://www.idigbio.org/videos/slides/08InvertNet_HUBsummitF.pptx}, author = {Chris Dietrich} } @article {1082, title = {An Integrative Platform for Research on Environmental Change, Species Discovery and Identification}, year = {2012}, keywords = {IDigBio Summit II}, url = {http://vimeo.com/album/2163675/video/54323290}, author = {Chris Dietrich} } @article {1081, title = {An Integrative Platform for Research on Environmental Change, Species Discovery and Identification}, year = {2012}, keywords = {IDigBio Summit II}, url = {http://vimeo.com/album/2163675/video/54323290}, author = {Chris Dietrich} } @article {2065, title = {Introduction to Web APIs}, year = {2015}, keywords = {Field to Database}, url = {https://www.idigbio.org/wiki/images/9/93/2015-03-12-F2DB-R_pkg_lesson.pdf}, author = {Francois Michonneau and Joanne Daly} } @article {777, title = {InvertNet}, year = {2013}, keywords = {Summit 3}, url = {https://www.idigbio.org/sites/default/files/workshop-presentations/summit3/Invertnet2_iDigBio_summitIII.pdf}, author = {Chris Dietrich} } @article {1761, title = {InvertNet: 2013-14 Progress and Goals}, year = {2014}, keywords = {Summit 2014}, url = {https://www.idigbio.org/wiki/images/d/da/InvertNetidigbio2014.pdf}, author = {Chris Dietrich} } @article {1793, title = {InvertNet: 2013-14 Progress and Goals}, year = {2014}, keywords = {Summit 2014}, url = {http://vimeo.com/album/3113100/video/110900201}, author = {Chris Dietrich} } @article {237, title = {InvertNet: a new paradigm for digital access to invertebrate collections}, journal = {ZooKeys}, volume = {209}, year = {2012}, month = {07/2012}, chapter = {165}, abstract = {InvertNet, one of the three Thematic Collection Networks (TCNs) funded in the first round of the U.S. National Science Foundation{\textquoteright}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. Limitations of previous approaches are discussed and possible solutions are proposed that incorporate advanced imaging and 3-D reconstruction technologies. InvertNet couples efficient digitization workflows with a highly robust network infrastructure capable of managing massive amounts of image data and related metadata and delivering high-quality images, including interactive 3-D reconstructions in real time via the Internet.}, keywords = {collection database, Collection digitization, EF-1115112, image processing}, doi = {10.3897/zookeys.209.3571}, url = {http://www.pensoft.net/journals/zookeys/article/3571/invertnet-a-new-paradigm-for-digital-access-to}, author = {Chris Dietrich}, editor = {John Hart and David Raila and Umberto Ravaioli and Nahil Sobh and Omar Sobh and Chris Taylor} } @article {1987, title = {InvertNet: A New Paradigm for Digital Access to Invertebrate Collections}, year = {2015}, keywords = {Digitizing Dried Insects Digitization Workshop}, url = {https://www.idigbio.org/wiki/images/4/43/InvertNetFieldMus2013.pdf}, author = {Chris Dietrich} } @article {884, title = {InvertNet: A New Paradigm for Digital Access to Invertebrates}, year = {2013}, keywords = {ASB Digitization Workshop}, url = {https://www.idigbio.org/wiki/images/e/e7/InvertNetASB2013.pdf}, author = {Chris Dietrich} } @article {999, title = {InvertNet: A New Paradigm for Digitization of Invertebrate Collections}, year = {2013}, keywords = {Summit 3}, url = {http://vimeo.com/album/2684234/video/84223536}, author = {Chris Dietrich} } @article {529, title = {Keeping an Eye on Biology}, journal = {Science}, volume = {339}, year = {2013}, month = {01/2013}, pages = {408-409}, type = {Essays on Science and Society}, chapter = {408}, abstract = {Genomic data sets offer opportunities for students to generate original findings without expensive laboratory equipment, extending the benefits of undergraduate research to the classroom (1{\textendash}4). Yet, working with data sets online can frustrate biology students who may miss connections to fascinating biological questions. Integrating organismal and molecular biology with bioinformatics can enhance student learning. We have developed a program in genomics, adapted for a plant (Chamaecrista fasciculata) and an animal (Aiptasia pallida), designed to support student learning with a Web-based guide (http://serc.carleton.edu/exploring_genomics/index.html) (see the first chart).}, keywords = {education, genomics}, doi = {10.1126/science.1229848}, url = {http://www.sciencemag.org/content/339/6118/408.full}, author = {Susan R. Singer and Jodi A. Schwarz and Cathryn A. Manduca and Sean P. Fox and Ellen R. Iverson and Benjamin J. Taylor and Steven B. Cannon and Gregory D. May and Sonja L. Maki and Andrew D. Farmer and Jeffrey J. Doyle} } @conference {253, title = {Label Recognition in Herbarium Specimens by using Database-Queries}, booktitle = {ICDM 2011 IEEE International Conference on Data Mining}, year = {2011}, month = {09/2011}, publisher = {IEEE}, organization = {IEEE}, address = {Vancouver, Canada}, abstract = {For hundreds of years plant specimens are collected in herbariums for scientific purposes. These plants are mounted on specimen sheets and labeled with the essential data such as the name of the collector, the date and the place it was found. To make them available for a wider public the specimen sheets get digitized for online use. The purpose of our project in cooperation with the Botanical Garden in Berlin (Germany) is the development of a software-system for the analysis of these high resolution images. There are different approaches like template matching or SURF for detecting stable objects like color-charts, rulers, barcodes or even labels (fig. 1) on specimens. This paper describes a new method for the automatic scale- and rotation-invariant recognition of prior defined label-types by using OCR-engine generated texts contained in a database.}, keywords = {database, label recognition, OCR-texts, rotation-invariant, scale-invariant, SURF, template matching}, author = {M Gehrke and KH Steinke and R Dzido} } @conference {2416, title = {Mapping Life: Quality Assessment of Novice and Computer Automated vs. Expert Georeferences}, booktitle = {TDWG 2015}, year = {2015}, keywords = {EF-1115210, Presentation, TDWG2015}, author = {Ellwood, Elizabeth R. and Bart, Henry and Doosey, Michael and Jue, Dean and Nelson, Gil and Rios, Nelson and Mast, Austin} } @article {2138, title = {Meeting report: Identifying practical applications of ontologies for biodiversity informatics}, journal = {Standards in Genomic Sciences C7 - 25}, volume = {10}, year = {2015}, pages = {1-6}, abstract = {This report describes the outcomes of a recent workshop, building on a series of workshops from the last three years with the goal if integrating genomics and biodiversity research, with a more specific goal here to express terms in Darwin Core and Audubon Core, where class constructs have been historically underspecified, into a Biological Collections Ontology (BCO) framework. For the purposes of this workshop, the BCO provided the context for fully defining classes as well as object and data properties, including domain and range information, for both the Darwin Core and Audubon Core. In addition, the workshop participants reviewed technical specifications and approaches for annotating instance data with BCO terms. Finally, we laid out proposed activities for the next 3 to 18 months to continue this work.}, keywords = {Ontology Biodiversity Population Community Darwin core OWL RDF Microbial ecology Sequencing}, doi = {10.1186/s40793-015-0014-0}, url = {http://dx.doi.org/10.1186/s40793-015-0014-0}, author = {Deck, John and Guralnick, Robert and Walls, Ramona and Blum, Stanley and Haendel, Melissa and Matsunaga, Andr{\'e}a and Wieczorek, John} } @article {683, title = {Mining Natural~History Collections for Invasive Species Data in New~York}, year = {2013}, keywords = {SPNHC, SPNHC 2013}, url = {https://www.idigbio.org/sites/default/files/workshop-presentations/spnhc2013/Dean-spnhc.pdf}, author = {Jennifer Dean} } @conference {2421, title = {Notes From Nature: Advancing a next generation citizen science platform for biodiversity transcription}, booktitle = {TDWG 2015}, year = {2015}, keywords = {EF-1115210, Presentation, TDWG2015}, author = {Guralnick, Robert Penn and Denslow, Michael W. and Mast, Austin} } @conference {254, title = {Object Recognition in Herbarium Specimens}, booktitle = {ICDM 2011 IEEE International Conference on Data Mining}, year = {2011}, month = {09/2011}, publisher = {IEEE}, organization = {IEEE}, address = {Vancouver, Canada}, abstract = {About 3.5 million dried plants on paper sheets are deposited in the Botanical Museum Berlin in Germany. The aim of our project is the image analysis of scanned high resolution images. There are many different objects contained in a herbarium sheet like ruler, barcode, stamps, color-chart, labels with printed title, red type designator, envelopes, hand-written and printed annotations and the plant. Some objects are very stable like the ruler, others are extremely variable like handwriting or plant. So each class of objects requires a special detection method. Algorithms like template matching or SURF can be applied to some of the stable objects. For variable objects like handwriting detection methods are already developed by the authors and are described in other papers.}, keywords = {best template, connected component analysis, hue space, object recognition, SURF, template matching}, author = {KH Steinke and M Gehrke and R Dzido} } @article {1093, title = {Public Participation in Digitization}, year = {2012}, keywords = {IDigBio Summit II}, url = {http://vimeo.com/album/2163675/video/55283855}, author = {Austin Mast and Betty Dunckel} } @conference {244, title = {Recognition of Humboldt{\textquoteright}s Handwriting in Complex Surroundings}, booktitle = {12th International Conference on Frontiers in Handwriting Recognition (ICFHR)}, year = {2010}, month = {11/2010}, address = {Kolkata}, abstract = {In the Botanic Museum of Berlin in Germany exist about 3.5 million dried plants on paper sheets. They were collected in the last two hundred years by many collectors among those was the famous researcher {\textquotedblleft}Alexander von Humboldt{\textquotedblright}. because e every collector left his handwriting on the sheet the question came up if it is possible to find out automatically which sheet belongs to Humboldt{\textquoteright}s collection. To solve the problem many challenging sub problems have to be solved before. First text regions have to be localized and extracted. Then printing is to be distinguished from handwriting. For the latter an off-line writer recognition procedure had to be developed in order to determine the writer of the handwriting. Often two or more writers can be found on one sheet. To make sure that the suspect writer is correct an interactive method is applied which transforms the static character into a dynamic form. Different mathematical procedures are used such as the reproduction of the write line of individual characters by Legendre polynomials. All methods were proved on the international IAMdatabase [3]. 93 writers with at least 5 samples were chosen from the IAM-database. By combining multiple characters (up to thirteen), the recognition rate rises considerably and reaches 98.7\%. A global statistical approach using the whole handwritten text results in a similar recognition rate of more than 98\%. By combining the methods by a ranking method a recognition rate of 99.5\% is achieved.}, keywords = {Legendre polynomials, text localization, writer recognition}, doi = {10.1109/ICFHR.2010.91}, url = {http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=\&arnumber=5693621}, author = {KH Steinke}, editor = {M Gehrke} } @article {1612, title = {Results and insights from the NCSU Insect Museum GigaPan project}, journal = {Zookeys}, volume = {209}, year = {2012}, month = {2012}, chapter = {115}, abstract = {Pinned insect specimens stored in museum collections are a fragile and valuable resource for entomological research. As such, they are usually kept away from viewing by the public and hard to access by experts. Here we present a method for mass imaging insect specimens, using GigaPan technology to achieve highly explorable, many-megapixel panoramas of insect museum drawers. We discuss the advantages and limitations of the system, and describe future avenues of collections research using this technology.}, keywords = {DBI-0847924}, url = {http://www.pensoft.net/journals/zookeys/article/3083/results-and-insights-from-the-ncsu-insect-museum-gigapan-project}, author = {M. A. Bertone and R. L. Blinn and T. M. Standfield and K. J. Dew and K. C. Seltmann and A. R. Deans} } @article {2211, title = {The Role of Human Infrastructure in Biodiversity Informatics: SERNEC as a model for Community Development}, year = {2015}, keywords = {Small Collections Symposium SPNHC 2015, SPNHC 2015}, url = {https://www.idigbio.org/wiki/images/b/b4/Murrell_spnhc.pdf}, author = {Zack Murrell and Michael Denslow and Joseph McKenna} } @article {1623, title = {Semantics in Support of Biodiversity Knowledge Discovery: An Introduction to the Biological Collections Ontology and Related Ontologies.}, journal = {PLoS ONE}, volume = {9}, year = {2014}, month = {03/2014}, chapter = {1}, abstract = {The study of biodiversity spans many disciplines and includes data pertaining to species distributions and abundances, genetic sequences, trait measurements, and ecological niches, complemented by information on collection and measurement protocols. A review of the current landscape of metadata standards and ontologies in biodiversity science suggests that existing standards such as the Darwin Core terminology are inadequate for describing biodiversity data in a semantically meaningful and computationally useful way. Existing ontologies, such as the Gene Ontology and others in the Open Biological and Biomedical Ontologies (OBO) Foundry library, provide a semantic structure but lack many of the necessary terms to describe biodiversity data in all its dimensions. In this paper, we describe the motivation for and ongoing development of a new Biological Collections Ontology, the Environment Ontology, and the Population and Community Ontology. These ontologies share the aim of improving data aggregation and integration across the biodiversity domain and can be used to describe physical samples and sampling processes (for example, collection, extraction, and preservation techniques), as well as biodiversity observations that involve no physical sampling. Together they encompass studies of: 1) individual organisms, including voucher specimens from ecological studies and museum specimens, 2) bulk or environmental samples (e.g., gut contents, soil, water) that include DNA, other molecules, and potentially many organisms, especially microbes, and 3) survey-based ecological observations. We discuss how these ontologies can be applied to biodiversity use cases that span genetic, organismal, and ecosystem levels of organization. We argue that if adopted as a standard and rigorously applied and enriched by the biodiversity community, these ontologies would significantly reduce barriers to data discovery, integration, and exchange among biodiversity resources and researchers.}, keywords = {EF-1115210}, url = {http://www.plosone.org/article/info\%3Adoi\%2F10.1371\%2Fjournal.pone.0089606}, author = {Ramona Wells and John Deck and Robert Guralnick and Steve Baskauf and Reed Beaman and Stanley Blum and Shawn Bowers and Pier Luigi Buttigieg and Neil Davies and Dag Endresen and Maria Alejandra Gandolfo and Robert Hanner and Alyssa Janning and Leonard Krishtalka and Matsunaga, Andr{\'e}a and Peter Midford and Norman Morrison and Eamonn O. Tuama and Mark Schidhauer and Barry Smith and Brian J. Stucky and Andrea Thomer and John Wieczorek and Jamie Whitacre and John Wooley} } @conference {2139, title = {A Specimen-based View of the World: Using the Biological Collections Ontology to Model Biodiversity Collections}, booktitle = {2014 ICBO Workshop: Starting an OBI-based Biobank Ontology}, year = {2014}, address = {Houston, TX, USA}, url = {http://ceur-ws.org/Vol-1309/paper8.pdf}, author = {Walls, Ramona and Guralnick, Robert and Deck, John and Matsunaga, Andr{\'e}a}, editor = {Brochhausen, Mathias and Haendel, Melissa and Stoeckert, Christian J. and Zheng, Jie} } @article {1318, title = {SPNHC 2014: Progress in Digitization: Creating a Swedish Digital Natural History Collection, e-BioColl.se}, year = {2014}, abstract = {Natural history collections constitute the major source of data for research in phylogenetics and systematics, and provide crucial information for analyses of long-term trends in ecology and environmental sciences. Recent mass-digitization efforts have opened up such collections abroad for transformative e-science approaches, but research dependent on Swedish objects is left behind. Out of an estimates 33 million Swedish specimens, almost 90\% are unavailable digitally, and it will take hundreds of years to eliminate this backlog at the current pace of digitization. To address this problem and provide a proof-of-concept version of an e-science platform for Swedish natural history collections allowing complete digitization within 10 years we plan to develop and test standardized, re-usable, industrial-level digitization processes where innovation and automation will bring down the cost of obtaining specimen images and geospatial and taxonomic metadata from specimen labels. Robotic techniques employed to image insect collections, and automated text recognition and citizen-science based crowd sourcing for extracting information from specimen labels during the digitization of 1.4 million specimens in the Gothenburg herbarium will provide a full-scale feasibility test of tools and concepts. The digitized information will immediately support outstanding research in Sweden and elsewhere on this unique material, and boost international initiatives (e g GBIF, LifeWatch and IPBES).}, keywords = {automation, Citizen Science, digitization, e-BioColl.se, e-science, optical character recognition, SPNHC 2014, SPNHC 2014: Progress in Digitization}, url = {https://www.idigbio.org/sites/default/files/workshop-presentations/spnhc2014/01_SPNHC_NRM_140626_KarinKarlsson.pdf}, author = {Karin Karlsson and Ericson, Per and Fredrik Ronquist and Anders Telenius and Stefan Daume and Kevin Holston} } @article {1331, title = {SPNHC 2014: Progress in Digitization: Georeferencing Fish Collections from the FishNet Network}, year = {2014}, abstract = {FishNet2 (www.fishnet2.net) is a global network of fish collection databases that gives researchers access to data on roughly 4 million fish species lots, representing over 30 million specimens. Before this project began, only about two-thirds of the records in Fishnet2 were georeferenced. The goals of this collaborative project were to georeference all localities without geographic coordinates and repatriate the results to data providers. The Collaborative Georeferencing Client (CoGe)of the GEOLocate Platform was used to georeference and verify the roughly 250,000 localities in FishNet2 lacking coordinates at the start of the project. Each of the twelve collaborating institutions hired a full-time georeferencing technician to verify and correct the CoGe generated geographic coordinates for localities assigned to his or her institution. Since January 2013, when the georeferencing phase of the project began, more than 244,000 localities of have been processed (214,000 corrected), and over 1 million specimens records have been processed (935,000 corrected). Records that could not be georeferenced were skipped and reasons for not correcting the coordinates were recorded. Every corrected record includes geographic coordinates in decimal degrees, an uncertainty radius, and most of the records have a user generated error polygon to define the uncertainty in the determinations.}, keywords = {Collaborative Georeferencing Client (CoGe), digitization, FishNet, GEOLocate, georeference, SPNHC 2014, SPNHC 2014: Progress in Digitization}, url = {https://www.idigbio.org/sites/default/files/workshop-presentations/spnhc2014/14_RIOS-spnhc2014.pdf}, author = {Nelson E. Rios and Henry L. Bart and Michael H. Doosey} } @article {1329, title = {SPNHC 2014: Progress in Digitization: Incorporating OCR into a digitisation and curation workflow}, year = {2014}, abstract = {The digitisation of natural history collections is a priority for many institutes for reasons including opening access to users around the world, incorporation of specimen data in research, disaster planning, etc. However, digitisation of natural history specimens is expensive and labour intensive. For this reason, digitisation of specimens has moved towards minimal data capture and imaging as part of large scale processes. The workflow can be summarised in the following steps: 1) minimal curation; 2) attach barcode as a unique identifier; 3) minimal data entry; 4) image specimen; 5) additional data entry. There has been some investigation by institutes into the use of Optical Character Recognition (OCR) within the digitsation and curation workflow. The Royal Botanic Garden Edinburgh (RBGE) now routinely processes all specimen images through OCR software. The OCR process is integrated into the overall digitisation and curation workflow and has been used to speed up the process of adding data to over 100,000 specimens. The following additional steps have been incorporated into the workflow at RBGE: 4a) assess condition of specimen; 4b) process image through OCR software; 5a) additional curation. The incorporation of OCR into digitisation workflows is being explored by the Synthesys project funded by the European Union within Framework 7, and by iDigBio funded by the United States Government within the National Science Foundation programme. The work being carried out at the Royal Botanic Garden Edinburgh to integrate OCR into the digitisation and curation workflow is discussed as part of the work of Synthesys and iDigBio.}, keywords = {digitization, optical character recognition, SPNHC 2014, SPNHC 2014: Progress in Digitization, workflow}, url = {https://www.idigbio.org/sites/default/files/workshop-presentations/spnhc2014/12_Haston_et_al_Incorporating_OCR.pdf}, author = {Elspeth Haston and Robyn Drinkwater and Robert Cubey} } @article {1858, title = {Stoneflies (Plecoptera), pre-European distributions and climate influenced future ranges in the Midwest}, year = {2014}, keywords = {ECN 2014}, url = {https://www.idigbio.org/wiki/images/7/79/DeWalt_ECN_2014.pdf}, author = {R.E. DeWalt and Y.Cao and J.L.Robinson and T. Tweddale and L.Hinz and S.A. Grubbs} } @article {1050, title = {Stonerose Interpretive Center and Eocene Fossil Site: an integrative model at the crossroads of research, public outreach and community involvement}, year = {2014}, keywords = {NAPC Symposium}, url = {https://www.idigbio.org/sites/default/files/workshop-presentations/napc-2014/mon-1.45-sternberg.pdf}, author = {Michael Sternberg and S. Bruce Archibald and Melanie L. DeVore and Kathleen B. Pigg} } @article {1863, title = {Using buprestid monitoring tools for obtaining diverse collections of forest insects}, year = {2014}, keywords = {ECN 2014}, url = {https://www.idigbio.org/wiki/images/2/2e/MJDECN2014.pdf}, author = {Michael Dominque and Joseph Francese and Warren Hellman and Melissa Fierke and Claire Rutledge} } @article {2248, title = {~Using digitized data to advance research }, year = {2015}, keywords = {ASM 2015}, url = {https://www.idigbio.org/wiki/images/b/b0/DelaSanchaDigBio.pdf}, author = {Noe U. de la Sancha} } @article {731, title = {Utility (and Shortcomings) of High Resolution Drawer Imaging for Remote Curation and Outreach}, year = {2010}, publisher = {North Carolina State University}, keywords = {Imaging, Technology}, url = {http://www.ecnweb.org/dev/files/17_Bertone_2010.pdf}, author = {M. Bertone and A. Deans} }