@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 {2418,
	title = {Accelerating Digitization of Biodiversity Specimens through Online Public Participation},
	year = {2015},
	abstract = {Biodiversity research specimens provide a historical baseline of diversity and distributions against which to compare new samples and project changes to diversity and distribution into the future. However, just ca. 10 percent of the estimated 1 billion specimens in U.S. collections have been digitized (e.g., databased, imaged, and/or georeferenced) with the data made available online. A goal of the biodiversity research community is to digitize most of the remaining specimens within a decade. However, meeting this ambitious goal requires increased collaboration, technological innovation, and broader engagement in digitization beyond the walls of biodiversity research collections. Engaging the public in digitization, rather than simply hiring more digitizers, promises to both serve the digitizing institutions and further public understanding of biodiversity science. We identify 24 digitization tasks that the public could participate in online and examples from three broad areas that will accelerate research progress: label and ledger transcribing/cataloging from digital images, georeferencing from collection locality descriptions, and specimen tagging/categorizing from images. We illustrate each activity, identify and compare useful tools, present relevant best practices and standards, and identify gaps in our knowledge and areas for improvement. We will also highlight the citizen science projects of iDigBio, NSF{\textquoteright}s National Resource for Advancing the Digitization of Biodiversity Collections. This includes Biospex (www.biospex.org), a system that provides project management functionality for public participation tools like Notes from Nature (www.notesfromnature.org).The field of public participation in digitization of biodiversity research specimens is clearly in a growth phase with many emerging opportunities for scientists, educators, and the public. The field will benefit from broader communication with complementary or overlapping projects in other fields, such as the digital humanities.},
	keywords = {AAAS2015, EF-1115210, poster},
	url = {https://aaas.confex.com/aaas/2015/webprogram/Paper15507.html},
	author = {Ellwood, Elizabeth R. and Guralnick, Robert and Riccardi, Greg and Rios, Nelson and Seltmann, Katja and Mast, Austin}
}
@article {1622,
	title = {Aiming Up: Natural History Collections as Emerging Resources for Innovative Undergraduate Education in Biology},
	journal = {BioScience},
	volume = {64},
	year = {2014},
	month = {08/2014},
	chapter = {725},
	abstract = {There is an emerging consensus that undergraduate biology education in the United States is at a crucial juncture, especially as we acknowledge the need to train a new generation of scientists to meet looming environmental and health crises. Digital resources for biology now available online provide an opportunity to transform biology curricula to include more authentic and inquiry-driven educational experiences. Digitized natural history collections have become tremendous assets for research in environmental and health sciences, but, to date, these data remain largely untapped by educators. Natural history collections have the potential to help transform undergraduate science education from passive learning into an active exploration of the natural world, including the exploration of the complex relationships among environmental conditions, biodiversity, and human well-being. By incorporating natural history specimens and their associated data into undergraduate curricula, educators can promote participatory learning and foster an understanding of essential interactions between organisms and their environments.},
	keywords = {EF-1115210},
	url = {http://www.academia.edu/7991735/Natural_History_Collections_as_Emerging_Resources_for_Innovative_Education},
	author = {Joseph A. Cook and Scott Edwards and Eileen A. Lacey and Robert P. Guralnick and Soltis, Pamela S. and Douglas E. Soltis and Corey K. Welch and Kayce C. Bell and Kurt E. Galbreath and Christopher Himes and Julie M. Allen and Tracy A. Heath and Ann C. Carnaval and Kimberly L. Cooper and Mark Liu and James Hanken and Stefanie Ickert-Bond}
}
@conference {2441,
	title = {Areas of endemism in the Nearctic: a case study of 1,566 species of Miridae (Insecta: Hemiptera) and their plant hosts},
	booktitle = {Entomological Collections Network 2015},
	year = {2015},
	keywords = {ECN2015, EF-1115210, Presentation},
	author = {Weirauch, Christiane and Schuh, Randall T and Seltmann, Katja C. and Schwarz, Michael and Johnson, Christine and Feist, Mary Ann and Soltis, Pamela S.}
}
@conference {2428,
	title = {Broadening participation in the biological sciences},
	booktitle = {SPNHC 2015},
	year = {2015},
	keywords = {EF-1115210, Presentation, SPNHC2015},
	author = {Nelson, Gil and Riccardi, Greg}
}
@conference {2424,
	title = {Closing the gap - building a strong and productive network between amateurs and professionals in Paleontology.},
	booktitle = {2015 GSA Annual Meeting},
	year = {2015},
	month = {11/2015},
	address = {Baltimore, Maryland},
	abstract = {The great natural history collections in museums and universities all over the country are the backbone of national and international research in taxonomy, biodiversity and evolution. The bulk of the collections has its origin in private engagement and was donated by private collectors and enthusiasts. Even the most iconic of fossils (e.g. Archaeopteryx lithographica, von Meyer 1861) stem from the playground of amateur paleontologists and private collectors. It is hard to imagine how much more of such icons may lie dormant unnoticed in private cabinets. The NSF funded FOSSIL Project is focused on attracting fossil hunters of all ages and level of experience to participate in academic research in general and special digital database like myFOSSIL and iDigBio in particular. Thirty representatives of U.S. fossil organizations completed an online survey about their clubs{\textquoteright} current activities and member interest in new initiatives. The majority of club members are active users of the Web, with 77\% of representatives reporting that members already use online image galleries. Ninety percent reported that club members would be interested in access to additional online digital resources, and 80\% or higher reported members to be interested in training in collection curation in either workshops or online webinars. To that end, the Fossil Project in partnership with iDigBio has begun providing training to amateurs that will allow them to contribute in meaningful ways to the digitization of fossil collections. Just a few advice in how to clean, prepare and image their fossils and how to upload the digital data might sometimes be enough to fulfill all the requirements needed to not just get access into the myFOSSIL database but also to be part of the FOSSIL and iDigBio world. In giving them the platform and appropriate guidance in terms of different types of tutorials, networking, personal interaction and discussion, we pave the way for a prospering and fruitful community. With respect to amateurs{\textquoteright} personal collections, we aim to increase their appreciation of the potential value of their collections when coupled with sound curatorial and imaging practices. As amateurs gain skills, we anticipate increased interest and participation in the national effort to digitize collections.

Geological Society of America Abstracts with Programs. Vol. 47, No. 7, p.748},
	keywords = {EF-1115210, GSA2015, poster},
	url = {https://gsa.confex.com/gsa/2015AM/webprogram/Paper268213.html},
	author = {Leder, Ronny M.}
}
@conference {1414,
	title = {A Computational- and Storage-Cloud for Integration of Biodiversity Collections},
	booktitle = {Proceedings of the 2013 IEEE 9th International Conference on e-Science},
	year = {2013},
	publisher = {IEEE},
	organization = {IEEE},
	address = {Beijing, China},
	abstract = {A core mission of the Integrated Digitized Biocollections (iDigBio) project is the building and deployment of a cloud computing environment customized to support the digitization workflow and integration of data from all U.S. nonfederal biocollections. iDigBio chose to use cloud computing technologies to deliver a cyberinfrastructure that is flexible, agile, resilient, and scalable to meet the needs of the biodiversity community. In this context, this paper describes the integration of open source cloud middleware, applications, and third party services using standard formats, protocols, and services. In addition, this paper demonstrates the value of the digitized information from collections in a broader scenario involving multiple disciplines.},
	keywords = {appliances, biocollections infrastructure, biodiversity, cloud computing, data access, data store, digitization, EF-1115210},
	doi = {10.1109/eScience.2013.48},
	url = {http://dx.doi.org/10.1109/eScience.2013.48},
	author = {Matsunaga, Andr{\'e}a and Thompson, Alex and Figueiredo, Renato J. and Germain-Aubrey, Charlotte C. and Collins, Matthew and Beaman, Reed S. and MacFadden, Bruce J. and Riccardi, Greg and Soltis, Pamela S. and Page, Lawrence M. and Fortes, Jos{\'e} A.B.}
}
@conference {2415,
	title = {Crowdsourcing Biodiversity Data Mobilization},
	booktitle = {TDWG 2015},
	year = {2015},
	keywords = {EF-1115210, Presentation, TDWG2015},
	author = {Ellwood, Elizabeth R.}
}
@conference {2432,
	title = {Data Carpentry: one comprehensive model for teaching biodiversity informatics data management, research skills, and training instructors},
	booktitle = {TDWG 2015},
	year = {2015},
	keywords = {EF-1115210, Presentation, TDWG2015},
	author = {Paul, Deborah L. and Teal, Tracy K and Collins, Matthew}
}
@conference {2431,
	title = {Enhancing your ecological research with iDigBio biological specimen data},
	booktitle = {Ecological Society of America},
	year = {2015},
	keywords = {EF-1115210, ESA2015, IGN 8-1, Presentation, Research},
	author = {Paul, Deborah L. and Ellwood, Elizabeth R.}
}
@conference {2437,
	title = {ePandda Project: increasing accessibility to digitized data from the paleontological and neontological communities},
	booktitle = {2015 GSA Annual Meeting},
	year = {2015},
	month = {2015},
	address = {Baltimore, Maryland},
	abstract = {The ePANDDA project, Enhancing PAleontological and Neontological Data Discovery API, is focused on the development of software tools that will connect three established, well-supported, and critically important data sources: the Paleobiology Database (PBDB, paleontological, literature-based), iDigPaleo (paleontological, specimen-based) and iDigBio (neontological and paleontological, specimen-based). At present, the ability to access and integrate data from across the geological and biological sciences is a cumbersome and time-consuming process, as the connectivity between modern and fossil, and specimen and literature-based resources does not currently exist. ePANDDA will use application programming interfaces (APIs) to streamline and normalize data acquisition, including retrieval from disparate data sources. This is a major shift in the way the geoscience community has traditionally approached data acquisition and publishing (e.g., building a new portal). It will allow for more growth and flexibility in which existing data portals can be utilized and facilitate coordination with future data initiatives in other geoscience disciplines.
Ultimately, for the researcher, the ePANDDA project will eliminate a significant barrier to data collection and processing, as users will be able to access and query multiple data sources at the same time from their preferred portal, resulting in a much richer, combined dataset. The development of APIs will provide researchers the opportunity to collaborate across disciplinary boundaries, to ask and answer new research questions affecting a diversity of fields (e.g., biogeographic/niche modeling, systematics, functional morphology, evolutionary biology, ecology, climatology, conservation biology, oceanography, and petroleum geology) and has the potential to change the nature and scope of the research questions that can be addressed by the scientific community.

Geological Society of America Abstracts with Programs. Vol. 47, No. 7, p.613},
	keywords = {239-11, EF-1115210, GSA2015, Presentation},
	url = {https://gsa.confex.com/gsa/2015AM/webprogram/Paper270315.html},
	author = {Smith, Dena M. and Butts, Susan H. and Gall, Lawrence and Karim, Talia S and Landman, Neil H. and Nelson, Gil and Norris, Christopher A and Sessa, Jocelyn A. and Uhen, Mark D.}
}
@article {225,
	title = {Five task clusters that enable efficient and effective digitization of biological collections},
	journal = {ZooKeys},
	volume = {209},
	year = {2012},
	month = {07/2012},
	chapter = {19},
	abstract = {This paper describes and illustrates five major clusters of related tasks (herein referred to as task clusters) that are common to efficient and effective practices in the digitization of biological specimen data and media. Examples of these clusters come from the observation of diverse digitization processes. The staff of iDigBio (The U.S. National Science Foundation{\textquoteright}s National Resource for Advancing Digitization of Biodiversity Collections) visited active biological and paleontological collections digitization programs for the purpose of documenting and assessing current digitization practices and tools. These observations identified five task clusters that comprise the digitization process leading up to data publication: (1) predigitization curation and staging, (2) specimen image capture, (3) specimen image processing, (4) electronic data capture, and (5) georeferencing locality descriptions. While not all institutions are completing each of these task clusters for each specimen, these clusters describe a composite picture of digitization of
biological and paleontological specimens across the programs that were observed. We describe these clusters, three workflow patterns that dominate the implemention of these clusters, and offer a set of workflow recommendations for digitization programs.},
	keywords = {ADBC, biodiversity informatics, Biological specimen collections, curation, digitization, EF-1115210, iDigBio, Imaging, paleontological specimen collections, task cluster, workflow},
	doi = {doi: 10.3897/zookeys.209.3135},
	url = {http://www.pensoft.net/journals/zookeys/article/3135/five-task-clusters-that-enable-efficient-and-effective-digitization-of-biological-collections},
	author = {Gil Nelson and Deborah L Paul and Gregory Riccardi and Austin R. Mast}
}
@conference {2430,
	title = {Got metadata? GBIF Task Force on accelerating discovery of biological collections data},
	booktitle = {Entomological Collections Network 2015},
	year = {2015},
	keywords = {ECN2015, EF-1115210, Presentation},
	author = {Paul, Deborah L.}
}
@conference {547,
	title = {iConference2013: Augmenting optical character recognition (OCR) for improved digitization: Strategies to access scientific data in natural history collections},
	booktitle = {iConference 2013},
	year = {2013},
	month = {02/2013},
	publisher = {iSchools},
	organization = {iSchools},
	address = {Ft. Worth, Texas},
	abstract = {The Augmenting OCR Working Group (A-OCR WG) at Integrated Digitized Biocollections (iDigBio) seeks to improve community OCR strategies and algorithms for faster, better parsing of OCR output derived from valuable data on natural history collection specimen labels. This task is exceedingly difficult because museum labels are often annotated, and vary in content, form and font. Under the National Science Foundation{\textquoteright}s (NSF) Advancing Digitization of Biological Collections (ADBC) program, iDigBio is building a cyberinfrastructure to aggregate quality data from museum specimens housed in collections across the United States for use by researchers, educators, environmentalists and the public. Since March of 2012, the A-OCR WG formed from community consensus to begin its role in this endeavor, defining reachable goals including setting up a hackathon concurrent with iConference 2013. This paper reports on the definition of some key problems identified by the A-OCR WG since these science problems will drive research and cyberinfrastructure development.},
	keywords = {EF-1115210, iConference2013, iDigBio, information analysis, information organization, information retrieval, information services, machine language, Natural Language, OCR, qualitative data analysis, research methods},
	doi = {10.9776/13266},
	url = {https://www.ideals.illinois.edu/bitstream/handle/2142/39427/266.pdf?sequence=4},
	author = {Deborah L Paul and Heidorn, P. Bryan}
}
@conference {546,
	title = {iConference2013: Improving the Character of Optical Character Recognition (OCR): iDigBio Augmenting OCR Working Group Seeks Collaborators and Strategies to Improve OCR Output and Parsing of OCR Output},
	booktitle = {iConference 2013},
	year = {2013},
	month = {02/2013},
	publisher = {iSchools},
	organization = {iSchools},
	address = {Ft. Worth, Texas},
	abstract = {There are an estimated 2 {\textendash} 3 billion museum specimens world {\textendash} wide (OECD 1999, Ari{\~n}o 2010). In an effort to increase the research value of their collections, institutions across the U. S. have been seeking new ways to cost effectively transcribe the label information associated with these specimen collections. Current digitization methods are still relatively slow, labor-intensive, and therefore expensive. New methods, such as optical character recognition (OCR), natural language processing, and human-in-the-loop assisted parsing are being explored to reduce these costs. The National Science Foundation (NSF), through the Advancing Digitization of Biodiversity Collections (ADBC) program, funded Integrated Digitized Biocollections (iDigBio) in 2011 to create a Home Uniting Biodiversity Collections (HUB) cyberinfrastructure to aggregate and collectively integrate specimen data and find ways to digitize specimen data faithfully and faster and disseminate the knowledge of how to achieve this. The iDigBio Augmenting OCR Working Group is part of this national effort. - speed up the overall digitization process, - lower the cost, - improve overall efficiency, - assure digitized data is fit-for-use (NIBA 2010, Chapman 2005), and - provide the resulting digitized data records to researchers more quickly. The iDigBio Augmenting OCR (A-OCR) working group is actively engaged in identifying opportunities for collaboration to leverage OCR tools and technologies that are successful (both within and outside of the biology digitization domain) and disseminate these tools to the public or seek funding for development.},
	keywords = {EF-1115210, iConference2013, iDigBio, information analysis, information organization, information retrieval, information services, machine language, Natural Language, OCR, qualitative data analysis, research methods},
	doi = {10.9776/13493},
	url = {https://www.ideals.illinois.edu/bitstream/handle/2142/42089/493.pdf?sequence=2},
	author = {Robert Anglin and Jason Best and Figueiredo, Renato and Gilbert, Edward and Gnanasambandam, Nathan and Gottschalk, Stephen and Haston, Elspeth and Heidorn, P. Bryan and Lafferty, Daryl and Lang, Peter and Nelson, Gil and Deborah L Paul and Ulate, William and Kimberly Watson and Zhang, Qianjin}
}
@article {569,
	title = {iConference2013: The Apiary Project: a workflow for text extraction and parsing for herbarium specimens},
	year = {2013},
	abstract = {The Apiary Project: combining OCR technology, OCR output from herbarium specimen or other images containing museum specimen data, well-developed regular expressions for parsing output to Darwin Core fields, and humans-in-the-digitization-loop for an elegant, sophisticated user-interface for a workflow designed to maximize the value of the human interaction, minimize steps, and speed data throughput.},
	keywords = {Augmenting Optical Character Recognition, collaboration, EF-1115210, Hackathon, iConference2013, Machine Learning, Natural Language Processing, parsing algorithms, Research, Transcription, workflow},
	url = {https://www.idigbio.org/sites/default/files/workshop-presentations/aocr-hackathon/JBest-Apiary-iConference.ppt},
	author = {Jason Best}
}
@proceedings {548,
	title = {iConference2013: Workshop -- Help iDigBio Reveal Hidden Data: iDigBio Augmenting OCR Working Group Needs You ($\#$CNFWSP11)},
	year = {2013},
	abstract = {Integrated Digitized Biodiversity Collections, iDigBio, is an initiative funded under the National Science Foundation{\textquoteright}s (NSF) Advancing Digitization of Biological Collections (ADBC) program set up to help natural history museums get specimen data for hundreds of millions of specimens out of drawers, off of labels, out of field notebooks, out of old publications and into integrated databases for everyone{\textquoteright}s use. The iDigBio Augmenting OCR Working Group needs your wisdom, knowledge and collaboration as part of our multi-faceted approach to improve OCR strategies and natural language processing (NLP) algorithms used in digitization. Our workshop panelists, members of our working group, are eager to introduce the iSchools community to our challenges and get your input in our break-out sessions. Our research areas of interest include: image segmentation, autocorrection of typographical errors, semantic autocorrection, autonormalization, automated text segmentation, generating consensus records and user interfaces for these tasks. We seek your insights, collective experiences and partnership in order to find ways to improve the digitization process to create a national searchable online specimen-based data set that is fit-for-use by scientists and the public. Some ideas generated in this session may be implemented at the iDigBio hackathon being held at the Botanical Research Institute of Texas (BRIT) during the iConference.
},
	keywords = {aocr, EF-1115210, iConference2013, iDigBio hackathon, information analysis, information organization, information retrieval, information services, iSchools, machine language, Natural Language, OCR, qualitative data analysis, research methods},
	doi = {10.9776/13471},
	url = {http://idigbio.adobeconnect.com/p6463wkhtx1/},
	author = {Paul, Deborah L. and Heidorn, P. Bryan and Best, Jason and Gilbert, Edward and Neill, Amanda and Nelson, Gil and Ulate, William}
}
@conference {1630,
	title = {iConference2013:Help iDigBio reveal hidden data: iDigBio Augmenting OCR working group needs you - Part II},
	year = {2013},
	publisher = {iSchools},
	organization = {iSchools},
	address = {Ft. Worth, Texas},
	abstract = {Integrated Digitized Biocollections (iDigBio) is a nation-wide effort funded by the National Science Foundation (NSF) to digitize data from hundreds of millions of natural history museum specimens. In a concerted five-part outreach effort, the iDigBio Augmenting Optical Character Recognition Working Group (A-OCR WG) coordinated a 2013 iConference Workshop, Poster, Notes submission, Alternative Event and a concurrent Hackathon hosted by the Botanical Research Institute of Texas (BRIT). The Workshop titled, " Help iDigBio Reveal Hidden Data: iDigBio Augmenting OCR Working Group Needs You" introduces the iSchools community to iDigBio and the A-OCR WG mission and challenges to improve digitization efficiency. This related Alternative Event provides the A-OCR WG an opportunity to report back to iConference Workshop attendees about our first experience using a Hackathon model to work on parsing and user interface design issues specific to our needs. We anticipate to a lively, open discussion with event attendees and future collaborators.},
	keywords = {EF-1115210, iConference2013, iDigBio},
	url = {http://hdl.handle.net/2142/42515},
	author = {Paul, Deborah L. and Heidorn, P. Bryan and Jason Best and Edward Gilbert and Amanda Neill and Ulate, William}
}
@conference {2429,
	title = {In Defense of Specimen Collecting, Natural History Collections, and Bioethics},
	booktitle = {SPNHC 2015},
	year = {2015},
	keywords = {EF-1115210, Presentation, SPNHC2015},
	author = {Page, Larry M.}
}
@article {238,
	title = {Integrating specimen databases and revisionary systematics},
	journal = {ZooKeys},
	volume = {209},
	year = {2012},
	month = {07/2012},
	chapter = {255},
	abstract = {Arguments are presented for the merit of integrating specimen databases into the practice of revisionary systematics. Work flows, data connections, data outputs, and data standardization are enumerated as critical aspects of such integration. Background information is provided on the use of {\textquotedblleft}barcodes{\textquotedblright} as unique specimen identifiers and on methods for efficient data capture. Examples are provided on how to achieve efficient workflows and data standardization, as well as data outputs and data integration.},
	keywords = {EF-1115210, revisionary systematics, specimen databases, WorkFlows},
	doi = {10.3897/zookeys.209.3288},
	url = {http://www.pensoft.net/journals/zookeys/article/3288/integrating-specimen-databases-and-revisionary-systematics},
	author = {Randall T. Schuh}
}
@conference {2422,
	title = {Introduction to Using Digitized Data},
	booktitle = {Ecological Collections Network 2015},
	year = {2015},
	keywords = {ECN2015, EF-1115210, Presentation},
	author = {James, Shelley A. and Bills, Christy and Nelson, Gil}
}
@conference {2439,
	title = {Lifemapper{\textquoteright}s species distribution modeling based on iDigBio Biocollections},
	booktitle = {SPNHC 2015},
	year = {2015},
	keywords = {EF-1115210, Presentation, SPNHC2015},
	author = {Stewart, Aimee and Matsunaga, Andr{\'e}a and Beach, James H. and Grady, C.J. and Cavner, Jeffrey and Fortes, Jos{\'e} A.B.}
}
@conference {2426,
	title = {A list of U.S.-based natural history collections},
	booktitle = {SPNHC 2015},
	year = {2015},
	keywords = {EF-1115210, Presentation, SPNHC2015},
	author = {Michonneau, Fran{\c c}ois and Page, Larry M.}
}
@article {2435,
	title = {Looking for treasures in a megadiverse country: natural collections in Ecuador},
	year = {2015},
	keywords = {EF-1115210, poster, SPNHC2015},
	author = {Segovia-Salcedo, Mar{\'\i}a C. and Acosta-Buena{\~n}o, N{\'e}stor A. and Carrasco Camacho, Luis}
}
@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}
}
@conference {2110,
	title = {Mapping Specifications for Ranked Hierarchical Trees in Data Integration Systems},
	booktitle = {2014 IEEE International Conference on Information Reuse and Integration (IRI 2014)},
	year = {2014},
	publisher = {IEEE},
	organization = {IEEE},
	address = {San Francisco, California, USA},
	abstract = {A popular approach to deal with data integration of heterogeneous data sources is to Extract, Transform and Load (ETL) data from disparate sources into a consolidated data store while addressing integration challenges including, but not limited to: structural differences in the source and target schemas, semantic differences in their vocabularies, and data encoding. This work focuses on the integration of tree-like hierarchical data or information that when modeled as a relational schema can take the shape of a flat schema, a self-referential schema or a hybrid schema. Examples include evolutionary taxonomies, geological time scales, and organizational charts. Given the observed complexity in developing ETL processes for this particular but common type of data, our work focuses on reducing the time and effort required to map and transform this data. Our research automates and simplifies the transformation from ranked self-referential to flat representations (and vice-versa), by: (a) proposing MSL+, an extension to IBM{\textquoteright}s Mapping Specification Language (MSL), to succinctly express the mapping between schemas while hiding the actual transformation implementation complexity from the user, and (b) implementing a transformation component for the Talend open-source ETL platform, called Tree Transformer (TT). We evaluated MSL+ and TT, in the context of biodiversity data integration, where this class of transformations is a recurring pattern. We demonstrate the effectiveness of MSL+ with respect to development time savings as well as a 2 to 25-fold performance improvement in transformation time achieved by TT when compared to existing implementations and to Talend built-in components.},
	keywords = {Data Integration, data transformation, EF-1115210, ETL, mapping language, self-referential schema},
	doi = {10.1109/IRI.2014.7051899},
	url = {http://ieeexplore.ieee.org/xpls/icp.jsp?arnumber=7051899},
	author = {Soomro, Sarfaraz and Matsunaga, Andr{\'e}a and Fortes, Jos{\'e} A.B.}
}
@conference {2434,
	title = {Measuring Megalodon: classroom driven research made possible with 3D technology},
	booktitle = {2015 GSA Annual Meeting},
	year = {2015},
	month = {2015},
	address = {Baltimore, Maryland},
	abstract = {The Florida Museum of Natural History has been collaborating with iDigBio and Duke University to incorporate 3D printing technology and compelling scientific research into K-12 classrooms. Recently, an associated dentition of Megalodon (Carcharocles megalodon), donated by amateur paleontologist Gordon Hubbell, was scanned and 3D printed for research and education purposes. Associated sets of Megalodon teeth are extremely rare and offer insurmountable information regarding the life history of this captivating creature. A lesson has since been developed, available on www.paleoteach.org, that integrates scientific research concerning body length estimates of Megalodon with 3D printing technology in order to develop an understanding of fundamental concepts in paleontology, geology, and biology. Body length estimates for Megalodon are commonly based off of the anatomy of the living Great White shark (Carcharodon carcharias), most prominent are a set of equations developed by Kenshu Shimada (2003) that estimates body length based off a linear relationship observed between crown height and body length for each tooth position. In this lesson, students are given teeth from the associated set at random and first asked to identify the tooth position of their isolated teeth, allowing them to compose a personal understanding of the tooth morphology. Subsequently, students estimate body length using the equations established by Shimada and their corresponding tooth positions, which requires solving a linear equation and, consequently, incorporates mathematics (i.e., STEM integration). A geometry extension was also developed that exploits the natural triangular shape of the teeth and the inherent dignathic heterodonty exhibited by Megalodon. Tooth dimensions vary, in terms of size and symmetry, between positions; which allows students to explore the geometric properties of triangles. Interestingly, upon testing these equations with the associated dentition, the students found that different tooth positions resulted in vastly different body length estimates. This had never been tested before and is in fact a new discovery to science made possible by a harmonious collaboration between technologic innovation, scientific institutions, researchers, amateur paleontologists, teachers, and students.

Geological Society of America Abstracts with Programs. Vol. 47, No. 7, p.99},
	keywords = {education, EF-1115210, GSA2015, poster},
	url = {https://gsa.confex.com/gsa/2015AM/webprogram/Paper266196.html},
	author = {Perez, Victor J. and Grant, Claudia and Hendrickson, Megan and Tovani, Jason}
}
@article {2105,
	title = {Natural History Collections as Emerging Resources for Innovative Education},
	journal = {BioScience},
	volume = {64},
	year = {2014},
	month = {08/2014},
	chapter = {725},
	abstract = {Nearly four decades ago, Roose \& Gottlieb (Roose \& Gottlieb 1976 Evolution 30, 818{\textendash}830. (doi:10.2307/2407821)) showed that the recently derived allotetraploids Tragopogon mirus and T. miscellus combined the allozyme profiles of their diploid parents (T. dubius and T. porrifolius, and T. dubius and T. pratensis, respectively). This classic paper addressed the link between genotype and biochemical phenotype and documented enzyme additivity in allopolyploids. Perhaps more important than their model of additivity, however, was their demonstration of novelty at the biochemical level. Enzyme multiplicity{\textemdash}the production of novel enzyme forms in the allopolyploids{\textemdash}can provide an extensive array of polymorphism for a polyploid individual and may explain, for example, the expanded ranges of polyploids relative to their diploid progenitors. In this paper, we extend the concept of evolutionary novelty in allopolyploids to a range of genetic and ecological features. We observe that the dynamic nature of polyploid genomes{\textemdash}with alterations in gene content, gene number, gene arrangement, gene expression and transposon activity{\textemdash}may generate sufficient novelty that every individual in a polyploid population or species may be unique. Whereas certain combinations of these features will undoubtedly be maladaptive, some unique combinations of newly generated variation may provide tremendous evolutionary potential and adaptive capabilities.},
	keywords = {EF-1115210},
	url = {https://www.idigbio.org/sites/default/files/sites/default/files/Cook\%20et\%20al\%20BioScience-2014-Cook-725-34.pdf},
	author = {Joseph A. Cook and Scott V. Edwards and Eileen A. Lacey and Robert P. Guralnick and Soltis, Pamela S. and Douglas E. Soltis and Corey K. Welch and Kayce C. Bell and Kurt E. Galbreath and Christopher Himes and Julie M. Allen and Tracy A. Heath and Ana C. Carnaval and Kimberly L. Cooper and Mark Liu and James Hanken and Stefanie Ickert-Bond}
}
@article {2103,
	title = {A New iDigBio Web Feature Links DNA Banks and Genetic Resources Repositories in the United States},
	journal = {DNA Banking for the 21st Century},
	year = {2014},
	month = {04/2014},
	abstract = {Collections of genetic resources have served the needs of molecular biologists for many decades, providing valu
able sources of materials for molecular studies of biodiversity and facilitating long-term archival of samples from pub
lished studies. However, the needs of the research community are rapidly changing and contributing to an increasing
demand for high-quality genetic resources. Curators and researchers in the United States (U.S.) have recently engaged
in an active dialogue about the future of these collections, as well as about best practices and standards for collecting
and preserving new materials. The discussion has reemphasized a previously identified need for networked data on
genetic resources to better link samples housed in U.S. collections with research consumers. However, there are no
comprehensive lists of DNA banks, genetic resources repositories, or tissue collections available, and significant gaps
remain in our knowledge about the types of genetic resources that are available as well as their physical localities. In
this paper, we describe a newly available web feature developed and maintained by Integrated Digitized Biocollections
(iDigBio) that is helping to compile the first comprehensive list of genetic resources collections in the U.S. Our new
tool provides information on a diverse set of collections and enables rapid searching of multiple collections.},
	keywords = {DNA bank, EF-1115210, genetic resources, iDigBio, natural history, tissue collections},
	issn = {10: 0-9808415-9-8},
	url = {https://www.idigbio.org/sites/default/files/sites/default/files/GoddenSoltis\%20DNA\%20Banking2014.pdf},
	author = {Soltis, Pamela S and Godden, Grant T}
}
@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 {2420,
	title = {Paleoteach: use of paleontological data for K-12 education},
	booktitle = {2015 GSA Annual Meeting},
	year = {2015},
	month = {11/2015},
	address = {Baltimore, Maryland},
	abstract = {PaleoTeach is a collaboration involving the Florida Museum of Natural History, and secondary science educators. The goal is to create curricula using high-quality 3D models for a K-12 audience. Fossils, present in required Earth Sciences curriculum, are oftentimes delicate or rare, and not universally suitable for classroom use. Therefore, 3D scanning and printing technology provides a unique opportunity to make these specimens available for K-12 education. In addition, paleontology is an interdisciplinary and engaging area of study that provides distinctive opportunities for STEM integration.
STEM integration is an instructional method that aims to emphasize the connections between science, technology, engineering, and math. This method helps introduce concepts in these subjects in a way that is more meaningful to students and also replicates the way science is practiced. PaleoTeach advances our understanding of the potential efficacy of the recently developed 3D scanning technology in K-12 science learning. This approach to integrate 3D data can improve the relevance of educational practices in our schools and broaden the impact of ongoing digitization efforts of paleontological research collections. Lessons that we have developed are rooted in the idea of STEM integration. For example, research on Carcharocles megalodon provides multiple opportunities for K-12 educators. Lessons have been designed to teach concepts of extinction and evolution (science) through the use of 3D printed teeth (technology). Students replicate scientific processes by measuring the teeth and calculating the size of the animal (math). Ultimately, they reconstruct the entire jaw by applying concepts of engineering. Like the study of C. megalodon, there are other examples from the fossil record (e.g., Titanoboa cerrejonensis and equid evolution) that can increase educators{\textquoteright} content knowledge and guide students through this integrated process. Furthermore, making specific fossils available for 3D reproduction can help educators introduce examples of important topics, such as climate change, extinction and evolution, fostering new learning opportunities in issues of current societal relevance.

Geological Society of America Abstracts with Programs. Vol. 47, No. 7, p.612},
	keywords = {EF-1115210, GSA2015, Presentation},
	url = {https://gsa.confex.com/gsa/2015AM/webprogram/Paper264381.html},
	author = {Grant, Claudia}
}
@article {2100,
	title = {Polyploidy and novelty: Gottlieb{\textquoteright}s legacy},
	journal = {Philosophical Transactions of the Royal Society B: Biological Sciences},
	volume = {369},
	year = {2015},
	month = {2014},
	chapter = {1},
	abstract = {There is an emerging consensus that undergraduate biology education in the United States is at a crucial juncture, especially as we acknowledge
the need to train a new generation of scientists to meet looming environmental and health crises. Digital resources for biology now available
online provide an opportunity to transform biology curricula to include more authentic and inquiry-driven educational experiences. Digitized
natural history collections have become tremendous assets for research in environmental and health sciences, but, to date, these data remain
largely untapped by educators. Natural history collections have the potential to help transform undergraduate science education from passive
learning into an active exploration of the natural world, including the exploration of the complex relationships among environmental
conditions, biodiversity, and human well-being. By incorporating natural history specimens and their associated data into undergraduate
curricula, educators can promote participatory learning and foster an understanding of essential interactions between organisms and their
environments.},
	keywords = {EF-1115210},
	doi = {http://dx.doi.org/10.1098/rstb.2013.0351},
	url = {https://www.idigbio.org/sites/default/files/sites/default/files/PSoltis\%20et\%20al\%20PhilTransRoySoc2014.pdf},
	author = {Pamela S. Soltis and Liu, Xiaoxian and Marchant, D. Blaine and Visger, Clayton J. and Douglas E. Soltis}
}
@article {2413,
	title = {Poster: ARPO-Augmented Reality for Public Outreach},
	year = {2015},
	keywords = {EF-1115210, poster, SPNHC2015},
	author = {Basham, Melody A. and Mast, Austin R. and Franz, Nico M.},
	editor = {Holmes, Kody}
}
@article {2102,
	title = {Preserving Biodiversity for Long-term Research: The Genetic Resources Repository of the Florida Museum of Natural History},
	journal = {DNA Banking for the 21st Century},
	year = {2014},
	month = {2014},
	chapter = {49},
	abstract = {The Genetic Resources Repository (GRR) of the Florida Museum of Natural History (FLMNH) is a centralized
facility that preserves DNA and other genetic resources of a wide array of organisms, mostly specimens derived from
research projects of the divisions of the FLMNH. In a period of six years the collection had rapid growth and now
encompasses 42,833 specimens with potential value for molecular studies that should prove instrumental to a broad
array of research programs worldwide. The establishment and different facets of organization and administration of
the GRR are here described, with the goal 0f contributing guidelines for the establishment of other genetic resources
collections.},
	keywords = {cryopreservation, DNA, EF-1115210, liquid nitrogen, Natural history collections, tissues},
	url = {https://www.idigbio.org/sites/default/files/sites/default/files/Endara\%20et\%20al\%20DNA\%20Banking\%202014.pdf},
	author = {Lorena Endara and Angelo Soto-Centeno and Terry A Lott and Pamela S. Soltis}
}
@conference {2427,
	title = {Providing the computing skills for the next generation of biodiversity scientists},
	booktitle = {SPNHC 2015},
	year = {2015},
	keywords = {EF-1115210, Presentation, SPNHC2015},
	author = {Michonneau, Fran{\c c}ois and Paul, Deborah L.}
}
@conference {1824,
	title = {Reaching Consensus in Crowdsourced Transcription of Biocollections Information},
	booktitle = {2014 IEEE 10th International Conference on e-Science},
	year = {2014},
	month = {Oct/2014},
	publisher = {IEEE},
	organization = {IEEE},
	address = {Guaruj{\'a}, Brazil},
	abstract = {Crowdsourcing can be a cost-effective method for tackling the problem of digitizing historical bio collections data, and a number of crowd sourcing platforms have been developed to facilitate interaction with the public and to design simple "Human Intelligence Tasks". However, the problem of reaching consensus on the response of the crowd is still challenging for tasks for which a simple majority vote is inadequate. This paper (a) describes the challenges faced when trying to reach consensus on data transcribed by different workers, (b) offers consensus algorithms for textual data and a consensus-based controller to assign a dynamic number of workers per task, and (c) proposes further enhancements of future crowd sourcing tasks in order to minimize the need for complex consensus algorithms. Experiments using the proposed algorithms show up to a 45-fold increase in ability to reach consensus when compared to majority voting using exact string matching. In addition, the controller is able to decrease the crowd sourcing cost by 55\% when compared to a strategy that uses a fixed number of workers.},
	keywords = {Accuracy, Approximation algorithms, biocollections infrastructure, biodiversity, consensus algorithms, crowdsourcing, digitization, EF-1115210, Heuristic algorithms, Materials, Optical character recognition software, Reliability},
	doi = {10.1109/eScience.2014.30},
	url = {http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=\&arnumber=6972249},
	author = {Matsunaga, Andr{\'e}a and Mast, Austin and Fortes, Jos{\'e} A.B.}
}
@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}
}
@inbook {2111,
	title = {Simplifying Extract-Transform-Load for Ranked Hierarchical Trees via Mapping Specifications},
	booktitle = {Formalisms for Reuse and Systems Integration},
	series = {Advances in Intelligent Systems and Computing},
	volume = {346},
	year = {2015},
	pages = {203-225},
	publisher = {Springer International Publishing},
	organization = {Springer International Publishing},
	abstract = {A popular approach to deal with data integration of heterogeneous data sources is to Extract, Transform and Load (ETL) data from disparate sources into a consolidated data store while addressing integration challenges including, but not limited to: structural differences in the source and target schemas, semantic differences in their vocabularies, and data encoding. This work focuses on the integration of tree-like hierarchical data or information that when modeled as a relational schema can take the shape of a flat schema, a self-referential schema or a hybrid schema. Examples include evolutionary taxonomies, geological time scales, and organizational charts. Given the observed complexity in developing ETL processes for this particular but common type of data, our work focuses on reducing the time and effort required to map and transform this data. Our research automates and simplifies all possible transformations involving ranked self-referential and flat representations, by: (a) proposing MSL+, an extension to IBM{\textquoteright}s Mapping Specification Language (MSL), to succinctly express the mapping between schemas while hiding the actual transformation implementation complexity from the user, and (b) implementing a transformation component for the Talend open-source ETL platform, called Tree Transformer (TT). We evaluated MSL+ and TT, in the context of biodiversity data integration, where this class of transformations is a recurring pattern. We demonstrate the effectiveness of MSL+ with respect to development time savings as well as a 2 to 25-fold performance improvement in transformation time achieved by TT when compared to existing implementations and to Talend built-in components.},
	keywords = {Data Integration, data transformation, EF-1115210, ETL, flat schema, hierarchical tree, mapping language, MSL, schema mapping, self-referential schema},
	issn = {978-3-319-16576-9},
	doi = {10.1007/978-3-319-16577-6_9},
	url = {http://dx.doi.org/10.1007/978-3-319-16577-6_9},
	author = {Soomro, Sarfaraz and Matsunaga, Andr{\'e}a and Fortes, Jos{\'e} A.B.},
	editor = {Bouabana-Tebibel, Thouraya and Rubin, Stuart H.}
}
@conference {2438,
	title = {Specimens full circle: collection to digitization to data use},
	booktitle = {SPNHC 2015},
	year = {2015},
	keywords = {EF-1115210, Presentation, SPNHC2015},
	author = {Smith, Dena M. and Paul, Deborah L. and Blagoderov, Vladimir}
}
@article {1618,
	title = {Temporal Calibration and Biochronology of the Centenario Fauna, Early Miocene of Panama},
	journal = {The Journal of Geology},
	volume = {122},
	year = {2014},
	month = {2014},
	chapter = {113},
	abstract = {New excavations along the Panama Canal have yielded a growing Early Miocene assemblage of mammals referred to as the Centenario Fauna. Despite the area{\textquoteright}s proximity to South America, the mammals of the Centenario Fauna have entirely North American affinities. The Centenario Fauna is distributed throughout a \~{}115-m stratigraphic interval encompassing the uppermost Culebra and Cucaracha Formations within the Panama Canal basin. Previously published ages constrain the age of the lower limit of the Centenario Fauna to no younger than \~{}19 Ma, but the upper limit has remained problematical. A fresh exposure of the Cucaracha tuff, a prominent marker horizon within our measured sections, has yielded two new radioisotopic determinations: (1) an 40Ar/39Ar age of 18.96 {\textpm} 0.90 Ma and (2) a U-Pb zircon age of 18.81 {\textpm} 0.30 Ma. In addition, magnetostratigraphic data indicate that the Centenario Fauna occurs within chron C5Er, from 18.78 to 19.05 Ma on the geomagnetic polarity timescale of Gee and Kent. These correlations further confirm the calibration of the latest Arikareean (Ar4) to early Hemingfordian (He1) transition in Nebraska, at the base of chron C5Er, at about 19.05 Ma. The Centenario Fauna occurs at the beginning of the Hemingfordian North American Land Mammal Age, i.e., He1. A broad faunal province existed during the early Hemingfordian that can be recognized across a north-south range of 5000 km throughout North America, with the southernmost limits defined by the Centenario Fauna of Panama.},
	keywords = {EF-1115210},
	url = {http://www.jstor.org/action/showArticleInfo?doi=10.1086\%2F675244},
	author = {MacFadden, Bruce J. and Jonathan Bloch and Helen Evans and David Foster and Gary Morgan and Aldo Rincon and Aaaron Wood}
}
@article {1616,
	title = {Toward broader impacts: Making sense of NSF{\textquoteright}s merit review criteria in the context of the National Science Digital Library},
	journal = {Journal of the American Society for Information Science and Technology},
	volume = {63},
	year = {2012},
	month = {2012},
	chapter = {1758},
	abstract = {Scholars in library and information science are under increasing pressure to seek external funding for research. The National Science Foundation (NSF), which is often the source of this funding, considers proposed projects based on the criteria of {\textquotedblleft}Intellectual Merit{\textquotedblright} and {\textquotedblleft}Broader Impacts.{\textquotedblright} However, these merit review criteria have been criticized as being insufficiently specific and not appropriate for all types of scientific research. In an effort to examine the extent to which funded projects represented Broader Impacts, the researchers performed a content analysis of the abstracts from projects in the National Science Digital Library, an NSF project that crossed many disciplines and applications, but is of particular relevance to information scientists. When the results of these analyses are placed in the context of the controversy surrounding the Broader Impacts merit review criterion, it is clear that this criterion is interpreted broadly and that even successful proposals often include aspirational or incomplete claims of impact. Because current proposed revisions to the merit review criteria that include emphases on demonstrable innovation and economic benefit will likely only complicate proposers{\textquoteright} abilities to describe their projects{\textquoteright} potentials, researchers may benefit from a greater understanding of Broader Impacts and how they can be clearly expressed to reviewers.},
	keywords = {DUE 0946953, DUE 1044315, EF-1115210},
	url = {http://onlinelibrary.wiley.com/doi/10.1002/asi.22693/abstract},
	author = {Marcia Mardis and Ellen S. Hoffman and Flora P McMartin}
}
@conference {2440,
	title = {Transforming accessibility to the rich, site-based, multi-taxon collections of field stations; a case study from Archbold Biological Station},
	booktitle = {SPNHC 2015},
	year = {2015},
	keywords = {EF-1115210, Presentation, SPNHC2015},
	author = {Swain, Hilary M. and Nelson, Gil}
}
@conference {2436,
	title = {Unlocking hidden potential: using museum specimens to engage and educate children with autism},
	booktitle = {SPNHC 2015},
	year = {2015},
	keywords = {education, EF-1115210, Presentation, SPNHC2015},
	author = {Singer, Randy A.}
}
@conference {2419,
	title = {Using museum data for niche modeling and phylogenetic diversity of Florida plants},
	booktitle = {Ecological Society of America 2015},
	year = {2015},
	keywords = {EF-1115210, ESA2015, IGN 8-3, Presentation},
	author = {Germain-Aubrey, Charlotte C. and Allen, Julie M. and Neubig, Kurt M. and Guralnick, Robert P. and Ponciano, Jose Miguel and Lamy, Thomas and Soltis, Douglas E. and Majure, Lucas and Soltis, Pamela S.}
}
@article {2104,
	title = {Variables affecting DNA preservation in archival plant specimens},
	journal = {DNA Banking for the 21st Century},
	year = {2014},
	month = {2014},
	chapter = {81},
	abstract = {Although the use of plant DNA in scientific research is now decades old now. we still know very little about the
best methods of DNA preservation. A few studies have addressed aspects of DNA quality and preservation . but a
broad sense of the quality of DNA in herbarium specimens and tissues specifically preserved for DNA usage is still
lacking. This article reviews the basic concepts ofDNA preservation, factors affecting DNA in herbarium specimens.
optimal methods for DNA extraction. and storage. To address lingering questions about the nature ofDNA quality
in archival plant specimens. we also evaluated - 2000 samples from herbarium specimens. as well as silica-dried and
frozen tissuesspecifically preserved for DNA usage. For herbarium specimens. we used materials spanning much of
angiosperm phylogenetic diversity to ascertain general trends of DNA degradation over time and to assesswhether
different clades had different rates of "expiration." Our results indicate different rates ofDNA degradation , but for
mostsamples. no matter the taxonomic group . we were unlikely to recover high-quality DNA after 30-40 years.
Nonetheless, given rapid technological advances and changes in DNA sequencing methods. even herbarium specimens
with highly degraded DNA may still be of use in molecular analyses. Additional herbarium specimens were
sampled for two different collection sets with drastically different curation histories bur of approximately the same
age. This analysis showed a vety marked difference in DNA quality between the two sets: the well-curared specimens
had excellent-quality DNA while the poorly curated samples had low-quality DNA. For frozen tissues, virtually all
samples had excellent quality. whether storage wasat -20{\textperiodcentered} or -BO{\textperiodcentered}C and whether tissue was pulverized or intact. For
silica-dried tissues, the results were much more heterogeneous, depending on the storage vessel. Samples stored in
vessels with poor seals yielded lower-quality DNA. To address the long-term viability of frozen DNA extracts, we
compared a set of 7-I2-year-old DNA extracts with new extracts of the same original silica-dried tissues and with
fresh, greenhouse-collected tissues of the same original material, these comparisons indicared less degradation in the
extracts than in rhe silica-preserved samples, although the differences were subtle. We also found that IS-year-old
photo-bleached, silica-dried samples Still had small amounts of high-molecular-weighr DNA. The long-term preservation
of DNA in archival samples remains problematic. bur we can besr preserve DNA by limiting the factors
that degrade it. Although the botanical community has been preserving tissues and DNA extracts for a limited
umespan, we can infer some basic conclusions from this and oth er studies . Recommended best practices are to freeze
tissues and extracts at as Iow a rernperarure as possible (e.g., -BO{\textperiodcentered}C). bur if that is not possible or practical. room
temperature storage of rlssues with silica in tightly sealed containers is a viable alternative , at least for the short term.},
	keywords = {EF-1115210},
	isbn = { 0-9808415-9-8},
	url = {https://www.idigbio.org/sites/default/files/sites/default/files/Neubig_et_al_2014_.pdf},
	author = {Kurt M. Neubig and Mark W. Whitten and Richard J. Abbott and Savannah Elliot and Douglas E. Soltis and Pamela S. Soltis}
}
@conference {2423,
	title = {WeDigBio: Worldwilde Engagement for the Digitization of Biocollections},
	booktitle = {SPNHC 2015},
	year = {2015},
	keywords = {EF-1115210, Presentation, SPNHC2015},
	author = {Kimberly, Paul G. and Flemons, Paul K.J. and Guralnick, Robert P. and Mast, Austin R. and Ellwood, Elizabeth R. and Paul, Deborah L. and Love, Kevin J.}
}
@conference {2414,
	title = {Whole-Dataset Analyses using Apache Spark},
	year = {2015},
	keywords = {EF-1115210, Presentation, TDWG2015},
	author = {Collins, Matthew and Poelen, Jorrit and Thompson, Alexander}
}
@article {2291,
	title = {Workforce-efficient consensus in crowdsourced transcription of biocollections information},
	journal = {Future Generation Computer Systems},
	year = {2015},
	abstract = {Abstract Crowdsourcing can be a cost-effective method for tackling the problem of digitizing historical biocollections data, and a number of crowdsourcing platforms have been developed to facilitate interaction with the public and to design simple {\^a}{\texteuro}{\oe}Human Intelligence Tasks{\^a}{\texteuro}. However, the problem of reaching consensus on the response of the crowd is still challenging for tasks for which a simple majority vote is inadequate. This paper (a) describes the challenges faced when trying to reach consensus on data transcribed by different workers, (b) offers consensus algorithms for textual data, (c) implements a consensus-based controller to assign a dynamic number of workers per task and per field of a task, (d) proposes the use of clustering to further eliminate redundant work and (e) proposes enhancements of future crowdsourcing task assignments in order to minimize the need for complex consensus algorithms. Experiments using the proposed algorithms show multifold increase in the ability to reach consensus when compared to majority voting using exact string matching. In addition, the workforce controller is able to decrease the crowdsourcing cost per task and per task field by 37\% and 50\%, respectively, when compared to a strategy that uses a fixed number of workers. The accuracy of clustering is also good and it has the potential to increase the quality of tasks that can be clustered.},
	keywords = {biocollections infrastructure, biodiversity, consensus algorithms, crowdsourcing, digitization, EF-1115210},
	doi = {http://dx.doi.org/10.1016/j.future.2015.07.004},
	url = {http://www.sciencedirect.com/science/article/pii/S0167739X15002277},
	author = {Matsunaga, Andr{\'e}a and Mast, Austin and Fortes, Jos{\'e} A. B.}
}
@conference {2425,
	title = {The Worldwide Engagement for Digitization of Biocollections (WeDigBio) Event},
	booktitle = {Botanical Society of America 2015},
	year = {2015},
	keywords = {BSA2015, EF-1115210, Presentation},
	author = {Mast, Austin R. and Kimberly, Paul and Flemons, Paul and Ellwood, Elizabeth and Love, Kevin and Paul, Deborah and Guralnick, Robert}
}
