Abstract Detail

Building a High-Resolution, Specimen-Based Picture of Life: Possibilities and Challenges

Macklin, James [1], Dou, Lei [2], Hanken, James [3], Kelley, Maureen [4], Lowery, David [4], Ludaescher, Bertram [2], Morris, Paul [4], Morris, Robert [5].

Introducing ApplePie: A botanical annotation network powered by Filtered Push.

We introduce ApplePie, a Filtered Push network implementation specifically designed for botanical applications. ApplePie will increase the efficiency of digitization workflows through rapid discovery of duplicate specimens, their clustering, generation of a consensus record, and both on-the-fly and bulk input of data into a collection database. ApplePie will also foster and manage the accumulation and dissemination of botanical knowledge through digital annotation, which for the first time will broker two-way flow of information from the aggregator (e.g., GBIF, iDigBio, domain portals) to the source of the primary object (herbaria). Curators and/or data managers can then "filter" the annotations that have been "pushed" to them and choose to accept or reject their addition to the collection database. Mapping of the annotations to collection databases will follow the AppleCore best practice documentation for use of TDWG DarwinCore in exchange of botanical specimen data, which currently is under development. The annotations themselves are communicated by using an extension to data of the Annotation Ontology, which has been developed by the biomedical community for use with publications. An annotation store will maintain all knowledge for the network, which may be accessed directly from integrated clients; non-network members can choose to have knowledge syndicated to them based on their interests using a web client, thus contributing to the accumulation of more knowledge.The annotations will contribute to an increase in data quality through asserting new determinations, adding knowledge about the collecting event (e.g., geo-references) or correcting errors, etc. We will demonstrate ApplePie integrating the Morphbank image repository, Symbiota Portal, and the Specify collection management system. We will also demonstrate a curation workflow tool, Kepler Kurator, built using the Kepler scientific workflow software platform. Kepler uses actors to connect data sources to services, which in this case aid in cleaning and assessing the quality of the data (e.g., Global Names Index, Biogeomancer, Flora of North America). This tool also incorporates semi-automated curation through syndicating problems to experts through e-mail and automated annotation using Filtered Push (NSF: #0960535).

Broader Impacts:

1 - Agriculture and Agri-Food Canada, Biodiversity, 960 Carling Avenue, Ottawa, ON, K1A 0C6, Canada
2 - University of California, Davis, UC Davis Genome Center, 451 Health Sciences Drive, Davis, CA, 95616, USA
3 - Harvard University, Museum of Comparative Zoology, 26 Oxford Street, Cambridge, MA, 02138, USA
4 - Harvard University, Harvard University Herbaria, 22 Divinity Avenue, Cambridge, MA, 02138, USA
5 - University of Massachusetts, Computer Science Department, 100 Morrissey Blvd., Boston, MA, 02125, USA

Keywords:
Annotation
Filtered Push
Software
Curation
Duplicate Specimens
natural history data
knowledge database
workflows.

Presentation Type: Symposium or Colloquium Presentation
Session: SY11
Location: Franklin A/Hyatt
Date: Wednesday, July 11th, 2012
Time: 4:45 PM
Number: SY11013
Abstract ID:605