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Proceedings of Life

Note: Because of the demise of the National Biological Information Network and subsequent loss of the cooperative agreement with Discover Life, the Proceedings of Life is currently unfunded. Until we have funds from elsewhere to continue its development, we will maintain its content and correct errors but not add new databases. -- July, 2011.

OVERVIEW

Discover Life is starting a scientific publication called the Proceedings of Life. This publication will be online, interactive, peer reviewed, and free to all users. It will provide authors with a means to get academic credit and a permanent scientific citation for building and maintaining high-quality databases on the web. The publication will use natural language processing and other software tools to allow authors to process documents and databases rapidly into interactive publications.

Scope

The Proceedings of Life will focus on making large amounts of high-quality data available to users. While not precluding hypothesis testing, modelling, and analysis, per se, contributions must be data rich. Their scope will include taxonomic catalogues, revisions, and checklists. In certain cases, to meet the requirements of the international codes of taxonomic nomenclature, the Proceedings will publish an electronic database that extends a conventional hard-copy publication that already exists or is published in parallel. Thus, for example, we envision digitizing parts of the historical literature, such as a taxonomic catalogue, and processing the text into structured databases and distribution maps.

We envision:

  • Publishing identification guides and databases that include text, images, videos, and sound recordings.
  • Generating web pages from taxonomic, environmental, and ecological datasets that document changes in the distribution and abundance of taxa.
  • Providing data to understand processes, such as birth, death, growth, and reproductive rates, and how these may be affected over time by climate change, invasive species, and other biotic and abiotic factors.
  • Organizations and individuals publishing site specific databases that rigorously document and monitor species occurrence, phenology, abundance, and interactions at schools, parks, and other potential study sites. Thus, the Proceedings of Life will have an entry point for young scientists to start collecting and publishing high-quality, original, reviewed findings.

EXAMPLES

The following examples demonstrate the technology that we currently have to process databases and text into interactive web pages. In the first example, we automatically processed several Excel files into the bee checklist and associated map database. In examples two and three, we used Discover Life's new natural language processor to database text from Word documents into the corresponding web documents. The associated text in the resulting HTML web pages is cross-linked at the individual record level with map points, checklists, images, and other information on Discover Life. For example, see CDFA43, a record generated from Alessandra Rung's Word document.

  1. Checklist of World Bees, Draft-18, 13 April, 2009.
    Please cite as Ascher, J. S. et al. 2009. Apoidea species guide.
    http://www.discoverlife.org/mp/20q?guide=Apoidea_species

  2. Catalogue of the Epiphloeinae (Coleoptera: Cleridae), Draft-1, May, 2009.
    Please do not cite. This is a working draft of an on-going project by Weston Opitz, Kansas Wesleyan University.

  3. Aulacigaster neoleucopeza,  Draft-1, June, 2009.
    Please do not cite. This is a working draft of a page of an on-going revision by Alessandra Rung, California Department of Food and Agriculture.

  4. Gordon, 1985,  Draft-1, June, 2009.

    Original citation: Gordon, R. D. 1985. The Coccinellidae (Coleoptera) of America North of Mexico. Journal of the New York Entomological Society Vol. 93(1):1-912.

    As part of the Lost Ladybug Project funded by the National Science Foundation, we are turning Gordon's published revision of coccinellids into an online database. So far we have scanned 908 of 912 pages, converted these pages to text with optical character recognition (OCR) software, and are now building HTML pages and associated database files. We have also extracted 702 of 706 images from Gordon's work and linked these into the online document above.

  5. Database of Hymenoptera in America north of Mexico  Draft-1, July, 2009.
    Please cite as follows:
    Pickering, J. 2009. Database of Hymenoptera in America north of Mexico.
    Proceedings of Life: http://www.discoverlife.org/proceedings/0000/6

    Source: This database is originally based on the Catalog of Hymenoptera in America North of Mexico, Volumes 1-3, prepared cooperatively by specialists under the direction of Karl V. Krombein, Paul D. Hurd, Jr., David R. Smith and B. D. Burks published by the Smithsonian Institution Press, Washington, D.C., 1979, and digitized by the Biodiversity Heritage Library, 2009. The draft is an on-going project.


SUBMITTED & UNDER REVIEW


NEXT STEPS
  • Form an editorial board (Gowaty, Hubbell, Mueller, Pickering, Schuh, Stephenson, PHER).
  • Define a submission and review process that includes:
    1. Rigorous scientific content but flexible, user-friendly technical requirements.
    2. Initial processing into a "draft-1" that provides authors with automated feedback of geographic errors, inconsistent nomenclature, typos, etc.
    3. Once these are corrected by the authors, a "draft-2" will be made open to the public and have a feedback mechanism for suggestions from the web community to the authors.
    4. Submission of the resulting "draft-3" for review by human editors.
    5. If accepted, the production of a "static published version" that can be cited and that never changes.
    6. A "current updated version" which after publication allows the authors to maintain, continuously correct, and expand their database.
    7. Re-review of updated versions upon authors' request, resulting in new static published versions. This could be done at 1 - 5 year intervals, depending on the extent of changes, to reward authors who continue to expand and improve their databases.
  • Seek partnerships with existing publications, such as the Canadian Journal of Arthropod Identification (Marshall).
  • Seek partnerships with digital content providers such as Biodiversity Heritage Library (Garnett).
  • Work with graphic designers to improve look and feel (Lowe, Mammola).
  • Work with organizations to get publications integrated with national and global efforts (NBII, GBIF).
  • Improve automatic error checking and correction of mistakes (Pickering, Parks).
  • Write policies that grant copyright to the contributing author(s) or, in cases where the Proceedings supplement existing publications, maintain copyright with the original publisher or other source (PHER).
  • Incorporate 'Terms of Use' similar to those used by GBIF to protect contributors intellectual property (PHER).
  • Develop a business plan to institutionalize the Proceedings and ensure their long-term viability (Weick). Through 2013, the Proceedings of Life is made possible by support to the Polistes Foundation through its second 5-year Cooperation Agreement with the National Biological Information Infrastructure (NBII).
  • Seek and process initial set of contributions from authors (Schuh, Herman, Rosenberg, Kjar, Gordon).

Contact

If you have suggestions or wish to participate in our endeavor, please contact John Pickering.


Updated: 7 August, 2009
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