Semi-automated workflows for acquiring specimen data from label images in herbarium collections

Taxon

Volumn 59, Issue 6, 2010, Pages 1830-1842

  Granzow de la Cerda, Íñigo ^a,c   Beach, James H ^b  

^a UNIVERSITY OF MICHIGAN   (United States)

^b UNIVERSITY OF KANSAS   (United States)

^c UNIVERSITAT AUTÒNOMA DE BARCELONA   (Spain)

Author keywords

Biological specimens; Central America; Data acquisition; Databases; Digital images; Digitization; Geo referencing; Herbarium collections; Mexico; Scientific workflows

Indexed keywords

COMPUTER SIMULATION; DATA ACQUISITION; DATA QUALITY; DATABASE; DIGITAL IMAGE; DIGITIZATION; HERBARIUM; SPECIMEN BANK;

EID: 78751556891     PISSN: 00400262     EISSN: None     Source Type: Journal    
DOI: 10.1002/tax.596014     Document Type: Article

References (44)

1. Bart, H.L. 2005. Geolocate. http://www.museum.tulane.edu/geolocate (accessed January 2010).
2. Beaman, R.S., Cellinese, N., Heidorn, P.B., Guo, Y., Green, A.M. & Thiers, B. 2006. HERBIS: Integrating digital imaging and label data capture for herbaria [Abstract]. Botany 2006, California State University - Chico. 28 July-2August 2006. http://www.2006.botanyconference.org/engine/search/index.php?func=detail&aid=402.
3. Beaman, R.S. & Conn, B.J. 2003. Automated geoparsing and georeferencing of Malaesian collection locality data. Telopea 10: 43-52.
4. Berry, P.M. 1998. Intelligent workflow for collection management: Workflow Management Systems (Workflow Engines). SRI International. http://www.ai.sri.com/~swim/resources/SOAworkflow.html (accessed January 2010).
5. Best, J.H., Moen, W.E. & Neill, A.K. 2009. A framework and workflow for extraction and parsing of herbarium specimen data [Abstract]. Proceedings of the Taxonomic Database Working Group (TDWG) 2009. http://www.tdwg.org/proceedings/article/view/567 (accessed July 2010).
6. Catalogue of Life. 2007. Annual Checklist, Species 2000 & ITIS Catalogue of Life Hierarchy, Edition 1 (2007). http://data.gbif.org/datasets/resource/1542 (accessed through GBIF data portal, July 2010).
7. Cavalcanti, M.C., Targino, R., Baião, F., Rössle, S.C., Bisch, P.M., Pires, P.F., Campos, M. L.M. & Mattoso, M. 2005. Managing structural genomic workflows using Web services. Data Knowl. Engin. 53: 45-74.
8. Conabio. 2006. Capital natural y bienestar social. México D.F.: Comisión Nacional para el Conocimiento y Uso de la Biodiversidad. Conn, B.J. 2003. Information standards in botanical databases: The limits to data interchange. Telopea 10: 53-60.
9. Davies, A.M.R., Bodensteiner, P., Pillukat, A. & Grau, J. 2002. INFOCOMP: The Compositae types digital imaging project in Munich. Sendtnera 8: 9-20.
10. Delgadillo, C. 2003. Catálogo de la Colección Briológica del Herbario Nacional de México. Actualización 2003. Herbario MEXU, Instituto de Biología, UNAM. Base de datos SNIB-Conabio, proyecto U006. Mexico.
11. Edwards, J.L., Lane, M.A. & Nielsen, E.S. 2000. Interoperability of biodiversity databases: Biodiversity information on every desktop. Science 289: 2312-2314.
12. Elith, J. & Leathwick, J.R. 2009. Species distribution models: Ecological explanation and prediction across space and time. Annual Rev. Ecol. Syst. 40: 677-697.
13. Ertter, B. 2000. Our undiscovered heritage: Past and future prospects for species-level botanical inventory. Madroño 47: 237-252.
14. Espejo-Serna, A., López-Ferrari, A.R. & Ugarte, I.S. 2004. A current estimate of angiosperm diversity in Mexico. Taxon 53: 127-130.
15. GBIF (Global Biodiversity Information Facility). 2002. Draft Report of the Meeting of the Digitization of Natural History Collections Scientific and Technical Advisory Group of the Global Biodiversity Information Facility. Copenhagen, Denmark.
16. Gold, C.M., Nantel, J. & Yang, W. 1996. Outside-in: An alternative approach to forest map digitizing. Int. J. Geogr. Inform. Syst. 10: 291-310.
17. Graham, G.H., Ferrier, S., Huettman, F., Moritz, C. & Peterson, A.T. 2004. New developments in museum-based informatics and applications in biodiversity analysis. Trends Ecol. Evol. 19: 497-503.
18. Greenberg, J., Spurgin, K. & Crystal, A. 2006. Functionalities forautomatic metadata generation applications: A survey of expert's opinions. Int. J. Metadata, Semantics and Ontologies 1: 3-20.
19. Greenwood, M. 2005. My Grid. http://www.mygrid.org.uk/wiki/bin/view/Mygrid/WorkflowLinks (accessed July 2010).
20. Guisan, A. & Thuiller, W. 2005. Predicting species distribution: Offering more than simple habitat models. Ecol. Lett. 8: 993-1009.
21. Guthrie, K. & Nygren, T. 2007. Aluka. Building a digital library of scholarly resources from Africa. http://www.aluka.org (accessed July 2010).
22. Heidorn, P.B. & Wei, Q. 2008. Automatic metadata extraction from museum specimen labels. Pp. 57-68 in: Greenberg, J. & Klas, W. (eds.), Metadata for semantic and social applications: Proceedings of the International Conference on Dublin Core and Metadata Applications, Berlin, 22-26 September 2008, DC 2008: Berlin,Germany. Göttingen: Universitätsverlag Göttingen.
23. INEGI. 2000. Principales resultados por localidad. XII Censo General de Población y Vivienda 2000. CD-ROM. Mexico Sistemas Nacionales Estadístico y de Información Geográfica, Instituto Nacional de Estadística, Geografía e Informática. http://www.inegi.org.mx/sistemas/biblioteca/detalle.aspx?c=14051&upc=0&s=est&tg=55&f=2&pf=Pob, accessed July 2010.
24. Kirkup, D., Malcolm, P., Christian, G. & Paton, A. 2005. Towards a digital African Flora. Taxon 54: 457-466.
25. Lafferty, D. & Landrum, L.R. 2009. SALIX, a semi-automatic label information extraction system using OCR [Abstract]. Botany & Mycology 2009, Snowbird, Utah, 25-29 July 2009. http://2009.botanyconference.org/engine/search/index.php?func=detail&aid=130 (accessed August 2010).
26. MacRander, A.M. & Haynes, R.R. 1990. SERFIS, a methodology for making multi-herbaria specimen databases a reality. Taxon 39: 433-441.
27. McPhillips, T.M. & Bowers, S. 2005. An approach for pipelining nested collections in scientific workflows. SIGMOD Record 34:12-17.
28. Mc-Vaugh, R. 1983-2001. Flora Novo-Galiciana, vols. 1-7. Ann Arbor:Univ. of Michigan Press.
29. Pankhurst, R.J. 2004. Computer technology for the future of SW Asiaticbotany. Turkish J. Bot. 28: 129-138.
30. Rzedowski, J. 1976. Catálogo de los herbarios institucionales mexicanos. México, D. F.: Sociedad Botánica de México.
31. Sarukhán, J., Koleff, P., Carabias, J., Soberón, J., Dirzo, R., Llorente-Bousquets, J., Halffter, G., González, R., March, I., Mohar, A., Anta, S. & de la Maza, J. 2009. Capital natural deMéxico. Síntesis: Conocimiento actual, evaluación y perspectivas de sustentabilidad. Mexico: Comisión Nacional para el Conocimiento y Uso de la Biodiversidad.
32. Schaub, M. & Dunn, C.P. 2002. VPlants: A virtual herbarium of the Chicago region. First Monday 7(5). http://firstmonday.org/htbin/cgiwrap/bin/ojs/index.php/fm/issue/view/145 (accessed January 2010).
33. Schmull, M., Heinrichs, J., Baier, R., Ullrich, D., Wagenitz, G., Groth, H., Hourticolon, S. & Gradstein, S.R. 2005. The type database at Göttingen (GOET)-a virtual herbarium online. Taxon 54: 251-254.
34. Shankar, S., Kini, A., DeWitt, D.J. & Naughton, J. 2005. Integrating databases and workflow systems. Sigmod Record 34: 5-11.
35. Sharp, A.J., Crum, H. & Eckel, P. 1994. The moss flora of Mexico. Bronx, New York: New York Botanical Garden Press.
36. Singh, M.P. & Vouk, M.A. [1996]. Scientific workflows: Scientific computing meets transactional workflows. http://www.csc.ncsu.edu/faculty/mpsingh/papers/databases/workflows/sciworkflows.html (accessed August 2010).
37. Smith, G.F. 2004. The African Plant Initiative: A big step for continental taxonomy. Taxon 53: 1023-1025.
38. Soberón, J. & Peterson, A.T. 2004. Biodiversity informatics: Managing and applying primary biodiversity data. Philos. Trans., Ser. B 359: 689-698.
39. Thiers, B. 2010. Index herbariorum database. http://sweetgum.nybg.org/ih/ (accessed July 2010).
40. Versteeg, R.J., Richardson, A.N. & Rowe, T. 2006. Web-accessible scientific workflow system for performance monitoring. Environm. Sci. Technol. 40: 2692-2698.
41. Villaseñor, J.L., Ortiz, E. & Redonda- Martínez, R. 2008. Catálogo de autores de plantas vasculares de México. México, D.F.: Instituto de Biología, UNAM, CONABIO. http://www.conabio.gob.mx/informacion/catalogo_autoridades/plantas/AutoresPlantas/AutoresPlantasMexicanas.pdf
42. Wieczorek, J.R. 2001. Georeferencing calculator. http://manisnet.org/GeorefGuide.html (accessed July 2010).
43. Wieczorek, J., Guo, Q. & Hijmans, R. 2004. The point-radius method for georeferencing locality descriptions and calculating associated uncertainty. Int. J. Geogr. Inform. Sci. 18: 745-767.
44. Wolf, C. & Holland, D. 2000. Digitizing and preserving plant images: Linking plant images and databases for public access. First Monday 5(6). http://firstmonday.org/htbin/cgiwrap/bin/ojs/index.php/fm/issue/view/120 (accessed January 2010).