IPlant's Taxonomic Name Resolution Service Naim Matasci BIO5 / The iPlant Collaborative tnrs.iplantc.org.

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Presentation transcript:

iPlant's Taxonomic Name Resolution Service Naim Matasci BIO5 / The iPlant Collaborative tnrs.iplantc.org

What is iPlant?

Empowering a New Plant Biology

TMU* Growth of Biological Collections (1600 – 2012) *TMU: Totally Made Up

If you can't find it, it doesn't exist

Data Reuse What's the correlation between leaf morphology and leaf economy (R. Walls)? Evolution of pit domatia (M. Donoghue)

iPlant Data Store Based on iRODS – Metadata driven – Storing, Sharing and Distributing Redundant (mirrors at TACC and UoA) Really, really, really big (6 PB + 40 PB LTS) Really, really, really fast

100GB: 29m15s iPlant Data Store Performance UC Berkeley to iDS 1 GB / 17.5 seconds Desktop PC (UA): Mac with 7.2K Internal Hard Drive External Drive: USB 2.0: 5.4k Hard Drive Flash Drive: USB 2.0 Patriot XT

PhytoBisque features Rich internet application (completely web based) Draws upon features from popular large scale photo sharing sites and high resolution aerial imagery (google maps) Ability to import and export over 100+ image formats, movies Ability to import extremely large image sets using iPlant data store Can display 20Kx20K image using standard web browser Manage data sets with tags, metadata management Utilizes distributed computing (connected to iPlant execute environment)

Taxonomic uncertainty 1.Non-existent names Misspellings Contamination Annotations Morphospecies Digitization issues (frame shifts, character encoding)Lexical variants (digitization conventions) 2.Synonymy Nomenclatural synonyms Taxonomic synonyms / concepts 3.Misidentifications, incomplete identifications

Non-existent names: Herbarium specimens *New World plant specimens, 34 herbaria, simple match against IPNI and TROPICOS, excluding authors Total specimens:1.1 million Unique species names:53,052 Published names (legitimate & illegitimate):44,532 Misspelled names:9371 (18%) Specimens with misspelled names:101,237 (9%)

Taxonomic Name Resolution Service Computer assisted standardization of plant names Corrects spelling errors and alternative spellings to a standard list of names Convert out-of-date names to currently accepted names

Future More sources – Standard source import with DwC support Better performance TNRastic API Integration with Global Names components

Web: Code: ource/TNRS API (provisional): TNRastic API:

Brad Boyle Brian Enquist Juan Antonio Raygoza Garay Nicole Hopkins Zhenyuan Lu Martha Narro Shannon Oliver William Piel Jill Yarmchuk Bob Magill (Missouri Botanical Garden) Chris Freeland (Missouri Botanical Garden) Chuck Miller (Missouri Botanical Garden) Peter Jorgensen (Missouri Botanical Garden) Amy Zanne (University of Missouri, St. Louis) Peter Stevens (Missouri Botanical Garden) Jay Paige (Missouri Botanical Garden) Bob Peet (University of North Carolina at Chapel Hill) Paul Morris (Harvard University) Alan Paton (Kew Royal Botanic Gardens and their International Plant Names Index) Tony Rees (Commonwealth Scientific and Industrial Research Organisation) Michael Giddens ( Dmitry Mozzherin (Global Biodiversity Information Facility) David Remsen (Global Biodiversity Information Facility) David Patterson (Encyclopedia of Life) Cam Webb (Harvard University) Missouri Botanical Garden (Tropicos) Funding provided by the National Science Foundation Plant Cyberinfrastructure Program (grant #DBI ).