New and Upcoming Lucid Identification Tools for Diagnosticians
Identification Technology Program (ITP), Fort Collins Laboratory Center for Plant Health Science and Technology (CPHST) USDA APHIS PPQ
Workshop: Technology Tools and the NPDN (Dr. Amanda Hodges, Organizer) 2nd NPDN National Meeting December 8, 2009; Miami, Florida 1 Preclearance inspection Off-shore intelligence Public cooperators USDA CPHST’s Biocontrol / IPM Identification Technology Program Port inspection (ITP) Industry Detection/ Prompt, Accurate Pest surveys Sample Triage Identification Pest databases Economic analyses Risk assessments Pest advisory groups Response Response Actionable Non-Actionable Quarantine treatments Emergency response Identification Aids Requested by ITP’s Clients
Field-oriented keys (macroscopic versus microscopic) Taxon-based keys with a wide geographical coverage Screening aid keys Keys to pests and diseases of concern Commodity-based keys (includes pests, diseases, etc.) Trade-based keys (includes pests, diseases, etc.) User-friendly keys (i.e., logical, simple terminology, etc.) Easily accessible keys - electronic-based (e.g., internet, PDA, CD, etc.) Why Electronic Format for Identification Keys?
Many scientific manuscripts include links to electronic keys
Numerous software packages available for electronic key development
Taxonomists know electronic keys are easier to develop
Taxonomists appreciate ease for updating an electronic key
Taxonomists reach a wider audience with electronic keys
Why Matrix Identification Key System [versus pathway (dichotomous) key system]?
Can start anywhere in the key with any character
Choose obvious (the easiest) characters first
Freedom from missing or obscure structures
Able to select more than one answer (state)
Dichotomous Key Example 22. Stamens as many as petals and opposite them, petals hooded . . . Rhamnaceae 22. Stamens as many as petals or alternate to them, petals not hooded 23. Leaves opposite ...... Rhizophoraceae 23. Leaves alternate 24. Ovary one-celled 25. Fruit a drupe, juice resinous or milky ...... Anacardiaceae 25. Fruit a capsule, juice not resinous or milky . . . . . Tamaricaceae 24. Ovary two to several celled, leaves simple, ovary sessile . Celastraceae SoftwareSoftware forfor MatrixMatrix--basedbased KeyKey DevelopmentDevelopment
Delta
Linnaeus Why Lucid Software for APHIS and Collaborators?
User Friendly
Intelligent
Robust
Up-To-Date
Widely Accepted
What is Lucid?
Software for developing and deploying interactive matrix-based identification, diagnostic, and training tools on CD and the Internet Lucid Identification Software
Lucid2 (Professional) • Windows operating system • Lucid2 Player required to use key (Lucid2 Player Standard - free download from the internet)
Lucid3 Builder (ca. US$482) • Runs on any Java-enabled operating system (e.g., Windows, Macintosh, Unix, etc.) • Lucid3 Builder required to build a tool • Lucid3 Player not necessary to use key, requires Java www.lucidcentral.org – to learn more; includes a tool search engine Lucid Terminology
• Feature (character): a distinctive trait, quality, or attribute used for recognizing, describing, or differentiating taxa (e.g., flower color, number of wings, etc.)
• State: the specific value of a feature or character shown in a specific taxon (e.g., red, 2, etc.)
• Entities (taxa): a category or unit, such as a species, genus, etc., based on a taxonomic system of classification (e.g., the taxa within the Buprestidae, etc.) Lucid Terminology (cont’d)
Lucid key can consist of: 1. a list of entities and a list of features and states 2. a matrix of score data 3. various images and HTML pages attached to the matrix
Lucid tool can consist of: 1. a Lucid key or Lucid keys 2. a home page and additional images and HTML pages not directly attached within the key matrix.
Lucid resource consists of: 1. two or more Lucid tools 2. a home page allowing access to each tool Lucid Home Page: www.lucidcentral.org To Join
Key search - Note the Four Panels
feature Entities state Features Available Remaining
Features Entities Chosen Discarded Example of underlying Lucid key matrix
Entities (Taxa)
Features (characters) & states AA LucidLucid KeyKey Lucid3 Key to Insect Orders
State image
State page
Entity image Fact sheet Entity Image Gallery State image
Entity Fact Sheet
Feature Page AA LucidLucid KeyKey Feature options Restart key Entity options Expand tree (highlight cell, click)
Feature Best Prune Thumbnails Redundants
Entity Thumbnails Lucid Tool – Home Pages (support pages outside key) Ants Moths
Wasps
Stiletto-flies Lucid Resource – Entry Page to Lucid Tools
Mites Scales Citrus During surveillance for LBAM (Tortricidae) in California, you came across this adult moth. Is it a Tortricid Moth (Family Tortricidae)?
Immediately we observe that the antennae taper towards the tip and the forewing length is 95 mm FindingFinding aa Lucid ToolTool
1. In your browser, type www.lucidcentral.org
2. Go to Keys Menu Bar, select: Search for keys
3. In the Search Field, type: Moth
4. Review results from search: Note LBAM ID
5. Click on “Visit” to the right of the title to gain access to the Lucid tool
Go to www.lucidcentral.org Lucid Identification Tools to Support Plant Protection
• Approximately 60% of the following tools have been developed by or in collaboration with CPHST ITP
• All ITP tools are available via the internet
• Some ITP tools are available on CD (no cost) upon request
• Other tools (not ITP): • 1) are available via the internet and/or
• 2) by purchasing the CD from the author or publisher DISEASESDISEASES
1. A Key to the Common Phytophthora species (Jean Beagle Ristaino, NCSU) [available early 2010 from APS; NPDN poster] DiseasesDiseases (continued)(continued)
2. Symptomatic Tool to Diseases and Commonly Confused Disorders of Citrus [available via the internet 01/2010]
3. Symptomatic Tool to Diseases and Disorders of Cultivated Palms [available via the internet 2010] BEETLES
1. The Bark and Ambrosia Beetles of Louisiana [available via the internet]
2. Key to Species of Hylesine Bark Beetles of the Southeastern United States (SPDN & NCSU) [available via www.lucidcentral.org]
3. Bark Beetles of the SE United States (SPDN & NCSU) [available 01/2010]
4. Bark Beetle Genera of North America (CSU, USFS) [available 01/2010] Beetles (cont’d)
5. Identification tool to the World Genera of Ambrosia Beetles (Cuculionidae: Xyleborina) (UW) [available 06/2010]
6. Identification Tool to North American Genera of Ironclad and Cylindrical Bark Beetles (Coleoptera: Zopheridae) (UNM) [available 02/2011]
7. Identification Tool to the Genera of Longhorn Wood Boring Beetles (Coleoptera: Cerambycidae: Onciderini) (UNM) [available 02/2011]
8. Identification Tool to the Genera of Buprestidae (UCD, CDFA, HU) [available 08/2010]
9. Identification Tool to the Genera of Bostrichidae (MSU) [available 2011] Beetles (cont’d)
Scope for Resource • World-wide; tools to families, tribes, and genera Current Tool • Family key (9 families) to adult and larvae [available via www.lucidcentral.org] THRIPSTHRIPS
1. Pest thrips of the world (only Thripidae) [CD AUS $49.95]
2. Pest thrips of North America: Associated with Domestic and Imported Crops [CD AUS $59.95]
3. Thrips ID: Pest Thrips of the World (9 families 180 pest species) [CD AUS $80.00]
4. World Thysanoptera (resource with access to Lucid tools for thrips) [access via the internet] Thrips (continued)
5. Thrips of California [available via www.lucidcentral.org]
Go to: http://keys.lucidcentral.org/keys/v3/thrips_of_california/Thrips_of_California.html GRASSHOPPERSGRASSHOPPERS
1. Grasshoppers of the Western United States, Edition 3 [available www.lucidcentral.org]
2. Edition 4, in development, will include a key to nymphs [available 2010] WHITEFLY Whitefly Fauna of the World [available via www.lucidcentral.org] MITES 1. Invasive Mite Identification [available www.lucidcentral.org] 2. Mites in Soil (5 keys to id 101 families) [CD AUS $85.00] 3. Mites of Quarantine Importance (key to 25 mite families) [CD purchase from author] Mites (continued) 4. Identification of Flat Mites (Acari: Tenuipalpidae) of the World: I. Brevipalpus and Raoiella
Raoiella indica Raoiella indica Raoiella indica Raoiella indica Male nymph Female adult Egg Female adult Scope • Eventually all taxa in family Status • Initiated phase 1 in fall 2009 (2-year project) • Key to all flat mite genera (ca. 34 genera) • Key to species of Brevipalpus (most commonly intercepted genus) • Key to species of Raoiella (includes red palm mite) SCALES [available via www.lucidcentral.org] FRUIT FLY
1. Dorsalis: An identification tool to the Bactrocera dorsalis complex [available only on CD] 2. Identification Tool for the Fruit Fly Species of Anastrepha (ARS) [available 2011] MOTHS 1. LBAM ID [available via www.lucidcentral.org] Moths (continued)
2. TortAI: Tortricids of Agricultural Importance [available 2012] ANTS
1. PIAkey: Identification guide to Invasive Ants of the Pacific Islands
Go to: http://keys.lucidcentral.org/keys/v3/PIAkey/ Ants (continued)
2. Introduced Ants of North 3. Identification tool to Solenopsis [2011] America [2011] Commodity Based – Cultivated Palms Commodity Based – Cultivated Palms
Draft home page to Lucid tool - Symptoms of Palm Diseases and Disorders
Resource Features • 12 individuals developing keys and tools for the resource 1. Key to general pests (SPDN, UF) 2. Tool to mites (FL-DPI) 3. Tool to beetles (FAMU) 4. Tool to scales (SPDN, FL-DPI, UF) 5. Symptomatic tool to diseases & abiotic disorders (UF) 6. Tool to cultivated palms (FL-DPI) • Available late 2010 Commodity Based – Cultivated Citrus
Draft of entry page to Lucid resource
Scope • USA and potential concern Tools • Symptomatic tool to diseases and commonly confused disorders (CHRP) [available 1/2010] • Identification tool to arthropod pests (SPDN, UF) [available 2010/2011] • Identification tool to cultivated citrus and related taxa (NCSU) [available 2011] Commodity Based – Cultivated Citrus (cont’d)
home page
key fact sheet Commodity Based – Exported California Table Grapes
Phase 1 [initiate 01/2010] 1. Tool to spiders • Key to adults • Key to eggs • DNA sequence search page 2. Tool to weed seeds
Future Phases 3. Tool to arthropod pests 4. Symptomatic tool to diseases & disorders 5. Key to cultivars Finding the Right Identification Aid, Tool, or Resource
• Many electronic identification tools/resources/keys exist • Different software programs used to create these tools • Some tools are relevant for plant protection and quarantine • Some tools are scientifically valuable and up-to-date • Some tools clearly define their scope (geography coverage, taxonomic coverage, etc)
How can ITP provide support to clients for quickly and efficiently locating the right identification resource? ID Source (IDentification reSOURCE)
• Database of links to relevant electronic tools and resources available via a URL address • ID Source will include the following resource types: • keys • fact sheets • image galleries • screening aids • descriptions • diagnostic tools • Each potential record evaluated and if relevant coded and input into database • Powerful search engine allows simple to more advanced search capabilities (taxonomy, geography, commodity, etc.) • Available 2011 USDA CPHST’s Identification Technology Program Team
Terrence Walters, ITP Coordinator [[email protected]]
Amanda Redford, ITP Technician [[email protected]]
Julia Scher, ITP Resource Developer
Jeff Drake, ITP Engineer