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Symbiota:A specimen database and
biodiversity data portal
Catoscopium nigritum (Hedw.) Brid. Photographer: Blanka Shaw
Lecanora horiza (Ach.) LindasyPhotographer: H.T. Lumbsch
Bouteloua rothrockii VaseyPhotographer: Sue Rutman
Amanita muscaria subsp. flavivolvata Singer Photographer: Scott T. Bates
Presented by
Kim Watson
Data Capture Course – 14 January 2014 – Accra, Ghana
http://symbiota.org
• Software package of open source, web-based tools
• Designed to integrate biological community knowledge and data
• Aid biologists with establishing specimen-based virtual floras
and faunas
http://symbiota.org/tiki/tiki-index.php?page=Contact+Us
Corinna Gries Ph.DUniv. of Wisconsin - Madison
Thomas Nash Ph.D.Arizona State University
Edward GilbertArizona State University
Symbiota: Active Portals
Community based biodiversity portals, representing a variety of organisms.
Single user interface comprised of distinct datasets• Many institutions’ collections• Taxonomic scope• Geographic scope
Framework architecture
Customize the look and feel• Cascading Style Sheets (CSS)• Configuration files
List of Active Nodes: http://symbiota.org/tiki/tiki-index.php?page=Data+Nodes
• Specimen search engine:
query by taxonomy,
geography, or collector
data
• Biodiversity inventories:
floristics, searchable
species lists
• Identification keys:
generate interactive
identification keys
View Images, dynamic distribution maps, descriptions, taxonomy
Symbiota: 3 Core Modules
https://www.idigbio.org/sites/default/files/workshop-presentations/wetcollections/Symbiota_2013-03-06.pdf
• Lichen Consortium
– 36 Collections
– 902,664 occurrences
• Bryophyte Consortium
– 28 Collections
– 1,300,135 occurrences
• Macrofungi Collection Consortium
– 23 Collections
– 686,042 occurrences
Symbiota: Example Portals
http://lichenportal.org/portal
http://mycoportal.org/portal
http://bryophyteportal.org/portal
www.idigbio.org/sites/default/files/workshop-presentations/wetcollections/Symbiota_2013-03-06.pdf
Biodiversity Content Management System
(CMS)
• Read-only user interface
• Password protected
– Web browser-based
– Globally accessible
– No special software
installation (free)
– Use of web services
• Snapshot or Live data
https://www.idigbio.org/sites/default/files/workshop-presentations/wetcollections/Symbiota_2013-03-06.pdf
Personal Specimen Management
• Data Entry
• Data Management
• Label Printing
• Cloud Management
– Web browser-based
– Password protected
– Globally accessible
https://www.idigbio.org/sites/default/files/workshop-presentations/wetcollections/Symbiota_2013-03-06.pdf
Data Entry From Label Images
Data schema is aligned to Darwin Core data exchange standard.
Checks for duplicate records across collections within a portal.
Data Entry using Optical Character Recognition (OCR)
• Tesseract OCR engine already installed; run on a specimen image= Open source: http://code.google.com/p/tesseract-ocr/
• Upload to Symbiota any text generated by other OCR engines
Data Entry using Crowd Sourcing Application
• Any user with a Symbiota login signature• Certain fields are locked (catalog number, scientific name)• Records to be captured by the Crowd can be thematic
(e.g. specific collector, geographic location, etc.)
http://taxonbytes.org/tdwg-2013-crowd-sourcing-and-community-management-capabilities-with-symbiota/
Georeferencing Tools• Capture Darwin Core Georeferencing data
• Georeference individual specimen records; link to GeoLocate
• Georeference batches of specimens at once (with the same locality)
Web Tutorial: http://symbiota.org/tiki/tikimovies/georef1.htm
Rapid Specimen Digitization Workflow
https://www.idigbio.org/sites/default/files/workshop-presentations/wetcollections/Symbiota_2013-03-06.pdf
Two Options for using Symbiota
for collection management
• Join and contribute to an existing portal:– Instructions: http://symbiota.org/tiki/tiki-
index.php?page=Specimen+Integration
– Costs: No cost for software or for contributing data
– Upload specimen data (Darwin Core format) and images
Symbiota: Active Portals
• Southwest Environmental Information Network (SEINet )
• Intermountain Regional Herbarium Network (IRHN)
• Consortium of North American Bryophyte Herbaria (CNABH)
• Consortium of North American Lichen Herbaria (CNALH)
• Mycology Collections Data Portal (MycoPortal)
• Consortium of Northeastern Herbaria Portal (CNH)
• Madrean Archipelago Biodiversity Assessment Project (MABA)
• Cooperative Taxonomic Resource for American Myrtaceae (CoTRAM)
• Herbario Virtual Austral Americano (HVAA)
http://symbiota.org/tiki/tiki-index.php?page=Data+Nodes
Two Options for using Symbiota
for collection management
• Join and contribute to an existing portal:– Instructions: http://symbiota.org/tiki/tiki-
index.php?page=Specimen+Integration
– Costs: No cost for software or for contributing data
– Upload specimen data (Darwin Core format) and images
• Establish a new portal:– Instructions: http://symbiota.org/tiki/tiki-
index.php?page=EstablishingNode
– Costs: this is server-based software running on a MySQL platform which requires server setup, server software, portal setup, ongoing IT personnel support and maintenance.
– Better for the creation of a regional flora/fauna through the integration
of numerous collections and biodiversity datasets.
https://www.idigbio.org/sites/default/files/workshop-presentations/wetcollections/Symbiota_2013-03-06.pdf
Sample Diagram of Portal Network
Considerations
• Does Symbiota meet the needs of your workflow for data capture?
• Does Symbiota satisfy your specimen data management needs for the long-term?
• Does Symbiota allow for the sharing of specimen data on the web?
Videos Online
“Symbiota: a specimen-based biodiversity portal platform”
– Presented by Edward Gilbert, Lead Developer for Symbiota
– Presentation: https://www.idigbio.org/sites/default/files/workshop-presentations/wetcollections/Symbiota_2013-03-06.pdf
– Video captured/provided by A. Townsend Peterson, in 4 parts
1. http://www.youtube.com/watch?v=mvWNELYEZ9g&feature=share&list=PLSm4rjXsJ4aNW83lJyYn1WH45xwbFXMtq&index=30
2. http://www.youtube.com/watch?v=oi7cBoUZ2ZA&feature=share&list=PLSm4rjXsJ4aNW83lJyYn1WH45xwbFXMtq&index=31
3. http://www.youtube.com/watch?v=vaWbrq0Gy9c&list=PLSm4rjXsJ4aNW83lJyYn1WH45xwbFXMtq&feature=share&index=32
4. http://www.youtube.com/watch?v=K2jcyLyr3cU&feature=share&list=PLSm4rjXsJ4aNW83lJyYn1WH45xwbFXMtq&index=33
Other Helpful Resources
Symbiota Homepage: http://symbiota.org
Compatible Symbiota fields (Darwin Core):http://symbiota.org/tiki/files/SymbiotaOccurrenceFields.pdf
Symbiota Spreadsheet Template:http://symbiota.org/tiki/files/OccurrenceTemplate.csv
iDigBio Software/Tool Comparison Worksheethttps://www.idigbio.org/sites/default/files/sites/default/files/Symbiota.pdf
Macrofungi Collection Consortium Procedures Manual:https://sites.google.com/site/macrofungicollectionconsortium/home/reference-documents/MaCC%20Reference%20manual%20version%2020%20May%202013.docx?attredirects=0&d=1
Macrofungi Collection Consortium Reference Documents:https://sites.google.com/site/macrofungicollectionconsortium/home/reference-documents