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