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Leveraging Filtered Push Technology to
Enhance Remote Taxonomic Identifications
Nico Franz1, Edward Gilbert1, Neil Cobb2 & Paul Morris3
1

School of Life Sciences, Arizona State University
2 Merriam-Powell Center, Northern Arizona University
3 Museum of Comparative Zoology, Harvard University
TDWD 2013 Annual Conference, Florence, Italy
Biodiversity Data Quality – Issues, Methods and Tools
October 29, 2013
Advancing Digitization of Biodiversity
Collections (NSF ADBC Program)
 Digitize 1 billion specimens in 10 years

Currently 9 Thematic Collection Networks with 130 participating institutions
SCAN member collections

ASU

Average ~ 480 miles apart

UNM

TAMU
UA
NMSU
NAU

TTU
CSU
DMNS

UCB
SCAN digitization objectives
• Digitize 1 million records for southwestern ground-dwelling arthropods
• Produce 16,000 high-resolution images of species; promote identifications
• Leverage an interactive identification & annotation workflow via Symbiota

Gerstaeckeria porosa (LeConte, 1876) – ASUHIC0017017

Crotanius trivittatus (Champion, 1908) – ASUHIC0012067
September, 2013: 510,262 records in SCAN
SCAN ADBC Collections
SCAN ADBC
Ground-Dwelling
Arthropod Records

•
•
•
•
•
•

510,262 specimens in Symbiota
300,984 (59%) georeferenced
338,836 (66%) identified to species
1,016 families
 Primary need:
8,056 genera
remote IDs
17,538 species

SCAN ADBC
Non-Target Taxa
Records

SCAN Broader Impact Collections

SCAN Non-ADBC
Broader Impact
Records
Deployment diagram – Symbiota & Filtered Push interaction

New FP Client Tools in Symbiota

Filtered Push3 Node

http://symbiota1.acis.ufl.edu/scan/portal/index.php

http://fp3.acis.ufl.edu/FPAnnotationProcessor-Web/

SCAN Symbiota Portal

• New, remotely added identifications are grounded in the Annotation Ontology.
• FP team has developed Symbiota-integrated PHP Client Tools that record and
push new annotations to the external FP infrastructure where statistics are kept.
Source: http://wiki.filteredpush.org/wiki/FP-Medium_deployment_for_SCAN
Current workings & look in SCAN
Homepage – http://symbiota1.acis.ufl.edu/scan/portal/index.php

Images
Image thumbnail gallery – some are insufficiently identified

ID = Epicaerus

ID = Scarabaeidae
More information – occurrence records, images – is clicks away
More information – occurrence records, images – is clicks away
Experts can log in and view a taxon-tailored IDs Needed tab

This is the scarab
in need of an ID
Experts can log in and view a taxon-tailored IDs Needed tab
Occurrence tab

This is the scarab
in need of an ID
Experts can log in and view a taxon-tailored IDs Needed tab
Occurrence tab

This is the scarab
in need of an ID

Images tab
Adding a new identification in the Determination History tab

 Scientific Name is linked to the
SCAN Taxonomic Thesaurus.
The fully integrated Symbiota tab for IDs is Filtered Push-enabled

• New = current ID
• Image remapping
• Submission to FP
Simultaneous ID recording internally (SCAN) and externally (FP)
Confirmation
in SCAN
Simultaneous ID recording internally (SCAN) and externally (FP)
Confirmation
in SCAN
AO translation

Confirmation
in FP3 node

Annotations
list view
Simultaneous ID recording internally (SCAN) and externally (FP)
Confirmation
in SCAN
AO translation

Confirmation
in FP3 node

Annotations
detail view

RDF / XML
translation
Future work – 1st production-level Symbiota / FP implementation
• Optimization of SCAN "IDs Needed" user interface – thumbnail view
• Roll-out to the SCAN expert community, creation of expert profiles in FP
• Expansion beyond SCAN members, diversified notification systems

"Curculionidae" ("Calles" sp.) – ASUHIC0031695
Acknowledgments
• TDWG 2013 Symposium organizers – Antonio Mauro Saraiva
• James Hanken, Maureen Kelly & David Lowery – http://wiki.filteredpush.org/wiki/
• ASUHIC digitization team – Sangmi Lee, David Fleming, Soon Flynn, Andrew Jansen,
Catherine Mercado, Joshua Persson, Sarah Shirota, Michael Shillingburg.
• NSF Award EF-1207107.

"Digitization TCN: Collaborative Research: Southwest Collections of Arthropods
Network (SCAN): a Model for Collections Digitization to Promote Taxonomic and Ecological Research."

https://sols.asu.edu

http://symbiota1.acis.ufl.edu/scan/portal/index.php

http://symbiota.org/tiki/tiki-index.php

http://taxonbytes.org

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Franz Et Al. SCAN - Southwest Collections of Arthropods Network: Leveraging Filtered Push Technology to Enhance Remote Taxonomic Identifications

  • 1. Leveraging Filtered Push Technology to Enhance Remote Taxonomic Identifications Nico Franz1, Edward Gilbert1, Neil Cobb2 & Paul Morris3 1 School of Life Sciences, Arizona State University 2 Merriam-Powell Center, Northern Arizona University 3 Museum of Comparative Zoology, Harvard University TDWD 2013 Annual Conference, Florence, Italy Biodiversity Data Quality – Issues, Methods and Tools October 29, 2013
  • 2. Advancing Digitization of Biodiversity Collections (NSF ADBC Program)  Digitize 1 billion specimens in 10 years Currently 9 Thematic Collection Networks with 130 participating institutions
  • 3. SCAN member collections ASU Average ~ 480 miles apart UNM TAMU UA NMSU NAU TTU CSU DMNS UCB
  • 4. SCAN digitization objectives • Digitize 1 million records for southwestern ground-dwelling arthropods • Produce 16,000 high-resolution images of species; promote identifications • Leverage an interactive identification & annotation workflow via Symbiota Gerstaeckeria porosa (LeConte, 1876) – ASUHIC0017017 Crotanius trivittatus (Champion, 1908) – ASUHIC0012067
  • 5. September, 2013: 510,262 records in SCAN SCAN ADBC Collections SCAN ADBC Ground-Dwelling Arthropod Records • • • • • • 510,262 specimens in Symbiota 300,984 (59%) georeferenced 338,836 (66%) identified to species 1,016 families  Primary need: 8,056 genera remote IDs 17,538 species SCAN ADBC Non-Target Taxa Records SCAN Broader Impact Collections SCAN Non-ADBC Broader Impact Records
  • 6. Deployment diagram – Symbiota & Filtered Push interaction New FP Client Tools in Symbiota Filtered Push3 Node http://symbiota1.acis.ufl.edu/scan/portal/index.php http://fp3.acis.ufl.edu/FPAnnotationProcessor-Web/ SCAN Symbiota Portal • New, remotely added identifications are grounded in the Annotation Ontology. • FP team has developed Symbiota-integrated PHP Client Tools that record and push new annotations to the external FP infrastructure where statistics are kept. Source: http://wiki.filteredpush.org/wiki/FP-Medium_deployment_for_SCAN
  • 7. Current workings & look in SCAN
  • 9. Image thumbnail gallery – some are insufficiently identified ID = Epicaerus ID = Scarabaeidae
  • 10. More information – occurrence records, images – is clicks away
  • 11. More information – occurrence records, images – is clicks away
  • 12. Experts can log in and view a taxon-tailored IDs Needed tab This is the scarab in need of an ID
  • 13. Experts can log in and view a taxon-tailored IDs Needed tab Occurrence tab This is the scarab in need of an ID
  • 14. Experts can log in and view a taxon-tailored IDs Needed tab Occurrence tab This is the scarab in need of an ID Images tab
  • 15. Adding a new identification in the Determination History tab  Scientific Name is linked to the SCAN Taxonomic Thesaurus.
  • 16. The fully integrated Symbiota tab for IDs is Filtered Push-enabled • New = current ID • Image remapping • Submission to FP
  • 17. Simultaneous ID recording internally (SCAN) and externally (FP) Confirmation in SCAN
  • 18. Simultaneous ID recording internally (SCAN) and externally (FP) Confirmation in SCAN AO translation Confirmation in FP3 node Annotations list view
  • 19. Simultaneous ID recording internally (SCAN) and externally (FP) Confirmation in SCAN AO translation Confirmation in FP3 node Annotations detail view RDF / XML translation
  • 20. Future work – 1st production-level Symbiota / FP implementation • Optimization of SCAN "IDs Needed" user interface – thumbnail view • Roll-out to the SCAN expert community, creation of expert profiles in FP • Expansion beyond SCAN members, diversified notification systems "Curculionidae" ("Calles" sp.) – ASUHIC0031695
  • 21. Acknowledgments • TDWG 2013 Symposium organizers – Antonio Mauro Saraiva • James Hanken, Maureen Kelly & David Lowery – http://wiki.filteredpush.org/wiki/ • ASUHIC digitization team – Sangmi Lee, David Fleming, Soon Flynn, Andrew Jansen, Catherine Mercado, Joshua Persson, Sarah Shirota, Michael Shillingburg. • NSF Award EF-1207107. "Digitization TCN: Collaborative Research: Southwest Collections of Arthropods Network (SCAN): a Model for Collections Digitization to Promote Taxonomic and Ecological Research." https://sols.asu.edu http://symbiota1.acis.ufl.edu/scan/portal/index.php http://symbiota.org/tiki/tiki-index.php http://taxonbytes.org