1. Integrating source modifiers with sequence data through a new GenBank submission module in Symbiota
Andrew N. Miller1, Phil Anders1, Neil Cobb2, Ben Brandt2, and Ed Gilbert3
1University of Illinois Urbana-Champaign
2Northern Arizona University
3Arizona State University
BCoN Meeting
Lawrence, KS
13 February, 2018

2. Collection Management Systems
Arctos
Emu
FileMaker Pro
Microsoft Access
Microsoft Excel
Paradox
Specify
Symbiota

3. What is Symbiota? Specimen search engine Floristic data
Species checklists
Surveys
Identification key
Image library
Distribution maps, descriptions, taxonomic information
Genetic data
Data aggregation

4. 37 Million Records, 40 Portals, 13 Thematic Collection Networks

5. Key Symbiota Websites
Homepage:
GitHub:
Citable publication:
Google Group (support):
Symbiota Working Group:

6. Source modifiers are seldom populated in GenBank records
The Problem
Source modifiers are seldom populated in GenBank records
specimen voucher
country
isolation source
host
collected by
collection date
identified by
latitude longitude
altitude

7. Fungi dataset (1,200,057 records)
(fungi[orgn] NOT srcdb refseq[prop] NOT wgs[keyword] NOT tsa[keyword] NOT uncultured[filter]) NOT gbdiv pat[prop]) AND (specimen_voucher[text] OR isolate[text] OR culture_collection[text] OR strain[text])
Source modifiers
specimen voucher 82%
country %
isolation source 29%
host %
collected by %
collection date %
identified by 0%
latitude longitude %
altitude %

8. Arthropod dataset (3,415,661 records)
Source modifiers
specimen voucher 29%
country %
isolation source 2%
host %
collected by %
collection date %
identified by 0%
latitude longitude %
altitude %

9. Plant dataset (3,715,413 records)
Source modifiers
specimen voucher 33%
country %
isolation source 2%
host %
collected by 0%
collection date %
identified by 0%
latitude longitude %
altitude %

10. Vertebrate dataset (6,748,218 records)
Source modifiers
specimen voucher 41%
country %
isolation source 2%
host %
collected by %
collection date %
identified by 0%
latitude longitude %
altitude %

11. Pull metadata directly from Collection Management System
The Solution
Pull metadata directly from Collection Management System
and submit to GenBank

12. Symbiota rRNA Submission Tool
User Profile info
Specimen metadata
Sequence
Send to GenBank

29. Genetic Data

30. Genetic Data

31. Genetic Data

32. PHP / MySQL
Open Source
Modular
Specimen
Floristic
Identification