Megan Milton & Mallory Van Wyngaarden - Managing Barcode Data Library Generation

Barcode of Life Data Systems (BOLD) www.boldsystems.org (v2.5) v3.boldsystems.org (v3.0 beta) Managing Barcode Data Library Generation Fourth International Barcode of Life Conference - Workshop Megan Milton and Mallory Van Wyngaarden Monday, November 28, 2011 – University of Adelaide, Australia

Barcode Library Generation

Barcode Library Generation
Needs
Scope (taxonomic and/or geographic)
Barcode standards compliance
Completion of data
Access by all participants
Quality control process
Data Curation/updates
Avoid duplication of effort
Computational power for analysis
Protection of data

BOLD Workbench
How BOLD addresses these needs:
Secure Data Storage
Online access anywhere
Permission based sharing
Taxonomy Browser (view progress so far)
Built-in Quality Control checks
Progress feeds/Activity log
Analysis tools on BOLD compute cluster

Requesting an Account
Requirements:
Valid Email Address
Institutional Affiliation
Password
User Registration Getting Started

Creating a Project
Project Identifiers
Project code
Project type
Markers
Primary
secondary
Campaign
Description
Project permissions
Getting Started Project Creation Form

Specimen Page Sequence Page Getting Started Barcode Record = Specimen data + Molecular data

Getting Started Standard Workflow - order of upload Specimen Data Images Traces Sequences

Specimen Data Submissions Single Specimen Upload Form
Specimen Data
Single Uploads
Identifiers
Taxonomy
Specimen Details
Collection data
Batch Uploads
New and updated records
Template spreadsheet
Submit through BOLD to Data Management Team

Image Submissions Image Library
Image Data
Required Fields
Sample ID
Process ID
Image File
Original Specimen
View Metadata
Licensing
Resolution
< 20 Megapixels
Assemble Package
Images (.jpeg format)
Spreadsheet (template)
Maximum zipped file size 190MB

Trace Submissions Trace File Viewer
Trace Files
Sequencing details:
Trace file in .ab1 or .scf
Phred File in .phd.1
PCR primers
Sequencing primer
Direction
Marker
Attribution to run site
Assemble Package
Electropherograms
Spreadsheet (template)
Maximum zipped file size 190MB

Primer Submissions Primer Database
Primer Database
Search by
Primer code
Submitter
Target marker
Reference/Citation

Primer Submissions Primer Submission Form
Primers
Required Fields
Primer code
Primer description
Target marker
Primer sequence
Reference/Citation
Direction
*Public/private

Sequence Submissions Sequence Page
Sequence Data
Required Fields
Aligned sequences in FASTA format
Header can use Process ID or Sample ID
Marker
Run Site (Institution)
< 1000 sequence per upload

Project Console
Project Permissions and Publication
Project manager only
Project Statistics
Upload/Downloads
Sequence Analysis
Specimen Aggregates
Activity Feed
Tags and Comments
Project Console Project Summary

Record List
Identification
Specimen Page
Specimen information
Image data
Sequence Page
Sequence(s), trace files and primer
Icons and flags
Tagging and Comments on multiple records
Record List and Icons Project Summary

Taxon ID Tree
Requires: good quality sequences, some level of taxonomy, images are recommended
Highlights common contaminations
Colourize by taxonomy, geography, etc
Helps to catch misidentifications
Add pictures for comparison
Use to help make identifications
Taxon ID Tree Data Validation

Nearest Neighbour
Tabular Format
Requires low level taxonomy
Highlights:
Low Divergence compared to nearest neighbour
Divergence that is less than the intra-specific
Nearest Neighbour Summary Data Validation

Editing Records
Review graphs and flags in Project Summary
Review and edit specimen page
Review sequence page
Sequence
Trace
Primer
Replace or delete images, traces, sequences
Specimen and Sequence Pages Data Curation

Publishing Project
Submitting to GenBank
Making projects public on BOLD
Publication Published Project

Bibliography Submissions Biblio Submission Form and Publication Database
Bibliography
Required Fields:
Title
Authors
Abstract
Journal details
Connect to BOLD records
Primary records
Secondary records

[email_address]

Megan Milton & Mallory Van Wyngaarden - Managing Barcode Data Library Generation

by Consortium for the Barcode of Life (CBOL)

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