megan milton & mallory van wyngaarden - managing barcode data library generation
DESCRIPTION
How to manage barcode data library generation using BOLD systemsTRANSCRIPT
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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
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Barcode Library Generation
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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
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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
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User Registration
Getting Started
Requesting an Account– Requirements:
• Valid Email Address
• Institutional Affiliation• Password
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Getting Started
Creating a Project– Project Identifiers
• Project code• Project type
– Markers• Primary• secondary
– Campaign– Description– Project permissions
Project Creation Form
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Specimen Page Sequence Page
Getting Started
Barcode Record = Specimen data + Molecular data
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Getting Started
Standard Workflow - order of upload
Specimen Data
Images
Traces
Sequences
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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
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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
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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
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Primer Submissions
Primer Database
Primer Database– Search by
• Primer code• Submitter• Target marker• Reference/Citation
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Primer Submissions
Primer Submission Form
Primers– Required Fields
• Primer code• Primer description• Target marker• Primer sequence• Reference/Citation• Direction• *Public/private
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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
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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
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Record List and Icons
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
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Taxon ID Tree
Data Validation
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
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Nearest Neighbour Summary
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
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Specimen and Sequence Pages
Data Curation
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
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Publication
Publishing Project– Submitting to GenBank– Making projects public
on BOLD
Published Project
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Bibliography Submissions
Biblio Submission Form and Publication Database
Bibliography• Required Fields:
• Title• Authors• Abstract• Journal details
• Connect to BOLD records• Primary records• Secondary records