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

User Registration

Getting Started

Requesting an Account– Requirements:

• Valid Email Address

• Institutional Affiliation• Password

Getting Started

Creating a Project– Project Identifiers

• Project code• Project type

– Markers• Primary• secondary

– Campaign– Description– Project permissions

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 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

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

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

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

Publication

Publishing Project– Submitting to GenBank– Making projects public

on BOLD

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

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