Jesse Xiao at the Data Publishing session at CODATA2017: Updates to the GigaDB open access data publishing platform. Wednesday 11th October in St Petersburg, Russia

1. Updates to the GigaDB open
access data publishing platform
Jesse Xiao
Jesse@gigasciencejournal.com
ORCID ID:0000-0003-3408-2852

2. About the Journal
GigaScience is an open access, open data,
open peer-review journal focusing on ‘big
data’ research from the life and biomedical
sciences

3. What is the point of publishing?
• To disseminate
information/knowledge/ideas.
• To present material so it can be
reasonably assessed for its level of
quality (and interest).
• To gain credit for career advancement.

4. Kahn, Goodman, & Mittleman. Dragging Scientific Publishing into the 21st Century 2014
http://genomebiology.com/2014/15/12/556
From Journal Delivery to PDF Delivery

5. Lack of Data and Software Availability
Impacts Reproducibility
1. Ioannidis et al., (2009). Repeatability of published microarray gene expression analyses. Nature Genetics 41: 14
2. Ioannidis JPA (2005) Why Most Published Research Findings Are False. PLoS Med 2(8)
Out of 18 microarray papers, results
from 10 could not be reproduced

6. Deconstructing a paper into accessible,
useable, trackable, interlinked units
Need to provide credit to
reward sharing and proper
organization of:
• Narrative
• Data/Metadata
availability/curation
• Software availability
• Interoperability
• Availability of workflows
• Transparent analyses
Data/
MetaData
Software
Methods
Narrative

7. Deconstructing a paper into accessible,
useable, trackable, interlinked units
Currently we provide credit
for this:
• Narrative
• Data/Metadata
availability/curation
• Software availability
• Interoperability
• Availability of workflows
• Transparent analyses
Data/
MetaData
Software
Methods
Narrative
Sometimes we publish these
as Methods Papers

8. Beyond the Narrative
Data And Tools

9. Getting past…
…look but don't touch

10. Data publishing
http://gigasciencejournal.com/
Launched July 2012. Publishes “Data Notes” for CC0 data. Uses ISA-Tab.

11. Data publishing
APC covers 1TB storage in GigaDB

12. FAIR DATA in GigaDB
Findable Accessible Interoperable Reusable

13. Findable
We have 373 published datasets in GigaDB,
& around 30 TB data. Every dataset has a DOI
and the individual dataset page.
Provides powerful search engine
and API search function
e.g.
http://gigadb.org/api/search

14. Accessible
All data in GigaDB can be accessed in the public ftp server.
We provide three stable ftp sites in 2 geographic locations (HK & Shenzhen)
1. ftp://penguin.genomics.cn // The main ftp server
2. ftp://ftp.cngb.org/pub/gigadb/ // The mirror ftp server in the cloud
3. ftp://ftp2.cngb.org/pub/gigadb// The mirror ftp server in the cloud
Download Speed
We are working with China National Gene Bank and will to use UDP protocol software
(Data Expedition) to provide faster data download speed.
The source code for all software and tools published in GigaDB can access in the Github
https://github.com/gigascience

15. Accessible via API
We provide a REST API to allow user retrieve and search all metadata held in GigaDB.
The current API returns result in XML (the XML file based on the database schema), and
we plan to have the option to also return results in JSON or ISA2.0-JSON in our next
version

16. Accessible via API
The website
http://www.gigadb.org/site/help#0
.1_API provides detailed
instructions on how to use the
GigaDB API

17. Interoperable and reusable
Integrating tools (inc Jbrowse genome browser …) to visualize data

18. First journal with deep integration with
Launched 2nd June 2016
Reward better handling of “wet” protocols…
• Create, share, modify forkeable protocols in repo.
• Download & run on smartphone app.
• Get discoverability, credit, DOIs for sharing methods.
• Create your own, or let us set up & you claim.
http://protocols.io/

19. The GigaDB dataset page embeds
the protocol.io in the iframe.
e.g. RNA extraction protocol

20. Interoperable and reusable
GigaDB provides an online submission wizard and excel spreadsheet to help
users curate their own metadata

21. https://codeocean.com/
Cloud-based executable research platform
Browse, share & run code on AWS
Creates compute capsule: encapsulation of
the data, code, and computation
environment
Integration into the paper, share via DOIs
First examples published in GigaScience
Integrated plugin into GigaDB
Share your code this way!
Interoperable and reusable

22. gigagalaxy.net
Reward Sharing of Workflows
Interoperable and reusable

23. http://www.gigasciencejournal.com/content/3/1/23
http://www.gigasciencejournal.com/content/4/1/19
Virtual Machines/containers
• Downloadable as virtual harddisk/available as Amazon Machine Image
• Now publishing many container (docker) submissions
Interoperable and reusable

24. How FAIR can we get?
Data sets
Analyses
Open-Paper
Open-Review
DOI:10.1186/2047-217X-1-18
>50,000 accesses
& >1000 citations
Open-Code
7 reviewers tested data in ftp server & named reports published
DOI:10.5524/100044
Open-Pipelines
Open-Workflows
DOI:10.5524/100038
Open-Data
78GB CC0 data
Code in sourceforge under GPLv3: http://soapdenovo2.sourceforge.net/
>40,000 downloads
Enabled code to being picked apart by bloggers in wiki
http://homolog.us/wiki/index.php?title=SOAPdenovo2

25. http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0127612
Quantifying how FAIR can we get

26. Methods
Answer
Metadata
softwareAnalysis
(Pipelines)
Workflows/
Environments
Idea
Study
Rewarding the
DOI, etc.
Publication
Publication
Publication
Data

27. www.gigasciencejournal.com
Give us your data, papers
& pipelines
Help GigaPanda
make it happen!
editorial@gigasciencejournal.com
database@gigasciencejournal.com
Contact us:

28. Thanks to:
Laurie Goodman, Editor in Chief
Nicole Nogoy, Editor
Hans Zauner, Assistant Editor
Peter Li, Lead Data Manager
Chris Hunter, Lead BioCurator
Xiao (Jesse) Si Zhe, Database Developer
Chen Qi, Shenzhen Office.
All of BGI
@GigaScience
facebook.com/GigaScience
gigasciencejournal.com/blog/
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www.gigadb.org
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