1. Christopher I Hunter Conference name Date
GigaDB explained
Christopher I Hunter
Conference name
Date

2. Presentation contents
GigaDB introduction
Data types hosted
Anatomy of a dataset DOI
Navigate GigaDB site
Search tool
Submission tool
The extensible metadata schema
Coffee Break
ISA tools introduction
ISA-Tab as an exchange format
ISA in action

3. GigaScience Database

4. Giga-overview GigaDB hosts biological data
(any type of data related to, or used in
biological studies)
Primarily associated with the BMC journal, GigaScience
Funded by BGI-Research and China National GeneBank

5. Currently ~160 datasets available
Genomic datasets represent majority of data(~70%)
~90% of all data from BGI (or partner) studies
But there 13 different types represented
All manually curated

6. Data types Various Nucleotide data types: Mass spectrometry:
Genomic, Transcriptomic, Metagenomic, Epigenomic, Genome mapping.
Mass spectrometry:
Proteomics, Metabolomics, MS-Imaging.
Software & Workflows
Other
Imaging, Neuroscience, Network analysis

7. Navigating the GigaDB website
Home page
Dataset DOI page
Data download options
Search tool
Submission:
Who should submit to GigaDB
How to submit data

9. Anatomy of a GigaDB entry
All relevant information is held together in packets called Datasets
Each dataset has a stable DOI page
If required there can be a hierarchy of datasets

10. Links to Google scholar and EuroPMC to see who has cited this dataset
Title
Study type(s)
Image
Citation
Description
Funders
Links to Google scholar and EuroPMC to see who has cited this dataset
submitter
Link to manuscript
Links to external resources
Cont.

11. Samples used in the study
Files listed as part of the study
History of dataset changes
Social media links
Links to other datasets of similar nature

12. Downloading the data FTP Conventional/easy to use
Can pull individually from web page
1 or multiple files using command line unix
Speed = upto 1 Mb/sec

13. Downloading the data Aspera Requires plugin download
Only available to use via web-app
1 or multiple files
Speed = upto 100 Mb/sec
(e.g. upto 100x faster than FTP)

14. Search tool
Search for the term “genome” in the search bar at the top of any dataset page:

15. Search tool

16. = GigaDB datasets = Samples = Files
It will only display files that contain matches to the search term

19. Submitting data to GigaDB
All data submitted to GigaDB must be fully consented for public release
Where appropriate data should be submitted to established public archives first. (e.g. INSDC)
At present we only host data associated with GigaScience journal articles, or by prior approval by the Editors of GigaScience.
Potential submitters should approach the editors and database curators by to discuss possible inclusion.

20. Submission Workflow Curator Review Validation checks Files GigaDB
Submit Excel spreadsheet or uses online wizard
Curator contacts submitter with DOI citation and to arrange file transfer (and resolve any other questions/issues).
Fail – submitter is provided error report
Curator Review
Submission
Validation checks
Files
DOI assigned
Submitter provides files by ftp or Aspera
GigaDB
Pass – dataset is uploaded to GigaDB.
XML is generated and registered with DataCite
Curator makes dataset public (can be set as future date if required)
DataCite XML file
Public GigaDB dataset
DOI /100003
Genomic data from the crab-eating macaque/cynomolgus monkey (Macaca fascicularis) (2011)

21. Submission Workflow Curator Review Validation checks Files GigaDB
Submit Excel spreadsheet or uses online wizard
Curator contacts submitter with DOI citation and to arrange file transfer (and resolve any other questions/issues).
Fail – submitter is provided error report
Curator Review
Submission
Validation checks
Files
DOI assigned
Submitter provides files by ftp or Aspera
GigaDB
Pass – dataset is uploaded to GigaDB.
XML is generated and registered with DataCite
Curator makes dataset public (can be set as future date if required)
DataCite XML file
Public GigaDB dataset
DOI /100003
Genomic data from the crab-eating macaque/cynomolgus monkey (Macaca fascicularis) (2011)

22. Submission
Once approved there are two options for submitting metadata;
offline using an Excel spreadsheet
online using the wizard
Soon to be a third option (ISA-tab)

23. Online vs Offline Guided Good for few large samples
Allows greater addition of linking
Limited documentation
Best for large number of samples/files

24. Submission wizard
Register, Log in, Goto your profile page:

28. Add all the links to related data

29. Add all the links to related data

30. Add all the links to related data

31. Add all the links to related data

32. Add all Sample metadata

33. Submission Workflow Curator Review Validation checks Files GigaDB
Submit Excel spreadsheet or uses online wizard
Curator contacts submitter with DOI citation and to arrange file transfer (and resolve any other questions/issues).
Fail – submitter is provided error report
Curator Review
Submission
Validation checks
Files
DOI assigned
Submitter provides files by ftp or Aspera
GigaDB
Pass – dataset is uploaded to GigaDB.
XML is generated and registered with DataCite
Curator makes dataset public (can be set as future date if required)
DataCite XML file
Public GigaDB dataset
DOI /100003
Genomic data from the crab-eating macaque/cynomolgus monkey (Macaca fascicularis) (2011)

34. Manual check /curate
After metadata has been submitted it is checked by a curator
A private upload area is assigned and user can upload data files by Aspera or FTP

35. Submission Workflow Curator Review Validation checks Files GigaDB
Submit Excel spreadsheet or uses online wizard
Curator contacts submitter with DOI citation and to arrange file transfer (and resolve any other questions/issues).
Fail – submitter is provided error report
Curator Review
Submission
Validation checks
Files
DOI assigned
Submitter provides files by ftp or Aspera
GigaDB
Pass – dataset is uploaded to GigaDB.
XML is generated and registered with DataCite
Curator makes dataset public (can be set as future date if required)
DataCite XML file
Public GigaDB dataset
DOI /100003
Genomic data from the crab-eating macaque/cynomolgus monkey (Macaca fascicularis) (2011)

36. Mint the DOI
Once all the files and metadata are stored and linked appropriately we will mint the DOI with out partners at DataCite.

37. Publish the dataset
Publication date = date on which DOI is released to public.
Immediately added to GigaDB RSS feed.
Any other promotion of datasets is done in conjunction with manuscript publication

38. Behind the scenes

39. The extensible metadata schema
Spectrum of data being hosted is very broad
Database needs to be:
Structured, but allow wide variety
Be able to incorporate multiple standards
Utilise ontologies
Link to multiple external sources

40. The GigaDB schema looks like this:

41. Just the Dataset tables

42. Just the Dataset tablesid
submitter_id
image_id
identifier
title
description
dataset_size
ftp_site
upload_status
excelfile
excelfile_md5
publication_date
modification_date
publisher_id
token

43. Just the Dataset tables

44. Store wide variety of attributes
attribute_name
definition
model
structured_comment_name
value_syntax
allowed_units
occurrence
ontology_link
note

45. Checklists
Different things are important in different experiment types
Various communities have standard checklists they try to adhere to
GigaDB can leverage those different checklists and integrate them where possible.

46. MIxS Genomic Standards Consortium (GSC) It includes:
Minimum Information about x Sequence
It includes:
set of core descriptors for sequence data
Set of measurements and observations describing the environment of the sample
Goes beyond the minimum, by defining ~370 attributes that could be used.
It is hoped that the adoption of this standard would elevate the quality, accessibility and utility of information that can be collected.

47. SRA & PX
The Sequence Read Archive (SRA) and the ProteomeXchange (PX) also both provide specific terms (attributes) that we can map to.

48. Other checklists
We are able to include attributes from any model or standard and link that from the attributes table
So if there is a recommended standard for a particular data-type we can incorporate it.

49. Ontologies Units Taxonomy Any that are defined in standards
Common ones in use:
DOID - Disease ontology
EFO - Experimental Factor ontology
SO - Sequence ontology
UBERON - cross-species ontology of anatomical structures
ENVO - ENVironment Ontology

50. Future developments Develop an Application programming Interface (API)
Including support for ISA format import and export
Improve dataset DOI display pages
Include experiment information
Improve submission wizard
Include bulk upload tables
Add ontology look-up automatically
Integrate other tools

51. That’s it for GigaDB.
Thanks for listening!
Any Questions?
Next up, ISA tools.

52. Christopher I Hunter Conference name Date
ISA tools
Christopher I Hunter
Conference name
Date

53. What is ISA?
Investigation
Study (and/or Sample)
Assay

54. What is ISA-tab?
ISA-tab is a general purpose, domain agnostic, flexible format to describe multi-omic experiments.
It can be used as a submission format to some archives and there are a suite of tools for conversion into other common formats.

56. What are ISA-tools? A suite of tools based on the ISA-tab format
Developed and maintained by a team at Oxford University, UK.
The main tool of interest here is the ISA-creator

58. Live demo Don’t panic, I have screen shots if it all goes wrong!

64. The Ontology lookup function

65. ISA Validation tool Default only checks ISA-tabs are formed correctly
Can be configured to check against checklists

66. ISA converter tool
The development team actively work on new converter tools
And are always happy to work with domain experts to make more

67. The ISA team http://www.isa-tools.org/ Susanna Sansone
Philippe Rocca-Serra
Alejandra Gonzalez-Beltran

68. That’s it for ISA.
Thanks for listening!
Any Questions?
Next up,
GigaScience software and workflows.