Data Policy
Bioplatforms Australia Stem Cells Collaborative Data Initiative
Data Policy
1. Introduction
The Bioplatforms Australia (Bioplatforms)-sponsored Stem Cells Collaborative Data Initiative[1] is generating a resource consisting of reference datasets of the core genome, transcript, protein and metabolite data to support national research efforts in Stem Cells biology.
The consortium reserves the right to conduct a ‘global analysis’ across these genome, transcript, protein and metabolite reference datasets and publish the results in the scientific literature. However, in accordance with the Bermuda[2] and Fort Lauderdale[3] agreements and the more recent Toronto Statement[4], which provide guidelines for scientific data sharing, Bioplatforms are committed to ensuring that data produced in this effort is shared at appropriate times and with as few restrictions as possible, to advance scientific discovery and maximize the value to the community from this Australian Government National Collaborative Research Infrastructure Strategy (NCRIS)-funded dataset.
This policy describes the data associated with the consortium, roles and responsibilities of various consortium members and data users and data release schedules.
2. Reference Dataset Description and overall data/information flow
The reference datasets to be produced by the consortium will cover four areas of stem cells research:
- Pluripotent Stem Cells - Pluripotent stages
- Pluripotent Stem Cells - Neural crest
- Pluripotent Stem Cells - Mesoderm Differentiation (Cardiac and blood)
- Pluripotent Stem Cells - Endoderm differentiation (Lymphatic)
Consortium members will discuss the experimental design for each of the study area above. DNA, RNA, protein and metabolite samples will be extracted and data produced from several Bioplatforms network data generation facilities to examine the genome, transcriptome, proteome and metabolome of each sample.
The following facilities will be generating data for the different “omics” type:
|
Omics Type |
Facility |
|
Genomics and Transcriptomics |
Ramaciotti Centre for Genomics, Sydney[5] |
|
Australian Genome Research Facility (AGRF), Melbourne[6] |
|
|
Metabolomics |
Metabolomics Australia, Bio21 Institute, Melbourne[7] |
|
Proteomics |
Australian Proteomics Analysis Facility (APAF), Sydney[8] |
|
Monash Biomedical Proteomics Facility (MBPF), Melbourne[9] |
Following production, raw data will be uploaded to a password-secured central data repository, which is physically located in Perth and managed by the Centre for Comparative Genomics (CCG)[10] on behalf of Bioplatforms.
To enable recovery in case of disaster, all data in the CCG-managed repository will be mirrored at a second site in Brisbane that is managed by the Queensland Cyber Infrastructure Foundation (QCIF)[11].
Data from the QCIF mirror of the central repository will be made available for direct download via a password protected web interface[12] to authorised users (see Section 3).
Metadata associated with each file and files names will be made publicly available via a web portal and associated Application Programming Interface (API), which is managed by CCG for Bioplatforms[13]. Access to the actual data files via the web portal and API will be restricted to authorised users and will require authentication through password use.
As and when determined by Bioplatforms, in consultation with various research champions, copies of the intermediate and analysed data may also be stored elsewhere. As noted above, when this option is executed, access to any copies of the data and metadata must be controlled under identical conditions as required for the primary copies.
Raw data will be shared with bioinformatics facilities and/or researchers at various sites around Australia to generate intermediate and analysed data for the consortium. These facilities will include (but are not necessarily limited to) the following:
|
Omics Type |
Facility |
|
Genomics and Transcriptomics |
Stemformatics[14] |
|
Metabolomics |
Stemformatics and Metabolomics Australia, Bio21 Institute, Melbourne |
|
Proteomics |
Stemformatics and Australian Proteomics Analysis Facility (APAF), Sydney |
|
Stemformatics and Monash Biomedical Proteomics Facility (MBPF), Melbourne |
Intermediate and/or analysed data will be uploaded by bioinformatics staff to the secure central data repository in Perth and mirrored in Brisbane as described above. Data downloads and API access will be provided under the same set-up as for the raw data.
Ultimately, the data generated in this project will be made available under open-access conditions to the international research community, through a variety of relevant established international data repositories including the European Nucleotide Archive (ENA)[15], ArrayExpress[16], ProteomeXchange[17] and MetaboLights[18] - See also Section 4 - Data sharing schedule).
3. Roles and Responsibilities
3.1 Data Initiators
Research champions, listed in Section 5, will assess the data request in consultation with Bioplatforms Australia and are responsible for:
- Outlining the scope of work and agreeing upon the analysis in consultation with Bioplatforms facilities;
- Provide the metadata information relevant for each piece of work.
- Consultation with Bioplatforms for the tasks outlined in Section 3.2.
3.2 Data Sponsor
Bioplatforms Australia, as the Data Sponsor, undertakes the overall duties of ownership, and is responsible for the following tasks (in consultation with various research champions):
- Defining the purpose of the data items;
- Defining access arrangements;
- Authorising any Data Users;
- Appointing a Data Custodian for copies of the data stored at various sites/on various systems.
3.3 Data Producers
Two broad types of data will be produced: raw and processed. Raw and processed data will be produced from the facilities listed in Section 2.
Producers of both raw and processed data are responsible for:
- Assigning a Data Custodian for copies of the data stored locally;
- Data generation and temporary storage;
- Ensuring data use is compliant with this policy;
- Quality assurance.
3.4 Data Infrastructure Providers
Data infrastructure providers provide data storage and/or compute infrastructure for the raw or processed data, and are responsible for:
- Assigning a Data Custodian for copies of the data stored locally.
3.5 Data Custodians
The Data Custodian undertakes the day-to-day management of each item of data stored at various sites/on various systems, and is responsible for:
- Data storage and disposal on that system;
- Ensuring data use is compliant with this and other policies/agreements;
- Providing access to Data Users that have been authorised by the Data Sponsor;
- Ensuring that any Data User who is given access to the data is aware of any data use policies (including this Policy) and their responsibilities.
3.6 Data Users
Data users include all end-users of the raw or processed data generated by the consortium. These comprise consortium researchers, any collaborators, training dataset users and any other approved members of the international research community.
The Data User is any party who has been granted access, by a Data Custodian, to any item of data. They are responsible for:
- Requesting authorisation from the Data Sponsor;
- Requesting access from the Data Custodian;
- Using and safeguarding information according to the conditions stipulated by the Data Sponsor and/or Custodian - including observing any relevant ethics approvals, legislation, data use policies (including this Policy and other relevant data use policies imposed by the Data Owner) and their responsibilities.
4. Data Sharing Schedule
Various data types will be made available at appropriate times throughout the multistep process of generating, processing, assembling, annotating and dispersing the reference datasets.
Broadly, this will fall into two phases: a “mediated-access” phase, where access to the data will be limited to members of the consortium and other authorised parties; and an “open-access” phase where the data will be made openly available from resources including International Data Repositories.
During the “mediated-access” phase, the process for gaining authorisation to access the data is to email data.access@bioplatforms.com with name, affiliation, specific data for which access is being requested and a brief outline of the intended data use. This information will be assessed by the Data Sponsor, Bioplatforms Australia, and the appropriate consortium research champion(s). If approved, Bioplatforms as the Data Sponsor will inform an appropriate Data Custodian to provide access. Data sharing and collaborative interactions are encouraged to advance scientific discovery and maximize the value to the community from this Australian Government (NCRIS)-funded dataset.
Data Release Timescales:
|
Data |
Schedule for release of data to authorised users during the “Mediated-access” phase |
Schedule for public release of data - resulting in the “Open-access” phase |
|
|
All Data sets |
Immediately following deposition of data into CCG data repository |
No earlier than 12 months from deposition of data into CCG data repository |
5. Consortium Group Members/Roles
|
Data Sponsor |
Bioplatforms Australia |
|
Research Champions |
Prof Ernst Wolvetang, University of Queensland |
|
Data Producers (raw) |
Ramaciotti Centre for Genomics, Sydney |
|
Data Producers (processed) |
Monash Biomedical Proteomics Facility (MBPF), Melbourne Stemformatics , Melbourne |
|
Data Infrastructure Providers |
Centre for Comparative Genomics (CCG), Perth Stemformatics, Melbourne |
|
Data Custodians
|
All the groups above are required to appoint a designated Data Custodian to ensure data assets generated throughout this project are managed according to the requirements of this policy |
Appendix 1
Example files types
Table 1: Examples of raw data file types generated
|
Omics Type |
Technology |
File type |
Data description |
|
Transcriptomics Single Cell |
Illumina NextSeq sequencing |
*.fastq |
Base call and quality information for all reads passing filtering |
|
Transcriptomics WholeRNA and SmallRNA |
Illumina HiSeq sequencing |
*.fastq |
Base call and quality information for all reads passing filtering |
|
Proteomics |
MS1 quantification on DDA data |
*.raw |
Raw mass spectrometry data |
|
MS2 quantification on DIA/SWATH data |
*.wiff *.wiff.scan |
1D IDA raw mass spectrometry data (individual samples) 2D IDA raw mass spectrometry data (pooled samples) SWATH mass spectrometry run files (individual samples) |
|
|
*.txt *.xlsx |
Spectral libraries to identify peptides acquired in SWATH-MS runs |
||
|
Metabolomics |
LC-MS analysis |
*.csv |
Raw LC-MS files |
Table 2: Examples of analysed data file types generated
|
Omics Type |
Technology |
File type |
Data description |
|
Transcriptomics Single cell |
Illumina NextSeq sequencing |
*.faa |
Chromosome - predicted protein sequences (amino acid FASTA) |
|
*.ffn |
Chromosome - predicted transcript sequences (nucleotide FASTA) |
||
|
*.fsa |
Chromosome - assembled sequence (nucleotide FASTA) |
||
|
*.gbk |
Chromosome - annotated sequence (Genbank flatfile) |
||
|
*.gff |
Chromosome - annotated sequence (General Feature Format 3.0) |
||
|
*.log
|
Chromosome - Prokka annotation log file (ASCII text) |
||
|
*.txt |
Chromosome - Prokka annotation summary statistics (ASCII text) |
||
|
Transcriptomics |
Illumina HiSeq sequencing |
*.fastq.bam |
Alignment file |
|
*.txt |
Gene list (raw counts) file |
||
|
Proteomics |
MS1 quantification on DDA data |
*.zip |
Zipped folder containing all intermediate and final MaxQuant search result files. The most important file is the proteinGroup.txt file within the combined/txt folder, which contains all quantitative information of all identified proteins |
|
*.sps |
Proprietary sps file containing all Perseus analysis steps. Version-specific to version 1.5.5.3. The MaxQuant proteinGroup.txt file was used as input. |
||
|
*.png |
Image showing distribution of CVs Image showing first 2 dimensions of a principal component analysis |
||
|
*txt |
Raw quantitative matrix summarising the analysis from Perseus. No imputation of missing values performed. Final quantitative matrix summarising the analysis from Perseus, with missing values imputed. |
||
|
MS2 quantification on DIA/SWATH data |
*.xlsx |
PeakView output containing ion, peptide and protein level peak area quantitation and additional information (FDR, score) |
|
|
Metabolomics |
LC-MS analysis |
*.csv |
Final metabolite profile (data matrix) for each sample replicate |
[1]http://www.bioplatforms.com/stem-cells/
[2] https://wellcome.ac.uk/funding/managing-grant/statement-genome-data-release
[3] https://www.genome.gov/pages/research/wellcomereport0303.pdf
[4] http://www.nature.com/nature/journal/v461/n7261/box/461168a_BX1.html
[5] http://www.ramaciotti.unsw.edu.au/
[7] http://www.bio21.unimelb.edu.au/metabolomics-australia
[8] http://www.proteome.org.au/
[9] http://monash.edu/proteomics/facility/
[10] https://ccg.murdoch.edu.au/
[12] https://downloads-qcif.bioplatforms.com/bpa/stemcell/
[13]https://data.bioplatforms.com/organization/about/bpa-stemcells
[14]http://www.stemformatics.org/#
The Stemformatics platform was developed for data sharing and collaboration by Stem Cells Australia. It is a community-focused collaborative platform to enable adoption of ‘omics data by clinicians and stem cells biologist. The data QC, processing and warehousing aspects will be performed by Stemformatics, as well as some additional integrative analyses on some of the different datasets.
[16] https://www.ebi.ac.uk/arrayexpress/
[17] http://www.proteomexchange.org/
[18] http://www.ebi.ac.uk/metabolights/
Version 1, 2018-02-15