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Frequently asked questions
The smallest amount of samples that still form a complete story
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Background
To answer this question, you need some information about our metadata model (the PISA-model) first.
FAIR data
At DataHub we believe in FAIR data. One of the aspects to accomplish FAIRness is to accompany datasets with rich, machine-readable and semantic metadata. Annotating data with proper metadata is often a cumbersome and boring process. As such, we have developed a web portal that uses intuitive forms to enter metadata about your data set.
ISA data model
The elements in this web form are inspired by the ISA data model that was originally developed by the ISA working group coordinated by the Oxford e-Research Centre. The ISA model was designed for use in omics-related domains, but is flexible enough for metadata modeling in other research domains. See Figure 1.
PISA - the DataHub implementation
At DataHub we use the ISA data model with an additional top-level category, i.e. P for Project, to be more aligned with the hierarchical folder structure in the iRODS system. Additionally we made design choices about cardinality of the individual levels in PISA.
Figure 1: The ISA model
PISA definitions
PISA is an acronym for Project, Investigation, Sample, Assay and forms a layered model; each layer being a level at which metadata can be entered. As such, each PISA-level has its own metadata template. See Figure 3.
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Currently, DataHub only provides metadata web forms for the Project- and Investigation-level. We will extend our functionality in the future to support user-friendly metadata entry on all PISA-levels. In the meantime we highly encourage each user to provide metadata on the Sample- and Assay levels as well, by using spreadsheets or other formats. For your convenience, we provide example spreadsheets as attachments to this page.
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Project
The highest level of organization. It encompasses all data from a same context.
Metadata on this level will typically be defined during your project intake process.
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Investigation
The smallest amount of samples that still form a complete story. The data that shape a complete investigation are therefore highly influenced by the research question.
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Conceptually, defining the scope of an investigation can be very challenging. The investigation should not be:
If you need help defining the scope of your investigation, please don't hesitate to contact us. |
Sample
Biological material that acts as a central unit in the experiment to which treatments or measurements are applied. Each investigation contains 1 to n samples. Each sample should be accompanied with proper metadata about biological origin, species, treatment, etc.
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Feel free to use this spreadsheet as starting point for your Sample metadata. |
Assay
Measurements performed on samples. Each sample in an investigation is associated with 1 to n assays. Each sample in an assay should be properly annotated with (technical) metadata about machine settings, machine type, measurement date, etc. and most importantly: the pointer to the resulting data file of this sample-assay combination.
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Feel free to use this spreadsheet as starting point for your Assay metadata. |
Figure 2: The tower of PISA as mascot for the PISA model
Figure 3: The DataHub PISA implementation
Mapping PISA to iRODS
Figure 4 shows the relationship between concepts in PISA and their corresponding element in the iRODS data structure.
- Project; metadata is registered in the iRODS database. Each project has its own path in iRODS.
- For example: /nlmumc/projects/P000000009
- Investigation; metadata is partly registered in the iRODS database and partly in the metadata.xml file. Each investigation is stored as a new Collection in iRODS.
- For example: /nlmumc/projects/P000000009/C000000002
- Sample; metadata is registered in spreadsheets, XML, RDF or any other preferred format by the researcher. Sample metadata is stored as file(s) in the Collection.
- For example: /nlmumc/projects/P000000009/C000000002/s_study_sample.txt
- Assay; metadata is registered in spreadsheets, XML, RDF or any other preferred format by the researcher. Sample metadata is stored as file(s) in the Collection.
- For example: /nlmumc/projects/P000000009/C000000002/a_transcription_micro_1.txt
- Data files; are stored in separate files or subfolders of the collection. It's up to the researcher how the data files are being organised, as long as there is a valid link from Assay-metadata to data file!
- For example: /nlmumc/projects/P000000009/C000000002/52078100929382020215419332913403.cel
- For example: /nlmumc/projects/P000000009/C000000002/microscope_data/sample_id_data_file.tif
Figure 4: Relationship between the PISA model and the data organisation in iRODS
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