The smallest amount of samples that still form a complete story

Table of Contents

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.

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.

Example of a Sample metadata spreadsheet
Example of an Assay metadata spreadsheet

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.

Project examples

PhD project
Consortium project
Clinical Study
Student's thesis project

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.

Investigation examples

Research Question	Investigation
What is the optimal setting for my microscope to measure slices of tissue X?	Microscope images of tissue X taken on different apertures, exposure time etc.
What is the dose- and time-effect of compound Y on HepG2 cells	Measurement results of different doses and time points from both the treated and control samples.
What is the level of CXCR4 expression in T-lymphocytes	qPCR results of expression of CXCR4- and corresponding household gene.

Conceptually, defining the scope of an investigation can be very challenging. The investigation should not be:

too small, because selection of samples belonging together can become difficult during the analysis phase
too large, because data in your collection can become too complicated and interrelated. Additionally, there is a risk that the duration of your sample collection phase transcends the maximum lifetime of a drop zone, being 3 months.

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.

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.

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

Page tree

What are investigations?