Use Cases for Laboratory Processes

The following use cases were developed by the Laboratory Protocols group.

Findability

Findability for comparative analysis

A user is seeking experimental data for the purpose of conducting a comparative analysis. Their primary interest lies in identifying and comparing experiments with specific factors. In individual experiments, these factors are not the primary focus of the studies; instead, they serve as fixed parameters within the experimental processes. These seemingly “uninteresting” parameters need to be easily accessible for their research. The user aims to search for various parameters, factors, and characteristics within the specific context of different parts of the experimental setup. For example, consider an experiment comprising two distinct processes: one for growth and another for measurement under heat stress, both involving the parameter “temperature.” However, for their comparative analysis, they are interested in a specific instance of this parameter, and they need the capability to search for it. Consequently, this parameter must be structured and accessible within the schema markup of the original experiment. In the event that all this information is associated with a dataset object, manual creation of the markup becomes necessary, as it demands a semantic understanding of formal parameters. The ISA’s straightforward process graph model excels in capturing these nuances. Therefore, we recommend integrating the LabProcess object type into Bioschemas, as this will facilitate the structured markup of the formal parameters associated with experiment steps.

Findability for fine-grained data acquisition

Improve the findability for datasets providing (raw) files which can be used for bioinformaticians to get data that was created using a dedicated facility or instrument. Imagine a bioinformatician developing a new image analysis algorithm to calculate plant growth based on drone images. Now he wants to improve the underlying calculation and need more drone images which have a minimal resolution or were generated with a certain camera sensor, he is not interested in the original experimental design, just looking for data based on any equipment.

Findability for Input-based dataset search

In a plant phenomic dataset that includes both direct measures and computed data elaborated to characterize the plant varieties, the LabProcess type will allow to document the relationship between datafiles. Hence, a user, through a search engine, would be able to identify reproducible datasets that include both raw and derived data. Also, a search engine would be able to point to raw data that have been used to extract specific traits. For instance, a raw images dataset from which a trait disease dataset has been derived could be easily found thanks to LabProcess, hence identifying potential training dataset for challenges such as the global wheat challenge.

Overview

Overview of LabProcess and how it relates to other specifications in Bioschemas, for instance LabProtcol and Sample.