New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
LabProcess Type Draft #669
Conversation
Extend labprocess_0.1-DRAFT example
small suggestion and fix typo
I really agree with the distinction of |
Hey @sgenehr, thank you for your input on this topic. I'm not quite sure I correctly got your proposition. Would the |
Yes, from the current proposal, I would understand a A Documentation could also specify which items were |
Ah okay, thanks for the clarification! We did not intend the In the annotation of research experiments we have in mind (based on ISA), the most important thing is to string As a short example, applying an RNA extraction protocol might be brought up. This of course consists of many steps, namely switching between differnt buffers, applying reagents, centrifuging etc.. You start with your input sample of cells and end up with your output RNA exract. This could be annotated using a single Of course this still does not represent a full Lab Experiment, so there might be some overarching type used that functions as a contextualizing collection for the |
Hi @gtsueng I think this PR is ready to go, could you please check it from DDE point of view? Thanks |
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
It looks good from the DDE side of things @ljgarcia
Description
This PR adds the new type draft
LabProcess
. ALabProcess
represents the specific application of aLabProtocol
to some input (biological material or data) to produce some output (biological material or data). The new type inherits these inputs and outputs from the Schema.org typeAction
(i.e. the propertiesobject
andresult
). Additionally, it adds properties for referencing the executed protocol (executesProtocol
) and parameter values of the process as key-value pairs (parameterValues
). This design is heavily inspired by the ISA process model.Motivation and context
Our overarching goal is to establish a distinct separation between LabProtocol (akin to a Recipe / SOP) and LabProcess (akin to the Action described by such LabProtocol, analogous to a lab notebook in a real-world scenario). The following details elaborate on the necessity for this differentiation and the specific use case we aim to address.
In our perspective, and in harmony with the ISA datamodel, we propose that a
LabProtocol
aligns more suitably with aHowTo
than aCreativeWork
. This clarification better reflects the instructional nature of a LabProtocol in guiding experimental procedures. A LabProcess, in contrast, aligns with anAction
.Thus, this PR goes hand-in-hand with the recent changes on
LabProtocol
(#661).We use the very generic Schema.org type
PropertyValue
to describe paramater values of processes in a structured way. This allows users to better annotate a wide range of laboratory processes, as the thePropertyValue
type covers any structured key-value pair or key-value-unit triplet (basically allowing any parameter that can be formalized). We hope that this improves findability of research data objects in the following use cases:Use Case 1 (Findability for comparative analysis)
A process graph encodes structured information for complex experimental setups consisting of multiple experimental steps. It therefore enables search for formal parameters (fixed parameters as well as factors) of specific processes.
Use Case 2 (Findability for fine-grained data acquistion)
A process graph enables semantic web markup and therefore findability of subsets of the data files since relevant metadata is not simply attached to the overall dataset.
Use Case 3 (Findability for Input-based dataset search)
A process graph enables search for samples or datafiles that were input of a specific experimental process, in addition to classic output-driven search.
Have these been tested?
We don't have any experience in the test setup for this repository, so please let us know what needs to be done!
Types of changes
Future TO-DOs
labEquipment
of the typeLabProtocol
is extended to includePropertyValue
.LabProcess
orLabProtocol
objects from aDataset
. Currently, there is no semantically sound property that describes this relation (onlyabout
is a rough match).