A data model for life-science experiments; FuGE

This post may be one in a series of responses to Cameron’s post on “Proposing a data model for Open Notebooks“. When I originally read this post I commented on the fact that a data model for experiments actually exists and that he may get some mileage out of it rather than starting from scratch and re-creating the wheel. Several discussions have followed on from this original post and Neil has picked up on it as well, with sentiments that I agree with.

I think a large part of this discussion confuses and conflates 3 issues which I believe to be separate;

  1. the representation of experiments – the data model
  2. the presentation or level of abstraction to the user (probably some what dependent on 3.)
  3. the implementation of the data model

With these three issues in mind, to start with, I am going back to the original post and respond to some of the comments.

What I’m suggesting is a standard format to describe experiments;…

A “standard” in the true sense of the word (established by consensus and approved by a recognized body) already exists to describe life-science experiments. It is a data model represented in UML called FuGE.

…..a default format for online notebooks. The object is to do a number of things. Firstly identify the page(s) as being an online laboratory notebook so that they can be aggregated or auto-processed as appropriate.

I see this as two different and separate things, the data model which represents experiments, and the presentation of the model to the user, in this case described as an online notebook. Page numbers are an arbitrary visual aid, they are not integral to modelling experiments

…Secondly to make rich metadata available in a human readable and machine processable form making mashups and other things possible using tools such as Yahoo! Pipes, Dapper, and the growing range of other interesting tools, but not to impose any unnecessary limitations on what that metadata might look like. ..

I am not going to deal with metadata here, as the post will probably be long enough. However, traditionally, metadata, (cv’s and ontologies) have been used to add specificity or meaning to the structured data. The choice of the metadata to use (or build) will be dependent on the application.

Another issue is the tables. My original thinking was that if we had a data model for tables then most of our problems would go away.

I am not sure I agree here. What is a table? I see it as a particular visual display mechanism that you have chosen to represent you results. The results can be modelled more accurately within the data model such as chemical-has_measurement, measurement has_numerical value and has_unit. I believe this statement is confusing the visual presentation of data with structuring the data.
However the argument against still stands. Anything that requires a fixed vocabulary is going to break

Well, anything that requires a fixed vocabulary is less flexible, breaking is something different. If it breaks doing the job it was designed to do then this is a problem. If it breaks when applied to a different application, then well, it was not designed for that application in the first place. FuGE is designed so that it provides a generic structure which can then be described or further specialised by the user/application by extending the model itself or by using cv’s/ontologies or free text. This provides the flexibility and in theory future proof.

Overall an experiment has inputs and outputs. These may be data or material objects. Procedures take inputs and generate outputs.[..] Broadly speaking there seem to be three types of item; material objects , data, and procedures (possibly also comments). For each of these we require a provenance (author), and a date

I would agree with you assessment of what classes are needed. This corresponds to what FuGE contains as illustrated in the digram below (click on image to see original)


In summary, the position I want to present is that FuGE is a data model to represent scientific experiments. Several domains are using it to represent their experiments from traditional biology/molecular biology to neurophysiology. I believe FuGE could form the underlying model for a “notebook” via an abstraction/presentation layer to the user. In how should it be implemented, blog, wiki, database, latex, XML, RDF, OWL, I am not going to hypothesis. However, a database implementation of the FuGE schema is already in development called SyMBA which abstracts away from the user presenting simple web forms to fill out the XML which is then stored as a relation database.

  1. #1 by harddriveman.com on March 1, 2015 - 8:08 pm

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