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@dweindl dweindl commented Jan 26, 2026

Rephrase and rearrange some extension-related parts:

  • Trying to make the PEtab 2.0 specs more self-contained
  • Separate process and specs for PEtab extensions
  • Avoid using "extension" to refer to different things

Rephrase and rearrange some extension-related parts:

* Trying to make the PEtab 2.0 specs more self-contained
* Separate process and specs for PEtab extensions
* Avoid using "extension" to refer to different things
@dweindl dweindl requested a review from a team as a code owner January 26, 2026 12:19
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This looks good. Do we have any extensions which are currently used? If yes it makes sense to list them on the webpage.

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dweindl commented Jan 26, 2026

Do we have any extensions which are currently used? If yes it makes sense to list them on the webpage.

There's this:

PEtab/README.md

Lines 112 to 128 in 26c4fb2

## PEtab extensions
Other standardization-related projects that extend or build on PEtab include:
* [PEtab Select](https://petab-select.readthedocs.io/en/latest/)
PEtab Select brings model selection to PEtab. It comprises both a
standardized way to define model selection problems in PEtab and a Python
library to work with these problems.
* [petabunit](https://github.com/matthiaskoenig/petabunit) (WIP)
A Python library that extends PEtab to annotate and convert physical units.
* [PEtab SciML](https://github.com/PEtab-dev/petab_sciml) (WIP)
PEtab SciML brings Scientific Machine Learning (SciML) models that
combine mechanistic and machine learning models to PEtab. It comprises
both a standardized way to define SciML problems, and a Python library
to work with these problems.

Extensions of this format (e.g., additional columns in the measurement table)
are allowed and encouraged. While such extensions can enhance plotting,
Additional non-standard columns are allowed in all PEtab tables.
While such extra column may, for example, contain metadata to enhance plotting,
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Suggested change
While such extra column may, for example, contain metadata to enhance plotting,
While such extra columns may, for example, contain metadata to enhance plotting,

Comment on lines +94 to +97
Additional non-standard columns are allowed in all PEtab tables.
While such extra column may, for example, contain metadata to enhance plotting,
downstream analysis, or improve efficiency in parameter estimation, they
should not alter the definition of the estimation problem itself.
must not alter the definition of the estimation problem itself.
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Does this contradict the ability of extensions to alter the definition through new columns?

Or does "non-standard" include both "core" and "extension" columns?

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4 participants