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Rename problems whose ID does not match the publication: * `Giordano_Nature2020` -> `Giordano_NatMed2020` (published in Nature Medicine) * `Schwen_PONE2014` -> `Schwen_PLoSOne2015` (published in 2015) * `Weber_BMC2015` -> `Weber_BMCSystBiol2015` (BMC is the publisher, not the journal) The new IDs use the ISO 4 journal abbreviation (as listed in PubMed). Other existing IDs use different abbreviations (e.g. `PNAS`, `MSB`, `JBC`); they are not wrong and are not changed here. The SBML model IDs and names are updated accordingly. The former IDs are still accepted by the accessor functions with a `FutureWarning` (`RENAMED_MODELS`), but are not part of `MODELS`. Co-Authored-By: Claude Opus 5.5 <[email protected]>
| | [Raimundez_PCB2020](problems/Raimundez_PCB2020/) | [v1](problems/Raimundez_PCB2020/v1/) | | Reaction network model of EGFR and MET signaling to ERK and AKT in two gastric cancer cell lines in response to EGF and the anti-EGFR antibody cetuximab. | | ||
| | [SalazarCavazos_MBoC2020](problems/SalazarCavazos_MBoC2020/) | [v1](problems/SalazarCavazos_MBoC2020/v1/) | | Reaction network model of EGFR dimerization, multisite phosphorylation and binding of the adaptor proteins GRB2 and SHC1, generated from a rule-based model. | | ||
| | [Schwen_PONE2014](problems/Schwen_PONE2014/) | [v1](problems/Schwen_PONE2014/v1/) | [v2](problems/Schwen_PONE2014/v2/) | Reaction network model of insulin binding, internalization and degradation in two subpopulations of isolated hepatocytes with low and high insulin binding. | | ||
| | [Schwen_PLoSOne2015](problems/Schwen_PLoSOne2015/) | [v1](problems/Schwen_PLoSOne2015/v1/) | [v2](problems/Schwen_PLoSOne2015/v2/) | Reaction network model of insulin binding, internalization and degradation in two subpopulations of isolated hepatocytes with low and high insulin binding. | |
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Schwen_PLoSOne2015 but Lang_PLOSComputBiol2019
Is PLoS still used?
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For the new names, I used the ISO 4 journal abbreviations. So far, the names appeared somewhat arbitrary. I think it makes sense to have some consistency, but I didn't want to touch all IDs (although I wouldn't be opposed to...). The ISO / PubMed / Medline abbreviations use PLoS despite the renaming.
If you prefer PLOS, I can switch.
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Ah right, it looks like even ISO 4 is inconsistent for different PLOS/PLoS journals.
For the PR, some standard should be set (ISO 4 is fine for me) and applied to all problem IDs.
The way to generate the problem ID should also be updated in the pull request template. Specifically e.g.
{LAST NAME OF FIRST AUTHOR}_{ISO 4 JOURNAL ABBREVIATION WITH NONALPHABET CHARACTERS STRIPPED}{YEAR OF PUBLICATION}
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Will do. Yeah, I think for PL[oO]S it depends on whether the respective journal already existed before the rebranding.
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Oh, but if we are breaking all IDs, I think we should also clarify some additional things:
- special characters in the first author's last name: Brännmark -> Brannmark vs. Fröhlich -> Froehlich
- how to handle collisions?
- different articles but same ID per the rule above: year gets suffix
a,b, ..., but the first one stays without suffix? - different problems within a single article:
_{variant}suffix?
- different articles but same ID per the rule above: year gets suffix
- how to handle multi-part last names?
- which year of publication - online or issue?
Anything else?
And note that some abbreviations may become a bit bulky, e.g., PNAS -> ProcNatlAcadSciUSA
Renames problems whose ID does not match the publication:
Giordano_Nature2020→Giordano_NatMed2020(published in Nature Medicine)Schwen_PONE2014→Schwen_PLoSOne2015(published in 2015)Weber_BMC2015→Weber_BMCSystBiol2015(BMC is the publisher, not the journal)The new IDs use the ISO 4 journal abbreviation (as listed in PubMed). Other existing IDs use different abbreviations (e.g.
PNAS,MSB,JBC,CellSystems); they are not wrong and are not changed here.The SBML model IDs and names are updated accordingly. The former IDs are still accepted by
get_problem,get_problem_yaml_path,get_simulation_df(v1 and v2), andget_metadata, with aFutureWarning; they are listed inRENAMED_MODELS, but are not part ofMODELS. Links to the old directories break.Closes #170.
Overlaps with #339: whichever is merged second needs the
referencesin the renamedmetadata.yamlfiles updated (BibTeX key = problem ID).🤖 Generated with Claude Code