Add publication references to the per-problem metadata

.github/pull_request_template.md

@@ -21,7 +21,7 @@
   - [ ] A visualization table is included, that can be used with the simulated data to reproduce figures from the original publication
   - [ ] The PEtab problem is valid (check with e.g. `petablint -vy problem.yaml`)
   - [ ] Labels (e.g. `parameterName` in the parameter table or `xLabel` in the visualization table) encode special characters with tex-style strings instead of unicode, e.g. use `H$_2$O` for water.
-- [ ] `problems/<ProblemID>/metadata.yaml` contains a single-sentence `short_description` of the problem and passes `bmp-check-metadata`
+- [ ] `problems/<ProblemID>/metadata.yaml` contains a single-sentence `short_description` of the problem and the `references` (DOI and BibTeX entry, key = problem ID) of the original publication(s), and passes `bmp-check-metadata`
 - [ ] The PEtab problem author(s) are assigned to the GitHub issue
 - [ ] The README has been updated with `bmp-create-overview  --update` (requires `pip install -e src/python` from the repository root)
   - [ ] The new PEtab problem row in the generated table has the correct reference (and other entries)

CONTRIBUTING.md

@@ -7,17 +7,16 @@ Each problem lives under `problems/<ProblemID>/`, with at least one of `v1/`/`v2
   `conditions.tsv`, `measurements.tsv`, `observables.tsv`, `parameters.tsv`, and optionally
   `simulations.tsv` and `visualizations.tsv`.
 - `v2/` holds the same problem in PEtab v2 format.
-- `metadata.yaml` contains version-independent metadata. Currently, this is a single-sentence
-  `short_description` of the problem, stating the type of model (e.g., biochemical reaction network,
-  compartmental epidemiological model), the biological system, and, where informative, the data.
-  For example:
-  ```yaml
-  short_description: Reaction network model of Epo-induced STAT5A/STAT5B phosphorylation and homo- and heterodimerization, fitted to quantitative mass spectrometry data.
-  ```
-  The file is validated against the `ProblemMetadata` model in
-  [`metadata.py`](src/python/benchmark_models_petab/metadata.py)
-  (check with `bmp-check-metadata`); the corresponding JSON schema is
-  [`metadata.schema.json`](src/python/benchmark_models_petab/schemas/metadata.schema.json).
+- `metadata.yaml` contains version-independent metadata:
+  - `short_description`: a single sentence stating the type of model (e.g., biochemical reaction
+    network, compartmental epidemiological model), the biological system, and, where informative,
+    the data.
+  - `references`: the publications the problem is based on, each with its `doi` and a `bibtex`
+    entry (one field per line, including a matching `doi` field). The first entry is the main
+    publication; its BibTeX key is the problem ID.
+
+  See [`problems/Boehm_JProteomeRes2014/metadata.yaml`](problems/Boehm_JProteomeRes2014/metadata.yaml)
+  for an example.
 - `resources/` (optional) holds anything else related to the problem that isn't part of the
   PEtab files themselves (e.g. raw data, scripts, notebooks, figures). There's no prescribed
   structure — organize it however fits your problem.

problems/Alkan_SciSignal2018/metadata.yaml

@@ -1 +1,14 @@
 short_description: Reaction network model of the DNA damage response and cell fate in cancer cells treated with chemotherapeutics, fitted to signaling and cell count data.
+references:
+  - doi: 10.1126/scisignal.aat0229
+    bibtex: |
+      @article{Alkan_SciSignal2018,
+        author = {Alkan, Ozan and Schoeberl, Birgit and Shah, Millie and Koshkaryev, Alexander and Heinemann, Tim and Drummond, Daryl C. and Yaffe, Michael B. and Raue, Andreas},
+        title = {Modeling chemotherapy-induced stress to identify rational combination therapies in the {DNA} damage response pathway},
+        journal = {Science Signaling},
+        year = {2018},
+        volume = {11},
+        number = {540},
+        pages = {eaat0229},
+        doi = {10.1126/scisignal.aat0229},
+      }

problems/Armistead_CellDeathDis2024/metadata.yaml

@@ -1 +1,14 @@
 short_description: Small reaction network model of sphingolipid metabolism with ceramide feedback, fitted to lipidomics data of wild-type and mutant zebrafish embryos.
+references:
+  - doi: 10.1038/s41419-024-07134-2
+    bibtex: |
+      @article{Armistead_CellDeathDis2024,
+        author = {Armistead, Joy and Höpfl, Sebastian and Goldhausen, Pierre and Müller-Hartmann, Andrea and Fahle, Evelin and Hatzold, Julia and Franzen, Rainer and Brodesser, Susanne and Radde, Nicole E. and Hammerschmidt, Matthias},
+        title = {A sphingolipid rheostat controls apoptosis versus apical cell extrusion as alternative tumour-suppressive mechanisms},
+        journal = {Cell Death \& Disease},
+        year = {2024},
+        volume = {15},
+        number = {10},
+        pages = {746},
+        doi = {10.1038/s41419-024-07134-2},
+      }

problems/Bachmann_MSB2011/metadata.yaml

@@ -1 +1,14 @@
 short_description: Reaction network model of Epo-induced JAK2/STAT5 signaling with two negative feedback regulators (SOCS3, CIS) in murine erythroid progenitor cells.
+references:
+  - doi: 10.1038/msb.2011.50
+    bibtex: |
+      @article{Bachmann_MSB2011,
+        author = {Bachmann, Julie and Raue, Andreas and Schilling, Marcel and Böhm, Martin E. and Kreutz, Clemens and Kaschek, Daniel and Busch, Hauke and Gretz, Norbert and Lehmann, Wolf D. and Timmer, Jens and Klingmüller, Ursula},
+        title = {Division of labor by dual feedback regulators controls {JAK2/STAT5} signaling over broad ligand range},
+        journal = {Molecular Systems Biology},
+        year = {2011},
+        volume = {7},
+        number = {1},
+        pages = {516},
+        doi = {10.1038/msb.2011.50},
+      }

problems/Beer_MolBioSystems2014/metadata.yaml

@@ -1 +1,14 @@
 short_description: Small kinetic model of bacterial growth and production of the blue pigment indigoidine by engineered variants of a non-ribosomal peptide synthetase.
+references:
+  - doi: 10.1039/c3mb70594c
+    bibtex: |
+      @article{Beer_MolBioSystems2014,
+        author = {Beer, Ralf and Herbst, Konrad and Ignatiadis, Nikolaos and Kats, Ilia and Adlung, Lorenz and Meyer, Hannah and Niopek, Dominik and Christiansen, Tania and Georgi, Fanny and Kurzawa, Nils and Meichsner, Johanna and Rabe, Sophie and Riedel, Anja and Sachs, Joshua and Schessner, Julia and Schmidt, Florian and Walch, Philipp and Niopek, Katharina and Heinemann, Tim and Eils, Roland and Di Ventura, Barbara},
+        title = {Creating functional engineered variants of the single-module non-ribosomal peptide synthetase {IndC} by {T} domain exchange},
+        journal = {Molecular BioSystems},
+        year = {2014},
+        volume = {10},
+        number = {7},
+        pages = {1709--1718},
+        doi = {10.1039/c3mb70594c},
+      }

problems/Bertozzi_PNAS2020/metadata.yaml

@@ -1 +1,14 @@
 short_description: SIR compartmental epidemiological model of the early COVID-19 outbreak in New York and California.
+references:
+  - doi: 10.1073/pnas.2006520117
+    bibtex: |
+      @article{Bertozzi_PNAS2020,
+        author = {Bertozzi, Andrea L. and Franco, Elisa and Mohler, George and Short, Martin B. and Sledge, Daniel},
+        title = {The challenges of modeling and forecasting the spread of {COVID-19}},
+        journal = {Proceedings of the National Academy of Sciences},
+        year = {2020},
+        volume = {117},
+        number = {29},
+        pages = {16732--16738},
+        doi = {10.1073/pnas.2006520117},
+      }

problems/Blasi_CellSystems2016/metadata.yaml

@@ -1 +1,14 @@
 short_description: Reaction network model of combinatorial histone H4 acetylation states generated by motif-specific acetylation reactions.
+references:
+  - doi: 10.1016/j.cels.2016.01.002
+    bibtex: |
+      @article{Blasi_CellSystems2016,
+        author = {Blasi, Thomas and Feller, Christian and Feigelman, Justin and Hasenauer, Jan and Imhof, Axel and Theis, Fabian J. and Becker, Peter B. and Marr, Carsten},
+        title = {Combinatorial Histone Acetylation Patterns Are Generated by Motif-Specific Reactions},
+        journal = {Cell Systems},
+        year = {2016},
+        volume = {2},
+        number = {1},
+        pages = {49--58},
+        doi = {10.1016/j.cels.2016.01.002},
+      }

problems/Boehm_JProteomeRes2014/metadata.yaml

@@ -1 +1,14 @@
 short_description: Reaction network model of Epo-induced STAT5A/STAT5B phosphorylation and homo- and heterodimerization, fitted to quantitative mass spectrometry data.
+references:
+  - doi: 10.1021/pr5006923
+    bibtex: |
+      @article{Boehm_JProteomeRes2014,
+        author = {Boehm, Martin E. and Adlung, Lorenz and Schilling, Marcel and Roth, Susanne and Klingmüller, Ursula and Lehmann, Wolf D.},
+        title = {Identification of Isoform-Specific Dynamics in Phosphorylation-Dependent {STAT5} Dimerization by Quantitative Mass Spectrometry and Mathematical Modeling},
+        journal = {Journal of Proteome Research},
+        year = {2014},
+        volume = {13},
+        number = {12},
+        pages = {5685--5694},
+        doi = {10.1021/pr5006923},
+      }

problems/Borghans_BiophysChem1997/metadata.yaml

@@ -1 +1,14 @@
 short_description: Three-variable ODE model of complex calcium oscillations with Ca2+-activated IP3 degradation, fitted to measured calcium bursting in a single hepatocyte.
+references:
+  - doi: 10.1016/s0301-4622(97)00010-0
+    bibtex: |
+      @article{Borghans_BiophysChem1997,
+        author = {Borghans, José A. M. and Dupont, Geneviève and Goldbeter, Albert},
+        title = {Complex intracellular calcium oscillations. {A} theoretical exploration of possible mechanisms},
+        journal = {Biophysical Chemistry},
+        year = {1997},
+        volume = {66},
+        number = {1},
+        pages = {25--41},
+        doi = {10.1016/s0301-4622(97)00010-0},
+      }

problems/Brannmark_JBC2010/metadata.yaml

@@ -1 +1,14 @@
 short_description: Reaction network model of insulin receptor and IRS1 phosphorylation with receptor endocytosis and feedback in primary human adipocytes.
+references:
+  - doi: 10.1074/jbc.M110.106849
+    bibtex: |
+      @article{Brannmark_JBC2010,
+        author = {Brännmark, Cecilia and Palmér, Robert and Glad, S. Torkel and Cedersund, Gunnar and Strålfors, Peter},
+        title = {Mass and Information Feedbacks through Receptor Endocytosis Govern Insulin Signaling as Revealed Using a Parameter-free Modeling Framework},
+        journal = {Journal of Biological Chemistry},
+        year = {2010},
+        volume = {285},
+        number = {26},
+        pages = {20171--20179},
+        doi = {10.1074/jbc.M110.106849},
+      }

problems/Bruno_JExpBot2016/metadata.yaml

@@ -1 +1,14 @@
 short_description: Enzyme kinetic model of the in vitro cleavage of carotenoids and apocarotenoids by Arabidopsis carotenoid cleavage dioxygenase 4 (CCD4).
+references:
+  - doi: 10.1093/jxb/erw356
+    bibtex: |
+      @article{Bruno_JExpBot2016,
+        author = {Bruno, Mark and Koschmieder, Julian and Wuest, Florian and Schaub, Patrick and Fehling-Kaschek, Mirjam and Timmer, Jens and Beyer, Peter and Al-Babili, Salim},
+        title = {Enzymatic study on {AtCCD4} and {AtCCD7} and their potential to form acyclic regulatory metabolites},
+        journal = {Journal of Experimental Botany},
+        year = {2016},
+        volume = {67},
+        number = {21},
+        pages = {5993--6005},
+        doi = {10.1093/jxb/erw356},
+      }

problems/Chen_MSB2009/metadata.yaml

@@ -1 +1,14 @@
 short_description: Large mass-action reaction network model of ErbB receptor signaling to ERK and AKT in response to EGF and heregulin.
+references:
+  - doi: 10.1038/msb.2008.74
+    bibtex: |
+      @article{Chen_MSB2009,
+        author = {Chen, William W. and Schoeberl, Birgit and Jasper, Paul J. and Niepel, Mario and Nielsen, Ulrik B. and Lauffenburger, Douglas A. and Sorger, Peter K.},
+        title = {Input–output behavior of {ErbB} signaling pathways as revealed by a mass action model trained against dynamic data},
+        journal = {Molecular Systems Biology},
+        year = {2009},
+        volume = {5},
+        number = {1},
+        pages = {239},
+        doi = {10.1038/msb.2008.74},
+      }

problems/Crauste_CellSystems2017/metadata.yaml

@@ -1 +1,14 @@
 short_description: Cell population model of CD8 T cell differentiation (naive, early/late effector, memory), fitted to cell counts in mice after vaccinia virus infection.
+references:
+  - doi: 10.1016/j.cels.2017.01.014
+    bibtex: |
+      @article{Crauste_CellSystems2017,
+        author = {Crauste, Fabien and Mafille, Julien and Boucinha, Lilia and Djebali, Sophia and Gandrillon, Olivier and Marvel, Jacqueline and Arpin, Christophe},
+        title = {Identification of Nascent Memory {CD8} {T} Cells and Modeling of Their Ontogeny},
+        journal = {Cell Systems},
+        year = {2017},
+        volume = {4},
+        number = {3},
+        pages = {306--317.e4},
+        doi = {10.1016/j.cels.2017.01.014},
+      }

problems/Elowitz_Nature2000/metadata.yaml

@@ -1 +1,14 @@
 short_description: Gene regulatory network model of the repressilator, a synthetic three-gene transcriptional oscillator in E. coli, fitted to a fluorescence time course.
+references:
+  - doi: 10.1038/35002125
+    bibtex: |
+      @article{Elowitz_Nature2000,
+        author = {Elowitz, Michael B. and Leibler, Stanislas},
+        title = {A synthetic oscillatory network of transcriptional regulators},
+        journal = {Nature},
+        year = {2000},
+        volume = {403},
+        number = {6767},
+        pages = {335--338},
+        doi = {10.1038/35002125},
+      }

problems/Fiedler_BMCSystBiol2016/metadata.yaml

@@ -1 +1,14 @@
 short_description: Reaction network model of RAF/MEK/ERK signaling with ERK feedback in HeLa cells, fitted to phospho-MEK/ERK data without and with RAF or MEK inhibitors.
+references:
+  - doi: 10.1186/s12918-016-0319-7
+    bibtex: |
+      @article{Fiedler_BMCSystBiol2016,
+        author = {Fiedler, Anna and Raeth, Sebastian and Theis, Fabian J. and Hausser, Angelika and Hasenauer, Jan},
+        title = {Tailored parameter optimization methods for ordinary differential equation models with steady-state constraints},
+        journal = {BMC Systems Biology},
+        year = {2016},
+        volume = {10},
+        number = {1},
+        pages = {80},
+        doi = {10.1186/s12918-016-0319-7},
+      }

problems/Froehlich_CellSystems2018/metadata.yaml

@@ -1 +1,14 @@
 short_description: Large-scale reaction network model of cancer signaling pathways, parameterized by cell-line-specific gene expression and fitted to drug response viability data.
+references:
+  - doi: 10.1016/j.cels.2018.10.013
+    bibtex: |
+      @article{Froehlich_CellSystems2018,
+        author = {Fröhlich, Fabian and Kessler, Thomas and Weindl, Daniel and Shadrin, Alexey and Schmiester, Leonard and Hache, Hendrik and Muradyan, Artur and Schütte, Moritz and Lim, Ji-Hyun and Heinig, Matthias and Theis, Fabian J. and Lehrach, Hans and Wierling, Christoph and Lange, Bodo and Hasenauer, Jan},
+        title = {Efficient Parameter Estimation Enables the Prediction of Drug Response Using a Mechanistic Pan-Cancer Pathway Model},
+        journal = {Cell Systems},
+        year = {2018},
+        volume = {7},
+        number = {6},
+        pages = {567--579.e6},
+        doi = {10.1016/j.cels.2018.10.013},
+      }

problems/Fujita_SciSignal2010/metadata.yaml

@@ -1 +1,14 @@
 short_description: Reaction network model of EGF-induced EGFR, Akt and S6 phosphorylation in PC12 cells under different EGF stimulation profiles.
+references:
+  - doi: 10.1126/scisignal.2000810
+    bibtex: |
+      @article{Fujita_SciSignal2010,
+        author = {Fujita, Kazuhiro A. and Toyoshima, Yu and Uda, Shinsuke and Ozaki, Yu-ichi and Kubota, Hiroyuki and Kuroda, Shinya},
+        title = {Decoupling of Receptor and Downstream Signals in the {Akt} Pathway by Its Low-Pass Filter Characteristics},
+        journal = {Science Signaling},
+        year = {2010},
+        volume = {3},
+        number = {132},
+        pages = {ra56},
+        doi = {10.1126/scisignal.2000810},
+      }

problems/Giordano_Nature2020/metadata.yaml

@@ -1 +1,14 @@
 short_description: Compartmental epidemiological model (SIDARTHE, distinguishing detected/undetected and symptom severity) of the COVID-19 epidemic in Italy.
+references:
+  - doi: 10.1038/s41591-020-0883-7
+    bibtex: |
+      @article{Giordano_Nature2020,
+        author = {Giordano, Giulia and Blanchini, Franco and Bruno, Raffaele and Colaneri, Patrizio and Di Filippo, Alessandro and Di Matteo, Angela and Colaneri, Marta},
+        title = {Modelling the {COVID-19} epidemic and implementation of population-wide interventions in {Italy}},
+        journal = {Nature Medicine},
+        year = {2020},
+        volume = {26},
+        number = {6},
+        pages = {855--860},
+        doi = {10.1038/s41591-020-0883-7},
+      }

problems/Isensee_JCB2018/metadata.yaml

@@ -1 +1,14 @@
 short_description: Reaction network model of cAMP-induced PKA activation and phosphorylation of its regulatory subunit in rat sensory neurons under pharmacological perturbations.
+references:
+  - doi: 10.1083/jcb.201708053
+    bibtex: |
+      @article{Isensee_JCB2018,
+        author = {Isensee, Jörg and Kaufholz, Melanie and Knape, Matthias J. and Hasenauer, Jan and Hammerich, Hanna and Gonczarowska-Jorge, Humberto and Zahedi, René P. and Schwede, Frank and Herberg, Friedrich W. and Hucho, Tim},
+        title = {{PKA-RII} subunit phosphorylation precedes activation by {cAMP} and regulates activity termination},
+        journal = {Journal of Cell Biology},
+        year = {2018},
+        volume = {217},
+        number = {6},
+        pages = {2167--2184},
+        doi = {10.1083/jcb.201708053},
+      }

problems/Lang_PLOSComputBiol2024/metadata.yaml

@@ -1 +1,14 @@
 short_description: Reaction network model of the human cell cycle, generated from a rule-based model and fitted to compartment-resolved single-cell imaging data of RPE-1 cells.
+references:
+  - doi: 10.1371/journal.pcbi.1011151
+    bibtex: |
+      @article{Lang_PLOSComputBiol2024,
+        author = {Lang, Paul F. and Penas, David R. and Banga, Julio R. and Weindl, Daniel and Novak, Bela},
+        title = {Reusable rule-based cell cycle model explains compartment-resolved dynamics of 16 observables in {RPE-1} cells},
+        journal = {PLOS Computational Biology},
+        year = {2024},
+        volume = {20},
+        number = {1},
+        pages = {e1011151},
+        doi = {10.1371/journal.pcbi.1011151},
+      }

problems/Laske_PLOSComputBiol2019/metadata.yaml

@@ -1 +1,14 @@
 short_description: Reaction network model of intracellular influenza A virus replication, fitted to viral RNA, genome import and virus release data in human A549 cells.
+references:
+  - doi: 10.1371/journal.pcbi.1006944
+    bibtex: |
+      @article{Laske_PLOSComputBiol2019,
+        author = {Laske, Tanja and Bachmann, Mandy and Dostert, Melanie and Karlas, Alexander and Wirth, Dagmar and Frensing, Timo and Meyer, Thomas F. and Hauser, Hansjörg and Reichl, Udo},
+        title = {Model-based analysis of influenza {A} virus replication in genetically engineered cell lines elucidates the impact of host cell factors on key kinetic parameters of virus growth},
+        journal = {PLOS Computational Biology},
+        year = {2019},
+        volume = {15},
+        number = {4},
+        pages = {e1006944},
+        doi = {10.1371/journal.pcbi.1006944},
+      }

problems/Liu_IFACPapersOnLine2025/metadata.yaml

@@ -1 +1,14 @@
 short_description: Population model of oncolytic virus therapy with uninfected and infected tumor cells and virus, fitted to tumor size data in zebrafish.
+references:
+  - doi: 10.1016/j.ifacol.2025.07.160
+    bibtex: |
+      @article{Liu_IFACPapersOnLine2025,
+        author = {Liu, Yuhong and Pathirana, Dilan and Hasenauer, Jan},
+        title = {Parameter Estimation and Model Selection for the Quantitative Analysis of Oncolytic Virus Therapy in Zebrafish},
+        journal = {IFAC-PapersOnLine},
+        year = {2025},
+        volume = {59},
+        number = {6},
+        pages = {289--294},
+        doi = {10.1016/j.ifacol.2025.07.160},
+      }

problems/Lucarelli_CellSystems2018/metadata.yaml

@@ -1 +1,14 @@
 short_description: Reaction network model of TGF-beta-induced SMAD complex formation and target gene expression.
+references:
+  - doi: 10.1016/j.cels.2017.11.010
+    bibtex: |
+      @article{Lucarelli_CellSystems2018,
+        author = {Lucarelli, Philippe and Schilling, Marcel and Kreutz, Clemens and Vlasov, Artyom and Boehm, Martin E. and Iwamoto, Nao and Steiert, Bernhard and Lattermann, Susen and Wäsch, Marvin and Stepath, Markus and Matter, Matthias S. and Heikenwälder, Mathias and Hoffmann, Katrin and Deharde, Daniela and Damm, Georg and Seehofer, Daniel and Muciek, Maria and Gretz, Norbert and Lehmann, Wolf D. and Timmer, Jens and Klingmüller, Ursula},
+        title = {Resolving the Combinatorial Complexity of {Smad} Protein Complex Formation and Its Link to Gene Expression},
+        journal = {Cell Systems},
+        year = {2018},
+        volume = {6},
+        number = {1},
+        pages = {75--89.e11},
+        doi = {10.1016/j.cels.2017.11.010},
+      }