Resolve R1-R8 desert_farm_leverage_points + add BioNumbers subset#26
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R1: CO2 fixation Time_min 7.69E-03 → 6.67E-02 (Bar-On natural kcat ceiling, 15/s)
R2: Replace Moore et al. 2013 mis-citations on Nutrient transport, Biochemical
synthesis, and Cell growth with Milo & Phillips (2015) Cell Biology by
the Numbers
R3: Rename Growth → Cell growth; tighten bounds to single algal cell scope
(Time 1e3-1e5 s, Space 1e-18 to 1e-14 m³). Population scales remain
covered by Community Ecology row.
R4: MD Space_max 1e-27 → 1e-22 m³ (modern atomistic-MD reach)
R5: Community Metabolic Models Time_min 99 → 1.00E+02 (formatting consistency)
R6: Fill empty Reference cells:
- Molecular Dynamics Models: Karplus & McCammon (2002) Nat Struct Biol 9:646
- Community Metabolic Models: Zakem et al. (2020) ISME J 14:288
- Biogeochemical Circulation Models: Levine et al. (2025) Annu Rev
Earth Planet Sci 53:595
R7: Rename Extraction → Fossil-fuel formation; Time bounds 3.16E+13 to
3.16E+15 s reflect formation duration rather than deposit age
R8: Extend CO2 fixation Reference text to justify both time and space bounds
25 entries justifying time/space bounds for Cell growth (8), Biochemical synthesis (8), and Nutrient transport (9) rows. Phototroph-specific where available; generic-organism proxies (E. coli, Xenopus, generic) used where phototroph data was unavailable. Each entry includes direct URL to BioNumbers page.
Schema, curation criteria, known gaps (including the Cell growth Time_min mismatch flagged by phototroph data), update procedure, and BioNumbers attribution per Milo et al. (2010) Nucleic Acids Res 38:D750.
The Time bound for cell division varies by ~3 OOM across phyla. The previous 'Cell growth' label silently scoped to phototrophs (since Time_min was set based on phototroph cell-cycle data). Rename makes the implicit organism scope explicit. Time_min 1.00E+03 → 7.56E+03 s (2.1 h, Synechococcus elongatus UTEX 2973 — currently fastest known photoautotroph). Anchored to Yu et al. (2015) Sci Rep 5:8132. Reference cell extended to cite both Milo & Phillips and Yu et al.
Sibling file to bionumbers_subset.csv for entries from primary literature where BioNumbers either has no value (NaN) or no entry. Initial entry: Synechococcus elongatus UTEX 2973 doubling time 2.1 h from Yu et al. (2015) Sci Rep 5:8132 — anchors the Time_min for the Photoautotroph cell growth row. BioNumbers entry 112484 exists for this strain but has NaN Value, hence the supplementary citation.
- Add phototroph_growth_supplementary.csv documentation and schema - Remove the 'Cell growth Time_min mismatch' known gap (now resolved by anchoring to UTEX 2973 in supplementary file) - Update curation criteria to reflect Photoautotroph cell growth rename and the BioNumbers-NaN → supplementary workflow - Restructure 'Known gaps' to reflect current state
Matches the R3 rename in desert_farm_leverage_points.csv. The supplementary file already used the new name; this aligns the BioNumbers subset so the Cited_in_row join key works for all 26 entries.
Discoverable cross-link from main CSV to data/references/ for the rows backed by curated BioNumbers / primary-literature data: Nutrient transport, Biochemical synthesis, Photoautotroph cell growth. Non-breaking — Reference column is free-form display text.
Per Madison's clarification: BioNumbers data is meant as a standalone resource for future work, not as a backing-data layer for the main CSV. Changes: - Drop (see data/references/) markers from 3 Reference cells in desert_farm_leverage_points.csv (main CSV stands alone) - Drop Cited_in_row column from bionumbers_subset.csv (no longer a join key into the main CSV) - Delete phototroph_growth_supplementary.csv (its only entry was UTEX 2973 / Yu 2015 / 2.1h doubling, already inline-cited in the main CSV's Photoautotroph cell growth Reference cell) - Rewrite README.md to describe bionumbers_subset.csv as a standalone phototroph reference set, removing all cross-linking schema docs
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Resolves R1–R8 data concerns + adds a standalone curated BioNumbers subset.
Supersedes #25 (which fell behind main during the BioNumbers addition; rebuilt fresh from current main per branch-hygiene rule).
Changes to
data/datasets/desert_farm_leverage_points.csvTime_min7.69e-3 → 6.67e-2 (Bar-On natural RuBisCO kcat ceiling, 15/s)Community EcologySpace_max1e-27 → 1e-22 m³ (modern atomistic MD reaches 100-nm boxes)Time_min99→1.00E+02New:
data/references/(standalone resource)Curated phototroph reference data, not coupled to the main CSV — kept as a resource for future work.
bionumbers_subset.csv— 25 entries from the BioNumbers database with stablebion_ididentifiers and direct URLs. Phototroph-relevant (cyanobacteria, green algae, diatoms) across cell generation/doubling times, biochemical synthesis rates (transcription/translation elongation), and small-molecule diffusion / transporter kinetics. Generic-organism proxies (e.g., E. coli, Xenopus) used where phototroph-specific entries were unavailable; flagged per-row inOrganism.README.md— schema, scope, attribution.