Biological rhythms dataset
Versioned frequencies of life, from sperm beat to embryonic heart rate, each with a DOI.
- Repository
biological-rhythms-dataseton GitHub- Cite
- doi:10.5281/zenodo.24038799 (all versions, via Zenodo)
- Layer
- Layer 1
- Licences
- PolyForm-Noncommercial-1.0.0 · CC-BY-NC-4.0
- Status
- released
Claims
| Claim | Level | Statement | Evidence |
|---|---|---|---|
bio:INTERPOLATION-AT-MEASUREMENTS v1.0.0 | P | Linear interpolation between two measurements taken at different times returns each measurement exactly at its own time. | |
bio:INTERPOLATION-BOUNDED v1.0.0 | P | Between two measurements, linear interpolation never leaves the range they span: it is at least the smaller measured value and at most the larger. | |
bio:HEART-RATE-WEEK-PLACEMENT v1.0.0 | M | heart_rate_at places the Ouyang et al. 2020 median for gestational week w at w + 0.5 weeks, the middle of that week. (Homo sapiens; Each binned median placed at the middle of its bin, checked against the regression of heart rate on gestational week in the paper's abstract) | |
bio:HEART-RATE-AT v1.0.0 | T | heart_rate_at(w) returns each Ouyang et al. 2020 weekly median exactly at the middle of its week (6.5, 7.5, 8.5, 9.5 and 10.5 weeks; bio:HEART-RATE-WEEK-PLACEMENT), interpolates linearly between neighbouring medians to within 1e-15 relative of an exact rational oracle, stays between the two bracketing medians in floating point too, and rejects weeks outside [6.5, 10.5]. |
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bio:CELL-COUNT-AT v1.0.0 | T | cell_count_at(h) is 1 before t2 and k from the mean time tk until the next division (k = 2 to 8), using the Lorenzo Rodríguez et al. 2026 means, and rejects hours below 0 or after t8, where the dataset has no division times. |
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bio:FREQUENCY-HZ v1.0.0 | T | frequency_hz(id) converts every period, frequency and rate in the dataset to its range in hertz with rhythm-units (f = 1/T for a period, bpm/60 for a rate), matching an exact rational oracle to within 1e-15 relative, and rejects durations, time points, stages and counts. |
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bio:DATASET-CONSISTENT v1.0.0 | T | data/rhythms.yaml matches its JSON Schema; every entry is one species, named in its id and its description, with a method and at least one source that has a DOI or PMID; and data/rhythms.json, data/rhythms.csv, the R claims in this ledger and the README tables are exactly what scripts/build.py generates from it, which CI checks on every push. | |
bio:IMPLEMENTATIONS-AGREE v1.0.0 | T | The Rust crate, the Python bindings and the WebAssembly bindings return the same records, unchanged from data/rhythms.json, and the same helper results on every shared golden vector. | |
bio:HUMAN-CA-SPIKE-INTERVAL v1.0.0 | R | Interval between Ca2+ spikes in human eggs at fertilisation: 10–35 min (range; n = 10 eggs with Ca2+ transients, of 26 inseminated). (Homo sapiens; Aequorin Ca2+ measurement with a photomultiplier in eggs donated during IVF treatment, zona-intact and zona-free, inseminated under perfusion) | |
bio:HUMAN-CA-SPIKE-DURATION v1.0.0 | R | Duration of each Ca2+ spike in human eggs at fertilisation: 120 s (approximate; n = 10 eggs with Ca2+ transients, of 26 inseminated). (Homo sapiens; Aequorin Ca2+ measurement with a photomultiplier in eggs donated during IVF treatment, zona-intact and zona-free, inseminated under perfusion) | |
bio:MOUSE-CA-SPIKE-INTERVAL v1.0.0 | R | Interval between Ca2+ transients in mouse eggs at fertilisation: 3.4 min (mean). (Mus musculus; Fluo-3 Ca2+ imaging of zona-free eggs during in vitro fertilisation) | |
bio:MOUSE-CA-FIRST-TRANSIENT-DURATION v1.0.0 | R | Duration of the first Ca2+ transient in mouse eggs at fertilisation: 2.3 min (mean). (Mus musculus; Fluo-3 Ca2+ imaging of zona-free eggs during in vitro fertilisation) | |
bio:MOUSE-CA-SPIKE-DURATION v1.0.0 | R | Duration of each later Ca2+ transient in mouse eggs at fertilisation: 0.5 min (mean). (Mus musculus; Fluo-3 Ca2+ imaging of zona-free eggs during in vitro fertilisation) | |
bio:MOUSE-ZINC-SPARK-INTERVAL v1.0.0 | R | Interval between zinc sparks in activated mouse eggs: 9.5 min (mean; n = 36 intervals between sparks). (Mus musculus; Imaging of zinc released into the medium with an extracellular zinc dye, alongside intracellular Ca2+ imaging) | |
bio:MOUSE-EGG-ZINC-VESICLES v1.0.0 | R | Number of zinc-loaded cortical vesicles in a mouse egg: 8,000 vesicles (estimate). (Mus musculus; Live zinc-probe imaging, scanning transmission electron microscopy with energy-dispersive spectroscopy, and X-ray fluorescence microscopy and tomography) | |
bio:MOUSE-ZINC-VESICLE-ATOMS v1.0.0 | R | Zinc atoms in one cortical vesicle of a mouse egg: 1,000,000 atoms (approximate). (Mus musculus; Live zinc-probe imaging, scanning transmission electron microscopy with energy-dispersive spectroscopy, and X-ray fluorescence microscopy and tomography) | |
bio:HUMAN-ZINC-SPARKS-PER-EGG v1.0.0 | R | Number of zinc sparks in a human egg activated with PLCζ: 1 spark (observed; n = 2 eggs that sparked, of 5 injected with hPLCζ cRNA). (Homo sapiens; Fluo-4 Ca2+ imaging and extracellular FluoZin-3 zinc imaging of discarded immature eggs from ICSI cycles, mostly matured in vitro; other eggs in the study were activated with Ca-ionomycin or ionomycin) | |
bio:HUMAN-SPERM-BEAT-DILUTED-SEMEN v1.0.0 | R | Flagellar beat frequency of human sperm swimming in diluted semen: 19 Hz (median; n = 205 cells). (Homo sapiens; High-speed imaging at 169.2 frames/s with automated flagellar tracking (FAST) of free-swimming progressive cells; three donors in total) | |
bio:HUMAN-SPERM-BEAT-VISCOUS v1.0.0 | R | Flagellar beat frequency of human sperm swimming in a high-viscosity medium: 10 Hz (median; n = 119 cells). (Homo sapiens; High-speed imaging at 169.2 frames/s with automated flagellar tracking (FAST) of free-swimming progressive cells; three donors in total) | |
bio:HUMAN-SPERM-BEAT-ADHERED v1.0.0 | R | Flagellar beat frequency of head-adhered human sperm before stimulation: 18.9 Hz (median; n = 34 cells from 4 donors). (Homo sapiens; High-speed imaging at 332 frames/s of head-adhered cells at 21 °C, the same cells before and after 4-aminopyridine (4-AP)) | |
bio:HUMAN-SPERM-BEAT-HYPERACTIVATED v1.0.0 | R | Flagellar beat frequency of head-adhered human sperm hyperactivated with 4-AP: 11.7 Hz (median; n = 34 cells from 4 donors). (Homo sapiens; High-speed imaging at 332 frames/s of head-adhered cells at 21 °C, the same cells before and after 4-aminopyridine (4-AP)) | |
bio:HUMAN-OVIDUCT-CILIA-BEAT v1.0.0 | R | Ciliary beat frequency in the human fallopian tube: 5.3 Hz (mean; n = 26 women (14 in the proliferative, 12 in the secretory phase)). (Homo sapiens; Light-intensity variation recording of ciliary beating in tubes removed at hysterectomy for benign conditions) | |
bio:MOUSE-OVIDUCT-CILIA-BEAT v1.0.0 | R | Ciliary beat frequency in the mouse fallopian tube: 23.3 Hz (mean; n = 19 mice). (Mus musculus; High-speed bright-field imaging at 35 °C of tube pieces held still by a motorised needle) | |
bio:HUMAN-UTERINE-CONTRACTIONS-LATE-FOLLICULAR v1.0.0 | R | Human uterine contraction frequency in the late follicular phase: 1.61 per min (as reported; n = 70 recordings analysed across all phases together, of 96 from 64 healthy women with natural cycles; the number in each phase is not recorded here). (Homo sapiens; Four-minute transvaginal ultrasound recordings analysed by speckle tracking; contraction frequency of the posterior uterine wall) | |
bio:HUMAN-UTERINE-CONTRACTIONS-MENSTRUAL v1.0.0 | R | Human uterine contraction frequency in the menstrual phase: 1.31 per min (as reported; n = 70 recordings analysed across all phases together, of 96 from 64 healthy women with natural cycles; the number in each phase is not recorded here). (Homo sapiens; Four-minute transvaginal ultrasound recordings analysed by speckle tracking; contraction frequency of the posterior uterine wall) | |
bio:HUMAN-UTERINE-CONTRACTIONS-LATE-LUTEAL v1.0.0 | R | Human uterine contraction frequency in the late luteal phase: 1.35 per min (as reported; n = 70 recordings analysed across all phases together, of 96 from 64 healthy women with natural cycles; the number in each phase is not recorded here). (Homo sapiens; Four-minute transvaginal ultrasound recordings analysed by speckle tracking; contraction frequency of the posterior uterine wall) | |
bio:HUMAN-EMBRYO-T2 v1.0.0 | R | Time from insemination to the 2-cell stage (t2) in human embryos: 27.48 h (mean; n = 2,523 correctly fertilised oocytes in the fresh-sperm group (the group size, not the number of embryos timed at each stage, which is not recorded here)). (Homo sapiens; Time-lapse imaging of embryos from oocyte-donation cycles fertilised with fresh ejaculated partner sperm (mostly ICSI); single-centre retrospective cohort of 469 cycles, 2013-2020) | |
bio:HUMAN-EMBRYO-T3 v1.0.0 | R | Time from insemination to the 3-cell stage (t3) in human embryos: 37.78 h (mean; n = 2,523 correctly fertilised oocytes in the fresh-sperm group (the group size, not the number of embryos timed at each stage, which is not recorded here)). (Homo sapiens; Time-lapse imaging of embryos from oocyte-donation cycles fertilised with fresh ejaculated partner sperm (mostly ICSI); single-centre retrospective cohort of 469 cycles, 2013-2020) | |
bio:HUMAN-EMBRYO-T4 v1.0.0 | R | Time from insemination to the 4-cell stage (t4) in human embryos: 40.4 h (mean; n = 2,523 correctly fertilised oocytes in the fresh-sperm group (the group size, not the number of embryos timed at each stage, which is not recorded here)). (Homo sapiens; Time-lapse imaging of embryos from oocyte-donation cycles fertilised with fresh ejaculated partner sperm (mostly ICSI); single-centre retrospective cohort of 469 cycles, 2013-2020) | |
bio:HUMAN-EMBRYO-T5 v1.0.0 | R | Time from insemination to the 5-cell stage (t5) in human embryos: 51.04 h (mean; n = 2,523 correctly fertilised oocytes in the fresh-sperm group (the group size, not the number of embryos timed at each stage, which is not recorded here)). (Homo sapiens; Time-lapse imaging of embryos from oocyte-donation cycles fertilised with fresh ejaculated partner sperm (mostly ICSI); single-centre retrospective cohort of 469 cycles, 2013-2020) | |
bio:HUMAN-EMBRYO-T6 v1.0.0 | R | Time from insemination to the 6-cell stage (t6) in human embryos: 54.25 h (mean; n = 2,523 correctly fertilised oocytes in the fresh-sperm group (the group size, not the number of embryos timed at each stage, which is not recorded here)). (Homo sapiens; Time-lapse imaging of embryos from oocyte-donation cycles fertilised with fresh ejaculated partner sperm (mostly ICSI); single-centre retrospective cohort of 469 cycles, 2013-2020) | |
bio:HUMAN-EMBRYO-T7 v1.0.0 | R | Time from insemination to the 7-cell stage (t7) in human embryos: 57.57 h (mean; n = 2,523 correctly fertilised oocytes in the fresh-sperm group (the group size, not the number of embryos timed at each stage, which is not recorded here)). (Homo sapiens; Time-lapse imaging of embryos from oocyte-donation cycles fertilised with fresh ejaculated partner sperm (mostly ICSI); single-centre retrospective cohort of 469 cycles, 2013-2020) | |
bio:HUMAN-EMBRYO-T8 v1.0.0 | R | Time from insemination to the 8-cell stage (t8) in human embryos: 61.51 h (mean; n = 2,523 correctly fertilised oocytes in the fresh-sperm group (the group size, not the number of embryos timed at each stage, which is not recorded here)). (Homo sapiens; Time-lapse imaging of embryos from oocyte-donation cycles fertilised with fresh ejaculated partner sperm (mostly ICSI); single-centre retrospective cohort of 469 cycles, 2013-2020) | |
bio:HUMAN-EMBRYO-TM v1.0.0 | R | Time from insemination to compaction (tM, morula) in human embryos: 87.75 h (mean; n = 2,523 correctly fertilised oocytes in the fresh-sperm group (the group size, not the number of embryos timed at each stage, which is not recorded here)). (Homo sapiens; Time-lapse imaging of embryos from oocyte-donation cycles fertilised with fresh ejaculated partner sperm (mostly ICSI); single-centre retrospective cohort of 469 cycles, 2013-2020) | |
bio:HUMAN-EMBRYO-TSB v1.0.0 | R | Time from insemination to the start of blastulation (tSB) in human embryos: 99.18 h (mean; n = 2,523 correctly fertilised oocytes in the fresh-sperm group (the group size, not the number of embryos timed at each stage, which is not recorded here)). (Homo sapiens; Time-lapse imaging of embryos from oocyte-donation cycles fertilised with fresh ejaculated partner sperm (mostly ICSI); single-centre retrospective cohort of 469 cycles, 2013-2020) | |
bio:HUMAN-EMBRYO-TB v1.0.0 | R | Time from insemination to the full blastocyst (tB) in human embryos: 104.5 h (mean; n = 2,523 correctly fertilised oocytes in the fresh-sperm group (the group size, not the number of embryos timed at each stage, which is not recorded here)). (Homo sapiens; Time-lapse imaging of embryos from oocyte-donation cycles fertilised with fresh ejaculated partner sperm (mostly ICSI); single-centre retrospective cohort of 469 cycles, 2013-2020) | |
bio:HUMAN-EMBRYO-TEB v1.0.0 | R | Time from insemination to the expanded blastocyst (tEB) in human embryos: 110.82 h (mean; n = 2,523 correctly fertilised oocytes in the fresh-sperm group (the group size, not the number of embryos timed at each stage, which is not recorded here)). (Homo sapiens; Time-lapse imaging of embryos from oocyte-donation cycles fertilised with fresh ejaculated partner sperm (mostly ICSI); single-centre retrospective cohort of 469 cycles, 2013-2020) | |
bio:HUMAN-EHR-6W v1.0.0 | R | Median human embryonic heart rate at 6 weeks of gestation: 117 bpm (median; n = 20,272 pregnancies measured in this gestational week (Table 3 of the paper; 30,416 across weeks 6-10)). (Homo sapiens; Early ultrasound measurements in singleton IVF-ET pregnancies with phenotypically normal live births after 37 weeks, 2010-2016; 5th, 50th and 95th percentiles by gestational week) | |
bio:HUMAN-EHR-7W v1.0.0 | R | Median human embryonic heart rate at 7 weeks of gestation: 146 bpm (median; n = 2,969 pregnancies measured in this gestational week (Table 3 of the paper; 30,416 across weeks 6-10)). (Homo sapiens; Early ultrasound measurements in singleton IVF-ET pregnancies with phenotypically normal live births after 37 weeks, 2010-2016; 5th, 50th and 95th percentiles by gestational week) | |
bio:HUMAN-EHR-8W v1.0.0 | R | Median human embryonic heart rate at 8 weeks of gestation: 174 bpm (median; n = 4,109 pregnancies measured in this gestational week (Table 3 of the paper; 30,416 across weeks 6-10)). (Homo sapiens; Early ultrasound measurements in singleton IVF-ET pregnancies with phenotypically normal live births after 37 weeks, 2010-2016; 5th, 50th and 95th percentiles by gestational week) | |
bio:HUMAN-EHR-9W v1.0.0 | R | Median human embryonic heart rate at 9 weeks of gestation: 176 bpm (median; n = 2,267 pregnancies measured in this gestational week (Table 3 of the paper; 30,416 across weeks 6-10)). (Homo sapiens; Early ultrasound measurements in singleton IVF-ET pregnancies with phenotypically normal live births after 37 weeks, 2010-2016; 5th, 50th and 95th percentiles by gestational week) | |
bio:HUMAN-EHR-10W v1.0.0 | R | Median human embryonic heart rate at 10 weeks of gestation: 174 bpm (median; n = 799 pregnancies measured in this gestational week (Table 3 of the paper; 30,416 across weeks 6-10)). (Homo sapiens; Early ultrasound measurements in singleton IVF-ET pregnancies with phenotypically normal live births after 37 weeks, 2010-2016; 5th, 50th and 95th percentiles by gestational week) | |
bio:HUMAN-SEGMENTATION-CLOCK-PERIOD v1.0.0 | R | Period of the human segmentation clock in presomitic mesoderm cells derived in vitro: 5 h (approximate). (Homo sapiens; Time-lapse imaging of oscillating segmentation-clock gene expression (such as HES7) in presomitic mesoderm induced in vitro from pluripotent stem cells) | |
bio:MOUSE-SEGMENTATION-CLOCK-PERIOD v1.0.0 | R | Period of the mouse segmentation clock in presomitic mesoderm cells derived in vitro: 2–3 h (range). (Mus musculus; Time-lapse imaging of oscillating segmentation-clock gene expression (such as HES7) in presomitic mesoderm induced in vitro from pluripotent stem cells) | |
bio:HUMAN-MAJOR-ZGA-STAGE v1.0.0 | R | Cell stage of major embryonic genome activation in human embryos: 4–8 cells (range). (Homo sapiens; Patterns of newly synthesised polypeptides in IVF embryos and their dependence on transcription) | |
bio:HUMAN-MINOR-ZGA-STAGE v1.0.0 | R | Cell stage at which human embryonic transcription begins (minor genome activation): 1 cell (observed). (Homo sapiens; High-resolution single-cell RNA sequencing of MII oocytes and bipronuclear one-cell embryos) | |
bio:MOUSE-MAJOR-ZGA-STAGE v1.0.0 | R | Cell stage of major zygotic genome activation in mouse embryos: 2 cells (as reported). (Mus musculus; Review of transcriptome and transcription-inhibition studies of mouse embryos) | |
bio:MOUSE-MINOR-ZGA-STAGE v1.0.0 | R | Cell stage of minor zygotic genome activation in mouse embryos: 1 cell (as reported). (Mus musculus; Review of transcriptome and transcription-inhibition studies of mouse embryos) | |
Depends on
rhythm-unitsreleasedevidence-kernelreleased
Used by
egg-activation-modelsreleasedfertilization-sonificationplannedfrequencies-of-lifeplannedfrequency-beginning-of-life-reportplannedegg-rhythm-predictorplanned
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