Validation status of Data Readers

WhiteEtAl1986

Data from White et al. 1986, The Structure of the Nervous System of the Nematode Caenorhabditis elegans, Phil. Trans. R. Soc. Lond. B3141–340 (also on WormAtlas).

The primary source of this data is https://www.wormatlas.org/neuronalwiring.html, and the []

TODO...

TODO: add expected data file: /home/runner/work/ConnectomeToolbox/ConnectomeToolbox/cect/validation//White_A_expected_data.yaml: [Errno 2] No such file or directory: '/home/runner/work/ConnectomeToolbox/ConnectomeToolbox/cect/validation//White_A_expected_data.yaml'

TODO: add expected data file: /home/runner/work/ConnectomeToolbox/ConnectomeToolbox/cect/validation//White_L4_expected_data.yaml: [Errno 2] No such file or directory: '/home/runner/work/ConnectomeToolbox/ConnectomeToolbox/cect/validation//White_L4_expected_data.yaml'

TODO: add expected data file: /home/runner/work/ConnectomeToolbox/ConnectomeToolbox/cect/validation//White_whole_expected_data.yaml: [Errno 2] No such file or directory: '/home/runner/work/ConnectomeToolbox/ConnectomeToolbox/cect/validation//White_whole_expected_data.yaml'

VarshneyEtAl2011

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BentleyEtAl2016

Data from: The Multilayer Connectome of Caenorhabditis elegans, Bentley et al. 2016, PLoS Comput Biol 12(12): e1005283

Connectivity was originally released in supplementary information: S1 Dataset ("Included are edge lists for monoamine and neuropeptide networks").

Data on the extrasynaptic connections was accessed using the Worm Neuro Atlas package in the WormNeuroAtlasMAReader.

TODO: add expected data file: /home/runner/work/ConnectomeToolbox/ConnectomeToolbox/cect/validation//WormNeuroAtlasMAReader_expected_data.yaml: [Errno 2] No such file or directory: '/home/runner/work/ConnectomeToolbox/ConnectomeToolbox/cect/validation//WormNeuroAtlasMAReader_expected_data.yaml'

TODO: add expected data file: /home/runner/work/ConnectomeToolbox/ConnectomeToolbox/cect/validation//WormNeuroAtlasPepReader_expected_data.yaml: [Errno 2] No such file or directory: '/home/runner/work/ConnectomeToolbox/ConnectomeToolbox/cect/validation//WormNeuroAtlasPepReader_expected_data.yaml'

CookEtAl2019

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TODO: add expected data file: /home/runner/work/ConnectomeToolbox/ConnectomeToolbox/cect/validation//Cook2019HermDataReader_expected_data.yaml: [Errno 2] No such file or directory: '/home/runner/work/ConnectomeToolbox/ConnectomeToolbox/cect/validation//Cook2019HermDataReader_expected_data.yaml'

TODO: add expected data file: /home/runner/work/ConnectomeToolbox/ConnectomeToolbox/cect/validation//Cook2019MaleDataReader_expected_data.yaml: [Errno 2] No such file or directory: '/home/runner/work/ConnectomeToolbox/ConnectomeToolbox/cect/validation//Cook2019MaleDataReader_expected_data.yaml'

CookEtAl2020

Data was taken from Cook et al. 2020, The connectome of the Caenorhabditis elegans pharynx, J Comp Neurol. 2020; 528: 2767–2784.

The connectivity data was released in 2 CSV files in the supplementary information for that paper:

cne24932-sup-0004-Supinfo4.csv described as "Complete edge list for pharyngeal reconstruction."
cne24932-sup-0005-Supinfo5.csv described as "Inferred gap junction connectivity between end-organs". These connections have been included and some of these tested below also.

These files were opened in Apple Numbers, and the weights (numbers of connections between pairs of cells, electrical or chemical) were read off, to provide checks listed below.

Validation tests for Cook2020DataReader (Chemical synaptic connections)

Pre	Post	Expected weight	Match
I1R	I2R	3	Yes
I1R	I2L	1	Yes
RIPL	pm3VL	4	Yes

TODO: add total num nonzero connections

Validation tests for Cook2020DataReader (Electrical connections)

Pre	Post	Expected weight	Match
M4	pm5VL	1	Yes
e2DR	e3D	2	Yes
g1AL	M3L	2	Yes
pm1	pm2VL	3	Yes
mc1V	pm3VL	3	Yes
mc3V	pm7VL	3	Yes

TODO: add total num nonzero connections

Validation PASSED on 2026-05-19 with cect v0.3.1

BrittinEtAl2021

Data taken from: A multi-scale brain map derived from whole-brain volumetric reconstructions, Christopher A. Brittin, Steven J. Cook, David H. Hall, Scott W. Emmons & Netta Cohen, Nature 591, 105–110, 2021.

Supplementary data file 3 (41586_2021_3284_MOESM5_ESM.xlsx) containing the M^δ, C^δ and G^δ reference graphs was downloaded and used in the BrittinDataReader.

The M⁴ graph is the example used in Connectome Toolbox. Values for the contact area/weights in tab M, with delta = 4 were used for this, and the values below were read from the spreadsheet.

Validation tests for BrittinDataReader (Contact connections)

Pre	Post	Expected weight	Match
ADAL	ADLL	11319.5	Yes
ADLL	ADAL	11319.5	Yes
ADLR	ADAR	11319.5	Yes
ADLR	ADAR	11319.5	Yes
ADAR	ADLR	11319.5	Yes
RID	RICL	10043.5	Yes
RICL	RID	10043.5	Yes
RICR	RID	10043.5	Yes
RIAR	SIBVR	5114.25	Yes
AQR	RIAL	2010.75	Yes
AQR	RIAR	2010.75	Yes
RIAR	AQR	2010.75	Yes
RIAL	AQR	2010.75	Yes

Expected number of nonzero connection weights: 3850 (matches)

Validation PASSED on 2026-05-19 with cect v0.3.1

WitvlietEtAl2021

Data on neuronal connectivity at different developmental stages of C. elegans from: Connectomes across development reveal principles of brain maturation Witvliet et al. Nature 2021.

While the paper's supplementary information contained connectivity matrices (here), these only contain the chemical connections.

The 8 spreadsheet files (witvliet_2020_1 L1.xlsx, witvliet_2020_2 L1.xlsx, ..., witvliet_2020_8 adult.xlsx) hosted on WormWiring, also contain electrical connectivity, and are saved to our repository here, and used for the readers.

The chemical connection weights below were read from the supplementary information spreadsheet, and the electrial connection weights were taken from the WormWiring spreadheet.

Validation tests for WitvlietDataReader1 (Chemical synaptic connections)

Pre	Post	Expected weight	Match
AWAL	AWBL	2	Yes
AINR	AUAL	2	Yes
RIAL	RMDVR	6	Yes

Expected number of nonzero connection weights: 775 (matches)

Validation tests for WitvlietDataReader1 (Electrical connections)

Pre	Post	Expected weight	Match
ASHL	ADAL	9	Yes
RMDR	SMDVR	1	Yes
IL1R	IL1VR	2	Yes

Expected number of nonzero connection weights: 164 (matches)

Validation PASSED on 2026-05-19 with cect v0.3.1

Validation tests for WitvlietDataReader2 (Chemical synaptic connections)

Pre	Post	Expected weight	Match
ADLR	ASKR	4	Yes
AUAL	RIBL	3	Yes
AWBL	AIZL	2	Yes

Expected number of nonzero connection weights: 986 (matches)

Validation tests for WitvlietDataReader2 (Electrical connections)

Pre	Post	Expected weight	Match
AVJR	RIS	1	Yes
OLLL	OLLR	2	Yes
RIH	RIR	1	Yes

Expected number of nonzero connection weights: 246 (matches)

Validation PASSED on 2026-05-19 with cect v0.3.1

Validation tests for WitvlietDataReader3 (Chemical synaptic connections)

Pre	Post	Expected weight	Match
ADLR	ASKR	4	Yes
FLPR	FLPL	3	Yes
RIVL	GLRVR	2	Yes

Expected number of nonzero connection weights: 1012 (matches)

Validation tests for WitvlietDataReader3 (Electrical connections)

Pre	Post	Expected weight	Match
OLLR	RIGR	1	Yes
OLLL	OLLR	2	Yes
SMDDL	SMDDR	1	Yes

Expected number of nonzero connection weights: 186 (matches)

Validation PASSED on 2026-05-19 with cect v0.3.1

Validation tests for WitvlietDataReader4 (Chemical synaptic connections)

Pre	Post	Expected weight	Match
AWCR	AWCL	5	Yes
RIML	MDR04	2	Yes
RIVL	MVR07	1	Yes

Expected number of nonzero connection weights: 1136 (matches)

Validation tests for WitvlietDataReader4 (Electrical connections)

Pre	Post	Expected weight	Match
ALML	AVDR	2	Yes
AVER	URYVL	1	Yes
SMDDL	SMDDR	1	Yes

Expected number of nonzero connection weights: 415 (matches)

Validation PASSED on 2026-05-19 with cect v0.3.1

Validation tests for WitvlietDataReader5 (Chemical synaptic connections)

Pre	Post	Expected weight	Match
ADLR	ASHR	3	Yes
ALNR	SAAVR	2	Yes
BAGR	RIBL	13	Yes

Expected number of nonzero connection weights: 1515 (matches)

Validation tests for WitvlietDataReader5 (Electrical connections)

Pre	Post	Expected weight	Match
ADAR	ASHR	2	Yes
ADLL	CEPshVL	1	Yes
OLQVL	RIGL	2	Yes

Expected number of nonzero connection weights: 578 (matches)

Validation PASSED on 2026-05-19 with cect v0.3.1

Validation tests for WitvlietDataReader6 (Chemical synaptic connections)

Pre	Post	Expected weight	Match
ASER	ASEL	1	Yes
ASKR	AIAR	18	Yes
ALML	CEPVL	3	Yes

Expected number of nonzero connection weights: 1525 (matches)

Validation tests for WitvlietDataReader6 (Electrical connections)

Pre	Post	Expected weight	Match
AIZR	AWCL	2	Yes
BAGR	RIR	1	Yes
DVA	OLQVL	1	Yes

Expected number of nonzero connection weights: 426 (matches)

Validation PASSED on 2026-05-19 with cect v0.3.1

Validation tests for WitvlietDataReader7 (Chemical synaptic connections)

Pre	Post	Expected weight	Match
AQR	BAGR	4	Yes
ALNR	SAAVR	11	Yes
CEPDL	OLLL	7	Yes

Expected number of nonzero connection weights: 2202 (matches)

Validation tests for WitvlietDataReader7 (Electrical connections)

Pre	Post	Expected weight	Match
ADAL	PVQL	2	Yes
SIAVL	SMDVR	1	Yes
SAADL	SMBDL	2	Yes

Expected number of nonzero connection weights: 576 (matches)

Validation PASSED on 2026-05-19 with cect v0.3.1

Validation tests for WitvlietDataReader8 (Chemical synaptic connections)

Pre	Post	Expected weight	Match
ASER	AWCR	9	Yes
ALNL	SAAVL	10	Yes
ALML	BDUL	9	Yes

Expected number of nonzero connection weights: 2186 (matches)

Validation tests for WitvlietDataReader8 (Electrical connections)

Pre	Post	Expected weight	Match
ADFL	AIAL	3	Yes
AFDR	AIZR	1	Yes
PVT	RIBL	2	Yes

Expected number of nonzero connection weights: 612 (matches)

Validation PASSED on 2026-05-19 with cect v0.3.1

RandiEtAl2023

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RipollSanchezEtAl2023

Data on neuropeptidergic signalling has been taken from: Ripoll-Sánchez et al. 2023, The neuropeptidergic connectome of C. elegans. Neuron, Volume 111, Issue 22, 2023, Pages 3570-3589.e5.

There is a GitHub repository referenced in the paper: https://github.com/LidiaRipollSanchez/Neuropeptide-Connectome. There are 3 different models used for the neuropeptidergic connectome (short-, medium- and long-range), and the following files have been used in Connectome Toolbox as the source of these models:

For each of these CSV files, the file was opened in Apple Numbers, and the weights (numbers of matched peptides expressed in pre cell with corresponding receptor in post cell) read off, to provide checks listed below.

Validation tests for RipollSanchezShortRangeReader (Peptidergic connections)

Pre	Post	Expected weight	Match
I3	I5	3	Yes
URBL	RMDDL	4	Yes
RIVR	HSNL	6	Yes

Expected number of nonzero connection weights: 31417 (matches)

Validation PASSED on 2026-05-19 with cect v0.3.1

Validation tests for RipollSanchezMidRangeReader (Peptidergic connections)

Pre	Post	Expected weight	Match
PVR	I3	6	Yes
SABVL	VC1	1	Yes
RIR	AVKR	5	Yes

Expected number of nonzero connection weights: 40425 (matches)

Validation PASSED on 2026-05-19 with cect v0.3.1

Validation tests for RipollSanchezLongRangeReader (Peptidergic connections)

Pre	Post	Expected weight	Match
I3	I5	3	Yes
URBL	RMDDL	4	Yes
RIVR	HSNL	6	Yes
PVR	I3	6	Yes
SABVL	VC1	1	Yes
RIR	AVKR	5	Yes
VC4	I4	1	Yes
ALA	HSNR	11	Yes

Expected number of nonzero connection weights: 53558 (matches)

Validation PASSED on 2026-05-19 with cect v0.3.1

YimEtAl2024

Data on the dauer connectivity was obtained from the supplementary information of: Yim et al. 2024, Comparative connectomics of dauer reveals developmental plasticity Nature Communications, 15:1546.

Supplementary Data 3 links to file 41467_2024_45943_MOESM6_ESM.xlsx.

This file has been added to our repository here.

Contactome based/non-normalised data

The spreadsheet above contained a sheet named "Dauer", from where the values for the contact area of connections were read. This file was opened in Excel and weights of selected connections were visually read from the cells, noting the pre and post cells and added to the connection test yaml file.

Normalised data

The spreadsheet above contained a sheet named "Dauer_normalized", from where the values for the "normalized" connections were read. This file was opened in Excel and weights of selected connections were visually read from the cells, noting the pre and post cells and added to the connection test yaml file.

Validation tests for Yim2024NonNormDataReader (Contact connections)

Pre	Post	Expected weight	Match
RIH	CEPshDL	7464.984227	Yes
PVNL	ALMR	97686.4	Yes
URYDR	URADR	33663.09403	Yes

Expected number of nonzero connection weights: 2198 (matches)

Validation PASSED on 2026-05-19 with cect v0.3.1

Validation tests for Yim2024DataReader (Chemical synaptic connections)

Pre	Post	Expected weight	Match
ADFR	AFDR	0.428024049927915	Yes
SMBDL	RMED	6.01978135910464	Yes
ASHL	RIPL	1.20804164634321	Yes

Expected number of nonzero connection weights: 2198 (matches)

Validation PASSED on 2026-05-19 with cect v0.3.1

WangEtAl2025

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TODO: add expected data file: /home/runner/work/ConnectomeToolbox/ConnectomeToolbox/cect/validation//Wang2024MaleDataReader_expected_data.yaml: [Errno 2] No such file or directory: '/home/runner/work/ConnectomeToolbox/ConnectomeToolbox/cect/validation//Wang2024MaleDataReader_expected_data.yaml'