Overview

Information on published connectomics data related to C. elegans. This is being developed as part of the OpenWorm project.

Please note: this is a Work in Progress! Please get in contact if you are interested in contributing to this resource!

Example plots

Some of the generated views of the connectomics datasets covered here. Click on the images for more details.

Historical publications on C. elegans connectomics

block-beta
columns 4

t1["<b>Anatomical - Chemical/electrical</b>"]
t2["<b>Extrasynaptic</b>"]
t4["<b>Gene/protein expression</b>"]
t3["<b>Functional</b>"]

  style t1 fill:#ff6666
  style t2 fill:#99bbff
  style t3 fill:#ff80ff
  style t4 fill:#85e085

block-beta

columns 4

  block:70sA
    columns 1
    space    
    A1("<b><a href='http://openworm.org/ConnectomeToolbox/Albertson_1976/'>Albertson and Thomson 1976</a></b>")
    space space space
  end

  block:70sB
    columns 1
    space
  end

  block:70sC
    columns 1
    space
  end

  block:70sD
    columns 1
    space
  end

  block:80sA
    columns 1
    A("<b><a href='http://openworm.org/ConnectomeToolbox/White_1986/' >White et al. 1986</a></b>")
    space
    B("<b><a href='http://openworm.org/ConnectomeToolbox/Durbin_1987/' >Durbin 1987</a></b>")
    space
    space
  end

  block:80sB
    columns 1
    space
  end

  block:80sC
    columns 1
    space
  end

  block:80sD
    columns 1
    space
  end

  block:90sA
    columns 1
    space
    A2("<b><a href='http://openworm.org/ConnectomeToolbox/Hall_1991/'>Hall & Russell 1991</a></b>") space space space
  end

  block:90sB
    columns 1
    space
  end

  block:90sC
    columns 1
    space
  end

  block:90sD
    columns 1
    space
  end

  block:00sA
    columns 1
    space
  end

  block:00sB
    columns 1
    space
  end

  block:00sC
    columns 1
    C("<b><a href='http://openworm.org/ConnectomeToolbox/Altun_2009/'>Altun et al. 2009</a></b>")
    space space space
  end

  block:00sD
    columns 1
    space
  end

  block:10sA
    columns 1
    D("<b><a href='http://openworm.org/ConnectomeToolbox/Varshney_2011/'>Varshney et al.2011</a></b>") 
    G("<b><a href='http://openworm.org/ConnectomeToolbox/Cook_2019/'>Cook et al. 2019</a></b>") 
    space
    space
  end

  block:10sB
    columns 1
    E1("<b><a href='http://openworm.org/ConnectomeToolbox/Serrano_2013/'>Serrano-Saiz et al. 2013</a></b>") 
    E("<b><a href='http://openworm.org/ConnectomeToolbox/Pereira_2015/'>Pereira et al. 2015</a></b>")
    E2("<b><a href='http://openworm.org/ConnectomeToolbox/Gendrel_2016/'>Gendrel, Hobert & Atlas 2016</a></b>")
    F("<b><a href='http://openworm.org/ConnectomeToolbox/Bentley_2016/'>Bentley et al. 2016</a></b>")
  end
  block:10sC
    columns 1
    space
  end
  block:10sD
    columns 1
    space
  end


  block:20sA
    columns 1
    I("<b><a href='http://openworm.org/ConnectomeToolbox/Cook_2020/'>Cook et al. 2020</a></b>")
    J("<b><a href='http://openworm.org/ConnectomeToolbox/Brittin_2021'>Brittin et al. 2021</a></b>")
    K("<b><a href='http://openworm.org/ConnectomeToolbox/Witvliet_2021'>Witvliet et al. 2021</a></b>")
    space
  end    

  block:20sB
    columns 1
    NP("<b><a href='http://openworm.org/ConnectomeToolbox/Ripoll_2023'>Ripoll-Sanchez et al. 2023</a></b>")
    space
    space
    space
  end    

  block:20sC
    columns 1
    L("<b><a href='http://openworm.org/ConnectomeToolbox/Taylor_2021'>Taylor et al. 2021</a></b>")
    M("<b><a href='http://openworm.org/ConnectomeToolbox/Yemini_2021'>Yemini et al. 2021</a></b>")
    N("<b><a href='http://openworm.org/ConnectomeToolbox/Beets_2023'>Beets et al. 2023</a></b>")
    space
  end    
  block:20sD
    columns 1
    H("<b><a href='http://openworm.org/ConnectomeToolbox/Fenyves_2020/'>Fenyves et al.2020</a></b>") 
    P("<b><a href='http://openworm.org/ConnectomeToolbox/Randi_2023'>Randi et al. 2023</a></b>")
    R("<b><a href='http://openworm.org/ConnectomeToolbox/Dag_2023'>Dag et al. 2023</a></b>")
    T("<b><a href='http://openworm.org/ConnectomeToolbox/Atanas_2023'>Atanas et al. 2023</a></b>")
  end     

    E --> H
    E1 --> H
    E2 --> H
    E --> F
    C --> L
    L --> M
    M --> N
    A --> B
    A1 --> A
    A1 --> I
    A  --> A2
    A --> D
    B --> D
    A2 --> D
    A --> G
    A --> I
    A --> J
    A --> F
    D --> F
    A --> NP
    A1 --> NP
    F --> NP
    L --> NP
    K --> NP
    D --> NP
    A --> P
    L --> P
    N --> P
    K --> P
    NP --> P
    F --> P
    M --> R
    T --> R
    A --> R
    K --> R
    A --> T
    K --> T

  style 70sA fill:#eeeeee
  style 70sB fill:#eeeeee
  style 70sC fill:#eeeeee
  style 70sD fill:#eeeeee

  style 80sA fill:#dddddd
  style 80sB fill:#dddddd
  style 80sC fill:#dddddd
  style 80sD fill:#dddddd

  style 90sA fill:#cccccc
  style 90sB fill:#cccccc
  style 90sC fill:#cccccc
  style 90sD fill:#cccccc

  style 00sA fill:#bbbbbb
  style 00sB fill:#bbbbbb
  style 00sC fill:#bbbbbb
  style 00sD fill:#bbbbbb

  style 10sA fill:#aaaaaa
  style 10sB fill:#aaaaaa
  style 10sC fill:#aaaaaa
  style 10sD fill:#aaaaaa

  style 20sA fill:#999999
  style 20sB fill:#999999
  style 20sC fill:#999999
  style 20sD fill:#999999

  style A1 fill:#ff6666
  style A fill:#ff6666
  style B fill:#ff6666
  style A2 fill:#ff6666
  style D fill:#ff6666
  style J fill:#ff6666
  style K fill:#ff6666
  style G fill:#ff6666
  style I fill:#ff6666

  style E fill:#99bbff
  style E1 fill:#99bbff
  style E2 fill:#99bbff
  style F fill:#99bbff
  style NP fill:#99bbff

  style H fill:#ff80ff
  style P fill:#ff80ff
  style R fill:#ff80ff
  style T fill:#ff80ff

  style C fill:#85e085
  style L fill:#85e085
  style M fill:#85e085
  style N fill:#85e085

Another view on the data

%%{ init: { 'flowchart': { 'curve': 'stepAfter' } } }%%
flowchart TD
    classDef anat fill:#ff6666
    classDef gene fill:#85e085
    classDef es fill:#99bbff
    classDef func fill:#ff80ff


    subgraph 1970-1980
    A1["<a href='http://openworm.org/ConnectomeToolbox/Albertson_1976/' >Albertson & Thomson 1976</a>"]:::anat
    end
    subgraph 1980-1990
    A["<a href='http://openworm.org/ConnectomeToolbox/White_1986/' >White et al. 1986</a>"]:::anat & B["<a href='http://openworm.org/ConnectomeToolbox/Durbin_1987/' >Durbin 1987</a>"]:::anat
    end

    subgraph 1990-2000
    A2["<a href='http://openworm.org/ConnectomeToolbox/Hall_1991/' >Hall & Russell 1991</a>"]:::anat
    end

    subgraph 2000-2010
    C["<a href='http://openworm.org/ConnectomeToolbox/Altun_2009/' >Altun et al. 2009</a>"]:::gene 
    end

    subgraph 2010-2020
    D["<a href='http://openworm.org/ConnectomeToolbox/Varshney_2011/' >Varshney et al.2011</a>"]:::anat & E["<a href='http://openworm.org/ConnectomeToolbox/Pereira_2015/' >Pereira et al. 2015</a>"]:::es & E1["<a href='http://openworm.org/ConnectomeToolbox/Serrano_2013/' >Serrano-Saiz et al. 2013</a>"]:::es  & E2["<a href='http://openworm.org/ConnectomeToolbox/Gendrel_2016/' >Gendrel, Hobert & Atlas 2016</a>"]:::es & F["<a href='http://openworm.org/ConnectomeToolbox/Bentley_2016/' >Bentley et al. 2016 </a>"]:::es & G["<a href='http://openworm.org/ConnectomeToolbox/Cook_2019/' >Cook et al. 2019</a>"]:::anat & H["<a href='http://openworm.org/ConnectomeToolbox/Fenyves_2020/' >Fenyves et al.2020</a>"]:::func & I["<a href='http://openworm.org/ConnectomeToolbox/Cook_2020/' >Cook et al. 2020</a>"]:::anat
    end

    subgraph 2020-2030
    J["<a href='http://openworm.org/ConnectomeToolbox/Brittin_2021' >Brittin et al. 2021</a>"]:::anat & K["<a href='http://openworm.org/ConnectomeToolbox/Witvliet_2021' >Witvliet et al. 2021</a>"]:::anat & L["<a href='http://openworm.org/ConnectomeToolbox/Taylor_2021' >Taylor et al. 2021</a>"]:::gene & M["<a href='http://openworm.org/ConnectomeToolbox/Yemini_2021' >Yemini et al. 2021</a>"]:::gene & N["<a href='http://openworm.org/ConnectomeToolbox/Beets_2023' >Beets et al. 2023</a>"]:::gene & P["<a href='http://openworm.org/ConnectomeToolbox/Randi_2023' >Randi et al. 2023</a>"]:::func & NP["<a href='http://openworm.org/ConnectomeToolbox/Ripoll_2023' >Ripoll-Sanchez et al. 2023</a>"]:::es & R["<a href='http://openworm.org/ConnectomeToolbox/Dag_2023' >Dag et al. 2023</a>"]:::func & T["<a href='http://openworm.org/ConnectomeToolbox/Atanas_2023' >Atanas et al. 2023</a>"]:::func
    end     


    E --> H
    E1 --> H
    E2 --> H
    E --> F
    C --> L
    L --> M
    M --> N
    A --> B
    A1 --> A
    A1 --> I
    A  --> A2
    A --> D
    B --> D
    A2 --> D
    A --> G
    A --> I
    A --> J
    A --> F
    D --> F
    A --> NP
    A1 --> NP
    F --> NP
    L --> NP
    K --> NP
    D --> NP
    A --> P
    L --> P
    N --> P
    K --> P
    NP --> P
    F --> P
    M --> R
    T --> R
    A --> R
    K --> R

Datasets

Papers	Features	Datasets
Albertson & Thomson 1976	Anatomical	N/A
White et al. 1986	Anatomical	White_A - White_L4 - White_whole
Durbin 1987	Anatomical	Work in progress: Durbin.txt
Hall & Russell 1991	Anatomical	N/A
Altun et al. 2009	Gene Expression	Work in progress: data
Varshney et al. 2011	Anatomical	Varshney 2011
Pereira et al. 2015	Extrasynaptic	Work in progress: Cholinergic neurons - NT_Map_herm - WormWiring - male_cholinergic - transcriptional_regulators
Bentley et al. 2016	Extrasynaptic	Bentley et al. 2016 Monoaminergic - Bentley et al. 2016 Peptidergic
Cook et al. 2019	Anatomical	Cook 2019 Hermaphrodite - Cook 2019 Male
Cook et al. 2020	Anatomical	Cook 2020
Fenyves et al. 2020	Functional	Work in progress: data
Brittin et al. 2021	Anatomical	Work in progress: data - parsed
Taylor et al. 2021	Gene Expression	Work in progress: data
Yemini et al. 2021	Gene Expression	Work in progress: data
Witvliet et al. 2021	Developmental	Witvliet1 - Witvliet2 - Witvliet3 - Witvliet4 - Witvliet5 - Witvliet6 - Witvliet7 - Witvliet8
Beets et al. 2023	Gene Expression	Work in progress: data
Dag et al. 2023	Functional	N/A
Atanas et al. 2023	Functional	Work in progress: data
Randi et al. 2023	Functional	WormNeuroAtlas: anatomical - WormNeuroAtlas: functional
Ripoll-Sanchez et al. 2023	Extrasynaptic	Ripoll-Sánchez 2023 (short) - Ripoll-Sánchez 2023 (mid) - Ripoll-Sánchez 2023 (long)