WormWideWeb-data

Adding a new paper/project

paper_id

Pick a unique paper_id e.g. atanas_kim_2023 and dag_nwabudike_kang_2023

Paper data

Add an entry in activity/papers.json e.g.:

{
  "paper_id": "atanas_kim_2023",
  "title_full": "Brain-wide representations of behavior spanning multiple timescales and states in C. elegans",
  "title_short": "Atanas & Kim et al., 2023",
  "neuropal_label": true,
  "encoding_data": true,
  "repository": {
    "type": "zenodo",
    "record_id": "19388374"
  }
}

• paper_id: unique paper id
• title_full: full title
• neuropal_label: true or false. if true, neorpal label must be in the repository
• encoding_data: true or false. if true, encoding data files must be in the repository
• repository: repository info. type: zenodo or dryad. record_id: use the record id for zenodo, the doi for dryad

Dataset types data

Add dataset types information entry for the paper, using the same paper_id. Commonly used data types such as neuropal don't need to be added.

Add the entry in activity/dataset_types.json e.g.:

{
  "atanas_kim_2023": [
    {
      "id": "baseline",
      "name": "Baseline",
      "color_background": "rgb(125,125,125)",
      "description": "Baseline dataset"
    },
    {
      "id": "heat",
      "name": "Heat",
      "color_background": "#dc3545",
      "description": "Heat stimulation experiment data"
    },
    {
      "id": "gfp",
      "name": "GFP",
      "color_background": "#198754",
      "description": "Control data with the GFP expression strain"
    }
  ]
}

Manifest

If already not there, create a csv file using the matching paper_id in activity/raw. The csv file should contain the following columns:

• filename: h5 file name
• checksum: sha256 checksum of the h5 file
• uid: unique id for the dataset
• θh_pos_is_ventral: true if positive/+ θh is ventral
• label: true if there's neuropal data
• type: dataset types from the dataset_types.json comma separated. e.g.: "baseline,neuropal"
• event: events e.g. "stim_begin_confocal=[300,600],food_encounter=[100]"
• t_range: time point range to display on the web app. e.g. skip if you want the full dataset. otherwise, specify as start:end e.g. "601:800"

Repository

Each zenodo or dryad repository must contain:

• processed_h5.tar.bz2: archive of h5 files

If the paper has encoding data (ouputs of generate_encoding_files in WormWideWebData.jl):

• neuron_categorization.h5.bz2
• encoding_changes_corrected.h5.bz2
• relative_encoding_strength_median.h5.bz2
• tuning_strength.h5.bz2
• sampled_tau_vals_median.h5.bz2
• fit_ranges.h5.bz2

If the paper has NeuroPAL labels (ouput of generate_neuropal_json in WormWideWebData.jl):

• neuropal_label.json.bz2