nomenclature
Overview
This repository contains code to generate the standardized Common Cell type Nomenclature (CCN) from an R "dendrogram", which will be presented in our manuscript soon to be resubmitted to eLife. The initial version of the CCN is described in detail on our website, here, with and updated version now published on eLife. We will (hopefully) update our website once the CCN is finalized. If you want to apply nomenclature of the format initially described, please use the initial release (not recommended).
Application of CCN to a taxonomy
To get started, download the scripts and data folders, and the follow the UPDATED directions in build_annotation_tables_SEAAD.rmd. An HTML version of this file is accessible AT THIS LINK.
----You can also install the NEW CCN R Package----.
This version includes updates for:
- Defining a standard CCN output (a zip file with key output files)
- Automation of cell set annotation based on a metadata file to minimize manual steps
- Adding child cell set accessions for building ontologies
- CCN R Package
- Single function application of CCN - Beta version now available in the CCN R Package
The original files are still available in the scripts folder (Link to original build_annotation_tables html).
Please visit the Cell Taxonomy category of our community forum to provide suggestions about the CCN itself.
We are currently saving used taxonomy_id IN THIS TABLE. Please choose a unique one and update the table accordingly if you use the CCN. A cell type taxonomy service is currently under construction at the Allen Institute, which will will replace this non-ideal system. CCN output for several of the taxonomies in this table are included in Supplementary File 1 from our paper on eLife.
Conversions to other formats
The CCN is intended to be a standardized format for researchers to save taxonomies resulting from any cell typing study. To facilitate ingest of these taxonomies into relevant databases and ontologies, we intend to provide conversion scripts (as available) from the CCN format to formats required by these external tools. If you would like to see scripts for conversions to other file formats, please email Jeremy Miller (jeremym at alleninstitute dot org).
Currently conversions are available for the Allen Institute Cell Type Taxonomy Service (CTTS). This is a tool for saving taxonomies in a database that is currently only available to Allen Institute employees. To convert to this format download the three "convert_to_CTTS" from this folder and follow the identical directions in the .Rmd or .html files.
License
The license for this package is available on Github at: https://github.com/AllenInstitute/allen_institute_nomenclature/blob/master/LICENSE
Level of Support
This tool will only be updated to correct errors and to reflect updates in the nomenclature schema.
Contribution Agreement
If you contribute code to this repository through pull requests or other mechanisms, you are subject to the Allen Institute Contribution Agreement, which is available in full at: https://github.com/AllenInstitute/allen_institute_nomenclature/blob/master/CONTRIBUTION