Contents
- The format is organized in multiple individual tables.
- The only mandatory table is the :ref:`core`.
- All other tables are either recommended for all experiment types, or optional depending on the experiment design and type.
- Each file must contain a single table.
- Accepted file formats for storing Tables are txt, csv and tsv.
- An underscore must be used as a word separator in header field
names and column headers to improve readability while not violating
common name restrictions in coding environments (dash
-
may be mistaken as subtraction of variables). - Each file has two parts: file header and data columns.
- In the file header, each line contains only one field.
- Header lines are denoted by
#
. In particular:##
denotes machine readable header lines. These lines must follow the following format##Key_A=Value_1
(e.g.,##FOF-CT_Version=v0.1
).#
denotes human readable header lines. These lines should follow the following format,#Term_X: free text description
(e.g.,#Lab_Name: name of the lab where the experiment was performed
).#^
denotes lines that define optional user specified columns. These lines provide the name of the column header and a description of the column content. Descriptions must be understandable and sufficient to ensure the interpretation and reproducibility of the results. These lines should follow the following format#^Term_X: free text description
(e.g.,#^Optional_Column_1: optional column 1 description
).
- Header names must use the underscore as a word separator (e.g., RNA_A_intensity).
- The file header contains required, conditionally-required, and optional fields.
- Conditionally-required fields are fields that are required when certains conditions are met (e.g., ##Intensity_Unit= is required any time an intensity metric is reported).
- All tables have to contain a mandatory header section.
##FOF-CT_Version= Data format version number. E.g. v0.2
##XYZ_Unit= The unit used to represent the XYZ location of bright Spots in this table. Note: use micron (instead of µm) to avoid problems with special, Greek symbols. Other allowed values are: nm, mm etc.
#Lab_Name: name of the lab where the experiment was performed
#Experimenter_Name: name of the person performing the experiment
#Experimenter_Contact: email address of the person performing the experiment
#Description: A free-text, description of the experiment and of the data recorded in this table. This description should provide a clear understanding of the process utilized to produce the data and contain sufficient details to ensure interpretation and reproducibility.
#Additional_Tables: AddTable1, AddTable2, AddTableN
##Columns=(C1, C2, C3, Cn)
In addition to all of the above,
##Genome_Assembly= Genome build. Note that the 4DN data portal only accepts GRCh38 for human and GRCm38 for mouse.
#Software_Title: The name of the Software(s) that were used in this case for localizing individual FISH-omics bright Spots and/or to produce three-dimensional (3D) polymeric chromatin Traces.
#Software_Type: The type of this Software. Allowed values: SpotLoc, Tracing, SpotLoc+Tracing, Other
#Software_Authors: The Name(s) of the individual Author(s) of this Software. In case there are more than one Authors, individual names should be listed as follows: Doe, John; Smith, Jane; etc,.
#Software_Description: A free-text description of this Software. This description should provide a detailed understanding of the algorithm and of the analysis parameters that were used, in order to guarantee interpretation and reproducibility.
#Software_Repository: The URL of any repository or archive where the Software executable release can be obtained.
#Software_Preferred_Citation_ID: The Unique Identifier for the preferred/primary publication describing this Software. Examples include Digital Object Identifier (DOI), PubMed Central Identifier (PMCID), ArXiv.org ID etc,.
- Tables contain required, conditionally-required, and optional columns.
- Conditionally-required columns are columns that are required when certain conditions are met (e.g., Cell_ID is required any time the experiment involves the identification of Cell boundaries).
- Column names should use the underscore as a word separator (e.g., Spot_ID).
- The first column is always either Spot_ID or another relevant ID (i.e., Trace_ID, Cell_ID, etc.). In the :ref:`core`, there are eight mandatory columns. All other columns are ordered at user's discretion.
- The order of the rows is at user's discretion.
- If an optional column does not contain any data (i.e., it is not used), it should be omitted.