Format description: overview
The format is organized in multiple individual tables.
The only mandatory table is the DNA-Spot/Trace Data core table.
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
#denotes human readable header lines. These lines should follow the following format,
#term: 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: 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.
Mandatory header lines (all tables)
##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)
Additional mandatory header lines (DNA spot/trace core and RNA tables)
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_PreferredCitationID: 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 DNA-Spot/Trace Data core table, 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.