4dn-dcic · andreacosolo · Sep 26, 2022 · Sep 26, 2022 · Sep 26, 2022 · Sep 26, 2022
diff --git a/docs/source/bio.rst b/docs/source/bio.rst
@@ -26,8 +26,8 @@ Example
 
 File Header
 -----------
-- The first line in the header is always "##FOF-CT_version=vX.X"
-- The second line in the header is always "##Table_namespace=4dn_FOF-CT_bio"
+- The first line in the header is always "##FOF-CT_Version=vX.X"
+- The second line in the header is always "##Table_Namespace=4dn_FOF-CT_bio"
 
 This Table can be indexed mandatorily by Spot_ID.
 

diff --git a/docs/source/cell.rst b/docs/source/cell.rst
@@ -24,8 +24,8 @@ Example
 
 File Header
 -----------
-- The first line in the header is always "##FOF-CT_version=vX.X"
-- The second line in the header is always "##Table_namespace=4dn_FOF-CT_cell"
+- The first line in the header is always "##FOF-CT_Version=vX.X"
+- The second line in the header is always "##Table_Namespace=4dn_FOF-CT_cell"
 
 The header MUST include a detailed description of each optional columns used.
 

diff --git a/docs/source/core.rst b/docs/source/core.rst
@@ -55,8 +55,8 @@ Example
 
 File Header
 -----------
-- The first line in the header is always "##FOF-CT_version=vX.X"
-- The second line in the header is always "##Table_namespace=4dn_FOF-CT_core"
+- The first line in the header is always "##FOF-CT_Version=vX.X"
+- The second line in the header is always "##Table_Namespace=4dn_FOF-CT_core"
 
 The header MUST contain a mandatory set of fields that describe the
 algorithm(s) that were used to identify and localize bright Spots and to

diff --git a/docs/source/demultiplexing.rst b/docs/source/demultiplexing.rst
@@ -26,8 +26,8 @@ DNA spots detected with multiplexed barcodes
 
 File Header
 -----------
-- The first line in the header is always "##FOF-CT_version=vX.X"
-- The second line in the header is always "##Table_namespace=4dn_FOF-CT_demultiplexing"
+- The first line in the header is always "##FOF-CT_Version=vX.X"
+- The second line in the header is always "##Table_Namespace=4dn_FOF-CT_demultiplexing"
 
 The header MUST contain a mandatory set of fields that describe any
 algorithm that was used to produce/process data in this table.

diff --git a/docs/source/examples/bio b/docs/source/examples/bio
@@ -1,10 +1,10 @@
-##FOF-CT_version=v0.1
-##Table_namespace=4dn_FOF-CT_bio
-##XYZ_unit=micron
-#^NL_distance:
-#^H4K27me3_distance:
-#additional_tables: 4dn_FOF-CT_rna, 4dn_FOF-CT_cell
-##columns=(Spot_ID, NL_distance, H4K27me3_distance)
+##FOF-CT_Version=v0.1
+##Table_Namespace=4dn_FOF-CT_bio
+##XYZ_Unit=micron
+#^NL_Distance:
+#^H4K27me3_Distance:
+#Additional_Tables: 4dn_FOF-CT_rna, 4dn_FOF-CT_cell
+##Columns=(Spot_ID, NL_Distance, H4K27me3_Distance)
 1, 1.345, 0.445
 2, 1.245, 0.005
 3, 1.005, 0.150
diff --git a/docs/source/examples/cell b/docs/source/examples/cell
@@ -1,13 +1,13 @@
-##FOF-CT_version=v0.1
-##Table_namespace=4dn_FOF-CT_cell
-##XYZ_unit=micron
-##Extra_Cell_ROI_type=Organoid
-#^RNA_A_nr: the number of detected bright Spots corresponding to RNA transcript A detected in this Cell, see also RNA Spot Data table
-#^RNA_B_nr: the number of detected bright Spots corresponding to RNA transcript B detected in this Cell, see also RNA Spot Data table
-#^cell_cycle_state: the Cell Cycle state in which this Cell is found as measured with the Fucci system. This column can contain one of the following values: G1, S, G2 or M.
-#^cell_volume: the volume of this Cell expressed in micron^3.
-#additional_tables: 4dn_FOF-CT_core, 4dn_FOF-CT_rna, 4dn_FOF-CT_trace
-##columns=(Cell_ID, Extra_Cell_ROI_ID, RNA_A_nr, RNA_B_nr, cell_cycle_state, cell_volume)
+##FOF-CT_Version=v0.1
+##Table_Namespace=4dn_FOF-CT_cell
+##XYZ_Unit=micron
+##Extra_Cell_ROI_Type=Organoid
+#^RNA_A_Nr: the number of detected bright Spots corresponding to RNA transcript A detected in this Cell, see also RNA Spot Data table
+#^RNA_B_Nr: the number of detected bright Spots corresponding to RNA transcript B detected in this Cell, see also RNA Spot Data table
+#^Cell_Cycle_State: the Cell Cycle state in which this Cell is found as measured with the Fucci system. This column can contain one of the following values: G1, S, G2 or M.
+#^Cell_Volume: the volume of this Cell expressed in micron^3.
+#Additional_Tables: 4dn_FOF-CT_core, 4dn_FOF-CT_rna, 4dn_FOF-CT_trace
+##Columns=(Cell_ID, Extra_Cell_ROI_ID, RNA_A_Nr, RNA_B_Nr, Cell_Cycle_State, Cell_Volume)
 1, 1, 10, 22, 1041.5, 12354.24, G1, 13453
 2, 1, 0, 11, 2041.3, 32234.24, G2, 35545
 3, 2, 10, 33, 101.5, 12354.24, S, 10010

diff --git a/docs/source/examples/core b/docs/source/examples/core
@@ -1,18 +1,18 @@
-##FOF-CT_version=v0.1
-##Table_namespace=4dn_FOF-CT_core
-##genome_assembly=GRCh38
-##XYZ_unit=micron
+##FOF-CT_Version=v0.1
+##Table_Namespace=4dn_FOF-CT_core
+##Genome_Assembly=GRCh38
+##XYZ_Unit=micron
 #Software_Title: ChrTracer3
 #Software_Type: SpotLoc+Tracing
 #Software_Authors: Mateo, LJ; Sinnott-Armstrong, N; Boettiger, AN
 #Software_Description: ChrTracer3 software was developed for analysis of raw DNA labeled images. As an input, it takes an.xlsx table containing information and folder names of the DNA experiment. As an output, it returns tab delimited.txt ﬁles with drift-corrected x, y, z positions for all labeled barcodes. These can be used directly to calculate the nm scale distances between all pairs of labeled loci. The current version of the software as of this writing is ChrTracer3.
 #Software_Repository: https://github.com/BoettigerLab/ORCA-public
-#Software_PreferredCitationID: https://doi.org/10.1038/s41596-020-00478-x
-#lab_name: Nobel
-#experimenter_name: John Doe
-#experimenter_contact: john.doe@email.com
-#additional_tables: 4dn_FOF-CT_quality, 4dn_FOF-CT_rna, 4dn_FOF-CT_trace, 4dn_FOF-CT_cell
-##columns=(Spot_ID, Trace_ID, X, Y, Z, Chrom, Chrom_Start, Chrom_End, Cell_ID)
+#Software_Preferred_Citation_ID: https://doi.org/10.1038/s41596-020-00478-x
+#Lab_Name: Nobel
+#Experimenter_Name: John Doe
+#Experimenter_Contact: john.doe@email.com
+#Additional_Tables: 4dn_FOF-CT_quality, 4dn_FOF-CT_rna, 4dn_FOF-CT_trace, 4dn_FOF-CT_cell
+##Columns=(Spot_ID, Trace_ID, X, Y, Z, Chrom, Chrom_Start, Chrom_End, Cell_ID)
 1, 1, 14.43, 41.43, 1.23, chr1, 0001, 1000, 1
 2, 1, 14.83, 41.83, 1.83, chr1, 1001, 2000, 1
 3, 1, 15.83, 42.83, 1.33, chr1, 2001, 3000, 1

diff --git a/docs/source/examples/demultiplexing b/docs/source/examples/demultiplexing
@@ -1,21 +1,21 @@
-##FOF-CT_version=v0.1
-##Table_namespace=4dn_FOF-CT_demultiplexing
-##XYZ_unit=micron
+##FOF-CT_Version=v0.1
+##Table_Namespace=4dn_FOF-CT_demultiplexing
+##XYZ_Unit=micron
 #Software_Title: ExampleLocalizationSoftware
 #Software_Type: SpotLoc
 #Software_Authors: Doe, J.
 #Software_Description: A pretty clear description
 #Software_Repository: https://github.com/repo_name_goes_here
-#Software_PreferredCitationID: https://doi.org/doi_goes_here
-#lab_name: Nobel
-#experimenter_name: John Doe
-#experimenter_contact: john.doe@email.com
-#additional_tables: 4dn_FOF-CT_core, 4dn_FOF-CT_quality
+#Software_Preferred_Citation_ID: https://doi.org/doi_goes_here
+#Lab_Name: Nobel
+#Experimenter_Name: John Doe
+#Experimenter_Contact: john.doe@email.com
+#Additional_Tables: 4dn_FOF-CT_core, 4dn_FOF-CT_quality
 #^Hyb: the labeling round in which this localization occurred
 #^Fluor: the fluorescent channel in which this localization was detected
 #^Brightness: the photon count for this localization event
 #^Fit_Quality: the quality of fit for this localization, on a relative scale of 0-1
-##columns=(Loc_ID, Spot_ID, X, Y, Z, Hyb, Fluor, Brightness, Fit_Quality)
+##Columns=(Loc_ID, Spot_ID, X, Y, Z, Hyb, Fluor, Brightness, Fit_Quality)
 1, 1, 2342, 2354, 545, 2, cy3, 1003, 0.83
 2, 1, 2342, 2354, 545, 2, cy5, 2000, 0.93
 3, 1, 2342, 2354, 545, 3, cy5, 1233, 0.85

diff --git a/docs/source/examples/extracell b/docs/source/examples/extracell
@@ -1,12 +1,12 @@
-##FOF-CT_version=v0.1
-##Table_namespace=4dn_FOF-CT_extracell
-##XYZ_unit=micron
-##Extra_Cell_ROI_type=Organoid
-#^Cell_A_nr: the number of identified Cells of type A identified to belong to this extracellular ROI.
-#^Cell_B_nr: the number of identified Cells of type B identified to belong to this extracellular ROI.
-#^ROI_volume: the volume of this extracellular ROI expressed in micron^3.
-#additional_tables: 4dn_FOF-CT_core, 4dn_FOF-CT_rna, 4dn_FOF-CT_trace
-##columns=(Extra_Cell_ROI, Cell_A_nr, Cell_B_nr, ROI_volume)
+##FOF-CT_Version=v0.1
+##Table_Namespace=4dn_FOF-CT_extracell
+##XYZ_Unit=micron
+##Extra_Cell_ROI_Type=Organoid
+#^Cell_A_Nr: the number of identified Cells of type A identified to belong to this extracellular ROI.
+#^Cell_B_Nr: the number of identified Cells of type B identified to belong to this extracellular ROI.
+#^ROI_Volume: the volume of this extracellular ROI expressed in micron^3.
+#Additional_Tables: 4dn_FOF-CT_core, 4dn_FOF-CT_rna, 4dn_FOF-CT_trace
+##Columns=(Extra_Cell_ROI, Cell_A_Nr, Cell_B_Nr, ROI_Volume)
 1, 10, 22, 13453
 2, 0, 11, 35545
 3, 10, 33, 10010

diff --git a/docs/source/examples/mapping b/docs/source/examples/mapping
@@ -1,13 +1,13 @@
-##FOF-CT_version=v0.1
-##Table_namespace=4dn_FOF-CT_mapping
-##XYZ_unit=micron
-##intensity_unit=a.u.
-##Sub_Cell_ROI_type=PML_body
-##ROI_boundaries_format=(X1,Y1 X2,Y2 Xn,Yn)
-#^ROI_volume: the volume of this ROI expressed in micron^3.
-#^ROI_intensity: the integrated average signal intensity measured within the boundaries of this ROI, of the marker used to identify this nuclear feature.
-#additional_tables: 4dn_FOF-CT_core, 4dn_FOF-CT_rna, 4dn_FOF-CT_trace
-##columns=(Sub_Cell_ROI_ID, ROI_boundaries, ROI_volume, ROI_intensity)
+##FOF-CT_Version=v0.1
+##Table_Namespace=4dn_FOF-CT_mapping
+##XYZ_Unit=micron
+##Intensity_Unit=a.u.
+##Sub_Cell_ROI_Type=PML_body
+##ROI_Boundaries_Format=(X1,Y1 X2,Y2 Xn,Yn)
+#^ROI_Volume: the volume of this ROI expressed in micron^3.
+#^ROI_Intensity: the integrated average signal intensity measured within the boundaries of this ROI, of the marker used to identify this nuclear feature.
+#Additional_Tables: 4dn_FOF-CT_core, 4dn_FOF-CT_rna, 4dn_FOF-CT_trace
+##Columns=(Sub_Cell_ROI_ID, ROI_Boundaries, ROI_Volume, ROI_Intensity)
 1, (0,0 1,2 3,5), 100, 1.00
 2, (0,0 2,3 4,6), 48, 0.90
 3, (0,0 3,2 7,5), 63, 0.67

diff --git a/docs/source/examples/quality b/docs/source/examples/quality
@@ -1,16 +1,16 @@
-##FOF-CT_version=v0.1
-##Table_namespace=4dn_FOF-CT_quality
-##XYZ_unit=micron
-##intensity_unit=photonCount
+##FOF-CT_Version=v0.1
+##Table_Namespace=4dn_FOF-CT_quality
+##XYZ_Unit=micron
+##Intensity_Unit=photonCount
 #Software_Title: SpotQualityCheck
 #Software_Type: QualityControl
 #Software_Authors: John Doe et al.
 #Software_Description: Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua.
 #Software_Repository: https://eample.com
-#Software_PreferredCitationID: https://doi.org/00000
-#lab_name: Nobel
-#experimenter_name: John Doe
-#experimenter_contact: john.doe@email.com
+#Software_Preferred_Citation_ID: https://doi.org/00000
+#Lab_Name: Nobel
+#Experimenter_Name: John Doe
+#Experimenter_Contact: john.doe@email.com
 #^Channel_ID: A unique identifier that refers to the Channel that was used to image this Spot.
 #^Peak_Intensity: The signal intensity of the brightest pixel within a bright Spot (i.e. local maximum).
 #^Raw_X: the original fit x-position relative to the camera and objective, (prior to drift correction, chromatic correction, or conversion to stage coordinates). This is the appropriate coordinate system for correcting optical aberrations. 
@@ -25,8 +25,8 @@
 #^X_Loc_Precision: lower and upper bound of 95% confidence interval on X-position after fit
 #^Y_Loc_Precision: lower and upper bound of 95% confidence interval on Y-position after fit
 #^Z_Loc_Precision: lower and upper bound of 95% confidence interval on Z-position after fit
-#additional_tables: 4dn_FOF-CT_core, 4dn_FOF-CT_rna, 4dn_FOF-CT_trace, 4dn_FOF-CT_cell
-##columns=(Spot_ID, Channel_ID, Peak_Intensity, Raw_X, Raw_Y, Raw_Z, X_Drift, Y_Drift, Z_Drift, X_Chromatic_Shift, Y_Chromatic_Shift, Z_Chromatic_Shift, X_Loc_Precision, Y_Loc_Precision, Z_Loc_Precision)
+#Additional_Tables: 4dn_FOF-CT_core, 4dn_FOF-CT_rna, 4dn_FOF-CT_trace, 4dn_FOF-CT_cell
+##Columns=(Spot_ID, Channel_ID, Peak_Intensity, Raw_X, Raw_Y, Raw_Z, X_Drift, Y_Drift, Z_Drift, X_Chromatic_Shift, Y_Chromatic_Shift, Z_Chromatic_Shift, X_Loc_Precision, Y_Loc_Precision, Z_Loc_Precision)
 1, 1, 100, 1.1, 1.05, 1.2, 0.1, 0.05, 0.2, 0.2, 0.2, 0.2, 0.01, 0.01, 0.01
 2, 1, 200, 1.11, 1.055, 1.22, 0.11, 0.055, 0.22, 0.22, 0.22, 0.22, 0.012, 0.012, 0.012
 3, 2, 500, 1.12, 1.054, 1.21, 0.12, 0.054, 0.21, 0.22, 0.22, 0.22, 0.012, 0.012, 0.012

diff --git a/docs/source/examples/rna b/docs/source/examples/rna
@@ -1,19 +1,19 @@
-##FOF-CT_version=v0.1
-##Table_namespace=4dn_FOF-CT_rna
-##genome_assembly=GRCh38
-##XYZ_unit=micron
+##FOF-CT_Version=v0.1
+##Table_Namespace=4dn_FOF-CT_rna
+##Genome_Assembly=GRCh38
+##XYZ_Unit=micron
 ##Gene_ID_type=Ensemble_V38
 #Software_Title: Xyz
 #Software_Type: SpotLoc
 #Software_Authors: Janet Doette
 #Software_Description: Lorem ipsum dolor sit amet, consectetur adipiscing elit. Maecenas sagittis est mollis, pulvinar tortor mattis, dignissim nisi. Nunc tincidunt volutpat lacus vitae bibendum.
 #Software_Repository: https://xyz.com
-#Software_PreferredCitationID: https://doi.org/xyz
-#lab_name: Nobel
-#experimenter_name: John Doe
-#experimenter_contact: john.doe@email.com
-#additional_tables: 4dn_FOF-CT_core, 4dn_FOF-CT_quality, 4dn_FOF-CT_cell
-##columns=(Spot_ID, X, Y, Z, RNA_name, Gene_ID, Transcript_ID, Cell_ID)
+#Software_Preferred_Citation_ID: https://doi.org/xyz
+#Lab_Name: Nobel
+#Experimenter_Name: John Doe
+#Experimenter_Contact: john.doe@email.com
+#Additional_Tables: 4dn_FOF-CT_core, 4dn_FOF-CT_quality, 4dn_FOF-CT_cell
+##Columns=(Spot_ID, X, Y, Z, RNA_name, Gene_ID, Transcript_ID, Cell_ID)
 1, 14.43, 41.43, 1.23, ACTB, ENSG00000075624, ENST00000646664.1, 1
 2, 14.83, 41.83, 1.83, GAPDH, ENSG00000111640, ENST00000229239.10, 1
 3, 15.83, 42.83, 1.33, MB, ENSG00000198125, ENST00000397326.7, 1
diff --git a/docs/source/examples/subcell b/docs/source/examples/subcell
@@ -1,12 +1,12 @@
-##FOF-CT_version=v0.1
-##Table_namespace=4dn_FOF-CT_subcell
-##XYZ_unit=micron
-##intensity_unit=a.u.
-##Sub_Cell_ROI_type=Nucleolus
-#^ROI_volume: the volume of this ROI expressed in micron^3.
+##FOF-CT_Version=v0.1
+##Table_Namespace=4dn_FOF-CT_subcell
+##XYZ_Unit=micron
+##Intensity_Unit=a.u.
+##Sub_Cell_ROI_Type=Nucleolus
+#^ROI_Volume: the volume of this ROI expressed in micron^3.
 #^ROI_intensity: the integrated average signal intensity of the marker of interest as measured within the boundaries of this ROI.
-#additional_tables: 4dn_FOF-CT_core, 4dn_FOF-CT_rna, 4dn_FOF-CT_trace
-##columns=(Sub_Cell_ROI_ID, Cell_ID, ROI_volume, ROI_intensity)
+#Additional_Tables: 4dn_FOF-CT_core, 4dn_FOF-CT_rna, 4dn_FOF-CT_trace
+##Columns=(Sub_Cell_ROI_ID, Cell_ID, ROI_Volume, ROI_intensity)
 1, 1, 1345, 3500
 2, 1, 3554, 1500
 3, 2, 1001, 2500

diff --git a/docs/source/examples/trace b/docs/source/examples/trace
@@ -1,12 +1,12 @@
-##FOF-CT_version=v0.1
-##Table_namespace=4dn_FOF-CT_trace
-##XYZ_unit=micron
-##intensity_unit=a.u.
-#^allele: This field records the Allele to which this Trace was mapped. This can be one of the following values: BL6, CAST.
-#^RNA_A_intensity: This records the intensity of the nascent RNA A expression signal associated with this Trace.
-#^NL_distance: This field records the distance of this Trace to the Nuclear Lamina.
-#additional_tables: 4dn_FOF-CT_core, 4dn_FOF-CT_cell
-##columns=(Trace_ID, allele, RNA_A_int, NL_distance)
+##FOF-CT_Version=v0.1
+##Table_Namespace=4dn_FOF-CT_trace
+##XYZ_Unit=micron
+##Intensity_Unit=a.u.
+#^Allele: This field records the Allele to which this Trace was mapped. This can be one of the following values: BL6, CAST.
+#^RNA_A_Intensity: This records the intensity of the nascent RNA A expression signal associated with this Trace.
+#^NL_Distance: This field records the distance of this Trace to the Nuclear Lamina.
+#Additional_Tables: 4dn_FOF-CT_core, 4dn_FOF-CT_cell
+##Columns=(Trace_ID, Allele, RNA_A_Intensity, NL_Distance)
 1, BL6, 43253, 0.235
 2, CAST, 40001, 0.563
 3, BL6, 1000, 0.135

diff --git a/docs/source/extracell.rst b/docs/source/extracell.rst
@@ -27,8 +27,8 @@ Example
 
 File Header
 -----------
-- The first line in the header is always "##FOF-CT_version=vX.X"
-- The second line in the header is always "##Table_namespace=4dn_FOF-CT_extracell"
+- The first line in the header is always "##FOF-CT_Version=vX.X"
+- The second line in the header is always "##Table_Namespace=4dn_FOF-CT_extracell"
 
 The header MUST include a detailed description of each optional columns used.
 

diff --git a/docs/source/format_overview.rst b/docs/source/format_overview.rst
@@ -25,56 +25,56 @@ File Header
 - Header lines are denoted by ``#``. In particular:
 
   - ``##`` denotes machine readable header lines. These lines must follow the
-    following format ``##Key1=Value1`` (e.g., ``##FOF-CT_version=v0.1``).
+    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: free text description`` (e.g.,
-    ``#lab_name: name of the lab where the experiment was performed``).
+    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: free text description`` (e.g.,
-    ``#^optional_column_1: optional column 1 description``).
+    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
+  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
+**##FOF-CT_Version=** Data format version number. E.g. v0.2
 
-**##XYZ_unit=** The unit used to represent the XYZ location of bright
+**##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
+#Lab_Name: name of the lab where the experiment was performed
 
-#experimenter_name: name of the person performing the experiment
+#Experimenter_Name: name of the person performing the experiment
 
-**#experimenter_contact:** email address of the person performing the
+**#Experimenter_Contact:** email address of the person performing the
 experiment
 
-**#description:** A free-text, description of the experiment and of the
+**#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
+**#Additional_Tables:** AddTable1, AddTable2, AddTableN
 
-**##columns=**\ (C1, C2, C3, Cn)
+**##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
+**##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
@@ -96,7 +96,7 @@ 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
+**#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,.