normalize-nodes
Overview¶
kgtk normalize-nodes
converts a KGTK node file to a KGTK edge file.
Relationship Names¶
By default, the input file's column headers are used as relationship
names in the output file's label
column. The --labels
option can be used to provide
a different set of relationship names in the output file.
Usage¶
usage: kgtk normalize-nodes [-h] [-i INPUT_FILE] [-o OUTPUT_FILE]
[-c COLUMNS [COLUMNS ...]]
[--labels LABELS [LABELS ...]]
[--id-column ID_COLUMN_NAME]
[-v [optional True|False]]
Normalize a KGTK node file into a KGTK edge file with a row for each column value in the input file.
optional arguments:
-h, --help show this help message and exit
-i INPUT_FILE, --input-file INPUT_FILE
The KGTK input file. (May be omitted or '-' for
stdin.)
-o OUTPUT_FILE, --output-file OUTPUT_FILE
The KGTK output file. (May be omitted or '-' for
stdout.)
-c COLUMNS [COLUMNS ...], --columns COLUMNS [COLUMNS ...]
Columns to remove as a space-separated list.
(default=all columns except id)
--labels LABELS [LABELS ...]
Label names to use as a space-separated list.
(default=column names)
--id-column ID_COLUMN_NAME
The name of the ID column. (default=id or alias)
-v [optional True|False], --verbose [optional True|False]
Print additional progress messages (default=False).
Examples¶
Sample Data: The First 18 Elements¶
Here is a file containing some physical properties and categories for the first 18 elements in the Period Table of Elements and Properties.
kgtk cat -i examples/docs/periodic_table_of_elements_1-18.tsv
id | AtomicNumber | Element | Symbol | AtomicMass | NumberofNeutrons | NumberofProtons | NumberofElectrons | Period | Group | Phase | Radioactive | Natural | Metal | Nonmetal | Metalloid | Type | AtomicRadius | Electronegativity | FirstIonization | Density | MeltingPoint | BoilingPoint | NumberOfIsotopes | Discoverer | Year | SpecificHeat | NumberofShells | NumberofValence |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
H | 1 | Hydrogen | H | 1.007 | 0 | 1 | 1 | 1 | 1 | gas | yes | yes | Nonmetal | 0.79 | 2.2 | 13.5984 | 8.99E-05 | 14.175 | 20.28 | 3 | Cavendish | 1766 | 14.304 | 1 | 1 | |||
He | 2 | Helium | He | 4.002 | 2 | 2 | 2 | 1 | 18 | gas | yes | yes | NobleGas | 0.49 | 24.5874 | 1.79E-04 | 4.22 | 5 | Janssen | 1868 | 5.193 | 1 | ||||||
Li | 3 | Lithium | Li | 6.941 | 4 | 3 | 3 | 2 | 1 | solid | yes | yes | AlkaliMetal | 2.1 | 0.98 | 5.3917 | 5.34E-01 | 453.85 | 1615 | 5 | Arfvedson | 1817 | 3.582 | 2 | 1 | |||
Be | 4 | Beryllium | Be | 9.012 | 5 | 4 | 4 | 2 | 2 | solid | yes | yes | AlkalineEarthMetal | 1.4 | 1.57 | 9.3227 | 1.85E+00 | 1560.15 | 2742 | 6 | Vaulquelin | 1798 | 1.825 | 2 | 2 | |||
B | 5 | Boron | B | 10.811 | 6 | 5 | 5 | 2 | 13 | solid | yes | yes | Metalloid | 1.2 | 2.04 | 8.298 | 2.34E+00 | 2573.15 | 4200 | 6 | Gay-Lussac | 1808 | 1.026 | 2 | 3 | |||
C | 6 | Carbon | C | 12.011 | 6 | 6 | 6 | 2 | 14 | solid | yes | yes | Nonmetal | 0.91 | 2.55 | 11.2603 | 2.27E+00 | 3948.15 | 4300 | 7 | Prehistoric | 0.709 | 2 | 4 | ||||
N | 7 | Nitrogen | N | 14.007 | 7 | 7 | 7 | 2 | 15 | gas | yes | yes | Nonmetal | 0.75 | 3.04 | 14.5341 | 1.25E-03 | 63.29 | 77.36 | 8 | Rutherford | 1772 | 1.04 | 2 | 5 | |||
O | 8 | Oxygen | O | 15.999 | 8 | 8 | 8 | 2 | 16 | gas | yes | yes | Nonmetal | 0.65 | 3.44 | 13.6181 | 1.43E-03 | 50.5 | 90.2 | 8 | Priestley|Scheele | 1774 | 0.918 | 2 | 6 | |||
F | 9 | Fluorine | F | 18.998 | 10 | 9 | 9 | 2 | 17 | gas | yes | yes | Halogen | 0.57 | 3.98 | 17.4228 | 1.70E-03 | 53.63 | 85.03 | 6 | Moissan | 1886 | 0.824 | 2 | 7 | |||
Ne | 10 | Neon | Ne | 20.18 | 10 | 10 | 10 | 2 | 18 | gas | yes | yes | Noble Gas | 0.51 | 21.5645 | 9.00E-04 | 24.703 | 27.07 | 8 | Ramsay_and_Travers | 1898 | 1.03 | 2 | 8 | ||||
Na | 11 | Sodium | Na | 22.99 | 12 | 11 | 11 | 3 | 1 | solid | yes | yes | AlkaliMetal | 2.2 | 0.93 | 5.1391 | 9.71E-01 | 371.15 | 1156 | 7 | Davy | 1807 | 1.228 | 3 | 1 | |||
Mg | 12 | Magnesium | Mg | 24.305 | 12 | 12 | 12 | 3 | 2 | solid | yes | yes | AlkalineEarthMetal | 1.7 | 1.31 | 7.6462 | 1.74E+00 | 923.15 | 1363 | 8 | Black | 1755 | 1.023 | 3 | 2 | |||
Al | 13 | Aluminum | Al | 26.982 | 14 | 13 | 13 | 3 | 13 | solid | yes | yes | Metal | 1.8 | 1.61 | 5.9858 | 2.70E+00 | 933.4 | 2792 | 8 | Wshler | 1827 | 0.897 | 3 | 3 | |||
Si | 14 | Silicon | Si | 28.086 | 14 | 14 | 14 | 3 | 14 | solid | yes | yes | Metalloid | 1.5 | 1.9 | 8.1517 | 2.33E+00 | 1683.15 | 3538 | 8 | Berzelius | 1824 | 0.705 | 3 | 4 | |||
P | 15 | Phosphorus | P | 30.974 | 16 | 15 | 15 | 3 | 15 | solid | yes | yes | Nonmetal | 1.2 | 2.19 | 10.4867 | 1.82E+00 | 317.25 | 553 | 7 | BranBrand | 1669 | 0.769 | 3 | 5 | |||
S | 16 | Sulfur | S | 32.065 | 16 | 16 | 16 | 3 | 16 | solid | yes | yes | Nonmetal | 1.1 | 2.58 | 10.36 | 2.07E+00 | 388.51 | 717.8 | 10 | Prehistoric | 0.71 | 3 | 6 | ||||
Cl | 17 | Chlorine | Cl | 35.453 | 18 | 17 | 17 | 3 | 17 | gas | yes | yes | Halogen | 0.97 | 3.16 | 12.9676 | 3.21E-03 | 172.31 | 239.11 | 11 | Scheele | 1774 | 0.479 | 3 | 7 | |||
Ar | 18 | Argon | Ar | 39.948 | 22 | 18 | 18 | 3 | 18 | gas | yes | yes | NobleGas | 0.88 | 15.7596 | 1.78E-03 | 83.96 | 87.3 | 8 | Rayleigh_and_Ramsay | 1894 | 0.52 | 3 | 8 |
Default Conversion¶
kgtk normalize-nodes -i examples/docs/periodic_table_of_elements_1-18.tsv
node1 | label | node2 |
---|---|---|
H | AtomicNumber | 1 |
H | Element | Hydrogen |
H | Symbol | H |
H | AtomicMass | 1.007 |
H | NumberofNeutrons | 0 |
H | NumberofProtons | 1 |
H | NumberofElectrons | 1 |
H | Period | 1 |
H | Group | 1 |
H | Phase | gas |
H | Natural | yes |
H | Nonmetal | yes |
H | Type | Nonmetal |
H | AtomicRadius | 0.79 |
H | Electronegativity | 2.2 |
H | FirstIonization | 13.5984 |
H | Density | 8.99E-05 |
H | MeltingPoint | 14.175 |
H | BoilingPoint | 20.28 |
H | NumberOfIsotopes | 3 |
H | Discoverer | Cavendish |
H | Year | 1766 |
H | SpecificHeat | 14.304 |
H | NumberofShells | 1 |
H | NumberofValence | 1 |
He | AtomicNumber | 2 |
He | Element | Helium |
He | Symbol | He |
He | AtomicMass | 4.002 |
He | NumberofNeutrons | 2 |
He | NumberofProtons | 2 |
He | NumberofElectrons | 2 |
He | Period | 1 |
He | Group | 18 |
He | Phase | gas |
He | Natural | yes |
He | Nonmetal | yes |
He | Type | NobleGas |
He | AtomicRadius | 0.49 |
He | FirstIonization | 24.5874 |
He | Density | 1.79E-04 |
He | BoilingPoint | 4.22 |
He | NumberOfIsotopes | 5 |
He | Discoverer | Janssen |
He | Year | 1868 |
He | SpecificHeat | 5.193 |
He | NumberofShells | 1 |
Li | AtomicNumber | 3 |
Li | Element | Lithium |
Li | Symbol | Li |
Li | AtomicMass | 6.941 |
Li | NumberofNeutrons | 4 |
Li | NumberofProtons | 3 |
Li | NumberofElectrons | 3 |
Li | Period | 2 |
Li | Group | 1 |
Li | Phase | solid |
Li | Natural | yes |
Li | Metal | yes |
Li | Type | AlkaliMetal |
Li | AtomicRadius | 2.1 |
Li | Electronegativity | 0.98 |
Li | FirstIonization | 5.3917 |
Li | Density | 5.34E-01 |
Li | MeltingPoint | 453.85 |
Li | BoilingPoint | 1615 |
Li | NumberOfIsotopes | 5 |
Li | Discoverer | Arfvedson |
Li | Year | 1817 |
Li | SpecificHeat | 3.582 |
Li | NumberofShells | 2 |
Li | NumberofValence | 1 |
Be | AtomicNumber | 4 |
Be | Element | Beryllium |
Be | Symbol | Be |
Be | AtomicMass | 9.012 |
Be | NumberofNeutrons | 5 |
Be | NumberofProtons | 4 |
Be | NumberofElectrons | 4 |
Be | Period | 2 |
Be | Group | 2 |
Be | Phase | solid |
Be | Natural | yes |
Be | Metal | yes |
Be | Type | AlkalineEarthMetal |
Be | AtomicRadius | 1.4 |
Be | Electronegativity | 1.57 |
Be | FirstIonization | 9.3227 |
Be | Density | 1.85E+00 |
Be | MeltingPoint | 1560.15 |
Be | BoilingPoint | 2742 |
Be | NumberOfIsotopes | 6 |
Be | Discoverer | Vaulquelin |
Be | Year | 1798 |
Be | SpecificHeat | 1.825 |
Be | NumberofShells | 2 |
Be | NumberofValence | 2 |
B | AtomicNumber | 5 |
B | Element | Boron |
B | Symbol | B |
B | AtomicMass | 10.811 |
B | NumberofNeutrons | 6 |
B | NumberofProtons | 5 |
B | NumberofElectrons | 5 |
B | Period | 2 |
B | Group | 13 |
B | Phase | solid |
B | Natural | yes |
B | Metalloid | yes |
B | Type | Metalloid |
B | AtomicRadius | 1.2 |
B | Electronegativity | 2.04 |
B | FirstIonization | 8.298 |
B | Density | 2.34E+00 |
B | MeltingPoint | 2573.15 |
B | BoilingPoint | 4200 |
B | NumberOfIsotopes | 6 |
B | Discoverer | Gay-Lussac |
B | Year | 1808 |
B | SpecificHeat | 1.026 |
B | NumberofShells | 2 |
B | NumberofValence | 3 |
C | AtomicNumber | 6 |
C | Element | Carbon |
C | Symbol | C |
C | AtomicMass | 12.011 |
C | NumberofNeutrons | 6 |
C | NumberofProtons | 6 |
C | NumberofElectrons | 6 |
C | Period | 2 |
C | Group | 14 |
C | Phase | solid |
C | Natural | yes |
C | Nonmetal | yes |
C | Type | Nonmetal |
C | AtomicRadius | 0.91 |
C | Electronegativity | 2.55 |
C | FirstIonization | 11.2603 |
C | Density | 2.27E+00 |
C | MeltingPoint | 3948.15 |
C | BoilingPoint | 4300 |
C | NumberOfIsotopes | 7 |
C | Discoverer | Prehistoric |
C | SpecificHeat | 0.709 |
C | NumberofShells | 2 |
C | NumberofValence | 4 |
N | AtomicNumber | 7 |
N | Element | Nitrogen |
N | Symbol | N |
N | AtomicMass | 14.007 |
N | NumberofNeutrons | 7 |
N | NumberofProtons | 7 |
N | NumberofElectrons | 7 |
N | Period | 2 |
N | Group | 15 |
N | Phase | gas |
N | Natural | yes |
N | Nonmetal | yes |
N | Type | Nonmetal |
N | AtomicRadius | 0.75 |
N | Electronegativity | 3.04 |
N | FirstIonization | 14.5341 |
N | Density | 1.25E-03 |
N | MeltingPoint | 63.29 |
N | BoilingPoint | 77.36 |
N | NumberOfIsotopes | 8 |
N | Discoverer | Rutherford |
N | Year | 1772 |
N | SpecificHeat | 1.04 |
N | NumberofShells | 2 |
N | NumberofValence | 5 |
O | AtomicNumber | 8 |
O | Element | Oxygen |
O | Symbol | O |
O | AtomicMass | 15.999 |
O | NumberofNeutrons | 8 |
O | NumberofProtons | 8 |
O | NumberofElectrons | 8 |
O | Period | 2 |
O | Group | 16 |
O | Phase | gas |
O | Natural | yes |
O | Nonmetal | yes |
O | Type | Nonmetal |
O | AtomicRadius | 0.65 |
O | Electronegativity | 3.44 |
O | FirstIonization | 13.6181 |
O | Density | 1.43E-03 |
O | MeltingPoint | 50.5 |
O | BoilingPoint | 90.2 |
O | NumberOfIsotopes | 8 |
O | Discoverer | Priestley |
O | Discoverer | Scheele |
O | Year | 1774 |
O | SpecificHeat | 0.918 |
O | NumberofShells | 2 |
O | NumberofValence | 6 |
F | AtomicNumber | 9 |
F | Element | Fluorine |
F | Symbol | F |
F | AtomicMass | 18.998 |
F | NumberofNeutrons | 10 |
F | NumberofProtons | 9 |
F | NumberofElectrons | 9 |
F | Period | 2 |
F | Group | 17 |
F | Phase | gas |
F | Natural | yes |
F | Nonmetal | yes |
F | Type | Halogen |
F | AtomicRadius | 0.57 |
F | Electronegativity | 3.98 |
F | FirstIonization | 17.4228 |
F | Density | 1.70E-03 |
F | MeltingPoint | 53.63 |
F | BoilingPoint | 85.03 |
F | NumberOfIsotopes | 6 |
F | Discoverer | Moissan |
F | Year | 1886 |
F | SpecificHeat | 0.824 |
F | NumberofShells | 2 |
F | NumberofValence | 7 |
Ne | AtomicNumber | 10 |
Ne | Element | Neon |
Ne | Symbol | Ne |
Ne | AtomicMass | 20.18 |
Ne | NumberofNeutrons | 10 |
Ne | NumberofProtons | 10 |
Ne | NumberofElectrons | 10 |
Ne | Period | 2 |
Ne | Group | 18 |
Ne | Phase | gas |
Ne | Natural | yes |
Ne | Nonmetal | yes |
Ne | Type | Noble Gas |
Ne | AtomicRadius | 0.51 |
Ne | FirstIonization | 21.5645 |
Ne | Density | 9.00E-04 |
Ne | MeltingPoint | 24.703 |
Ne | BoilingPoint | 27.07 |
Ne | NumberOfIsotopes | 8 |
Ne | Discoverer | Ramsay_and_Travers |
Ne | Year | 1898 |
Ne | SpecificHeat | 1.03 |
Ne | NumberofShells | 2 |
Ne | NumberofValence | 8 |
Na | AtomicNumber | 11 |
Na | Element | Sodium |
Na | Symbol | Na |
Na | AtomicMass | 22.99 |
Na | NumberofNeutrons | 12 |
Na | NumberofProtons | 11 |
Na | NumberofElectrons | 11 |
Na | Period | 3 |
Na | Group | 1 |
Na | Phase | solid |
Na | Natural | yes |
Na | Metal | yes |
Na | Type | AlkaliMetal |
Na | AtomicRadius | 2.2 |
Na | Electronegativity | 0.93 |
Na | FirstIonization | 5.1391 |
Na | Density | 9.71E-01 |
Na | MeltingPoint | 371.15 |
Na | BoilingPoint | 1156 |
Na | NumberOfIsotopes | 7 |
Na | Discoverer | Davy |
Na | Year | 1807 |
Na | SpecificHeat | 1.228 |
Na | NumberofShells | 3 |
Na | NumberofValence | 1 |
Mg | AtomicNumber | 12 |
Mg | Element | Magnesium |
Mg | Symbol | Mg |
Mg | AtomicMass | 24.305 |
Mg | NumberofNeutrons | 12 |
Mg | NumberofProtons | 12 |
Mg | NumberofElectrons | 12 |
Mg | Period | 3 |
Mg | Group | 2 |
Mg | Phase | solid |
Mg | Natural | yes |
Mg | Metal | yes |
Mg | Type | AlkalineEarthMetal |
Mg | AtomicRadius | 1.7 |
Mg | Electronegativity | 1.31 |
Mg | FirstIonization | 7.6462 |
Mg | Density | 1.74E+00 |
Mg | MeltingPoint | 923.15 |
Mg | BoilingPoint | 1363 |
Mg | NumberOfIsotopes | 8 |
Mg | Discoverer | Black |
Mg | Year | 1755 |
Mg | SpecificHeat | 1.023 |
Mg | NumberofShells | 3 |
Mg | NumberofValence | 2 |
Al | AtomicNumber | 13 |
Al | Element | Aluminum |
Al | Symbol | Al |
Al | AtomicMass | 26.982 |
Al | NumberofNeutrons | 14 |
Al | NumberofProtons | 13 |
Al | NumberofElectrons | 13 |
Al | Period | 3 |
Al | Group | 13 |
Al | Phase | solid |
Al | Natural | yes |
Al | Metal | yes |
Al | Type | Metal |
Al | AtomicRadius | 1.8 |
Al | Electronegativity | 1.61 |
Al | FirstIonization | 5.9858 |
Al | Density | 2.70E+00 |
Al | MeltingPoint | 933.4 |
Al | BoilingPoint | 2792 |
Al | NumberOfIsotopes | 8 |
Al | Discoverer | Wshler |
Al | Year | 1827 |
Al | SpecificHeat | 0.897 |
Al | NumberofShells | 3 |
Al | NumberofValence | 3 |
Si | AtomicNumber | 14 |
Si | Element | Silicon |
Si | Symbol | Si |
Si | AtomicMass | 28.086 |
Si | NumberofNeutrons | 14 |
Si | NumberofProtons | 14 |
Si | NumberofElectrons | 14 |
Si | Period | 3 |
Si | Group | 14 |
Si | Phase | solid |
Si | Natural | yes |
Si | Metalloid | yes |
Si | Type | Metalloid |
Si | AtomicRadius | 1.5 |
Si | Electronegativity | 1.9 |
Si | FirstIonization | 8.1517 |
Si | Density | 2.33E+00 |
Si | MeltingPoint | 1683.15 |
Si | BoilingPoint | 3538 |
Si | NumberOfIsotopes | 8 |
Si | Discoverer | Berzelius |
Si | Year | 1824 |
Si | SpecificHeat | 0.705 |
Si | NumberofShells | 3 |
Si | NumberofValence | 4 |
P | AtomicNumber | 15 |
P | Element | Phosphorus |
P | Symbol | P |
P | AtomicMass | 30.974 |
P | NumberofNeutrons | 16 |
P | NumberofProtons | 15 |
P | NumberofElectrons | 15 |
P | Period | 3 |
P | Group | 15 |
P | Phase | solid |
P | Natural | yes |
P | Nonmetal | yes |
P | Type | Nonmetal |
P | AtomicRadius | 1.2 |
P | Electronegativity | 2.19 |
P | FirstIonization | 10.4867 |
P | Density | 1.82E+00 |
P | MeltingPoint | 317.25 |
P | BoilingPoint | 553 |
P | NumberOfIsotopes | 7 |
P | Discoverer | BranBrand |
P | Year | 1669 |
P | SpecificHeat | 0.769 |
P | NumberofShells | 3 |
P | NumberofValence | 5 |
S | AtomicNumber | 16 |
S | Element | Sulfur |
S | Symbol | S |
S | AtomicMass | 32.065 |
S | NumberofNeutrons | 16 |
S | NumberofProtons | 16 |
S | NumberofElectrons | 16 |
S | Period | 3 |
S | Group | 16 |
S | Phase | solid |
S | Natural | yes |
S | Nonmetal | yes |
S | Type | Nonmetal |
S | AtomicRadius | 1.1 |
S | Electronegativity | 2.58 |
S | FirstIonization | 10.36 |
S | Density | 2.07E+00 |
S | MeltingPoint | 388.51 |
S | BoilingPoint | 717.8 |
S | NumberOfIsotopes | 10 |
S | Discoverer | Prehistoric |
S | SpecificHeat | 0.71 |
S | NumberofShells | 3 |
S | NumberofValence | 6 |
Cl | AtomicNumber | 17 |
Cl | Element | Chlorine |
Cl | Symbol | Cl |
Cl | AtomicMass | 35.453 |
Cl | NumberofNeutrons | 18 |
Cl | NumberofProtons | 17 |
Cl | NumberofElectrons | 17 |
Cl | Period | 3 |
Cl | Group | 17 |
Cl | Phase | gas |
Cl | Natural | yes |
Cl | Nonmetal | yes |
Cl | Type | Halogen |
Cl | AtomicRadius | 0.97 |
Cl | Electronegativity | 3.16 |
Cl | FirstIonization | 12.9676 |
Cl | Density | 3.21E-03 |
Cl | MeltingPoint | 172.31 |
Cl | BoilingPoint | 239.11 |
Cl | NumberOfIsotopes | 11 |
Cl | Discoverer | Scheele |
Cl | Year | 1774 |
Cl | SpecificHeat | 0.479 |
Cl | NumberofShells | 3 |
Cl | NumberofValence | 7 |
Ar | AtomicNumber | 18 |
Ar | Element | Argon |
Ar | Symbol | Ar |
Ar | AtomicMass | 39.948 |
Ar | NumberofNeutrons | 22 |
Ar | NumberofProtons | 18 |
Ar | NumberofElectrons | 18 |
Ar | Period | 3 |
Ar | Group | 18 |
Ar | Phase | gas |
Ar | Natural | yes |
Ar | Nonmetal | yes |
Ar | Type | NobleGas |
Ar | AtomicRadius | 0.88 |
Ar | FirstIonization | 15.7596 |
Ar | Density | 1.78E-03 |
Ar | MeltingPoint | 83.96 |
Ar | BoilingPoint | 87.3 |
Ar | NumberOfIsotopes | 8 |
Ar | Discoverer | Rayleigh_and_Ramsay |
Ar | Year | 1894 |
Ar | SpecificHeat | 0.52 |
Ar | NumberofShells | 3 |
Ar | NumberofValence | 8 |
Convert Specific Columns¶
kgtk normalize-nodes -i examples/docs/periodic_table_of_elements_1-18.tsv \
--columns AtomicNumber Element Symbol AtomicMass
node1 | label | node2 |
---|---|---|
H | AtomicNumber | 1 |
H | Element | Hydrogen |
H | Symbol | H |
H | AtomicMass | 1.007 |
He | AtomicNumber | 2 |
He | Element | Helium |
He | Symbol | He |
He | AtomicMass | 4.002 |
Li | AtomicNumber | 3 |
Li | Element | Lithium |
Li | Symbol | Li |
Li | AtomicMass | 6.941 |
Be | AtomicNumber | 4 |
Be | Element | Beryllium |
Be | Symbol | Be |
Be | AtomicMass | 9.012 |
B | AtomicNumber | 5 |
B | Element | Boron |
B | Symbol | B |
B | AtomicMass | 10.811 |
C | AtomicNumber | 6 |
C | Element | Carbon |
C | Symbol | C |
C | AtomicMass | 12.011 |
N | AtomicNumber | 7 |
N | Element | Nitrogen |
N | Symbol | N |
N | AtomicMass | 14.007 |
O | AtomicNumber | 8 |
O | Element | Oxygen |
O | Symbol | O |
O | AtomicMass | 15.999 |
F | AtomicNumber | 9 |
F | Element | Fluorine |
F | Symbol | F |
F | AtomicMass | 18.998 |
Ne | AtomicNumber | 10 |
Ne | Element | Neon |
Ne | Symbol | Ne |
Ne | AtomicMass | 20.18 |
Na | AtomicNumber | 11 |
Na | Element | Sodium |
Na | Symbol | Na |
Na | AtomicMass | 22.99 |
Mg | AtomicNumber | 12 |
Mg | Element | Magnesium |
Mg | Symbol | Mg |
Mg | AtomicMass | 24.305 |
Al | AtomicNumber | 13 |
Al | Element | Aluminum |
Al | Symbol | Al |
Al | AtomicMass | 26.982 |
Si | AtomicNumber | 14 |
Si | Element | Silicon |
Si | Symbol | Si |
Si | AtomicMass | 28.086 |
P | AtomicNumber | 15 |
P | Element | Phosphorus |
P | Symbol | P |
P | AtomicMass | 30.974 |
S | AtomicNumber | 16 |
S | Element | Sulfur |
S | Symbol | S |
S | AtomicMass | 32.065 |
Cl | AtomicNumber | 17 |
Cl | Element | Chlorine |
Cl | Symbol | Cl |
Cl | AtomicMass | 35.453 |
Ar | AtomicNumber | 18 |
Ar | Element | Argon |
Ar | Symbol | Ar |
Ar | AtomicMass | 39.948 |
Convert Specific Columns with Alternate Relationship Names¶
--labels LABEL ...
allows you to specify the relationsip symbols used in the
output KGTK edge file. When this option is specified, one lable must be
supplied for each column extracted.
kgtk normalize-nodes -i examples/docs/periodic_table_of_elements_1-18.tsv \
--columns AtomicNumber Element AtomicMass \
--labels atomic_number element atomic_mass
node1 | label | node2 |
---|---|---|
H | atomic_number | 1 |
H | element | Hydrogen |
H | atomic_mass | 1.007 |
He | atomic_number | 2 |
He | element | Helium |
He | atomic_mass | 4.002 |
Li | atomic_number | 3 |
Li | element | Lithium |
Li | atomic_mass | 6.941 |
Be | atomic_number | 4 |
Be | element | Beryllium |
Be | atomic_mass | 9.012 |
B | atomic_number | 5 |
B | element | Boron |
B | atomic_mass | 10.811 |
C | atomic_number | 6 |
C | element | Carbon |
C | atomic_mass | 12.011 |
N | atomic_number | 7 |
N | element | Nitrogen |
N | atomic_mass | 14.007 |
O | atomic_number | 8 |
O | element | Oxygen |
O | atomic_mass | 15.999 |
F | atomic_number | 9 |
F | element | Fluorine |
F | atomic_mass | 18.998 |
Ne | atomic_number | 10 |
Ne | element | Neon |
Ne | atomic_mass | 20.18 |
Na | atomic_number | 11 |
Na | element | Sodium |
Na | atomic_mass | 22.99 |
Mg | atomic_number | 12 |
Mg | element | Magnesium |
Mg | atomic_mass | 24.305 |
Al | atomic_number | 13 |
Al | element | Aluminum |
Al | atomic_mass | 26.982 |
Si | atomic_number | 14 |
Si | element | Silicon |
Si | atomic_mass | 28.086 |
P | atomic_number | 15 |
P | element | Phosphorus |
P | atomic_mass | 30.974 |
S | atomic_number | 16 |
S | element | Sulfur |
S | atomic_mass | 32.065 |
Cl | atomic_number | 17 |
Cl | element | Chlorine |
Cl | atomic_mass | 35.453 |
Ar | atomic_number | 18 |
Ar | element | Argon |
Ar | atomic_mass | 39.948 |
Using An Alternate ID¶
--id-column ID_COLUMN_NAME
specifies a column to be used instead of
the normal id
column for the source of the node1
values in the output file.
kgtk normalize-nodes -i examples/docs/periodic_table_of_elements_1-18.tsv \
--columns AtomicNumber Symbol AtomicMass \
--labels atomic_number symbol atomic_mass \
--id-column Element
node1 | label | node2 |
---|---|---|
Hydrogen | atomic_number | 1 |
Hydrogen | symbol | H |
Hydrogen | atomic_mass | 1.007 |
Helium | atomic_number | 2 |
Helium | symbol | He |
Helium | atomic_mass | 4.002 |
Lithium | atomic_number | 3 |
Lithium | symbol | Li |
Lithium | atomic_mass | 6.941 |
Beryllium | atomic_number | 4 |
Beryllium | symbol | Be |
Beryllium | atomic_mass | 9.012 |
Boron | atomic_number | 5 |
Boron | symbol | B |
Boron | atomic_mass | 10.811 |
Carbon | atomic_number | 6 |
Carbon | symbol | C |
Carbon | atomic_mass | 12.011 |
Nitrogen | atomic_number | 7 |
Nitrogen | symbol | N |
Nitrogen | atomic_mass | 14.007 |
Oxygen | atomic_number | 8 |
Oxygen | symbol | O |
Oxygen | atomic_mass | 15.999 |
Fluorine | atomic_number | 9 |
Fluorine | symbol | F |
Fluorine | atomic_mass | 18.998 |
Neon | atomic_number | 10 |
Neon | symbol | Ne |
Neon | atomic_mass | 20.18 |
Sodium | atomic_number | 11 |
Sodium | symbol | Na |
Sodium | atomic_mass | 22.99 |
Magnesium | atomic_number | 12 |
Magnesium | symbol | Mg |
Magnesium | atomic_mass | 24.305 |
Aluminum | atomic_number | 13 |
Aluminum | symbol | Al |
Aluminum | atomic_mass | 26.982 |
Silicon | atomic_number | 14 |
Silicon | symbol | Si |
Silicon | atomic_mass | 28.086 |
Phosphorus | atomic_number | 15 |
Phosphorus | symbol | P |
Phosphorus | atomic_mass | 30.974 |
Sulfur | atomic_number | 16 |
Sulfur | symbol | S |
Sulfur | atomic_mass | 32.065 |
Chlorine | atomic_number | 17 |
Chlorine | symbol | Cl |
Chlorine | atomic_mass | 35.453 |
Argon | atomic_number | 18 |
Argon | symbol | Ar |
Argon | atomic_mass | 39.948 |
Note
This example assumes that the input files contains an id
field, but
another field is being substituted for it. If the input file does not
contain an id
field at all, the expert option --mode=NONE
is also needed.
Expert Example: CSV Input File without id
Field¶
If the input file does not have an id
field, the option --id-column ID_COLUMN_NAME
may
be used to select a substitute for the id
column. The expert option --mode=NONE
is also needed. This example also illustrates using a CSV file as an input file,
using the expert option --input-format csv
.
kgtk normalize-nodes -i examples/docs/periodic_table_of_elements_1-18.csv \
--mode=NONE --input-format csv \
--columns AtomicNumber Symbol AtomicMass \
--labels atomic_number symbol atomic_mass \
--id-column Element
node1 | label | node2 |
---|---|---|
Hydrogen | atomic_number | 1 |
Hydrogen | symbol | H |
Hydrogen | atomic_mass | 1.007 |
Helium | atomic_number | 2 |
Helium | symbol | He |
Helium | atomic_mass | 4.002 |
Lithium | atomic_number | 3 |
Lithium | symbol | Li |
Lithium | atomic_mass | 6.941 |
Beryllium | atomic_number | 4 |
Beryllium | symbol | Be |
Beryllium | atomic_mass | 9.012 |
Boron | atomic_number | 5 |
Boron | symbol | B |
Boron | atomic_mass | 10.811 |
Carbon | atomic_number | 6 |
Carbon | symbol | C |
Carbon | atomic_mass | 12.011 |
Nitrogen | atomic_number | 7 |
Nitrogen | symbol | N |
Nitrogen | atomic_mass | 14.007 |
Oxygen | atomic_number | 8 |
Oxygen | symbol | O |
Oxygen | atomic_mass | 15.999 |
Fluorine | atomic_number | 9 |
Fluorine | symbol | F |
Fluorine | atomic_mass | 18.998 |
Neon | atomic_number | 10 |
Neon | symbol | Ne |
Neon | atomic_mass | 20.18 |
Sodium | atomic_number | 11 |
Sodium | symbol | Na |
Sodium | atomic_mass | 22.99 |
Magnesium | atomic_number | 12 |
Magnesium | symbol | Mg |
Magnesium | atomic_mass | 24.305 |
Aluminum | atomic_number | 13 |
Aluminum | symbol | Al |
Aluminum | atomic_mass | 26.982 |
Silicon | atomic_number | 14 |
Silicon | symbol | Si |
Silicon | atomic_mass | 28.086 |
Phosphorus | atomic_number | 15 |
Phosphorus | symbol | P |
Phosphorus | atomic_mass | 30.974 |
Sulfur | atomic_number | 16 |
Sulfur | symbol | S |
Sulfur | atomic_mass | 32.065 |
Chlorine | atomic_number | 17 |
Chlorine | symbol | Cl |
Chlorine | atomic_mass | 35.453 |
Argon | atomic_number | 18 |
Argon | symbol | Ar |
Argon | atomic_mass | 39.948 |