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	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