semtools

Translate term lists

Take a list of code terms and pas to name terms

Input

GO:0005499
GO:0005502
GO:0016918

The script takes a input file with one code term per line and translates the list to term names

semtools -O GO -i terms.txt -l names

Click to see results
GO:0005499 vitamin D binding
GO:0005502 11-cis retinal binding
GO:0016918 retinal binding

Get children terms

Use a list of parent terms to obtain a list of child terms

We use -C to specify whic terms use as parents to obtain all childs (from the next level to the finale leafs in the ontology). Then, all childs for the specified parents are unified in one list.

semtools -C GO:0019842,GO:0002060 -O GO

Click to see results
GO:0005499
GO:0005502
GO:0016918
GO:0005503
GO:0005542
GO:0008431
GO:0009374
GO:0019841
GO:0030170
GO:0070279
GO:0030975
GO:0030976
GO:0031177
GO:0031418
GO:0031419
GO:0070280
GO:0070281
GO:0070282
GO:1902098
GO:1902271
GO:1902118
GO:1904768
GO:0002055
GO:0002057
GO:0160050

Use a list of parent terms to obtain a list of parent-child term names

With '/' character previous to the term list specified with -C flag we an use modificators such 'r' to obtain pairs parent-child and 'n' to translate term codes to term names.

semtools -C 'rn/GO:0019842,GO:0002060' -O GO

Click to see results
vitamin D binding D3 vitamins binding
retinal binding 11-cis retinal binding
retinal binding all-trans retinal binding
retinol binding all-trans-retinol binding
vitamin B6 binding pyridoxal phosphate binding
vitamin B6 binding pyridoxal binding
vitamin B6 binding pyridoxamine binding
vitamin B6 binding pyridoxine binding
D3 vitamins binding calcitriol binding
D3 vitamins binding calcidiol binding
vitamin binding vitamin D binding
vitamin binding folic acid binding
vitamin binding vitamin E binding
vitamin binding biotin binding
vitamin binding retinal binding
vitamin binding retinol binding
vitamin binding thiamine binding
vitamin binding thiamine pyrophosphate binding
vitamin binding phosphopantetheine binding
vitamin binding L-ascorbic acid binding
vitamin binding cobalamin binding
vitamin binding vitamin B6 binding
purine nucleobase binding adenine binding
purine nucleobase binding guanine binding
purine nucleobase binding xanthine binding

Use a list of child terms to obtain a list of parent-child term names limiting the levels

Others -C modificators are 'a' which assumes that the given terms are childs and that the user desires the parent terms of these childs. The numbers of levels checked (parents or childs without 'a' or not) could be controlled with 'hN' where N must be an integrate with the number of hops (i.e. 'h2' means that the command only must check the next/previous two levels of the ontology)

semtools -C 'rah2n/GO:0019842,GO:0002060' -O GO

Click to see results
nucleobase binding purine nucleobase binding
small molecule binding heterocyclic compound binding
organic cyclic compound binding nucleobase binding
heterocyclic compound binding nucleobase binding
small molecule binding vitamin binding
binding small molecule binding
binding organic cyclic compound binding

Take a list of code terms and remove whose terms with a given parent

Input

Show imput data
GO:0005499
GO:0005502
GO:0016918
GO:0005503
GO:0005542
GO:0008431
GO:0009374
GO:0019841
GO:0030170
GO:0070279
GO:0030975
GO:0030976
GO:0031177
GO:0031418
GO:0031419
GO:0070280
GO:0070281
GO:0070282

To filter a list of code terms the -F flag must be used with a string that with specifices white lists (p, to keep terms with a given parent) or black list (n, to remove terms with a given parent). Parents are listed as comma separated term list flanked by '(' and ')'. The string can include several especifications of this estructure. The flag '--list' specifies that the input file is one item per line list.

semtools -i terms.txt -F 'n(GO:0070279)' --list -O GO

Click to see results
GO:0005499
GO:0005502
GO:0016918
GO:0005503
GO:0005542
GO:0008431
GO:0009374
GO:0019841
GO:0070279
GO:0030975
GO:0030976
GO:0031177
GO:0031418
GO:0031419