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#9 Amino acid ontology
Following the Tuesday discussion, I have created a
lineage for canonical amino acid residues from
bioontology as follows:
%CHEBI:24432 biological function ontology
%CHEBI:33694 biopolymers
%CHEBI:33695 information biopolymers
%CHEBI:16541 proteins
<CHEBI:33700 canonical amino-acid residues
%CHEBI:29948 L-alanine residue
%CHEBI:29950 L-cysteine residue
%CHEBI:29958 L-aspartic acid residue
%CHEBI:29972 L-glutamic acid residue
%CHEBI:29997 L-phenylalanine residue
%CHEBI:29947 glycine residue
%CHEBI:29979 L-histidine residue
%CHEBI:30009 L-isoleucine residue
%CHEBI:29967 L-lysine residue
%CHEBI:29983 L-methionine residue
%CHEBI:29956 L-asparagine residue
%CHEBI:30017 L-proline residue
%CHEBI:30011 L-glutamine residue
%CHEBI:29952 L-arginine residue
%CHEBI:29999 L-serine residue
%CHEBI:30013 L-threonine residue
%CHEBI:30000 L-selenocysteine residue
%CHEBI:30015 L-valine residue
%CHEBI:29954 L-tryptophan residue
%CHEBI:29975 L-tyrosine residue
%CHEBI:30006 L-leucine residue
%CHEBI:33716 N-terminal canonical amino-acid residues
%CHEBI:33717 C-terminal canonical amino-acid residues
%CHEBI:33726 canonical amino-acid residue anions
%CHEBI:33727 canonical amino-acid residue cations
%CHEBI:33728 canonical amino-acid residue radicals
On the molecular structure side, the lineage is as
...
%CHEBI:24833 oxoacids
%CHEBI:33575 carboxylic acids
%CHEBI:33709 amino acids
%CHEBI:33704 α-amino acids
%CHEBI:15705 L-α-amino acids
...
etc.
One detailed example is provided for cysteine and all
its forms (ions, radicals, groups, residues etc.).
Please have a look and send your comments.
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Cysteine has been given a thorough treatment and this can
serve as a model for classifying the other alpha-amino
acids.
A possibility for simplifying the structure is to delete
the subclass 'sulfur amino acids' which has but two
members, cysteine and methionine. However this then might
create a gap at the end of the branch 'sulfur molecular
entities' -> 'organosulfur compunds' -> 'sulfur-containing
carboxylic acids' -> 'sulfur amino acids'. This route
enables users to navigate down from sulfur molecular
entities to cysteine, which could well be useful to
biologists. Any opinions on the fors and againsts of
deleting this subclass?
Also, in view of discussions which took place on 17/1/06, I
propose deletion of the various familes of amino acids
(e.g. CHEBI:26650 serine family amino acids). These are
based on biosynthetic routes and are inappropriate for a
chemical ontology, belonging more in a reactions database.