LiteFold/GO huggingface dataset:
fatty acid catabolic process (GO:0009062)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of a fatty acid, any of the aliphatic monocarboxylic acids that can be liberated by hydrolysis from naturally occurring fats and oils. Fatty acids are predominantly straight-chain acids of 4 to 24 carbon atoms, which may be saturated or unsaturated; branched fatty acids and hydroxy fatty acids also occur, and very long chain acids of over 30 carbons are found in waxes.
Synonyms: fatty acid breakdown; fatty acid catabolism; fatty acid degradation
amino acid catabolic process (GO:0009063)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of amino acids, organic acids containing one or more amino substituents.
Synonyms: amino acid breakdown; amino acid catabolism; amino acid degradation; cellular amino acid catabolic process
obsolete glutamine family amino acid metabolic process (GO:0009064)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways involving amino acids of the glutamine family, comprising arginine, glutamate, glutamine and proline.
Synonyms: glutamine family amino acid metabolism
Comment: The reason for obsoletion is that this is an unnecessary grouping term.
obsolete glutamine family amino acid catabolic process (GO:0009065)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the breakdown of amino acids of the glutamine family, comprising arginine, glutamate, glutamine and proline.
Synonyms: glutamine family amino acid breakdown; glutamine family amino acid catabolism; glutamine family amino acid degradation
Comment: The reason for obsoletion is that this term is an unnecessary grouping term.
obsolete aspartate family amino acid metabolic process (GO:0009066)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways involving amino acids of the aspartate family, comprising asparagine, aspartate, lysine, methionine and threonine.
Synonyms: aspartate family amino acid metabolism
Comment: The reason for obsoletion is that this is an unnecessary grouping term.
aspartate family amino acid biosynthetic process (GO:0009067)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of amino acids of the aspartate family, comprising asparagine, aspartate, lysine, methionine and threonine.
Synonyms: aspartate family amino acid anabolism; aspartate family amino acid biosynthesis; aspartate family amino acid formation; aspartate family amino acid synthesis
obsolete serine family amino acid metabolic process (GO:0009069)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways involving amino acids of the serine family, comprising cysteine, glycine, homoserine, selenocysteine and serine.
Synonyms: serine family amino acid metabolism
Comment: The reason for obsoletion is that this is an unnecessary grouping term.
serine family amino acid biosynthetic process (GO:0009070)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of amino acids of the serine family, comprising cysteine, glycine, homoserine, selenocysteine and serine.
Synonyms: serine family amino acid anabolism; serine family amino acid biosynthesis; serine family amino acid formation; serine family amino acid synthesis
obsolete serine family amino acid catabolic process (GO:0009071)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the breakdown of amino acids of the serine family, comprising cysteine, glycine, homoserine, selenocysteine and serine.
Synonyms: serine family amino acid breakdown; serine family amino acid catabolism; serine family amino acid degradation
Comment: The reason for obsoletion is that this is an unnecessary grouping term.
aromatic amino acid metabolic process (GO:0009072)
Namespace: biological_process
Definition: The chemical reactions and pathways involving aromatic amino acid family, amino acids with aromatic ring (phenylalanine, tyrosine, tryptophan).
Synonyms: aromatic amino acid family metabolic process; aromatic amino acid family metabolism
aromatic amino acid family biosynthetic process (GO:0009073)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of aromatic amino acid family, amino acids with aromatic ring (phenylalanine, tyrosine, tryptophan).
Synonyms: aromatic amino acid family anabolism; aromatic amino acid family biosynthesis; aromatic amino acid family biosynthetic process, shikimate pathway; aromatic amino acid family formation; aromatic amino acid family synthesis
aromatic amino acid family catabolic process (GO:0009074)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of aromatic amino acid family, amino acids with aromatic ring (phenylalanine, tyrosine, tryptophan).
Synonyms: aromatic amino acid family breakdown; aromatic amino acid family catabolism; aromatic amino acid family degradation
obsolete histidine family amino acid metabolic process (GO:0009075)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways involving amino acids of the histidine family.
Synonyms: histidine family amino acid metabolic process; histidine family amino acid metabolism
Comment: This term was made obsolete because it was an unnecessary grouping term, as histidine would be the only member of this family.
obsolete histidine family amino acid biosynthetic process (GO:0009076)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the formation of amino acids of the histidine family.
Synonyms: histidine family amino acid anabolism; histidine family amino acid biosynthesis; histidine family amino acid biosynthetic process; histidine family amino acid formation; histidine family amino acid synthesis
Comment: This term was made obsolete because it was an unnecessary grouping term, as histidine would be the only member of this family.
obsolete histidine family amino acid catabolic process (GO:0009077)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the breakdown of amino acids of the histidine family.
Synonyms: histidine family amino acid breakdown; histidine family amino acid catabolic process; histidine family amino acid catabolism; histidine family amino acid degradation
Comment: This term was made obsolete because it was an unnecessary grouping term, as histidine would be the only member of this family.
obsolete pyruvate family amino acid metabolic process (GO:0009078)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways involving any amino acid that requires pyruvate for its synthesis, e.g. alanine.
Synonyms: pyruvate family amino acid metabolism
Comment: This term was obsoleted because it is an unnecessary grouping class.
pyruvate family amino acid biosynthetic process (GO:0009079)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of any amino acid that requires pyruvate for its synthesis, e.g. alanine.
Synonyms: pyruvate family amino acid anabolism; pyruvate family amino acid biosynthesis; pyruvate family amino acid formation; pyruvate family amino acid synthesis
obsolete pyruvate family amino acid catabolic process (GO:0009080)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the breakdown of any amino acid that requires pyruvate for its synthesis, e.g. alanine.
Synonyms: pyruvate family amino acid breakdown; pyruvate family amino acid catabolism; pyruvate family amino acid degradation
Comment: The reason for obsoletion is that this is an unnecessary grouping term
branched-chain amino acid metabolic process (GO:0009081)
Namespace: biological_process
Definition: The chemical reactions and pathways involving amino acids containing a branched carbon skeleton, comprising isoleucine, leucine and valine.
Synonyms: branched chain family amino acid metabolism
branched-chain amino acid biosynthetic process (GO:0009082)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of amino acids containing a branched carbon skeleton, comprising isoleucine, leucine and valine.
Synonyms: branched chain family amino acid anabolism; branched chain family amino acid biosynthesis; branched chain family amino acid biosynthetic process; branched chain family amino acid formation; branched chain family amino acid synthesis
branched-chain amino acid catabolic process (GO:0009083)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of amino acids containing a branched carbon skeleton, comprising isoleucine, leucine and valine.
Synonyms: branched chain family amino acid breakdown; branched chain family amino acid catabolic process; branched chain family amino acid catabolism; branched chain family amino acid degradation
L-glutamine family amino acid biosynthetic process (GO:0009084)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of amino acids of the glutamine family, comprising arginine, glutamate, glutamine and proline.
Synonyms: glutamine family amino acid anabolism; glutamine family amino acid biosynthesis; glutamine family amino acid formation; glutamine family amino acid synthesis
obsolete methionine biosynthetic process (GO:0009086)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the de novo formation of L-methionine (2-amino-4-(methylthio)butanoic acid), a sulfur-containing, essential amino acid found in peptide linkage in proteins.
Synonyms: methionine anabolism; methionine biosynthesis; methionine formation; methionine synthesis
Comment: The reason for obsoletion is that this term was an unnecessary grouping term.
L-methionine catabolic process (GO:0009087)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of L-methionine.
Synonyms: methionine breakdown; methionine catabolism; methionine degradation
obsolete L-lysine biosynthetic process via diaminopimelate (GO:0009089)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the formation of lysine, via the intermediate diaminopimelate.
Synonyms: diaminopimelate pathway; diaminopimelic acid pathway; lysine anabolism via diaminopimelate; lysine biosynthesis via diaminopimelic acid; lysine biosynthetic process via diaminopimelic acid; lysine formation via diaminopimelate; lysine synthesis via diaminopimelate
Comment: The reason for obsoletion is that this term represents a GO-CAM model.
L-homoserine biosynthetic process (GO:0009090)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of homoserine, alpha-amino-gamma-hydroxybutyric acid.
Synonyms: homoserine anabolism; homoserine biosynthesis; homoserine formation; homoserine synthesis
obsolete L-homoserine catabolic process (GO:0009091)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the breakdown of homoserine, alpha-amino-gamma-hydroxybutyric acid.
Synonyms: homoserine breakdown; homoserine catabolism; homoserine degradation
Comment: This term was obsoleted because there is no evidence that a specific pathway for L-homoserine degradation exists.
obsolete cysteine catabolic process (GO:0009093)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the breakdown of cysteine, 2-amino-3-mercaptopropanoic acid.
Synonyms: cysteine breakdown; cysteine catabolism; cysteine degradation
Comment: The reason for obsoletion is that a more specific term has been created.
L-phenylalanine biosynthetic process (GO:0009094)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of L-phenylalanine, the L-enantiomer of 2-amino-3-phenylpropanoic acid, i.e. (2S)-2-amino-3-phenylpropanoic acid.
Synonyms: L-phenylalanine anabolism; L-phenylalanine biosynthesis; L-phenylalanine formation; L-phenylalanine synthesis; phenylalanine biosynthesis; phenylalanine biosynthetic process; phenylalanine biosynthetic process, prephenate pathway; phenylalanine biosynthetic process, shikimate pathway
aromatic amino acid family biosynthetic process, prephenate pathway (GO:0009095)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of phenylalanine and tyrosine from other compounds, including chorismate, via the intermediate prephenate.
Synonyms: aromatic amino acid family anabolism, prephenate pathway; aromatic amino acid family biosynthetic process via prephenate; aromatic amino acid family biosynthetic process via prephenate(2-); aromatic amino acid family formation, prephenate pathway; aromatic amino acid family synthesis, prephenate pathway
obsolete isoleucine biosynthetic process (GO:0009097)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the formation of isoleucine, (2R*,3R*)-2-amino-3-methylpentanoic acid.
Synonyms: isoleucine anabolism; isoleucine biosynthesis; isoleucine formation; isoleucine synthesis
Comment: The reason for obsoletion is that more specific terms were created.
L-leucine biosynthetic process (GO:0009098)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of L-leucine, 2-amino-4-methylpentanoic acid.
Synonyms: L-leucine anabolism; L-leucine biosynthesis; L-leucine formation; L-leucine synthesis; leucine biosynthetic process
L-valine biosynthetic process (GO:0009099)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of valine, 2-amino-3-methylbutanoic acid.
Synonyms: valine anabolism; valine biosynthesis; valine formation; valine synthesis
glycoprotein metabolic process (GO:0009100)
Namespace: biological_process
Definition: The chemical reactions and pathways involving glycoproteins, a protein that contains covalently bound glycose (i.e. monosaccharide) residues; the glycose occurs most commonly as oligosaccharide or fairly small polysaccharide but occasionally as monosaccharide.
Synonyms: glycoprotein metabolism
glycoprotein biosynthetic process (GO:0009101)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of glycoproteins, a protein that contains covalently bound glycose (i.e. monosaccharide) residues; the glycose occurs most commonly as oligosaccharide or fairly small polysaccharide but occasionally as monosaccharide.
Synonyms: glycoprotein anabolism; glycoprotein biosynthesis; glycoprotein formation; glycoprotein synthesis
biotin biosynthetic process (GO:0009102)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of biotin, cis-tetrahydro-2-oxothieno(3,4-d)imidazoline-4-valeric acid.
Synonyms: biotin anabolism; biotin biosynthesis; biotin formation; biotin synthesis; vitamin B7 biosynthesis; vitamin B7 biosynthetic process; vitamin H biosynthesis; vitamin H biosynthetic process
lipopolysaccharide biosynthetic process (GO:0009103)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of lipopolysaccharides, any of a group of related, structurally complex components of the outer membrane of Gram-negative bacteria.
Synonyms: lipopolysaccharide anabolism; lipopolysaccharide biosynthesis; lipopolysaccharide formation; lipopolysaccharide synthesis; LPS biosynthetic process
lipopolysaccharide catabolic process (GO:0009104)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of lipopolysaccharides, any of a group of related, structurally complex components of the outer membrane of Gram-negative bacteria.
Synonyms: lipopolysaccharide breakdown; lipopolysaccharide catabolism; lipopolysaccharide degradation; LPS catabolic process
lipoate metabolic process (GO:0009106)
Namespace: biological_process
Definition: The chemical reactions and pathways involving lipoate, 1,2-dithiolane-3-pentanoate, the anion derived from lipoic acid.
Synonyms: lipoate metabolism; lipoic acid metabolic process; lipoic acid metabolism
lipoate biosynthetic process (GO:0009107)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of lipoate, 1,2-dithiolane-3-pentanoate, the anion derived from lipoic acid.
Synonyms: lipoate anabolism; lipoate biosynthesis; lipoate formation; lipoate synthesis; lipoic acid anabolism; lipoic acid biosynthesis; lipoic acid biosynthetic process; lipoic acid formation; lipoic acid synthesis
obsolete coenzyme biosynthetic process (GO:0009108)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the formation of coenzymes, any of various nonprotein organic cofactors that are required, in addition to an enzyme and a substrate, for an enzymatic reaction to proceed.
Synonyms: coenzyme anabolism; coenzyme and prosthetic group biosynthesis; coenzyme and prosthetic group biosynthetic process; coenzyme biosynthesis; coenzyme formation; coenzyme synthesis
Comment: 1. Making inferences in GO about compounds based on the coenzyme role curated by ChEBI creates relationships that are not always true which violates ontological principles for GO; therefore we will cease making these inferences. 2. It is not meaningful to group biosynthetic processes that are not all metabolically related by the fact that they may be used as a coenzyme.
obsolete coenzyme catabolic process (GO:0009109)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the breakdown of coenzymes, any of various nonprotein organic cofactors that are required, in addition to an enzyme and a substrate, for an enzymatic reaction to proceed.
Synonyms: coenzyme and prosthetic group catabolic process; coenzyme and prosthetic group catabolism; coenzyme breakdown; coenzyme catabolism; coenzyme degradation
Comment: 1. Making inferences in GO about compounds based on the coenzyme role curated by ChEBI creates relationships that are not always true which violates ontological principles for GO; therefore we will cease making these inferences. 2. It is not meaningful to group catabolic processes that are not all metabolically related by the fact that they may be used as a coenzyme.
vitamin biosynthetic process (GO:0009110)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of a vitamin, one of a number of unrelated organic substances that occur in many foods in small amounts and that are necessary in trace amounts for the normal metabolic functioning of the body.
Synonyms: vitamin anabolism; vitamin biosynthesis; vitamin formation; vitamin synthesis
nucleobase metabolic process (GO:0009112)
Namespace: biological_process
Definition: The chemical reactions and pathways involving a nucleobase, a nitrogenous base that is a constituent of a nucleic acid, e.g. the purines: adenine, guanine, hypoxanthine, xanthine and the pyrimidines: cytosine, uracil, thymine.
Synonyms: nucleobase metabolism
purine nucleobase biosynthetic process (GO:0009113)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of purine nucleobases, one of the two classes of nitrogen-containing ring compounds found in DNA and RNA, which include adenine and guanine.
Synonyms: purine base anabolism; purine base biosynthesis; purine base biosynthetic process; purine base formation; purine base synthesis
hypoxanthine catabolic process (GO:0009114)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of hypoxanthine, 6-hydroxy purine, an intermediate in the degradation of adenylate. Its ribonucleoside is known as inosine and its ribonucleotide as inosinate.
Synonyms: hypoxanthine breakdown; hypoxanthine catabolism; hypoxanthine degradation; hypoxanthine oxidation
xanthine catabolic process (GO:0009115)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of xanthine, 2,6-dihydroxypurine, a purine formed in the metabolic breakdown of guanine but not present in nucleic acids.
Synonyms: xanthine breakdown; xanthine catabolism; xanthine degradation; xanthine oxidation
nucleoside metabolic process (GO:0009116)
Namespace: biological_process
Definition: The chemical reactions and pathways involving a nucleoside, a nucleobase linked to either beta-D-ribofuranose (a ribonucleoside) or 2-deoxy-beta-D-ribofuranose, (a deoxyribonucleoside), e.g. adenosine, guanosine, inosine, cytidine, uridine and deoxyadenosine, deoxyguanosine, deoxycytidine and thymidine (= deoxythymidine).
Synonyms: nucleoside metabolism
nucleotide metabolic process (GO:0009117)
Namespace: biological_process
Definition: The chemical reactions and pathways involving a nucleotide, a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the glycose moiety; may be mono-, di- or triphosphate; this definition includes cyclic nucleotides (nucleoside cyclic phosphates).
Synonyms: nucleotide metabolism
regulation of nucleoside metabolic process (GO:0009118)
Namespace: biological_process
Definition: Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving nucleosides.
Synonyms: regulation of nucleoside metabolism
ribonucleoside metabolic process (GO:0009119)
Namespace: biological_process
Definition: The chemical reactions and pathways involving any ribonucleoside, a nucleoside in which purine or pyrimidine base is linked to a ribose (beta-D-ribofuranose) molecule.
Synonyms: ribonucleoside metabolism
2'-deoxyribonucleoside metabolic process (GO:0009120)
Namespace: biological_process
Definition: The chemical reactions and pathways involving any one of a family of organic molecules consisting of a purine or pyrimidine base covalently bonded to a sugar deoxyribose (a deoxyribonucleoside).
Synonyms: deoxyribonucleoside metabolic process; deoxyribonucleoside metabolism
nucleoside monophosphate metabolic process (GO:0009123)
Namespace: biological_process
Definition: The chemical reactions and pathways involving a nucleoside monophosphate, a compound consisting of a nucleobase linked to a deoxyribose or ribose sugar esterified with phosphate on the sugar.
Synonyms: nucleoside monophosphate metabolism
nucleoside monophosphate biosynthetic process (GO:0009124)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of a nucleoside monophosphate, a compound consisting of a nucleobase linked to a deoxyribose or ribose sugar esterified with phosphate on the sugar.
Synonyms: nucleoside monophosphate anabolism; nucleoside monophosphate biosynthesis; nucleoside monophosphate formation; nucleoside monophosphate synthesis
nucleoside monophosphate catabolic process (GO:0009125)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of a nucleoside monophosphate, a compound consisting of a nucleobase linked to a deoxyribose or ribose sugar esterified with phosphate on the sugar.
Synonyms: nucleoside monophosphate breakdown; nucleoside monophosphate catabolism; nucleoside monophosphate degradation
purine nucleoside monophosphate metabolic process (GO:0009126)
Namespace: biological_process
Definition: The chemical reactions and pathways involving purine nucleoside monophosphate, a compound consisting of a purine base linked to a ribose or deoxyribose sugar esterified with phosphate on the sugar.
Synonyms: purine nucleoside monophosphate metabolism