Adding missing CHEBI xps

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Metabolism

Issues still to resolve

  • salvage/cycle terms?
  • further qualifications e.g. aerobic, anaerobic (in PATO? make new genus terms in GO), de novo (define in terms of inputs and outputs), neutral
  • particular protein types e.g. amyloid precursor protein, FasL, CD4 and glycoproteins
  • dependencies e.g. anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process, modification-dependent protein catabolic process (has_part protein modification or starts_with protein modification)
  • location e.g. angiotensin catabolic process in blood, ascospore wall chitin catabolic process, capsule polysaccharide biosynthetic process, cell wall (1->3)-alpha-glucan biosynthetic process

(where a cc, use occurs_in? More complex - needs more consideration).

  • amino acid family terms - no xps for these
  • RNA/DNA - specific sequence binding terms, TFs (SO?) - requires separate set. Use what's in CHEBI for now.
  • fermentation (type of catabolism?)

Other oddities:

GO:0002812	biosynthetic process of antibacterial peptides active against Gram-negative bacteria
GO:0002815	biosynthetic process of antibacterial peptides active against Gram-positive bacteria
GO:0019254	carnitine metabolic process, CoA-linked
GO:0019616	catechol catabolic process, meta-cleavage
GO:0019615	catechol catabolic process, ortho-cleavage
GO:0030995	cell septum edging catabolic process
GO:0050653	chondroitin sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process
GO:0050652	dermatan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process

GO:0010406	classical arabinogalactan protein metabolic process
GO:0006112	energy reserve metabolic process
GO:0009244	lipopolysaccharide core region biosynthetic process
GO:0046401	lipopolysaccharide core region metabolic process
GO:0006515	misfolded or incompletely synthesized protein catabolic process
GO:0018131	oxazole or thiazole biosynthetic process
GO:0046484	oxazole or thiazole metabolic process
GO:0010597	green leaf volatile biosynthetic process
GO:0046951 ! ketone body biosynthetic process
GO:0046952 ! ketone body catabolic process
GO:0006490 ! oligosaccharide-lipid intermediate biosynthetic process
GO:0006730 ! one-carbon metabolic process
GO:0010192 ! mucilage biosynthetic process
"Mucilage is a thick, gluey substance produced by most plants and some microorganisms. It is a polar glycoprotein and an exopolysaccharide." - is this a chemical or a cc?

see also

GO:0048358 ! mucilage pectin biosynthetic process
GO:0048357 ! pedicel mucilage biosynthetic process


GO:0016053 ! organic acid biosynthetic process
GO:0016054 ! organic acid catabolic process
GO:0006082 ! organic acid metabolic process

acid is_a role: these should be defined as organic molecular entities that has_role acid

GO:0006733 ! oxidoreduction coenzyme metabolic process
GO:0010403 ! pectic arabinogalactan I metabolic process
GO:0010401 ! pectic galactan metabolic process

Transport

  • secretion:
[Term]
id: GO:0032310  ! prostaglandin secretion
intersection_of: GO:0046903  ! secretion
intersection_of: results_in_transport_of CHEBI:59326  ! prostaglandin

are these sufficient? How is it distinguished from regular transport? Secretion is export from tissue or cell.

  • transmembrane
  • export, efflux/import, influx
  • from X/into X (generally X = cc)
  • across (e.g. protein transport across periplasmic space)
  • by (e.g. protein transport by the Tat complex)
  • within (e.g. protein transport within lipid bilayer)
  • qualifiers: high-affinity,
  • dependencies e.g. sodium-dependent
  • coupled e.g. ATP synthesis-coupled