Adding missing CHEBI xps

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