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?)
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?
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
[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.
- 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