#######################################
# jeden spravny prazdny zaznam pre vas :)

ENTITY ID:
ENTITY NAME:
CLASSIFICATION:
LOCATIONS:
STATES:
COMPOSITION:
DESCRIPTION:
LINKS:
ORGANISM:
NOTES:

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# Compartments

ENTITY ID:	pbr
ENTITY NAME:	photobioreactor
CLASSIFICATION:	compartment
LOCATIONS:	
STATES:
COMPOSITION:
DESCRIPTION:	Machine, which is used to study cell growth and metabolic activity of cyanobacteria by measuring secondary metabolites as O2, CO2 or ethanol in medium.
LINKS:	doi::10.1002/elsc.200800123
ORGANISM:
NOTES:	


ENTITY ID:	bub
ENTITY NAME:	bubbles
CLASSIFICATION:	compartment
LOCATIONS:	pbr
STATES:
COMPOSITION:
DESCRIPTION:	Gas-phase: bubbles
LINKS:
ORGANISM:
NOTES:	


ENTITY ID:	hsp
ENTITY NAME:	headspace
CLASSIFICATION:	compartment
LOCATIONS:	pbr
STATES:
COMPOSITION:
DESCRIPTION:	Gas-phase: headspace
LINKS:
ORGANISM:
NOTES:	


ENTITY ID:	liq
ENTITY NAME:	medium
CLASSIFICATION:	compartment
LOCATIONS:	pbr
STATES:
COMPOSITION:
DESCRIPTION:	Liquid medium, where cells are situated.
LINKS:	
NOTES:	


ENTITY ID:	ext
ENTITY NAME:	extracellular space
CLASSIFICATION:	compartment
LOCATIONS:
STATES:
COMPOSITION:
DESCRIPTION: That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.	
LINKS:
ORGANISM:
NOTES:


ENTITY ID:	cell
ENTITY NAME:	cell
CLASSIFICATION:	biological entity, compartment
LOCATIONS:	liq
STATES:
COMPOSITION:
DESCRIPTION:	The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope. [source: GOC:go_curators] 
LINKS:	go::0005623
ORGANISM:
NOTES:	


ENTITY ID:	cax
ENTITY NAME:	carboxysome
CLASSIFICATION:	compartment
LOCATIONS: cell	
STATES:	
COMPOSITION:
DESCRIPTION: Microcompartiment surrounded by a protein shell. Plays major role in Carbon Concentrating Mechanism (CCM).	
LINKS:	doi::10.1128/MMBR.00061-12.
ORGANISM:
NOTES:
	

ENTITY ID:	pps
ENTITY NAME:	periplasmic space
CLASSIFICATION:	cellular component, compartment
LOCATIONS:	cell
STATES:
COMPOSITION:
DESCRIPTION:	The region between cytoplasmic membrane and cell wall.
LINKS:	go::0042597
ORGANISM:
NOTES:	


ENTITY ID:	cyt
ENTITY NAME:	cytosol
CLASSIFICATION:	compartment, cellular component
LOCATIONS:	cell
STATES:
COMPOSITION:
DESCRIPTION:	It is liquid content of cytoplasm.
LINKS:	 go::0005829 
ORGANISM:
NOTES:	


ENTITY ID:	cym
ENTITY NAME:	cytoplasmic membrane
CLASSIFICATION:	cellular component, compartment
LOCATIONS:	cell
STATES:
COMPOSITION:
DESCRIPTION:	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. 
LINKS:	go::0005886
ORGANISM:
NOTES:	


ENTITY ID:	tlm
ENTITY NAME:	thylakoid membrane
CLASSIFICATION:	compartment, cellular component
LOCATIONS:	cell
STATES:COMPOSITION:
DESCRIPTION:	A membrane enriched in complexes formed of reaction centers, accessory pigments and electron carriers, in which photosynthetic reactions take place. 
LINKS:	go::0034357
ORGANISM:
NOTES:	


ENTITY ID:	lum
ENTITY NAME:	lumen
CLASSIFICATION:	cellular component, compartment
LOCATIONS:	tlm
STATES:
COMPOSITION:
DESCRIPTION: 	The volume enclosed by a thylakoid membrane. 	
LINKS:	go::0031977
ORGANISM:
NOTES:	


# Entities (note compartments have the same format)


ENTITY ID:	h
ENTITY NAME:	proton
CLASSIFICATION:	subatomic particle
LOCATIONS:	cyt, lum, liq, pps, cym, cax, ext
STATES:	{+}
COMPOSITION:
DESCRIPTION:	
LINKS:	chebi::24636
ORGANISM:
NOTES:	


ENTITY ID:	CO2
ENTITY NAME:	carbon dioxide
CLASSIFICATION:	small molecule
LOCATIONS:	lum, cell, liq, bub, hsp, pps, cyt, ext, cax
STATES:
COMPOSITION:
DESCRIPTION:	Carbon dioxide (chemical formula CO2) is a naturally occurring chemical compound composed of two oxygen atoms covalently bonded to a single carbon atom. It is a gas at standard temperature and pressure and exists in Earth's atmosphere in this state, as a trace gas at a concentration of 0.039 per cent by volume.
LINKS:	chebi::16526, pubchem::280
ORGANISM:
NOTES:	


ENTITY ID:	H2O
ENTITY NAME:	water
CLASSIFICATION:	small molecule
LOCATIONS:	cell, liq, pps, lum, cyt, cax, ext
STATES:
COMPOSITION:
DESCRIPTION: An oxygen hydride consisting of an oxygen atom that is covalently bonded to two hydrogen atoms.	
LINKS:	kegg::C00001,  	chebi::15377 
ORGANISM:
NOTES:	


ENTITY ID:	HCO3
ENTITY NAME:	hydrogencarbonate
CLASSIFICATION:	small molecule
LOCATIONS:	cyt, cell, liq, ext, cax
STATES:	{-}
COMPOSITION:
DESCRIPTION:	The carbon oxoanion resulting from the removal of a proton from carbonic acid.
LINKS:	chebi::17544
ORGANISM:
NOTES:	


ENTITY ID:	OH
ENTITY NAME:	hydroxide
CLASSIFICATION:	
LOCATIONS:	liq
STATES:	{-}
COMPOSITION:
DESCRIPTION:	
LINKS:	chebi::16234
ORGANISM:
NOTES:	


#######################################
# jeden spravny prazdny zaznam pre vas :)

RULE ID:
RULE EQUATION:
RULE NAME:
CLASSIFICATION:
MODIFIER:
DESCRIPTION:
LINKS:
NOTES:

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# Rules


RULE ID:
RULE NAME:	Carbon dioxide hydration
RULE EQUATION:	"CO2::liq" + "H2O::liq" <=>  "HCO3{-}::liq" + "h{+}::liq"
CLASSIFICATION:	
MODIFIER:
DESCRIPTION:	Carbon dioxide hydration
LINKS:	
NOTES:


RULE ID:	
RULE NAME:	Water self-dissociation
RULE EQUATION:	"H2O::liq" <=> "h{+}::liq"+ "OH{-}::liq"
CLASSIFICATION:	
MODIFIER:	
DESCRIPTION:	Water self-dissociation.
LINKS:	
NOTES:


RULE ID:	
RULE NAME:	Carbon dioxide hydroxylation
RULE EQUATION:	"CO2::liq" + "OH{-}::liq" <=> "HCO3{-}::liq"
CLASSIFICATION:	
MODIFIER:
DESCRIPTION:	Carbon dioxide hydroxylation/dehydroxylation
LINKS:	
NOTES:


RULE ID:	
RULE NAME:	Bubble-liquid carbon dioxide transfer
RULE EQUATION:	"CO2::bub" <=> "CO2::liq"
CLASSIFICATION:		
MODIFIER:
DESCRIPTION:	Bubble-liquid carbon dioxide transfer
LINKS:	
NOTES:


RULE ID:	
RULE NAME:	Carbon dioxide excretion
RULE EQUATION:	"CO2::cell" <=> "CO2::liq"
CLASSIFICATION:	
MODIFIER:	
DESCRIPTION:	Carbon dioxide excretion by the cells.
LINKS:	
NOTES:


RULE ID:	
RULE NAME:	Bicarbonate excretion
RULE EQUATION:	"HCO3{-}::cell" <=> "HCO3{-}::liq"
CLASSIFICATION:	
MODIFIER:
DESCRIPTION:	Bicarbonate excretion from cells.
LINKS:	
NOTES:
	

RULE ID:	R671
RULE NAME:	R671
RULE EQUATION:	"CO2::cyt" => "CO2::ext"
CLASSIFICATION: 	Transport
MODIFIER:	
DESCRIPTION:	
LINKS:	
NOTES:


RULE ID:	R672
RULE NAME:	R672
RULE EQUATION:	"H2O::ext" <=> "H2O::cyt"
CLASSIFICATION: 	Transport
MODIFIER:	
DESCRIPTION:	
LINKS:	
NOTES: evid/relia::A	
	

RULE ID:	R718
RULE NAME:	R718
RULE EQUATION:	"h{+}::cyt" <=> "h{+}::cax"
CLASSIFICATION: 	Transport
MODIFIER:	
DESCRIPTION:	
LINKS:	
NOTES:


RULE ID:	R719
RULE NAME:	R719
RULE EQUATION:	"O2::cyt" => "O2::cax"
CLASSIFICATION: 	Transport
MODIFIER:	
DESCRIPTION:	
LINKS:	
NOTES:


RULE ID:	R720
RULE NAME:	R720
RULE EQUATION:	"HCO3{-}::cyt" => "HCO3{-}::cax"
CLASSIFICATION: 	Transport
MODIFIER:	
DESCRIPTION:	
LINKS:	
NOTES: