Question

Reading nested tags in SBML with SBMLR (R package)

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srinadee • 0

@srinadee-8283

Last seen 9.5 years ago

Hello,

I have a SBML file. I want to create a tale including the ReactionID, Reaction Name, Reactant Species and Gene Association. Below is the structure of one reaction.

<reaction id="R_DM_4CRSOL" name="Sink needed to allow p-Cresol to leave system" reversible="false">
<notes>
<html xmlns="http://www.w3.org/1999/xhtml">
<p>GENE_ASSOCIATION: B21_02644</p>
<p>SUBSYSTEM: </p>
</html>
</notes>
<listOfReactants>
<speciesReference species="M_4crsol_c" stoichiometry="1"/>
<speciesReference species="M_4crsol_c_boundary" stoichiometry="1"/>
</listOfReactants>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> FLUX_VALUE </ci>
</math>
<listOfParameters>
<parameter id="LOWER_BOUND" value="0" units="mmol_per_gDW_per_hr"/>
.........
<parameter id="FLUX_VALUE" value="0" units="mmol_per_gDW_per_hr"/>
</listOfParameters>
</kineticLaw>
</reaction>

Below is the code I wrote to get the list of reactions and the corresponding metabolites.

library(SBMLR)
sampleFile = readSBML("Sample.xml")
reactions = summary(sampleFile$reactions) #list of reactions
reactants = sampleFile$reactions$R_DM_4CRSOL$reactants #metabolites for each reaction

sampleFile doesn't identify the name attribute or the html tags related to gene association. Can someone please help on this? Thank you

sbml sbmlr r • 1.8k views

ADD COMMENT • link updated 9.5 years ago by radivot ▴ 20 • written 9.5 years ago by srinadee • 0

score 2 · Accepted Answer · 2015-06-27

My goal when I wrote SBMLR was to bring SBML models into R for the purpose of solving differential equations. Things not critical to simulations did not necessarily come into the R object. Reading your file into R below shows what made it and where it ended up. So it looks like all notes in reactions and species went into one global note for the whole model. Because rsbml uses libsbml, and SBMLR does not, I suspect it does a better job of preserving SBML.

library(SBMLR)
sampleFile = readSBML("~/ccf/SB/Sample.xml")
sampleFile

$sbml
xmlns level version
"http://www.sbml.org/sbml/level2" "2" "1"

$id
NULL

$notes
[1] "FORMULA: C21H39N2O8PRS" "CHARGE: -1" "FORMULA: C4H7NO3" "CHARGE: 0"
[5] "FORMULA: C2H2O6P" "CHARGE: -3" "GENE_ASSOCIATION: B21_02644" "SUBSYSTEM:"
[9] "GENE_ASSOCIATION:" "SUBSYSTEM:" "GENE_ASSOCIATION:" "SUBSYSTEM:"

$compartments
$compartments$p
$compartments$p$id
[1] "p"

$compartments$p$size
[1] 1

$compartments$p$name
[1] "Periplasm"

$compartments$c
$compartments$c$id
[1] "c"

$compartments$c$size
[1] 1

$compartments$c$name
[1] "Cytoplasm"

$compartments$e
$compartments$e$id
[1] "e"

$compartments$e$size
[1] 1

$compartments$e$name
[1] "Extracellular"

$species
$species$M_4crsol_c
$species$M_4crsol_c$id
[1] "M_4crsol_c"

$species$M_4crsol_c$ic
[1] 0

$species$M_4crsol_c$compartment
[1] "c"

$species$M_4crsol_c$bc
[1] FALSE

$species$M_4crsol_c_boundary
$species$M_4crsol_c_boundary$id
[1] "M_4crsol_c_boundary"

$species$M_4crsol_c_boundary$ic
[1] 0

$species$M_4crsol_c_boundary$compartment
[1] "c"

$species$M_4crsol_c_boundary$bc
[1] FALSE

$species$M_5drib_c
$species$M_5drib_c$id
[1] "M_5drib_c"

$species$M_5drib_c$ic
[1] 0

$species$M_5drib_c$compartment
[1] "c"

$species$M_5drib_c$bc
[1] FALSE

$globalParameters
list()

$rules
list()

$reactions
$reactions$R_DM_4CRSOL
$reactions$R_DM_4CRSOL$id
[1] "R_DM_4CRSOL"

$reactions$R_DM_4CRSOL$reversible
[1] FALSE

$reactions$R_DM_4CRSOL$reactants
[1] "M_4crsol_c" "M_4crsol_c_boundary"

$reactions$R_DM_4CRSOL$parameters
LOWER_BOUND OBJECTIVE_COEFFICIENT UPPER_BOUND FLUX_VALUE
0 0 1000 0

$reactions$R_DM_4CRSOL$mathmlLaw
<ci>FLUX_VALUE</ci>

$reactions$R_DM_4CRSOL$exprLaw
FLUX_VALUE

$reactions$R_DM_4CRSOL$strLaw
[1] "FLUX_VALUE"

$reactions$R_DM_4CRSOL$law
function (r, p = NULL)
{
LOWER_BOUND = p["LOWER_BOUND"]
OBJECTIVE_COEFFICIENT = p["OBJECTIVE_COEFFICIENT"]
UPPER_BOUND = p["UPPER_BOUND"]
FLUX_VALUE = p["FLUX_VALUE"]
M_4crsol_c = r["M_4crsol_c"]
M_4crsol_c_boundary = r["M_4crsol_c_boundary"]
FLUX_VALUE
}
<environment: 0x11f689ea0>

$reactions$R_DM_5DRIB
$reactions$R_DM_5DRIB$id
[1] "R_DM_5DRIB"

$reactions$R_DM_5DRIB$reversible
[1] FALSE

$reactions$R_DM_5DRIB$reactants
[1] "M_5drib_c" "M_4crsol_c_boundary"

$reactions$R_DM_5DRIB$parameters
LOWER_BOUND OBJECTIVE_COEFFICIENT UPPER_BOUND FLUX_VALUE
0 0 1000 0

$reactions$R_DM_5DRIB$mathmlLaw
<ci>FLUX_VALUE</ci>

$reactions$R_DM_5DRIB$exprLaw
FLUX_VALUE

$reactions$R_DM_5DRIB$strLaw
[1] "FLUX_VALUE"

$reactions$R_DM_5DRIB$law
function (r, p = NULL)
{
LOWER_BOUND = p["LOWER_BOUND"]
OBJECTIVE_COEFFICIENT = p["OBJECTIVE_COEFFICIENT"]
UPPER_BOUND = p["UPPER_BOUND"]
FLUX_VALUE = p["FLUX_VALUE"]
M_5drib_c = r["M_5drib_c"]
M_4crsol_c_boundary = r["M_4crsol_c_boundary"]
FLUX_VALUE
}
<environment: 0x11f39b380>

$reactions$R_DM_AACALD
$reactions$R_DM_AACALD$id
[1] "R_DM_AACALD"

$reactions$R_DM_AACALD$reversible
[1] FALSE

$reactions$R_DM_AACALD$reactants
[1] "M_4crsol_c_boundary" "M_4crsol_c"

$reactions$R_DM_AACALD$parameters
LOWER_BOUND OBJECTIVE_COEFFICIENT UPPER_BOUND FLUX_VALUE
0 0 1000 0

$reactions$R_DM_AACALD$mathmlLaw
<ci>FLUX_VALUE</ci>

$reactions$R_DM_AACALD$exprLaw
FLUX_VALUE

$reactions$R_DM_AACALD$strLaw
[1] "FLUX_VALUE"

$reactions$R_DM_AACALD$law
function (r, p = NULL)
{
LOWER_BOUND = p["LOWER_BOUND"]
OBJECTIVE_COEFFICIENT = p["OBJECTIVE_COEFFICIENT"]
UPPER_BOUND = p["UPPER_BOUND"]
FLUX_VALUE = p["FLUX_VALUE"]
M_4crsol_c_boundary = r["M_4crsol_c_boundary"]
M_4crsol_c = r["M_4crsol_c"]
FLUX_VALUE
}
<environment: 0x1027c1668>

attr(,"class")
[1] "SBMLR"