Import GPML format to the MINERVA Platform and export as GPML from MINERVA are not symmetrical due to differences between both formats. Tables below contain information on how particular reactions and elements are mapped between formats (from GPML to CellDesigner and opposite direction CellDesigner to GPML).
To learn more, see example 8 - GPML file display.
Import GPML to MINERVA#
| GPML format | MINERVA (CellDesigner based format) |
|---|---|
| DATA NODES | SPECIES |
| ———– | ———————————– |
| gene | gene |
| ———– | ———————————– |
| metabolite | simple molecule |
| ———– | ———————————– |
| pathway | phenotype |
| ———– | ———————————– |
| protein | protein |
| ———– | ———————————– |
| RNA | RNA |
| ———– | ———————————– |
| unknown | unknown |
| ———– | ———————————– |
| complex | complex |
| ———– | ———————————– |
| group | hypothetical complex |
| ———– | ———————————– |
| MIM INTERACTIONS | REACTIONS |
| mim-necessary-stimulation | reduced physical stimulation |
| ———– | ———————————— |
| mim-binding | unknown transition |
| ———– | ———————————— |
| mim-conversion | state transition |
| ———– | ———————————— |
| mim-stimulation | reduced physical stimulation |
| ———– | ———————————— |
| mim-modification | positive influence |
| ———– | ———————————— |
| mim-catalysis | positive influence |
| ———– | ———————————— |
| mim-inhibition | negative influence |
| ———– | ———————————— |
| mim-cleavage | state transition |
| ———– | ———————————— |
| mim-covalent-bond | reversible unknown transition |
| ———– | ———————————— |
| mim-branching-left | reversible unknown transition |
| ———– | ———————————— |
| mim-branching-right | reversible unknown transition |
| ———– | ———————————— |
| mim-transcription-translation | state transition |
| ———– | ———————————— |
| mim-gap | reversible unknown transition |
| BASIC INTERACTIONS | REACTIONS |
| new-line | reversible unknown transition |
| ———– | ———————————– |
| new-arrow | state transition |
| ———– | ———————————– |
| new-dashedline | reversible unknown transition |
| ———– | ———————————– |
| new-dashedarrow | unknown positive influence |
| ———– | ———————————– |
| new-elbow | reversible unknown transition |
| ———– | ———————————– |
| new-curve | reversible unknown transition |
| ———– | ———————————– |
| new-tbar | negative influence |
| GRAPHICAL ELEMENTS | PATHWAYS |
| ALL elements except degraded and new-line | pathway |
| ——————— | —————————- |
| new-line | the element is not displayed |
| ———————— | —————————- |
| degraded | degraded |
| CELLULAR COMPARTMENTS | COMPARTMENTS |
| ALL compartments | compartment |
Export as GPML from MINERVA#
| MINERVA (CellDesigner based format) | GPML format |
|---|---|
| SPECIES | DATA NODES |
| —————- | ———————————– |
| gene | gene |
| —————- | ———————————– |
| RNA | RNA |
| —————- | ———————————– |
| antisense RNA | RNA |
| —————- | ———————————– |
| simple molecule | metabolite |
| —————- | ———————————– |
| drug | metabolite |
| —————- | ———————————– |
| ion | metabolite |
| —————- | ———————————– |
| phenotype | pathway |
| —————- | ———————————– |
| protein | protein |
| —————- | ———————————– |
| truncated protein | protein |
| ———– | ———————————– |
| ion channel | protein |
| ———– | ———————————– |
| receptor | protein |
| ———– | ———————————– |
| degraded | degraded (graphical element) |
| ———– | ———————————– |
| unknown | unknown |
| ———– | ———————————– |
| complex | complex |
| REACTIONS | INTERACTIONS |
| ———– | ———————————– |
| state transition | new-arrow |
| ———– | ———————————– |
| transcription | mim-conversion |
| ———– | ———————————– |
| translation | mim-conversion |
| ———– | ———————————– |
| known transition omitted | mim-conversion |
| ———– | ———————————– |
| transport | mim-conversion |
| ———– | ———————————– |
| unknown transition | mim-gap |
| ———– | ———————————– |
| reversible state transition | new-arrow-arrow |
| ———– | ———————————– |
| dissociation | mim-conversion |
| ———– | ———————————– |
| heterodimer association | mim-binding |
| ———– | ———————————– |
| truncation | mim-conversion |
| ———– | ———————————– |
| boolean reaction | mim-conversion |
| REACTIONS reduced notation | INTERACTIONS |
| positive influence | mim-modification |
| ———– | ———————————– |
| negative influence | mim-inhibition |
| ———– | ———————————– |
| reduced physical stimulation | mim-necessary-stimulation |
| ———– | ———————————– |
| reduced modulation | mim-conversion |
| ———– | ———————————– |
| reduced trigger | mim-conversion |
| ———– | ———————————– |
| unknown positive influence | new-arrow dashed |
| ———– | ———————————– |
| unknown negative influence | mim-inhibition dashed |
| ———– | ———————————– |
| unknown reduced physical stimulation | mim-conversion dashed |
| ———– | ———————————– |
| unknown reduced modulation | mim-conversion dashed |
| ———– | ———————————– |
| unknown reduced trigger | mim-conversion dashed |
| REACTIONS modulation | INTERACTIONS |
| catalysis | mim-catalysis |
| ———– | ———————————– |
| inhibition | mim-conversion dashed |
| ———– | ———————————– |
| physical stimulation | mim-necessary-stimulation |
| ———– | ———————————– |
| trigger | mim-modification |
| ———– | ———————————– |
| modulation | mim-modification |
| ———– | ———————————– |
| any above modulation unknown | any above interaction dashed |
| PATHWAY / COMPARTMENT | RECTANGLE (graphical element) |