Some stats about databases
- PE: PhysicalEntities
- CMPLX: Complexes
- SMLM: SmallMolecules
- CL: Classes
- R: Reactions
- CTRL: Controls
-
int
: Not supported
Note: For Kegg, PID, Reactome, files comes from PathwayCommons. The Kegg version contains only metabolism data.
DB | PE | R | PE inheritance of CL attributes | PE duplicates-groups | Proteins in R | SMLM in Reactions | CMPLX/CL | CMPLX/CL w/ components | CL-CL used | Nested CL | CL in CTRL |
---|---|---|---|---|---|---|---|---|---|---|---|
PID v9 | 10526 | 6504 | 11124 | 699-339 | 6337 | 570 | 66 | 2 | 403-273 | 23 |
363 |
Kegg v10 | 3536 | 1786 | 3536 | 135-61 | 0 | 7190 | 0 | 0 | 0-0 | 0 | 0 |
Reactome v9 | 42349 | 10253 | ? |
2333-692 | 8218 | 12490 | 665 | 0 | 4224-1597 | 573 |
1140 |
EMT CellD* | 1716 | 2074 | 1716 | 90-39 | NC #6 | NC #6 | 0 | 0 | 0 | 0 | 0 |
*See #6
Types of controls:
DB | CTRL | CL Catalysis | CL TemplateReactionRegulation | CL Control | Entities on both sides of R | Modulation | Doesn't control R | CTRL w/ many controllers |
---|---|---|---|---|---|---|---|---|
PID v9 | 6195 | 3800 | 2023 | 322 | 50 | 0 | 0 | 0 |
Kegg v10 | 2716 | 1782 | 0 | 0 | 934 | 0 | 0 | 545 |
Reactome v9 | 6606 | 4929 | 43 | 1516 | 94 | 24 |
24 |
0 |
EMT CellD* | 558 | 494 | 0 | 64 | 0 | 0 | 0 |
*See #6
Cadbiom models
DB | Cadbiom entities | Cadbiom transitions |
---|---|---|
PID v9 | 9572 | 10813 |
Kegg v10 | 2359 | 5220 |
Reactome v9 | NC | NC |
EMT CellD | 1515 | 1784 |
Direction of Interactions
DB | BiochemicalReaction REVERSIBLE | BiochemicalReaction LEFT_TO_RIGHT | Catalysis LEFT_TO_RIGHT | Degradation LEFT_TO_RIGHT |
---|---|---|---|---|
PID v9 | 0 | 0 | 3793 | 0 |
Kegg v10 | 18154 |
5163 | 0 | 0 |
Reactome v9 | 0 | 36053 | 0 | 0 |
EMT CellD* | 0 | 0 | 0 | 0 |
*See #6
Note:
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX biopax3: <http://www.biopax.org/release/biopax-level3.owl#>
PREFIX XMLSchema: <http://www.w3.org/2001/XMLSchema#>
SELECT ?conversionDirection ?reactionType count(?conversionDirection)
FROM <http://biopax.org/lvl3>
FROM <http://www.pathwaycommons.org/v10/kegg>
WHERE
{
?reaction rdf:type ?reactionType .
?reactionType rdfs:subClassOf* biopax3:Interaction .
OPTIONAL {?reaction biopax3:conversionDirection ?conversionDirection . }
OPTIONAL {?reaction biopax3:catalysisDirection ?conversionDirection . }
}
GROUP BY ?reactionType ?conversionDirection
Edited by VIGNET Pierre