Commit 2db83592 authored by VIGNET Pierre's avatar VIGNET Pierre
Browse files

[doc] Update databases metrics, links to the new models etc.

parent ddc3f4ef
......@@ -77,71 +77,77 @@ Advanced users will be able to create their own models from a SPARQL endpoint as
Obtaining these data from the models is also explained in the chapter `Query the Cadbiom model`_.
Here is a table of the raw data in various BioPAX databases:
Here is a table of the number of the BioPAX types found in various databases:
.. csv-table::
:header: Metrics - Databases , PID , Kegg , Reactome , CellDesigner
Entity,,,,27426??
Pathway,745,122,2148,13
Gene,,,,
PhysicalEntity,,,1447,1718/11922??
Protein,6194,1872,24676,6851
Complex,4137,,11715,2323/2358??
SmallMolecule,173,1664,3574,0/555??
Dna,,,645,1030
Rna,22,,292,0/1164??
Interaction,,,,
BiochemicalReaction,1824,1782,10197,6863
ComplexAssembly,2722,,,1743
TemplateReaction,1492,,39,
Transport,312,,,699
MolecularInteraction,,4,,
Degradation,,,17,
TransportWithBiochemicalReaction,154,,,
Catalysis,3800,1782,4929,6186
Control,322/2380??,,1516/1522??,
TemplateReactionRegulation,2023,,43,
Modulation,,,24,
:header: Metrics - Databases , PID , Kegg , Reactome , ACSN
Entity , , , , 27426\*
Pathway , 745 , 122 , 2139 , 13
Gene , , , ,
PhysicalEntity , , , 1447 , 1718/11922\*
Protein , 6194 , 1872 , 24676 , 6851
Complex , 4137 , , 11715 , 2323/2358\*
SmallMolecule , 173 , 1664 , 3574 , 0/555\*
Dna , , , 645 , 1030
Rna , 22 , , 292 , 0/1164\*
Interaction , , , ,
BiochemicalReaction , 1824 , 1782 , 10197 , 6863
ComplexAssembly , 2722 , , , 1743
TemplateReaction , 1492 , , 39 ,
Transport , 312 , , , 699
MolecularInteraction , , 4 , ,
Degradation , , , 17 ,
TransportWithBiochemicalReaction, 154 , , ,
Catalysis , 3800 , 1782 , 4929 , 6186
Control , 322 , , 1516 ,
TemplateReactionRegulation , 2023 , , 43 ,
Modulation , , , 24 ,
\*: Number before cleaning of incorrect/duplicate types in triplestore.
i.e. the entire database, for the Entity type.
Here is a table presenting some metrics interpreted according to the raw BioPAX data obtained:
.. csv-table::
:header: Metrics - Databases , PID , Kegg , Reactome , CellDesigner
:header: Metrics - Databases , PID , Kegg , Reactome , ACSN
Retrieved PhysicalEntities , 10526 , 3536 , 42349 , 1716
Total of duplicated entities , 699 , 135 , 2333 , 90
Nb of groups of duplicated entities , 339 , 61 , 692 , 39
Classes , 403 , 0 , 4224 , 0
Used classes , 273 , 0 , 1597 , 0
Nested classes , 23 , 0 , 573 , 0
Total of duplicated entities , 699 , 135 , 2341 , 74
Nb of groups of duplicated entities , 339 , 61 , 696 , 23
Classes , 403 , 0 , 4229 , 0
Used classes , 304 , 0 , 1611 , 0
Nested classes , 23 , 0 , 574 , 0
Classes with ModificationFeatures , 157 , 0 , 0 , 0
Classes/complexes , 66 , 0 , 669 , 0
Final number of entities (after processing) , , , ,
Retrieved Reactions , 6504 , 1786 , 10253 , 2074
Proteins involved as reactants , 6337 , 0 , 8218 , NA
SmallMolecules involved as reactants , 570 , 7190 , 12490 , NA
Complexes involved as reactants , , , , NA
Retrieved Reactions , 6504 , 1786 , 10253 , 9305
Proteins involved as reactants , 3304 , 0 , 4777 , 4840
SmallMolecules involved as reactants , 128 , 1571 , 2604 , NA
Complexes involved as reactants , 3733 , 0 , 7642 , 2217
Retrieved Controls , 6195 , 2716 , 6606 , 558
Retrieved Controls , 6145 , 1782 , 6512 , 6186
Catalysis control , 3800 , 1782 , 4929 , 494
Reactions with similar entities as reactants and products , 50 , 934 , 94 , 64
Reactions with similar entities as reactants and products , 50 , 934 , 94 , 333
Controls of other controls , 0 , 0 , 24 , 0
Here is the the characteristics of the generated models:
.. csv-table::
:header: Metrics - Databases, PID , Kegg , Reactome , CellDesigner
:header: Metrics - Databases, PID , Kegg , Reactome , ACSN
Cadbiom entities , 9445 , 2363 , NA , 10234
Cadbiom entities , 9788 , 2604 , NA , 10313
Genes , 788 , 2 , NA , 1035
, :download:`csv <./_static/demo_files/models_sept_2019/genes_pid.csv>`/:download:`json <./_static/demo_files/models_sept_2019/model_summary_genes_pid.json>`, :download:`csv <./_static/demo_files/models_sept_2019/genes_kegg.csv>`/:download:`json <./_static/demo_files/models_sept_2019/model_summary_genes_kegg.json>`, NA, :download:`csv <./_static/demo_files/models_sept_2019/genes_cg.csv>`/:download:`json <./_static/demo_files/models_sept_2019/model_summary_genes_cg.json>`
Boundaries , 3769 , 1179 , NA , 3614
, :download:`csv <./_static/demo_files/models_sept_2019/boundaries_pid.csv>`/:download:`json <./_static/demo_files/models_sept_2019/model_summary_boundaries_pid.json>`, :download:`csv <./_static/demo_files/models_sept_2019/boundaries_kegg.csv>`/:download:`json <./_static/demo_files/models_sept_2019/model_summary_boundaries_kegg.json>`, NA, :download:`csv <./_static/demo_files/models_sept_2019/boundaries_cg.csv>`/:download:`json <./_static/demo_files/models_sept_2019/model_summary_boundaries_cg.json>`
Transitions , 10212 , 5220 , NA , 11315
Events , 6700 , 1570 , NA , 8740
Models , :download:`bcx file <./_static/demo_files/models_sept_2019/model_without_scc_pid.bcx>`, :download:`bcx file <./_static/demo_files/models_sept_2019/model_without_scc_kegg.bcx>`, NA, :download:`bcx file <./_static/demo_files/models_sept_2019/model_without_scc_cg.bcx>`
, :download:`csv <./_static/demo_files/models_mars_2020/genes_pid.csv>`/:download:`json <./_static/demo_files/models_mars_2020/model_summary_genes_pid.json>`, :download:`csv <./_static/demo_files/models_mars_2020/genes_kegg.csv>`/:download:`json <./_static/demo_files/models_mars_2020/model_summary_genes_kegg.json>`, NA, :download:`csv <./_static/demo_files/models_mars_2020/genes_acsn.csv>`/:download:`json <./_static/demo_files/models_mars_2020/model_summary_genes_acsn.json>`
Boundaries , 3925 , 1420 , NA , 3693
, :download:`csv <./_static/demo_files/models_mars_2020/boundaries_pid.csv>`/:download:`json <./_static/demo_files/models_mars_2020/model_summary_boundaries_pid.json>`, :download:`csv <./_static/demo_files/models_mars_2020/boundaries_kegg.csv>`/:download:`json <./_static/demo_files/models_mars_2020/model_summary_boundaries_kegg.json>`, NA, :download:`csv <./_static/demo_files/models_mars_2020/boundaries_acsn.csv>`/:download:`json <./_static/demo_files/models_mars_2020/model_summary_boundaries_acsn.json>`
Transitions , 11036 , 5220 , NA , 11394
Events , 7501 , 1570 , NA , 8819
Models , :download:`bcx file <./_static/demo_files/models_mars_2020/model_pid_without_scc.bcx>`, :download:`bcx file <./_static/demo_files/models_mars_2020/model_kegg_without_scc.bcx>`, NA, :download:`bcx file <./_static/demo_files/models_mars_2020/model_acsn_without_scc.bcx>`
Note: Use *"Save as"* after a right click on the download links if your browser tries to open files in a new tab...
.. todo::
Explain these data
......@@ -824,7 +830,7 @@ The generated model will be placed in the ``./output`` folder;
we will focus on the model with specific alterations
intended to optimize the operation of Cadbiom and its solver: ``./output/model_without_scc.bcx``.
(Download link: :download:`pid_model_without_scc.bcx <./_static/demo_files/models_sept_2019/model_without_scc_pid.bcx>`)
(Download link: :download:`pid_model_without_scc.bcx <./_static/demo_files/models_mars_2020/model_pid_without_scc.bcx>`)
.. note:: Small graphs can be queried and converted from the GUI of Cadbiom.
......
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