October 25, 2007
Paxtools Level2 persistency layer available!
Paxtools persistency layer for BioPAX Level 2 specification is available from the BioPAX sourceforge CVS.
Paxtools is a Domain Object Model(DOM) for BioPAX, providing software tools such as editors, exporters, importers, visualization tools and analysis algorithms with an API for manipulating BioPAX models. The Paxtools core model is developed at CBIO, MSKCC and the persistency layer is developed by INOH database.
#NOTE: Currently we only have a "dev" version in the CVS.
[documents]
Find out here how to set up your Paxtools with a backbone DBMS.
The javadoc for the Paxtools Level2 persistency layer API is available here.
You can also get the pdf file of the paxtools poster abstract at ISMB 2007 here.
Continue reading"Paxtools Level2 persistency layer available!"
Posted by KenFukuda : 10:47 AM | TrackBacks (0)
October 03, 2007
MoleculeRole Ontology Ver.2.22
The latest MoleculeRole Ontology is Ver2.22
MoleculeRole Ontology is an ontology for proteins.
You can download it from the OBO site and from our download page.
Statistics
==========
All entries 8821
Chemicals 592
Proteins 8228
Obsoletes 25
UniProt ACs 5572
GO IDs 344
InterPro ACs 32
KEGG COMPOUND IDs 587
PubMed IDs 99
Continue reading"MoleculeRole Ontology Ver.2.22"
Posted by SatokoYamamoto : 05:44 PM | TrackBacks (0)
Event Ontology Ver.1.62
The latest Event Ontology is Ver.1.62
Event Ontology is an ontology of pathways.
It classifies pathways, sub-pathways and other biological phenomena to form a DAG structure.
You can download it from the OBO site and from our download page.
Statistics
==========
All entries 2781
Obsoletes 37
definition 470
GO IDs 406
KEGG PATHWAY IDs 184
Reactome IDs 110
PSI-MI IDs 68
Continue reading"Event Ontology Ver.1.62"
Posted by NorikoSakai : 05:33 PM | TrackBacks (0)
March 31, 2007
INOH release 1.5 has been released (BioPAX format included)
Additional curation and bug fixes to BioPAX level2 export has been done.
The data is available from our download site.
==========
Statistics
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BioPAX Level2 instances:
control 105
catalysis 451
conversion 133
biochemicalReaction 469
complexAssembly 688
transport 124
physicalEntityParticipant 2479
sequenceParticipant 5104
pathway 332
pathwayStep 1670
complex 1621
dna 143
protein 2606
rna 60
smallMolecule 126
Continue reading"INOH release 1.5 has been released (BioPAX format included)"
Posted by KenFukuda : 11:47 AM | TrackBacks (0)
March 29, 2007
MoleculeRole Ontology Ver.2.21
The latest MoleculeRole Ontology is Ver2.21
MoleculeRole Ontology is an ontology for proteins.
You can download it from the OBO site and from our download page.
Statistics
==========
All entries 8649
Chemicals 592
Proteins 8056
Obsoletes 25
UniProt ACs 5465
GO IDs 329
InterPro ACs 32
KEGG COMPOUND IDs 587
PubMed IDs 81
Continue reading"MoleculeRole Ontology Ver.2.21"
Posted by SatokoYamamoto : 11:35 AM | TrackBacks (0)
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