INOH Pathway Database: October 2007 Archives

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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.

Paxtools provides a complete domain object model (DOM) in Java that enables users manipulating and evaluating BioPAX. It also provides state-of-the-art persistence services based on Java Persistence API. Finally Paxtools implement a fail-fast validation framework, mitigating the cost of potential pitfalls for the developers. Paxtools was designed to be modular, lightweight and platform independent to be easily embedded into applications.

[quoted from the ISMB2007 poster abstract]

Posted by KenFukuda : 10:47 AM | TrackBacks

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

MoleculeRole Ontology Release Notes
=====================
Version: 2.22 (Oct 3, 2007)

Molecule Role is a hierarchical ontology which contains the molecular functional group names, the abstract molecule names and the concrete molecule names collected from literature manually. This classification is based on a conceptual classification of molecular roles in protein interaction and signal transduction.

Changes from version 2.1x
=====================
KEGG metabolic pathway related molecules (500~ chemicals and 300~ proteins) were added.

Changes from version 2.0x
=====================
Over 13,000 synonyms were added from EntrezGene, HGNC, FlyBase, OMIM, MGI and RGD database in an automatic way, using UniProt ACs manually collected in Molecule Role.

Changes from version 1.xx
=====================
The ontologies and definitions are provided together in a single OBO format flat file. This data is NOT also available in the GO flat file format as an ontology file and a definitions file.

Protein sequences (=UniProt ACs) in the DbXrefs of protein leaf-class entries have been separated as new protein leaf-class entries. The parents-children relationship type is "sequence_of". The relationships of "Concrete-Names (e.g. ERK1)" and protein sequences (e.g. P27361) have been defined explicitly.

More information about MoleculeRole Ontology
---------------------
Satoko Yamamoto, Takao Asanuma, Toshihisa Takagi, Ken Ichiro Fukuda. The Molecule Role Ontology: an ontology for annotation of signal transduction pathway molecules in the scientific literature. Comparative and Functional Genomics 2004 Volume 5, Issue 6-7, p 528-536. (http://www3.interscience.wiley.com/cgi-bin/fulltext/109860932/HTMLSTART)

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

Posted by SatokoYamamoto : 05:44 PM | TrackBacks

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

Event Ontology Release Notes
=====================
Version: 1.62 (3rd Oct. 2007)

Event Ontology is an ontology that organizes the concepts and terms of pathway objects such as sub-pathways, biological processes and experimental environments appearing in the cellular pathway (e.g. signal transductions, disease pathways, metabolic pathways, etc.) The concepts in the Event Ontology were manually extracted from scientific articles and text books. Each concept has a link to Gene Ontology if possible.

Changes from version 1.61
=====================
[Added terms and definitions]

1. terms related to genetic interaction (e.g., IEV_0003393:synthetic interaction)
2. subpathways related to EPO signaling pathway (e.g., IEV_0003438:Binding of EPO receptor and STAT3)
3. subpathways related to TNFR signaling pathway (e.g., IEV_0003418:Proteasome degradation of c-FLIP)
4. etc.

More information about Event Ontology
---------------------
Tatsuya Kushida, Toshihisa Takagi and Ken Ichiro Fukuda, Event Ontology: A Pathway-Centric Ontology for Biological Processes. Pacific Symposium on Biocomputing 11:152-163(2006).