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).
Statistics
==========
All entries 2781
Obsoletes 37
definition 470
GO IDs 406
KEGG PATHWAY IDs 184
Reactome IDs 110
PSI-MI IDs 68
Posted by NorikoSakai : 05:33 PM | TrackBacks
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
MoleculeRole Ontology Release Notes
=====================
Version: 2.21 (Mar 28, 2006)
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 8649
Chemicals 592
Proteins 8056
Obsoletes 25
UniProt ACs 5465
GO IDs 329
InterPro ACs 32
KEGG COMPOUND IDs 587
PubMed IDs 81
Posted by SatokoYamamoto : 11:35 AM | TrackBacks
March 28, 2007
Event Ontology Ver.1.61
The latest Event Ontology is Ver.1.61
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 2723
Obsoletes 21
definition 455
GO IDs 400
KEGG PATHWAY IDs 184
Reactome IDs 110
PSI-MI IDs 53
Event Ontology Release Notes
=====================
Version: 1.61 (28th Mar. 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 1.60
=====================
[Added terms and definitions]
1. terms related to MAPKKK cascade (e.g., IEV_0003381:Phosphorylation of MKK4 by TAK1)
2. terms related to IL-1 signaling, TLR signaling (e.g., IEV_0003384:Phosphorylation of TAB2 and TAK1)
3. definitions related to Metabolic pathway (e.g., IEV_0001411:Glutamate metabolism)
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).
Statistics
==========
All entries 2723
Obsoletes 21
definition 455
GO IDs 400
KEGG PATHWAY IDs 184
Reactome IDs 110
PSI-MI IDs 53
Posted by NorikoSakai : 07:11 PM | TrackBacks
November 01, 2006
MoleculeRole Ontology Ver.2.20
The latest MoleculeRole Ontology is Ver2.20
MoleculeRole Ontology is an ontology for proteins.
You can download it from the OBO site and from our download page.
Statistics
==========
All entries 8457
Chemicals 592
Proteins 7864
Obsoletes 23
UniProt ACs 5286
GO IDs 322
InterPro ACs 32
KEGG COMPOUND IDs 587
PubMed IDs 78
MoleculeRole Ontology Release Notes
=====================
Version: 2.20 (Nov 1, 2006)
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 8457
Chemicals 592
Proteins 7864
Obsoletes 23
UniProt ACs 5286
GO IDs 322
InterPro ACs 32
KEGG COMPOUND IDs 587
PubMed IDs 78
Posted by SatokoYamamoto : 04:59 PM | TrackBacks
August 23, 2006
Event Ontology Ver.1.60
The latest Event Ontology is Ver.1.60
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.
Event Ontology Release Notes
=====================
Version: 1.60 (23th Aug. 2006)
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 1.59
=====================
[Added terms and definitions]
1. terms related to molecular interaction (e.g., IEV_0002721:enzymatic reaction)
2. definitions related to pathway (e.g., IEV_0000208:IKK-NF-kappaB cascade)
3. 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).
Statistics
==========
All entries 2666
Obsoletes 21
definition 299
GO IDs 259
KEGG PATHWAY IDs 173
Reactome IDs 110
PSI-MI IDs 53
Posted by KenFukuda : 10:19 AM | TrackBacks
March 17, 2006
MoleculeRole Ontology Ver.2.11
The latest MoleculeRole Ontology is Ver2.11
MoleculeRole Ontology is an ontology for proteins.
You can download it from the OBO site and from our download page.
Statistics
==========
All entries 7236
Chemicals 86
Proteins 7149
Obsoletes 19
UniProt ACs 4619
GO IDs 315
InterPro ACs 31
KEGG COMPOUND IDs 85
PubMed IDs 66
MoleculeRole Ontology Release Notes
=====================
Version: 2.11 (Mar 17, 2006)
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 2.0x
=====================
Over 13,000 synonyms were added from EntrezGene, HGNC, FlyBase, OMIM, MGI and RGD database in 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 7236
Chemicals 86
Proteins 7149
Obsoletes 19
UniProt ACs 4619
GO IDs 315
InterPro ACs 31
KEGG COMPOUND IDs 85
PubMed IDs 66
Posted by SatokoYamamoto : 07:23 PM | TrackBacks
February 08, 2006
Event Ontology Ver.1.59
The latest Event Ontology is Ver.1.59
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 2665
Obsoletes 22
definition 291
GO IDs 253
KEGG PATHWAY IDs 173
Reactome IDs 110
PSI-MI IDs 51
Event Ontology Release Notes
=====================
Version: 1.59 (8th Feb. 2006)
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 1.57
=====================
[Added terms]
1. terms related to molecular interaction (e.g., IEV_0002674:Formylation)
2. terms related to genetic interaction (e.g., IEV_0002683:suppression)
3. terms related to Nervous system development (e.g., IEV_0002707:Neural tube formation)
4. subpathways related to TPO signaling pathway (e.g., IEV_0002658:Binding of TPO receptor and STAT3)
5. etc.
More information about Event Ontology
---------------------
Tatsuya Kushida, Toshihisa Takagi and Ken Ichiro Fukuda, Event ontology: a pathway-centric ontology for biological processes, Proc. Pacific Symposium on Biocomputing, 2006. (in press)
Statistics
==========
All entries 2665
Obsoletes 22
definition 291
GO IDs 253
KEGG PATHWAY IDs 173
Reactome IDs 110
PSI-MI IDs 51
Posted by NorikoSakai : 04:05 PM | TrackBacks
February 01, 2006
Location Ontology Ver1.00
Location Ontology is a cellular compartment ontology.
Location Ontology Release Notes
=====================
Version: 1.00 (Dec 12, 2005)
Statistics
==========
all entries 49
obsolete 2
definition 42
GO IDs 47
Posted by KenFukuda : 07:20 PM | TrackBacks
Event Ontology Ver.1.58
The latest Event Ontology is Ver.1.58
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 2659
Obsoletes 22
definition 207
GO IDs 202
KEGG PATHWAY IDs 173
Reactome IDs 110
PSI-MI IDs 51
Event Ontology Release Notes
=====================
Version: 1.58 (29th Nov. 2005)
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 1.57
=====================
[Added terms]
1. terms related to molecular interaction (e.g., IEV_0002674:Formylation)
2. terms related to genetic interaction (e.g., IEV_0002683:suppression)
3. terms related to Nervous system development (e.g., IEV_0002707:Neural tube formation)
4. subpathways related to TPO signaling pathway (e.g., IEV_0002658:Binding of TPO receptor and STAT3)
5. etc.
More information about Event Ontology
---------------------
Tatsuya Kushida, Toshihisa Takagi and Ken Ichiro Fukuda, Event ontology: a pathway-centric ontology for biological processes, Proc. Pacific Symposium on Biocomputing, 2006. (in press)
Statistics
==========
All entries 2659
Obsoletes 22
definition 207
GO IDs 202
KEGG PATHWAY IDs 173
Reactome IDs 110
PSI-MI IDs 51
Posted by KenFukuda : 03:27 PM | TrackBacks
MoleculeRole Ontology Ver.2.10
The latest MoleculeRole Ontology is Ver2.10
MoleculeRole Ontology is an ontology for proteins.
You can download it from the OBO site and from our download page.
Statistics
==========
All entries 7184
Chemicals 85
Proteins 7098
Obsoletes 18
UniProt ACs 4582
GO IDs 314
InterPro ACs 31
KEGG COMPOUND IDs 85
PubMed IDs 64
MoleculeRole Ontology Release Notes
=====================
Version: 2.10 (Dec 27, 2005)
Molecule Role is a hierarchical ontology which contains molecular functional group names, abstract molecule names and 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 2.0x
=====================
Over 13,000 synonyms were added from EntrezGene, HGNC, FlyBase, OMIM, MGI and RGD database in 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 7184
Chemicals 85
Proteins 7098
Obsoletes 18
UniProt ACs 4582
GO IDs 314
InterPro ACs 31
KEGG COMPOUND IDs 85
PubMed IDs 64
Posted by KenFukuda : 03:12 PM | TrackBacks