April 13, 2009, at 05:05 PM by 155.52.91.161 -

Changed lines 3-4 from:

The StemNet project aims to improve the treatment of cancer patients based on a sepcial form of stem cell transplantation (HSCT). To accelerate research in this area, the project uses text mining techniques, such as automated test annotation to form structured databases out of unstructured scientific literature.

to:

The StemNet project aims to improve the treatment of cancer patients based on a sepcial form of stem cell transplantation (HSCT). To accelerate research in this area, the project uses text mining techniques, such as automated test annotation to form structured databases out of unstructured scientific literature.

Changed lines 8-10 from:

the StemNet project is the ontology. StemNet utilizes ontologies from the OBO Foundry, including the Gene Ontology and the Cell Ontology.
An ontology which is arising directly out of the StemNet project is MaHCO the MaHCO-HLA Ontology is a sub-domain. The long-term goal is the full integration of these ontologies into the Sequence Ontology.

to:

the StemNet project is the ontology. StemNet utilizes ontologies from the OBO Foundry, including the Gene Ontology and the Cell Ontology.

An ontology which is arising directly out of the StemNet project is MaHCO the MaHCO-HLA Ontology is a sub-domain. The long-term goal is the full integration of these ontologies into the Sequence Ontology.

April 13, 2009, at 05:05 PM by 155.52.91.161 -

Deleted line 8:

April 13, 2009, at 05:05 PM by 155.52.91.161 -

Changed lines 3-4 from:

The StemNet project aims to improve the treatment of cancer patients based on a sepcial form of stem cell transplantation (HSCT). To accelerate research in this area, the project uses text mining techniques, such as automated test annotation to form structured databases out of unstructured scientific literature.

to:

The StemNet project aims to improve the treatment of cancer patients based on a sepcial form of stem cell transplantation (HSCT). To accelerate research in this area, the project uses text mining techniques, such as automated test annotation to form structured databases out of unstructured scientific literature.

Changed lines 8-11 from:

the StemNet project is the ontology. StemNet utilizes ontologies from the OBO Foundry, including the Gene Ontology and the Cell Ontology.

An ontology which is arising directly out of the StemNet project is MaHCO the MaHCO-HLA Ontology is a sub-domain. The long-term goal is the full integration of these ontologies into the Sequence Ontology.

to:

the StemNet project is the ontology. StemNet utilizes ontologies from the OBO Foundry, including the Gene Ontology and the Cell Ontology.
An ontology which is arising directly out of the StemNet project is MaHCO the MaHCO-HLA Ontology is a sub-domain. The long-term goal is the full integration of these ontologies into the Sequence Ontology.

April 13, 2009, at 04:58 PM by 155.52.91.161 -

Added lines 12-14:

(:include Main/Viewing and Browsing:) (:include Main/MaHCO:) (:include Main/MaHCO_HLA:)

Added lines 16-19:

(:include Main/Applications:) (:include Main/Publications:) (:include Main/Changes:) (:include Main/Links:)

April 13, 2009, at 04:56 PM by 155.52.91.161 -

Changed lines 12-71 from:

Viewing And Browsing

There are different ways of browisng the ontologies contained in the OWL files below, but here are several options

Protégé is a java-based stand alone graphical user interface for viewing and editing ontologies. It is loaded with features.
BioPortal is a web-based repository which hosts many important biomedical ontologies, including MaHCO. You can click here to go directly to the built-in explorer for browing MaHCO.
OwlSight is a web-based ontology browser requiring no installation. To use it, go here, click the "Launch OwlSight" button, and you will be presented with a new window. Click on the "File" menu at the top and choose "Load Ontology". Copy and paste the following:: input text authorid "http://purl.org/stemnet/MHC/MaHCO.owl" size=40 into the "Ontology URI" field and click "Browse".

MaHCO

MHC, or major histocompatibility complex is a gene complex found in jawed vertebrates. The genes found on this region of the genome include several important genes which encode proteins which are responsible for presenting peptides on the cell surface for inspection by cells of the immune system. In human, such genes are called HLA (human leukocyte antigen). MaHCO contains terms necessary for describing and categorizing concepts related to MHC, in general, and for a number of model species, and also for humans. Important resources include the international ImMunoGeneTics information system (IMGT), and the Immuno Polymorphism Database (IPD).

Files

MaHCO.owl
Figure of upper classes of MaHCO (very large)
Figure of a subset of classes including HLA allele examples (also very large)

Date Changed

April 13th, 2009

Dependencies

Note that MaHCO.owl uses an import statement to include the classes found in MaHCO_HLA.owl. Please download both files if you intend to work offline.
Dublin core: http://protege.stanford.edu/plugins/owl/dc/protege-dc.owl

HLA Ontology

Human MHC genes, or HLA genes, have major clinical relevance for transplantation and other blood and immune system related illnesses. Because of the high level of polymorphism found in these genes in the human population, thousands of variants have been identified. A systematic and official standard for the organization of HLA sequences has been provide by the HLA Nomenclature Comittee. The official curated source of HLA sequences is the IMGT/HLA Database. The ]]HLA Dictionary]], as well as the HLA Informatics Group website include other important resources.

The MaCHO-HLA Ontology is an attempt to apply the logical principles on ontologies to help combine the aforementioned resources into a universal structured source of HLA information. HLA research, as well as clinical processes, requires complicated software systems to process HLA data. This ontology is a resource for such software developers who need a formalized structure for their databases and systems which is maintained and up-to-date with the latest IMGT/HLA database releases.

Files

MaHCO_HLA.owl
MaHCO_HLA.xml

These files do not include serological nomenclature, and instead only use "Two Digit" HLA resolution: MaHCO_HLA_twodigit.owl MaHCO_HLA_twodigit.xml

Date Changed

April 16th, 2008

Dependencies

Dublin core: http://protege.stanford.edu/plugins/owl/dc/protege-dc.owl

Publications

Beisswanger E, DeLuca DS, Blasczyk R, Hahn U. An Ontology for Major Histocompatibility Complex (MHC) Alleles and Molecules. Proceedings of the AMIA 2007 Annual Symposium, Chicago, IL, USA, Nov. 10-14, 2007.

DeLuca DS, Beisswanger E, Hahn U, Blasczyk R. An automatically curated MHC ontology for intelligent immunogenetic information retrieval. J Immunol 178, LB9- (2007).

Applications

semedico HLA Module Explorer

to:

(:include Main/Forum:)

April 13, 2009, at 04:52 PM by 155.52.91.161 -

Changed lines 18-21 from:

OwlSight is a web-based ontology browser requiring no installation. To use it, go here, click the "Launch OwlSight" button, and you will be presented with a new window. Click on the "File" menu at the top and choose "Load Ontology". Copy and paste the following: "http://purl.org/stemnet/MHC/MaHCO.owl" into the "Ontology URI" field and click "Browse".

to:

OwlSight is a web-based ontology browser requiring no installation. To use it, go here, click the "Launch OwlSight" button, and you will be presented with a new window. Click on the "File" menu at the top and choose "Load Ontology". Copy and paste the following:: (:input text authorid "http://purl.org/stemnet/MHC/MaHCO.owl" size=40:) into the "Ontology URI" field and click "Browse".

April 13, 2009, at 04:35 PM by 155.52.91.161 -

Changed lines 42-43 from:

The HLA Ontology is an attempt to apply the logical principles on ontologies to help combine the aforementioned resources into a universal structured source of HLA information. HLA research, as well as clinical processes, requires complicated software systems to process HLA data. This ontology is a resource for such software developers who need a formalized structure for their databases and systems which is maintained and up-to-date with the latest IMGT/HLA database releases.

to:

The MaCHO-HLA Ontology is an attempt to apply the logical principles on ontologies to help combine the aforementioned resources into a universal structured source of HLA information. HLA research, as well as clinical processes, requires complicated software systems to process HLA data. This ontology is a resource for such software developers who need a formalized structure for their databases and systems which is maintained and up-to-date with the latest IMGT/HLA database releases.

Changed lines 46-48 from:

MaHCO_HLA.owl MaHCO_HLA.xml

to:

MaHCO_HLA.owl
MaHCO_HLA.xml

April 13, 2009, at 04:34 PM by 155.52.91.161 -

Changed lines 28-31 from:

MaHCO.owl Figure ? of upper classes of MaHCO (very large) Figure of a subset of classes including HLA allele examples (also very large)

to:

MaHCO.owl
Figure of upper classes of MaHCO (very large)
Figure of a subset of classes including HLA allele examples (also very large)

April 13, 2009, at 02:16 PM by 155.52.91.161 -

Changed line 28 from:

MaHCO.owl

to:

MaHCO.owl

Changed lines 30-31 from:

Figure ? of a subset of classes including HLA allele examples (also very large)

to:

Figure of a subset of classes including HLA allele examples (also very large)

Changed lines 47-49 from:

MaHCO_HLA.owl ? MaHCO_HLA.xml ?

to:

MaHCO_HLA.owl MaHCO_HLA.xml

Changed lines 51-53 from:

MaHCO_HLA_twodigit.owl ? MaHCO_HLA_twodigit.xml ?

to:

MaHCO_HLA_twodigit.owl MaHCO_HLA_twodigit.xml

April 13, 2009, at 12:26 PM by 155.52.91.161 -

Changed lines 12-18 from:

Viewing

There are different ways of browisng the ontologies contained in the OWL files below, but here are two options #Protégé is a java-based stand alone graphical user interface for viewing and editing ontologies. It is loaded with features.

OwlSight is a web-based ontology browser requiring no installation. To use it, go here, click the "Launch OwlSight" button, and you will be presented with a new window. Click on the "File" menu at the top and choose "Load Ontology". Copy and paste the following:

http://purl.org/stemnet/MHC/MaHCO.owl into the "Ontology URI" field and click "Browse".

to:

Viewing And Browsing

There are different ways of browisng the ontologies contained in the OWL files below, but here are several options

Protégé is a java-based stand alone graphical user interface for viewing and editing ontologies. It is loaded with features.
BioPortal is a web-based repository which hosts many important biomedical ontologies, including MaHCO. You can click here to go directly to the built-in explorer for browing MaHCO.
OwlSight is a web-based ontology browser requiring no installation. To use it, go here, click the "Launch OwlSight" button, and you will be presented with a new window. Click on the "File" menu at the top and choose "Load Ontology". Copy and paste the following: "http://purl.org/stemnet/MHC/MaHCO.owl" into the "Ontology URI" field and click "Browse".

April 13, 2009, at 12:18 PM by 155.52.91.161 -

Changed line 1 from:

StemNet Ontologies

to:

MaHCO - An MHC Ontology

Changed lines 23-24 from:

Files

to:

Files

April 13, 2009, at 10:52 AM by 155.52.91.161 -

Changed lines 3-7 from:

The StemNet project aims to improve the treatment of cancer patients based on a sepcial form of stem cell transplantation (HSCT). To accelerate research in this area, the project uses text mining techniques, such as automated test annotation to form structured databases out of unstructured scientific literature.

to:

The StemNet project aims to improve the treatment of cancer patients based on a sepcial form of stem cell transplantation (HSCT). To accelerate research in this area, the project uses text mining techniques, such as automated test annotation to form structured databases out of unstructured scientific literature.

Changed lines 8-14 from:

the StemNet project is the ontology. StemNet utilizes ontologies from the OBO Foundry, including the Gene Ontology and the Cell Ontology.

An ontology which is arising directly out of the StemNet project is MaHCO the MaHCO-HLA Ontology is a sub-domain. The long-term goal is the full integration of these ontologies into the Sequence Ontology.

to:

the StemNet project is the ontology. StemNet utilizes ontologies from the OBO Foundry, including the Gene Ontology and the Cell Ontology.

An ontology which is arising directly out of the StemNet project is MaHCO the MaHCO-HLA Ontology is a sub-domain. The long-term goal is the full integration of these ontologies into the Sequence Ontology.

Changed lines 14-16 from:

There are different ways of browisng the ontologies contained in the OWL files below, but here are two options

Protégé is a java-based stand alone graphical user interface for viewing and editing ontologies. It is loaded with features.
OwlSight is a web-based ontology browser requiring no installation. To use it, go here, click the "Launch OwlSight" button, and you will be presented with a new window. Click on the "File" menu at the top and choose "Load Ontology". Copy and paste the following:

to:

There are different ways of browisng the ontologies contained in the OWL files below, but here are two options #Protégé is a java-based stand alone graphical user interface for viewing and editing ontologies. It is loaded with features.

OwlSight is a web-based ontology browser requiring no installation. To use it, go here, click the "Launch OwlSight" button, and you will be presented with a new window. Click on the "File" menu at the top and choose "Load Ontology". Copy and paste the following:

Changed lines 21-29 from:

MHC, or major histocompatibility complex is a gene complex found in jawed vertebrates. The genes found on this region of the genome include several important genes which encode proteins which are responsible for presenting peptides on the cell surface for inspection by cells of the immune system. In human, such genes are called HLA (human leukocyte antigen). MaHCO contains terms necessary for describing and categorizing concepts related to MHC, in general, and for a number of model species, and also for humans. Important resources include the international ImMunoGeneTics information system (IMGT), and the Immuno Polymorphism Database (IPD).

to:

MHC, or major histocompatibility complex is a gene complex found in jawed vertebrates. The genes found on this region of the genome include several important genes which encode proteins which are responsible for presenting peptides on the cell surface for inspection by cells of the immune system. In human, such genes are called HLA (human leukocyte antigen). MaHCO contains terms necessary for describing and categorizing concepts related to MHC, in general, and for a number of model species, and also for humans. Important resources include the international ImMunoGeneTics information system (IMGT), and the Immuno Polymorphism Database (IPD).

Changed lines 38-51 from:

Human MHC genes, or HLA genes, have major clinical relevance for transplantation and other blood and immune system related illnesses. Because of the high level of polymorphism found in these genes in the human population, thousands of variants have been identified. A systematic and official standard for the organization of HLA sequences has been provide by the HLA Nomenclature Comittee. The official curated source of HLA sequences is the IMGT/HLA Database. The ]]HLA Dictionary]], as well as the HLA Informatics Group

 website include other important resources.

The HLA Ontology is an attempt to apply the logical principles on ontologies to help combine the aforementioned resources into a universal structured source of HLA information. HLA research, as well as clinical processes, requires complicated software systems to process HLA data. This ontology is a resource for such software developers who need a formalized structure for their databases and systems which is maintained and up-to-date with the latest IMGT/HLA database releases.

to:

Human MHC genes, or HLA genes, have major clinical relevance for transplantation and other blood and immune system related illnesses. Because of the high level of polymorphism found in these genes in the human population, thousands of variants have been identified. A systematic and official standard for the organization of HLA sequences has been provide by the HLA Nomenclature Comittee. The official curated source of HLA sequences is the IMGT/HLA Database. The ]]HLA Dictionary]], as well as the HLA Informatics Group website include other important resources.

The HLA Ontology is an attempt to apply the logical principles on ontologies to help combine the aforementioned resources into a universal structured source of HLA information. HLA research, as well as clinical processes, requires complicated software systems to process HLA data. This ontology is a resource for such software developers who need a formalized structure for their databases and systems which is maintained and up-to-date with the latest IMGT/HLA database releases.

Deleted line 43:

Deleted line 46:

Deleted line 52:

Changed lines 56-62 from:

<ul>

	<li>Dublin core: http://protege.stanford.edu/plugins/owl/dc/protege-dc.owl

</ul>

to:

Dublin core: http://protege.stanford.edu/plugins/owl/dc/protege-dc.owl

Deleted line 59:

Deleted lines 63-64:

Deleted line 65:

April 13, 2009, at 10:49 AM by 155.52.91.161 -

Changed lines 22-23 from:

OwlSight is a web-based ontology browser requiring no installation. To use it, go here,

		click the "Launch OwlSight" button, and you will be presented with a new window. Click on the "File" menu at the top and choose "Load Ontology". Copy and pase the following:

to:

OwlSight is a web-based ontology browser requiring no installation. To use it, go here, click the "Launch OwlSight" button, and you will be presented with a new window. Click on the "File" menu at the top and choose "Load Ontology". Copy and paste the following:

Changed lines 24-25 from:

into the "Ontolgy URI" field and click "Browse".

to:

into the "Ontology URI" field and click "Browse".

Changed line 39 from:

a target='_new' href='./MHC/MaHCO.owl|MaHCO.owl]]

to:

MaHCO.owl

April 13, 2009, at 10:45 AM by 155.52.91.161 -

Added lines 1-106:

StemNet Ontologies

StemNet

The StemNet project aims to improve the treatment of cancer patients based on a sepcial form of stem cell transplantation (HSCT). To accelerate research in this area, the project uses text mining techniques, such as automated test annotation to form structured databases out of unstructured scientific literature.

Ontologies

An important tool for the StemNet project is the ontology. StemNet utilizes ontologies from the OBO Foundry, including the Gene Ontology and the Cell Ontology.

An ontology which is arising directly out of the StemNet project is MaHCO the MaHCO-HLA Ontology is a sub-domain. The long-term goal is the full integration of these ontologies into the Sequence Ontology.

Viewing

There are different ways of browisng the ontologies contained in the OWL files below, but here are two options

Protégé is a java-based stand alone graphical user interface for viewing and editing ontologies. It is loaded with features.
OwlSight is a web-based ontology browser requiring no installation. To use it, go here,

		click the "Launch OwlSight" button, and you will be presented with a new window. Click on the "File" menu at the top and choose "Load Ontology". Copy and pase the following:

http://purl.org/stemnet/MHC/MaHCO.owl into the "Ontolgy URI" field and click "Browse".

MaHCO

MHC, or major histocompatibility complex is a gene complex found in jawed vertebrates. The genes found on this region of the genome include several important genes which encode proteins which are responsible for presenting peptides on the cell surface for inspection by cells of the immune system. In human, such genes are called HLA (human leukocyte antigen). MaHCO contains terms necessary for describing and categorizing concepts related to MHC, in general, and for a number of model species, and also for humans. Important resources include the international ImMunoGeneTics information system (IMGT), and the Immuno Polymorphism Database (IPD).

Files

a target='_new' href='./MHC/MaHCO.owl|MaHCO.owl]] Figure ? of upper classes of MaHCO (very large) Figure ? of a subset of classes including HLA allele examples (also very large)

Date Changed

April 13th, 2009

Dependencies

Note that MaHCO.owl uses an import statement to include the classes found in MaHCO_HLA.owl. Please download both files if you intend to work offline.
Dublin core: http://protege.stanford.edu/plugins/owl/dc/protege-dc.owl

HLA Ontology

Human MHC genes, or HLA genes, have major clinical relevance for transplantation and other blood and immune system related illnesses. Because of the high level of polymorphism found in these genes in the human population, thousands of variants have been identified. A systematic and official standard for the organization of HLA sequences has been provide by the HLA Nomenclature Comittee. The official curated source of HLA sequences is the IMGT/HLA Database. The ]]HLA Dictionary]], as well as the HLA Informatics Group

 website include other important resources.

The HLA Ontology is an attempt to apply the logical principles on ontologies to help combine the aforementioned resources into a universal structured source of HLA information. HLA research, as well as clinical processes, requires complicated software systems to process HLA data. This ontology is a resource for such software developers who need a formalized structure for their databases and systems which is maintained and up-to-date with the latest IMGT/HLA database releases.

Files

MaHCO_HLA.owl ? MaHCO_HLA.xml ?

These files do not include serological nomenclature, and instead only use "Two Digit" HLA resolution: MaHCO_HLA_twodigit.owl ? MaHCO_HLA_twodigit.xml ?

Date Changed

April 16th, 2008

Dependencies

<ul>

	<li>Dublin core: http://protege.stanford.edu/plugins/owl/dc/protege-dc.owl

</ul>

Publications

Beisswanger E, DeLuca DS, Blasczyk R, Hahn U. An Ontology for Major Histocompatibility Complex (MHC) Alleles and Molecules. Proceedings of the AMIA 2007 Annual Symposium, Chicago, IL, USA, Nov. 10-14, 2007.

DeLuca DS, Beisswanger E, Hahn U, Blasczyk R. An automatically curated MHC ontology for intelligent immunogenetic information retrieval. J Immunol 178, LB9- (2007).

Applications

semedico HLA Module Explorer

MaHCO
	Main / Home Page	Edit Page \| Page History \| Wiki Help Print \| Search:

Main.HomePage History

Viewing And Browsing

MaHCO

Files

Date Changed

Dependencies

HLA Ontology

Files

Date Changed

Dependencies

Publications

Applications

Viewing

Viewing And Browsing

StemNet Ontologies

MaHCO - An MHC Ontology

Files

Files

StemNet Ontologies

StemNet

Ontologies

Viewing

MaHCO

Files

Date Changed

Dependencies

HLA Ontology

Files

Date Changed

Dependencies

Publications

Applications