https://www.bioontology.org//mediawiki/api.php?action=feedcontributions&feedformat=atom&user=Skanel 2026-06-05T11:18:47Z User contributions MediaWiki 1.35.9 https://www.bioontology.org//mediawiki/index.php?title=OWLConverter&diff=8532 2009-03-05T02:23:47Z

<p>Skanel: New page: The OWL Converter is a plugin for OBOEdit to convert OBO format files into OWL files and vice-versa (keeping in mind that OWL to OBO conversions can lose information if one encodes things ...</p> <hr /> <div>The OWL Converter is a plugin for OBOEdit to convert OBO format files into OWL files and vice-versa (keeping in mind that OWL to OBO conversions can lose information if one encodes things in OWL that cannot be expressed in OBO). It is also developed in a manner such that it can also work as a standalone conversion program.</div>

Skanel https://www.bioontology.org//mediawiki/index.php?title=Ontology_News&diff=8226 2008-11-19T01:50:16Z

<p>Skanel: New page: Please see the main [http://www.bioontology.org/news.html NCBO News Site]</p> <hr /> <div>Please see the main [http://www.bioontology.org/news.html NCBO News Site]</div>

Skanel https://www.bioontology.org//mediawiki/index.php?title=BioPortal_FAQ&diff=8187 2008-11-11T23:20:27Z

<p>Skanel: /* What is BioPortal? */</p> <hr /> <div>'''Frequently Asked Questions (FAQ)'''<br /> <br /> =General=<br /> <br /> ==NCBO==<br /> <br /> Advancing biology and medicine with tools and methodologies for the structured organization of knowledge. <br /> <br /> ===What is NCBO?===<br /> <br /> The National Center for Biomedical Ontology (http://www.biontology.org) is a consortium of leading biologists, clinicians, informaticians, and ontologists who develop innovative technology and methods that allow scientists to create, disseminate, and manage biomedical information and knowledge in machine-processable form. Our vision is that all biomedical knowledge and data are disseminated on the Internet using principled ontologies, such that the knowledge and data are semantically interoperable and useful for furthering biomedical science and clinical care. The Center’s products and technologies include BioPortal, Phenote+, Open Biomedical Resources (OBR), Biomedical Annotations Repository (BAR), and Open Biomedical Data (OBD). Partner technologies include LexGrid, Protege, and Jambalaya. The products and technologies are used to deliver repositories and tools for accessing and using this biomedical information in research. The Center collaborates with biomedical researchers conducting Driving Biological Projects (DBPs) to enable their research and to stimulate technology development in the Center. The Center is undertaking outreach and educational activities to train the future generation of researchers in using biomedical ontologies and the Center’s tools to enhance scientific discovery.<br /> <br /> ==What is an ontology?==<br /> An ontology is a formal representation of a set of concepts/nodes within a domain and the relationships between those concepts. It is used to reason about the properties of that domain, and may be used to define the domain.<br /> <br /> ==Where are the ontologies?==<br /> <br /> Ontologies are available from BioPortal 2.0 at http://bioportal.bioontology.org. <br /> <br /> ===How do I submit an ontology?===<br /> <br /> The current protocol is:<br /> <br /> 1) Go to BioPortal 2.0 at http://bioportal.bioontology.org<br /> <br /> 2) If you haven't already, click on the &quot;Register&quot; link in the top right hand corner. <br /> <br /> 3) After you have registered as a user, &quot;Sign In&quot; as that user.<br /> <br /> 4) Click on the &quot;Browse&quot; tab (or click on the following link: http://bioportal.bioontology.org)<br /> <br /> 5) Click on the &quot;Submit Ontology&quot; button and follow the instructions.<br /> <br /> ==What is an annotation?==<br /> <br /> ==Where are the annotations?==<br /> <br /> ===How do I submit an annotation?===<br /> <br /> =Ontology Content=<br /> <br /> ==Building Ontologies==<br /> <br /> ===How do I go about building an ontology?===<br /> <br /> There are a plethora of tools for building ontologies. Below are two preferred tools for building OWL and OBO ontologies:<br /> <br /> 1) Protege (http://protege.stanford.edu/) - OWL ontologies<br /> <br /> 2) OBOEdit (http://oboedit.org/) - OBO ontologies<br /> <br /> ===What is the OBO Foundry?===<br /> <br /> A collaborative experiment, involving a group of OBO ontology developers who have agreed in advance to the adoption of a growing set of principles specifying best practices in ontology development. These principles are designed to foster interoperability of ontologies within the broader OBO framework, and also to ensure a gradual improvement of quality and formal rigor in ontologies, in ways designed to meet the increasing needs of data and information integration in the biomedical domain. See http://obofoundry.org/<br /> <br /> =NCBO Products=<br /> The NCBO has selected the Java/J2EE software infrastructure as the development of choice for all products.<br /> <br /> ==What is BioPortal?==<br /> A Web-based application for searching, sharing, visualizing, and analyzing a large repository of biomedical ontologies, terminologies, and annotations. BioPortal 2.0, the current release, is available at: http://bioportal.bioontology.org/. <br /> <br /> BioPortal 2.0 allows for mappings between concepts, bulk export of mappings, visualization of concepts and relationships within ontologies, notes, and navigation of multiple ontologies through tabbed browsing. To see a demo of BioPortal 2.0, please visit http://bioontology.org/videos/demos/BioPortal_2.0_Demo.html.<br /> <br /> ==What is Open Biomedical Resources?==<br /> A set of annotations generated automatically. These annotations are presented through integration with BioPortal UI which enables researchers to search for biomedical resources associated (or annotated) with specific ontology terms.<br /> <br /> ==What is Open Biomedical Services?==<br /> A set of inter-related Java-based REST/SOAP services that use ontologies in BioPortal to perform concept recognition, ontology traversal, concept expansion, and to determine concept similarity. <br /> <br /> ==What is Biomedical Annotation Repository?==<br /> TBD<br /> <br /> ==What is Phenote?==<br /> A Java client application for manual creation and storage of biomedical annotations (starting with phenotype annotations) using terms from multiple ontologies.<br /> <br /> ==What is Open Biomedical Data?==<br /> A database of manually generated biomedical annotations (starting with phenotype annotations) summarizing key attributes such as anatomy, phenotype, and genetic features. The annotations are currently loaded directly from a Phenote file, which contains the manually created annotations.<br /> <br /> ===incomplete is-a paths===<br /> <br /> Many OBO ontologies are currently incomplete with respect to all classes/terms having an is-a parent. Many tools (including OBO-Edit and AmiGO) deliberately allow the conflation of relations when presenting the ontology as a DAG or a tree to the user. However, other tools (including Protege and SWOOP) do not. This means that some OBO ontologies can look unusual when viewed with these other tools (lots of classes appear at the root level).<br /> <br /> This is currently being addressed by the maintainers of OBO ontologies. An effort is underway to complete the is-a parentage in the GO cellular component ontology (biological process will be more difficult). The Plant Ontology Consortium are completing the is-a parentage in the plant anatomical structure ontology.<br /> <br /> Until this work is complete, some OBO ontologies may look unusual when viewed in conventional ontology browsing and editing tools. With some of these tools, there may be some configurations which allow other relations to be conflated with the is-a relation when presenting the ontology as a DAG or tree view.<br /> <br /> One option is to automatically create an is-a parent to the ontology root for every non-root class/term which lacks any is-a parents. Note that this may create inconsistencies in the ontology if the genuine is-a parent is somewhere deeper in the ontology hierarchy; nevertheless this step may be necessary before presenting some OBO ontologies to tools such as reasoners.<br /> <br /> =Details=<br /> <br /> ==What is NCBO Core 1?==<br /> <br /> ==What is NCBO Core 2?==<br /> <br /> ==Ontology Metadata==<br /> The NCBO is planning to leverage the Ontology Metadata Vocabulary (OMV) format to store all ontology meta data. Please see the following web site for more information on the format (http://omv.ontoware.org/).<br /> <br /> ==OBO Format==<br /> <br /> Questions about the OBO text and xml formats<br /> <br /> ===What is OBO Format?===<br /> <br /> ===Is OBO Format different from the old GO format?===<br /> <br /> Yes. The old dag-edit format (i.e. the one in which indentation was used to denote the GO hierarchy) is STRONGLY deprecated.<br /> <br /> ===Where can I find the spec?===<br /> <br /> You can find details on the 1.0 spec on the GO home page<br /> http://www.geneontology.org/GO.format.shtml#oboflat<br /> <br /> This spec is somewhat underspecified<br /> <br /> The 1.2 spec is in preparation, and will be released to coincide with the first production OBO-Edit release sometime early in 2006<br /> <br /> You can find a preliminary version of the spec here:<br /> HTML -- http://www.godatabase.org/dev/doc/obo_format_spec.html<br /> PDF -- http://www.godatabase.org/dev/doc/obo_format_spec.pdf<br /> Ascii text -- http://www.godatabase.org/dev/doc/obo_format_spec.txt<br /> <br /> ===Why not use XML?===<br /> <br /> There is also an obo-xml format. See<br /> <br /> http://www.godatabase.org/dev/xml<br /> <br /> Currently only available as DTD. Relax-NG and XSD coming soon.<br /> <br /> ===Is there a UML model?===<br /> <br /> Yes, there is a UML translation of the obo format in progress, produced by Harold Solbrig of Mayo clinic; see:<br /> <br /> http://informatics.mayo.edu/schema/OBO/UMLModel/HTML/<br /> <br /> ===What tools support Obo-Format?===<br /> <br /> The following are *ontology* tools that support the OBO format. There are many other tools for the analysis of gene ontology data which also happen to read the OBO format - see http://www.geneontology.org/GO.tools.shtml for a list<br /> <br /> ; OBO-Edit<br /> : (naturally!). You should use this rather than DAG-Edit (DAG-Edit still supports obo-1.0 format), as DAG-Edit is deprecated as of 2006.<br /> <br /> ; COBRA<br /> : developed by Stuart Aitken as part of http://www.xspan.org. COBRA is a java ontology editor/viewer for aligning ontologies<br /> <br /> ; go-perl<br /> : http://search.cpan.org/~cmungall/go-perl<br /> <br /> ==Using Protege with OBO ontologies==<br /> <br /> You have two options here - use the Protege OBO plugin, or convert to a format which Protege understands.<br /> <br /> The OBO plugin was developed at the University of Washington, and is no longer supported.<br /> <br /> You can convert any obo-format file to OWL and use Protege-OWL (but not Protege-classic); see the next entry.<br /> <br /> Note that when you look at many of the OBO ontologies in Protege (classic or Protege-OWL) you will see that there are large amounts of classes apparently at the root level. This is because OBO ontologies have historically not been complete with respect to all classes having a superclass (is-a parent). This is currently being addressed. See the FAQ entry on this subject.<br /> <br /> ===Can I convert Obo-format to OWL?===<br /> <br /> Yes. At this present time, the best way of foing this is to use the xslts included in go-perl.<br /> Download and install:<br /> http://search.cpan.org/~cmungall/go-perl/<br /> Then run the script<br /> <br /> go2owl myontology.obo<br /> <br /> This functionality will soon be available from oboedit<br /> <br /> For more details on the mapping, see:<br /> <br /> http://www.fruitfly.org/~cjm/obol/doc/mapping-obo-to-owl.html<br /> <br /> ===OK, but can I just download OBO ontologies as OWL without doing the conversion myself?===<br /> <br /> You can, at least for some OBO ontologies. This is an experimental service, and will eventually be subsumed into the services provided by cBio:<br /> <br /> http://www.fruitfly.org/~cjm/obo-download<br /> <br /> ===Can I convert Obo-format files to Protege-classic?===<br /> <br /> Not yet. In theory it should not be hard to provide an XSL for this. The reverse transformation may be more difficult.<br /> <br /> <br /> <br /> ==OBD==<br /> <br /> ===What is OBD?===<br /> <br /> OBD is a database for storing data typed using OBO ontologies<br /> <br /> ===Where is it?===<br /> <br /> In development!<br /> <br /> ===Is there a demo?===<br /> <br /> See http://www.fruitfly.org/~cjm/obd<br /> <br /> ===Datasets===<br /> <br /> See the above URL for now</div>

Skanel https://www.bioontology.org//mediawiki/index.php?title=BioPortal_FAQ&diff=8185 2008-11-11T19:07:26Z

<p>Skanel: /* What is BioPortal? */</p> <hr /> <div>'''Frequently Asked Questions (FAQ)'''<br /> <br /> =General=<br /> <br /> ==NCBO==<br /> <br /> Advancing biology and medicine with tools and methodologies for the structured organization of knowledge. <br /> <br /> ===What is NCBO?===<br /> <br /> The National Center for Biomedical Ontology (http://www.biontology.org) is a consortium of leading biologists, clinicians, informaticians, and ontologists who develop innovative technology and methods that allow scientists to create, disseminate, and manage biomedical information and knowledge in machine-processable form. Our vision is that all biomedical knowledge and data are disseminated on the Internet using principled ontologies, such that the knowledge and data are semantically interoperable and useful for furthering biomedical science and clinical care. The Center’s products and technologies include BioPortal, Phenote+, Open Biomedical Resources (OBR), Biomedical Annotations Repository (BAR), and Open Biomedical Data (OBD). Partner technologies include LexGrid, Protege, and Jambalaya. The products and technologies are used to deliver repositories and tools for accessing and using this biomedical information in research. The Center collaborates with biomedical researchers conducting Driving Biological Projects (DBPs) to enable their research and to stimulate technology development in the Center. The Center is undertaking outreach and educational activities to train the future generation of researchers in using biomedical ontologies and the Center’s tools to enhance scientific discovery.<br /> <br /> ==What is an ontology?==<br /> An ontology is a formal representation of a set of concepts/nodes within a domain and the relationships between those concepts. It is used to reason about the properties of that domain, and may be used to define the domain.<br /> <br /> ==Where are the ontologies?==<br /> <br /> Ontologies are available from BioPortal 2.0 at http://bioportal.bioontology.org. <br /> <br /> ===How do I submit an ontology?===<br /> <br /> The current protocol is:<br /> <br /> 1) Go to BioPortal 2.0 at http://bioportal.bioontology.org<br /> <br /> 2) If you haven't already, click on the &quot;Register&quot; link in the top right hand corner. <br /> <br /> 3) After you have registered as a user, &quot;Sign In&quot; as that user.<br /> <br /> 4) Click on the &quot;Browse&quot; tab (or click on the following link: http://bioportal.bioontology.org)<br /> <br /> 5) Click on the &quot;Submit Ontology&quot; button and follow the instructions.<br /> <br /> ==What is an annotation?==<br /> <br /> ==Where are the annotations?==<br /> <br /> ===How do I submit an annotation?===<br /> <br /> =Ontology Content=<br /> <br /> ==Building Ontologies==<br /> <br /> ===How do I go about building an ontology?===<br /> <br /> There are a plethora of tools for building ontologies. Below are two preferred tools for building OWL and OBO ontologies:<br /> <br /> 1) Protege (http://protege.stanford.edu/) - OWL ontologies<br /> <br /> 2) OBOEdit (http://oboedit.org/) - OBO ontologies<br /> <br /> ===What is the OBO Foundry?===<br /> <br /> A collaborative experiment, involving a group of OBO ontology developers who have agreed in advance to the adoption of a growing set of principles specifying best practices in ontology development. These principles are designed to foster interoperability of ontologies within the broader OBO framework, and also to ensure a gradual improvement of quality and formal rigor in ontologies, in ways designed to meet the increasing needs of data and information integration in the biomedical domain. See http://obofoundry.org/<br /> <br /> =NCBO Products=<br /> The NCBO has selected the Java/J2EE software infrastructure as the development of choice for all products.<br /> <br /> ==What is BioPortal?==<br /> A Web-based application for accessing, sharing, visualizing, analyzing, uploading, and searching a large repository of biomedical ontologies, terminologies, and annotations. BioPortal 2.0 is the current release accessible through the following URL: http://bioportal.bioontology.org/. <br /> BioPortal 2.0 allows for mappings between concepts, bulk export of mappings, vizualization of concepts and relationships within ontologies, marginal notes, and navigation of multiple ontologies through tabbed browsing. To see a demo of BioPortal 2.0, please visit http://bioontology.org/videos/demos/BioPortal_2.0_Demo.html.<br /> <br /> ==What is Open Biomedical Resources?==<br /> A set of annotations generated automatically. These annotations are presented through integration with BioPortal UI which enables researchers to search for biomedical resources associated (or annotated) with specific ontology terms.<br /> <br /> ==What is Open Biomedical Services?==<br /> A set of inter-related Java-based REST/SOAP services that use ontologies in BioPortal to perform concept recognition, ontology traversal, concept expansion, and to determine concept similarity. <br /> <br /> ==What is Biomedical Annotation Repository?==<br /> TBD<br /> <br /> ==What is Phenote?==<br /> A Java client application for manual creation and storage of biomedical annotations (starting with phenotype annotations) using terms from multiple ontologies.<br /> <br /> ==What is Open Biomedical Data?==<br /> A database of manually generated biomedical annotations (starting with phenotype annotations) summarizing key attributes such as anatomy, phenotype, and genetic features. The annotations are currently loaded directly from a Phenote file, which contains the manually created annotations.<br /> <br /> ===incomplete is-a paths===<br /> <br /> Many OBO ontologies are currently incomplete with respect to all classes/terms having an is-a parent. Many tools (including OBO-Edit and AmiGO) deliberately allow the conflation of relations when presenting the ontology as a DAG or a tree to the user. However, other tools (including Protege and SWOOP) do not. This means that some OBO ontologies can look unusual when viewed with these other tools (lots of classes appear at the root level).<br /> <br /> This is currently being addressed by the maintainers of OBO ontologies. An effort is underway to complete the is-a parentage in the GO cellular component ontology (biological process will be more difficult). The Plant Ontology Consortium are completing the is-a parentage in the plant anatomical structure ontology.<br /> <br /> Until this work is complete, some OBO ontologies may look unusual when viewed in conventional ontology browsing and editing tools. With some of these tools, there may be some configurations which allow other relations to be conflated with the is-a relation when presenting the ontology as a DAG or tree view.<br /> <br /> One option is to automatically create an is-a parent to the ontology root for every non-root class/term which lacks any is-a parents. Note that this may create inconsistencies in the ontology if the genuine is-a parent is somewhere deeper in the ontology hierarchy; nevertheless this step may be necessary before presenting some OBO ontologies to tools such as reasoners.<br /> <br /> =Details=<br /> <br /> ==What is NCBO Core 1?==<br /> <br /> ==What is NCBO Core 2?==<br /> <br /> ==Ontology Metadata==<br /> The NCBO is planning to leverage the Ontology Metadata Vocabulary (OMV) format to store all ontology meta data. Please see the following web site for more information on the format (http://omv.ontoware.org/).<br /> <br /> ==OBO Format==<br /> <br /> Questions about the OBO text and xml formats<br /> <br /> ===What is OBO Format?===<br /> <br /> ===Is OBO Format different from the old GO format?===<br /> <br /> Yes. The old dag-edit format (i.e. the one in which indentation was used to denote the GO hierarchy) is STRONGLY deprecated.<br /> <br /> ===Where can I find the spec?===<br /> <br /> You can find details on the 1.0 spec on the GO home page<br /> http://www.geneontology.org/GO.format.shtml#oboflat<br /> <br /> This spec is somewhat underspecified<br /> <br /> The 1.2 spec is in preparation, and will be released to coincide with the first production OBO-Edit release sometime early in 2006<br /> <br /> You can find a preliminary version of the spec here:<br /> HTML -- http://www.godatabase.org/dev/doc/obo_format_spec.html<br /> PDF -- http://www.godatabase.org/dev/doc/obo_format_spec.pdf<br /> Ascii text -- http://www.godatabase.org/dev/doc/obo_format_spec.txt<br /> <br /> ===Why not use XML?===<br /> <br /> There is also an obo-xml format. See<br /> <br /> http://www.godatabase.org/dev/xml<br /> <br /> Currently only available as DTD. Relax-NG and XSD coming soon.<br /> <br /> ===Is there a UML model?===<br /> <br /> Yes, there is a UML translation of the obo format in progress, produced by Harold Solbrig of Mayo clinic; see:<br /> <br /> http://informatics.mayo.edu/schema/OBO/UMLModel/HTML/<br /> <br /> ===What tools support Obo-Format?===<br /> <br /> The following are *ontology* tools that support the OBO format. There are many other tools for the analysis of gene ontology data which also happen to read the OBO format - see http://www.geneontology.org/GO.tools.shtml for a list<br /> <br /> ; OBO-Edit<br /> : (naturally!). You should use this rather than DAG-Edit (DAG-Edit still supports obo-1.0 format), as DAG-Edit is deprecated as of 2006.<br /> <br /> ; COBRA<br /> : developed by Stuart Aitken as part of http://www.xspan.org. COBRA is a java ontology editor/viewer for aligning ontologies<br /> <br /> ; go-perl<br /> : http://search.cpan.org/~cmungall/go-perl<br /> <br /> ==Using Protege with OBO ontologies==<br /> <br /> You have two options here - use the Protege OBO plugin, or convert to a format which Protege understands.<br /> <br /> The OBO plugin was developed at the University of Washington, and is no longer supported.<br /> <br /> You can convert any obo-format file to OWL and use Protege-OWL (but not Protege-classic); see the next entry.<br /> <br /> Note that when you look at many of the OBO ontologies in Protege (classic or Protege-OWL) you will see that there are large amounts of classes apparently at the root level. This is because OBO ontologies have historically not been complete with respect to all classes having a superclass (is-a parent). This is currently being addressed. See the FAQ entry on this subject.<br /> <br /> ===Can I convert Obo-format to OWL?===<br /> <br /> Yes. At this present time, the best way of foing this is to use the xslts included in go-perl.<br /> Download and install:<br /> http://search.cpan.org/~cmungall/go-perl/<br /> Then run the script<br /> <br /> go2owl myontology.obo<br /> <br /> This functionality will soon be available from oboedit<br /> <br /> For more details on the mapping, see:<br /> <br /> http://www.fruitfly.org/~cjm/obol/doc/mapping-obo-to-owl.html<br /> <br /> ===OK, but can I just download OBO ontologies as OWL without doing the conversion myself?===<br /> <br /> You can, at least for some OBO ontologies. This is an experimental service, and will eventually be subsumed into the services provided by cBio:<br /> <br /> http://www.fruitfly.org/~cjm/obo-download<br /> <br /> ===Can I convert Obo-format files to Protege-classic?===<br /> <br /> Not yet. In theory it should not be hard to provide an XSL for this. The reverse transformation may be more difficult.<br /> <br /> <br /> <br /> ==OBD==<br /> <br /> ===What is OBD?===<br /> <br /> OBD is a database for storing data typed using OBO ontologies<br /> <br /> ===Where is it?===<br /> <br /> In development!<br /> <br /> ===Is there a demo?===<br /> <br /> See http://www.fruitfly.org/~cjm/obd<br /> <br /> ===Datasets===<br /> <br /> See the above URL for now</div>

Skanel https://www.bioontology.org//mediawiki/index.php?title=BioPortal_FAQ&diff=8184 2008-11-11T19:07:11Z

<p>Skanel: /* What is BioPortal? */</p> <hr /> <div>'''Frequently Asked Questions (FAQ)'''<br /> <br /> =General=<br /> <br /> ==NCBO==<br /> <br /> Advancing biology and medicine with tools and methodologies for the structured organization of knowledge. <br /> <br /> ===What is NCBO?===<br /> <br /> The National Center for Biomedical Ontology (http://www.biontology.org) is a consortium of leading biologists, clinicians, informaticians, and ontologists who develop innovative technology and methods that allow scientists to create, disseminate, and manage biomedical information and knowledge in machine-processable form. Our vision is that all biomedical knowledge and data are disseminated on the Internet using principled ontologies, such that the knowledge and data are semantically interoperable and useful for furthering biomedical science and clinical care. The Center’s products and technologies include BioPortal, Phenote+, Open Biomedical Resources (OBR), Biomedical Annotations Repository (BAR), and Open Biomedical Data (OBD). Partner technologies include LexGrid, Protege, and Jambalaya. The products and technologies are used to deliver repositories and tools for accessing and using this biomedical information in research. The Center collaborates with biomedical researchers conducting Driving Biological Projects (DBPs) to enable their research and to stimulate technology development in the Center. The Center is undertaking outreach and educational activities to train the future generation of researchers in using biomedical ontologies and the Center’s tools to enhance scientific discovery.<br /> <br /> ==What is an ontology?==<br /> An ontology is a formal representation of a set of concepts/nodes within a domain and the relationships between those concepts. It is used to reason about the properties of that domain, and may be used to define the domain.<br /> <br /> ==Where are the ontologies?==<br /> <br /> Ontologies are available from BioPortal 2.0 at http://bioportal.bioontology.org. <br /> <br /> ===How do I submit an ontology?===<br /> <br /> The current protocol is:<br /> <br /> 1) Go to BioPortal 2.0 at http://bioportal.bioontology.org<br /> <br /> 2) If you haven't already, click on the &quot;Register&quot; link in the top right hand corner. <br /> <br /> 3) After you have registered as a user, &quot;Sign In&quot; as that user.<br /> <br /> 4) Click on the &quot;Browse&quot; tab (or click on the following link: http://bioportal.bioontology.org)<br /> <br /> 5) Click on the &quot;Submit Ontology&quot; button and follow the instructions.<br /> <br /> ==What is an annotation?==<br /> <br /> ==Where are the annotations?==<br /> <br /> ===How do I submit an annotation?===<br /> <br /> =Ontology Content=<br /> <br /> ==Building Ontologies==<br /> <br /> ===How do I go about building an ontology?===<br /> <br /> There are a plethora of tools for building ontologies. Below are two preferred tools for building OWL and OBO ontologies:<br /> <br /> 1) Protege (http://protege.stanford.edu/) - OWL ontologies<br /> <br /> 2) OBOEdit (http://oboedit.org/) - OBO ontologies<br /> <br /> ===What is the OBO Foundry?===<br /> <br /> A collaborative experiment, involving a group of OBO ontology developers who have agreed in advance to the adoption of a growing set of principles specifying best practices in ontology development. These principles are designed to foster interoperability of ontologies within the broader OBO framework, and also to ensure a gradual improvement of quality and formal rigor in ontologies, in ways designed to meet the increasing needs of data and information integration in the biomedical domain. See http://obofoundry.org/<br /> <br /> =NCBO Products=<br /> The NCBO has selected the Java/J2EE software infrastructure as the development of choice for all products.<br /> <br /> ==What is BioPortal?==<br /> A Web-based application for accessing, sharing, visualizing, analyzing, uploading, and searching a large repository of biomedical ontologies, terminologies, and annotations. BioPortal 2.0 is the current release accessible through the following URL: http://bioportal.bioontology.org/. BioPortal 2.0 allows for mappings between concepts, bulk export of mappings, vizualization of concepts and relationships within ontologies, marginal notes, and navigation of multiple ontologies through tabbed browsing. To see a demo of BioPortal 2.0, please visit http://bioontology.org/videos/demos/BioPortal_2.0_Demo.html.<br /> <br /> ==What is Open Biomedical Resources?==<br /> A set of annotations generated automatically. These annotations are presented through integration with BioPortal UI which enables researchers to search for biomedical resources associated (or annotated) with specific ontology terms.<br /> <br /> ==What is Open Biomedical Services?==<br /> A set of inter-related Java-based REST/SOAP services that use ontologies in BioPortal to perform concept recognition, ontology traversal, concept expansion, and to determine concept similarity. <br /> <br /> ==What is Biomedical Annotation Repository?==<br /> TBD<br /> <br /> ==What is Phenote?==<br /> A Java client application for manual creation and storage of biomedical annotations (starting with phenotype annotations) using terms from multiple ontologies.<br /> <br /> ==What is Open Biomedical Data?==<br /> A database of manually generated biomedical annotations (starting with phenotype annotations) summarizing key attributes such as anatomy, phenotype, and genetic features. The annotations are currently loaded directly from a Phenote file, which contains the manually created annotations.<br /> <br /> ===incomplete is-a paths===<br /> <br /> Many OBO ontologies are currently incomplete with respect to all classes/terms having an is-a parent. Many tools (including OBO-Edit and AmiGO) deliberately allow the conflation of relations when presenting the ontology as a DAG or a tree to the user. However, other tools (including Protege and SWOOP) do not. This means that some OBO ontologies can look unusual when viewed with these other tools (lots of classes appear at the root level).<br /> <br /> This is currently being addressed by the maintainers of OBO ontologies. An effort is underway to complete the is-a parentage in the GO cellular component ontology (biological process will be more difficult). The Plant Ontology Consortium are completing the is-a parentage in the plant anatomical structure ontology.<br /> <br /> Until this work is complete, some OBO ontologies may look unusual when viewed in conventional ontology browsing and editing tools. With some of these tools, there may be some configurations which allow other relations to be conflated with the is-a relation when presenting the ontology as a DAG or tree view.<br /> <br /> One option is to automatically create an is-a parent to the ontology root for every non-root class/term which lacks any is-a parents. Note that this may create inconsistencies in the ontology if the genuine is-a parent is somewhere deeper in the ontology hierarchy; nevertheless this step may be necessary before presenting some OBO ontologies to tools such as reasoners.<br /> <br /> =Details=<br /> <br /> ==What is NCBO Core 1?==<br /> <br /> ==What is NCBO Core 2?==<br /> <br /> ==Ontology Metadata==<br /> The NCBO is planning to leverage the Ontology Metadata Vocabulary (OMV) format to store all ontology meta data. Please see the following web site for more information on the format (http://omv.ontoware.org/).<br /> <br /> ==OBO Format==<br /> <br /> Questions about the OBO text and xml formats<br /> <br /> ===What is OBO Format?===<br /> <br /> ===Is OBO Format different from the old GO format?===<br /> <br /> Yes. The old dag-edit format (i.e. the one in which indentation was used to denote the GO hierarchy) is STRONGLY deprecated.<br /> <br /> ===Where can I find the spec?===<br /> <br /> You can find details on the 1.0 spec on the GO home page<br /> http://www.geneontology.org/GO.format.shtml#oboflat<br /> <br /> This spec is somewhat underspecified<br /> <br /> The 1.2 spec is in preparation, and will be released to coincide with the first production OBO-Edit release sometime early in 2006<br /> <br /> You can find a preliminary version of the spec here:<br /> HTML -- http://www.godatabase.org/dev/doc/obo_format_spec.html<br /> PDF -- http://www.godatabase.org/dev/doc/obo_format_spec.pdf<br /> Ascii text -- http://www.godatabase.org/dev/doc/obo_format_spec.txt<br /> <br /> ===Why not use XML?===<br /> <br /> There is also an obo-xml format. See<br /> <br /> http://www.godatabase.org/dev/xml<br /> <br /> Currently only available as DTD. Relax-NG and XSD coming soon.<br /> <br /> ===Is there a UML model?===<br /> <br /> Yes, there is a UML translation of the obo format in progress, produced by Harold Solbrig of Mayo clinic; see:<br /> <br /> http://informatics.mayo.edu/schema/OBO/UMLModel/HTML/<br /> <br /> ===What tools support Obo-Format?===<br /> <br /> The following are *ontology* tools that support the OBO format. There are many other tools for the analysis of gene ontology data which also happen to read the OBO format - see http://www.geneontology.org/GO.tools.shtml for a list<br /> <br /> ; OBO-Edit<br /> : (naturally!). You should use this rather than DAG-Edit (DAG-Edit still supports obo-1.0 format), as DAG-Edit is deprecated as of 2006.<br /> <br /> ; COBRA<br /> : developed by Stuart Aitken as part of http://www.xspan.org. COBRA is a java ontology editor/viewer for aligning ontologies<br /> <br /> ; go-perl<br /> : http://search.cpan.org/~cmungall/go-perl<br /> <br /> ==Using Protege with OBO ontologies==<br /> <br /> You have two options here - use the Protege OBO plugin, or convert to a format which Protege understands.<br /> <br /> The OBO plugin was developed at the University of Washington, and is no longer supported.<br /> <br /> You can convert any obo-format file to OWL and use Protege-OWL (but not Protege-classic); see the next entry.<br /> <br /> Note that when you look at many of the OBO ontologies in Protege (classic or Protege-OWL) you will see that there are large amounts of classes apparently at the root level. This is because OBO ontologies have historically not been complete with respect to all classes having a superclass (is-a parent). This is currently being addressed. See the FAQ entry on this subject.<br /> <br /> ===Can I convert Obo-format to OWL?===<br /> <br /> Yes. At this present time, the best way of foing this is to use the xslts included in go-perl.<br /> Download and install:<br /> http://search.cpan.org/~cmungall/go-perl/<br /> Then run the script<br /> <br /> go2owl myontology.obo<br /> <br /> This functionality will soon be available from oboedit<br /> <br /> For more details on the mapping, see:<br /> <br /> http://www.fruitfly.org/~cjm/obol/doc/mapping-obo-to-owl.html<br /> <br /> ===OK, but can I just download OBO ontologies as OWL without doing the conversion myself?===<br /> <br /> You can, at least for some OBO ontologies. This is an experimental service, and will eventually be subsumed into the services provided by cBio:<br /> <br /> http://www.fruitfly.org/~cjm/obo-download<br /> <br /> ===Can I convert Obo-format files to Protege-classic?===<br /> <br /> Not yet. In theory it should not be hard to provide an XSL for this. The reverse transformation may be more difficult.<br /> <br /> <br /> <br /> ==OBD==<br /> <br /> ===What is OBD?===<br /> <br /> OBD is a database for storing data typed using OBO ontologies<br /> <br /> ===Where is it?===<br /> <br /> In development!<br /> <br /> ===Is there a demo?===<br /> <br /> See http://www.fruitfly.org/~cjm/obd<br /> <br /> ===Datasets===<br /> <br /> See the above URL for now</div>

Skanel https://www.bioontology.org//mediawiki/index.php?title=BioPortal_FAQ&diff=8183 2008-11-11T19:06:23Z

<p>Skanel: /* What is BioPortal? */</p> <hr /> <div>'''Frequently Asked Questions (FAQ)'''<br /> <br /> =General=<br /> <br /> ==NCBO==<br /> <br /> Advancing biology and medicine with tools and methodologies for the structured organization of knowledge. <br /> <br /> ===What is NCBO?===<br /> <br /> The National Center for Biomedical Ontology (http://www.biontology.org) is a consortium of leading biologists, clinicians, informaticians, and ontologists who develop innovative technology and methods that allow scientists to create, disseminate, and manage biomedical information and knowledge in machine-processable form. Our vision is that all biomedical knowledge and data are disseminated on the Internet using principled ontologies, such that the knowledge and data are semantically interoperable and useful for furthering biomedical science and clinical care. The Center’s products and technologies include BioPortal, Phenote+, Open Biomedical Resources (OBR), Biomedical Annotations Repository (BAR), and Open Biomedical Data (OBD). Partner technologies include LexGrid, Protege, and Jambalaya. The products and technologies are used to deliver repositories and tools for accessing and using this biomedical information in research. The Center collaborates with biomedical researchers conducting Driving Biological Projects (DBPs) to enable their research and to stimulate technology development in the Center. The Center is undertaking outreach and educational activities to train the future generation of researchers in using biomedical ontologies and the Center’s tools to enhance scientific discovery.<br /> <br /> ==What is an ontology?==<br /> An ontology is a formal representation of a set of concepts/nodes within a domain and the relationships between those concepts. It is used to reason about the properties of that domain, and may be used to define the domain.<br /> <br /> ==Where are the ontologies?==<br /> <br /> Ontologies are available from BioPortal 2.0 at http://bioportal.bioontology.org. <br /> <br /> ===How do I submit an ontology?===<br /> <br /> The current protocol is:<br /> <br /> 1) Go to BioPortal 2.0 at http://bioportal.bioontology.org<br /> <br /> 2) If you haven't already, click on the &quot;Register&quot; link in the top right hand corner. <br /> <br /> 3) After you have registered as a user, &quot;Sign In&quot; as that user.<br /> <br /> 4) Click on the &quot;Browse&quot; tab (or click on the following link: http://bioportal.bioontology.org)<br /> <br /> 5) Click on the &quot;Submit Ontology&quot; button and follow the instructions.<br /> <br /> ==What is an annotation?==<br /> <br /> ==Where are the annotations?==<br /> <br /> ===How do I submit an annotation?===<br /> <br /> =Ontology Content=<br /> <br /> ==Building Ontologies==<br /> <br /> ===How do I go about building an ontology?===<br /> <br /> There are a plethora of tools for building ontologies. Below are two preferred tools for building OWL and OBO ontologies:<br /> <br /> 1) Protege (http://protege.stanford.edu/) - OWL ontologies<br /> <br /> 2) OBOEdit (http://oboedit.org/) - OBO ontologies<br /> <br /> ===What is the OBO Foundry?===<br /> <br /> A collaborative experiment, involving a group of OBO ontology developers who have agreed in advance to the adoption of a growing set of principles specifying best practices in ontology development. These principles are designed to foster interoperability of ontologies within the broader OBO framework, and also to ensure a gradual improvement of quality and formal rigor in ontologies, in ways designed to meet the increasing needs of data and information integration in the biomedical domain. See http://obofoundry.org/<br /> <br /> =NCBO Products=<br /> The NCBO has selected the Java/J2EE software infrastructure as the development of choice for all products.<br /> <br /> ==What is BioPortal?==<br /> A Web-based application for accessing, sharing, visualizing, analyzing, uploading, and searching a large repository of biomedical ontologies, terminologies, and annotations. BioPortal 2.0 is the current release accessible through the following URL: http://bioportal.bioontology.org/. BioPortal 2.0 allows for mappings between concepts, bulk export of said mappings, vizualization of concepts and relationships within ontologies, marginal notes, and navigation of multiple ontologies through tabbed browsing. To see a demo of BioPortal 2.0, please visit http://bioontology.org/videos/demos/BioPortal_2.0_Demo.html.<br /> <br /> ==What is Open Biomedical Resources?==<br /> A set of annotations generated automatically. These annotations are presented through integration with BioPortal UI which enables researchers to search for biomedical resources associated (or annotated) with specific ontology terms.<br /> <br /> ==What is Open Biomedical Services?==<br /> A set of inter-related Java-based REST/SOAP services that use ontologies in BioPortal to perform concept recognition, ontology traversal, concept expansion, and to determine concept similarity. <br /> <br /> ==What is Biomedical Annotation Repository?==<br /> TBD<br /> <br /> ==What is Phenote?==<br /> A Java client application for manual creation and storage of biomedical annotations (starting with phenotype annotations) using terms from multiple ontologies.<br /> <br /> ==What is Open Biomedical Data?==<br /> A database of manually generated biomedical annotations (starting with phenotype annotations) summarizing key attributes such as anatomy, phenotype, and genetic features. The annotations are currently loaded directly from a Phenote file, which contains the manually created annotations.<br /> <br /> ===incomplete is-a paths===<br /> <br /> Many OBO ontologies are currently incomplete with respect to all classes/terms having an is-a parent. Many tools (including OBO-Edit and AmiGO) deliberately allow the conflation of relations when presenting the ontology as a DAG or a tree to the user. However, other tools (including Protege and SWOOP) do not. This means that some OBO ontologies can look unusual when viewed with these other tools (lots of classes appear at the root level).<br /> <br /> This is currently being addressed by the maintainers of OBO ontologies. An effort is underway to complete the is-a parentage in the GO cellular component ontology (biological process will be more difficult). The Plant Ontology Consortium are completing the is-a parentage in the plant anatomical structure ontology.<br /> <br /> Until this work is complete, some OBO ontologies may look unusual when viewed in conventional ontology browsing and editing tools. With some of these tools, there may be some configurations which allow other relations to be conflated with the is-a relation when presenting the ontology as a DAG or tree view.<br /> <br /> One option is to automatically create an is-a parent to the ontology root for every non-root class/term which lacks any is-a parents. Note that this may create inconsistencies in the ontology if the genuine is-a parent is somewhere deeper in the ontology hierarchy; nevertheless this step may be necessary before presenting some OBO ontologies to tools such as reasoners.<br /> <br /> =Details=<br /> <br /> ==What is NCBO Core 1?==<br /> <br /> ==What is NCBO Core 2?==<br /> <br /> ==Ontology Metadata==<br /> The NCBO is planning to leverage the Ontology Metadata Vocabulary (OMV) format to store all ontology meta data. Please see the following web site for more information on the format (http://omv.ontoware.org/).<br /> <br /> ==OBO Format==<br /> <br /> Questions about the OBO text and xml formats<br /> <br /> ===What is OBO Format?===<br /> <br /> ===Is OBO Format different from the old GO format?===<br /> <br /> Yes. The old dag-edit format (i.e. the one in which indentation was used to denote the GO hierarchy) is STRONGLY deprecated.<br /> <br /> ===Where can I find the spec?===<br /> <br /> You can find details on the 1.0 spec on the GO home page<br /> http://www.geneontology.org/GO.format.shtml#oboflat<br /> <br /> This spec is somewhat underspecified<br /> <br /> The 1.2 spec is in preparation, and will be released to coincide with the first production OBO-Edit release sometime early in 2006<br /> <br /> You can find a preliminary version of the spec here:<br /> HTML -- http://www.godatabase.org/dev/doc/obo_format_spec.html<br /> PDF -- http://www.godatabase.org/dev/doc/obo_format_spec.pdf<br /> Ascii text -- http://www.godatabase.org/dev/doc/obo_format_spec.txt<br /> <br /> ===Why not use XML?===<br /> <br /> There is also an obo-xml format. See<br /> <br /> http://www.godatabase.org/dev/xml<br /> <br /> Currently only available as DTD. Relax-NG and XSD coming soon.<br /> <br /> ===Is there a UML model?===<br /> <br /> Yes, there is a UML translation of the obo format in progress, produced by Harold Solbrig of Mayo clinic; see:<br /> <br /> http://informatics.mayo.edu/schema/OBO/UMLModel/HTML/<br /> <br /> ===What tools support Obo-Format?===<br /> <br /> The following are *ontology* tools that support the OBO format. There are many other tools for the analysis of gene ontology data which also happen to read the OBO format - see http://www.geneontology.org/GO.tools.shtml for a list<br /> <br /> ; OBO-Edit<br /> : (naturally!). You should use this rather than DAG-Edit (DAG-Edit still supports obo-1.0 format), as DAG-Edit is deprecated as of 2006.<br /> <br /> ; COBRA<br /> : developed by Stuart Aitken as part of http://www.xspan.org. COBRA is a java ontology editor/viewer for aligning ontologies<br /> <br /> ; go-perl<br /> : http://search.cpan.org/~cmungall/go-perl<br /> <br /> ==Using Protege with OBO ontologies==<br /> <br /> You have two options here - use the Protege OBO plugin, or convert to a format which Protege understands.<br /> <br /> The OBO plugin was developed at the University of Washington, and is no longer supported.<br /> <br /> You can convert any obo-format file to OWL and use Protege-OWL (but not Protege-classic); see the next entry.<br /> <br /> Note that when you look at many of the OBO ontologies in Protege (classic or Protege-OWL) you will see that there are large amounts of classes apparently at the root level. This is because OBO ontologies have historically not been complete with respect to all classes having a superclass (is-a parent). This is currently being addressed. See the FAQ entry on this subject.<br /> <br /> ===Can I convert Obo-format to OWL?===<br /> <br /> Yes. At this present time, the best way of foing this is to use the xslts included in go-perl.<br /> Download and install:<br /> http://search.cpan.org/~cmungall/go-perl/<br /> Then run the script<br /> <br /> go2owl myontology.obo<br /> <br /> This functionality will soon be available from oboedit<br /> <br /> For more details on the mapping, see:<br /> <br /> http://www.fruitfly.org/~cjm/obol/doc/mapping-obo-to-owl.html<br /> <br /> ===OK, but can I just download OBO ontologies as OWL without doing the conversion myself?===<br /> <br /> You can, at least for some OBO ontologies. This is an experimental service, and will eventually be subsumed into the services provided by cBio:<br /> <br /> http://www.fruitfly.org/~cjm/obo-download<br /> <br /> ===Can I convert Obo-format files to Protege-classic?===<br /> <br /> Not yet. In theory it should not be hard to provide an XSL for this. The reverse transformation may be more difficult.<br /> <br /> <br /> <br /> ==OBD==<br /> <br /> ===What is OBD?===<br /> <br /> OBD is a database for storing data typed using OBO ontologies<br /> <br /> ===Where is it?===<br /> <br /> In development!<br /> <br /> ===Is there a demo?===<br /> <br /> See http://www.fruitfly.org/~cjm/obd<br /> <br /> ===Datasets===<br /> <br /> See the above URL for now</div>

Skanel https://www.bioontology.org//mediawiki/index.php?title=BioPortal_FAQ&diff=8181 2008-11-11T19:01:58Z

<p>Skanel: /* What is BioPortal? */</p> <hr /> <div>'''Frequently Asked Questions (FAQ)'''<br /> <br /> =General=<br /> <br /> ==NCBO==<br /> <br /> Advancing biology and medicine with tools and methodologies for the structured organization of knowledge. <br /> <br /> ===What is NCBO?===<br /> <br /> The National Center for Biomedical Ontology (http://www.biontology.org) is a consortium of leading biologists, clinicians, informaticians, and ontologists who develop innovative technology and methods that allow scientists to create, disseminate, and manage biomedical information and knowledge in machine-processable form. Our vision is that all biomedical knowledge and data are disseminated on the Internet using principled ontologies, such that the knowledge and data are semantically interoperable and useful for furthering biomedical science and clinical care. The Center’s products and technologies include BioPortal, Phenote+, Open Biomedical Resources (OBR), Biomedical Annotations Repository (BAR), and Open Biomedical Data (OBD). Partner technologies include LexGrid, Protege, and Jambalaya. The products and technologies are used to deliver repositories and tools for accessing and using this biomedical information in research. The Center collaborates with biomedical researchers conducting Driving Biological Projects (DBPs) to enable their research and to stimulate technology development in the Center. The Center is undertaking outreach and educational activities to train the future generation of researchers in using biomedical ontologies and the Center’s tools to enhance scientific discovery.<br /> <br /> ==What is an ontology?==<br /> An ontology is a formal representation of a set of concepts/nodes within a domain and the relationships between those concepts. It is used to reason about the properties of that domain, and may be used to define the domain.<br /> <br /> ==Where are the ontologies?==<br /> <br /> Ontologies are available from BioPortal 2.0 at http://bioportal.bioontology.org. <br /> <br /> ===How do I submit an ontology?===<br /> <br /> The current protocol is:<br /> <br /> 1) Go to BioPortal 2.0 at http://bioportal.bioontology.org<br /> <br /> 2) If you haven't already, click on the &quot;Register&quot; link in the top right hand corner. <br /> <br /> 3) After you have registered as a user, &quot;Sign In&quot; as that user.<br /> <br /> 4) Click on the &quot;Browse&quot; tab (or click on the following link: http://bioportal.bioontology.org)<br /> <br /> 5) Click on the &quot;Submit Ontology&quot; button and follow the instructions.<br /> <br /> ==What is an annotation?==<br /> <br /> ==Where are the annotations?==<br /> <br /> ===How do I submit an annotation?===<br /> <br /> =Ontology Content=<br /> <br /> ==Building Ontologies==<br /> <br /> ===How do I go about building an ontology?===<br /> <br /> There are a plethora of tools for building ontologies. Below are two preferred tools for building OWL and OBO ontologies:<br /> <br /> 1) Protege (http://protege.stanford.edu/) - OWL ontologies<br /> <br /> 2) OBOEdit (http://oboedit.org/) - OBO ontologies<br /> <br /> ===What is the OBO Foundry?===<br /> <br /> A collaborative experiment, involving a group of OBO ontology developers who have agreed in advance to the adoption of a growing set of principles specifying best practices in ontology development. These principles are designed to foster interoperability of ontologies within the broader OBO framework, and also to ensure a gradual improvement of quality and formal rigor in ontologies, in ways designed to meet the increasing needs of data and information integration in the biomedical domain. See http://obofoundry.org/<br /> <br /> =NCBO Products=<br /> The NCBO has selected the Java/J2EE software infrastructure as the development of choice for all products.<br /> <br /> ==What is BioPortal?==<br /> A Web-based application for accessing, sharing, visualizing, analyzing, uploading, and searching a large repository of biomedical ontologies, terminologies, and annotations. BioPortal 2.0 is the current release accessible through the following URL: http://bioportal.bioontology.org/. To see a demo of BioPortal 2.0, please visit http://bioontology.org/videos/demos/BioPortal_2.0_Demo.html.<br /> <br /> ==What is Open Biomedical Resources?==<br /> A set of annotations generated automatically. These annotations are presented through integration with BioPortal UI which enables researchers to search for biomedical resources associated (or annotated) with specific ontology terms.<br /> <br /> ==What is Open Biomedical Services?==<br /> A set of inter-related Java-based REST/SOAP services that use ontologies in BioPortal to perform concept recognition, ontology traversal, concept expansion, and to determine concept similarity. <br /> <br /> ==What is Biomedical Annotation Repository?==<br /> TBD<br /> <br /> ==What is Phenote?==<br /> A Java client application for manual creation and storage of biomedical annotations (starting with phenotype annotations) using terms from multiple ontologies.<br /> <br /> ==What is Open Biomedical Data?==<br /> A database of manually generated biomedical annotations (starting with phenotype annotations) summarizing key attributes such as anatomy, phenotype, and genetic features. The annotations are currently loaded directly from a Phenote file, which contains the manually created annotations.<br /> <br /> ===incomplete is-a paths===<br /> <br /> Many OBO ontologies are currently incomplete with respect to all classes/terms having an is-a parent. Many tools (including OBO-Edit and AmiGO) deliberately allow the conflation of relations when presenting the ontology as a DAG or a tree to the user. However, other tools (including Protege and SWOOP) do not. This means that some OBO ontologies can look unusual when viewed with these other tools (lots of classes appear at the root level).<br /> <br /> This is currently being addressed by the maintainers of OBO ontologies. An effort is underway to complete the is-a parentage in the GO cellular component ontology (biological process will be more difficult). The Plant Ontology Consortium are completing the is-a parentage in the plant anatomical structure ontology.<br /> <br /> Until this work is complete, some OBO ontologies may look unusual when viewed in conventional ontology browsing and editing tools. With some of these tools, there may be some configurations which allow other relations to be conflated with the is-a relation when presenting the ontology as a DAG or tree view.<br /> <br /> One option is to automatically create an is-a parent to the ontology root for every non-root class/term which lacks any is-a parents. Note that this may create inconsistencies in the ontology if the genuine is-a parent is somewhere deeper in the ontology hierarchy; nevertheless this step may be necessary before presenting some OBO ontologies to tools such as reasoners.<br /> <br /> =Details=<br /> <br /> ==What is NCBO Core 1?==<br /> <br /> ==What is NCBO Core 2?==<br /> <br /> ==Ontology Metadata==<br /> The NCBO is planning to leverage the Ontology Metadata Vocabulary (OMV) format to store all ontology meta data. Please see the following web site for more information on the format (http://omv.ontoware.org/).<br /> <br /> ==OBO Format==<br /> <br /> Questions about the OBO text and xml formats<br /> <br /> ===What is OBO Format?===<br /> <br /> ===Is OBO Format different from the old GO format?===<br /> <br /> Yes. The old dag-edit format (i.e. the one in which indentation was used to denote the GO hierarchy) is STRONGLY deprecated.<br /> <br /> ===Where can I find the spec?===<br /> <br /> You can find details on the 1.0 spec on the GO home page<br /> http://www.geneontology.org/GO.format.shtml#oboflat<br /> <br /> This spec is somewhat underspecified<br /> <br /> The 1.2 spec is in preparation, and will be released to coincide with the first production OBO-Edit release sometime early in 2006<br /> <br /> You can find a preliminary version of the spec here:<br /> HTML -- http://www.godatabase.org/dev/doc/obo_format_spec.html<br /> PDF -- http://www.godatabase.org/dev/doc/obo_format_spec.pdf<br /> Ascii text -- http://www.godatabase.org/dev/doc/obo_format_spec.txt<br /> <br /> ===Why not use XML?===<br /> <br /> There is also an obo-xml format. See<br /> <br /> http://www.godatabase.org/dev/xml<br /> <br /> Currently only available as DTD. Relax-NG and XSD coming soon.<br /> <br /> ===Is there a UML model?===<br /> <br /> Yes, there is a UML translation of the obo format in progress, produced by Harold Solbrig of Mayo clinic; see:<br /> <br /> http://informatics.mayo.edu/schema/OBO/UMLModel/HTML/<br /> <br /> ===What tools support Obo-Format?===<br /> <br /> The following are *ontology* tools that support the OBO format. There are many other tools for the analysis of gene ontology data which also happen to read the OBO format - see http://www.geneontology.org/GO.tools.shtml for a list<br /> <br /> ; OBO-Edit<br /> : (naturally!). You should use this rather than DAG-Edit (DAG-Edit still supports obo-1.0 format), as DAG-Edit is deprecated as of 2006.<br /> <br /> ; COBRA<br /> : developed by Stuart Aitken as part of http://www.xspan.org. COBRA is a java ontology editor/viewer for aligning ontologies<br /> <br /> ; go-perl<br /> : http://search.cpan.org/~cmungall/go-perl<br /> <br /> ==Using Protege with OBO ontologies==<br /> <br /> You have two options here - use the Protege OBO plugin, or convert to a format which Protege understands.<br /> <br /> The OBO plugin was developed at the University of Washington, and is no longer supported.<br /> <br /> You can convert any obo-format file to OWL and use Protege-OWL (but not Protege-classic); see the next entry.<br /> <br /> Note that when you look at many of the OBO ontologies in Protege (classic or Protege-OWL) you will see that there are large amounts of classes apparently at the root level. This is because OBO ontologies have historically not been complete with respect to all classes having a superclass (is-a parent). This is currently being addressed. See the FAQ entry on this subject.<br /> <br /> ===Can I convert Obo-format to OWL?===<br /> <br /> Yes. At this present time, the best way of foing this is to use the xslts included in go-perl.<br /> Download and install:<br /> http://search.cpan.org/~cmungall/go-perl/<br /> Then run the script<br /> <br /> go2owl myontology.obo<br /> <br /> This functionality will soon be available from oboedit<br /> <br /> For more details on the mapping, see:<br /> <br /> http://www.fruitfly.org/~cjm/obol/doc/mapping-obo-to-owl.html<br /> <br /> ===OK, but can I just download OBO ontologies as OWL without doing the conversion myself?===<br /> <br /> You can, at least for some OBO ontologies. This is an experimental service, and will eventually be subsumed into the services provided by cBio:<br /> <br /> http://www.fruitfly.org/~cjm/obo-download<br /> <br /> ===Can I convert Obo-format files to Protege-classic?===<br /> <br /> Not yet. In theory it should not be hard to provide an XSL for this. The reverse transformation may be more difficult.<br /> <br /> <br /> <br /> ==OBD==<br /> <br /> ===What is OBD?===<br /> <br /> OBD is a database for storing data typed using OBO ontologies<br /> <br /> ===Where is it?===<br /> <br /> In development!<br /> <br /> ===Is there a demo?===<br /> <br /> See http://www.fruitfly.org/~cjm/obd<br /> <br /> ===Datasets===<br /> <br /> See the above URL for now</div>

Skanel https://www.bioontology.org//mediawiki/index.php?title=BioPortal_FAQ&diff=8178 2008-11-11T18:50:28Z

<p>Skanel: /* What is BioPortal? */</p> <hr /> <div>'''Frequently Asked Questions (FAQ)'''<br /> <br /> =General=<br /> <br /> ==NCBO==<br /> <br /> Advancing biology and medicine with tools and methodologies for the structured organization of knowledge. <br /> <br /> ===What is NCBO?===<br /> <br /> The National Center for Biomedical Ontology (http://www.biontology.org) is a consortium of leading biologists, clinicians, informaticians, and ontologists who develop innovative technology and methods that allow scientists to create, disseminate, and manage biomedical information and knowledge in machine-processable form. Our vision is that all biomedical knowledge and data are disseminated on the Internet using principled ontologies, such that the knowledge and data are semantically interoperable and useful for furthering biomedical science and clinical care. The Center’s products and technologies include BioPortal, Phenote+, Open Biomedical Resources (OBR), Biomedical Annotations Repository (BAR), and Open Biomedical Data (OBD). Partner technologies include LexGrid, Protege, and Jambalaya. The products and technologies are used to deliver repositories and tools for accessing and using this biomedical information in research. The Center collaborates with biomedical researchers conducting Driving Biological Projects (DBPs) to enable their research and to stimulate technology development in the Center. The Center is undertaking outreach and educational activities to train the future generation of researchers in using biomedical ontologies and the Center’s tools to enhance scientific discovery.<br /> <br /> ==What is an ontology?==<br /> An ontology is a formal representation of a set of concepts/nodes within a domain and the relationships between those concepts. It is used to reason about the properties of that domain, and may be used to define the domain.<br /> <br /> ==Where are the ontologies?==<br /> <br /> Currently found in BioPortal 1.0 at http://www.bioontology.org/ncbo/faces/pages/ontology_list.xhtml. We will be rolling out BioPortal 2.0 in August 2008 which will include all ontologies currently found in BioPortal 1.0.<br /> <br /> ===How do I submit an ontology?===<br /> <br /> The current protocol is:<br /> <br /> 1) Go to BioPortal 1.0 at http://www.bioontology.org/ncbo/faces/index.xhtml.<br /> <br /> 2) If you haven't already, click on the &quot;Register&quot; link in the top right hand corner. <br /> <br /> 3) After you have registered as a user, &quot;Sign In&quot; as that user.<br /> <br /> 4) Click on the &quot;Browse&quot; tab (or click on the following link: http://www.bioontology.org/ncbo/faces/pages/ontology_list.xhtml)<br /> <br /> 5) Click on the &quot;Submit Ontology&quot; button and follow the instructions.<br /> <br /> ==What is an annotation?==<br /> <br /> ==Where are the annotations?==<br /> <br /> ===How do I submit an annotation?===<br /> <br /> =Ontology Content=<br /> <br /> ==Building Ontologies==<br /> <br /> ===How do I go about building an ontology?===<br /> <br /> There are a plethora of tools for building ontologies. Below are two preferred tools for building OWL and OBO ontologies:<br /> <br /> 1) Protege (http://protege.stanford.edu/) - OWL ontologies<br /> <br /> 2) OBOEdit (http://oboedit.org/) - OBO ontologies<br /> <br /> ===What is the OBO Foundry?===<br /> <br /> A collaborative experiment, involving a group of OBO ontology developers who have agreed in advance to the adoption of a growing set of principles specifying best practices in ontology development. These principles are designed to foster interoperability of ontologies within the broader OBO framework, and also to ensure a gradual improvement of quality and formal rigor in ontologies, in ways designed to meet the increasing needs of data and information integration in the biomedical domain. See http://obofoundry.org/<br /> <br /> =NCBO Products=<br /> The NCBO has selected the Java/J2EE software infrastructure as the development of choice for all products.<br /> <br /> ==What is BioPortal?==<br /> A web-based application for accessing, sharing, visualizing, analyzing, uploading, and searching a large repository of biomedical ontologies, terminologies, and annotations. BioPortal 2.0 is the current release accessible through the following URL: http://bioportal.bioontology.org/. To see a demo of BioPortal 2.0, please visit http://bioontology.org/videos/demos/BioPortal_2.0_Demo.html.<br /> <br /> ==What is Open Biomedical Resources?==<br /> A set of annotations generated automatically. These annotations are presented through integration with BioPortal UI which enables researchers to search for biomedical resources associated (or annotated) with specific ontology terms.<br /> <br /> ==What is Open Biomedical Services?==<br /> A set of inter-related Java-based REST/SOAP services that use ontologies in BioPortal to perform concept recognition, ontology traversal, concept expansion, and to determine concept similarity. <br /> <br /> ==What is Biomedical Annotation Repository?==<br /> TBD<br /> <br /> ==What is Phenote?==<br /> A Java client application for manual creation and storage of biomedical annotations (starting with phenotype annotations) using terms from multiple ontologies.<br /> <br /> ==What is Open Biomedical Data?==<br /> A database of manually generated biomedical annotations (starting with phenotype annotations) summarizing key attributes such as anatomy, phenotype, and genetic features. The annotations are currently loaded directly from a Phenote file, which contains the manually created annotations.<br /> <br /> ===incomplete is-a paths===<br /> <br /> Many OBO ontologies are currently incomplete with respect to all classes/terms having an is-a parent. Many tools (including OBO-Edit and AmiGO) deliberately allow the conflation of relations when presenting the ontology as a DAG or a tree to the user. However, other tools (including Protege and SWOOP) do not. This means that some OBO ontologies can look unusual when viewed with these other tools (lots of classes appear at the root level).<br /> <br /> This is currently being addressed by the maintainers of OBO ontologies. An effort is underway to complete the is-a parentage in the GO cellular component ontology (biological process will be more difficult). The Plant Ontology Consortium are completing the is-a parentage in the plant anatomical structure ontology.<br /> <br /> Until this work is complete, some OBO ontologies may look unusual when viewed in conventional ontology browsing and editing tools. With some of these tools, there may be some configurations which allow other relations to be conflated with the is-a relation when presenting the ontology as a DAG or tree view.<br /> <br /> One option is to automatically create an is-a parent to the ontology root for every non-root class/term which lacks any is-a parents. Note that this may create inconsistencies in the ontology if the genuine is-a parent is somewhere deeper in the ontology hierarchy; nevertheless this step may be necessary before presenting some OBO ontologies to tools such as reasoners.<br /> <br /> =Details=<br /> <br /> ==What is NCBO Core 1?==<br /> <br /> ==What is NCBO Core 2?==<br /> <br /> ==Ontology Metadata==<br /> The NCBO is planning to leverage the Ontology Metadata Vocabulary (OMV) format to store all ontology meta data. Please see the following web site for more information on the format (http://omv.ontoware.org/).<br /> <br /> ==OBO Format==<br /> <br /> Questions about the OBO text and xml formats<br /> <br /> ===What is OBO Format?===<br /> <br /> ===Is OBO Format different from the old GO format?===<br /> <br /> Yes. The old dag-edit format (i.e. the one in which indentation was used to denote the GO hierarchy) is STRONGLY deprecated.<br /> <br /> ===Where can I find the spec?===<br /> <br /> You can find details on the 1.0 spec on the GO home page<br /> http://www.geneontology.org/GO.format.shtml#oboflat<br /> <br /> This spec is somewhat underspecified<br /> <br /> The 1.2 spec is in preparation, and will be released to coincide with the first production OBO-Edit release sometime early in 2006<br /> <br /> You can find a preliminary version of the spec here:<br /> HTML -- http://www.godatabase.org/dev/doc/obo_format_spec.html<br /> PDF -- http://www.godatabase.org/dev/doc/obo_format_spec.pdf<br /> Ascii text -- http://www.godatabase.org/dev/doc/obo_format_spec.txt<br /> <br /> ===Why not use XML?===<br /> <br /> There is also an obo-xml format. See<br /> <br /> http://www.godatabase.org/dev/xml<br /> <br /> Currently only available as DTD. Relax-NG and XSD coming soon.<br /> <br /> ===Is there a UML model?===<br /> <br /> Yes, there is a UML translation of the obo format in progress, produced by Harold Solbrig of Mayo clinic; see:<br /> <br /> http://informatics.mayo.edu/schema/OBO/UMLModel/HTML/<br /> <br /> ===What tools support Obo-Format?===<br /> <br /> The following are *ontology* tools that support the OBO format. There are many other tools for the analysis of gene ontology data which also happen to read the OBO format - see http://www.geneontology.org/GO.tools.shtml for a list<br /> <br /> ; OBO-Edit<br /> : (naturally!). You should use this rather than DAG-Edit (DAG-Edit still supports obo-1.0 format), as DAG-Edit is deprecated as of 2006.<br /> <br /> ; COBRA<br /> : developed by Stuart Aitken as part of http://www.xspan.org. COBRA is a java ontology editor/viewer for aligning ontologies<br /> <br /> ; go-perl<br /> : http://search.cpan.org/~cmungall/go-perl<br /> <br /> ==Using Protege with OBO ontologies==<br /> <br /> You have two options here - use the Protege OBO plugin, or convert to a format which Protege understands.<br /> <br /> The OBO plugin was developed at the University of Washington, and is no longer supported.<br /> <br /> You can convert any obo-format file to OWL and use Protege-OWL (but not Protege-classic); see the next entry.<br /> <br /> Note that when you look at many of the OBO ontologies in Protege (classic or Protege-OWL) you will see that there are large amounts of classes apparently at the root level. This is because OBO ontologies have historically not been complete with respect to all classes having a superclass (is-a parent). This is currently being addressed. See the FAQ entry on this subject.<br /> <br /> ===Can I convert Obo-format to OWL?===<br /> <br /> Yes. At this present time, the best way of foing this is to use the xslts included in go-perl.<br /> Download and install:<br /> http://search.cpan.org/~cmungall/go-perl/<br /> Then run the script<br /> <br /> go2owl myontology.obo<br /> <br /> This functionality will soon be available from oboedit<br /> <br /> For more details on the mapping, see:<br /> <br /> http://www.fruitfly.org/~cjm/obol/doc/mapping-obo-to-owl.html<br /> <br /> ===OK, but can I just download OBO ontologies as OWL without doing the conversion myself?===<br /> <br /> You can, at least for some OBO ontologies. This is an experimental service, and will eventually be subsumed into the services provided by cBio:<br /> <br /> http://www.fruitfly.org/~cjm/obo-download<br /> <br /> ===Can I convert Obo-format files to Protege-classic?===<br /> <br /> Not yet. In theory it should not be hard to provide an XSL for this. The reverse transformation may be more difficult.<br /> <br /> <br /> <br /> ==OBD==<br /> <br /> ===What is OBD?===<br /> <br /> OBD is a database for storing data typed using OBO ontologies<br /> <br /> ===Where is it?===<br /> <br /> In development!<br /> <br /> ===Is there a demo?===<br /> <br /> See http://www.fruitfly.org/~cjm/obd<br /> <br /> ===Datasets===<br /> <br /> See the above URL for now</div>

Skanel https://www.bioontology.org//mediawiki/index.php?title=Main_Page&diff=6954 2008-05-10T19:42:59Z

<p>Skanel: </p> <hr /> <div>Welcome to the '''NCBO Public WIKI'''. This WIKI provides information about collaborative ontology development efforts, dissemination events conducted by the NCBO and publically shared materials from the NCBO. <br /> Please visit our [http://www.bioontology.org Main Site] for more information and materials.<br /> <br /> <br /> === NCBO Links ===<br /> *[http://www.bioontology.org/ NCBO Home page]<br /> *[http://www.bioontology.org/wiki/index.php/NCBO_FAQ NCBO FAQ]<br /> *[http://www.bioontology.org/wiki/index.php/News_Events_Publications NCBO News, Events and Publications]<br /> <br /> === Shared Materials===<br /> <br /> *[[Public Requirements Redirect|Public Requirements]]<br /> <br /> *[[Shared Materials]]<br /> <br /> *[[Evaluation Activities]]<br /> <br /> === NCBC Links ===<br /> <br /> *[http://www.bisti.nih.gov/ncbc/ Home page of National Centers for Biomedical Computing]<br /> <br /> *[http://wiki.na-mic.org/Wiki/index.php/SDIWG:Software_and_Data_Integration_Working_Group NCBC Software and Data Integration Working Group (SDIWG) and Centers Discussion]<br /> <br /> *[http://wiki.na-mic.org/Wiki/index.php/SDIWG:_NCBC_Scientific_Ontologies NCBC Scientific Ontologies Working Group]<br /> <br /> === Ontology Development Area ===<br /> <br /> Below are wikis for some of the current OBO ontologies. Each wiki is housed on the bioontologies.org wiki, in its own partition (wikispace) of the main wiki<br /> <br /> *[[PATO:Main_Page]] - An ontology of phenotypic qualities<br /> <br /> *[[RO:Main_Page]] - OBO Relations ontology<br /> <br /> *[[CARO:Main_Page]] - Reference anatomical ontology<br /> <br /> *[[CL:Main_Page]] - OBO Cell ontology<br /> <br /> *[[SO:Main_Page]] - Sequence Ontology<br /> <br /> *[[Disease:Main_Page]] - Disease Ontology, and other ontologies pertaining to diseases and disorders<br /> <br /> *[[OCI:Main_Page]] - Ontology of Clinical Investigation<br /> <br /> Note that each ontology lives in its own wikispace which corresponds to the [[OBO:IDSpace]] of that ontology. Note for wiki editors: all wiki pages that are to be considered local to a particular ontology should be prefixed with that IDSpace.<br /> <br /> === Software Development Area ===<br /> *[[OboInOwl:Main_Page]] - Mapping between OBO and OWL formats<br /> *[[Phenote:Main_Page]] - A Phenotype Annotation Tool using Ontologies<br /> *[[Bioportal:Main_Page]]</div>

Skanel https://www.bioontology.org//mediawiki/index.php?title=Education&diff=6953 2008-05-10T19:41:04Z

<p>Skanel: </p> <hr /> <div>===Publications===<br /> *Please see the main [http://www.bioontology.org/publications.html NCBO Publications Site]<br /> <br /> === RSS Feeds ===<br /> *Ontology articles in Pubmed in last 60 days [http://eutils.ncbi.nlm.nih.gov/entrez/eutils/erss.cgi?rss_guid=0gcn-LTgvdDj0y38wqDUuwq_R5x8QZnS3TX7HIwZ7Jn Feed]<br /> <br /> ===Educational Documents, Videos and Slides===<br /> <br /> To see old and new educational materials created and supplied by the NCBO, please visit our main [http://www.bioontology.org/education.html Education Page]<br /> <br /> ===Journals of Interest===<br /> ====Bio[medical] Informatics====<br /> *[http://www.jamia.org/ Journal of American Medical Informatics Association]<br /> *[http://www.elsevier.com/wps/find/journaldescription.cws_home/622857/description#description Journal of Biomedical Informatics]<br /> *[http://bioinformatics.oxfordjournals.org/ Bioinformatics]<br /> *[http://www.biomedcentral.com/bmcbioinformatics/ BMC Bioinformatics]<br /> *[http://bib.oxfordjournals.org/ Briefings in Bioinformatics]<br /> *[http://www.worldscinet.com/jbcb/jbcb.shtml Journal of Bioinformatics and Computational Biology]<br /> *[http://www.elsevier.com/wps/find/journaldescription.cws_home/506040/description?navopenmenu=-2 International Journal of Medical Informatics]<br /> *for more journals, see http://www.hiww.org/jou.html<br /> <br /> ====Ontologies====<br /> *[http://www.applied-ontology.org/ Journal of Applied Ontology]<br /> <br /> ====Biomedical====<br /> *[http://www.genomebiology.com/ Genome Biology]<br /> *[http://www.nature.com/nbt/index.html Nature Biotechnology]<br /> *[http://www.elsevier.com/wps/find/journaldescription.cws_home/351/description?navopenmenu=-2 Computers in Biology and Medicine]<br /> *[http://www.liebertpub.com/publication.aspx?pub_id=43 Omics: A journal of Integrative Biology]<br /> *[http://www.elsevier.com/wps/find/journaldescription.cws_home/505627/description?navopenmenu=-2 Artificial Intelligence in Medicine]<br /> <br /> ===Symposia and Meetings===<br /> *[http://iswc2008.semanticweb.org/ ISWC] by [http://www.iswsa.org/ SWSA]<br /> *[http://www.amia.org/meetings/ AMIA]<br /> *[http://www.eswc2008.org/index.html ESWC]<br /> *[http://www.iscb.org/ismb2008/index.php ISMB]<br /> *[http://psb.stanford.edu PSB]<br /> *[http://www2007.org/ WWW Conference]<br /> *[http://www.csd.abdn.ac.uk/kcap07/index.php KCAP/EKAW]<br /> *[http://kr-med.org/2008/index.html KR-MED]<br /> *[http://www.w3.org/2001/sw/hcls/ HCLSIG]</div>

Skanel https://www.bioontology.org//mediawiki/index.php?title=Education&diff=6952 2008-05-10T19:40:45Z

<p>Skanel: </p> <hr /> <div>===Publications===<br /> *Please see the main [http://www.bioontology.org/publications.html NCBO Publications Site]<br /> <br /> === RSS Feeds ===<br /> *Ontology articles in Pubmed in last 60 days [http://eutils.ncbi.nlm.nih.gov/entrez/eutils/erss.cgi?rss_guid=0gcn-LTgvdDj0y38wqDUuwq_R5x8QZnS3TX7HIwZ7Jn Feed]<br /> <br /> ==Educational Documents, Videos and Slides==<br /> <br /> To see old and new educational materials created and supplied by the NCBO, please visit our main [http://www.bioontology.org/education.html Education Page]<br /> <br /> ===Journals of Interest===<br /> ====Bio[medical] Informatics====<br /> *[http://www.jamia.org/ Journal of American Medical Informatics Association]<br /> *[http://www.elsevier.com/wps/find/journaldescription.cws_home/622857/description#description Journal of Biomedical Informatics]<br /> *[http://bioinformatics.oxfordjournals.org/ Bioinformatics]<br /> *[http://www.biomedcentral.com/bmcbioinformatics/ BMC Bioinformatics]<br /> *[http://bib.oxfordjournals.org/ Briefings in Bioinformatics]<br /> *[http://www.worldscinet.com/jbcb/jbcb.shtml Journal of Bioinformatics and Computational Biology]<br /> *[http://www.elsevier.com/wps/find/journaldescription.cws_home/506040/description?navopenmenu=-2 International Journal of Medical Informatics]<br /> *for more journals, see http://www.hiww.org/jou.html<br /> <br /> ====Ontologies====<br /> *[http://www.applied-ontology.org/ Journal of Applied Ontology]<br /> <br /> ====Biomedical====<br /> *[http://www.genomebiology.com/ Genome Biology]<br /> *[http://www.nature.com/nbt/index.html Nature Biotechnology]<br /> *[http://www.elsevier.com/wps/find/journaldescription.cws_home/351/description?navopenmenu=-2 Computers in Biology and Medicine]<br /> *[http://www.liebertpub.com/publication.aspx?pub_id=43 Omics: A journal of Integrative Biology]<br /> *[http://www.elsevier.com/wps/find/journaldescription.cws_home/505627/description?navopenmenu=-2 Artificial Intelligence in Medicine]<br /> <br /> ===Symposia and Meetings===<br /> *[http://iswc2008.semanticweb.org/ ISWC] by [http://www.iswsa.org/ SWSA]<br /> *[http://www.amia.org/meetings/ AMIA]<br /> *[http://www.eswc2008.org/index.html ESWC]<br /> *[http://www.iscb.org/ismb2008/index.php ISMB]<br /> *[http://psb.stanford.edu PSB]<br /> *[http://www2007.org/ WWW Conference]<br /> *[http://www.csd.abdn.ac.uk/kcap07/index.php KCAP/EKAW]<br /> *[http://kr-med.org/2008/index.html KR-MED]<br /> *[http://www.w3.org/2001/sw/hcls/ HCLSIG]</div>

Skanel https://www.bioontology.org//mediawiki/index.php?title=Education&diff=6951 2008-05-10T19:40:07Z

<p>Skanel: </p> <hr /> <div>===Publications===<br /> *Please see the main [http://www.bioontology.org/publications.html NCBO Publications Site]<br /> <br /> === RSS Feeds ===<br /> *Ontology articles in Pubmed in last 60 days [http://eutils.ncbi.nlm.nih.gov/entrez/eutils/erss.cgi?rss_guid=0gcn-LTgvdDj0y38wqDUuwq_R5x8QZnS3TX7HIwZ7Jn Feed]<br /> <br /> ===Journals of Interest===<br /> ====Bio[medical] Informatics====<br /> *[http://www.jamia.org/ Journal of American Medical Informatics Association]<br /> *[http://www.elsevier.com/wps/find/journaldescription.cws_home/622857/description#description Journal of Biomedical Informatics]<br /> *[http://bioinformatics.oxfordjournals.org/ Bioinformatics]<br /> *[http://www.biomedcentral.com/bmcbioinformatics/ BMC Bioinformatics]<br /> *[http://bib.oxfordjournals.org/ Briefings in Bioinformatics]<br /> *[http://www.worldscinet.com/jbcb/jbcb.shtml Journal of Bioinformatics and Computational Biology]<br /> *[http://www.elsevier.com/wps/find/journaldescription.cws_home/506040/description?navopenmenu=-2 International Journal of Medical Informatics]<br /> *for more journals, see http://www.hiww.org/jou.html<br /> <br /> ====Ontologies====<br /> *[http://www.applied-ontology.org/ Journal of Applied Ontology]<br /> <br /> ====Biomedical====<br /> *[http://www.genomebiology.com/ Genome Biology]<br /> *[http://www.nature.com/nbt/index.html Nature Biotechnology]<br /> *[http://www.elsevier.com/wps/find/journaldescription.cws_home/351/description?navopenmenu=-2 Computers in Biology and Medicine]<br /> *[http://www.liebertpub.com/publication.aspx?pub_id=43 Omics: A journal of Integrative Biology]<br /> *[http://www.elsevier.com/wps/find/journaldescription.cws_home/505627/description?navopenmenu=-2 Artificial Intelligence in Medicine]<br /> <br /> ===Symposia and Meetings===<br /> *[http://iswc2008.semanticweb.org/ ISWC] by [http://www.iswsa.org/ SWSA]<br /> *[http://www.amia.org/meetings/ AMIA]<br /> *[http://www.eswc2008.org/index.html ESWC]<br /> *[http://www.iscb.org/ismb2008/index.php ISMB]<br /> *[http://psb.stanford.edu PSB]<br /> *[http://www2007.org/ WWW Conference]<br /> *[http://www.csd.abdn.ac.uk/kcap07/index.php KCAP/EKAW]<br /> *[http://kr-med.org/2008/index.html KR-MED]<br /> *[http://www.w3.org/2001/sw/hcls/ HCLSIG]</div>

Skanel https://www.bioontology.org//mediawiki/index.php?title=Dissemination_Wiki&diff=6950 2008-05-10T19:37:32Z

<p>Skanel: </p> <hr /> <div>==NCBO Dissemination ==<br /> <br /> What follows is a list of events organized under the auspices of the NCBO's Dissemination Core (PI: [http://ontology.buffalo.edu/smith Barry Smith]), together with information pertaining to related events and resources relevant to the NCBO's mission.<br /> <br /> ==Educational Documents, Videos and Slides==<br /> <br /> To see old and new educational materials created and supplied by the NCBO, please visit our [http://www.bioontology.org/education.html Education Page]<br /> <br /> ==NCBO Dissemination Workshops, Events and Meetings==<br /> <br /> *'''Forthcoming Events:'''<br /> <br /> ::For forthcoming events of all types, please refer to the new NCBO [http://www.bioontology.org/events.html Events Page]<br /> <br /> *'''Past:'''<br /> <br /> ::*'''[[Workshops and Training Events 2008 | 2008]]'''<br /> <br /> ::*'''[[Workshops and Training Events 2007 | 2007]]'''<br /> <br /> ::*'''[[Workshops and Training Events 2006 | 2006]]'''<br /> <br /> ::*'''[[Meetings and Events | Past Meetings]]'''<br /> <br /> ::*'''[[Related Events 2007 | Related 2007 Events]]'''<br /> <br /> ::*'''[[Related Events 2006 | Related 2006 Events]]'''<br /> <br /> == Ontology Training: Video and Audio Presentations ==<br /> <br /> '''[http://bmir.stanford.edu/people/view.php/mark_a_musen/ Mark Musen]'''<br /> <br /> *If we build it, will they come? Social-engineering of new technology to disseminate biomedical ontologies (Ontolog Form, December 6, 2007)<br /> ::[http://ontolog.cim3.net/cgi-bin/wiki.pl?ConferenceCall_2007_12_06 Details]<br /> ::[http://ontolog.cim3.net/file/resource/presentation/MarkMusen_20071206/NCBO--MarkMusen_20071206.pdf Slides]<br /> ::[http://ontolog.cim3.net/file/resource/presentation/MarkMusen_20071206/NCBO-BioPortal--MarkMusen_Ontolog-AudioRecording_conf-133566_20071206.mp3 Audio]<br /> <br /> '''[http://ontology.buffalo.edu/smith Barry Smith]'''<br /> <br /> *Ontology Evaluation in Biomedicine: The OBO Foundry (Ontolog Forum, December 21, 2006)<br /> ::[http://ontolog.cim3.net/cgi-bin/wiki.pl?ConferenceCall_2005_10_13 Details]<br /> ::[http://ontolog.cim3.net/file/work/OntologyMeasurementEvaluation/2006-12-21_OntologyEvaluationInBiomedicine/OBO-Foundry--BarrySmith_20061221.ppt Slides]<br /> ::[http://obofoundry.org/OntologDec06.mp3 Audio]<br /> <br /> *How to Build an Ontology (Tutorial, Stanford University, October 25, 2006)<br /> ::[http://stream.buffalo.edu/shared/research/phismith/Stanford10-25-06/Tutorial.rm Realplayer]<br /> ::[http://stream.buffalo.edu/shared/research/phismith/Stanford10-25-06/Tutorial.WMV Windows Mediaplayer]<br /> <br /> *Presentations at the Workshop on [http://www.bioontology.org/wiki/index.php/Workshop_on_Ontology_of_Images Ontology of Images] {Stanford University, March 24-25, 2006)<br /> ::[http://med.stanford.edu/irt/mmt/video/ontology/ontology-03-24-2006-09.ram Basic Principles]<br /> ::[http://med.stanford.edu/irt/mmt/video/ontology/ontology-03-24-2006-11.ram Towards an Ontology for the Imaging Domain]<br /> <br /> *The HL7 Reference Information Model<br /> ::[http://stream.buffalo.edu/shared/research/phismith/regenstrief.mpg Presentation] at the Regenstrief Institute, Indianapolis, November 9, 2005<br /> <br /> '''NCBO Workshops on Biomedical Ontology'''<br /> <br /> *The Ontology of Images: March 24-25, 2006 in Stanford, CA.<br /> ::[http://www.bioontology.org/wiki/index.php/Workshop_on_Ontology_of_Images#Webcast Webcast]<br /> <br /> *The Ontology of Diseases: November 6-7, 2006 in Baltimore, MD. <br /> ::[http://www.bioontology.org/wiki/index.php/Workshop_on_Ontology_of_Diseases#Agenda Slides and Audio Presentations]</div>

Skanel https://www.bioontology.org//mediawiki/index.php?title=Dissemination_Wiki&diff=6949 2008-05-09T23:43:26Z

<p>Skanel: /* NCBO Dissemination Workshops, Events and Meetings */</p> <hr /> <div>==NCBO Dissemination ==<br /> <br /> What follows is a list of events organized under the auspices of the NCBO's Dissemination Core (PI: [http://ontology.buffalo.edu/smith Barry Smith]), together with information pertaining to related events and resources relevant to the NCBO's mission.<br /> <br /> ==NCBO Dissemination Workshops, Events and Meetings ==<br /> <br /> *'''Forthcoming Events:'''<br /> <br /> ::For forthcoming events of all types, please refer to the new NCBO [http://www.bioontology.org/events.html Events Page]<br /> <br /> *'''Past:'''<br /> <br /> ::*'''[[Workshops and Training Events 2008 | 2008]]'''<br /> <br /> ::*'''[[Workshops and Training Events 2007 | 2007]]'''<br /> <br /> ::*'''[[Workshops and Training Events 2006 | 2006]]'''<br /> <br /> ::*'''[[Meetings and Events | Past Meetings]]'''<br /> <br /> ::*'''[[Related Events 2007 | Related 2007 Events]]'''<br /> <br /> ::*'''[[Related Events 2006 | Related 2006 Events]]'''<br /> <br /> == Ontology Training: Video and Audio Presentations ==<br /> <br /> '''[http://bmir.stanford.edu/people/view.php/mark_a_musen/ Mark Musen]'''<br /> <br /> *If we build it, will they come? Social-engineering of new technology to disseminate biomedical ontologies (Ontolog Form, December 6, 2007)<br /> ::[http://ontolog.cim3.net/cgi-bin/wiki.pl?ConferenceCall_2007_12_06 Details]<br /> ::[http://ontolog.cim3.net/file/resource/presentation/MarkMusen_20071206/NCBO--MarkMusen_20071206.pdf Slides]<br /> ::[http://ontolog.cim3.net/file/resource/presentation/MarkMusen_20071206/NCBO-BioPortal--MarkMusen_Ontolog-AudioRecording_conf-133566_20071206.mp3 Audio]<br /> <br /> '''[http://ontology.buffalo.edu/smith Barry Smith]'''<br /> <br /> *Ontology Evaluation in Biomedicine: The OBO Foundry (Ontolog Forum, December 21, 2006)<br /> ::[http://ontolog.cim3.net/cgi-bin/wiki.pl?ConferenceCall_2005_10_13 Details]<br /> ::[http://ontolog.cim3.net/file/work/OntologyMeasurementEvaluation/2006-12-21_OntologyEvaluationInBiomedicine/OBO-Foundry--BarrySmith_20061221.ppt Slides]<br /> ::[http://obofoundry.org/OntologDec06.mp3 Audio]<br /> <br /> *How to Build an Ontology (Tutorial, Stanford University, October 25, 2006)<br /> ::[http://stream.buffalo.edu/shared/research/phismith/Stanford10-25-06/Tutorial.rm Realplayer]<br /> ::[http://stream.buffalo.edu/shared/research/phismith/Stanford10-25-06/Tutorial.WMV Windows Mediaplayer]<br /> <br /> *Presentations at the Workshop on [http://www.bioontology.org/wiki/index.php/Workshop_on_Ontology_of_Images Ontology of Images] {Stanford University, March 24-25, 2006)<br /> ::[http://med.stanford.edu/irt/mmt/video/ontology/ontology-03-24-2006-09.ram Basic Principles]<br /> ::[http://med.stanford.edu/irt/mmt/video/ontology/ontology-03-24-2006-11.ram Towards an Ontology for the Imaging Domain]<br /> <br /> *The HL7 Reference Information Model<br /> ::[http://stream.buffalo.edu/shared/research/phismith/regenstrief.mpg Presentation] at the Regenstrief Institute, Indianapolis, November 9, 2005<br /> <br /> '''NCBO Workshops on Biomedical Ontology'''<br /> <br /> *The Ontology of Images: March 24-25, 2006 in Stanford, CA.<br /> ::[http://www.bioontology.org/wiki/index.php/Workshop_on_Ontology_of_Images#Webcast Webcast]<br /> <br /> *The Ontology of Diseases: November 6-7, 2006 in Baltimore, MD. <br /> ::[http://www.bioontology.org/wiki/index.php/Workshop_on_Ontology_of_Diseases#Agenda Slides and Audio Presentations]</div>

Skanel https://www.bioontology.org//mediawiki/index.php?title=Dissemination_Wiki&diff=6948 2008-05-09T23:42:47Z

<p>Skanel: /* NCBO Dissemination Workshops, Events and Meetings */</p> <hr /> <div>==NCBO Dissemination ==<br /> <br /> What follows is a list of events organized under the auspices of the NCBO's Dissemination Core (PI: [http://ontology.buffalo.edu/smith Barry Smith]), together with information pertaining to related events and resources relevant to the NCBO's mission.<br /> <br /> ==NCBO Dissemination Workshops, Events and Meetings ==<br /> <br /> *'''Forthcoming Events:'''<br /> <br /> ::For forthcoming events of all types, please refer to the new [http://www.bioontology.org/events.html Events Page]<br /> <br /> *'''Past:'''<br /> <br /> ::*'''[[Workshops and Training Events 2008 | 2008]]'''<br /> <br /> ::*'''[[Workshops and Training Events 2007 | 2007]]'''<br /> <br /> ::*'''[[Workshops and Training Events 2006 | 2006]]'''<br /> <br /> ::*'''[[Meetings and Events | Past Meetings]]'''<br /> <br /> ::*'''[[Related Events 2007 | Related 2007 Events]]'''<br /> <br /> ::*'''[[Related Events 2006 | Related 2006 Events]]'''<br /> <br /> == Ontology Training: Video and Audio Presentations ==<br /> <br /> '''[http://bmir.stanford.edu/people/view.php/mark_a_musen/ Mark Musen]'''<br /> <br /> *If we build it, will they come? Social-engineering of new technology to disseminate biomedical ontologies (Ontolog Form, December 6, 2007)<br /> ::[http://ontolog.cim3.net/cgi-bin/wiki.pl?ConferenceCall_2007_12_06 Details]<br /> ::[http://ontolog.cim3.net/file/resource/presentation/MarkMusen_20071206/NCBO--MarkMusen_20071206.pdf Slides]<br /> ::[http://ontolog.cim3.net/file/resource/presentation/MarkMusen_20071206/NCBO-BioPortal--MarkMusen_Ontolog-AudioRecording_conf-133566_20071206.mp3 Audio]<br /> <br /> '''[http://ontology.buffalo.edu/smith Barry Smith]'''<br /> <br /> *Ontology Evaluation in Biomedicine: The OBO Foundry (Ontolog Forum, December 21, 2006)<br /> ::[http://ontolog.cim3.net/cgi-bin/wiki.pl?ConferenceCall_2005_10_13 Details]<br /> ::[http://ontolog.cim3.net/file/work/OntologyMeasurementEvaluation/2006-12-21_OntologyEvaluationInBiomedicine/OBO-Foundry--BarrySmith_20061221.ppt Slides]<br /> ::[http://obofoundry.org/OntologDec06.mp3 Audio]<br /> <br /> *How to Build an Ontology (Tutorial, Stanford University, October 25, 2006)<br /> ::[http://stream.buffalo.edu/shared/research/phismith/Stanford10-25-06/Tutorial.rm Realplayer]<br /> ::[http://stream.buffalo.edu/shared/research/phismith/Stanford10-25-06/Tutorial.WMV Windows Mediaplayer]<br /> <br /> *Presentations at the Workshop on [http://www.bioontology.org/wiki/index.php/Workshop_on_Ontology_of_Images Ontology of Images] {Stanford University, March 24-25, 2006)<br /> ::[http://med.stanford.edu/irt/mmt/video/ontology/ontology-03-24-2006-09.ram Basic Principles]<br /> ::[http://med.stanford.edu/irt/mmt/video/ontology/ontology-03-24-2006-11.ram Towards an Ontology for the Imaging Domain]<br /> <br /> *The HL7 Reference Information Model<br /> ::[http://stream.buffalo.edu/shared/research/phismith/regenstrief.mpg Presentation] at the Regenstrief Institute, Indianapolis, November 9, 2005<br /> <br /> '''NCBO Workshops on Biomedical Ontology'''<br /> <br /> *The Ontology of Images: March 24-25, 2006 in Stanford, CA.<br /> ::[http://www.bioontology.org/wiki/index.php/Workshop_on_Ontology_of_Images#Webcast Webcast]<br /> <br /> *The Ontology of Diseases: November 6-7, 2006 in Baltimore, MD. <br /> ::[http://www.bioontology.org/wiki/index.php/Workshop_on_Ontology_of_Diseases#Agenda Slides and Audio Presentations]</div>

Skanel https://www.bioontology.org//mediawiki/index.php?title=Workshops_and_Training_Events_2008&diff=6947 2008-05-09T23:42:03Z

<p>Skanel: New page: ::'''April 12-13, 2008''' ::Introduction to Biomedical Ontologies, 2-Day Training Event, Buffalo, NY ::'''March 27-28, 2008''' ::[[Networks | Workshop on Ontologies of Cellular Netw...</p> <hr /> <div>::'''April 12-13, 2008'''<br /> <br /> ::[[Introduction to Biomedical Ontologies]], 2-Day Training Event, Buffalo, NY<br /> <br /> ::'''March 27-28, 2008'''<br /> <br /> ::[[Networks | Workshop on Ontologies of Cellular Networks]], Newark, NJ. <br /> <br /> ::'''February 26-27, 2008'''<br /> <br /> ::[[JCOR | Joint JCOR-NCBO International Biomedical Ontology Dissemination Workshop]], Tokyo, Japan.</div>

Skanel https://www.bioontology.org//mediawiki/index.php?title=Dissemination_Wiki&diff=6946 2008-05-09T23:38:43Z

<p>Skanel: consolidation of events and meetings</p> <hr /> <div>==NCBO Dissemination ==<br /> <br /> What follows is a list of events organized under the auspices of the NCBO's Dissemination Core (PI: [http://ontology.buffalo.edu/smith Barry Smith]), together with information pertaining to related events and resources relevant to the NCBO's mission.<br /> <br /> ==NCBO Dissemination Workshops, Events and Meetings ==<br /> <br /> *'''Forthcoming Events:'''<br /> <br /> ::For forthcoming events of all types, please refer to the new [http://www.bioontology.org/events.html Events Page]<br /> <br /> *'''Past:'''<br /> <br /> ::'''April 12-13, 2008'''<br /> <br /> ::[[Introduction to Biomedical Ontologies]], 2-Day Training Event, Buffalo, NY<br /> <br /> ::'''March 27-28, 2008'''<br /> <br /> ::[[Networks | Workshop on Ontologies of Cellular Networks]], Newark, NJ. <br /> <br /> ::'''February 26-27, 2008'''<br /> <br /> ::[[JCOR | Joint JCOR-NCBO International Biomedical Ontology Dissemination Workshop]], Tokyo, Japan. <br /> <br /> ::*'''[[Workshops and Training Events 2007 | 2007]]'''<br /> <br /> ::*'''[[Workshops and Training Events 2006 | 2006]]'''<br /> <br /> ::*'''[[Meetings and Events | Past Meetings]]'''<br /> <br /> ::*'''[[Related Events 2007 | Related 2007 Events]]'''<br /> <br /> ::*'''[[Related Events 2006 | Related 2006 Events]]'''<br /> <br /> <br /> == Ontology Training: Video and Audio Presentations ==<br /> <br /> '''[http://bmir.stanford.edu/people/view.php/mark_a_musen/ Mark Musen]'''<br /> <br /> *If we build it, will they come? Social-engineering of new technology to disseminate biomedical ontologies (Ontolog Form, December 6, 2007)<br /> ::[http://ontolog.cim3.net/cgi-bin/wiki.pl?ConferenceCall_2007_12_06 Details]<br /> ::[http://ontolog.cim3.net/file/resource/presentation/MarkMusen_20071206/NCBO--MarkMusen_20071206.pdf Slides]<br /> ::[http://ontolog.cim3.net/file/resource/presentation/MarkMusen_20071206/NCBO-BioPortal--MarkMusen_Ontolog-AudioRecording_conf-133566_20071206.mp3 Audio]<br /> <br /> '''[http://ontology.buffalo.edu/smith Barry Smith]'''<br /> <br /> *Ontology Evaluation in Biomedicine: The OBO Foundry (Ontolog Forum, December 21, 2006)<br /> ::[http://ontolog.cim3.net/cgi-bin/wiki.pl?ConferenceCall_2005_10_13 Details]<br /> ::[http://ontolog.cim3.net/file/work/OntologyMeasurementEvaluation/2006-12-21_OntologyEvaluationInBiomedicine/OBO-Foundry--BarrySmith_20061221.ppt Slides]<br /> ::[http://obofoundry.org/OntologDec06.mp3 Audio]<br /> <br /> *How to Build an Ontology (Tutorial, Stanford University, October 25, 2006)<br /> ::[http://stream.buffalo.edu/shared/research/phismith/Stanford10-25-06/Tutorial.rm Realplayer]<br /> ::[http://stream.buffalo.edu/shared/research/phismith/Stanford10-25-06/Tutorial.WMV Windows Mediaplayer]<br /> <br /> *Presentations at the Workshop on [http://www.bioontology.org/wiki/index.php/Workshop_on_Ontology_of_Images Ontology of Images] {Stanford University, March 24-25, 2006)<br /> ::[http://med.stanford.edu/irt/mmt/video/ontology/ontology-03-24-2006-09.ram Basic Principles]<br /> ::[http://med.stanford.edu/irt/mmt/video/ontology/ontology-03-24-2006-11.ram Towards an Ontology for the Imaging Domain]<br /> <br /> *The HL7 Reference Information Model<br /> ::[http://stream.buffalo.edu/shared/research/phismith/regenstrief.mpg Presentation] at the Regenstrief Institute, Indianapolis, November 9, 2005<br /> <br /> '''NCBO Workshops on Biomedical Ontology'''<br /> <br /> *The Ontology of Images: March 24-25, 2006 in Stanford, CA.<br /> ::[http://www.bioontology.org/wiki/index.php/Workshop_on_Ontology_of_Images#Webcast Webcast]<br /> <br /> *The Ontology of Diseases: November 6-7, 2006 in Baltimore, MD. <br /> ::[http://www.bioontology.org/wiki/index.php/Workshop_on_Ontology_of_Diseases#Agenda Slides and Audio Presentations]</div>

Skanel https://www.bioontology.org//mediawiki/index.php?title=Dissemination_Wiki&diff=6945 2008-05-09T23:20:06Z

<p>Skanel: </p> <hr /> <div>==NCBO Dissemination ==<br /> <br /> What follows is a list of events organized under the auspices of the NCBO's Dissemination Core (PI: [http://ontology.buffalo.edu/smith Barry Smith]), together with information pertaining to related events and resources relevant to the NCBO's mission.<br /> <br /> ==NCBO Dissemination Workshops and Training Events ==<br /> <br /> *'''Forthcoming:'''<br /> <br /> ::'''June 20, 2008'''<br /> <br /> ::[[Evolutionary Biology and Ontologies]], Minneapolis, MN (collocated with [http://www.cce.umn.edu/conferences/evolution/ Evolution 2008])<br /> <br /> ::'''July 19, 2008'''<br /> <br /> ::[[How to Make Useful Ontologies for Biomedicine]], Tutorial at ISMB 2008, Toronto, Canada.<br /> <br /> <br /> *'''Past:'''<br /> <br /> ::'''April 12-13, 2008'''<br /> <br /> ::[[Introduction to Biomedical Ontologies]], 2-Day Training Event, Buffalo, NY<br /> <br /> ::'''March 27-28, 2008'''<br /> <br /> ::[[Networks | Workshop on Ontologies of Cellular Networks]], Newark, NJ. <br /> <br /> ::'''February 26-27, 2008'''<br /> <br /> ::[[JCOR | Joint JCOR-NCBO International Biomedical Ontology Dissemination Workshop]], Tokyo, Japan. <br /> <br /> ::*'''[[Workshops and Training Events 2007 | 2007]]'''<br /> <br /> ::*'''[[Workshops and Training Events 2006 | 2006]]'''<br /> <br /> == Meetings and Events ==<br /> <br /> *'''[http://www.bioontology.org/events.html Forthcoming]'''<br /> <br /> *'''[[Meetings and Events | Past Meetings]]'''<br /> <br /> *'''[[Related Events 2007 | 2007 Events]]'''<br /> <br /> *'''[[Related Events 2006 | 2006 Events]]'''<br /> <br /> == Ontology Training: Video and Audio Presentations ==<br /> <br /> '''[http://bmir.stanford.edu/people/view.php/mark_a_musen/ Mark Musen]'''<br /> <br /> *If we build it, will they come? Social-engineering of new technology to disseminate biomedical ontologies (Ontolog Form, December 6, 2007)<br /> ::[http://ontolog.cim3.net/cgi-bin/wiki.pl?ConferenceCall_2007_12_06 Details]<br /> ::[http://ontolog.cim3.net/file/resource/presentation/MarkMusen_20071206/NCBO--MarkMusen_20071206.pdf Slides]<br /> ::[http://ontolog.cim3.net/file/resource/presentation/MarkMusen_20071206/NCBO-BioPortal--MarkMusen_Ontolog-AudioRecording_conf-133566_20071206.mp3 Audio]<br /> <br /> '''[http://ontology.buffalo.edu/smith Barry Smith]'''<br /> <br /> *Ontology Evaluation in Biomedicine: The OBO Foundry (Ontolog Forum, December 21, 2006)<br /> ::[http://ontolog.cim3.net/cgi-bin/wiki.pl?ConferenceCall_2005_10_13 Details]<br /> ::[http://ontolog.cim3.net/file/work/OntologyMeasurementEvaluation/2006-12-21_OntologyEvaluationInBiomedicine/OBO-Foundry--BarrySmith_20061221.ppt Slides]<br /> ::[http://obofoundry.org/OntologDec06.mp3 Audio]<br /> <br /> *How to Build an Ontology (Tutorial, Stanford University, October 25, 2006)<br /> ::[http://stream.buffalo.edu/shared/research/phismith/Stanford10-25-06/Tutorial.rm Realplayer]<br /> ::[http://stream.buffalo.edu/shared/research/phismith/Stanford10-25-06/Tutorial.WMV Windows Mediaplayer]<br /> <br /> *Presentations at the Workshop on [http://www.bioontology.org/wiki/index.php/Workshop_on_Ontology_of_Images Ontology of Images] {Stanford University, March 24-25, 2006)<br /> ::[http://med.stanford.edu/irt/mmt/video/ontology/ontology-03-24-2006-09.ram Basic Principles]<br /> ::[http://med.stanford.edu/irt/mmt/video/ontology/ontology-03-24-2006-11.ram Towards an Ontology for the Imaging Domain]<br /> <br /> *The HL7 Reference Information Model<br /> ::[http://stream.buffalo.edu/shared/research/phismith/regenstrief.mpg Presentation] at the Regenstrief Institute, Indianapolis, November 9, 2005<br /> <br /> '''NCBO Workshops on Biomedical Ontology'''<br /> <br /> *The Ontology of Images: March 24-25, 2006 in Stanford, CA.<br /> ::[http://www.bioontology.org/wiki/index.php/Workshop_on_Ontology_of_Images#Webcast Webcast]<br /> <br /> *The Ontology of Diseases: November 6-7, 2006 in Baltimore, MD. <br /> ::[http://www.bioontology.org/wiki/index.php/Workshop_on_Ontology_of_Diseases#Agenda Slides and Audio Presentations]</div>

Skanel https://www.bioontology.org//mediawiki/index.php?title=Dissemination_Wiki&diff=6944 2008-05-09T23:19:44Z

<p>Skanel: /* Past Meetings and Events */</p> <hr /> <div>==NCBO Dissemination ==<br /> <br /> What follows is a list of events organized under the auspices of the NCBO's Dissemination Core (PI: [http://ontology.buffalo.edu/smith Barry Smith]), together with information pertaining to related events and resources relevant to the NCBO's mission.<br /> <br /> ==NCBO Dissemination Workshops and Training Events ==<br /> <br /> *'''Forthcoming:'''<br /> <br /> ::'''June 20, 2008'''<br /> <br /> ::[[Evolutionary Biology and Ontologies]], Minneapolis, MN (collocated with [http://www.cce.umn.edu/conferences/evolution/ Evolution 2008])<br /> <br /> ::'''July 19, 2008'''<br /> <br /> ::[[How to Make Useful Ontologies for Biomedicine]], Tutorial at ISMB 2008, Toronto, Canada.<br /> <br /> <br /> *'''Past:'''<br /> <br /> ::'''April 12-13, 2008'''<br /> <br /> ::[[Introduction to Biomedical Ontologies]], 2-Day Training Event, Buffalo, NY<br /> <br /> ::'''March 27-28, 2008'''<br /> <br /> ::[[Networks | Workshop on Ontologies of Cellular Networks]], Newark, NJ. <br /> <br /> ::'''February 26-27, 2008'''<br /> <br /> ::[[JCOR | Joint JCOR-NCBO International Biomedical Ontology Dissemination Workshop]], Tokyo, Japan. <br /> <br /> ::*'''[[Workshops and Training Events 2007 | 2007]]'''<br /> <br /> ::*'''[[Workshops and Training Events 2006 | 2006]]'''<br /> <br /> == Meetings and Events ==<br /> <br /> *'''[http://www.bioontology.org/events.html Forthcoming]'''<br /> <br /> *'''[[Meetings and Events | Past Meetings]]'''<br /> <br /> *'''[[Related Events 2007 | 2007 Events]]'''<br /> <br /> *'''[[Related Events 2006 | 2006 Events]]'''<br /> <br /> ==Other Meetings==<br /> <br /> *'''[http://www.bioontology.org/events.html Forthcoming]'''<br /> <br /> == Ontology Training: Video and Audio Presentations ==<br /> <br /> '''[http://bmir.stanford.edu/people/view.php/mark_a_musen/ Mark Musen]'''<br /> <br /> *If we build it, will they come? Social-engineering of new technology to disseminate biomedical ontologies (Ontolog Form, December 6, 2007)<br /> ::[http://ontolog.cim3.net/cgi-bin/wiki.pl?ConferenceCall_2007_12_06 Details]<br /> ::[http://ontolog.cim3.net/file/resource/presentation/MarkMusen_20071206/NCBO--MarkMusen_20071206.pdf Slides]<br /> ::[http://ontolog.cim3.net/file/resource/presentation/MarkMusen_20071206/NCBO-BioPortal--MarkMusen_Ontolog-AudioRecording_conf-133566_20071206.mp3 Audio]<br /> <br /> '''[http://ontology.buffalo.edu/smith Barry Smith]'''<br /> <br /> *Ontology Evaluation in Biomedicine: The OBO Foundry (Ontolog Forum, December 21, 2006)<br /> ::[http://ontolog.cim3.net/cgi-bin/wiki.pl?ConferenceCall_2005_10_13 Details]<br /> ::[http://ontolog.cim3.net/file/work/OntologyMeasurementEvaluation/2006-12-21_OntologyEvaluationInBiomedicine/OBO-Foundry--BarrySmith_20061221.ppt Slides]<br /> ::[http://obofoundry.org/OntologDec06.mp3 Audio]<br /> <br /> *How to Build an Ontology (Tutorial, Stanford University, October 25, 2006)<br /> ::[http://stream.buffalo.edu/shared/research/phismith/Stanford10-25-06/Tutorial.rm Realplayer]<br /> ::[http://stream.buffalo.edu/shared/research/phismith/Stanford10-25-06/Tutorial.WMV Windows Mediaplayer]<br /> <br /> *Presentations at the Workshop on [http://www.bioontology.org/wiki/index.php/Workshop_on_Ontology_of_Images Ontology of Images] {Stanford University, March 24-25, 2006)<br /> ::[http://med.stanford.edu/irt/mmt/video/ontology/ontology-03-24-2006-09.ram Basic Principles]<br /> ::[http://med.stanford.edu/irt/mmt/video/ontology/ontology-03-24-2006-11.ram Towards an Ontology for the Imaging Domain]<br /> <br /> *The HL7 Reference Information Model<br /> ::[http://stream.buffalo.edu/shared/research/phismith/regenstrief.mpg Presentation] at the Regenstrief Institute, Indianapolis, November 9, 2005<br /> <br /> '''NCBO Workshops on Biomedical Ontology'''<br /> <br /> *The Ontology of Images: March 24-25, 2006 in Stanford, CA.<br /> ::[http://www.bioontology.org/wiki/index.php/Workshop_on_Ontology_of_Images#Webcast Webcast]<br /> <br /> *The Ontology of Diseases: November 6-7, 2006 in Baltimore, MD. <br /> ::[http://www.bioontology.org/wiki/index.php/Workshop_on_Ontology_of_Diseases#Agenda Slides and Audio Presentations]</div>

Skanel https://www.bioontology.org//mediawiki/index.php?title=Dissemination_Wiki&diff=6943 2008-05-09T23:18:36Z

<p>Skanel: /* Other Meetings */</p> <hr /> <div>==NCBO Dissemination ==<br /> <br /> What follows is a list of events organized under the auspices of the NCBO's Dissemination Core (PI: [http://ontology.buffalo.edu/smith Barry Smith]), together with information pertaining to related events and resources relevant to the NCBO's mission.<br /> <br /> ==NCBO Dissemination Workshops and Training Events ==<br /> <br /> *'''Forthcoming:'''<br /> <br /> ::'''June 20, 2008'''<br /> <br /> ::[[Evolutionary Biology and Ontologies]], Minneapolis, MN (collocated with [http://www.cce.umn.edu/conferences/evolution/ Evolution 2008])<br /> <br /> ::'''July 19, 2008'''<br /> <br /> ::[[How to Make Useful Ontologies for Biomedicine]], Tutorial at ISMB 2008, Toronto, Canada.<br /> <br /> <br /> *'''Past:'''<br /> <br /> ::'''April 12-13, 2008'''<br /> <br /> ::[[Introduction to Biomedical Ontologies]], 2-Day Training Event, Buffalo, NY<br /> <br /> ::'''March 27-28, 2008'''<br /> <br /> ::[[Networks | Workshop on Ontologies of Cellular Networks]], Newark, NJ. <br /> <br /> ::'''February 26-27, 2008'''<br /> <br /> ::[[JCOR | Joint JCOR-NCBO International Biomedical Ontology Dissemination Workshop]], Tokyo, Japan. <br /> <br /> ::*'''[[Workshops and Training Events 2007 | 2007]]'''<br /> <br /> ::*'''[[Workshops and Training Events 2006 | 2006]]'''<br /> <br /> == Past Meetings and Events ==<br /> <br /> *'''[[Related Events 2007 | 2007 Events]]'''<br /> <br /> *'''[[Related Events 2006 | 2006 Events]]'''<br /> <br /> *'''[[Meetings and Events | Past Meetings]]'''<br /> <br /> ==Other Meetings==<br /> <br /> *'''[http://www.bioontology.org/events.html Forthcoming]'''<br /> <br /> == Ontology Training: Video and Audio Presentations ==<br /> <br /> '''[http://bmir.stanford.edu/people/view.php/mark_a_musen/ Mark Musen]'''<br /> <br /> *If we build it, will they come? Social-engineering of new technology to disseminate biomedical ontologies (Ontolog Form, December 6, 2007)<br /> ::[http://ontolog.cim3.net/cgi-bin/wiki.pl?ConferenceCall_2007_12_06 Details]<br /> ::[http://ontolog.cim3.net/file/resource/presentation/MarkMusen_20071206/NCBO--MarkMusen_20071206.pdf Slides]<br /> ::[http://ontolog.cim3.net/file/resource/presentation/MarkMusen_20071206/NCBO-BioPortal--MarkMusen_Ontolog-AudioRecording_conf-133566_20071206.mp3 Audio]<br /> <br /> '''[http://ontology.buffalo.edu/smith Barry Smith]'''<br /> <br /> *Ontology Evaluation in Biomedicine: The OBO Foundry (Ontolog Forum, December 21, 2006)<br /> ::[http://ontolog.cim3.net/cgi-bin/wiki.pl?ConferenceCall_2005_10_13 Details]<br /> ::[http://ontolog.cim3.net/file/work/OntologyMeasurementEvaluation/2006-12-21_OntologyEvaluationInBiomedicine/OBO-Foundry--BarrySmith_20061221.ppt Slides]<br /> ::[http://obofoundry.org/OntologDec06.mp3 Audio]<br /> <br /> *How to Build an Ontology (Tutorial, Stanford University, October 25, 2006)<br /> ::[http://stream.buffalo.edu/shared/research/phismith/Stanford10-25-06/Tutorial.rm Realplayer]<br /> ::[http://stream.buffalo.edu/shared/research/phismith/Stanford10-25-06/Tutorial.WMV Windows Mediaplayer]<br /> <br /> *Presentations at the Workshop on [http://www.bioontology.org/wiki/index.php/Workshop_on_Ontology_of_Images Ontology of Images] {Stanford University, March 24-25, 2006)<br /> ::[http://med.stanford.edu/irt/mmt/video/ontology/ontology-03-24-2006-09.ram Basic Principles]<br /> ::[http://med.stanford.edu/irt/mmt/video/ontology/ontology-03-24-2006-11.ram Towards an Ontology for the Imaging Domain]<br /> <br /> *The HL7 Reference Information Model<br /> ::[http://stream.buffalo.edu/shared/research/phismith/regenstrief.mpg Presentation] at the Regenstrief Institute, Indianapolis, November 9, 2005<br /> <br /> '''NCBO Workshops on Biomedical Ontology'''<br /> <br /> *The Ontology of Images: March 24-25, 2006 in Stanford, CA.<br /> ::[http://www.bioontology.org/wiki/index.php/Workshop_on_Ontology_of_Images#Webcast Webcast]<br /> <br /> *The Ontology of Diseases: November 6-7, 2006 in Baltimore, MD. <br /> ::[http://www.bioontology.org/wiki/index.php/Workshop_on_Ontology_of_Diseases#Agenda Slides and Audio Presentations]</div>

Skanel https://www.bioontology.org//mediawiki/index.php?title=Dissemination_Wiki&diff=6942 2008-05-09T23:18:25Z

<p>Skanel: /* Past Meetings and Events */</p> <hr /> <div>==NCBO Dissemination ==<br /> <br /> What follows is a list of events organized under the auspices of the NCBO's Dissemination Core (PI: [http://ontology.buffalo.edu/smith Barry Smith]), together with information pertaining to related events and resources relevant to the NCBO's mission.<br /> <br /> ==NCBO Dissemination Workshops and Training Events ==<br /> <br /> *'''Forthcoming:'''<br /> <br /> ::'''June 20, 2008'''<br /> <br /> ::[[Evolutionary Biology and Ontologies]], Minneapolis, MN (collocated with [http://www.cce.umn.edu/conferences/evolution/ Evolution 2008])<br /> <br /> ::'''July 19, 2008'''<br /> <br /> ::[[How to Make Useful Ontologies for Biomedicine]], Tutorial at ISMB 2008, Toronto, Canada.<br /> <br /> <br /> *'''Past:'''<br /> <br /> ::'''April 12-13, 2008'''<br /> <br /> ::[[Introduction to Biomedical Ontologies]], 2-Day Training Event, Buffalo, NY<br /> <br /> ::'''March 27-28, 2008'''<br /> <br /> ::[[Networks | Workshop on Ontologies of Cellular Networks]], Newark, NJ. <br /> <br /> ::'''February 26-27, 2008'''<br /> <br /> ::[[JCOR | Joint JCOR-NCBO International Biomedical Ontology Dissemination Workshop]], Tokyo, Japan. <br /> <br /> ::*'''[[Workshops and Training Events 2007 | 2007]]'''<br /> <br /> ::*'''[[Workshops and Training Events 2006 | 2006]]'''<br /> <br /> == Past Meetings and Events ==<br /> <br /> *'''[[Related Events 2007 | 2007 Events]]'''<br /> <br /> *'''[[Related Events 2006 | 2006 Events]]'''<br /> <br /> *'''[[Meetings and Events | Past Meetings]]'''<br /> <br /> ==Other Meetings==<br /> <br /> *'''[http://www.bioontology.org/events.html Forthcoming]'''<br /> <br /> *'''[[Meetings and Events | Past]]'''<br /> <br /> == Ontology Training: Video and Audio Presentations ==<br /> <br /> '''[http://bmir.stanford.edu/people/view.php/mark_a_musen/ Mark Musen]'''<br /> <br /> *If we build it, will they come? Social-engineering of new technology to disseminate biomedical ontologies (Ontolog Form, December 6, 2007)<br /> ::[http://ontolog.cim3.net/cgi-bin/wiki.pl?ConferenceCall_2007_12_06 Details]<br /> ::[http://ontolog.cim3.net/file/resource/presentation/MarkMusen_20071206/NCBO--MarkMusen_20071206.pdf Slides]<br /> ::[http://ontolog.cim3.net/file/resource/presentation/MarkMusen_20071206/NCBO-BioPortal--MarkMusen_Ontolog-AudioRecording_conf-133566_20071206.mp3 Audio]<br /> <br /> '''[http://ontology.buffalo.edu/smith Barry Smith]'''<br /> <br /> *Ontology Evaluation in Biomedicine: The OBO Foundry (Ontolog Forum, December 21, 2006)<br /> ::[http://ontolog.cim3.net/cgi-bin/wiki.pl?ConferenceCall_2005_10_13 Details]<br /> ::[http://ontolog.cim3.net/file/work/OntologyMeasurementEvaluation/2006-12-21_OntologyEvaluationInBiomedicine/OBO-Foundry--BarrySmith_20061221.ppt Slides]<br /> ::[http://obofoundry.org/OntologDec06.mp3 Audio]<br /> <br /> *How to Build an Ontology (Tutorial, Stanford University, October 25, 2006)<br /> ::[http://stream.buffalo.edu/shared/research/phismith/Stanford10-25-06/Tutorial.rm Realplayer]<br /> ::[http://stream.buffalo.edu/shared/research/phismith/Stanford10-25-06/Tutorial.WMV Windows Mediaplayer]<br /> <br /> *Presentations at the Workshop on [http://www.bioontology.org/wiki/index.php/Workshop_on_Ontology_of_Images Ontology of Images] {Stanford University, March 24-25, 2006)<br /> ::[http://med.stanford.edu/irt/mmt/video/ontology/ontology-03-24-2006-09.ram Basic Principles]<br /> ::[http://med.stanford.edu/irt/mmt/video/ontology/ontology-03-24-2006-11.ram Towards an Ontology for the Imaging Domain]<br /> <br /> *The HL7 Reference Information Model<br /> ::[http://stream.buffalo.edu/shared/research/phismith/regenstrief.mpg Presentation] at the Regenstrief Institute, Indianapolis, November 9, 2005<br /> <br /> '''NCBO Workshops on Biomedical Ontology'''<br /> <br /> *The Ontology of Images: March 24-25, 2006 in Stanford, CA.<br /> ::[http://www.bioontology.org/wiki/index.php/Workshop_on_Ontology_of_Images#Webcast Webcast]<br /> <br /> *The Ontology of Diseases: November 6-7, 2006 in Baltimore, MD. <br /> ::[http://www.bioontology.org/wiki/index.php/Workshop_on_Ontology_of_Diseases#Agenda Slides and Audio Presentations]</div>

Skanel https://www.bioontology.org//mediawiki/index.php?title=Dissemination_Wiki&diff=6941 2008-05-09T23:17:15Z

<p>Skanel: /* Related Events */</p> <hr /> <div>==NCBO Dissemination ==<br /> <br /> What follows is a list of events organized under the auspices of the NCBO's Dissemination Core (PI: [http://ontology.buffalo.edu/smith Barry Smith]), together with information pertaining to related events and resources relevant to the NCBO's mission.<br /> <br /> ==NCBO Dissemination Workshops and Training Events ==<br /> <br /> *'''Forthcoming:'''<br /> <br /> ::'''June 20, 2008'''<br /> <br /> ::[[Evolutionary Biology and Ontologies]], Minneapolis, MN (collocated with [http://www.cce.umn.edu/conferences/evolution/ Evolution 2008])<br /> <br /> ::'''July 19, 2008'''<br /> <br /> ::[[How to Make Useful Ontologies for Biomedicine]], Tutorial at ISMB 2008, Toronto, Canada.<br /> <br /> <br /> *'''Past:'''<br /> <br /> ::'''April 12-13, 2008'''<br /> <br /> ::[[Introduction to Biomedical Ontologies]], 2-Day Training Event, Buffalo, NY<br /> <br /> ::'''March 27-28, 2008'''<br /> <br /> ::[[Networks | Workshop on Ontologies of Cellular Networks]], Newark, NJ. <br /> <br /> ::'''February 26-27, 2008'''<br /> <br /> ::[[JCOR | Joint JCOR-NCBO International Biomedical Ontology Dissemination Workshop]], Tokyo, Japan. <br /> <br /> ::*'''[[Workshops and Training Events 2007 | 2007]]'''<br /> <br /> ::*'''[[Workshops and Training Events 2006 | 2006]]'''<br /> <br /> == Past Meetings and Events ==<br /> <br /> *'''[[Related Events 2007 | 2007 Events]]'''<br /> <br /> *'''[[Related Events 2006 | 2006 Events]]'''<br /> <br /> ==Other Meetings==<br /> <br /> *'''[http://www.bioontology.org/events.html Forthcoming]'''<br /> <br /> *'''[[Meetings and Events | Past]]'''<br /> <br /> == Ontology Training: Video and Audio Presentations ==<br /> <br /> '''[http://bmir.stanford.edu/people/view.php/mark_a_musen/ Mark Musen]'''<br /> <br /> *If we build it, will they come? Social-engineering of new technology to disseminate biomedical ontologies (Ontolog Form, December 6, 2007)<br /> ::[http://ontolog.cim3.net/cgi-bin/wiki.pl?ConferenceCall_2007_12_06 Details]<br /> ::[http://ontolog.cim3.net/file/resource/presentation/MarkMusen_20071206/NCBO--MarkMusen_20071206.pdf Slides]<br /> ::[http://ontolog.cim3.net/file/resource/presentation/MarkMusen_20071206/NCBO-BioPortal--MarkMusen_Ontolog-AudioRecording_conf-133566_20071206.mp3 Audio]<br /> <br /> '''[http://ontology.buffalo.edu/smith Barry Smith]'''<br /> <br /> *Ontology Evaluation in Biomedicine: The OBO Foundry (Ontolog Forum, December 21, 2006)<br /> ::[http://ontolog.cim3.net/cgi-bin/wiki.pl?ConferenceCall_2005_10_13 Details]<br /> ::[http://ontolog.cim3.net/file/work/OntologyMeasurementEvaluation/2006-12-21_OntologyEvaluationInBiomedicine/OBO-Foundry--BarrySmith_20061221.ppt Slides]<br /> ::[http://obofoundry.org/OntologDec06.mp3 Audio]<br /> <br /> *How to Build an Ontology (Tutorial, Stanford University, October 25, 2006)<br /> ::[http://stream.buffalo.edu/shared/research/phismith/Stanford10-25-06/Tutorial.rm Realplayer]<br /> ::[http://stream.buffalo.edu/shared/research/phismith/Stanford10-25-06/Tutorial.WMV Windows Mediaplayer]<br /> <br /> *Presentations at the Workshop on [http://www.bioontology.org/wiki/index.php/Workshop_on_Ontology_of_Images Ontology of Images] {Stanford University, March 24-25, 2006)<br /> ::[http://med.stanford.edu/irt/mmt/video/ontology/ontology-03-24-2006-09.ram Basic Principles]<br /> ::[http://med.stanford.edu/irt/mmt/video/ontology/ontology-03-24-2006-11.ram Towards an Ontology for the Imaging Domain]<br /> <br /> *The HL7 Reference Information Model<br /> ::[http://stream.buffalo.edu/shared/research/phismith/regenstrief.mpg Presentation] at the Regenstrief Institute, Indianapolis, November 9, 2005<br /> <br /> '''NCBO Workshops on Biomedical Ontology'''<br /> <br /> *The Ontology of Images: March 24-25, 2006 in Stanford, CA.<br /> ::[http://www.bioontology.org/wiki/index.php/Workshop_on_Ontology_of_Images#Webcast Webcast]<br /> <br /> *The Ontology of Diseases: November 6-7, 2006 in Baltimore, MD. <br /> ::[http://www.bioontology.org/wiki/index.php/Workshop_on_Ontology_of_Diseases#Agenda Slides and Audio Presentations]</div>

Skanel https://www.bioontology.org//mediawiki/index.php?title=MediaWiki:Sidebar&diff=6632 2008-03-07T19:12:17Z

<p>Skanel: Removed meetings and events page from sidebar;can still be accessed from Dissemination#othermeetings page</p> <hr /> <div>* navigation<br /> ** mainpage|mainpage<br /> ** News_Events_Publications|News, Events, Pubs<br /> ** Dissemination_Wiki|Dissemination<br /> ** Education|Education<br /> ** Ontology_News|Ontology News<br /> ** Ontology_Evaluation|Ontology Evaluation<br /> ** NCBO_FAQ|NCBO FAQ<br /> ** Shared_Materials|Shared Materials<br /> ** Public_Requirements|Public RQs<br /> ** Glossary|Glossary<br /> ** recentchanges-url|recentchanges<br /> ** helppage|help</div>

Skanel https://www.bioontology.org//mediawiki/index.php?title=Dissemination_Wiki&diff=6631 2008-03-07T19:11:15Z

<p>Skanel: </p> <hr /> <div>==NCBO Dissemination ==<br /> <br /> What follows is a list of events organized under the auspices of the NCBO's Dissemination Core (PI: [http://ontology.buffalo.edu/smith Barry Smith]), together with information pertaining to related events and resources relevant to the NCBO's mission.<br /> <br /> ==NCBO Dissemination Workshops and Training Events ==<br /> <br /> *'''Forthcoming:'''<br /> <br /> ::'''March 27-28, 2008'''<br /> <br /> ::[[Networks | Workshop on Ontologies of Cellular Networks]], Newark, NJ. <br /> <br /> ::'''April 12-13, 2008'''<br /> <br /> ::[[Introduction to Biomedical Ontologies]], 2-Day Training Event, Buffalo, NY<br /> <br /> ::'''June 20, 2008'''<br /> <br /> ::[[Evolutionary Biology and Ontologies]], Minneapolis, MN (collocated with [http://www.cce.umn.edu/conferences/evolution/ Evolution 2008])<br /> <br /> ::'''July 19, 2008'''<br /> <br /> ::[[How to Make Useful Ontologies for Biomedicine]], Tutorial at ISMB 2008, Toronto, Canada.<br /> <br /> <br /> *'''Past:'''<br /> <br /> ::'''February 26-27, 2008'''<br /> <br /> ::[[JCOR | Joint JCOR-NCBO International Biomedical Ontology Dissemination Workshop]], Tokyo, Japan. This event is being scheduled as part of the [http://abelard.flet.keio.ac.jp/ontology/ Inaugural Conference] of JCOR: The Japanese Center for Ontological Research.<br /> <br /> <br /> ::*'''[[Workshops and Training Events 2007 | 2007]]'''<br /> <br /> ::*'''[[Workshops and Training Events 2006 | 2006]]'''<br /> <br /> == Related Events ==<br /> <br /> *''' Forthcoming:'''<br /> <br /> ::'''September 8, 2008'''<br /> <br /> ::The Nature of Psychiatric Disease and Its Classification ([[Psychiatric Disease]]), University at Buffalo, NY.<br /> <br /> *'''[[Related Events 2007 | 2007]]'''<br /> <br /> *'''[[Related Events 2006 | 2006]]'''<br /> <br /> ==Other Meetings==<br /> <br /> *'''[http://www.bioontology.org/events.html Forthcoming]'''<br /> <br /> *'''[[Meetings and Events | Past]]'''<br /> <br /> == Ontology Training: Video and Audio Presentations ==<br /> <br /> '''[http://bmir.stanford.edu/people/view.php/mark_a_musen/ Mark Musen]'''<br /> <br /> *If we build it, will they come? Social-engineering of new technology to disseminate biomedical ontologies (Ontolog Form, December 6, 2007)<br /> ::[http://ontolog.cim3.net/cgi-bin/wiki.pl?ConferenceCall_2007_12_06 Details]<br /> ::[http://ontolog.cim3.net/file/resource/presentation/MarkMusen_20071206/NCBO--MarkMusen_20071206.pdf Slides]<br /> ::[http://ontolog.cim3.net/file/resource/presentation/MarkMusen_20071206/NCBO-BioPortal--MarkMusen_Ontolog-AudioRecording_conf-133566_20071206.mp3 Audio]<br /> <br /> '''[http://ontology.buffalo.edu/smith Barry Smith]'''<br /> <br /> *Ontology Evaluation in Biomedicine: The OBO Foundry (Ontolog Forum, December 21, 2006)<br /> ::[http://ontolog.cim3.net/cgi-bin/wiki.pl?ConferenceCall_2005_10_13 Details]<br /> ::[http://ontolog.cim3.net/file/work/OntologyMeasurementEvaluation/2006-12-21_OntologyEvaluationInBiomedicine/OBO-Foundry--BarrySmith_20061221.ppt Slides]<br /> ::[http://obofoundry.org/OntologDec06.mp3 Audio]<br /> <br /> *How to Build an Ontology (Tutorial, Stanford University, October 25, 2006)<br /> ::[http://stream.buffalo.edu/shared/research/phismith/Stanford10-25-06/Tutorial.rm Realplayer]<br /> ::[http://stream.buffalo.edu/shared/research/phismith/Stanford10-25-06/Tutorial.WMV Windows Mediaplayer]<br /> <br /> *Presentations at the Workshop on [http://www.bioontology.org/wiki/index.php/Workshop_on_Ontology_of_Images Ontology of Images] {Stanford University, March 24-25, 2006)<br /> ::[http://med.stanford.edu/irt/mmt/video/ontology/ontology-03-24-2006-09.ram Basic Principles]<br /> ::[http://med.stanford.edu/irt/mmt/video/ontology/ontology-03-24-2006-11.ram Towards an Ontology for the Imaging Domain]<br /> <br /> *The HL7 Reference Information Model<br /> ::[http://stream.buffalo.edu/shared/research/phismith/regenstrief.mpg Presentation] at the Regenstrief Institute, Indianapolis, November 9, 2005</div>

Skanel https://www.bioontology.org//mediawiki/index.php?title=Main_Page&diff=6630 2008-03-07T19:05:33Z

<p>Skanel: /* NCBO Links */</p> <hr /> <div>Welcome to the '''NCBO Public WIKI'''. This WIKI provides information about collaborative ontology development efforts, &lt;br&gt;<br /> dissemination events conducted by the NCBO and publically shared materials from the NCBO.<br /> <br /> <br /> === NCBO Links ===<br /> *[http://www.bioontology.org/ NCBO Home page]<br /> *[http://www.bioontology.org/wiki/index.php/NCBO_FAQ NCBO FAQ]<br /> *[http://www.bioontology.org/wiki/index.php/News_Events_Publications NCBO News, Events and Publications]<br /> <br /> === Shared Materials===<br /> <br /> *[[Public Requirements Redirect|Public Requirements]]<br /> <br /> *[[Shared Materials]]<br /> <br /> *[[Evaluation Activities]]<br /> <br /> === NCBC Links ===<br /> <br /> *[http://www.bisti.nih.gov/ncbc/ Home page of National Centers for Biomedical Computing]<br /> <br /> *[http://wiki.na-mic.org/Wiki/index.php/SDIWG:Software_and_Data_Integration_Working_Group NCBC Software and Data Integration Working Group (SDIWG) and Centers Discussion]<br /> <br /> *[http://wiki.na-mic.org/Wiki/index.php/SDIWG:_NCBC_Scientific_Ontologies NCBC Scientific Ontologies Working Group]<br /> <br /> === Ontology Development Area ===<br /> <br /> Below are wikis for some of the current OBO ontologies. Each wiki is housed on the bioontologies.org wiki, in its own partition (wikispace) of the main wiki<br /> <br /> *[[PATO:Main_Page]] - An ontology of phenotypic qualities<br /> <br /> *[[RO:Main_Page]] - OBO Relations ontology<br /> <br /> *[[CARO:Main_Page]] - Reference anatomical ontology<br /> <br /> *[[CL:Main_Page]] - OBO Cell ontology<br /> <br /> *[[SO:Main_Page]] - Sequence Ontology<br /> <br /> *[[Disease:Main_Page]] - Disease Ontology, and other ontologies pertaining to diseases and disorders<br /> <br /> *[[OCI:Main_Page]] - Ontology of Clinical Investigation<br /> <br /> Note that each ontology lives in its own wikispace which corresponds to the [[OBO:IDSpace]] of that ontology. Note for wiki editors: all wiki pages that are to be considered local to a particular ontology should be prefixed with that IDSpace.<br /> <br /> === Software Development Area ===<br /> *[[OboInOwl:Main_Page]] - Mapping between OBO and OWL formats<br /> *[[Phenote:Main_Page]] - A Phenotype Annotation Tool using Ontologies<br /> *[[Bioportal:Main_Page]]</div>

Skanel https://www.bioontology.org//mediawiki/index.php?title=Main_Page&diff=6629 2008-03-07T19:03:53Z

<p>Skanel: /* NCBO Links */</p> <hr /> <div>Welcome to the '''NCBO Public WIKI'''. This WIKI provides information about collaborative ontology development efforts, &lt;br&gt;<br /> dissemination events conducted by the NCBO and publically shared materials from the NCBO.<br /> <br /> <br /> === NCBO Links ===<br /> *[http://www.bioontology.org/ NCBO Home page]<br /> *[http://www.bioontology.org/wiki/index.php/NCBO_FAQ NCBO FAQ]<br /> *[[News_Events_Publications]]<br /> <br /> === Shared Materials===<br /> <br /> *[[Public Requirements Redirect|Public Requirements]]<br /> <br /> *[[Shared Materials]]<br /> <br /> *[[Evaluation Activities]]<br /> <br /> === NCBC Links ===<br /> <br /> *[http://www.bisti.nih.gov/ncbc/ Home page of National Centers for Biomedical Computing]<br /> <br /> *[http://wiki.na-mic.org/Wiki/index.php/SDIWG:Software_and_Data_Integration_Working_Group NCBC Software and Data Integration Working Group (SDIWG) and Centers Discussion]<br /> <br /> *[http://wiki.na-mic.org/Wiki/index.php/SDIWG:_NCBC_Scientific_Ontologies NCBC Scientific Ontologies Working Group]<br /> <br /> === Ontology Development Area ===<br /> <br /> Below are wikis for some of the current OBO ontologies. Each wiki is housed on the bioontologies.org wiki, in its own partition (wikispace) of the main wiki<br /> <br /> *[[PATO:Main_Page]] - An ontology of phenotypic qualities<br /> <br /> *[[RO:Main_Page]] - OBO Relations ontology<br /> <br /> *[[CARO:Main_Page]] - Reference anatomical ontology<br /> <br /> *[[CL:Main_Page]] - OBO Cell ontology<br /> <br /> *[[SO:Main_Page]] - Sequence Ontology<br /> <br /> *[[Disease:Main_Page]] - Disease Ontology, and other ontologies pertaining to diseases and disorders<br /> <br /> *[[OCI:Main_Page]] - Ontology of Clinical Investigation<br /> <br /> Note that each ontology lives in its own wikispace which corresponds to the [[OBO:IDSpace]] of that ontology. Note for wiki editors: all wiki pages that are to be considered local to a particular ontology should be prefixed with that IDSpace.<br /> <br /> === Software Development Area ===<br /> *[[OboInOwl:Main_Page]] - Mapping between OBO and OWL formats<br /> *[[Phenote:Main_Page]] - A Phenotype Annotation Tool using Ontologies<br /> *[[Bioportal:Main_Page]]</div>

Skanel https://www.bioontology.org//mediawiki/index.php?title=Main_Page&diff=6628 2008-03-07T19:02:48Z

<p>Skanel: /* NCBO Links */</p> <hr /> <div>Welcome to the '''NCBO Public WIKI'''. This WIKI provides information about collaborative ontology development efforts, &lt;br&gt;<br /> dissemination events conducted by the NCBO and publically shared materials from the NCBO.<br /> <br /> <br /> === NCBO Links ===<br /> *[http://www.bioontology.org/ NCBO Home page]<br /> *[http://www.bioontology.org/wiki/index.php/NCBO_FAQ NCBO FAQ]<br /> *[[News, Events, Pubs]]<br /> <br /> === Shared Materials===<br /> <br /> *[[Public Requirements Redirect|Public Requirements]]<br /> <br /> *[[Shared Materials]]<br /> <br /> *[[Evaluation Activities]]<br /> <br /> === NCBC Links ===<br /> <br /> *[http://www.bisti.nih.gov/ncbc/ Home page of National Centers for Biomedical Computing]<br /> <br /> *[http://wiki.na-mic.org/Wiki/index.php/SDIWG:Software_and_Data_Integration_Working_Group NCBC Software and Data Integration Working Group (SDIWG) and Centers Discussion]<br /> <br /> *[http://wiki.na-mic.org/Wiki/index.php/SDIWG:_NCBC_Scientific_Ontologies NCBC Scientific Ontologies Working Group]<br /> <br /> === Ontology Development Area ===<br /> <br /> Below are wikis for some of the current OBO ontologies. Each wiki is housed on the bioontologies.org wiki, in its own partition (wikispace) of the main wiki<br /> <br /> *[[PATO:Main_Page]] - An ontology of phenotypic qualities<br /> <br /> *[[RO:Main_Page]] - OBO Relations ontology<br /> <br /> *[[CARO:Main_Page]] - Reference anatomical ontology<br /> <br /> *[[CL:Main_Page]] - OBO Cell ontology<br /> <br /> *[[SO:Main_Page]] - Sequence Ontology<br /> <br /> *[[Disease:Main_Page]] - Disease Ontology, and other ontologies pertaining to diseases and disorders<br /> <br /> *[[OCI:Main_Page]] - Ontology of Clinical Investigation<br /> <br /> Note that each ontology lives in its own wikispace which corresponds to the [[OBO:IDSpace]] of that ontology. Note for wiki editors: all wiki pages that are to be considered local to a particular ontology should be prefixed with that IDSpace.<br /> <br /> === Software Development Area ===<br /> *[[OboInOwl:Main_Page]] - Mapping between OBO and OWL formats<br /> *[[Phenote:Main_Page]] - A Phenotype Annotation Tool using Ontologies<br /> *[[Bioportal:Main_Page]]</div>

Skanel https://www.bioontology.org//mediawiki/index.php?title=News_Events_Publications&diff=6627 2008-03-07T19:02:04Z

<p>Skanel: New page: Please see the new [http://www.bioontology.org/news.html NCBO News Site] You can also find information on the latest NCBO [http://www.bioontology.org/publications.html Publications] and [...</p> <hr /> <div>Please see the new [http://www.bioontology.org/news.html NCBO News Site]<br /> <br /> You can also find information on the latest NCBO [http://www.bioontology.org/publications.html Publications] and [http://www.bioontology.org/events.html Events]</div>

Skanel https://www.bioontology.org//mediawiki/index.php?title=MediaWiki:Sidebar&diff=6626 2008-03-07T19:01:47Z

<p>Skanel: </p> <hr /> <div>* navigation<br /> ** mainpage|mainpage<br /> ** News_Events_Publications|News, Events, Pubs<br /> ** Dissemination_Wiki|Dissemination<br /> ** Education|Education<br /> ** Ontology_News|Ontology News<br /> ** Meetings_and_Events|Meetings and Events<br /> ** Ontology_Evaluation|Ontology Evaluation<br /> ** NCBO_FAQ|NCBO FAQ<br /> ** Shared_Materials|Shared Materials<br /> ** Public_Requirements|Public RQs<br /> ** Glossary|Glossary<br /> ** recentchanges-url|recentchanges<br /> ** helppage|help</div>

Skanel https://www.bioontology.org//mediawiki/index.php?title=News_Events_Pubs&diff=6625 2008-03-07T19:00:40Z

<p>Skanel: New page: Please see the new [http://www.bioontology.org/news.html NCBO News Site] You can also find information on the latest NCBO [http://www.bioontology.org/publications.html Publications] and [...</p> <hr /> <div>Please see the new [http://www.bioontology.org/news.html NCBO News Site]<br /> <br /> You can also find information on the latest NCBO [http://www.bioontology.org/publications.html Publications] and [http://www.bioontology.org/events.html Events]</div>

Skanel https://www.bioontology.org//mediawiki/index.php?title=MediaWiki:Sidebar&diff=6624 2008-03-07T18:59:56Z

<p>Skanel: </p> <hr /> <div>* navigation<br /> ** mainpage|mainpage<br /> ** News_Events_Pubs|News, Events, Pubs<br /> ** Dissemination_Wiki|Dissemination<br /> ** Education|Education<br /> ** Ontology_News|Ontology News<br /> ** Meetings_and_Events|Meetings and Events<br /> ** Ontology_Evaluation|Ontology Evaluation<br /> ** NCBO_FAQ|NCBO FAQ<br /> ** Shared_Materials|Shared Materials<br /> ** Public_Requirements|Public RQs<br /> ** Glossary|Glossary<br /> ** recentchanges-url|recentchanges<br /> ** helppage|help</div>

Skanel https://www.bioontology.org//mediawiki/index.php?title=MediaWiki:Sidebar&diff=6623 2008-03-07T18:59:31Z

<p>Skanel: </p> <hr /> <div>* navigation<br /> ** mainpage|mainpage<br /> ** News_Events_Pubs|News Events &amp; Pubs<br /> ** Dissemination_Wiki|Dissemination<br /> ** Education|Education<br /> ** Ontology_News|Ontology News<br /> ** Meetings_and_Events|Meetings and Events<br /> ** Ontology_Evaluation|Ontology Evaluation<br /> ** NCBO_FAQ|NCBO FAQ<br /> ** Shared_Materials|Shared Materials<br /> ** Public_Requirements|Public RQs<br /> ** Glossary|Glossary<br /> ** recentchanges-url|recentchanges<br /> ** helppage|help</div>

Skanel https://www.bioontology.org//mediawiki/index.php?title=MediaWiki:Sidebar&diff=6622 2008-03-07T18:58:57Z

<p>Skanel: </p> <hr /> <div>* navigation<br /> ** mainpage|mainpage<br /> ** NCBO_News_Events_Pubs|NCBO News Events Pubs<br /> ** Dissemination_Wiki|Dissemination<br /> ** Education|Education<br /> ** Ontology_News|Ontology News<br /> ** Meetings_and_Events|Meetings and Events<br /> ** Ontology_Evaluation|Ontology Evaluation<br /> ** NCBO_FAQ|NCBO FAQ<br /> ** Shared_Materials|Shared Materials<br /> ** Public_Requirements|Public RQs<br /> ** Glossary|Glossary<br /> ** recentchanges-url|recentchanges<br /> ** helppage|help</div>

Skanel https://www.bioontology.org//mediawiki/index.php?title=Main_Page&diff=6621 2008-03-07T18:58:31Z

<p>Skanel: /* NCBO Links */</p> <hr /> <div>Welcome to the '''NCBO Public WIKI'''. This WIKI provides information about collaborative ontology development efforts, &lt;br&gt;<br /> dissemination events conducted by the NCBO and publically shared materials from the NCBO.<br /> <br /> <br /> === NCBO Links ===<br /> *[http://www.bioontology.org/ NCBO Home page]<br /> *[http://www.bioontology.org/wiki/index.php/NCBO_FAQ NCBO FAQ]<br /> *[[NCBO News]]<br /> <br /> === Shared Materials===<br /> <br /> *[[Public Requirements Redirect|Public Requirements]]<br /> <br /> *[[Shared Materials]]<br /> <br /> *[[Evaluation Activities]]<br /> <br /> === NCBC Links ===<br /> <br /> *[http://www.bisti.nih.gov/ncbc/ Home page of National Centers for Biomedical Computing]<br /> <br /> *[http://wiki.na-mic.org/Wiki/index.php/SDIWG:Software_and_Data_Integration_Working_Group NCBC Software and Data Integration Working Group (SDIWG) and Centers Discussion]<br /> <br /> *[http://wiki.na-mic.org/Wiki/index.php/SDIWG:_NCBC_Scientific_Ontologies NCBC Scientific Ontologies Working Group]<br /> <br /> === Ontology Development Area ===<br /> <br /> Below are wikis for some of the current OBO ontologies. Each wiki is housed on the bioontologies.org wiki, in its own partition (wikispace) of the main wiki<br /> <br /> *[[PATO:Main_Page]] - An ontology of phenotypic qualities<br /> <br /> *[[RO:Main_Page]] - OBO Relations ontology<br /> <br /> *[[CARO:Main_Page]] - Reference anatomical ontology<br /> <br /> *[[CL:Main_Page]] - OBO Cell ontology<br /> <br /> *[[SO:Main_Page]] - Sequence Ontology<br /> <br /> *[[Disease:Main_Page]] - Disease Ontology, and other ontologies pertaining to diseases and disorders<br /> <br /> *[[OCI:Main_Page]] - Ontology of Clinical Investigation<br /> <br /> Note that each ontology lives in its own wikispace which corresponds to the [[OBO:IDSpace]] of that ontology. Note for wiki editors: all wiki pages that are to be considered local to a particular ontology should be prefixed with that IDSpace.<br /> <br /> === Software Development Area ===<br /> *[[OboInOwl:Main_Page]] - Mapping between OBO and OWL formats<br /> *[[Phenote:Main_Page]] - A Phenotype Annotation Tool using Ontologies<br /> *[[Bioportal:Main_Page]]</div>

Skanel https://www.bioontology.org//mediawiki/index.php?title=NCBO_News&diff=6620 2008-03-07T18:57:19Z

<p>Skanel: </p> <hr /> <div>Please see the new [http://www.bioontology.org/news.html NCBO News Site]<br /> <br /> You can also find information on the latest NCBO [http://www.bioontology.org/publications.html Publications] and [http://www.bioontology.org/events.html Events]</div>

Skanel https://www.bioontology.org//mediawiki/index.php?title=Meetings_and_Events&diff=6619 2008-03-07T18:54:28Z

<p>Skanel: </p> <hr /> <div>== Upcoming meetings ==<br /> Please see NCBO [http://www.bioontology.org/events.html Events Page] for Upcoming events and meetings<br /> <br /> <br /> <br /> == Past meetings ==<br /> <br /> * '''Phenotype Ontology (Upper Level) workshop'''<br /> **2007?<br /> <br /> *'''All NCBCs Ontology workshop'''<br /> **Fall 2007, with Andreas Califano, Columbia, NY<br /> <br /> *'''Dagstuhl Seminar: Ontologies and Text Mining for Life Sciences'''<br /> **July 23-27, 2007: Schloss Dagstuhl, Germany<br /> **Organizers: Ulf Leser, Dietrich Rebholz-Schuhmann &amp; Michael Ashburner<br /> ** Attending: Michael Ashburner<br /> **[http://www.dagstuhl.de/07301 http://www.dagstuhl.de/07301]<br /> <br /> *'''[http://cbms07.biomap.org/ Ontologies for Biomedical Systems II at 20th IEEE CBMS 2007]'''<br /> **June 20-22, 2007, Maribor, Slovenia<br /> <br /> *'''Reasoning with Biomedical Ontologies'''<br /> **June 20-23, 2007: Schloss Dagstuhl, Germany <br /> **Attending: Deborah McGuinness, Fabian Neuhaus, Nigam Shah, Barry Smith.<br /> <br /> *'''Workshop on Clinical Trial Ontology'''<br /> **May 16-17 2007, venue TBD<br /> **[[Workshop on Clinical Trial Ontology | information about Clinical Trial Ontology workshop]]<br /> <br /> *'''[http://www.dagstuhl.de/de/programm/kalender/semhp/?semid=29453 Dagstuhl Seminar: Ontology Interoperability in Biomedicine]'''<br /> **March 27-30, 2007, Dagstuhl, Germany<br /> **Attending: Barry Smith, Michael Ashburner, Mark Musen, Nigam Shah, Fabian Neuhaus, Suzanna Lewis, Werner Ceusters<br /> **Invitation only<br /> <br /> *'''Phenotype Ontology (Workshop)'''<br /> **December 1-2, 2006, Clark Center, Stanford, CA<br /> **[[PATO_Meeting| PATO meeting agenda]]<br /> **Attending: Suzanna Lewis, Chris Mungall, Mark Gibson, Nicole Washington, Nigam Shah, Fabian Neuhaus, Michael Ashburner, Monte Westerfield<br /> <br /> *'''Panel on the Future of HL7'''<br /> **AMIA Anual Symposium<br /> **November 14, 3.30-5.00pm., Washington DC<br /> **http://ontology.buffalo.edu/HL7/panel.htm<br /> **Attending: Barry Smith<br /> <br /> *'''Tutorial on Genomics Knowledge Representation for Clinical Trials'''<br /> **AMIA Annual Symposium<br /> **November 12, 2006, Washington DC<br /> **http://ontology.buffalo.edu/06/AMIAWorkshop.htm <br /> <br /> *'''Biomedical Ontology in Action'''<br /> **KR-MED 2006<br /> **November 8, 2006, Baltimore<br /> **http://www.imbi.uni-freiburg.de/medinf/kr-med-2006/index.html<br /> **Attending: Werner Ceusters, Barry Smith<br /> <br /> *'''Workshop on Ontology of Diseases'''<br /> **In association with FOIS 2006 (Formal Ontology and Information Systems)<br /> **November 6-7, 2006, John Hopkins University, Baltimore<br /> **[[Workshop on Ontology of Diseases | information on the Disease Ontology Workshop]]<br /> **Attending: Werner Ceusters, Christopher Chute, Suzanna Lewis, Chris Mungall, Fabian Neuhaus, Nigam Shah, Barry Smith, Monte Westerfield<br /> <br /> *'''Fall NCBO Project Meeting'''<br /> **Oct. 23-25, 2006, Stanford<br /> ** All Hands meeting<br /> ** Advisory Comm. &amp; NIH Program &amp; Science officers invited<br /> <br /> *'''Workshop on Philosophy of Biology'''<br /> **October 14-15, 2006, Buffalo, NY<br /> **http://ontology.buffalo.edu/06/pob <br /> **Attending: Werner Ceusters, Barry Smith<br /> <br /> *'''American Society of Human Genetics'''<br /> **October 9-13, 2006, New Orleans, LA<br /> **[http://genetics.faseb.org/genetics/ashg/menu-annmeet.shtml http://genetics.faseb.org/genetics/ashg/menu-annmeet.shtml]<br /> **Presentation to find collaborators, also ontology workshop<br /> <br /> *'''Genomics Standards Consortium Workshop<br /> **National Institute for Environmental e-Science (NIEeS)<br /> **September 11-13, 2006, Hinxton, UK.<br /> ** [http://www.niees.ac.uk/events/egenomics2006/index.shtml http://www.niees.ac.uk/events/egenomics2006/index.shtml]<br /> **Attending: Suzanna Lewis, Michael Ashburner, George Gkoutos<br /> <br /> *'''Anatomy Ontology Workshop'''<br /> **September 8-9, 2006, Seattle<br /> **[[Anatomy Ontology Workshop | information on the Anatomy Ontology Workshop]]<br /> **Attending: Michael Ashburner, Melissa Haendel, Suzanna Lewis, Chris Mungall, Fabian Neuhaus, Nigam Shah, Barry Smith, David Sutherland, Monte Westerfield <br /> <br /> *'''Tutorial on Standards and Ontologies<br /> **Medical Informatics Europe<br /> **August 27, 2006, Maastricht, Netherlands.<br /> **http://ontology.buffalo.edu/06/MIE_Tutorial.htm<br /> **Attending: Werner Ceusters, Barry Smith<br /> <br /> *'''IEEE Computational Systems Bioinformatics, 2006'''<br /> **August 14-18, 2006. Stanford University<br /> **[http://www.lifesciencessociety.org/CSB2006/index.html http://www.lifesciencessociety.org/CSB2006/index.html]<br /> ** Attending: Mark Musen (Keynote), rest of Stanford group (tutorial in bioontologies/semantic web)<br /> <br /> *'''ISMB, 2006'''<br /> **August 6-10, 2006, Fortaleza, Brazil.<br /> ** [http://ismb2006.cbi.cnptia.embrapa.br/ http://ismb2006.cbi.cnptia.embrapa.br/]<br /> ** Attending: Michael Ashburner, Suzanna Lewis (Keynote speaker for Bio-ontologies SIG)<br /> <br /> *'''In Silico Analysis of Proteins. Celebrating the 20th Anniversary of Swiss-Prot'''<br /> **Jul 30- August 4, 2006, Fortaleza, Brazil.<br /> ** [http://www.swissprot20.org/ http://www.swissprot20.org/]<br /> ** Attending: Michael Ashburner, Suzanna Lewis<br /> <br /> *'''Functional Genomics investigation Ontology (FuGO) 2nd Workshop'''<br /> **July 24-28, 2006, Hinxton, UK<br /> **http://fugo.sourceforge.net/news/index.php<br /> **Attending: Barry Smith<br /> <br /> *'''9th International Protege Conference'''<br /> **July 23-26, 2006, Stanford, CA<br /> **[http://protege.stanford.edu/conference/2006/ http://protege.stanford.edu/conference/2006/]<br /> ** Attending: Chris Callendar, Christopher Chute, Tricia d'Entremont, Chris Mungall, Mark Musen, Natasha Noy, Daniel Rubin, Nigam Shah, Kaustubh Supekar<br /> <br /> *'''NCBC All Hands Meeting'''<br /> **July 17-19, 2006, NIH, Bethesda, MD<br /> **Attending: Michael Ashburner, James Buntrock, Chris Callendar, Simona Carini, Louis Goldberg, Deborah McGuinness, Chris Mungall,Mark Musen, Fabian Neuhaus, Daniel Rubin, Nigam Shah, Barry Smith, Nicole Washington, Monte Westerfield <br /> **[http://www.bisti.nih.gov/ahm2006/ http://www.bisti.nih.gov/ahm2006/]<br /> **[http://www.bisti.nih.gov/ahm2006/ncbo_dissemination.htm Ontology: A Vision for the Future and Its Realization] Dissemination Event<br /> ***Organizers: Mark Musen, Barry Smith<br /> <br /> * '''Core 1 &amp; 2 Project Meeting'''<br /> ** June 27-28, 2006, Berkeley, CA<br /> ** Attending: Julie Moseley, Lynn Murphy, Mark Musen, Daniel Rubin, Nigam Shah, Archana Vembakam (Stanford); Suzanna Lewis, Sima Misra, Chris Mungall, ShengQiang Shu, Nicole Washington (Berkeley); James Buntrock, Christopher Chute, Harold Solbrig (Mayo); Margaret-Anne Storey (UVic); Sherri De Coronado (NIH)<br /> ** Working plan for core 1 &amp; 2 goals<br /> <br /> * '''Core 1 &amp; 2 Meeting'''<br /> ** June 9, 2006, Berkeley, CA<br /> ** Attending: Dilvan Moreira, Lynn Murphy, Daniel Rubin, Nigam Shah, Archana Vembakam (Stanford); Suzanna Lewis, Chris Mungall, ShengQiang Shu, Nicole Washington (Berkeley); James Buntrock, Harold Solbrig (Mayo by phone); Chris Callendar (UVic by phone)<br /> <br /> *'''Training Course in Biomedical Ontologies'''<br /> **[http://ontology.buffalo.edu/06/os2/index.html http://ontology.buffalo.edu/06/os2/index.html]<br /> **May 21-24, 2006, Schloss Dagstuhl, Germany<br /> **Attending: Werner Ceusters, Mark Musen, Barry Smith<br /> <br /> *'''NSF/RCN workshop on ontology and phylogeny'''<br /> **May 21-24, St. Louis, MO<br /> **Attending: Michael Ashburner, Suzanna Lewis, Monte Westerfield<br /> <br /> *'''Phenotype Annotation Meeting'''<br /> **May 17-20, Hinxton, UK<br /> **Attending: Michael Ashburner, Mark Gibson, George Gkoutos, Suzanna Lewis, Gillian Millburn, Chris Mungall, Fabian Neuhaus, Erik Segerdell, Nigam Shah, Monte Westerfield<br /> **[[Agenda PaTO | PATO meeting agenda]]<br /> <br /> *'''Fish Evolutionary Biology Working Group Meeting'''<br /> **April 9-11, National Evolutionary Synthesis Center (NESCent), Durham, NC<br /> **Attending: Mark Gibson,Paula Mabee, Chris Mungall, Monte Westerfield<br /> <br /> *'''Gene Ontology Workshop'''<br /> **March 31-April 3, 2006, St. Croix<br /> ** Attending: Michael Ashburner, Suzanna Lewis, Chris Mungall, Barry Smith<br /> <br /> * '''Bio-IT LifeSciences Conference'''<br /> **April 3-6, 2006, Boston, MA'''<br /> **[http://www.lifesciencesexpo.com/live/26/ http://www.lifesciencesexpo.com/live/26/]<br /> ** Speaker: Michael Ashburner, Ben Franklin Award Lecture.<br /> <br /> *'''Workshop on Ontology of Images'''<br /> **March 24-25, 2006, Stanford, CA<br /> **[http://www.loni.ucla.edu/CCB/ CCB NCBC] and others with biomedical image ontologies<br /> **[Workshop on Ontology of Images | info on Ontology of Images workshop]<br /> ** Attending: Suzanna Lewis, Chris Mungall, Mark Musen, Daniel Rubin, Nigam Shah, Barry Smith, Kaushtubh Supekar<br /> <br /> *'''Immunology Ontology Workshop: NIAID'''<br /> **March 21-22, 2006, Gaitherburg, MD<br /> ** Attending: Suzanna Lewis (speaker), Mark Musen (Session chair), Barry Smith<br /> <br /> *'''Semantic Technology Conference'''<br /> **March 6-9, 2006, San Jose, CA<br /> ** [http://www.semantic-conference.com/ http://www.semantic-conference.com/ ]<br /> ** Attending: Deborah McGuinness (Keynote, tutorial), Mark Musen (speaker), Daniel Rubin, Kaustubh Superkar (speaker) <br /> <br /> *'''NIH NCRR Animal Models workshop'''<br /> **March 6-7, 2006, Bethesda, MD<br /> ** Attending: Monte Westerfield<br /> <br /> *'''[[Minutes &amp; presentations, March 2-4, 2006 Project meeting|cBio Project Meeting]]'''<br /> **March 2-4, 2006, Stanford, CA<br /> ** [[Agenda, Project Meeting, Thursday, March 2-Saturday, March 4, 2006|Agenda]]<br /> **[http://www.smi.stanford.edu/research/cbio/cbio_meeting.html http://www.smi.stanford.edu/research/cbio/cbio_meeting.html]<br /> **Entire project, NIH Program &amp; Lead Science officers <br /> <br /> *'''BIRN ontology workshop'''<br /> **February 28-March 1, 2006, Stanford, CA<br /> ** Attending: Christopher Chute, Suzanna Lewis, Mark Musen, Daniel Rubin, Nigam Shah, Barry Smith<br /> <br /> *'''NLM vocabulary collection and distribution meeting'''<br /> **February 27-28, 2006, NLM, Washington, DC<br /> ** Attending: James Buntrock, Christopher Chute, Tom Johnson, Chris Mungall, Deepak Sharma, Harold Solbrig<br /> <br /> *'''NIAID meeting'''<br /> **February, 2006, Washington, DC<br /> **Attending: Mark Musen<br /> <br /> *'''cBio Phenotype Annotation tool specification'''<br /> **February 21-23, 2006, Berkeley, CA<br /> ** Attending: Melissa Haendel, Sierra Taylor (ZFIN); John Day-Richter, Mark Gibson, Suzanna Lewis, Chris Mungall, ShengQiang Shu (Berkeley)<br /> <br /> *'''Mini-Syposium on Semantic Enrichment of Scientific Literature'''<br /> **February 20, 2006 at the European Bioinformatics Institute, Hinxton, UK<br /> **Attending: Michael Ashburner (speaker)<br /> <br /> *'''cBio OBD specification'''<br /> **February 17, 2006, Berkeley, CA<br /> ** Attending: Ben Olasov, Ida Sim (UCSF); Mark Gibson, Suzanna Lewis, Sima Misra, Chris Mungall, ShengQiang Shu (Berkeley); Daniel Rubin (Stanford by phone)<br /> <br /> *'''FuGO meeting'''<br /> ** February 13-15, 2006, Philadelphia, PA<br /> **[http://fugo.sourceforge.net/news/index.php http://fugo.sourceforge.net/news/index.php]<br /> **Attending: Barry Smith<br /> <br /> *'''Fourth Semantic Interoperability for E-Government Conference'''<br /> ** February 9-10, 2006, MITRE, McLean, VA<br /> ** [http://colab.cim3.net/cgi-bin/wiki.pl?FourthSemanticInteroperabilityforEGovernmentConference_2006_2_0910 http://colab.cim3.net/cgi-bin/wiki.pl?FourthSemanticInteroperabilityforEGovernmentConference_2006_2_0910]<br /> **Attending: Barry Smith<br /> <br /> *'''NIAID BRC3 and Inter Operability Working Group meeting'''<br /> ** February 6-7, 2006, Philadelphia, PA<br /> ** [http://www.niaid.nih.gov/dmid/genomes/brc/brc3.htm http://www.niaid.nih.gov/dmid/genomes/brc/brc3.htm]<br /> ** Attending: Suzanna Lewis, Barry Smith<br /> <br /> *'''PharmGKB and cBiO meeting'''<br /> ** January 31, 2006, Stanford, CA<br /> ** Attending: Daniel Rubin (Stanford); Suzanna Lewis, Sima Misra (Berkeley); Russ Altman, Tina Boussard, Teri Klein, Mark Woon (PharmGKB)<br /> <br /> *'''Pacific Symposium on Biocomputing, 2006'''<br /> **January 2-6, 2006, Maui, HI<br /> **Michael Ashburner (Keynote)<br /> **[http://psb.stanford.edu/ http://psb.stanford.edu/]<br /> <br /> *'''NCBC Meeting'''<br /> **Dec. 15-16, NIH, Bethesda, MD<br /> **Attending: Mark Musen, Suzanna Lewis, Monte Westerfield<br /> **Introducting new NCBCs to each other and NIH staff<br /> <br /> *'''Phenotype Annotation Meeting''' <br /> **December 11-12, 2005, [http://www.visitasilomar.com/ Asilomar conference center]<br /> ** Attending: Melissa Haendel, Paula Mabee, Erik Segerdell, Monte Westerfield (ZFIN); Gillian Millburn (FlyBase); Mark Gibson, Suzanna Lewis, Chris Mungall (Berkeley); Chris Callendar, Sean Falconer, Margaret-Anne Storey (UVic)<br /> ** Define requirements of phenotype annotation tools<br /> <br /> *'''International Biocurator Meeting'''<br /> **December 8-11, 2005, Asilomar, CA<br /> **[http://biocurator.org/intnlbiocurator.html http://biocurator.org/intnlbiocurator.html]<br /> **Attending: Sima Misra (organizer), Chris Mungall (speaker), Monte Westerfield (speaker)<br /> <br /> *'''National Bioinformatics Network, South Africa'''<br /> **December 2, 2005, University of Cape Town, SA<br /> **Michael Ashburner (Keynote)<br /> <br /> *'''Phenotype Ontology Content Workshop'''<br /> **Nov. 19-20, 2005, Cold Spring Harbor, NY<br /> ** Attending: Michael Ashburner, John Day-Richter, George Gkoutos, Suzanna Lewis, Chris Mungall, Mark Musen, Erik Segerdell, Nigam Shah, Monte Westerfield <br /> ** [[Media:PhenoAgenda.doc]]<br /> <br /> *'''Stanford/Mayo/Berkeley Meetings'''<br /> **Nov. 21, 10am-3pm, Stanford, CA; Nov. 22, 10am-3pm, Berkeley, CA<br /> ** Attending: Lynn Murphy, Mark Musen, Daniel Rubin, Nigam Shah, Archana Vembakam, (Stanford); Nomi Harris, Suzanna Lewis, Sima Misra, Chris Mungall, ShengQiang Shu (Berkeley); James Buntrock, Deepak Sharma, Harold Solbrig (Mayo by phone)<br /> <br /> *'''Forbes Dewey Meeting'''<br /> **Late October, MIT, Cambridge, MA<br /> **Michael Ashburner, chair<br /> **Goal to see if anonymous foundation would pay for ontology content unification, standards, collaboration, etc.<br /> <br /> *'''Genome Informatics Meeting'''<br /> **Oct. 28-Nov. 1, 2005, Cold Spring Harbor, NY<br /> **Suzanna Lewis (organizer, speaker)<br /> <br /> *'''Workshop on Bio-Ontologies'''<br /> **October 28, 2005, Buffalo, NY<br /> **[http://ontology.buffalo.edu/05/bio-ontologies.pdf http://ontology.buffalo.edu/05/bio-ontologies.pdf]<br /> **Presenting: Suzanna Lewis, Frank Hartel, Sumi Yoshikawa, Olivier Bodenreider, David Hill<br /> **Training session: making ontologies better<br /> <br /> *'''1st International Annual Conference, Brazilian Association for Bioinformatics and Computational Biology'''<br /> **October, 2005, Caxambu, Brazil<br /> **Michael Ashburner (Keynote)<br /> <br /> *'''Applied Biosystems Inc., Science Meeting'''<br /> **September, 2005, Asilomar, CA<br /> **Michael Ashburner (Keynote)<br /> <br /> *'''MGED8, Bergen'''<br /> **September, 2005<br /> **Michael Ashburner (Keynote)</div>

Skanel https://www.bioontology.org//mediawiki/index.php?title=MediaWiki:Sidebar&diff=6618 2008-03-07T18:51:36Z

<p>Skanel: re-ordered</p> <hr /> <div>* navigation<br /> ** mainpage|mainpage<br /> ** NCBO_News|NCBO News<br /> ** Dissemination_Wiki|Dissemination<br /> ** Education|Education<br /> ** Ontology_News|Ontology News<br /> ** Meetings_and_Events|Meetings and Events<br /> ** Ontology_Evaluation|Ontology Evaluation<br /> ** NCBO_FAQ|NCBO FAQ<br /> ** Shared_Materials|Shared Materials<br /> ** Public_Requirements|Public RQs<br /> ** Glossary|Glossary<br /> ** recentchanges-url|recentchanges<br /> ** helppage|help</div>

Skanel https://www.bioontology.org//mediawiki/index.php?title=Dissemination_Wiki&diff=6617 2008-03-07T18:46:59Z

<p>Skanel: /* NCBO Dissemination Workshops and Training Events */</p> <hr /> <div>==NCBO Dissemination ==<br /> <br /> What follows is a list of events organized under the auspices of the NCBO's Dissemination Core (PI: [http://ontology.buffalo.edu/smith Barry Smith]), together with information pertaining to related events and resources relevant to the NCBO's mission.<br /> <br /> ==NCBO Dissemination Workshops and Training Events ==<br /> <br /> *'''Forthcoming:'''<br /> <br /> ::'''March 27-28, 2008'''<br /> <br /> ::[[Networks | Workshop on Ontologies of Cellular Networks]], Newark, NJ. <br /> <br /> ::'''April 12-13, 2008'''<br /> <br /> ::[[Introduction to Biomedical Ontologies]], 2-Day Training Event, Buffalo, NY<br /> <br /> ::'''June 20, 2008'''<br /> <br /> ::[[Evolutionary Biology and Ontologies]], Minneapolis, MN (collocated with [http://www.cce.umn.edu/conferences/evolution/ Evolution 2008])<br /> <br /> ::'''July 19, 2008'''<br /> <br /> ::[[How to Make Useful Ontologies for Biomedicine]], Tutorial at ISMB 2008, Toronto, Canada.<br /> <br /> <br /> *'''Past:'''<br /> <br /> ::'''February 26-27, 2008'''<br /> <br /> ::[[JCOR | Joint JCOR-NCBO International Biomedical Ontology Dissemination Workshop]], Tokyo, Japan. This event is being scheduled as part of the [http://abelard.flet.keio.ac.jp/ontology/ Inaugural Conference] of JCOR: The Japanese Center for Ontological Research.<br /> <br /> <br /> ::*'''[[Workshops and Training Events 2007 | 2007]]'''<br /> <br /> ::*'''[[Workshops and Training Events 2006 | 2006]]'''<br /> <br /> == Related Events ==<br /> <br /> *''' Forthcoming:'''<br /> <br /> ::'''September 8, 2008'''<br /> <br /> ::The Nature of Psychiatric Disease and Its Classification ([[Psychiatric Disease]]), University at Buffalo, NY.<br /> <br /> *'''[[Related Events 2007 | 2007]]'''<br /> <br /> *'''[[Related Events 2006 | 2006]]'''<br /> <br /> == Ontology Training: Video and Audio Presentations ==<br /> <br /> '''[http://bmir.stanford.edu/people/view.php/mark_a_musen/ Mark Musen]'''<br /> <br /> *If we build it, will they come? Social-engineering of new technology to disseminate biomedical ontologies (Ontolog Form, December 6, 2007)<br /> ::[http://ontolog.cim3.net/cgi-bin/wiki.pl?ConferenceCall_2007_12_06 Details]<br /> ::[http://ontolog.cim3.net/file/resource/presentation/MarkMusen_20071206/NCBO--MarkMusen_20071206.pdf Slides]<br /> ::[http://ontolog.cim3.net/file/resource/presentation/MarkMusen_20071206/NCBO-BioPortal--MarkMusen_Ontolog-AudioRecording_conf-133566_20071206.mp3 Audio]<br /> <br /> '''[http://ontology.buffalo.edu/smith Barry Smith]'''<br /> <br /> *Ontology Evaluation in Biomedicine: The OBO Foundry (Ontolog Forum, December 21, 2006)<br /> ::[http://ontolog.cim3.net/cgi-bin/wiki.pl?ConferenceCall_2005_10_13 Details]<br /> ::[http://ontolog.cim3.net/file/work/OntologyMeasurementEvaluation/2006-12-21_OntologyEvaluationInBiomedicine/OBO-Foundry--BarrySmith_20061221.ppt Slides]<br /> ::[http://obofoundry.org/OntologDec06.mp3 Audio]<br /> <br /> *How to Build an Ontology (Tutorial, Stanford University, October 25, 2006)<br /> ::[http://stream.buffalo.edu/shared/research/phismith/Stanford10-25-06/Tutorial.rm Realplayer]<br /> ::[http://stream.buffalo.edu/shared/research/phismith/Stanford10-25-06/Tutorial.WMV Windows Mediaplayer]<br /> <br /> *Presentations at the Workshop on [http://www.bioontology.org/wiki/index.php/Workshop_on_Ontology_of_Images Ontology of Images] {Stanford University, March 24-25, 2006)<br /> ::[http://med.stanford.edu/irt/mmt/video/ontology/ontology-03-24-2006-09.ram Basic Principles]<br /> ::[http://med.stanford.edu/irt/mmt/video/ontology/ontology-03-24-2006-11.ram Towards an Ontology for the Imaging Domain]<br /> <br /> *The HL7 Reference Information Model<br /> ::[http://stream.buffalo.edu/shared/research/phismith/regenstrief.mpg Presentation] at the Regenstrief Institute, Indianapolis, November 9, 2005</div>

Skanel https://www.bioontology.org//mediawiki/index.php?title=Dissemination_Wiki&diff=6616 2008-03-07T18:40:30Z

<p>Skanel: /* Related Events */</p> <hr /> <div>==NCBO Dissemination ==<br /> <br /> What follows is a list of events organized under the auspices of the NCBO's Dissemination Core (PI: [http://ontology.buffalo.edu/smith Barry Smith]), together with information pertaining to related events and resources relevant to the NCBO's mission.<br /> <br /> ==NCBO Dissemination Workshops and Training Events ==<br /> <br /> *'''[[Workshops and Training Events 2006 | 2006]]'''<br /> <br /> *'''[[Workshops and Training Events 2007 | 2007]]'''<br /> <br /> *'''Forthcoming:'''<br /> <br /> ::'''February 26-27, 2008'''<br /> <br /> ::[[JCOR | Joint JCOR-NCBO International Biomedical Ontology Dissemination Workshop]], Tokyo, Japan. This event is being scheduled as part of the [http://abelard.flet.keio.ac.jp/ontology/ Inaugural Conference] of JCOR: The Japanese Center for Ontological Research.<br /> <br /> ::'''March 27-28, 2008'''<br /> <br /> ::[[Networks | Workshop on Ontologies of Cellular Networks]], Newark, NJ. <br /> <br /> ::'''April 12-13, 2008'''<br /> <br /> ::[[Introduction to Biomedical Ontologies]], 2-Day Training Event, Buffalo, NY<br /> <br /> ::'''June 20, 2008'''<br /> <br /> ::[[Evolutionary Biology and Ontologies]], Minneapolis, MN (collocated with [http://www.cce.umn.edu/conferences/evolution/ Evolution 2008])<br /> <br /> ::'''July 19, 2008'''<br /> <br /> ::[[How to Make Useful Ontologies for Biomedicine]], Tutorial at ISMB 2008, Toronto, Canada.<br /> <br /> == Related Events ==<br /> <br /> *''' Forthcoming:'''<br /> <br /> ::'''September 8, 2008'''<br /> <br /> ::The Nature of Psychiatric Disease and Its Classification ([[Psychiatric Disease]]), University at Buffalo, NY.<br /> <br /> *'''[[Related Events 2007 | 2007]]'''<br /> <br /> *'''[[Related Events 2006 | 2006]]'''<br /> <br /> == Ontology Training: Video and Audio Presentations ==<br /> <br /> '''[http://bmir.stanford.edu/people/view.php/mark_a_musen/ Mark Musen]'''<br /> <br /> *If we build it, will they come? Social-engineering of new technology to disseminate biomedical ontologies (Ontolog Form, December 6, 2007)<br /> ::[http://ontolog.cim3.net/cgi-bin/wiki.pl?ConferenceCall_2007_12_06 Details]<br /> ::[http://ontolog.cim3.net/file/resource/presentation/MarkMusen_20071206/NCBO--MarkMusen_20071206.pdf Slides]<br /> ::[http://ontolog.cim3.net/file/resource/presentation/MarkMusen_20071206/NCBO-BioPortal--MarkMusen_Ontolog-AudioRecording_conf-133566_20071206.mp3 Audio]<br /> <br /> '''[http://ontology.buffalo.edu/smith Barry Smith]'''<br /> <br /> *Ontology Evaluation in Biomedicine: The OBO Foundry (Ontolog Forum, December 21, 2006)<br /> ::[http://ontolog.cim3.net/cgi-bin/wiki.pl?ConferenceCall_2005_10_13 Details]<br /> ::[http://ontolog.cim3.net/file/work/OntologyMeasurementEvaluation/2006-12-21_OntologyEvaluationInBiomedicine/OBO-Foundry--BarrySmith_20061221.ppt Slides]<br /> ::[http://obofoundry.org/OntologDec06.mp3 Audio]<br /> <br /> *How to Build an Ontology (Tutorial, Stanford University, October 25, 2006)<br /> ::[http://stream.buffalo.edu/shared/research/phismith/Stanford10-25-06/Tutorial.rm Realplayer]<br /> ::[http://stream.buffalo.edu/shared/research/phismith/Stanford10-25-06/Tutorial.WMV Windows Mediaplayer]<br /> <br /> *Presentations at the Workshop on [http://www.bioontology.org/wiki/index.php/Workshop_on_Ontology_of_Images Ontology of Images] {Stanford University, March 24-25, 2006)<br /> ::[http://med.stanford.edu/irt/mmt/video/ontology/ontology-03-24-2006-09.ram Basic Principles]<br /> ::[http://med.stanford.edu/irt/mmt/video/ontology/ontology-03-24-2006-11.ram Towards an Ontology for the Imaging Domain]<br /> <br /> *The HL7 Reference Information Model<br /> ::[http://stream.buffalo.edu/shared/research/phismith/regenstrief.mpg Presentation] at the Regenstrief Institute, Indianapolis, November 9, 2005</div>

Skanel https://www.bioontology.org//mediawiki/index.php?title=MediaWiki:Sidebar&diff=6615 2008-03-07T18:38:04Z

<p>Skanel: removed collaborators link - moved to bioont. site</p> <hr /> <div>* navigation<br /> ** mainpage|mainpage<br /> ** NCBO_News|NCBO News<br /> ** NCBO_FAQ|NCBO FAQ<br /> ** Public_Requirements|Public RQs<br /> ** Shared_Materials|Shared Materials<br /> ** Dissemination_Wiki|Dissemination<br /> ** Education|Education<br /> ** Ontology_News|Ontology News<br /> ** Meetings_and_Events|Meetings and Events<br /> ** Ontology_Evaluation|Ontology Evaluation<br /> ** Glossary|Glossary<br /> ** recentchanges-url|recentchanges<br /> ** helppage|help</div>

Skanel https://www.bioontology.org//mediawiki/index.php?title=Education&diff=6607 2008-03-06T00:49:41Z

<p>Skanel: /* Symposia and Meetings */</p> <hr /> <div>===Publications===<br /> *Please see the main [http://www.bioontology.org/publications.html NCBO Publications Site]<br /> <br /> === RSS Feeds ===<br /> *Ontology articles in Pubmed in last 60 days [http://eutils.ncbi.nlm.nih.gov/entrez/eutils/erss.cgi?rss_guid=0gcn-LTgvdDj0y38wqDUuwq_R5x8QZnS3TX7HIwZ7Jn Feed Location]<br /> <br /> ===Journals of Interest===<br /> ====Bio[medical] Informatics====<br /> *[http://www.jamia.org/ Journal of American Medical Informatics Association]<br /> *[http://www.elsevier.com/wps/find/journaldescription.cws_home/622857/description#description Journal of Biomedical Informatics]<br /> *[http://bioinformatics.oxfordjournals.org/ Bioinformatics]<br /> *[http://www.biomedcentral.com/bmcbioinformatics/ BMC Bioinformatics]<br /> *[http://bib.oxfordjournals.org/ Briefings in Bioinformatics]<br /> *[http://www.worldscinet.com/jbcb/jbcb.shtml Journal of Bioinformatics and Computational Biology]<br /> *[http://www.elsevier.com/wps/find/journaldescription.cws_home/506040/description?navopenmenu=-2 International Journal of Medical Informatics]<br /> *for more journals, see http://www.hiww.org/jou.html<br /> <br /> ====Ontologies====<br /> *[http://www.applied-ontology.org/ Journal of Applied Ontology]<br /> <br /> ====Biomedical====<br /> *[http://www.genomebiology.com/ Genome Biology]<br /> *[http://www.nature.com/nbt/index.html Nature Biotechnology]<br /> *[http://www.elsevier.com/wps/find/journaldescription.cws_home/351/description?navopenmenu=-2 Computers in Biology and Medicine]<br /> *[http://www.liebertpub.com/publication.aspx?pub_id=43 Omics: A journal of Integrative Biology]<br /> *[http://www.elsevier.com/wps/find/journaldescription.cws_home/505627/description?navopenmenu=-2 Artificial Intelligence in Medicine]<br /> <br /> ===Symposia and Meetings===<br /> *[http://iswc2008.semanticweb.org/ ISWC] by [http://www.iswsa.org/ SWSA]<br /> *[http://www.amia.org/meetings/ AMIA]<br /> *[http://www.eswc2008.org/index.html ESWC]<br /> *[http://www.iscb.org/ismb2008/index.php ISMB]<br /> *[http://psb.stanford.edu PSB]<br /> *[http://www2007.org/ WWW Conference]<br /> *[http://www.csd.abdn.ac.uk/kcap07/index.php KCAP/EKAW]<br /> *[http://kr-med.org/2008/index.html KR-MED]<br /> *[http://www.w3.org/2001/sw/hcls/ HCLSIG]</div>

Skanel https://www.bioontology.org//mediawiki/index.php?title=Education&diff=6606 2008-03-06T00:41:51Z

<p>Skanel: /* Biomedical */</p> <hr /> <div>===Publications===<br /> *Please see the main [http://www.bioontology.org/publications.html NCBO Publications Site]<br /> <br /> === RSS Feeds ===<br /> *Ontology articles in Pubmed in last 60 days [http://eutils.ncbi.nlm.nih.gov/entrez/eutils/erss.cgi?rss_guid=0gcn-LTgvdDj0y38wqDUuwq_R5x8QZnS3TX7HIwZ7Jn Feed Location]<br /> <br /> ===Journals of Interest===<br /> ====Bio[medical] Informatics====<br /> *[http://www.jamia.org/ Journal of American Medical Informatics Association]<br /> *[http://www.elsevier.com/wps/find/journaldescription.cws_home/622857/description#description Journal of Biomedical Informatics]<br /> *[http://bioinformatics.oxfordjournals.org/ Bioinformatics]<br /> *[http://www.biomedcentral.com/bmcbioinformatics/ BMC Bioinformatics]<br /> *[http://bib.oxfordjournals.org/ Briefings in Bioinformatics]<br /> *[http://www.worldscinet.com/jbcb/jbcb.shtml Journal of Bioinformatics and Computational Biology]<br /> *[http://www.elsevier.com/wps/find/journaldescription.cws_home/506040/description?navopenmenu=-2 International Journal of Medical Informatics]<br /> *for more journals, see http://www.hiww.org/jou.html<br /> <br /> ====Ontologies====<br /> *[http://www.applied-ontology.org/ Journal of Applied Ontology]<br /> <br /> ====Biomedical====<br /> *[http://www.genomebiology.com/ Genome Biology]<br /> *[http://www.nature.com/nbt/index.html Nature Biotechnology]<br /> *[http://www.elsevier.com/wps/find/journaldescription.cws_home/351/description?navopenmenu=-2 Computers in Biology and Medicine]<br /> *[http://www.liebertpub.com/publication.aspx?pub_id=43 Omics: A journal of Integrative Biology]<br /> *[http://www.elsevier.com/wps/find/journaldescription.cws_home/505627/description?navopenmenu=-2 Artificial Intelligence in Medicine]<br /> <br /> ===Symposia and Meetings===<br /> *ISWC<br /> *AMIA<br /> *ESWC<br /> *ISMB<br /> *PSB<br /> *WWW Conference<br /> *KCAP/EKAW<br /> *KR-MED<br /> *HCLSIG</div>

Skanel https://www.bioontology.org//mediawiki/index.php?title=Education&diff=6605 2008-03-06T00:33:30Z

<p>Skanel: /* Ontologies */</p> <hr /> <div>===Publications===<br /> *Please see the main [http://www.bioontology.org/publications.html NCBO Publications Site]<br /> <br /> === RSS Feeds ===<br /> *Ontology articles in Pubmed in last 60 days [http://eutils.ncbi.nlm.nih.gov/entrez/eutils/erss.cgi?rss_guid=0gcn-LTgvdDj0y38wqDUuwq_R5x8QZnS3TX7HIwZ7Jn Feed Location]<br /> <br /> ===Journals of Interest===<br /> ====Bio[medical] Informatics====<br /> *[http://www.jamia.org/ Journal of American Medical Informatics Association]<br /> *[http://www.elsevier.com/wps/find/journaldescription.cws_home/622857/description#description Journal of Biomedical Informatics]<br /> *[http://bioinformatics.oxfordjournals.org/ Bioinformatics]<br /> *[http://www.biomedcentral.com/bmcbioinformatics/ BMC Bioinformatics]<br /> *[http://bib.oxfordjournals.org/ Briefings in Bioinformatics]<br /> *[http://www.worldscinet.com/jbcb/jbcb.shtml Journal of Bioinformatics and Computational Biology]<br /> *[http://www.elsevier.com/wps/find/journaldescription.cws_home/506040/description?navopenmenu=-2 International Journal of Medical Informatics]<br /> *for more journals, see http://www.hiww.org/jou.html<br /> <br /> ====Ontologies====<br /> *[http://www.applied-ontology.org/ Journal of Applied Ontology]<br /> <br /> ====Biomedical====<br /> *Genome Biology<br /> *Nature Biotechnology<br /> *Computers in Biology and Medicine<br /> *Omics: A journal of Integrative Biology<br /> *Applied Bioinformatics<br /> *Artificial Intelligence in Medicine<br /> <br /> ===Symposia and Meetings===<br /> *ISWC<br /> *AMIA<br /> *ESWC<br /> *ISMB<br /> *PSB<br /> *WWW Conference<br /> *KCAP/EKAW<br /> *KR-MED<br /> *HCLSIG</div>

Skanel https://www.bioontology.org//mediawiki/index.php?title=Education&diff=6604 2008-03-06T00:32:19Z

<p>Skanel: /* Bio[medical] Informatics */</p> <hr /> <div>===Publications===<br /> *Please see the main [http://www.bioontology.org/publications.html NCBO Publications Site]<br /> <br /> === RSS Feeds ===<br /> *Ontology articles in Pubmed in last 60 days [http://eutils.ncbi.nlm.nih.gov/entrez/eutils/erss.cgi?rss_guid=0gcn-LTgvdDj0y38wqDUuwq_R5x8QZnS3TX7HIwZ7Jn Feed Location]<br /> <br /> ===Journals of Interest===<br /> ====Bio[medical] Informatics====<br /> *[http://www.jamia.org/ Journal of American Medical Informatics Association]<br /> *[http://www.elsevier.com/wps/find/journaldescription.cws_home/622857/description#description Journal of Biomedical Informatics]<br /> *[http://bioinformatics.oxfordjournals.org/ Bioinformatics]<br /> *[http://www.biomedcentral.com/bmcbioinformatics/ BMC Bioinformatics]<br /> *[http://bib.oxfordjournals.org/ Briefings in Bioinformatics]<br /> *[http://www.worldscinet.com/jbcb/jbcb.shtml Journal of Bioinformatics and Computational Biology]<br /> *[http://www.elsevier.com/wps/find/journaldescription.cws_home/506040/description?navopenmenu=-2 International Journal of Medical Informatics]<br /> *for more journals, see http://www.hiww.org/jou.html<br /> <br /> ====Ontologies====<br /> *Journal of Applied Ontology<br /> <br /> ====Biomedical====<br /> *Genome Biology<br /> *Nature Biotechnology<br /> *Computers in Biology and Medicine<br /> *Omics: A journal of Integrative Biology<br /> *Applied Bioinformatics<br /> *Artificial Intelligence in Medicine<br /> <br /> ===Symposia and Meetings===<br /> *ISWC<br /> *AMIA<br /> *ESWC<br /> *ISMB<br /> *PSB<br /> *WWW Conference<br /> *KCAP/EKAW<br /> *KR-MED<br /> *HCLSIG</div>

Skanel https://www.bioontology.org//mediawiki/index.php?title=BioPortal_FAQ&diff=6603 2008-03-06T00:19:42Z

<p>Skanel: /* What is OBO? */</p> <hr /> <div>Frequently Asked Questions <br /> <br /> This FAQ is currently in alpha - please be patient...<br /> <br /> =General=<br /> <br /> ==NCBO==<br /> <br /> ===What is NCBO?===<br /> <br /> National Center for Biomedical Ontology http://www.bioontology.org<br /> <br /> ==OBO==<br /> <br /> ===What is OBO?===<br /> <br /> Open Biomedical Ontologies<br /> <br /> ===Where are the ontologies?===<br /> <br /> Currently on http://obo.sourceforge.net<br /> <br /> Soon to be moving to the NCBO site<br /> <br /> ===How do I submit an ontology?===<br /> <br /> The current protocol is:<br /> <br /> Send an email to the obo-discuss mailing list, even if the ontology is in planning stages<br /> <br /> If the ontology satisfies basic criteria, we will add it to the OBO metadata and it will appear on the OBO site<br /> <br /> Soon we will have an ontology submission service on the NCBO website<br /> <br /> =Ontology Content=<br /> <br /> ==Building Ontologies==<br /> <br /> ===How do I go about building an ontology?===<br /> <br /> ===What is the OBO Foundry?===<br /> <br /> A collaborative experiment, involving a group of ontology developers who have agreed in advance to the adoption of a growing set of principles specifying best practices in ontology development. These principles are designed to foster interoperability of ontologies within the broader OBO framework, and also to ensure a gradual improvement of quality and formal rigor in ontologies, in ways designed to meet the increasing needs of data and information integration in the biomedical domain.<br /> <br /> ===Where is the OBO Foundry?===<br /> <br /> See http://obofoundry.org/<br /> <br /> ==Current Ontologies==<br /> <br /> ===incomplete is-a paths===<br /> <br /> Many OBO ontologies are currently incomplete with respect to all classes/terms having an is-a parent. Many tools (including OBO-Edit and AmiGO) deliberately allow the conflation of relations when presenting the ontology as a DAG or a tree to the user. However, other tools (including Protege and SWOOP) do not. This means that some OBO ontologies can look unusual when viewed with these other tools (lots of classes appear at the root level).<br /> <br /> This is currently being addressed by the maintainers of OBO ontologies. An effort is underway to complete the is-a parentage in the GO cellular component ontology (biological process will be more difficult). The Plant Ontology Consortium are completing the is-a parentage in the plant anatomical structure ontology.<br /> <br /> Until this work is complete, some OBO ontologies may look unusual when viewed in conventional ontology browsing and editing tools. With some of these tools, there may be some configurations which allow other relations to be conflated with the is-a relation when presenting the ontology as a DAG or tree view.<br /> <br /> One option is to automatically create an is-a parent to the ontology root for every non-root class/term which lacks any is-a parents. Note that this may create inconsistencies in the ontology if the genuine is-a parent is somewhere deeper in the ontology hierarchy; nevertheless this step may be necessary before presenting some OBO ontologies to tools such as reasoners.<br /> <br /> =Technical=<br /> <br /> Questions for cores 1 and 2<br /> <br /> ==OBO Format==<br /> <br /> Questions about the OBO text and xml formats<br /> <br /> ===What is OBO Format?===<br /> <br /> ===Is OBO Format different from the old GO format?===<br /> <br /> Yes. The old dag-edit format (i.e. the one in which indentation was used to denote the GO hierarchy) is STRONGLY deprecated.<br /> <br /> ===Where can I find the spec?===<br /> <br /> You can find details on the 1.0 spec on the GO home page<br /> http://www.geneontology.org/GO.format.shtml#oboflat<br /> <br /> This spec is somewhat underspecified<br /> <br /> The 1.2 spec is in preparation, and will be released to coincide with the first production OBO-Edit release sometime early in 2006<br /> <br /> You can find a preliminary version of the spec here:<br /> HTML -- http://www.godatabase.org/dev/doc/obo_format_spec.html<br /> PDF -- http://www.godatabase.org/dev/doc/obo_format_spec.pdf<br /> Ascii text -- http://www.godatabase.org/dev/doc/obo_format_spec.txt<br /> <br /> ===Why not use XML?===<br /> <br /> There is also an obo-xml format. See<br /> <br /> http://www.godatabase.org/dev/xml<br /> <br /> Currently only available as DTD. Relax-NG and XSD coming soon.<br /> <br /> ===Is there a UML model?===<br /> <br /> Yes, there is a UML translation of the obo format in progress, produced by Harold Solbrig of Mayo clinic; see:<br /> <br /> http://informatics.mayo.edu/schema/OBO/UMLModel/HTML/<br /> <br /> ===What tools support Obo-Format?===<br /> <br /> The following are *ontology* tools that support the OBO format. There are many other tools for the analysis of gene ontology data which also happen to read the OBO format - see http://www.geneontology.org/GO.tools.shtml for a list<br /> <br /> ; OBO-Edit<br /> : (naturally!). You should use this rather than DAG-Edit (DAG-Edit still supports obo-1.0 format), as DAG-Edit is deprecated as of 2006.<br /> <br /> ; COBRA<br /> : developed by Stuart Aitken as part of http://www.xspan.org. COBRA is a java ontology editor/viewer for aligning ontologies<br /> <br /> ; go-perl<br /> : http://search.cpan.org/~cmungall/go-perl<br /> <br /> ==Using Protege with OBO ontologies==<br /> <br /> You have two options here - use the Protege OBO plugin, or convert to a format which Protege understands.<br /> <br /> The OBO plugin was developed at the University of Washington, and is no longer supported.<br /> <br /> You can convert any obo-format file to OWL and use Protege-OWL (but not Protege-classic); see the next entry.<br /> <br /> Note that when you look at many of the OBO ontologies in Protege (classic or Protege-OWL) you will see that there are large amounts of classes apparently at the root level. This is because OBO ontologies have historically not been complete with respect to all classes having a superclass (is-a parent). This is currently being addressed. See the FAQ entry on this subject.<br /> <br /> ===Can I convert Obo-format to OWL?===<br /> <br /> Yes. At this present time, the best way of foing this is to use the xslts included in go-perl.<br /> Download and install:<br /> http://search.cpan.org/~cmungall/go-perl/<br /> Then run the script<br /> <br /> go2owl myontology.obo<br /> <br /> This functionality will soon be available from oboedit<br /> <br /> For more details on the mapping, see:<br /> <br /> http://www.fruitfly.org/~cjm/obol/doc/mapping-obo-to-owl.html<br /> <br /> ===OK, but can I just download OBO ontologies as OWL without doing the conversion myself?===<br /> <br /> You can, at least for some OBO ontologies. This is an experimental service, and will eventually be subsumed into the services provided by cBio:<br /> <br /> http://www.fruitfly.org/~cjm/obo-download<br /> <br /> ===Can I convert Obo-format files to Protege-classic?===<br /> <br /> Not yet. In theory it should not be hard to provide an XSL for this. The reverse transformation may be more difficult.<br /> <br /> ==Ontology Metadata==<br /> <br /> ==OBD==<br /> <br /> ===What is OBD?===<br /> <br /> OBD is a database for storing data typed using OBO ontologies<br /> <br /> ===Where is it?===<br /> <br /> In development!<br /> <br /> ===Is there a demo?===<br /> <br /> See http://www.fruitfly.org/~cjm/obd<br /> <br /> ===Datasets===<br /> <br /> See the above URL for now</div>

Skanel https://www.bioontology.org//mediawiki/index.php?title=BioPortal_FAQ&diff=6602 2008-03-06T00:18:49Z

<p>Skanel: /* What is OBO? */</p> <hr /> <div>Frequently Asked Questions <br /> <br /> This FAQ is currently in alpha - please be patient...<br /> <br /> =General=<br /> <br /> ==NCBO==<br /> <br /> ===What is NCBO?===<br /> <br /> National Center for Biomedical Ontology http://www.bioontology.org<br /> <br /> ==OBO==<br /> <br /> ===What is OBO?===<br /> <br /> Open Biomedical Ontologies [http://www.bioontology.org/repositories.html#obo (OBO)]<br /> <br /> ===Where are the ontologies?===<br /> <br /> Currently on http://obo.sourceforge.net<br /> <br /> Soon to be moving to the NCBO site<br /> <br /> ===How do I submit an ontology?===<br /> <br /> The current protocol is:<br /> <br /> Send an email to the obo-discuss mailing list, even if the ontology is in planning stages<br /> <br /> If the ontology satisfies basic criteria, we will add it to the OBO metadata and it will appear on the OBO site<br /> <br /> Soon we will have an ontology submission service on the NCBO website<br /> <br /> =Ontology Content=<br /> <br /> ==Building Ontologies==<br /> <br /> ===How do I go about building an ontology?===<br /> <br /> ===What is the OBO Foundry?===<br /> <br /> A collaborative experiment, involving a group of ontology developers who have agreed in advance to the adoption of a growing set of principles specifying best practices in ontology development. These principles are designed to foster interoperability of ontologies within the broader OBO framework, and also to ensure a gradual improvement of quality and formal rigor in ontologies, in ways designed to meet the increasing needs of data and information integration in the biomedical domain.<br /> <br /> ===Where is the OBO Foundry?===<br /> <br /> See http://obofoundry.org/<br /> <br /> ==Current Ontologies==<br /> <br /> ===incomplete is-a paths===<br /> <br /> Many OBO ontologies are currently incomplete with respect to all classes/terms having an is-a parent. Many tools (including OBO-Edit and AmiGO) deliberately allow the conflation of relations when presenting the ontology as a DAG or a tree to the user. However, other tools (including Protege and SWOOP) do not. This means that some OBO ontologies can look unusual when viewed with these other tools (lots of classes appear at the root level).<br /> <br /> This is currently being addressed by the maintainers of OBO ontologies. An effort is underway to complete the is-a parentage in the GO cellular component ontology (biological process will be more difficult). The Plant Ontology Consortium are completing the is-a parentage in the plant anatomical structure ontology.<br /> <br /> Until this work is complete, some OBO ontologies may look unusual when viewed in conventional ontology browsing and editing tools. With some of these tools, there may be some configurations which allow other relations to be conflated with the is-a relation when presenting the ontology as a DAG or tree view.<br /> <br /> One option is to automatically create an is-a parent to the ontology root for every non-root class/term which lacks any is-a parents. Note that this may create inconsistencies in the ontology if the genuine is-a parent is somewhere deeper in the ontology hierarchy; nevertheless this step may be necessary before presenting some OBO ontologies to tools such as reasoners.<br /> <br /> =Technical=<br /> <br /> Questions for cores 1 and 2<br /> <br /> ==OBO Format==<br /> <br /> Questions about the OBO text and xml formats<br /> <br /> ===What is OBO Format?===<br /> <br /> ===Is OBO Format different from the old GO format?===<br /> <br /> Yes. The old dag-edit format (i.e. the one in which indentation was used to denote the GO hierarchy) is STRONGLY deprecated.<br /> <br /> ===Where can I find the spec?===<br /> <br /> You can find details on the 1.0 spec on the GO home page<br /> http://www.geneontology.org/GO.format.shtml#oboflat<br /> <br /> This spec is somewhat underspecified<br /> <br /> The 1.2 spec is in preparation, and will be released to coincide with the first production OBO-Edit release sometime early in 2006<br /> <br /> You can find a preliminary version of the spec here:<br /> HTML -- http://www.godatabase.org/dev/doc/obo_format_spec.html<br /> PDF -- http://www.godatabase.org/dev/doc/obo_format_spec.pdf<br /> Ascii text -- http://www.godatabase.org/dev/doc/obo_format_spec.txt<br /> <br /> ===Why not use XML?===<br /> <br /> There is also an obo-xml format. See<br /> <br /> http://www.godatabase.org/dev/xml<br /> <br /> Currently only available as DTD. Relax-NG and XSD coming soon.<br /> <br /> ===Is there a UML model?===<br /> <br /> Yes, there is a UML translation of the obo format in progress, produced by Harold Solbrig of Mayo clinic; see:<br /> <br /> http://informatics.mayo.edu/schema/OBO/UMLModel/HTML/<br /> <br /> ===What tools support Obo-Format?===<br /> <br /> The following are *ontology* tools that support the OBO format. There are many other tools for the analysis of gene ontology data which also happen to read the OBO format - see http://www.geneontology.org/GO.tools.shtml for a list<br /> <br /> ; OBO-Edit<br /> : (naturally!). You should use this rather than DAG-Edit (DAG-Edit still supports obo-1.0 format), as DAG-Edit is deprecated as of 2006.<br /> <br /> ; COBRA<br /> : developed by Stuart Aitken as part of http://www.xspan.org. COBRA is a java ontology editor/viewer for aligning ontologies<br /> <br /> ; go-perl<br /> : http://search.cpan.org/~cmungall/go-perl<br /> <br /> ==Using Protege with OBO ontologies==<br /> <br /> You have two options here - use the Protege OBO plugin, or convert to a format which Protege understands.<br /> <br /> The OBO plugin was developed at the University of Washington, and is no longer supported.<br /> <br /> You can convert any obo-format file to OWL and use Protege-OWL (but not Protege-classic); see the next entry.<br /> <br /> Note that when you look at many of the OBO ontologies in Protege (classic or Protege-OWL) you will see that there are large amounts of classes apparently at the root level. This is because OBO ontologies have historically not been complete with respect to all classes having a superclass (is-a parent). This is currently being addressed. See the FAQ entry on this subject.<br /> <br /> ===Can I convert Obo-format to OWL?===<br /> <br /> Yes. At this present time, the best way of foing this is to use the xslts included in go-perl.<br /> Download and install:<br /> http://search.cpan.org/~cmungall/go-perl/<br /> Then run the script<br /> <br /> go2owl myontology.obo<br /> <br /> This functionality will soon be available from oboedit<br /> <br /> For more details on the mapping, see:<br /> <br /> http://www.fruitfly.org/~cjm/obol/doc/mapping-obo-to-owl.html<br /> <br /> ===OK, but can I just download OBO ontologies as OWL without doing the conversion myself?===<br /> <br /> You can, at least for some OBO ontologies. This is an experimental service, and will eventually be subsumed into the services provided by cBio:<br /> <br /> http://www.fruitfly.org/~cjm/obo-download<br /> <br /> ===Can I convert Obo-format files to Protege-classic?===<br /> <br /> Not yet. In theory it should not be hard to provide an XSL for this. The reverse transformation may be more difficult.<br /> <br /> ==Ontology Metadata==<br /> <br /> ==OBD==<br /> <br /> ===What is OBD?===<br /> <br /> OBD is a database for storing data typed using OBO ontologies<br /> <br /> ===Where is it?===<br /> <br /> In development!<br /> <br /> ===Is there a demo?===<br /> <br /> See http://www.fruitfly.org/~cjm/obd<br /> <br /> ===Datasets===<br /> <br /> See the above URL for now</div>

Skanel https://www.bioontology.org//mediawiki/index.php?title=BioPortal_FAQ&diff=6601 2008-03-06T00:17:19Z

<p>Skanel: /* What is NCBO? */</p> <hr /> <div>Frequently Asked Questions <br /> <br /> This FAQ is currently in alpha - please be patient...<br /> <br /> =General=<br /> <br /> ==NCBO==<br /> <br /> ===What is NCBO?===<br /> <br /> National Center for Biomedical Ontology http://www.bioontology.org<br /> <br /> ==OBO==<br /> <br /> ===What is OBO?===<br /> <br /> Open Biomedical Ontologies<br /> <br /> ===Where are the ontologies?===<br /> <br /> Currently on http://obo.sourceforge.net<br /> <br /> Soon to be moving to the NCBO site<br /> <br /> ===How do I submit an ontology?===<br /> <br /> The current protocol is:<br /> <br /> Send an email to the obo-discuss mailing list, even if the ontology is in planning stages<br /> <br /> If the ontology satisfies basic criteria, we will add it to the OBO metadata and it will appear on the OBO site<br /> <br /> Soon we will have an ontology submission service on the NCBO website<br /> <br /> =Ontology Content=<br /> <br /> ==Building Ontologies==<br /> <br /> ===How do I go about building an ontology?===<br /> <br /> ===What is the OBO Foundry?===<br /> <br /> A collaborative experiment, involving a group of ontology developers who have agreed in advance to the adoption of a growing set of principles specifying best practices in ontology development. These principles are designed to foster interoperability of ontologies within the broader OBO framework, and also to ensure a gradual improvement of quality and formal rigor in ontologies, in ways designed to meet the increasing needs of data and information integration in the biomedical domain.<br /> <br /> ===Where is the OBO Foundry?===<br /> <br /> See http://obofoundry.org/<br /> <br /> ==Current Ontologies==<br /> <br /> ===incomplete is-a paths===<br /> <br /> Many OBO ontologies are currently incomplete with respect to all classes/terms having an is-a parent. Many tools (including OBO-Edit and AmiGO) deliberately allow the conflation of relations when presenting the ontology as a DAG or a tree to the user. However, other tools (including Protege and SWOOP) do not. This means that some OBO ontologies can look unusual when viewed with these other tools (lots of classes appear at the root level).<br /> <br /> This is currently being addressed by the maintainers of OBO ontologies. An effort is underway to complete the is-a parentage in the GO cellular component ontology (biological process will be more difficult). The Plant Ontology Consortium are completing the is-a parentage in the plant anatomical structure ontology.<br /> <br /> Until this work is complete, some OBO ontologies may look unusual when viewed in conventional ontology browsing and editing tools. With some of these tools, there may be some configurations which allow other relations to be conflated with the is-a relation when presenting the ontology as a DAG or tree view.<br /> <br /> One option is to automatically create an is-a parent to the ontology root for every non-root class/term which lacks any is-a parents. Note that this may create inconsistencies in the ontology if the genuine is-a parent is somewhere deeper in the ontology hierarchy; nevertheless this step may be necessary before presenting some OBO ontologies to tools such as reasoners.<br /> <br /> =Technical=<br /> <br /> Questions for cores 1 and 2<br /> <br /> ==OBO Format==<br /> <br /> Questions about the OBO text and xml formats<br /> <br /> ===What is OBO Format?===<br /> <br /> ===Is OBO Format different from the old GO format?===<br /> <br /> Yes. The old dag-edit format (i.e. the one in which indentation was used to denote the GO hierarchy) is STRONGLY deprecated.<br /> <br /> ===Where can I find the spec?===<br /> <br /> You can find details on the 1.0 spec on the GO home page<br /> http://www.geneontology.org/GO.format.shtml#oboflat<br /> <br /> This spec is somewhat underspecified<br /> <br /> The 1.2 spec is in preparation, and will be released to coincide with the first production OBO-Edit release sometime early in 2006<br /> <br /> You can find a preliminary version of the spec here:<br /> HTML -- http://www.godatabase.org/dev/doc/obo_format_spec.html<br /> PDF -- http://www.godatabase.org/dev/doc/obo_format_spec.pdf<br /> Ascii text -- http://www.godatabase.org/dev/doc/obo_format_spec.txt<br /> <br /> ===Why not use XML?===<br /> <br /> There is also an obo-xml format. See<br /> <br /> http://www.godatabase.org/dev/xml<br /> <br /> Currently only available as DTD. Relax-NG and XSD coming soon.<br /> <br /> ===Is there a UML model?===<br /> <br /> Yes, there is a UML translation of the obo format in progress, produced by Harold Solbrig of Mayo clinic; see:<br /> <br /> http://informatics.mayo.edu/schema/OBO/UMLModel/HTML/<br /> <br /> ===What tools support Obo-Format?===<br /> <br /> The following are *ontology* tools that support the OBO format. There are many other tools for the analysis of gene ontology data which also happen to read the OBO format - see http://www.geneontology.org/GO.tools.shtml for a list<br /> <br /> ; OBO-Edit<br /> : (naturally!). You should use this rather than DAG-Edit (DAG-Edit still supports obo-1.0 format), as DAG-Edit is deprecated as of 2006.<br /> <br /> ; COBRA<br /> : developed by Stuart Aitken as part of http://www.xspan.org. COBRA is a java ontology editor/viewer for aligning ontologies<br /> <br /> ; go-perl<br /> : http://search.cpan.org/~cmungall/go-perl<br /> <br /> ==Using Protege with OBO ontologies==<br /> <br /> You have two options here - use the Protege OBO plugin, or convert to a format which Protege understands.<br /> <br /> The OBO plugin was developed at the University of Washington, and is no longer supported.<br /> <br /> You can convert any obo-format file to OWL and use Protege-OWL (but not Protege-classic); see the next entry.<br /> <br /> Note that when you look at many of the OBO ontologies in Protege (classic or Protege-OWL) you will see that there are large amounts of classes apparently at the root level. This is because OBO ontologies have historically not been complete with respect to all classes having a superclass (is-a parent). This is currently being addressed. See the FAQ entry on this subject.<br /> <br /> ===Can I convert Obo-format to OWL?===<br /> <br /> Yes. At this present time, the best way of foing this is to use the xslts included in go-perl.<br /> Download and install:<br /> http://search.cpan.org/~cmungall/go-perl/<br /> Then run the script<br /> <br /> go2owl myontology.obo<br /> <br /> This functionality will soon be available from oboedit<br /> <br /> For more details on the mapping, see:<br /> <br /> http://www.fruitfly.org/~cjm/obol/doc/mapping-obo-to-owl.html<br /> <br /> ===OK, but can I just download OBO ontologies as OWL without doing the conversion myself?===<br /> <br /> You can, at least for some OBO ontologies. This is an experimental service, and will eventually be subsumed into the services provided by cBio:<br /> <br /> http://www.fruitfly.org/~cjm/obo-download<br /> <br /> ===Can I convert Obo-format files to Protege-classic?===<br /> <br /> Not yet. In theory it should not be hard to provide an XSL for this. The reverse transformation may be more difficult.<br /> <br /> ==Ontology Metadata==<br /> <br /> ==OBD==<br /> <br /> ===What is OBD?===<br /> <br /> OBD is a database for storing data typed using OBO ontologies<br /> <br /> ===Where is it?===<br /> <br /> In development!<br /> <br /> ===Is there a demo?===<br /> <br /> See http://www.fruitfly.org/~cjm/obd<br /> <br /> ===Datasets===<br /> <br /> See the above URL for now</div>

Skanel https://www.bioontology.org//mediawiki/index.php?title=MediaWiki:Sidebar&diff=6600 2008-03-05T23:55:28Z

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Skanel https://www.bioontology.org//mediawiki/index.php?title=Education&diff=6599 2008-03-05T23:54:11Z

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Skanel https://www.bioontology.org//mediawiki/index.php?title=Education&diff=6598 2008-03-05T23:53:55Z

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