https://www.bioontology.org//mediawiki/api.php?action=feedcontributions&feedformat=atom&user=Cjm2 2026-06-05T11:12:33Z User contributions MediaWiki 1.35.9 https://www.bioontology.org//mediawiki/index.php?title=Degrees_of_Annotation&diff=3182 2006-05-15T23:15:33Z

<p>Cjm2: </p> <hr /> <div>&quot;Annotation&quot; has various definitions. One of them (from wikipedia) is -<br /> Annotation is information associated with a particular point [or item] in a document or other piece of information.<br /> <br /> In the context of the bio* domain, annotation referes to some descriptive text that assists in the interpretation of the primary information [about an item] at hand. There can be various levels of annotation for example:<br /> <br /> * If the assembled genome coming out of a sequence assembly program is the primary information then the assignment of &quot;labels&quot; such as 'start site', 'exon', 'intron' to different parts of the sequence is an annotation.<br /> <br /> * At the second level this annotation itself [the statement about the boundries of 'start site', 'exon', 'intron'] is a conceptual item called a gene. Which is further &quot;annotated&quot; to have a particular 'function' or 'location' in the cell.<br /> <br /> * At a still higher level this annotation [about the function or location] is an item that is &quot;annotated&quot; to be relevant only in a certain genetic or experimental context.<br /> <br /> so defining the boundry between an information item (or data) and an annotation is dependent on the use case.<br /> <br /> Note from cjm: I have minor disagreements with most of the above. I think in the bio* domain annotations are much more than descriptive text. It is typically highly structured data. I think this is glossing over a lot - from base calling through assemblies and compute pipelines (the results of which are sometimes called annotations, although the word is typically only used for human-curated data). As well as simply labeling, there is a lot more going on with annotating intron-exon structure before functional annotation even starts. Why are genes conceptual items and exons aren't? Not sure what the final point means. But yes, the basic idea that annotation refers to different things at different levels is correct, so we should ban use of the word annotation as it is inherently ambiguous.</div>

Cjm2 https://www.bioontology.org//mediawiki/index.php?title=BioPortal_FAQ&diff=2380 2006-02-27T03:15:35Z

<p>Cjm2: </p> <hr /> <div>Frequently Asked Questions within cBio<br /> <br /> This FAQ is currently in alpha - please be patient...<br /> <br /> =General=<br /> <br /> ==cBio==<br /> <br /> ===What is cBio===<br /> <br /> ===What does cBio stand for?===<br /> <br /> ==OBO==<br /> <br /> ===What is OBO?===<br /> <br /> ===Where are the ontologies?===<br /> <br /> Currently on http://obo.sourceforge.net<br /> <br /> Soon to be moving to the cBio 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 cBio 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 Gold standard?===<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>

Cjm2 https://www.bioontology.org//mediawiki/index.php?title=File:Core2-2006-Jan.ppt&diff=2055 2006-01-12T19:34:34Z

<p>Cjm2: This was the presentation delivered by core 2 at the initial cbio meeting in 2005. It has aged a little, and was partially updated in Jan 2006; some parts are still out of date.</p> <hr /> <div>This was the presentation delivered by core 2 at the initial cbio meeting in 2005. It has aged a little, and was partially updated in Jan 2006; some parts are still out of date.</div>

Cjm2 https://www.bioontology.org//mediawiki/index.php?title=BioPortal_FAQ&diff=2040 2006-01-11T23:13:09Z

<p>Cjm2: /* Can I convert Obo-format to OWL? */</p> <hr /> <div>Frequently Asked Questions within cBio<br /> <br /> This FAQ is currently in alpha - please be patient...<br /> <br /> =General=<br /> <br /> ==cBio==<br /> <br /> ===What is cBio===<br /> <br /> ===What does cBio stand for?===<br /> <br /> ==OBO==<br /> <br /> ===What is OBO?===<br /> <br /> ===Where are the ontologies?===<br /> <br /> Currently on http://obo.sourceforge.net<br /> <br /> Soon to be moving to the cBio 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 cBio 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 Gold standard?===<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 /> <br /> The 1.2 spec is in preparation, and will be released to coincide with the first production OBO-Edit release before the end of 2005<br /> <br /> ===Why not use an XML format?===<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 /> <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>

Cjm2 https://www.bioontology.org//mediawiki/index.php?title=BioPortal_FAQ&diff=2039 2006-01-11T23:12:37Z

<p>Cjm2: /* Can I convert Obo-format to OWL? */</p> <hr /> <div>Frequently Asked Questions within cBio<br /> <br /> This FAQ is currently in alpha - please be patient...<br /> <br /> =General=<br /> <br /> ==cBio==<br /> <br /> ===What is cBio===<br /> <br /> ===What does cBio stand for?===<br /> <br /> ==OBO==<br /> <br /> ===What is OBO?===<br /> <br /> ===Where are the ontologies?===<br /> <br /> Currently on http://obo.sourceforge.net<br /> <br /> Soon to be moving to the cBio 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 cBio 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 Gold standard?===<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 /> <br /> The 1.2 spec is in preparation, and will be released to coincide with the first production OBO-Edit release before the end of 2005<br /> <br /> ===Why not use an XML format?===<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 /> <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 /> 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>

Cjm2 https://www.bioontology.org//mediawiki/index.php?title=BioPortal_FAQ&diff=2038 2006-01-11T23:09:45Z

<p>Cjm2: /* Can I convert Obo-format to OWL? */</p> <hr /> <div>Frequently Asked Questions within cBio<br /> <br /> This FAQ is currently in alpha - please be patient...<br /> <br /> =General=<br /> <br /> ==cBio==<br /> <br /> ===What is cBio===<br /> <br /> ===What does cBio stand for?===<br /> <br /> ==OBO==<br /> <br /> ===What is OBO?===<br /> <br /> ===Where are the ontologies?===<br /> <br /> Currently on http://obo.sourceforge.net<br /> <br /> Soon to be moving to the cBio 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 cBio 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 Gold standard?===<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 /> <br /> The 1.2 spec is in preparation, and will be released to coincide with the first production OBO-Edit release before the end of 2005<br /> <br /> ===Why not use an XML format?===<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 /> <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. You can do this using 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 /> For more details, 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>

Cjm2 https://www.bioontology.org//mediawiki/index.php?title=BioPortal_FAQ&diff=2037 2006-01-11T23:07:36Z

<p>Cjm2: /* Can I convert Obo-format to OWL? */</p> <hr /> <div>Frequently Asked Questions within cBio<br /> <br /> This FAQ is currently in alpha - please be patient...<br /> <br /> =General=<br /> <br /> ==cBio==<br /> <br /> ===What is cBio===<br /> <br /> ===What does cBio stand for?===<br /> <br /> ==OBO==<br /> <br /> ===What is OBO?===<br /> <br /> ===Where are the ontologies?===<br /> <br /> Currently on http://obo.sourceforge.net<br /> <br /> Soon to be moving to the cBio 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 cBio 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 Gold standard?===<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 /> <br /> The 1.2 spec is in preparation, and will be released to coincide with the first production OBO-Edit release before the end of 2005<br /> <br /> ===Why not use an XML format?===<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 /> <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!<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>

Cjm2 https://www.bioontology.org//mediawiki/index.php?title=Phenotype_Reading_List&diff=1991 2006-01-10T21:16:02Z

<p>Cjm2: </p> <hr /> <div>=Phenotype readling list=<br /> <br /> I have some of these in my endnote library, but endnote is terrible<br /> for collecting non-bio references. I'm guessing the CS and logiv<br /> people use Latex? If so, if they post their bibtexes here I can<br /> compile both an endnote and a bibtex library.<br /> <br /> ==Intro to phenotypes for non-biologists==<br /> <br /> This list is very fly-centric. If someone can contribute zebrafish and<br /> human clinical genetics pointers that would be great. <br /> <br /> ===Genetics of Development===<br /> <br /> Only looked briefly at this, but seems like it might be a useful non-biologists intro. Nice images.<br /> <br /> http://www.learner.org/channel/courses/biology/units/gendev/<br /> <br /> ===EBI Introduction to cell biology===<br /> <br /> This is microarray centric (we'll need to turn our attention to this technology at some point), but still v useful for the non-biologist<br /> <br /> http://www.ebi.ac.uk/microarray/biology_intro.html<br /> <br /> ===Drysdale R: Phenotypic data in FlyBase=== <br /> Brief Bioinform 2001,2(1):68-80.<br /> <br /> This is an ideal intro for folks familiar with biological databases<br /> looking to make the first step into genetics and phenotypes.<br /> <br /> ===Essential Developmental Biology===<br /> by J. M. W. Slack<br /> <br /> http://books.google.com/books?ie=UTF-8&amp;hl=en&amp;id=BXfdbKLTiZQC&amp;dq=essential+developmental+biology&amp;prev=http://books.google.com/books%3Flr%3D%26client%3Dfirefox-a%26q%3Dessential%2Bdevelopmental%2Bbiology&amp;lpg=PP5&amp;pg=PP5&amp;printsec=4&amp;sig=FIivE3wd7u_AC9ojAEdW-BpD90A<br /> <br /> I found this to be a really useful and accessible introduction to<br /> developmental biology. Remember, many of the phenotypes we're dealing<br /> with will be developmental. It may be challenging for those with<br /> virtually no biology, but I'd still highly recommend it. Covers fly,<br /> zebrafish and other major model organisms.<br /> <br /> ===Other books===<br /> <br /> These two are standard texts for molecular biology - this will have a lot of the background material for understanding phenotypes:<br /> <br /> Alberts, B. , Bray, D. , Lewis J. , Raff, M., Roberts, K., Watson, J.D.: Molecular biology of the cell. New York, Garland Publishing, 1994<br /> <br /> Lewin B: Genes VII, New York, Oxford University Press, 2000<br /> <br /> This may also be useful:<br /> <br /> The Shape of Life : Genes, Development, and the Evolution of Animal Form (Paperback)<br /> by Rudolf A. Raff<br /> <br /> <br /> ===THE ART AND DESIGN OF GENETIC SCREENS===<br /> <br /> This is actually a whole collection of reviews in Nature Reviews<br /> Genetics coverisg zebrafish, mouse, etc. Go to their website and<br /> search on the above:<br /> <br /> http://search.nature.com/search/?sp_a=sp1001702d&amp;sp_sfvl_field=subject%7Cujournal&amp;sp_t=results&amp;sp_q_1=Nature+Reviews+Genetics&amp;sp_x_1=ujournal&amp;sp_p_1=phrase&amp;go.x=0&amp;go.y=0&amp;sp-q=the+art+and+design+of+genetic+screens<br /> <br /> Here's the one on zebrafish<br /> http://www.nature.com/nrg/journal/v2/n12/abs/nrg1201-956a_fs.html;jsessionid=C33F00DB1D1DF6C5E26BCD324FFE25B4<br /> <br /> These are highly recommended for the tools developers<br /> <br /> ===The Making of a Fly: The Genetics of Animal Design [BOOK]===<br /> <br /> http://www.amazon.com/gp/product/0632030488/103-3091658-4208606?v=glance&amp;n=283155<br /> <br /> May be hard going for those without any knowledge of genetics<br /> <br /> ===Drosophila: A Laboratory Handbook, Michael Ashburner [BOOK]===<br /> aka the grey book<br /> http://www.cshlpress.com/default.tpl?action=full&amp;cart=1133810703113928&amp;--eqskudatarq=467&amp;newtitle=Drosophila%3A%20A%20Laboratory%20Handbook%2C%20Second%20Edition<br /> <br /> Everything you ever wanted to know about Drosophila genetics but were<br /> afraid to ask Michael. This may be a little overwhelming for the CS<br /> folks<br /> <br /> ==Formal ontology and logic==<br /> <br /> References on formal ontology and logic and qualities that are tied to<br /> qualities<br /> <br /> ===A formal theory of substances, qualities, and universals.===<br /> <br /> Neuhaus, F., Grenon, P., Smith, B.: In Varzi, A., Vieu, L., eds.:<br /> Formal Ontology in Information Systems (FOIS’04), Turin, Italy, IOS<br /> Press (2004) 49–59<br /> <br /> Available from: http://ontology.buffalo.edu/bfo/SQU.pdf<br /> <br /> This paper may be heavy-going for those without a background in logic,<br /> but I would still highly recommend the first couple of pages to<br /> everyone involved in this project.<br /> <br /> ===Stanford Encyclopedia of Philosophy===<br /> <br /> Entry on properties: http://plato.stanford.edu/entries/properties/<br /> <br /> I think properties here are used in the sense that Fabian Neuhaus and<br /> I would use &quot;quality&quot;, rather than in the looser sense that a CS or<br /> OWL person may use the term.<br /> <br /> Entry on determinate vs determinable: http://plato.stanford.edu/entries/determinate-determinables/<br /> <br /> I was hesitant about adding this one. Inquiring minds may want to<br /> check this out. Determinate vs determinable roughly corresponds to<br /> value vs attribute<br /> <br /> ==Data modeling==<br /> <br /> ===J. Diederich. Basic properties for biological databases: character development and support===<br /> in Math. Comput. Modelling 25 (1997), 109-127.<br /> <br /> Required reading for everyone in the project. 1997, but it anticipated<br /> many of the problems we are facing. This has more of a systematics<br /> focus, but really the design of ontologies for phenotypic characters<br /> should be independent of whether we are applying this to genetic<br /> screens or to phylogenetic classisification.<br /> <br /> ==See also an application of the work from this paper in:<br /> Diederich, J., R. Fortuner and J. Milton. 1997. Construction and integration<br /> of large character sets for nematode morpho-anatomical data. ''Fundam. appl. Nematol.'' 20: 409-424<br /> <br /> ===Papers by George===<br /> <br /> George gets his own section here. The GB is paper is a good<br /> introduction to the EAV model as it was originally formulated in 2003.<br /> <br /> <br /> Gkoutos GV, Green EC, Mallon AM, Hancock JM, Davidson D: Building<br /> mouse phenotype ontologies. Pac Symp Biocomput 2004:178-189.3.<br /> http://helix-web.stanford.edu/psb04/gkoutos.pdf<br /> <br /> Gkoutos GV, Green EC, Mallon AM, Hancock JM, Davidson D: Using<br /> ontologies to describe mouse phenotypes. Genome Biol 2005, 6(1):R8.4.<br /> http://dx.doi.org/10.1186/gb-2004-6-1-r8<br /> <br /> G. V. Gkoutos, E. C. J. Green, A.-M. Mallon, A. Blake, S. Greenaway 1, J. M. Hancock, D. Davidson<br /> Ontologies for the description of mouse phenotypes<br /> MRC Mammalian Genetics Unit, Harwell, UK<br /> http://doi.wiley.com/10.1002/cfg.430<br /> <br /> Gkoutos GV, Green EC, Greenaway S, Blake A, Mallon AM, Hancock JM:<br /> CRAVE: a database, middleware and visualization system for phenotype<br /> ontologies. Bioinformatics 2005, 21(7):1257-1262.<br /> http://www.bioinformatics.oupjournals.org/cgi/doi/10.1093/bioinformatics/bti147<br /> <br /> <br /> [[User:Cjm|Cjm]] 12:03, 5 December 2005 (PST)</div>

Cjm2 https://www.bioontology.org//mediawiki/index.php?title=BioPortal_FAQ&diff=1957 2006-01-03T12:48:40Z

<p>Cjm2: /* incomplete is-a paths */</p> <hr /> <div>Frequently Asked Questions within cBio<br /> <br /> This FAQ is currently in alpha - please be patient...<br /> <br /> =General=<br /> <br /> ==cBio==<br /> <br /> ===What is cBio===<br /> <br /> ===What does cBio stand for?===<br /> <br /> ==OBO==<br /> <br /> ===What is OBO?===<br /> <br /> ===Where are the ontologies?===<br /> <br /> Currently on http://obo.sourceforge.net<br /> <br /> Soon to be moving to the cBio 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 cBio 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 Gold standard?===<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 /> <br /> The 1.2 spec is in preparation, and will be released to coincide with the first production OBO-Edit release before the end of 2005<br /> <br /> ===Why not use an XML format?===<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 /> <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! See <br /> <br /> http://www.godatabase.org/dev/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>

Cjm2 https://www.bioontology.org//mediawiki/index.php?title=BioPortal_FAQ&diff=1956 2006-01-02T12:38:38Z

<p>Cjm2: </p> <hr /> <div>Frequently Asked Questions within cBio<br /> <br /> This FAQ is currently in alpha - please be patient...<br /> <br /> =General=<br /> <br /> ==cBio==<br /> <br /> ===What is cBio===<br /> <br /> ===What does cBio stand for?===<br /> <br /> ==OBO==<br /> <br /> ===What is OBO?===<br /> <br /> ===Where are the ontologies?===<br /> <br /> Currently on http://obo.sourceforge.net<br /> <br /> Soon to be moving to the cBio 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 cBio 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 Gold standard?===<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 <br /> <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 /> <br /> The 1.2 spec is in preparation, and will be released to coincide with the first production OBO-Edit release before the end of 2005<br /> <br /> ===Why not use an XML format?===<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 /> <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! See <br /> <br /> http://www.godatabase.org/dev/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>

Cjm2 https://www.bioontology.org//mediawiki/index.php?title=BioPortal_FAQ&diff=1955 2006-01-02T12:35:41Z

<p>Cjm2: </p> <hr /> <div>Frequently Asked Questions within cBio<br /> <br /> This FAQ is currently in alpha - please be patient...<br /> <br /> =General=<br /> <br /> ==cBio==<br /> <br /> ===What is cBio===<br /> <br /> ===What does cBio stand for?===<br /> <br /> ==OBO==<br /> <br /> ===What is OBO?===<br /> <br /> ===Where are the ontologies?===<br /> <br /> Currently on http://obo.sourceforge.net<br /> <br /> Soon to be moving to the cBio 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 cBio 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 Gold standard?===<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<br /> <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 /> <br /> The 1.2 spec is in preparation, and will be released to coincide with the first production OBO-Edit release before the end of 2005<br /> <br /> ===Why not use an XML format?===<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 /> <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! See <br /> <br /> http://www.godatabase.org/dev/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>

Cjm2 https://www.bioontology.org//mediawiki/index.php?title=BioPortal_FAQ&diff=1954 2006-01-02T12:33:40Z

<p>Cjm2: </p> <hr /> <div>Frequently Asked Questions within cBio<br /> <br /> =General=<br /> <br /> ==cBio==<br /> <br /> ===What is cBio===<br /> <br /> ===What does cBio stand for?===<br /> <br /> ==OBO==<br /> <br /> ===What is OBO?===<br /> <br /> ===Where are the ontologies?===<br /> <br /> Currently on http://obo.sourceforge.net<br /> <br /> Soon to be moving to the cBio 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 cBio 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 Gold standard?===<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 /> <br /> The 1.2 spec is in preparation, and will be released to coincide with the first production OBO-Edit release before the end of 2005<br /> <br /> ===Why not use an XML format?===<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 /> <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! See <br /> <br /> http://www.godatabase.org/dev/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>

Cjm2 https://www.bioontology.org//mediawiki/index.php?title=Phenotype_Reading_List&diff=1835 2005-12-12T21:57:20Z

<p>Cjm2: /* Papers by George */</p> <hr /> <div>=Phenotype readling list=<br /> <br /> I have some of these in my endnote library, but endnote is terrible<br /> for collecting non-bio references. I'm guessing the CS and logiv<br /> people use Latex? If so, if they post their bibtexes here I can<br /> compile both an endnote and a bibtex library.<br /> <br /> ==Intro to phenotypes for non-biologists==<br /> <br /> This list is very fly-centric. If someone can contribute zebrafish and<br /> human clinical genetics pointers that would be great. <br /> <br /> ===Genetics of Development===<br /> <br /> Only looked briefly at this, but seems like it might be a useful non-biologists intro. Nice images.<br /> <br /> http://www.learner.org/channel/courses/biology/units/gendev/<br /> <br /> ===EBI Introduction to cell biology===<br /> <br /> This is microarray centric (we'll need to turn our attention to this technology at some point), but still v useful for the non-biologist<br /> <br /> http://www.ebi.ac.uk/microarray/biology_intro.html<br /> <br /> ===Drysdale R: Phenotypic data in FlyBase=== <br /> Brief Bioinform 2001,2(1):68-80.<br /> <br /> This is an ideal intro for folks familiar with biological databases<br /> looking to make the first step into genetics and phenotypes.<br /> <br /> ===Essential Developmental Biology===<br /> by J. M. W. Slack<br /> <br /> http://books.google.com/books?ie=UTF-8&amp;hl=en&amp;id=BXfdbKLTiZQC&amp;dq=essential+developmental+biology&amp;prev=http://books.google.com/books%3Flr%3D%26client%3Dfirefox-a%26q%3Dessential%2Bdevelopmental%2Bbiology&amp;lpg=PP5&amp;pg=PP5&amp;printsec=4&amp;sig=FIivE3wd7u_AC9ojAEdW-BpD90A<br /> <br /> I found this to be a really useful and accessible introduction to<br /> developmental biology. Remember, most of the phenotypes we're dealing<br /> with will be developmental. It may be challenging for those with<br /> virtually no biology, but I'd still highly recommend it. Covers fly,<br /> zebrafish and other major model organisms.<br /> <br /> ===Other books===<br /> <br /> Alberts, B. , Bray, D. , Lewis J. , Raff, M., Roberts, K., Watson, J.D.: Molecular biology of the cell. New York, Garland Publishing, 1994<br /> <br /> Lewin B: Genes VII, New York, Oxford University Press, 2000<br /> <br /> <br /> ===THE ART AND DESIGN OF GENETIC SCREENS===<br /> <br /> This is actually a whole collection of reviews in Nature Reviews<br /> Genetics coverisg zebrafish, mouse, etc. Go to their website and<br /> search on the above:<br /> <br /> http://search.nature.com/search/?sp_a=sp1001702d&amp;sp_sfvl_field=subject%7Cujournal&amp;sp_t=results&amp;sp_q_1=Nature+Reviews+Genetics&amp;sp_x_1=ujournal&amp;sp_p_1=phrase&amp;go.x=0&amp;go.y=0&amp;sp-q=the+art+and+design+of+genetic+screens<br /> <br /> Here's the one on zebrafish<br /> http://www.nature.com/nrg/journal/v2/n12/abs/nrg1201-956a_fs.html;jsessionid=C33F00DB1D1DF6C5E26BCD324FFE25B4<br /> <br /> These are highly recommended for the tools developers<br /> <br /> ===The Making of a Fly: The Genetics of Animal Design [BOOK]===<br /> <br /> http://www.amazon.com/gp/product/0632030488/103-3091658-4208606?v=glance&amp;n=283155<br /> <br /> May be hard going for those without any knowledge of genetics<br /> <br /> ===Drosophila: A Laboratory Handbook, Michael Ashburner [BOOK]===<br /> aka the grey book<br /> http://www.cshlpress.com/default.tpl?action=full&amp;cart=1133810703113928&amp;--eqskudatarq=467&amp;newtitle=Drosophila%3A%20A%20Laboratory%20Handbook%2C%20Second%20Edition<br /> <br /> Everything you ever wanted to know about Drosophila genetics but were<br /> afraid to ask Michael. This may be a little overwhelming for the CS<br /> folks<br /> <br /> ==Formal ontology and logic==<br /> <br /> References on formal ontology and logic and qualities that are tied to<br /> qualities<br /> <br /> ===A formal theory of substances, qualities, and universals.===<br /> <br /> Neuhaus, F., Grenon, P., Smith, B.: In Varzi, A., Vieu, L., eds.:<br /> Formal Ontology in Information Systems (FOIS’04), Turin, Italy, IOS<br /> Press (2004) 49–59<br /> <br /> Available from: http://ontology.buffalo.edu/bfo/SQU.pdf<br /> <br /> This paper may be heavy-going for those without a background in logic,<br /> but I would still highly recommend the first couple of pages to<br /> everyone involved in this project.<br /> <br /> ===Stanford Encyclopedia of Philosophy===<br /> <br /> Entry on properties: http://plato.stanford.edu/entries/properties/<br /> <br /> I think properties here are used in the sense that Fabian Neuhaus and<br /> I would use &quot;quality&quot;, rather than in the looser sense that a CS or<br /> OWL person may use the term.<br /> <br /> Entry on determinate vs determinable: http://plato.stanford.edu/entries/determinate-determinables/<br /> <br /> I was hesitant about adding this one. Inquiring minds may want to<br /> check this out. Determinate vs determinable roughly corresponds to<br /> value vs attribute<br /> <br /> ==Data modeling==<br /> <br /> ===Basic properties for biological databases: character development and support===<br /> in Math. Comput. Modelling 25 (1997), 109-127.<br /> <br /> Required reading for everyone in the project. 1997, but it anticipated<br /> many of the problems we are facing. This has more of a systematics<br /> focus, but really the design of ontologies for phenotypic characters<br /> should be independent of whether we are applying this to genetic<br /> screens or to phylogenetic classisification.<br /> <br /> ===Papers by George===<br /> <br /> George gets his own section here. The GB is paper is a good<br /> introduction to the EAV model as it was originally formulated in 2003.<br /> <br /> <br /> Gkoutos GV, Green EC, Mallon AM, Hancock JM, Davidson D: Building<br /> mouse phenotype ontologies. Pac Symp Biocomput 2004:178-189.3.<br /> http://helix-web.stanford.edu/psb04/gkoutos.pdf<br /> <br /> Gkoutos GV, Green EC, Mallon AM, Hancock JM, Davidson D: Using<br /> ontologies to describe mouse phenotypes. Genome Biol 2005, 6(1):R8.4.<br /> http://dx.doi.org/10.1186/gb-2004-6-1-r8<br /> <br /> G. V. Gkoutos 1 *, E. C. J. Green 1, A.-M. Mallon 1, A. Blake 1, S. Greenaway 1, J. M. Hancock 1, D. Davidson 2<br /> Ontologies for the description of mouse phenotypes<br /> MRC Mammalian Genetics Unit, Harwell, UK<br /> http://doi.wiley.com/10.1002/cfg.430<br /> <br /> Gkoutos GV, Green EC, Greenaway S, Blake A, Mallon AM, Hancock JM:<br /> CRAVE: a database, middleware and visualization system for phenotype<br /> ontologies. Bioinformatics 2005, 21(7):1257-1262.<br /> http://www.bioinformatics.oupjournals.org/cgi/doi/10.1093/bioinformatics/bti147<br /> <br /> <br /> [[User:Cjm|Cjm]] 12:03, 5 December 2005 (PST)</div>

Cjm2 https://www.bioontology.org//mediawiki/index.php?title=File:OBDarchitecture.png&diff=1816 2005-12-11T00:30:05Z

<p>Cjm2: foo</p> <hr /> <div>foo</div>

Cjm2 https://www.bioontology.org//mediawiki/index.php?title=File:OBDdataflow.png&diff=1815 2005-12-11T00:29:09Z

<p>Cjm2: OBD data exchange</p> <hr /> <div>OBD data exchange</div>

Cjm2 https://www.bioontology.org//mediawiki/index.php?title=Phenotype_Reading_List&diff=1804 2005-12-07T23:48:51Z

<p>Cjm2: </p> <hr /> <div>=Phenotype readling list=<br /> <br /> I have some of these in my endnote library, but endnote is terrible<br /> for collecting non-bio references. I'm guessing the CS and logiv<br /> people use Latex? If so, if they post their bibtexes here I can<br /> compile both an endnote and a bibtex library.<br /> <br /> ==Intro to phenotypes for non-biologists==<br /> <br /> This list is very fly-centric. If someone can contribute zebrafish and<br /> human clinical genetics pointers that would be great. <br /> <br /> ===Genetics of Development===<br /> <br /> Only looked briefly at this, but seems like it might be a useful non-biologists intro. Nice images.<br /> <br /> http://www.learner.org/channel/courses/biology/units/gendev/<br /> <br /> ===EBI Introduction to cell biology===<br /> <br /> This is microarray centric (we'll need to turn our attention to this technology at some point), but still v useful for the non-biologist<br /> <br /> http://www.ebi.ac.uk/microarray/biology_intro.html<br /> <br /> ===Drysdale R: Phenotypic data in FlyBase=== <br /> Brief Bioinform 2001,2(1):68-80.<br /> <br /> This is an ideal intro for folks familiar with biological databases<br /> looking to make the first step into genetics and phenotypes.<br /> <br /> ===Essential Developmental Biology===<br /> by J. M. W. Slack<br /> <br /> http://books.google.com/books?ie=UTF-8&amp;hl=en&amp;id=BXfdbKLTiZQC&amp;dq=essential+developmental+biology&amp;prev=http://books.google.com/books%3Flr%3D%26client%3Dfirefox-a%26q%3Dessential%2Bdevelopmental%2Bbiology&amp;lpg=PP5&amp;pg=PP5&amp;printsec=4&amp;sig=FIivE3wd7u_AC9ojAEdW-BpD90A<br /> <br /> I found this to be a really useful and accessible introduction to<br /> developmental biology. Remember, most of the phenotypes we're dealing<br /> with will be developmental. It may be challenging for those with<br /> virtually no biology, but I'd still highly recommend it. Covers fly,<br /> zebrafish and other major model organisms.<br /> <br /> ===Other books===<br /> <br /> Alberts, B. , Bray, D. , Lewis J. , Raff, M., Roberts, K., Watson, J.D.: Molecular biology of the cell. New York, Garland Publishing, 1994<br /> <br /> Lewin B: Genes VII, New York, Oxford University Press, 2000<br /> <br /> <br /> ===THE ART AND DESIGN OF GENETIC SCREENS===<br /> <br /> This is actually a whole collection of reviews in Nature Reviews<br /> Genetics coverisg zebrafish, mouse, etc. Go to their website and<br /> search on the above:<br /> <br /> http://search.nature.com/search/?sp_a=sp1001702d&amp;sp_sfvl_field=subject%7Cujournal&amp;sp_t=results&amp;sp_q_1=Nature+Reviews+Genetics&amp;sp_x_1=ujournal&amp;sp_p_1=phrase&amp;go.x=0&amp;go.y=0&amp;sp-q=the+art+and+design+of+genetic+screens<br /> <br /> Here's the one on zebrafish<br /> http://www.nature.com/nrg/journal/v2/n12/abs/nrg1201-956a_fs.html;jsessionid=C33F00DB1D1DF6C5E26BCD324FFE25B4<br /> <br /> These are highly recommended for the tools developers<br /> <br /> ===The Making of a Fly: The Genetics of Animal Design [BOOK]===<br /> <br /> http://www.amazon.com/gp/product/0632030488/103-3091658-4208606?v=glance&amp;n=283155<br /> <br /> May be hard going for those without any knowledge of genetics<br /> <br /> ===Drosophila: A Laboratory Handbook, Michael Ashburner [BOOK]===<br /> aka the grey book<br /> http://www.cshlpress.com/default.tpl?action=full&amp;cart=1133810703113928&amp;--eqskudatarq=467&amp;newtitle=Drosophila%3A%20A%20Laboratory%20Handbook%2C%20Second%20Edition<br /> <br /> Everything you ever wanted to know about Drosophila genetics but were<br /> afraid to ask Michael. This may be a little overwhelming for the CS<br /> folks<br /> <br /> ==Formal ontology and logic==<br /> <br /> References on formal ontology and logic and qualities that are tied to<br /> qualities<br /> <br /> ===A formal theory of substances, qualities, and universals.===<br /> <br /> Neuhaus, F., Grenon, P., Smith, B.: In Varzi, A., Vieu, L., eds.:<br /> Formal Ontology in Information Systems (FOIS’04), Turin, Italy, IOS<br /> Press (2004) 49–59<br /> <br /> Available from: http://ontology.buffalo.edu/bfo/SQU.pdf<br /> <br /> This paper may be heavy-going for those without a background in logic,<br /> but I would still highly recommend the first couple of pages to<br /> everyone involved in this project.<br /> <br /> ===Stanford Encyclopedia of Philosophy===<br /> <br /> Entry on properties: http://plato.stanford.edu/entries/properties/<br /> <br /> I think properties here are used in the sense that Fabian Neuhaus and<br /> I would use &quot;quality&quot;, rather than in the looser sense that a CS or<br /> OWL person may use the term.<br /> <br /> Entry on determinate vs determinable: http://plato.stanford.edu/entries/determinate-determinables/<br /> <br /> I was hesitant about adding this one. Inquiring minds may want to<br /> check this out. Determinate vs determinable roughly corresponds to<br /> value vs attribute<br /> <br /> ==Data modeling==<br /> <br /> ===Basic properties for biological databases: character development and support===<br /> in Math. Comput. Modelling 25 (1997), 109-127.<br /> <br /> Required reading for everyone in the project. 1997, but it anticipated<br /> many of the problems we are facing. This has more of a systematics<br /> focus, but really the design of ontologies for phenotypic characters<br /> should be independent of whether we are applying this to genetic<br /> screens or to phylogenetic classisification.<br /> <br /> ===Papers by George===<br /> <br /> George gets his own section here. The GB is paper is a good<br /> introduction to the EAV model as it was originally formulated in 2003.<br /> <br /> Gkoutos GV, Green EC, Mallon AM, Hancock JM, Davidson D: Building<br /> mouse phenotype ontologies. Pac Symp Biocomput 2004:178-189.3.<br /> <br /> Gkoutos GV, Green EC, Mallon AM, Hancock JM, Davidson D: Using<br /> ontologies to describe mouse phenotypes. Genome Biol 2005, 6(1):R8.4.<br /> <br /> Gkoutos GV, Green EC, Greenaway S, Blake A, Mallon AM, Hancock JM:<br /> CRAVE: a database, middleware and visualization system for phenotype<br /> ontologies. Bioinformatics 2005, 21(7):1257-1262.<br /> <br /> [[User:Cjm|Cjm]] 12:03, 5 December 2005 (PST)</div>

Cjm2 https://www.bioontology.org//mediawiki/index.php?title=Phenotype_Reading_List&diff=1803 2005-12-07T00:19:26Z

<p>Cjm2: </p> <hr /> <div>=Phenotype readling list=<br /> <br /> I have some of these in my endnote library, but endnote is terrible<br /> for collecting non-bio references. I'm guessing the CS and logiv<br /> people use Latex? If so, if they post their bibtexes here I can<br /> compile both an endnote and a bibtex library.<br /> <br /> ==Intro to phenotypes for non-biologists==<br /> <br /> This list is very fly-centric. If someone can contribute zebrafish and<br /> human clinical genetics pointers that would be great. <br /> <br /> ===EBI Introduction to cell biologists===<br /> <br /> This is microarray centric (we'll need to turn our attention to this technology at some point), but still v useful for the non-biologist<br /> <br /> http://www.ebi.ac.uk/microarray/biology_intro.html<br /> <br /> ===Drysdale R: Phenotypic data in FlyBase=== <br /> Brief Bioinform 2001,2(1):68-80.<br /> <br /> This is an ideal intro for folks familiar with biological databases<br /> looking to make the first step into genetics and phenotypes.<br /> <br /> ===Essential Developmental Biology===<br /> by J. M. W. Slack<br /> <br /> http://books.google.com/books?ie=UTF-8&amp;hl=en&amp;id=BXfdbKLTiZQC&amp;dq=essential+developmental+biology&amp;prev=http://books.google.com/books%3Flr%3D%26client%3Dfirefox-a%26q%3Dessential%2Bdevelopmental%2Bbiology&amp;lpg=PP5&amp;pg=PP5&amp;printsec=4&amp;sig=FIivE3wd7u_AC9ojAEdW-BpD90A<br /> <br /> I found this to be a really useful and accessible introduction to<br /> developmental biology. Remember, most of the phenotypes we're dealing<br /> with will be developmental. It may be challenging for those with<br /> virtually no biology, but I'd still highly recommend it. Covers fly,<br /> zebrafish and other major model organisms.<br /> <br /> ===Other books===<br /> <br /> Alberts, B. , Bray, D. , Lewis J. , Raff, M., Roberts, K., Watson, J.D.: Molecular biology of the cell. New York, Garland Publishing, 1994<br /> <br /> Lewin B: Genes VII, New York, Oxford University Press, 2000<br /> <br /> <br /> ===THE ART AND DESIGN OF GENETIC SCREENS===<br /> <br /> This is actually a whole collection of reviews in Nature Reviews<br /> Genetics coverisg zebrafish, mouse, etc. Go to their website and<br /> search on the above:<br /> <br /> http://search.nature.com/search/?sp_a=sp1001702d&amp;sp_sfvl_field=subject%7Cujournal&amp;sp_t=results&amp;sp_q_1=Nature+Reviews+Genetics&amp;sp_x_1=ujournal&amp;sp_p_1=phrase&amp;go.x=0&amp;go.y=0&amp;sp-q=the+art+and+design+of+genetic+screens<br /> <br /> Here's the one on zebrafish<br /> http://www.nature.com/nrg/journal/v2/n12/abs/nrg1201-956a_fs.html;jsessionid=C33F00DB1D1DF6C5E26BCD324FFE25B4<br /> <br /> These are highly recommended for the tools developers<br /> <br /> ===The Making of a Fly: The Genetics of Animal Design [BOOK]===<br /> <br /> http://www.amazon.com/gp/product/0632030488/103-3091658-4208606?v=glance&amp;n=283155<br /> <br /> May be hard going for those without any knowledge of genetics<br /> <br /> ===Drosophila: A Laboratory Handbook, Michael Ashburner [BOOK]===<br /> aka the grey book<br /> http://www.cshlpress.com/default.tpl?action=full&amp;cart=1133810703113928&amp;--eqskudatarq=467&amp;newtitle=Drosophila%3A%20A%20Laboratory%20Handbook%2C%20Second%20Edition<br /> <br /> Everything you ever wanted to know about Drosophila genetics but were<br /> afraid to ask Michael. This may be a little overwhelming for the CS<br /> folks<br /> <br /> ==Formal ontology and logic==<br /> <br /> References on formal ontology and logic and qualities that are tied to<br /> qualities<br /> <br /> ===A formal theory of substances, qualities, and universals.===<br /> <br /> Neuhaus, F., Grenon, P., Smith, B.: In Varzi, A., Vieu, L., eds.:<br /> Formal Ontology in Information Systems (FOIS’04), Turin, Italy, IOS<br /> Press (2004) 49–59<br /> <br /> Available from: http://ontology.buffalo.edu/bfo/SQU.pdf<br /> <br /> This paper may be heavy-going for those without a background in logic,<br /> but I would still highly recommend the first couple of pages to<br /> everyone involved in this project.<br /> <br /> ===Stanford Encyclopedia of Philosophy===<br /> <br /> Entry on properties: http://plato.stanford.edu/entries/properties/<br /> <br /> I think properties here are used in the sense that Fabian Neuhaus and<br /> I would use &quot;quality&quot;, rather than in the looser sense that a CS or<br /> OWL person may use the term.<br /> <br /> Entry on determinate vs determinable: http://plato.stanford.edu/entries/determinate-determinables/<br /> <br /> I was hesitant about adding this one. Inquiring minds may want to<br /> check this out. Determinate vs determinable roughly corresponds to<br /> value vs attribute<br /> <br /> ==Data modeling==<br /> <br /> ===Basic properties for biological databases: character development and support===<br /> in Math. Comput. Modelling 25 (1997), 109-127.<br /> <br /> Required reading for everyone in the project. 1997, but it anticipated<br /> many of the problems we are facing. This has more of a systematics<br /> focus, but really the design of ontologies for phenotypic characters<br /> should be independent of whether we are applying this to genetic<br /> screens or to phylogenetic classisification.<br /> <br /> ===Papers by George===<br /> <br /> George gets his own section here. The GB is paper is a good<br /> introduction to the EAV model as it was originally formulated in 2003.<br /> <br /> Gkoutos GV, Green EC, Mallon AM, Hancock JM, Davidson D: Building<br /> mouse phenotype ontologies. Pac Symp Biocomput 2004:178-189.3.<br /> <br /> Gkoutos GV, Green EC, Mallon AM, Hancock JM, Davidson D: Using<br /> ontologies to describe mouse phenotypes. Genome Biol 2005, 6(1):R8.4.<br /> <br /> Gkoutos GV, Green EC, Greenaway S, Blake A, Mallon AM, Hancock JM:<br /> CRAVE: a database, middleware and visualization system for phenotype<br /> ontologies. Bioinformatics 2005, 21(7):1257-1262.<br /> <br /> [[User:Cjm|Cjm]] 12:03, 5 December 2005 (PST)</div>

Cjm2 https://www.bioontology.org//mediawiki/index.php?title=BioPortal_FAQ&diff=1777 2005-12-06T01:17:51Z

<p>Cjm2: </p> <hr /> <div>Frequently Asked Questions within cBio<br /> <br /> =General=<br /> <br /> ==cBio==<br /> <br /> ===What is cBio===<br /> <br /> ===What does cBio stand for?===<br /> <br /> ==OBO==<br /> <br /> ===What is OBO?===<br /> <br /> ===Where are the ontologies?===<br /> <br /> Currently on http://obo.sourceforge.net<br /> <br /> Soon to be moving to the cBio 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 cBio 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 Gold standard?===<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 /> <br /> The 1.2 spec is in preparation, and will be released to coincide with the first production OBO-Edit release before the end of 2005<br /> <br /> ===What tools support Obo-Format?===<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 /> ; Blip<br /> <br /> The following tools have limited support:<br /> <br /> * Protege (only for 1.0 - even then, may be problematic?). Requires OBO plugin.<br /> <br /> Note that you can load OWL files into Protege-OWL; see below<br /> <br /> ===Why not an XML format?===<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 /> ===Can I convert Obo-format to OWL?===<br /> <br /> Yes! See <br /> <br /> http://www.godatabase.org/dev/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>

Cjm2 https://www.bioontology.org//mediawiki/index.php?title=BioPortal_FAQ&diff=1776 2005-12-06T01:16:09Z

<p>Cjm2: </p> <hr /> <div>Frequently Asked Questions within cBio<br /> <br /> =General=<br /> <br /> ==cBio==<br /> <br /> ===What is cBio===<br /> <br /> ===What does cBio stand for?===<br /> <br /> ==OBO==<br /> <br /> ===What is OBO?===<br /> <br /> ===Where are the ontologies?===<br /> <br /> Currently on http://obo.sourceforge.net<br /> <br /> Soon to be moving to the cBio 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 cBio website<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 /> <br /> The 1.2 spec is in preparation, and will be released to coincide with the first production OBO-Edit release before the end of 2005<br /> <br /> ===What tools support Obo-Format?===<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 /> ; Blip<br /> <br /> The following tools have limited support:<br /> <br /> * Protege (only for 1.0 - even then, may be problematic?). Requires OBO plugin.<br /> <br /> Note that you can load OWL files into Protege-OWL; see below<br /> <br /> ===Why not an XML format?===<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 /> ===Can I convert Obo-format to OWL?===<br /> <br /> Yes! See <br /> <br /> http://www.godatabase.org/dev/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<br /> <br /> =Ontology Content=<br /> <br /> ==Building Ontologies==<br /> <br /> ==Submitting ontologies to OBO==</div>

Cjm2 https://www.bioontology.org//mediawiki/index.php?title=BioPortal_FAQ&diff=1775 2005-12-06T01:09:09Z

<p>Cjm2: </p> <hr /> <div>Frequently Asked Questions within cBio<br /> <br /> =General=<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 /> <br /> The 1.2 spec is in preparation, and will be released to coincide with the first production OBO-Edit release before the end of 2005<br /> <br /> ===What tools support Obo-Format?===<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 /> ; Blip<br /> <br /> The following tools have limited support:<br /> <br /> * Protege (only for 1.0 - even then, may be problematic?). Requires OBO plugin.<br /> <br /> Note that you can load OWL files into Protege-OWL; see below<br /> <br /> ===Why not an XML format?===<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 /> ===Can I convert Obo-format to OWL?===<br /> <br /> Yes! See <br /> <br /> http://www.godatabase.org/dev/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.</div>

Cjm2 https://www.bioontology.org//mediawiki/index.php?title=BioPortal_FAQ&diff=1774 2005-12-06T01:05:57Z

<p>Cjm2: </p> <hr /> <div>Frequently Asked Questions within cBio<br /> <br /> =General=<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 /> <br /> The 1.2 spec is in preparation, and will be released to coincide with the first production OBO-Edit release before the end of 2005<br /> <br /> ===What tools support Obo-Format?===<br /> <br /> * OBO-Edit (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 /> <br /> ; go-perl<br /> : http://search.cpan.org/~cmungall/go-perl<br /> <br /> * Blip<br /> <br /> The following tools have limited support:<br /> <br /> * Protege (only for 1.0 - even then, may be problematic?). Requires OBO plugin.<br /> <br /> Note that you can load OWL files into Protege-OWL; see below<br /> <br /> ===Why not an XML format?===<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 /> ===Can I convert Obo-format to OWL?===<br /> <br /> Yes! See <br /> <br /> http://www.godatabase.org/dev/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.</div>

Cjm2 https://www.bioontology.org//mediawiki/index.php?title=Main_Page&diff=1773 2005-12-06T00:44:33Z

<p>Cjm2: /* Developers Area */</p> <hr /> <div>Welcome to the cBiO WIKI!&lt;br&gt;<br /> <br /> <br /> === cBio Links ===<br /> *[http://www.bioontology.org/ cBio Home page]<br /> <br /> *[http://datebook.stanford.edu:88/cBiO_Calendar cBio calendar]<br /> <br /> *[[CBiO_Email_Lists]]<br /> <br /> === cBio Work Materials===<br /> <br /> *[[Teleconference Instructions]]<br /> <br /> *[[Meeting Agendas and Minutes]]<br /> <br /> *[[Meetings and Events]]<br /> <br /> *[[Action Items]]<br /> <br /> *[[Shared Materials]]<br /> <br /> *[[Possible Collaborations]]<br /> <br /> *[[Evaluation Activities]]<br /> <br /> === NCBC Links ===<br /> <br /> *[http://www.bisti.nih.gov/ncbc/ NCBC Home page]<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 /> === Developers Area ===<br /> *[[OBO Development]]<br /> *[[OBD Development]]<br /> *[[Phenotype Reading List]]<br /> *[[cBio FAQ]]<br /> <br /> <br /> <br /> <br /> <br /> Please see [http://meta.wikipedia.org/wiki/MediaWiki_i18n documentation on customizing the interface]<br /> and the [http://meta.wikipedia.org/wiki/MediaWiki_User%27s_Guide User's Guide] for usage and configuration help.</div>

Cjm2 https://www.bioontology.org//mediawiki/index.php?title=Phenotype_Reading_List&diff=1761 2005-12-05T20:03:09Z

<p>Cjm2: </p> <hr /> <div>=Phenotype readling list=<br /> <br /> I have some of these in my endnote library, but endnote is terrible<br /> for collecting non-bio references. I'm guessing the CS and logiv<br /> people use Latex? If so, if they post their bibtexes here I can<br /> compile both an endnote and a bibtex library.<br /> <br /> ==Intro to phenotypes for non-biologists==<br /> <br /> This list is very fly-centric. If someone can contribute zebrafish and<br /> human clinical genetics pointers that would be great. <br /> <br /> ===Drysdale R: Phenotypic data in FlyBase=== <br /> Brief Bioinform 2001,2(1):68-80.<br /> <br /> This is an ideal intro for folks familiar with biological databases<br /> looking to make the first step into genetics and phenotypes.<br /> <br /> ===Essential Developmental Biology===<br /> by J. M. W. Slack<br /> <br /> http://books.google.com/books?ie=UTF-8&amp;hl=en&amp;id=BXfdbKLTiZQC&amp;dq=essential+developmental+biology&amp;prev=http://books.google.com/books%3Flr%3D%26client%3Dfirefox-a%26q%3Dessential%2Bdevelopmental%2Bbiology&amp;lpg=PP5&amp;pg=PP5&amp;printsec=4&amp;sig=FIivE3wd7u_AC9ojAEdW-BpD90A<br /> <br /> I found this to be a really useful and accessible introduction to<br /> developmental biology. Remember, most of the phenotypes we're dealing<br /> with will be developmental. It may be challenging for those with<br /> virtually no biology, but I'd still highly recommend it. Covers fly,<br /> zebrafish and other major model organisms.<br /> <br /> ===THE ART AND DESIGN OF GENETIC SCREENS===<br /> <br /> This is actually a whole collection of reviews in Nature Reviews<br /> Genetics coverisg zebrafish, mouse, etc. Go to their website and<br /> search on the above:<br /> <br /> http://search.nature.com/search/?sp_a=sp1001702d&amp;sp_sfvl_field=subject%7Cujournal&amp;sp_t=results&amp;sp_q_1=Nature+Reviews+Genetics&amp;sp_x_1=ujournal&amp;sp_p_1=phrase&amp;go.x=0&amp;go.y=0&amp;sp-q=the+art+and+design+of+genetic+screens<br /> <br /> Here's the one on zebrafish<br /> http://www.nature.com/nrg/journal/v2/n12/abs/nrg1201-956a_fs.html;jsessionid=C33F00DB1D1DF6C5E26BCD324FFE25B4<br /> <br /> These are highly recommended for the tools developers<br /> <br /> ===The Making of a Fly: The Genetics of Animal Design [BOOK]===<br /> <br /> http://www.amazon.com/gp/product/0632030488/103-3091658-4208606?v=glance&amp;n=283155<br /> <br /> May be hard going for those without any knowledge of genetics<br /> <br /> ===Drosophila: A Laboratory Handbook, Michael Ashburner [BOOK]===<br /> aka the grey book<br /> http://www.cshlpress.com/default.tpl?action=full&amp;cart=1133810703113928&amp;--eqskudatarq=467&amp;newtitle=Drosophila%3A%20A%20Laboratory%20Handbook%2C%20Second%20Edition<br /> <br /> Everything you ever wanted to know about Drosophila genetics but were<br /> afraid to ask Michael. This may be a little overwhelming for the CS<br /> folks<br /> <br /> ==Formal ontology and logic==<br /> <br /> References on formal ontology and logic and qualities that are tied to<br /> qualities<br /> <br /> ===A formal theory of substances, qualities, and universals.===<br /> <br /> Neuhaus, F., Grenon, P., Smith, B.: In Varzi, A., Vieu, L., eds.:<br /> Formal Ontology in Information Systems (FOIS’04), Turin, Italy, IOS<br /> Press (2004) 49–59<br /> <br /> Available from: http://ontology.buffalo.edu/bfo/SQU.pdf<br /> <br /> This paper may be heavy-going for those without a background in logic,<br /> but I would still highly recommend the first couple of pages to<br /> everyone involved in this project.<br /> <br /> ===Stanford Encyclopedia of Philosophy===<br /> <br /> Entry on properties: http://plato.stanford.edu/entries/properties/<br /> <br /> I think properties here are used in the sense that Fabian Neuhaus and<br /> I would use &quot;quality&quot;, rather than in the looser sense that a CS or<br /> OWL person may use the term.<br /> <br /> Entry on determinate vs determinable: http://plato.stanford.edu/entries/determinate-determinables/<br /> <br /> I was hesitant about adding this one. Inquiring minds may want to<br /> check this out. Determinate vs determinable roughly corresponds to<br /> value vs attribute<br /> <br /> ==Data modeling==<br /> <br /> ===Basic properties for biological databases: character development and support===<br /> in Math. Comput. Modelling 25 (1997), 109-127.<br /> <br /> Required reading for everyone in the project. 1997, but it anticipated<br /> many of the problems we are facing. This has more of a systematics<br /> focus, but really the design of ontologies for phenotypic characters<br /> should be independent of whether we are applying this to genetic<br /> screens or to phylogenetic classisification.<br /> <br /> ===Papers by George===<br /> <br /> George gets his own section here. The GB is paper is a good<br /> introduction to the EAV model as it was originally formulated in 2003.<br /> <br /> Gkoutos GV, Green EC, Mallon AM, Hancock JM, Davidson D: Building<br /> mouse phenotype ontologies. Pac Symp Biocomput 2004:178-189.3.<br /> <br /> Gkoutos GV, Green EC, Mallon AM, Hancock JM, Davidson D: Using<br /> ontologies to describe mouse phenotypes. Genome Biol 2005, 6(1):R8.4.<br /> <br /> Gkoutos GV, Green EC, Greenaway S, Blake A, Mallon AM, Hancock JM:<br /> CRAVE: a database, middleware and visualization system for phenotype<br /> ontologies. Bioinformatics 2005, 21(7):1257-1262.<br /> <br /> [[User:Cjm|Cjm]] 12:03, 5 December 2005 (PST)</div>

Cjm2 https://www.bioontology.org//mediawiki/index.php?title=Main_Page&diff=1760 2005-12-05T20:00:20Z

<p>Cjm2: /* Developers Area */</p> <hr /> <div>Welcome to the cBiO WIKI!&lt;br&gt;<br /> <br /> <br /> === cBio Links ===<br /> *[http://www.bioontology.org/ cBio Home page]<br /> <br /> *[http://datebook.stanford.edu:88/cBiO_Calendar cBio calendar]<br /> <br /> *[[CBiO_Email_Lists]]<br /> <br /> === cBio Work Materials===<br /> <br /> *[[Teleconference Instructions]]<br /> <br /> *[[Meeting Agendas and Minutes]]<br /> <br /> *[[Meetings and Events]]<br /> <br /> *[[Action Items]]<br /> <br /> *[[Shared Materials]]<br /> <br /> *[[Possible Collaborations]]<br /> <br /> *[[Evaluation Activities]]<br /> <br /> === NCBC Links ===<br /> <br /> *[http://www.bisti.nih.gov/ncbc/ NCBC Home page]<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 /> === Developers Area ===<br /> *[[OBO Development]]<br /> *[[OBD Development]]<br /> *[[Phenotype Reading List]]<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> Please see [http://meta.wikipedia.org/wiki/MediaWiki_i18n documentation on customizing the interface]<br /> and the [http://meta.wikipedia.org/wiki/MediaWiki_User%27s_Guide User's Guide] for usage and configuration help.</div>

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