NCBO Wiki - User contributions [en]

OboInOwl:Main Page

2008-02-15T21:52:53Z

Dilvan: /* OBO Converter Protege tab: */

=Mapping OBO to OWL=

This wiki is for discussing the mapping between Obo1.2 format and OWL. The [http://www.godatabase.org/dev/doc/mapping-obo-to-owl.html first version] of this mapping is at http://www.godatabase.org/dev/doc/mapping-obo-to-owl.html. We have finished work on a newer version of this mapping. This page provides a brief background for the effort and provides links to the relevant tools (plugins for OBOEdit and Protege) that implement the mapping.

The Gene Ontology and a significant number of biomedical ontologies are in the OBO-format. The OBO format, which originated along with the Gene Ontology, has evolved to support the needs of the biomedical ontologies that fall under the Open Biomedical Ontologies (OBO) umbrella. The OBO-format aims to have 1) human readability, 2) ease of parsing, 3) extensibility and 4) minimal redundancy. The OBO-format currently forms the backbone of most GO based annotation and data analysis tools.

In parallel with the developments in bio-ontologies, ontologies in general have become more prevalent in information technology; with the most visible push coming from the W3C in the form of the W3C recommendation of the Web Ontology Language (OWL) as an international standard for ontologies on the web. There has also been a corresponding increase in the number, diversity and quality of the tools available to construct, maintain and view ontologies in OWL.

As bio-ontologies become more popular and grow in size as well as complexity, they are becoming the focus of attention of the larger computer science research community. On one hand there is significant interest in using the life sciences domain as a “focus” for W3C semantic web activity. In this light, biological data annotated using OBO ontologies is a prime resource and there is great interest from the Semantic Web community to access the ontologies and the annotated data in OWL format. On the other hand, if bio-ontologies are to benefit from the rapid progress being made in computer science – especially the semantic web technologies – bio-ontologies need to interoperate with other ontologies which are in the OWL format. The relatively newer biomedical ontologies (such as BioPAX) are already in OWL. The NCI-thesaurus, being developed by the National Cancer Institute, is also in OWL.

As a result, there is a strong need to map the OBO-format to OWL and provide tools that enable the end user to perform the translation at the click of a button in a stable ontology editing environment without worrying about underlying formats.

=Mail Lists=

We have created the OBO to OWL mapping remaining faithful to the (declared) semantics of the OBO format. At places where we found the format to be vague, we have tightened the semantics and have update the documentation accordingly. We make the mapping tools available for other researchers to use and evaluate the mapping. Please feel free to contact us on these mailing lists if you find anything lacking, have suggestions or have any kind of feedback.

[https://lists.sourceforge.net/lists/listinfo/obo-format Obo Format List]

Also of interest: [https://lists.sourceforge.net/lists/listinfo/obo-crossproduct Obo Cross-Product List]

=The Mapping=

We have made the mapping available as an online Google spreadsheet. You can view the sheet at http://spreadsheets.google.com/ccc?key=pWN_4sBrd9l1Umn1LN8WuQQ. If you want edits rights (or already have them) to leave comments then use the following link http://spreadsheets.google.com/ccc?key=o06770842196506107736.4732937099693365844

=Tools for the mapping=

== Protege plugins ==

== OBO Converter Protege tab: ==

The OBO Converter is a Tab plugin for Protégé to convert OBO format files into OWL files and vice-versa (keeping in mind that OWL to OBO conversions can lose information if one encodes things in OWL that cannot be expressed in OBO). It is also developed in a manner such that it can also work as a standalone conversion program.

'''Tab User Guide'''

The OBO Converter Tab basically reads OBO files (OBO 1.0 and 1.2) into Protégé OWL projects and saves those projects back as OBO 1.0 files. The Tab has two main panels, one to read OBO files and one to write (save) them.

The save operation is straightforward as the user chooses the file name and the conversion is done. The read operation has the same functionality plus a set of options that can alter the way an OBO file is read (see figure).

[[Image:OBOConverter.jpg]]

Read Options:

'''1 Class name generation'''

A Combo box allows users to choose the way the OWL class names will be generated from the OBO format file Terms. There are 3 options:

* OBO id will generate the name from the OBO term id that is the option that generates the OWL id in the way described in the mapping.
* Class name will generate the name from the OBO term name, be careful as those names may not be unique. If the names are not unique, there will be a parser error.
* Class name + OBO id will generate the name from the combination of the OBO term name and id.

In all cases, characters other than letters (a-z, A-Z) or numbers will be converted to underscore characters (_). Ex: the OBO term name “nurse cell” will be converted to the OWL class name nurse_cell.

The default behavior of the Tab is to generate the OWL id in the way described in the mapping and uses the OBO id to generate class names. If the user wants to see the OBO name of the classes, instead of their meaningless ids, Protégé has an option to display the OWL class label as the class identifier. As OWL labels can have language identifiers (such as en for English), converted OBO ontologies can now have names in different languages all pointing to the same entities.

The other options are targeted to users that want to create their ontology using a specific OBO ontology as a start point, but need to name their entities in a different way. Those users are not interested in maintaining naming compatibility with OBO.

'''2 Exclusion of namespaces'''

In OBO format, it is possible to define more than one ontology in each file using the OBO namespace: tag (Note that OBO namespaces have no connection with OWL namespaces). For instance, the Gene Ontology is actually composed by three independent ontologies defined in the same file (gene_ontology.obo) using three different namespaces (''biological_process'', ''molecular_funtion'' and ''cellular_component''). When the OBO Converter Tab reads such file types, it collapses all ontologies in one and namespace information is stored as annotation, which may not be the intention of the user. The OBO Converter Tab has a panel where the user can specify which namespaces he does not want to be read from a file.

Example: In the gene_ontology.obo file, if the namespaces ''biological_process'' and ''molecular_function'' are selected (for not being read), only the ''cellular_component'' ontology will be read.

'''3 Default namespace URI'''

It is the author responsibility to set the default namespace URI for the OWL ontology. That information is not available in the OBO format file. The OBO Converter Tab has a panel where the author can enter this URI. If it does not enter one, whatever default URI Protégé is using becomes the default namespace URI for the OWL ontology.

Downloads:

[http://smi-protege.stanford.edu/svn/obo-converter/trunk/ Source code for OBO Converter Tab]
[http://stanford.edu/~dilvan/oboconverter.zip Binaries for OBO Converter Tab]
[http://protege.cim3.net/cgi-bin/wiki.pl?OBOConverter Page at Protege Site]

== OBO Explorer Protege tab: ==

The OWL format for OBO files uses anonymous nodes to represent definitions, synonyms, and DbxRefs, and the generic Protégé GUI components are not immediately suitable to display and edit them. The existing graphical components also do not allow the user to easily access or edit the lexical information associated with an OBO term. The OBO Explorer tab allows the user to do so in an interface that is similar to that of OBO-edit. This provides the user with the flexibility to edit these lexical features (such as synonyms and dbxrefs) in an intuitive manner.

[http://www.aiai.ed.ac.uk/project/cobra-ct/COBrA_downloads.htm OBO Explorer Tab]

[[Image:OBOExplorer.jpg]]

== OboEdit OWL plugin ==
We have also added the functionality to save an OBO format file as an OWL file from within OBOEdit. We have a development version of the OWL Export/Import plugin for OboEdit available. Just download the distribution file, unzip it and copy its content to <OboEdit>/extensions folder. Start OboEdit and you should find the option "OWL Adapter" for loading ontologies, File->Load Terms..., and for saving, File->Save as...

[http://smi-protege.stanford.edu/~nigam/OboEditPlugin.zip OboEdit OWL plugin].

If you have problems with big ontologies, try to increase the size of the memory available to OboEdit.

== obo2owl xslt ==

The oboxml_to_owl.xsl mapping now implements the OboInOwl mapping for obo-xml:

[http://geneontology.cvs.sourceforge.net/geneontology/go-dev/xml/xsl/oboxml_to_owl.xsl?view=log XSLT]

This will be bundled with [http://search.cpan.org/~cmungall/go-perl/ go-perl-0.07] and higher

Sample ontologies exported from obo to owl are available [http://www.berkeleybop.org/ontologies here]

== obo2owl and owl2obo using PERL ==

The '''onto-perl''' package implements the '''OboInOwl''' mapping. In order to run the PERL conversion scripts, first install the latest [http://search.cpan.org/~easr/ onto-perl] distribution like any other CPAN module (those modules deal with the '''OBO''' and '''OWL''' ontology parsing tasks among other things). Then, in order to convert from '''OBO to OWL''', execute the '''obo2owl.pl''' script by providing the '''input OBO''' file and, alternatively, specifying the '''output''' file location (by default the standard output) like in the following line:

<code>$./obo2owl.pl my_ontology.obo > my_ontology.owl</code>

This conversion script has been tested with some ontologies such as [http://www.cellcycleontology.org CCO] and [http://www.geneontology.org/ GO]. Moreover, the produced '''OWL''' files were successfully loaded into '''Protege'''. Besides, these OWL files were checked with [http://projects.semwebcentral.org/projects/vowlidator/ vowlidator] and [http://owl-eclipse.projects.semwebcentral.org/ SWeDE].

Finally, to convert back from '''OWL to OBO''', use the '''owl2obo.pl''' conversion script by providing the '''input OWL''' file. This script completes the conversion circuit ('''obo2owl <=> owl2obo'''):

<code>$./owl2obo.pl my_ontology.owl > my_ontology.obo</code>

'''N.B.:''' Input OBO files should follow the OBO spec [http://www.geneontology.org/GO.format.obo-1_0.shtml 1.0] or [http://www.geneontology.org/GO.format.obo-1_2.shtml 1.2]. Output OBO files follow the spec '''1.2'''.

[[Image:obo2owl.png|center]]

=URIs=

Added a separate page on mapping OBO IDs to URIs:

[[OboInOwl:URIs]]

=Overview of Other Mapping efforts=

We are aware that there are several other groups that have created an OBO to OWL mapping to address immediate needs of their research groups. We have compiled a summary of the various OBO to OWL conversion efforts that we are aware of. Email me (nigam .AT. stanford.edu) with additions/deletions as you come across them.

[http://spreadsheets.google.com/ccc?key=pWN_4sBrd9l1Umn1LN8WuQQ Spread sheet comparing the mappings]

See also: Christine Golbreich and Ian Horrocks, "The OBO to OWL mapping, GO to OWL 1.1!", OWLED 2007 [http://www.med.univ-rennes1.fr/lim/doc_175.pdf]

=Progress Notes=

I've overhauled the obo2owl mapping. I've pretty much followed Alan's
recommendations (I made a lot of purely internal changes to the xslt too though which should make it much clearer). Hope these work for you Stuart. Sorry about the churn
- but this will definitely be worth it in the end.

Example OWL file can be found here (also attached):

http://geneontology.cvs.sourceforge.net/*checkout*/geneontology/go-dev/xml/examples/gotest.owl

(note that this example includes a cross-product example)

The OWL is generated from either of the following:

http://geneontology.cvs.sourceforge.net/*checkout*/geneontology/go-dev/xml/examples/gotest.obo
http://geneontology.cvs.sourceforge.net/*checkout*/geneontology/go-dev/xml/examples/gotest.obo-xml

The XSL can be found here:

http://geneontology.cvs.sourceforge.net/*checkout*/geneontology/go-dev/xml/xsl/obo2owl.xsl
http://geneontology.cvs.sourceforge.net/*checkout*/geneontology/go-dev/xml/xsl/obo2owl_obo_in_owl_metamodel.xsl

The XSL actually serves as fairly reasonable documentation about what's going on - but we'll also come up with a friendlier description once it's finalised

You can convert the obo-xml directly with the xslt. If you want to
convert from obo you'll need the latest version of go-perl (from cvs)

Here are the changes and things still pending:

Adopted Alan Ruttenberg's metamodel changes (see obo-format list)

split into 2 separate xsl files

subset (ontology views) now more consistent with obo
* the oboInOwl class is SubsetDef
* this does not appear in the owl:Ontology section, it stands alone
(subsets can be used across ontologies)

namespace changes -
* the metamodel is now called oboInOwl
(the format is owned by GO, so this maps to a GO URI)
* the default ontology content namespace is now bioont
(the URI for this will be some bioontologies.org URI)
* slashes not hashes or underscores
- example: rdf:about="oboContent/GO/0000001"

fixed rdf:about/resource/ID issues
- ID is never used
- about and resource now used in correct places

CHECKED

- validates as DL in http://phoebus.cs.man.ac.uk:9999/OWL/Validator
- works in SWOOP
- works in Protege-OWL (but looks odd)

TODO

do we need an equivalentClass for intersectionOf?
SWOOP saves this without

decide on final URI scheme
- Can we make the URIs less verbose? Use entities - or is this frowned on?

new obo tags for obsoletion
handling obsoletes

decide on whether the oboInOwl metamodel should be exported as
part of the content export, or linked to separately;
and if linked to separately, do we need an owl:imports?

OboInOwl:Main Page

2008-02-15T21:51:47Z

Dilvan: /* OBO Converter Protege tab: */

=Mapping OBO to OWL=

This wiki is for discussing the mapping between Obo1.2 format and OWL. The [http://www.godatabase.org/dev/doc/mapping-obo-to-owl.html first version] of this mapping is at http://www.godatabase.org/dev/doc/mapping-obo-to-owl.html. We have finished work on a newer version of this mapping. This page provides a brief background for the effort and provides links to the relevant tools (plugins for OBOEdit and Protege) that implement the mapping.

The Gene Ontology and a significant number of biomedical ontologies are in the OBO-format. The OBO format, which originated along with the Gene Ontology, has evolved to support the needs of the biomedical ontologies that fall under the Open Biomedical Ontologies (OBO) umbrella. The OBO-format aims to have 1) human readability, 2) ease of parsing, 3) extensibility and 4) minimal redundancy. The OBO-format currently forms the backbone of most GO based annotation and data analysis tools.

In parallel with the developments in bio-ontologies, ontologies in general have become more prevalent in information technology; with the most visible push coming from the W3C in the form of the W3C recommendation of the Web Ontology Language (OWL) as an international standard for ontologies on the web. There has also been a corresponding increase in the number, diversity and quality of the tools available to construct, maintain and view ontologies in OWL.

As bio-ontologies become more popular and grow in size as well as complexity, they are becoming the focus of attention of the larger computer science research community. On one hand there is significant interest in using the life sciences domain as a “focus” for W3C semantic web activity. In this light, biological data annotated using OBO ontologies is a prime resource and there is great interest from the Semantic Web community to access the ontologies and the annotated data in OWL format. On the other hand, if bio-ontologies are to benefit from the rapid progress being made in computer science – especially the semantic web technologies – bio-ontologies need to interoperate with other ontologies which are in the OWL format. The relatively newer biomedical ontologies (such as BioPAX) are already in OWL. The NCI-thesaurus, being developed by the National Cancer Institute, is also in OWL.

As a result, there is a strong need to map the OBO-format to OWL and provide tools that enable the end user to perform the translation at the click of a button in a stable ontology editing environment without worrying about underlying formats.

=Mail Lists=

We have created the OBO to OWL mapping remaining faithful to the (declared) semantics of the OBO format. At places where we found the format to be vague, we have tightened the semantics and have update the documentation accordingly. We make the mapping tools available for other researchers to use and evaluate the mapping. Please feel free to contact us on these mailing lists if you find anything lacking, have suggestions or have any kind of feedback.

[https://lists.sourceforge.net/lists/listinfo/obo-format Obo Format List]

Also of interest: [https://lists.sourceforge.net/lists/listinfo/obo-crossproduct Obo Cross-Product List]

=The Mapping=

We have made the mapping available as an online Google spreadsheet. You can view the sheet at http://spreadsheets.google.com/ccc?key=pWN_4sBrd9l1Umn1LN8WuQQ. If you want edits rights (or already have them) to leave comments then use the following link http://spreadsheets.google.com/ccc?key=o06770842196506107736.4732937099693365844

=Tools for the mapping=

== Protege plugins ==

== OBO Converter Protege tab: ==

The OBO Converter is a Tab plugin for Protégé to convert OBO format files into OWL files and vice-versa (keeping in mind that OWL to OBO conversions can lose information if one encodes things in OWL that cannot be expressed in OBO). It is also developed in a manner such that it can also work as a standalone conversion program.

'''Tab User Guide'''

The OBO Converter Tab basically reads OBO files (OBO 1.0 and 1.2) into Protégé OWL projects and saves those projects back as OBO 1.0 files. The Tab has two main panels, one to read OBO files and one to write (save) them.

The save operation is straightforward as the user chooses the file name and the conversion is done. The read operation has the same functionality plus a set of options that can alter the way an OBO file is read (see figure).

[[Image:OBOConverter.jpg]]

Read Options:

'''1 Class name generation'''

A Combo box allows users to choose the way the OWL class names will be generated from the OBO format file Terms. There are 3 options:

* OBO id will generate the name from the OBO term id that is the option that generates the OWL id in the way described in the mapping.
* Class name will generate the name from the OBO term name, be careful as those names may not be unique. If the names are not unique, there will be a parser error.
* Class name + OBO id will generate the name from the combination of the OBO term name and id.

In all cases, characters other than letters (a-z, A-Z) or numbers will be converted to underscore characters (_). Ex: the OBO term name “nurse cell” will be converted to the OWL class name nurse_cell.

The default behavior of the Tab is to generate the OWL id in the way described in the mapping and uses the OBO id to generate class names. If the user wants to see the OBO name of the classes, instead of their meaningless ids, Protégé has an option to display the OWL class label as the class identifier. As OWL labels can have language identifiers (such as en for English), converted OBO ontologies can now have names in different languages all pointing to the same entities.

The other options are targeted to users that want to create their ontology using a specific OBO ontology as a start point, but need to name their entities in a different way. Those users are not interested in maintaining naming compatibility with OBO.

'''2 Exclusion of namespaces'''

In OBO format, it is possible to define more than one ontology in each file using the OBO namespace: tag (Note that OBO namespaces have no connection with OWL namespaces). For instance, the Gene Ontology is actually composed by three independent ontologies defined in the same file (gene_ontology.obo) using three different namespaces (''biological_process'', ''molecular_funtion'' and ''cellular_component''). When the OBO Converter Tab reads such file types, it collapses all ontologies in one and namespace information is stored as annotation, which may not be the intention of the user. The OBO Converter Tab has a panel where the user can specify which namespaces he does not want to be read from a file.

Example: In the gene_ontology.obo file, if the namespaces ''biological_process'' and ''molecular_function'' are selected (for not being read), only the ''cellular_component'' ontology will be read.

'''3 Default namespace URI'''

It is the author responsibility to set the default namespace URI for the OWL ontology. That information is not available in the OBO format file. The OBO Converter Tab has a panel where the author can enter this URI. If it does not enter one, whatever default URI Protégé is using becomes the default namespace URI for the OWL ontology.

Downloads:

[http://smi-protege.stanford.edu/svn/obo-converter/trunk/ Source code for OBO Converter Tab]
[http://smi-protege.stanford.edu/~dilvan/oboconverter.zip Binaries for OBO Converter Tab]
[http://protege.cim3.net/cgi-bin/wiki.pl?OBOConverter Page at Protege Site]

== OBO Explorer Protege tab: ==

The OWL format for OBO files uses anonymous nodes to represent definitions, synonyms, and DbxRefs, and the generic Protégé GUI components are not immediately suitable to display and edit them. The existing graphical components also do not allow the user to easily access or edit the lexical information associated with an OBO term. The OBO Explorer tab allows the user to do so in an interface that is similar to that of OBO-edit. This provides the user with the flexibility to edit these lexical features (such as synonyms and dbxrefs) in an intuitive manner.

[http://www.aiai.ed.ac.uk/project/cobra-ct/COBrA_downloads.htm OBO Explorer Tab]

[[Image:OBOExplorer.jpg]]

== OboEdit OWL plugin ==
We have also added the functionality to save an OBO format file as an OWL file from within OBOEdit. We have a development version of the OWL Export/Import plugin for OboEdit available. Just download the distribution file, unzip it and copy its content to <OboEdit>/extensions folder. Start OboEdit and you should find the option "OWL Adapter" for loading ontologies, File->Load Terms..., and for saving, File->Save as...

[http://smi-protege.stanford.edu/~nigam/OboEditPlugin.zip OboEdit OWL plugin].

If you have problems with big ontologies, try to increase the size of the memory available to OboEdit.

== obo2owl xslt ==

The oboxml_to_owl.xsl mapping now implements the OboInOwl mapping for obo-xml:

[http://geneontology.cvs.sourceforge.net/geneontology/go-dev/xml/xsl/oboxml_to_owl.xsl?view=log XSLT]

This will be bundled with [http://search.cpan.org/~cmungall/go-perl/ go-perl-0.07] and higher

Sample ontologies exported from obo to owl are available [http://www.berkeleybop.org/ontologies here]

== obo2owl and owl2obo using PERL ==

The '''onto-perl''' package implements the '''OboInOwl''' mapping. In order to run the PERL conversion scripts, first install the latest [http://search.cpan.org/~easr/ onto-perl] distribution like any other CPAN module (those modules deal with the '''OBO''' and '''OWL''' ontology parsing tasks among other things). Then, in order to convert from '''OBO to OWL''', execute the '''obo2owl.pl''' script by providing the '''input OBO''' file and, alternatively, specifying the '''output''' file location (by default the standard output) like in the following line:

<code>$./obo2owl.pl my_ontology.obo > my_ontology.owl</code>

This conversion script has been tested with some ontologies such as [http://www.cellcycleontology.org CCO] and [http://www.geneontology.org/ GO]. Moreover, the produced '''OWL''' files were successfully loaded into '''Protege'''. Besides, these OWL files were checked with [http://projects.semwebcentral.org/projects/vowlidator/ vowlidator] and [http://owl-eclipse.projects.semwebcentral.org/ SWeDE].

Finally, to convert back from '''OWL to OBO''', use the '''owl2obo.pl''' conversion script by providing the '''input OWL''' file. This script completes the conversion circuit ('''obo2owl <=> owl2obo'''):

<code>$./owl2obo.pl my_ontology.owl > my_ontology.obo</code>

'''N.B.:''' Input OBO files should follow the OBO spec [http://www.geneontology.org/GO.format.obo-1_0.shtml 1.0] or [http://www.geneontology.org/GO.format.obo-1_2.shtml 1.2]. Output OBO files follow the spec '''1.2'''.

[[Image:obo2owl.png|center]]

=URIs=

Added a separate page on mapping OBO IDs to URIs:

[[OboInOwl:URIs]]

=Overview of Other Mapping efforts=

We are aware that there are several other groups that have created an OBO to OWL mapping to address immediate needs of their research groups. We have compiled a summary of the various OBO to OWL conversion efforts that we are aware of. Email me (nigam .AT. stanford.edu) with additions/deletions as you come across them.

[http://spreadsheets.google.com/ccc?key=pWN_4sBrd9l1Umn1LN8WuQQ Spread sheet comparing the mappings]

See also: Christine Golbreich and Ian Horrocks, "The OBO to OWL mapping, GO to OWL 1.1!", OWLED 2007 [http://www.med.univ-rennes1.fr/lim/doc_175.pdf]

=Progress Notes=

I've overhauled the obo2owl mapping. I've pretty much followed Alan's
recommendations (I made a lot of purely internal changes to the xslt too though which should make it much clearer). Hope these work for you Stuart. Sorry about the churn
- but this will definitely be worth it in the end.

Example OWL file can be found here (also attached):

http://geneontology.cvs.sourceforge.net/*checkout*/geneontology/go-dev/xml/examples/gotest.owl

(note that this example includes a cross-product example)

The OWL is generated from either of the following:

http://geneontology.cvs.sourceforge.net/*checkout*/geneontology/go-dev/xml/examples/gotest.obo
http://geneontology.cvs.sourceforge.net/*checkout*/geneontology/go-dev/xml/examples/gotest.obo-xml

The XSL can be found here:

http://geneontology.cvs.sourceforge.net/*checkout*/geneontology/go-dev/xml/xsl/obo2owl.xsl
http://geneontology.cvs.sourceforge.net/*checkout*/geneontology/go-dev/xml/xsl/obo2owl_obo_in_owl_metamodel.xsl

The XSL actually serves as fairly reasonable documentation about what's going on - but we'll also come up with a friendlier description once it's finalised

You can convert the obo-xml directly with the xslt. If you want to
convert from obo you'll need the latest version of go-perl (from cvs)

Here are the changes and things still pending:

Adopted Alan Ruttenberg's metamodel changes (see obo-format list)

split into 2 separate xsl files

subset (ontology views) now more consistent with obo
* the oboInOwl class is SubsetDef
* this does not appear in the owl:Ontology section, it stands alone
(subsets can be used across ontologies)

namespace changes -
* the metamodel is now called oboInOwl
(the format is owned by GO, so this maps to a GO URI)
* the default ontology content namespace is now bioont
(the URI for this will be some bioontologies.org URI)
* slashes not hashes or underscores
- example: rdf:about="oboContent/GO/0000001"

fixed rdf:about/resource/ID issues
- ID is never used
- about and resource now used in correct places

CHECKED

- validates as DL in http://phoebus.cs.man.ac.uk:9999/OWL/Validator
- works in SWOOP
- works in Protege-OWL (but looks odd)

TODO

do we need an equivalentClass for intersectionOf?
SWOOP saves this without

decide on final URI scheme
- Can we make the URIs less verbose? Use entities - or is this frowned on?

new obo tags for obsoletion
handling obsoletes

decide on whether the oboInOwl metamodel should be exported as
part of the content export, or linked to separately;
and if linked to separately, do we need an owl:imports?

User:Dilvan

2007-04-04T00:20:26Z

Dilvan: /* BioAnnotation Tab for Protege */

Test page:

== OWL Export/Import plugin for OboEdit ==

That is the development version of the OWL Export/Import plugin for OboEdit . Just download the distribution file, unzip it and copy its content to <OboEdit>/extensions folder. Start OboEdit and you should find the option "OWL Adapter" for loading ontologies, File->Load Terms..., and for saving, File->Save as...

[http://smi-cbio01.stanford.edu/~nigam/OboEditPlugin.zip Download plugin (for OBOEdit 1.002)].

If you have problems with big ontologies, try to increase the size of the memory available to OboEdit.

== BioAnnotation Tab for Protege ==

That is the development version of the BioAnnotation Tab for Protege.
To install:

1- Download the distribution files for the OBO Converter Tab and BioAnnotation Tab from this page. If you have a different version of those plugins, uninstall them and use the ones from this page.

2- Unzip them in the Protege plugin directory (<Protege install directory>/plugins).

3- Create a Protege OWL project, and import the GO ontology in OWL (there is a copy in this page).

4- In the Protege menu, choose Project->Configure...->Annotation Tab.

5- In the Annotation Tab, you now can read GO Annotation Format files from the MODs (or other sources), using "Annotation Input File ..." and "Start!".

The NCBI taxonomy (used in the GO annotation) is not imported, just referenced (it is too big to import). So you will only see a reference to the species you are working with.

[[Media:Oboconverter.zip|Download OBO Converter plugin]]
[[Media:BioAnnotation.zip|Download BioAnnotation plugin]]
[[Media:Go_ontology.zip|Download GO Ontology in OWL]]

Please, keep in mind that this is a beta version of this tab. If you have problems with big files, try to increase the size of the memory available to Protege.

If you just want to see the GO Annotation files in OWL, download the ''Saccharomyces cerevisiae'' or the ''Homo sapiens'' GO Annotations in OWL. Both files import the GO ontology in OWL, so you have to have it in your disk. You can use your preferred OWL editor to read them:

[[Media:Yeast_annotations.zip|Download Yeast GO Annotations in OWL]]
[[Media:Human_annotations.zip|Download Human GO Annotations in OWL]]

If you use Protege, to see the annotations on restrictions (relationships), right click on them and choose "Edit Annotation Properties ...".

TIP: When using Protege to display any of the OWL files above, you have the option of showing the classes more meaningful labels in place of their rdf:ID names, just:

1- In menu OWL->Preferences... in the Visibility Tab choose owl:Class

2- In the Forms Tab select owl:Class and in the Form Editor choose Display Slot: rdfs:label

NOTE: In the AMIA-2007 paper referring to this Tab, there are links to the NCBI Entrez Gene site pointing out misinterpretations of the GO Annotation File Format. Since the submission of this paper, the authors contacted the NCBI and they recognized and corrected their mistake (at least on the Entrez Gene browser).

User:Dilvan

2007-04-04T00:19:59Z

Dilvan: /* BioAnnotation Tab for Protege */

Test page:

== OWL Export/Import plugin for OboEdit ==

That is the development version of the OWL Export/Import plugin for OboEdit . Just download the distribution file, unzip it and copy its content to <OboEdit>/extensions folder. Start OboEdit and you should find the option "OWL Adapter" for loading ontologies, File->Load Terms..., and for saving, File->Save as...

[http://smi-cbio01.stanford.edu/~nigam/OboEditPlugin.zip Download plugin (for OBOEdit 1.002)].

If you have problems with big ontologies, try to increase the size of the memory available to OboEdit.

== BioAnnotation Tab for Protege ==

That is the development version of the BioAnnotation Tab for Protege.
To install:

1- Download the distribution files for the OBO Converter Tab and BioAnnotation Tab from this page. If you have a different version of those plugins, uninstall them and use the ones from this page.

2- Unzip them in the Protege plugin directory (<Protege install directory>/plugins).

3- Create a Protege OWL project, and import the GO ontology in OWL (there is a copy in this page).

4- In the Protege menu, choose Project->Configure...->Annotation Tab.

5- In the Annotation Tab, you now can read GO Annotation Format files from the MODs (or other sources), using "Annotation Input File ..." and "Start!".

The NCBI taxonomy (used in the GO annotation) is not imported, just referenced (it is too big to import). So you will only see a reference to the species you are working with.

[[Media:Oboconverter.zip|Download OBO Converter plugin]]
[[Media:BioAnnotation.zip|Download BioAnnotation plugin]]
[[Media:Go_ontology.zip|Download GO Ontology in OWL]]

Please, keep in mind that this is a beta version of this tab. If you have problems with big files, try to increase the size of the memory available to Protege.

If you just want to see the GO Annotation files in OWL, download the ''Saccharomyces cerevisiae'' or the ''Homo sapiens'' GO Annotations in OWL. Both files import the GO ontology in OWL, so you have to have it in your disk. You can use your preferred OWL editor to read them:

[[Media:Yeast_annotations.zip|Download Yeast GO Annotations in OWL]]
[[Media:Human_annotations.zip|Download Human GO Annotations in OWL]]

If you use Protege, to see the annotations on restrictions (relationships), right click on them and choose "Edit Annotation Properties ...".

TIP: When using Protege to display any of the OWL files above, you have the option of showing the classes more meaningful labels in place of their rdf:ID names, just:
1- In menu OWL->Preferences... in the Visibility Tab choose owl:Class
2- In the Forms Tab select owl:Class and in the Form Editor choose Display Slot: rdfs:label

NOTE: In the AMIA-2007 paper referring to this Tab, there are links to the NCBI Entrez Gene site pointing out misinterpretations of the GO Annotation File Format. Since the submission of this paper, the authors contacted the NCBI and they recognized and corrected their mistake (at least on the Entrez Gene browser).

User:Dilvan

2007-03-27T21:15:51Z

Dilvan: /* BioAnnotation Tab for Protege */

Test page:

== OWL Export/Import plugin for OboEdit ==

That is the development version of the OWL Export/Import plugin for OboEdit . Just download the distribution file, unzip it and copy its content to <OboEdit>/extensions folder. Start OboEdit and you should find the option "OWL Adapter" for loading ontologies, File->Load Terms..., and for saving, File->Save as...

[http://smi-cbio01.stanford.edu/~nigam/OboEditPlugin.zip Download plugin (for OBOEdit 1.002)].

If you have problems with big ontologies, try to increase the size of the memory available to OboEdit.

== BioAnnotation Tab for Protege ==

That is the development version of the BioAnnotation Tab for Protege.
To install:

1- Download the distribution files for the OBO Converter Tab and BioAnnotation Tab from this page. If you have a different version of those plugins, uninstall them and use the ones from this page.

2- Unzip them in the Protege plugin directory (<Protege install directory>/plugins).

3- Create a Protege OWL project, and import the GO ontology in OWL (there is a copy in this page).

4- In the Protege menu, choose Project->Configure...->Annotation Tab.

5- In the Annotation Tab, you now can read GO Annotation Format files from the MODs (or other sources), using "Annotation Input File ..." and "Start!".

The NCBI taxonomy (used in the GO annotation) is not imported, just referenced (it is too big to import). So you will only see a reference to the species you are working with.

[[Media:Oboconverter.zip|Download OBO Converter plugin]]
[[Media:BioAnnotation.zip|Download BioAnnotation plugin]]
[[Media:Go_ontology.zip|Download GO Ontology in OWL]]

Please, keep in mind that this is a beta version of this tab. If you have problems with big files, try to increase the size of the memory available to Protege.

If you just want to see the GO Annotation files in OWL, download the ''Saccharomyces cerevisiae'' or the ''Homo sapiens'' GO Annotations in OWL. Both files import the GO ontology in OWL, so you have to have it in your disk. You can use your preferred OWL editor to read them:

[[Media:Yeast_annotations.zip|Download Yeast GO Annotations in OWL]]
[[Media:Human_annotations.zip|Download Human GO Annotations in OWL]]

If you use Protege, to see the annotations on restrictions (relationships), right click on them and choose "Edit Annotation Properties ...".

NOTE: In the AMIA-2007 paper referring to this Tab, there are links to the NCBI Entrez Gene site pointing out misinterpretations of the GO Annotation File Format. Since the submission of this paper, the authors contacted the NCBI and they recognized and corrected their mistake (at least on the Entrez Gene browser).

User:Dilvan

2007-03-27T18:23:50Z

Dilvan: /* BioAnnotation Tab for Protege */

Test page:

== OWL Export/Import plugin for OboEdit ==

That is the development version of the OWL Export/Import plugin for OboEdit . Just download the distribution file, unzip it and copy its content to <OboEdit>/extensions folder. Start OboEdit and you should find the option "OWL Adapter" for loading ontologies, File->Load Terms..., and for saving, File->Save as...

[http://smi-cbio01.stanford.edu/~nigam/OboEditPlugin.zip Download plugin (for OBOEdit 1.002)].

If you have problems with big ontologies, try to increase the size of the memory available to OboEdit.

== BioAnnotation Tab for Protege ==

That is the development version of the BioAnnotation Tab for Protege.
To install:

1- Download the distribution files for the OBO Converter Tab and BioAnnotation Tab from this page. If you have a different version of those plugins, uninstall them and use the ones from this page.

2- Unzip them in the Protege plugin directory (<Protege install directory>/plugins).

3- Create a Protege OWL project, and import the GO ontology in OWL (there is a copy in this page).

4- In the Protege menu, choose Project->Configure...->Annotation Tab.

5- In the Annotation Tab, you now can read GO Annotation Format files from the MODs (or other sources), using "Annotation Input File ..." and "Start!".

The NCBI taxonomy (used in the GO annotation) is not imported, just referenced (it is too big to import). So you will only see a reference to the species you are working with.

[[Media:Oboconverter.zip|Download OBO Converter plugin]]
[[Media:BioAnnotation.zip|Download BioAnnotation plugin]]
[[Media:Go_ontology.zip|Download GO Ontology in OWL]]

Please, keep in mind that this is a beta version of this tab. If you have problems with big files, try to increase the size of the memory available to Protege.

If you just want to see the GO Annotation files in OWL, download the ''Saccharomyces cerevisiae'' or the ''Homo sapiens'' GO Annotations in OWL. Both files import the GO ontology in OWL, so you have to have it in your disk. You can use your preferred OWL editor to read them:

[[Media:Yeast_annotations.zip|Download Yeast GO Annotations in OWL]]
[[Media:Human_annotations.zip|Download Human GO Annotations in OWL]]

If you use Protege, to see the annotations on restrictions (relationships), right click on them and choose "Edit Annotation Properties ...".

NOTE: In the AMIA-2007 paper referring to this Tab, there are links to the NCBI Entrez Gene site pointing out misinterpretations of the GO Annotation File Format. Since the submission of this paper, the authors contacted the NCBI and they recognized and corrected their mistake.

User:Dilvan

2007-03-27T18:06:44Z

Dilvan: /* BioAnnotation Tab for Protege */

Test page:

== OWL Export/Import plugin for OboEdit ==

That is the development version of the OWL Export/Import plugin for OboEdit . Just download the distribution file, unzip it and copy its content to <OboEdit>/extensions folder. Start OboEdit and you should find the option "OWL Adapter" for loading ontologies, File->Load Terms..., and for saving, File->Save as...

[http://smi-cbio01.stanford.edu/~nigam/OboEditPlugin.zip Download plugin (for OBOEdit 1.002)].

If you have problems with big ontologies, try to increase the size of the memory available to OboEdit.

== BioAnnotation Tab for Protege ==

That is the development version of the BioAnnotation Tab for Protege.
To install:

1- Download the distribution files for the OBO Converter Tab and BioAnnotation Tab from this page. If you have a different version of those plugins, uninstall them and use the ones from this page.

2- Unzip them in the Protege plugin directory (<Protege install directory>/plugins).

3- Create a Protege OWL project, and import the GO ontology in OWL (there is a copy in this page).

4- In the BioAnnotation Tab read a GO Annotation Format file from one of the MODs.

The NCBI taxonomy is not imported, just referenced (it is too big to import). So you will only see a reference to the species you are working with.

[[Media:Oboconverter.zip|Download OBO Converter plugin]]
[[Media:BioAnnotation.zip|Download BioAnnotation plugin]]
[[Media:Go_ontology.zip|Download GO Ontology in OWL]]

Please, keep in mind that this is a beta version of this tab. If you have problems with big files, try to increase the size of the memory available to Protege.

If you just want to see the GO Annotation files in OWL, download the ''Saccharomyces cerevisiae'' or the ''Homo sapiens'' GO Annotations in OWL. Both files import the GO ontology in OWL, so you have to have it in your disk. You can use your preferred OWL editor to read them:

[[Media:Yeast_annotations.zip|Download Yeast GO Annotations in OWL]]
[[Media:Human_annotations.zip|Download Human GO Annotations in OWL]]

If you use Protege, to see the annotations on restrictions (relationships), right click on them and choose "Edit Annotation Properties ...".

NOTE: In the AMIA-2007 paper referring to this Tab, there are links to the NCBI Entrez Gene site pointing out misinterpretations of the GO Annotation File Format. Since the submission of this paper, the authors contacted the NCBI and they recognized and corrected their mistake.

User:Dilvan

2007-03-27T17:37:05Z

Dilvan: /* BioAnnotation Tab for Protege */

Test page:

== OWL Export/Import plugin for OboEdit ==

That is the development version of the OWL Export/Import plugin for OboEdit . Just download the distribution file, unzip it and copy its content to <OboEdit>/extensions folder. Start OboEdit and you should find the option "OWL Adapter" for loading ontologies, File->Load Terms..., and for saving, File->Save as...

[http://smi-cbio01.stanford.edu/~nigam/OboEditPlugin.zip Download plugin (for OBOEdit 1.002)].

If you have problems with big ontologies, try to increase the size of the memory available to OboEdit.

== BioAnnotation Tab for Protege ==

That is the development version of the BioAnnotation Tab for Protege.
To install:

1- Download the distribution files for the OBO Converter Tab and BioAnnotation Tab from this page. If you have a different version of those plugins, uninstall them and use the ones from this page.

2- Unzip them in the Protege plugin directory (<Protege install directory>/plugins).

3- Create a Protege OWL project, and import the GO ontology in OWL (there is a copy in this page).

4- In the BioAnnotation Tab read a GO Annotation Format file from one of the MODs.

The NCBI taxonomy is not imported, just referenced (it is too big to import). So you will only see a reference to the species you are working with.

[[Media:Oboconverter.zip|Download OBO Converter plugin]]
[[Media:BioAnnotation.zip|Download BioAnnotation plugin]]
[[Media:Go_ontology.zip|Download GO Ontology in OWL]]

Please, keep in mind that this is a beta version of this tab. If you have problems with big files, try to increase the size of the memory available to Protege.

If you just want to see the GO Annotation files in OWL, download the ''Saccharomyces cerevisiae'' or the ''Homo sapiens'' GO Annotations in OWL. Both files import the GO ontology in OWL, so you have to have it in your disk. You can use your preferred OWL editor to read them:

[[Media:Yeast_annotations.zip|Download Yeast GO Annotations in OWL]]
[[Media:Human_annotations.zip|Download Human GO Annotations in OWL]]

NOTE: In the AMIA-2007 paper referring to this Tab, there are links to the NCBI Entrez Gene site pointing out misinterpretations of the GO Annotation File Format. Since the submission of this paper, the authors contacted the NCBI and they recognized and corrected their mistake.

User:Dilvan

2007-03-27T17:35:05Z

Dilvan: /* BioAnnotation Tab for Protege */

Test page:

== OWL Export/Import plugin for OboEdit ==

That is the development version of the OWL Export/Import plugin for OboEdit . Just download the distribution file, unzip it and copy its content to <OboEdit>/extensions folder. Start OboEdit and you should find the option "OWL Adapter" for loading ontologies, File->Load Terms..., and for saving, File->Save as...

[http://smi-cbio01.stanford.edu/~nigam/OboEditPlugin.zip Download plugin (for OBOEdit 1.002)].

If you have problems with big ontologies, try to increase the size of the memory available to OboEdit.

== BioAnnotation Tab for Protege ==

That is the development version of the BioAnnotation Tab for Protege.
To install:

1- Download the distribution files for the OBO Converter Tab and BioAnnotation Tab from this page. If you have a different version of those plugins, uninstall them and use the ones from this page.

2- Unzip them in the Protege plugin directory (<Protege install directory>/plugins).

3- Create a Protege OWL project, and import the GO ontology in OWL (there is a copy in this page).

4- In the BioAnnotation Tab read a GO Annotation Format file from one of the MODs.

The NCBI taxonomy is not imported, just referenced (it is too big to import). So you will only see a reference to the species you are working with.

[[Media:Oboconverter.zip|Download OBO Converter plugin]]
[[Media:BioAnnotation.zip|Download BioAnnotation plugin]]
[[Media:Go_ontology.zip|Download GO Ontology in OWL]]

Please, keep in mind that this is a beta version of this tab. If you have problems with big files, try to increase the size of the memory available to Protege.

If you just want to see the GO Annotation files in OWL, download the ''Saccharomyces cerevisiae'' or the ''Homo sapiens'' GO Annotations in OWL. Both files import the GO ontology in OWL, so you have to have it in your disk. You can use your preferred OWL editor to read them:

[[Media:Yeast_annotations.zip|Download Yeast GO Annotations in OWL]]
[[Media:Human_annotations.zip|Download Human GO Annotations in OWL]]

NOTE: In the Amia paper referring to this Tab, there are links to the NCBI Entrez Gene site pointing out misinterpretations of the GO Annotation File Format. Since the submission of this paper, the authors contacted the NCBI and they recognized and corrected their mistake.

User:Dilvan

2007-03-27T17:27:24Z

Dilvan: /* BioAnnotation Tab for Protege */

Test page:

== OWL Export/Import plugin for OboEdit ==

That is the development version of the OWL Export/Import plugin for OboEdit . Just download the distribution file, unzip it and copy its content to <OboEdit>/extensions folder. Start OboEdit and you should find the option "OWL Adapter" for loading ontologies, File->Load Terms..., and for saving, File->Save as...

[http://smi-cbio01.stanford.edu/~nigam/OboEditPlugin.zip Download plugin (for OBOEdit 1.002)].

If you have problems with big ontologies, try to increase the size of the memory available to OboEdit.

== BioAnnotation Tab for Protege ==

That is the development version of the BioAnnotation Tab for Protege.
To install:

1- Download the distribution files for the OBO Converter Tab and BioAnnotation Tab from this page. If you have a different version of those plugins, uninstall them and use the ones from this page.

2- Unzip them in the Protege plugin directory (<Protege install directory>/plugins).

3- Create a Protege OWL project, and import the GO ontology in OWL (there is a copy in this page).

4- In the BioAnnotation Tab read a GO Annotation Format file from one of the MODs.

The NCBI taxonomy is not imported, just referenced (it is too big to import). So you will only see a reference to the species you are working with.

[[Media:Oboconverter.zip|Download OBO Converter plugin]]
[[Media:BioAnnotation.zip|Download BioAnnotation plugin]]
[[Media:Go_ontology.zip|Download GO Ontology in OWL]]

Please, keep in mind that this is a beta version of this tab. If you have problems with big files, try to increase the size of the memory available to Protege.

If you just want to see the GO Annotation files in OWL, download the ''Saccharomyces cerevisiae'' or the ''Homo sapiens'' GO Annotations in OWL. Both files import the GO ontology in OWL, so you have to have it in your disk. You can use your prefered OWL editor to read them:

[[Media:Yeast_annotations.zip|Download Yeast GO Annotations in OWL]]
[[Media:Human_annotations.zip|Download Human GO Annotations in OWL]]

NOTE: In the Amia paper refering to this Tab, there are links to the NCBI Entrez Gene site pointing out misinterpretations of the GO Annotation File Format. Since the submission of this paper, the authors contacted the NCBI and they corrected their mistake.

User:Dilvan

2007-03-27T17:26:38Z

Dilvan: /* BioAnnotation Tab for Protege */

Test page:

== OWL Export/Import plugin for OboEdit ==

That is the development version of the OWL Export/Import plugin for OboEdit . Just download the distribution file, unzip it and copy its content to <OboEdit>/extensions folder. Start OboEdit and you should find the option "OWL Adapter" for loading ontologies, File->Load Terms..., and for saving, File->Save as...

[http://smi-cbio01.stanford.edu/~nigam/OboEditPlugin.zip Download plugin (for OBOEdit 1.002)].

If you have problems with big ontologies, try to increase the size of the memory available to OboEdit.

== BioAnnotation Tab for Protege ==

That is the development version of the BioAnnotation Tab for Protege.
To install:

1- Download the distribution files for the OBO Converter Tab and BioAnnotation Tab from this page. If you have a different version of those plugins, uninstall them and use the ones from this page.

2- Unzip them in the Protege plugin directory (<Protege install directory>/plugins).

3- Create a Protege OWL project, and import the GO ontology in OWL (there is a copy in this page).

4- In the BioAnnotation Tab read a GO Annotation Format file from one of the MODs.

The NCBI taxonomy is not imported, just referenced (it is too big to import). So you will only see a reference to the species you are working with.

[[Media:Oboconverter.zip | Download OBO Converter plugin]].
[[Media:BioAnnotation.zip | Download BioAnnotation plugin]].
[[Media:Go_ontology.zip | Download GO Ontology in OWL]].

Please, keep in mind that this is a beta version of this tab. If you have problems with big files, try to increase the size of the memory available to Protege.

If you just want to see the GO Annotation files in OWL, download the ''Saccharomyces cerevisiae'' or the ''Homo sapiens'' GO Annotations in OWL. Both files import the GO ontology in OWL, so you have to have it in your disk. You can use your prefered OWL editor to read them:

[[Media:Yeast_annotations.zip | Download Yeast GO Annotations in OWL]].
[[Media:Human_annotations.zip | Download Human GO Annotations in OWL]].

NOTE: In the Amia paper refering to this Tab, there are links to the NCBI Entrez Gene site pointing out misinterpretations of the GO Annotation File Format. Since the submission of this paper, the authors contacted the NCBI and they corrected their mistake.

User:Dilvan

2007-03-27T17:26:11Z

Dilvan: /* BioAnnotation Tab for Protege */

Test page:

== OWL Export/Import plugin for OboEdit ==

That is the development version of the OWL Export/Import plugin for OboEdit . Just download the distribution file, unzip it and copy its content to <OboEdit>/extensions folder. Start OboEdit and you should find the option "OWL Adapter" for loading ontologies, File->Load Terms..., and for saving, File->Save as...

[http://smi-cbio01.stanford.edu/~nigam/OboEditPlugin.zip Download plugin (for OBOEdit 1.002)].

If you have problems with big ontologies, try to increase the size of the memory available to OboEdit.

== BioAnnotation Tab for Protege ==

That is the development version of the BioAnnotation Tab for Protege.
To install:

1- Download the distribution files for the OBO Converter Tab and BioAnnotation Tab from this page. If you have a different version of those plugins, uninstall them and use the ones from this page.

2- Unzip them in the Protege plugin directory (<Protege install directory>/plugins).

3- Create a Protege OWL project, and import the GO ontology in OWL (there is a copy in this page).

4- In the BioAnnotation Tab read a GO Annotation Format file from one of the MODs.

The NCBI taxonomy is not imported, just referenced (it is too big to import). So you will only see a reference to the species you are working with.

[[Media:Oboconverter.zip | Download OBO Converter plugin]].
[[Media:BioAnnotation.zip | Download BioAnnotation plugin].
[[Media:Go_ontology.zip | Download GO Ontology in OWL].

Please, keep in mind that this is a beta version of this tab. If you have problems with big files, try to increase the size of the memory available to Protege.

If you just want to see the GO Annotation files in OWL, download the ''Saccharomyces cerevisiae'' or the ''Homo sapiens'' GO Annotations in OWL. Both files import the GO ontology in OWL, so you have to have it in your disk. You can use your prefered OWL editor to read them:

[[Media:Yeast_annotations.zip | Download Yeast GO Annotations in OWL].
[[Media:Human_annotations.zip | Download Human GO Annotations in OWL].

NOTE: In the Amia paper refering to this Tab, there are links to the NCBI Entrez Gene site pointing out misinterpretations of the GO Annotation File Format. Since the submission of this paper, the authors contacted the NCBI and they corrected their mistake.

User:Dilvan

2007-03-27T17:24:39Z

Dilvan: /* BioAnnotation Tab for Protege */

Test page:

== OWL Export/Import plugin for OboEdit ==

That is the development version of the OWL Export/Import plugin for OboEdit . Just download the distribution file, unzip it and copy its content to <OboEdit>/extensions folder. Start OboEdit and you should find the option "OWL Adapter" for loading ontologies, File->Load Terms..., and for saving, File->Save as...

[http://smi-cbio01.stanford.edu/~nigam/OboEditPlugin.zip Download plugin (for OBOEdit 1.002)].

If you have problems with big ontologies, try to increase the size of the memory available to OboEdit.

== BioAnnotation Tab for Protege ==

That is the development version of the BioAnnotation Tab for Protege.
To install:

1- Download the distribution files for the OBO Converter Tab and BioAnnotation Tab from this page. If you have a different version of those plugins, uninstall them and use the ones from this page.

2- Unzip them in the Protege plugin directory (<Protege install directory>/plugins).

3- Create a Protege OWL project, and import the GO ontology in OWL (there is a copy in this page).

4- In the BioAnnotation Tab read a GO Annotation Format file from one of the MODs.

The NCBI taxonomy is not imported, just referenced (it is too big to import). So you will only see a reference to the species you are working with.

[[Media:Oboconverter.zip | Download OBO Converter plugin]].
[http://www.bioontology.org/wiki/index.php/Image:BioAnnotation.zip Download BioAnnotation plugin].
[http://www.bioontology.org/wiki/index.php/Image:Go_ontology.zip Download GO Ontology in OWL].

Please, keep in mind that this is a beta version of this tab. If you have problems with big files, try to increase the size of the memory available to Protege.

If you just want to see the GO Annotation files in OWL, download the ''Saccharomyces cerevisiae'' or the ''Homo sapiens'' GO Annotations in OWL. Both files import the GO ontology in OWL, so you have to have it in your disk. You can use your prefered OWL editor to read them:

[http://www.bioontology.org/wiki/index.php/Image:Yeast_annotations.zip Download Yeast GO Annotations in OWL].
[http://www.bioontology.org/wiki/index.php/Image:Human_annotations.zip Download Human GO Annotations in OWL].

NOTE: In the Amia paper refering to this Tab, there are links to the NCBI Entrez Gene site pointing out misinterpretations of the GO Annotation File Format. Since the submission of this paper, the authors contacted the NCBI and they corrected their mistake.

User:Dilvan

2007-03-27T17:23:18Z

Dilvan: /* BioAnnotation Tab for Protege */

Test page:

== OWL Export/Import plugin for OboEdit ==

That is the development version of the OWL Export/Import plugin for OboEdit . Just download the distribution file, unzip it and copy its content to <OboEdit>/extensions folder. Start OboEdit and you should find the option "OWL Adapter" for loading ontologies, File->Load Terms..., and for saving, File->Save as...

[http://smi-cbio01.stanford.edu/~nigam/OboEditPlugin.zip Download plugin (for OBOEdit 1.002)].

If you have problems with big ontologies, try to increase the size of the memory available to OboEdit.

== BioAnnotation Tab for Protege ==

That is the development version of the BioAnnotation Tab for Protege.
To install:

1- Download the distribution files for the OBO Converter Tab and BioAnnotation Tab from this page. If you have a different version of those plugins, uninstall them and use the ones from this page.

2- Unzip them in the Protege plugin directory (<Protege install directory>/plugins).

3- Create a Protege OWL project, and import the GO ontology in OWL (there is a copy in this page).

4- In the BioAnnotation Tab read a GO Annotation Format file from one of the MODs.

The NCBI taxonomy is not imported, just referenced (it is too big to import). So you will only see a reference to the species you are working with.

[[[Media:Oboconverter.zip | Download OBO Converter plugin]].
[http://www.bioontology.org/wiki/index.php/Image:BioAnnotation.zip Download BioAnnotation plugin].
[http://www.bioontology.org/wiki/index.php/Image:Go_ontology.zip Download GO Ontology in OWL].

Please, keep in mind that this is a beta version of this tab. If you have problems with big files, try to increase the size of the memory available to Protege.

If you just want to see the GO Annotation files in OWL, download the ''Saccharomyces cerevisiae'' or the ''Homo sapiens'' GO Annotations in OWL. Both files import the GO ontology in OWL, so you have to have it in your disk. You can use your prefered OWL editor to read them:

[http://www.bioontology.org/wiki/index.php/Image:Yeast_annotations.zip Download Yeast GO Annotations in OWL].
[http://www.bioontology.org/wiki/index.php/Image:Human_annotations.zip Download Human GO Annotations in OWL].

NOTE: In the Amia paper refering to this Tab, there are links to the NCBI Entrez Gene site pointing out misinterpretations of the GO Annotation File Format. Since the submission of this paper, the authors contacted the NCBI and they corrected their mistake.

User:Dilvan

2007-03-27T17:16:04Z

Dilvan: /* BioAnnotation Tab for Protege */

Test page:

== OWL Export/Import plugin for OboEdit ==

That is the development version of the OWL Export/Import plugin for OboEdit . Just download the distribution file, unzip it and copy its content to <OboEdit>/extensions folder. Start OboEdit and you should find the option "OWL Adapter" for loading ontologies, File->Load Terms..., and for saving, File->Save as...

[http://smi-cbio01.stanford.edu/~nigam/OboEditPlugin.zip Download plugin (for OBOEdit 1.002)].

If you have problems with big ontologies, try to increase the size of the memory available to OboEdit.

== BioAnnotation Tab for Protege ==

That is the development version of the BioAnnotation Tab for Protege.
To install:

1- Download the distribution files for the OBO Converter Tab and BioAnnotation Tab from this page. If you have a different version of those plugins, uninstall them and use the ones from this page.

2- Unzip them in the Protege plugin directory (<Protege install directory>/plugins).

3- Create a Protege OWL project, and import the GO ontology in OWL (there is a copy in this page).

4- In the BioAnnotation Tab read a GO Annotation Format file from one of the MODs.

The NCBI taxonomy is not imported, just referenced (it is too big to import). So you will only see a reference to the species you are working with.

[[[Media:Oboconverter.zip]] Download OBO Converter plugin].
[http://www.bioontology.org/wiki/index.php/Image:BioAnnotation.zip Download BioAnnotation plugin].
[http://www.bioontology.org/wiki/index.php/Image:Go_ontology.zip Download GO Ontology in OWL].

Please, keep in mind that this is a beta version of this tab. If you have problems with big files, try to increase the size of the memory available to Protege.

If you just want to see the GO Annotation files in OWL, download the ''Saccharomyces cerevisiae'' or the ''Homo sapiens'' GO Annotations in OWL. Both files import the GO ontology in OWL, so you have to have it in your disk. You can use your prefered OWL editor to read them:

[http://www.bioontology.org/wiki/index.php/Image:Yeast_annotations.zip Download Yeast GO Annotations in OWL].
[http://www.bioontology.org/wiki/index.php/Image:Human_annotations.zip Download Human GO Annotations in OWL].

NOTE: In the Amia paper refering to this Tab, there are links to the NCBI Entrez Gene site pointing out misinterpretations of the GO Annotation File Format. Since the submission of this paper, the authors contacted the NCBI and they corrected their mistake.

User:Dilvan

2007-03-27T17:14:01Z

Dilvan: /* BioAnnotation Tab for Protege */

Test page:

== OWL Export/Import plugin for OboEdit ==

That is the development version of the OWL Export/Import plugin for OboEdit . Just download the distribution file, unzip it and copy its content to <OboEdit>/extensions folder. Start OboEdit and you should find the option "OWL Adapter" for loading ontologies, File->Load Terms..., and for saving, File->Save as...

[http://smi-cbio01.stanford.edu/~nigam/OboEditPlugin.zip Download plugin (for OBOEdit 1.002)].

If you have problems with big ontologies, try to increase the size of the memory available to OboEdit.

== BioAnnotation Tab for Protege ==

That is the development version of the BioAnnotation Tab for Protege.
To install:

1- Download the distribution files for the OBO Converter Tab and BioAnnotation Tab from this page. If you have a different version of those plugins, uninstall them and use the ones from this page.

2- Unzip them in the Protege plugin directory (<Protege install directory>/plugins).

3- Create a Protege OWL project, and import the GO ontology in OWL (there is a copy in this page).

4- In the BioAnnotation Tab read a GO Annotation Format file from one of the MODs.

The NCBI taxonomy is not imported, just referenced (it is too big to import). So you will only see a reference to the species you are working with.

[[Media:Oboconverter.zip] Download OBO Converter plugin].
[http://www.bioontology.org/wiki/index.php/Image:BioAnnotation.zip Download BioAnnotation plugin].
[http://www.bioontology.org/wiki/index.php/Image:Go_ontology.zip Download GO Ontology in OWL].

Please, keep in mind that this is a beta version of this tab. If you have problems with big files, try to increase the size of the memory available to Protege.

If you just want to see the GO Annotation files in OWL, download the ''Saccharomyces cerevisiae'' or the ''Homo sapiens'' GO Annotations in OWL. Both files import the GO ontology in OWL, so you have to have it in your disk. You can use your prefered OWL editor to read them:

[http://www.bioontology.org/wiki/index.php/Image:Yeast_annotations.zip Download Yeast GO Annotations in OWL].
[http://www.bioontology.org/wiki/index.php/Image:Human_annotations.zip Download Human GO Annotations in OWL].

NOTE: In the Amia paper refering to this Tab, there are links to the NCBI Entrez Gene site pointing out misinterpretations of the GO Annotation File Format. Since the submission of this paper, the authors contacted the NCBI and they corrected their mistake.

User:Dilvan

2007-03-27T17:12:33Z

Dilvan: /* BioAnnotation Tab for Protege */

Test page:

== OWL Export/Import plugin for OboEdit ==

That is the development version of the OWL Export/Import plugin for OboEdit . Just download the distribution file, unzip it and copy its content to <OboEdit>/extensions folder. Start OboEdit and you should find the option "OWL Adapter" for loading ontologies, File->Load Terms..., and for saving, File->Save as...

[http://smi-cbio01.stanford.edu/~nigam/OboEditPlugin.zip Download plugin (for OBOEdit 1.002)].

If you have problems with big ontologies, try to increase the size of the memory available to OboEdit.

== BioAnnotation Tab for Protege ==

That is the development version of the BioAnnotation Tab for Protege.
To install:

1- Download the distribution files for the OBO Converter Tab and BioAnnotation Tab from this page. If you have a different version of those plugins, uninstall them and use the ones from this page.

2- Unzip them in the Protege plugin directory (<Protege install directory>/plugins).

3- Create a Protege OWL project, and import the GO ontology in OWL (there is a copy in this page).

4- In the BioAnnotation Tab read a GO Annotation Format file from one of the MODs.

The NCBI taxonomy is not imported, just referenced (it is too big to import). So you will only see a reference to the species you are working with.

[[Media:Oboconverter.zip]]
[http://www.bioontology.org/wiki/index.php/Image:Oboconverter.zip Download OBO Converter plugin].
[http://www.bioontology.org/wiki/index.php/Image:BioAnnotation.zip Download BioAnnotation plugin].
[http://www.bioontology.org/wiki/index.php/Image:Go_ontology.zip Download GO Ontology in OWL].

Please, keep in mind that this is a beta version of this tab. If you have problems with big files, try to increase the size of the memory available to Protege.

If you just want to see the GO Annotation files in OWL, download the ''Saccharomyces cerevisiae'' or the ''Homo sapiens'' GO Annotations in OWL. Both files import the GO ontology in OWL, so you have to have it in your disk. You can use your prefered OWL editor to read them:

[http://www.bioontology.org/wiki/index.php/Image:Yeast_annotations.zip Download Yeast GO Annotations in OWL].
[http://www.bioontology.org/wiki/index.php/Image:Human_annotations.zip Download Human GO Annotations in OWL].

NOTE: In the Amia paper refering to this Tab, there are links to the NCBI Entrez Gene site pointing out misinterpretations of the GO Annotation File Format. Since the submission of this paper, the authors contacted the NCBI and they corrected their mistake.

User:Dilvan

2007-03-27T17:10:49Z

Dilvan: /* BioAnnotation Tab for Protege */

Test page:

== OWL Export/Import plugin for OboEdit ==

That is the development version of the OWL Export/Import plugin for OboEdit . Just download the distribution file, unzip it and copy its content to <OboEdit>/extensions folder. Start OboEdit and you should find the option "OWL Adapter" for loading ontologies, File->Load Terms..., and for saving, File->Save as...

[http://smi-cbio01.stanford.edu/~nigam/OboEditPlugin.zip Download plugin (for OBOEdit 1.002)].

If you have problems with big ontologies, try to increase the size of the memory available to OboEdit.

== BioAnnotation Tab for Protege ==

That is the development version of the BioAnnotation Tab for Protege.
To install:

1- Download the distribution files for the OBO Converter Tab and BioAnnotation Tab from this page. If you have a different version of those plugins, uninstall them and use the ones from this page.

2- Unzip them in the Protege plugin directory (<Protege install directory>/plugins).

3- Create a Protege OWL project, and import the GO ontology in OWL (there is a copy in this page).

4- In the BioAnnotation Tab read a GO Annotation Format file from one of the MODs.

The NCBI taxonomy is not imported, just referenced (it is too big to import). So you will only see a reference to the species you are working with.

[[Media:Example.ogg]][[Image:Oboconverter.zip]]
[http://www.bioontology.org/wiki/index.php/Image:Oboconverter.zip Download OBO Converter plugin].
[http://www.bioontology.org/wiki/index.php/Image:BioAnnotation.zip Download BioAnnotation plugin].
[http://www.bioontology.org/wiki/index.php/Image:Go_ontology.zip Download GO Ontology in OWL].

Please, keep in mind that this is a beta version of this tab. If you have problems with big files, try to increase the size of the memory available to Protege.

If you just want to see the GO Annotation files in OWL, download the ''Saccharomyces cerevisiae'' or the ''Homo sapiens'' GO Annotations in OWL. Both files import the GO ontology in OWL, so you have to have it in your disk. You can use your prefered OWL editor to read them:

[http://www.bioontology.org/wiki/index.php/Image:Yeast_annotations.zip Download Yeast GO Annotations in OWL].
[http://www.bioontology.org/wiki/index.php/Image:Human_annotations.zip Download Human GO Annotations in OWL].

NOTE: In the Amia paper refering to this Tab, there are links to the NCBI Entrez Gene site pointing out misinterpretations of the GO Annotation File Format. Since the submission of this paper, the authors contacted the NCBI and they corrected their mistake.

User:Dilvan

2007-03-27T17:08:10Z

Dilvan: /* BioAnnotation Tab for Protege */

Test page:

== OWL Export/Import plugin for OboEdit ==

That is the development version of the OWL Export/Import plugin for OboEdit . Just download the distribution file, unzip it and copy its content to <OboEdit>/extensions folder. Start OboEdit and you should find the option "OWL Adapter" for loading ontologies, File->Load Terms..., and for saving, File->Save as...

[http://smi-cbio01.stanford.edu/~nigam/OboEditPlugin.zip Download plugin (for OBOEdit 1.002)].

If you have problems with big ontologies, try to increase the size of the memory available to OboEdit.

== BioAnnotation Tab for Protege ==

That is the development version of the BioAnnotation Tab for Protege.
To install:

1- Download the distribution files for the OBO Converter Tab and BioAnnotation Tab from this page.

2- Unzip them in the Protege plugin directory (<Protege install directory>/plugins).

3- Create a Protege OWL project, and import the GO ontology in OWL (there is a copy in this page).

4- In the BioAnnotation Tab read a GO Annotation Format file from one of the MODs.

The NCBI taxonomy is not imported, just referenced (it is too big to import). So you will only see a reference to the species you are working with.

[http://www.bioontology.org/wiki/index.php/Image:Oboconverter.zip Download OBO Converter plugin].
[http://www.bioontology.org/wiki/index.php/Image:BioAnnotation.zip Download BioAnnotation plugin].
[http://www.bioontology.org/wiki/index.php/Image:Go_ontology.zip Download GO Ontology in OWL].

Please, keep in mind that this is a beta version of this tab. If you have problems with big files, try to increase the size of the memory available to Protege.

If you just want to see the GO Annotation files in OWL, download the ''Saccharomyces cerevisiae'' or the ''Homo sapiens'' GO Annotations in OWL. Both files import the GO ontology in OWL, so you have to have it in your disk. You can use your prefered OWL editor to read them:

[http://www.bioontology.org/wiki/index.php/Image:Yeast_annotations.zip Download Yeast GO Annotations in OWL].
[http://www.bioontology.org/wiki/index.php/Image:Human_annotations.zip Download Human GO Annotations in OWL].

NOTE: In the Amia paper refering to this Tab, there are links to the NCBI Entrez Gene site pointing out misinterpretations of the GO Annotation File Format. Since the submission of this paper, the authors contacted the NCBI and they corrected their mistake.

User:Dilvan

2007-03-27T17:07:20Z

Dilvan: /* BioAnnotation Tab for Protege */

Test page:

== OWL Export/Import plugin for OboEdit ==

That is the development version of the OWL Export/Import plugin for OboEdit . Just download the distribution file, unzip it and copy its content to <OboEdit>/extensions folder. Start OboEdit and you should find the option "OWL Adapter" for loading ontologies, File->Load Terms..., and for saving, File->Save as...

[http://smi-cbio01.stanford.edu/~nigam/OboEditPlugin.zip Download plugin (for OBOEdit 1.002)].

If you have problems with big ontologies, try to increase the size of the memory available to OboEdit.

== BioAnnotation Tab for Protege ==

That is the development version of the BioAnnotation Tab for Protege.
To install:

1- Download the distribution files for the OBO Converter Tab and BioAnnotation Tab from this page.

2- Unzip them in the Protege plugin directory (<Protege install directory>/plugins).

3- Create a Protege OWL project, and import the GO ontology in OWL (there is a copy in this page).

4- In the BioAnnotation Tab read a GO Annotation Format file from one of the MODs.

The NCBI taxonomy is not imported, just referenced (it is too big to import). So you will only see a reference to the species you are working with.

[http://www.bioontology.org/wiki/index.php/Image:Oboconverter.zip Download OBO Converter plugin].
[http://www.bioontology.org/wiki/index.php/Image:BioAnnotation.zip Download BioAnnotation plugin].
[http://www.bioontology.org/wiki/index.php/Image:Go_ontology.zip Download GO Ontology in OWL].

Please, keep in mind that this is a beta version of this tab. If you have problems with big files, try to increase the size of the memory available to Protege.

If you just want to see the GO Annotation files in OWL, download the ''Saccharomyces cerevisiae'' or the ''Homo sapiens'' GO Annotations in OWL. Both files import the GO ontology in OWL, so you have to have it in your disk. You can use your prefered OWL editor to read them:

[http://www.bioontology.org/wiki/index.php/Image:Yeast_annotations.zip Download Yeast GO Annotations].
[http://www.bioontology.org/wiki/index.php/Image:Human_annotations.zip Download Human GO Annotations].

NOTE: In the Amia paper refering to this Tab, there are links to the NCBI Entrez Gene site pointing out misinterpretations of the GO Annotation File Format. Since the submission of this paper, the authors contacted the NCBI and they corrected their mistake.

User:Dilvan

2007-03-27T17:06:55Z

Dilvan: /* BioAnnotation Tab for Protege */

Test page:

== OWL Export/Import plugin for OboEdit ==

That is the development version of the OWL Export/Import plugin for OboEdit . Just download the distribution file, unzip it and copy its content to <OboEdit>/extensions folder. Start OboEdit and you should find the option "OWL Adapter" for loading ontologies, File->Load Terms..., and for saving, File->Save as...

[http://smi-cbio01.stanford.edu/~nigam/OboEditPlugin.zip Download plugin (for OBOEdit 1.002)].

If you have problems with big ontologies, try to increase the size of the memory available to OboEdit.

== BioAnnotation Tab for Protege ==

That is the development version of the BioAnnotation Tab for Protege.
To install:

1- Download the distribution files for the OBO Converter Tab and BioAnnotation Tab from this page.

2- Unzip them in the Protege plugin directory (<Protege install directory>/plugins).

3- Create a Protege OWL project, and import the GO ontology in OWL (there is a copy in this page).

4- In the BioAnnotation Tab read a GO Annotation Format file from one of the MODs.

The NCBI taxonomy is not imported, just referenced (it is too big to import). So you will only see a reference to the species you are working with.

[Image:Oboconverter.zip Download OBO Converter plugin].
[http://www.bioontology.org/wiki/index.php/Image:BioAnnotation.zip Download BioAnnotation plugin].
[http://www.bioontology.org/wiki/index.php/Image:Go_ontology.zip Download GO Ontology in OWL].

Please, keep in mind that this is a beta version of this tab. If you have problems with big files, try to increase the size of the memory available to Protege.

If you just want to see the GO Annotation files in OWL, download the ''Saccharomyces cerevisiae'' or the ''Homo sapiens'' GO Annotations in OWL. Both files import the GO ontology in OWL, so you have to have it in your disk. You can use your prefered OWL editor to read them:

[http://www.bioontology.org/wiki/index.php/Image:Yeast_annotations.zip Download Yeast GO Annotations].
[http://www.bioontology.org/wiki/index.php/Image:Human_annotations.zip Download Human GO Annotations].

NOTE: In the Amia paper refering to this Tab, there are links to the NCBI Entrez Gene site pointing out misinterpretations of the GO Annotation File Format. Since the submission of this paper, the authors contacted the NCBI and they corrected their mistake.

File:BioAnnotation.zip

2007-03-27T17:06:04Z

Dilvan: Bio Annotation Tab for Protege 3.2.1.

Bio Annotation Tab for Protege 3.2.1.

User:Dilvan

2007-03-27T17:04:48Z

Dilvan: /* BioAnnotation Tab for Protege */

Test page:

== OWL Export/Import plugin for OboEdit ==

That is the development version of the OWL Export/Import plugin for OboEdit . Just download the distribution file, unzip it and copy its content to <OboEdit>/extensions folder. Start OboEdit and you should find the option "OWL Adapter" for loading ontologies, File->Load Terms..., and for saving, File->Save as...

[http://smi-cbio01.stanford.edu/~nigam/OboEditPlugin.zip Download plugin (for OBOEdit 1.002)].

If you have problems with big ontologies, try to increase the size of the memory available to OboEdit.

== BioAnnotation Tab for Protege ==

That is the development version of the BioAnnotation Tab for Protege.
To install:

1- Download the distribution files for the OBO Converter Tab and BioAnnotation Tab from this page.

2- Unzip them in the Protege plugin directory (<Protege install directory>/plugins).

3- Create a Protege OWL project, and import the GO ontology in OWL (there is a copy in this page).

4- In the BioAnnotation Tab read a GO Annotation Format file from one of the MODs.

The NCBI taxonomy is not imported, just referenced (it is too big to import). So you will only see a reference to the species you are working with.

[http://www.bioontology.org/wiki/index.php/Image:Oboconverter.zip Download OBO Converter plugin].
[http://smi-cbio01.snford.edu/~nigam/ Download BioAnnotation plugin].
[http://www.bioontology.org/wiki/index.php/Image:Go_ontology.zip Download GO Ontology in OWL].

Please, keep in mind that this is a beta version of this tab. If you have problems with big files, try to increase the size of the memory available to Protege.

If you just want to see the GO Annotation files in OWL, download the ''Saccharomyces cerevisiae'' or the ''Homo sapiens'' GO Annotations in OWL. Both files import the GO ontology in OWL, so you have to have it in your disk. You can use your prefered OWL editor to read them:

[http://www.bioontology.org/wiki/index.php/Image:Yeast_annotations.zip Download Yeast GO Annotations].
[http://www.bioontology.org/wiki/index.php/Image:Human_annotations.zip Download Human GO Annotations].

NOTE: In the Amia paper refering to this Tab, there are links to the NCBI Entrez Gene site pointing out misinterpretations of the GO Annotation File Format. Since the submission of this paper, the authors contacted the NCBI and they corrected their mistake.

File:Oboconverter.zip

2007-03-27T17:04:09Z

Dilvan: OBO Converter Tab for Protege 3.2.1.

OBO Converter Tab for Protege 3.2.1.

User:Dilvan

2007-03-27T17:02:24Z

Dilvan: /* BioAnnotation Tab for Protege */

Test page:

== OWL Export/Import plugin for OboEdit ==

That is the development version of the OWL Export/Import plugin for OboEdit . Just download the distribution file, unzip it and copy its content to <OboEdit>/extensions folder. Start OboEdit and you should find the option "OWL Adapter" for loading ontologies, File->Load Terms..., and for saving, File->Save as...

[http://smi-cbio01.stanford.edu/~nigam/OboEditPlugin.zip Download plugin (for OBOEdit 1.002)].

If you have problems with big ontologies, try to increase the size of the memory available to OboEdit.

== BioAnnotation Tab for Protege ==

That is the development version of the BioAnnotation Tab for Protege.
To install:

1- Download the distribution files for the OBO Converter Tab and BioAnnotation Tab from this page.

2- Unzip them in the Protege plugin directory (<Protege install directory>/plugins).

3- Create a Protege OWL project, and import the GO ontology in OWL (there is a copy in this page).

4- In the BioAnnotation Tab read a GO Annotation Format file from one of the MODs.

The NCBI taxonomy is not imported, just referenced (it is too big to import). So you will only see a reference to the species you are working with.

[http://smi-cbio01.stford.edu/~nigam/OboEditPlugin.zip Download OBO Converter plugin].
[http://smi-cbio01.snford.edu/~nigam/ Download BioAnnotation plugin].
[http://www.bioontology.org/wiki/index.php/Image:Go_ontology.zip Download GO Ontology in OWL].

Please, keep in mind that this is a beta version of this tab. If you have problems with big files, try to increase the size of the memory available to Protege.

If you just want to see the GO Annotation files in OWL, download the ''Saccharomyces cerevisiae'' or the ''Homo sapiens'' GO Annotations in OWL. Both files import the GO ontology in OWL, so you have to have it in your disk. You can use your prefered OWL editor to read them:

[http://www.bioontology.org/wiki/index.php/Image:Yeast_annotations.zip Download Yeast GO Annotations].
[http://www.bioontology.org/wiki/index.php/Image:Human_annotations.zip Download Human GO Annotations].

NOTE: In the Amia paper refering to this Tab, there are links to the NCBI Entrez Gene site pointing out misinterpretations of the GO Annotation File Format. Since the submission of this paper, the authors contacted the NCBI and they corrected their mistake.

File:Human annotations.zip

2007-03-27T17:01:09Z

Dilvan: GO Annotations for human (Homo sapiens).

GO Annotations for human (Homo sapiens).

File:Yeast annotations.zip

2007-03-27T17:00:18Z

Dilvan: GO annotations for yeast (Saccharomyces cerevisiae).

GO annotations for yeast (Saccharomyces cerevisiae).

User:Dilvan

2007-03-27T16:58:13Z

Dilvan: /* BioAnnotation Tab for Protege */

Test page:

== OWL Export/Import plugin for OboEdit ==

That is the development version of the OWL Export/Import plugin for OboEdit . Just download the distribution file, unzip it and copy its content to <OboEdit>/extensions folder. Start OboEdit and you should find the option "OWL Adapter" for loading ontologies, File->Load Terms..., and for saving, File->Save as...

[http://smi-cbio01.stanford.edu/~nigam/OboEditPlugin.zip Download plugin (for OBOEdit 1.002)].

If you have problems with big ontologies, try to increase the size of the memory available to OboEdit.

== BioAnnotation Tab for Protege ==

That is the development version of the BioAnnotation Tab for Protege.
To install:

1- Download the distribution files for the OBO Converter Tab and BioAnnotation Tab from this page.

2- Unzip them in the Protege plugin directory (<Protege install directory>/plugins).

3- Create a Protege OWL project, and import the GO ontology in OWL (there is a copy in this page).

4- In the BioAnnotation Tab read a GO Annotation Format file from one of the MODs.

The NCBI taxonomy is not imported, just referenced (it is too big to import). So you will only see a reference to the species you are working with.

[http://smi-cbio01.stford.edu/~nigam/OboEditPlugin.zip Download OBO Converter plugin].
[http://smi-cbio01.snford.edu/~nigam/OboEditPlugin.zip Download BioAnnotation plugin].
[http://www.bioontology.org/wiki/index.php/Image:Go_ontology.zip Download GO Ontology in OWL].

Please, keep in mind that this is a beta version of this tab. If you have problems with big files, try to increase the size of the memory available to Protege.

If you just want to see the GO Annotation files in OWL, download the ''Saccharomyces cerevisiae'' or the ''Homo sapiens'' GO Annotations in OWL. Both files import the GO ontology in OWL, so you have to have it in your disk. You can use your prefered OWL editor to read them:

[http://smi-cbio01.staord.edu/~nigam/OboEditPlugin.zip Download Yeast GO Annotations].
[http://smi-cbio01.stanrd.edu/~nigam/OboEditPlugin.zip Download Human GO Annotations].

NOTE: In the Amia paper refering to this Tab, there are links to the NCBI Entrez Gene site pointing out misinterpretations of the GO Annotation File Format. Since the submission of this paper, the authors contacted the NCBI and they corrected their mistake.

File:Go ontology.zip

2007-03-27T16:57:17Z

Dilvan: GO ontology in OWL.

GO ontology in OWL.

User:Dilvan

2007-03-27T07:45:17Z

Dilvan: /* BioAnnotation Tab for Protege */

Test page:

== OWL Export/Import plugin for OboEdit ==

That is the development version of the OWL Export/Import plugin for OboEdit . Just download the distribution file, unzip it and copy its content to <OboEdit>/extensions folder. Start OboEdit and you should find the option "OWL Adapter" for loading ontologies, File->Load Terms..., and for saving, File->Save as...

[http://smi-cbio01.stanford.edu/~nigam/OboEditPlugin.zip Download plugin (for OBOEdit 1.002)].

If you have problems with big ontologies, try to increase the size of the memory available to OboEdit.

== BioAnnotation Tab for Protege ==

That is the development version of the BioAnnotation Tab for Protege.
To install:

1- Download the distribution files for the OBO Converter Tab and BioAnnotation Tab from this page.

2- Unzip them in the Protege plugin directory (<Protege install directory>/plugins).

3- Create a Protege OWL project, and import the GO ontology in OWL (there is a copy in this page).

4- In the BioAnnotation Tab read a GO Annotation Format file from one of the MODs.

The NCBI taxonomy is not imported, just referenced (it is too big to import). So you will only see a reference to the species you are working with.

[http://smi-cbio01.stford.edu/~nigam/OboEditPlugin.zip Download OBO Converter plugin].
[http://smi-cbio01.snford.edu/~nigam/OboEditPlugin.zip Download BioAnnotation plugin].
[http://smi-cbio01.snford.edu/~nigam/OboEditPlugin.zip Download GO Annotation in OWL].

Please, keep in mind that this is a beta version of this tab. If you have problems with big files, try to increase the size of the memory available to Protege.

If you just want to see the GO Annotation files in OWL, download the ''Saccharomyces cerevisiae'' or the ''Homo sapiens'' GO Annotations in OWL. Both files import the GO ontology in OWL, so you have to have it in your disk. You can use your prefered OWL editor to read them:

[http://smi-cbio01.staord.edu/~nigam/OboEditPlugin.zip Download Yeast GO Annotations].
[http://smi-cbio01.stanrd.edu/~nigam/OboEditPlugin.zip Download Human GO Annotations].

NOTE: In the Amia paper refering to this Tab, there are links to the NCBI Entrez Gene site pointing out misinterpretations of the GO Annotation File Format. Since the submission of this paper, the authors contacted the NCBI and they corrected their mistake.

User:Dilvan

2007-03-27T07:32:37Z

Dilvan: /* BioAnnotation Tab for Protege */

Test page:

== OWL Export/Import plugin for OboEdit ==

That is the development version of the OWL Export/Import plugin for OboEdit . Just download the distribution file, unzip it and copy its content to <OboEdit>/extensions folder. Start OboEdit and you should find the option "OWL Adapter" for loading ontologies, File->Load Terms..., and for saving, File->Save as...

[http://smi-cbio01.stanford.edu/~nigam/OboEditPlugin.zip Download plugin (for OBOEdit 1.002)].

If you have problems with big ontologies, try to increase the size of the memory available to OboEdit.

== BioAnnotation Tab for Protege ==

That is the development version of the BioAnnotation Tab for Protege.
To install:

1- Download the distribution files for the OBO Converter Tab and BioAnnotation Tab from this page.

2- Unzip them in the Protege plugin directory (<Protege install directory>/plugins).

3- Create a Protege OWL project, and import the GO ontology in OWL (there is a copy in this page).

4- In the BioAnnotation Tab read a GO Annotation Format file from one of the MODs.

The NCBI taxonomy is not imported, just referenced (it is too big to import). So you will only see a reference to the species you are working with.

[http://smi-cbio01.stanford.edu/~nigam/OboEditPlugin.zip Download OBO Converter plugin].
[http://smi-cbio01.stanford.edu/~nigam/OboEditPlugin.zip Download BioAnnotation plugin].
[http://smi-cbio01.stanford.edu/~nigam/OboEditPlugin.zip Download GO Annotation in OWL].

Please, keep in mind that this is a beta version of this tab. If you have problems with big files, try to increase the size of the memory available to Protege.

If you just want to see the GO Annotation files in OWL, download the ''Saccharomyces cerevisiae'' or the ''Homo sapiens'' GO Annotations in OWL. Both files import the GO ontology in OWL, so you have to have it in your disk. You can use your prefered OWL editor to read them:

[http://smi-cbio01.stanford.edu/~nigam/OboEditPlugin.zip Download Yeast GO Annotations].
[http://smi-cbio01.stanford.edu/~nigam/OboEditPlugin.zip Download Human GO Annotations].

NOTE: In the Amia paper refering to this Tab, there are links to the NCBI Entrez Gene site pointing out misinterpretations of the GO Annotation File Format. Since the submission of this paper, the authors contacted the NCBI and they corrected their mistake.

User:Dilvan

2007-03-27T07:28:19Z

Dilvan: /* BioAnnotation Tab for Protege */

OboInOwl:Main Page

2007-03-20T22:22:38Z

Dilvan: /* OBO Converter Protege tab: */

=OBO in OWL: Mapping and Tools=

This wiki is for discussing the mapping between Obo1.2 format and OWL. The [http://www.godatabase.org/dev/doc/mapping-obo-to-owl.html first version] of this mapping is at http://www.godatabase.org/dev/doc/mapping-obo-to-owl.html. We have finished work on a newer version of this mapping. This page provides a brief background for the effort and provides links to the relevant tools (plugins for OBOEdit and Protege) that implement the mapping.

The Gene Ontology and a significant number of biomedical ontologies are in the OBO-format. The OBO format, which originated along with the Gene Ontology, has evolved to support the needs of the biomedical ontologies that fall under the Open Biomedical Ontologies (OBO) umbrella. The OBO-format aims to have 1) human readability, 2) ease of parsing, 3) extensibility and 4) minimal redundancy. The OBO-format currently forms the backbone of most GO based annotation and data analysis tools.

In parallel with the developments in bio-ontologies, ontologies in general have become more prevalent in information technology; with the most visible push coming from the W3C in the form of the W3C recommendation of the Web Ontology Language (OWL) as an international standard for ontologies on the web. There has also been a corresponding increase in the number, diversity and quality of the tools available to construct, maintain and view ontologies in OWL.

As bio-ontologies become more popular and grow in size as well as complexity, they are becoming the focus of attention of the larger computer science research community. On one hand there is significant interest in using the life sciences domain as a “focus” for W3C semantic web activity. In this light, biological data annotated using OBO ontologies is a prime resource and there is great interest from the Semantic Web community to access the ontologies and the annotated data in OWL format. On the other hand, if bio-ontologies are to benefit from the rapid progress being made in computer science – especially the semantic web technologies – bio-ontologies need to interoperate with other ontologies which are in the OWL format. The relatively newer biomedical ontologies (such as BioPAX) are already in OWL. The NCI-thesaurus, being developed by the National Cancer Institute, is also in OWL.

As a result, there is a strong need to map the OBO-format to OWL and provide tools that enable the end user to perform the translation at the click of a button in a stable ontology editing environment without worrying about underlying formats.

=Mail Lists=

We have created the OBO to OWL mapping remaining faithful to the (declared) semantics of the OBO format. At places where we found the format to be vague, we have tightened the semantics and have update the documentation accordingly. We make the mapping tools available for other researchers to use and evaluate the mapping. Please feel free to contact us on these mailing lists if you find anything lacking, have suggestions or have any kind of feedback.

[https://lists.sourceforge.net/lists/listinfo/obo-format Obo Format List]

Also of interest: [https://lists.sourceforge.net/lists/listinfo/obo-crossproducts Obo Cross-Product List]

=The Mapping=

We have made the mapping available as an online Google spreadsheet. You can view the sheet at http://spreadsheets.google.com/ccc?key=pWN_4sBrd9l1Umn1LN8WuQQ. If you want edits rights (or already have them) to leave comments then use the following link http://spreadsheets.google.com/ccc?key=o06770842196506107736.4732937099693365844

=Tools for the mapping=

== Protege plugins ==

== OBO Converter Protege tab: ==

The OBO Converter is a Tab plugin for Protégé to convert OBO format files into OWL files and vice-versa (keeping in mind that OWL to OBO conversions can lose information if one encodes things in OWL that cannot be expressed in OBO). It is also developed in a manner such that it can also work as a standalone conversion program.

'''Tab User Guide'''

The OBO Converter Tab basically reads OBO files (OBO 1.0 and 1.2) into Protégé OWL projects and saves those projects back as OBO 1.0 files. The Tab has two main panels, one to read OBO files and one to write (save) them.

The save operation is straightforward as the user chooses the file name and the conversion is done. The read operation has the same functionality plus a set of options that can alter the way an OBO file is read (see figure).

[[Image:OBOConverter.jpg]]

Read Options:

'''1 Class name generation'''

A Combo box allows users to choose the way the OWL class names will be generated from the OBO format file Terms. There are 3 options:

* OBO id will generate the name from the OBO term id that is the option that generates the OWL id in the way described in the mapping.
* Class name will generate the name from the OBO term name, be careful as those names may not be unique. If the names are not unique, there will be a parser error.
* Class name + OBO id will generate the name from the combination of the OBO term name and id.

In all cases, characters other than letters (a-z, A-Z) or numbers will be converted to underscore characters (_). Ex: the OBO term name “nurse cell” will be converted to the OWL class name nurse_cell.

The default behavior of the Tab is to generate the OWL id in the way described in the mapping and uses the OBO id to generate class names. If the user wants to see the OBO name of the classes, instead of their meaningless ids, Protégé has an option to display the OWL class label as the class identifier. As OWL labels can have language identifiers (such as en for English), converted OBO ontologies can now have names in different languages all pointing to the same entities.

The other options are targeted to users that want to create their ontology using a specific OBO ontology as a start point, but need to name their entities in a different way. Those users are not interested in maintaining naming compatibility with OBO.

'''2 Exclusion of namespaces'''

In OBO format, it is possible to define more than one ontology in each file using the OBO namespace: tag (Note that OBO namespaces have no connection with OWL namespaces). For instance, the Gene Ontology is actually composed by three independent ontologies defined in the same file (gene_ontology.obo) using three different namespaces (''biological_process'', ''molecular_funtion'' and ''cellular_component''). When the OBO Converter Tab reads such file types, it collapses all ontologies in one and namespace information is stored as annotation, which may not be the intention of the user. The OBO Converter Tab has a panel where the user can specify which namespaces he does not want to be read from a file.

Example: In the gene_ontology.obo file, if the namespaces ''biological_process'' and ''molecular_function'' are selected (for not being read), only the ''cellular_component'' ontology will be read.

'''3 Default namespace URI'''

It is the author responsibility to set the default namespace URI for the OWL ontology. That information is not available in the OBO format file. The OBO Converter Tab has a panel where the author can enter this URI. If it does not enter one, whatever default URI Protégé is using becomes the default namespace URI for the OWL ontology.

Downloads:

[http://smi-protege.stanford.edu/svn/obo-converter/trunk/ Source code for OBO Converter Tab]
[http://smi-cbio01.stanford.edu/~nigam/OBOConverter.zip Binaries for OBO Converter Tab]
[http://protege.cim3.net/cgi-bin/wiki.pl?OBOConverter Page at Protege Site]

== OBO Explorer Protege tab: ==

The OWL format for OBO files uses anonymous nodes to represent definitions, synonyms, and DbxRefs, and the generic Protégé GUI components are not immediately suitable to display and edit them. The existing graphical components also do not allow the user to easily access or edit the lexical information associated with an OBO term. The OBO Explorer tab allows the user to do so in an interface that is similar to that of OBO-edit. This provides the user with the flexibility to edit these lexical features (such as synonyms and dbxrefs) in an intuitive manner.

[http://www.aiai.ed.ac.uk/project/cobra-ct/COBrA_downloads.htm OBO Explorer Tab]

[[Image:OBOExplorer.jpg]]

== OboEdit OWL plugin ==
We have also added the functionality to save an OBO format file as an OWL file from within OBOEdit. We have a development version of the OWL Export/Import plugin for OboEdit available. Just download the distribution file, unzip it and copy its content to <OboEdit>/extensions folder. Start OboEdit and you should find the option "OWL Adapter" for loading ontologies, File->Load Terms..., and for saving, File->Save as...

[http://smi-cbio01.stanford.edu/~nigam/OboEditPlugin.zip OboEdit OWL plugin].

If you have problems with big ontologies, try to increase the size of the memory available to OboEdit.

== obo2owl xslt ==

The oboxml_to_owl.xsl mapping now implements the OboInOwl mapping for obo-xml:

[http://geneontology.cvs.sourceforge.net/geneontology/go-dev/xml/xsl/oboxml_to_owl.xsl?view=log XSLT]

This will be bundled with [http://search.cpan.org/~cmungall/go-perl/ go-perl-0.07] and higher

Sample ontologies exported from obo to owl are available [http://www.berkeleybop.org/ontologies here]

=URIs=

Added a separate page on mapping OBO IDs to URIs:

[[OboInOwl:URIs]]

=Overview of Other Mapping efforts=

We are aware that there are several other groups that have created an OBO to OWL mapping to address immediate needs of their research groups. We have compiled a summary of the various OBO to OWL conversion efforts that we are aware of. Email me (nigam .AT. stanford.edu) with additions/deletions as you come across them.

[http://spreadsheets.google.com/ccc?key=pWN_4sBrd9l1Umn1LN8WuQQ Spread sheet comparing the mappings]

=Progress Notes=

I've overhauled the obo2owl mapping. I've pretty much followed Alan's
recommendations (I made a lot of purely internal changes to the xslt too though which should make it much clearer). Hope these work for you Stuart. Sorry about the churn
- but this will definitely be worth it in the end.

Example OWL file can be found here (also attached):

http://geneontology.cvs.sourceforge.net/*checkout*/geneontology/go-dev/xml/examples/gotest.owl

(note that this example includes a cross-product example)

The OWL is generated from either of the following:

http://geneontology.cvs.sourceforge.net/*checkout*/geneontology/go-dev/xml/examples/gotest.obo
http://geneontology.cvs.sourceforge.net/*checkout*/geneontology/go-dev/xml/examples/gotest.obo-xml

The XSL can be found here:

http://geneontology.cvs.sourceforge.net/*checkout*/geneontology/go-dev/xml/xsl/obo2owl.xsl
http://geneontology.cvs.sourceforge.net/*checkout*/geneontology/go-dev/xml/xsl/obo2owl_obo_in_owl_metamodel.xsl

The XSL actually serves as fairly reasonable documentation about what's going on - but we'll also come up with a friendlier description once it's finalised

You can convert the obo-xml directly with the xslt. If you want to
convert from obo you'll need the latest version of go-perl (from cvs)

Here are the changes and things still pending:

Adopted Alan Ruttenberg's metamodel changes (see obo-format list)

split into 2 separate xsl files

subset (ontology views) now more consistent with obo
* the oboInOwl class is SubsetDef
* this does not appear in the owl:Ontology section, it stands alone
(subsets can be used across ontologies)

namespace changes -
* the metamodel is now called oboInOwl
(the format is owned by GO, so this maps to a GO URI)
* the default ontology content namespace is now bioont
(the URI for this will be some bioontologies.org URI)
* slashes not hashes or underscores
- example: rdf:about="oboContent/GO/0000001"

fixed rdf:about/resource/ID issues
- ID is never used
- about and resource now used in correct places

CHECKED

- validates as DL in http://phoebus.cs.man.ac.uk:9999/OWL/Validator
- works in SWOOP
- works in Protege-OWL (but looks odd)

TODO

do we need an equivalentClass for intersectionOf?
SWOOP saves this without

decide on final URI scheme
- Can we make the URIs less verbose? Use entities - or is this frowned on?

new obo tags for obsoletion
handling obsoletes

decide on whether the oboInOwl metamodel should be exported as
part of the content export, or linked to separately;
and if linked to separately, do we need an owl:imports?

OboInOwl:Main Page

2007-03-20T22:04:38Z

Dilvan: /* OBO Converter Protege tab: */

=OBO in OWL: Mapping and Tools=

This wiki is for discussing the mapping between Obo1.2 format and OWL. The [http://www.godatabase.org/dev/doc/mapping-obo-to-owl.html first version] of this mapping is at http://www.godatabase.org/dev/doc/mapping-obo-to-owl.html. We have finished work on a newer version of this mapping. This page provides a brief background for the effort and provides links to the relevant tools (plugins for OBOEdit and Protege) that implement the mapping.

The Gene Ontology and a significant number of biomedical ontologies are in the OBO-format. The OBO format, which originated along with the Gene Ontology, has evolved to support the needs of the biomedical ontologies that fall under the Open Biomedical Ontologies (OBO) umbrella. The OBO-format aims to have 1) human readability, 2) ease of parsing, 3) extensibility and 4) minimal redundancy. The OBO-format currently forms the backbone of most GO based annotation and data analysis tools.

In parallel with the developments in bio-ontologies, ontologies in general have become more prevalent in information technology; with the most visible push coming from the W3C in the form of the W3C recommendation of the Web Ontology Language (OWL) as an international standard for ontologies on the web. There has also been a corresponding increase in the number, diversity and quality of the tools available to construct, maintain and view ontologies in OWL.

As bio-ontologies become more popular and grow in size as well as complexity, they are becoming the focus of attention of the larger computer science research community. On one hand there is significant interest in using the life sciences domain as a “focus” for W3C semantic web activity. In this light, biological data annotated using OBO ontologies is a prime resource and there is great interest from the Semantic Web community to access the ontologies and the annotated data in OWL format. On the other hand, if bio-ontologies are to benefit from the rapid progress being made in computer science – especially the semantic web technologies – bio-ontologies need to interoperate with other ontologies which are in the OWL format. The relatively newer biomedical ontologies (such as BioPAX) are already in OWL. The NCI-thesaurus, being developed by the National Cancer Institute, is also in OWL.

As a result, there is a strong need to map the OBO-format to OWL and provide tools that enable the end user to perform the translation at the click of a button in a stable ontology editing environment without worrying about underlying formats.

=Mail Lists=

We have created the OBO to OWL mapping remaining faithful to the (declared) semantics of the OBO format. At places where we found the format to be vague, we have tightened the semantics and have update the documentation accordingly. We make the mapping tools available for other researchers to use and evaluate the mapping. Please feel free to contact us on these mailing lists if you find anything lacking, have suggestions or have any kind of feedback.

[https://lists.sourceforge.net/lists/listinfo/obo-format Obo Format List]

Also of interest: [https://lists.sourceforge.net/lists/listinfo/obo-crossproducts Obo Cross-Product List]

=The Mapping=

We have made the mapping available as an online Google spreadsheet. You can view the sheet at http://spreadsheets.google.com/ccc?key=pWN_4sBrd9l1Umn1LN8WuQQ. If you want edits rights (or already have them) to leave comments then use the following link http://spreadsheets.google.com/ccc?key=o06770842196506107736.4732937099693365844

=Tools for the mapping=

== Protege plugins ==

== OBO Converter Protege tab: ==

The OBO Converter is a Tab plugin for Protégé to convert OBO format files into OWL files and vice-versa (keeping in mind that OWL to OBO conversions can lose information if one encodes things in OWL that cannot be expressed in OBO). It is also developed in a manner such that it can also work as a standalone conversion program.

'''Tab User Guide'''

The OBO Converter Tab basically reads OBO files (OBO 1.0 and 1.2) into Protégé OWL projects and saves those projects back as OBO 1.0 files. The Tab has two main panels, one to read OBO files and one to write (save) them.

The save operation is straightforward as the user chooses the file name and the conversion is done. The read operation has the same functionality plus a set of options that can alter the way an OBO file is read (see figure).

[[Image:OBOConverter.jpg]]

Read 0ptions:

'''1 Class name generation'''

A Combo box allows users to choose the way the OWL class names will be generated from the OBO format file Terms. There are 3 options:

* OBO id will generate the name from the OBO term id that is the option that generates the OWL id in the way described in the mapping.
* Class name will generate the name from the OBO term name, be careful as those names may not be unique. If the names are not unique, there will be a parser error.
* Class name + OBO id will generate the name from the combination of the OBO term name and id.

In all cases, characters other than letters (a-z, A-Z) or numbers will be converted to underscore characters (_). Ex: the OBO term name “nurse cell” will be converted to the OWL class name nurse_cell.

The default behavior of the Tab is to generate the OWL id in the way described in the mapping and uses the OBO id to generate class names. If the user wants to see the OBO name of the classes, instead of their meaningless ids, Protégé has an option to display the OWL class label as the class identifier. As OWL labels can have language identifiers (such as en for English), converted OBO ontologies can now have names in different languages all pointing to the same entities.

The other options are targeted to users that want to create their ontology using a specific OBO ontology as a start point, but need to name their entities in a different way. Those users are not interested in maintaining naming compatibility with OBO.

'''2 Exclusion of namespaces'''

In OBO format, it is possible to define more than one ontology in each file using the OBO namespace: tag (Note that OBO namespaces have no connection with OWL namespaces). For instance, the Gene Ontology is actually composed by three independent ontologies defined in the same file (gene_ontology.obo) using three different namespaces (''biological_process'', ''molecular_funtion'' and ''cellular_component''). When the OBO Converter Tab reads such file types, it collapses all ontologies in one and namespace information is stored as annotation, which may not be the intention of the user. The OBO Converter Tab has a panel where the user can specify which namespaces he does not want to be read from a file.

Example: In the gene_ontology.obo file, if the namespaces ''biological_process'' and ''molecular_function'' are selected (for not being read), only the ''cellular_component'' ontology will be read.

'''3 Default namespace URI'''

It is the author responsibility to set the default namespace URI for the OWL ontology. That information is not available in the OBO format file. The OBO Converter Tab has a panel where the author can enter this URI. If it does not enter one, whatever default URI Protégé is using becomes the default namespace URI for the OWL ontology.

Downloads:

[http://smi-protege.stanford.edu/svn/obo-converter/trunk/ Source code for OBO Converter Tab]
[http://smi-cbio01.stanford.edu/~nigam/OBOConverter.zip Binaries for OBO Converter Tab]
[http://protege.cim3.net/cgi-bin/wiki.pl?OBOConverter Page at Protege Site]

== OBO Explorer Protege tab: ==

The OWL format for OBO files uses anonymous nodes to represent definitions, synonyms, and DbxRefs, and the generic Protégé GUI components are not immediately suitable to display and edit them. The existing graphical components also do not allow the user to easily access or edit the lexical information associated with an OBO term. The OBO Explorer tab allows the user to do so in an interface that is similar to that of OBO-edit. This provides the user with the flexibility to edit these lexical features (such as synonyms and dbxrefs) in an intuitive manner.

[http://www.aiai.ed.ac.uk/project/cobra-ct/COBrA_downloads.htm OBO Explorer Tab]

[[Image:OBOExplorer.jpg]]

== OboEdit OWL plugin ==
We have also added the functionality to save an OBO format file as an OWL file from within OBOEdit. We have a development version of the OWL Export/Import plugin for OboEdit available. Just download the distribution file, unzip it and copy its content to <OboEdit>/extensions folder. Start OboEdit and you should find the option "OWL Adapter" for loading ontologies, File->Load Terms..., and for saving, File->Save as...

[http://smi-cbio01.stanford.edu/~nigam/OboEditPlugin.zip OboEdit OWL plugin].

If you have problems with big ontologies, try to increase the size of the memory available to OboEdit.

== obo2owl xslt ==

The oboxml_to_owl.xsl mapping now implements the OboInOwl mapping for obo-xml:

[http://geneontology.cvs.sourceforge.net/geneontology/go-dev/xml/xsl/oboxml_to_owl.xsl?view=log XSLT]

This will be bundled with [http://search.cpan.org/~cmungall/go-perl/ go-perl-0.07] and higher

Sample ontologies exported from obo to owl are available [http://www.berkeleybop.org/ontologies here]

=URIs=

Added a separate page on mapping OBO IDs to URIs:

[[OboInOwl:URIs]]

=Overview of Other Mapping efforts=

We are aware that there are several other groups that have created an OBO to OWL mapping to address immediate needs of their research groups. We have compiled a summary of the various OBO to OWL conversion efforts that we are aware of. Email me (nigam .AT. stanford.edu) with additions/deletions as you come across them.

[http://spreadsheets.google.com/ccc?key=pWN_4sBrd9l1Umn1LN8WuQQ Spread sheet comparing the mappings]

=Progress Notes=

I've overhauled the obo2owl mapping. I've pretty much followed Alan's
recommendations (I made a lot of purely internal changes to the xslt too though which should make it much clearer). Hope these work for you Stuart. Sorry about the churn
- but this will definitely be worth it in the end.

Example OWL file can be found here (also attached):

http://geneontology.cvs.sourceforge.net/*checkout*/geneontology/go-dev/xml/examples/gotest.owl

(note that this example includes a cross-product example)

The OWL is generated from either of the following:

http://geneontology.cvs.sourceforge.net/*checkout*/geneontology/go-dev/xml/examples/gotest.obo
http://geneontology.cvs.sourceforge.net/*checkout*/geneontology/go-dev/xml/examples/gotest.obo-xml

The XSL can be found here:

http://geneontology.cvs.sourceforge.net/*checkout*/geneontology/go-dev/xml/xsl/obo2owl.xsl
http://geneontology.cvs.sourceforge.net/*checkout*/geneontology/go-dev/xml/xsl/obo2owl_obo_in_owl_metamodel.xsl

The XSL actually serves as fairly reasonable documentation about what's going on - but we'll also come up with a friendlier description once it's finalised

You can convert the obo-xml directly with the xslt. If you want to
convert from obo you'll need the latest version of go-perl (from cvs)

Here are the changes and things still pending:

Adopted Alan Ruttenberg's metamodel changes (see obo-format list)

split into 2 separate xsl files

subset (ontology views) now more consistent with obo
* the oboInOwl class is SubsetDef
* this does not appear in the owl:Ontology section, it stands alone
(subsets can be used across ontologies)

namespace changes -
* the metamodel is now called oboInOwl
(the format is owned by GO, so this maps to a GO URI)
* the default ontology content namespace is now bioont
(the URI for this will be some bioontologies.org URI)
* slashes not hashes or underscores
- example: rdf:about="oboContent/GO/0000001"

fixed rdf:about/resource/ID issues
- ID is never used
- about and resource now used in correct places

CHECKED

- validates as DL in http://phoebus.cs.man.ac.uk:9999/OWL/Validator
- works in SWOOP
- works in Protege-OWL (but looks odd)

TODO

do we need an equivalentClass for intersectionOf?
SWOOP saves this without

decide on final URI scheme
- Can we make the URIs less verbose? Use entities - or is this frowned on?

new obo tags for obsoletion
handling obsoletes

decide on whether the oboInOwl metamodel should be exported as
part of the content export, or linked to separately;
and if linked to separately, do we need an owl:imports?

OboInOwl:Main Page

2007-03-20T22:00:01Z

Dilvan: /* Protege plugins */

=OBO in OWL: Mapping and Tools=

This wiki is for discussing the mapping between Obo1.2 format and OWL. The [http://www.godatabase.org/dev/doc/mapping-obo-to-owl.html first version] of this mapping is at http://www.godatabase.org/dev/doc/mapping-obo-to-owl.html. We have finished work on a newer version of this mapping. This page provides a brief background for the effort and provides links to the relevant tools (plugins for OBOEdit and Protege) that implement the mapping.

The Gene Ontology and a significant number of biomedical ontologies are in the OBO-format. The OBO format, which originated along with the Gene Ontology, has evolved to support the needs of the biomedical ontologies that fall under the Open Biomedical Ontologies (OBO) umbrella. The OBO-format aims to have 1) human readability, 2) ease of parsing, 3) extensibility and 4) minimal redundancy. The OBO-format currently forms the backbone of most GO based annotation and data analysis tools.

In parallel with the developments in bio-ontologies, ontologies in general have become more prevalent in information technology; with the most visible push coming from the W3C in the form of the W3C recommendation of the Web Ontology Language (OWL) as an international standard for ontologies on the web. There has also been a corresponding increase in the number, diversity and quality of the tools available to construct, maintain and view ontologies in OWL.

As bio-ontologies become more popular and grow in size as well as complexity, they are becoming the focus of attention of the larger computer science research community. On one hand there is significant interest in using the life sciences domain as a “focus” for W3C semantic web activity. In this light, biological data annotated using OBO ontologies is a prime resource and there is great interest from the Semantic Web community to access the ontologies and the annotated data in OWL format. On the other hand, if bio-ontologies are to benefit from the rapid progress being made in computer science – especially the semantic web technologies – bio-ontologies need to interoperate with other ontologies which are in the OWL format. The relatively newer biomedical ontologies (such as BioPAX) are already in OWL. The NCI-thesaurus, being developed by the National Cancer Institute, is also in OWL.

As a result, there is a strong need to map the OBO-format to OWL and provide tools that enable the end user to perform the translation at the click of a button in a stable ontology editing environment without worrying about underlying formats.

=Mail Lists=

We have created the OBO to OWL mapping remaining faithful to the (declared) semantics of the OBO format. At places where we found the format to be vague, we have tightened the semantics and have update the documentation accordingly. We make the mapping tools available for other researchers to use and evaluate the mapping. Please feel free to contact us on these mailing lists if you find anything lacking, have suggestions or have any kind of feedback.

[https://lists.sourceforge.net/lists/listinfo/obo-format Obo Format List]

Also of interest: [https://lists.sourceforge.net/lists/listinfo/obo-crossproducts Obo Cross-Product List]

=The Mapping=

We have made the mapping available as an online Google spreadsheet. You can view the sheet at http://spreadsheets.google.com/ccc?key=pWN_4sBrd9l1Umn1LN8WuQQ. If you want edits rights (or already have them) to leave comments then use the following link http://spreadsheets.google.com/ccc?key=o06770842196506107736.4732937099693365844

=Tools for the mapping=

== Protege plugins ==

== OBO Converter Protege tab: ==

The OBO Converter is a Tab plugin for Protégé to convert OBO format files into OWL files and vice-versa (keeping in mind that OWL to OBO conversions can lose information if one encodes things in OWL that cannot be expressed in OBO). It is also developed in a manner such that it can also work as a standalone conversion program.

'''Tab User Guide'''

The OBO Converter Tab basically reads OBO files (OBO 1.0 and 1.2) into Protégé OWL projects and saves those projects back as OBO 1.0 files. The Tab has two main panels, one to read OBO files and one to write (save) them.

The save operation is straightforward as the user chooses the file name and the conversion is done. The read operation has the same functionality plus a set of options that can alter the way an OBO file is read (see figure).

[[Image:OBOConverter.jpg]]

Read 0ptions:

'''1 Class name generation'''

A Combo box allows users to choose the way the OWL class names will be generated from the OBO format file Terms. There are 3 options:

* OBO id will generate the name from the OBO term id that is the option that generates the OWL id in the way described in the mapping.
* Class name will generate the name from the OBO term name, be careful as those names may not be unique. If the names are not unique, there will be a parser error.
* Class name + OBO id will generate the name from the combination of the OBO term name and id.

In all cases, characters other than letters (a-z, A-Z) or numbers will be converted to underscore characters (_). Ex: the OBO term name “nurse cell” will be converted to the OWL class name nurse_cell.

The default behavior of the Tab is to generate the OWL id in the way described in the mapping and uses the OBO id to generate class names. If the user wants to see the OBO name of the classes, instead of their meaningless ids, Protégé has an option to display the OWL class label as the class identifier. As OWL labels can have language identifiers (such as en for English), converted OBO ontologies can now have names in different languages all pointing to the same entities.

The other options are targeted to users that want to create their ontology using a specific OBO ontology as a start point, but need to name their entities in a different way. Those users are not interested in maintaining naming compatibility with OBO.

'''2 Exclusion of namespaces'''

In OBO format, it is possible to define more than one ontology in each file using the OBO namespace: tag (Note that OBO namespaces have no connection with OWL namespaces). For instance, the Gene Ontology is actually composed by three independent ontologies defined in the same file (gene_ontology.obo) using three different namespaces (biological_process, molecular_funtion and cellular_component). When the OBO Converter Tab reads such types of file, it collapses all ontologies in one and namespace information is stored as annotation, which may not be the intention of the user. The OBO Converter Tab has a panel where the user can specify which namespaces he does not want to be read from a file.

Example: In the gene_ontology.obo file, if the namespaces ''biological_process'' and ''molecular_function'' are not read, only the ''cellular_component'' ontology will be read.

'''3 Default namespace URI'''

It is the author responsibility to set the default namespace URI for the OWL ontology. That information is not available in the OBO format file. The OBO Converter Tab has a panel where the author can enter this URI. If it does not enter one, whatever default URI Protégé is using becomes the default namespace.

Downloads:

[http://smi-protege.stanford.edu/svn/obo-converter/trunk/ Source code for OBO Converter Tab]
[http://smi-cbio01.stanford.edu/~nigam/OBOConverter.zip Binaries for OBO Converter Tab]
[http://protege.cim3.net/cgi-bin/wiki.pl?OBOConverter Page at Protege Site]

== OBO Explorer Protege tab: ==

The OWL format for OBO files uses anonymous nodes to represent definitions, synonyms, and DbxRefs, and the generic Protégé GUI components are not immediately suitable to display and edit them. The existing graphical components also do not allow the user to easily access or edit the lexical information associated with an OBO term. The OBO Explorer tab allows the user to do so in an interface that is similar to that of OBO-edit. This provides the user with the flexibility to edit these lexical features (such as synonyms and dbxrefs) in an intuitive manner.

[http://www.aiai.ed.ac.uk/project/cobra-ct/COBrA_downloads.htm OBO Explorer Tab]

[[Image:OBOExplorer.jpg]]

== OboEdit OWL plugin ==
We have also added the functionality to save an OBO format file as an OWL file from within OBOEdit. We have a development version of the OWL Export/Import plugin for OboEdit available. Just download the distribution file, unzip it and copy its content to <OboEdit>/extensions folder. Start OboEdit and you should find the option "OWL Adapter" for loading ontologies, File->Load Terms..., and for saving, File->Save as...

[http://smi-cbio01.stanford.edu/~nigam/OboEditPlugin.zip OboEdit OWL plugin].

If you have problems with big ontologies, try to increase the size of the memory available to OboEdit.

== obo2owl xslt ==

The oboxml_to_owl.xsl mapping now implements the OboInOwl mapping for obo-xml:

[http://geneontology.cvs.sourceforge.net/geneontology/go-dev/xml/xsl/oboxml_to_owl.xsl?view=log XSLT]

This will be bundled with [http://search.cpan.org/~cmungall/go-perl/ go-perl-0.07] and higher

Sample ontologies exported from obo to owl are available [http://www.berkeleybop.org/ontologies here]

=URIs=

Added a separate page on mapping OBO IDs to URIs:

[[OboInOwl:URIs]]

=Overview of Other Mapping efforts=

We are aware that there are several other groups that have created an OBO to OWL mapping to address immediate needs of their research groups. We have compiled a summary of the various OBO to OWL conversion efforts that we are aware of. Email me (nigam .AT. stanford.edu) with additions/deletions as you come across them.

[http://spreadsheets.google.com/ccc?key=pWN_4sBrd9l1Umn1LN8WuQQ Spread sheet comparing the mappings]

=Progress Notes=

I've overhauled the obo2owl mapping. I've pretty much followed Alan's
recommendations (I made a lot of purely internal changes to the xslt too though which should make it much clearer). Hope these work for you Stuart. Sorry about the churn
- but this will definitely be worth it in the end.

Example OWL file can be found here (also attached):

http://geneontology.cvs.sourceforge.net/*checkout*/geneontology/go-dev/xml/examples/gotest.owl

(note that this example includes a cross-product example)

The OWL is generated from either of the following:

http://geneontology.cvs.sourceforge.net/*checkout*/geneontology/go-dev/xml/examples/gotest.obo
http://geneontology.cvs.sourceforge.net/*checkout*/geneontology/go-dev/xml/examples/gotest.obo-xml

The XSL can be found here:

http://geneontology.cvs.sourceforge.net/*checkout*/geneontology/go-dev/xml/xsl/obo2owl.xsl
http://geneontology.cvs.sourceforge.net/*checkout*/geneontology/go-dev/xml/xsl/obo2owl_obo_in_owl_metamodel.xsl

The XSL actually serves as fairly reasonable documentation about what's going on - but we'll also come up with a friendlier description once it's finalised

You can convert the obo-xml directly with the xslt. If you want to
convert from obo you'll need the latest version of go-perl (from cvs)

Here are the changes and things still pending:

Adopted Alan Ruttenberg's metamodel changes (see obo-format list)

split into 2 separate xsl files

subset (ontology views) now more consistent with obo
* the oboInOwl class is SubsetDef
* this does not appear in the owl:Ontology section, it stands alone
(subsets can be used across ontologies)

namespace changes -
* the metamodel is now called oboInOwl
(the format is owned by GO, so this maps to a GO URI)
* the default ontology content namespace is now bioont
(the URI for this will be some bioontologies.org URI)
* slashes not hashes or underscores
- example: rdf:about="oboContent/GO/0000001"

fixed rdf:about/resource/ID issues
- ID is never used
- about and resource now used in correct places

CHECKED

- validates as DL in http://phoebus.cs.man.ac.uk:9999/OWL/Validator
- works in SWOOP
- works in Protege-OWL (but looks odd)

TODO

do we need an equivalentClass for intersectionOf?
SWOOP saves this without

decide on final URI scheme
- Can we make the URIs less verbose? Use entities - or is this frowned on?

new obo tags for obsoletion
handling obsoletes

decide on whether the oboInOwl metamodel should be exported as
part of the content export, or linked to separately;
and if linked to separately, do we need an owl:imports?

OboInOwl:Main Page

2007-03-20T21:55:45Z

Dilvan: /* Protege plugins */

=OBO in OWL: Mapping and Tools=

This wiki is for discussing the mapping between Obo1.2 format and OWL. The [http://www.godatabase.org/dev/doc/mapping-obo-to-owl.html first version] of this mapping is at http://www.godatabase.org/dev/doc/mapping-obo-to-owl.html. We have finished work on a newer version of this mapping. This page provides a brief background for the effort and provides links to the relevant tools (plugins for OBOEdit and Protege) that implement the mapping.

The Gene Ontology and a significant number of biomedical ontologies are in the OBO-format. The OBO format, which originated along with the Gene Ontology, has evolved to support the needs of the biomedical ontologies that fall under the Open Biomedical Ontologies (OBO) umbrella. The OBO-format aims to have 1) human readability, 2) ease of parsing, 3) extensibility and 4) minimal redundancy. The OBO-format currently forms the backbone of most GO based annotation and data analysis tools.

In parallel with the developments in bio-ontologies, ontologies in general have become more prevalent in information technology; with the most visible push coming from the W3C in the form of the W3C recommendation of the Web Ontology Language (OWL) as an international standard for ontologies on the web. There has also been a corresponding increase in the number, diversity and quality of the tools available to construct, maintain and view ontologies in OWL.

As bio-ontologies become more popular and grow in size as well as complexity, they are becoming the focus of attention of the larger computer science research community. On one hand there is significant interest in using the life sciences domain as a “focus” for W3C semantic web activity. In this light, biological data annotated using OBO ontologies is a prime resource and there is great interest from the Semantic Web community to access the ontologies and the annotated data in OWL format. On the other hand, if bio-ontologies are to benefit from the rapid progress being made in computer science – especially the semantic web technologies – bio-ontologies need to interoperate with other ontologies which are in the OWL format. The relatively newer biomedical ontologies (such as BioPAX) are already in OWL. The NCI-thesaurus, being developed by the National Cancer Institute, is also in OWL.

As a result, there is a strong need to map the OBO-format to OWL and provide tools that enable the end user to perform the translation at the click of a button in a stable ontology editing environment without worrying about underlying formats.

=Mail Lists=

We have created the OBO to OWL mapping remaining faithful to the (declared) semantics of the OBO format. At places where we found the format to be vague, we have tightened the semantics and have update the documentation accordingly. We make the mapping tools available for other researchers to use and evaluate the mapping. Please feel free to contact us on these mailing lists if you find anything lacking, have suggestions or have any kind of feedback.

[https://lists.sourceforge.net/lists/listinfo/obo-format Obo Format List]

Also of interest: [https://lists.sourceforge.net/lists/listinfo/obo-crossproducts Obo Cross-Product List]

=The Mapping=

We have made the mapping available as an online Google spreadsheet. You can view the sheet at http://spreadsheets.google.com/ccc?key=pWN_4sBrd9l1Umn1LN8WuQQ. If you want edits rights (or already have them) to leave comments then use the following link http://spreadsheets.google.com/ccc?key=o06770842196506107736.4732937099693365844

=Tools for the mapping=

== Protege plugins ==

'''OBO Converter Protege tab:'''

The OBO Converter is a Tab plugin for Protégé to convert OBO format files into OWL files and vice-versa (keeping in mind that OWL to OBO conversions can lose information if one encodes things in OWL that cannot be expressed in OBO). It is also developed in a manner such that it can also work as a standalone conversion program.

'''Tab User Guide'''

The OBO Converter Tab basically reads OBO files (OBO 1.0 and 1.2) into Protégé OWL projects and saves those projects back as OBO 1.0 files. The Tab has two main panels, one to read OBO files and one to write (save) them.

The save operation is straightforward as the user chooses the file name and the conversion is done. The read operation has the same functionality plus a set of options that can alter the way an OBO file is read (see figure).

[[Image:OBOConverter.jpg]]

Read 0ptions:

1 Class name generation
A Combo box allows users to choose the way the OWL class names will be generated from the OBO format file Terms. There are 3 options:

* OBO id will generate the name from the OBO term id that is the option that generates the OWL id in the way described in the mapping.
* Class name will generate the name from the OBO term name, be careful as those names may not be unique. If the names are not unique, there will be a parser error.
* Class name + OBO id will generate the name from the combination of the OBO term name and id.
In all cases, characters other than letters (a-z, A-Z) or numbers will be converted to underscore characters (_). Ex: the OBO term name “nurse cell” will be converted to the OWL class name nurse_cell.
The default behavior of the Tab is to generate the OWL id in the way described in the mapping and uses the OBO id to generate class names. If the user wants to see the OBO name of the classes, instead of their meaningless ids, Protégé has an option to display the OWL class label as the class identifier. As OWL labels can have language identifiers (such as en for English), converted OBO ontologies can now have names in different languages all pointing to the same entities.
The other options are targeted to users that want to create their ontology using a specific OBO ontology as a start point, but need to name their entities in a different way. Those users are not interested in maintaining naming compatibility with OBO.

2 Exclusion of namespaces

In OBO format, it is possible to define more than one ontology in each file using the OBO namespace: tag (Note that OBO namespaces have no connection with OWL namespaces). For instance, the Gene Ontology is actually composed by three independent ontologies defined in the same file (gene_ontology.obo) using three different namespaces (biological_process, molecular_funtion and cellular_component). When the OBO Converter Tab reads such types of file, it collapses all ontologies in one and namespace information is stored as annotation, which may not be the intention of the user. The OBO Converter Tab has a panel where the user can specify which namespaces he does not want to be read from a file.
Example: In the gene_ontology.obo file, if the namespaces biological_process and molecular_function are not read, only the cellular_component ontology will be read.

3 Default namespace URI

It is the author responsibility to set the default namespace URI for the OWL ontology. That information is not available in the OBO format file. The OBO Converter Tab has a panel where the author can enter this URI. If it does not enter one, whatever default URI Protégé is using becomes the default namespace.

Downloads:

[http://smi-protege.stanford.edu/svn/obo-converter/trunk/ Source code for OBO Converter Tab]
[http://smi-cbio01.stanford.edu/~nigam/OBOConverter.zip Binaries for OBO Converter Tab]
[http://protege.cim3.net/cgi-bin/wiki.pl?OBOConverter Page at Protege Site]

'''OBO Explorer Protege tab:'''

The OWL format for OBO files uses anonymous nodes to represent definitions, synonyms, and DbxRefs, and the generic Protégé GUI components are not immediately suitable to display and edit them. The existing graphical components also do not allow the user to easily access or edit the lexical information associated with an OBO term. The OBO Explorer tab allows the user to do so in an interface that is similar to that of OBO-edit. This provides the user with the flexibility to edit these lexical features (such as synonyms and dbxrefs) in an intuitive manner.

[http://www.aiai.ed.ac.uk/project/cobra-ct/COBrA_downloads.htm OBO Explorer Tab]

[[Image:OBOExplorer.jpg]]

== OboEdit OWL plugin ==
We have also added the functionality to save an OBO format file as an OWL file from within OBOEdit. We have a development version of the OWL Export/Import plugin for OboEdit available. Just download the distribution file, unzip it and copy its content to <OboEdit>/extensions folder. Start OboEdit and you should find the option "OWL Adapter" for loading ontologies, File->Load Terms..., and for saving, File->Save as...

[http://smi-cbio01.stanford.edu/~nigam/OboEditPlugin.zip OboEdit OWL plugin].

If you have problems with big ontologies, try to increase the size of the memory available to OboEdit.

== obo2owl xslt ==

The oboxml_to_owl.xsl mapping now implements the OboInOwl mapping for obo-xml:

[http://geneontology.cvs.sourceforge.net/geneontology/go-dev/xml/xsl/oboxml_to_owl.xsl?view=log XSLT]

This will be bundled with [http://search.cpan.org/~cmungall/go-perl/ go-perl-0.07] and higher

Sample ontologies exported from obo to owl are available [http://www.berkeleybop.org/ontologies here]

=URIs=

Added a separate page on mapping OBO IDs to URIs:

[[OboInOwl:URIs]]

=Overview of Other Mapping efforts=

We are aware that there are several other groups that have created an OBO to OWL mapping to address immediate needs of their research groups. We have compiled a summary of the various OBO to OWL conversion efforts that we are aware of. Email me (nigam .AT. stanford.edu) with additions/deletions as you come across them.

[http://spreadsheets.google.com/ccc?key=pWN_4sBrd9l1Umn1LN8WuQQ Spread sheet comparing the mappings]

=Progress Notes=

I've overhauled the obo2owl mapping. I've pretty much followed Alan's
recommendations (I made a lot of purely internal changes to the xslt too though which should make it much clearer). Hope these work for you Stuart. Sorry about the churn
- but this will definitely be worth it in the end.

Example OWL file can be found here (also attached):

http://geneontology.cvs.sourceforge.net/*checkout*/geneontology/go-dev/xml/examples/gotest.owl

(note that this example includes a cross-product example)

The OWL is generated from either of the following:

http://geneontology.cvs.sourceforge.net/*checkout*/geneontology/go-dev/xml/examples/gotest.obo
http://geneontology.cvs.sourceforge.net/*checkout*/geneontology/go-dev/xml/examples/gotest.obo-xml

The XSL can be found here:

http://geneontology.cvs.sourceforge.net/*checkout*/geneontology/go-dev/xml/xsl/obo2owl.xsl
http://geneontology.cvs.sourceforge.net/*checkout*/geneontology/go-dev/xml/xsl/obo2owl_obo_in_owl_metamodel.xsl

The XSL actually serves as fairly reasonable documentation about what's going on - but we'll also come up with a friendlier description once it's finalised

You can convert the obo-xml directly with the xslt. If you want to
convert from obo you'll need the latest version of go-perl (from cvs)

Here are the changes and things still pending:

Adopted Alan Ruttenberg's metamodel changes (see obo-format list)

split into 2 separate xsl files

subset (ontology views) now more consistent with obo
* the oboInOwl class is SubsetDef
* this does not appear in the owl:Ontology section, it stands alone
(subsets can be used across ontologies)

namespace changes -
* the metamodel is now called oboInOwl
(the format is owned by GO, so this maps to a GO URI)
* the default ontology content namespace is now bioont
(the URI for this will be some bioontologies.org URI)
* slashes not hashes or underscores
- example: rdf:about="oboContent/GO/0000001"

fixed rdf:about/resource/ID issues
- ID is never used
- about and resource now used in correct places

CHECKED

- validates as DL in http://phoebus.cs.man.ac.uk:9999/OWL/Validator
- works in SWOOP
- works in Protege-OWL (but looks odd)

TODO

do we need an equivalentClass for intersectionOf?
SWOOP saves this without

decide on final URI scheme
- Can we make the URIs less verbose? Use entities - or is this frowned on?

new obo tags for obsoletion
handling obsoletes

decide on whether the oboInOwl metamodel should be exported as
part of the content export, or linked to separately;
and if linked to separately, do we need an owl:imports?

OboInOwl:Main Page

2007-03-20T21:50:34Z

Dilvan: /* Protege plugins */

=OBO in OWL: Mapping and Tools=

This wiki is for discussing the mapping between Obo1.2 format and OWL. The [http://www.godatabase.org/dev/doc/mapping-obo-to-owl.html first version] of this mapping is at http://www.godatabase.org/dev/doc/mapping-obo-to-owl.html. We have finished work on a newer version of this mapping. This page provides a brief background for the effort and provides links to the relevant tools (plugins for OBOEdit and Protege) that implement the mapping.

The Gene Ontology and a significant number of biomedical ontologies are in the OBO-format. The OBO format, which originated along with the Gene Ontology, has evolved to support the needs of the biomedical ontologies that fall under the Open Biomedical Ontologies (OBO) umbrella. The OBO-format aims to have 1) human readability, 2) ease of parsing, 3) extensibility and 4) minimal redundancy. The OBO-format currently forms the backbone of most GO based annotation and data analysis tools.

In parallel with the developments in bio-ontologies, ontologies in general have become more prevalent in information technology; with the most visible push coming from the W3C in the form of the W3C recommendation of the Web Ontology Language (OWL) as an international standard for ontologies on the web. There has also been a corresponding increase in the number, diversity and quality of the tools available to construct, maintain and view ontologies in OWL.

As bio-ontologies become more popular and grow in size as well as complexity, they are becoming the focus of attention of the larger computer science research community. On one hand there is significant interest in using the life sciences domain as a “focus” for W3C semantic web activity. In this light, biological data annotated using OBO ontologies is a prime resource and there is great interest from the Semantic Web community to access the ontologies and the annotated data in OWL format. On the other hand, if bio-ontologies are to benefit from the rapid progress being made in computer science – especially the semantic web technologies – bio-ontologies need to interoperate with other ontologies which are in the OWL format. The relatively newer biomedical ontologies (such as BioPAX) are already in OWL. The NCI-thesaurus, being developed by the National Cancer Institute, is also in OWL.

As a result, there is a strong need to map the OBO-format to OWL and provide tools that enable the end user to perform the translation at the click of a button in a stable ontology editing environment without worrying about underlying formats.

=Mail Lists=

We have created the OBO to OWL mapping remaining faithful to the (declared) semantics of the OBO format. At places where we found the format to be vague, we have tightened the semantics and have update the documentation accordingly. We make the mapping tools available for other researchers to use and evaluate the mapping. Please feel free to contact us on these mailing lists if you find anything lacking, have suggestions or have any kind of feedback.

[https://lists.sourceforge.net/lists/listinfo/obo-format Obo Format List]

Also of interest: [https://lists.sourceforge.net/lists/listinfo/obo-crossproducts Obo Cross-Product List]

=The Mapping=

We have made the mapping available as an online Google spreadsheet. You can view the sheet at http://spreadsheets.google.com/ccc?key=pWN_4sBrd9l1Umn1LN8WuQQ. If you want edits rights (or already have them) to leave comments then use the following link http://spreadsheets.google.com/ccc?key=o06770842196506107736.4732937099693365844

=Tools for the mapping=

== Protege plugins ==

'''OBO Converter Protege tab:'''

The OBO Converter is a Tab plugin for Protégé to convert OBO format files into OWL files and vice-versa (keeping in mind that OWL to OBO conversions can lose information if one encodes things in OWL that cannot be expressed in OBO). It is also developed in a manner such that it can also work as a standalone conversion program.

'''Tab User Guide'''

The OBO Converter Tab basically reads OBO files (OBO 1.0 and 1.2) into Protégé OWL projects and saves those projects back as OBO 1.0 files. The Tab has two main panels, one to read OBO files and one to write (save) them.

The save operation is straightforward as the user chooses the file name and the conversion is done. The read operation has the same functionality plus a set of options that can alter the way an OBO file is read (see figure).

[[Image:OBOConverter.jpg]]

There are options toUsers have

1- Users can choose the way the OWL class names will be generated from the OBO format file Terms. There are 3 options:

*OBO id This option will generate the name from the OBO term id. This is the default option and generates the OWL id in the way described in our mapping.
*Class name This option will generate the name from the OBO term name. This has to be used with care because the names are not required to be unique. If the names are not unique, there will be a parser error.
*Class name + OBO id This option will generate the name from the combination of the OBO term name and id.

In all cases, characters other than letters (a-z, A-Z) or numbers will be converted to underscore characters (_). Ex: the OBO term name “nurse cell” will be converted to the OWL class name nurse_cell.
The default behavior of the Tab is to generate the OWL class names from the OBO id. If the user wants to see the OBO name, instead of their meaningless ids, as the class identifier, Protégé has an option to display the OWL class label as the identifier. As OWL labels can also have language identifiers (such as en for English), converted OBO ontologies can now have names in different languages all pointing to the same entities allowing for language localization while preserving the OBO ids. The other options are targeted to users that want to create their ontology using a specific OBO ontology as a start point, but want to name their entities in a different way.

Downloads:

[http://smi-protege.stanford.edu/svn/obo-converter/trunk/ Source code for OBO Converter Tab]
[http://smi-cbio01.stanford.edu/~nigam/OBOConverter.zip Binaries for OBO Converter Tab]
[http://protege.cim3.net/cgi-bin/wiki.pl?OBOConverter Instructions for OBO Converter Tab]

'''OBO Explorer Protege tab:'''

The OWL format for OBO files uses anonymous nodes to represent definitions, synonyms, and DbxRefs, and the generic Protégé GUI components are not immediately suitable to display and edit them. The existing graphical components also do not allow the user to easily access or edit the lexical information associated with an OBO term. The OBO Explorer tab allows the user to do so in an interface that is similar to that of OBO-edit. This provides the user with the flexibility to edit these lexical features (such as synonyms and dbxrefs) in an intuitive manner.

[http://www.aiai.ed.ac.uk/project/cobra-ct/COBrA_downloads.htm OBO Explorer Tab]

[[Image:OBOExplorer.jpg]]

== OboEdit OWL plugin ==
We have also added the functionality to save an OBO format file as an OWL file from within OBOEdit. We have a development version of the OWL Export/Import plugin for OboEdit available. Just download the distribution file, unzip it and copy its content to <OboEdit>/extensions folder. Start OboEdit and you should find the option "OWL Adapter" for loading ontologies, File->Load Terms..., and for saving, File->Save as...

[http://smi-cbio01.stanford.edu/~nigam/OboEditPlugin.zip OboEdit OWL plugin].

If you have problems with big ontologies, try to increase the size of the memory available to OboEdit.

== obo2owl xslt ==

The oboxml_to_owl.xsl mapping now implements the OboInOwl mapping for obo-xml:

[http://geneontology.cvs.sourceforge.net/geneontology/go-dev/xml/xsl/oboxml_to_owl.xsl?view=log XSLT]

This will be bundled with [http://search.cpan.org/~cmungall/go-perl/ go-perl-0.07] and higher

Sample ontologies exported from obo to owl are available [http://www.berkeleybop.org/ontologies here]

=URIs=

Added a separate page on mapping OBO IDs to URIs:

[[OboInOwl:URIs]]

=Overview of Other Mapping efforts=

We are aware that there are several other groups that have created an OBO to OWL mapping to address immediate needs of their research groups. We have compiled a summary of the various OBO to OWL conversion efforts that we are aware of. Email me (nigam .AT. stanford.edu) with additions/deletions as you come across them.

[http://spreadsheets.google.com/ccc?key=pWN_4sBrd9l1Umn1LN8WuQQ Spread sheet comparing the mappings]

=Progress Notes=

I've overhauled the obo2owl mapping. I've pretty much followed Alan's
recommendations (I made a lot of purely internal changes to the xslt too though which should make it much clearer). Hope these work for you Stuart. Sorry about the churn
- but this will definitely be worth it in the end.

Example OWL file can be found here (also attached):

http://geneontology.cvs.sourceforge.net/*checkout*/geneontology/go-dev/xml/examples/gotest.owl

(note that this example includes a cross-product example)

The OWL is generated from either of the following:

http://geneontology.cvs.sourceforge.net/*checkout*/geneontology/go-dev/xml/examples/gotest.obo
http://geneontology.cvs.sourceforge.net/*checkout*/geneontology/go-dev/xml/examples/gotest.obo-xml

The XSL can be found here:

http://geneontology.cvs.sourceforge.net/*checkout*/geneontology/go-dev/xml/xsl/obo2owl.xsl
http://geneontology.cvs.sourceforge.net/*checkout*/geneontology/go-dev/xml/xsl/obo2owl_obo_in_owl_metamodel.xsl

The XSL actually serves as fairly reasonable documentation about what's going on - but we'll also come up with a friendlier description once it's finalised

You can convert the obo-xml directly with the xslt. If you want to
convert from obo you'll need the latest version of go-perl (from cvs)

Here are the changes and things still pending:

Adopted Alan Ruttenberg's metamodel changes (see obo-format list)

split into 2 separate xsl files

subset (ontology views) now more consistent with obo
* the oboInOwl class is SubsetDef
* this does not appear in the owl:Ontology section, it stands alone
(subsets can be used across ontologies)

namespace changes -
* the metamodel is now called oboInOwl
(the format is owned by GO, so this maps to a GO URI)
* the default ontology content namespace is now bioont
(the URI for this will be some bioontologies.org URI)
* slashes not hashes or underscores
- example: rdf:about="oboContent/GO/0000001"

fixed rdf:about/resource/ID issues
- ID is never used
- about and resource now used in correct places

CHECKED

- validates as DL in http://phoebus.cs.man.ac.uk:9999/OWL/Validator
- works in SWOOP
- works in Protege-OWL (but looks odd)

TODO

do we need an equivalentClass for intersectionOf?
SWOOP saves this without

decide on final URI scheme
- Can we make the URIs less verbose? Use entities - or is this frowned on?

new obo tags for obsoletion
handling obsoletes

decide on whether the oboInOwl metamodel should be exported as
part of the content export, or linked to separately;
and if linked to separately, do we need an owl:imports?

User:Dilvan

2007-03-15T00:29:32Z

Dilvan: /* OWL Export/Import plugin for OboEdit */

OboInOwl:Main Page

2007-02-14T19:31:44Z

Dilvan: /* OboInOwl */

=OBO in OWL: Mapping and Tools=

This wiki is for discussing the mapping between Obo1.2 format and OWL. The [http://www.godatabase.org/dev/doc/mapping-obo-to-owl.html first version] of this mapping is at http://www.godatabase.org/dev/doc/mapping-obo-to-owl.html. We have finished work on a newer version of this mapping. This page provides a brief background for the effort and provides links to the relevant tools (plugins for OBOEdit and Protege) that implement the mapping.

The Gene Ontology and a significant number of biomedical ontologies are in the OBO-format. The OBO format, which originated along with the Gene Ontology, has evolved to support the needs of the biomedical ontologies that fall under the Open Biomedical Ontologies (OBO) umbrella. The OBO-format aims to have 1) human readability, 2) ease of parsing, 3) extensibility and 4) minimal redundancy. The OBO-format currently forms the backbone of most GO based annotation and data analysis tools.

In parallel with the developments in bio-ontologies, ontologies in general have become more prevalent in information technology; with the most visible push coming from the W3C in the form of the W3C recommendation of the Web Ontology Language (OWL) as an international standard for ontologies on the web. There has also been a corresponding increase in the number, diversity and quality of the tools available to construct, maintain and view ontologies in OWL.

As bio-ontologies become more popular and grow in size as well as complexity, they are becoming the focus of attention of the larger computer science research community. On one hand there is significant interest in using the life sciences domain as a “focus” for W3C semantic web activity. In this light, biological data annotated using OBO ontologies is a prime resource and there is great interest from the Semantic Web community to access the ontologies and the annotated data in OWL format. On the other hand, if bio-ontologies are to benefit from the rapid progress being made in computer science – especially the semantic web technologies – bio-ontologies need to interoperate with other ontologies which are in the OWL format. The relatively newer biomedical ontologies (such as BioPAX) are already in OWL. The NCI-thesaurus, being developed by the National Cancer Institute, is also in OWL.

As a result, there is a strong need to map the OBO-format to OWL and provide tools that enable the end user to perform the translation at the click of a button in a stable ontology editing environment without worrying about underlying formats.

=Mail Lists=

We have created the OBO to OWL mapping remaining faithful to the (declared) semantics of the OBO format. At places where we found the format to be vague, we have tightened the semantics and have update the documentation accordingly. We make the mapping tools available for other researchers to use and evaluate the mapping. Please feel free to contact us on these mailing lists if you find anything lacking, have suggestions or have any kind of feedback.

[https://lists.sourceforge.net/lists/listinfo/obo-format Obo Format List]

Also of interest: [https://lists.sourceforge.net/lists/listinfo/obo-crossproducts Obo Cross-Product List]

=The Mapping=

We have made the mapping available as an online Google spreadsheet. You can view the sheet at http://spreadsheets.google.com/ccc?key=pWN_4sBrd9l1Umn1LN8WuQQ. If you want edits rights (or already have them) to leave comments then use the following link http://spreadsheets.google.com/ccc?key=o06770842196506107736.4732937099693365844

=Tools for the mapping=

== Protege plugins ==

'''OBO Converter Protege tab:'''

The OBO Converter is a Tab plugin for Protégé to convert OBO format files into OWL files and vice-versa (keeping in mind that OWL to OBO conversions can lose information if one encodes things in OWL that cannot be expressed in OBO). It is also developed in a manner such that it can also work as a standalone conversion program.

The OBO Converter Tab basically reads OBO files into Protégé OWL projects and saves those projects back as OBO 1.0 files. The Tab has two main panels, one to read OBO files and one to write (save) them. The save operation is straightforward as the user chooses the file name and the conversion is done. The read operation has the same functionality plus a set of options that can alter the way an OBO file is read (see figure).

[[Image:OBOConverter.jpg]]

users to choose the way the OWL class names will be generated from the OBO format file Terms. There are 3 options:

*OBO id This option will generate the name from the OBO term id. This is the default option and generates the OWL id in the way described in our mapping.
*Class name This option will generate the name from the OBO term name. This has to be used with care because the names are not required to be unique. If the names are not unique, there will be a parser error.
*Class name + OBO id This option will generate the name from the combination of the OBO term name and id.

In all cases, characters other than letters (a-z, A-Z) or numbers will be converted to underscore characters (_). Ex: the OBO term name “nurse cell” will be converted to the OWL class name nurse_cell.
The default behavior of the Tab is to generate the OWL class names from the OBO id. If the user wants to see the OBO name, instead of their meaningless ids, as the class identifier, Protégé has an option to display the OWL class label as the identifier. As OWL labels can also have language identifiers (such as en for English), converted OBO ontologies can now have names in different languages all pointing to the same entities allowing for language localization while preserving the OBO ids. The other options are targeted to users that want to create their ontology using a specific OBO ontology as a start point, but want to name their entities in a different way.

Downloads:

[http://smi-protege.stanford.edu/svn/obo-converter/trunk/ Source code for OBO Converter Tab]
[http://smi-cbio01.stanford.edu/~nigam/OBOConverter.zip Binaries for OBO Converter Tab]
[http://protege.cim3.net/cgi-bin/wiki.pl?OBOConverter Instructions for OBO Converter Tab]

'''OBO Explorer Protege tab:'''

The OWL format for OBO files uses anonymous nodes to represent definitions, synonyms, and DbxRefs, and the generic Protégé GUI components are not immediately suitable to display and edit them. The existing graphical components also do not allow the user to easily access or edit the lexical information associated with an OBO term. The OBO Explorer tab allows the user to do so in an interface that is similar to that of OBO-edit. This provides the user with the flexibility to edit these lexical features (such as synonyms and dbxrefs) in an intuitive manner.

[http://www.aiai.ed.ac.uk/project/cobra-ct/COBrA_downloads.htm OBO Explorer Tab]

[[Image:OBOExplorer.jpg]]

== OboEdit OWL plugin ==
We have also added the functionality to save an OBO format file as an OWL file from within OBOEdit. We have a development version of the OWL Export/Import plugin for OboEdit available. Just download the distribution file, unzip it and copy its content to <OboEdit>/extensions folder. Start OboEdit and you should find the option "OWL Adapter" for loading ontologies, File->Load Terms..., and for saving, File->Save as...

[http://smi-cbio01.stanford.edu/~nigam/OboEditPlugin.zip OboEdit OWL plugin].

If you have problems with big ontologies, try to increase the size of the memory available to OboEdit.

== obo2owl xslt ==

The oboxml_to_owl.xsl mapping now implements the OboInOwl mapping for obo-xml:

[http://geneontology.cvs.sourceforge.net/geneontology/go-dev/xml/xsl/oboxml_to_owl.xsl?view=log XSLT]

This will be bundled with [http://search.cpan.org/~cmungall/go-perl/ go-perl-0.07] and higher

Sample ontologies exported from obo to owl are available [http://www.berkeleybop.org/ontologies here]

=URIs=

Added a separate page on mapping OBO IDs to URIs:

[[OboInOwl:URIs]]

=Overview of Other Mapping efforts=

We are aware that there are several other groups that have created an OBO to OWL mapping to address immediate needs of their research groups. We have compiled a summary of the various OBO to OWL conversion efforts that we are aware of. Email me (nigam .AT. stanford.edu) with additions/deletions as you come across them.

[http://spreadsheets.google.com/ccc?key=pWN_4sBrd9l1Umn1LN8WuQQ Spread sheet comparing the mappings]

=Progress Notes=

I've overhauled the obo2owl mapping. I've pretty much followed Alan's
recommendations (I made a lot of purely internal changes to the xslt too though which should make it much clearer). Hope these work for you Stuart. Sorry about the churn
- but this will definitely be worth it in the end.

Example OWL file can be found here (also attached):

http://geneontology.cvs.sourceforge.net/*checkout*/geneontology/go-dev/xml/examples/gotest.owl

(note that this example includes a cross-product example)

The OWL is generated from either of the following:

http://geneontology.cvs.sourceforge.net/*checkout*/geneontology/go-dev/xml/examples/gotest.obo
http://geneontology.cvs.sourceforge.net/*checkout*/geneontology/go-dev/xml/examples/gotest.obo-xml

The XSL can be found here:

http://geneontology.cvs.sourceforge.net/*checkout*/geneontology/go-dev/xml/xsl/obo2owl.xsl
http://geneontology.cvs.sourceforge.net/*checkout*/geneontology/go-dev/xml/xsl/obo2owl_obo_in_owl_metamodel.xsl

The XSL actually serves as fairly reasonable documentation about what's going on - but we'll also come up with a friendlier description once it's finalised

You can convert the obo-xml directly with the xslt. If you want to
convert from obo you'll need the latest version of go-perl (from cvs)

Here are the changes and things still pending:

Adopted Alan Ruttenberg's metamodel changes (see obo-format list)

split into 2 separate xsl files

subset (ontology views) now more consistent with obo
* the oboInOwl class is SubsetDef
* this does not appear in the owl:Ontology section, it stands alone
(subsets can be used across ontologies)

namespace changes -
* the metamodel is now called oboInOwl
(the format is owned by GO, so this maps to a GO URI)
* the default ontology content namespace is now bioont
(the URI for this will be some bioontologies.org URI)
* slashes not hashes or underscores
- example: rdf:about="oboContent/GO/0000001"

fixed rdf:about/resource/ID issues
- ID is never used
- about and resource now used in correct places

CHECKED

- validates as DL in http://phoebus.cs.man.ac.uk:9999/OWL/Validator
- works in SWOOP
- works in Protege-OWL (but looks odd)

TODO

do we need an equivalentClass for intersectionOf?
SWOOP saves this without

decide on final URI scheme
- Can we make the URIs less verbose? Use entities - or is this frowned on?

new obo tags for obsoletion
handling obsoletes

decide on whether the oboInOwl metamodel should be exported as
part of the content export, or linked to separately;
and if linked to separately, do we need an owl:imports?

User:Dilvan

2007-01-17T18:46:41Z

Dilvan: /* OWL Export/Import plugin for OboEdit */

User:Dilvan

2007-01-17T18:35:38Z

Dilvan: /* OWL Export/Import plugin for OboEdit */

User:Dilvan

2006-12-23T03:26:10Z

Dilvan: /* OWL Export/Import plugin for OboEdit */

User:Dilvan

2006-12-23T03:24:38Z

Dilvan: /* OWL Export/Import plugin for OboEdit */

User:Dilvan

2006-12-23T03:23:29Z

Dilvan: /* OWL Export/Import plugin for OboEdit */

User:Dilvan

2006-12-23T02:59:36Z

Dilvan:

User:Dilvan

2006-12-23T02:53:07Z

Dilvan:

Test page:

'''OWL Export/Import plugin for OboEdit'''

That is the development version of the OWL Export/Import plugin for OboEdit . Just download the distribution file, unzip it and copy its content to <OboEdit>/extensions folder. Start OboEdit and you should find the option "OWL Adapter" for loading ontologies, File->Load Terms..., and for saving, File->Save as...

[[Download plugin]].