UCSDBioLit Wiki & Documentation Rss Feed

Updated Wiki: Home

AlexWade — Mon, 25 Feb 2013 23:00:59 GMT

Project Description
A Word add-in that enables the annotation of Word documents based on terms that appear in Ontologies

Read the latest press release here.

Summary
Microsoft Research Connections' goal with this project is to enable communities who maintain ontologies to more easily experiment and to enhance the experience of authors who use Microsoft Word for content creation, incorporating semantic knowledge into the content. This add-in should simplify the development and validation of ontologies, by making ontologies more accessible to a wide audience of authors and by enabling semantic content to be integrated in the authoring experience, capturing the author’s intent and knowledge at the source, and facilitating downstream discoverability.

The goal of the add-in is to assist scientists in writing a manuscript that is easily integrated with existing and pending electronic resources. The major aims of this project are to add semantic information as XML mark-up to the manuscript using ontologies and controlled vocabularies (from the National Center for Biomedical Ontology) and identifiers from major biological databases, and to integrate manuscript content with existing public data repositories.

As part of the publishing workflow and archiving process, the terms added by the add-in, providing the semantic information, can be extracted from Word files, as they are stored as custom XML tags as part of the content. The semantic knowledge can then be preserved as the documented is converted to other formats, such as HTML or the XML format from the National Library of Medicine, which is commonly used for archiving.

The full benefit of semantic-rich content will result from an end-to-end approach to the preservation of semantics and metadata through the publishing pipeline, starting with capturing knowledge from the subject experts, the authors, and enabling this knowledge to be preserved when published, as well as made available to search engines and presented to people consuming the content.

This project resulted from an initial and ongoing collaboration between Microsoft External Research and Dr. Phil Bourne and Dr. Lynn Fink, at the University of California San Diego. Additional collaboration with the staff from Science Commons aims to make the add-in relevant to a wider audience and also to preserve semantic data along the publishing pipeline.

Audience
This project is focused on researchers and software developers in domains utilizing ontologies– as well as publishers, archivists, and early adopters in the scientific, technical, and scholarly publishing fields.

Specific features

Inline Syntax Coloring of Informative Words
Built-in Knowledge of Ontologies and Controlled Vocabularies maintained and delivered by NCBO
Built-in Knowledge of Biological Databases (Protein Data Bank, UniProtKB, NCBI GenBank/RefSeq)
Automatic Detection of Identifiers
Custom Semantic Markup

Getting Started

Trying out the add-in:
- You will need Microsoft Word 2007 or Microsoft Word 2010 (32-bit or 64-bit) running on Windows XP, Windows Vista or Windows 7.
- Open the test document from the Releases tab in this page and enable Term Recognition in the Ontology tab within Word

If you have installed a previous version of the add-in, you may need to follow these instructions to achieve a full uninstall.

Examining the source code and contributing to the project:
- Navigate to the Source Code tab
- You can use the free version of Visual Studio (Visual C# 2008 Express Edition) to build the project
- Add comments in the Discussion tab, and report problems under Issue Tracker

Design Documentation
Design Documents

Semantic Tagging

When a word or set of words is tagged by the add-in, the word is wrapped with some tags that associate it with the ontology term. The example below shows the word "astrocyte" being tagged with the Cell Line ontology.

<w:customXml w:uri="http://biolit.ucsd.edu/biolitschema1" w:element="named-content">
 <w:customXmlPr>
   <w:attr w:name="content-type" w:val="biolit" /> 
   <w:attr w:name="id" w:val="ncbo_id=40962;term_id=CL:0000127;term=astrocyte;url=http://purl.org/obo/owl/CL#CL_0000127" /> 
  </w:customXmlPr>
  <w:proofErr w:type="gramStart" /> 
  <w:smartTag w:uri="BioLitTags" w:element="Term">
   <w:r w:rsidRPr="00FA60F6">
    <w:rPr>
     <w:highlight w:val="yellow" /> 
    </w:rPr>
    <w:t>astrocyte</w:t> 
    </w:r>
  </w:smartTag>
  <w:proofErr w:type="gramEnd" /> 
</w:customXml>

If the Word file (docx) is to be transformed to other formats, this set of tags would need to be processed using xslt or other technologies. Note that there are other CodePlex projects available which implement transformations of docx files to other formats, which one can start from.

Background
Cyberinfrastructure is integral to all aspects of conducting experimental research and distributing those results. However, it has yet to make a similar impact on the way we communicate that information. Peer-reviewed publications have long been the currency of scientific research as they are the fundamental unit through which scientists communicate with and evaluate each other. However, in striking contrast to the data, publications have yet to benefit from the opportunities offered by cyberinfrastructure. While the means of distributing publications has vastly improved, publishers have done little else to capitalize on the electronic medium. In particular, semantic information describing the content of these publications is sorely lacking, as is the integration of this information with data in public repositories. This is confounding considering that many basic tools for marking-up and integrating publication content in this manner already exist, such as a centralized literature database, relevant ontologies, and machine-readable document standards. We propose to address this delay in the maturation of scholarly communication by developing open source tools to facilitate the semantic mark-up of new manuscripts and the submission of those manuscripts directly to a journal’s electronic publishing system.

Updated Wiki: Home

erteam — Fri, 07 May 2010 23:24:37 GMT

Project Description
A Word add-in that enables the annotation of Word documents based on terms that appear in Ontologies

Read the latest press release here.

Summary
Microsoft External Research’s goal with this project is to enable communities who maintain ontologies to more easily experiment and to enhance the experience of authors who use Microsoft Word for content creation, incorporating semantic knowledge into the content. This add-in should simplify the development and validation of ontologies, by making ontologies more accessible to a wide audience of authors and by enabling semantic content to be integrated in the authoring experience, capturing the author’s intent and knowledge at the source, and facilitating downstream discoverability.

The goal of the add-in is to assist scientists in writing a manuscript that is easily integrated with existing and pending electronic resources. The major aims of this project are to add semantic information as XML mark-up to the manuscript using ontologies and controlled vocabularies (from the National Center for Biomedical Ontology) and identifiers from major biological databases, and to integrate manuscript content with existing public data repositories.

As part of the publishing workflow and archiving process, the terms added by the add-in, providing the semantic information, can be extracted from Word files, as they are stored as custom XML tags as part of the content. The semantic knowledge can then be preserved as the documented is converted to other formats, such as HTML or the XML format from the National Library of Medicine, which is commonly used for archiving.

The full benefit of semantic-rich content will result from an end-to-end approach to the preservation of semantics and metadata through the publishing pipeline, starting with capturing knowledge from the subject experts, the authors, and enabling this knowledge to be preserved when published, as well as made available to search engines and presented to people consuming the content.

This project resulted from an initial and ongoing collaboration between Microsoft External Research and Dr. Phil Bourne and Dr. Lynn Fink, at the University of California San Diego. Additional collaboration with the staff from Science Commons aims to make the add-in relevant to a wider audience and also to preserve semantic data along the publishing pipeline.

Audience
This project is focused on researchers and software developers in domains utilizing ontologies– as well as publishers, archivists, and early adopters in the scientific, technical, and scholarly publishing fields.

Specific features

Inline Syntax Coloring of Informative Words
Built-in Knowledge of Ontologies and Controlled Vocabularies maintained and delivered by NCBO
Built-in Knowledge of Biological Databases (Protein Data Bank, UniProtKB, NCBI GenBank/RefSeq)
Automatic Detection of Identifiers
Custom Semantic Markup

Getting Started

Trying out the add-in:
- You will need Microsoft Word 2007 or Microsoft Word 2010 (32-bit or 64-bit) running on Windows XP, Windows Vista or Windows 7.
- Open the test document from the Releases tab in this page and enable Term Recognition in the Ontology tab within Word

If you have installed a previous version of the add-in, you may need to follow these instructions to achieve a full uninstall.

Examining the source code and contributing to the project:
- Navigate to the Source Code tab
- You can use the free version of Visual Studio (Visual C# 2008 Express Edition) to build the project
- Add comments in the Discussion tab, and report problems under Issue Tracker

<w:customXml w:uri="http://biolit.ucsd.edu/biolitschema1" w:element="named-content">
 <w:customXmlPr>
   <w:attr w:name="content-type" w:val="biolit" /> 
   <w:attr w:name="id" w:val="ncbo_id=40962;term_id=CL:0000127;term=astrocyte;url=http://purl.org/obo/owl/CL#CL_0000127" /> 
  </w:customXmlPr>
  <w:proofErr w:type="gramStart" /> 
  <w:smartTag w:uri="BioLitTags" w:element="Term">
   <w:r w:rsidRPr="00FA60F6">
    <w:rPr>
     <w:highlight w:val="yellow" /> 
    </w:rPr>
    <w:t>astrocyte</w:t> 
    </w:r>
  </w:smartTag>
  <w:proofErr w:type="gramEnd" /> 
</w:customXml>

Updated Wiki: uninstallhelp

jlfink — Wed, 16 Dec 2009 13:09:08 GMT

Full Uninstall of Earlier Add-in Versions

If you have previously installed and uninstalled earlier versions, there may be files that were not fully uninstalled. The following directions will explain how to remove any old files.

Uninstall the Ontology Add-in for Word 2007

Open the Control Panel

Select the Programs group

Select Uninstall a Program

Select Ontology Add-in for Word 2007 and click Uninstall

Remove Any Remaining Files

Start Word

Select Word Options from the main menu

Select the Add-ins tab

In the lower panel, you’ll see a section for Inactive Application Add-ins.

Uninstall any remaining XML Schema

There may be several items with the type XML Schema listed that are part of the Ontology Add-in. These need to be manually removed as follows:

At the bottom of the panel is a drop down box labeled Manage.

Change the selection in the Manage box to XML Schema and click the Go… button

The Templates and Add-ins dialog should appear. You’ll notice that the XML schema you need to remove should be on this list.

Click the Schema Library… button to remove them

The Schema Library dialog will appear.

Select each schema you want to remove and click the Delete Schema button

Repeat the previous step until you have deleted all Ontology Add-in schemas.

Click OK to close the Schema Library dialog the click OK to close the Templates and Add-ins dialog

Exit Word

Install the Latest Version

Restart your computer (just to be safe)

Reinstall the latest Ontology Add-in for Word 2007

Contributed by Mike Galos

Updated Wiki: uninstallhelp

jlfink — Wed, 16 Dec 2009 13:08:22 GMT

Full Uninstall of Earlier Add-in Versions

If you have previously installed and uninstalled earlier versions, there may be files that were not fully uninstalled. The following directions will explain how to remove any old files.

Uninstall the Ontology Add-in for Word 2007

Open the Control Panel

Select the Programs group

Select Uninstall a Program

Select Ontology Add-in for Word 2007 and click Uninstall

Remove Any Remaining Files

Start Word

Select Word Options from the main menu

Select the Add-ins tab

In the lower panel, you’ll see a section for Inactive Application Add-ins.

Uninstall any remaining XML Schema

Change the selection in the Manage box to XML Schema and click the Go… button

The Templates and Add-ins dialog should appear. You’ll notice that the XML schema you need to remove should be on this list.

Click the Schema Library… button to remove them

The Schema Library dialog will appear.

Select each schema you want to remove and click the Delete Schema button

Repeat the previous step until you have deleted all Ontology Add-in schemas.

Click OK to close the Schema Library dialog the click OK to close the Templates and Add-ins dialog

Exit Word

Install the Latest Version

Restart your computer (just to be safe)

Reinstall the latest Ontology Add-in for Word 2007

Updated Wiki: uninstallhelp

jlfink — Wed, 16 Dec 2009 13:07:45 GMT

Full Uninstall of Earlier Add-in Versions

If you have previously installed and uninstalled earlier versions, there may be files that were not fully uninstalled. The following directions will explain how to remove any old files.

Uninstall the Ontology Add-in for Word 2007

Open the Control Panel

Select the Programs group

Select Uninstall a Program

Select Ontology Add-in for Word 2007 and click Uninstall

Remove Any Remaining Files

Start Word

Select Word Options from the main menu

Select the Add-ins tab

In the lower panel, you’ll see a section for Inactive Application Add-ins.

Uninstall any remaining XML Schema

Change the selection in the Manage box to XML Schema and click the Go… button

The Templates and Add-ins dialog should appear. You’ll notice that the XML schema you need to remove should be on this list.

image

Click the Schema Library… button to remove them

The Schema Library dialog will appear.

Select each schema you want to remove and click the Delete Schema button

image

Repeat the previous step until you have deleted all Ontology Add-in schemas.

Click OK to close the Schema Library dialog the click OK to close the Templates and Add-ins dialog

Exit Word

Install the Latest Version

Restart your computer (just to be safe)

Reinstall the latest Ontology Add-in for Word 2007

Updated Wiki: Home

jlfink — Wed, 16 Dec 2009 13:00:19 GMT

Project Description
A Word 2007 add-in that enables the annotation of Word documents based on terms that appear in Ontologies

Read the latest press release here.

Summary
Microsoft External Research’s goal with this project is to enable communities who maintain ontologies to more easily experiment and to enhance the experience of authors who use Microsoft Word for content creation, incorporating semantic knowledge into the content. This add-in should simplify the development and validation of ontologies, by making ontologies more accessible to a wide audience of authors and by enabling semantic content to be integrated in the authoring experience, capturing the author’s intent and knowledge at the source, and facilitating downstream discoverability.

The goal of the add-in is to assist scientists in writing a manuscript that is easily integrated with existing and pending electronic resources. The major aims of this project are to add semantic information as XML mark-up to the manuscript using ontologies and controlled vocabularies (from the National Center for Biomedical Ontology) and identifiers from major biological databases, and to integrate manuscript content with existing public data repositories.

As part of the publishing workflow and archiving process, the terms added by the add-in, providing the semantic information, can be extracted from Word files, as they are stored as custom XML tags as part of the content. The semantic knowledge can then be preserved as the documented is converted to other formats, such as HTML or the XML format from the National Library of Medicine, which is commonly used for archiving.

The full benefit of semantic-rich content will result from an end-to-end approach to the preservation of semantics and metadata through the publishing pipeline, starting with capturing knowledge from the subject experts, the authors, and enabling this knowledge to be preserved when published, as well as made available to search engines and presented to people consuming the content.

This project resulted from an initial and ongoing collaboration between Microsoft External Research and Dr. Phil Bourne and Dr. Lynn Fink, at the University of California San Diego. Additional collaboration with the staff from Science Commons aims to make the add-in relevant to a wider audience and also to preserve semantic data along the publishing pipeline.

Audience
This project is focused on researchers and software developers in domains utilizing ontologies– as well as publishers, archivists, and early adopters in the scientific, technical, and scholarly publishing fields.

Specific features

Inline Syntax Coloring of Informative Words
Built-in Knowledge of Ontologies and Controlled Vocabularies maintained and delivered by NCBO
Built-in Knowledge of Biological Databases (Protein Data Bank, UniProtKB, NCBI GenBank/RefSeq)
Automatic Detection of Identifiers
Custom Semantic Markup

Getting Started

Trying out the add-in:
- You will need Microsoft Word 2007 (Windows XP or Windows Vista)
- Open the test document from the Releases tab in this page and enable Term Recognition in the Ontology tab within Word

If you have installed a previous version of the add-in, you may need to follow these instructions to achieve a full uninstall.

Examining the source code and contributing to the project:
- Navigate to the Source Code tab
- You can use the free version of Visual Studio (Visual C# 2008 Express Edition) to build the project
- Add comments in the Discussion tab, and report problems under Issue Tracker

<w:customXml w:uri="http://biolit.ucsd.edu/biolitschema1" w:element="named-content">
 <w:customXmlPr>
   <w:attr w:name="content-type" w:val="biolit" /> 
   <w:attr w:name="id" w:val="ncbo_id=40962;term_id=CL:0000127;term=astrocyte;url=http://purl.org/obo/owl/CL#CL_0000127" /> 
  </w:customXmlPr>
  <w:proofErr w:type="gramStart" /> 
  <w:smartTag w:uri="BioLitTags" w:element="Term">
   <w:r w:rsidRPr="00FA60F6">
    <w:rPr>
     <w:highlight w:val="yellow" /> 
    </w:rPr>
    <w:t>astrocyte</w:t> 
    </w:r>
  </w:smartTag>
  <w:proofErr w:type="gramEnd" /> 
</w:customXml>

Updated Wiki: uninstallhelp

jlfink — Wed, 16 Dec 2009 13:00:10 GMT

Full Uninstall of Earlier Add-in Versions

If you have previously installed and uninstalled earlier versions, there may be files that were not fully uninstalled. The following directions will explain how to remove any old files.

Uninstall the Ontology Add-in for Word 2007

Open the Control Panel

Select the Programs group

Select Uninstall a Program

Select Ontology Add-in for Word 2007 and click Uninstall

Remove Any Remaining Files

Start Word

Select Word Options from the main menu

Select the Add-ins tab

In the lower panel, you’ll see a section for Inactive Application Add-ins.

Uninstall any remaining XML Schema

Change the selection in the Manage box to XML Schema and click the Go… button

The Templates and Add-ins dialog should appear. You’ll notice that the XML schema you need to remove should be on this list.

Click the Schema Library… button to remove them

The Schema Library dialog will appear.

Select each schema you want to remove and click the Delete Schema button

Repeat the previous step until you have deleted all Ontology Add-in schemas.

Click OK to close the Schema Library dialog the click OK to close the Templates and Add-ins dialog

Exit Word

Install the Latest Version

Restart your computer (just to be safe)

Reinstall the latest Ontology Add-in for Word 2007

Updated Wiki: Home

jlfink — Wed, 16 Dec 2009 12:22:34 GMT

Inline Syntax Coloring of Informative Words
Built-in Knowledge of Ontologies and Controlled Vocabularies maintained and delivered by NCBO
Built-in Knowledge of Biological Databases (Protein Data Bank, UniProtKB, NCBI GenBank/RefSeq)
Automatic Detection of Identifiers
Custom Semantic Markup

Getting Started

Trying out the add-in:
- You will need Microsoft Word 2007 (Windows XP or Windows Vista)
- Download and install the latest Technology Preview release of the add-in
- Open the test document from the Releases tab in this page and enable Term Recognition in the Ontology tab within Word
Examining the source code and contributing to the project:
- Navigate to the Source Code tab
- You can use the free version of Visual Studio (Visual C# 2008 Express Edition) to build the project
- Add comments in the Discussion tab, and report problems under Issue Tracker

<w:customXml w:uri="http://biolit.ucsd.edu/biolitschema1" w:element="named-content">
 <w:customXmlPr>
   <w:attr w:name="content-type" w:val="biolit" /> 
   <w:attr w:name="id" w:val="ncbo_id=40962;term_id=CL:0000127;term=astrocyte;url=http://purl.org/obo/owl/CL#CL_0000127" /> 
  </w:customXmlPr>
  <w:proofErr w:type="gramStart" /> 
  <w:smartTag w:uri="BioLitTags" w:element="Term">
   <w:r w:rsidRPr="00FA60F6">
    <w:rPr>
     <w:highlight w:val="yellow" /> 
    </w:rPr>
    <w:t>astrocyte</w:t> 
    </w:r>
  </w:smartTag>
  <w:proofErr w:type="gramEnd" /> 
</w:customXml>

Updated Wiki: Home

jlfink — Tue, 17 Mar 2009 07:42:59 GMT

Inline Syntax Coloring of Informative Words
Built-in Knowledge of Ontologies and Controlled Vocabularies maintained and delivered by NCBO
Built-in Knowledge of Biological Databases (Protein Data Bank, UniProtKB, NCBI GenBank/RefSeq)
Automatic Detection of Identifiers
Custom Semantic Markup

Getting Started

Trying out the add-in:

You will need Microsoft Word 2007 (Windows XP or Windows Vista)
Download and install the latest Technology Preview release of the add-in
Open the test document from the Releases tab in this page and enable Term Recognition in the Ontology tab within Word

Examining the source code and contributing to the project:

Navigate to the Source Code tab
You can use the free version of Visual Studio (Visual C# 2008 Express Edition) to build the project
Add comments in the Discussion tab, and report problems under Issue Tracker

<w:customXml w:uri="http://biolit.ucsd.edu/biolitschema" w:element="biolit-term">
    <w:customXmlPr>
        <w:attr w:name="id" w:val="DOID:4" /> 
        <w:attr w:name="type" w:val="Human disease" /> 
        <w:attr w:name="status" w:val="true" /> 
        <w:attr w:name="OntName" w:val="Human disease" /> 
        <w:attr w:name="url" w:val="http://purl.org/obo/owl/DOID#DOID_4" /> 
    </w:customXmlPr>
    <w:smartTag w:uri="BioLitTags" w:element="tag1">
        <w:r>
            <w:t>disease</w:t> 
        </w:r>
    </w:smartTag>
</w:customXml>

Updated Wiki: Home

jlfink — Fri, 13 Mar 2009 18:45:41 GMT

Project Description
A Word 2007 add-in that enables the annotation of Word documents based on terms that appear in Ontologies

Summary
Microsoft External Research’s goal with this project is to enable communities who maintain ontologies to more easily experiment and to enhance the experience of authors who use Microsoft Word for content creation, incorporating semantic knowledge into the content. This add-in should simplify the development and validation of ontologies, by making ontologies more accessible to a wide audience of authors and by enabling semantic content to be integrated in the authoring experience, capturing the author’s intent and knowledge at the source, and facilitating downstream discoverability.

The goal of the add-in is to assist scientists in writing a manuscript that is easily integrated with existing and pending electronic resources. The major aims of this project are to add semantic information as XML mark-up to the manuscript using ontologies and controlled vocabularies (from the National Center for Biomedical Ontology) and identifiers from major biological databases, and to integrate manuscript content with existing public data repositories.

As part of the publishing workflow and archiving process, the terms added by the add-in, providing the semantic information, can be extracted from Word files, as they are stored as custom XML tags as part of the content. The semantic knowledge can then be preserved as the documented is converted to other formats, such as HTML or the XML format from the National Library of Medicine, which is commonly used for archiving.

The full benefit of semantic-rich content will result from an end-to-end approach to the preservation of semantics and metadata through the publishing pipeline, starting with capturing knowledge from the subject experts, the authors, and enabling this knowledge to be preserved when published, as well as made available to search engines and presented to people consuming the content.

This project resulted from an initial and ongoing collaboration between Microsoft External Research and Dr. Phil Bourne and Dr. Lynn Fink, at the University of California San Diego. Additional collaboration with the staff from Science Commons aims to make the add-in relevant to a wider audience and also to preserve semantic data along the publishing pipeline.

Audience
This project is focused on researchers and software developers in domains utilizing ontologies– as well as publishers, archivists, and early adopters in the scientific, technical, and scholarly publishing fields.

Specific features

Inline Syntax Coloring of Informative Words
Built-in Knowledge of Ontologies and Controlled Vocabularies maintained and delivered by NCBO
Built-in Knowledge of Biological Databases (Protein Data Bank, UniProtKB, NCBI GenBank/RefSeq)
Automatic Detection of Identifiers
Custom Semantic Markup

Getting Started

Trying out the add-in:

You will need Microsoft Word 2007 (Windows XP or Windows Vista)
Download and install the latest Technology Preview release of the add-in
Open the test document from the Releases tab in this page and enable Term Recognition in the Ontology tab within Word

Examining the source code and contributing to the project:

Navigate to the Source Code tab
You can use the free version of Visual Studio (Visual C# 2008 Express Edition) to build the project
Add comments in the Discussion tab, and report problems under Issue Tracker

<w:customXml w:uri="http://biolit.ucsd.edu/biolitschema" w:element="biolit-term">
    <w:customXmlPr>
        <w:attr w:name="id" w:val="DOID:4" /> 
        <w:attr w:name="type" w:val="Human disease" /> 
        <w:attr w:name="status" w:val="true" /> 
        <w:attr w:name="OntName" w:val="Human disease" /> 
        <w:attr w:name="url" w:val="http://purl.org/obo/owl/DOID#DOID_4" /> 
    </w:customXmlPr>
    <w:smartTag w:uri="BioLitTags" w:element="tag1">
        <w:r>
            <w:t>disease</w:t> 
        </w:r>
    </w:smartTag>
</w:customXml>

Updated Wiki: Ontologies and Controlled Vocabularies

jlfink — Fri, 13 Mar 2009 03:02:50 GMT

NCBO Ontology Availability

The add-in currently downloads the following NCBO ontologies:

Amphibian gross anatomy

Biological imaging methods

Biological process

BRENDA tissue / enzyme source

C. elegans development

C. elegans phenotype

Cell type

Cellular component

Cereal plant trait

Dictyostelium discoideum anatomy

Drosophila development

Drosophila gross anatomy

Environment Ontology

Event (INOH pathway ontology)

Fungal gross anatomy

Human developmental anatomy, abstract version

Human developmental anatomy, timed version

Human disease

Infectious disease

Mammalian phenotype

Mass spectrometry

Molecular function

Mosquito gross anatomy

Mouse adult gross anatomy

Mouse pathology

Pathogen transmission

Pathway ontology

Physico-chemical methods and properties

Physico-chemical process

Plant environmental conditions

Plant growth and developmental stage

Plant structure

Protein-protein interaction

Spider Ontology

Teleost anatomy and development

Tick gross anatomy

Xenopus anatomy and development

Zebrafish anatomy and development

Updated Wiki: Home

jlfink — Fri, 13 Mar 2009 02:59:14 GMT

Project Description
A Word 2007 add-in that enables the annotation of Word documents based on terms that appear in Ontologies

Summary
Microsoft External Research’s goal with this project is to enable communities who maintain ontologies to more easily experiment and to enhance the experience of authors who use Microsoft Word for content creation, incorporating semantic knowledge into the content. This add-in should simplify the development and validation of ontologies, by making ontologies more accessible to a wide audience of authors and by enabling semantic content to be integrated in the authoring experience, capturing the author’s intent and knowledge at the source, and facilitating downstream discoverability.

The goal of the add-in is to assist scientists in writing a manuscript that is easily integrated with existing and pending electronic resources. The major aims of this project are to add semantic information as XML mark-up to the manuscript using ontologies and controlled vocabularies (using OBO), and to integrate manuscript content with existing public data repositories.

As part of the publishing workflow and archiving process, the terms added by the add-in, providing the semantic information, can be extracted from Word files, as they are stored as custom XML tags as part of the content. The semantic knowledge can then be preserved as the documented is converted to other formats, such as HTML or the XML format from the National Library of Medicine, which is commonly used for archiving.

The full benefit of semantic-rich content will result from an end-to-end approach to the preservation of semantics and metadata through the publishing pipeline, starting with capturing knowledge from the subject experts, the authors, and enabling this knowledge to be preserved when published, as well as made available to search engines and presented to people consuming the content.

This project resulted from an initial and ongoing collaboration between Microsoft External Research and Dr. Phil Bourne and Dr. Lynn Fink, at the University of California San Diego. Additional collaboration with the staff from Science Commons aims to make the add-in relevant to a wider audience and also to preserve semantic data along the publishing pipeline.

Audience
This project is focused on researchers and software developers in domains utilizing ontologies– as well as publishers, archivists, and early adopters in the scientific, technical, and scholarly publishing fields.

Specific features

Inline Syntax Coloring of Informative Words
Built-in Knowledge of Ontologies and Controlled Vocabularies maintained and delivered by NCBO
Built-in Knowledge of Biological Databases (Protein Data Bank, UniProtKB, NCBI GenBank/RefSeq)
Automatic Detection of Identifiers
Custom Semantic Markup

Getting Started

Trying out the add-in:

You will need Microsoft Word 2007 (Windows XP or Windows Vista)
Download and install the latest Technology Preview release of the add-in
Open the test document from the Releases tab in this page and enable Term Recognition in the Ontology tab within Word

Examining the source code and contributing to the project:

Navigate to the Source Code tab
You can use the free version of Visual Studio (Visual C# 2008 Express Edition) to build the project
Add comments in the Discussion tab, and report problems under Issue Tracker

<w:customXml w:uri="http://biolit.ucsd.edu/biolitschema" w:element="biolit-term">
    <w:customXmlPr>
        <w:attr w:name="id" w:val="DOID:4" /> 
        <w:attr w:name="type" w:val="Human disease" /> 
        <w:attr w:name="status" w:val="true" /> 
        <w:attr w:name="OntName" w:val="Human disease" /> 
        <w:attr w:name="url" w:val="http://purl.org/obo/owl/DOID#DOID_4" /> 
    </w:customXmlPr>
    <w:smartTag w:uri="BioLitTags" w:element="tag1">
        <w:r>
            <w:t>disease</w:t> 
        </w:r>
    </w:smartTag>
</w:customXml>

Updated Wiki: Home

jlfink — Fri, 13 Mar 2009 02:21:18 GMT

Project Description
A Word 2007 add-in that enables the annotation of Word documents based on terms that appear in Ontologies

Summary
Microsoft External Research’s goal with this project is to enable communities who maintain ontologies to more easily experiment and to enhance the experience of authors who use Microsoft Word for content creation, incorporating semantic knowledge into the content. This add-in should simplify the development and validation of ontologies, by making ontologies more accessible to a wide audience of authors and by enabling semantic content to be integrated in the authoring experience, capturing the author’s intent and knowledge at the source, and facilitating downstream discoverability.

The goal of the add-in is to assist scientists in writing a manuscript that is easily integrated with existing and pending electronic resources. The major aims of this project are to add semantic information as XML mark-up to the manuscript using ontologies and controlled vocabularies (using OBO), and to integrate manuscript content with existing public data repositories.

As part of the publishing workflow and archiving process, the terms added by the add-in, providing the semantic information, can be extracted from Word files, as they are stored as custom XML tags as part of the content. The semantic knowledge can then be preserved as the documented is converted to other formats, such as HTML or the XML format from the National Library of Medicine, which is commonly used for archiving.

The full benefit of semantic-rich content will result from an end-to-end approach to the preservation of semantics and metadata through the publishing pipeline, starting with capturing knowledge from the subject experts, the authors, and enabling this knowledge to be preserved when published, as well as made available to search engines and presented to people consuming the content.

This project resulted from an initial and ongoing collaboration between Microsoft External Research and Dr. Phil Bourne and Dr. Lynn Fink, at the University of California San Diego. Additional collaboration with the staff from Science Commons aims to make the add-in relevant to a wider audience and also to preserve semantic data along the publishing pipeline.

Audience
This project is focused on researchers and software developers in domains utilizing ontologies– as well as publishers, archivists, and early adopters in the scientific, technical, and scholarly publishing fields.

Specific features

Inline Syntax Coloring of Informative Words
Built-in Knowledge of Ontologies and Controlled Vocabularies maintained and delivered by NCBO
Built-in Knowledge of Biological Databases (Protein Data Bank, UniProtKB, NCBI GenBank/RefSeq)
Automatic Detection of Identifiers
Custom Semantic Markup

Getting Started

Trying out the add-in:

You will need Microsoft Word 2007 (Windows XP or Windows Vista)
Download and install the latest Technology Preview release of the add-in
Open the test document from the Releases tab in this page and enable Term Recognition in the Ontology tab within Word

Examining the source code and contributing to the project:

Navigate to the Source Code tab
You can use the free version of Visual Studio (Visual C# 2008 Express Edition) to build the project
Add comments in the Discussion tab, and report problems under Issue Tracker

<w:customXml w:uri="http://biolit.ucsd.edu/biolitschema" w:element="biolit-term">
    <w:customXmlPr>
        <w:attr w:name="id" w:val="DOID:4" /> 
        <w:attr w:name="type" w:val="Human disease" /> 
        <w:attr w:name="status" w:val="true" /> 
        <w:attr w:name="OntName" w:val="Human disease" /> 
        <w:attr w:name="url" w:val="http://purl.org/obo/owl/DOID#DOID_4" /> 
    </w:customXmlPr>
    <w:smartTag w:uri="BioLitTags" w:element="tag1">
        <w:r>
            <w:t>disease</w:t> 
        </w:r>
    </w:smartTag>
</w:customXml>

Updated Wiki: Home

jlfink — Fri, 13 Mar 2009 02:20:52 GMT

Project Description
A Word 2007 add-in that enables the annotation of Word documents based on terms that appear in Ontologies

Summary
Microsoft External Research’s goal with this project is to enable communities who maintain ontologies to more easily experiment and to enhance the experience of authors who use Microsoft Word for content creation, incorporating semantic knowledge into the content. This add-in should simplify the development and validation of ontologies, by making ontologies more accessible to a wide audience of authors and by enabling semantic content to be integrated in the authoring experience, capturing the author’s intent and knowledge at the source, and facilitating downstream discoverability.

The goal of the add-in is to assist scientists in writing a manuscript that is easily integrated with existing and pending electronic resources. The major aims of this project are to add semantic information as XML mark-up to the manuscript using ontologies and controlled vocabularies (using OBO), and to integrate manuscript content with existing public data repositories.

As part of the publishing workflow and archiving process, the terms added by the add-in, providing the semantic information, can be extracted from Word files, as they are stored as custom XML tags as part of the content. The semantic knowledge can then be preserved as the documented is converted to other formats, such as HTML or the XML format from the National Library of Medicine, which is commonly used for archiving.

The full benefit of semantic-rich content will result from an end-to-end approach to the preservation of semantics and metadata through the publishing pipeline, starting with capturing knowledge from the subject experts, the authors, and enabling this knowledge to be preserved when published, as well as made available to search engines and presented to people consuming the content.

This project resulted from an initial and ongoing collaboration between Microsoft External Research and Dr. Phil Bourne and Dr. Lynn Fink, at the University of California San Diego. Additional collaboration with the staff from Science Commons aims to make the add-in relevant to a wider audience and also to preserve semantic data along the publishing pipeline.

Audience
This project is focused on researchers and software developers in domains utilizing ontologies– as well as publishers, archivists, and early adopters in the scientific, technical, and scholarly publishing fields.

Specific features

Inline Syntax Coloring of Informative Words
Built-in Knowledge of Ontologies and Controlled Vocabularies maintained and delivered by NCBO
Built-in Knowledge of Biological Databases (Protein Data Bank, UniProtKB, NCBI GenBank/RefSeq)
Automatic Detection of Identifiers
Custom Semantic Markup

Getting Started

Trying out the add-in:

You will need Microsoft Word 2007 (Windows XP or Windows Vista)
Download and install the latest Technology Preview release of the add-in
Open the test document from the Releases tab in this page and enable Term Recognition in the Ontology tab within Word

Examining the source code and contributing to the project:

Navigate to the Source Code tab
You can use the free version of Visual Studio (Visual C# 2008 Express Edition) to build the project
Add comments in the Discussion tab, and report problems under Issue Tracker

<w:customXml w:uri="http://biolit.ucsd.edu/biolitschema" w:element="biolit-term">
    <w:customXmlPr>
        <w:attr w:name="id" w:val="DOID:4" /> 
        <w:attr w:name="type" w:val="Human disease" /> 
        <w:attr w:name="status" w:val="true" /> 
        <w:attr w:name="OntName" w:val="Human disease" /> 
        <w:attr w:name="url" w:val="http://purl.org/obo/owl/DOID#DOID_4" /> 
    </w:customXmlPr>
    <w:smartTag w:uri="BioLitTags" w:element="tag1">
        <w:r>
            <w:t>disease</w:t> 
        </w:r>
    </w:smartTag>
</w:customXml>

Updated Wiki: Home

pablofe — Tue, 10 Mar 2009 21:24:06 GMT

Project Description
A Word 2007 add-in that enables the annotation of Word documents based on terms that appear in Ontologies

Summary
Microsoft External Research’s goal with this project is to enable communities who maintain ontologies to more easily experiment and to enhance the experience of authors who use Microsoft Word for content creation, incorporating semantic knowledge into the content. This add-in should simplify the development and validation of ontologies, by making ontologies more accessible to a wide audience of authors and by enabling semantic content to be integrated in the authoring experience, capturing the author’s intent and knowledge at the source, and facilitating downstream discoverability.

The goal of the add-in is to assist scientists in writing a manuscript that is easily integrated with existing and pending electronic resources. The major aims of this project are to add semantic information as XML mark-up to the manuscript using ontologies and controlled vocabularies (using OBO), and to integrate manuscript content with existing public data repositories.

As part of the publishing workflow and archiving process, the terms added by the add-in, providing the semantic information, can be extracted from Word files, as they are stored as custom XML tags as part of the content. The semantic knowledge can then be preserved as the documented is converted to other formats, such as HTML or the XML format from the National Library of Medicine, which is commonly used for archiving.

The full benefit of semantic-rich content will result from an end-to-end approach to the preservation of semantics and metadata through the publishing pipeline, starting with capturing knowledge from the subject experts, the authors, and enabling this knowledge to be preserved when published, as well as made available to search engines and presented to people consuming the content.

This project resulted from an initial and ongoing collaboration between Microsoft External Research and Dr. Phil Bourne and Dr. Lynn Fink, at the University of California San Diego. Additional collaboration with the staff from Science Commons aims to make the add-in relevant to a wider audience and also to preserve semantic data along the publishing pipeline.

Audience
This project is focused on researchers and software developers in domains utilizing ontologies– as well as publishers, archivists, and early adopters in the scientific, technical, and scholarly publishing fields.

Specific features

Inline Syntax Coloring of Informative Words
Built-in Knowledge of Ontologies and Controlled Vocabularies
Automatic Detection of Identifiers
Custom Semantic Markup

Getting Started

Trying out the add-in:

You will need Microsoft Word 2007 (Windows XP or Windows Vista)
Download and install the latest Technology Preview release of the add-in
Open the test document from the Releases tab in this page and enable Term Recognition in the Ontology tab within Word

Examining the source code and contributing to the project:

Navigate to the Source Code tab
You can use the free version of Visual Studio (Visual C# 2008 Express Edition) to build the project
Add comments in the Discussion tab, and report problems under Issue Tracker

<w:customXml w:uri="http://biolit.ucsd.edu/biolitschema" w:element="biolit-term">
    <w:customXmlPr>
        <w:attr w:name="id" w:val="DOID:4" /> 
        <w:attr w:name="type" w:val="Human disease" /> 
        <w:attr w:name="status" w:val="true" /> 
        <w:attr w:name="OntName" w:val="Human disease" /> 
        <w:attr w:name="url" w:val="http://purl.org/obo/owl/DOID#DOID_4" /> 
    </w:customXmlPr>
    <w:smartTag w:uri="BioLitTags" w:element="tag1">
        <w:r>
            <w:t>disease</w:t> 
        </w:r>
    </w:smartTag>
</w:customXml>

Updated Wiki: Home

pablofe — Tue, 10 Mar 2009 21:21:04 GMT

Project Description
A Word 2007 add-in that enables the annotation of Word documents based on terms that appear in Ontologies

Summary
Microsoft External Research’s goal with this project is to enable communities who maintain ontologies to more easily experiment and to enhance the experience of authors who use Microsoft Word for content creation, incorporating semantic knowledge into the content. This add-in should simplify the development and validation of ontologies, by making ontologies more accessible to a wide audience of authors and by enabling semantic content to be integrated in the authoring experience, capturing the author’s intent and knowledge at the source, and facilitating downstream discoverability.

The goal of the add-in is to assist scientists in writing a manuscript that is easily integrated with existing and pending electronic resources. The major aims of this project are to add semantic information as XML mark-up to the manuscript using ontologies and controlled vocabularies (using OBO), and to integrate manuscript content with existing public data repositories.

As part of the publishing workflow and archiving process, the terms added by the add-in, providing the semantic information, can be extracted from Word files, as they are stored as custom XML tags as part of the content. The semantic knowledge can then be preserved as the documented is converted to other formats, such as HTML or the XML format from the National Library of Medicine, which is commonly used for archiving.

The full benefit of semantic-rich content will result from an end-to-end approach to the preservation of semantics and metadata through the publishing pipeline, starting with capturing knowledge from the subject experts, the authors, and enabling this knowledge to be preserved when published, as well as made available to search engines and presented to people consuming the content.

This project resulted from an initial and ongoing collaboration between Microsoft External Research and Dr. Phil Bourne and Dr. Lynn Fink, at the University of California San Diego. Additional collaboration with the staff from Science Commons aims to make the add-in relevant to a wider audience and also to preserve semantic data along the publishing pipeline.

Audience
This project is focused on researchers and software developers in domains utilizing ontologies– as well as publishers, archivists, and early adopters in the scientific, technical, and scholarly publishing fields.

Specific features

Inline Syntax Coloring of Informative Words
Built-in Knowledge of Ontologies and Controlled Vocabularies
Automatic Detection of Identifiers
Custom Semantic Markup

Getting Started

Trying out the add-in:

You will need Microsoft Word 2007 (Windows XP or Windows Vista)
Download and install the latest Technology Preview release of the add-in
Check that the SmartTags feature in Word is enabled:

Click the Microsoft Office Button (circle on the top left)
Click the Word Options button
In the categories pane click Add-ins
In the Manage box, towards the bottom of the dialog, select Smart Tags, and then click Go
Select the Label data with smart tags check box

Open the test document from the Releases tab and follow the instructions in the page

Examining the source code and contributing to the project:

Navigate to the Source Code tab
You can use the free version of Visual Studio (Visual C# 2008 Express Edition) to build the project
Add comments in the Discussion tab, and report problems under Issue Tracker

<w:customXml w:uri="http://biolit.ucsd.edu/biolitschema" w:element="biolit-term">
    <w:customXmlPr>
        <w:attr w:name="id" w:val="DOID:4" /> 
        <w:attr w:name="type" w:val="Human disease" /> 
        <w:attr w:name="status" w:val="true" /> 
        <w:attr w:name="OntName" w:val="Human disease" /> 
        <w:attr w:name="url" w:val="http://purl.org/obo/owl/DOID#DOID_4" /> 
    </w:customXmlPr>
    <w:smartTag w:uri="BioLitTags" w:element="tag1">
        <w:r>
            <w:t>disease</w:t> 
        </w:r>
    </w:smartTag>
</w:customXml>

Updated Wiki: Home

pablofe — Tue, 10 Mar 2009 21:19:18 GMT

Project Description
A Word 2007 add-in that enables the annotation of Word documents based on terms that appear in Ontologies

Summary
Microsoft External Research’s goal with this project is to enable communities who maintain ontologies to more easily experiment and to enhance the experience of authors who use Microsoft Word for content creation, incorporating semantic knowledge into the content. This add-in should simplify the development and validation of ontologies, by making ontologies more accessible to a wide audience of authors and by enabling semantic content to be integrated in the authoring experience, capturing the author’s intent and knowledge at the source, and facilitating downstream discoverability.

The goal of the add-in is to assist scientists in writing a manuscript that is easily integrated with existing and pending electronic resources. The major aims of this project are to add semantic information as XML mark-up to the manuscript using ontologies and controlled vocabularies (using OBO), and to integrate manuscript content with existing public data repositories.

As part of the publishing workflow and archiving process, the terms added by the add-in, providing the semantic information, can be extracted from Word files, as they are stored as custom XML tags as part of the content. The semantic knowledge can then be preserved as the documented is converted to other formats, such as HTML or the XML format from the National Library of Medicine, which is commonly used for archiving.

The full benefit of semantic-rich content will result from an end-to-end approach to the preservation of semantics and metadata through the publishing pipeline, starting with capturing knowledge from the subject experts, the authors, and enabling this knowledge to be preserved when published, as well as made available to search engines and presented to people consuming the content.

This project resulted from an initial and ongoing collaboration between Microsoft External Research and Dr. Phil Bourne and Dr. Lynn Fink, at the University of California San Diego. Additional collaboration with the staff from Science Commons aims to make the add-in relevant to a wider audience and also to preserve semantic data along the publishing pipeline.

Audience
This project is focused on researchers and software developers in domains utilizing ontologies– as well as publishers, archivists, and early adopters in the scientific, technical, and scholarly publishing fields.

Specific features

Inline Syntax Coloring of Informative Words
Built-in Knowledge of Ontologies and Controlled Vocabularies
Automatic Detection of Identifiers
Custom Semantic Markup

Getting Started

Trying out the add-in:

You will need Microsoft Word 2007 (Windows XP or Windows Vista)
Download and install the latest Technology Preview release of the add-in
Check that the SmartTags feature in Word is enabled:

Click the Microsoft Office Button (circle on the top left)
Click the Word Options button
In the categories pane click Add-ins
In the Manage box, towards the bottom of the dialog, select Smart Tags, and then click Go
Select the Label data with smart tags check box

Open the test document from the Releases tab and follow the instructions in the page

Examining the source code and contributing to the project:

Navigate to the Source Code tab
You can use the free version of Visual Studio (Visual C# 2008 Express Edition) to build the project
Add comments in the Discussion tab, and report problems under Issue Tracker

<w:customXml w:uri="http://biolit.ucsd.edu/biolitschema" w:element="biolit-term">
    <w:customXmlPr>
        <w:attr w:name="id" w:val="DOID:4" /> 
        <w:attr w:name="type" w:val="Human disease" /> 
        <w:attr w:name="status" w:val="true" /> 
        <w:attr w:name="OntName" w:val="Human disease" /> 
        <w:attr w:name="url" w:val="http://purl.org/obo/owl/DOID#DOID_4" /> 
    </w:customXmlPr>
    <w:smartTag w:uri="BioLitTags" w:element="tag1">
        <w:r>
            <w:t>disease</w:t> 
        </w:r>
    </w:smartTag>
</w:customXml>

If the Word file (docx) needs to be transformed to other formats, this set of tags would need to be processed using xslt or other technologies. Note that there are other CodePlex projects available which implement transformations of docx files to other formats which one can start from.

Background
Cyberinfrastructure is integral to all aspects of conducting experimental research and distributing those results. However, it has yet to make a similar impact on the way we communicate that information. Peer-reviewed publications have long been the currency of scientific research as they are the fundamental unit through which scientists communicate with and evaluate each other. However, in striking contrast to the data, publications have yet to benefit from the opportunities offered by cyberinfrastructure. While the means of distributing publications has vastly improved, publishers have done little else to capitalize on the electronic medium. In particular, semantic information describing the content of these publications is sorely lacking, as is the integration of this information with data in public repositories. This is confounding considering that many basic tools for marking-up and integrating publication content in this manner already exist, such as a centralized literature database, relevant ontologies, and machine-readable document standards. We propose to address this delay in the maturation of scholarly communication by developing open source tools to facilitate the semantic mark-up of new manuscripts and the submission of those manuscripts directly to a journal’s electronic publishing system.

Updated Wiki: Home

pablofe — Tue, 10 Mar 2009 20:57:21 GMT

Project Description
A Word 2007 add-in that enables the annotation of Word documents based on terms that appear in Ontologies

Summary
Microsoft External Research’s goal with this project is to enable communities who maintain ontologies to more easily experiment and to enhance the experience of authors who use Microsoft Word for content creation, incorporating semantic knowledge into the content. This add-in should simplify the development and validation of ontologies, by making ontologies more accessible to a wide audience of authors and by enabling semantic content to be integrated in the authoring experience, capturing the author’s intent and knowledge at the source, and facilitating downstream discoverability.

The goal of the add-in is to assist scientists in writing a manuscript that is easily integrated with existing and pending electronic resources. The major aims of this project are to add semantic information as XML mark-up to the manuscript using ontologies and controlled vocabularies (using OBO), and to integrate manuscript content with existing public data repositories.

As part of the publishing workflow and archiving process, the terms added by the add-in, providing the semantic information, can be extracted from Word files, as they are stored as custom XML tags as part of the content. The semantic knowledge can then be preserved as the documented is converted to other formats, such as HTML or the XML format from the National Library of Medicine, which is commonly used for archiving.

The full benefit of semantic-rich content will result from an end-to-end approach to the preservation of semantics and metadata through the publishing pipeline, starting with capturing knowledge from the subject experts, the authors, and enabling this knowledge to be preserved when published, as well as made available to search engines and presented to people consuming the content.

This project resulted from an initial and ongoing collaboration between Microsoft External Research and Dr. Phil Bourne and Dr. Lynn Fink, at the University of California San Diego. Additional collaboration with the staff from Science Commons aims to make the add-in relevant to a wider audience and also to preserve semantic data along the publishing pipeline.

Audience
This project is focused on researchers and software developers in domains utilizing ontologies– as well as publishers, archivists, and early adopters in the scientific, technical, and scholarly publishing fields.

Specific features

Inline Syntax Coloring of Informative Words
Built-in Knowledge of Ontologies and Controlled Vocabularies
Automatic Detection of Identifiers
Custom Semantic Markup

Getting Started

Trying out the add-in:

You will need Microsoft Word 2007 (Windows XP or Windows Vista)
Download and install the latest Technology Preview release of the add-in
Check that the SmartTags feature in Word is enabled:

Click the Microsoft Office Button (circle on the top left)
Click the Word Options button
In the categories pane click Add-ins
In the Manage box, towards the bottom of the dialog, select Smart Tags, and then click Go
Select the Label data with smart tags check box

Open the test document from the Releases tab and follow the instructions in the page

Examining the source code and contributing to the project:

Navigate to the Source Code tab
You can use the free version of Visual Studio (Visual C# 2008 Express Edition) to build the project
Add comments in the Discussion tab, and report problems under Issue Tracker

Design Documentation
Design Documents

"Semantic Tagging"

When a word or set of words is tagged by the add-in, the word is wrapped with some tags that associate it with the ontology term. The example below shows the word "disease" being tagged with Human Disease ontology.

<w:customXml w:uri="http://biolit.ucsd.edu/biolitschema" w:element="biolit-term">
<w:customXmlPr>
<w:attr w:name="id" w:val="DOID:4" />
<w:attr w:name="type" w:val="Human disease" />
<w:attr w:name="status" w:val="true" />
<w:attr w:name="OntName" w:val="Human disease" />
<w:attr w:name="url" w:val="http://purl.org/obo/owl/DOID#DOID_4" />
</w:customXmlPr>
<w:smartTag w:uri="BioLitTags" w:element="tag1">
<w:r>
<w:t>disease</w:t>
</w:r>
</w:smartTag>
</w:customXml>

If the Word file (docx) needs to be transformed to other formats, this set of tags would need to be processed using xslt or other technologies. Note that there are other CodePlex projects available which implement transformations of docx files to other formats which one can start from.

Background
Cyberinfrastructure is integral to all aspects of conducting experimental research and distributing those results. However, it has yet to make a similar impact on the way we communicate that information. Peer-reviewed publications have long been the currency of scientific research as they are the fundamental unit through which scientists communicate with and evaluate each other. However, in striking contrast to the data, publications have yet to benefit from the opportunities offered by cyberinfrastructure. While the means of distributing publications has vastly improved, publishers have done little else to capitalize on the electronic medium. In particular, semantic information describing the content of these publications is sorely lacking, as is the integration of this information with data in public repositories. This is confounding considering that many basic tools for marking-up and integrating publication content in this manner already exist, such as a centralized literature database, relevant ontologies, and machine-readable document standards. We propose to address this delay in the maturation of scholarly communication by developing open source tools to facilitate the semantic mark-up of new manuscripts and the submission of those manuscripts directly to a journal’s electronic publishing system.

Updated Wiki: Home

pablofe — Tue, 10 Mar 2009 17:02:38 GMT

Project Description
A Word 2007 add-in that enables the annotation of Word documents based on terms that appear in Ontologies

Summary
Microsoft External Research’s goal with this project is to enable communities who maintain ontologies to more easily experiment and to enhance the experience of authors who use Microsoft Word for content creation, incorporating semantic knowledge into the content. This add-in should simplify the development and validation of ontologies, by making ontologies more accessible to a wide audience of authors and by enabling semantic content to be integrated in the authoring experience, capturing the author’s intent and knowledge at the source, and facilitating downstream discoverability.

The goal of the add-in is to assist scientists in writing a manuscript that is easily integrated with existing and pending electronic resources. The major aims of this project are to add semantic information as XML mark-up to the manuscript using ontologies and controlled vocabularies (using OBO), and to integrate manuscript content with existing public data repositories.

As part of the publishing workflow and archiving process, the terms added by the add-in, providing the semantic information, can be extracted from Word files, as they are stored as custom XML tags as part of the content. The semantic knowledge can then be preserved as the documented is converted to other formats, such as HTML or the XML format from the National Library of Medicine, which is commonly used for archiving.

The full benefit of semantic-rich content will result from an end-to-end approach to the preservation of semantics and metadata through the publishing pipeline, starting with capturing knowledge from the subject experts, the authors, and enabling this knowledge to be preserved when published, as well as made available to search engines and presented to people consuming the content.

This project resulted from an initial and ongoing collaboration between Microsoft External Research and Dr. Phil Bourne and Dr. Lynn Fink, at the University of California San Diego. Additional collaboration with the staff from Science Commons aims to make the add-in relevant to a wider audience and also to preserve semantic data along the publishing pipeline.

Audience
This project is focused on researchers and software developers in domains utilizing ontologies– as well as publishers, archivists, and early adopters in the scientific, technical, and scholarly publishing fields.

Specific features

Inline Syntax Coloring of Informative Words
Built-in Knowledge of Ontologies and Controlled Vocabularies
Automatic Detection of Identifiers
Custom Semantic Markup

Getting Started

Trying out the add-in:

You will need Microsoft Word 2007 (Windows XP or Windows Vista)
Download and install the latest Technology Preview release of the add-in
Check that the SmartTags feature in Word is enabled:

Click the Microsoft Office Button (circle on the top left)
Click the Word Options button
In the categories pane click Add-ins
In the Manage box, towards the bottom of the dialog, select Smart Tags, and then click Go
Select the Label data with smart tags check box

Open the test document from the Releases tab and follow the instructions in the page

Examining the source code and contributing to the project:

Navigate to the Source Code tab
You can use the free version of Visual Studio (Visual C# 2008 Express Edition) to build the project
Add comments in the Discussion tab, and report problems under Issue Tracker

Design Documentation
Design Documents

Background
Cyberinfrastructure is integral to all aspects of conducting experimental research and distributing those results. However, it has yet to make a similar impact on the way we communicate that information. Peer-reviewed publications have long been the currency of scientific research as they are the fundamental unit through which scientists communicate with and evaluate each other. However, in striking contrast to the data, publications have yet to benefit from the opportunities offered by cyberinfrastructure. While the means of distributing publications has vastly improved, publishers have done little else to capitalize on the electronic medium. In particular, semantic information describing the content of these publications is sorely lacking, as is the integration of this information with data in public repositories. This is confounding considering that many basic tools for marking-up and integrating publication content in this manner already exist, such as a centralized literature database, relevant ontologies, and machine-readable document standards. We propose to address this delay in the maturation of scholarly communication by developing open source tools to facilitate the semantic mark-up of new manuscripts and the submission of those manuscripts directly to a journal’s electronic publishing system.

Updated Wiki: Home

pablofe — Tue, 10 Mar 2009 17:01:54 GMT

Project Description
A Word 2007 add-in that enables the annotation of Word documents based on terms that appear in Ontologies

Summary
Microsoft External Research’s goal with this project is to enable communities who maintain ontologies to more easily experiment and to enhance the experience of authors who use Microsoft Word for content creation, incorporating semantic knowledge into the content. This add-in should simplify the development and validation of ontologies, by making ontologies more accessible to a wide audience of authors and by enabling semantic content to be integrated in the authoring experience, capturing the author’s intent and knowledge at the source, and facilitating downstream discoverability.

The goal of the add-in is to assist scientists in writing a manuscript that is easily integrated with existing and pending electronic resources. The major aims of this project are to add semantic information as XML mark-up to the manuscript using ontologies and controlled vocabularies (using OBO), and to integrate manuscript content with existing public data repositories.

As part of the publishing workflow and archiving process, the terms added by the add-in, providing the semantic information, can be extracted from Word files, as they are stored as custom XML tags as part of the content. The semantic knowledge can then be preserved as the documented is converted to other formats, such as HTML or the XML format from the National Library of Medicine, which is commonly used for archiving.

The full benefit of semantic-rich content will result from an end-to-end approach to the preservation of semantics and metadata through the publishing pipeline, starting with capturing knowledge from the subject experts, the authors, and enabling this knowledge to be preserved when published, as well as made available to search engines and presented to people consuming the content.

This project resulted from an initial and ongoing collaboration between Microsoft External Research and Dr. Phil Bourne and Dr. Lynn Fink, at the University of California San Diego. Additional collaboration with the staff from Science Commons aims to make the add-in relevant to a wider audience and also to preserve semantic data along the publishing pipeline.

Audience
This project is focused on researchers and software developers in domains utilizing ontologies– as well as publishers, archivists, and early adopters in the scientific, technical, and scholarly publishing fields.

Specific features

Inline Syntax Coloring of Informative Words
Built-in Knowledge of Ontologies and Controlled Vocabularies
Automatic Detection of Identifiers
Custom Semantic Markup

Getting Started

Trying out the add-in:

You will need Microsoft Word 2007 (Windows XP or Windows Vista)
Download and install the latest Technology Preview release of the add-in
Check that the SmartTags feature in Word is enabled:

Click the Microsoft Office Button (circle on the top left)
Click the Word Options button
In the categories pane click Add-ins
In the Manage box, towards the bottom of the dialog, select Smart Tags, and then click Go
Select the Label data with smart tags check box

Open the test document from the Releases tab and follow the instructions in the page

Examining the source code and contributing to the project:

Navigate to the Source Code tab
You can use the free version of Visual Studio (Visual C# 2008 Express Edition) to build the project
Add comments in the Discussion tab, and report problems under Issue Tracker

Architecture
To be added...

Design Documentation
Design Documents

Background
Cyberinfrastructure is integral to all aspects of conducting experimental research and distributing those results. However, it has yet to make a similar impact on the way we communicate that information. Peer-reviewed publications have long been the currency of scientific research as they are the fundamental unit through which scientists communicate with and evaluate each other. However, in striking contrast to the data, publications have yet to benefit from the opportunities offered by cyberinfrastructure. While the means of distributing publications has vastly improved, publishers have done little else to capitalize on the electronic medium. In particular, semantic information describing the content of these publications is sorely lacking, as is the integration of this information with data in public repositories. This is confounding considering that many basic tools for marking-up and integrating publication content in this manner already exist, such as a centralized literature database, relevant ontologies, and machine-readable document standards. We propose to address this delay in the maturation of scholarly communication by developing open source tools to facilitate the semantic mark-up of new manuscripts and the submission of those manuscripts directly to a journal’s electronic publishing system.