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<article xmlns:xlink="http://www.w3.org/1999/xlink">
  <front>
    <journal-meta />
    <article-meta>
      <title-group>
        <article-title>Semantic Authoring By Tagging with Annotea Social Bookmarks and Topics</article-title>
      </title-group>
      <contrib-group>
        <contrib contrib-type="author">
          <string-name>Marja-Riitta Koivunen Annotea</string-name>
          <email>marja@annotea.org</email>
        </contrib>
      </contrib-group>
      <abstract>
        <p>Annotea is a framework that supports Semantic Web based collaboration and authoring via Annotea objects, such as social annotations, bookmarks, and topics. Social bookmarks and topics can be used for semantic authoring in many levels. They let ordinary users tag interesting Web documents with their own personal concepts (folksonomies). These concepts can be simple or form hierarchies, and they can be linked to more standard concepts when users become aware of them. Collections of the concepts and the bookmarks under them can be stored to bookmark documents or services as metadata and easily shared with other users. Annotea users can also literally semantically author pages with link collections and categories. They can use the title and description information of the topics and bookmarks to create the page content. This content from the bookmark and topics hierarchies is then easily converted to XHTML Web pages by using XSLT scripts. Annotea presentation objects further support authoring and customized presentations by separating the presentation and the application data. While Annotea precedes tagging and social bookmarking services and tools popular today it still provides better flexibility, extendibility, and reuse of the bookmark and topic data with help of the Semantic Web technologies.</p>
      </abstract>
      <kwd-group>
        <kwd>Social bookmarks</kwd>
        <kwd>social topics</kwd>
        <kwd>Semantic Web</kwd>
        <kwd>semantic authoring</kwd>
        <kwd>ontologies</kwd>
        <kwd>tagging</kwd>
        <kwd>folksonomies</kwd>
      </kwd-group>
    </article-meta>
  </front>
  <body>
    <sec id="sec-1">
      <title>Categories and Subject Descriptors</title>
    </sec>
    <sec id="sec-2">
      <title>1. INTRODUCTION</title>
      <p>
        Annotea is a framework for semantic annotations [
        <xref ref-type="bibr" rid="ref19">26</xref>
        ],
bookmarks, and topics focusing on sharing of the objects and
collaboration in document context[
        <xref ref-type="bibr" rid="ref11">18</xref>
        ]. Annotea [
        <xref ref-type="bibr" rid="ref10">4, 17</xref>
        ] gets its
inspiration from observing users’ needs and problems and
developing user scenarios based on those observations [
        <xref ref-type="bibr" rid="ref11">18</xref>
        ].
Annotea sees humans as meaning makers. They create concepts,
make associations, comment, clarify, annotate, review, organize,
bookmark, tag, and file information into categories or organize it
into folders. When humans learn something new they augment
and modify their existing cognitive models with new personal
concepts. Typically, these concepts are vague at first but as they
become more precise they can be shared with other users and
developed further collaboratively.
      </p>
      <p>Ordinary users who are not familiar with semantic Web can do
semantic authoring with intuitively familiar Annotea objects,
such as annotations, discussions threads, bookmarks, and topics
(tags). For instance, Annotea social bookmarks allow users to
recall earlier visited Web resources, such as Web documents,
services, music, images and blogs. As a side effect, the user also
authors metadata about the bookmarked resources. When
published and shared, this information can be useful not only for
the user but also for other users and applications.</p>
      <p>Users can also choose to use Annotea to author and maintain
Web pages consisting of link collections and categories. In this
case, users semantically author bookmark and topic information,
such as title and description information, which can be used to
form Web pages that were earlier manually written and
maintained.</p>
      <p>
        Annotea topics [
        <xref ref-type="bibr" rid="ref11 ref12 ref14 ref9">18, 19, 21, 16</xref>
        ] support user defined simple
concepts (tags). Instead of forcing the users to invest in learning
standard ontologies before they can start developing their ideas,
Annotea supports the innovation process by letting users start
from their own personal ontologies (folksonomies). Gradually,
when the user learns about connections her concepts and
standard, commonly used concepts, it is possible to link the
personal topics to them.
      </p>
      <p>
        Annotea uses the Semantic Web technologies for implementing
the solutions but hides the Semantic Web from the ordinary
users under the familiar objects and easy user interfaces. From
the user point of view, the Annotea topics can be used for Web
tagging just like in the popular Web tagging services [
        <xref ref-type="bibr" rid="ref4 ref6">11, 13</xref>
        ]
that followed Annotea. However, the Semantic Web metadata
basis [9] makes Annotea more flexible, easily extendible, and
interoperable supporting user needs and applications also
beyond tagging. The user can select bookmark stores relevant to
her tasks and seamlessly merge Annotea objects from these
stores to support task related queries.
      </p>
      <p>
        Annotea objects can be presented to the users in many
innovative ways and by different tools. Typically, the objects are
explored in the context of the Web resources they refer to,
examined in selected topic hierarchies, and searched by using
different properties. Amaya browser/editor [1] and lately
Annotea Ubimarks [7] have been used to demonstrate some
capabilities of Annotea objects. In addition, many other clients,
such as Annozilla [8], have been developed outside the Annotea
team. The bookmark files can also be presented in normal
browsers as XHTML pages by using selected XSLT style sheets.
In Annotea the bookmarks and topics can be stored locally or
shared both with individual users on different devices and with
different user groups. Unlike simple tagging or bookmark
formats, such as XBEL [
        <xref ref-type="bibr" rid="ref20">27</xref>
        ], Annotea bookmarks and topics
help collaboration and finding relevant information even when
users use different terms for similar concepts. This is is often the
case in cross disciplinary fields, such as life science, user
experience or even in marketing and research where users are
awarded from finding original concepts instead of using the
already existing ones. While services, such as Linkagogo [
        <xref ref-type="bibr" rid="ref15">22</xref>
        ]
help in interpreting between different formats, the simple
formats often don’t have enough identification information to
easily separate or merge concepts.
      </p>
      <p>In addition to supporting tools for creating and retrieving
bookmarks, the Annotea bookmarks can be used as user profiles
for different services. This helps users find the information
relevant to them at a certain context. Annotea bookmarks and
topics can also contain information not just about the user but
his or her social network. Again, this can be used to support the
finding of more relevant information. Bookmarks and topics can
also be used in applications organizing blog type information.
Finally, as shared bookmarks are easy to create we hope to
eventually see enough commonly available bookmark and topic
data to be able to see network effects in applications using the
published bookmark repositories collectively. These
applications can provide more relevant results. Furthermore,
when dat a mining and search engines type applications mine the
topics and different connections between the topics it is possible
to make many new innovative discoveries connecting fields that
were not aware of each other because they used different
terminologies.</p>
    </sec>
    <sec id="sec-3">
      <title>2. ANNOTEA ARCHITECTURE</title>
      <p>Different annotation and tagging applications can be built on top
of Annotea architecture that includes Annotea stores, Annotea
objects, such as the bookmarks and topics, and protocols.
Annotea stores are RDF metadata stores that store Annotea
objects. Objects from various stores can be easily merged and
viewed together. Many currently popular tagging services
violate the principle of user control and do not give users a
choice of where to store the bookmarks and topics. The Annotea
objects can be stored in local files, global Web servers and/or
Web documents containing the metadata.</p>
      <p>Web documents offer users an easy alternative to get started
without a server. The same authentication and protection
mechanisms can be used as for any other Web document. A
document can also be used to archive snapshots of the selected
Annotea objects stored on the server. For instance, a version of a
document can be stored together with annotations for that
version.</p>
      <p>
        Annotea objects have URIs and properties. They all store some
basic tracking information, such as who created them and when.
The Annotea schemas [2, 3, 6] define only a few specifically
Annotea related properties for Annotea objects. To improve
reuse and decrease unnecessary inferencing the rest of the
properties are adopted from other well-established schemas,
such as Dublin Core. Annotea usage documents [
        <xref ref-type="bibr" rid="ref13">20</xref>
        ] and server
protocols [
        <xref ref-type="bibr" rid="ref18">25</xref>
        ] help define the basic annotation/bookmarking
framework [
        <xref ref-type="bibr" rid="ref7">14</xref>
        ] for Annotea objects. Finally, model user
interfaces [1,7] demonstrate the use of the objects.
      </p>
      <p>New properties can be easily added to Annotea objects. For
instance, Annotea Ubimarks lets the author add a URI to his
personal and social network information by using foaf:maker
(see Figure 1). When provided, this social network information
can be used as additional help when trying to find related
documents.</p>
      <p>
        Annotea [
        <xref ref-type="bibr" rid="ref10 ref7">14 , 17</xref>
        ] has demonstrated storing annotations and
replies to different annotation servers. Annotea protocol for the
metadata stores is based on HTTP. Annotea bookmarks and
topics can use a similar protocol or standard Web queries. We
have done some experiments with this. Currently, the model
implementations use HTTP, FTP, and possibly also other Web
protocols to store the bookmarks and topics as Web documents.
This approach can be applied for annotations and replies as well.
Annotea applications and user interfaces provide different
views of the Annotea objects. When the interfaces are attached
to browsers users can seamlessly collaborate via Annotea
objects in the context of the Web documents or other Web
resources. In addition, Annotea objects can be used in many
other kinds of applications and user interfaces. For instance,
bookmark collections on a selected topic can be used as user
defined profiles for services or bookmark repositories for
selected domains can be used to order the results from search
agents, such as Yahoo Search or Google, in a more meaningful
way for the user [
        <xref ref-type="bibr" rid="ref17">24</xref>
        ].
      </p>
    </sec>
    <sec id="sec-4">
      <title>3. ANNOTEA BOOKMARK AND TOPIC</title>
    </sec>
    <sec id="sec-5">
      <title>OBJECTS</title>
      <p>While the first phase of Annotea development concentrated on
annotations, early on many user scenarios were developed,
presented, and discussed about social bookmarks and topics
(tags). These were implemented during the second development
phase, when the need for categories was high on the users’ wish
list. Especially status categories were needed to mark the
processed annotations.</p>
      <p>
        We wanted to make sure that Annotea could easily support not
only annotation categories but also our other scenarios related to
categories. We also wanted an easy user metaphor that would
work well with the already existing metaphors. As a result, we
decided to implement the social bookmark and topic objects as a
variation of the semantic annotations [
        <xref ref-type="bibr" rid="ref19">26</xref>
        ]. Our goal was to
experiment with these objects and use the experiences later to
also improve the annotation implementations.
&lt;?xml version="1.0"?&gt;
&lt;RDF:RDF xmlns:foaf="http://xmlns.com/foaf/0.1/"
xmlns:dc="http://purl.org/dc/elements/1.1/"
xmlns:bm="http://www.w3.org/2002/01/bookmark#"
xmlns:a="http://www.w3.org/2000/10/annotation-ns#"
xmlns:RDFS="http://www.w3.org/2000/01/rdf-schema#"
xmlns:RDF="http://www.w3.org/1999/02/22-rdf-syntax-ns#"&gt;
&lt;bm:Bookmark RDF:about = "http://mydomain.org/AnnoteaURI/exBookmark"
dc:title = "The Whole Brain Atlas"
dc:date = "Mon, 15 May 2006 14:28:32 GMT"
a:created = "Mon, 15 May 2006 14:28:32 GMT"
dc:description = "The Whole Brain Atlas is intended as
an introduction to basic neuroanatomy, with emphasis
on the pathoanatomy of several leading central nervous
system diseases."
dc:creator = "Marja"&gt;
&lt;bm:recalls RDF:resource =
      </p>
      <p>"http://www.med.harvard.edu/AANLIB/home.html"/&gt;
&lt;foaf:maker RDF:resource =</p>
      <p>"http://www.annotea.org/marja#marja"/&gt;
&lt;bm:hasTopic RDF:resource = "http://mydomain.org/AnnoteaURI/exTopic"/&gt;
&lt;RDFS:seeAlso RDF:resource =</p>
      <p>"http://big.sfn.org/NDG/site/eavData.asp?o=28952"/&gt;
&lt;/bm:Bookmark&gt;</p>
      <p>The bookmark metaphor was great for our purposes. Ordinary
users are not only familiar with it but have often used traditional
bookmark interfaces. Furthermore, the bookmark user interfaces
have a lot of enhancement possibilities that benefit from the
Semantic Web approach. For instance, the user interface can
utilize the document context to find similar bookmarks and
topics..</p>
    </sec>
    <sec id="sec-6">
      <title>3.1 Annotea Object Identification</title>
      <p>Like other Annotea objects, the bookmark and the topic objects
have their own identification URI. This URI ensures that
Annotea objects retain their identity globally even when objects
are merged together from different data stores, or moved to
another location along with a bookmark file, or sent to another
user by e-mail.</p>
      <p>Not all users have their own Web domains. Therefore, the
current Annotea Ubimarks implementation uses URIs that are
unique UUIDs, such as
"urn:uid:025f3d84-57bd-11da-924db619a79a047d". The UUIDs can be easily created without
owning a Web domain. Resolving the objects content based on
the UUID would need more work, but that is not usually a
problem. .</p>
      <p>Alternatively, the user can choose HTTP addresses in her own
domain with date info by defining an URI path, for instance,
"http://mydomain.org/AnnoteaURI/". Similarly, a
bookmark server can create URIs. If the URI changes in the
server or for some other reason, the correspondence between
two Annotea objects can be defined by using the owl:sameAs
property.</p>
    </sec>
    <sec id="sec-7">
      <title>3.2 Bookmark and Topic Properties</title>
      <p>Annotea does not define all bookmark and topic properties by
itself. It uses properties from well known vocabularies, such as
Dublin Core. Applications already familiar with these properties
know how to deal with them also in Annotea object context
without any extra processing. RDF for a sample bookmark and a
topic is presented in Figure 1.</p>
      <p>Bookmarks and topics have many common properties with other
Annotea objects. For instance, the objects can have a title
(dc:title), a longer description (dc:description), information
about their author (dc:creator and foaf:maker), the creation date
(a:created), the modification date (dc:date), and links to other
related information (RDFS:seeAlso)</p>
      <p>In addition, a bookmark has information about the page it recalls
(bm:recalls), and zero or more topics (bm:hasTopic). A
topic has information about its parent topic
(bm:subTopicOf). In addition, new properties can be easily
added.</p>
    </sec>
    <sec id="sec-8">
      <title>4. VIEWING ANNOTEA BOOKMARKS</title>
    </sec>
    <sec id="sec-9">
      <title>AND TOPICS</title>
      <p>Annotea objects can be presented to users without a need to
know anything about the Semantic Web. The bookmark
metaphor nicely supports semantic authoring and presentation of
Annotea bookmark and topic objects, their collections, and
context sensitive views to these objects.</p>
      <p>The Annotea topics can be anything the user wants them to be.
They can start with vague meaning and gradually become more
robust and better understood. When user discovers other related
concepts in a better established ontologies, her own concepts
can be linked to those.</p>
    </sec>
    <sec id="sec-10">
      <title>4.1 Bookmark and Topic Object View</title>
      <p>Users can explore the bookmark or the topic information in
simple forms. For instance, in Figure 2 the “Bookmark view”
presents the bookmark’s RDF properties and values.
Properties can be added to Annotea objects and different
presentations may show different sets of properties. With
guidance information about the properties, such as the
presentation order and the preferred widgets, the presentations
could be created automatically. This is the next step for the new
Annotea presentation objects.</p>
    </sec>
    <sec id="sec-11">
      <title>4.2 Viewing Collections of Bookmarks and</title>
    </sec>
    <sec id="sec-12">
      <title>Topics</title>
      <p>
        Annotea topics allow authors create and maintain shared
classifications or topics [
        <xref ref-type="bibr" rid="ref8">15</xref>
        ]. A bookmark can be cataloged
under one or more topics and presented to the user in a
hierarchy view resembling a folder hierarchy. In Figure 3 the
“View Bookmark Hierarchy” window shows a hierarchy of
“Annotea related projects”. Clicking the bookmark title in the
hierarchy view shows the recalled page while clicking the
properties icon presents the bookmark view (see Figure 2).
Clicking a topic always shows its properties in a topic view.
The Semantic information in Figure 3 bookmark hierarchy was
originally copied from the Web page shown in the bottom
browser window. The bookmark document was so easy to
update with Annotea Ubimarks that in many cases the updates to
the original Web page lacked behind. Fortunately, it was quite
easy to create a corresponding XHTML page directly from the
bookmark document semantics with an XSLT transformation.
The top browser window in Figure 3 shows one example of
such a transformed page. The style of the generated page can be
easily changed to bear even closer resemblance to the original
page. This is semantic authoring at its best as the user gets
benefits from semantics that was created without any extra work
or learning.
      </p>
    </sec>
    <sec id="sec-13">
      <title>4.3 Viewing Bookmarks and Topics in</title>
    </sec>
    <sec id="sec-14">
      <title>Context</title>
      <p>
        Context dependent views of Annotea objects are characteristic
to Annotea applications. For instance, Annotea Ubimarks user
interface provides information about related Web documents in
the current document context. When a user browses through the
Web pages and finds something interesting she can look for the
“Pagemarks” icon. This icon means that one or more users has
bookmarked the current page. The “Pagemarks” icon can be
clicked to open a view listing all the bookmarks on the page.
These bookmarks and their topics can be easily followed to find
related documents in the currently subscribed bookmark stores,
some of which may provide information from Web crawlers.
Users collaborating in related research areas can benefit from
the bookmark and topic information. They can find related
topics and bookmarks. For instance, in Figure 4 the user has
bookmarked a gene page in Amigo. When she browses the page
later and clicks the “Pagemarks” and the topic icons, she finds
more information about the genes involved in CML leukemia
made by other researchers in other departments of the institution
or in other institutions. In the future, the user generated
information can be combined with automatic categorizations,
such as created in MagPie [
        <xref ref-type="bibr" rid="ref5">12</xref>
        ] or in Trailblazer [
        <xref ref-type="bibr" rid="ref3">10</xref>
        ] to help the
user to find also non-bookmarked relevant documents and make
new innovative associations.
      </p>
    </sec>
    <sec id="sec-15">
      <title>4.4 Defining Custom Bookmark Orders</title>
      <p>The order of the bookmarks can be defined by using Annotea
presentation objects [5]. They can be attached to another
resource, such as a topic, to guide its presentation. For instance,
it can define the order of the selected bookmarks under a topic.
The rest of the topics are presented alphabetically. The
presentation objects let users define customized orders for a
shared hierarchy. A sample presentation object is presented in
Figure 5.</p>
    </sec>
    <sec id="sec-16">
      <title>4.5 Defining Multiple Root Topics</title>
      <p>
        The topic hierarchies do not have to have a common root topic.
It is possible to have several roots. This lets the user also view
hierarchies even when some topics are temporarily unavailable.
Hierarchies containing several root topics can be also viewed in
multifaceted displays, such as the ones used in mSpace [
        <xref ref-type="bibr" rid="ref16">23</xref>
        ].
Because of multiple roots it is easy to define concept hierarchies
that are intended to be used in parallel with other concepts.
Workflow status (see Figure 6) and content label hierarchies
(Figure 7) are such examples.
      </p>
    </sec>
    <sec id="sec-17">
      <title>5. CONCLUSIONS</title>
      <p>Annotea has been pioneering with social bookmarking, tagging,
and folksonomy applications on the Web. Annotea social
bookmarks and topics provide ordinary users familiar metaphors
for authoring and sharing reusable and easily extendible
Semantic Web metadata without a need to learn or understand
the Semantic Web.</p>
      <p>Many Web pages containing links and categories can be chosen
to be semantically authored as Annotea bookmark files and
transformed with XSLT into XHTML pages. This makes
maintaining the links easy.</p>
      <p>Annotea users are not limited to use one service for their
bookmarks and topics. They can subscribe several local or
global data stores containing the various Annotea objects they
are interested in at each moment. Web documents offer users an
easy starting point. Semantic Web gives supports for easy
merging and querying of Annotea metadata from several
different sources.</p>
      <p>Annotea object metadata is uniquely identifiable and includes
information of its creator and creation dates. It can be easily
extended, customized, combined, and reused in many
applications and services. It can provide additional organization
for data mining and search engine applications, chatrooms, and
blogs.</p>
      <p>Different views to the data, including document context
dependent views, can be easily created. Overall, Annotea
bookmarks and topics can provide huge benefits and flexibility
for Semantic authoring without adding complexity for the user
interface.</p>
    </sec>
    <sec id="sec-18">
      <title>6. ACKNOWLEDGMENTS</title>
      <p>Many people including Jose Kahan, Eric Prud'hommeaux
and Ralph Swick have contributed to Annotea.. I also
want to thank Siegfried Handshuh, Martin Dzbor and Pat
Croke for support and many inspiring discussions.
7. REFERENCES
[1] Amaya homepage, http://www.w3.org/Amaya
[2] Annotea annotation schema,</p>
      <p>http://www.w3.org/2000/10/annotation-ns
[3] Annotea bookmark schema,</p>
      <p>http://www.w3.org/2002/01/bookmark#
[4] Annotea homepage at W3C,</p>
      <p>http://www.w3.org/2001/Annotea
[5] Annotea presentation schema (draft),</p>
      <p>http://www.annotea.org/schemas/2006/04/presentation
[6] Annotea thread schema, http://www.w3.org/2001/03/thread
[7] Annotea Ubimarks homepage,</p>
      <p>http://www.annotea.org/mozilla/ubi.html
[8] Annozilla home page, http://annozilla.mozdev.org/</p>
    </sec>
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