Tony Hammond, profile picture
Uploaded byTony Hammond
PPT, PDF754 views

Agile Descriptions

The document discusses various topics related to Web 2.0 including web feeds, markup tagging, collaborative filtering, social networking, and text mining. It provides examples of using microformats to add semantics to web pages through tags like XFN for social networks, hCard for contact information, and hCalendar for events. It also discusses using RDFa and embedded RDF for metadata and tools for tagging like Delicious, Flickr, CiteULike, and Connotea.

Embed presentation

Download to read offline
Agile Descriptions Tony Hammond Nature Publishing Group [email_address]
Web 2.0 Stuff Some topics to consider: Web Feeds Markup Tagging Collaborative Filtering Social Networking Text Mining
Web Feeds Feeds = news, blogs, podcasts, ... Feed formats are RSS / Atom Feeds are just Rivers of Metadata XML documents polled by subscribers <item> / <entry> = <title>, <link>, <description> / <summary> Administrative metadata Descriptive metadata (dc, prism, mods, ...) Common description model - RDF
Markup Two main approaches to adding semantics to documents: Embedded Metadata Content hidden from user ‘ Blob’ added to page content Exposed Metadata Microformats (  F’s) RDFa = RDF w/attributes eRDF = embedded RDF
Embedded Metadata (i) HTTP headers - exchanged in request HTTP entities - in GET, PUT, POST HTML <head> <meta> HTML <head> / <body> HTML comments HTML comments as RDF ‘islands’
Embedded Metadata (ii) Binary data: XMP PDF’s (and arbitrary binary files) EXIF JPEG’s (digital photos) ID3 tags MP3’s (audio files)
Exposed Metadata -  F’s  F’s qualify display content  F’s add semantic tier to existing structure  F’s limit search indexing abuse  F = nested markup layered on top of host markup environment (HTML/XML) Examples: rel-license, rel-tag, ... hCard, hCalendar, hReview, xFolk, XFN, ...
 F’s Design patterns with semantics Content becomes ‘live’ Can replace custom APIs A poorboy semantic web XMDP profiles GRDDL (W3C Draft - Last Call)  F -> RDF
rel-license - Licenses <a rel=&quot;license&quot; href=&quot; http://.../licenses &quot; > CC </a> Target of URI is license for current page
rel-tag - Tags <a rel=&quot;tag&quot; href=&quot; http://.../tag/microformats &quot; > uF’s </a> Target of URI is tag for current page Last URI path element is tag Preceding URI string is tag space
XFN – Social Networks Example: Ingrid’s blogroll: <a href=&quot; http://.../... &quot; rel=&quot;friend met&quot; >Josh</a> <a href=&quot; http://.../... &quot; rel=&quot;met acquaintance&quot; >Kat</a> <a href=&quot; http://.../... &quot; rel=&quot;co-worker friend met&quot; >Mary</a> <a href=&quot; http://.../... &quot;> Nick </a> Target of URI is typically blog or personal site List of rel attributes indicates personal relationship
XFN (i)
XFN (ii) #1 #4 #2 #3
hCard - Addresses <div class=&quot;vcard&quot; > <a class=&quot;url fn&quot; href=&quot; http://.../... &quot; > Tony Hammond </a> <span class=&quot;org&quot; > Nature Publishing Group </span> <span class=&quot;tel&quot; > <span class=&quot;type&quot; > work </span> <span class=&quot;value&quot; > +44-20-7843-4659 </span> </span> </div> Use vCard (RFC 2426) as basis Nest vCard objects into nested XHTML Make vCard object/property names lcase
hCalendar - Events <div class=&quot;vevent&quot; > <a class=&quot;url&quot; href=&quot; http://.../... &quot; > <span class=&quot;summary&quot; > Future of ... </span> <abbr class=&quot;dtstart&quot; title=&quot; 2007-03-08 &quot; > March 8 </abbr> <abbr class=&quot;dtend&quot; title=&quot; 2007-03-08 &quot; > March 8 </abbr> at <span class=“location&quot; > Google, Inc. </span> </a> </div> Use iCalendar (RFC 2445) as basis Nest iCalendar objects into nested XHTML Make iCalendar object/property names lcase
hReview - Reviews <li class=&quot;hreview&quot; > <h3 class=&quot;item summary&quot; ><a href=&quot;/reviews/programming/web+standards&quot; class=&quot;fn&quot; rel=&quot;self bookmark&quot; > Web standards </a></h3> <div class=&quot;reviewer vcard&quot; > <p class=&quot;icon&quot; > <a href=&quot;/users/katemonkey&quot;><img src=&quot;/images/icons/katemonkey.png&quot; class=&quot;photo&quot;/></a> </p> <p class=&quot;description&quot; > Web standards help designers and developers create the pedantic web. </p> <p class=&quot;by-line&quot; > a <a href=&quot;/reviews/programming&quot;> programming </a> review by <a href=&quot;/users/katemonkey&quot; class=&quot;fn url&quot; > katemonkey </a> that was written <a title=&quot;2007-01-27 11:09:21&quot; class=&quot;dtreviewed&quot; href=&quot;/reviews/date/2007/01/27/&quot;> on 27 th January </a> and has been rated by 3 users as a good review. </p> </div> </li>
xFolk - Bookmarks <div class=&quot;folkentry&quot; > <div> <a class=&quot;taggedlink&quot; href=&quot; http://.../... &quot; > bookmark </a> </div> <div class=&quot;description&quot; > A description ... </div> <div class=&quot;meta&quot; > <a rel=&quot;tag&quot; href=&quot; http://.../tag/tag &quot; > tag </a> </div> </div>
hcite - Citations <li class=&quot;hcite&quot; xml:lang=&quot;en&quot;> <div class=&quot;publisher vcard&quot; > <!-- publisher data as hCard --> <span class=&quot;fn org&quot; > ABC Publishing Co. </span> <span class=&quot;country-name&quot; > United Kingdom </span> ... </div> <div class=&quot;creator vcard&quot; > <!-- author(s) data as hCard --> <span class=&quot;fn n&quot; > <span class=&quot;given-name&quot; > John <span class=&quot;family-name&quot; > Doe </span></span> ... </div> <span class=&quot;fn&quot; > Foobar! </span> <span class=&quot;description&quot; > World Class Book about foobar </span> <span class=&quot;volume&quot; > 1 </span> <span class=&quot;issue&quot; > 1 </span> <span class=&quot;pages&quot; > 1-10 </span> <span class=&quot;format&quot; > article </span> <span class=&quot;identifier&quot; > 12345678 </span> <a class=&quot;keyword&quot; rel=&quot;tag&quot; href=&quot; /tags/foo &quot;> foo </a> Published <abbr class=&quot;dtpublished&quot; title=&quot; 20060101 &quot;> January 1st 2006 </abbr> Copyright <abbr class=&quot;copyright&quot; title=&quot; 20060101 &quot;> 2006 </abbr> </li>
Tagging Tags as simple labels Tags as personal ‘aides-memoire’ Bottom-up rather than top-down Just-in-time vs just-in-case Folksonomies user categories group tag clouds, clustering
Tag Namespaces Tags as simple text tokens Tags as globally unique URIs Naming authority issues DNS- & Registry-based authorities Persistence Per application namespaces Per user, per application namespaces
Tag Terms Any lessons from dynamic vs static typed programming languages? Static compilation provides for type safety Dynamic compilation allows typing on demand Unit tests substitute for type checking at compilation time
Flickr / Photo Clusters
Connotea / Many Eyes
Unalog / Starlight Tag “python” Tag “iceland”
Tagging Tools Let’s look at some cases: del.icio.us – general tagging tool Flickr – photo tagging tool CiteULike – scolarly tagging Connotea – scholarly tagging Unalog – library tagging tool HubMed – an interface to PubMed
del.icio.us <item rdf:about=&quot; http://orlabs.oclc.org/Identities/ &quot;> <title> WorldCat Identities </title> <link> http://orlabs.oclc.org/Identities/ </link> <description> pages for people </description> <dc:creator> hublicious </dc:creator> <dc:date> 2007-02-14T10:37:46Z </dc:date> <dc:subject> person </dc:subject> <dc:subject> identifier </dc:subject> <dc:subject> oclc </dc:subject> <taxo:topics> <rdf:Bag> <rdf:li resource=&quot; http://del.icio.us/tag/person &quot;/> <rdf:li resource=&quot; http://del.icio.us/tag/identifier &quot;/> <rdf:li resource=&quot; http://del.icio.us/tag/oclc &quot;/> </rdf:Bag> </taxo:topics> </item>
Flickr <entry> <title> The Eclipsified Moon </title> <link rel=&quot;alternate&quot; type=&quot;text/html“ href=&quot; http://www.flickr.com/photos/alf/409522855/ &quot;/> <id> tag:flickr.com,2005:/photo/409522855 </id> <published> 2007-03-04T04:53:33Z </published> <updated> 2007-03-04T04:53:33Z </updated> <dc:date.Taken> 2007-03-03T23:34:23-08:00 </dc:date.Taken> <content type=&quot;html”> ... </content> <author> <name> balloon in a sock </name> <uri> http://www.flickr.com/people/alf/ </uri> </author> <link rel=&quot;license&quot; type=&quot;text/html&quot; href=&quot; http://.../licenses/by-nc/2.0/ &quot; /> <link rel=&quot;enclosure&quot; type=&quot;image/jpeg“ href=&quot; http://.../133/409522855_6ed97bbd2a_o.jpg &quot; /> <category term=&quot; moon &quot; scheme=&quot; http://www.flickr.com/photos/tags/ &quot; /> <category term=&quot; eclipse &quot; scheme=&quot; http://www.flickr.com/photos/tags/ &quot; /> </entry>
Cite U Like CiteULike (i)
Cite U Like CiteULike (ii) <item rdf:about= http://www.citeulike.org/user/timflutre/article/1139879 > <title> Dating the tree of life. </title> <link> http://www.citeulike.org/user/timflutre/article/1139879 </link> <description> ... </description> <dc:title> Dating the tree of life. </dc:title> <dc:creator> MJ Benton </dc:creator> <dc:creator> FJ Ayala </dc:creator> <dc:identifier> doi:10.1126/science.1077795 </dc:identifier> <dc:source> Science, Vol. 300, No. 5626. (13 June 2003), pp. 1698-1700. </dc:source> <prism:publicationName> Science </prism:publicationName> <prism:issn> 1095-9203 </prism:issn> <prism:volume> 300 </prism:volume> <prism:number> 5626 </prism:number> <prism:startingPage> 1698 </prism:startingPage> <prism:endingPage> 1700 </prism:endingPage> <category> evolution </category> <category> molecular_clock </category> </item>
Connotea (i) <item rdf:about=&quot; http://.../user/penguin/uri/ceac242dfd66979fe07ac5ebf8381afc &quot;> <title> Induction of IL-10 suppressors in lung transplant patients by CD4+25+ regulatory T cells through CTLA-4 signaling. </title> <link> http://.../user/penguin/uri/ceac242dfd66979fe07ac5ebf8381afc </link> <description> Posted by penguin to test on Wed Feb 21 2007 </description> <dc:creator> penguin </dc:creator> <dc:date> 2007-02-21T10:22:00Z </dc:date> <dc:subject> test </dc:subject> <slash:comments> 0 </slash:comments> <content:encoded><![CDATA[ ... ]]></content:encoded> <connotea:uri> <dcTerms:URI/> </connotea:uri> <annotate:reference rdf:resource=&quot; http://.../comments/uri/ceac242dfd66979fe07ac5ebf8381afc &quot;/> </item>
Connotea (ii) <dcterms:URI rdf:about=&quot; http://www.hubmed.org/display.cgi?uids=17015751 &quot;> <dc:title> Induction of IL-10 suppressors in lung transplant patients by CD4+25+ regulatory T cells through CTLA-4 signaling. </dc:title> <dc:creator> Ankit Bharat </dc:creator> <dc:creator> Ryan Fields </dc:creator> <dc:creator> Elbert Trulock </dc:creator> <dc:creator> G Patterson </dc:creator> <dc:creator> Thalachallour Mohanakumar </dc:creator> <dc:identifier> info:pmid/17015751 </dc:identifier> <dc:date> 2006-10-15 </dc:date> <prism:publicationName> Journal of immunology (Baltimore, Md. : 1950) </prism:publicationName> <prism:issn></prism:issn> <prism:volume> 177 </prism:volume> <prism:number> 8 </prism:number> <prism:startingPage> 5631 </prism:startingPage> <prism:endingPage> 5638 </prism:endingPage> </dcterms:URI>
Unalog (i)
Unalog (ii) <mods> <titleInfo><title> 3quarksdaily </title></titleInfo> <typeOfResource> text </typeOfResource> <physicalDescription> <form authority=&quot;marcform&quot;> electronic </form> </physicalDescription> <location> <url> http://.../2006/07/random_walks_he.html </url> </location> <note> Mode of access: Internet. </note> <subject> <topic> jackchick </topic> <topic> fear </topic> <topic> altercall </topic> </subject> <recordInfo> ... </recordInfo> </mods>
HubMed (i) <item rdf:about=&quot; info:pmid/17015751 &quot;> <rdf:type rdf:resource=&quot; http://purl.oclc.org/NET/nknouf/ns/bibtex#Article &quot;/> <title> Induction of IL-10 suppressors in lung transplant patients by CD4+25+ regulatory T cells through CTLA-4 signaling. </title> <link> http://www.hubmed.org/display.cgi?uids=17015751 </link> <description> stored by aorchid </description> <dc:date> 2006 </dc:date> <dc:title> Induction of IL-10 suppressors in lung transplant patients by CD4+25+ regulatory T cells through CTLA-4 signaling. </dc:title> <dc:subject> bos </dc:subject> <dc:subject> treg </dc:subject> </item> <tags:Tagging> ... <tags:taggedResource rdf:resource=&quot; info:pmid/17015751 &quot;/> ... </tags:Tagging>
HubMed (ii) <tags:Tagging rdf:about=&quot; http://.../tags/users/aorchid/item/17015751 &quot;> <tags:taggedBy rdf:resource=&quot; http://.../tags/users#aorchid &quot;/> <tags:taggedOn></tags:taggedOn> <tags:taggedResource rdf:resource=&quot; info:pmid/17015751 &quot;/> <tags:taggedWithTag> <tags:Tag rdf:about=&quot; http://.../tags/users/aorchid/tags#bos &quot;> <tags:tagName> bos </tags:tagName> </tags:Tag> </tags:taggedWithTag> <tags:taggedWithTag> <tags:Tag rdf:about=&quot; http://.../tags/users/aorchid/tags#treg &quot;> <tags:tagName> treg </tags:tagName> </tags:Tag> </tags:taggedWithTag> </tags:Tagging>
Collaborative Filtering Amazon Wikipedia Last.fm Technorati Digg Postgenomic Dissect Medicine
Postgenomic
Chemical blogspace
Dissect Medicine
Dissect Medicine
Social Networking MySpace YouTube Facebook Friendster LinkedIn Nature Network
Nature Network
Nature Network
Nature Network
Nature Network
Nature Network
Nature Network
Nature Network
Nature Network
Text Mining OTMI
OTMI Open Text Mining Interface [email_address] nature.com/otmi Repository *.tar.gz, *.otmi - content *.opml - navigation opentextmining.org/ Wiki Resources (draft spec, scripts)
OTMI - Goals Publish machine-readable full text to Enable text mining Allow document categorization Allow domain entities (e.g. chemical compounds, genomes, etc) to be mapped Entity maps can be published in turn and related back to original document
OTMI – Details OTMI = Atom <entry> document OTMI += document sections OTMI += vectors (word frequencies) OTMI += ‘snippets’ (nonlinear full text) OTMI += references (with DOI) OTMI filters stopwords (e.g. NLM)
OTMI – Entry (i) <atom:entry xmlns:otmi=‘...’ xmlns:prism=‘...‘ xmlns:atom=‘...'> <atom:title>Structural biology Dangerous liaisons on neurons</atom:title> <atom:author> <atom:name>Giampietro Schiavo</atom:name> </atom:author> <atom:id>info:doi/10.1038/nature05410</atom:id> <atom:link href='http://dx.doi.org/10.1038/nature05410' /> <atom:link href='http://.../nature/journal/v444/n7122/otmi/nature05410.otmi‘ rel='self' /> <atom:link href='http://opentextmining.org/' rel='related' /> <atom:published>2006-12-21T00:00:00Z</atom:published> <atom:updated>2006-12-21T00:00:00Z</atom:updated> <atom:rights type='html'>(c) 2006 Nature Publishing Group</atom:rights> <prism:publicationName>Nature</prism:publicationName> <prism:volume>444</prism:volume> <prism:number>7122</prism:number> <prism:startingPage>1019</prism:startingPage> <prism:endingPage>1020</prism:endingPage> <prism:issn>0028-0836</prism:issn> <prism:eIssn /> <otmi:data/> </atom:entry>
OTMI – Entry (ii) <otmi:data> <otmi:stoplist href='http://www.nature.com/nature/journal/v444/n7122/otmi/otmi-stoplist.xml' /> <otmi:section name='body'> <otmi:section name='other'> <otmi:vectors> ... </otmi:vectors> <otmi:snippets> ... </otmi:snippets> </otmi:section> </otmi:section> <otmi:figure> ... </otmi:figure> <otmi:references> ... </otmi:references> </otmi:data>
OTMI – Entry (ii) / Vectors <otmi:vectors> <otmi:split-regex>(?-mix:\s+\W+|\W+\s+|\s+|\/)</otmi:split-regex> ... <otmi:vector count='9'>vesicles</otmi:vector> <otmi:vector count='8'>al</otmi:vector> <otmi:vector count='8'>et</otmi:vector> <otmi:vector count='8'>protein</otmi:vector> <otmi:vector count='8'>synaptic</otmi:vector> <otmi:vector count='8'>vesicle</otmi:vector> <otmi:vector count='7'>chain</otmi:vector> <otmi:vector count='7'>neuron</otmi:vector> ... </otmi:vectors>
OTMI – Entry (iii) <otmi:data> <otmi:stoplist href='http://www.nature.com/nature/journal/v444/n7122/otmi/otmi-stoplist.xml' /> <otmi:section name='body'> <otmi:section name='other'> <otmi:vectors> ... </otmi:vectors> <otmi:snippets> ... </otmi:snippets> </otmi:section> </otmi:section> <otmi:figure> ... </otmi:figure> <otmi:references> ... </otmi:references> </otmi:data>
OTMI – Entry (iii) / Snippets <otmi:snippets> <otmi:split-regex>(?-mix:\.\s+(?=[A-Z]))</otmi:split-regex> ... <otmi:snippet>The amino acids lining this cleft are very similar to those found in BoNT/G (ref. 10 ), but differ in the other toxin family members, which explains why different BoNTs recognize distinct protein receptors</otmi:snippet> <otmi:snippet>The model predicts that the interaction of BoNTs with both PSGs and protein receptors is necessary to explain their awesome potency , with a different protein receptor being recognized by each BoNT</otmi:snippet> <otmi:snippet>The rigid character of this interaction might be further enhanced by the association of the toxins heavy chain with nearby negatively charged lipid molecules, which play an accessory role in stabilizing the toxin on membranes </otmi:snippet> <otmi:snippet>The simplest possibility is that BoNT/B binds to PSGs and synaptotagmin within the lumen of a synaptic vesicle that is fused to the neuron membrane</otmi:snippet> <otmi:snippet>The toxins then escape from the vesicle lumen when the vesicles are acidified as they reload with neurotransmitters</otmi:snippet> <otmi:snippet>The two binding sites would firmly anchor the tip of BoNT/B to the vesicles inner surface, constraining the toxins mobility</otmi:snippet> ... </otmi:snippets>
OTMI – Entry (iv) <otmi:data> <otmi:stoplist href='http://www.nature.com/nature/journal/v444/n7122/otmi/otmi-stoplist.xml' /> <otmi:section name='body'> <otmi:section name='other'> <otmi:vectors> ... </otmi:vectors> <otmi:snippets> ... </otmi:snippets> </otmi:section> </otmi:section> <otmi:figure> ... </otmi:figure> <otmi:references> ... </otmi:references> </otmi:data>
OTMI – Entry (iv) / Figs <otmi:figure> <otmi:title> <otmi:reduced-text>Possible binding sites botulinum neurotoxin B (BoNT/B) neurons. Crystal studies Jin et al . Chai et al . suggest BoNT/B invades neurons stowing away carriers known synaptic vesicles. forming complex lipid molecules (polysialogangliosides, PSGs) vesicle protein ( synaptotagmin or synaptotagmin II) neuronal membrane. complex stabilized interactions neighbouring acidic lipid molecules (orange). BoNT/B enter open vesicles neurons membrane, one three possible sequences. , BoNT/B enters vesicle directly forms required complex. b , BoNT/B binds first PSGs membrane, transferred synaptic vesicle containing synaptotagmin. c , BoNT/B forms full complex membrane, synaptotagmin left behind inaccurate vesicle recycling. transferred lumen vesicle.</otmi:reduced-text> </otmi:title> <otmi:caption> <otmi:reduced-text>Possible binding sites botulinum neurotoxin B (BoNT/B) neurons. Crystal studies Jin et al . Chai et al . suggest BoNT/B invades neurons stowing away carriers known synaptic vesicles. forming complex lipid molecules (polysialogangliosides, PSGs) vesicle protein ( synaptotagmin or synaptotagmin II) neuronal membrane. complex stabilized interactions neighbouring acidic lipid molecules (orange). BoNT/B enter open vesicles neurons membrane, one three possible sequences. , BoNT/B enters vesicle directly forms required complex. b , BoNT/B binds first PSGs membrane, transferred synaptic vesicle containing synaptotagmin. c , BoNT/B forms full complex membrane, synaptotagmin left behind inaccurate vesicle recycling. transferred lumen vesicle.</otmi:reduced-text> </otmi:caption> </otmi:figure>
OTMI – Entry (v) <otmi:data> <otmi:stoplist href='http://www.nature.com/nature/journal/v444/n7122/otmi/otmi-stoplist.xml' /> <otmi:section name='body'> <otmi:section name='other'> <otmi:vectors> ... </otmi:vectors> <otmi:snippets> ... </otmi:snippets> </otmi:section> </otmi:section> <otmi:figure> ... </otmi:figure> <otmi:references> ... </otmi:references> </otmi:data>
OTMI – Entry (v) / Refs <otmi:references> <otmi:ref-id>info:doi/10.1038/nature05387</otmi:ref-id> <otmi:ref-id>info:doi/10.1038/nature05411</otmi:ref-id> <otmi:ref-id>info:doi/10.1016/0968-0004(86)90282-3</otmi:ref-id> <otmi:ref-id>info:doi/10.1016/0014-5793(95)01471-3</otmi:ref-id> <otmi:ref-id>info:doi/10.1083/jcb.200305098</otmi:ref-id> <otmi:ref-id>info:doi/10.1074/jbc.M403945200</otmi:ref-id> <otmi:ref-id>info:doi/10.1126/science.1123654</otmi:ref-id> <otmi:ref-id>info:doi/10.1016/j.febslet.2006.02.074</otmi:ref-id> <otmi:ref-id>info:doi/10.1083/jcb.200508170</otmi:ref-id> <otmi:refs-noid>3</otmi:refs-noid> </otmi:references>
snoitpircseD eligA Tony Hammond Nature Publishing Group [email_address]

More Related Content

PPT
Tor2
byDixie Foster
 
PPTX
1-04: HTML Elements
byapnwebdev
 
PPT
RDFa: The Semantic Web's Missing Link
byMark Birbeck
 
ODP
An Overview on PROV-AQ: Provenance Access and Query
byOlaf Hartig
 
PDF
Findability Bliss Through Web Standards
byAarron Walter
 
PPTX
"RDFa - what, why and how?" by Mike Hewett and Shamod Lacoul
byShamod Lacoul
 
PPT
Xml Zoe
byzoepster
 
PDF
RDFa: introduction, comparison with microdata and microformats and how to use it
byJose Luis Lopez Pino
 
Tor2
byDixie Foster
 
1-04: HTML Elements
byapnwebdev
 
RDFa: The Semantic Web's Missing Link
byMark Birbeck
 
An Overview on PROV-AQ: Provenance Access and Query
byOlaf Hartig
 
Findability Bliss Through Web Standards
byAarron Walter
 
"RDFa - what, why and how?" by Mike Hewett and Shamod Lacoul
byShamod Lacoul
 
Xml Zoe
byzoepster
 
RDFa: introduction, comparison with microdata and microformats and how to use it
byJose Luis Lopez Pino
 

What's hot

PPTX
Creating Linked Data 2/5 Semtech2011
byJuan Sequeda
 
PPT
OpenSocial - GTUG Stockholm Meeting Oct 1 2009
byJacob Gyllenstierna
 
PPT
Introduction To Xml
bybdebruin
 
PPT
CrossRef Secondary Query: Practice and Problems (2011 CrossRef Workshops)
byCrossref
 
PPT
Google and Google Scholar
byjopitts
 
PPT
The Semantic Web An Introduction
byshaouy
 
PPT
How To Create Personal Web Pages On My Web
bysritikumar
 
PPT
Webpages And Dynamic Content
bymaycourse
 
PPS
Google Search Techniques
byDuc Chau
 
KEY
HTML presentation for beginners
byjeroenvdmeer
 
PDF
Pdfsamplefile
byTesting Spammer
 
PPT
Google search tips
byYashwant Shet Talaulikar
 
PPT
Enhance Your Google Search
byValentini Mellas
 
PPT
Google searching techniques
byabbas mohd
 
PDF
Introduction to Html
byOmerMahdi
 
PPTX
Effective web search techniques
byaliciafe0215
 
PPT
Google
bysunil sharma
 
Creating Linked Data 2/5 Semtech2011
byJuan Sequeda
 
OpenSocial - GTUG Stockholm Meeting Oct 1 2009
byJacob Gyllenstierna
 
Introduction To Xml
bybdebruin
 
CrossRef Secondary Query: Practice and Problems (2011 CrossRef Workshops)
byCrossref
 
Google and Google Scholar
byjopitts
 
The Semantic Web An Introduction
byshaouy
 
How To Create Personal Web Pages On My Web
bysritikumar
 
Webpages And Dynamic Content
bymaycourse
 
Google Search Techniques
byDuc Chau
 
HTML presentation for beginners
byjeroenvdmeer
 
Pdfsamplefile
byTesting Spammer
 
Google search tips
byYashwant Shet Talaulikar
 
Enhance Your Google Search
byValentini Mellas
 
Google searching techniques
byabbas mohd
 
Introduction to Html
byOmerMahdi
 
Effective web search techniques
byaliciafe0215
 
Google
bysunil sharma
 

Viewers also liked

PPT
Bionlp 07
byTony Hammond
 
PPT
Handle 08
byTony Hammond
 
PDF
Biokimika
byJuan Arbulu Arin
 
PDF
Prokariotoen pareta zelularra 1
byJuan Arbulu Arin
 
PPTX
Iswc 2014-hammond-pasin-presentation-final
byTony Hammond
 
PPT
Jisc
byTony Hammond
 
PDF
Google docs aurkezpena
byJuan Arbulu Arin
 
PPTX
Techniques used in RDF Data Publishing at Nature Publishing Group
byTony Hammond
 
PPT
OpenURL - The Rough Guide
byTony Hammond
 
Bionlp 07
byTony Hammond
 
Handle 08
byTony Hammond
 
Biokimika
byJuan Arbulu Arin
 
Prokariotoen pareta zelularra 1
byJuan Arbulu Arin
 
Iswc 2014-hammond-pasin-presentation-final
byTony Hammond
 
Jisc
byTony Hammond
 
Google docs aurkezpena
byJuan Arbulu Arin
 
Techniques used in RDF Data Publishing at Nature Publishing Group
byTony Hammond
 
OpenURL - The Rough Guide
byTony Hammond
 

Similar to Agile Descriptions

PPT
What is hot on the web right now - A W3C perspective
byArmin Haller
 
PPT
Web Topics
byPraveen AP
 
PPT
Making the Web searchable
byPeter Mika
 
PPT
Web 3 0
byRobin Hastings
 
PPTX
How I built the demo's
byGlenn Jones
 
PPTX
How to connect social media with open standards
byGlenn Jones
 
PDF
Web3.0 or The semantic web
byDarren Wood
 
PPTX
webtech unit for educational purposes 4.pptx
byabhinavas9207
 
PDF
Microformats HTML to API
byelliando dias
 
PDF
Understanding the Standards Gap
byDan Brickley
 
PPT
Microformats at Web 2.0 Expo April 2007
byJohn Allsopp
 
PPT
The Semantic Web
byBarry Smith
 
PDF
Microformats I: What & Why
byRachael L Moore
 
ODP
Journalism and the Semantic Web
byKurt Cagle
 
ODP
Future Of Web Languages
byMark Birbeck
 
PDF
Applying Semantic Extensions And New Services To Drupal Sem Tech June 2010
byAI4BD GmbH
 
PDF
Is linked data something for me?
byChristophe Guéret
 
PPT
Web 3 0
byDigital Marketing Team Lead @ Startappz
 
PPT
Microformats
byAaron Grogg
 
KEY
Open Standards for the Semantic Web: XML / RDF(S) / OWL / SOAP
byPieter De Leenheer
 
What is hot on the web right now - A W3C perspective
byArmin Haller
 
Web Topics
byPraveen AP
 
Making the Web searchable
byPeter Mika
 
Web 3 0
byRobin Hastings
 
How I built the demo's
byGlenn Jones
 
How to connect social media with open standards
byGlenn Jones
 
Web3.0 or The semantic web
byDarren Wood
 
webtech unit for educational purposes 4.pptx
byabhinavas9207
 
Microformats HTML to API
byelliando dias
 
Understanding the Standards Gap
byDan Brickley
 
Microformats at Web 2.0 Expo April 2007
byJohn Allsopp
 
The Semantic Web
byBarry Smith
 
Microformats I: What & Why
byRachael L Moore
 
Journalism and the Semantic Web
byKurt Cagle
 
Future Of Web Languages
byMark Birbeck
 
Applying Semantic Extensions And New Services To Drupal Sem Tech June 2010
byAI4BD GmbH
 
Is linked data something for me?
byChristophe Guéret
 
Web 3 0
byDigital Marketing Team Lead @ Startappz
 
Microformats
byAaron Grogg
 
Open Standards for the Semantic Web: XML / RDF(S) / OWL / SOAP
byPieter De Leenheer
 

Recently uploaded

PPSX
AppSec Role Based Training OWASP Global AppSec USA 2025-11-06
byRobert Grupe, CSSLP CISSP PE PMP
 
PDF
Control Access to Files - RHCSA (RH124).pdf
byLinuxCert Guru
 
PDF
MathML Core in WebKit
byIgalia
 
PDF
ENTSO-E's Response to the European Commission Call for Evidence on the Strate...
byReynir Orn Bachmann Gudmundsson
 
PDF
Access Linux File System in RHEL - RHCSA (RH124).pdf
byLinuxCert Guru
 
PDF
#MakeAIMatter for HR Professionals | AI Transformation Workshop by Tekdi Tech...
byParth Lawate
 
PPTX
AI and Linux in 2025 - Jay LaCroix, Learn Linux TV
byAll Things Open
 
PDF
Getting started with Agent Framework.pdf
byNilesh Gule
 
PDF
"Visual Guide to DSA: Big O Notation, Data Structures, and Algorithms Fundame...
byNusrat Gulbarga
 
PDF
Cybersecurity in ASEAN and Singapore Columbia SIPA 2025.pdf
byBenjamin Ang
 
PDF
Install and Update Software - RHCSA (RH124).pdf
byLinuxCert Guru
 
PPTX
Getting Started with MSP360 Backup for M365/Google
byMSP360
 
PPTX
Expanding Your Toolbox: Beginners Guide to Controlling Kubernetes Logs
byEric D. Schabell
 
PDF
WebXR in Android and Linux with OpenXR
byIgalia
 
PDF
Open Source SecurityCon 2025 in Atlanta - Transparency Exchange API: Where To...
byPavel Shukhman
 
PDF
Private Governance: How Decentralized Mechanisms Can Regulate the Crypto Economy
byFederico Ast
 
PDF
Analyze and Store Logs - RHCSA (RH124).pdf
byLinuxCert Guru
 
PDF
Career Blueprint: Mentor Tracks & Career Clinic - Part 2
byDianaGray10
 
PPTX
Governance, Deployment & Methodologies for Agentic Automation [2/3]
bysuhanisingh58689
 
PDF
Manage Networking in RHEL - RHCSA (RH124).pdf
byLinuxCert Guru
 
AppSec Role Based Training OWASP Global AppSec USA 2025-11-06
byRobert Grupe, CSSLP CISSP PE PMP
 
Control Access to Files - RHCSA (RH124).pdf
byLinuxCert Guru
 
MathML Core in WebKit
byIgalia
 
ENTSO-E's Response to the European Commission Call for Evidence on the Strate...
byReynir Orn Bachmann Gudmundsson
 
Access Linux File System in RHEL - RHCSA (RH124).pdf
byLinuxCert Guru
 
#MakeAIMatter for HR Professionals | AI Transformation Workshop by Tekdi Tech...
byParth Lawate
 
AI and Linux in 2025 - Jay LaCroix, Learn Linux TV
byAll Things Open
 
Getting started with Agent Framework.pdf
byNilesh Gule
 
"Visual Guide to DSA: Big O Notation, Data Structures, and Algorithms Fundame...
byNusrat Gulbarga
 
Cybersecurity in ASEAN and Singapore Columbia SIPA 2025.pdf
byBenjamin Ang
 
Install and Update Software - RHCSA (RH124).pdf
byLinuxCert Guru
 
Getting Started with MSP360 Backup for M365/Google
byMSP360
 
Expanding Your Toolbox: Beginners Guide to Controlling Kubernetes Logs
byEric D. Schabell
 
WebXR in Android and Linux with OpenXR
byIgalia
 
Open Source SecurityCon 2025 in Atlanta - Transparency Exchange API: Where To...
byPavel Shukhman
 
Private Governance: How Decentralized Mechanisms Can Regulate the Crypto Economy
byFederico Ast
 
Analyze and Store Logs - RHCSA (RH124).pdf
byLinuxCert Guru
 
Career Blueprint: Mentor Tracks & Career Clinic - Part 2
byDianaGray10
 
Governance, Deployment & Methodologies for Agentic Automation [2/3]
bysuhanisingh58689
 
Manage Networking in RHEL - RHCSA (RH124).pdf
byLinuxCert Guru
 

Agile Descriptions

  • 1.
    Agile Descriptions TonyHammond Nature Publishing Group [email_address]
  • 2.
    Web 2.0 StuffSome topics to consider: Web Feeds Markup Tagging Collaborative Filtering Social Networking Text Mining
  • 3.
    Web Feeds Feeds = news, blogs, podcasts, ... Feed formats are RSS / Atom Feeds are just Rivers of Metadata XML documents polled by subscribers <item> / <entry> = <title>, <link>, <description> / <summary> Administrative metadata Descriptive metadata (dc, prism, mods, ...) Common description model - RDF
  • 4.
    Markup Twomain approaches to adding semantics to documents: Embedded Metadata Content hidden from user ‘ Blob’ added to page content Exposed Metadata Microformats (  F’s) RDFa = RDF w/attributes eRDF = embedded RDF
  • 5.
    Embedded Metadata (i)HTTP headers - exchanged in request HTTP entities - in GET, PUT, POST HTML <head> <meta> HTML <head> / <body> HTML comments HTML comments as RDF ‘islands’
  • 6.
    Embedded Metadata (ii)Binary data: XMP PDF’s (and arbitrary binary files) EXIF JPEG’s (digital photos) ID3 tags MP3’s (audio files)
  • 7.
    Exposed Metadata -  F’s  F’s qualify display content  F’s add semantic tier to existing structure  F’s limit search indexing abuse  F = nested markup layered on top of host markup environment (HTML/XML) Examples: rel-license, rel-tag, ... hCard, hCalendar, hReview, xFolk, XFN, ...
  • 8.
     F’s Designpatterns with semantics Content becomes ‘live’ Can replace custom APIs A poorboy semantic web XMDP profiles GRDDL (W3C Draft - Last Call)  F -> RDF
  • 9.
    rel-license - Licenses<a rel=&quot;license&quot; href=&quot; http://.../licenses &quot; > CC </a> Target of URI is license for current page
  • 10.
    rel-tag - Tags<a rel=&quot;tag&quot; href=&quot; http://.../tag/microformats &quot; > uF’s </a> Target of URI is tag for current page Last URI path element is tag Preceding URI string is tag space
  • 11.
    XFN – SocialNetworks Example: Ingrid’s blogroll: <a href=&quot; http://.../... &quot; rel=&quot;friend met&quot; >Josh</a> <a href=&quot; http://.../... &quot; rel=&quot;met acquaintance&quot; >Kat</a> <a href=&quot; http://.../... &quot; rel=&quot;co-worker friend met&quot; >Mary</a> <a href=&quot; http://.../... &quot;> Nick </a> Target of URI is typically blog or personal site List of rel attributes indicates personal relationship
  • 12.
  • 13.
    XFN (ii) #1#4 #2 #3
  • 14.
    hCard - Addresses<div class=&quot;vcard&quot; > <a class=&quot;url fn&quot; href=&quot; http://.../... &quot; > Tony Hammond </a> <span class=&quot;org&quot; > Nature Publishing Group </span> <span class=&quot;tel&quot; > <span class=&quot;type&quot; > work </span> <span class=&quot;value&quot; > +44-20-7843-4659 </span> </span> </div> Use vCard (RFC 2426) as basis Nest vCard objects into nested XHTML Make vCard object/property names lcase
  • 15.
    hCalendar - Events<div class=&quot;vevent&quot; > <a class=&quot;url&quot; href=&quot; http://.../... &quot; > <span class=&quot;summary&quot; > Future of ... </span> <abbr class=&quot;dtstart&quot; title=&quot; 2007-03-08 &quot; > March 8 </abbr> <abbr class=&quot;dtend&quot; title=&quot; 2007-03-08 &quot; > March 8 </abbr> at <span class=“location&quot; > Google, Inc. </span> </a> </div> Use iCalendar (RFC 2445) as basis Nest iCalendar objects into nested XHTML Make iCalendar object/property names lcase
  • 16.
    hReview - Reviews<li class=&quot;hreview&quot; > <h3 class=&quot;item summary&quot; ><a href=&quot;/reviews/programming/web+standards&quot; class=&quot;fn&quot; rel=&quot;self bookmark&quot; > Web standards </a></h3> <div class=&quot;reviewer vcard&quot; > <p class=&quot;icon&quot; > <a href=&quot;/users/katemonkey&quot;><img src=&quot;/images/icons/katemonkey.png&quot; class=&quot;photo&quot;/></a> </p> <p class=&quot;description&quot; > Web standards help designers and developers create the pedantic web. </p> <p class=&quot;by-line&quot; > a <a href=&quot;/reviews/programming&quot;> programming </a> review by <a href=&quot;/users/katemonkey&quot; class=&quot;fn url&quot; > katemonkey </a> that was written <a title=&quot;2007-01-27 11:09:21&quot; class=&quot;dtreviewed&quot; href=&quot;/reviews/date/2007/01/27/&quot;> on 27 th January </a> and has been rated by 3 users as a good review. </p> </div> </li>
  • 17.
    xFolk - Bookmarks<div class=&quot;folkentry&quot; > <div> <a class=&quot;taggedlink&quot; href=&quot; http://.../... &quot; > bookmark </a> </div> <div class=&quot;description&quot; > A description ... </div> <div class=&quot;meta&quot; > <a rel=&quot;tag&quot; href=&quot; http://.../tag/tag &quot; > tag </a> </div> </div>
  • 18.
    hcite - Citations<li class=&quot;hcite&quot; xml:lang=&quot;en&quot;> <div class=&quot;publisher vcard&quot; > <!-- publisher data as hCard --> <span class=&quot;fn org&quot; > ABC Publishing Co. </span> <span class=&quot;country-name&quot; > United Kingdom </span> ... </div> <div class=&quot;creator vcard&quot; > <!-- author(s) data as hCard --> <span class=&quot;fn n&quot; > <span class=&quot;given-name&quot; > John <span class=&quot;family-name&quot; > Doe </span></span> ... </div> <span class=&quot;fn&quot; > Foobar! </span> <span class=&quot;description&quot; > World Class Book about foobar </span> <span class=&quot;volume&quot; > 1 </span> <span class=&quot;issue&quot; > 1 </span> <span class=&quot;pages&quot; > 1-10 </span> <span class=&quot;format&quot; > article </span> <span class=&quot;identifier&quot; > 12345678 </span> <a class=&quot;keyword&quot; rel=&quot;tag&quot; href=&quot; /tags/foo &quot;> foo </a> Published <abbr class=&quot;dtpublished&quot; title=&quot; 20060101 &quot;> January 1st 2006 </abbr> Copyright <abbr class=&quot;copyright&quot; title=&quot; 20060101 &quot;> 2006 </abbr> </li>
  • 19.
    Tagging Tagsas simple labels Tags as personal ‘aides-memoire’ Bottom-up rather than top-down Just-in-time vs just-in-case Folksonomies user categories group tag clouds, clustering
  • 20.
    Tag Namespaces Tags as simple text tokens Tags as globally unique URIs Naming authority issues DNS- & Registry-based authorities Persistence Per application namespaces Per user, per application namespaces
  • 21.
    Tag Terms Anylessons from dynamic vs static typed programming languages? Static compilation provides for type safety Dynamic compilation allows typing on demand Unit tests substitute for type checking at compilation time
  • 22.
  • 23.
  • 24.
    Unalog / StarlightTag “python” Tag “iceland”
  • 25.
    Tagging Tools Let’slook at some cases: del.icio.us – general tagging tool Flickr – photo tagging tool CiteULike – scolarly tagging Connotea – scholarly tagging Unalog – library tagging tool HubMed – an interface to PubMed
  • 26.
    del.icio.us <item rdf:about=&quot;http://orlabs.oclc.org/Identities/ &quot;> <title> WorldCat Identities </title> <link> http://orlabs.oclc.org/Identities/ </link> <description> pages for people </description> <dc:creator> hublicious </dc:creator> <dc:date> 2007-02-14T10:37:46Z </dc:date> <dc:subject> person </dc:subject> <dc:subject> identifier </dc:subject> <dc:subject> oclc </dc:subject> <taxo:topics> <rdf:Bag> <rdf:li resource=&quot; http://del.icio.us/tag/person &quot;/> <rdf:li resource=&quot; http://del.icio.us/tag/identifier &quot;/> <rdf:li resource=&quot; http://del.icio.us/tag/oclc &quot;/> </rdf:Bag> </taxo:topics> </item>
  • 27.
    Flickr <entry> <title>The Eclipsified Moon </title> <link rel=&quot;alternate&quot; type=&quot;text/html“ href=&quot; http://www.flickr.com/photos/alf/409522855/ &quot;/> <id> tag:flickr.com,2005:/photo/409522855 </id> <published> 2007-03-04T04:53:33Z </published> <updated> 2007-03-04T04:53:33Z </updated> <dc:date.Taken> 2007-03-03T23:34:23-08:00 </dc:date.Taken> <content type=&quot;html”> ... </content> <author> <name> balloon in a sock </name> <uri> http://www.flickr.com/people/alf/ </uri> </author> <link rel=&quot;license&quot; type=&quot;text/html&quot; href=&quot; http://.../licenses/by-nc/2.0/ &quot; /> <link rel=&quot;enclosure&quot; type=&quot;image/jpeg“ href=&quot; http://.../133/409522855_6ed97bbd2a_o.jpg &quot; /> <category term=&quot; moon &quot; scheme=&quot; http://www.flickr.com/photos/tags/ &quot; /> <category term=&quot; eclipse &quot; scheme=&quot; http://www.flickr.com/photos/tags/ &quot; /> </entry>
  • 28.
    Cite U Like CiteULike (i)
  • 29.
    Cite U Like CiteULike (ii) <item rdf:about= http://www.citeulike.org/user/timflutre/article/1139879 > <title> Dating the tree of life. </title> <link> http://www.citeulike.org/user/timflutre/article/1139879 </link> <description> ... </description> <dc:title> Dating the tree of life. </dc:title> <dc:creator> MJ Benton </dc:creator> <dc:creator> FJ Ayala </dc:creator> <dc:identifier> doi:10.1126/science.1077795 </dc:identifier> <dc:source> Science, Vol. 300, No. 5626. (13 June 2003), pp. 1698-1700. </dc:source> <prism:publicationName> Science </prism:publicationName> <prism:issn> 1095-9203 </prism:issn> <prism:volume> 300 </prism:volume> <prism:number> 5626 </prism:number> <prism:startingPage> 1698 </prism:startingPage> <prism:endingPage> 1700 </prism:endingPage> <category> evolution </category> <category> molecular_clock </category> </item>
  • 30.
    Connotea (i) <itemrdf:about=&quot; http://.../user/penguin/uri/ceac242dfd66979fe07ac5ebf8381afc &quot;> <title> Induction of IL-10 suppressors in lung transplant patients by CD4+25+ regulatory T cells through CTLA-4 signaling. </title> <link> http://.../user/penguin/uri/ceac242dfd66979fe07ac5ebf8381afc </link> <description> Posted by penguin to test on Wed Feb 21 2007 </description> <dc:creator> penguin </dc:creator> <dc:date> 2007-02-21T10:22:00Z </dc:date> <dc:subject> test </dc:subject> <slash:comments> 0 </slash:comments> <content:encoded><![CDATA[ ... ]]></content:encoded> <connotea:uri> <dcTerms:URI/> </connotea:uri> <annotate:reference rdf:resource=&quot; http://.../comments/uri/ceac242dfd66979fe07ac5ebf8381afc &quot;/> </item>
  • 31.
    Connotea (ii) <dcterms:URIrdf:about=&quot; http://www.hubmed.org/display.cgi?uids=17015751 &quot;> <dc:title> Induction of IL-10 suppressors in lung transplant patients by CD4+25+ regulatory T cells through CTLA-4 signaling. </dc:title> <dc:creator> Ankit Bharat </dc:creator> <dc:creator> Ryan Fields </dc:creator> <dc:creator> Elbert Trulock </dc:creator> <dc:creator> G Patterson </dc:creator> <dc:creator> Thalachallour Mohanakumar </dc:creator> <dc:identifier> info:pmid/17015751 </dc:identifier> <dc:date> 2006-10-15 </dc:date> <prism:publicationName> Journal of immunology (Baltimore, Md. : 1950) </prism:publicationName> <prism:issn></prism:issn> <prism:volume> 177 </prism:volume> <prism:number> 8 </prism:number> <prism:startingPage> 5631 </prism:startingPage> <prism:endingPage> 5638 </prism:endingPage> </dcterms:URI>
  • 32.
  • 33.
    Unalog (ii) <mods><titleInfo><title> 3quarksdaily </title></titleInfo> <typeOfResource> text </typeOfResource> <physicalDescription> <form authority=&quot;marcform&quot;> electronic </form> </physicalDescription> <location> <url> http://.../2006/07/random_walks_he.html </url> </location> <note> Mode of access: Internet. </note> <subject> <topic> jackchick </topic> <topic> fear </topic> <topic> altercall </topic> </subject> <recordInfo> ... </recordInfo> </mods>
  • 34.
    HubMed (i) <itemrdf:about=&quot; info:pmid/17015751 &quot;> <rdf:type rdf:resource=&quot; http://purl.oclc.org/NET/nknouf/ns/bibtex#Article &quot;/> <title> Induction of IL-10 suppressors in lung transplant patients by CD4+25+ regulatory T cells through CTLA-4 signaling. </title> <link> http://www.hubmed.org/display.cgi?uids=17015751 </link> <description> stored by aorchid </description> <dc:date> 2006 </dc:date> <dc:title> Induction of IL-10 suppressors in lung transplant patients by CD4+25+ regulatory T cells through CTLA-4 signaling. </dc:title> <dc:subject> bos </dc:subject> <dc:subject> treg </dc:subject> </item> <tags:Tagging> ... <tags:taggedResource rdf:resource=&quot; info:pmid/17015751 &quot;/> ... </tags:Tagging>
  • 35.
    HubMed (ii) <tags:Taggingrdf:about=&quot; http://.../tags/users/aorchid/item/17015751 &quot;> <tags:taggedBy rdf:resource=&quot; http://.../tags/users#aorchid &quot;/> <tags:taggedOn></tags:taggedOn> <tags:taggedResource rdf:resource=&quot; info:pmid/17015751 &quot;/> <tags:taggedWithTag> <tags:Tag rdf:about=&quot; http://.../tags/users/aorchid/tags#bos &quot;> <tags:tagName> bos </tags:tagName> </tags:Tag> </tags:taggedWithTag> <tags:taggedWithTag> <tags:Tag rdf:about=&quot; http://.../tags/users/aorchid/tags#treg &quot;> <tags:tagName> treg </tags:tagName> </tags:Tag> </tags:taggedWithTag> </tags:Tagging>
  • 36.
    Collaborative Filtering AmazonWikipedia Last.fm Technorati Digg Postgenomic Dissect Medicine
  • 37.
  • 38.
  • 39.
  • 40.
  • 41.
    Social Networking MySpace YouTube Facebook Friendster LinkedIn Nature Network
  • 42.
  • 43.
  • 44.
  • 45.
  • 46.
  • 47.
  • 48.
  • 49.
  • 50.
  • 51.
    OTMI Open TextMining Interface [email_address] nature.com/otmi Repository *.tar.gz, *.otmi - content *.opml - navigation opentextmining.org/ Wiki Resources (draft spec, scripts)
  • 52.
    OTMI - GoalsPublish machine-readable full text to Enable text mining Allow document categorization Allow domain entities (e.g. chemical compounds, genomes, etc) to be mapped Entity maps can be published in turn and related back to original document
  • 53.
    OTMI – DetailsOTMI = Atom <entry> document OTMI += document sections OTMI += vectors (word frequencies) OTMI += ‘snippets’ (nonlinear full text) OTMI += references (with DOI) OTMI filters stopwords (e.g. NLM)
  • 54.
    OTMI – Entry(i) <atom:entry xmlns:otmi=‘...’ xmlns:prism=‘...‘ xmlns:atom=‘...'> <atom:title>Structural biology Dangerous liaisons on neurons</atom:title> <atom:author> <atom:name>Giampietro Schiavo</atom:name> </atom:author> <atom:id>info:doi/10.1038/nature05410</atom:id> <atom:link href='http://dx.doi.org/10.1038/nature05410' /> <atom:link href='http://.../nature/journal/v444/n7122/otmi/nature05410.otmi‘ rel='self' /> <atom:link href='http://opentextmining.org/' rel='related' /> <atom:published>2006-12-21T00:00:00Z</atom:published> <atom:updated>2006-12-21T00:00:00Z</atom:updated> <atom:rights type='html'>(c) 2006 Nature Publishing Group</atom:rights> <prism:publicationName>Nature</prism:publicationName> <prism:volume>444</prism:volume> <prism:number>7122</prism:number> <prism:startingPage>1019</prism:startingPage> <prism:endingPage>1020</prism:endingPage> <prism:issn>0028-0836</prism:issn> <prism:eIssn /> <otmi:data/> </atom:entry>
  • 55.
    OTMI – Entry(ii) <otmi:data> <otmi:stoplist href='http://www.nature.com/nature/journal/v444/n7122/otmi/otmi-stoplist.xml' /> <otmi:section name='body'> <otmi:section name='other'> <otmi:vectors> ... </otmi:vectors> <otmi:snippets> ... </otmi:snippets> </otmi:section> </otmi:section> <otmi:figure> ... </otmi:figure> <otmi:references> ... </otmi:references> </otmi:data>
  • 56.
    OTMI – Entry(ii) / Vectors <otmi:vectors> <otmi:split-regex>(?-mix:\s+\W+|\W+\s+|\s+|\/)</otmi:split-regex> ... <otmi:vector count='9'>vesicles</otmi:vector> <otmi:vector count='8'>al</otmi:vector> <otmi:vector count='8'>et</otmi:vector> <otmi:vector count='8'>protein</otmi:vector> <otmi:vector count='8'>synaptic</otmi:vector> <otmi:vector count='8'>vesicle</otmi:vector> <otmi:vector count='7'>chain</otmi:vector> <otmi:vector count='7'>neuron</otmi:vector> ... </otmi:vectors>
  • 57.
    OTMI – Entry(iii) <otmi:data> <otmi:stoplist href='http://www.nature.com/nature/journal/v444/n7122/otmi/otmi-stoplist.xml' /> <otmi:section name='body'> <otmi:section name='other'> <otmi:vectors> ... </otmi:vectors> <otmi:snippets> ... </otmi:snippets> </otmi:section> </otmi:section> <otmi:figure> ... </otmi:figure> <otmi:references> ... </otmi:references> </otmi:data>
  • 58.
    OTMI – Entry(iii) / Snippets <otmi:snippets> <otmi:split-regex>(?-mix:\.\s+(?=[A-Z]))</otmi:split-regex> ... <otmi:snippet>The amino acids lining this cleft are very similar to those found in BoNT/G (ref. 10 ), but differ in the other toxin family members, which explains why different BoNTs recognize distinct protein receptors</otmi:snippet> <otmi:snippet>The model predicts that the interaction of BoNTs with both PSGs and protein receptors is necessary to explain their awesome potency , with a different protein receptor being recognized by each BoNT</otmi:snippet> <otmi:snippet>The rigid character of this interaction might be further enhanced by the association of the toxins heavy chain with nearby negatively charged lipid molecules, which play an accessory role in stabilizing the toxin on membranes </otmi:snippet> <otmi:snippet>The simplest possibility is that BoNT/B binds to PSGs and synaptotagmin within the lumen of a synaptic vesicle that is fused to the neuron membrane</otmi:snippet> <otmi:snippet>The toxins then escape from the vesicle lumen when the vesicles are acidified as they reload with neurotransmitters</otmi:snippet> <otmi:snippet>The two binding sites would firmly anchor the tip of BoNT/B to the vesicles inner surface, constraining the toxins mobility</otmi:snippet> ... </otmi:snippets>
  • 59.
    OTMI – Entry(iv) <otmi:data> <otmi:stoplist href='http://www.nature.com/nature/journal/v444/n7122/otmi/otmi-stoplist.xml' /> <otmi:section name='body'> <otmi:section name='other'> <otmi:vectors> ... </otmi:vectors> <otmi:snippets> ... </otmi:snippets> </otmi:section> </otmi:section> <otmi:figure> ... </otmi:figure> <otmi:references> ... </otmi:references> </otmi:data>
  • 60.
    OTMI – Entry(iv) / Figs <otmi:figure> <otmi:title> <otmi:reduced-text>Possible binding sites botulinum neurotoxin B (BoNT/B) neurons. Crystal studies Jin et al . Chai et al . suggest BoNT/B invades neurons stowing away carriers known synaptic vesicles. forming complex lipid molecules (polysialogangliosides, PSGs) vesicle protein ( synaptotagmin or synaptotagmin II) neuronal membrane. complex stabilized interactions neighbouring acidic lipid molecules (orange). BoNT/B enter open vesicles neurons membrane, one three possible sequences. , BoNT/B enters vesicle directly forms required complex. b , BoNT/B binds first PSGs membrane, transferred synaptic vesicle containing synaptotagmin. c , BoNT/B forms full complex membrane, synaptotagmin left behind inaccurate vesicle recycling. transferred lumen vesicle.</otmi:reduced-text> </otmi:title> <otmi:caption> <otmi:reduced-text>Possible binding sites botulinum neurotoxin B (BoNT/B) neurons. Crystal studies Jin et al . Chai et al . suggest BoNT/B invades neurons stowing away carriers known synaptic vesicles. forming complex lipid molecules (polysialogangliosides, PSGs) vesicle protein ( synaptotagmin or synaptotagmin II) neuronal membrane. complex stabilized interactions neighbouring acidic lipid molecules (orange). BoNT/B enter open vesicles neurons membrane, one three possible sequences. , BoNT/B enters vesicle directly forms required complex. b , BoNT/B binds first PSGs membrane, transferred synaptic vesicle containing synaptotagmin. c , BoNT/B forms full complex membrane, synaptotagmin left behind inaccurate vesicle recycling. transferred lumen vesicle.</otmi:reduced-text> </otmi:caption> </otmi:figure>
  • 61.
    OTMI – Entry(v) <otmi:data> <otmi:stoplist href='http://www.nature.com/nature/journal/v444/n7122/otmi/otmi-stoplist.xml' /> <otmi:section name='body'> <otmi:section name='other'> <otmi:vectors> ... </otmi:vectors> <otmi:snippets> ... </otmi:snippets> </otmi:section> </otmi:section> <otmi:figure> ... </otmi:figure> <otmi:references> ... </otmi:references> </otmi:data>
  • 62.
    OTMI – Entry(v) / Refs <otmi:references> <otmi:ref-id>info:doi/10.1038/nature05387</otmi:ref-id> <otmi:ref-id>info:doi/10.1038/nature05411</otmi:ref-id> <otmi:ref-id>info:doi/10.1016/0968-0004(86)90282-3</otmi:ref-id> <otmi:ref-id>info:doi/10.1016/0014-5793(95)01471-3</otmi:ref-id> <otmi:ref-id>info:doi/10.1083/jcb.200305098</otmi:ref-id> <otmi:ref-id>info:doi/10.1074/jbc.M403945200</otmi:ref-id> <otmi:ref-id>info:doi/10.1126/science.1123654</otmi:ref-id> <otmi:ref-id>info:doi/10.1016/j.febslet.2006.02.074</otmi:ref-id> <otmi:ref-id>info:doi/10.1083/jcb.200508170</otmi:ref-id> <otmi:refs-noid>3</otmi:refs-noid> </otmi:references>
  • 63.
    snoitpircseD eligA TonyHammond Nature Publishing Group [email_address]