Agile Descriptions

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="license" href=" http://.../licenses " > CC </a>

Target of URI is license for current page

rel-tag - Tags

<a rel="tag" href=" http://.../tag/microformats " > 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=" http://.../... " rel="friend met" >Josh</a>

<a href=" http://.../... " rel="met acquaintance" >Kat</a>

<a href=" http://.../... " rel="co-worker friend met" >Mary</a>

<a href=" http://.../... "> 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="vcard" >

<a class="url fn" href=" http://.../... " > Tony Hammond </a>

<span class="org" > Nature Publishing Group </span>

<span class="tel" >

<span class="type" > work </span>

<span class="value" > +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="vevent" >

<a class="url" href=" http://.../... " >

<span class="summary" > Future of ... </span>

<abbr class="dtstart" title=" 2007-03-08 " > March 8 </abbr>

<abbr class="dtend" title=" 2007-03-08 " > March 8 </abbr>

at

<span class=“location" > 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="hreview" >

<h3 class="item summary" ><a href="/reviews/programming/web+standards" class="fn" rel="self bookmark" > Web standards </a></h3>

<div class="reviewer vcard" >

<p class="icon" >

<a href="/users/katemonkey"><img src="/images/icons/katemonkey.png" class="photo"/></a>

</p>

<p class="description" > Web standards help designers and developers create the pedantic web. </p>

<p class="by-line" >

a <a href="/reviews/programming"> programming </a> review by

<a href="/users/katemonkey" class="fn url" > katemonkey </a>

that was written

<a title="2007-01-27 11:09:21" class="dtreviewed" href="/reviews/date/2007/01/27/"> on 27 th January </a> and has been rated by 3 users as a good review.

</p>

</div>

</li>

xFolk - Bookmarks

<div class="folkentry" >

<div>

<a class="taggedlink" href=" http://.../... " > bookmark </a>

</div>

<div class="description" > A description ... </div>

<div class="meta" >

<a rel="tag" href=" http://.../tag/tag " > tag </a>

</div>

</div>

hcite - Citations

<li class="hcite" xml:lang="en">

<div class="publisher vcard" >

<span class="fn org" > ABC Publishing Co. </span>

<span class="country-name" > United Kingdom </span>

...

</div>

<div class="creator vcard" >

<span class="fn n" >

<span class="given-name" > John <span class="family-name" > Doe </span></span>

...

</div>

<span class="fn" > Foobar! </span>

<span class="description" > World Class Book about foobar </span>

<span class="volume" > 1 </span>

<span class="issue" > 1 </span>

<span class="pages" > 1-10 </span>

<span class="format" > article </span>

<span class="identifier" > 12345678 </span>

<a class="keyword" rel="tag" href=" /tags/foo "> foo </a>

Published <abbr class="dtpublished" title=" 20060101 "> January 1st 2006 </abbr>

Copyright <abbr class="copyright" title=" 20060101 "> 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=" http://orlabs.oclc.org/Identities/ ">

<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=" http://del.icio.us/tag/person "/>

<rdf:li resource=" http://del.icio.us/tag/identifier "/>

<rdf:li resource=" http://del.icio.us/tag/oclc "/>

</rdf:Bag>

</taxo:topics>

</item>

Flickr

<entry>

<title> The Eclipsified Moon </title>

<link rel="alternate" type="text/html“ href=" http://www.flickr.com/photos/alf/409522855/ "/>

<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="html”> ... </content>

<author>

<name> balloon in a sock </name>

<uri> http://www.flickr.com/people/alf/ </uri>

</author>

<link rel="license" type="text/html" href=" http://.../licenses/by-nc/2.0/ " />

<link rel="enclosure" type="image/jpeg“ href=" http://.../133/409522855_6ed97bbd2a_o.jpg " />

<category term=" moon " scheme=" http://www.flickr.com/photos/tags/ " />

<category term=" eclipse " scheme=" http://www.flickr.com/photos/tags/ " />

</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=" http://.../user/penguin/uri/ceac242dfd66979fe07ac5ebf8381afc ">

<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=" http://.../comments/uri/ceac242dfd66979fe07ac5ebf8381afc "/>

</item>

Connotea (ii)

<dcterms:URI rdf:about=" http://www.hubmed.org/display.cgi?uids=17015751 ">

<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="marcform"> 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=" info:pmid/17015751 "> <rdf:type rdf:resource=" http://purl.oclc.org/NET/nknouf/ns/bibtex#Article "/> <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=" info:pmid/17015751 "/> ... </tags:Tagging>

HubMed (ii)

<tags:Tagging rdf:about=" http://.../tags/users/aorchid/item/17015751 ">

<tags:taggedBy rdf:resource=" http://.../tags/users#aorchid "/>

<tags:taggedOn></tags:taggedOn>

<tags:taggedResource rdf:resource=" info:pmid/17015751 "/>

<tags:taggedWithTag>

<tags:Tag rdf:about=" http://.../tags/users/aorchid/tags#bos ">

<tags:tagName> bos </tags:tagName>

</tags:Tag>

</tags:taggedWithTag>

<tags:taggedWithTag>

<tags:Tag rdf:about=" http://.../tags/users/aorchid/tags#treg ">

<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

Social Networking

MySpace

YouTube

Facebook

Friendster

LinkedIn

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: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: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>