Bringing a publisher’s
content to the
Life Science researcher
Alf Eaton
Nature Publishing Group

Why?
Find
Browse
Store

Search

HubMed
Whatizit: GO, UniProt; Wikipedia

GoPubMed

GoPubMed

Search
Recognise entities, including synonyms.
Discover and suggest connections
between entities.

NextBio

Freebase

Browse
Diabetes
Cancer
Cell Migration

Cell Migration Gateway

Chemical Blogspace
(PostGenomic: open source aggregator)

Increase the visibility of articles
Increased readership
Increased citations

Text mining
Abstracts
Full text
Access
OTMI

OTMI
opentextmining.org
Atom Entry elements
Metadata
Sentences
References

Extract

Garten, Niclas, Altman (Stanford University), in press

Metadata
Authors, Dates, Title, Journal, Abstract
PRISM, Dublin Core
References

Entities
People, Places, Companies
(Reuters OpenCalais)
Genes, Proteins, Molecules, Products

Full text
Sharable
NLM DTD Text mining
annotations

iHOP
Gene/protein entities
Interactions between proteins
MeSH
Gene Ontology

Interaction
Author/editor verification

Annotation formats
Inline
Stand-off
Splice annotations into XML using PHP or
Javascript
XPath and character offsets for positioning
Can store inline, eg in Marklogic, using start/
end markers

Possible shared
annotation formats
Atom
RDF
UIMA
Annotea
Zotero, Diigo

Atom
Extensible
Hierarchical content model
Atom Publishing Protocol

RDF
Completely extensible
Arbitrary attributes
Generic data storage
SPARQL queries

Licensing
Non-commercial (some rights reserved)
Attribution
Joint ownership
Facts vs creative arrangement
Redistribution (share-alike)
Preserve value

Participation
Vote annotations up/down
Highlight/suggest new annotations
Knowledge mapping (Mind Maps)

Semgine myMap

Communication
Bookmarks (Connotea)
Links to sections/paragraphs/figures/data
Blog posts

Structured HTML
Microformats
RDFa
Yahoo! search
Microcitation

APIs
Make content available to :
Researchers/scientists (desktop, mobile,
web)
Machines/indexers
Artists/visualizers
Integrate with data web