Bringing a publisher’s content to the

Life Science researcher

Alf EatonNature Publishing Group

Find

Why?

BrowseStore

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

NLM DTD Text miningSharableannotations

iHOP

Gene/protein entities

Interactions between proteins

MeSH

Gene Ontology

Interaction

Author/editor verification

Annotation formats

Splice annotations into XML using PHP or Javascript

XPath and character offsets for positioning

Can store inline, eg in Marklogic, using start/end markers

Inline

Stand-off

Possible sharedannotation 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

Knowledge mapping (Mind Maps)

Vote annotations up/down

Highlight/suggest new annotations

Semgine myMap

Communication

Bookmarks (Connotea)

Links to sections/paragraphs/figures/data

Blog posts

Microformats

RDFa

Yahoo! search

Microcitation

Structured HTML

APIs

Researchers/scientists (desktop, mobile, web)

Machines/indexers

Artists/visualizers

Integrate with data web

Make content available to :