Bringing a publisher’s content to the Life Science researcher
description
Transcript of Bringing a publisher’s content to the Life Science researcher
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 :