Bringing a publisher’s content to the Life Science researcher
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Transcript of Bringing a publisher’s content to the Life Science researcher
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Bringing a publisher’s content to the
Life Science researcher
Alf EatonNature Publishing Group
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Find
Why?
BrowseStore
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Search
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HubMed
Whatizit: GO, UniProt; Wikipedia
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GoPubMed
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GoPubMed
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Search
Recognise entities, including synonyms.
Discover and suggest connections between entities.
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NextBio
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Freebase
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Browse
Diabetes
Cancer
Cell Migration
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Cell Migration Gateway
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Chemical Blogspace
(PostGenomic: open source aggregator)
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Increase the visibility of articles
Increased readership
Increased citations
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Text mining
Abstracts
Full text
Access
OTMI
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OTMI
opentextmining.org
Atom Entry elements
Metadata
Sentences
References
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Extract
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Garten, Niclas, Altman (Stanford University), in press
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Metadata
Authors, Dates, Title, Journal, Abstract
PRISM, Dublin Core
References
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Entities
People, Places, Companies(Reuters OpenCalais)
Genes, Proteins, Molecules, Products
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Full text
NLM DTD Text miningSharableannotations
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iHOP
Gene/protein entities
Interactions between proteins
MeSH
Gene Ontology
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Interaction
Author/editor verification
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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
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Possible sharedannotation formats
Atom
RDF
UIMA
Annotea
Zotero, Diigo
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Atom
Extensible
Hierarchical content model
Atom Publishing Protocol
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RDF
Completely extensible
Arbitrary attributes
Generic data storage
SPARQL queries
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Licensing
Non-commercial (some rights reserved)
Attribution
Joint ownership
Facts vs creative arrangement
Redistribution (share-alike)
Preserve value
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Participation
Knowledge mapping (Mind Maps)
Vote annotations up/down
Highlight/suggest new annotations
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Semgine myMap
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Communication
Bookmarks (Connotea)
Links to sections/paragraphs/figures/data
Blog posts
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Microformats
RDFa
Yahoo! search
Microcitation
Structured HTML
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APIs
Researchers/scientists (desktop, mobile, web)
Machines/indexers
Artists/visualizers
Integrate with data web
Make content available to :
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