Database Publishing at Nature

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Database Publishing at Nature

• Timo Hannay
• Nature Publishing Group
• 7 October 2005

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Overview

• Publishing collaborations Making databases more
  like journals
• NPG New Technology Making journals more like
  databases
• Tagging and social bookmarking New methods of
  annotation and navigation

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Database publishing at NPG

• The AfCS-Nature Signaling Gateway
  (http//www.signaling-gateway.org/)
• The CMC-Nature Cell Migration Gateway
  (http//www.cellmigration.org/)
• Forthcoming collaborations with NCI and several
  other groups

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The AfCS-Nature Signaling Gateway

• A freely available online resource for anyone
  interested in cellular signalling
• A collaboration with the research community
  through the Alliance for Cellular Signaling
• An experiment in the next generation of online,
  database-driven scientific publications

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The Signaling Gateway
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The Molecule Pages

• Comprehensive, structured data for 3,700
  proteins involved in cellular signalling
• Some information automatically fed in from other
  online databases and updated monthly
• Other information entered by selected expert
  authors and updated annually
• Author-entered data peer-reviewed by NPG
• Fully citable using digital object identifiers
  (DOIs)

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Using Digital Object Identifiers
http//dx.doi.org/10.1038/35057062
Correct URL at publishers website
Nature 409, 860 - 921 (2001)
doi10.1038/35057062
IDF/CrossRef databases

• Allows unambiguous identification of paper
• Allows readers to find the paper online
• Allows publishers to cross-link reference lists
• Guaranteed not to change (even if the publisher
  changes)

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The Molecule Pages A scientific publication
The Molecule Pages has the same features as a
traditional journal, except that the information
it contains is more highly structured and
queryable.
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Overview

• Publishing collaborations Making databases more
  like journals
• NPG New Technology Making journals more like
  databases
• Tagging and social bookmarking New methods of
  annotation and navigation

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Great underestimated technologies of our age
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Scientific papers as structured data objects
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Experimental article metadata database

• Initial data to be included
• Author and institute details
• Scientific
• Molecules (InChI)
• Genes (Entrez Gene)
• Proteins (UniProt)
• Cellular processes, functions, locations (GO)
• Species (NCBI)
• Citation annotations (controlled vocabulary)

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Support for structured data sets

• Developing support for
• Systems Biology Markup Language
• CellML
• Chemical Markup Language
• Others

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SVG Figures as interactive data objects
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Automated scientific markup and linking
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Increasing structure in text markup (1)
The old way (no semantic markup) ltpgt...gp120
binding to CXCR4 or CCR5 activates PYK2 and
FAKlt/pgt Now (key entities and concepts marked
up) ltpgt...ltprotein id"urnlsiduniprot.orguni
protP03378"gtgp120lt/proteingt ltaction
id"urnlsidgeneontology.orggo000548"gtbindinglt/
actiongt to ltprotein id"urnlsiduniprot.orgunipr
otP48061"gtCXCR4lt/proteingt or ltprotein
id"urnlsiduniprot.orguniprotP10147"gtCCR5lt/pro
teingt ltaction id"urnlsidgeneontology.orggo000
8047"gtactivateslt/actiongt ltprotein
id"urnlsiduniprot.orguniprotO43150"gtPYK2lt/pro
teingt and ltprotein id"urnlsiduniprot.orgunipro
tQ05397"gtFAKlt/proteingtlt/pgt
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Increasing structure in text markup (2)
The new way (full RDF/XML) ltpgt... ltrdfGraph
xmlnsrdf"http//www.w3.org/1999/02/22-rdf-syntax
-ns" xmlnsgo"urnlsidgeneontology.orggo"
xmlnsuniprot"urnlsiduniprot.orguniprot"gt
ltgo000548gt ltuniprotProtein
rdfresource"urnlsiduniprot.orguniprotP03378"
/gt ltuniprotProtein rdfresource"urnlsiduni
prot.orguniprotP48061"/gt ltgo0008047
rdfresource"urnlsiduniprot.orguniprotO43150"
/gt ltgo0008047 rdfresource"urnlsiduniprot.
orguniprotQ05397"/gt lt/go000548gt
ltgo000548gt ltuniprotProtein
rdfresource"urnlsiduniprot.orguniprotP03378"
/gt ltuniprotProtein rdfresource"urnlsiduni
prot.orguniprotP10147"/gt ltgo0008047
rdfresource"urnlsiduniprot.orguniprotO43150"
/gt ltgo0008047 rdfresource"urnlsiduniprot.
orguniprotQ05397"/gt lt/go000548gt
ltrdflabelgtgp120 binding to CXCR4 or CCR5
activates PYK2 and FAKlt/rdflabelgt lt/rdfGraphgt lt
/pgt
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Why go to all this effort?
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Views from the database side
Before the end of the next decade, pathway
databases will become scientific journals and
journals will become databases. Biologists will
be greatly empowered, and bioinformatics will
continue its long evolution. Lincoln Stein
(Reactome) Is a biological database any
different than a biological journal? I am working
toward reaching an answer of, no, there is no
difference. Phil Bourne (Protein Data Bank)
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Overview

• Publishing collaborations Making databases more
  like journals
• NPG New Technology Making journals more like
  databases
• Tagging and social bookmarking New methods of
  annotation and navigation

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A few uses for Connotea

• Keeping bookmarks and references in order
• Sharing links and ideas within a team (perhaps
  geographically dispersed)
• Providing readers with a (dynamic) list of
  further or related reading
• Encouraging readers to share relevant links with
  the author and with each other