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Hufton-npg-scientific data and semantic publishing-nfdp13


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Presentation by Andrew Hufton on Nature Publishing Group's Scientific Data journal and semantic publishing given at the Now and Future of Data Publishing Symposium, 22 May 2013, Oxford, UK

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Hufton-npg-scientific data and semantic publishing-nfdp13

  1. 1. Now and Future of Data Publishing 2013 Andrew L. Hufton Managing Editor Scientific Data Helping you publish, discover, and reuse research data
  2. 2. Scientific Data ● Descriptions of scientifically valuable datasets ● Includes standardized machine-readable experimental metadata ● Open-access with CC0 experimental metadata ● Rigorous peer review ensures data quality and standards 2
  3. 3. Structured information enhances narrative content online Design Type(s) genetic modification design comparative LC/MS- based profiling Factor Type(s) genotype replicate Measurement Type(s) metabolite profiling Metabolite profiling during early development in Xenopus laevis Background & Summary Methods Technical Validation Usage Notes Samples/ Subjects Assays References Export PDF ISA-Tab Related Articles … Associated Data Records … Supporting Files … Background & Summary The organizer is the primary patterning center during early vertebrate gastrulation. As might be expected for a tissue with such capabilities, the organizer is complex. Studies in multiple species, including frogs and mice, have shown that the organizer has distinct regions that induce head and trunk, and these abilities decisively change as development proceeds. At the molecular level, the organizer's inductive properties are mediated by factors that inhibit the BMP, Wnt, and Nodal signaling pathways. BMP inhibitors, including the secreted molecule Noggin, can induce a partial secondary axis that lacks a head and notochord. However, BMP inhibition alone cannot sustain the expression of most organizer genes past late gastrula without the addition of Wnt inhibitors, such as Dkk-1 [1]. Furthermore, Wnt inhibitors alone cannot induce secondary structures, but when combined with Noggin can induce a complete secondary axis, including properly patterned head and trunk tissues. Therefore, inhibition of both pathways generates the complete spectrum of molecules required for total organizer function and maintenance, illustrating that regional differences in organizer activity are created by the mixes of inhibitors present and active within particular regions (reviewed in [2-4]).
  4. 4. Challenges ● Collecting metadata from authors who may not be data standards experts ● Standardizing experimental metadata across many disparate fields ● Working with existing data repositories, rather than against them 4
  5. 5. How we are tackling these challenges? ● ISA-tab provides a common metadata format ● Primary data to be stored in community repositories, not journal-specific resources ● Support for community ontologies ● Professional in-house curation 5
  6. 6. 6 Authors can submit structured information in multiple ways Submit ISA-tab files directly OR Submission tools and simple templates help authors provide the information without special tools In-house curator standardizes the structured content
  7. 7. Local metadata format Nature Nature Genetics Journal Journal Scientific Reports Nature Methods Journal Journal Other NPG titles
  8. 8. Calling for submissions in Fall 2013, launching in Spring 2014
  9. 9. Thanks! Andrew L. Hufton Managing Editor Scientific Data