Ngsp
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Transcript of Ngsp
Next Generation Scientific Publishing:
Challenges and Directions
European Bioinformatics Institute 21 June 2013
Tim ClarkMassachusetts General Hospital
MassGeneral Institute of Neurodegenerative DiseaseHarvard Medical School
© 2013 Massachusetts General Hospital
Contents•Historical background•What is a scientific article?•Some problems in scientific communication•Next generation scientific publishing
(NGSP)•Taking NGSP forward•Conclusion
Historical background
Linear document format
1665 2012
Origins of linear format
•Linear format originated pre-1665 with personal correspondence amongst experimentalists & mathematicians.
•1665 scientific paper format was transported to the Web, PDFs
•Lives in a complex ecosystem• Incomplete Web exploitation & transition•Tension between linear & object formats
circle @ Oxford 1640-59
circle @ Gresham College, London 1645-60
Royal Society 1660-present
“Invisible Colleges”
Scientific journals
Royal Society 1660-present
Académie des Sciences 1666-present
Jan 1665
Mar 1665
Then and nowprintin
g
c. 1450
Scientific
Journal166
5
General PostOffice
1660
IBM S/360
Internet Web
1964
1980s
1991
Printcultur
e
Webcultur
e
Information
Technology
the Web
the Internet
Incomplete transition to Web
•Scientific article information model is limited, because it is mostly narrative.
•Critical information should ideally be computationally extractable and re-mixable.
•Yet as humans we require narratives.•We need narratives + computable
objects.
What is a scientific article?
Definition: A scientific article is a defeasible argument for assertions, based on a detailed narrative of observations, which are reproducible in principle, supported by exhibited data and supporting methods, and contextualized with other relevant findings in the domain. It exists in a complex ecosystem of technologies, people and activities.
Defeasible argument
•May be challenged and proven wrong.•May be “true” today but not tomorrow.•Inference to best explanation (IBE),
abductive reasoning (Peirce), etc.•Defeasible reasoning is a big topic in
AI.
Exhibited data...
Philos Trans R Soc Lond 1(4):56 Brain. 2010 Nov;133(Pt 11) 3336-3348.
(at least, enough to be convincing!)
...and reproducible methods
Boyle’s air pump, from New Experiments (1660) Illumina NGS system
Scientific communications
ecosystem
Interlocking systems of activity
Some problems in scientific
communication c. 2013
Some problems in the ecosystem• Intractable publication volumes [1]
• Invalid, distorted and copied citations [3,4,5]
• Growing volume of retractions [5,6]• 2/3 of retractions due to misconduct [7]• Research non-reproducibility [8]• Lack of transparency in publication
process [9]• Methods non-re-usability [10]• Flawed assessment metrics [11-12]
Non-reproduciblity
11%
Begley CG and Ellis LM, Nature 2012, 483(7391):531-533
Citation distortionadapted from supporting data, Greenberg SA, British Medical Journal 2009, 339:b2680
The copied citation• Citation analysis of one sample of publications
(in ethnobotany) found that “the majority of citing texts do not consider the theoretical contributions made by the articles cited”.
• I.e., author of Work A makes statement, cites Work B, and then copies several references, unread, from Work B as well, assuming they are relevant too.
• Ramos et al. Scientometrics 2012, 92(3):711-719
Not to mention...•Closed access publishing model•Walled garden systems,•Text mining & remixing prohibitions,
and•Insane rising costs imposed on
libraries.•Open access publishing model•Researcher cost burden unaccounted
for by funding agencies.
Some efforts at coping
• Mandatory open access (US, UK, Universities)
• Data access: archiving and citation, institutional data policies, “data papers”, etc. (various)
• Methods: cataloging & annotation (NIF, publishers)
• Open annotation (W3C Community) & tools
• Velocity: Alzforum, StemBook, Open Wetware, blogs, webinars, Wikipedia coordination, etc.
• Velocity: preprint servers (ArXiv, DASH, PMC, etc.)
• Advocacy groups: FORCE11, DELSA, DORA, Amsterdam Manifesto, etc.
Next Generation Scientific Publishing
What does NextGen Scientific Publishing look
like?•There is transparency of all data & methods. •Big data + small data (the very long
tail).•Articles are deconstructable * text-
minable * remixable * computable.•Information moves quickly and is
verifiable. •Open annotation for narrative + objects.•There are no walled gardens: a service-
oriented open-access economy.
Data re-usability• The main reason to exhibit data is not
necessarily to reuse it...it is (minimally) to prove that1. you have it and are willing to show it,2. it is reasonable to think that you derived
it as you say you did, and you openly share these methods.
• Data that is re-usable is special:• Re-usable data is itself a research method
with its own special requirements.• See: Data Papers.
Data papers•Data should be surfaced in a re-usable
way.•Incentivize the extra effort required.•Concept being developed by a few
publishers with differing implementation ideas.
•Questions: what is reusability? at what level?
Our Data Papers requirements
•Only inherently reusable data is published as a Data Paper•Normalize identifiers
•Reverse normal “ratio” of text:data•Amsterdam data citation principles
•All data is searchable w/ or w/o the paper•Global metadata catalog in stable
archive
Methods re-usability
•Open methods are the basis of science.•“Standing on the shoulders of giants” = •reusing maths, software, instruments,
reagents, models, protocols, etc. •But method citations can be very obscure;•you cannot reuse a secret. •See: alchemy, necromancy, divination.
Computational semantics
•Entity-extraction: NIF, Utopia, etc. •Topic-based: Threads •Statement-based: SWAN,
nanopublications•Argument-based:
micropublications
Open annotation• Open model• Annotate any web document• Transferable, selectively sharable• Highlights, comments, semantics, video• Entities, topics, statements, arguments• W3C Open Annotation Community• http://www.w3.org/community/
openannotation/
Open annotation model
Complex annotation
Discussion as annotation
Annotation tools
Creating digital abstracts in Domeo
Digital article summary
Digital article summary{:MP3 rdf:type mp:Micropublication; mp:name "MP(a3)"; mp:description "Digital summary of Spillman et al. 2010"; pav:authoredBy [ a foaf:Person ; foaf:name "Tim Clark" ]; pav:createdBy [ a foaf:Person ; foaf:name "Tim Clark" ]; pav:createdOn "2013-03-06T09:49:12-05:00"^^xsd:dateTime ; mp:argues :C3; mp:supportedBy <info:doi:10.1371/journal.pone.0009979> .} .
:MP3 = {:S1 rdf:type mp:Statement; mp:hasContent "Rapamycin [is] an inhibitor of the mTOR pathway." ; mp:supportedBy <info:doi/10.1038/nature08221> .:S2 rdf:type mp:Statement; mp:hasContent "PDAPP mice accumulate soluble and deposited Aβ and develop AD-like synaptic deficits as well as cognitive impairment and hippocampal atrophy." ; mp:supportedBy <info:doi/10.1073/pnas.96.6.3228> .
:S3 rdf:type mp:Statement; mp:hasContent "Rapamycin-fed transgenic PDAPP mice showed improved learning (Figure 1a) and memory (Figure 1b). We observed significant deficits in learning and memory in control-fed transgenic PDAPP animals." ; mp:supportedBy <http://www.jneurosci.org/content/20/11/4050> .
:M1 rdf:type mp:Procedure; mp:hasName "Rapamycin-supplemented mouse diet protocol" ; mp:hasContent "We fed a rapamycin-supplemented diet... or control chow to groups of PDAPP mice and littermate non-transgenic controls for 13 weeks. At the end of treatment (7 mo), learning and memory were tested using the Morris water maze." .
:M2 rdf:type mp:Material; mp:hasName "PDAPP J20"; mp:hasDescription "Lennart Mucke's PDAPP J20 transgenic mice, as obtained from JAX, stock#006293" ; mp:describedBy: <http://jaxmice.jax.org/strain/006293.html> .
:D1 rdf:type mp:Data; pav:retrievedFrom <http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0009979#pone-0009979-g001>; mp:supportedBy :M1, :M2 .
:C3 rdf:type mp:Claim; mp:hasContent "Inhibition of mTOR by rapamycin can slow or block AD progression in a transgenic mouse model of the disease." ; mp:supportedBy :S1, :S2, :S3, :D1.} .
Mixing nano, micro, entities, topics
Navigable citation networks
Figure from Greenberg SA, British Medical Journal 2009, 339:b2680
Taking NGSP forward
The Future of Research Communications and eScholarship • Open community of scholars, librarians,
archivists, publishers and research funders.• Goal is to facilitate more rapid change &
improvement in scholarly communications through effective use of information technologies.
• Founded 2011 at a workshop held at Leibniz Zentrum für Informatik, Schloss Dagstuhl, DE.
• Check it out & join online at http://force11.org
Summary•Incomplete transition of scientific
publishing to the Web•Big problems with the current system•NextGen Scientific Publishing will be: •open, transparent, remixable, fast•and we will annotate it on the Web.
Acknowledgements• Lab: Paolo Ciccarese, Stephane Corlosquet, Sudeshna Das,
Patti Davis, Emily Merrill, Marco Ocana
• Collaborators: Brad Allen, Neil Andrews, Anita Bandrowski, Phil Bourne, Suzanne Brewerton, Monika Byrne, Merce Crosas, Anita De Waard, Lisa Girard, Carole Goble, Tudor Grosza, Paul Groth, Keith Gutfreund, Hamed Hassanzadeh, Ivan Herman, Brad Hyman, Adrian Ivinson, Derek Marren, Maryann Martone, Pat McCaffery, Steve Pettifer, Brock Reeve, Rob Sanderson, Holly Schmidt, Herbert Van de Sompel and Thomas Wilkin; and our colleagues at the Mass. Alzheimer Disease Research Center
• Funding: Eli Lilly, Elsevier, Harvard Neuro Discovery Center, Harvard Stem Cell Institute, EMD Serono, NIH (NIA, NIDA), and two anonymous foundations.
• Very special thanks to: Carole Goble & Brad Hyman
References1. Hunter L, Cohen KB: Biomedical language processing: what's beyond PubMed?
Molecular cell 2006, 21(5):589-594.2. Greenberg SA: How citation distortions create unfounded authority: analysis
of a citation network. British Medical Journal 2009, 339:b2680.3. Greenberg SA: Understanding belief using citation networks. Journal of
Evaluation in Clinical Practice 2011, 17(2):389-393.4. Ramos, M., J. Melo, and U. Albuquerque, Citation behavior in popular scientific
papers: what is behind obscure citations? The case of ethnobotany. Scientometrics, 2012. 92(3): p. 711-719.
5. Lawless J: The bad science scandal: how fact-fabrication is damaging UK's global name for research. In: The Independent. 2013.
6. Noorden RV: Science publishing: The trouble with retractions. Nature 2011, 478:26-28.
7. Fang FC, et al: Misconduct accounts for the majority of retracted scientific publications. Proceedings of the National Academy of Sciences 2012, 109(42):17028-17033.
8. Begley CG, Ellis LM: Drug development: Raise standards for preclinical cancer research. Nature 2012, 483(7391):531-533.
9. Marcus A, Oransky I: Bring On the Transparency Index. In: The Scientist. Midland, Ontario, CA: LabX Media Group; 2012.
10.Bandrowski AE, et al: A hybrid human and machine resource curation pipeline for the Neuroscience Information Framework. Database 2012: bas005.
11.Randy S, Mark P: Reforming research assessment. eLife 2013, 2.12.Alberts B: Impact Factor Distortions. Science 2013, 340(6134):787.