The presentation discussed the future of scientific communication, noting that open access to digital data and methods will be key to enabling reproducibility and maximizing data integration to advance discovery, but that both technological innovations and changes to incentives and rewards systems will be needed to fully realize more open and interactive models of sharing research.

1. The Future of Research
Communication
Judith Blake
The Jackson Laboratory

2. My Perspective
Future open access to digital data will speed discovery
Data generation is getting easier, data analysis is
getting harder, we are drowning in data
Key to scientific discourse is the ability to reproduce
and verify results - currently difficult for computational
results that do not include code and data upon
publication
Current „academic‟ publication and rewards systems
are inadequate for measuring scientific contributions
Digital data repositories, open access
publications, electronic journals, and semantic web
enhancements will all contribute to the success of
future of science communications
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3. Outline
1. Improving knowledge communication
- Vision: What are the communication functionalities
needed?
- Technology: What are the tools for doing this?
2. Impacting our world
- Social Aspects: How do we quantify impact of
use/reward system?
- Coolness: How do we make it attractive to do/ use?
3. Overcoming obstacles
-Financial Considerations: How do we make is
sustainable?
-Getting the ball rolling: How do we start? Rocky ISBC 12/8/11

4. “Where Computer Scientists
Meet”
Elsevier, Wiley, ISI, (Highwire), PLoS, 14 Universities, European Commission, UKRoyal
Society Rocky ISBC 12/8/11

5. The Reasoned Argument
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6. Managing
Biological
Information is
Nothing New
Roxy Laybourne and
others, photo by Chip Clark
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Bird Collections at the Smithsonian Natural History Museum

7. TCTCTCCCCCGCCCCCCAGGCTCCCCCGGTCGCTCTCCTCCGGCGGTCGCCCGCGCTCGGTGGATGTGGC
From the birth of the field of genetics until a decade ago,
TGGCAGCTGCCGCCCCCTCCCTCGCTCGCCGCCTGCTCTTCCTCGGCCCTCCGCCTCCTCCCCTCCTCCT it was generally assumed
TCTCGTCTTCAGCCGCTCCTCTCGCCGCCGCCTCCACAGCCTGGGCCTCGCCGCGATGCCGGAGAAGAGG its function. In the vast
that the parental origin of a gene could have no effect on
CCCTTCGAGCGGCTGCCTGCCGATGTCTCCCCCATCAACTACAGCCTTTGCCTCAAGCCCGACTTGCTGG this paradigm has appeared
majority of studies carried out during the last 90 years,
to hold true. However, with increasingly sophisticated genetic and embryological
ACTTCACCTTCGAGGGCAAGCTGGAGGCCGCCGCCCAGGTGAGGCAGGCGACTAATCAGATTGTGATGAA
investigations in the mouse, important exceptions to this rule have been uncovered
TTGTGCTGATATTGATATTATTACAGCTTCATATGCACCAGAAGGAGATGAAGAAATACATGCTACAGGA
over the last decade. First, the results of nuclear transplantation experiments carried
TTTAACTATCAGAATGAAGATGAAAAAGTCACCTTGTCTTTCCCTAGTACTCTGCAAACAGGTACGGGAA
out with single-cell fertilized embryos have demonstrated an absolute requirement for
CCTTAAAGATAGATTTTGTTGGAGAGCTGAATGACAAAATGAAAGGTTTCTATAGAAGTAAATATACTAC
both a maternally-derived and a paternally-derived pronculeus to allow full-term
CCCTTCTGGAGAGGTGCGCTATGCTGCTGTAACACAGTTTGAGGCTACTGATGCCCGAAGGGCTTTTCCT
development (McGrath and Solter, 1983). Second, in animals that receive both
TGCTGGGATGAGCCTGCTATCAAAGCAACTTTTGATATCTCATTGGTTGTTCCTAAAGACAGAGTAGCTT
homologs of certain chromosomes or subchromosomal regions from one parent and
TATCAAACATGAATGTAATTGACCGGAAACCATACCCTGATGATGAAAATTTAGTGGAAGTGAAGTTTGC
not the other (through the mating of translocation heterozygotes as described in
CCGCACACCTGTTATGTCTACATATCTGGTGGCATTTGTTGTGGGTGAATATGACTTTGTAGAAACAAGGobserved including enhanced
Section 5.2.3), dramatic effects on development can be
TCAAAAGATGGTGTGTGTGTCCGTGTTTACACTCCTGTTGGCAAAGCAGAGCAAGGAAAATTTGCGTTAG Kirk, 1985). Third, either of
or retarded growth and outright lethality (Cattanach and
two deletions that cover a small region of mouse chromosome 17 can be transmitted
AGGTTGCTGCTAAAACCTTGCCTTTTTATAAGGACTACTTCAATGTTCCTTATCCTCTACCTAAAATTGA
TCTCATTGCTATTGCAGACTTTGCAGCTGGTGCCATGGAGAACTGGGGCCTTGTTACTTATAGGGAGACTdeletions cause prenatal
normally from a father to his offspring, but these same
lethality when they are maternally transmitted (Johnson, 1974; Winking and
GCATTGCTTATTGATCCAAAAAATTCCTGTTCTTCATCCCGCCAGTGGGTTGCTCTGGTTGTGGGACATG
Silver, 1984). Fourth, similar parent-of-origin effects have been observed on the
AACTCGCCCATCAATGGTTTGGAAATCTTGTTACTATGGAATGGTGGACTCATCTTTGGTTAAATGAAGG
TTTTGCATCCTGGATTGAATATCTGTGTGTAGACCACTGCTTCCCAGAGTATGATATTTGGACTCAGTTT knock-out allele at the Igf2
phenotypes expressed by animals that carry a targeted
locus (DeChiara et al., 1991). Finally, molecular techniques have been used to directly
GTTTCTGCTGATTACACCCGTGCCCAGGAGCTTGACGCCTTAGATAACAGCCATCCTATTGAAGTCAGTG
The trouble with facts is that there are so many of
demonstrate the expression of transcripts from one parental allele and not the other
TGGGCCATCCATCTGAGGTTGATGAGATATTTGATGCTATATCATATAGCAAAGGTGCATCTGTCATCCG
at the Igf2r locus (Barlow et al., 1991) and the H19 locus (Bartolomei et al., 1991). The
them.
AATGCTGCATGACTACATTGGGGATAAGGACTTTAAGAAAGGAATGAACATGTATTTAACCAAGTTCCAA
accumulated data indicate that a subset of mouse genes (on the order of 0.2%) will
CAAAAGAATGCTGCCACAGAGGATCTCTGGGAAAGTTTAGAAAATGCTAGTGGTAAACCTATAGCAGCTG The Gentle Reader (1903)
Samuel Crothers:
function differently in normal embryos depending on whether they have been
GTTTCTGCTGATTACACCCGTGCCCAGGAGCTTGACGCCTTAGATAACAGCCATCCTATTGAAGTCAGTG
inherited through the male or the female gamete, such that one allele will be expressed
TGGGCCATCCATCTGAGGTTGATGAGATATTTGATGCTATATCATATAGCAAAGGTGCATCTGTCATCCG
and the other will be silent. Genomic imprinting is the term that has been coined to
AATGCTGCATGACTACATTGGGGATAAGGACTTTAAGAAAGGAATGAACATGTATTTAACCAAGTTCCAA by a gene varies depending
describe this situation in which the phenotype expressed
on its parental origin (Sapienza, 1989). Further experiments have demonstrated
CAAAAGAATGCTGCCACAGAGGATCTCTGGGAAAGTTTAGAAAATGCTAGTGGTAAACCTATAGCAGCTG
that, in general, the "imprint" is erased and regenerated during gametogenesis so
that the function of an imprintable gene is fully determined by the sex of its
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progenitor alone, and not by earlier ancestors.

8. Manual (mostly) curation of the biomedical literature
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9. The knowledge is in
the details
Curators use controlled
terms from structured
vocabularies
(ontologies) to annotate
complex biological
systems described in
the literature
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10. Crash Blossoms
and other semantic ambiguities
translating what we say into
what we mean: data, words
and knowledge
“Violinist Linked to JAL Crash
Blossoms”
“Squad Helps Dog Bite
“MacArthur Flies Back toVictim”
Front”
“Red Tape Holds Up New
Bridge.” Rocky ISBC 12/8/11

11. Today there are many biomedical ontologies…
Open Biomedical
Ontologies
http://www.obofoundry.org/
The „s link to the
term request
trackers for the
listed ontologies.
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12. Something very important and very weird is happening to the book right
now: It‟s shedding its papery corpus and transmigrating into a bodiless
digital form, right before our eyes. We‟re witnessing the bibliographical
equivalent of the rapture. If anything we may be lowballing the weirdness
of it all. Rocky ISBC 12/8/11
Lev Grossman, NYTimes Book Review Sept

13. Semantic Web
Semantic Web Layer Cake (Berners-Lee, 2000)
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14. …..into the Future
The current back-propagation of biomedical literature
of semantic integration using ontologies is not scalable
to necessary level of granularity and context needed
A key element of data integration is the mark-up of
data at the time of generation
Reasoned Argument communication includes
providing methods and data to enable
reproducibility, and requires
open access to the semantically enriched
discussion, machine-readable metadata, accessible
datasets, peer review discussions, and possibility of
testing for reproducibility Rocky ISBC 12/8/11

15. 1 - Improving Knowledge
Communication
What are functionalities needed
detail methods, both wet and dry
provide data with appropriate metadata
support interactive results, i.e., tables and figures
track metrics of utility, usage, and impact
Technology
electronic lab books that are easy and functional
data collection and repositories that provide standards
and persistence
new models for data interconnections
real-time metrics available
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16. What‟s Changing - 2
Peer Review
Journal Impact (the Myth of Impact Factors)
Supplementary Material (i.e., the DATA) missing
and or incomplete
Metrics of Impact of Research
Persistence of Data
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17. Peer Review-1 – bad review
hard to engage expert reviews for multi-component
research
The Scientist
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18. Large computation analysis
require multiple coordinated
reviews
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Slide from Carol Bult

19. Peer Review – bad review 2
Computation analysis verity depends on data input
Ascertainment bias refers to a systematic
distortion in measuring the true frequency of
Faculty of
way in which 12/8/1
a phenomenon due to the Rocky ISBC the
1000 1
data are collected.

20. We need to enable
reproducibility
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21. Rocky ISBC 12/8/11

22. Research data is simply not
available
50 highest impact research journals
1st 10 original research articles of 2009
88% of journals had „some‟ statement on sharing
of data
50% of articles did not meet journal standards
9% of articles in full compliance
algorithms and meta-date required for
reproducibility not required by any journal
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Alsheikh-Ali et al., PLoS One 2011;6(9):e24357. Epub 2011
Sep 7.

23. Changing Incentives to Publish -
1
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24. Changing Incentives to Publish - 2
Nature Medicine 16, 744 (2010) doi:10.1038/nm0710-744
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25. 2 - Impacting Our World
Open Access to data within supportive
environment accelerates knowledge
discovery
Social Aspects:
How do we quantify impact of use/reward
system?
Coolness:
How do we make it attractive to do/ use?
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26. Sharing Data – Crowd Sourcing
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27. Interactive Communication
Imbedded links to data for figures
Immediate access to referenced material
Interactive community
Blogs and commentary
Analytics of impact
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28. Initiatives to Access Data
uvm biomedical figuresearch
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29. Interactive Publications
Jonathan Eisen's Blogspot – 9/6/11
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30. Metrics of Paper Impact -1
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31. 3 – Overcoming Obstacles
New Publication Models
Data Preservation –
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32. publish your data – Rocky ISBC 12/8/11
datadryad.org

33. Key Points
Communication of research methods, data and results is
changing.
Access to research is limited outside northern hemisphere -
institutional access missing – thus limiting the globalization of
science.
Utility of research depends on inter-connections and access to
data and results; cloud-sourcing of science imminent.
The reward mechanism (tenure /cash) via publication record is
changing, but slowly for most of us.
The business model of scientific publishing is under great stress.
Government investment mechanisms for support and sharing of
science endeavors are under intense discussion.
New research communication mechanisms are coming; some
are already here. Rocky ISBC 12/8/11

34. Summary
We must continue to support the Reasoned Argument
- in context of massive amounts of digital data, this includes
comprehensive data access to maximize data integration
and enable reproducibility
The necessary upheaval in scientific communication
requires both technological and sociological
innovations
YOU can be part of this sea change in research
communication
Rocky ISBC 12/8/11

35. FoRCe Workshop Mouse Genome
Informatics
Gene Ontology Consortium
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36. Acknowledgements
MGI PIs
Carol Bult, Janan Eppig, Jim Kadin, Joel Richardson, Martin Ringwald
GO Consortium PIs and Council
Michael Ashburner, Mike Cherry, Suzanna Lewis, Paul Thomas, Paul
Sternberg;
Rolf Apweiler, Rex Chisholm, Eva Huala
GO @ MGI
Alex Diehl, Mary Dolan, David Hill,
Li Ni, Harold Drabkin, Li Ni,
Dmitry Sitnikov
Funding: NIH-NHGRI P-41 grants to MGI and GOC; GM080646 to
PRO Rocky ISBC 12/8/11