1.
brian m. bot | sage bionetworks | @BrianMBot
department of defense breast cancer research program
vision setting meeting 2015
biomedical research in an
increasingly digital world

2.
biomedical research in an increasingly digital world

3.
biomedical research in an increasingly digital world

4.
6%
21%
8%
11%
54%
cannot
reproduce
can
reproduce in
principle
can reproduce
w/discrepancies
can reproduce from
processed data w/
discrepancies
can
reproduce
partially
the status quo tolerates
poor communication of
findings
Ioannidis A. et al. Nature Genetics 2009

5.
“Scientists often study the past as
obsessively as historians because few
other professions depend so acutely on it.
Every experiment is a conversation with
a prior experiment,
every new theory a refutation of the old”
-Siddhartha Mukherjee, The Emperor of All Maladies

6.
scientific method
1. define a question
2. gather information and resources (background research)
3. form a hypothesis
8. retest (frequently done by other scientists)
4. test hypothesis experimentally
5. analyze experimental data
7. publish results
6. draw conclusions based on data

7.
7. publish results

8.
finitein
∞
...

9.
sage bionetworks
~40 FTEs
1/2 research - 1/3 platform - 1/6 leadership/support

10.
sage bionetworks
a non-profit organization which pilots a
variety of components that are necessary
to build a scientific research commons
focused on a world where biomedical research
will fundamentally change to be
more open and collaborative
supports communities of researchers
working collaboratively across disciplines

11.
sage bionetworks
focused on a world where biomedical research
will fundamentally change to be
more open and collaborative

12.
focused on a world where biomedical research
will fundamentally change to be
more open and collaborative
open
sage bionetworks

13.
open access
focused on a world where biomedical research
will fundamentally change to be
more open and collaborative
sage bionetworks

14.
accessibility
focused on a world where biomedical research
will fundamentally change to be
more open and collaborative
sage bionetworks

15.
open access
focused on a world where biomedical research
will fundamentally change to be
more open and collaborative
sage bionetworks

16.
open science
focused on a world where biomedical research
will fundamentally change to be
more open and collaborative
sage bionetworks

17.
science
focused on a world where biomedical research
will fundamentally change to be
more open and collaborative
sage bionetworks

18.
a non-profit organization which pilots a
variety of components that are necessary
to build a scientific research commons
focused on a world where biomedical research
will fundamentally change to be
more open and collaborative
supports communities of researchers
working collaboratively across disciplines
sage bionetworks

19.
a non-profit organization which pilots a
variety of components that are necessary
to build a scientific research commons
tool for
collaborative
science
re-imagined
informed
consent
patients
as
partners
sage bionetworks

20.
a non-profit organization which pilots a
variety of components that are necessary
to build a scientific research commons
enables sharing of all resources (data, code, results)
and their relationships to one another
provides mechanism to communicate in real time instead of
only at time of publication
supports open scientific collaborations for
clear, reproducible science
sage bionetworks

21.
a non-profit organization which pilots a
variety of components that are necessary
to build a scientific research commons
enables sharing of all resources (data, code, results)
and their relationships to one another
sage bionetworks

22.
tool for
collaborative
science
re-imagined
informed
consent
patients
as
partners
a non-profit organization which pilots a
variety of components that are necessary
to build a scientific research commons
sage bionetworks

23.
“biomedical research needs to empower patients with the
voice and the tools they need to manage their health,
understand their disease and partner in research”
a non-profit organization which pilots a
variety of components that are necessary
to build a scientific research commons
sage bionetworks
patients as partners

24.
a non-profit organization which pilots a
variety of components that are necessary
to build a scientific research commons
sage bionetworks
“participants will be provided real-time graphical
representations of their data, access to their own data at
will (to provide to healthcare professionals, donate to other
studies, etc.), and also research notifications when new
insights are available”
sharing two ways

25.
a non-profit organization which pilots a
variety of components that are necessary
to build a scientific research commons
sage bionetworks

26.
tool for
collaborative
science
re-imagined
informed
consent
patients
as
partners
a non-profit organization which pilots a
variety of components that are necessary
to build a scientific research commons
sage bionetworks

27.
a non-profit organization which pilots a
variety of components that are necessary
to build a scientific research commons
written by a doctor
reviewed by a lawyer
edited by a committee
sage bionetworks

28.
a non-profit organization which pilots a
variety of components that are necessary
to build a scientific research commons
interaction design prioritizes
the user and the experience
patient-centered consent (pcc) toolkit
sage bionetworks

29.
a non-profit organization which pilots a
variety of components that are necessary
to build a scientific research commons
deploy consent as a process via mobile, web
patient-centered consent (pcc) toolkit
sage bionetworks

30.
a non-profit organization which pilots a
variety of components that are necessary
to build a scientific research commons
assist informedness for complex documents
patient-centered consent (pcc) toolkit
sage bionetworks

31.
a non-profit organization which pilots a
variety of components that are necessary
to build a scientific research commons
nouns and verbs
patient-centered consent (pcc) toolkit
sage bionetworks

32.
a non-profit organization which pilots a
variety of components that are necessary
to build a scientific research commons
sentences via animation
patient-centered consent (pcc) toolkit
sage bionetworks

33.
sage bionetworks
metadata&
survey&
sensor&tasks&
wearables&
Consent&
Toolkit&
Bridge&
Server&
Synapse&
Stores&study&data&
Assigns&study&code&
De<iden=fies&&
Syndicates&
Consent&
Data&capture&
No=fica=ons&
Study<specific&folder&
Auto<deposit&aAer&embargo&period&
Authorized&users&

34.
a non-profit organization which pilots a
variety of components that are necessary
to build a scientific research commons
focused on a world where biomedical research
will fundamentally change to be
more open and collaborative
supports communities of researchers
working collaboratively across disciplines
sage bionetworks

35.
supports communities of researchers
working collaboratively across disciplines
end game is not collaboration

36.
supports communities of researchers
working collaboratively across disciplines
accelerate research

37.
supports communities of researchers
working collaboratively across disciplines
end disease

38.
supports communities of researchers
working collaboratively across disciplines
end breast cancer

39.
end breast cancer
incentives of the individual
don’t align with
greater goals of the field

40.
collaboration around common data
collaboration around common question

41.
“systematic exploration of the entire
spectrum of genomic changes involved in
more than 20 types of human cancer”

42.
TCGA Pan-Cancer Consortium
analysis of:
12 tumor types
6 molecular profiling platforms

43.
18NPG papers
68core projects
248researchers
28institutions
1070datasets
1723results
TCGA Pan-Cancer Consortium

44.
TCGA Pan-Cancer Consortium

45.
doi:10.7303/syn1710680.4
TCGA Pan-Cancer Consortium

46.
collaboration around common data
collaboration around common question

47.
CRC Subtyping Consortium

48.
A
B
C
D
E
F
1
2
3
4
5
6
CRC Subtyping Consortium

49.
A
B
C
D
E
F
1
2
3
4
5
6
...
CRC Subtyping Consortium

50.
collaborative analyses
cloud-based file storage
CRC Subtyping Consortium

51.
code associated
with results
CRC Subtyping Consortium

52.
CRC Subtyping Consortium

53.
collaboration around
common data and question

54.
public / private partnership between NIH,
10 biopharmaceutical companies
and several non-profit organizations
Accelerating Medicines Partnership

55.
Accelerating Medicines Partnership
($ Millions)
Total
Project
Total NIH
Total
Industry
Alzheimer’s
Disease
129.5 67.6 61.9
Type 2
Diabetes
58.4 30.4 28
Rheumatoid
Arthritis
41.6 20.9 20.7
TOTAL 229.5 118.9 110.6

56.
Accelerating Medicines Partnership
Target
Discovery
Target
Discovery
Target
Discovery
Target
Discovery
Target
Validation
Target
Validation
Target
Validation
Target
Validation
Shared
Information for
Target Identification
coordinate sharing of early-phase
target identification insights

57.
harmonize
incentives of the individual
with the greater goals of the field

58.
department of defense breast cancer research program
vision setting meeting 2015
brian m. bot
——————
brian.bot@sagebase.org
@BrianMBot
sage bionetworks
biomedical research in an
increasingly digital world