An invited talk for Lilly's Global IT Seminar Meeting In November 2016 on the subject of data, machine learning, AI, semantic web, text mining and spinach!

1. Data: The Good, The Bad
& The Ugly
Lee Harland
@SciBitely
http://www.scibite.com
http://www.slideshare.net/scibitely
Lee Harland
Lilly Global IT Meeting November 2016

2. Context
• This is an invited talk I gave at Lilly’s Internal Global IT meeting on the
subject of “data”

3. The Good

4. http://www.nejm.org/doi/full/10.1056/NEJMp1606181

8. What matters to me!

9. The Bad

10. + =
…. (Promotion of) the nutritional importance of spinach over
other foods, lead to an increase of over 30 per cent in its
consumption during the 1920s and 30s.
The action of S. Oleracea on cardiovascular
output and muscular tone

11. Bad, Bad Data Point
1870 35.2 mg Fe/100g
1937 3.52 mg Fe/100g
The mythical strength-giving properties of
spinach are ... credited to a simple mistake
concerning the iron content of the vegetable.
In 1870, Dr E von Wolf published figures
which were accepted until the 1930s, when
they were rechecked
This revealed that a decimal point had been
placed wrongly and that the real figure was
only one tenth of Dr von Wolf's claim

12. Still Making Headlines After 140 Years
2013

13. There Is No
Decimal Point
Error

14. X X

15. X

16. Spinach: One Small Data Point, One Huge Mess
1870 35.2 mg Fe/100g
1937 3.52 mg Fe/100g
✓
✓
Both Values Are Correct – The difference is down to the assay conditions

17. http://www.merriam-webster.com/dictionary/provenance

18. 35.2
35.2
The datapoint + its provenance
(experimental context)
What people saw

19. So What?

20. ……estimates for the reproducibility of preclinical research range
from 51 percent to 89 percent. They estimate that at least half of
all U.S. preclinical biomedical research funding—about
$28 billion annually—is therefore squandered……
http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1002165

21. http://www.merriam-webster.com/dictionary/provenance

22. Provenance Is A Critical Component of Reproducibility
What L cells, where from,
how old, epigenetic profile
etc etc?
When, how often, in what
way, using what
system?????
What, when, how?
Could you accurately reproduce this experiment from this method?
* I was responsible for
this paragraph

23. http://www.nature.com/nrd/journal/v10/n9/full/nrd3439-c1.html
A first-of-a-kind analysis of Bayer's internal efforts to validate 'new drug
target' claims now not only supports this view but suggests that 50%
may be an underestimate; the company's in-house
experimental data do not match literature claims in
65% of target-validation projects, leading to project
discontinuation.

24. This is where
Informatics & Data
Science can add real
value to
Drug Discovery

25. Open PHACTS https://www.openphacts.org/

26. Open PHACTS: Adding Provenance To Data
http://nanopub.org/

27. .sub:Head {
this: np:hasAssertion sub:assertion ;
np:hasProvenance sub:provenance ;
np:hasPublicationInfo sub:pubinfo ;
a np:Nanopublication .
}
sub:assertion {
nx:NX_P35712 bfo:BFO_0000066 ts:TS-0276 ; # Protein NX_P35712 is localized in tissue TS-0276
ro:has_quality "positive" .
}
sub:provenance {
<http://www.nextprot.org/help/quality_criteria/silver> a eco:ECO_0000205 ;
rdfs:label "neXtProt silver"^^xsd:string .
sub:_1 a efo:EFO_00027688 .
sub:_10 a eco:ECO_0000218 .
sub:_2 a eco:ECO_0000218 .
sub:_9 a efo:EFO_00027688 .
sub:assertion prv:usedData <http://bgee.unil.ch/bgee/bgee?page=expression&action=data&stage_id=HsapDO:0000087&amp;organ_id=EV:0100115&amp;gene_id=ENSG00000110693> ,
<http://bgee.unil.ch/bgee/bgee?page=expression&action=data&stage_id=HsapDO:0000088&amp;organ_id=EV:0100115&amp;gene_id=ENSG00000110693> ,
<http://bgee.unil.ch/bgee/bgee?page=expression&action=data&stage_id=HsapDO:0000090&amp;organ_id=EV:0100115&amp;gene_id=ENSG00000110693&amp;stage_children=on> ,
<http://bgee.unil.ch/bgee/bgee?page=expression&action=data&stage_id=HsapDO:0000092&amp;organ_id=EV:0100115&amp;gene_id=ENSG00000110693&amp;stage_children=on> ,
<http://bgee.unil.ch/bgee/bgee?page=expression&action=data&stage_id=HsapDO:0000094&amp;organ_id=EV:0100115&amp;gene_id=ENSG00000110693&amp;stage_children=on> ;
wi:evidence <http://www.nextprot.org/help/quality_criteria/silver> ;
a eco:ECO_0000220 ;
rdfs:comment " data, NX_P35712 is expressed in Endometrium"^^xsd:string ;
prov:wasDerivedFrom sub:_1 , sub:_3 , sub:_5 , sub:_7 , sub:_9 ;
prov:wasGeneratedBy sub:_10 , sub:_2 , sub:_4 , sub:_6 , sub:_8 .
}
sub:pubinfo {
sub:_11 a eco:ECO_0000205 .
sub:_12 a eco:ECO_0000205 . sub:_15 a eco:ECO_0000205 .
this: dcterms:created "2014-09-19T00:00:00.0Z"^^xsd:dateTime ;
dcterms:rights <http://creativecommons.org/licenses/by/3.0/> ;
dcterms:rightsHolder <http://nextprot.org> ;
prv:usedData "neXtProt database" ;
pav:authoredBy "CALIPHO project" , <http://orcid.org/0000-0001-6710-1373> , <http://orcid.org/0000-0001-6818-334X> , <http://orcid.org/0000-0002-1303-2189> , <http://orcid.org/0000-0003-1813-6857> ;
pav:versionNumber "3" ;
prov:wasGeneratedBy sub:_11 , sub:_12 , sub:_13 , sub:_14 , sub:_15 .
}
http://nanopub.org

28. https://explorer.openphacts.org

29. One of the few user interfaces where provenance is intrinsically “there”

30. The Ugly

31. 80-90% of all potentially
usable business information
may originate in
unstructured form
https://en.wikipedia.org/wiki/Unstructured_data
The Ugly

32. “Carboxypeptidase B2” “Thrombin-Activatable
Fibrinolysis Inhibitor”
“Plasma CPU”
The True Picture
(they are the same thing)

33. It hasn’t just got 3 names its got LOTS
carboxypeptidase B-like protein OR thrombin-activatable fibrinolysis
inhibitor OR CPB type 2 OR Carboxypeptidase type B2 OR
plasma carboxypeptidase type B OR carboxypeptidase type B2 OR
CPB2 OR Plasma carboxypeptidase type B OR CPB-2 OR
carboxypeptidase B2 (plasma),carboxypeptidase U OR
Carboxypeptidase type U OR carboxypeptidase type U OR plasma
carboxypeptidase B2 OR carboxy-peptidylase U OR thrombin-
activable fibrinolysis inhibitor OR plasma carboxypeptidase type
B2 OR carboxypeptidase B2 (plasma OR CPU OR
carboxypeptidase B2 OR PCPB OR pCPB OR Carboxypeptidase U
OR plasma carboxypeptidase B OR TAFI OR Carboxypeptidase B2
OR Plasma carboxypeptidase B OR Thrombin-activable
fibrinolysis inhibitor OR carboxypeptidase B2 plasma OR
carboxypeptidase R

34. “We also manually standardized
data related to lab measurement
units and terminology related to
patient race and ethnicity,
geographical study regions, and
names of drugs and drug
families. “
Yet Another Issue

35. (an accident waiting to happen)

36. VARCHAR2
PROJ_TITLE
EXPERIMENT_INFO
ASSAY_DESCRIPTION
KEYWORDS
USER_PROFILE SUMMARY
EXPT_METADATA
SETTINGS_INFO
REPORT_TEXT
EXPT_NAME
Databases: Where Knowledge Goes To Die
MEETING_MINUTES
PROJ_ACTIONS
ASSAY_CONLCUSION
COHORT_DESC
INCLUSION_CRITERIA
POLICY_DETAILS
PROJECT_OVERVIEW
RATIONALE
JUSTIFICATION

37. Text2Data MicroService
TERMite
Supports basic
keyword search only
TEXT Rich substrate for search
and discovery & insight
DATA

38. Just What Is “The Data”?
•Mentions of all
• Genes, Diseases, Drugs, Tissues, Cells, Techniques,
Assays, Measures, Protocols, Compounds, Regimens,
Companies, People, Locations, Pathologies, Adverse
Events, Pathways, Metabolism, Manufacturing Concepts,
QC/QA, Pathogens, Strains, Animals … and so on...
•… And their relationships to each other
•… And their locations (section, database column)
•… Inferring relationships between documents/entries
•… Regardless of actual keyword used

39. Systems Integration Guide
http://yourcompany.com/termite?
text=<content>
app=<application name>
index=<e.g. page, table or column name>

40. ELN
Screening
Registry
PDM
Registry
Project
Management
Sharepoint
Whats going on, right now

41. Trending Today

44. Why Give Ugly Data A Makeover?
• ELN annotation using Bioassay Ontology
• Find all experiments using any Cell Flourescence technique”
• Pharmacovigilance
• Monitoring newsfeeds & internal data for safety signals
• Automatic Process Notification
• Alert groups based on content of CRO documents Etc
• Synergise Both Semantic Technology & Information Professionals
• Re-energise Therapeutic Area Literature Searching
• Build Knowledge Chains (Assertional Provenance)
• Project Management à ELN Data à Screen SOP

45. Before I go…..

46. Spinach: The Truth Is Out There!
Spinach is high
in iron (!)
..oxalic acid in spinach prevents
more than 90% of iron from being
absorbed..
Acknowledgement

47. Acknowledgements
IMI Open PHACTS Team
(many more involved, I just
don’t have a photo L )
http://openphacts.org
SciBite Team
http://scibite.com