ICIC 2017: Open data in chemistry: the fast track to scientific content

InfoChem Copyright © 2017
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Dr. Josef EiblmaierICIC 2017, Heidelberg, Germany, October 24th
Open data in chemistry: the fast track to
scientific content
Dr. Josef Eiblmaier, Dr. Heinz Saller, Dr. Dorothee Geppert
Heidelberg, October 24th 2017
Outline

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Outline
» The project NERO 2
» PubChem
» A show case
» Relevance ranking
» Outlook: further opportunities
© cora / PIXELIO, www.pixelio.de
Outline

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2015: The Networked: Springer Chemistry Demonstrator
© Stephanie Hofschlaeger / pixelio.de
» Large scale automatic extraction of chemical
entities from SpringerLink documents
» Joint definition of output formats (inline and standoff
XML)
» Semantic enrichment of chemically relevant
SpringerLink documents (> 2,700 titles)
» Creation of a chemical registry including all
chemistry sources of Springer / InfoChem having
structural information
» Implementation of an online-demonstrator, Interlink
different data repositories via the chemical structure
The project NERO 2

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Discoverability and accessability Showcase data for SciGraph
» Position Springer Nature as a thoughtleader in Open Data
» Raise attractiveness of Springer Nature for authors
» Set the basis to enhance content and functionality of Springer Nature
» Strengthen our position in chemistry via Open Data
Project NERO 2 (Named Entity Recognition of Organic Compounds)
The project NERO 2

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The Content
Journal articles, Major Reference Works,
eBooks (1846 - 2017) from:
» Biomedical and Life Sciences
» Chemistry and Material Science
» Earth and Environmental Science
» Engineering
» Medicine
» Physics and Astronomy
Chemistry related journals
» Nature Communications
» Scientific Reports
» Nature Reviews Materials
» Nature Reviews Chemistry
» Nature Chemistry
» Nature Chemical Biology
The project NERO 2

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Concept
InChIKeys +
7-Chlor-1-methyl-5-phenyl-
3-hydro-1,4-benzodiazepin-2-on
The project NERO 2

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Results
Count Comment
Input documents 7,133,996
Selected SpringerLink subject
collections, 6 Nature journals
Documents containing significant
chemistry
3,981,327
Containing at least one compound
with relevance value > 0.1
Documents having a PMID 858,934 Also available via PubMed
Documents Open/free access 294,380
Unique chemical compounds 604,506
Compound -> DOI links 26,839,100
The project NERO 2

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Discoverability?
2.1 million SpringerLink
documents on PubMed
1.188 million visits on
SpringerLink
(July 2016) = 6%!
Only little Springer Nature content
(compounds) on PubChem
No significant traffic
generated from
PubChem!
The project NERO 2

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» 93,890,677 compounds
» 1,252,816 Bio assays
» 10,341 protein targets
» 22,104 gene targets
» On the order of 100k searches per day, via
API: 2 – 12M *
» 1.7 million monthly visits in last 3 months**
* Evan Bolton, Lead Scientist at NCBI, October 15th , 2017
** Natalia Manrique, Analyst in Market Intelligence SpringerNature
*** Noorden, Richard Van (27 March 2012). "Chemistry's web of data expands". Nature.
PubChem is the first major public database to connect
cheminformatics to bioinformatics and thereby provide a
unique information resource for pharmaceutical research.
(Steve Bryant, NIH)
PubChem is the largest known public repository of
biological and chemical data (Tudor I. Oprea (University of
New Mexico) )
PubChem is the world's largest free
chemical database ***
PubChem

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» 93,890,677 compounds
» 1,252,816 Bio assays
» 10,341 protein targets
» 22,104 gene targets
» On the order of 100k searches per day, via
API: 2 – 12M *
» 1.7 million monthly visits in last 3 months**
* Evan Bolton, Lead Scientist at NCBI, October 15th , 2017
** Natalia Manrique, Analyst in Market Intelligence SpringerNature
*** Noorden, Richard Van (27 March 2012). "Chemistry's web of data expands". Nature.
PubChem is the first major public database to connect
cheminformatics to bioinformatics and thereby provide a
unique information resource for pharmaceutical research.
(Steve Bryant, NIH)
PubChem is the largest known public repository of
biological and chemical data (Tudor I. Oprea (University of
New Mexico) )
PubChem is the world's largest free
chemical database ***
PubChem

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PubChem

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Literature information in PubChem: associations between PubChem records and scientific articles, Sunghwan Kim,corresponding author Paul A.
Thiessen, Tiejun Cheng, Bo Yu, Benjamin A. Shoemaker, Jiyao Wang, Evan E. Bolton, Yanli Wang, and Stephen H. Bryant, J Cheminform. 2016; 8: 32
PubChem

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Concept
604,506 NERO2 Compounds
extracted from SpringerLink and
nature.com documents
• InChIKeys
• DOIs (SpringerLink / Nature documents)
• relevance values
• journal titles
• article/chapter titles
• publication year
PubChem

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Concept
604,506 NERO2 Compounds
extracted from SpringerLink and
nature.com documents
• InChIKeys
• DOIs (SpringerLink / Nature documents)
• relevance values
• journal titles
• article/chapter titles
• publication year
Upload
Link to SpringerLink
Link to nature.com
Link to Biomed Central
PubChem

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Distribution of Documents and Compounds
PubChem

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PubChem

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3,981,327 documents / 604,506 compounds
PubChem

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Documents in PubMed? Open / Free Access?
3,981,327 documents
PubChem

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Novelty? Druglikeness?
604,506 compounds
* Compounds satisfied Lipinski's Rule of Five in evaluating druglikeness. (https://en.wikipedia.org/wiki/Lipinski%27s_rule_of_five)
PubChem

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Show Case Temozolomide
» Oral chemotherapy drug (brain tumor)
» ‘Temodar’ (Merck US)
» ‘Temcad’ (Cadila Pharmaceuticals)
A show case

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» ‘Temodar’ (Merck US): 233 hits
» ‘Temcad’ (Cadila Pharmaceuticals): 2 hits
» ‘Temozolomid’: (German INN): 608 hits
» ‘Temozolomide’: (English INN) 7,583 hits
» ‚85622-93-1‘: 7 hits
» ‚BPEGJWRSRHCHSN-UHFFFAOYSA-N ‘: 0 hits
» Methazolastone: (FDA SRS): 27 hits
A show case
Show Case Temozolomide

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A show case

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A show case

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A show case

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A show case

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A show case

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A show case

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A show case

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A show case

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A show case

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A show case

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A show case

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Relevance Ranking? Why?
?
Relevance ranking

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?
Relevance ranking

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Main questions
» Which are the most relevant compounds in one
article/chapter?
» Which are the most relevant articles/chapters
for a given compound?
Task
Add a relevance value to every unique structure
per document and create
InchIKey <-> DOI <-> RV triples
Relevance ranking

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The Algorithm
RV 𝑠, 𝑑 = 𝑆𝐹 ∙ 𝐼𝐷𝐹 + 𝐷𝑆 ∙ 𝐶𝑆
SF∙IDF structure frequency – inverse document frequency, 𝑆𝐹∙𝐼𝐷𝐹 =
𝑓(𝑠,𝑑)
𝑓 𝑤𝑜𝑟𝑑𝑠
(𝑑)
log
𝑁
𝑛 𝑠
f: #structure s in d; fwords: #words in d; N: #docs; ns: #docs with structure s
DS document structure
CS chemistry related contributions
Relevance ranking

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Challenges: Acronyms and Numbered Compounds
Acronyms:
“… specific bioactivity of (2S,3R)-3-amino-2-hydroxy-4-
phenylbutanic acid (AHPA) was measured …
in the following text only referred to as ‚AHPA‘
Numbered compounds:
“… preparation of 3-(tritylthio)propionic acid (6) is done
in a solution of …“
in the following text only referred to as ‚compound 6‘ or ‚6‘.
Relevance ranking

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Challenges: Ambiguities
Diethylazodicarboxylate
‚DEAD‘
Moexipril
Perdix ®
Hexen
(German)
Relevance ranking

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The Other Way Round: Which Chemicals are Important in 1 Article?
Effects of Sublethal Doses of Acetamiprid and Thiamethoxam on the Behavior of the
Honeybee (Apis mellifera)
Acetamiprid and thiamethoxam are insecticides introduced for pest control, but they can also affect non-target insects such
as honeybees. In insects, these neonicotinoid insecticides are known to act on acetylcholine nicotinic receptors but the
behavioral effects of low doses are not yet fully understood. The effects of acetamiprid and thiamethoxam were studied
after acute sublethal treatment on the behavior of the honeybee (Apis mellifera) under controlled laboratory conditions. The
drugs were either administered orally or applied topically on the thorax. After oral consumption acetamiprid increased
sensitivity to antennal stimulation by sucrose solutions at doses of 1 μg/bee and impaired long-term retention of olfactory
learning at the dose of 0.1 μg/bee. Acetamiprid thoracic application induced no effect in these behavioral assays but
increased locomotor activity (0.1 and 0.5 μg/bee) and water-induced proboscis extension reflex (0.1, 0.5, and 1 μg/bee).
Unlike acetamiprid, thiamethoxam had no effect on bees’ behavior under the conditions used. Our results suggest a
particular vulnerability of honeybee behavior to sublethal doses of acetamiprid.
Rank Name RV
1 acetamiprid 3.4422
2 thiamethoxam 2.6834
3 sucrose 0.9561
4 imidacloprid 0.4630 14 mentions in text, comparison
5 acetylcholine 0.3052
6 clothianidin 0.1245 3 mentions in text, metabolite of thiamethoxam
7 6-chloropyridine-3-carboxylicacid 0.0919
8 acetone 0.0537
9 phenylpyrazoles 0.0404
10 thiacloprid 0.0404
11 methyllycaconitine 0.0388
12 Fipronil 0.037
13 acetonitrile 0.033
14 nicotine 0.0199
Relevance ranking

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Relevance Ranking Verification
467 Springer articles from NERO1 were analyzed by chemistry subject matter experts
Quality of Relevance Ranking in 94 % good or okay
89%
5%
6%
good ok wrong
Relevance ranking

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Springer Nature SciGraph
www.springernature.com/scigraph

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Springer Nature SciGraph Data Landscape
Compounds
600K
www.springernature.com/scigraph

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» NIH
 Evan Bolton
 Jan Zhang
 Ben Shoemaker
 The PubChem Team
» Springer Nature
 Henning Schönenberger
 Markus Kaindl
 The SciGraph Team
» The InfoChem Team
Acknowledgements
© P. Storz / PIXELIO, www.pixelio.de

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InfoChem GmbH: www.infochem.de, www.spresi.com, info@infochem.de
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ICIC 2017: Open data in chemistry: the fast track to scientific content

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