The document discusses Sciwalker, a platform integrating open access and private data sources for life and material sciences, featuring normalized patents, scientific articles, and analytics tools. It includes a compound registration system along with a comprehensive database of unique molecules, compounds, and relevant ontologies for various scientific fields. Additionally, it highlights technology integration and data management capabilities, emphasizing fast data processing and visualization tools.

1. Nizza , April 8
SciWalker
integrating open access & private sources

2. Ontologies: we understand life and material sciences.
Data Streams: normalized patents, scientific articles (open source and behind
paywalls) & news etc.
Software & Analytics tools: indexing, extracting compound properties, combining
internal & external sources - documents, databases, linked data.
We support our customers by ...

3. Compound Registration
OC|processor - chemistry annotator
dictionary
WebAPI190000000809
if no
register
deliver OCID
and data
• provides chemistry registration system based on InChI
• unique, stable OCID
• substructure searchable (JChem SQL Database)
• synonyms & classification connected to OCID
• can be used for local compounds in DB’s or documents as well
is it known?… composition comprising a neonicotinoid
such as imidacloprid <190000000809> and a …
formula &
molpuzzler
name-2-
structure
image-2-
structure
class/group
classify
compound
store
other applications
[O-][N+](=O)NC1=NCCN1CC1=CC=C(Cl)N=C1

4. About 50.000 new compounds per month from new patents and articles
Growth of registered unique compounds

5. Compound Registration
your chemistry
WebAPI190000000809
if no
register
deliver OCID
and data
is it known?
[O-][N+](=O)NC1=NCCN1CC1=CC=C(Cl)N=C1
Call WebAPI client
compound
store
Get the client & description at our public FTP transfer.ontochem.com
User: Mievoogh pwd: phae9Goo
other applications
compound
database

6. ● Molecules: about 126 million unique InChI compounds from OntoChem registration server, 74 million
nucleotide and 11 million peptide sequences = 211 million unique molecules
○ OntoChem, PubChem, ChEMBL, Zinc, DssTox
○ Nucleotide sequences, protein and peptide sequences
● Ontologies - public OCID and hierarchy
○ anatomy, biomarker, chemistry, clinicalTrials, compound_classes, cosmetology, drugs, effects,
herbal_drugs, human_genes, inorganic_materials, institutions, magnitudes, methods,
natural_products, nutrition, proteins, regions, species, substances, toxicity
● Genes & Proteins
○ GWAS - Genome wide association studies, ClinVar
● Clinical & Drug Data
○ ClinicalTrials.gov, Drug Central, Drug labels
“SciWalker Open Data” in BigQuery

7. Use Examples

8. Data on
Sitagliptin ?
SciWalker + BigQuery
WebAPI
compound link-outs

9. Application structure changes
Qlik
Backend API
Middleware
Frontend
OIS API
Backend
OIS
Middleware
Looker
Tableau
Google API
BigQuery
Google Data
Studio
so far new
Integrity
COSMIC
GWAS
Text sources Databases
PMC
MedLine
Patents
Integrity
COSMIC
GWAS
Text sources Databases
PMC
MedLine
Patents
Frontend
BigQuery
your data

10. ● Technology integration:
○ Lucene or SQL indexes: speed with indexed data
○ BigQuery: fast sorting, deduplication and aggregation of non-indexed data
○ Seamless prototyping of OLAP search and visualization using Google Data Studio, Tableau,
Looker, Qlik …
● Data integration:
○ Faster integration of novel data sources
○ JOIN operations on different sources: public + third party + private data
○ Scalability and speed
○ BigQuery: large amount of open access data
Advantages of hybrid BigQuery architectures

11. sciwalker-open-data:sequences.proteins
seq = DRVYIHPF
Searching for patents with AT2 sequences in BQ

12. Q: What tetrazole containing drug candidates are in how many clinical trials for which diseases ?
A: from 303.973 published tetrazoles, 35 compounds were in 926 trials:
Answering pharma related questions

13. Ian Wetherbee
@Google
https://datastudio.
google.com/u/0/re
porting/1xKxWJ9R
TOaJCjjzrBgB2p_
s-
OstfCikt/page/M6y
j

14. Thanks to
Stephen Boyer, Collabra
Ian Wetherbee, Google
Aleksandar Kapisoda, Karlheinz Spenny, Boehringer-Ingelheim
Team, OntoChem