Improving Online Chemistry One Structure at a Time fileMetabolic pathway databases ADME/Tox data...
Transcript of Improving Online Chemistry One Structure at a Time fileMetabolic pathway databases ADME/Tox data...
![Page 1: Improving Online Chemistry One Structure at a Time fileMetabolic pathway databases ADME/Tox data –eTOX for example Blogs/Wikis and Open Notebook Science Contributing Open Source](https://reader030.fdocuments.us/reader030/viewer/2022041222/5e0c0ed41767650c30300884/html5/thumbnails/1.jpg)
Improving Online Chemistry –
One Structure at a Time
Antony WilliamsAstraZeneca, February 10th 2012
![Page 2: Improving Online Chemistry One Structure at a Time fileMetabolic pathway databases ADME/Tox data –eTOX for example Blogs/Wikis and Open Notebook Science Contributing Open Source](https://reader030.fdocuments.us/reader030/viewer/2022041222/5e0c0ed41767650c30300884/html5/thumbnails/2.jpg)
We Have …Too Much Data!!!
![Page 3: Improving Online Chemistry One Structure at a Time fileMetabolic pathway databases ADME/Tox data –eTOX for example Blogs/Wikis and Open Notebook Science Contributing Open Source](https://reader030.fdocuments.us/reader030/viewer/2022041222/5e0c0ed41767650c30300884/html5/thumbnails/3.jpg)
It is so difficult to navigate…
What’s the
structure?
Are they in
our file?
What’s
similar?
What’s the
target?Pharmacology
data?
Known
Pathways?
Working On
Now?Connections
to disease?
Expressed in
right cell type?
Competitors?
IP?
![Page 4: Improving Online Chemistry One Structure at a Time fileMetabolic pathway databases ADME/Tox data –eTOX for example Blogs/Wikis and Open Notebook Science Contributing Open Source](https://reader030.fdocuments.us/reader030/viewer/2022041222/5e0c0ed41767650c30300884/html5/thumbnails/4.jpg)
Literature Patents NewsPipeline SAR CSRs SafetyIn vivo Etc
Pharma Information..and the web…
![Page 5: Improving Online Chemistry One Structure at a Time fileMetabolic pathway databases ADME/Tox data –eTOX for example Blogs/Wikis and Open Notebook Science Contributing Open Source](https://reader030.fdocuments.us/reader030/viewer/2022041222/5e0c0ed41767650c30300884/html5/thumbnails/5.jpg)
The World of Online Chemistry
Property databases
Compound aggregators
Screening assay results
Scientific publications
Encyclopedic articles (Wikipedia)
Metabolic pathway databases
ADME/Tox data – eTOX for example
Blogs/Wikis and Open Notebook Science
Contributing Open Source code to projects
![Page 6: Improving Online Chemistry One Structure at a Time fileMetabolic pathway databases ADME/Tox data –eTOX for example Blogs/Wikis and Open Notebook Science Contributing Open Source](https://reader030.fdocuments.us/reader030/viewer/2022041222/5e0c0ed41767650c30300884/html5/thumbnails/6.jpg)
PubChem
![Page 7: Improving Online Chemistry One Structure at a Time fileMetabolic pathway databases ADME/Tox data –eTOX for example Blogs/Wikis and Open Notebook Science Contributing Open Source](https://reader030.fdocuments.us/reader030/viewer/2022041222/5e0c0ed41767650c30300884/html5/thumbnails/7.jpg)
ChEMBL
![Page 8: Improving Online Chemistry One Structure at a Time fileMetabolic pathway databases ADME/Tox data –eTOX for example Blogs/Wikis and Open Notebook Science Contributing Open Source](https://reader030.fdocuments.us/reader030/viewer/2022041222/5e0c0ed41767650c30300884/html5/thumbnails/8.jpg)
Collaborative Knowledge Management
![Page 9: Improving Online Chemistry One Structure at a Time fileMetabolic pathway databases ADME/Tox data –eTOX for example Blogs/Wikis and Open Notebook Science Contributing Open Source](https://reader030.fdocuments.us/reader030/viewer/2022041222/5e0c0ed41767650c30300884/html5/thumbnails/9.jpg)
e-Science and Primary Data
How much data generated in a lab, that COULDgo public, is lost forever?
![Page 10: Improving Online Chemistry One Structure at a Time fileMetabolic pathway databases ADME/Tox data –eTOX for example Blogs/Wikis and Open Notebook Science Contributing Open Source](https://reader030.fdocuments.us/reader030/viewer/2022041222/5e0c0ed41767650c30300884/html5/thumbnails/10.jpg)
e-Science and Primary Data
How much data generated in a lab, that COULDgo public, is lost forever?
Public Domain reference databases of value?
Syntheses
Properties
Spectra
CIFs
Images
![Page 11: Improving Online Chemistry One Structure at a Time fileMetabolic pathway databases ADME/Tox data –eTOX for example Blogs/Wikis and Open Notebook Science Contributing Open Source](https://reader030.fdocuments.us/reader030/viewer/2022041222/5e0c0ed41767650c30300884/html5/thumbnails/11.jpg)
e-Science and Primary Data
How much data generated in a lab, that COULDgo public, is lost forever?
Public Domain reference databases of value?
Syntheses
Properties
Spectra
CIFs
Images
Much of chemistry is chemical structure-based –where and how could we host these data?
![Page 12: Improving Online Chemistry One Structure at a Time fileMetabolic pathway databases ADME/Tox data –eTOX for example Blogs/Wikis and Open Notebook Science Contributing Open Source](https://reader030.fdocuments.us/reader030/viewer/2022041222/5e0c0ed41767650c30300884/html5/thumbnails/12.jpg)
RSC’s ChemSpider
![Page 13: Improving Online Chemistry One Structure at a Time fileMetabolic pathway databases ADME/Tox data –eTOX for example Blogs/Wikis and Open Notebook Science Contributing Open Source](https://reader030.fdocuments.us/reader030/viewer/2022041222/5e0c0ed41767650c30300884/html5/thumbnails/13.jpg)
We Want to Answer Questions
Questions a chemist might ask…
What is the melting point of n-heptanol?
What is the chemical structure of Xanax?
Chemically, what is phenolphthalein?
What are the stereocenters of cholesterol?
Where can I find publications about xylene?
What are the different trade names for Ketoconazole?
What is the NMR spectrum of Aspirin?
What are the safety handling issues for Thymol Blue?
![Page 14: Improving Online Chemistry One Structure at a Time fileMetabolic pathway databases ADME/Tox data –eTOX for example Blogs/Wikis and Open Notebook Science Contributing Open Source](https://reader030.fdocuments.us/reader030/viewer/2022041222/5e0c0ed41767650c30300884/html5/thumbnails/14.jpg)
Available Information…
Linked to vendors, safety data, toxicity, metabolism
![Page 15: Improving Online Chemistry One Structure at a Time fileMetabolic pathway databases ADME/Tox data –eTOX for example Blogs/Wikis and Open Notebook Science Contributing Open Source](https://reader030.fdocuments.us/reader030/viewer/2022041222/5e0c0ed41767650c30300884/html5/thumbnails/15.jpg)
Available Information….
![Page 16: Improving Online Chemistry One Structure at a Time fileMetabolic pathway databases ADME/Tox data –eTOX for example Blogs/Wikis and Open Notebook Science Contributing Open Source](https://reader030.fdocuments.us/reader030/viewer/2022041222/5e0c0ed41767650c30300884/html5/thumbnails/16.jpg)
Crowdsourced “Annotations”
Users can add
Descriptions/Syntheses/Commentaries
Links to PubMed articles
Links to articles via DOIs
Add spectral data
Add Crystallographic Information Files
Add photos
Add MP3 files
Add Videos
![Page 17: Improving Online Chemistry One Structure at a Time fileMetabolic pathway databases ADME/Tox data –eTOX for example Blogs/Wikis and Open Notebook Science Contributing Open Source](https://reader030.fdocuments.us/reader030/viewer/2022041222/5e0c0ed41767650c30300884/html5/thumbnails/17.jpg)
![Page 18: Improving Online Chemistry One Structure at a Time fileMetabolic pathway databases ADME/Tox data –eTOX for example Blogs/Wikis and Open Notebook Science Contributing Open Source](https://reader030.fdocuments.us/reader030/viewer/2022041222/5e0c0ed41767650c30300884/html5/thumbnails/18.jpg)
Spectra
![Page 19: Improving Online Chemistry One Structure at a Time fileMetabolic pathway databases ADME/Tox data –eTOX for example Blogs/Wikis and Open Notebook Science Contributing Open Source](https://reader030.fdocuments.us/reader030/viewer/2022041222/5e0c0ed41767650c30300884/html5/thumbnails/19.jpg)
Data on the Web
![Page 20: Improving Online Chemistry One Structure at a Time fileMetabolic pathway databases ADME/Tox data –eTOX for example Blogs/Wikis and Open Notebook Science Contributing Open Source](https://reader030.fdocuments.us/reader030/viewer/2022041222/5e0c0ed41767650c30300884/html5/thumbnails/20.jpg)
![Page 21: Improving Online Chemistry One Structure at a Time fileMetabolic pathway databases ADME/Tox data –eTOX for example Blogs/Wikis and Open Notebook Science Contributing Open Source](https://reader030.fdocuments.us/reader030/viewer/2022041222/5e0c0ed41767650c30300884/html5/thumbnails/21.jpg)
Chemistry Data online is messy
We have inherited errors
All public compound databases, including ours, have errors
“Incorrect” structures – assertions, timelines etc
“Incorrect” names associated with structures
Properties
Links
Publications
ENORMOUS CHALLENGE
![Page 22: Improving Online Chemistry One Structure at a Time fileMetabolic pathway databases ADME/Tox data –eTOX for example Blogs/Wikis and Open Notebook Science Contributing Open Source](https://reader030.fdocuments.us/reader030/viewer/2022041222/5e0c0ed41767650c30300884/html5/thumbnails/22.jpg)
What could create change?
Harvard Business Review (2010)
“One change would make a substantial difference [to drug R&D]: the creation of
agreed-upon standards for digitally representing drug assets.”
Consider drug structures ONLY…
![Page 23: Improving Online Chemistry One Structure at a Time fileMetabolic pathway databases ADME/Tox data –eTOX for example Blogs/Wikis and Open Notebook Science Contributing Open Source](https://reader030.fdocuments.us/reader030/viewer/2022041222/5e0c0ed41767650c30300884/html5/thumbnails/23.jpg)
The Structure of Vitamin K?
![Page 24: Improving Online Chemistry One Structure at a Time fileMetabolic pathway databases ADME/Tox data –eTOX for example Blogs/Wikis and Open Notebook Science Contributing Open Source](https://reader030.fdocuments.us/reader030/viewer/2022041222/5e0c0ed41767650c30300884/html5/thumbnails/24.jpg)
MeSH
A lipid cofactor that is required for normal blood clotting. Several forms of vitamin K have been identified: VITAMIN K 1 (phytomenadione) derived from plants, VITAMIN K 2 (menaquinone) from bacteria, and synthetic naphthoquinone provitamins, VITAMIN K 3 (menadione). Vitamin K 3 provitamins, after being alkylated in vivo, exhibit the antifibrinolytic activity of vitamin K. Green leafy vegetables, liver, cheese, butter, and egg yolk are good sources of vitamin K
![Page 25: Improving Online Chemistry One Structure at a Time fileMetabolic pathway databases ADME/Tox data –eTOX for example Blogs/Wikis and Open Notebook Science Contributing Open Source](https://reader030.fdocuments.us/reader030/viewer/2022041222/5e0c0ed41767650c30300884/html5/thumbnails/25.jpg)
The Structure of Vitamin K1?
![Page 26: Improving Online Chemistry One Structure at a Time fileMetabolic pathway databases ADME/Tox data –eTOX for example Blogs/Wikis and Open Notebook Science Contributing Open Source](https://reader030.fdocuments.us/reader030/viewer/2022041222/5e0c0ed41767650c30300884/html5/thumbnails/26.jpg)
What is the Structure of Vitamin K1?
![Page 27: Improving Online Chemistry One Structure at a Time fileMetabolic pathway databases ADME/Tox data –eTOX for example Blogs/Wikis and Open Notebook Science Contributing Open Source](https://reader030.fdocuments.us/reader030/viewer/2022041222/5e0c0ed41767650c30300884/html5/thumbnails/27.jpg)
CAS’s Common Chemistry
![Page 28: Improving Online Chemistry One Structure at a Time fileMetabolic pathway databases ADME/Tox data –eTOX for example Blogs/Wikis and Open Notebook Science Contributing Open Source](https://reader030.fdocuments.us/reader030/viewer/2022041222/5e0c0ed41767650c30300884/html5/thumbnails/28.jpg)
Wikipedia
![Page 29: Improving Online Chemistry One Structure at a Time fileMetabolic pathway databases ADME/Tox data –eTOX for example Blogs/Wikis and Open Notebook Science Contributing Open Source](https://reader030.fdocuments.us/reader030/viewer/2022041222/5e0c0ed41767650c30300884/html5/thumbnails/29.jpg)
![Page 30: Improving Online Chemistry One Structure at a Time fileMetabolic pathway databases ADME/Tox data –eTOX for example Blogs/Wikis and Open Notebook Science Contributing Open Source](https://reader030.fdocuments.us/reader030/viewer/2022041222/5e0c0ed41767650c30300884/html5/thumbnails/30.jpg)
![Page 31: Improving Online Chemistry One Structure at a Time fileMetabolic pathway databases ADME/Tox data –eTOX for example Blogs/Wikis and Open Notebook Science Contributing Open Source](https://reader030.fdocuments.us/reader030/viewer/2022041222/5e0c0ed41767650c30300884/html5/thumbnails/31.jpg)
ChEBI – Manual Curation
![Page 32: Improving Online Chemistry One Structure at a Time fileMetabolic pathway databases ADME/Tox data –eTOX for example Blogs/Wikis and Open Notebook Science Contributing Open Source](https://reader030.fdocuments.us/reader030/viewer/2022041222/5e0c0ed41767650c30300884/html5/thumbnails/32.jpg)
![Page 33: Improving Online Chemistry One Structure at a Time fileMetabolic pathway databases ADME/Tox data –eTOX for example Blogs/Wikis and Open Notebook Science Contributing Open Source](https://reader030.fdocuments.us/reader030/viewer/2022041222/5e0c0ed41767650c30300884/html5/thumbnails/33.jpg)
![Page 34: Improving Online Chemistry One Structure at a Time fileMetabolic pathway databases ADME/Tox data –eTOX for example Blogs/Wikis and Open Notebook Science Contributing Open Source](https://reader030.fdocuments.us/reader030/viewer/2022041222/5e0c0ed41767650c30300884/html5/thumbnails/34.jpg)
![Page 35: Improving Online Chemistry One Structure at a Time fileMetabolic pathway databases ADME/Tox data –eTOX for example Blogs/Wikis and Open Notebook Science Contributing Open Source](https://reader030.fdocuments.us/reader030/viewer/2022041222/5e0c0ed41767650c30300884/html5/thumbnails/35.jpg)
“2-methyl-3-(3,7,11,15-tetramethylhexadec-2-enyl)naphthalene-1,4-dione”
Variants of systematic names on PubChem
2-methyl-3-[(E,7R,11R)-3,7,11,15-tetramethyl
2-methyl-3-[(E,7S,11R)-3,7,11,15-tetramethyl
2-methyl-3-[(E,7R,11S)-3,7,11,15-tetramethyl
2-methyl-3-[(E,7S,11S)-3,7,11,15-tetramethyl
2-methyl-3-[(E,11S)-3,7,11,15-tetramethyl
2-methyl-3-[(E)-3,7,11,15-tetramethyl
2-methyl-3-(3,7,11,15-tetramethyl
2-methyl-3-[(E)-3,7,11,15-tetramethyl
![Page 36: Improving Online Chemistry One Structure at a Time fileMetabolic pathway databases ADME/Tox data –eTOX for example Blogs/Wikis and Open Notebook Science Contributing Open Source](https://reader030.fdocuments.us/reader030/viewer/2022041222/5e0c0ed41767650c30300884/html5/thumbnails/36.jpg)
What’s Methane?
![Page 37: Improving Online Chemistry One Structure at a Time fileMetabolic pathway databases ADME/Tox data –eTOX for example Blogs/Wikis and Open Notebook Science Contributing Open Source](https://reader030.fdocuments.us/reader030/viewer/2022041222/5e0c0ed41767650c30300884/html5/thumbnails/37.jpg)
What’s Methane?
![Page 38: Improving Online Chemistry One Structure at a Time fileMetabolic pathway databases ADME/Tox data –eTOX for example Blogs/Wikis and Open Notebook Science Contributing Open Source](https://reader030.fdocuments.us/reader030/viewer/2022041222/5e0c0ed41767650c30300884/html5/thumbnails/38.jpg)
What ELSE is Methane???
![Page 39: Improving Online Chemistry One Structure at a Time fileMetabolic pathway databases ADME/Tox data –eTOX for example Blogs/Wikis and Open Notebook Science Contributing Open Source](https://reader030.fdocuments.us/reader030/viewer/2022041222/5e0c0ed41767650c30300884/html5/thumbnails/39.jpg)
![Page 40: Improving Online Chemistry One Structure at a Time fileMetabolic pathway databases ADME/Tox data –eTOX for example Blogs/Wikis and Open Notebook Science Contributing Open Source](https://reader030.fdocuments.us/reader030/viewer/2022041222/5e0c0ed41767650c30300884/html5/thumbnails/40.jpg)
EPA’s DailyMed
![Page 41: Improving Online Chemistry One Structure at a Time fileMetabolic pathway databases ADME/Tox data –eTOX for example Blogs/Wikis and Open Notebook Science Contributing Open Source](https://reader030.fdocuments.us/reader030/viewer/2022041222/5e0c0ed41767650c30300884/html5/thumbnails/41.jpg)
EPA’s DailyMed
![Page 42: Improving Online Chemistry One Structure at a Time fileMetabolic pathway databases ADME/Tox data –eTOX for example Blogs/Wikis and Open Notebook Science Contributing Open Source](https://reader030.fdocuments.us/reader030/viewer/2022041222/5e0c0ed41767650c30300884/html5/thumbnails/42.jpg)
EPA’s DailyMed
![Page 43: Improving Online Chemistry One Structure at a Time fileMetabolic pathway databases ADME/Tox data –eTOX for example Blogs/Wikis and Open Notebook Science Contributing Open Source](https://reader030.fdocuments.us/reader030/viewer/2022041222/5e0c0ed41767650c30300884/html5/thumbnails/43.jpg)
With Great Fanfare…
![Page 44: Improving Online Chemistry One Structure at a Time fileMetabolic pathway databases ADME/Tox data –eTOX for example Blogs/Wikis and Open Notebook Science Contributing Open Source](https://reader030.fdocuments.us/reader030/viewer/2022041222/5e0c0ed41767650c30300884/html5/thumbnails/44.jpg)
NPC Browser http://tripod.nih.gov/npc/
![Page 45: Improving Online Chemistry One Structure at a Time fileMetabolic pathway databases ADME/Tox data –eTOX for example Blogs/Wikis and Open Notebook Science Contributing Open Source](https://reader030.fdocuments.us/reader030/viewer/2022041222/5e0c0ed41767650c30300884/html5/thumbnails/45.jpg)
NPC Browser http://tripod.nih.gov/npc/
![Page 46: Improving Online Chemistry One Structure at a Time fileMetabolic pathway databases ADME/Tox data –eTOX for example Blogs/Wikis and Open Notebook Science Contributing Open Source](https://reader030.fdocuments.us/reader030/viewer/2022041222/5e0c0ed41767650c30300884/html5/thumbnails/46.jpg)
![Page 47: Improving Online Chemistry One Structure at a Time fileMetabolic pathway databases ADME/Tox data –eTOX for example Blogs/Wikis and Open Notebook Science Contributing Open Source](https://reader030.fdocuments.us/reader030/viewer/2022041222/5e0c0ed41767650c30300884/html5/thumbnails/47.jpg)
Openness and Quality IssuesWilliams and Ekins, DDT, 16: 747-750 (2011)
Science Translational Medicine 2011
![Page 48: Improving Online Chemistry One Structure at a Time fileMetabolic pathway databases ADME/Tox data –eTOX for example Blogs/Wikis and Open Notebook Science Contributing Open Source](https://reader030.fdocuments.us/reader030/viewer/2022041222/5e0c0ed41767650c30300884/html5/thumbnails/48.jpg)
Content is King and Quality Costs Curated Chemistry “content” is expensive to create
Patent searching
Structures and properties
Drug databases
Literature databases
Chemical Abstracts Service (CAS), the “Gold Standard” in Chemistry related information 104 years of content
>50 million substances
Proprietary platform
![Page 49: Improving Online Chemistry One Structure at a Time fileMetabolic pathway databases ADME/Tox data –eTOX for example Blogs/Wikis and Open Notebook Science Contributing Open Source](https://reader030.fdocuments.us/reader030/viewer/2022041222/5e0c0ed41767650c30300884/html5/thumbnails/49.jpg)
The EXPERTS must get it right?!
![Page 50: Improving Online Chemistry One Structure at a Time fileMetabolic pathway databases ADME/Tox data –eTOX for example Blogs/Wikis and Open Notebook Science Contributing Open Source](https://reader030.fdocuments.us/reader030/viewer/2022041222/5e0c0ed41767650c30300884/html5/thumbnails/50.jpg)
Wikipedia, C&E News, PubChemC&E News (from ACS)
![Page 51: Improving Online Chemistry One Structure at a Time fileMetabolic pathway databases ADME/Tox data –eTOX for example Blogs/Wikis and Open Notebook Science Contributing Open Source](https://reader030.fdocuments.us/reader030/viewer/2022041222/5e0c0ed41767650c30300884/html5/thumbnails/51.jpg)
Feedback from Steve Ritter
“Although CAS and C&EN are both part of the ACS Publications Division, we at C&EN still have to pay for our SciFinder access, strangely enough.”
“It would be nice to have an authoritative web-based source of standard, well-drawn structures for chemists to go to so they can freely cut and paste structures into their papers, PowerPoint presentations, and anything else they might need. Maybe Wikipedia will be that source one day.”
![Page 52: Improving Online Chemistry One Structure at a Time fileMetabolic pathway databases ADME/Tox data –eTOX for example Blogs/Wikis and Open Notebook Science Contributing Open Source](https://reader030.fdocuments.us/reader030/viewer/2022041222/5e0c0ed41767650c30300884/html5/thumbnails/52.jpg)
Public Domain Databases
Our databases are a mess…
Non-curated databases are proliferating errors
We source and deposit data between databases
Original sources of errors hard to determine
Curation is time-consuming and challenging
![Page 53: Improving Online Chemistry One Structure at a Time fileMetabolic pathway databases ADME/Tox data –eTOX for example Blogs/Wikis and Open Notebook Science Contributing Open Source](https://reader030.fdocuments.us/reader030/viewer/2022041222/5e0c0ed41767650c30300884/html5/thumbnails/53.jpg)
Stop Whining – Fix it
![Page 54: Improving Online Chemistry One Structure at a Time fileMetabolic pathway databases ADME/Tox data –eTOX for example Blogs/Wikis and Open Notebook Science Contributing Open Source](https://reader030.fdocuments.us/reader030/viewer/2022041222/5e0c0ed41767650c30300884/html5/thumbnails/54.jpg)
Crowdsourced Curation
Crowd-sourced curation: identify/tag errors, edit names, synonyms, identify records to deprecate
![Page 55: Improving Online Chemistry One Structure at a Time fileMetabolic pathway databases ADME/Tox data –eTOX for example Blogs/Wikis and Open Notebook Science Contributing Open Source](https://reader030.fdocuments.us/reader030/viewer/2022041222/5e0c0ed41767650c30300884/html5/thumbnails/55.jpg)
Search “Vitamin H”
![Page 56: Improving Online Chemistry One Structure at a Time fileMetabolic pathway databases ADME/Tox data –eTOX for example Blogs/Wikis and Open Notebook Science Contributing Open Source](https://reader030.fdocuments.us/reader030/viewer/2022041222/5e0c0ed41767650c30300884/html5/thumbnails/56.jpg)
“Curate” Identifiers
![Page 57: Improving Online Chemistry One Structure at a Time fileMetabolic pathway databases ADME/Tox data –eTOX for example Blogs/Wikis and Open Notebook Science Contributing Open Source](https://reader030.fdocuments.us/reader030/viewer/2022041222/5e0c0ed41767650c30300884/html5/thumbnails/57.jpg)
“Curate” Identifiers
![Page 58: Improving Online Chemistry One Structure at a Time fileMetabolic pathway databases ADME/Tox data –eTOX for example Blogs/Wikis and Open Notebook Science Contributing Open Source](https://reader030.fdocuments.us/reader030/viewer/2022041222/5e0c0ed41767650c30300884/html5/thumbnails/58.jpg)
“Curate” Identifiers
![Page 59: Improving Online Chemistry One Structure at a Time fileMetabolic pathway databases ADME/Tox data –eTOX for example Blogs/Wikis and Open Notebook Science Contributing Open Source](https://reader030.fdocuments.us/reader030/viewer/2022041222/5e0c0ed41767650c30300884/html5/thumbnails/59.jpg)
Standards : Structure Standardization
![Page 60: Improving Online Chemistry One Structure at a Time fileMetabolic pathway databases ADME/Tox data –eTOX for example Blogs/Wikis and Open Notebook Science Contributing Open Source](https://reader030.fdocuments.us/reader030/viewer/2022041222/5e0c0ed41767650c30300884/html5/thumbnails/60.jpg)
Standards : Structure Standardization
![Page 61: Improving Online Chemistry One Structure at a Time fileMetabolic pathway databases ADME/Tox data –eTOX for example Blogs/Wikis and Open Notebook Science Contributing Open Source](https://reader030.fdocuments.us/reader030/viewer/2022041222/5e0c0ed41767650c30300884/html5/thumbnails/61.jpg)
Standards : Structure Standardization
![Page 62: Improving Online Chemistry One Structure at a Time fileMetabolic pathway databases ADME/Tox data –eTOX for example Blogs/Wikis and Open Notebook Science Contributing Open Source](https://reader030.fdocuments.us/reader030/viewer/2022041222/5e0c0ed41767650c30300884/html5/thumbnails/62.jpg)
What needs to happen?
Standards
Standardization of structures ChEBI/PubChem sharing
InChI adoption
![Page 63: Improving Online Chemistry One Structure at a Time fileMetabolic pathway databases ADME/Tox data –eTOX for example Blogs/Wikis and Open Notebook Science Contributing Open Source](https://reader030.fdocuments.us/reader030/viewer/2022041222/5e0c0ed41767650c30300884/html5/thumbnails/63.jpg)
The InChI Identifier
![Page 64: Improving Online Chemistry One Structure at a Time fileMetabolic pathway databases ADME/Tox data –eTOX for example Blogs/Wikis and Open Notebook Science Contributing Open Source](https://reader030.fdocuments.us/reader030/viewer/2022041222/5e0c0ed41767650c30300884/html5/thumbnails/64.jpg)
Multiple Layers
![Page 65: Improving Online Chemistry One Structure at a Time fileMetabolic pathway databases ADME/Tox data –eTOX for example Blogs/Wikis and Open Notebook Science Contributing Open Source](https://reader030.fdocuments.us/reader030/viewer/2022041222/5e0c0ed41767650c30300884/html5/thumbnails/65.jpg)
InChIStrings Hash to InChIKeys
![Page 66: Improving Online Chemistry One Structure at a Time fileMetabolic pathway databases ADME/Tox data –eTOX for example Blogs/Wikis and Open Notebook Science Contributing Open Source](https://reader030.fdocuments.us/reader030/viewer/2022041222/5e0c0ed41767650c30300884/html5/thumbnails/66.jpg)
Vancomycin – Search the Internet
![Page 67: Improving Online Chemistry One Structure at a Time fileMetabolic pathway databases ADME/Tox data –eTOX for example Blogs/Wikis and Open Notebook Science Contributing Open Source](https://reader030.fdocuments.us/reader030/viewer/2022041222/5e0c0ed41767650c30300884/html5/thumbnails/67.jpg)
Vancomycin
Search Molecular
SKELETON
Search Full Molecule
![Page 68: Improving Online Chemistry One Structure at a Time fileMetabolic pathway databases ADME/Tox data –eTOX for example Blogs/Wikis and Open Notebook Science Contributing Open Source](https://reader030.fdocuments.us/reader030/viewer/2022041222/5e0c0ed41767650c30300884/html5/thumbnails/68.jpg)
Full Skeleton Search: 104 Hits
![Page 69: Improving Online Chemistry One Structure at a Time fileMetabolic pathway databases ADME/Tox data –eTOX for example Blogs/Wikis and Open Notebook Science Contributing Open Source](https://reader030.fdocuments.us/reader030/viewer/2022041222/5e0c0ed41767650c30300884/html5/thumbnails/69.jpg)
Full Molecule Search: 4 Hits
![Page 70: Improving Online Chemistry One Structure at a Time fileMetabolic pathway databases ADME/Tox data –eTOX for example Blogs/Wikis and Open Notebook Science Contributing Open Source](https://reader030.fdocuments.us/reader030/viewer/2022041222/5e0c0ed41767650c30300884/html5/thumbnails/70.jpg)
Crowdsourcing Works
>130 people have deposited data and participated in data curation
Different level curators check each other
More curators and depositors are encouraged!
![Page 71: Improving Online Chemistry One Structure at a Time fileMetabolic pathway databases ADME/Tox data –eTOX for example Blogs/Wikis and Open Notebook Science Contributing Open Source](https://reader030.fdocuments.us/reader030/viewer/2022041222/5e0c0ed41767650c30300884/html5/thumbnails/71.jpg)
What needs to happen?
Standards
Standardization of structures ChEBI/PubChem sharing
InChI adoption
Collaboration
Stop reinventing the wheel
Share data, share efforts and speed the process
![Page 72: Improving Online Chemistry One Structure at a Time fileMetabolic pathway databases ADME/Tox data –eTOX for example Blogs/Wikis and Open Notebook Science Contributing Open Source](https://reader030.fdocuments.us/reader030/viewer/2022041222/5e0c0ed41767650c30300884/html5/thumbnails/72.jpg)
Antony Williams vs Identifiers
Passport ID
Dad, Tony, others
SSN
Green Card
License5 email addresses
ChemSpiderman (blog,
Twitter account,
Facebook, Friendfeed)
OpenID
….
![Page 73: Improving Online Chemistry One Structure at a Time fileMetabolic pathway databases ADME/Tox data –eTOX for example Blogs/Wikis and Open Notebook Science Contributing Open Source](https://reader030.fdocuments.us/reader030/viewer/2022041222/5e0c0ed41767650c30300884/html5/thumbnails/73.jpg)
Aspirin names and synonyms
• Text searches depend on correct association
• 335 suggested identifiers for Aspirin just on PubChem!
• Disambiguation dictionaries are necessary, not just for authors!
![Page 74: Improving Online Chemistry One Structure at a Time fileMetabolic pathway databases ADME/Tox data –eTOX for example Blogs/Wikis and Open Notebook Science Contributing Open Source](https://reader030.fdocuments.us/reader030/viewer/2022041222/5e0c0ed41767650c30300884/html5/thumbnails/74.jpg)
![Page 75: Improving Online Chemistry One Structure at a Time fileMetabolic pathway databases ADME/Tox data –eTOX for example Blogs/Wikis and Open Notebook Science Contributing Open Source](https://reader030.fdocuments.us/reader030/viewer/2022041222/5e0c0ed41767650c30300884/html5/thumbnails/75.jpg)
The Final Search Strategy
![Page 76: Improving Online Chemistry One Structure at a Time fileMetabolic pathway databases ADME/Tox data –eTOX for example Blogs/Wikis and Open Notebook Science Contributing Open Source](https://reader030.fdocuments.us/reader030/viewer/2022041222/5e0c0ed41767650c30300884/html5/thumbnails/76.jpg)
All Those Names, One Structure
![Page 77: Improving Online Chemistry One Structure at a Time fileMetabolic pathway databases ADME/Tox data –eTOX for example Blogs/Wikis and Open Notebook Science Contributing Open Source](https://reader030.fdocuments.us/reader030/viewer/2022041222/5e0c0ed41767650c30300884/html5/thumbnails/77.jpg)
Curated Dictionaries Matter
![Page 78: Improving Online Chemistry One Structure at a Time fileMetabolic pathway databases ADME/Tox data –eTOX for example Blogs/Wikis and Open Notebook Science Contributing Open Source](https://reader030.fdocuments.us/reader030/viewer/2022041222/5e0c0ed41767650c30300884/html5/thumbnails/78.jpg)
Success Depends on Dictionaries
![Page 79: Improving Online Chemistry One Structure at a Time fileMetabolic pathway databases ADME/Tox data –eTOX for example Blogs/Wikis and Open Notebook Science Contributing Open Source](https://reader030.fdocuments.us/reader030/viewer/2022041222/5e0c0ed41767650c30300884/html5/thumbnails/79.jpg)
Validated Name-Structure Dictionaries
Chemical name dictionaries are used for: Text-mining (publications, patents)
Used to index PubMed and link to Google Patents
Linking to other databases – think Biology! When structures are not available drug names link
Searching the web Names link to structures link to InChIs
![Page 80: Improving Online Chemistry One Structure at a Time fileMetabolic pathway databases ADME/Tox data –eTOX for example Blogs/Wikis and Open Notebook Science Contributing Open Source](https://reader030.fdocuments.us/reader030/viewer/2022041222/5e0c0ed41767650c30300884/html5/thumbnails/80.jpg)
I want to know about “Vincristine”
If all algorithms work then
everything on the page is
correct by default except the
name-structure relationship!
![Page 81: Improving Online Chemistry One Structure at a Time fileMetabolic pathway databases ADME/Tox data –eTOX for example Blogs/Wikis and Open Notebook Science Contributing Open Source](https://reader030.fdocuments.us/reader030/viewer/2022041222/5e0c0ed41767650c30300884/html5/thumbnails/81.jpg)
Vincristine: Identifiers and Properties
![Page 82: Improving Online Chemistry One Structure at a Time fileMetabolic pathway databases ADME/Tox data –eTOX for example Blogs/Wikis and Open Notebook Science Contributing Open Source](https://reader030.fdocuments.us/reader030/viewer/2022041222/5e0c0ed41767650c30300884/html5/thumbnails/82.jpg)
Vincristine: PatentsLinked by Name
![Page 83: Improving Online Chemistry One Structure at a Time fileMetabolic pathway databases ADME/Tox data –eTOX for example Blogs/Wikis and Open Notebook Science Contributing Open Source](https://reader030.fdocuments.us/reader030/viewer/2022041222/5e0c0ed41767650c30300884/html5/thumbnails/83.jpg)
Vincristine: ArticlesLinked by Name
![Page 84: Improving Online Chemistry One Structure at a Time fileMetabolic pathway databases ADME/Tox data –eTOX for example Blogs/Wikis and Open Notebook Science Contributing Open Source](https://reader030.fdocuments.us/reader030/viewer/2022041222/5e0c0ed41767650c30300884/html5/thumbnails/84.jpg)
ChemSpider Everywhere:
What do computers want?
Web services
![Page 85: Improving Online Chemistry One Structure at a Time fileMetabolic pathway databases ADME/Tox data –eTOX for example Blogs/Wikis and Open Notebook Science Contributing Open Source](https://reader030.fdocuments.us/reader030/viewer/2022041222/5e0c0ed41767650c30300884/html5/thumbnails/85.jpg)
Mass Spec Analysis
![Page 86: Improving Online Chemistry One Structure at a Time fileMetabolic pathway databases ADME/Tox data –eTOX for example Blogs/Wikis and Open Notebook Science Contributing Open Source](https://reader030.fdocuments.us/reader030/viewer/2022041222/5e0c0ed41767650c30300884/html5/thumbnails/86.jpg)
ChemSpider Interface
![Page 87: Improving Online Chemistry One Structure at a Time fileMetabolic pathway databases ADME/Tox data –eTOX for example Blogs/Wikis and Open Notebook Science Contributing Open Source](https://reader030.fdocuments.us/reader030/viewer/2022041222/5e0c0ed41767650c30300884/html5/thumbnails/87.jpg)
![Page 88: Improving Online Chemistry One Structure at a Time fileMetabolic pathway databases ADME/Tox data –eTOX for example Blogs/Wikis and Open Notebook Science Contributing Open Source](https://reader030.fdocuments.us/reader030/viewer/2022041222/5e0c0ed41767650c30300884/html5/thumbnails/88.jpg)
Tinuvin 328
![Page 89: Improving Online Chemistry One Structure at a Time fileMetabolic pathway databases ADME/Tox data –eTOX for example Blogs/Wikis and Open Notebook Science Contributing Open Source](https://reader030.fdocuments.us/reader030/viewer/2022041222/5e0c0ed41767650c30300884/html5/thumbnails/89.jpg)
Position sorted by references
![Page 90: Improving Online Chemistry One Structure at a Time fileMetabolic pathway databases ADME/Tox data –eTOX for example Blogs/Wikis and Open Notebook Science Contributing Open Source](https://reader030.fdocuments.us/reader030/viewer/2022041222/5e0c0ed41767650c30300884/html5/thumbnails/90.jpg)
Position 1 only
![Page 91: Improving Online Chemistry One Structure at a Time fileMetabolic pathway databases ADME/Tox data –eTOX for example Blogs/Wikis and Open Notebook Science Contributing Open Source](https://reader030.fdocuments.us/reader030/viewer/2022041222/5e0c0ed41767650c30300884/html5/thumbnails/91.jpg)
Web Services
![Page 92: Improving Online Chemistry One Structure at a Time fileMetabolic pathway databases ADME/Tox data –eTOX for example Blogs/Wikis and Open Notebook Science Contributing Open Source](https://reader030.fdocuments.us/reader030/viewer/2022041222/5e0c0ed41767650c30300884/html5/thumbnails/92.jpg)
Web Services Open Up Collaboration
Agilent, Bruker, Waters and Thermo all use our web-based services for compound lookup
Many academic sites integrating directly –metabonomics, name lookup, semantic markup
Mobile app integration
Commercial structure drawing packages
![Page 93: Improving Online Chemistry One Structure at a Time fileMetabolic pathway databases ADME/Tox data –eTOX for example Blogs/Wikis and Open Notebook Science Contributing Open Source](https://reader030.fdocuments.us/reader030/viewer/2022041222/5e0c0ed41767650c30300884/html5/thumbnails/93.jpg)
ChemSpider Everywhere : Embed
![Page 94: Improving Online Chemistry One Structure at a Time fileMetabolic pathway databases ADME/Tox data –eTOX for example Blogs/Wikis and Open Notebook Science Contributing Open Source](https://reader030.fdocuments.us/reader030/viewer/2022041222/5e0c0ed41767650c30300884/html5/thumbnails/94.jpg)
ChemSpider Everywhere: Spectral Game
![Page 95: Improving Online Chemistry One Structure at a Time fileMetabolic pathway databases ADME/Tox data –eTOX for example Blogs/Wikis and Open Notebook Science Contributing Open Source](https://reader030.fdocuments.us/reader030/viewer/2022041222/5e0c0ed41767650c30300884/html5/thumbnails/95.jpg)
ChemSpider Everywhere
Crowdsourced Curation of Spectra
![Page 96: Improving Online Chemistry One Structure at a Time fileMetabolic pathway databases ADME/Tox data –eTOX for example Blogs/Wikis and Open Notebook Science Contributing Open Source](https://reader030.fdocuments.us/reader030/viewer/2022041222/5e0c0ed41767650c30300884/html5/thumbnails/96.jpg)
ChemSpider Everywhere : ChemMobi
![Page 97: Improving Online Chemistry One Structure at a Time fileMetabolic pathway databases ADME/Tox data –eTOX for example Blogs/Wikis and Open Notebook Science Contributing Open Source](https://reader030.fdocuments.us/reader030/viewer/2022041222/5e0c0ed41767650c30300884/html5/thumbnails/97.jpg)
Structure Database Lookup
![Page 98: Improving Online Chemistry One Structure at a Time fileMetabolic pathway databases ADME/Tox data –eTOX for example Blogs/Wikis and Open Notebook Science Contributing Open Source](https://reader030.fdocuments.us/reader030/viewer/2022041222/5e0c0ed41767650c30300884/html5/thumbnails/98.jpg)
ChemSpider Resources for Chemistry
![Page 99: Improving Online Chemistry One Structure at a Time fileMetabolic pathway databases ADME/Tox data –eTOX for example Blogs/Wikis and Open Notebook Science Contributing Open Source](https://reader030.fdocuments.us/reader030/viewer/2022041222/5e0c0ed41767650c30300884/html5/thumbnails/99.jpg)
It is so difficult to navigate…
What’s the
structure?
Are they in
our file?
What’s
similar?
What’s the
target?Pharmacology
data?
Known
Pathways?
Working On
Now?Connections
to disease?
Expressed in
right cell type?
Competitors?
IP?
![Page 100: Improving Online Chemistry One Structure at a Time fileMetabolic pathway databases ADME/Tox data –eTOX for example Blogs/Wikis and Open Notebook Science Contributing Open Source](https://reader030.fdocuments.us/reader030/viewer/2022041222/5e0c0ed41767650c30300884/html5/thumbnails/100.jpg)
Open PHACTS Project Develop a set of robust standards…
Implement the standards in a semantic integration hub
Deliver services to support drug discovery programs in pharma and public domain
22 partners, 8 pharmaceutical companies, 3 biotechs
36 months project
Guiding principle is open access, open usage, open source
- Key to standards adoption -
![Page 101: Improving Online Chemistry One Structure at a Time fileMetabolic pathway databases ADME/Tox data –eTOX for example Blogs/Wikis and Open Notebook Science Contributing Open Source](https://reader030.fdocuments.us/reader030/viewer/2022041222/5e0c0ed41767650c30300884/html5/thumbnails/101.jpg)
![Page 102: Improving Online Chemistry One Structure at a Time fileMetabolic pathway databases ADME/Tox data –eTOX for example Blogs/Wikis and Open Notebook Science Contributing Open Source](https://reader030.fdocuments.us/reader030/viewer/2022041222/5e0c0ed41767650c30300884/html5/thumbnails/102.jpg)
Internet Data
The Future
Commercial Software
Pre-competitive Data
Open Science
Open Data
Publishers
Educators
Open Databases
Chemical Vendors
Small organic molecules
Undefined materials
Organometallics
Nanomaterials
Polymers
Minerals
Particle bound
Links to Biologicals
![Page 103: Improving Online Chemistry One Structure at a Time fileMetabolic pathway databases ADME/Tox data –eTOX for example Blogs/Wikis and Open Notebook Science Contributing Open Source](https://reader030.fdocuments.us/reader030/viewer/2022041222/5e0c0ed41767650c30300884/html5/thumbnails/103.jpg)
The Future of Chemistry on the Web?
Public compound databases federate & build a linked environment of validated data!
Data validation needs are not ignored
Publishers layer on information to make publications discoverable
Public-Private databases can be linked
Open Data proliferate
The “Semantic Web” in action
![Page 104: Improving Online Chemistry One Structure at a Time fileMetabolic pathway databases ADME/Tox data –eTOX for example Blogs/Wikis and Open Notebook Science Contributing Open Source](https://reader030.fdocuments.us/reader030/viewer/2022041222/5e0c0ed41767650c30300884/html5/thumbnails/104.jpg)
Acknowledgments
The ChemSpider team
Our data providers, depositors, collaborators and curators
Software providers – OpenEye, ChemDoodle, ACD/Labs, GGA Software, Open Source (Jmol, JSpecView, OpenBabel)
![Page 105: Improving Online Chemistry One Structure at a Time fileMetabolic pathway databases ADME/Tox data –eTOX for example Blogs/Wikis and Open Notebook Science Contributing Open Source](https://reader030.fdocuments.us/reader030/viewer/2022041222/5e0c0ed41767650c30300884/html5/thumbnails/105.jpg)
Thank you
Email: [email protected]
Twitter: ChemConnector
Blog: www.chemspider.com/blog
Personal Blog: www.chemconnector.com
SLIDES: www.slideshare.net/AntonyWilliams