How the Web Has Weaved a Web of Interlinked Chemistry Data Antony Williams ACS Anaheim March 29 th 2011
How the web has weaved a web of interlinked chemistry data final
Jan 20, 2015
The internet has provided access to unprecedented quantities of data. In the domain of chemistry specifically over the past decade the web has become populated with tens of millions of chemical structures and related properties of assays together with tens of thousands of spectra and syntheses. The data have, to a large extent, remained disparate and disconnected. In recent years with the wave of Web 2.0 participation any chemist can contribute to both the sharing and validation of chemistry-related data whether it be via Wikipedia, the online encyclopedia, or one of the multiple public compound databases. The presentation will offer a perspective of what is available today, our experiences of building a public compound database to link together the internet and a suggested path forward for enabling even greater integration and connectivity for chemistry data for the masses to both use and participate in developing.
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How the Web Has Weaved a Web of Interlinked Chemistry Data
Antony WilliamsACS Anaheim March 29th 2011
Data on the Web
Where is Chemistry Online? Property databases Compound aggregators Screening assay results Scientific publications Encyclopedic articles (Wikipedia) Metabolic pathway databases ADME/Tox data Blogs/Wikis and Open Notebook Science Contributing Open Source code to projects
How to Connect Chemicals…
Chemistry on the Internet
100s of websites serving up chemistry data, SDF files of structures and data
RSC’s ChemSpider “links” chemistry on the internet Over 25 million compounds, over 400 data sources Allows community deposition, curation, annotation Integrating properties, publications, patents, media Text, structure, substructure, similarity searching
www.chemspider.com
Search for a Chemical
We Have Delivered the Vision
“Build a Structure Centric Community toServe Chemists”
Integrate chemical structure data on the web
How Did We Build It? We deal in Molfiles or SDF files
We do rudimentary filtering prior to deposition – valence checking, charge imbalance etc.
We have our own “business logic” to standardize
We use InChI to “aggregate tautomers”
Link out to external sites where possible using IDs
Inherited Errors
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
The Structure of Vitamin K?
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
The Structure of Vitamin K1?
What is the Structure of Vitamin K1?
CAS’s Common Chemistry
Wikipedia
ChEBI – Manual Curation
PubChem
“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
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
Consider searching each of these chemical databases by chemical name (systematic name, trade name or synonym). Please mark each online resource according to how much you generally trust the results.
To report at Denver ACS…
An examination of quality in databases – inter/intra lab comparison of processes for 150 drugs
Five separate organizations, 8 individuals
The Wikipedia List of the “200 Top Selling Drugs”
Vytorin: Ezetimibe/Simvastatin
Vytorin: Ezetimibe/Simvastatin
Vytorin: Ezetimibe/Simvastatin
Vytorin: Ezetimibe/Simvastatin
Vytorin: Ezetimibe/Simvastatin
Taxol: Paclitaxel 44 structures
Taxol: Paclitaxel Bioassay Data
Taxol: Paclitaxel Bioassay Data
Most Bioassay data associated with structure with one ambiguous stereocenter
Drug Name Generic Name ChEBI ChemSpiderCAS Com.
Chem ChemIDPlus DailyMed DrugBank PubChem Wikipedia
SpirivaTiotropium Bromide
No Hits No Hits 4/0
DepakoteValproate semisodium No
Structure
Basen Voglibose No Hits No Hits 2/1 Symbicort 1) Budesonide 8/1 Symbicort 2) Formoterol WRONG No Hits 6/1 Vytorin 1) Ezetimibe No Hits Vytorin 2) Simvastatin 2/1 Taxol Paclitaxel 44/1 Thalidomid Thalidomide No Hits Zocor Simvastatin 2/1 Crestor Rosuvastatin No Hits 2/1
Entity-Extraction and Mark-up
Entity-Extraction and Mark-up
Success Depends on Dictionaries
Nature Chemistry
RSC Prospect
Validated “Dictionaries”
The following resources do NOT have structures to link to ChemSpider…but are linked:
Google Scholar PubMed DailyMed RSC Databases and Backfile
How did we link these resources to ChemSpider? Validated Name Look-up!
Extend the Vision
“Build a Structure Centric Community toServe Chemists”
Integrate chemical structure data on the web Create a “structure-based hub” to information,
data and algorithmic predictions
Integrate other services..
We will integrate to systems of values to the community
Many interfaces now available for integration NMRShiftDB ACD/Labs Name Generation ChemAxon Chemicalize What others???
Extend the Vision
“Build a Structure Centric Community toServe Chemists”
Integrate chemical structure data on the web Create a “structure-based hub” to information,
data and algorithmic predictions Let chemists contribute their own data Allow the community to curate/correct data
How Did We Build It (cont.)
Ask users to 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
Complex Data and Information
Kind Contributions!
Crowdsourcing “Vitamin H”
“Curate” Identifiers
“Curate” Identifiers
Crowdsourcing Works
>130 people have deposited data and participated in data curation
Different level curators check each other
More curators and depositors are encouraged!
Accessibility and Reuse
It’s a shame to go it alone!!!
Can we “collectively” improve the quality of chemistry on the Internet?
All DBs should take comments!
Proof-of-concept curation sharing
Presently collaborating with DrugBank to enable “curation sharing”
Setting up services for monitoring curations and edits – starting with “identifiers”
The Social Network
Career-wise NOT having a personal presence online will be a detriment Self-marketing Establishing a profile Getting on the record Collaborative Science Demonstrating a skill set Measured using alternative metrics Contributing to the public peer review process
Social Networking Tools
A growing number of social networking tools:
Facebook Twitter Linked-In Flickr YouTube Blogs Communities Collaborative environments
Chemistry Social Networking
Methods of sharing MY chemistry online include: Wikis or blogs Slideshare for presentations YouTube for videos Flickr, Wikimedia etc. for images PubChem for assay data NMRShiftDB for NMR assignments GoogleDocs for data
Drivers in the Social Network Anonymity is a choice in the social networks
Anonymity in peer-review will likely become less important and may be generational
I may want acknowledgment if… I share my data I review a paper I share my expertise
The Alt-Metrics Manifesto
http://altmetrics.org/manifesto/
Enabled by ORCID…
What will enhance OUR network?
The “semantic web”
Mobile technologies
More participation
Use of standards: JCAMP, InChI
RDF and the semantic web
Using RDF permalinks
http://www.chemspider.com/Chemical-Structure.7787.rdf
Using a Search Term
http://www.chemspider.com/rdf.ashx?q=cyclohexane
http://rdf.chemspider.com/cyclohexane
Enabled through InChIs
Mobile Support
Licensing “My Work” Online The complex nature of licensing “my” chemistry
Blogs - copyrighted and creative commons Wikis - mixed licensing, depends on the host(s) Data – much value in sharing data as “Open Data”
Often, people can make money from your work!
Police your own “licensing” – how many people have read the Facebook and Twitter agreements?!
Who declares data as Open? Data licensing is very interesting and can spark
“interesting” conversations. Opinions differ: Are images data? Are assertions data? What on a ChemSpider record is data?
We allow people to declare their data as Open and add an Open Data button at upload
Acknowledgments
RSC|ChemSpider team All data source providers >100 curators and annotators, and growing… Service providers:
ACD/Labs ChemAxon GGA Software Services Google PubMed ….
ChemSpider Training Session
ChemSpider: A Community Resource for Chemical Data
Wednesday, March 30th
8:30-11:00 AM
Anaheim Convention Center, Room 211 A
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