How the web has weaved a web of interlinked chemistry data final

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