Text mining for chemistry and building a public platform for document markup Antony Williams

Searching and Reading Articles… Online search tools for chemistry articles are generally text-based Searching articles based on chemical structure and substructure is very expensive.. but is changing Text-mining is a “hot area” of research ….but what is public? What depends on public curation?

Online search tools for chemistry articles are generally text-based

Searching articles based on chemical structure and substructure is very expensive.. but is changing

Text-mining is a “hot area” of research ….but what is public? What depends on public curation?

Text-Based Search Tools Google Pubmed Google Scholar Publishers websites And 10s of other resources….

Google

Pubmed

Google Scholar

Publishers websites

And 10s of other resources….

Vancomycin Through PubChem

Vancomycin Text Searches Pubmed Google Scholar

Pubmed

Google Scholar

Online Structure Searching of Articles Some capabilities from publishers starting to show up

Some capabilities from publishers starting to show up

Publishers should adopt/add InChIs RSC and Nature Publishing Group have!

ChemMantis - Single Click Mark-up

Name-Structure Pairs

Converting Detected Names… Names are searched against a validated dictionary (this expands as ChemSpider is curated If not found then they are passed through a Name to Structure algorithm If they cannot convert then ChemSpider is searched for non-validated names

Names are searched against a validated dictionary (this expands as ChemSpider is curated

If not found then they are passed through a Name to Structure algorithm

If they cannot convert then ChemSpider is searched for non-validated names

RED Underline Non-validated, Cannot Convert through NTS “Names” can be added to Suppress List

“Names” can be added to Suppress List

BLUE Underline Name to Structure Converted

Deposit Structures

Entity Extraction built around modified algorithms from SureChem Optimized for “publications” Dictionaries for chemical entities, groups, reactions, elements, families, species… Dictionaries can be expanded – presently adding PDB

Entity Extraction built around modified algorithms from SureChem

Optimized for “publications”

Dictionaries for chemical entities, groups, reactions, elements, families, species…

Dictionaries can be expanded – presently adding PDB

Species..

What do you do with a markup system? Test it, Show it off and make it available… Tested on chemistry articles so why not HOST articles? …and create an online journal…

Test it, Show it off and make it available…

Tested on chemistry articles so why not HOST articles?

…and create an online journal…

The ChemSpider Journal

Open Access Community Journal

Deposit Article Import URL or Document Copy-Paste Markup

Import URL or Document

Copy-Paste

Markup

Copy-Paste Version Martin Walker Monthly Article

Chemical names

Names, Elements, Groups, Families

Outlinks

Mark Up Open Access Article

Online Journals and Live Data

A Community Resource of Spectra Spectra deposited on ChemSpider as “Open Data” are available to anybody to “Embed” in their articles, blogs, wikis etc

Spectra deposited on ChemSpider as “Open Data” are available to anybody to “Embed” in their articles, blogs, wikis etc

Present Dictionaries Chemical names - ChemSpider Validated Names Reactions - Wikipedia Named Reactions and RSC Reaction Ontology reactions Species – Wikipedia “species” To add – New Dictionaries PDB codes IUPAC Gold Book

Chemical names - ChemSpider Validated Names

Reactions - Wikipedia Named Reactions and RSC Reaction Ontology reactions

Species – Wikipedia “species”

To add – New Dictionaries

PDB codes

IUPAC Gold Book

Conclusions The internet enables chemistry – and at a reduced cost Web 2.0 is here and improving quality – to benefit 3.0 Question Quality! Crowdsourcing for expansion, curation and integration Classical models may die quite quickly – business models must change soon or fail Publishers – heed the profileration of InChIs for Chemistry

The internet enables chemistry – and at a reduced cost

Web 2.0 is here and improving quality – to benefit 3.0

Question Quality!

Crowdsourcing for expansion, curation and integration

Classical models may die quite quickly – business models must change soon or fail

Publishers – heed the profileration of InChIs for Chemistry