DeepLit WikiHyperGlossary: Connecting Documents to Data and Discourse

Michael A. Bauer, Andrew P. Cornell, Daniel Berleant, Robert E. Belford 08/17/2015 ACS National Meeting DIVISION: Division of Chemical Information SESSION: The Growing Impact of Openness in Chemistry: A Symposium in Honor of JC Bradley

Unprecedented access to Information

Libraries

Art Galleries Data Warehouses

Distant Locations

Browsers Vs. Burrowers

Connecting Documents to Data

ANY DOCUMENT

ENHANCED DOCUMENT

Video

Images

Expert Knowledge

Audio Overlay

Instantly a document of your choosing is connected to a wealth of information.

Links created

WHG Core

Content Management

User Management

WHG Database

Data Request to WHG

(JavaScript)

WHG Portlet Document

Parsing

Content Retrieval

Remote Content

MySQL

Click Event

Document

Processed

Populate

Submit

Privileged Access (Login)

Glossary

XML Bulk

Importing

Glossary/Term Management Portal

User Administration Portal

Open Access (Public)

Compare to Glossary

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WikiHyperGlossary (WHG)

Commitment to Open Source Software Architecture Tools  Perl   General purpose programming language.  

Catalyst   Model View Controller framework for the Perl language.  

ExtJS   JavaScript application framework for building interactive web applications.

MySQL   MySQL is an open source database management system.  

Integrated Applications  

JSmol   JSmol extends the Java-based molecular visualization applet Jmol (jmol.sourceforge.net) to an HTML5 JavaScript-only web app.  

JSME   JSME is a free molecule editor written in JavaScript.  

TinyMCE   TinyMCE is a platform independent web based Javascript HTML WYSIWYG editor module.  

Balloon  Balloon creates 3D atomic coordinates from molecular connectivity data via distance geometry and conformer ensembles using a multi-objective genetic algorithm.  

Web Services  ChemEdDL Models 360   http://www.chemeddl.org/ resources/models360/models.php  

ChemSpider  

ChemSpider is a free chemical structure database with access to a range of web services. http://www.chemspider.com/ •  SMILESToInChI (Convert Smiles to InChI) •  Convert (Uses OpenBabel Internally to convert) •  GetCompoundThumbnail •  SimpleSearch

CACTUS  This service resolves different chemical structure identifiers and allows converting a given structure identifier into another representation or structure identifier. http://cactus.nci.nih.gov/chemical/structure  

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Submit URL

Submit Text

WHG Start

WHG Processed Doc

Chemical

Definition

ChemSpider

JSME 2D

JSMOL 3D

Protein

Definition

JSMOL 3D

No Type

Definition

WHG Word Types

Definition ChemSpider Search

JsMol (3D) ChemEdDL JSME (2D)

Click “ozone”

Processed Text

WHG Portlets

Definition

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WHG Definition

Select Term (Chemical)

Query ChemEdDL

Display Enhanced JSmol

Display Basic JSmol

Jsmol Returned

Save Mol2 File

Mol2 file on WHG Server

ChemSpider* InChI->SMILES

Balloon (SMILES->mol2)

ChemSpider* InChI->InChI Key

Yes No

Yes No

3D Molecular Structure

2D Molecular Editor

Alter Structure

Submit

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C

D

Term and Glossary Management

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C

Edit Term Panel

<?xml version="1.0" encoding="UTF-8" standalone="yes"?> <dictionary xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"> <entry term="abiotic"> <definition>Not associated with living organisms. Synonymous with abiological.</definition> <type>No Type</type> <identifier></ identifier> </entry> <entry term="DDT"> <definition>p,p'-dichlorodiphenyltrichloroethane[4,4'-(2,2,2-trichloroethane-1,1-diyl)bis(chlorobenzene).</definition> <type>Chemical</type> <identifier>InChI=1S/C14H9Cl5/c15-11-5-1-9(2-6-11)13(14(17,18)19)10-3-7-12(16)8-4-10/h1-8,13H</ identifier> </entry> <entry term="3-alpha-HSD type 2"> <definition>A long 15 part Uniprot database definition would fit here).</definition> <type>Protein</type> <identifier>P42330</ identifier> </entry> </dictionary>

Bulk Upload

WikiHyperGlossary Integration

www.jikitou.com

Near Future

WHG DB

WikiHyperGlossary

getGlossaryList

pullGlossary

pushGlossary

MS Word

Authenticated User

GET

POST

WHG Services

Data Manipulation

HG

WHG Plugin

Education

Document Review

Glossary Hosting &

Generation Catalog Service

Journal Peer Review Tech Transfer

Legislative Review USPTO

MOOCs

Electronic Lab Notebooks

Online Textbooks

Catalogs

Publishers Information Literacy Service

Glossary Aggregation

Interactive Learning

Far Future

WikiHyperGlossary Additional Info

www.hyperglossary.org https://github.com/DeepLit/WHG

Contact Info § Robert Belford (rebelford@ualr.edu) § Michael Bauer (mbauer2@uams.edu)

Questions?