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
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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
A
B
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
A
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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
A B
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>