ChemXSeer

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Introduction

ChemXSeer is "an integrated digital library and database allowing for intelligent search of documents in the chemistry domain and data obtained from chemical kinetics"[1] that was designed by faculty, students, and researchers at Pennsylvania State University.[2] The database is freely accessible online, and the ChemXSeer website describes the following features of the tool:[1]

  • Chemical Entity Search: The tool identifies chemical formulae and chemical names, disambiguates the terms from other general terms, and tags them. Novel similarity scores, ranking functions and search methods are used to enable searching for chemical entities.
  • TableSeer: This tool automatically identifies tables in digital documents and extracts the contents in the cells of the tables. The contents are stored in a queryable table in a database. TableSeer extracts table metadata, and uses a novel ranking function to search for tables relevant to user queries.
  • Databases: Our data repository contains experimental data obtained from various sources. Our tools can process, store and link data in multiple formats, e.g., Excel, XML, Gaussian, and Charmm. A metadata add-on can help annotate the data and link multiple datasets.
Users can register to create an account on ChemXSeer, although all search functions and tools seem to be freely accessible without an account.

Use

From the homepage of ChemXSeer, users can access the following search forms and tools:

  • Search Keywords/Formulae/Name - Use a keyword search form to search through over 44,500 articles by keyword, chemical formula, or chemical name. Users can sort results by Citation, year, or recency, and they can also choose to conduct the search in other search engines (Google Scholar, Yahoo!, Ask, etc). Full record views include a link to the PDF version of the full-text articles, citations, abstract, chemical formulas, and a list of chemical names identified.
  • Table Tools - Table Search (currently not available) and Table Extractor. The current version of Table Extractor "does not support the reversed tables, image tables, and a part of tables with the below captions."[3]
  • Search Data - Search data through a keyword form (name or formula), Gaussian search form (select elements from periodic table), a CHARMM Calculation search form, or select specific data tables and attributes to view through the "Database Viewer" option. From the homepage menu, users can also access a keyword search form to search Excel data ("Kinetics Database" search option) and an "All Types" form that searches all calculation data.
  • Upload Data Files - Upload files from your personal computer to ChemXSeer.
  • Tools - Download the Excel Add-in Tool for ChemXSeer (versions for Windows and MAC).
  • Publications - View PDF versions of publications by researchers working on ChemXSeer.


Sources

  1. 1.0 1.1 "About ChemXSeer." ChemXSeer website, http://chemxseer.ist.psu.edu/about/index.html. Accessed September 21, 2011.
  2. "Project Personnel." ChemXSeer website, http://chemxseer.ist.psu.edu/about/personnel.html. Accessed September 21, 2011.
  3. "ChemXSeer Table Data and Metadata Extraction - Alpha." ChemXSeer website, http://chemxseer.ist.psu.edu/ChemXSeerTableExtractor/TableExtractorServlet. Accessed September 21, 2011.

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