We report on the Gaussian file search system designed as part of the ChemXSeer digital library. Gaussian files are produced by the Gaussian software [4], a software package used for calculating molecular electronic structure and properties. The output files are semi-structured, allowing relatively easy access to the Gaussian attributes and metadata. Our system is currently capable of searching Gaussian documents using a boolean combination of atoms (chemical elements) and attributes. We have also implemented a faceted browsing feature on three important Gaussian attribute types - Basis Set, Job Type and Method Used. The faceted browsing feature enables a user to view and process a smaller, filtered subset of documents.
Among other purely chemistry-domain digital libraries, OREChem ChemXSeer by Li, et al @cite_4 integrates semantic web technology with the basic ChemXSeer framework. The Chemical Education Digital Library @cite_5 and the JCE (Journal of Chemical Education) Digital Library @cite_6 focus on organizing instructional and educational materials in Chemistry. Both these projects are supported by NSF under the National Science Digital Library (NSDL). In contrast with these studies, our focus here is to design a search functionality on Gaussian files that helps domain experts locate attribute information more easily.
@cite_5 @cite_4 @cite_6
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Representing the semantics of unstructured scientific publications will certainly facilitate access and search and hopefully lead to new discoveries. However, current digital libraries are usually limited to classic flat structured metadata even for scientific publications that potentially contain rich semantic metadata. In addition, how to search the scientific literature of linked semantic metadata is an open problem. We have developed a semantic digital library oreChem ChemxSeer that models chemistry papers with semantic metadata. It stores and indexes extracted metadata from a chemistry paper repository Chemx Seer using "compound objects". We use the Open Archives Initiative Object Reuse and Exchange (OAI-ORE) (http: www.openarchives.org ore standard to define a compound object that aggregates metadata fields related to a digital object. Aggregated metadata can be managed and retrieved easily as one unit resulting in improved ease-of-use and has the potential to improve the semantic interpretation of shared data. We show how metadata can be extracted from documents and aggregated using OAI-ORE. ORE objects are created on demand; thus, we are able to search for a set of linked metadata with one query. We were also able to model new types of metadata easily. For example, chemists are especially interested in finding information related to experiments in documents. We show how paragraphs containing experiment information in chemistry papers can be extracted and tagged based on a chemistry ontology with 470 classes, and then represented in ORE along with other document-related metadata. Our algorithm uses a classifier with features that are words that are typically only used to describe experiments, such as "apparatus", "prepare", etc. Using a dataset comprised of documents from the Royal Society of Chemistry digital library, we show that the our proposed methodperforms well in extracting experiment-related paragraphs from chemistry documents. The ChemEd Digital Library is one of eleven Pathways projects in the National Science Digital Library, a major project supported by the NSF to improve science education nationwide, that aims to provide broad access to a rich, reliable, and authoritative collection of materials. This article presents an open-source object-oriented C11 library of classes and routines to perform tensor algebra. The primary purpose of the library is to enable postHartree–Fock electronic structure methods; however, the code is general enough to be applicable in other areas of physical and computational sciences. The library supports tensors of arbitrary order (dimensionality), size, and symmetry. Implemented data structures and algorithms operate on large tensors by splitting them into smaller blocks, storing them both in core memory and in files on disk, and applying divide-and-conquer-type parallel algorithms to perform tensor algebra. The library offers a set of general tensor symmetry algorithms and a full implementation of tensor symmetries typically found in electronic structure theory: permutational, spin, and molecular point group symmetry. The Q-Chem electronic structure software uses this library to drive coupled-cluster, equation-of-motion, and algebraicdiagrammatic construction methods. V C 2013 Wiley Periodicals, Inc. ChemSpider is a free, online chemical database offering access to physical and chemical properties, molecular structure, spectral data, synthetic methods, safety information, and nomenclature for almost 25 million unique chemical compounds sourced and linked to almost 400 separate data sources on the Web. ChemSpider is quickly becoming the primary chemistry Internet portal and it can be very useful for both chemical teaching and research.