Saturday, October 20, 2007

PubChem: A Public Chemical Portal


PubChem provides information on the biological activities of small molecules. PubChem includes substance information, compound structures, and bioactivity data in three primary databases, PCSubstance, PCCompound, and PCBioAssay, respectively.

PubChem Substance: Search deposited chemical substance records using names, synonyms or keywords. Links to biological property information and depositor web sites are provided. The PubChem substance database contains chemical structures, synonyms, registration IDs, description, related ... [Web sites], database cross-reference links to PubMed, protein 3D structures, and biological screening results. If the contents of a chemical sample are known, the description includes links to PubChem Compound.


PubChem Compound: Search unique chemical structures using names, synonyms or keywords. Links to available biological property information are provided for each compound. The PubChem Compound Database contains validated chemical depiction information that is provided to describe substances in PubChem Substance. Structures stored within PubChem Compound are pre-clustered and cross-referenced by identity and similarity groups. Additionally, calculated properties and descriptors are available for searching and filtering of chemical structures.Users can perform a term/keyword search in a same manner as for substance database. In addition, the PubChem compound database also provides a chemical property search.

PubChem BioAssay: Search bioassay records using terms from the bioassay description, for example "cancer cell line". Links to active compounds and bioassay results are provided. The PubChem BioAssay Database contains bioactivity screens of chemical substances described in PubChem Substance. It provides searchable descriptions of each bioassay, including descriptions of the conditions and readouts specific to a screening protocol.

Structure Search: Search PubChem's Compound database using a chemical structure as the query. PubChem Structure Search allows PubChem Compound Database to be queried using a chemical structure. Chemical structure queries may be sketched using the PubChem Sketcher. You may also specify the structural query input by PubChem Compound Identifier (CID), SMILES, SMARTS, InChI, Molecular Formula, or by upload of a supported structure file format.

The Substance/Compound database, where possible, provides links to bioassay description, literature, references, and assay data points. The BioAssay database also includes links back to the Substance/Compound database.

PubChem Help
This document provides tips and examples for searches of the three PubChem databases by text term/keyword, as well as tips for searching PubChem Compound by chemical properties.

[http://pubchem.ncbi.nlm.nih.gov/help.html]

PubChem is integrated with Entrez, NCBI's primary search engine, and also provides compound neighboring, sub/superstructure, similarity structure, bioactivity data, and other searching features.

PubChem is a component of NIH's Molecular Libraries Roadmap Initiative.

Thursday, October 18, 2007

Gerry McKiernan, Science and Technology Librarian

Gerry McKiernan
Science and Technology Librarian
152 Parks Library

515- 294-9886
gerrymck@iastate.edu

Gerry McKiernan, Associate Professor and Science and Technology Librarian, currently has primary responsibilities for Instruction, Reference and Research Services and Collection Development in Chemical and Biological Engineering; Civil, Contruction, and Environmental Engineering; Environment Sciences; Industrial and Manufacturing Systems Engineering; and Mechanical Engineering.


He currently serves as a member of the editorial board and columnist for Science & Technology Libraries (Haworth) and has served as a contributing editor for Library Hi Tech News and the Journal of Internet Cataloging (Haworth). He has been a member of the editorial board of The Serials Librarian (Haworth) since Fall 2002.

He has delivered numerous presentations for local, state, national, and international conferences, programs, and workshops. These include meetings of the American Library Association, the Michigan Library Association, and the North American Serials Interest Group (NASIG); an Open Forum on Metadata Registries, WiLSWorld; as well as Internet Librarian 2003 and the Workshop on Peer Review in the Age of Open Archives (Trieste, Italy).

In 2005, McKiernan gave invited presentations at Digital Libraries à la Carte: Choices for the Future at Tilburg University, The Netherlands; and at The Role of Open Access Publishing in Science, the preconference held prior to Globalization of Information: Agriculture at the Crossroads, the XIth IAALD World Congress/USAIN Biennial Conference 2005, Lexington, Kentucky. 2005, McKiernan has also given selected presentations at the 12th ACRL National Conference, Minneapolis, Minnesota; and at the LITA National Forum 2005, San Jose, California, and the LITA National Forum 2007, Denver, Colorado.

McKiernan has been employed by the Iowa State University Library since April 1987. Prior to joining ISU, McKiernan has served as the Museum Librarian at the Carnegie Museum of Natural History, Pittsburgh, and as an Assistant Librarian with the Library of the New York Botanical Garden in the Bronx, his home town.

He received his Masters of Science degree in Library Science from the University of Illinois-Urbana-Champaign in 1975 and his undergraduate degree in Anthropology from Lehman College of the City University of New York, The Bronx.

McKiernan currently maintains several blogs relating to alternative energy, notably The Bioeconomy Blog [http://bioeconomyblog.blogspot.com/] and The Bioenergy Blog [http://thebioenergyblog.blogspot.com/].

In addition, he maintains Friends, a blog devoted to"social networking sites for engaged library services" [http://onlinesocialnetworks.blogspot.com/]

McKiernan and his wife of 26 years, Karen M. Anglin, are the parents of three daughters, Kate, Kristen, and Beth, and live in Ames, Iowa.

Women in Chemistry Oral History Project

Women in Chemistry Oral History Project, MS-650, Archives of Women in Science and Engineering, Special Collections Department, Iowa State University Library.

The Archives of Women in Science and Engineering (Iowa State University Library) is sponsoring an oral history project focused on women who have devoted their careers to the study of chemistry in the post World War II era. The project, funded by the ISU Library, the Camille and Henry Dreyfus Foundation, and private donors, will document the careers and experiences of women in chemistry and chemical engineering to illustrate the critical role of women in science.


Collection description

This collection, organized alphabetically by name, contains biographical information, photographs, published material, and oral history interview transcripts. Some transcripts are unavailable due to their being revised. Additional transcripts will be added continuously.

The master audio cassettes of each interview are restricted. Reference copies are available for researchers ... .

List of interviewees available

CHEMnetBASE: A Database of Full-Text Chemistry Handbooks


CHEMnetBase includes descriptive and numerical data on chemical, physical and biological properties of compounds; systematic and common names of compounds; literature references; structure diagrams and their associated connection tables.


[ http://www.chemnetbase.com/]


CHEMnetBase includes:


  • Combined Chemical Dictionary (CCD)


    • Dictionary of Commonly Cited Compounds


    • Dictionary of Drugs (Formerly Pharmasource).


    • Dictionary of Inorganic and Organometallic Compounds


    • Dictionary of Natural Products


    • Dictionary of Organic Compounds

  • Handbook of Chemistry & Physics


  • Polymers: A Property Database


  • Properties of Organic Compounds

  • CRCPress Periodic Table Online


  • The Dictionaries available in the Combined Chemical Dictionary can be searched individually or concurrently with all other dictionaries.

    The Combined Chemical Dictionary database contains data for more than 500,000 substances.

    In general, CCD contains the following compounds:


  • The basic fundamental organic and inorganic compounds of simple structure, including the elements, inorganic binary and ternary compounds (hydrides, halides, oxides, sulfides).

  • Comprehensive coverage of virtually every known natural product including those of unknown structure.


  • All currently marketed drugs, including all those listed in generic name compilations (US Adopted Names, International Nonproprietary Names, British Approved Names, Japanese Accepted Names), as well as those undergoing clinical trials.


  • Compounds with an established use such as catalysts, solvents, starting materials, synthetic reagents, analytical reagents.


  • Important coordination compounds, e.g. amines, phosphines, alkoxy complexes, and major well-characterised bioinorganics.


  • Organometallic compounds representative of all important structural types

  • Important biochemicals and minerals.

  • Other compounds of particular interest because of their chemical, structural or biological properties, including many newly synthesised compounds of active research interest.

  • [http://ccd.chemnetbase.com/intro/index.jsp#compound]

    Searching each CHEMnetBase resource is Free-Of-Charge. One can browse, perform searches and view search hitlists.


    A current subscription is required to view andor print full entries.


    CHEMnetBASE is only available to multi-user organizations on a site license basis; it is not available for individual subscription.


    [http://www.chemnetbase.com/about.html]