Faculty of 1000 Biology: By Scientists for Scientists

Faculty of 1000Faculty of 1000 Biology (F1000 Biology) is described as a “next generation literature awareness tool.” Its purpose is to help researchers identify trends and highly regarded papers through reviews and recommendations, generated by over 2,300 leading researchers from around the world, including 21 faculty members from the University of Pittsburgh.

F1000 Biology is run by scientists for scientists and is useful because it:

    • systematically organizes and evaluates the mass literature
    • can identify key papers in areas outside of your area of expertise or in journals outside of your normal browsing sphere
    • can confirm the importance of specific papers
    • provides quick suggestions for journal club articles

Each article is assigned a rating and one of seven classification types, as shown below.

Faculty of 1000Faculty of 1000

The HSLS Molecular Biology Information Service has integrated F1000 Biology into the search interface on the MolBio home page. This Vivisimo-driven search, found under the Recommended Articles tab, allows researchers to limit their search results to titles recommended by F1000 Biology. Articles are clustered on the right of the results page by subtopic, rating, or classification.

See F1000 Biology’s FAQ page for more information on this useful tool.

~ Melissa Ratajeski and Carrie Iwema

Fugitive Literature Captured by PsycEXTRA

The HSLS online collection now includes PsycEXTRA, a database that captures difficult-to-find “fugitive” or “gray” literature in the fields of psychology, behavioral science, and health. To access this resource, type “PsycEXTRA” into the search.HSLS box on the HSLS homepage.

What is fugitive or gray literature?
Gray literature consists of publications “…produced on all levels of government, academics, business and industry in print and electronic formats, but which is not controlled by commercial publishers.”1 Gray literature can be difficult to locate because it is disseminated outside the traditional path of peer-reviewed journal/book scholarship.

Why is PsycEXTRA useful?

    • PsycEXTRA is useful for locating obscure scientific or scholarly literature outside the traditional commercial publication path.

    • It fills the gap by bringing together material which is usually not covered in standard bibliographic databases such as MEDLINE and PsycINFO.

    • PDFs are included for a major portion of the publications listed in the database. The variety of materials available in PsycEXTRA include: research reports, policy statements, annual reports, curricula, standards, conference papers and abstracts, fact sheets, consumer brochures, newsletters, pamphlets, directories, popular magazines, white papers, and grant information.

    • Currency: new research in psychology and the behavioral sciences often emerges first in the form of technical reports and conference papers, long before it reaches the journal literature. PsycEXTRA can help to identify the first appearance of this research.

    • Patient Education: clear, concise explanations of behavior health issues, often found in consumer brochures and newsletters, are accessible through PsycEXTRA.

For more information visit PsycEXTRA’s FAQ page.

Examples of timely topics available in PsycEXTRA:

    • Information-Processing Skills Related to Working Memory in Individuals With Asperger’s Disorder (Conference Paper)
    • PASRR Screening for Mental Illness in Nursing Facility Applicants and Residents (White Paper)
    • Caring for Veterans with Traumatic Brain Injury, Act of 2007: [H.R. 2201] (Legislation)
    • Durham Study to Probe Benefits of Guided Imagery for PTSD [US Department of Veterans Affairs] (Press Release)

1New frontiers in gray literature. Fourth International Conference on Gray Literature: GL 1999. Proceedings; 4–5 Oct 1999; Washington, DC, and Amsterdam, The Netherlands: GrayNet, 1999.

~ Rebecca Abromitis

Director’s Reflections . . . NIH Public Access Mandate: Dates to Remember and Helpful Web Sites

color-picture_be-caption-smaller.jpgNIH investigators should be aware of two important dates related to the new NIH Public Access Policy. This legislation requires that all journal articles reporting on NIH-funded research be deposited into the National Library of Medicine’s online archive, PubMed Central. These two dates are April 7, 2008 and May 25, 2008.

Beginning on April 7, all applicable peer-reviewed articles accepted for publication must be in compliance with this mandate. To comply authors must:

    • inform the journal that the article is subject to the Policy when submitting for publication.
    • make sure that any copyright transfer or other publication agreement has appropriate language, allowing the article to be submitted to NIH, in accordance with the Policy.
    • must take responsibility for submitting the article to PubMed Central on acceptance, unless the journal has explicitly agreed to do this on the author’s behalf.

Beginning on May 25, relevant citations included in NIH applications, proposals and progress reports must include the PubMed Central reference number (PMCID). Citations that fall under this policy are those that are authored or co-authored by the investigator, or that arose from the investigator’s NIH award.

Helpful Web Sites

    HSLS NIH Public Access Policy includes detailed instructions and citation examples, as well as quick links to the NIH Manuscript Submission site, and NIH’s informative “Frequently Asked Questions” page. You can also link to a listing of journals that will submit articles to PubMed Central on behalf of authors.
    • The Association of Research Libraries (ARL) has a web-based Guide for Research Institutions focusing on issues of institutional compliance.
    • The Scholarly Publishing and Research Coalition (SPARC) web page offers detailed compliance and background information about the NIH Policy. Of particular note is SPARC’s information for authors, including explanations of author’s rights and sample addenda to publishing agreements to retain these rights.
    • The RoMEO (Rights MEtadata for Open Archiving) Project Web site has information on publisher copyright and archiving policies, searchable by journal title or publisher name.

The Jing Project: A Free and Easy Screen Capture Tool

Jing ProjectA picture is worth a thousand words. This is the idea behind the Jing Project, an application that allows users to capture images on their computer screens and share them as still pictures or videos. Imagine the possibilities! Create a video to show your colleague how to create an automatic e-mail alert in PubMed. Send your IT department a screen shot of the error message you received. Narrate a picture slideshow to send to your mom.

The Jing Project was developed by TechSmith, the company that created the products Camtasia and SnagIt, and was released to the public as a way to gather feedback on the strengths and weaknesses of the application. The company is honest in saying that the product is free, for now.

Jing is available for Windows and Mac users and is quickly installed. Images and videos captured using the product can be saved as .swf files or uploaded directly to Screencast.com, a hosting site owned by TechSmith. When the files are uploaded to Screencast.com or another available server, such as your department’s, a url address is created, allowing you to share information without the need to send sizable attachments via e-mail or instant messaging. See the Jing Project’s FAQ page for more information about Screencast.com accounts and technology requirements.

Screen shots can be modified with tools such as highlighting, text boxes, and arrows. Videos can be narrated, but editing is not possible. Jing is intended for the creation of short videos in comparison to Camtasia or Apreso software that can be used to record lengthier lectures.

Think outside the box and give Jing a try! HSLS reference librarians will be using Jing to answer some of the questions received through Ask A Librarian.

~ Melissa Ratajeski

BIOBASE Knowledge Library: Featuring TRANSFAC & ExPlain

Is your research focused on regulation of gene expression? Do you use microarrays, ChIP-on-chip, or protein arrays? Are you interested in uncovering the biology behind a list of differentially expressed genes? If so, you will want to explore a recent addition to the HSLS molecular biology resources collection, the BIOBASE Knowledge Library (BKL).

BKL is a Web-based bioinformatics suite offering three databases and two DNA sequence analysis tools.

You can search these databases for genes or proteins of interest and retrieve expertly-extracted literature findings on function, mutant phenotype, interactions with other proteins, gene expression, promoter location, transcription factor binding sites in promoter regions, cellular localization, and posttranslational modifications.

TRANSFAC: contains information on transcription factors, their experimentally-verified binding sites, DNA-binding profiles, and regulated genes.

• TRANSPATH: a database on biological pathways that provides information on signaling molecules, metabolic enzymes, second messengers, endogenous metabolytes, miRNAs, and the reactions they are involved in, resulting in a complex network of interconnected chains of reactions and pathways.

• PROTEOME: a collection of six protein databases covering information on yeast, human, mouse, rat, worm, human pathogenic fungi, S. pombe, and G protein-coupled receptors proteins.

The real power of this systems biology-driven product comes from its two software programs.

• MATCH: a tool that helps you locate transcription regulatory elements in your sequence of interest. It uses a library of mononucleotide weight matrices from TRANSFAC. Searches may be limited to a specific taxonomic group (vertebrates, plants, etc.) or to a particular tissue (adipose, muscle, liver, etc.) by selecting the appropriate matrix.

• ExPlain: a novel tool for interpretation of gene expression data. It predicts key regulatory molecules which are the actual cause for observed gene expression changes present in an experimental data set. Utilizing data from the TRANSFAC and PROTEOME databases, promoters of differentially expressed genes are analyzed and specific combinations of transcription factors regulating these genes are identified. Then the TRANSPATH database is used to analyze signal transduction networks present upstream of these transcription factors, thus providing a list of key signaling molecules that may be the potential cause of the observed gene expression profile.

Registration Information
To receive access privileges for the BKL databases and tools, please contact the HSLS Molecular Biology Information Service.

~ Ansuman Chattopadhyay and Carrie Iwema

NLM Drug Information Portal

Drug Information Portal
The NLM Drug Information Portal is a quick and easy-to-use gateway to selected drug information resources from the National Library of Medicine (NLM) and major governmental agencies. Coverage includes over 12,000 drugs, spanning from their entry into clinical trials, through FDA approval, and into the marketplace.

    • Resources in this portal include MEDLINEPlus, PubMed, ClinicalTrials.gov, DailyMed, Dietary Supplements Database, LactMed, HSDB, PubChem, Drugs@FDA and AIDSInfo.
    • Information can be located for the intended audience, such as consumer or researcher or by its class, such as prescription or over-the-counter.
    • A search can be completed using a drug’s trade name or generic name.
    • Not all experimental drugs or untested folk remedies are covered in this portal.

For more information on this resource see the NLM Drug Information Portal FAQs.

~ Charlie Wessel

New to TOXNET: Carcinogenic Potency Database

, a collection of toxicology and environmental health databases, recently included a new resource, the Carcinogenic Potency Database (CPDB), developed by scientists at the University of California, Berkeley, and the Lawrence Berkeley National Laboratory. The information contained in the CPDB can be useful for completing cancer risk assessments.

CPDB provides:

    • access to results on 1,547 chemicals from 6,540 chronic, long-term animal cancer tests, conducted since the 1950s
    • for each experiment, information on the species, strain, and gender of the test animal
    • protocol features such as dose duration, administration route, dose level and experiment duration
    • analyses of dose-response curve shape, carcinogenic potency, and statistical significance
    • experimental results including tumor type, tumor incidence, and target organ
    • author’s opinion as to the chemical’s carcinogenicity, and literature citations

The CPDB reports on animal cancer tests that are both positive and negative for carcinogenicity and standardizes the assorted literature of animal cancer tests that have been published in the general literature or reported by the National Cancer Institute and the National Toxicology Program.

The CPDB can be searched as a part of TOXNET, or independently, by chemical name or Chemical Abstracts Service Registry Number (RN). Supplemental information regarding CPDB can be found on Berkeley’s Carcinogenic Potency Project’s homepage.

~ Carolyn Biglow

E-books: Information One Click Away

HSLS offers access to over 1,000 electronic books (e-books). Use the online alphabetic title or subject lists to browse the collection. Search the full-text of HSLS e-books using the program developed by HSLS with Vivisimo technology. Vivisimo clusters the results of the full-text search by topic or e-book source, allowing users to narrow their search in just one click.

~ Leslie Czechowski

HSLS Update Archives Now Searchable

The online archives of the HSLS Update newsletter are now searchable. Use the search box located in the right margin of the newsletter, to find topics of interest or locate the specific details from articles you have read in the past. Note that links and information are up-to-date at time of publication; archived information may no longer be current.