Science Intelligence and InfoPros

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Archive for July 2012

Searching by chemical structures into a SharePoint environment

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Authors of this article have assembled different features to allow a user to search by chemical structures or reactions into the company content managed by SharePoint.

The use of SharePoint® collaboration software for content management has become a critical part of today’s drug discovery process. SharePoint 2010 software has laid a foundation which enables researchers to collaborate and search on various contents.

The amount of data generated during a transition of a single compound from preclinical discovery to commercialization can easily range in terabytes, thus there is a greater demand of a chemically aware search algorithm that supplements SharePoint which enables researchers to query for information in a more intuitive and effective way.

Thus by supplementing SharePoint with Chemically Aware™ features provides a great value to the pharmaceutical and biotech companies and makes drug discovery more efficient. Using several tools we have integrated SharePoint with chemical, compound, and reaction databases, thereby improving the traditional search engine capability and enhancing the user experience. (…)

CASP uses SharePoint software to run most of its processes, but to get the chemically rich features it uses tools like Accelrys JDraw and Pipeline Pilot to help render the chemical structure and help search documents with embedded chemical structures. Using the Accelrys Direct cartridge, one can perform various types of structure searches like Sub Structure similarity, Flex match, or exact structure similarity. One can also connect to the Pipeline Pilot protocol and retrieve information like IUPAC name, or any of the molecular properties in a SharePoint database list.

Read the full article at:

Tallapragada K, Chewning J, Kombo D, Ludwick B. Making SharePoint® Chemically Aware™. J Cheminform. 2012 Jan 12;4(1):1. Available from: [Accessed 9th July 2012]

Written by hbasset

July 9, 2012 at 5:50 pm

Posted in 03: Storage

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Build your Product Literature Database with Quosa Virtual Library

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Commercial info from QUOSA, a company recently acquired by Elsevier:

You need a consolidated literature archive capturing all of the full-text articles, conference abstracts, patents and related documents relevant to your products or project, perhaps complete with tagging specific to your company.

QUOSA provides:

  • Automated alerts and import of the full-text literature, integrated with your preferred search platforms
  • A robust, copyright-compliant archive structure with fully configurable meta-data and tagging architecture
  • Easy- to-use access options, including browser-based search, email and RSS Alerts, dynamic links, and automatically generated reporting templates

Written by hbasset

July 9, 2012 at 5:32 pm

iPad 2.0 and Librarians

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A stimulating article from the latest issue of TILT (IFLA):

As more and more of our library clientele are becoming techno-savvy, librarians and other information professionals must not only keep abreast of the technology in order to assist them but must lead the charge. (…)

Many of the apps are “must haves” for librarians and information professionals that I will address later in this article including how the iPad 2.0 can be considered the “go to device” for librarians and information professionals.

Some suggestions of application:

– The iWorks suite should be at the top of every information professionals list. They can use iWorks for presentations, documents, and spreadsheets. iWorks is the equivalent to Microsoft Office

– Information professionals have access to exciting and informative courses on any topic imaginable through Apple’s iTunes U. They can subscribe to courses, take self-paced classes, and get access to learning materials from some of the most erudite scholars in education

 Information professionals can use Drop box for storing, retrieving and sending large files and can synchronize all of their Calendars through the Calendar application

Librarians and information professionals can collaborate with colleagues all over the world using the Facetime and Skype applications.

Some of the popular Apps that librarians have recommended are included below. Top 10 iPad Apps for Librarians by Andy Burkhardt (Information Tyrannosaur) –

Joiner, Ida A. iPad 2.0: Information Professionals Don’t Leave Home Without It! TILT (Trends and Issues in Libray Technologies), July 2012. Available from: [Accessed 9th July 2012]

Written by hbasset

July 9, 2012 at 5:01 pm

Posted in InfoPros

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Pharma funding and publishing bias in High-impact journals

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Journal BMJ has published the results of a case-control study titled “High reprint orders in medical journals and pharmaceutical industry funding”. The study analysed the extent to which funding and study design were associated with high reprint orders, and the financial implications of the same.
Reprints of published articles are seen as a potential valuable means of disseminating information. The pharmaceutical industry is thought to be the largest purchaser of reprints, which constitute the most common form of promotional material circulated among doctors, after gifts and sample medicines.

Since pharmaceutical companies may purchase from journals copies of articles funded by them, reprints may represent a possible source of conflict of interest leading to publication bias. Orders may be worth large sums of money and possibly influence the chance of a paper being published. This is particularly so as the present framework allows editors to be responsible for a journal’s finances apart from its content.

Also, studies sponsored by pharmaceutical companies are reportedly more likely to be published in journals with high impact factors, as against those without Big Pharma funding.

The study authors sought information on reprint orders from the Journal of the American Medical Association, Lancet, New England Journal of Medicine, Annals of Internal Medicine and BMJ. Of the five, only two – the Lancet and the BMJ – consented to provide the data. The researchers found that high reprint articles, irrespective of journal, were significantly more likely to be sponsored by the pharmaceutical industry. Some of the reprint orders were substantial, equating to a large amount of income generated. Thus reprint orders could potentially be a source of publication bias, although the study was not designed with that in mind.


Written by hbasset

July 9, 2012 at 4:44 pm

95% of librarians believe in OA future

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According a study provided by an OA european publisher.

The survey revealed high levels of awareness of OA – 95% of the respondents stated they were very or quite familiar with the OA model.  Librarians highlight a number of benefits of OA publishing models:

  • Ease of access to content
  • Increased visibility, usage and impact for authors
  • Improved sharing and collaboration
  • Improved public engagement with research
  • Broad benefits for society of improved access to research
  • Improved return on investment for funders of research


  • 78% of respondents support OA publishing, with only 5.5% stating they oppose the model.
  • 95% believe OA is already delivering benefits, or will do in the future.

Librarians did express some concern about OA publishing models.  In particular that the charges levied by publishers would create a barrier for authors with limited access to funding, while opening up the potential for ‘vanity’ publishing for those with funds.”

The full article:

Skelton, Val. How OA is changing the role of librarians, Information Today Europe, 5th of July 2012, Available from: [Accessed 9th July 2012]

Written by hbasset

July 9, 2012 at 4:37 pm

Posted in Journals

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Biblimed: a review by Intellogist

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BibliMed is a free search interface that accesses MEDLINE data and provides unique search and viewing features like a tag cloud of MeSH term suggestions to add to your search and a list of books relevant to your query. 

BibliMed may not include the command line search option that makes PubMed attractive to expert searchers, but the intuitive and creative search features on BibliMed will be very useful for students and novice searchers who aren’t comfortable crafting complex queries and using MeSH terms

Read Further at:

Mornini, Joelle. The Intuitive Alternative to PubMed: Search MEDLINE on BibliMed. Intellogist, 1st of July 2012. Available from:[Accessed 10th July 2012]

Written by hbasset

July 8, 2012 at 1:56 pm

Posted in literature

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