Category Archives: Scientific Data Management

BenchSci, an antibody-finding search engine free to academics

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The Peter B. Lewis Library is pleased to present BenchSci to the Princeton research community.

Registration is free to all scientists with a princeton.edu or affiliated institutional emails at https://www.benchsci.com

BenchSci is a online platform designed to help scientists find antibodies from publications. Their proprietary machine-learning algorithm was trained by PhD-level scientists to identify and understand the usage of commercial antibodies in the research literature.

When searching for a specific protein target, BenchSci curates published data in the form of figures to simplify the literature search process. The figures can then be filtered by specific experimental contexts cited in the paper such as techniques, tissue, cell lines, and more, to help users pinpoint antibodies that have been published under experimental conditions matching their study interest.

For more information about BenchSci, please refer to this article: https://blog.benchsci.com/7-features-to-find-antibodies

To learn how to navigate BenchSci, please watch this short video: https://youtu.be/EFaDwTtqlv4

For further inquiries or feedback, contact Maurice Shen, PhD, the Head of Academic Relations at BenchSci, at maurice@benchsci.com

Data Management Plan Presentation – Wed., March 28th

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Data Management Plan Presentation

Wednesday, March 28, 12:00 – 1:00 pm

347 Lewis Science Library, Washington Road & Ivy Lane
[Lunch will be provided. RSVP here.]

This one-hour presentation by PU librarians, OIT and PICSciE/Research Computing staff is open to Princeton researchers, graduate students and grants personnel. Please share with those who may benefit from this presentation.

Topics

  • Why manage research data?
  • Elements of data management
  • How to write a data management plan
  • Common data management issues
  • Best practices for managing research data
  • Resources and support on campus

Encyclopedia of Life — now 10 years old!

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STS Science Resources

The Encyclopedia of Life is 10 years old!  It is freely available on the web.  From their statistics, as of May 11, 2017, they have 5.5 million pages.  Responsibilities are shared by interested groups and individuals.  “The founding partners of the project include the Field Museum of Natural History, Harvard University, the Marine Biological Laboratory, the Smithsonian Institution, and the Biodiversity Heritage Library.  The Missouri Botanical Garden later joined, and negotiations are ongoing with the Atlas of Living Australia.  Other partners are the American Museum of Natural History (New York), Natural History Museum (London), New York Botanical Garden, and the Royal Botanic Gardens (Kew).”

 From https://en.wikinews.org/wiki/Scientists_to_bring_all_species_together_in_Encyclopedia_of_Life

There is also a Wikipedia article about the EOL: https://en.wikipedia.org/wiki/Encyclopedia_of_Life

Efforts began with plants, animals and fungi.  It appears now that microorganisms have been added, as they’d hoped.  If one searches for tuberculosis, there are many hits,  but many are not very productive.  Searching on the Genus is the key – Mycobacterium.   The site provides the NCBI ( National Center for Biotechnology Information) taxonomy for these organisms.  There are many  entries on Staphylococcus species.  Not all hits will be productive, and they urge inquirers to request information.

There are tabs for:  Overview, Detail, Data, Media (including some videos), Maps, Names, Communities (which include related EOL groups, e.g. “Birds of America”), Collections (on-line databases), Resources, Literature and Updates.  These headings also serve as filters or limits.

I tried cardinal, but Cardinalis cardinalis — the scientific name, Genus and species — works  best, if you are looking for our most common red bird.

There are data which indicate species to species interactions, from this site:  http://www.globalbioticinteractions.org/  There are many links to many collections.

I looked up cedar and from starting to browse through <6400 entries, I soon (within the first page of 25) came upon Cedrus libani, and found much information, including a video about the restoration of the “Cedars of Lebanon”.   The page steers one to many “traits” including the IUCN (International Union for Conservation of Nature) status, which is “vulnerable” for this tree:   Its populations are declining.   Searching can be a bit tricky.  Scientific name works best.

 

Best of the Web, GEN (Vol. 37, No. 8) SciPy PYTHON

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“Computer programming is becoming (or rather, already has become) an essential skill for modern-day life scientists. A popular programming language in many fields is Python, in large part due to its open-source development. As a result, there exist many free resources available to both experienced and novice Python users. A large collection of such resources can be found on SciPy.org, home of a number of scientific and computational software packages/libraries for Python. In addition to offering free downloads of those packages, the SciPy website also includes SciPy Central (a collection of useful Python code snippets), a blog, documentation for the various software packages, and a place for users to report bugs. Site visitors in search of even more information can browse the SciPy Cookbook, a collection of user-contributed “recipes” that span topics such as graphics, linear algebra, simple plotting, and differential equations.”

Genetic Engineering & Biotechnology News, April 15, 2017,  URL:scipy.org

Rated “Excellent”, free software downloads, good documentation

Global Stat: GlobalStat.eu

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From Library Journal, Mar. 1, 2017, “Best Free Resources 2016”, by Gary Price:

“From the European University Institute, this database compiles publicly available data from over 100 sources offering statistical information on globalization sustainability and human development. Users can search on a range of topics including income distribution, energy consumption, water resources, dwellings, migration, land use, food production, nutrition, school enrollment, and life expectancy and create data visualizations.  See the list of underlying sources by clicking the sources/entities link at the bottom left of the main page.”  http://www.globalstat.eu

Project Euclid — Repository for math and statistics

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The goal of Project Euclid—a project of the Cornell University Library—is to provide an online repository for mathematics and statistics publications, with the goal of offering content as open-access. The website hosts full journals and book series from dozens of publishers, with topics that range from statistics and probability, applied mathematics, logic, and computer science. Site visitors can search the collection by a number of parameters such as authors, keyword, or full text, and each article or journal on the website is conveniently marked with an indicator that tells whether the content is freely accessible without a subscription. (Approximately 70% of content on the site is currently open-access.) Additionally, the website provides support for researchers, librarians, and publishers. Project Euclid is a convenient collection of mathematical journals and articles all together in one place.

“Excellent” rating ****  No weak points

Source:  “Best of the Web”, GEN: Genetic Engineering & Biotechnology News, Nov. 15,  2016, p.42.

New Weather Satellite: post on Dan’s Wild Wild Science Journal

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New Era In Meteorology is Days Away

by Dan Satterfield

This Saturday evening, NASA will launch the GOES-R weather satellite, and a new 21st century era in weather and climate prediction will begin. This will be the equivalent of going from an old black and white TV, to an HD flat screen in color, and if all goes well it will revolutionize forecasting. I […]

Read more of this post

Dan Satterfield | November 15, 2016 at 3:18 am | URL: http://wp.me/s1t6W8-43555

 

Data USA — Visualization of free public data — MIT

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Website makes government data easier to find
Steve Lohr writes: “For years, the federal government, states, and some cities have enthusiastically made vast troves of data open to the public. A project coming out of the MIT Media Lab seeks to harness that data and make it available to a wider audience. The project, called Data USA, bills itself as ‘the most comprehensive visualization of US public data.’ It is free, and its software code is open source, meaning that developers can build custom applications by adding other data.”…

New York Times, Apr. 4DATA USA

Emerging trends and top innovators in science & technology — Thomson-Reuters

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Follow the links to learn about some of the…

http://ip-science.thomsonreuters.com/

  • 2015 Top 100 Global Innovators
  • Predicting the World in 2025  (Emerging trends in Science & Technology)
  • Innovation — from Discovery to Delivery (video)  (Controlling the innovation life cycle)

  • “US Thomson Reuters announces the world’s most influential scientific minds – 18 Jan 2016

    The Intellectual Property (IP) and Science business of Thomson Reuters, has announced the release of ‘The World’s Most Influential Scientific Minds,’ a citation analysis identifying the scientists – as determined by their fellow researchers – who have made the most significant global impact within their respective field of study.

    The two-part study includes an 11 year assessment of research paper citations to determine the leaders within 21 broad fields of science and a ranking of 2015’s top scientists or ‘hottest researchers,’ revealing significant growth in cancer genomics and improvements in converting solar cells into renewable energy.

    The report draws on data and analysis performed by Thomson Reuters IP & and Science bibliometric experts via InCites™ Essential Science Indicators℠, a leading web-based research analytics platform and a unique compilation of science performance metrics and trend data based on scholarly paper publication counts and citation data from the Web of Science™, the premier web-based environment for scientific and scholarly research.

    The longer-range study, widely known as the Highly Cited Researchers, recognises nearly 3,000 scientists who published the greatest number of articles ranking among the top one percent by citations received in their respective fields in each paper’s year of publication. Analysts assessed more than 120,000 papers indexed between 2003 and 2013 throughout each area of study.

    The 2015 hottest researchers ranking spotlights the scientific community’s emerging trends and 19 innovators, who recently published at least 14 papers with notably high levels of citations. The list was identified by tabulating citations within the Web of Science recorded during calendar year 2014 for papers published between 2012 and 2014.

    Stacey B. Gabriel of the Broad Institute of MIT and Harvard tops the list for the second consecutive year for her contributions to the Cancer Genome Atlas project, providing molecular portraits of tumors afflicting the breast, lung and other areas of the body. Her most recent papers examine the genetic underpinnings of schizophrenia and Alzheimer’s. She is followed by newcomer, Oxford University’s Henry J. Snaith, a physics and material scientist for his work on perovskite solar cells to advance solar energy technology. ”

    Brought to you by Scope e-Knowledge Center, a world-leading provider of abstraction, indexing, entity extraction and knowledge organisation models (Taxonomies, Thesauri and Ontologies).

    Click here  Jan. 18, 2016

The Cambridge Structural Database has reached no. 800,000

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“The Cambridge Crystallographic Data Centre is delighted to announce that there are now over 800,000 entries in the Cambridge Structural Database. The 800,000th entry is a copper-containing metal-organic crystal structure determined by researchers in Spain and published in Crystal Growth & Design.

You can read more about this structure and the significance of this milestone at http://www.ccdc.cam.ac.uk/NewsandEvents/News/Pages/NewsItem.aspx?newsid=42 and in our blog post at http://www.ccdc.cam.ac.uk/Community/Blog/pages/BlogPost.aspx?bpid=58.

We take this opportunity to express our appreciation for the immense contribution made by researchers past and present to the continuing growth and success of the Cambridge Structural Database.”

As reported to the CHMINF-L on Oct. 23, 2015, by

Dr Ian Bruno: Director, Strategic Partnerships

The Cambridge Crystallographic Data Centre (CCDC)

Tel: +44-1223-336013   Email: bruno@ccdc.cam.ac.uk