Category Archives: Collections & Databases

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

National Service Center for Environmental Publications

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https://www.epa.gov/nscep
EPA Publications
“You can search, retrieve, download, print, and order EPA technical, scientific, and educational materials from this site – all free of charge!”
LAST UPDATED ON JANUARY 9, 2018

Springer Nature Experiments Database — an indexed searching tool

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German “Springer Nature launches Springer Nature Experiments – a free-to-use research solution for the life sciences – 12 Oct 2017

Springer Nature has launched a new, free-to-use research solution, Springer Nature Experiments, to help researchers in the life sciences advance discovery by accessing the most relevant protocols and methods to support their research projects.

Protocols are ‘recipes’ used in laboratory research to support the design and implementation of reproducible experiments. The step-by-step instructions help researchers recreate an experiment by typically including information on the materials required, equipment and set-up. Methods are new scientific procedures for solving existing problems. Together, these two different types of content are the cornerstone for scientists to successfully conduct their research.

Springer Nature publishes the largest available collection of protocols and methods for the life sciences with content from SpringerProtocols, Nature Methods, Nature Protocols and Protocol Exchange – the free repository for scientists to share their protocols with the scientific community. Springer Nature Experiments provides access to all of these through a single easy-to-use platform, designed to save researchers’ time.

The platform uses advanced knowledge models to categorise content based on techniques and organisms – the two most commonly used search categories identified in user research. With the help of cutting-edge artificial intelligence and text mining technologies, these terms are recognised and extracted from the content, enabling users to perform searches and narrow down their results quickly and easily.

In addition, users can evaluate and compare protocols prior to accessing the full-text with the help of protocol landing pages. These summarize key information such as the keywords mentioned, article history and citations which gives an indication of whether the protocol has been used successfully in other research projects.

Springer Nature Experiments is accessible online at https://experiments.springernature.com. Springer Nature will officially launch the new research solution at the Frankfurt Book Fair 2017.”

Source:  Knowledgespeak Newsletter

Come hear about IOP Concise Physics e-books — Lewis 225 Friday noon

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On behalf of Morgan & Claypool Publishers, we would like to invite you to please join us

for a publishing presentation featuring the IOP Concise Physics e-Book collection.

Friday, October 13th at 12:15 PM

Lunch to Follow

Lewis Library (Room 225)

Joel Claypool (Vice President & Publisher) and Susanne Filler (Executive Editor) will:

  • Present the current state of the print and digital publishing industry
  • Demonstrate the industry-leading multimedia capabilities of the award-winning collection published in partnership with the Institute of Physics (IOP)
  • Discuss the publishing process from the initial proposal stage through to final publication

In 2014, Morgan & Claypool Publishers partnered with the Institute of Physics Publishing (IOPP) to establish the IOP Concise Physics series, which is an award-winning collection of e-books written for students, teachers, and researchers. The IOP digital library has a growing worldwide dissemination via IOP’s large network of libraries and consortia, with over 600 institutions having unlimited access including Princeton University via:

https://pulsearch.princeton.edu/catalog?q1=IOP+concise+physics.&f1=in_series&search_field=advanced

The books within this series are intended to be shorter works (approximately 60-150 pages) with rapid publication timeframes.  Highlights include:

  • Full color in the print and e-book formats available for multiple e-reader devices
  • Multimedia capabilities such as unlimited videos and animations and no DRM
  • 115 published books with 250-plus manuscripts currently in development on emerging topics, cutting edge research, and innovative teaching methods

The IOP Concise Physics collection is actively seeking new book projects, and Joel Claypool and Susanne Filler would be happy to discuss this opportunity with you as well as elaborate on the expedited publishing process and streamlined workflow from the initial proposal stage through to final publication

For additional information about IOP Concise Physics, please visit

morganclaypoolpublishers.com/iop  /  iopscience.org

For additional books by Morgan & Claypool, please visit: http://library.princeton.edu/resource/4329

Please contact Susanne Filler at filler@morganclaypool.com / 908-630-7188 with any questions.

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.

 

UK Medical Heritage Library

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UK” The UK Medical Heritage Library now available online for free – 10 May 2017

A £1m project to digitise more than 15 million pages of 19th century medical texts has been completed and the material is now available online for free. It has taken three years to convert these historic published works for use in the 21st century by learners, teachers and researchers.

Covering much more than just medical sciences, this enormous library of text and images encompasses consumer health, sport and fitness, diet and nutrition, along with some weird and wonderful historical medical practices such as phrenology and hydrotherapy.

The project was jointly funded by education technology solutions not-for-profit, Jisc, and Wellcome Library, which contributed its entire 19th century collection, along with content from nine partner institutions: Royal College of Physicians of London, Royal College of Physicians of Edinburgh, Royal College of Surgeons of England, University College London, University of Leeds, University of Glasgow, London School of Hygiene and Tropical Medicine, King’s College London and the University of Bristol. As a collective, this will make a valuable resource for the exploration of medical humanities.

The aim has been to create a comprehensive online resource for the history of medicine and related sciences, which significantly increases the availability of digitised text for teaching, learning and research.

The collection, called the UK Medical Heritage Library, is completely open and can now be accessed for free via Jisc’s Historical Texts resource or via the Wellcome Library’s website.

Brought to you by Scope e-Knowledge Center, a world-leading provider of Abstracting & Indexing (A&I) Services, Knowledge Modeling Services (Taxonomies, Thesauri and Ontologies), Metadata Enrichment & Entity Extraction Services.”

Click here

Source:  Knowledgespeak Newsletter

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.

National Geographic enables free 8×11 printing of USGS topos

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Here are some useful USGS map tips from Emily Wild, Hydrologist/Librarian at the USGS:

This may be of interest if you and(or) your library users are looking for an easy-to-use tool to search, download, and easily print (by using 8×11 printer) for topographic maps published by the U.S. Geological Survey (USGS).

– Examples of recent USGS Denver Library inquiries and instruction of USGS topographic maps include, but not limited to: outdoor recreation, emergency management, disaster planning, search and rescue, bureau of investigations searches and(or) instruction, military, educational outreach, citizen science, and so on.
– Go to the “FREE!! Printable USGS PDF Quads” web site available from National Geographic:

http://www.natgeomaps.com/trail-maps/pdf-quads

– Search selected area

– Click on thumbnail image of the USGS topographic map to open pdf

– Download and(or) print the pages,

~~~~~~~

Just some quick reminders about features available for using USGS Topographic Maps:

– USGS Topographic Maps can be uploaded into Google Earth by using this USGS National Geologic Map Data Base (NGMDB) access point to search, download, and import the KMZ files : http://ngmdb.usgs.gov/maps/TopoView/

– The geopdf versions of USGS Topographic Maps can be annotated, measured, etc when users download the free TerraGo Toolbar : http://info.terragotech.com/download/terrago-toolbar

– Library users mention that the transparency feature and snapshot of all USGS topographic maps through time for a point on Earth are useful features in the USGS-ESRI’s “USGS Historical Topographic Map Explorer”

http://historicalmaps.arcgis.com/usgs/

– the how-to is available online through GPO at : http://www.fdlp.gov/all-newsletters/community-insights/2045-tricks-and-tips-for-finding-and-using-usgs-topographic-maps

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And as an aside, many library users still find this map source useful for historical research of the United States :

Atlas of the Historical Geography of the United States

http://dsl.richmond.edu/historicalatlas

~~~~~~~

Enjoy the day/weekend,

Emily

Disclaimer: the use of trade, product, or firm names is for descriptive purposes only and does not imply endorsement by the U.S. Government.

Emily C. Wild

Librarian (Physical Scientist)
U.S. Geological Survey, Denver Library
Denver Federal Center
ph: (303) 236-1003
ecwild@usgs.gov

USGS Libraries: http://library.usgs.gov

Training: http://go.usa.gov/cBfmG

Profile: https://profile.usgs.gov/ecwild

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

GenBank has reached 200 billion base pairs from > 350,000 spp.

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“Almost the number of stars in the Milky Way.” Through this stellar comparison, the National Institutes of Health proudly announced in 2005 that the content of their computerized collection of DNA sequences called GenBank had reached 50 billion bases or units of DNA. Today, it contains far more, over 200 billion bases from over 350,000 different species, making it one of the largest scientific database in the world.

Here is the announcement of the availability of the Nirenberg papers: “GenBank & The Early Years of “Big Data”

http://circulatingnow.nlm.nih.gov/2016/03/03/genbank-the-early-years-of-big-data/

“Deciphering the Genetic Code: A 50 Year Anniversary” January, 2015

Marshall Nirenberg in the lab in early 1960’s, when he completed the first summary document of the genetic code — how triplets (DNA sequences) direct amino acids to form proteins.  Pictures of the group and more about the papers are here:

http://circulatingnow.nlm.nih.gov/2015/01/21/deciphering-the-genetic-code-a-50-year-anniversary/

A young man in a lab coat and plastic gloves holds up a glass tube in a laboratory.