Library Workshops – NCBI Resources, SciFinder, Patents, PubMed

This month’s hands-on workshops to learn more about some of the best resources for your science and engineering research. Classes are free, but registration is strongly encouraged. Note that some classes are in the Geisel Library Building, and others are at the Biomedical Library Building.

 

The UC San Diego Library is hosting a live-streaming webinar from the University of Michigan’s National Center for Biotechnology Information (NCBI) Discovery Workshops, which will be held May 5 & 6. Each 2.5-hour session consists of hands-on work emphasizing a different set of NCBI resources, using specific examples to highlight important features of the resources and tools. The workshops will be broadcast in the Biomedical Library’s Classroom 3, and computers are available.

Gene Expression Resources at the NCBI (register)
May 5 (Tues),
Biomed Lib Bldg, Classroom 3
10:00 – 12:30 pm

You will find, display and analyze microarray and sequence-based expression data that are stored in the Gene Expression Omnibus (GEO), Sequence Read Archive (SRA), UniGene, and Epigenomics databases to investigate the potential for expression of transcript splice variants and examine the levels of expression under varied experimental conditions as well as in different tissues and disease states. You will analyze Microarray data the on-demand GEO2R tool and will explore the precomputed transcript analyses that are displayed on the UniGene and GEO Profiles pages. You will explore genome-aligned RNA-Seq data through the Gene database’s sequence viewer displays and analyze raw RNA-Seq reads in the SRA database using NCBI’s SRA-BLAST service.

NCBI Genomes, Assemblies and Annotation Products: Microbiome to Human (register)
May 6 (Wed),
Biomed Lib Bldg, Classroom 3
10:00 – 12:30 pm

NCBI BioProject, BioSample, Genomes and Assembly databases Annotation products from the Eukaryotic and Microbial genome annotation pipelines Environmental and organismal metagenomes Accessing wgs data in the Sequence Read Archive (SRA) Specialized genomic and SRA BLAST services Downloading genome sequences and next-gen reads from the NCBI FTP and Aspera sites.


SciFinder Essentials for Chemists and Non-Chemists (register)
May 6 (Wed),
Geisel Lib Bldg, Classroom 1
10:00 – 11:30 am

SciFinder is one of the core information resources for exploring the chemical literature, but it’s not just for chemists. It can also be helpful to researchers in engineering, environmental sciences, physics, and radiology and other health sciences.

This hands-on workshop will cover the SciFinder essentials: topic and author searching, improving your search results, accessing the full text articles, and how SciFinder compares with other databases like Web of Science. You’ll also learn to search CAS Registry to find chemical substance information, and get an introduction to the built-in editor for drawing chemical structures and reactions.

Patents & Patent Searching (register)
May 13 (Wed),
Geisel Lib Bldg, Classroom 1
1:00 – 2:30 pm

Patents are critically important in protecting intellectual property and companies are investing fortunes in them to safeguard their inventions. It is estimated that between 2010 and 2012 in the smartphone industry alone, over $20 billion was spent on patent purchases and litigation. Without the protection afforded by patent coverage, technological innovation would dry up.

In this class, you will learn how patents protect your intellectual property and what rights they confer, what to expect in the patent application process, how to read and interpret patent documents, and why international patents matter. Learn how you can work with the UCSD Technology Transfer Office to manage and protect your inventions. Finally, learn about free web search engines you can use to discover if your invention has already been patented. Even if you don’t have an invention on the drawing board, this class will give you valuable insight into how patents work.

PubMed Essentials (register)
May 14 (Thurs),
Biomed Lib Bldg, Classroom 3
11:00 – 12:30 pm

This hands-on workshop focuses on what every user needs to know about PubMed, whether doing a search for a specific author or topic using keywords. Learn to focus your results with limits, become familiar with the features of the advanced search screen, and know how to use UC E-Links to easily get to full text articles.

PubMed: Beyond the Essentials (register)
May 28 (Thurs),
Biomed Lib Bldg, Classroom 3
11:00 am – 12:30 pm

Move beyond the basics to refine and expand your searching skills. Learn about MeSH terms and how to use them in a search. Use MyNCBI and its numerous tools to keep you updated and to customize PubMed for your most frequent types of searches. Great for the frequent searcher.

New Interface for Access World News

Access World News provides access to local, regional, and national U.S. newspapers as well as full-text content of key international sources. Access World News (via Newsbank) has a new interface.

Watch this short video to learn how to search and locate different types of news content, including videos, transcripts, and online-only content.

access world news

Highlights include the following:

Searching
• More navigators by which the content can be explored
• Searches can be refined either before or after conducting a search
• Searches can be edited directly on the search form which remains at the top of the result list

Navigation
• Tool Bar for access to Search History, Document View History, Saved Articles (My Collection) and Other NewsBank Products is available on all screens
• Email, Cite and Print commands are more prominent on the article page
• Add to My Collection, Print or Email are available under each article on the results page
• Source Type icons appear in each article returned on the search results page

Functionality
• Result list can be sorted before or after entering a search
• URLs for all screens are persistent and can be bookmarked for future use
• Citing requires fewer clicks to get to a preferred format, and more formats are available
• The Browse Issues option is accessible from within articles
• Two options to return to the beginning screen are available: Clickable NewsBank Logo and New Search link under logo
• Enhanced source list provides the ability to search for titles and information about sources.

Categories: Databases, Research Tips Tags:

Images & Media

Looking for images or media to jazz up your class presentations? Check out these guides–

Image Guide: Image Copyright, Citation & Publication Information

Images and Video (from the Communication Research Guide)

Original footage: Public Domain Images

Categories: Databases, Technology Tips

February Workshops – PubMed, Refworks, and Patents

The Library’s Febrary workshops (complete list for Winter 2015)

PubMed Essentials
Feb 4 (Wed), 2:00 – 3:30 pm
Biomed Lib Bldg, Classroom 3
Register

This hands-on workshop focuses on what every user needs to know about PubMed, whether doing a search for a specific author or topic using keywords. Learn to focus your results with limits, become familiar with the features of the advanced search screen, and know how to use UC E-Links to easily get to full text articles.

PubMed: Beyond the Essentials
Feb 18 (Wed), 2:00 – 3:30 pm
Biomed Lib Bldg, Classroom 3
Register

Move beyond the basics to refine and expand your searching skills. Learn about MeSH terms and how to use them in a search. Use MyNCBI and its numerous tools to keep you updated and to customize PubMed for your most frequent types of searches. Great for the frequent searcher.

Patents & Patent Searching
Feb. 12, 2015 (Tues), 10:00 am – 12:00 pm
Geisel Lib Classroom 1
Register

Patents are critically important in protecting intellectual property and companies are investing fortunes in them to safeguard their inventions. It is estimated that between 2010 and 2012 in the smartphone industry alone, over $20 billion was spent on patent purchases and litigation. Without the protection afforded by patent coverage, technological innovation would dry up.

In this class, you will learn how patents protect your intellectual property and what rights they confer, what to expect in the patent application process, how to read and interpret patent documents, and why international patents matter. Learn how you can work with the UCSD Technology Transfer Office to manage and protect your inventions. Finally, learn about free web search engines you can use to discover if your invention has already been patented. Even if you don’t have an invention on the drawing board, this class will give you valuable insight into how patents work.

Refworks
Feb 18 (Wed), 10:30 am – 12:00 pm
Geisel Lib Bldg Classroom 3
Register

Learn how to organize your references and instantly format your research papers, articles, and other publications using APA, NLM and hundreds of other writing styles. You’ll also learn how to download references using your favorite research databases and library catalogs. Collaborate with other authors via the RefShare tool.

New UCSD Database – MarinLit (Marine Natural Products)

marinlit_logoroyal-society-of-chemistry-logo

The UCSD Library recently licensed the MarinLit Database. Once available only to individuals through the University of Canterbury, it was acquired in late 2013 by the Royal Society of Chemistry and now offered to campuses with a site license.

MarinLit is a text and structural searchable database of the marine natural product literature, with some unique search features and dereplication tools that are not available in our other chemical information resources. This database will be useful to anyone researching marine natural products at SIO, SSPPS, and the Department of Chemistry and Biochemistry. There are numerous ways to search the database, including:

  • Bibliographic Information: article title and citation, author, trivial name
  • Taxonomy
  • Location
  • Compound (for dereplication of newly isolated compounds): name, structure, molecular formula, mass, UV maxima, functional groups, NMR predicted shifts

If you have questions about using MarinLit, please contact Amy Butros (abutros@ucsd.edu) or Teri Vogel (tmvogel@ucsd.edu).

Library Workshops in January – EndNote and SciFinder

The Library’s January workshops (complete list for Winter 2015)

EndNote

Jan 20 (Tues), 2:00 – 3:30 pm
Geisel Lib Bldg Classroom 1
Register

Writing a research paper and need to manage your references? Using EndNote already, but want to learn about its “power” features (e.g., Connect, “Cite While You Write,” etc.)? Take this workshop to learn to build your own EndNote reference library and work with Word to write your paper and seamlessly create bibliographies. Attendees from all departments are welcome.

Special EndNote instructor, Doug Nguyen, from Thomson-Reuters will be teaching the session.

—————-

SciFinder Essentials for Chemists and Non-Chemists

Jan 29 (Thurs), 10:00 – 11:30 am
Biomed Lib Bldg Classroom 3
Register

SciFinder is one of the core information resources for exploring the chemical literature, but it’s not just for chemists. It can also be helpful to researchers in engineering, environmental sciences, physics, and radiology and other health sciences.

This hands-on workshop will cover the SciFinder essentials: topic and author searching, improving your search results, accessing the full text articles, and how SciFinder compares with other databases like Web of Science. You’ll also learn to search CAS Registry to find chemical substance information, and get an introduction to the built-in editor for drawing chemical structures and reactions.

Cambridge Structural Database 2015

The 2015 Cambridge Structural Database System (CSDS) is available for UCSD faculty, staff, and students to download and install. The regular UC distribution site at UCLA will be updated with the 2015 CSDS shortly, but until then you can access the files directly from the Cambridge Crystallographic Data Centre (CCDC).

  • Go to the CCDC download page.
  • Enter your email address and the UCSD site and confirmation codes, which you can find here. If off campus, you’ll need VPN or proxy to reach this page.
  • You will receive an email from CCDC with the links to download CSDS (Windows, OSX, Linux), along with additional Windows and/or Linux programs: DASH, IsoStar, SuperStar, and GoldSuite. It usually takes a few hours for the files to download, and these links are good for 24 hours.

Once you have the CSDS file, you can install the programs. It is recommended that you uninstall CSDS 2014 first. The first time you run CSDS, you will be prompted to register with the site and confirmation codes.

The Cambridge Structural Database is a repository of more than 700,000 organic and organometallic crystal structures, searchable by chemical name, molecular formula, elements, experimental details, and literature reference information like author. If you have questions about CSDS, please contact Teri Vogel.

UC Libraries Become Hub for Digital Public Library of America

The Digital Public Library of America (DPLA) DPLA 2brings together the riches of America’s libraries, archives, and museums, and makes them freely available to the world online. An online library into the United States’ historical and cultural heritage, DPLA aggregates metadata — or information describing an item — and thumbnails for millions of photographs, manuscripts, books, sounds, moving images, and more.

The UC Libraries have recently joined the Digital Public Library of America (DPLA) as a Content Hub. In our role as a DPLA Content Hub, the California Digital Library will be sharing metadata records from Calisphere, a website containing approximately 250,000 digital primary source objects contributed by libraries, archives, and museums across the state of California– including unique content from across the UC Libraries. Because of the increased exposure, the UC Libraries’ digital resources will have a broader, nationwide audience that will be able to find and discover unique collections maintained across the UC Libraries.

Browse and search DPLA’s collections by timeline, physical location via a map, a virtual bookshelf, and faceted search. You can also save and share customized lists of items; explore digital exhibitions; and interact with DPLA-powered apps in the app library. Never has our cultural heritage been so easy to explore!

ChemBioOffice 14 and SciFinder

The campus-wide site license for ChemBioOffice/ChemDraw is funded by ACMS and the Department of Chemistry and Biochemistry, and administered by ACMS. Questions about the license or registration codes should be directed to software@ucsd.edu. For questions about SciFinder, contact Teri Vogel.

UCSD faculty, staff and students can now download the new ChemBioOffice 14. Among the enhancements, you can send your ChemDraw structure and reaction queries directly to SciFinder without having to copy/paste or import into the SciFinder structure editor. Instructions and technical information after the jump.

Read more…

Natural Standard Database Access Restored

Access to the Natural Standard database on integrative medicine was not available for UCSD users in April and much of May due to licensing and renewal problems. CDL/UCSF licensing efforts have concluded and we now have access again. Thank you for your patience. The new site is https://naturalmedicines.therapeuticresearch.com/

Additional resources for natural product medicine include the following:

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