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Reaxys 2.0 Migration

 

Logo for Reaxys Database

Reaxys is a web-based tool for the retrieval of chemistry information and data from published literature, including journals and patents.Chemists at Berkeley are active users of Reaxys, doing 1000’s of searches/month!

Elsevier has rolled out a new version of Reaxys (Reaxys 2.0) that has a number of enhanced features, including:

  1.       An increasingly simple user interface.  The opening page has spaces to (a) type in the search query in a search bar or (b) type in the name of the structure or draw the structure.
  2.       Search functions using the querylets to increase the specificity of the search and reduces the time that the user has to filter the results post search.
  3.       Search functions that contain auto suggest. Similarly it also searches for singular/plural and synonyms
  4.       Using Boolean operators (obviously one of Elsevier’s strengths)
  5.       Listing hits in the initial screen (post search).  No secondary search needed.
  6.       A big increase in the number of searchable Asian patents

The migration is Reaxys 2.0 is ongoing, but migration should be completed by November 30, 2017. Soon UCB users will be directed to the new interface, but will continue to have the option to use the old interface for the foreseeable future.

JAMAevidence: Using Evidence to Improve Care

JAMAevidence

JAMAevidence helps clinical decision makers identify the best available evidence.

Check out their guides to the systematic consideration of the validity, importance, and applicability of claims about the assessment of health problems and the outcomes of health care.

Try it out!

Engineering Academic Challenge!

The Elsevier Engineering Academic Challenge is back! The team-based challenge lasts for five weeks and began on September 18. Register here to get started and win prizes!

 

quote about EAC

UPDATE: Elsevier Data Publishing Requirements

Last spring, we posted about data publishing requirements from Elsevier, Springer/Nature, and AAAS. At the time, Elsevier was the most lenient on their data publishing policies and used language that was suggestive and encouraging of data publishing. As of September 5th, 2017, that is no longer the case. Elsevier has signed on to the Transparency and Openness Guidelines (TOP) through the Center for Open Science. We talk and write a lot about transparency, openness, and sharing in science; however, there is a disconnect between the conversations and the daily workflows and practice of scientists. I was once told, after giving a workshop on data sharing, that I was an idealist trying to preach to realists. In order to close that gap, we need more publishers, like Elsevier, to make the ideal a reality, and enforce strict guidelines on data sharing and publishing.

Elsevier Logo

 

Let’s take a look at the 5 new data sharing requirements, which will be implemented for 1800 of Elsevier’s titles:

Option A:  you are encouraged to

  • deposit your research data in a relevant repository
  • cite this dataset in your article

Option B: you are encouraged to

  • deposit your research data in a relevant repository
  • cite this dataset in your article
  • link this dataset in your article
  • If you can’t do this, be prepared to explain why!

Option C: you are required to

  • deposit your research data in a relevant repository
  • cite this dataset in your article
  • link this dataset in your article
  • if you can’t do this, be prepared to explain why!

Option D: you are required to

  • deposit your research data in a relevant repository
  • cite this dataset in your article
  • link this dataset in your article

Option E: you are required to

  • deposit your research data in a relevant repository
  • cite this dataset in your article
  • link this dataset in your article
  • peer reviewers will review the data prior to publication

The new Elsevier policy is similar in nature to Springer/Nature with their tiered system of requirements. It’s important to check with your individual journal to see which option it falls under. Ideally, you will always follow option E, where you make your data openly available, cited, linked, and provide the proper amount of metadata to go through the peer review process or be reused by another researcher.

 

If you have any questions about how to enrich the metadata of your dataset, or where to deposit your research data, please email researchdata@berkeley.edu!

 

 

Workshops on Scopus for literature searching and research impact

Want to make the most of our subscription to Scopus to improve your literature searching or evaluate your research impact? Attend one of our upcoming Scopus workshops! The Library is hosting two back-to-back workshops on September 28 to provide tips on using this large abstract and citation database covering the peer-reviewed literature across disciplines.

Scopus banner image

Advanced Literature Searching with Scopus
September 28 | 2-3 p.m. | Bechtel Engineering Center, Kresge Engineering Library Training Room 110MD

Want to improve your literature searching and save yourself time? This workshop will cover advanced searching with Scopus, a large abstract and citation database covering the peer-reviewed literature: scholarly journals, books, and conference proceedings. The database covers publications in science, technology, medicine, social sciences, arts, and humanities. Come learn useful tips and techniques for finding relevant publications for your literature reviews.

Scopus Tools for Assessing Research Impact
September 28 | 3-4 p.m. | Bechtel Engineering Center, Kresge Engineering Library Training Room 110MD

This workshop will cover tools and techniques available in the citation database Scopus for maximizing and assessing your research impact. Topics to be covered include: citation analysis for authors, comparing journals with CiteScore, linking your Scopus Author ID to your ORCID ID, and using PlumX metrics in Scopus.

We encourage you to register online for these workshops but drop-ins will also be welcome as space allows.

Maps & More: Hamilton!

Please mark your calendars for the first Maps and More pop-up exhibit of the semester!
Friday, September 22, 11 am – noon
Earth Sciences & Map Library, 50 McCone Hall
Hamilton, in Maps informational poster

You’ve listened to the musical, now put some names to places with maps related to Alexander Hamilton’s life and exploits. This month’s Maps and More collections show-and-tell event is offered in coordination with the On the Same Page program. Featuring maps and atlases from the Earth Sciences & Map Library collection, this exhibit helps put some geographic context to key events in Hamilton, from his birth in the West Indies to his years in Philadelphia and New York and his deadly duel on the banks of the Hudson.

 
We’re delighted to have history graduate student Nicole Viglini guest curating this pop-up exhibit. Nicole’s research interests include themes of race, culture, class, and gender in early and nineteenth-century America and the Caribbean.
 
We hope to see you there!
Susan Powell
Sam Teplitzky
 
ps: Save the date for next month’s Maps and More on Wednesday, Oct. 18, 11 am – noon with mapmaker Stace Wright of Eureka Cartography!

Data Practices and Publishing Workshop Series

On Tuesday, September 5th and Tuesday, September 12th, the Kresge Engineering Library and Research Data Management will be holding a series of two data management workshops designed for researchers who are in the midst navigating the research data lifecycle.

research data lifecycle

https://www.jisc.ac.uk/guides/research-data-management

During the first workshop, Efficient Research Data Practices, we’ll tear apart the above cycle and identify where each attendee currently falls in the data lifecycle. We’ll address pitfalls, tips, and tools for each step of the process that includes creating data management plans; setting up secure storage for the active data management phase; and how to prepare your data for publication while adhering to publisher and funder requirements.

 

The second workshop, Data Sharing: Publishing and Archiving, will take a deep dive into metadata creation and preparing data for publication and archiving. We’ll discuss why data publication is so important and we’ll identify individual publisher requirements for datasets. Daniella Lowenberg, formerly a publication manager for PLoS, and now the Research Data Specialist for the California Digital Library will be joining us.

 

Please register for the workshops by clicking on the below links and we look forward to seeing you!

Efficient Research Data Practices: September 5, 4:00 – 5:00, Kresge Engineering Library – 110MD Bechtel Engineering Center

Data Sharing: Publishing and Archiving: September 12, 4:00 – 5:00, Kresge Engineering Library – 110MD Bechtel Engineering Center

Advanced PubMed workshop

PubMed logo

Want to make your searches for biomedical information more effective and efficient? The Library’s Life and Health Sciences Division is holding a hands-on workshop on advanced features of PubMed, including:

  • How to use filters to focus search results on specific article types, publication dates and more
  • How to add field tags to find articles by author, title, journal, and other criteria
  • How Medical Subject Headings (MeSH) can help you find additional relevant information
  • How to use My NCBI to save searches, set up alerts, and display results in your preferred format
  • How PubMed links to information in other NCBI resources

Location: Bioscience Library Training Room, 2101 VLSB
Date: Tuesday, September 5, repeated Wednesday, September 6
Time: 12 – 1 pm

No pre-registration is required; all are welcome.

Questions? Please contact Elliott Smith at esmith@library.berkeley.edu

For additional workshops on NCBI bioinformatics tools, citation managers, searching Scopus, writing and collaboration tools, data visualization, productivity tools and techniques, and other topics, please see the Science Libraries Events Calendar.

NCBI bioinformatics tools: An introduction

NCBI-Logo_sm

A hands-on workshop introducing NCBI bioinformatics tools such as PubMed, Gene, Protein, Nucleotide, and BLAST:

  • Starting with a disease, syndrome, or process, identify the genes/proteins involved
  • Starting with an organism and a protein, find the protein sequence and gene coding region
  • Starting with a sequence, identify the gene/protein and source

The workshop will cover selecting the proper tools for your question, navigating through the interlinked NCBI databases, and saving your results. It will be offered twice:

  • Dates: Tuesday August 29 (add to bCal) and Wednesday August 30 (add to bCal)
  • Time: 12 – 1 pm
  • Location: Bioscience Library Training Room, 2101 VLSB

Open to all interested students and researchers; no registration is required.

Questions? Contact esmith@library.berkeley.edu

For additional workshops on citation managers, searching PubMed and Scopus, writing and collaboration tools, data visualization, productivity tools and techniques, and other topics, please see the Science Libraries Events Calendar.

5 things you didn’t know about solar eclipses

Total solar eclipse (CC via Flickr)

It’s bird! It’s a plane! It’s — an eclipse?

On Monday, the moon will completely cover the sun and cast a shadow across the country, marking the first total solar eclipse visible in the United States since Feb. 26, 1979 — and the first one whose path has traveled from one American coast to the next in 99 years.

Although the forthcoming solar spectacle will be fully visible only from a 70-mile-wide, 3,000-mile-long band — “the path of totality” — which stretches from Oregon to South Carolina, you won’t have to travel far to get your eclipse fix.

Earth and physical sciences librarian Sam Teplitzky, who recently chose the items for a Cal Day eclipse extravaganza in the Physics Library and a Maps and More pop-up event at the Earth Sciences Library, says she has noticed a surge in interest in the topic.

“We’ve had several patrons use the eclipse-related maps to help chart their own eclipse-chasing plans,” she says, “and the new books I purchased related to next week’s eclipse have been checked out all summer.”

Those who can’t make it to the path of totality to witness the full-on phenomenon in person can check out the eclipse-centric displays here on campus. One, on view until Oct. 1, is outside of the Earth Sciences & Map Library (open weekdays from 9 to 5 p.m.), in the lower level of the lobby of McCone Hall. The other, which will be up through the end of the month, is at the main reading room of the Physics-Astronomy Library (open weekdays from 1 to 5 p.m.).

Eclipse exhibit

Eclipse resources are on display at the Earth Sciences & Map Library until Oct. 1. (Photo by Cade Johnson for the University Library)

Eclipse books on display

The main reading room of the Physics-Astronomy Library will feature eclipse materials through August. (Photo by Cade Johnson for the University Library)

Bonita Dyess, circulation supervisor at the Earth Sciences & Map Library, was instrumental in putting together the eclipse displays.

“I hope people gain a different outlook on our science libraries from looking at our displays,” she says. “I also hope they gain a better understanding of what a total eclipse truly is and how rare this extraordinary event occurs, especially in the U.S.”

We pored over many of the eclipse-related offerings at the Library, full of little-known tidbits and fun facts. Here are just a few things we learned.

1. Eclipse chasing is old.
Heading to Oregon in time for the big event? You’re not alone. Many eclipse enthusiasts are making their way the path of totality — from Boiler Bay in Oregon to Charleston, South Carolina — for primo viewing. But eclipse chasing isn’t new: It is said to have started in 1715. In fact, that year, Sir Isaac Newton created diagrams of the eclipse in England for the public, according to “Total Solar Eclipses and How to Observe Them.”

Interested in the history of eclipse chasing? Rebecca Joslin’s “Chasing Eclipses: The Total Solar Eclipses of 1905, 1914, 1925” tackles the subject, and its beautiful imagery makes it one of librarian Teplitzky’s top eclipse-related picks at the Library.

2. Eclipses come with their own weather.
Like a neighborhood in San Francisco, eclipses are said to come with their own microclimates. Solar eclipses are associated with a drop in temperature — the moon is blocking the sun, after all. Tracking software, however, isn’t sophisticated enough to predict the the weather changes they trigger, according to “Total Solar Eclipses.”

But rapidly fluctuating weather? That’s something all of us in the Bay Area are used to.

3. According to legend, a dragon (or frog or vampire or werewolf or dog) ate the sun.
Eclipses have been explained throughout the years in legends and lore, which vary from culture to culture. The Chinese and Indonesians, for example, historically held that the eclipse is caused by a giant dragon eating the sun, accounting for its apparent disappearance. In fact, the Mandarin word for eclipse is “shi,” which means “eat.

Eclipse myths involving creatures eating the sun are not uncommon, although the beast ingesting the planets can vary depending on the stories’ origins. In Bolivia, it was a huge dog; in Vietnam, a ginormous frog; a werewolf in Serbia; and a vampire in Siberia, according to the fascinating tome “Total Eclipses: Science, Observations, Myths and Legends.”

4. Eclipses have appeared in many books throughout history — including maybe the Bible.
Eclipses are featured in some of the most highly regarded works in history, including those by Shakespeare (“King Lear”) and Mark Twain (“A Connecticut Yankee in King Arthur’s Court”). Even one of the “Twilight” books is called “Eclipse.”

Most notably, though, is that the Scriptures may depict a solar eclipse. The Bible mentions three hours of darkness in the daytime during Jesus’ crucifixion, according to “Total Eclipses.” But whether this was a religious miracle or a normal (albeit rare) astronomical occurrence — or something else entirely — remains up for debate.

5. Someday, solar eclipses will no longer be visible.
The moon is drifting away from the Earth at a rate of 38 mm per year — which is the thickness of about five iPhones stacked on top of one another. Someday, the moon will appear so small in the sky, it will be unable to obscure the sun, according to “Total Solar Eclipses.”

But don’t worry, chasers — it won’t happen anytime soon.

How to see the eclipse

If you do want to see the eclipse but are stuck in the Bay Area on Monday, fear not: Although the region doesn’t lie on the path of totality, we can catch a glimpse of a partial (or about 75 percent) eclipse — that is, if Karl the Fog is cooperative.

Set your alarm to 10:15 a.m. — or a few minutes earlier, for some wiggle room — so you don’t miss it.

If you don’t end up seeing it in person, of course, there’s the Eclipse Megamovie Project, a crowdsourced venture spearheaded by UC Berkeley and Google, which pulls together volunteer-submitted images of the eclipse from across the country. So, like the sun come Monday, you’ll be covered.

Librarian Teplitzky says, if the weather allows, she’ll likely step outside to look at the eclipse — “with my eclipse glasses,” she adds, referring to the protective eyewear that filters out harmful rays.

You’ll want to nab a pair, even if you’re watching from the Bay Area. After all, you wouldn’t want to risk your eyesight for when the next total solar eclipse is visible in the United States — in 2024.

Sources: ABC Channel 7, American Astronomical Society, “Chasing Eclipses: The Total Solar Eclipses of 1905, 1914, 1925,” NASA, “Total Eclipses: Science, Observations, Myths and Legends”, “Total Solar Eclipses and How to Observe Them,” Washington Post

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