CHEM 184/284 (Chemical Literature) - Huber - Winter 2022: Lecture 16

A two-credit course in the techniques and tools for effective searching the literature of chemistry, biochemistry, chemical engineering and related fields.

Lecture 16: The New Web & Mobile Science

Science on the Web...2.0?

  • The Internet was originally a network of networks, with protocols devised to allow users - originally the military and scientific researchers - to exchange data.  As it grew, the 'Net became more and more used for commercial purposes.
  • Widespread public use of the Internet really took off with the invention of the World Wide Web protocols at CERN in 1989, and the release of the first Web browser capable of hangling multiple file formats, Mosaic, in 1993 by the National Center for Supercomputing Applications.
  • The Web soon supplanted most other means of transferring information.  By the late 90's Web-based electronic journals began to proliferate, scientific databases began to migrate to the Web.  But now the driving influences for much of Web development were coming from commercial and popular sources.
  • Now, scientists are finding ways to make use of tools developed for non-scientific purposes.

The Many Faces of Google™

The Google search engine, introduced in the late 1990's, quickly became the most popular search engine in the world, and still holds that distinction.  But besides the search engine proper, Google has spun off a number of projects, many of which are of interest to chemists and other scientists.

Google Scholar (http://scholar.google.com/) - an alternative for scholarly searching

  • Google Scholar is an initiative by the folks at Google to make scholarly information (journal articles, books, dissertations, preprints, etc.) available through the familiar Google interface. See About Google Scholar for their mission statement.
  • Clicking the triple bar icon on the upper left gives you access to the "Advanced Search" options.
  • Once you do a search, note that Google Scholar gives you some of the features common in article databases like Web of Science and SciFinder. You have (limited) refinement options, you can sort by either relevance or publication date, and you can create search alerts.  It also allows you to find citing references in Google Scholar.
  • Google is contracting with major publishers to allow the Google indexing robots access to their subscription websites, and with the OCLC WorldCat library catalog, in addition to sites on the publicly-accessible Web (e.g. PubMed, arXiv, government technical reports collections, open access journals.)  Note that sources indexed in Google Scholar are not necessarily peer-reviewed: see  "Publishers withdraw over 120 gibberish papers" for a description of how one researcher, as a test, created a fake author and fake papers, got them listed in Google Scholar and made his non-existent author a highly ranked scientist.
  • In addition to the documents themselves, Google Scholar extracts the cited references from the documents and so can "find" documents which are not themselves available on the Web.
  • Google Scholar also publishes their own lists of journal metrics (https://scholar.google.com/citations?view_op=top_venues&hl=en&vq=en) Their lists are based on an h-index for articles published in the last five years. (See lectures 9-3 and 17 for more on metrics.)
  • Some studies have been conducted comparing the results of Google Scholar searches with those in more traditional broad-scope indexing services, such as Web of Science. See, for instance, Bauer, Kathleen and Bakkalbasi, Nina, "An Examination of Citation Counts in a New Scholarly Communication Environment", D-Lib Magazine, 11(9), Sept. 2005 at http://www.dlib.org/dlib/september05/bauer/09bauer.html. So far, results are mixed.
  • Note that Google Scholar searches, like Google searches, can give variable results from one day to another, for reasons other than the growth of the database. Google Scholar is more stable than its general counterpart, but not so much as a traditional indexing database
  • Google Scholar does not provide specialized subject indexing, or chemical substance indexing, though documents which provide SMILES or InChI strings as chemical descriptors can compensate for that.
  • The University of California is collaborating with Google to provide UC-e-Links connections for Google Scholar searches done from UC IP addresses (though the familiar white-and-gold UCe-Links icon does not appear.)

Google Books (http://books.google.com/)

  • Google Books Search is an ongoing project from Google to index books and provide full-text access to books which are either out-of-copyright, or for which permission has been obtained from the copyright holders to make them available online. Recently, they have added the Google play store to sell electronic versions of books suitable for downloading to various e-readers.
  • Click on the Tools link to reveal a menu bar that allows to to limit by type of book, type of document, time range, and sort options.
  • Here's an example of a Google Book Search on fullerene*. It retrieves over 154,000 titles. Notice that not all of the books have "fullerenes" in the title; the indexing digs into the content of the books. Note, too, that since this is a fairly recent topic, the vast majority of the books do not provide full text online, but only a limited preview -- only about 60 have available free full text...and about half of those are not dealing with the chemical substance "fullerene".  If you wish to limit your searches to books with free full-text, click on the Tools menu and use the "Any books" menu or use the Advanced search option (see below).
  • Here is an example of a result for which the full text is available. Note that the link took us to a page on which the search term is used.
  • Note that Google Books lets you limit your results using the drop-down Tools menu at the top of our resutls display.  To do that before you run your search, you must use the Advanced Book Search at http://books.google.com/advanced_book_search? and limit to "Full view only".  Doing so on the fullerene search reduces the hits fromsome 74,000 to less than thirty.
  • Google has partnered with a number of academic libraries, including the University of California, to begin digitizing and indexing their out-of-copyright collections and make them available on the Web. These include some of the largest libraries in the world. Eventually, millions of books will be available through Google Book Search.
  • Google Books has recently begun adding backfiles of magazines to its holdings, including such interesting titles as Popular Science, Popular Mechanics, and Bulletin if the Atomic Scientists.
  • Google's digitization project has led to considerable controversy. Publishers distrust Google's willingness to respect copyright laws. A settlement with the Authors Guild and American Association of Publishers has resolved many of these problems, at least in the United States. Officials in non-English speaking nations have expressed fears that this project will marginalize non-English literature, and have moved to create their own national digitization projects.
  • Some attempts to do similar projects have failed (Microsoft tried...and gave up.)  A non-profit group created the  HathiTrust Digital Library (http://www.hathitrust.org/) as an alternative to Google Books, but it, too. has encountered controvery and has a relatively small number of items whose full text is generally available due to public domain status.

Google Patent Search (http://www.google.com/?tbm=pts&hl=en)

  • Google originally undertook to digitize the full body of United States patents, creting PDF images of the patents, and using optical character recognition to index the text.  Google Patents now includes patents from the WIPO, European Patent Office, Canada, China, Germany, Japan, South Korea, Russia, United Kingdom, France, Spain, Belgium, Denmark, Finland, Luxembourg, Netherlands, Austria, Australia, Brazil, Switzerland and Taiwan. (and will doubtless add more over time.)
  • The basic search is a keyword search of the digitized full text.  Advanced Patent Search (http://www.google.com/advanced_patent_search?) allows you to search specific fields (ncluding patent number, inventor, assignee, classification codes, publication date, etc.)
  • Over 7 million US patents have been digitized. 
  • Note that the OCR process is subject to errors, so searching older patents can be a hit-or-miss proposition, even over and above the challenges of dealing with patent language.  Google has cleaned up some of the OCR errors, so searching mistakes are fare less frequent than they once were.
  • For more informaion, see About Google Patents.

Google Images (http://images.google.com/)

  • Google Images specializes in searching for images: photographs, but also tables, graphs, charts...and structure diagrams.
  • Google Images keyword searching depends on how the images have been labeled on the original HTML document, so don't expect a comprehensive search of all images of, say, ferrocene, on the Web. But it can be useful for finding structure diagrams, illustrations of laboratory procedures and the like.
  • You can also upload an image, and discover websites where that image has been posted. This is a great way to discover the sources of images from social media and other Web sites that may have been uncredited on the site where you found them.
  • Once you've done a search (by keyword or image), click on the Search Tools tab to refine your results by Size, Color, Type, Time or Usage Rights.  The latter can help you find images that you can reuse in your own documents without specially requesting permission from the copyright holder.

Google Drive (http://accounts.google.com/)

  • Google has merged most of their personalized services: Gmail e-mail service, Google+ social networking and Google Docs, into a single account under the heading of Google Drive.
  • One major feature is the set of applications formerly known as Google Docs. In one sense, these are simply alternatives to conventional word processing, spreadsheet, presentation, drawing and form creation software, with locally mounted software replaced by a Web interface, and document storage on remote servers - in the "cloud".
  • Its relevance to scholarly endeavor, however, is as a collaborative tool - enabling users to easily share these documents with one another.
  • Lots of other folks are in the collaborative applications business these days.  See, for example, Zoho.com at http://www.zoho.com/

Alerting services and RSS

  • Most sources of information on the Web depend on the user going out and tracking them down. This is sometimes referred to as "pulling" information. Services which send desired information to the user automatically are said to "push" information. Many of the electronic databases we have examined have some form of alerting service which allows you to set up a search, and then automatically receive selected pieces of data on a regular basis without further effort. Some online journals allow you to receive tables of contents; some online newspapers have e-mail news features.
  • More recently, a new approach to "pushing" information out to users has come into vogue: RSS. The following description is borrowed from Engineering Village 2 which has an RSS feature for Compendex and its other databases:
    • "RSS stands for Really Simple Syndication or Rich Site Summary. It is an XML-based format for content syndication. RSS is a way of publishing and distributing content from one Web site to another. It's an easy way for you to keep updated automatically on web sources that you follow."
    • "You need to have an RSS reader or aggregator to make use of RSS. RSS readers will display information feeds from your selected sites on your computer without visiting each Web site. You will automatically receive the most current information whenever these sources are updated. It will also allow you to share information with others in your research or study group."
    • "With an RSS aggregator, you will be able to find technical information from Engineering Village 2, latest news from your library (if your library is providing an RSS feed), or latest technology news from the New York Times."
    • "There are several types of RSS readers. Some are Web-based, such as My Yahoo, Bloglines or NewsGator, some are extensions of Web browsers such as Mozilla Firefox and some are desktop readers like FeedDemon or Awasu. 
  • The main advantage for the user of RSS over more traditional alerting services is that your RSS aggregator can pool RSS feeds from a variety of sources into a single location for you.
  • You can see an example of a collection of RSS feeds on the Help by Subject: Chemistry & Biochemistry page at http://guides.library.ucsb.edu/chemistry, which displays feeds from C&ENews, Chemistry World, and ChemSpider's The Spinneret.

Blogs: What are they, and should I care?

  • Blogs are part of the general class of social networking software, which includes phenomena like MySpace and FaceBook. While the latter two haven't made strong inroads into the sciences, other forms of social network software are gaining in importance, especially in science education. See, for example, this article from Chemical & Engineering News about a 2007 symposium in the ACS Division of Chemical Education.
  • Blog is short for Weblog. It is a class of software to allow easy publication on the Web, readily organizable, and with the possibility of allowing other users to add comments to your publication. For a capsule description of blog basics see What Are Weblogs? at http://www.userland.com/whatAreWeblogs. For an extensive collection of information on blogs, see Weblogs Compendium at http://chnm.gmu.edu/digitalhistory/links/cached/chapter6/6_13g_blogtools.htm
  • Most blogs are sort of personal diaries/newsletters/collections of random thoughts. However, blogs are being used for some types of systematic scientific information, replacing more static lists of web sources. See, for example, About: Chemistry. Other blogs are more news oriented, some using teams of writers/bloggers to cover the field, such as Chemistry Blog.  A blog aimed at the educated non-specialist is The Culture of Chemistry at http://cultureofchemistry.fieldofscience.com/Useful Chemistry (http://usefulchem.blogspot.com/) presents the work of a particular research group at Drexel University, heavily devoted to open science and opten data.  If you look carefully at these, you will notice that even high-quality blogs, launched by authors with the best intentions, can languish without new posts for long periods of time.
  • Some journal publishers are launching blogs at their websites to facilitate communication among their authors, editors and readers. See, for example, the NCBI Insights, BMC Chemistry and Nature blogs.
  • The Royal Society of Chemistry (RSC) has a blog site at http://blogs.rsc.org/ with a nice mix of newsy and entertaining entries.
  •  The WWW Chemistry Guide has a good short list of chemistry blogs. You can also find many examples by searching "chemistry blogs" or "chemistry blogspot" (Blogspot is a very popular blog-hosting site) on Google or other internet search engine.
  • Note that many blogs offer RSS feeds so that you can easily keep track of new postings.
  • The basic blog platform can be used as a vehicle for scholarly publishing.  One such recent effort wass Annotum (http://annotum.org/) using the WordPress blog software.  You can find a gallery of Annotum-based sites at http://annotum.tumblr.com/ . Whether it will have any significant impact on scholarly publishiwas apparently negligible, as Annotum's final release was in 2016 and it hasn't been revived.
  • Not exactly a blog, but an outstanding example of using the Web for "micropublishing" of chemical information, ChemSpider Synthetic Pages (CSSP) (http://cssp.chemspider.com/) allows researchers to publish experimental details on individual reactions, even failed reactions (which can be very valuable information!).  Peer review is provided after-the-fact by user comments.  For more about CSSP, see their "About" section at http://cssp.chemspider.com/About.aspx

Wikis: Do It Yourself Web guides made easy

  • Wikis are a concept which has been around for a surprisingly long time: the first was created in 1995. Wikis are designed to allow easy creation of web pages. Like blogs, other users can comment on the contents of a wiki, but unlike blogs, any user can edit the content of a page. They can be used for communities of common interest to build shared resources. For more information, see the article "Wiki" in the Wikipedia at http://en.wikipedia.org/wiki/Main_Page.
  • The Wikipedia is a good example of a resource being built by its user community. Anyone can add articles or edit existing articles in this "free encyclopedia". However, an informal community of chemist-volunteers has been working hard to make sure that quality chemistry information is being added to Wikipedia. They have created the Wikipedia Chemistry Portal at http://en.wikipedia.org/wiki/Portal:Chemistry, a great place to start exploring the chemicstry-related resources to be found there. Recently, Chemical Abstracts Service agreed to begin verifying the CAS Registry Numbers listed for major chemicals in Wikipedia aprticles.
  • Other wikis are devoted exclusively to chemistry, such as Chemistry Wiki. (It is, alas, largely unchanged for some thre years now.) Most of these are much smaller and less well-developed than the Wikipedia Chemistry Portal. Searching on "chemistry wikis" or "chemistry wikispaces" on Google or other internet search engine can track down interesting possibilities.
  • Wikis are taking off as teaching tools, both in general and for specific courses. ChemEd Collaborative, a Wiki project of the Chemical Education Digital Library (ChemEd DL) is a good example of a group project utilizing Wiki tools.
  • As with blogs, some journal publishers have tried adding Wiki sites to their online journals. However, these experiments have mostly been failures.
  • Some information scientists have proposed using wiki software as an alternative, "free", method of scientific publication, which would allow an author to publish, peer reviewers to critique, editors to edit and readers in general to comment, all easily and interactively. Such concepts have not yet been widely tested.
  • Note that blogs and wikis, perhaps even more than the average Web site, are subject to clutter with garbage. A critical eye is needed to separate the gems and gold from the trash. Even for generally high-quality products such as Wikipedia, a good rule of thumb is "Wikis can be a good place to start a search, but they should never be where you finish your search."

Podcasts and streaming video -- the audio/video Web

  • Podcasts are the popular term for audio and video segments "broadcast" via the Web, and viewable/listenable on devices like the iPod, as well as more full-featured computers.
  • In addition to the recreational uses of podcasting, there are now many sources of scientific information being released as podcasts:
  • Some conferences are recording their symposia and publishing them on the web as podcasts.
  • YouTube (a division of Google), the massively popular site for distributing video clips  is also the home to some educational and scientific material. A search on "chemistry lectures" on YouTube yields over 2.2 million hits as of March 2018. Note that, as with most YouTube content, the professionalism and quality of the videos vary dramatically. Some are created by students capturing a lecture with their cellphones; some are created by the chemistry departments and are much slicker. Unfortunately, the only way to discover which is which is trial and error. Note, too, that many YouTube videos come and go, sometimes because the person being recorded decides he/she doesn't want his/her presentation put up on the Web without their permission. The  Filter options let you limit by date uploaded, length, features, or choose a sort order.
  • Vimeo https://vimeo.com/ is another popular site for video hosting, if not quite so ubiquitous as YouTube. The UCSB Library, for example, uses a Vimeo site to host itutorial videos. A searchfor "chemistry" on Vimeo yileded 29,400 hits. You can refine by category (such as "instructinal"), length, when added, etc.
  • A large number of prestigious universities (including Oxford, Stanford and MIT) are now making lectures available through Apple's iTunes U at https://apps.apple.com/us/app/itunes-u/id490217893 with a huge array of excellent lectures on chemistry topics.
  • The University of California - Irvine chemistry department is now offering an entire undergraduate curriculum worth of chemistry lectures free on the Web under a Creative Commons license: Open Chemistry (http://ocw.uci.edu/openchem/)  Since there are no laboratories, discussions or exams associated with the lecture material, these are not credit-bearing classes, or part of a degree program, but are merely offered as instructional tools.
  • Also of note, though not open-access, is JoVE, the "Journal of Visualized Experments"  https://jove.com This is a curated collections of video recordings of experiments with explanatory text and vocie-overs in a wide range of science and engineering fields. The UCSB Library subscribes to a number of these subject segments, and, temporarily during the pandemic, has access to all of them. The Education series are particularly useful as a supplement to undergraduate lab courses, especially when in person labs are inaccessible.

Networking -- social and professional

Web sites designed to facilitate networking have become extremely popular in recent years, and they do have uses for chemists.

  • Friendster was the first social networking site, founded in 2002 in Mountain View, CA and went live in 2003. Though it still has a large user community, especially in Asia, it has been somewhat eclipsed in the United States by later arrivals.
  • LinkedIn, also founded in 2002, is a heavily business-oriented site, aimed at professional networking, including job-seeking and employee-seeking, though it does have numerous personal interest groups available. Its privacy features are stronger than in some other social networking sites.
  • MySpace launched in 2003, inspired by Friendster, and grew rapidly through heavy promotion and a useful feature set. In 2005, it (and its parent company, eUniverse) were purchased by Rupert Murdoch's News Corporation, and merged into its Fox Interactive Media division. It is extrememly popular with musicians, as it allows to upload, distribute and/or sell MP3's of their music. MySpace Forums includes a section of science forums.. Many observers suspect that MySpace may be doomed in the long run.
  • Facebook started as a networking site for Harvard University students in 2004. It subsequently expanded to add other college, high school students, selected companies, and, in 2006, anyone over 13 with a valid e-mail address. It is now the most popular social networking site in the U.S. Facebook members can post personal information, create networks of "friends", "groups" of people interested in a common topic, "fan pages" devoted to any topic, "events", both on and offline, and a wide range of applications, from games to search tools for databases and catalogs. While still mainly a social tool, it has become a place for groups and committees to share news and publicize their activities. Here, for example, is the Facebook page for the UCSB Chem Club (Note: you must have a Facebook account, and log in, to join the group.) JACS also has a Facebook page which is publicly accessible. Facebook's priacy policies, frequently subject to change, are a matter of considerble controversy.
  • Reddit, the social news site, has a variety of subject-oriented "communities", including a Chemistry community
  • Twitter is a hybrid of social networking and blogging, designed to allow users to post short (140 chararcter or less) messages which are delivered to those who sign up for them. It's popularity as a social medium may have even surpassed that of Facebook.  The American Chemical Society and the Royal Society of Chemistr have siste on Twitter.  See also a now somewhat dated article from Chemical & Engineering News on Twitter use by chemists, Real-Time Community (http://cen.acs.org/articles/91/i8/Real-Time-Community.html-
  • Instagram is a network oriented to sharing phtos and videos, now owned by Facebook. It now has an Instagram for Business section. The American Chemical Society now has its own Instagram channel, amerchemsociety. So does the Royal Society of Chemistry, roysochem
  • An example of a more specialized social networking site is LibraryThing. This site allows you to create an online catalog of your personal library, and share it with the world, as a way to find other books you may be interested in, and people who share your interests.
  • There are also social networking sites designed for students to pool their knowledge. Cram.com allows to to create, post and share "flash cards" as study aids. Much like del.icio.us links, sets of cards are tagged by their creators for easy searching. Here's a set tagged as "chemistry". StudyBlue.com allows you create files of flashcards, wiki notes, study groups and networks of friends. It requires you to register, but there is a demo login that allows you to see its capabilities.
  • Academia.edu and ResearchGate are two very popular commercial sites aimed at scholars and researchers.  You can create a profile, and provide bibliographies of your work.  Note that may users post copies of their work on these sites, but frequently do so in violation of copyright.
  • Getting in on the networking game, the American Chemical Society has created the ACS Network, a site where ACS members, student affiliates or "global partners" (defined as anyone with access to ACS journal subscriptions...like UC students and faculty), can network. Members can post a profile, resume or vita; participate in discussion groups, and share documents collaboratively.

Chemistry on the move - mobile science!

When "smartphones" first appeared, some asked, "Who would ever want to do serious literature searching/journal reading/data seeking/etc. on a tiny phone screen?"  As it turns out...a LOT of people. With every faster Internet connectivity via phones running iOS, Android, etc., and the introduction of tablet computing, scientists in the factory or in the field can have almost as good access to scholarly resources as they would in their offices or libraries.

  • Mobile applications can be divided broadly into two categories: apps - stand-alone programs that run on the mobile device and may take advantage ot their Internet connectivity, and mobile-adapted Web services - which operate through a standard Web browser on the mobile device, with adaptations to deal with the smaller screens and/or lack of certain tools (Java, Flash) in the mobile environment.
  • Apps, like traditional software, need to be customized for the operating system of the device on which you wish to use them.  As a result the easiest way to track down useful apps is to go the the appropriate online "store" and search there.
  • Access to apps for the Apple iPhone requires installation of App Store.  However, you can see some representative educational apps at this iTunes Preview site (https://apps.apple.com/us/genre/ios-education/id6017)
  • The Android Market, merged into Google Play may be viewed directly.  A search of "chemistry" in Feb. 2022 displayed 250 hits. There are actually more available, but only 250 will display at a time. Make your search more specific to see more. The overall answer set may be sorted by relevance or popularity, filtered to either free or paid apps, and filtered by safety level (i.e., maturity level - a parents helper).
  • The Windows Phone store has many of the same apps, though perhaps not quite so many as for iOS or Android.  Here's a search for "chemistry", which yielded 250 apps in Feb. 2022  Note that the site has a refinement option to separate games from "serious" software.
  • Some companies have created mobile app versions of their desktop softare and sell or distribute them on their own websites.  See for example, iChemLabs ChemDoodle Mobile.
  • Many journal and database publishers, including ACS and RSC have created apps for one or both iOS and Android for accessing their content.
  • Other publishers have gone the "mobile-adapted Web" route.  Many have special URL's for their mobile versions.
  • Here's a recent article that may be of interest:

 

© 2022 Charles F. Huber

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This work by Charles F. Huber is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License.
Based on a work at guides.library.ucsb.edu


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