Chemical Literature (Chem 184/284)

Lecture 12, Part II: SciFinder Web, Part 1

Chemical Abstracts Online

• Just as Chemical Abstracts is the single most important printed tool for chemical information, so its online counterpart is the most important electronic source.
• Electronic CA is made available through several vendors, including DIALOG, DataStar, Ovid, Orbit, Questel, ESA-IRS, and STN International, and in several formats, including STN Online, STNEasy (web menu interface), STNWeb (web command interface), SciFinder (client-server menu interface) and SciFinder Scholar (similar to SciFinder, for academic institutions) . We will be primarily using SciFinder Scholar.
• If you would like more information on the command language version of STN, see the following pages: Author Searching, Subject Searching, Substance Searching, Structure Searching.

STN International

• Chemical Abstracts Service (CAS) (Columbus, Ohio)
• Fachinformationzentrum Karlrsruhe (FIZ Karlsruhe) (Karlsruhe, Germany)
• Japan Information Center for Science and Technology (JICST) (Tokyo, Japan)

Key Features of the Various Forms of CA Online

• STN Online
  • Available only to account holders with STN International; pricing is by records displayed and connect time and/or subject terms used.
  • All CA databases are available, as well as numerous others from other sci-tech database producers.
  • Multiple databases may be browsed (EXPAND command) or searched simultaneously. Answer sets may be combined, and duplicate identified or removed.
  • Uses Messenger command language.
  • Full power of CA databases is available...to those who have mastered the command language.
  • Connection by direct TELNET connection.
  • For easiest searching, especially structure searching, you need to use STN Express, interface and communication software for Windows and Mac computers. STN Express is designed to expedite STN online searching in many ways.
  • With current versions of STN Express, user can jump to full text records from selected publishers and patent offices where available.
• STNWeb
  • Available only to account holders with STN International; pricing is by records displayed and connect time and/or subject terms used.
  • All CA databases are available, as well as numerous others from other sci-tech database producers.
  • Multiple databases may be browsed (EXPAND command) or searched simultaneously.
  • Uses Messenger command language.
  • Full power of CA databases is available...to those who have mastered the command language.
  • Connection through the World Wide Web.
  • Requires Netscape Navigator 4.X or higher or Internet Explorer 4.X or higher, with JavaScript enabled. Structure drawing requires a free, downloadable plugin.
  • Through "ChemPort Connection", user can jump to full text records from selected publishers and patent offices.
• STNEasy
  • Available only to account holders with STN International; pricing is by search and by answers displayed.
  • Most but not all CA databases are available, as well as numerous others from other sci-tech database producers.
  • Multiple databases may be searched simultaneously.
  • Uses a Web forms and menu interface.
  • Cannot use all the sophisticated features of Messenger -- the Web interface is simplified.
  • Connections through the World Wide Web.
  • Requires Netscape Navigator 4.5 or higher, or Internet Explorer 5.0 or higher.
  • Through "ChemPort Connection", user can jump to full text records from selected publishers and patent offices.
• SciFinder
  • Available only to subscribers at specified terminals.
  • Pricing is per "task" or by annual subscription.
  • Selected CA databases plus MEDLINE available.
  • Client-server system. Requires special SciFinder client software.
  • Designed for use by practicing chemists, the interface contains many built-in features to allow the user to take advantage of Messenger features without knowing the command language.
  • Client is available only for Windows and Mac operating systems.
  • Through "ChemPort Connection", user can jump to full text records from selected publishers and patent offices.
• SciFinder Scholar
  • Available site-wide at subscribing campuses; number of simultaneous users is limited.
  • Pricing is by annual subscription.
  • Client-server system. Requires special SciFinder client software.
  • Selected CA databases and MEDLINE available.
  • Designed for use by practicing chemists, the interface contains many built-in features to allow the user to take advantage of Messenger features without knowing the command language. Features of SciFinder Scholar usually lag behind those of SciFinder by one or two versions at any given time.
  • Client is available only for Windows and Mac operating systems.
  • Through "ChemPort Connection", user can jump to full text records from selected publishers and patent offices.
• SciFinder Web
  • Newly released in 2008.
  • Available site-wide at subscribing institutions; number of simultaneous users is limited.
  • Pricing is by annual subscription.
  • Web interface. Structure searching uses a Java applet.
  • Selected CA databases and MEDLINE available.
  • LIke the SciFinder client products, SciFinder Web is designed for use by the practicing chemist. Not all features of the client have been implemented yet in this version, but both academic and commercial customers use the same Web interface. Some features have been implemented in a more sophisticted fashion than in the current SciFinder client.
  • SciFinder Web is usable on Windows, Mac or Unix systems. Java and Javascript must be enabled. Works with Internet Explorer v. 6.0 or higher and Mozilla Firefox v. 2.0 or higher.
  • Through "ChemPort Connection", user can jump to full text records from selected publishers and patent offices. Pop-up blockers must be turned off or set to accept pop-ups from cas.org.

What You Can Search in SciFinder Web

• In SciFinder Web at present, you can search the following:
  • The Chemical Abstracts document database (CAPLUS). Documents from 1907 to the present (plus selected records pre-1906) have bibliographic information, abstracts, and full subject and substance indexing (by CAS Registry Number.) Total number of records: about 27 million as of Jan. 2008. Updated daily.
  • The Chemical Abstracts substance file (REGISTRY). Substances indexed by Chemical Abstracts since 1957, plus substances from other sources (regulatory agencies, chemical catalogs, etc.) Includes Registry Numbers, chemical names, molecular formulas. Searchable structure diagrams are available for most simple comounds. Many proteins and nucleic acids have sequence information (displayble but not directly searchable in SFW). Many compound records have predicted and/or experimental chemical data for selected properties. In SFW, this information cannot be searched directly, but can be used to refine searches. Over 93 million records as of Feb. 2008 (33 million simple substances; 60 million biosequences).
  • The Chemical Abstracts reaction file (CASREACT). Organic reactions from journal literature from 1907 to present, and patents from 1982 to present. Structure searchable for reactants and products, with reaction sites and atoms specifiable. Over 600,000 documents indexed, with some 14.5 million reactions as of Feb. 2008.
  • The Chemical Abstracts chemical catalogs file (CHEMCATS). Information (including pricing) on over 19.1 million substances from over 900 suppliers' catalogs and chemical libraries. In SFW, commercial availability information is linked to substance records but may not be searched directly.
  • The Chemical Abstracts chemical regulatory database (CHEMLIST). Lists regulatory information from a host of national and international agencies on about 246,000 substances as of Feb. 2008. In SFW, regulatory information is linked to substance records but may not be directly searched.
  • MEDLINE (PubMed). The National Library of Medicine's database may be searched simultaneously with the CAPLUS database in SFS. Over 16 million records from 1950 to present. Updated five times/week, with a complete annual reload to update subject headings.

Getting Started in SciFinder Web (SFW)   (For SciFinder Scholar (SFS), see here.)

Registration

• SciFinder Web requires no client software, but it does require advance registration by each user. Each institutional subscriber has its own registration page for SciFinder Web. For UCSB students faculty and staff, you will find the link to that page here at http://www.library.ucsb.edu/eresources/databases/scifinder.html. Note that access to this page is restricted to UCSB IP addresses. To go to this page from off campus, you will need to log in using the campus proxy server or VPN server. See the Off Campus Access page at http://www.library.ucsb.edu/help/offcampus.html for details.
• Note: descriptions and screen shots in these lectures are for the SciFinder Web version as seen on Firefox 2.0 on a Windows XP_ machine. The look on other operating systems may vary slightly.

• Above is the first screen you'll see after clicking on the registration link. Click the "Next>>" button to begin registration.
• On the screen below, fill in the information required. Notice that some information is optional. You must use a valid "ucsb.edu" e-mail address, such as "smith@umail.ucsb.edu" or "jones@chem.ucsb.edu". E-mail addresses from other providers (e.g. gmail,aol, yahoo) will not be accepted. Only one SFW username and password may be created per e-mail address.

• After you have completed registration, you will receive an e-mail at the address you entered on the form verifying your registration. You must then follow the instructions on the e-mail to verify that you are the valid user of that e-mail address and complete the registration process.

Logging In to SciFinder Web

• Now that you are registered, you may proceed to the SciFinder Web login page. You can find a link to it on the UCSB SciFinder page above, or you may connect directly at https://scifinder.cas.org/ If you are using a public workstation, DO NOT check the box "Remember my username"!!

• When it successfully connects, you will see the SFS User Agreement. You must click the "Accept" button, agreeing to the terms, before you can proceed. SciFinder Web requires that the user be currently affiliated with the academic institution providing the service, and that the research be for teaching or academic purposes, not commercial research.
  

• You will now be taken to the SciFinder web opening screen below.

Breakdown of the Opening Screen of SciFinder Web

Category Selection Bar

• On the left top of the screen are icons for selecting what type of item you are searching for: "References", "Substances" or "Reactions". The default selection is "References", unless you change it in your Preferences (see below). Clicking on one of the other icons will change the display in the search area below.

Session and Personalization Options

• At the upper right of the screen are lins for some of the personalization options:
  • "Answer Sets" enables you to view answer sets which you have saved on the SciFinder Web server. Thanks to the registration process, each user has a personal space on the server for answer set storage.
  • "Keep Me Posted" is SFW's term for search alerts. When you perform a search on SFW, you can save that search and arrange for it to be run when the database is updated. The new results will saved, and appear in the "Keep Me Posted: section when you next log on. You may choose (in Preferences) to have them e-mailed to the e-mail address you supplied when registering.
  • "History" displays your search history for that session. When you sign out, the search history is erased.
  • "Preferences", at present, allows you to select which type of search is the default on your opening screen, and whether "Keep Me Posted" results will be e-mailed to you.
  • "Help" -- Clicking the Help button opens up a separate window with help topics browsable by table of contents or by alphabetical index, or searchable by keyword. The opening screen introduces some of the new and familiar features of SciFinder Web.
  • "Sign Out" Click here to end your session. Remember: Always sign out as soon as you are finished with your session to free up your port for other users!

Main Search Window (for References)

• The image below is the Search Window for exploring References by Research Topic. We will see some of the other screens for exploring references later on in this lecture, and the Search Windows for Substances and Reactions in later lectures.

• On the left of this area, you may select which type of search you wish to perform. For References, the options are:
  • Research Topic-- searches the title, abstract and index terms of reference records (eequivalent to a "keyword" search in many databases.), discussed in detail in the next lecture.
  • Author Name -- Author search, discussed in detail below.
  • Company Name -- Search for institutions where the authors performed their research, including companies, academic institutions, government labs, etc., discussed in detail below.
  • Document Identifier -- Find a known document by CAS Accession Number, Patent Number (or Patent Application Number), or PubMed ID.
  • Journal -- Find known journal articles by combinations of journal name (including abbreviations and acronyms, such as J. Amer. Chem. Soc. or JACS), volume, issue, starting page, words in the article title, author name or publication year (or range of years).
  • Patent -- Find known patents by combinations of patent numbers, assignee's name or inventor's name or publication year (or range of years).
• Note that the search window will change depending on which option you select.

Limits

• The lower middle part of the screen contains the options for limiting the search in the search window above.
• The options will vary depending on the type of search selected. For a "Research Topic" search, you may limit by pubication year or range of years, document type (e.g. journal article, patent, dissertation), language, author name or company name.

Explore References by Author Name

• Above is an example of the author search screen for SciFinder Web. Some tips for entering author names:
  • Enter as much of the name as you know.
  • Enter spaces, hyphens, and apostrophes as you would if you were handwriting the name.
  • Replace special characters with equivalent character(s), for example, use either a or ae for ä.
  • Select "Look for alternative spellings of the last name" to account for name variations and typographical differences.
  • For complicated names, such as Von Braun or hyphenated names, or names from non-Roman alphabets which may be transliterated in different ways, try multiple searches and determine which give the best results.

• Select the author names you wish to search by clicking the box next to the name.
• In this case, I selected all the possibilities except for "Ford". Note the buttons for selecting or deselecting all authors, and, above them, the total number of authors in the list, and the number selected.
• Also note the "breadcrumb" giving the history of the search: Author Name "Ford, Peter C". You can use these to retrace your steps in complicated searches. To the left of that is a "Keep Me Posted" button. Clicking it will create a search alert from the search listed to its right.
• Now click on "Get References". The system will automatically retrieve an answer set corresponding to the names you have selected. Answers will be displayed most recently indexed first. If your answer set has more than 10,000 references, only the first 10,000 will be displayable. However, the full answer set may be Refined to get segments of the set.

Breakdown of the Results Display in SciFinder Web

• Starting just below the SciFinder logo: Note that the "breadcrumb" trail has grown and now shows the number of references found in the search.
• Next to the References heading are links for extracting information from the reference answer set:
  • Get Substances -- Creates a list of the substances indexed in the answer set.
  • Get Reactions -- Creates a list of the (organic) reactions indexed in the answer set.
  • Get Cited -- Creates an answer set of the references (which were indexed by CAS) cited in the documents in your starting answer set. Note that cited reference information is only available for journal articles since 1997, and patents since 1999.
  • Get Citing -- Creates an answer set of the references (indexed by CAS) which cite one or more of the documents in the answer set. Since citation information is only availble from 1997 forward, this will only retrieve documents published since then.
• Note that each of these functions may be applied either to the entire answer set or to selected documents. To select, check the box to the left of the desired document.
• Just below that, there is a bar giving the total number of documents in the answer set, the number selected at present and the options to "Keep Selected" or "Delete Selected". Clicking the former will remove all unselected references from the answer set; clicking the latter will remove the selected documents from the answer set. These features can be used to weed out unwanted answers from an answer set. Warning; Do not use either of these before you have finished viewing the entire answer set (or as much of it as you need). You may delete desired answers which you haven't examined yet.
• Just below that on the left are buttons to select or deselect all records.
• To the right, are links to jump through the llst of references. By default, SFW displays records in reverse chronological order by date of indexing. Each screen displays 20 records, so in this case, there are 40 screens for the 782 references.
• On the right of the screen is the Analysis of the answer set. This collects the information from a selected field of the reference records and displays them in order of descending frequency. The default analysis is be Author Name, but you may also select from the drop-down menu: CAS Registry Number, CA Section Title (the 80 subject sections of print CA), Company/Organization, Database (CAPLUS or MEDLINE), Document Type, Index Terms (subject headings), Journal Name, Language, Publication Year, or Supplementary Terms. The screen automatically displays the top ten items in the list. To see more, click on the "Show More" button. This will open up a sub-window with a scrollable display of the top 500 items in the analysis list. You may then select items from the list to narrow your answer set to references containing that author, index term, etc. Note that, unlike SciFinder Scholar, SciFinder Web does not offer the option of listing the Analysis list in alphabetical order.

• Below the Analysis list on the right are options for Refining (i.e., narrowing) the answer set by Research Topic, Author Name, Company Name, Document Type, Publication Year, Language or Database. Note that the entry window will change depending on which option you select.
• In the center of the screen is the actual display of references. Each record displays:
  • Title of the reference. Clicking this title will display the full record for the reference (see below).
  • Authors/inventors
  • Source information, e.g. journal name or patenting authority, year of publication, language and source database
  • The abstract, or the first 100 words thereof.
  • Links to the Substances, Reactions, Citing References and Full Text. Note: The presence of the link does not imply that the items in question are necessarily available for that document.
  • The full text link is a link to the ChemPort system, which in the UC system uses UCe-Links to link to article full text (as well as other UCe-Links functionality, see below.)

  
  

  Full Records ("Reference Detail") for References in SciFinder Web

  
  
  
  
  
  • Note at the top, how the "trail of breadcrumbs" continues to expand. You can always jump back to an earlier stage by clicking on the appropriate link.
  • Below that, you have links to get the Substances, Reactions, Cited References, Citing References and Full Text for this particular document.
  • To the right are links for Saving, Printing and Exporting your answer or answer set.
  • On the right hand side, you find the source information, company/organization of the lead author, CAS accesssion number, and publisher and language of the article (for recent papers.)
  • In the center, you find the title, authors, full abstract, "indexing" (i.e. section codes), "concepts" (i.e. index terms or subject headings, with subheadings), substances (identified by Registry Number, with subheadings and role indicators), supplementary terms, and at the bottom, for references since 1997, the cited reference list for the document in the order in which they are cited in the paper.
  • Note that the Registry numbers are hot-linked. Clicking on one takes you to the Registry Record for that substance (We will examine this in detail in a later lecture.)
  • Note that most of the cited references are also hot-linked. Clicking on one of them will take you to the full CAS record for that document.
  • Patent records (see below) include patent family data where available, and the patent classification codes (IPC codes for all patents, and US codes for US patents.)

  
  
  
  
  
  
  
  

  Saving, Printing, Exporting

  • Select the results you wish to save, print or export by clicking the Selection Box to the left of the answer(s).
  • Save saves the desired set of answers on the SciFinder Web server under your personal account. You must give the answer set a title, and you can add descriptive notes.
  • Print creates a formatted list of answers in a new window which you can then print with your browser's print function. You have a choice of summary or detailed records. Note: The summary view does not contain the full bibliographic information you would need to cite the records! Always use the detailed view!
  • Export saves the answer set on your local workstation. You must choose a file name and a file type:
    • Answer Key eXchange (.akx) -- This format preserves hot links. However, it may only be opened in the SciFinder Scholar client, or a software package call SubScape. Up to 20,000 answers may be saved, but the maximum file size is 1MB.
    • Portable Document Format (.pdf) -- This is the familiar Adobe Acrobat document format. You may choose to have the answers in summary or detailed form. Hot-links in the records are not active. A maximum of 500 records may be exported in this format at a time.
    • Answer Keys (.txt) -- This is plain ASCII text which saves only the CAS Accession number (for references) or CAS Registry Number (for substances). You cannot save reaction records in this format. Only 500 records at a time may be saved.
    • Quoted Format (.txt) -- This is a format which can be imported by spreadsheet software (e.g. Microsoft Excel) or database software (such as Microsoft Access.) It does not preserve links, and only 500 records at a time may be downloaded.
    • Tagged Format (.txt) -- This is a format designed for import into bibliographic database software, such as EndNote and EndNote Web. It does not preserve highlighting, and can save only 500 answers at a time.
  • Note that, at present, there is no direct e-mail option within SciFinder Web.

  Explore By Company Name

  • This feature is useful for exploring the research efforts of a given company, agency or academic institution.

  

  • Below is a portion of the "Company name" answer set obtained by searching "3M". A search of "Minnesota Mining" gave the exact same result. Look at he Analysis by Company/Organization at the right. Note that the search has a degree of built-in "intelligence" and will find (at least in many cases) alternate forms of a company name. However, it cannot keep track of all mergers, acquisitions, spinoffs, and name changes.
  
  • In the case of non-corporate institutions, there is frequently no attempt at cross-referencing. Compare (below) the total number of answers and the Analysis by Company/Organization of an answer set generated by searching "Santa Barbara" with that for "UCSB".
  • For academic institutions, you may need to do multiple searches with different synonyms and analyze/refine and combine them to get a truly comprehensive or accurate search.
  • Note, too, that only the company/organization of the lead researcher is listed. If a faculty member is collaborating on a project, his or her institution may not be the one named. Use "company name" as a limiting tool with caution.
  

  

  Features of SciFinder Scholar unavailable in SciFinder Web

  As of Feb. 2008, neither duplicate record removal nor combine sets are available in SciFinder Web. It is expected that these features will be added in future releases.

  This page created by Chuck Huber (huber@library.ucsb.edu).
  Updated: 02/12/08 10:22:56