STN on the Web Documentation


Table of Contents

Login Page
Login Screen
Login Page Toolbar
Session Page
Session Screen
Session Page Toolbar
Session Transcripts
Help
Full text
Citation Searching
Hypertext Links
CAS Registry Number Hypertext Links
Derwent Hypertext Links
Search Assistant
Results Assistant
Chemical Structure Searching
Patent Hypertext Links
Patent Graphic Images
Patent Family Assistant
Upload Command File
STN AnaVist Assistant
STN Viewer Assistant
Sequence Assistant
CAS REGISTRY BLAST ® Similarity Searching
Sequence Searches in DGENE and PCTGEN
Upload Sequences in DGENE and PCTGEN

Login Page

The Login Page consists of the Login Screen and the Login Page Toolbar . The Login Screen consists of the entry boxes for starting an STN session. The Toolbar offers various options that are available before starting an STN session.

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Login Screen

To start an STN session, click in the Login ID box on the Login Screen and enter your login ID. Then click in the Password box and enter your password. Click the Login button. After a few moments, the STN Session Page will appear.

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Login Page Toolbar

The Login Page Toolbar provides information about STN® on the Web and STN® in the News and Help folders, links to download the Structure and Sequence Plug-ins, and links to Standard and Academic (if available) login screens:

  • News

This folder contains the latest news about STN on the Web and STN (via the STNews Archive).

  • Help

This folder contains many links to detailed information about STN on the Web and STN.

  • Get Structure
    Plug-in

This button offers access to information on how to download, install, and use the free graphical structure query plug-in.

  • Get Sequence Plug-in

This button offers access to information on how to download, install, and use the free BLAST sequence search plug-in.

  • Standard Login

This button opens the Login Page.

  • Academic Login

This button opens the Login Page for Academic Programs.

  • Feedback

This button opens a browser e-mail window to send a message to the STN Help Desk.

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Session Page

The Session Page consists of the Session Screen and the Session Page Toolbar. The Session Screen shows the session history and features a command entry box at the bottom. The Toolbar offers links to help messages, user documentation, news messages about STN, the search assistants, and session control features.

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Session Screen

The Session Screen shows the latest (most recent) part of the STN session. To look at earlier parts of the session, use the scroll bar on the right side of the screen to scroll up and down in the session history. The complete history of the session is available in the session screen for the duration of the session. After the session is ended (Logoff), the portion of the session history that is available in the Session Screen will depend on the size of the browser cache.

See also Session Transcripts for information on downloading a complete session history.

You may also control the session output with the "Hide session output" and "Show session output" buttons in the right hand corner of the bottom frame of the session page. These buttons toggle the session output shown in the session window on and off. This does not affect what is being recorded in the session transcript.

The Session Screen features a command entry box at the bottom. This box allows entry of STN commands that can be submitted either with a carriage return or by clicking the Submit button at the right side of the box. There is a limit of 256 characters for the commands and terms that may be submitted, including blanks and other special characters.

A three-line toggle switch is available to the right of the command entry box. This switch toggles the command entry box from one line status to multiple line status, and back. In multiple line status, the last 3 entry lines are shown in the box. Use the scrollbar to scroll up and down within the box. While the command entry box is in multiple line status, carriage return key may be used only to enter additional lines, and the Submit button must be used to submit the commands.

Three additional buttons are available to the right of the Submit button: |< , <, and >

See also Upload Command File for information on how to upload command (script) files to an STN on the Web session.

Records that are displayed in the Session Screen may contain hyperlinks. These are marked with a blue underline. See also Hypertext Links, CAS Registry Number Hypertext Links and Patent Hypertext Links for information on other types of hyperlinks. Records may also offer a Full text button, which gives access to the full text options for the source document.

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Session Page Toolbar

The Session Page Toolbar provides the same News and Help folders as the Login Page Toolbar, plus additional functions that support the STN session:

  • News

This folder contains the latest news about STN on the Web and STN (via the STNews Archive). It also contains a shortcut to display the current Online News in the session window.

  • Help

This folder contains many links to detailed information about STN on the Web and STN.

  • Assistants

This folder provides a toolbar with access to a variety of powerful Assistant tools to help you get the information you need.

  • Transcripts

This button offers access to all your transcripts for the last 4 days as well as the transcript on / off option.

  • => Command Line

This button immediately restores the session screen to the default command line status.

  • Logoff Hold

This button suspends your session for up to 120 minutes. When clicked, the LOG H command is entered and submitted. If you log back in with the same login ID within the 120 minutes, you will be reconnected to this suspended session.

  • Logoff
This button terminates your session. When clicked, the LOGOFF Y command is entered and submitted. If you want to suspend your session rather than terminate it, use the Logoff Hold button.

  • Feedback

This button opens a browser e-mail window to send a message to the STN Help Desk.

  • Send Break

This button sends a break signal to STN to stop processing the current command.

At the bottom of the Session Page toolbar are two information hyperlinks: STN Commands List and File-Specific Helps List. Click on either for further links to information on these topics.

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Session Transcripts

During an active STN on the Web session and after logoff of a session, the Transcript Assistant gives you all the information you need about your session transcripts. During a session, click the Transcript Assistant button on the left navigation bar to enter the Transcript Assistant. After logoff, click the Retrieve Transcript button at the bottom of the left navigation bar.

The Transcript Assistant page offers:

At logon the session transcript capture is automatically ON. A colored box on the Transcript Assistant page displays the capture status. Capture OFF/ON may be changed by simply clicking the hyperlink. When changed to ON, the session transcript from that point is appended to any existing transcript for that continuing session. The capture status is also displayed in the browser status line.

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Help

There are various options for obtaining help information.

Help for STN commands is available by clicking the STN Commands List hyperlink located at the bottom of the Session Page Toolbar. When you click this hyperlink, a new browser window is opened showing a list of all the STN commands. Click on a command to obtain details for the selected command.

File-specific help is available by clicking the File-Specific Help List hyperlink located at the bottom of the Session Toolbar. When you click this hyperlink, the HELP DIR command is submitted and the list of helps for the current file displays in the session screen. Each help message is hyperlinked to further information on the topic.

Help may also be obtained by clicking in the Help folder in the Session Page Toolbar. This folder offers help on Commands, Databases, and STN on the Web.

The HELP command can be used in the command entry box. Enter HELP followed by an option, e.g., HELP DUPLICATE. The help message will be displayed in the session screen. HELP messages are available for the STN command language and for file-specific features. Enter HELP MESSAGES to see a hyperlinked list of detailed information on what HELP messages are available. Enter HELP DIRECTORY to see a hyperlinked list of the file-specific helps that are available for the current file.

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Full text

Any time that you display a record in a format that includes the record's source information, the Full-text button appears at the beginning of the record. Click the button to see what full-text options are available for that record. A new browser window will open and will link you to the STN Full Text Solution. You may order the full text via fax or mail delivery, or via direct electronic access, if available.

Please Note: When you click the Full-text button, the clock used for connect-time billing of your STN session is stopped. The clock starts again when the next STN command is submitted, either directly from the command line or from one of the Assistants.

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Citation Searching

The Citing References button allows the user to find documents that cite the retrieved reference. The system checks to see if the document has been cited by other documents in CAPLUS and SCISEARCH and retrieves the citing records from these two databases. The Citing References button can be found in records from more than 40 STN databases including: AEROSPACE, AGRICOLA, ANABSTR, BIOSIS, BIOTECHNO, CABA, CAPLUS, COMPENDEX, EMBASE, ENERGY, FROSTI, FSTA, INSPEC, MEDLINE, METADEX, RAPRA and SCISEARCH.

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Hypertext Links

There are two types of hypertext links appearing in your session window, external and internal.

External hyperlinks are URLs for web sites outside your STN on the Web session, e.g., the homepage of a conference organizer in a CONF file record. When you click on an external link, a new browser window is opened, displaying the selected web page. The browser window with your STN on the Web session is still active in the background. These external links will also be available in your session transcripts.

Internal hyperlinks give you further information in your session environment, e.g., CAS Registry Numbers and help messages. Help messages are hyperlinked so you can easily switch between different help messages with a single click. Internal hyperlinks are active during the entire STN on the Web session. Internal hyperlinks do not appear in your session transcript. See also >Patent Hypertext Links.

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CAS Registry Number Hypertext Links

CAS Registry Numbers are displayed as hypertext links in STN records. Click on a CAS Registry Number hyperlink in a given record. Automatically, the REGISTRY file is entered and the substance identification data, including the structure diagram, for that CAS Registry Number is displayed in the session screen. The system then returns to an arrow prompt in the previous STN file when the hyperlink was clicked. Enter DISPLAY HISTORY to verify the current file.

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Derwent Hypertext Links

Records that are related in Derwent databases have hypertext links for Derwent World Patents Index (DWPI) accession numbers. The feature links patent records in BIOTECHABS, BIOTECHDS, CROPU, DGENE, PCI, DJSMONLINE, WPINDEX, WPIDS, and WPIX.

A click on the DWPI accession number in a DWPI record initiates an STNindex search for further records in other Derwent files on that patent. The result is reported on a separate screen, where the user can select the hit files and retrieve the relevant records. The session screen redisplays with the results in an L-number answer set.

Another type of Derwent hypertext link is available for patent records in BIOTECHABS, BIOTECHDS, CROPU, DGENE, PCI, and DJSMONLINE. The link is present for the DWPI accession number in the Other Source (OS) field. A click of the link allows the user to display the corresponding DWPI record. When the hypertext link is clicked, a screen displays a table of DWPI display formats. The user selects the appropriate format and clicks the Display button. The DWPI record is displayed in the session window in the selected format, followed by automatic re-entry into the file from which the procedure was initiated.

This feature is also available for DWPI accession numbers in the Cross Reference (CR) field in WPINDEX, WPIDS, WPIX.

WPINDEX, WPIDS, WPIX contain bibliographic and substance records. Hyperlinks (in the DCSE, KW fields), enable crossover linking between the two types of records.

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Search Assistant

The Search Assistant leads the user, step by step, through the search in any STN database without needing to know the STN command language.

The Search Assistant is available from the Search Assistants folder in the left-hand toolbar during an online session. Database cluster(s) or individual database(s) may be selected from a list. Search fields and Boolean operators may be selected from a pull-down menu. Browse Index and Search may be invoked with a mouse-click. In a multi-file environment the Search Preview option is a cost effective way to identify STN databases that contain answers relevant to the search question. Content related Help is available at any stage of the search with a mouse-click. The STN command interaction for the search is covered in the session history and in the transcript, if transcript is on.

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Results Assistant

The Results Assistant leads the user, step by step, through display, sort and duplicate procedures without needing to know the STN command language.

The Results Assistant is available from the left-hand toolbar during an online session. After selecting the answer set from a list the user may start sort or duplicate detection procedures with a mouse-click. The required selections and specifications to run a sort or duplicate detection procedure are offered on subsequent pages for selection. After running a sort or duplicate detection procedure the system returns to the Results Assistant to run a Display, Print Offline or Print Email. The required selections and specifications needed for Display, Print Offline or Print Email are offered on subsequent pages. Content related Help is available at any stage of the different menus per mouse-click. The STN command interaction for the sort, duplicate detection and display procedures is covered in the session history and in the transcript, if transcript is on. >

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Chemical Structure Searching

Chemical structure searching is available by using the online STN commands (STRUCTURE and SCREEN), or by using the Structure Assistant.

Click on the Get Structure Plug-in button on the Login Page Toolbar or on the Structure Query button on the Session Page Toolbar for more information about the Structure Assistant.

Help on the STN commands can be obtained by clicking on the button in the Help Folder of the Session Page Toolbar.

Various manuals about structure searching are available via the button in the Customer Support folder on the Login Page.

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Patent Hypertext Links

Patent, application, and priority numbers in STN records are hyperlinked to initiate retrieval of the original document via STN's Full Text Options.

A hyperlink in the OSDW field of the INPADOCDB file enables crossover linking to corresponding WPI records.

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Patent Graphic Images

Some STN patent files (PATDPA and WPIDS/WPINDEX) offer patent graphic images. These can be displayed using one of the display formats that include the image, e.g., ALLG. The images appear integrated in the text and require no further handling. The html transcripts available with the Download Transcript option also contain the images integrated in the text.

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Patent Family Assistant

The Patent Family Assistant is located in the Assistants folder and can be used to extract the first member from each patent family, remove twin multiple basics from patent families in CA/CAplus answer sets, and customize displays of patent family results.

Extract the first member from each patent family automatically creates an answer set of the first member of each patent family after an FSORT. (For documentation on FSORT, see: ). There is a limit of 5,000 records when using this feature. You have the option to include or exclude non-patent documents from your answer set by using the check box; by default non-patent answers are excluded.

Remove twin multiple basics from patent families in CA/CAplus allows you to manage the multiple basic patent content of your CA/CAplus answer set. You have the option to retain the WO basic patent, the national basic patent with oldest priority, the patent with the oldest application date or the patent with the oldest publication date. The CA/CAplus answer set you process with this feature can be of any size as long as no more than 5,000 of the patents in it include the Chemical Indexing Equivalent tag in their Source fields. The feature works with CA/CAplus answer sets only; multi-file answer sets are not allowed. Patents without the Chemical Indexing Equivalent tag and non-patent documents will be automatically retained in the answer set created after the feature is executed.

Customize displays of patent family results allows you to specify different display formats for the first member of a patent family, and any other members of that family. This allows you to save time in entering display formats and save money by choosing less expensive formats for family member displays. This feature works with answer sets of 5,000 records or less.

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Upload Command File

STN on the Web offers the option to create complex search strategies offline, and then upload these command (script) files to an STN on the Web session for efficient execution, thereby minimizing connect time charges for typing in and correcting commands. Command scripts can be submitted one line at a time or all at once. A script command line may be edited before it is submitted.

The content of the command file must be plain text data. It cannot be a Word file, Excel spreadsheet, etc. A common Windows program to create the file would be Notepad.

You can enter any valid STN command into the command file. When you want to refer to previous search steps you should use variable L-Numbers instead of fixed L-Numbers.

Instead of:

s cat
s dog
s L1-L2

use:

s cat \>_line1
s dog \>_line2
s _line1-_line2

What does this do?

The "\>_lineX" construct tells STN on the Web to do the search and remember the L-number the search created in variable _lineX. The "X" can be anything from 0 to 999. Once that variable is defined, it can be used in later commands where an L-number would normally be specified. This way, no matter what L-numbers exist in your session, when the command file is invoked, the proper L-numbers will be used.

To upload a command file click on the "Upload Command File" button on the navigation bar. Three new buttons appear near the command entry box: Browse, Open File and Cancel Upload. With the Browse button you may select a command file on your local machine for upload. A new window opens where you can browse and select a file. With the Open button in that window the filename and directory of the command file is transferred to the command entry box. With the Open button near the entry box the command file is displayed in the command entry box. Now you can check, if the commands need additional editing. The command script can then be submitted one line at a time or all at once by clicking the corresponding buttons.

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STN AnaVist Assistant

The STN AnaVist Assistant is located in the Assistants folder on the left-hand navigation pane in your online session. To use the STN AnaVist Assistant:

STN AnaVist projects are limited to 20,000 records.

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STN Viewer Assistant

The STN Viewer Assistant, located in the Assistants folder on the left-hand navigation pane, is used to send full-text patent documents from STN on the Web answer sets to STN Viewer for evaluation. There is a limit of 1,000 records when using this feature.

Conduct desired search then select STN Viewer Assistant. Select the L# to evaluate with STN Viewer, and click Continue. When the selection of records is completed, you will be prompted to Launch STN Viewer. Your STN login ID and password will be needed to launch STN Viewer. Use STN Viewer to view, evaluate, and navigate through STN full-text patent documents. Note: it may take a few minutes for the records to be loaded into STN Viewer. Remember to logoff of STN on the Web if you are finished searching. Use STN Viewer HELP for any questions.

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Sequence Assistant

The Sequence Assistant provides two options: CAS Registry BLAST ® Similarity Searching, and Searching of sequences from patents in DGENE, PCTGEN and USGENE with BLAST ®, GETSIM or GETSEQ.

Refer to CAS Registry BLAST Similarity Searching for a description of CAS Registry BLAST searching. Refer to Sequence Searches in DGENE, PCTGEN and USGENE for information on the menu-driven BLAST, GETSIM and GETSEQ searches in DGENE.

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CAS Registry BLAST Similarity Searching

CAS REGISTRY BLAST ® similarity searching allows similarity searching of peptide and nucleotide sequences in the CAS Registry file using the BLAST ® (Basic Local Alignment Search Tool) algorithm. The CAS Registry file includes sequences from patents, journal literature, and GenBank ®. After the CAS REGISTRY BLAST similarity search, use the familiar STN on the Web command language and features to search and display references for the sequences retrieved by the BLAST algorithms.

To obtain a sequence plug-in

Sequence Plug-in is required for BLAST similarity searching in the CAS Registry file. To obtain the plug-in, click Get Sequence Plug-in on the tool bar on the left side of the screen. Follow the instructions.

To run a BLAST search

Launch CAS Registry BLAST from the Sequence Search Assistant page. Select one of the three options to manage your online session during the BLAST search, and click the Launch CAS Registry BLAST button. If you have already installed the Sequence Plug-in, the BLAST interface appears with Main and New Search windows.

To enter a sequence, select Similar Sequences in the New Search window and enter the name to be used to track and save the search results (optional), type the sequence or copy/paste the sequence from another application, or download a sequence from an existing file by clicking Read from File.

Select a BLAST program in the Program Selection window. Select a database subset, or search the entire database. The subset selection varies depending on the BLAST program. Specify BLAST settings or take the default values that have been set to optimize most types of nucleic and amino acid sequence searching.

To view BLAST results

After your search is initiated, the Main Window is automatically updated with the status of the submitted search, along with the status of previously run searches. Details for results may be viewed after the word Complete appears in the Status column. In the Main Window, highlight the line with your sequence search results and click View. The BLAST Report is displayed.

To transfer sequences to the CAS Registry file

In the BLAST Report window, select the sequences to be transferred to the CAS Registry file. To select all of the sequences, choose Select All from the Edit menu. To select all the sequences for an entire range in the Alignment Scores section, click the bar for the desired range. You may also click the selection box for any individual sequence to select it for transfer to STN.

Click the Transfer RNs button. The system transfers the CAS Registry Numbers from the most recent BLAST search, and provides a message that the Registry Number Transfer is complete. You can transfer any sequence result sets from the Main Window. Highlight the desired sequence result set in the Main Window and click View. In the BLAST Report window, select the sequences to be transferred.

To retrieve transferred sequences

Return to your STN on the Web session after the Registry Number transfer is complete.

Select Retrieve RNs from BLAST on the Sequence Assistant page. Search the final L-number query generated by the transfer from BLAST to STN. To retrieve references to the transferred sequences, search the L-number created by the Registry file search in bibliographic files such as CAPLUS.

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Sequence Searches in DGENE, PCTGEN and USGENE

The DGENE (Derwent Geneseq) file is a unique database of nucleic and peptide sequences which have been extracted from basic patent documents of the 40 issuing authorities covered by the Derwent World Patents Index (file WPINDEX/WPIDS/WPIX). More than half of the sequence data that appears in DGENE is not available in any other public sequence database. The file covers patent literature from 1981 to present and is updated every two weeks.

PCTGEN covers nucleotide and amino acid sequence information submitted electronically to the World Intellectual Property Organisation (WIPO) by patent applicants. The file contains nucleotide and peptide sequences and bibliographic data. Sequence and patent application information is compiled in this file as given by the patent applicant. The file comprises data from August 2001 to present and is updated weekly.

USGENE covers all peptide and nucleic acid sequences from the published applications and issued patents of the United States Patent and Trademark Office (USPTO). The USGENE database includes extensive bibliographic and text search options, including abstracts and patent claims. The file covers data from 1982 to present and is updated weekly. New sequences are available within one week of publication.

To run a sequence search

Polypeptide and nucleic acid sequences in DGENE, PCTGEN and USGENE are searchable using three options (please note that multifile sequence searching is not possible)

Launch the menu-driven sequence searches from the Sequence Assistant page. After selecting one of the offered databases, the search option (BLAST, GETSIM or GETSEQ) and the type of search (Protein or Nucleotide) the "Continue" button leads you to another page where you can enter your sequence query. >Three options for sequence input are available:

Note that sequence queries uploaded in one file may also be used for sequence searches in the other file (concerning DGENE, PCTGEN and USGENE). This is not possible with sequences input manually. On the following page select the search mode (Online, Offline or Alert). The "Advanced parameters" link on the same page allows to specify some additional settings depending on the selected search option. Or take the default values that have been set to optimize most types of nucleic and amino acid sequence searching.

To get the search results

After your search is initiated with the "Search" button, the results are presented directly or may be viewed later depending on the selected search mode (Online, Offline, Alert).

In Online mode the status of the submitted search is automatically displayed. When the search is completed the results are presented graphically and you are asked how many answers you would like to keep. With "Create Answer Set" an L-number (answer set) will be created and presented on the final page of the Sequence Assistant. Two options for proceeding are offered. You may switch to the Results Assistant or you may continue in command line mode. The Results Assistant leads you, step by step, through sort and display processing without needing to know the STN command language.

Offline and Alert status and results are accessible by using the corresponding buttons on the bottom of the Sequence Assistant page. Choose the database in which to check BATCH or ALERT searches and view, process and display results.

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Upload Sequences in DGENE, PCTGEN and USGENE

Complex biosequence queries can be created offline and then uploaded to an STN on the Web session, for use in RUN GETSEQ, RUN GETSIM or RUN BLAST packages in DGENE, PCTGEN and in USGENE in command line mode.

To upload a run command sequence query choose the corresponding button to upload the sequence in the DGENE, PCTGEN or USGENE file. Browse to select a sequence file from the local machine and click the Upload button. The Kermit transfer protocol performing the upload is started automatically. The created L-number may be used with the RUN command for sequence search in DGENE, PCTGEN or USGENE. You may view the entire uploaded sequence query with the command 'D LQUE' and the corresponding L-number of the uploaded sequence. Please note that a sequence uploaded in one file can be used as well for a sequence search in the other (concerning DGENE, PCTGEN and USGENE). For details on sequence searching in DGENE, PCTGEN and USGENE, enter HELP SEQ at an arrow prompt in each file.

Refer to Sequence Searches in DGENE, PCTGEN and USGENE for information on the menu-driven BLAST, GETSIM and GETSEQ searches.

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