KJC IT Team | Tutorial »Refbase« Author: PG/FM | Version: 17.02.2010 | Page 1 of 25
Tutorial »Refbase« 1 What is Refbase? ...... 2 2 How to access the Cluster bibliography ...... 2 3 How to use the Cluster bibliography ...... 4 3.1 Start page ...... 4 3.2 Quick search ...... 4 3.3 Simple search ...... 5 3.4 Advanced search ...... 6 3.5 Search results ...... 6 3.6 Adding records ...... 12 3.6.1 Mandatory fields (grey fields) ...... 15 3.6.2 Facultative fields (white fields)...... 16 3.6.3 User fields (yellow fields) ...... 17 4 Direct import of RIS-Files from Bibliographic catalogues ...... 18 4.1 Data Import from HOLLIES ...... 18 4.2 Data Import from WorldCat ...... 19 5 Bibliographic data migration between Endnote and Refbase ...... 19 5.1 Import bibliographic entries from Endnote into Refbase ...... 19 5.1.1 Export Endnote entries to XML ...... 19 5.1.2 Import the XML file to Refbase ...... 22 5.2 Import bibliographic entries from Refbase into Endnote ...... 24 5.2.1 Export entries from Refbase...... 24 5.2.2 Import entries into Endnote ...... 24
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1 What is Refbase?
The Cluster Bibliography Database (http://kjc-fs-cluster.kjc.uni-heidelberg.de/refbase), as a part of the Heidelberg Research Architecture (HRA) is implemented with the Open Source Software refbase (http://www.refbase.net). It provides the possibility to share bibliographical entries and the asso- ciated texts in PDF format. As part of the HRA it will in future be integrated into cluster wide search facilities. This database can also be seen as the basis of the Cluster Virtual library and is integrated into respec- tive service infrastructure. Cluster projects can get help for bulk uploading own bibliographic refer- ence collections, that have been collected, e.g., with Endnote. There also is a scan and OCR service for inputting and full-text indexing new texts into the data base. For more information about these services, please contact [email protected]. Of course you can also input ma- terial with the help of the refbase web interface with cluster account. This text is a short guide how to login and use this HRA resource.
2 How to access the Cluster bibliography
To access the database, please use the following URL: http://kjc-fs-cluster.kjc.uni-heidelberg.de/refbase. This link is also available via the Cluster Website http://www.asia-europe.uni-heidelberg.de via: “Research” “Heidelberg Research Architecture” “HRA Databases” “Cluster Database” “Cluster Bibliographical Database”
You will see the bibliography start page in Figure 1. For searching metadata you don't have to login, but just start using it. Since the cluster bibliography contains the actual texts as PDF files, it is pass- word protected. Thus for read access you need to login with your Cluster account to get the PDF files.
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Figure 1: Refbase start page.
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3 How to use the Cluster bibliography
3.1 Start page
The start page gives you access to several retrieval possibilities. On the top of all pages you will find the main menu which has the items “show all”, “simple search” and “advanced search”. These will be discussed below. With the menu item “home” you will always get back to this start page. The main window provides you with some fixed searches, namely for All entries that have recently been added (today, yesterday, last 7 days) All entries that have recently been edited (today, yesterday, last 7 days) All entries published in a certain year All entries sorted by creation date in reverse chronological order The start page also provides you with some information about the data base. At the bottom of all pages there again is a menu with the items “home”, “show Records”, “Extract Citations”, and “Help”. The latter leads you to the refbase web page, which might contain informa- tion that helps you. This manual should answer most of your questions though. As to the other two menu items (besides “home”), please see the respective sections below.
3.2 Quick search
Figure 2: Quick search window.
For quick searches you can use the input field on the upper right of every page, where there is an associated drop-down menu, where you can choose to search within the fields author, title, publica- tion (i.e. the title of the publication which contains the referred to article), keyword, abstract. When searching, refbase performs a "contains" search by default. This means that refbase will return all records where the searched field contains the specified search string (in some search engines this is equivalent to “*string*”). Beware: refbase has implemented the feature of auto completion, which means that it will make on the fly searches in the respective field while you are typing and provide you with a list of possible
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KJC IT Team | Tutorial »Refbase« Author: PG/FM | Version: 17.02.2010 | Page 5 of 25 completions. This can be handy, but this can also sometimes (especially in “contains” searches) be a nuisance. Just click on an empty part of the page to stop auto completion. This quick search will accommodate most demands concerning searches. If you want to perform more complex searches, you can use simple and advanced search.
3.3 Simple search
Simple search allows you to search in more than one field within one search run. You will find only those entries that meet all search criteria (logical AND-search).
Figure 3: Simple search window.
Hereby you can select whether you want to have a "contains" search like in quick search, which is the default setting here, or whether you want to have a different search behavior, namely: “Does not contain” which is the opposite of “contains” “is equal to” which means that the field has to exactly contain the search string and nothing else “is not equal to” which is the opposite of the latter “starts with” which means that the fields content has to start with the search string but may end anything (in some search engines this is equivalent to "*string"). “ends with” which means that the fields content may start with anything but has exactly to end with the search string (in some search engines this is equivalent to "string*"). It is allowed to search for in the fields Author, Title, Year, Publication, Volume and Pages.
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With the help of the check boxes on the right you can specify which fields of the found entries shall be displayed in the result list. By default all these 6 fields are checked and thus will be displayed in the list. Below the field definitions you can specify display options, mainly how many entries you want to have displayed in the list per page. The checkbox “Display links” is of no relevance. Below the display options you can specify the sorting order of the results where you can specify up to three criteria and whether to sort these ascending or descending. You again have the 6 mentioned fields to choose from. The default is to sort by author (ascending), within one author by year des- cending, and within the entries of one author in one year the publication ascending.
3.4 Advanced search
The advanced search window provides you with even more search possibilities. Basically it functions just like simple search, the only difference is that you now can search within any field available. Be aware that most of these fields are left blank in most of the entries and it doesn’t make a lot of sense to search them.
Figure 4: Advanced search window.
3.5 Search results
After performing one of the above mentioned fixed or individual search possibilities (they all are activated via the “search”-button by the way) you will receive a list of the found entries. In the header part you will be notified how many entries have been found and how many of these are displayed on the first result page. In the same line you also have two links:
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"RSS" a link to the RSS interface, which allows you to subscribe to a dynamic RSS feed, that notifies you of any changes to the results of your search. For more information about RSS please consult http://en.wikipedia.org/wiki/RSS or the IT-Support team.
Figure 5: Header of the result page.
In the main window you will find the first page of the list of found entries. The other pages of the result list can be accessed by clicking on the page numbers displayed at the top and at the bottom of the list.
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Figure 6: List of several pages.
Figure 7: Area to open Search and Display Options.
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Figure 8: Search and Display Options opened.
On the upper right you have a link “Search and Display Options” where you can modify the display, basically:
perform searches within the result list (with the possibility to exclude the results of the second search) add or hide fields to be included in the list change the setting for the number entries to be displayed per page
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Figure 9: Icons at the end of the list items.
At the end of each list item you find following icons which are links, you can click on:
leads you to the details of the entry namely displays all the fields
leads you to additional information about the record in the web (be aware: for publications this will perform a search for the ISBN-number and leads you to places where you could buy the publication, for articles a search is performed in a cross reference data base to which the cluster has no access yet)
will only be shown after you logged into the database and allows you to download the PDF file
will only be shown after you logged into the database and allows you to edit the record.
After you click on the PDF icon , a pop up window will be shown with following text and down- load button with PDF filename:
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Figure 10: Pop up download window.
Figure 11: Export of citations.
At the bottom of the result list you can to download the list as citations in different formats: RTF (Rich Text Format) to include the list in a word file Html PDF LaTex (an Open Source text processing software) By using the checkboxes on the left of each list item you can control which list items to download.
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3.6 Adding records
One has to be logged in with Cluster account to add or edit a record. You will get this account from IT Support. Please write a message to [email protected]. You can use the quick login in the start page or click the login link any time to go to the login window.
Figure 12: quick login and Login link.
Figure 13: Login window.
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After login with this account you have additional items in the main menu. The most important is “Add record”, which leads you to the input form.
Figure 14: Enhanced menu after login.
You will see several input-fields, which are grouped. Groups are indicated by color-coding (colors may vary with used browser, used style sheets etc.)
Grey fields: such as author, title, year and publication (these are mandatory fields, which are necessary for correct citation of references)
White fields: such as abstract, keywords and ISBN (these are facultative fields, which are not necessary for correct citation, but these fields will give an additional benefit to the database, for searching abstracts etc.)
Yellow fields: such as marked, user keys and related (these fields are facultative fields, which are only visible for the logged in user. This allows a personalization of a common used refer- ences)
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Figure 15: Input form in simple mode.
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You can also switch to extended mode any time when you filling the form.
Figure 16: Input form in extended mode.
Filling the fields Hints for filling the fields should be displayed when moving the mouse over a field. More information is given below and at the definition page for the refs MySQL table.
3.6.1 Mandatory fields (grey fields)
Author - the author(s) of the publication. several authors separated by semicolon (;) example: Mo, Fei; Granskog,MA; Virkanen, J is Editor - Yes if author is Editor. only relevant for books (Type: "book whole") please activate, if persons, entered in author-field are editors of the publication
Title - the title of the publication. no dot at the end; species-names can be set as italic by surrounding by underscore example: Feeding of _Sprattus sprattus_ in the Baltic Sea
Type - defines the type of the publication
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Year - the year of the publication; enter in four-digit-style example: 245
Publication - complete name of publication; insert here the complete (!) name of the book (if Type=Book Chapter) or of the Journal (if Type=Journal Article) examples: The northern North Atlantic: A changing environment
Pages - defines which pages of the publication are covered with the reference enter range of pages, when using Types "Journal Articles" and "Book Chapter"; enter total number of pages including "pp" (without dot) when using Types"Book Whole" and "Ma- nuscript" examples: 35-42 (article or book chapter starts at page 35 and ends at page 42) 620 pp (book has 620 pages in total
KJC-Member Publication check this if the Publication from KJC member.
Cluster Publication check this if it is a KJC Publication
3.6.2 Facultative fields (white fields)
Keywords - the keywords given by the author contains keywords, as given in the article; multiple items should be seperated by semicolon (";") (your personal keywords can be entered under User Keys) example: Vlibrary; Baltic Sea; hydroacoustic; Sprat; Herring; GAM
Publisher - The publisher of a publication example: American Geophysical Union
Place of Publication - The place of publication example: Washington, DC
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Language - langrage of the body text example: English with germen footnotes
ISBN: If the publication is a book (chapter), specify it's ISBN number in this field example: 0-12-026143-X
3.6.3 User fields (yellow fields)
User Keys - user's personal keywords other users could not see this entry example: KJC; 2010-01-15; home;
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4 Direct import of RIS-Files from Bibliographic catalogues
Refbase is capable of importing bibliographic information saved in the so called RIS-notation (which is available both Text an XML Format). Modern bibliographic databases give users the possibility to export a single record or a list of records as RIS-file. These files can be uploaded directly into refbase or saved in your personal citation- manager (e.g. EndNote, Zotero or Citavi). Two of the most interesting metadata sources for Cluster Refbase are: Harvard HOLLIS: http://discovery.lib.harvard.edu/ (not HOLLIS Classic) WorldCat: http://www.worldcat.org/
4.1 Data Import from HOLLIES
The following example will show how to import a bibliographic record from Harvard HOLLIES to ref- base. Search for a title in HOLLIES and switch to detailed record view by clicking on the title.
Detail View of a search result in HOLLIES.
The result should look like the figure above. Click “Export to EndNote” and save the file. The file name should be something like export-id000123456.ris. This file can be imported as described in 5.1.2 Import XML to Refbase.
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4.2 Data Import from WorldCat
The following example will show how to import a bibliographic record from worldcat to refbase. Search for a title in worldcat.org.
Detail View of a search result in WORLDCAT.
The result should look like the figure above. Click “Zitieren/Exportieren”, then “nach EndNote expor- tieren”and save the file. The file name should be something like WorldCat_35465453241.ris. This file can be imported as described in 5.1.2 Import XML to Refbase.
5 Bibliographic data migration between Endnote and Refbase
The following describes how to import and export data between Endnote application and the Ref- base database.
5.1 Import bibliographic entries from Endnote into Refbase
5.1.1 Export Endnote entries to XML
Choose the entries you want to export either by clicking on them or using the select all function in Endnote.
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Figure 17: select in Endnote.
Click on the command File – Export
Figure 18: export in Endnote.
Choose the export format to XML and output style to RefMan (RIS) Export. Then click the save button. The XML file, e.g., endnote-export.xml is generated in the chosen directo- ry.
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Figure 19: Choose the export format to XML.
Figure 20: Choose the output style to RefMan (RIS)
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Figure 21: save XML file.
5.1.2 Import the XML file to Refbase
Log into the Refbase web application using your user account in the web page (Refer to 3.6) http://kjc-fs-cluster.kjc.uni-heidelberg.de/refbase/
Figure 22: import button after login.
In the import window, choose the exported xml file and click import.
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Figure 23: import selection
After successful import, a confirmation window appears.
Figure 24: import confirm
Note: At the moment refbase does not support as much types of publication as endnote does. En- tries of other types than those registered in refbase are saved as entries of the type “Miscellaneous”. We are constantly adjusting the database to your needs. Please let us ([email protected] heidelberg.de) know if you have proposals for further improving refbase.
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5.2 Import bibliographic entries from Refbase into Endnote
5.2.1 Export entries from Refbase
First you must choose the entries you want to export from refbase. Change the Export format to Endnote.
Figure 25: select entries
Choose the directory to save endnote-export.enw from the window and click OK. The endnote- export.enw file will be saved in the chosen directory.
Figure 26: save endnote-export.enw
5.2.2 Import entries into Endnote
Choose the File - import in Endnote application. Choose the endnote-export.enw file in the feld Im- port Data File and import option as endnote library.
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Figure 27: save endnote-export.enw
Depending on the number of entries, a progress bar appears.
Figure 28: save progress
After successful import, a window appears confirming the number of successfully imported entries.
Figure 29: save confirm
For further information please contact the KJC IT Team: [email protected] +49 (0) 62 21 – 54 40 91 Karl Jaspers Centre, Room 005
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