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Drupal Training Series

Drupal Training Series. Foundations for OSU Drupal 6 Keep it Cited With Bibliography. What We’ll Be Covering…. What is Biblio? Manual Biblio Entries Journal Article Entry Book Entry Biblio Components Publication List Author List Keyword List Biblio Imports Single Import BibTex

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Drupal Training Series

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  1. Drupal Training Series • Foundations for OSU Drupal 6 • Keep it Cited With Bibliography

  2. What We’ll Be Covering… • What is Biblio? • Manual Biblio Entries • Journal Article Entry • Book Entry • Biblio Components • Publication List • Author List • Keyword List • Biblio Imports • Single Import • BibTex • DOI Lookup • PubMed Lookup • Batch Import • Biblio Configuration • Sorting • Styling • Syndication • Summary

  3. Getting Started • As a reminder, to get to your personal development site go to: • http://drupaldev.cws.oregonstate.edu/training/<yourONIDname>/login • From there, log in with your ONID information. • After logging in, please open a second tab in your browser and go to CWS Training at • http://oregonstate.edu/cws/training • Locate the name of this workshop in the list and click it. This will take you to a page describing the course with download links at the bottom of the page. • Download the lab materials to your desktop and unzip them.

  4. Bibliography Overview • The Bibliography module, also commonly referred to as Biblio, is a contributed module that provides a robust method of managing and displaying bibliographic entries on a Drupal site. • Bibliographic entries can be used for a few different reasons: • A list of documents published by faculty or staff that may be of further interest to an audience • A list of published material that further supports content on a site • An inventory list of publications within a group that may be available as resources to an audience • The Biblio module also tracks authors and keywords, has numerous import/export options, and is integrated with Views.

  5. Manual Biblio Entries: Overview • Bibliographic entries are created using the Biblio content type, found at Create content > Biblio. • This content type is just a little bit different from others used in the OSU Drupal 6 system as it possesses a Publication Type field, which offers thirty-one different informational templates to users who create manual entries. • These templates include, but are not limited, the following: • Articles • Journal • Newspaper • Magazine • Web • Books • Cases • Statutes • Let’s start our Biblio exploration by creating a couple of different types of manual entries: Journal Article and Book.

  6. Manual Biblio Entries: Ex. 01 Create a Journal Article Entry 1 • The Journal Article submission form contains fields relative to this particular publication type, roughly grouped as follows: • Publication type and ID This is basic information about the type of article (Journal), title, and year of publication. • Author information Many authoring option types are available, including editors, and corporate authors. • Journal and article info Specific information regarding the journal and where to locate the article within the journal • Location info Various methods for locating the article including ISBN and Keywords • Using the ex-01.doc lab materials, add the supplied Journal Article information. Remember to click Save when completed. 2 3 4

  7. Manual Biblio Entries: Ex. 01 Create a Journal Article Entry - Completed • The result is a nicely formatted table of information about this particular article. • Clicking on the Authors links will take you to a list of all publications by that Author. • Clicking on a Keyword link will take you to a list of all publications listed in your site that contain that keyword.

  8. Manual Biblio Entries: Ex. 02 Create a Magazine Article Entry 1 • The Magazine Article submission form contains fields relative to this particular publication type, roughly grouped as follows: • Publication type and ID This is basic information about the type of article (Magazine), title, and year of publication. • Author information Many authoring option types are available, including editors, and corporate authors. • Journal and article info Specific information regarding the journal and where to locate the article within the journal • Location info Various methods for locating the article including ISBN and Keywords • Abstract Add in some summary text to provide an overview of the article. • Using the ex-02.doc lab materials, add the supplied Magazine Article information. Remember to click Save when completed. 2 3 4 5

  9. Manual Biblio Entries: Ex. 02 Create a Magazine Article Entry - Completed • The completed Magazine Article publication type has many of the same information fields as the Journal Article publication type – but there are a few differences. • For example, the Magazine Article type offers Edition and Frequency fields, whereas the Journal Article type does not. • The Journal Article type has a Start Page field where the Magazine Article type does not.

  10. Manual Biblio Entries: Now You Do It – Ex. 03 Create a Book Entry • Now, using the ex-03.doc lab materials, go to Create Content > Biblio and create a Book publication type. Don’t confuse this with the Book page content type – the two are completely different items.

  11. Biblio Components: Ex. 04 Publications List – Sorting and Grouping 1 • Now that we have some Biblio content, let’s see what features Biblio has. The most obvious to start with is the publications list: • To get to the publications list, click on the Biblio link in the Navigation menu – by default, the publications list will be grouped based on the publication Type • To group by author, click on the Author link at the top of the screen • To group by title, click on the Title link at the top of the screen • To group by year of publication, click on the Year link at the top of the screen • Note that for all of these links, when one is active, a small triangle appears next to it. Clicking on this triangle will sort items from ascending to descending. 2 3 4

  12. Biblio Components: Ex. 04 Publications List – Filtering • To filter publication list items, do the following: • From the main Biblio panel, click on the Filter tab • Select one of the radio button options: Author Type Year Keyword • Select a value from the corresponding drop down box • Click the Filter button • The filtered result set will appear • To clear the filter, just click the Clear All Filters link 1 3 2 4 5 6

  13. Biblio Components: Ex. 05 Authors List • To view all of the authors listed through Biblio, do the following: • In the Navigation menu, go to Biblio > Authors • The authors list will appear as a tabled list with an alphabar in the header. • Clicking on an authors name will provide a filtered list of publications based on the author’s name • The number next to the authors name is the number of publications the author has listed in Biblio • Clicking on the edit link will take you to edit the author’s information 2 3 4 5 1

  14. Biblio Components: Ex. 05 Authors List – Using the Alphabar • If the author list becomes large, the alphabar can be used to quickly filter authors alphabetically: • Click on the letter A in the alphabar • This will return all authors whose last names begin with the letter A • To clear the filter, click the Show ALL link 1 3 2

  15. Corrected Biblio Components: Ex. 05 Authors List – Edit Author • You may have noticed the misspelling in one of our author’s names. Biblio has to use some specific patterns to separate names and sometimes gets thrown by names that contain abbreviations. It’s easy to fix, though: • Locate the Clair, B.S. author and click the corresponding edit link • When the Edit author information screen appears, remove the St. from the First Name field • Add the St. to the Last Name field • Click the Save button 1 2 3 4

  16. Biblio Components: Ex. 06 Keyword List • In addition to tracking publications and authors, Biblio also tracks all keywords that are associated with publications in the system: • In the Navigation menu, go to Biblio > Keywords • The keywords list will appear as a tabled list with an alphabar in the header. • Clicking on a keyword will provide a filtered list of publications based on the keyword • The number next to the authors name is the number of publications the keyword is associated with in Biblio • Clicking on the edit link will take you to edit the keyword 2 1 5 3 4

  17. Biblio Components: Ex. 06 Keyword List – Edit Keyword • To edit a keyword in the keyword list: • Click on the keyword’s corresponding edit link • A keyword edit page will appear. Make any desired changes. • Click the Save button 1 Corrected 2 3

  18. Imports & Exports: Overview • Perhaps Biblio’s greatest asset is its import and export flexibility. • There are many different bibliographic import formats. Biblio works with the following: • BibTeX • End Note Tagged • End Note 7 XML • End Note 8 XML • MARC • RIS • There are also different methods for importing bibliographic information. Biblio offers three different methods: • Paste entry • Lookup • File import • We’ll take a look at a few of these different formats and methods.

  19. Imports & Exports: Ex. 07 Single Imports – BibTeX Overview • BibTeX is a cross-platform software application used to create and structure lists of bibliographic references. BibTeX is commonly used with the LaTeX typesetting system. • BibTeX code may be imported into Biblio in one of two ways: either as an import file with the extension .bib, or as a .txt file, in which the code is pasted directly into the Biblio submission form, versus uploaded.

  20. Imports & Exports: Ex. 07 Single Imports – BibTeX Paste • BibTeX code can be pasted straight into the interface by doing the following: • Open the ex-07a.txt lab materials and copy the code • Go to Create content > Biblio • Click on the Paste field set to expand it • Paste the code into the BibTex field • Click the Populate using BibTex button. 1 2 3 4 5

  21. Imports & Exports: Ex. 07 Single Imports – BibTeX Paste – Save 1 • After clicking the Populate using BibTex button, you will be redirected to the content’s edit form: • Add any additional information (such as keywords) if desired • Click the Save button 2

  22. Imports & Exports: Ex. 07 Single Imports – BibTeX Paste – Completed • The completed BibTeX import will then display.

  23. Imports & Exports: Ex. 07 Single Imports – DOI Overview • The Digital Object Identifier (DOI) system is used for identifying content objects in a digital environment. • DOI names are assigned to items for use on digital networks. They are used to provide current information, including where the object (or information about it) can be found on the Internet. • A DOI name is persistent, which means that information about a digital object – such as meta data or location - may change over time, but the DOI name will not change. More information about DOI can be found at http://www.doi.org. • CrossRef is a not-for-profit association which provides a collaborative reference linking service for scholarly information. This group provides a free DOI lookup service at http://www.crossref.org/guestquery/. If a scholarly publication is listed with CrossRef, the associated DOI number will be made available here. We’ll start by registering with CrossRef.

  24. Imports & Exports: Ex. 07 Single Imports – DOI Overview – CrossRef Registration • To register with CrossRef, go to their site at http://www.crossref.org/requestaccount/ and do the following: • In the Email field, enter your OSU e-mail address • In the Organization field enter Oregon State University • Click the I agree to the Terms and conditions checkbox • Enter the CAPTCHA information • Click the Submit button • You will receive a confirmation message • Open your e-mail client – a verification e-mail from CrossRef should be there • Click the verification link, which will take you back to CrossRef • Enter CAPTCHA one final time • Click the Submit button 1 2 3 4 5 6 7 8

  25. Imports & Exports: Ex. 07 Single Imports – DOI Overview – Add CrossRef Acct Info • To add your CrossRef account information to your Drupal site: • In your Navigation menu go to My Account > Edit tab • Click on the Biblio settings fieldset to open it • Click on the CrossRef Login Information fieldset to open it • In the CrossRef OpenURL Account ID field, enter the same e-mail address you used to register with CrossRef • Click the Save button 1 2 3 4 5

  26. Imports & Exports: Ex. 07 Single Imports – DOI Lookup • Lookups are, by far, the simplest import method. To import a DOI Lookup, do the following: • From the ex-07b.txt lab materials, copy the first DOI Lookup number (10.2307/1499632) • In the Navigation menu, go to Create content > Biblio • Click on the DOI Lookup fieldset to open it • Paste the DOI number into the DOI field • Click the Populate using DOI button 1 2 3 4 5

  27. Imports & Exports: Ex. 07 Single Imports – DOI Lookup – Save • After clicking the Populate using DOI button, you will be redirected to the content’s edit form: • Add any additional information (such as keywords) if desired • Click the Save button 1 2

  28. Imports & Exports: Ex. 07 Single Imports – DOI Lookup – Completed • The completed DOI import will then display. • This task is performed so quickly that a second DOI number has been provided in the ex-07b.txt lab materials. Add this one as well.

  29. Imports & Exports: Ex. 07 Single Imports – PubMed Overview • PubMed is a service of the US National Library of Medicine (NLM)® that does the following: • Provides free access to MEDLINE®, the NLM® database of indexed citations and abstracts to medical, nursing, dental, veterinary, health care, and preclinical sciences journal articles • Includes additional life sciences journals not in MEDLINE® • Adds new citations Tuesday through Saturday • For specific information about PubMed, go to http://www.nlm.nih.gov/services/pubmed.html • Biblio can import PubMed Lookups based on the PubMed ID number (PMID). PubMed.org provides a free and comprehensive search service located at http://www.ncbi.nlm.nih.gov/pubmed/.

  30. Imports & Exports: Ex. 07 Single Imports – PubMed Lookup • To import a PubMed Lookup, do the following: • From the ex-07c.txt lab materials, copy the first PMID number (11707550) • In the Navigation menu, go to Create content > Biblio • Click on the PubMed Lookup fieldset to open it • Paste the PMID number into the PubMed ID field • Click the Populate using PubMed button 1 2 3 4 5

  31. Imports & Exports: Ex. 07 Single Imports – PubMed Lookup – Save • After clicking the Populate using PubMed button, you will be redirected to the content’s edit form: • Add any additional information (such as keywords) if desired • Click the Save button 1 2

  32. Imports & Exports: Ex. 07 Single Imports – PubMed Lookup – Completed • The completed PubMed import will then display. • You may note that large abstracts, such as the one shown here, may not display paragraph breaks. Additional paragraph breaks can be added by clicking on the Edit tab and adding them manually, if desired. • A second PubMed number has been provided in the ex-07c.txt lab materials. Add this one as well.

  33. Imports & Exports: Ex. 07 Single Imports – RIS Overview • The RIS file format is a standardized tag format developed by Research Information Systems, Incorporated. • This format is used by many different digital libraries including : • Institute of Electrical and Electronics Engineers (IEEE) Xplore • http://ieeexplore.ieee.org/Xplore/guesthome.jsp • Association for Computing Machinery (ACM) portal • http://portal.acm.org/portal.cfm • Summit Libraries Catalog • http://summit.worldcat.org • The RIS file format uses the .ris extension. On a Windows operating system, content within this file format is best viewed using WordPad (right click on the file and choose Open With > WordPad). • Biblio offers the ability to import .ris files via a file upload.

  34. Imports & Exports: Ex. 07 Single Imports – RIS File Import • To upload an RIS file, do the following: • In the Navigation menu, go to Biblio > Import • Click on the Browse button, browse to the ex-07d.ris file in the lab materials, and select it • In the File Type field, select RIS • Uncheck the Batch Process checkbox • If the Set user ID field does not contain your username, select your username from the field • Click the Import button • A confirmation message will appear if the import was successful 1 2 3 4 5 6 7

  35. Imports & Exports: Ex. 07 Single Imports – RIS File Import – Completed • To locate the new import, in the Navigation menu, click on Biblio and the click on the America Eats book title.

  36. Imports & Exports: Progress to Date • Take a look at the publications list now, by clicking on the Biblio link in the Navigation menu. You may also want to take a look at the authors list. The information has grown substantially, and quickly, thanks to imports. • Even greater efficiencies can be gained, though, by utilizing a bulk import operation…

  37. Imports & Exports: Ex. 08 Batch Imports – File Preparation Overview • Biblio allows for batch importing of bibliographic records which, when available, are the most efficient methods of importing data. • If several smaller files are provided, and they are all the same file format, they can be combined into one larger file and then imported all at once. We’ll use the .ris format as an example. • At left is a single .ris file with multiple records inside of it. • Note how each record begins with a TY, ends with an ER – , and is separated with a space. • To prepare a document like this, simply open one .ris file in WordPad and paste other .ris records from other .ris files into the first, following this format.

  38. Imports & Exports: Ex. 08 Batch Imports – Upload RIS Batch File • Uploading a batch .ris file works in almost the exact same manner as uploading a file with a single record in it: • In the Navigation menu, go to Biblio > Import • Click on the Browse button, browse to the ex-08.ris file in the lab materials, and select it • In the File Type field, select RIS • Leave the Batch Process checked • If the Set user ID field does not contain your username, select your username from the field • Click the Import button • An upload progress bar will appear • A confirmation message will appear if the import was successful 1 2 3 4 5 6 7 8

  39. Imports & Exports: Completed Imports • Take another look at the publications and author lists and it becomes obvious why imports, when available, are the best way to go. • Note that there are some “authors” in the list that may need to be edited in the actual content type. A good example is the author “Writer’s Program…” – this probably would better fit Other Author Affiliations in the Other Biblio Fields group rather than Author.

  40. Imports & Exports: Ex. 09 Exports – Single • To export a single file, go to the publications list at Navigation > Biblio and do the following: • Click one of the links at the end of an entry • Tagged • XML • BibTex • A dialog box will open, choose to save the file • Click the OK button • A file will download in the location specified • Rename the file 1 2 3 5 4

  41. Imports & Exports: Ex. 09 Exports – Single – Completed • Chances are the file will look odd because Windows may not recognize the file extension. If this occurs, right click on the file, select Open With > Choose Program > WordPad. You may also want to check the Always Use the Selected Program to Open This Kind of File checkbox as well. • Once this is done, the icon will change. • Open the file to view the contents.

  42. Imports & Exports: Ex. 10 Exports – Batch • To export all records, go to the publications list at Navigation > Biblio and do the following: • Click one of the links in the upper right corner, after the words Export 24 results: • Tagged • XML • BibTex • A dialog box will open, choose Save File • Click the OK button • A file will download in the location specified • Rename the file 1 2 3 4 5

  43. Imports & Exports: Ex. 10 Exports – Batch – Completed • When the file is opened, multiple records will show. • Currently, Biblio is not able to export subsets, but if there are particular entries that you do not want in this file, just locate them, delete them, and save.

  44. Configuration: Overview • Biblio offers a great deal of flexibility in regards to configurations – more than can be covered in this particular workshop alone. • Biblio configurations can be found at Administer > Site configuration > Biblio settings. This configuration suite contains six main tabs, with sub-items available for some tabs. • Preferences • Fields • Authors • Keywords • Import • Export • We’ll focus on some Preference, Field, and Author configurations.

  45. Configuration: Ex. 11 Preferences – Keywords • Biblio’sKeyword feature can work in conjunction with Taxonomy: • Keyword separator field If a different character to separate multiple keywords is preferred, enter it here • Automatically remove orphaned keywords checkbox • Copy selected taxonomy terms to biblio keyword database checkbox If a Taxonomy vocabulary is associated with the Biblio content type and a term is selected, it will automatically be copied into the Biblio keyword database • Use keywords from biblio entries as taxonomy “free tags” checkbox Will auto-populate a chosen Taxonomy vocabulary with keywords in the Biblio database 1 2 3 4 • For the Taxonomy related features to work, you must have a Taxonomy Vocabulary built and have it associated with the Biblio content type. • To learn about Taxonomy, come visit the Developing Site Structures workshop.

  46. Configuration: Ex. 11 Preferences – Links – Disable Service Links • Biblio offers several different configurations regarding both the appearance and functionality of links. • We’ll start with the Export and Google Scholar Links service links which can be disabled as desired by simply unchecking the items. Without Service Links With Service Links

  47. Configuration: Ex. 11 Preferences – Links – Link Behaviors • Additional link behavior options are included, as follows: • Links open in new browser option Opens linked page in a new browser tab or window. This is especially helpful if links are external. • Carry “inline” mode through to all links option This is used when the default Drupal search feature is enabled to help keep the result appearance intact. It is not necessary for OSU Drupal 6. • Hyperlink titles using supplied URL option If a URL to a specific publication is available, it can be entered in the Biblio submission form and traffic can be routed directly to that publication instead of the Biblio entry. • Hyperlink author names option This creates a hyperlink on an author’s name which will then filter all publications based on that particular author. 1 2 3 4

  48. Configuration: Ex. 11 Preferences – Sorting • Default grouping and sorting methods can be configured in a number of ways. • At left, below, is the default sorting, by publication type, with sorting tools displayed as links. • At right, below, is a sort by author name with sorting tools displayed as tabs.

  49. Configuration: Ex. 11 Preferences – Styling – Overview • Different disciplines, industries, and institutions may use different bibliographic styles – some common examples are: • Modern Language Association (MLA) Literature, arts, and the humanities • Council of Science Editors (CSE) Natural sciences, chemistry, mathematics, and physics • Chicago Newspapers, books, magazines, and non-scholarly publications • Additionally, it’s not uncommon for groups to often have their own custom citation format. • Biblio is capable of rendering eight different, common citation format styles, and also provides some options for how the node is laid out and whether annotations should be displayed or not.

  50. Configuration: Ex. 11 Preferences – Styling – Style Formats • There are a few different styling elements to consider: • Text to display…no year of publication field Sometimes the year of publication is not known or provided. Biblio can be set up to automatically enter a brief note to handle a null year of publication field. • Text to display…publication set to 9998 field If a publication is currently In Press (which means it hasn’t been officially published yet) the code 9998 will often be used. Biblio can be set up to automatically enter a brief note to handle items that are in process. • Style options Eight different, popular citation formats available • Node Layout options Choose between the default node style or the original, less styled version • Annotations selection box If you would like to include annotations, select a field 1 2 3 4 5

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