Import Literature References from Database Files

Learn how to intake literature reference information from external databases.

Note: Depending on your Admin’s configuration, object, field, and section labels, lifecycle states, and workflows may differ from the general information on this page. Refer to your organization’s business processes for guidance.

About Importing Literature References

Vault SafetyDocs can import literature references in bulk from third-party databases.

When you create a Search Term in your Vault as part of a literature review, you can select an action to import articles from a database in the following formats:

Research Information Systems (RIS) files
ZIP files, when importing from the Japan Pharmaceutical Information Center (JAPIC). Vault uses the D-SDI.txt file within these ZIP files for literature reference information.

These files include reference information for all the articles that show up as search results when you query databases using that specific search term.

Vault then creates a Literature Article record for each article included in the imported database file and maps all relevant information from the file to these records. Once your Literature Article records are created and all fields are populated, you can proceed with your literature review as usual.

Automating the literature intake process reduces the need for manual data entry, significantly decreasing the potential for errors and speeding up your literature review process.

Prerequisites

Your Admin must configure the following features in your Vault:

Upload a Database File

To upload an RIS or JAPIC ZIP file to your Vault, use the Database Export document classification. See Adding Documents for instructions.

To link an uploaded file to the related Search Term, populate the Literature Search Term field with the search term used to find the articles included in the RIS file.

To learn about other subtypes and classifications of literature documents, see Working with Literature Documents.

Import Literature References

Once you have uploaded the database file to your Vault, complete the following steps to start importing your literature references:

Navigate to Literature > Literature Reviews.
Select the Literature Review that contains the Search Term record associated with your file.
In the Search Terms section, select the associated Search Term.
From the All Actions menu, select Import Articles from File.

Result

The following results take place:

The file is imported and for each reference within it, Literature Article records are created under the selected Literature Review.
For JAPIC ZIP files, Vault can also create a document in your Library for every article document contained in the ZIP file. Vault associates each document with a Literature Article record by matching the document number in its name with the Document Number field on the Literature Article record.

Note: This action can import files in the following formats only:

RIS files
ZIP files (if the Literature Database field on the Search Term record is set to JAPIC)

Any other file format will cause the import to fail and both the Search Term record and the uploaded file will enter the Error state. You will receive a notification indicating that the import has failed. If needed, verify the file format and try again.

Duplicate Handling

Vault identifies duplicate references using the DOI field for RIS files and the Document Number field for JAPIC ZIP files. Once duplicates have been identified, Vault does the following:

Creates an initial Literature Article record.
Creates Literature Article records for the duplicate references and sets their Duplicate Literature Review and Duplicate Literature Article fields to point to the initial record.
For documents associated with these duplicate records, sets the Literature Article field to point to the initial record.

Search Expression Number Matching

When you import literature articles using a JAPIC ZIP file, Vault runs a search to identify if the value in each article’s Search Expression Number field matches the value of this field in an existing Literature Search Term or Literature Standard Search Term record. Based on this search, Vault does the following:

If a Literature Search Term record with a matching Search Expression Number exists in your Vault, Vault creates a Literature Article record and links it to the matching Literature Search Term record.
If a Literature Standard Search Term record with a matching Search Expression Number exists in your Vault, the following processes take place:
- Vault creates a Literature Search Term record and maps the Search Expression Number, Product and Product Family fields from the matched Literature Standard Search Term record.
- Then, Vault creates a Literature Article record and links it to the new matching Literature Search Term record.
If no Literature Search Term record or Literature Standard Search Term record with a matching Search Expression Number exists in your Vault, the following processes take place:
- Vault creates a Literature Search Term record and populates the Search Expression Number field with the current Search Expression Number.
- Then, Vault creates a Literature Article record and links it to this new Literature Search Term record.

Field Mapping from Database Files

When Vault imports literature reference information from an RIS file or a D-SDI.txt file within a JAPIC ZIP file, it creates a Literature Article record for each article included within it. All relevant information is mapped from the file to the fields in those Literature Article records.

Field Mapping from RIS Files

The following sections provide a breakdown of this mapping when RIS files are imported:

Literature Article Section

In this section, Vault maps general information about the article as it appears in the RIS file. The following table outlines how Vault maps this information from the file to fields in your Vault:

RIS Tag	Description	Populated Field
TY	Type of Reference	Reference Type See Reference Type Mapping for a list of RIS abbreviations for the value of the TY tag and how Vault interprets them to populate this field.
AB	Abstract	Abstract
AN	Accession Number	Accession Number
CN	Call Number	Call Number
DA	Date	Date of Publication If the file does not contain a DA value, Vault maps: the Y1 value to the Day and Month components of this field the PY value to the Year component of this field If the file does not contain a Y1 value either, Vault sets the Day and Month to "1 January".
CY	Place of Publication	Place of Publication
CP	City/Place of Publication	Place of Publication If the value of CP conflicts with the CY tag, Vault maps it to the Literature Additional Information section.
DB	Name of Database	Database Name If the file does not contain a DB value, Vault populates this field with the value in the Literature Database field on the associated Search Term record.
DO	DOI	DOI
DP	Database Provider	Database Provider
EP	End Page	End Page
ET	Edition	Edition
ID	Reference ID	Reference ID
IS	Issue Number	Issue Number
J1	Periodical Name - User Abbreviation 1	Abbreviated Title of Journal
JA	Periodical Name - Standard Abbreviation 1	Abbreviated Title of Journal If the value of JA conflicts with the JF, J1, or T2 tags, Vault maps it to the Literature Additional Information section.
JF	Journal or Periodical Name - Full Format	Abbreviated Title of Journal If the value of JF conflicts with the J1 or T2 tags, Vault maps it to the Literature Additional Information section.
JO	Journal or Periodical Name - Full Format	Abbreviated Title of Journal If the value of JO conflicts with the JF, J1, or T2 tags, Vault maps it to the Literature Additional Information section.
KW	Keywords	Keywords In case of multiple keywords, Vault maps them all to this field and separates them with commas.
L1	Link to PDF of the article	URL (PDF)
L2	Link to full text of the article	URL (Full Text)
LA	Language	Language
N1	Notes	Article Notes
N2	Abstract	Abstract If the value of N2 conflicts with the AB tag, Vault maps it to the Literature Additional Information section.
PB	Publisher	Publisher
SE	Section	Section
SN	ISBN/ISSN	ISBN/ISSN
SP	Start Page	Start Page
ST	Short Title	Title of Article If the value of ST conflicts with the T1 or TI tags, Vault maps it to the Literature Additional Information section.
T2	Secondary Title	Abbreviated Title of Journal If the value of T2 conflicts with the JF or J1 tags, Vault maps it to the Literature Additional Information section. This tag contains the Secondary Title value for all reference types except Whole Book (BOOK) and Unpublished Work (UNPB). Secondary Titles for these reference types are mapped to the BT tag in the Literature Additional Information section.
TI	Title	Title of Article If the file does not contain a TI value, Vault maps the T1 value to this field.
TT	Translated Title	Title (English)
UR	URL	Link If the file does not contain a UR value, Vault maps the value of the LK tag to this field.
VL	Volume Number	Volume
Y2	Access Date	Access Date

Reference Type Mapping

The following table outlines how Vault interprets Reference Type abbreviations from RIS files to set the value in the Reference Type field:

Abbreviation	Vault Mapping
ABST	Abstract
ADVS	Audiovisual Material
AGGR	Aggregated Database
ANCIENT	Ancient Text
ART	Art Work
BILL	Bill
BLOG	Blog
BOOK	Whole book
CASE	Case
CHAP	Book chapter
CHART	Chart
CLSWK	Classical Work
COMP	Computer Program
CONF	Conference Proceeding
CPAPER	Conference Paper
CTLG	Catalog
DATA	Data File
DBASE	Online Database
DICT	Dictionary
EBOOK	Electronic Book
ECHAP	Electronic Book Section
EDBOOK	Edited Book
EJOUR	Electronic Article
WEB	Web Page
ENCYC	Encyclopedia
EQUA	Equation
FIGURE	Figure
GEN	Generic
GOVDOC	Government Document
GRANT	Grant
HEAR	Hearing
ICOMM	Internet Communication
INPR	In Press
JFULL	Journal (full)
JOUR	Journal
LEGAL	Legal Rule or Regulation
MANSCPT	Manuscript
MAP	Map
MGZN	Magazine Article
MPCT	Motion Picture
MULTI	Online Multimedia
MUSIC	Music Score
NEWS	Newspaper
PAMP	Pamphlet
PAT	Patent
PCOMM	Personal Communication
RPRT	Report
SER	Serial Publication
SLIDE	Slide
SOUND	Sound Recording
STAND	Standard
STAT	Statute
THES	Thesis/Dissertation
UNBILL	Unenacted Bill
UNPB	Unpublished Work
VIDEO	Video Recording

Literature Author Section

In this section, Vault maps information about the article’s authors as it appears in the RIS file. The following table outlines how Vault maps this information from the file to fields in your Vault:

RIS Tag	Description	Field Populated
A1	Primary Authors	The complete author reference is populated in the Value field. The author's last name is populated in the Last Name field. The author's first name is populated in the First Name field. The Author Type field is set to Primary.
A2	Secondary Authors	The complete author reference is populated in the Value field. The author's last name is populated in the Last Name field. The author's first name is populated in the First Name field. The Author Type field is set to Non-Primary.
A3	Tertiary Authors	The complete author reference is populated in the Value field. The author's last name is populated in the Last Name field. The author's first name is populated in the First Name field. The Author Type field is set to Non-Primary.
A4	Subsidiary Authors	The complete author reference is populated in the Value field. The author's last name is populated in the Last Name field. The author's first name is populated in the First Name field. The Author Type field is set to Non-Primary.
AU	Author	The complete author reference is populated in the Value field. The author's last name is populated in the Last Name field. The author's first name is populated in the First Name field. The Author Type field is set to Primary only if: There is no A1 tag in the file This is the first instance of the AU tag
ED	Editor	The complete author reference is populated in the Value field. The author's last name is populated in the Last Name field. The author's first name is populated in the First Name field. The Author Type field is set to Editor.
TA	Translated Author	The complete author reference is populated in the Value field. The author's last name is populated in the Last Name field. The author's first name is populated in the First Name field. The Author Type field is set to Translator.

Literature Additional Information Section

In this section, Vault maps any additional information about the article as it appears in the RIS file that was not covered in the Literature Article and Literature Author sections. Vault creates a record for every section of additional information with its corresponding tag and value from the RIS file. The Tag field is populated with the RIS tag, and the Value field is populated with the corresponding information.

Vancouver Citation

When an article’s type of reference is Journal, Vault generates a Vancouver Citation for it by mapping relevant field values to that Literature Article record’s Vancouver Citation section. Vault generates this citation in the following format:

{List of all literature authors, separated by commas}. {Title of Article}. {Abbreviated Title of Journal}. {Date of Publication} [cited {Access Date}]; {Volume}({Issue Number}): {Start Page}-{End Page}. Available from {Database Name} DOI:{DOI}

Field Mapping from JAPIC ZIP Files

The following sections provide a breakdown of this mapping when ZIP files are imported from JAPIC:

Literature Article Section

In this section, Vault maps general information about the article as it appears in the JAPIC ZIP file. The following table outlines how Vault maps this information from the file to fields in your Vault:

Column in JAPIC ZIP File	Populated Field
検索式番号 (Search Expression Number)	Search Expression Number For more information about this field, see the Search Expression Number Matching section.
文書番号 (Document Number)	Document Number
標題 (Title)	Title of Article
所属機関 (Institution)	Institution
雑誌名 (Journal Title)	Abbreviated Title of Journal
ISSN	ISSN/ISBN
学会名 (Conference Name)	Conference
巻 (Volume)	Volume
号 (Issue)	Issue Number
頁 (Page)	Start Page and End Page
発行年月日 (Date of Publication)	Date of Publication
全キーワード詳細 (All Keyword Details)	Keywords In case of multiple keywords, Vault maps them all to this field and separates them with commas.
文献URL (Literature URL)	URL
発送日 (Sent Date)	Access Date

Literature Author Section

In this section, Vault maps information about the article’s authors as it appears in the JAPIC ZIP file. Vault maps values in the Author Name column of the JAPIC ZIP file to the Raw field on the article’s Literature Author section.

Vancouver Citation

Vault uses the same logic and process to generate a Vancouver Citation for JAPIC ZIP files as for RIS files. The only exception is when the Conference Name column is populated in the imported JAPIC ZIP file. In this case, Vault generates the citation in the following format:

{list of literature_author__v.raw__v (comma separated)}. {title_of_article__v}. {conference_name__v}. {date_of_publication__v}

Translate Imported Literature Abstracts

If your database file includes references from non-English literature articles, Vault can automatically send any available abstracts for translation. Auto-translation allows you to quickly determine if the associated articles contain any ICSRs or new Safety information, and eliminates the need for external translation tools.

Prerequisites

To use this feature, your Admin must set up Literature Abstract Translations in your Vault. See the following pages for the steps to complete:

Enable Literature Abstract Translation: Enable the Amazon Translate Connection
Enable Literature Abstract Translation: Configure Layouts
Configure Literature Abstract Translation Settings

Once the required configuration is complete and you import references into your Vault, any abstracts that are in a non-English language are automatically sent to Amazon Translate for translation into English. Vault maps translated abstracts to the Abstract (English) field of their respective Literature Article record.

Note: When the translated abstracts are sent back to Vault SafetyDocs, they are simply imported as received. Vault does not perform quality checks on the content.

To learn more, see Considerations for Abstract Translations.

Considerations for Importing Literature References

When importing literature reference information from a database file, keep the following things in mind:

If any articles within the file have duplicate DOIs or ISSN/ISBNs, Vault imports only one (1) to prevent duplicate records in your Vault. Vault sends a notification indicating that some articles have been skipped from import due to matching unique identifiers.
If the value of any tag exceeds the character limit of the field to which it is being mapped, Vault truncates the value to that field’s maximum character length. Vault also adds the value to the Literature Additional Information section as a new record. For information on truncated fields, see the Notes field of the Literature Article record.
If any or all articles fail to be imported, Vault sends a notification.