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SyRF User Guide

Preparing References Before Upload

Before uploading your references to SyRF, perform these essential preparation steps:

Contents

1. Deduplicate Your Search Results

If you searched multiple databases, your combined results likely contain duplicate references for the same study.

Important: SyRF does not perform deduplication during the upload process. You must remove duplicates before creating your upload file. Failure to do so will result in multiple entries for the same study within SyRF, complicating your screening process.

  • Recommended Tool: We strongly recommend using the free ASySD deduplication tool to automate this crucial step. Other reference management software (like EndNote) also offers deduplication features.

2. Choose and Prepare Your Upload File Format

SyRF accepts three file formats for uploading your deduplicated references:

  • EndNote XML (.xml): Recommended if you manage your references in EndNote Desktop or Zotero. Exported together with your PDFs, it lets SyRF link each study to its PDF.
  • Comma Separated Value (.csv): A flexible format suitable for spreadsheets or exports from other reference managers (like Zotero). This format also allows the optional inclusion of pre-existing screening decisions.
  • Research Information Systems (.ris): A standard export available from reference managers including Zotero and EndNote and databases including Web of Science. RIS imports bibliographic fields and each reference’s first PDF attachment path; it does not import screening decisions.

Option A: Using EndNote XML (.xml)

Compatibility: SyRF accepts EndNote XML from EndNote Desktop and from Zotero (and other software that writes the same format). EndNote’s tagged-text export and EndNote library files (.enl, .enlx) can’t be imported: export as XML instead.

Follow these steps to export from EndNote Desktop:

  1. Import & Finalize: Ensure all deduplicated references for this Systematic Search are in your EndNote library.
  2. (Optional) Find Full Text: To attach PDFs within EndNote before exporting, select the relevant references (e.g., Ctrl+A or Cmd+A for all), then go to References -> Find Full Text. (See Managing Full-Text PDFs for details on how SyRF handles PDFs).
  3. Select References: In your EndNote library, highlight all references you intend to upload (Ctrl+A or Cmd+A).

    Warning: If no references are selected, EndNote might only export the first reference in your library, leading to an incomplete upload.

  4. Export: Go to File -> Export.
  5. Configure Export Settings:
    • Set Save as type (Windows) or Format (Mac) to XML (*.xml).
    • Ensure the Output style is set to Show All Fields or a similarly comprehensive style to include maximum data.
  6. Save: Name your file (e.g., ProjectName_Search_Date.xml) and save it. This .xml file is ready for upload.

Exporting EndNote XML from Zotero

  1. In Zotero, right-click your library (or the collection holding this search’s references) and choose Export Library… (or Export Collection…).
  2. Set Format to EndNote XML.
  3. Tick Export Files if you want SyRF to link your PDFs.
  4. Click OK and choose where to save. Zotero creates an export folder holding the .xml file and a PDF folder with your attachments.
  5. Upload the .xml file. When you later bulk upload PDFs, choose the PDF folder inside the export folder.

SyRF imports titles, authors, abstracts, journal, year, DOI, URL, keywords, author addresses and reference type. Other fields (for example volume, pages or language) stay in your original file and are listed as import notes on the search, with how many records had them.

An EndNote XML file can hold up to 256 MiB and 100,000 references. Every record needs a title; if any record has none, nothing from the file is imported and the search lists the records to fix.

XML Upload Error? Refer to the SyRF FAQ for troubleshooting common XML upload issues.

Option B: Using a Spreadsheet CSV (.csv) (With Optional Screening Decisions)

Note: This option is recommended if you are not using EndNote or if you want to include pre-existing screening decisions in your upload.

You can prepare your reference list using spreadsheet software (like Microsoft Excel, Google Sheets, LibreOffice Calc) and save it as a .csv file.

  1. Create Your Spreadsheet: Open a new or existing spreadsheet.

  2. Required Column Headings: Your spreadsheet must include the following column headings exactly as spelled and cased. Include all columns, even if you don’t have data for every field for every reference.

    Column Name Description
    Title Title of the study
    Authors Authors separated by semicolons, e.g., Smith J; Doe A
    PublicationName Journal or publication name
    AlternateName Alternative name(s) for the study (if any)
    Abstract Study abstract
    Url Web link to the study (if available)
    AuthorAddress Corresponding author’s address
    Year Publication year, format: YYYY (e.g., 2023)
    Doi Digital Object Identifier
    ReferenceType Reference type (e.g., journal article, book)
    Keywords Relevant keywords separated by semicolons
    PdfRelativePath Relative path to associated PDF
    CustomId Optional identifier for your own reference to be included in SyRF data exports

    Systematic Search CSV Upload Template: A template CSV file with the correct headings and example data is available: Download Template

  3. Populate Data: Fill in the reference details under the corresponding headings. *Empty Fields: It’s acceptable to have empty cells if data is missing for a particular reference. Do not delete the columns themselves.
  4. (Optional) Include Pre-existing Screening Decisions:
    • If screening was partially done outside SyRF, you can import these decisions. Add a separate column for *each screener whose decisions you want to import.
    • Name these columns descriptively (e.g., Screener_Alice_TitleAbstract, Screener_Bob_FullText). You’ll map these to SyRF users during the upload. *Use 1 for inclusion and 0 for exclusion in these columns. Leave cells blank if no decision was recorded for that screener/study; they will be ignored.
  5. Remove Extra Columns: Ensure your file only contains the required columns listed above, plus any optional screening decision columns. Extraneous columns can cause errors or invalid data during upload.
  6. Save as CSV:
    • In your spreadsheet software, choose File -> Save As or File -> Download.
    • Select the file type CSV (Comma delimited) (*.csv) or CSV (Comma Separated Values) (*.csv). Encoding should typically be UTF-8 if prompted.

    Screenshot showing how to save as CSV in Excel

Option C: Using RIS (.ris)

  1. In your reference manager or database, select the deduplicated references you want to upload.
  2. Choose its RIS export option and save the resulting .ris file. SyRF supports common RIS exports from Zotero, EndNote, and Web of Science.
  3. Keep the file at or below 256 MiB and 100,000 references. The generated UTF-8 copy must also fit within 256 MiB, so a near-limit legacy-encoded file may need to be split before upload. Each record must contain a reference type (TY), a title (TI or T1), and an end marker (ER); if any record breaks these rules, nothing from the file is imported and the search lists the records to fix.
  4. If the exporter offers an encoding choice, use UTF-8. SyRF also accepts UTF-8 with a byte-order mark, UTF-16 LE/BE with a byte-order mark, and Windows-1252.

SyRF maps common titles, authors, abstracts, years, publication names, DOI, URL, keywords, reference types and the first PDF attachment path (L1) into the current Study fields. Unsupported RIS fields are retained in the stored original/augmented upload but are not added to the Study record; the completed search shows a warning when data was omitted or normalised.

PDF attachments in RIS. If you export from Zotero or EndNote with files, each reference’s first PDF attachment (the L1 field) is kept as the study’s PDF path, ready for bulk PDF upload. Absolute paths on your computer, web addresses and paths that climb out of the library folder are refused, and extra or non-PDF attachments are not attached; the completed search lists them. When you later upload PDFs, choose the folder that contains the exported files: for Zotero RIS, the export folder that contains files/; for EndNote RIS, the library’s PDF folder.

Next Steps

Once you have prepared your references file, proceed to the Upload Process to add your Systematic Search to your SyRF project.