Capture Discoveries in a PDF Lab Notebook: Part 1

Portfolio IllustrationAn Electronic Lab Notebook (ELN) is digital container for documents and data which is part of the research and development of drugs and medical devices. By replacing paper, you can save money and protect important data and discoveries.

Enterprise class ELN products are available and are good choices for large organizations. For example, CambridgeSoft’s Chemistry E-Notebook offers integration with Adobe Acrobat and enterprise content management systems.

However, what do you do if you are a smaller organization or have a limited budget?

One option to consider is a digitally signed PDF Portfolio, a container structure introduced with Acrobat 9.

A PDF Portfolio is a new concept in Acrobat 9, although it builds upon the PDF Package functionality in Acrobat 8. It’s easiest to think of a PDF Portfolio as a briefcase—or Portfolio— which can hold many types of documents in addition, of course, to PDF.

For example, you could have PDFs, Word Files, Excel documents, instrument data files and more that “live” inside a single PDF document.

PDF Portfolios offer professional-looking Flash-based navigation. Creating a useful interface to your files is simple using the pre-built layouts. In addition, you can “brand” the portfolio with a universal header:

A PDF Portfolio used as a Lab Notebook

The entire PDF Portfolio may be digitally signed on the Portfolio Cover Sheet to protect your important discoveries.

This entry is Part 1 in a series of articles. To start, I’ll present some background information on PDF Portfolios and how they work.

Subsequent articles will cover how to create and customize PDF Portfolios. Read on!

What is a PDF Portfolio?

Most of us think of a PDF as a single document with many pages. A PDF Portfolio has the .PDF extension like any other PDF document. However, a PDF Portfolio is a different type of PDF with some unique capabilities.

A Container
A PDF Portfolio is a single PDF document which acts as a container for other documents. It offers a useful interface for working with the documents inside:

Home View
In this case a grid view, but there are many other options available.
List View
A spreadsheet-like list of all of the documents in the Portfolio. It is easy to add new columns and sort data.
View PDF and non-PDF content without leaving the Portfolio context

PDF Portfolios are searchable. In fact, a PDF Portfolio may contain an embedded full-text index.
Text "hits" can be returned for PDF and many other file types such as text, CSV, etc. Hits are shown in context in the document.

PDF Portfolios have integrated Search

Welcome Page
The Portfolio Welcome page is shown by default whenever a PDF Portfolio is opened. It may contain text and graphics. You could use this page to record a summary of discoveries.

The Portfolio Welcome page is displayed when a Portfolio is opened.

PDF Portfolios may contain folders, a convenient way to organize your documents.

A folder displayed in Grid View


Customizable List View
The List View of the Portfolio may be customized.

Additional columns (text, number, date) may be added.

A default sort order based on data in the columns may be imposed.

An unlimited number of columns is available and they may appear in any order desired.

Preview Files
You can preview the files inside a PDF Portfolio without having to open them in a separate application. Inside a Portfolio, you can natively view PDF documents (of course!), but also a variety of other formats:


Media Formats: SWF, FLV, MP3

Text Formats: .txt and many other text file types


Note: Acrobat takes advantage of the OS or application viewing capabilities provided by either Windows Vista or Office 2007.

An Excel spreadsheet previewed inside a PDF Portfolio

Cover Sheet
To capture discoveries, the Portfolio Cover Sheet may be digitally signed. The Cover Sheet is the backbone PDF which contains all the other documents.

A Portfolio Cover Sheet signed by a researcher and supervisor
using an industry-standard SAFE


How does a Portfolio open in previous versions of Acrobat?

A PDF Portfolio is an PDF 1.7, Extension Level 3 document. To fully utilize a PDF Portfolio, the viewer would need Adobe Reader 9 or above. That said, PDF Portfolios may be opened in Reader 8 without an warning message while still retaining most of their useful structure.

PDF Portfolios open as PDF Packages
in Adobe Reader 8. The user
will see a cover page with this text: "For the best experience, open this
PDF portfolio in Acrobat 9 or Adobe Reader 9, or later."

PDF Portfolios may be opened in Acrobat 6 and 7, but the user experience is decidedly lacking.

Don’t confuse the version of a PDF Portfolio (PDF 1.8, L3) with that of the PDF files contained within.

A PDF Portfolio can contain PDFs of any version. For example, the Portfolio you created could contain PDF 1.4 files for agency compliance.


A PDF Portfolio can’t replace an enterprise-class ELN on their own. However, the compelling interface for working with groups of documents in a digitally signed container offers a nice alternative for smaller organizations and labs.

In forthcoming articles in this series, I’ll discuss how to create and digitally sign a Portfolio.

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