# Presentation: 066997

## PubMed Central

- Martha Fishel
- National Library of Medicine
- CENDI Meeting
- September 15,  2004

## What is PubMed Central?

- Digital archive of life sciences journals
- includes health policy, bioinformatics and other fields
- Participation is open to journals:
- covered by a major abstracting/indexing service
- or, that have 3 editorial board members with current grants from major non-profit funding agencies
- Free access to full-text articles and supporting data
- Integrated with PubMed and other bibliographic and factual databases in NCBI’s Entrez network

## PMC Basic Policy

- Journal deposits an authoritative electronic copy that meets PMC data quality standards
- full-text XML
- original high-resolution graphics
- PDF
- supplementary data
- Journal may delay free access  (up to 2 years)
- research articles usually free in one year or less
- Copyright is retained by publisher or author
- Deposits – and free access permissions – are permanent
- journal may stop depositing new material but may not withdraw material already deposited

## Back Issue Digitization

- Objective: Create a complete digital archive of PMC journals back to volume 1
- Cover-to-cover digital copy of everything up to where journal began producing electronic copy
- (includes articles, covers, TOCs, advertisements and administrative matter)
- Publisher gets free, unencumbered copy

## Back Issue Digitization

- 1st set of scanned journals covered 62 titles (and title variations) for approximately 2.5 million pages
- As of September 2004, 193,436 scanned articles are included in PMC
- Starting September 2004, a new cooperative agreement with the Wellcome Trust and JISC in UK to cover an additional 1.7 million pages or more

## Titles Scanned Back to Volume 1

- Antimicrobial Agents and Chemotherapy v.1,1972
- BMLA v. 1,1911
- Clinical Microbiology Reviews v. 1, 1988
- J of Bacteriology v.1, 1916
- J Clinical Investigation v.1, 1924
- J Clinical Microbiology v.1, 1975
- J Virology v. 1, 1967
- Molecular and Cellular Biology v.1, 1981
- Nucleic Acids Research v.1, 1974
- Texas Heart Institute Journal v.1, 1974

## Scanning Specifications

- 1-bit B&W 600 dpi G4 TIFFs
- 8-bit 300 dpi grayscale TIFF
- 24-bit 300 dpi color TIFF for illustrations
- Unedited prime OCR (5-pass engine)
- PDF with hidden text (searchable OCR “hidden behind” pg. images)

## Digitized Samples

- Secure permission to digitize
- Acquire disposable content
- Donor sources include publishers, associations, individuals
- Create issue-level inventory
- Prepare content for digitization – create journal style sheets
- Pack and ship materials

- Back Issue Scanning Tasks

## QA Tasks

-   Receive deliverables (DVDs) at NLM (NCBI)
-   Run automated QA programs
-   Mark random issues from each title for manual QA
-   Perform QA (NLM contractor compares digitized   image to original volumes pulled from NLM shelves)
-   Accept or Reject a batch based on rigid criteria

## QA Criteria

- XML Character and Tag accuracy – 99.95%
- Inventory Error – 100%
- Image quality – 100%
- Distortion
- Color
- Visible pixilation
- OCR quality – 100% for completeness and zoning (unedited)
- PDF sequence and source accuracy – 100%

## Sample Batch Status Report

| XML | # of samples | # of samples failed  | % failed | Status |
| --- | --- | --- | --- | --- |
| Tag content accuracy (99.95%) | 5135 tags | 12 tags | 0.23% | Failed |
| PDF | # of samples | # of samples failed  | % failed | Status |
| Visible skew (99%) | 675 pages | 1 page | 0.15% | OK |
| OCR file | # of samples | # of samples failed  | % failed | Status |
| Full Page Image | # of samples | # of samples failed  | % failed | Status |
| Illustration Image | # of samples | # of samples failed  | % failed | Status |
| Other | # of samples | # of samples failed  | % failed | Status |
| Recommended action |   |   |   | Reject |

## Final data Preparation

-   Update Inventory database indicating issues returned
-   Format TIFFs, PDFs, Organize journal parts
-   Load to Preview Site for publisher review
-   Load to Live PMC site
-   Retain indefinitely!

## Progress to Date 

- 25,000:         Issues received
- 1.8 million:   pages scanned
- 156,000:        XML Citations created

## Challenges To Date

-    Locating old, rare copies  in good condition
-    Scanning and delivering fill-in pages at NLM
-    Feeding the pipeline
-    Maintaining even workflow at NLM
-    Quality Assurance (understanding requirements)

## Find Out More

- 		PubMed Central home
- 			_[http://www.pubmedcentral.gov/](http://www.pubmedcentral.gov/)_
- 		NLM Journal XML DTDs
- 			_[http://dtd.nlm.nih.gov/](http://dtd.nlm.nih.gov/)_