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Web-based pathology annotation

In the HPA program, the objective has been that all immunohistochemistry images should be manually annotated by a certified pathologist. A web-based annotation tool was developed taking advantage that all tissue images was scanned to generate high resolution digital images. A “annotation jamboree” was organized in which a large number of Scandinavian pathologists came together and performed annotation of hundreds of thousands of pathology images. However, due to the increased throughput of images, a new strategy to keep up with the production of images was necessary. A dedicated site with pathologists was set-up in Mumbai, India headed by Dr Sanjay Navani. This HPA affiliated site have now annotated more than 10 million images published on the open access resource (Human Protein Atlas).

Key publication

Other selected publications

  • Björling E et al., A web-based tool for in silico biomarker discovery based on tissue-specific protein profiles in normal and cancer tissues. Mol Cell Proteomics. (2008)
    PubMed: 17913849 DOI: 10.1074/mcp.M700411-MCP200

  • Pontén F et al., A global view of protein expression in human cells, tissues, and organs. Mol Syst Biol. (2009)
    PubMed: 20029370 DOI: 10.1038/msb.2009.93

  • Uhlen M et al., Towards a knowledge-based Human Protein Atlas. Nat Biotechnol. (2010)
    PubMed: 21139605 DOI: 10.1038/nbt1210-1248

Figure legend: Web-based annotation. A. Annotation jamboree session with pathologists from the Scandinavian countries. B. The pathologist at the HPA site in Mumbai, India.

Key facts

  • The immunohistochemistry images of HPA have been annotated by certified pathologists
  • A web-based annotation tool has been developed and used for analysis of more than 10 million images
  • An annotation jamboree was arranged to allow pathologists to interact during the annotations
  • A dedicated HPA site was set-up in Mumbai, India with medical pathology experts.