Question About Organ Attribution in the PUMA Dataset

Hello,

Thank you for organizing the PUMA challenge and providing this dataset. I have a question regarding the organ attribution of the samples. The paper mentions that the data comes from different organs, such as bone, liver, lung, and brain. However, there is no clear indication in the file names or labels specifying which sample belongs to which organ.

Could you clarify how we can determine the organ source for each sample? Is there any additional metadata available, or another way to obtain this information?

I appreciate your help!

Best regards, Tong

Dear Tong Wang,

Is this helpful:

• 'training_set_metastatic_roi_001': 'soft tissue',
• 'training_set_metastatic_roi_002': 'soft tissue',
• 'training_set_metastatic_roi_003': 'lymph node',
• 'training_set_metastatic_roi_004': 'skin',
• 'training_set_metastatic_roi_005': 'soft tissue',
• 'training_set_metastatic_roi_006': 'soft tissue',
• 'training_set_metastatic_roi_007': 'brain',
• 'training_set_metastatic_roi_008': 'lung',
• 'training_set_metastatic_roi_009': 'brain',
• 'training_set_metastatic_roi_010': 'soft tissue',
• 'training_set_metastatic_roi_011': 'brain',
• 'training_set_metastatic_roi_012': 'brain',
• 'training_set_metastatic_roi_013': 'skin',
• 'training_set_metastatic_roi_014': 'skin',
• 'training_set_metastatic_roi_015': 'lymph node',
• 'training_set_metastatic_roi_016': 'soft tissue',
• 'training_set_metastatic_roi_017': 'lymph node',
• 'training_set_metastatic_roi_018': 'brain',
• 'training_set_metastatic_roi_019': 'soft tissue',
• 'training_set_metastatic_roi_020': 'lymph node',
• 'training_set_metastatic_roi_021': 'gastrointestinal tract',
• 'training_set_metastatic_roi_022': 'brain',
• 'training_set_metastatic_roi_023': 'lymph node',
• 'training_set_metastatic_roi_024': 'liver',
• 'training_set_metastatic_roi_025': 'lymph node',
• 'training_set_metastatic_roi_026': 'soft tissue',
• 'training_set_metastatic_roi_027': 'skin',
• 'training_set_metastatic_roi_028': 'brain',
• 'training_set_metastatic_roi_029': 'soft tissue',
• 'training_set_metastatic_roi_030': 'lymph node',
• 'training_set_metastatic_roi_031': 'lung',
• 'training_set_metastatic_roi_032': 'lymph node',
• 'training_set_metastatic_roi_033': 'brain',
• 'training_set_metastatic_roi_034': 'skin',
• 'training_set_metastatic_roi_035': 'liver',
• 'training_set_metastatic_roi_036': 'lymph node',
• 'training_set_metastatic_roi_037': 'gastrointestinal tract',
• 'training_set_metastatic_roi_038': 'liver',
• 'training_set_metastatic_roi_039': 'lymph node',
• 'training_set_metastatic_roi_040': 'brain',
• 'training_set_metastatic_roi_041': 'bone',
• 'training_set_metastatic_roi_042': 'soft tissue',
• 'training_set_metastatic_roi_043': 'skin',
• 'training_set_metastatic_roi_044': 'lymph node',
• 'training_set_metastatic_roi_045': 'liver',
• 'training_set_metastatic_roi_046': 'skin',
• 'training_set_metastatic_roi_047': 'soft tissue',
• 'training_set_metastatic_roi_048': 'lymph node',
• 'training_set_metastatic_roi_049': 'liver',
• 'training_set_metastatic_roi_050': 'lymph node',
• 'training_set_metastatic_roi_051': 'lung',
• 'training_set_metastatic_roi_052': 'brain',
• 'training_set_metastatic_roi_053': 'lymph node',
• 'training_set_metastatic_roi_054': 'brain',
• 'training_set_metastatic_roi_055': 'lymph node',
• 'training_set_metastatic_roi_056': 'gastrointestinal tract',
• 'training_set_metastatic_roi_057': 'lung',
• 'training_set_metastatic_roi_058': 'liver',
• 'training_set_metastatic_roi_059': 'liver',
• 'training_set_metastatic_roi_060': 'gastrointestinal tract',
• 'training_set_metastatic_roi_061': 'gastrointestinal tract',
• 'training_set_metastatic_roi_062': 'skin',
• 'training_set_metastatic_roi_063': 'skin',
• 'training_set_metastatic_roi_064': 'gastrointestinal tract',
• 'training_set_metastatic_roi_065': 'brain',
• 'training_set_metastatic_roi_066': 'skin',
• 'training_set_metastatic_roi_067': 'lymph node',
• 'training_set_metastatic_roi_068': 'soft tissue',
• 'training_set_metastatic_roi_069': 'liver',
• 'training_set_metastatic_roi_070': 'gastrointestinal tract',
• 'training_set_metastatic_roi_071': 'lymph node',
• 'training_set_metastatic_roi_072': 'gastrointestinal tract',
• 'training_set_metastatic_roi_073': 'brain',
• 'training_set_metastatic_roi_074': 'bone',
• 'training_set_metastatic_roi_075': 'soft tissue',
• 'training_set_metastatic_roi_076': 'lung',
• 'training_set_metastatic_roi_077': 'skin',
• 'training_set_metastatic_roi_078': 'liver',
• 'training_set_metastatic_roi_079': 'skin',
• 'training_set_metastatic_roi_080': 'lymph node',
• 'training_set_metastatic_roi_081': 'soft tissue',
• 'training_set_metastatic_roi_082': 'liver',
• 'training_set_metastatic_roi_083': 'skin',
• 'training_set_metastatic_roi_084': 'skin',
• 'training_set_metastatic_roi_085': 'lung',
• 'training_set_metastatic_roi_086': 'lymph node',
• 'training_set_metastatic_roi_087': 'skin',
• 'training_set_metastatic_roi_088': 'lymph node',
• 'training_set_metastatic_roi_089': 'liver',
• 'training_set_metastatic_roi_090': 'liver',
• 'training_set_metastatic_roi_091': 'lung',
• 'training_set_metastatic_roi_092': 'skin',
• 'training_set_metastatic_roi_093': 'skin',
• 'training_set_metastatic_roi_094': 'skin',
• 'training_set_metastatic_roi_095': 'skin',
• 'training_set_metastatic_roi_096': 'skin',
• 'training_set_metastatic_roi_097': 'skin',
• 'training_set_metastatic_roi_098': 'lung',
• 'training_set_metastatic_roi_099': 'soft tissue',
• 'training_set_metastatic_roi_100': 'liver',
• 'training_set_metastatic_roi_101': 'soft tissue',
• 'training_set_metastatic_roi_102': 'skin',
• 'training_set_metastatic_roi_103': 'skin',

What kind of other metadata would you like to have?

Kind regards, Mark

Dear Mark,

Thank you very much for your detailed response — it’s extremely helpful!

Just to clarify, do only metastatic cases spread to different organs in this dataset? Also, could you let me know which organs are involved in primary tumors?

Best regards, Tong Wang

Dear Tong Wang,

Just to clarify, do only metastatic cases spread to different organs in this dataset? No, primary cases could also have spread. I looked into the pathology archive to find cases of malignant melanoma but I did not look specifically into whether the patient developed a metastasis.

Also, could you let me know which organs are involved in primary tumors? We excluded uveal and mucosal melanoma lesions so lesion would be primarily be from the skin.

Kind regards, Mark

Thank you, Mark. Your response was very helpful to me. I truly appreciate it once again.

Yours sincerely, Tong