CSV report of biomarker descriptions

[nutjob4life]

🤔 Tell Us About the Feature

Develop a CSV report for biomarker descriptions. This could use the RDF directly or could query the portal database. The descriptions should include the general description of the biomarker and each organ-specific description.

🎇 What Solution You'd Like

The CSV should have these columns:

1. Biomarker ID
2. Biomarker HGNC name
3. General description
4. Bladder description, or blank if unavailable
5. Blood description, or blank if unavailable
6. Bone description, or blank if unavailable
7. Brain description, or blank if unavailable
8. etc.

The list of organs is:

['Bladder', 'Blood', 'Bone', 'Brain', 'Breast', 'Bronchus', 'Cartilage', 'Cervix', 'Colon', 'Esophagus', 'Head & neck, NOS', 'Hypopharynx', 'Kidney', 'Larynx', 'Liver', 'Lung', 'Lymph nodes', 'Mouth', 'Nasopharynx', 'Nose', 'Oral Cavity', 'Oropharynx', 'Ovary', 'Pancreas', 'Placenta', 'Prostate', 'Rectum', 'Skin', 'Stomach', 'Testis', 'Throat', 'Thyroid', 'Uterus', 'Vagina']

For the organ-specific description, use the following fields:

• description
• performance_comment

Use both if available (concatenated)

〽️ Alternative Ideas

This could also be gleaned from the RDF so no portal code or BMDB code is really necessary.

🗺 Context

Meeting 2025-06-06.

[nutjob4life]

@AshishMahabal take a look at the issue text above; does that sounds correct?

[AshishMahabal]

Yep. That looks great. I didn't know there were so many 'organs' with at least one entry in our biomarker files.

[nutjob4life]

I've adjusted this a bit:

• Although the official list of organs (from the DMCC) is quite long, those actually in-use by biomarkers is just 10 (['Bladder', 'Breast', 'Colon', 'Esophagus', 'Head and Neck', 'Liver', 'Lung', 'Ovary', 'Pancreas', 'Prostate'])
• For some biomarkers' organs, there was both a description and a performance comment
  • The issue text above preferred the description if it was available
  • However for some biomarkers (CXCL8 for example), the description was "No additional data available." which hid much more useful information in the performance comment
    • So I've included both when possible

[nutjob4life]

File sent to Dan and Shubham but LFT does not @AshishMahabal.