Added new 'density' term

[ar-ibrahim]

• NTR: breast density New term request for Verma PMID: 37345113 EBISPOT/efo#2107

[ar-ibrahim]

• The paper defines breast density as the amount of fibroglandular versus fatty tissue in the breast, so I wonder if using the PATO quality mass density accurately reflects that. Existing OBA terms like nucleosome density, use the PATO quality amount. Is this a comparable case?

[rays22]

They are looking at the composition of breast tissue in a population. One of the major tissue components is adipose tissue. They call this trait 'breast density', because they are looking at pixel densities of mammographs in 2D. I think the PATO quality composition --> fatty PATO:0002114 captures the gist of the genetic trait they are measuring.

• Entity: UBERON:0000310 breast
• Attribute: PATO:0002114 fatty

I would suggest to add a synonym like breast tissue density so that it is easier to find based on the original breast density term used in the paper.

[rays22]

Please, make sure that only the

OBA:2050351	breast density	UBERON:0000310	breast	PATO:0001019	mass density	breast tissue density	PMID:37345113	https://orcid.org/0000-0001-6757-4744

line is added to src/patterns/data/default/entity_attribute.tsv and nothing else is taken away or added.

[rays22]

It seems that you are editing an earlier version of this file. Here you are undoing some edits that are unrelated to your addition of the density term.

[rays22]

Suggested fix

Typically, a simple way to fix this and similar errors is as follows:

1. Save the information (in this case 1 line from the src/patterns/data/default/entity_attribute.tsv file) that you want to add in a place outside of your github controlled PR branch (e.g. in a temporary textfile or a spreadsheet on your machine). You will want to add this back later:

OBA:2050351	breast density	UBERON:0000310	breast	PATO:0001019	mass density	breast tissue density	PMID:37345113	https://orcid.org/0000-0001-6757-4744

2. Replace src/patterns/data/default/entity_attribute.tsv in your branch with the latest version of this file from the master branch. You can do that in many different ways. Here is how to do it on the command line:

git checkout master -- path/to/your/folder/entity_attribute.tsv

4. Add back the line that you have removed in step 1 to the entity_attribute.tsv table.
5. Update definitions.owl:

sh run.sh make ../patterns/definitions.owl

6. Check in the 2 updated files (entity_attribute.tsv, definitions.owl) and commit to github.
7. Push your changes from your local machine to github.
8. Check if the only difference in entity_attribute.tsv between your branch and the master branch is the one line that you wanted to add.
   Let the QC and automatic actions complete and the PR is ready for review/merge.

[rays22]

Looks fine, including the new term from your previous PR (305) in definitions.owl .