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How to Download Phenotype Annotations from SGD

September 17, 2026

Q: Is it possible to download a flat file for all phenotype annotations?

The short answer is yes! There are two easy ways to get all of the phenotype annotations at SGD.

Option 1: The SGD Downloads Site

SGD maintains a Downloads site, which you can reach via the “Download” link in the black toolbar that runs across the top of most SGD pages, or directly at:

http://sgd-archive.yeastgenome.org/

To find the phenotype annotations:

  1. Since this is curated data, select “curation.”
  2. Next, select “literature.”
  3. This brings you to: http://sgd-archive.yeastgenome.org/curation/literature/
  4. Here you’ll find a file named phenotype_data.tab, along with an associated README file named phenotype_data.README that explains the file’s contents in detail.

This file is updated weekly and contains all of the phenotypes annotated at SGD.

Option 2: AllianceMine (“Get Data”)

You can also retrieve phenotype annotations through AllianceMine. Look for the “Get Data” link in the black toolbar that runs across the top right of most SGD pages, or go directly to:

https://www.alliancegenome.org/bluegenes/alliancemine

From there:

  1. Navigate to “Templates.”
  2. Use “filter by category” and select “Phenotypes.”
  3. You’ll find two precomposed templates (queries) for phenotypes: both will give you the same data.
  4. Select, for example, “Retrieve all phenotypes for all genes.” This brings you to a page with a results preview of phenotype annotations.
  5. Click “View [count] rows” at the bottom to load the file in your browser. Because phenotype annotation is ongoing, the number of rows grows over time.

From here, you have two options:

  • Export (top right) and open the downloaded file in Excel (or a similar program), or
  • Use the built-in filters first to retrieve a subset of the data, then download.

Questions?

As always, if you have questions about downloading data, or anything else at SGD, don’t hesitate to reach out. Chances are, if you’re wondering about it, someone else is too!

Categories: Tutorial

Tags: user question