create unique id for genes by meganrm · Pull Request #420 · AllenCell/cell-catalog

meganrm · 2026-02-10T22:25:32Z

Problem

a number of genes have the same gene symbol but are visualizing different structures

Solution

I made a unique identifier. I tried other methods of automatically creating a unique ID, but struggled to figure out a good solution that worked for all of them. Since this is probably not going to be an ongoing problem I think it's an ok solution. If we were planning on making a lot of new cell lines, I would want to create checks to make sure the id is actually unique.

Type of change

Please delete options that are not relevant.

Bug fix (non-breaking change which fixes an issue)

Steps to Verify:

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Copilot

Pull request overview

This PR introduces a unique geneId to disambiguate gene entries that share the same symbol, and updates CMS/Gatsby linking so cell line genetic modifications reference that unique identifier.

Changes:

Add required geneId field to gene-name content and switch Netlify CMS slugs/value fields to use it.
Update Gatsby schema customization and mappings so genetic_modifications.gene links by geneId rather than symbol.
Update existing gene-name and cell-line markdown content to populate and reference geneId values.

Reviewed changes

Copilot reviewed 120 out of 120 changed files in this pull request and generated 4 comments.

Show a summary per file

File	Description
static/admin/config.yml	Add `geneId` field and update CMS relations/slugging to rely on `geneId`.
src/templates/normal-catalog.tsx	Extend GraphQL query to include `id` and `fields.slug`.
src/templates/gene-name.tsx	Extend GraphQL query to include `fields.slug`.
src/pages/gene-names/ubtf.md	Add `geneId` frontmatter.
src/pages/gene-names/tuba1b.md	Add `geneId` frontmatter.
src/pages/gene-names/ttn.md	Add `geneId` frontmatter.
src/pages/gene-names/tomm20.md	Add `geneId` frontmatter.
src/pages/gene-names/tnni1.md	Add `geneId` frontmatter.
src/pages/gene-names/tjp1.md	Add `geneId` frontmatter.
src/pages/gene-names/tfam.md	Add `geneId` frontmatter.
src/pages/gene-names/terf2.md	Add `geneId` frontmatter.
src/pages/gene-names/st6gal1.md	Add `geneId` frontmatter.
src/pages/gene-names/sox2.md	Add `geneId` frontmatter.
src/pages/gene-names/son.md	Add `geneId` frontmatter.
src/pages/gene-names/smc1a.md	Add `geneId` frontmatter.
src/pages/gene-names/slc25a17.md	Add `geneId` frontmatter.
src/pages/gene-names/sec61b.md	Add `geneId` frontmatter.
src/pages/gene-names/rab5a.md	Add `geneId` frontmatter.
src/pages/gene-names/pxn.md	Add `geneId` frontmatter.
src/pages/gene-names/polr2a.md	Add `geneId` frontmatter.
src/pages/gene-names/pcna.md	Add `geneId` frontmatter.
src/pages/gene-names/nup153.md	Add `geneId` frontmatter.
src/pages/gene-names/npm1.md	Add `geneId` frontmatter.
src/pages/gene-names/myl7.md	Add `geneId` frontmatter.
src/pages/gene-names/myl2.md	Add `geneId` frontmatter.
src/pages/gene-names/myh7.md	Add `geneId` frontmatter.
src/pages/gene-names/myh3.md	Add `geneId` frontmatter.
src/pages/gene-names/myh10.md	Add `geneId` frontmatter.
src/pages/gene-names/map1lc3b.md	Add `geneId` frontmatter.
src/pages/gene-names/lmnb1.md	Add `geneId` frontmatter.
src/pages/gene-names/lmna.md	Add `geneId` frontmatter.
src/pages/gene-names/lamp1.md	Add `geneId` frontmatter.
src/pages/gene-names/hist1h2bj.md	Add `geneId` frontmatter.
src/pages/gene-names/gja1.md	Add `geneId` frontmatter.
src/pages/gene-names/g3bp1.md	Add `geneId` frontmatter.
src/pages/gene-names/fus.md	Add `geneId` frontmatter.
src/pages/gene-names/fbl.md	Add `geneId` frontmatter.
src/pages/gene-names/ezh2.md	Add `geneId` frontmatter.
src/pages/gene-names/eomes.md	Add `geneId` frontmatter.
src/pages/gene-names/dsp.md	Add `geneId` frontmatter.
src/pages/gene-names/dmd.md	Add `geneId` frontmatter.
src/pages/gene-names/dcp1a.md	Add `geneId` frontmatter.
src/pages/gene-names/ctnnb1.md	Add `geneId` frontmatter.
src/pages/gene-names/ctcf.md	Add `geneId` frontmatter.
src/pages/gene-names/clybl-dcas9-krab.md	Add `geneId` frontmatter.
src/pages/gene-names/clybl safe harbor.md	Add `geneId` frontmatter.
src/pages/gene-names/cetn2.md	Add `geneId` frontmatter.
src/pages/gene-names/cdh5.md	Add `geneId` frontmatter.
src/pages/gene-names/cdh1.md	Add `geneId` frontmatter.
src/pages/gene-names/cbx1.md	Add `geneId` frontmatter.
src/pages/gene-names/atp2a2.md	Add `geneId` frontmatter.
src/pages/gene-names/actn2.md	Add `geneId` frontmatter.
src/pages/gene-names/actb.md	Add `geneId` frontmatter.
src/pages/gene-names/aavs1-mitochondrial.md	Add `geneId` frontmatter.
src/pages/gene-names/aavs1-megfp.md	Add new gene-name entry with `geneId`.
src/pages/gene-names/aavs1-caax.md	Add `geneId` frontmatter.
src/pages/cell-line/AICS-99-20/index.md	Update `genetic_modifications.gene` to use `geneId`.
src/pages/cell-line/AICS-96-74/index.md	Update `genetic_modifications.gene` to use `geneId`.
src/pages/cell-line/AICS-95-18/index.md	Update `genetic_modifications.gene` to use `geneId`.
src/pages/cell-line/AICS-94-24/index.md	Update `genetic_modifications.gene` to use `geneId`.
src/pages/cell-line/AICS-93-25/index.md	Update `genetic_modifications.gene` to use `geneId`.
src/pages/cell-line/AICS-90-391/index.md	Update `genetic_modifications.gene` to use `geneId`.
src/pages/cell-line/AICS-89-61/index.md	Update multiple `genetic_modifications.gene` entries to use `geneId`.
src/pages/cell-line/AICS-88-83/index.md	Update `genetic_modifications.gene` to use `geneId`.
src/pages/cell-line/AICS-87-31/index.md	Update `genetic_modifications.gene` to use `geneId`.
src/pages/cell-line/AICS-86-147/index.md	Update multiple `genetic_modifications.gene` entries to use `geneId`.
src/pages/cell-line/AICS-84-18/index.md	Update multiple `genetic_modifications.gene` entries to use `geneId`.
src/pages/cell-line/AICS-83-5/index.md	Update `genetic_modifications.gene` to use `geneId`.
src/pages/cell-line/AICS-83-124/index.md	Update `genetic_modifications.gene` to use `geneId`.
src/pages/cell-line/AICS-82-1/index.md	Update `genetic_modifications.gene` to use `geneId`.
src/pages/cell-line/AICS-80-69/index.md	Update `genetic_modifications.gene` to use `geneId`.
src/pages/cell-line/AICS-78-79/index.md	Update multiple `genetic_modifications.gene` entries to use `geneId`.
src/pages/cell-line/AICS-75-85/index.md	Update `genetic_modifications.gene` to use `geneId`.
src/pages/cell-line/AICS-74-26/index.md	Update `genetic_modifications.gene` to use `geneId`.
src/pages/cell-line/AICS-70-in-progress/index.md	Update `genetic_modifications.gene` to use `geneId`.
src/pages/cell-line/AICS-69-88/index.md	Update `genetic_modifications.gene` to use `geneId`.
src/pages/cell-line/AICS-68-9/index.md	Update `genetic_modifications.gene` to use `geneId`.
src/pages/cell-line/AICS-63-96/index.md	Update `genetic_modifications.gene` to use `geneId`.
src/pages/cell-line/AICS-61-36/index.md	Update `genetic_modifications.gene` to use `geneId`.
src/pages/cell-line/AICS-60-27/index.md	Update `genetic_modifications.gene` to use `geneId`.
src/pages/cell-line/AICS-59-36/index.md	Update multiple `genetic_modifications.gene` entries to use `geneId`.
src/pages/cell-line/AICS-58-67/index.md	Update `genetic_modifications.gene` to use `geneId`.
src/pages/cell-line/AICS-57-50/index.md	Update `genetic_modifications.gene` to use `geneId`.
src/pages/cell-line/AICS-54-91/index.md	Update `genetic_modifications.gene` to use `geneId` (AAVS1 variant).
src/pages/cell-line/AICS-53-16/index.md	Update `genetic_modifications.gene` to use `geneId`.
src/pages/cell-line/AICS-52-3/index.md	Update `genetic_modifications.gene` to use `geneId`.
src/pages/cell-line/AICS-5-50/index.md	Update `genetic_modifications.gene` to use `geneId`.
src/pages/cell-line/AICS-48-39/index.md	Update `genetic_modifications.gene` to use `geneId`.
src/pages/cell-line/AICS-46-51/index.md	Update `genetic_modifications.gene` to use `geneId`.
src/pages/cell-line/AICS-40-35/index.md	Update `genetic_modifications.gene` to use `geneId`.
src/pages/cell-line/AICS-40-13/index.md	Update `genetic_modifications.gene` to use `geneId`.
src/pages/cell-line/AICS-37-172/index.md	Update `genetic_modifications.gene` to use `geneId`.
src/pages/cell-line/AICS-36-6/index.md	Use `geneId` for AAVS1 entry and reformat YAML content.
src/pages/cell-line/AICS-36-28/index.md	Use `geneId` for AAVS1 entry and reformat YAML content.
src/pages/cell-line/AICS-34-62/index.md	Update `genetic_modifications.gene` to use `geneId`.
src/pages/cell-line/AICS-33-115/index.md	Update `genetic_modifications.gene` to use `geneId`.
src/pages/cell-line/AICS-32-19/index.md	Update `genetic_modifications.gene` to use `geneId`.
src/pages/cell-line/AICS-31-35/index.md	Update `genetic_modifications.gene` to use `geneId`.
src/pages/cell-line/AICS-30-22/index.md	Update `genetic_modifications.gene` to use `geneId`.
src/pages/cell-line/AICS-25-44/index.md	Update `genetic_modifications.gene` to use `geneId`.
src/pages/cell-line/AICS-25-1/index.md	Update `genetic_modifications.gene` to use `geneId`.
src/pages/cell-line/AICS-24-80/index.md	Update `genetic_modifications.gene` to use `geneId`.
src/pages/cell-line/AICS-23-20/index.md	Update `genetic_modifications.gene` to use `geneId`.
src/pages/cell-line/AICS-22-37/index.md	Update `genetic_modifications.gene` to use `geneId`.
src/pages/cell-line/AICS-17-65/index.md	Update `genetic_modifications.gene` to use `geneId`.
src/pages/cell-line/AICS-16-184/index.md	Update `genetic_modifications.gene` to use `geneId`.
src/pages/cell-line/AICS-14-6/index.md	Update `genetic_modifications.gene` to use `geneId`.
src/pages/cell-line/AICS-13-210/index.md	Update `genetic_modifications.gene` to use `geneId`.
src/pages/cell-line/AICS-126-68/index.md	Update `genetic_modifications.gene` to use `geneId`.
src/pages/cell-line/AICS-126-41/index.md	Update `genetic_modifications.gene` to use `geneId`.
src/pages/cell-line/AICS-122-77/index.md	Update `genetic_modifications.gene` to use `geneId`.
src/pages/cell-line/AICS-120-204/index.md	Update multiple `genetic_modifications.gene` entries to use `geneId` (incl AAVS1 variant).
src/pages/cell-line/AICS-12-105/index.md	Update `genetic_modifications.gene` to use `geneId`.
src/pages/cell-line/AICS-114-35/index.md	Update `genetic_modifications.gene` to use `geneId`.
src/pages/cell-line/AICS-114-32/index.md	Update `genetic_modifications.gene` to use `geneId`.
src/pages/cell-line/AICS-11-27/index.md	Update `genetic_modifications.gene` to use `geneId`.
src/pages/cell-line/AICS-102-330/index.md	Update `genetic_modifications.gene` to use `geneId` (AAVS1 variant).
src/pages/cell-line/AICS-10-55/index.md	Update `genetic_modifications.gene` to use `geneId`.
gatsby-node.js	Update `@link` to join genes by `frontmatter.geneId` and reformat strings.
gatsby-config.js	Update Gatsby field mapping to target new gene identifier.

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gatsby-config.js

static/admin/config.yml

src/pages/gene-names/clybl safe harbor.md

static/admin/config.yml

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

…l-catalog-2.1 into fix/non-unique-genes

netlify · 2026-02-10T22:30:41Z

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Pull request overview

Copilot reviewed 120 out of 120 changed files in this pull request and generated no new comments.

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netlify · 2026-02-10T22:35:42Z

✅ Deploy Preview for cell-catalog ready!

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interim17

Read through this and it seems reasonable, approving. I'm reviewing without running the code because I'm afk. Can circle back to run if desired.

rugeli · 2026-02-11T18:59:27Z

src/pages/gene-names/clybl-safe-harbor.md

@@ -1,5 +1,6 @@
 ---
 templateKey: gene-name
+geneId: "clybl-safe-harbor"
 symbol: CLYBL safe harbor
 name: citramalyl-CoA lyase safe harbor
 protein: dCas9-KRAB


nit(preventative): should we rename this file to "src/pages/gene-names/clybl-safe-harbor.md" to keep filenames slugified and consistent?

rugeli · 2026-02-11T18:59:50Z

static/admin/config.yml

+          - {
+                label: "Gene ID",
+                name: "geneId",
+                widget: "string",
+                required: true,
+                hint: "Unique identifier for this gene entry. If the gene symbol is unique, you can use that as the gene ID. Otherwise, you can create a unique ID (lowercase no spaces) using a combination of the gene symbol and other relevant information (e.g., species, isoform).",
+                pattern: ["^[a-z0-9-]+$", "Must be lowercase, using only letters, numbers, and hyphens (no spaces)."]
+            }


Good idea to add gene id, love the regex validation and error msg!

rugeli

Built locally and played around with the preview site, gene related display and search&filter work well!

create unique id for genes

250f14a

meganrm requested a review from Copilot February 10, 2026 22:25

Copilot AI reviewed Feb 10, 2026

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meganrm and others added 4 commits February 10, 2026 14:28

Update gatsby-config.js

065b760

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

Update static/admin/config.yml

a358cbb

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

use dashes

4220d92

Merge branch 'fix/non-unique-genes' of https://github.com/meganrm/cel…

015e024

…l-catalog-2.1 into fix/non-unique-genes

meganrm requested a review from Copilot February 10, 2026 22:32

Copilot AI reviewed Feb 10, 2026

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meganrm requested review from interim17 and rugeli February 10, 2026 22:33

interim17 approved these changes Feb 11, 2026

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rugeli reviewed Feb 11, 2026

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rugeli approved these changes Feb 11, 2026

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change file name to match id

037d21d

meganrm merged commit 26027a4 into main Feb 11, 2026
7 checks passed

meganrm deleted the fix/non-unique-genes branch February 11, 2026 21:21

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create unique id for genes#420

create unique id for genes#420
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fix/non-unique-genes

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meganrm commented Feb 10, 2026

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