Tutorial

This is the guided, end-to-end path: start from nothing and finish with a working viewer that shows the full UniProt annotation for a protein plus your own track, recoloured to match your site. It’s one continuous example on a single protein: P05067, amyloid precursor protein, the reference accession used throughout these docs.

Each step ends with a Try it live link that opens the exact setup in the playground, so you can see it render and edit it without leaving the browser. When you want the full detail behind a step, follow the links to the how-to guides.

The quickest way to follow along is the Starter Kit: a no-build template repository you can copy and open straight in the browser. You can also work in your own page served by any static file server or your app’s dev server, or use the playground for the config-only steps. No build tooling is required.

Note

These docs describe the unreleased 5.0 config surface (rows:, kind:, extends:). The current npm release, protvista-uniprot@4.9.3, predates it and will not read the configs below — Step 1 shows how to get a matching build.

Step 1: Add the component and point it at an accession

<protvista-uniprot> is a web component: a custom element that works in any page with no bundler or framework. Load it once and drop the tag in with an accession:

<script type="module" src="./protvista-uniprot.mjs"></script>

<protvista-uniprot accession="P05067"></protvista-uniprot>

protvista-uniprot.mjs is the component’s built ES-module bundle. Until 5.0 is published to npm, build it from source and copy it next to your page:

git clone https://github.com/ebi-webcomponents/protvista
cd protvista
yarn install && yarn build
# then copy dist/protvista-uniprot.mjs next to your HTML page

That single attribute gives you the full default UniProt viewer for the protein: domains, variants, binding sites, structure coverage, AlphaFold confidence, and more. No config required.

Try it live

Open the default viewer for P05067. Swap the accession in the header to view any other protein.

Embed the viewer covers both ways to load the component and every attribute (config-src, notooltip, nostructure, …).

Step 2: Add your own track from a CSV

Now bring your own annotations. A features track can read a CSV file directly: point data: at the file and the .csv extension picks the parser for you: no adapter: needed.

Say your lab has flagged some hotspot regions. Put them in a CSV with the feature-record columns type,start,end,description,score:

type,start,end,description,score
DOMAIN,18,289,Extracellular domain (custom re-annotation),0.95
BINDING,132,140,Predicted heparin-binding site,0.87
REGION,290,340,Acidic-rich linker region,0.6
MUTAGEN,614,614,Lab-observed loss-of-function point mutation,0.75

Then describe a viewer that shows just that file as one standalone track (a rows: entry with data: and no tracks: needs no group wrapper):

accession: P05067
rows:
  - id: hotspots
    label: Hotspots
    kind: features
    data: ./hotspots.csv
    description: Hotspot regions identified by our lab's pipeline

Save the config as my-config.yaml next to hotspots.csv and point the element at it:

<protvista-uniprot config-src="./my-config.yaml"></protvista-uniprot>

Caution

data: ./hotspots.csv is fetched relative to the hosting page, not the config file. If a file-backed track renders empty, this is the usual cause: serve the page from the same directory as the data, or use an absolute URL.

Try it live

Open the CSV track in the playground. It renders the same config against a hosted copy of hotspots.csv.

Load your own data covers the full feature record and the TSV, JSON, and BED formats.

Step 3: Layer it onto the full UniProt viewer

A standalone track is a viewer of its own. More often you want your track on top of everything UniProt already provides. Instead of rebuilding the default viewer, extends it: you inherit all its sources, groups, and themes, and declare only your addition.

The custom data can be simpler here — the default viewer supplies the rest:

type,start,end,description,score
DOMAIN,18,289,Custom re-annotation of the extracellular domain,0.9
BINDING,614,614,Lab-observed candidate binding residue,0.72

accession: P05067
extends: /src/default-config.yaml

rows:
  - id: MY_LAB
    label: My lab
    tracks:
      - id: hotspots
        kind: features
        data: ./hotspots.csv
        description: Hotspot regions identified by our lab's pipeline, layered on top of the canonical UniProt viewer

That’s the whole config: the full canonical viewer, with a My lab group added at the end.

Caution

extends: /src/default-config.yaml resolves only when the page is served from this repo’s root; a deployed site must point extends at a hosted copy instead — either your own, or the published package on a CDN: https://cdn.jsdelivr.net/npm/protvista-uniprot@5.0.0/dist/default-config.yaml (available once 5.0.0 ships, as above). See Author a config for the merge rules and the full caveat.

Try it live

Open the full default viewer to see the base you’re extending. To see it combined with your track, switch extends: to the CDN URL above — that form resolves from any page, once 5.0.0 ships.

Step 4: Style it

Finally, make it yours. There are two levers, no rebuild required.

No code: from the config. A theme: block recolours the viewer chrome directly, so an author who doesn’t write CSS can still brand the viewer. labelColor sets the row-label panel; the optional accentColor sets focus rings and the datatable’s active-row marker:

theme:
  labelColor: '#e8f5e9'
  accentColor: '#2e7d32'

Try it live

Open the inline-data preset, which carries a theme: block — edit the colours and press Run.

From your page’s CSS. For full control, <protvista-uniprot> exposes --protvista-* design tokens and ::part hooks — set them in ordinary CSS on the page:

protvista-uniprot {
  --protvista-color-accent: #7b2d8e;
  --protvista-group-label-bg: #efe6f5;
}

Caution

The two levers are not additive: a config theme: wins. labelColor and accentColor are applied as inline styles on the element, so they override page CSS targeting the same tokens — including both tokens in the example above. Pick one lever, or force the CSS with !important. See No-code theming from the config.

Theme the viewer lists every token and the datatable ::part hooks.

You’re done

You went from an empty page to a viewer that shows the full UniProt annotation for a protein, adds your own track from a CSV, and matches your site’s colours.

Where to go next:

• Author a config — every field a config can hold.
• Load your own data — TSV, JSON, BED, and inline data.
• Theme the viewer — the full token and ::part reference.
• Configuration vs data — what your config controls versus what a data provider supplies.
• Escape hatches — custom parsers, kinds, and themes when the built-ins aren’t enough.
• Playground — edit any config live and share it by link.
• Starter Kit — a no-build template repository to copy and go.
• Runnable examples — the CI-validated configs this tutorial draws from.

Licensed under CC BY 4.0.