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Client for InterPro 99.0 #596

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merged 193 commits into from
Mar 23, 2024
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00342d2
storybook with 2 basic stories
gustavo-salazar Jan 12, 2024
152e92f
Merge branch 'dev' into storybook-again
gustavo-salazar Jan 12, 2024
582696a
first stories
gustavo-salazar Jan 15, 2024
2be8156
Merge branch 'dev' into storybook-again
gustavo-salazar Jan 15, 2024
cf7c4db
description, button and dropdownbutton stories
gustavo-salazar Jan 15, 2024
29aaf30
storybook: simpleTable
gustavo-salazar Jan 15, 2024
3714721
storybook: removing onboarding
gustavo-salazar Jan 15, 2024
88009d4
storybook: adding jsdoc comment on the components of the current srto…
gustavo-salazar Jan 16, 2024
ac80b14
storybook: GOTerms story
gustavo-salazar Jan 16, 2024
2a7b4aa
storybook: FullScreen story
gustavo-salazar Jan 16, 2024
7f26f8f
storybook: Connected Table story
gustavo-salazar Jan 16, 2024
027cd47
storybook: Link story
gustavo-salazar Jan 16, 2024
c2a0ddd
storybook: Number story
gustavo-salazar Jan 16, 2024
94ded81
storybook: MemberDBSelector story
gustavo-salazar Jan 16, 2024
b07fea0
storybook: Popups story
gustavo-salazar Jan 16, 2024
9741cc2
storybook: References story
gustavo-salazar Jan 16, 2024
74a2bcf
storybook: Tabs story + detaching Tabs syling from foundation and EBI…
gustavo-salazar Jan 18, 2024
b026208
strotybook: FullyLoadedTable Story
gustavo-salazar Jan 18, 2024
82a50cd
strotybook: Title Story + minor styling touches in title
gustavo-salazar Jan 18, 2024
4d7a41f
strotybook: autodocs for Title story
gustavo-salazar Jan 18, 2024
472baaf
strotybook: ToggleSwitch story + styling and decoupling from ebi-globals
gustavo-salazar Jan 18, 2024
0d10a51
strotybook: Tooltip story
gustavo-salazar Jan 19, 2024
6bf3887
strotybook: Skylign story
gustavo-salazar Jan 19, 2024
304d837
strotybook: ProteinViewer story
gustavo-salazar Jan 19, 2024
63e4102
strotybook: Callout story + reating a Callout component
gustavo-salazar Jan 19, 2024
8225c23
Using the new Callout component on all TSX components
gustavo-salazar Jan 19, 2024
2e4e89a
removing forced eror message from home
gustavo-salazar Jan 22, 2024
62891eb
<Callout> in js files
gustavo-salazar Jan 22, 2024
a6322c5
flow and jest fixes
gustavo-salazar Jan 22, 2024
97cb3fd
new Component Car with its story and used in Proteome and Taxonomy ta…
gustavo-salazar Jan 23, 2024
f4a3cbf
using Card in Entry, Protein, Set and Structure
gustavo-salazar Jan 23, 2024
2ddb3a7
remove SarsCov proteome page
gustavo-salazar Jan 23, 2024
959cf59
Using the new Card component for EntryCard
gustavo-salazar Jan 23, 2024
8c42aec
flow fix
gustavo-salazar Jan 23, 2024
f509afc
new component CounterIcon and using it in Entry page
gustavo-salazar Jan 24, 2024
b79b5b5
TS: Extracting SummaryCunterEntries
gustavo-salazar Jan 24, 2024
800baed
Using CounterIcon for Protein page
gustavo-salazar Jan 24, 2024
0a95170
TS: Extracting SummaryCunterProteins
gustavo-salazar Jan 24, 2024
5252d11
TS: Extracting SummaryCunterStructures and using ConterIcon on it
gustavo-salazar Jan 24, 2024
88aa15c
TS: Extracting SummaryCunterSets and using ConterIcon on it
gustavo-salazar Jan 24, 2024
2506ef5
TS: Extracting SummaryCunterProteome and using ConterIcon on it
gustavo-salazar Jan 25, 2024
9fbcb6f
TS: Proteome/Card
gustavo-salazar Jan 25, 2024
1a2e8b3
TS: Extracting SummaryCunterTaxonomy and using ConterIcon on it
gustavo-salazar Jan 25, 2024
a096e4d
TS: Extracting EntryCard from Enrtry page
gustavo-salazar Jan 25, 2024
ad67cb3
Using COunterIcon in the Entry Card of the home page
gustavo-salazar Jan 25, 2024
0851c97
TS: home/EntryCard
gustavo-salazar Jan 25, 2024
2d2d036
cleaning CSSs
gustavo-salazar Jan 25, 2024
a332e37
storybook: reorganising the stories
gustavo-salazar Jan 25, 2024
7938e14
storybook: first CounterCards
gustavo-salazar Jan 25, 2024
0dc5f7c
TS: Extracting ProteinCard
gustavo-salazar Jan 25, 2024
695cee1
storybook: ProteinCard
gustavo-salazar Jan 25, 2024
e02c8ae
TS: Extracting StructureCard from Structure page
gustavo-salazar Jan 26, 2024
7441bc2
storybook: StructureCard
gustavo-salazar Jan 26, 2024
d8b1e3e
TS: extract TaxonomyCard for page + storybook: TaxonomyCard
gustavo-salazar Jan 26, 2024
290ae5a
storybook: ProteomeCard
gustavo-salazar Jan 26, 2024
57fa779
TS: extract SetCard for page + storybook: SetCard
gustavo-salazar Jan 26, 2024
1b3f1b0
storybook: CounterIcon
gustavo-salazar Jan 26, 2024
819c378
removing the tmp/ folder that had the old storybook files
gustavo-salazar Jan 26, 2024
1961586
Using Card in BlogEntries and movingcthe some of the cards styling in…
gustavo-salazar Jan 26, 2024
cc3bae0
TS: BlogEntries
gustavo-salazar Jan 26, 2024
2c4e172
storybook: BlogEntry Card
gustavo-salazar Jan 26, 2024
115f806
TS:Tool car + storybook: Home Tool Card
gustavo-salazar Jan 29, 2024
bae6551
remove unused help and about pages
gustavo-salazar Jan 29, 2024
42ae163
TS: InfoBanner
gustavo-salazar Jan 29, 2024
9447204
TS: Help/Publication + Removing unused code
gustavo-salazar Jan 29, 2024
ad7ad91
using Card in Abput/Interproscan
gustavo-salazar Jan 29, 2024
2c035fb
TS: About/InterProScan
gustavo-salazar Jan 29, 2024
f78d9f2
TS: HelpBanner
gustavo-salazar Jan 29, 2024
a4cc9b4
storybook: Help and Info Cards
gustavo-salazar Jan 29, 2024
f3403a3
removing last usage of css flex-card, now everything uses <Card>
gustavo-salazar Jan 29, 2024
a956d0c
update storybook
gustavo-salazar Jan 29, 2024
87a34e7
Merge branch 'storybook-again' into callout-in-js
gustavo-salazar Jan 29, 2024
3825c63
Merge branch 'storybook-again' into card-component
gustavo-salazar Jan 29, 2024
e9b70ed
Apply suggestions from code review
gustavo-salazar Feb 1, 2024
4cf1e6c
Apply suggestions from code review - missed those somehow
gustavo-salazar Feb 1, 2024
0b976a5
sugestions from PR
gustavo-salazar Feb 1, 2024
972f666
Merge branch 'storybook-again' of https://github.com/ProteinsWebTeam/…
gustavo-salazar Feb 1, 2024
7467681
missing sugestion from PR
gustavo-salazar Feb 1, 2024
b8e26f1
Merge branch 'storybook-again' into callout-in-js
gustavo-salazar Feb 1, 2024
59d3cae
Apply suggestions from code review
gustavo-salazar Feb 1, 2024
ab483b8
Merge branch 'callout-in-js' of https://github.com/ProteinsWebTeam/in…
gustavo-salazar Feb 1, 2024
ecb92f5
re-enable mouseleave in ToastDisplay
gustavo-salazar Feb 1, 2024
d2a7eae
Fixes #573, update text
matthiasblum Feb 1, 2024
c02396a
Fixes #572: add external link to "Citing Pfam" page
matthiasblum Feb 1, 2024
b7c8c18
Update link texts
matthiasblum Feb 1, 2024
e50629d
Update icons
matthiasblum Feb 1, 2024
a589520
Update text
matthiasblum Feb 1, 2024
1f41044
Update some links
matthiasblum Feb 1, 2024
9377942
Add missing whitespace
matthiasblum Feb 1, 2024
c07b300
Fixes #569: use undo icon
matthiasblum Feb 1, 2024
c79b131
Update tooltip text to remove tech term
matthiasblum Feb 1, 2024
7714939
Fixes #555: only show section if at least one reference
matthiasblum Feb 1, 2024
b5a325e
Update snapshots
matthiasblum Feb 1, 2024
de32bca
Merge branch 'storybook-again' into card-component
gustavo-salazar Feb 2, 2024
187b20c
jsons are dealt by webpack automatically - shouldnt be an assset
gustavo-salazar Feb 2, 2024
d1d705e
Merge pull request #567 from ProteinsWebTeam/storybook-again
gustavo-salazar Feb 5, 2024
1c3f77e
Merge pull request #568 from ProteinsWebTeam/callout-in-js
gustavo-salazar Feb 5, 2024
ba19356
Apply suggestions from code review
gustavo-salazar Feb 5, 2024
8f92c2d
Apply suggestions from code review 2
gustavo-salazar Feb 5, 2024
649a802
Update stories/InterProUI/CounterCards/ProteinCard.stories.tsx
gustavo-salazar Feb 5, 2024
ed61cf9
solve merge conflict
gustavo-salazar Feb 5, 2024
4870cc6
Merge dev into tiny-fixes
matthiasblum Feb 5, 2024
e8b8480
Update snapshot
matthiasblum Feb 5, 2024
4149271
storybug bugfix for protein viewer
gustavo-salazar Feb 5, 2024
18339f9
adding a margin if the card header has a tag
gustavo-salazar Feb 5, 2024
e1beaa2
adding a min width to cards + and link to organisim in protein cards
gustavo-salazar Feb 5, 2024
ea0ae85
Merge pull request #571 from ProteinsWebTeam/card-component
gustavo-salazar Feb 5, 2024
2a91a71
Merge branch 'dev' into tiny-fixes
gustavo-salazar Feb 5, 2024
98324d6
Merge pull request #574 from ProteinsWebTeam/tiny-fixes
matthiasblum Feb 6, 2024
a0658aa
specifying the type of counter required in any mention of extra_fields
gustavo-salazar Feb 6, 2024
7cc291c
updating test to include regex for granular counters
gustavo-salazar Feb 6, 2024
4d2fba6
puppeteer script to navigate browse
gustavo-salazar Feb 12, 2024
d2e409b
updating x-refrences
gustavo-salazar Feb 13, 2024
e2bdc28
downsizing the LLM warning
gustavo-salazar Feb 13, 2024
59f0d4b
Apply suggestions from code review
gustavo-salazar Feb 14, 2024
492989a
Merge pull request #579 from ProteinsWebTeam/granular-counters
gustavo-salazar Feb 14, 2024
ab0925a
Apply suggestions from code review
gustavo-salazar Feb 15, 2024
6f0f0f1
Apply suggestions from code review
gustavo-salazar Feb 15, 2024
2c3caab
snapshot update
gustavo-salazar Feb 15, 2024
cbf4a27
Merge pull request #582 from ProteinsWebTeam/small-llm-callout
gustavo-salazar Feb 16, 2024
b063790
Merge pull request #583 from ProteinsWebTeam/x-references
gustavo-salazar Feb 16, 2024
caf1d46
#FIX 580: It only contains the issue, as the real problem is in the n…
gustavo-salazar Feb 19, 2024
8426fcc
#FIX 575: when click on a family in clan viewer checks if the command…
gustavo-salazar Feb 19, 2024
6b3509f
Replace AlphafoldMenuLink for anormal menu link using in-alphafold to…
gustavo-salazar Feb 20, 2024
21529ff
Do not convert external resource name to upper case
matthiasblum Feb 20, 2024
e9158db
alphafold links in similar proteins
gustavo-salazar Feb 20, 2024
0419446
alphafold links for protein subpages
gustavo-salazar Feb 20, 2024
4c124ed
Merge pull request #584 from ProteinsWebTeam/xref-db-name-no-uppercase
matthiasblum Feb 21, 2024
0ae8fd9
TS: EntryMenuLink
gustavo-salazar Feb 22, 2024
d3ff575
TS: EntryMenuLink - fixing tests
gustavo-salazar Feb 22, 2024
9ef0e40
Update icon used for reviewed proteins
matthiasblum Feb 22, 2024
fed8197
TS: EntryMenu + null allowed in InterProLocation type
gustavo-salazar Feb 23, 2024
46641a2
Merge pull request #586 from ProteinsWebTeam/reviewed-icon
gustavo-salazar Feb 23, 2024
8351e46
Apply suggestions from code review
gustavo-salazar Feb 23, 2024
3b1cc90
adding alphafold links in browse by protein
gustavo-salazar Feb 23, 2024
3cd0ba0
badges for LLM entries
gustavo-salazar Feb 26, 2024
1cee64a
TS: version badge + 🎉 .celebration
gustavo-salazar Feb 26, 2024
05dce50
Merge pull request #585 from ProteinsWebTeam/has-alphafold
gustavo-salazar Feb 27, 2024
c2bbb56
ups, we should celebrate 100, not 99
gustavo-salazar Feb 27, 2024
81eeaf8
FIX #564: bit hacky - but there are only so many hours my brain can t…
gustavo-salazar Feb 28, 2024
14badc2
FIX #576: setting a max width for the mol* div, so it doesnt grwo ove…
gustavo-salazar Feb 29, 2024
9aae07a
FIX #577 styling sunburst flex row
gustavo-salazar Feb 29, 2024
7153464
FIX #578: Styling the toggleswitch and adding a width prop to force a…
gustavo-salazar Feb 29, 2024
f80e1de
FIX #482: passing search object to tooltip AND not refreshing form un…
gustavo-salazar Mar 1, 2024
49952a1
Getting the Proteome description from UniProt API
gustavo-salazar Mar 1, 2024
0f2a20b
Adding RFam link in proteome page
gustavo-salazar Mar 1, 2024
ccb77a9
removing unused icon for new structureal model
gustavo-salazar Mar 4, 2024
b28c35b
Update src/components/VersionBadge/style.css
gustavo-salazar Mar 4, 2024
564f613
Update src/components/Proteome/Summary/UniProtDescription/index.tsx
gustavo-salazar Mar 4, 2024
d3c46b4
Merge pull request #589 from ProteinsWebTeam/ts-version-badge
gustavo-salazar Mar 4, 2024
12ef1e9
Merge pull request #593 from ProteinsWebTeam/ts-has-alphafold
gustavo-salazar Mar 4, 2024
e228814
Merge pull request #591 from ProteinsWebTeam/proteome-page
gustavo-salazar Mar 4, 2024
972c2b7
Merge branch 'dev' into entry-AI
gustavo-salazar Mar 4, 2024
b1c4423
solving conflicts
gustavo-salazar Mar 4, 2024
fe8ad22
removing entry LLM badge and simplifying callout
gustavo-salazar Mar 4, 2024
bdf9de3
TS: DownloadForm/URLParameters
gustavo-salazar Mar 4, 2024
fa9e9fa
TS: DownloadForm/ApiLink
gustavo-salazar Mar 5, 2024
4307b9f
TS: DownloadForm/Controls
gustavo-salazar Mar 5, 2024
60605df
TS: DownloadForm/DataPreviewAndProgressProvider
gustavo-salazar Mar 5, 2024
110b637
extracting DownloadForm/InputGroup
gustavo-salazar Mar 5, 2024
23aaef2
TS: DownloadForm/DBChoiceInput
gustavo-salazar Mar 5, 2024
8f54d2d
story for InputGroup
gustavo-salazar Mar 5, 2024
3099644
TS: DownloadForm/Estimate
gustavo-salazar Mar 6, 2024
bf9725b
TS: DownloadForm/FormatSelector
gustavo-salazar Mar 6, 2024
5e18f85
TS: DownloadForm/ProgressAnimation
gustavo-salazar Mar 6, 2024
5eeae7c
TS: DownloadForm/Snippet
gustavo-salazar Mar 6, 2024
d43296c
TS: DownloadForm/TextExplanation
gustavo-salazar Mar 6, 2024
dffda6c
TS: DownloadForm
gustavo-salazar Mar 6, 2024
3ba2e7e
style fixes
gustavo-salazar Mar 6, 2024
af29d6d
style filter
gustavo-salazar Mar 7, 2024
1676fe5
Adding AI mini badge to fields AI-generated
gustavo-salazar Mar 7, 2024
f0d789a
re-enabling member DB selector in proteomes
gustavo-salazar Mar 7, 2024
ef0d28b
adding the check for memberDB to the puppeteer script
gustavo-salazar Mar 7, 2024
d9fd2aa
Apply suggestions from code review
gustavo-salazar Mar 11, 2024
7fca5bd
Merge pull request #588 from ProteinsWebTeam/entry-AI
gustavo-salazar Mar 11, 2024
97d55ca
Apply suggestions from code review
gustavo-salazar Mar 11, 2024
2c4fe48
TS: passing the rest of props when calling mapStateToProps in new loa…
gustavo-salazar Mar 11, 2024
9ebb347
fixing issues reported in PR
gustavo-salazar Mar 11, 2024
15fda10
change from PR review
gustavo-salazar Mar 11, 2024
fa37b4b
Merge pull request #590 from ProteinsWebTeam/minor-issues
gustavo-salazar Mar 12, 2024
55d5ca0
Merge pull request #594 from ProteinsWebTeam/TS-downloadform
gustavo-salazar Mar 12, 2024
aa44ba7
Merge branch 'dev' into proteome-page
gustavo-salazar Mar 12, 2024
903b3cc
fixing unrelated DownloadForm test error
gustavo-salazar Mar 12, 2024
68c862a
fixing DownloadForm test error
gustavo-salazar Mar 12, 2024
430ae9b
adding pivot pages if there are too many pages in numeric pagination
gustavo-salazar Mar 12, 2024
a847e14
TS: extracting PaginationItem from Table/Footer
gustavo-salazar Mar 12, 2024
9c2f23c
TS: extracting CursorPaginationLink from Table/Footer
gustavo-salazar Mar 12, 2024
8bdfca0
TS: extracting NumberedPaginationLink from Table/Footer
gustavo-salazar Mar 12, 2024
e4d08bb
TS: Table/Footer
gustavo-salazar Mar 12, 2024
e915c72
Merge pull request #598 from ProteinsWebTeam/ipscan-pagination
gustavo-salazar Mar 14, 2024
98ac068
Merge pull request #599 from ProteinsWebTeam/TS-Table-Footer
gustavo-salazar Mar 14, 2024
9d66b04
Merge pull request #595 from ProteinsWebTeam/proteome-page
gustavo-salazar Mar 14, 2024
8116c46
minor edits to puppeteer script
gustavo-salazar Mar 15, 2024
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8 changes: 7 additions & 1 deletion .eslintrc.js
Original file line number Diff line number Diff line change
Expand Up @@ -444,7 +444,13 @@ module.exports = {
settings,
parser,
parserOptions,
extends: extending,
extends: [
'plugin:react/recommended',
'plugin:react/jsx-runtime',
'plugin:jsx-a11y/recommended',
'prettier',
'plugin:storybook/recommended',
],
plugins,
env,
rules,
Expand Down
38 changes: 0 additions & 38 deletions .storybook/interpro.theme.js

This file was deleted.

9 changes: 9 additions & 0 deletions .storybook/interpro.theme.ts
Original file line number Diff line number Diff line change
@@ -0,0 +1,9 @@
import { create } from '@storybook/theming/create';

export default create({
base: 'light',
brandTitle: 'InterPro 7',
brandUrl: 'https://www.ebi.ac.uk/interpro',
brandImage:
'https://raw.githubusercontent.com/ProteinsWebTeam/interpro7-client/master/src/images/logo/logo_InterPro.png',
});
59 changes: 0 additions & 59 deletions .storybook/main.js

This file was deleted.

98 changes: 98 additions & 0 deletions .storybook/main.ts
Original file line number Diff line number Diff line change
@@ -0,0 +1,98 @@
import type { StorybookConfig } from '@storybook/react-webpack5';
import * as path from 'path';
import TsconfigPathsPlugin from 'tsconfig-paths-webpack-plugin';
import postCSSImport from 'postcss-import';
import postcssPresetEnv from 'postcss-preset-env';
import { RuleSetRule } from 'webpack';

const config: StorybookConfig = {
stories: [
'../stories/**/*.mdx',
'../stories/**/*.stories.@(js|jsx|mjs|ts|tsx)',
],
addons: [
'@storybook/addon-links',
'@storybook/addon-essentials',
'@storybook/addon-interactions',
'@storybook/addon-styling-webpack',
{
name: '@storybook/addon-styling-webpack',

options: {
rules: [
{
test: /\.css$/,
sideEffects: true,
use: [
require.resolve('style-loader'),
{
loader: require.resolve('css-loader'),
options: {
modules: {
mode: 'local',
localIdentName: '[folder]_[name]__[local]___[hash:2]',
},
importLoaders: 1,
},
},
{
loader: require.resolve('postcss-loader'),
options: {
implementation: require.resolve('postcss'),
postcssOptions: {
plugins: [postCSSImport, postcssPresetEnv({ stage: 0 })],
},
},
},
],
},
],
},
},
],
framework: {
name: '@storybook/react-webpack5',
options: {
builder: {
useSWC: true,
},
},
},
docs: {
autodocs: 'tag',
},
async webpackFinal(config) {
// do mutation to the config
if (!config.resolve) config.resolve = {};
if (!config.resolve.modules) config.resolve.modules = [];
if (!config.module) config.module = {};
if (!config.module.rules) config.module.rules = [];
config.resolve.plugins = [
new TsconfigPathsPlugin({
configFile: path.resolve('.', 'stories', 'tsconfig.json'),
}),
];
config.resolve.modules.push(path.resolve('.', 'src'));

const cssRule = config.module.rules.find((rule) =>
((rule as RuleSetRule).test || '').toString().includes('.css')
);

(cssRule as RuleSetRule).exclude = /((clanviewer))\.css$/i;

config.module.rules.push({
test: /((clanviewer))\.css$/i,
use: [{ loader: 'style-loader' }, { loader: 'css-loader' }],
});
config.module.rules.push({
test: /\.yml$/i,
use: [{ loader: 'yaml-loader' }],
});
config.module.rules.push({
test: /\.(jpe?g|png|gif|svg|avif)$/i,
type: 'asset/resource',
});
return config;
},
};
export default config;
6 changes: 0 additions & 6 deletions .storybook/manager.js

This file was deleted.

6 changes: 6 additions & 0 deletions .storybook/manager.ts
Original file line number Diff line number Diff line change
@@ -0,0 +1,6 @@
import { addons } from '@storybook/manager-api';
import interproTheme from './interpro.theme';

addons.setConfig({
theme: interproTheme,
});
28 changes: 28 additions & 0 deletions .storybook/preview.tsx
Original file line number Diff line number Diff line change
@@ -0,0 +1,28 @@
import React from 'react';
import type { Preview } from '@storybook/react';

const preview: Preview = {
parameters: {
actions: { argTypesRegex: '^on[A-Z].*' },
controls: {
matchers: {
color: /(background|color)$/i,
date: /Date$/i,
},
},
},
decorators: [
(Story) => (
<>
<link
rel="stylesheet"
href="https://assets.emblstatic.net/vf/v2.5.10/css/styles.css"
/>

<Story />
</>
),
],
};

export default preview;
5 changes: 5 additions & 0 deletions .storybook/tsconfig.json
Original file line number Diff line number Diff line change
@@ -0,0 +1,5 @@
{
"extends": "../tsconfig.json",
"include": ["src/**/*", "../src/custom.d.ts"]
}

4 changes: 3 additions & 1 deletion config.yml.example
Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,9 @@ root:
repeatsDB: https://repeatsdb.bio.unipd.it/api/search
disprot: https://disprot.org/api/
LLMFeedback: https://docs.google.com/forms/d/e/1FAIpQLSc9lPkgGOZBpnyLiHF87AbUYdAWyx_3YFTNNg4MGQEcqAK4jQ/viewform?usp=pp_url&entry.128814244=

Rfam: https://www.ebi.ac.uk/ebisearch/ws/rest/rfam
UniProt: https://rest.uniprot.org/

title: InterPro

github:
Expand Down
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