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Binary file added src/assets/mave-registry-logo.png
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36 changes: 28 additions & 8 deletions src/components/screens/AboutView.vue
Original file line number Diff line number Diff line change
Expand Up @@ -60,9 +60,18 @@
class="h-7 object-contain object-left"
:src="partner.logoSrc"
/>
<div v-else class="flex h-7 items-center text-sm font-bold text-link">{{ partner.name }}</div>
<div class="text-sm font-bold text-text-primary">{{ partner.name }}</div>
<div v-else class="flex h-7 items-center text-sm font-bold text-text-primary">{{ partner.name }}</div>
<div class="text-xs leading-relaxed text-text-muted">{{ partner.description }}</div>
<a
v-if="partner.url"
:aria-label="partner.name + ' (opens in new tab)'"
class="mt-auto inline-block text-sm font-semibold text-link"
:href="partner.url"
rel="noopener noreferrer"
target="_blank"
>
Visit site &rarr;
</a>
</div>
</div>
</div>
Expand All @@ -83,7 +92,7 @@
<div class="px-6 py-6">
<a
aria-label="Zulip (opens in new tab)"
class="text-base font-bold text-text-primary no-underline"
class="text-base font-bold text-link no-underline"
href="https://zulip.com/"
rel="noopener"
target="_blank"
Expand Down Expand Up @@ -198,8 +207,9 @@ import {useHead} from '@unhead/vue'
import MvLayout from '@/components/layout/MvLayout.vue'
import MvPageHeader from '@/components/layout/MvPageHeader.vue'
import igvfLogo from '@/assets/igvf-tag.png'
import maveRegistryLogo from '@/assets/mave-registry-logo.png'
import zulipLogo from '@/assets/zulip-logo.png'
import {GITHUB_API_URL, GITHUB_UI_URL} from '@/lib/links'
import {GITHUB_API_URL, GITHUB_UI_URL, MAVE_REGISTRY, IGVF_URL, CLINGEN_URL, GA4GH_URL, CLINVAR_URL} from '@/lib/links'

const DATA_MODEL_STEPS = [
{
Expand All @@ -223,24 +233,34 @@ const PARTNERS = [
{
name: 'IGVF Consortium',
description: 'Functional genomics data from the Impact of Genomic Variation on Function consortium.',
logoSrc: igvfLogo
logoSrc: igvfLogo,
url: IGVF_URL
},
{
name: 'ClinGen',
description: 'Clinical Genome Resource — calibrated MaveDB score sets contribute to variant evidence curation.',
logoSrc: ''
logoSrc: '',
url: CLINGEN_URL
},
{
name: 'GA4GH',
description:
'Global Alliance for Genomics and Health — MaveDB is a Driver Project for the Genomic Knowledge Standards Work Stream.',
logoSrc: ''
logoSrc: '',
url: GA4GH_URL
},
{
name: 'ClinVar',
description:
'ClinVar is a public database of variant interpretations, providing a resource for clinical and research communities.',
logoSrc: ''
logoSrc: '',
url: CLINVAR_URL
},
{
name: 'MaveRegistry',
description: 'A registry for sharing and tracking progress on MAVE experiments.',
logoSrc: maveRegistryLogo,
url: MAVE_REGISTRY
}
]

Expand Down
22 changes: 20 additions & 2 deletions src/components/screens/HelpScreen.vue
Original file line number Diff line number Diff line change
Expand Up @@ -55,6 +55,23 @@
</Accordion>
</div>

<!-- Clinical application -->
<div class="rounded-lg border border-border bg-white px-8 py-7">
<h2 class="mb-4 text-lg font-bold text-sage">Clinical application</h2>
<p class="text-sm leading-relaxed text-text-secondary">
The Alliance for Variant Effects (AVE) maintains a
<a
aria-label="Clinical Application of Variant Effect Data (opens in new tab)"
class="text-link"
:href="AVE_CLINICAL_APPLICATION"
rel="noopener noreferrer"
target="_blank"
>Clinical Application of Variant Effect Data</a
>
page covering how MAVE functional scores can be used in clinical genomics and for variant interpretation.
</p>
</div>

<!-- Contact us -->
<div class="rounded-lg border border-border bg-white px-8 py-7">
<h2 class="mb-4 text-lg font-bold text-sage">Contact us</h2>
Expand Down Expand Up @@ -89,7 +106,7 @@ import AccordionContent from 'primevue/accordioncontent'

import MvLayout from '@/components/layout/MvLayout.vue'
import MvPageHeader from '@/components/layout/MvPageHeader.vue'
import {ZULIP_CHAT, GITHUB_UI_ISSUES} from '@/lib/links'
import {ZULIP_CHAT, GITHUB_UI_ISSUES, AVE_CLINICAL_APPLICATION} from '@/lib/links'

const CHANNELS = [
{
Expand Down Expand Up @@ -174,7 +191,8 @@ export default defineComponent({
channels: CHANNELS,
faqs: FAQS,
ZULIP_CHAT,
GITHUB_UI_ISSUES
GITHUB_UI_ISSUES,
AVE_CLINICAL_APPLICATION
}
}
})
Expand Down
14 changes: 13 additions & 1 deletion src/components/screens/SearchVariantsScreen.vue
Original file line number Diff line number Diff line change
Expand Up @@ -12,6 +12,17 @@
calibrations, provide intuitive visualizations, and export structured evidence compatible with ACMG/AMP
variant classification guidelines.
</p>
<p class="mx-auto mt-2.5 max-w-[580px] text-sm leading-relaxed text-gray-500 md:text-base">
Learn more about
<a
aria-label="Clinical Application of Variant Effect Data (opens in new tab)"
class="font-medium text-sage-dark hover:underline"
:href="AVE_CLINICAL_APPLICATION"
rel="noopener noreferrer"
target="_blank"
>evaluating MAVE functional assays and integrating them into clinical practice</a
>.
</p>
</section>

<!-- SEARCH BAND -->
Expand Down Expand Up @@ -675,6 +686,7 @@ import {components} from '@/schema/openapi'
import {getScoreSetShortName} from '@/lib/score-sets'
import {clinVarHgvsSearchStringRegex, hgvsSearchStringRegex} from '@/lib/mave-hgvs'
import {SEARCH_COLORS} from '@/data/search'
import {AVE_CLINICAL_APPLICATION} from '@/lib/links'
import {
HOW_IT_WORKS_STEPS,
MAVEMD_COLLECTION_URN,
Expand Down Expand Up @@ -714,7 +726,7 @@ export default defineComponent({
const router = useRouter()
const toast = useToast()
const {getEntity} = useEntityCache()
return {route, router, toast, getEntity, getScoreSetShortName, scoreSetUrnFromVariantUrn}
return {route, router, toast, getEntity, getScoreSetShortName, scoreSetUrnFromVariantUrn, AVE_CLINICAL_APPLICATION}
},

data: function () {
Expand Down
8 changes: 8 additions & 0 deletions src/lib/links.ts
Original file line number Diff line number Diff line change
Expand Up @@ -12,6 +12,14 @@ export const GITHUB_API_ISSUES = `${GITHUB_API_URL}/issues`

export const MAVEDB_PRODUCTION = 'https://mavedb.org'

export const AVE_CLINICAL_APPLICATION = 'https://www.varianteffect.org/clinical-application/'
export const MAVE_REGISTRY = 'https://registry.varianteffect.org/'

export const IGVF_URL = 'https://www.igvf.org/'
export const CLINGEN_URL = 'https://clinicalgenome.org/'
export const GA4GH_URL = 'https://www.ga4gh.org/'
export const CLINVAR_URL = 'https://www.ncbi.nlm.nih.gov/clinvar/'

/**
* Build a Zulip link to report a dataset issue for a specific URN.
*/
Expand Down