Merge branch 'main' of https://github.com/progenetix/progenetix-web

progenetix · Feb 21, 2024 · c905f2f · c905f2f
2 parents 5781320 + 8273c2c
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diff --git a/docs/common/classifications-and-ontologies.md b/docs/common/classifications-and-ontologies.md
@@ -55,7 +55,7 @@ For terms with a `pgx` prefix, the [identifiers.org resolver](http://identifiers
 * based on [NCIt neoplasm core](https://evs.nci.nih.gov/ftp1/NCI_Thesaurus/Neoplasm/About_Core.html)
 but now extended based on the whole "neoplasia" subtree of the NCI Thesaurus (`NCIT:C3262` and child terms)
 * first implementation of NCIt concepts mapping in January 2017, then for a subset of arrayMap samples
-* now providing ICD-O 3 <=> NCIt mappings through the [ICDOntoologies](https://github.com/progenetix/ICDOntologies) mapping project with a [front-end an API](http://progenetix.org/service-collection/ontologymaps/) on the website
+* now providing ICD-O 3 <=> NCIt mappings through the [ICDOntoologies](https://github.com/progenetix/ICDOntologies) mapping project with a [front-end an API](http://progenetix.org/service-collection/ontologymappings/) on the website
 
 #### Current NCIt sample codes
 

diff --git a/docs/services.md b/docs/services.md
@@ -98,10 +98,10 @@ exact gene symbol match
     - when using the REST syntax also only the exact match will be returned
 
 
-### Ontology Cross-Mapping (`ontologymaps`)
+### Ontology Cross-Mapping (`ontologymappings`)
 
-The `ontologymaps` service provides equivalency mapping between ICD-O and other
-classification systems, notably NCIt. The mappings are represented in the [ICDOntologies](https://github.com/progenetix/ICDOntologies) project and accessible trough a front-end in the [Progenetix Services area](http://progenetix.org/service-collection/ontologymaps).
+The `ontologymappings` service provides equivalency mapping between ICD-O and other
+classification systems, notably NCIt. The mappings are represented in the [ICDOntologies](https://github.com/progenetix/ICDOntologies) project and accessible trough a front-end in the [Progenetix Services area](http://progenetix.org/service-collection/ontologymappings).
 
 #### ICD-O Representation
 
@@ -131,23 +131,23 @@ Our resources use an internal representation of ICD-O 3 codes since no official
 
 ##### NCIt and ICD-O 3
 
-* [progenetix.org/services/ontologymaps/?filters=pgx:icdom-85003](http://progenetix.org/services/ontologymaps/?filters=pgx:icdom-85003)
-* [http://progenetix.org/services/ontologymaps/?filters=NCIT](http://progenetix.org/services/ontologymaps/?filters=NCIT)
-* [progenetix.org/services/ontologymaps/?filters=pgx:icdom-85003,pgx:icdot-C50.9](http://progenetix.org/services/ontologymaps/?filters=pgx:icdom-85003,pgx:icdot-C50.9)
-* [progenetix.org/services/ontologymaps/?filters=icdom-85,icdot-C50&filterPrecision=start](http://progenetix.org/services/ontologymaps/?filters=icdom-85,icdot-C50&filterPrecision=start)
+* [progenetix.org/services/ontologymappings/?filters=pgx:icdom-85003](http://progenetix.org/services/ontologymappings/?filters=pgx:icdom-85003)
+* [http://progenetix.org/services/ontologymappings/?filters=NCIT](http://progenetix.org/services/ontologymappings/?filters=NCIT)
+* [progenetix.org/services/ontologymappings/?filters=pgx:icdom-85003,pgx:icdot-C50.9](http://progenetix.org/services/ontologymappings/?filters=pgx:icdom-85003,pgx:icdot-C50.9)
+* [progenetix.org/services/ontologymappings/?filters=icdom-85,icdot-C50&filterPrecision=start](http://progenetix.org/services/ontologymappings/?filters=icdom-85,icdot-C50&filterPrecision=start)
     - As in the example above, but by stemmming the query parameters and providing the `filterPrecision=start` pragma, the response will now be a list of matched data objects (inputs and equivalents)
 
 ##### UBERON and ICD-O 3 Topography
 
-* [progenetix.org/services/ontologymaps/?filters=UBERON&filterPrecision=start](http://progenetix.org/services/ontologymaps/?filters=UBERON&filterPrecision=start)
+* [progenetix.org/services/ontologymappings/?filters=UBERON&filterPrecision=start](http://progenetix.org/services/ontologymappings/?filters=UBERON&filterPrecision=start)
     - all mappings
-* [progenetix.org/services/ontologymaps/?filters=UBERON,icdot-C0&filterPrecision=start](http://progenetix.org/services/ontologymaps/?filters=UBERON,icdot-C0&filterPrecision=start)
+* [progenetix.org/services/ontologymappings/?filters=UBERON,icdot-C0&filterPrecision=start](http://progenetix.org/services/ontologymappings/?filters=UBERON,icdot-C0&filterPrecision=start)
     - all `C0...` ICD-O T matches
     - limited to `UBERON` mappings since the prefix was given, too (otherwise all the NCIT mappings would also be listed for these ICD-O T code matches)
 
 #### More Information
 
-* [Web Interface for ICD & NCIT](http://progenetix.org/service-collection/ontologymaps)
+* [Web Interface for ICD & NCIT](http://progenetix.org/service-collection/ontologymappings)
 * [Interface for ICD & UBERON](http://progenetix.org/service-collection/uberonmaps)
 
 

diff --git a/src/components/Layout.js b/src/components/Layout.js
@@ -174,11 +174,11 @@ function Side({ onClick }) {
           isSub="isSub"
         />
         <MenuInternalLinkItem
-          href="/service-collection/ontologymaps"
+          href="/service-collection/ontologymappings"
           label="Services"
         />
         <MenuInternalLinkItem
-          href="/service-collection/ontologymaps"
+          href="/service-collection/ontologymappings"
           label="NCIt Mappings"
           isSub="isSub"
         />

diff --git a/src/hooks/api.js b/src/hooks/api.js
@@ -274,7 +274,7 @@ export function useProgenetixRefPublicationList({ geoCity, geodistanceKm }) {
   return useProgenetixApi(url)
 }
 
-export const ontologymapsBaseUrl = `${SITE_DEFAULTS.API_PATH}services/ontologymaps?`
+export const ontologymapsBaseUrl = `${SITE_DEFAULTS.API_PATH}services/ontologymappings?`
 
 export function ontologymapsUrl({ filters, filterPrecision }) {
   let params = new URLSearchParams({ filters: filters })

diff --git a/src/modules/service-pages/OntologymapsPage.js b/src/modules/service-pages/OntologymapsPage.js
@@ -28,7 +28,7 @@ export default function OntologymapsPage() {
           className="Layout__img__topright Layout__img__width-160"
         />
         <p>
-          The <strong>ontologymaps</strong> service provides equivalency mapping
+          The <strong>ontologymappings</strong> service provides equivalency mapping
           between ICD-O and other classification systems, notably NCIt and
           UBERON. It makes use of the sample-level mappings for NCIT and ICD-O 3
           codes developed for the individual samples in the Progenetix

diff --git a/src/modules/service-pages/UBERONmapsPage.js b/src/modules/service-pages/UBERONmapsPage.js
@@ -28,7 +28,7 @@ export default function UBERONmapsPage() {
           className="Layout__img__topright Layout__img__width-40"
         />
         <p>
-          The <strong>ontologymaps</strong> service provides equivalency mapping
+          The <strong>ontologymappings</strong> service provides equivalency mapping
           between ICD-O and other classification systems, notably NCIt and
           UBERON. It makes use of the sample-level mappings developed for the
           individual samples in the Progenetix collection.