diff --git a/docs/common/classifications-and-ontologies.md b/docs/common/classifications-and-ontologies.md index 594e0daf..545b5ac3 100644 --- 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 index 48c7d61b..2b779b98 100644 --- 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 index 8311beb1..7380193f 100644 --- a/src/components/Layout.js +++ b/src/components/Layout.js @@ -174,11 +174,11 @@ function Side({ onClick }) { isSub="isSub" /> diff --git a/src/hooks/api.js b/src/hooks/api.js index 62f976e0..e1680c8e 100644 --- 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 index 487fc151..e9ee5d96 100644 --- 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" />

- The ontologymaps service provides equivalency mapping + The ontologymappings 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 index 9c6b7710..b6058416 100644 --- 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" />

- The ontologymaps service provides equivalency mapping + The ontologymappings 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.