diff --git a/docs/doc_manual.rst b/docs/doc_manual.rst index be46f51f..95a0b3ca 100644 --- a/docs/doc_manual.rst +++ b/docs/doc_manual.rst @@ -44,10 +44,25 @@ This card shows the avaible gene pathogenicity scores for a gene such as: Associated Conditions ===================== -This card shows the avaible information on the phenotypes associated to the respective gene as HPO terms and known OMIM phenotypes. +This card shows the avaible information on the conditiosn associated to the respective gene. + +First, the card will display information on membership in the ACMG Supplementary Findings list, if the gene is contained. + +Second, the card will show diseases associated via OMIM, OrphaNet or PanelApp. +The confidence corresponds to the highest evidence of the link (high, medium, or low). +A link from OMIM has high confidence, as does have a link from OrphaNet with "Assessed" label. +Orphanet links that are "Not yet assessed" have a link of low strength. +Link strength from PanelApp are taken from the green/amber/red labels in PanelApp. +Currently, links from PanelApp are only made if the gene-phenotype link is tagged with an Orphanet or OMIM disease. +Clicking on the disease sheet will show you the OMIM and Orphanet terms that are integrated into the card. + +Below, you can see a list of PanelApp panels associated with the gene. +You can see the panel name, the version, confidence, and labeled mode of inheritance. +Clicking on the panel sheet will show you the full list of phenotypes labeled in the panel. + Note than you can use the button "numeric terms" in the lower left corner to show or hide the corresponding numeric HPO term and OMIM phenotype IDs; with the button "show links" right next you can activate and deactivate the corresponding link-outs of the displayed HPO terms and OMIM phenotypes. At the bottom of the card you can also find more link-outs to further websites with gene-phenotype information, such as JAX and Orphanet. -Note that you can also use the "More" button on the lower right of the card to show associated Orphanet disorders and their respective link-outs. +Note that you can also use the "More" button on the lower right of the card to directly show non-integrated OMIM and Orphanet disorders and their respective link-outs. If you have logged in and provided case specific phenotype information with HPO terms you can find the gene-to-phenotype rank (i.e. how well your case's HPO terms fit the gene's associated HPO terms) in the grey box on the right. diff --git a/frontend/src/assets/__tests__/BRCA1GeneInfo.json b/frontend/src/assets/__tests__/BRCA1GeneInfo.json index d2880410..a335054d 100644 --- a/frontend/src/assets/__tests__/BRCA1GeneInfo.json +++ b/frontend/src/assets/__tests__/BRCA1GeneInfo.json @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:56f7d3d6c5675405612f4ee44d05eabef387d4b998a50a7e12b86d685f89304d -size 41213 +oid sha256:fc87b085bfb6c974639219589283b2a68273169fa465800cfae0845560b8fe2e +size 62219 diff --git a/frontend/src/components/GeneDetails/ConditionsCard.vue b/frontend/src/components/GeneDetails/ConditionsCard.vue index e426dbe8..d4b9a6c4 100644 --- a/frontend/src/components/GeneDetails/ConditionsCard.vue +++ b/frontend/src/components/GeneDetails/ConditionsCard.vue @@ -1,11 +1,11 @@