Merge branch 'master' into nlharris-patch-11

Author: nataled

_config.yml

@@ -1428,9 +1428,9 @@ ontologies:
   browsers:
   - label: DO
     title: DO Browser
-    url: http://www.disease-ontology.org/
+    url: https://disease-ontology.org/
   build:
-    source_url: https://github.com/DiseaseOntology/DiseaseDriversOntology/tree/main/src/ontology/disdriv.owl
+    source_url: https://raw.githubusercontent.com/DiseaseOntology/DiseaseDriversOntology/refs/heads/main/src/ontology/disdriv.owl
   contact:
     email: lynn.schriml@gmail.com
     github: lschriml
@@ -1440,7 +1440,7 @@ ontologies:
     ExO ontology exposure stressors. An application ontology. Built in collaboration
     with EnvO, ExO, ECTO and ChEBI.
   domain: health
-  homepage: http://www.disease-ontology.org
+  homepage: https://disease-ontology.org/
   id: disdriv
   layout: ontology_detail
   license:
@@ -1465,13 +1465,13 @@ ontologies:
   - description: Human Disease Ontology
     examples:
     - description: fetal alcohol syndrome, has exposure stressor some alcohol
-      url: https://www.disease-ontology.org/?id=DOID:0050665
-    user: https://www.disease-ontology.org
+      url: https://disease-ontology.org/?id=DOID:0050665
+    user: https://disease-ontology.org/
 - activity_status: active
   browsers:
   - label: DO
     title: DO Browser
-    url: http://www.disease-ontology.org/do
+    url: https://disease-ontology.org/do
   build:
     infallible: 1
     method: obo2owl
@@ -1481,11 +1481,11 @@ ontologies:
     github: lschriml
     label: Lynn Schriml
     orcid: 0000-0001-8910-9851
-  depicted_by: http://www.disease-ontology.org/media/images/DO_logo.jpg
+  depicted_by: https://disease-ontology.org/media/images/DO_logo_teal.png
   description: An ontology for describing the classification of human diseases organized
     by etiology.
   domain: health
-  homepage: http://www.disease-ontology.org
+  homepage: https://disease-ontology.org
   id: doid
   in_foundry_order: 1
   layout: ontology_detail
@@ -1531,8 +1531,8 @@ ontologies:
   - description: MGI disease model annotations use DO
     examples:
     - description: physical disorder
-      url: http://www.informatics.jax.org/disease/DOID:0080015
-    user: http://www.informatics.jax.org/disease
+      url: https://www.informatics.jax.org/disease/DOID:0080015
+    user: https://www.informatics.jax.org/disease
   - description: Immune Epitope Database
     examples:
     - description: Antibody and T cell epitopes associated with human diseases

ontology/chebi.md

@@ -15,7 +15,7 @@ contact:
   github: amalik01
   label: Adnan Malik
   orcid: 0000-0001-8123-5351
-depicted_by: https://www.ebi.ac.uk/chebi/images/ChEBI_logo.png
+depicted_by: https://www.ebi.ac.uk/chebi/chebi_logo.svg
 description: A structured classification of molecular entities of biological interest focusing on 'small' chemical compounds.
 domain: chemistry and biochemistry
 homepage: http://www.ebi.ac.uk/chebi

ontology/disdriv.md

@@ -5,17 +5,17 @@ title: Disease Drivers Ontology
 browsers:
 - title: DO Browser
   label: DO
-  url: http://www.disease-ontology.org/
+  url: https://disease-ontology.org/
 build:
-  source_url: https://github.com/DiseaseOntology/DiseaseDriversOntology/tree/main/src/ontology/disdriv.owl
+  source_url: https://raw.githubusercontent.com/DiseaseOntology/DiseaseDriversOntology/refs/heads/main/src/ontology/disdriv.owl
 contact:
   email: lynn.schriml@gmail.com
   github: lschriml
   label: Lynn Schriml
   orcid: 0000-0001-8910-9851
 description: Ontology for drivers and triggers of human diseases, built to classify ExO ontology exposure stressors. An application ontology. Built in collaboration with EnvO, ExO, ECTO and ChEBI.
 domain: health
-homepage: http://www.disease-ontology.org
+homepage: https://disease-ontology.org/
 license:
   label: CC0 1.0
   url: https://creativecommons.org/publicdomain/zero/1.0/
@@ -34,7 +34,7 @@ usages:
 - description: Human Disease Ontology
   examples:
   - description: fetal alcohol syndrome, has exposure stressor some alcohol
-    url: https://www.disease-ontology.org/?id=DOID:0050665
-  user: https://www.disease-ontology.org
+    url: https://disease-ontology.org/?id=DOID:0050665
+  user: https://disease-ontology.org/
 activity_status: active
 ---

ontology/doid.md

@@ -5,7 +5,7 @@ title: Human Disease Ontology
 browsers:
 - title: DO Browser
   label: DO
-  url: http://www.disease-ontology.org/do
+  url: https://disease-ontology.org/do
 build:
   infallible: 1
   method: obo2owl
@@ -15,10 +15,10 @@ contact:
   github: lschriml
   label: Lynn Schriml
   orcid: 0000-0001-8910-9851
-depicted_by: http://www.disease-ontology.org/media/images/DO_logo.jpg
+depicted_by: https://disease-ontology.org/media/images/DO_logo_teal.png
 description: An ontology for describing the classification of human diseases organized by etiology.
 domain: health
-homepage: http://www.disease-ontology.org
+homepage: https://disease-ontology.org
 in_foundry_order: 1
 license:
   label: CC0 1.0
@@ -53,8 +53,8 @@ usages:
 - description: MGI disease model annotations use DO
   examples:
   - description: physical disorder
-    url: http://www.informatics.jax.org/disease/DOID:0080015
-  user: http://www.informatics.jax.org/disease
+    url: https://www.informatics.jax.org/disease/DOID:0080015
+  user: https://www.informatics.jax.org/disease
 - description: Immune Epitope Database
   examples:
   - description: Antibody and T cell epitopes associated with human diseases
@@ -70,4 +70,4 @@ Creating a comprehensive classification of human diseases organized by etiology.
 This file is equivalent to doid-non-classified.obo.
 
 - DO provides an additional OBO file, [doid-merged.obo](https://raw.githubusercontent.com/DiseaseOntology/HumanDiseaseOntology/master/src/ontology/doid-merged.obo). 
- for the [AGR](http://www.alliancegenome.org) that includes [OMIM](http://omim.org) to DO associations as xrefs plus defined  relationships between OMIM susceptibility IDs and DO terms.  
+ for the [AGR](https://www.alliancegenome.org) that includes [OMIM](https://omim.org) to DO associations as xrefs plus defined  relationships between OMIM susceptibility IDs and DO terms.  

registry/ontologies.jsonld

@@ -1947,11 +1947,11 @@
                 {
                     "label": "DO",
                     "title": "DO Browser",
-                    "url": "http://www.disease-ontology.org/"
+                    "url": "https://disease-ontology.org/"
                 }
             ],
             "build": {
-                "source_url": "https://github.com/DiseaseOntology/DiseaseDriversOntology/tree/main/src/ontology/disdriv.owl"
+                "source_url": "https://raw.githubusercontent.com/DiseaseOntology/DiseaseDriversOntology/refs/heads/main/src/ontology/disdriv.owl"
             },
             "contact": {
                 "email": "lynn.schriml@gmail.com",
@@ -1961,7 +1961,7 @@
             },
             "description": "Ontology for drivers and triggers of human diseases, built to classify ExO ontology exposure stressors. An application ontology. Built in collaboration with EnvO, ExO, ECTO and ChEBI.",
             "domain": "health",
-            "homepage": "http://www.disease-ontology.org",
+            "homepage": "https://disease-ontology.org/",
             "id": "disdriv",
             "layout": "ontology_detail",
             "license": {
@@ -1994,10 +1994,10 @@
                     "examples": [
                         {
                             "description": "fetal alcohol syndrome, has exposure stressor some alcohol",
-                            "url": "https://www.disease-ontology.org/?id=DOID:0050665"
+                            "url": "https://disease-ontology.org/?id=DOID:0050665"
                         }
                     ],
-                    "user": "https://www.disease-ontology.org"
+                    "user": "https://disease-ontology.org/"
                 }
             ]
         },
@@ -2007,7 +2007,7 @@
                 {
                     "label": "DO",
                     "title": "DO Browser",
-                    "url": "http://www.disease-ontology.org/do"
+                    "url": "https://disease-ontology.org/do"
                 }
             ],
             "build": {
@@ -2021,10 +2021,10 @@
                 "label": "Lynn Schriml",
                 "orcid": "0000-0001-8910-9851"
             },
-            "depicted_by": "http://www.disease-ontology.org/media/images/DO_logo.jpg",
+            "depicted_by": "https://disease-ontology.org/media/images/DO_logo_teal.png",
             "description": "An ontology for describing the classification of human diseases organized by etiology.",
             "domain": "health",
-            "homepage": "http://www.disease-ontology.org",
+            "homepage": "https://disease-ontology.org",
             "id": "doid",
             "in_foundry_order": 1,
             "layout": "ontology_detail",
@@ -2088,10 +2088,10 @@
                     "examples": [
                         {
                             "description": "physical disorder",
-                            "url": "http://www.informatics.jax.org/disease/DOID:0080015"
+                            "url": "https://www.informatics.jax.org/disease/DOID:0080015"
                         }
                     ],
-                    "user": "http://www.informatics.jax.org/disease"
+                    "user": "https://www.informatics.jax.org/disease"
                 },
                 {
                     "description": "Immune Epitope Database",