Fix a few menu items (with help from Claude, but it was actually terrible at recognizing broken links - it cited some that are fine and missed others that are broken). Also reordered a few of the software projects to put older ones lower on the list, and added a few words of explanation to two ontology names.

Author: nlharris

_data/sidebar_doc.yml

@@ -47,7 +47,7 @@ entries:
           url: /project/agr
 
         - title: BioPortal
-          url: /project/bioportal
+          url: /project/BioPortal
 
         - title: "National Microbiome Data Collaborative (NMDC)"
           url: /project/nmdc
@@ -83,14 +83,8 @@ entries:
       print: true
       items:  
         - title: OntoGPT
-          url: /project/GPT
+          url: /project/AI
 
-        - title: AmiGO and GOlr
-          url: /software/amigo
-
-        - title: Noctua
-          url: /software/noctua
-
         - title: Biolink Model
           url: /software/biolink-model
 
@@ -118,10 +112,16 @@ entries:
         - title: Ontology Development Kit
           url: /software/odk
 
+         - title: AmiGO and GOlr
+          url: /software/amigo
+
+        - title: Noctua
+          url: /software/noctua
+
         - title: k-BOOM
           url: /software/kboom
 
-        - title: BioMake
+        - title: BioMake (inactive)
           url: /software/biomake
 
         - title: PAINT
@@ -143,7 +143,7 @@ entries:
         - title: Environment Ontology
           url: /ontology/envo
 
-        - title: Uberon
+        - title: Uberon anatomy ontology
           url: /ontology/uberon
 
         - title: FANTOM5 Ontology
@@ -152,7 +152,7 @@ entries:
         - title: Mondo disease ontology
           url: /ontology/mondo
 
-        - title: Phenotype ontologies
+        - title: uPheno phenotype ontology
           url: /ontology/upheno
 
         - title: Relation Ontology

ontology/envo/index.md

@@ -19,7 +19,7 @@ The primary developers of ENVO are Pier Luigi Buttigieg and [Chris Mungall](/peo
 
 <iframe src="//www.slideshare.net/slideshow/embed_code/key/DghA7gkMn0dmgc" width="595" height="485" frameborder="0" marginwidth="0" marginheight="0" scrolling="no" style="border:1px solid #CCC; border-width:1px; margin-bottom:5px; max-width: 100%;" allowfullscreen> </iframe> <div style="margin-bottom:5px"> <strong> <a href="//www.slideshare.net/cmungall/envo-gsc-2015" title="ENVO GSC 2015" target="_blank">ENVO GSC 2015</a> </strong> from <strong><a href="https://www.slideshare.net/cmungall" target="_blank">Chris Mungall</a></strong> </div>
 
-![img](http://media.springernature.com/lw785/springer-static/image/art%3A10.1186%2Fs13326-016-0097-6/MediaObjects/13326_2016_97_Fig2_HTML.gif)
+![img](https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0f6e/5035502/b984f5a506ce/13326_2016_97_Fig2_HTML.jpg)
 
 ## References
 

software/paint/index.md

@@ -16,7 +16,7 @@ For a more complete description, please see the publication on the GO Phylogenet
 Rather than a pairwise paradigm, PAINT uses this more accurate phylogenetic model to infer gene function by homology.  PAINT annotation is intended to capture actual inferences about the evolution of gene function within a gene family: the gain, inheritance, modification and loss of function over evolutionary time.  Inference is a two-step process, and involves directly annotating a phylogenetic tree.  In the first step, experimental GO annotations for extant sequences are used to make inferences about when a given function may have first evolved.  In PAINT, this is referred to as "up-propagation", in which ancestral genes are annotated based on information about extant sequences.  In the second step, "down-propagation", ancestral annotations are used to make inferences about unannotated extant sequences, based on the principle of inheritance from the common ancestor, and allowing for modification and even loss of function during evolution.
 
 
-![img](http://wiki.geneontology.org/images/2/25/PAINT_msa.png)
+![img](https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e7ff/3178059/ba1a6874867a/bbr042f4.jpg)
 
 ## References