fix: graph-database doc title + sweep angle-bracket /dev/* legacy links (closes #85)

adamjohnwright · adamjohnwright · commit cd6b4612c952 · 2026-05-20T15:03:09.000Z
Two distinct problems on the graph-database documentation pages: - projects/website-angular/content/documentation/dev/graph-database/neo4j-desktop.mdx had `title: Untitled` as its frontmatter literally, so the rendered page (and the section anchor) read "Untitled". Now "Neo4j Desktop". - Line 68 of graph-database.mdx pointed at `<https://reactome.org/dev/graph-database/extract-participating-molecules>` -- the angle-bracket-wrapped absolute legacy URL. The #88 link sweep matched `(/dev/X)` and `(https://reactome.org/dev/X)` but not the `(<https://reactome.org/dev/X>)` markdown variant. Clicking it navigated users off beta into the prod chrome, which Leo (rightly) flagged as broken-feeling. Sweep the angle-bracket variant across all six MDX files that had it (graph-database.mdx + five news articles).
diff --git a/projects/website-angular/content/about/news/111-international-open-access-week-analysis-tools.mdx b/projects/website-angular/content/about/news/111-international-open-access-week-analysis-tools.mdx
@@ -13,4 +13,4 @@ Following up on the International [Open Access week](<http://www.openaccessweek.
 
 Pathway analysis methods have a broad range of applications in physiological and biomedical research. Our analysis suite currently implements an overrepresentation analysis, an expression data analysis and a species comparison tool. Using this service, users can submit their sample (list of identifiers) to get as result the most significants pathways. Results are overlaid in the different modules of our Pathway Browser and can be exported to different formats including a [PDF report](</about/news/107-new-tool-to-generate-analysis-pdf-reports>).
 
-A light-weight client is integrated in our [Pathway Browser](</PathwayBrowser/#TOOL=AT>). The tool suite is available via a [RESTFul Web Service](</AnalysisService/>) so all the available analysis tools can be easily integrated into third party software. More documentation for developers is available at our [developer's zone](</documentation/dev/analysis>)[.](<https://reactome.org/dev/analysis.>)
+A light-weight client is integrated in our [Pathway Browser](</PathwayBrowser/#TOOL=AT>). The tool suite is available via a [RESTFul Web Service](</AnalysisService/>) so all the available analysis tools can be easily integrated into third party software. More documentation for developers is available at our [developer's zone](</documentation/dev/analysis>)[.](</documentation/dev/analysis.>)
diff --git a/projects/website-angular/content/about/news/114-graphdb-content-service.mdx b/projects/website-angular/content/about/news/114-graphdb-content-service.mdx
@@ -13,4 +13,4 @@ Since version 57 we provide our data in a [Neo4j](<https://neo4j.com/>) [graph d
 
 The graph database also benefits Reactome in other aspects like (i) the creation of complex data quality assessment (QA) queries or (ii) supporting software that requires data pattern analysis, e.g. [reactions classification](<https://github.com/reactome/rxn-classifier>). QA queries are executed during each quarterly release to identify instances that need to be checked out and corrected by Reactome curators ensuring that high-quality content is delivered to the final user. The reactions classifier project, for example, uses Cypher to formalise the concepts presented in [Jupe et al. (2014)](<https://doi.org/10.1093/database/bau060>) to generate a series of reports that help curators classify the reactions in Reactome.
 
-The [Content Service](<https://reactome.org/dev/content-service>) constitutes an easy API, based on the Representational State Transfer (REST) protocol, that provides access to the Reactome knowledgebase. It includes a set of methods classified in groups according to their functionality. For instance, expanding the pathways group reveals a set of methods that provide specific information about pathways such as the contained Events or the participating PhysicalEntities.
+The [Content Service](</documentation/dev/content-service>) constitutes an easy API, based on the Representational State Transfer (REST) protocol, that provides access to the Reactome knowledgebase. It includes a set of methods classified in groups according to their functionality. For instance, expanding the pathways group reveals a set of methods that provide specific information about pathways such as the contained Events or the participating PhysicalEntities.
diff --git a/projects/website-angular/content/about/news/124-deprecated-support-for-reactome-restful-api.mdx b/projects/website-angular/content/about/news/124-deprecated-support-for-reactome-restful-api.mdx
@@ -7,6 +7,6 @@ tags: ["about", "news", "124-deprecated-support-for-reactome-restful-api"]
 
 ##  Deprecated support for Reactome RESTful API 
 
-As of Version 68 (March 2019), the RESTful API is deprecated and will be superceded by our ContentService. The ContentService is currently available through our website at <https://reactome.org/ContentService/> and is designed for bioinformaticians, computer scientists, and software developers to access our pathway data. See more details about this API at [https://reactome.org/dev/content-service. ](<https://reactome.org/dev/content-service.>)
+As of Version 68 (March 2019), the RESTful API is deprecated and will be superceded by our ContentService. The ContentService is currently available through our website at <https://reactome.org/ContentService/> and is designed for bioinformaticians, computer scientists, and software developers to access our pathway data. See more details about this API at [https://reactome.org/dev/content-service. ](</documentation/dev/content-service.>)
 
 If you have questions or concerns regarding this announcement, please email [help@reactome.org](<mailto:help@reactome.org>).
diff --git a/projects/website-angular/content/about/news/275-v93-released.mdx b/projects/website-angular/content/about/news/275-v93-released.mdx
@@ -21,7 +21,7 @@ Annotation Statistics. Reactome comprises 15,890 human reactions organized into
 
 Other news: 
 
-As of Reactome V93, our Docker images are no longer available on DockerHub and have been migrated to AWS Elastic Container Registry (ECR). Users should pull images from AWS ECR moving forward. Updated access instructions are available in our [documentation](<https://reactome.org/dev/graph-database#GetStarted>).
+As of Reactome V93, our Docker images are no longer available on DockerHub and have been migrated to AWS Elastic Container Registry (ECR). Users should pull images from AWS ECR moving forward. Updated access instructions are available in our [documentation](</documentation/dev/graph-database#GetStarted>).
 
 As of Reactome V94, the following files will no longer be available: “Protégé 2.0 ontology files”, and “Events in the BioPAX level 2 format”. If you require these files for your work, please let our team know via [help@reactome.org](<mailto:help@reactome.org>).
 
diff --git a/projects/website-angular/content/about/news/279-v94-released.mdx b/projects/website-angular/content/about/news/279-v94-released.mdx
@@ -21,7 +21,7 @@ Annotation Statistics. Reactome comprises 16,002 human reactions organized into
 
 **Other news** : 
 
-As of Reactome V93, our Docker images are no longer available on DockerHub and have been migrated to AWS Elastic Container Registry (ECR). Users should pull images from AWS ECR moving forward. Updated access instructions are available in our [documentation](<https://reactome.org/dev/graph-database#GetStarted>).
+As of Reactome V93, our Docker images are no longer available on DockerHub and have been migrated to AWS Elastic Container Registry (ECR). Users should pull images from AWS ECR moving forward. Updated access instructions are available in our [documentation](</documentation/dev/graph-database#GetStarted>).
 
 As of Reactome V94, the following files will no longer be available: “Protégé 2.0 ontology files”, and “Events in the BioPAX level 2 format”. If you require these files for your work, please let our team know via [help@reactome.org](<mailto:help@reactome.org>).
 
diff --git a/projects/website-angular/content/documentation/dev/graph-database.mdx b/projects/website-angular/content/documentation/dev/graph-database.mdx
@@ -65,7 +65,7 @@ docker run --name reactome-graphdb -e NEO4J_AUTH=neo4j/$NEO4J_PASSWORD -p 7474:7
 Username: neo4j  
 Password: (set via $NEO4J_PASSWORD or default if not set)
 
-You now have a docker image containing Neo4j and the Reactome graph database. You can create custom queries using Cypher and submit your own queries. Please refer to our [extracting pathway participating molecules](<https://reactome.org/dev/graph-database/extract-participating-molecules>) tutorial to introduce yourself to using Cypher to query the Reactome Graph Database.
+You now have a docker image containing Neo4j and the Reactome graph database. You can create custom queries using Cypher and submit your own queries. Please refer to our [extracting pathway participating molecules](</documentation/dev/graph-database/extract-participating-molecules>) tutorial to introduce yourself to using Cypher to query the Reactome Graph Database.
 
 #### 2\. Neo4j Desktop
 
diff --git a/projects/website-angular/content/documentation/dev/graph-database/neo4j-desktop.mdx b/projects/website-angular/content/documentation/dev/graph-database/neo4j-desktop.mdx
@@ -1,5 +1,5 @@
 ---
-title: Untitled
+title: Neo4j Desktop
 category: "documentation"
 ---
 

Original file line number	Diff line number	Diff line change
`@@ -13,4 +13,4 @@ Following up on the International [Open Access week](<http://www.openaccessweek.`
`13`	`13`
`14`	`14`	Pathway analysis methods have a broad range of applications in physiological and biomedical research. Our analysis suite currently implements an overrepresentation analysis, an expression data analysis and a species comparison tool. Using this service, users can submit their sample (list of identifiers) to get as result the most significants pathways. Results are overlaid in the different modules of our Pathway Browser and can be exported to different formats including a [PDF report](</about/news/107-new-tool-to-generate-analysis-pdf-reports>).
`15`	`15`
`16`		`-A light-weight client is integrated in our [Pathway Browser](</PathwayBrowser/#TOOL=AT>). The tool suite is available via a [RESTFul Web Service](</AnalysisService/>) so all the available analysis tools can be easily integrated into third party software. More documentation for developers is available at our [developer's zone](</documentation/dev/analysis>)[.](<https://reactome.org/dev/analysis.>)`
	`16`	`+A light-weight client is integrated in our [Pathway Browser](</PathwayBrowser/#TOOL=AT>). The tool suite is available via a [RESTFul Web Service](</AnalysisService/>) so all the available analysis tools can be easily integrated into third party software. More documentation for developers is available at our [developer's zone](</documentation/dev/analysis>)[.](</documentation/dev/analysis.>)`
Original file line number	Diff line number	Diff line change
`@@ -13,4 +13,4 @@ Since version 57 we provide our data in a [Neo4j](<https://neo4j.com/>) [graph d`
`13`	`13`
`14`	`14`	The graph database also benefits Reactome in other aspects like (i) the creation of complex data quality assessment (QA) queries or (ii) supporting software that requires data pattern analysis, e.g. [reactions classification](<https://github.com/reactome/rxn-classifier>). QA queries are executed during each quarterly release to identify instances that need to be checked out and corrected by Reactome curators ensuring that high-quality content is delivered to the final user. The reactions classifier project, for example, uses Cypher to formalise the concepts presented in [Jupe et al. (2014)](<https://doi.org/10.1093/database/bau060>) to generate a series of reports that help curators classify the reactions in Reactome.
`15`	`15`
`16`		`-The [Content Service](<https://reactome.org/dev/content-service>) constitutes an easy API, based on the Representational State Transfer (REST) protocol, that provides access to the Reactome knowledgebase. It includes a set of methods classified in groups according to their functionality. For instance, expanding the pathways group reveals a set of methods that provide specific information about pathways such as the contained Events or the participating PhysicalEntities.`
	`16`	`+The [Content Service](</documentation/dev/content-service>) constitutes an easy API, based on the Representational State Transfer (REST) protocol, that provides access to the Reactome knowledgebase. It includes a set of methods classified in groups according to their functionality. For instance, expanding the pathways group reveals a set of methods that provide specific information about pathways such as the contained Events or the participating PhysicalEntities.`