Merge pull request #41 from EBISPOT/repo_rename

Updated all relevant files to new repo name

README.md

@@ -7,14 +7,14 @@ The Human Ancestry Ontology (HAncestro) provides a systematic description of the
 
 The following HANCESTRO release files are provided 
 
-* https://github.com/EBISPOT/ancestro/blob/main/hancestro.owl
-* https://github.com/EBISPOT/ancestro/blob/main/hancestro_inferred.owl - pre-inferred version of HANCESTRO
-* https://github.com/EBISPOT/ancestro/blob/main/hancestro_bfo.owl - version of HANCESTRO fitted into the BFO upper hierarchy for ease of integration with other ontologies
+* https://github.com/EBISPOT/hancestro/blob/main/hancestro.owl
+* https://github.com/EBISPOT/hancestro/blob/main/hancestro_inferred.owl - pre-inferred version of HANCESTRO
+* https://github.com/EBISPOT/hancestro/blob/main/hancestro_bfo.owl - version of HANCESTRO fitted into the BFO upper hierarchy for ease of integration with other ontologies
 
 
 ### Contact Details ###
 
-For questions and comments and to report any issues, please email Dani Welter at danielle.welter@uni.lu. To submit a feature request, submit a ticket via the [HANCESTRO Github issue tracker](https://github.com/EBISPOT/ancestro/issues).
+For questions and comments and to report any issues, please email Dani Welter at danielle.welter@uni.lu. To submit a feature request, submit a ticket via the [HANCESTRO Github issue tracker](https://github.com/EBISPOT/hancestro/issues).
 
 
 ### Licence ###
@@ -41,11 +41,11 @@ Date Released: 16 February 2023
 
 Class Count: 585 
 
-- Addition of new terms for `Singaporean Malay (HANCESTRO:0597)` and `Singaporean Indian (HANCESTRO:0598)` (as per [request #26](https://github.com/EBISPOT/ancestro/issues/26))
-- Reclassification of `Martu Australian Aboriginal` from `uncategorised population` to `Aboriginal Australian` and addition of definition and synonyms (as per [request #25](https://github.com/EBISPOT/ancestro/issues/25)
-- Corrected typo in label for `Hungarian` (as per [request #21](https://github.com/EBISPOT/ancestro/issues/21))
+- Addition of new terms for `Singaporean Malay (HANCESTRO:0597)` and `Singaporean Indian (HANCESTRO:0598)` (as per [request #26](https://github.com/EBISPOT/hancestro/issues/26))
+- Reclassification of `Martu Australian Aboriginal` from `uncategorised population` to `Aboriginal Australian` and addition of definition and synonyms (as per [request #25](https://github.com/EBISPOT/hancestro/issues/25)
+- Corrected typo in label for `Hungarian` (as per [request #21](https://github.com/EBISPOT/hancestro/issues/21))
 
-See the [release notes](https://github.com/EBISPOT/ancestro/releases) for details of most recent changes.
+See the [release notes](https://github.com/EBISPOT/hancestro/releases) for details of most recent changes.
 
 
 Please note that as of v2.3 of the ontology, all identifiers have changed for ANCESTRO to HANCESTRO.
@@ -71,7 +71,7 @@ Editors of this ontology should use the edit version, [src/ontology/hancestro-ed
 
 ## Contact
 
-Please use this GitHub repository's [Issue tracker](https://github.com/EBISPOT/ancestro/issues) to request new terms/classes or report errors or specific concerns related to the ontology.
+Please use this GitHub repository's [Issue tracker](https://github.com/EBISPOT/hancestro/issues) to request new terms/classes or report errors or specific concerns related to the ontology.
 
 ## Acknowledgements
 

docs/faq.md

@@ -22,7 +22,7 @@ HANCESTRO is released whenever new terms have been added, although generally no
 
 ## How can I request new terms? ##
 
-Please use our [Github tracker](https://github.com/EBISPOT/ancestro/issues) to request new terms. Please provide as much information as possible, including
+Please use our [Github tracker](https://github.com/EBISPOT/hancestro/issues) to request new terms. Please provide as much information as possible, including
 - label (name) of the new term
 - definition
 - for new ancestry groups, please provide links to at least 2 scientific publications referencing and describing the ancestry group in question

docs/index.md

@@ -6,9 +6,9 @@ The Human Ancestry Ontology (HAncestro) provides a systematic description of the
 
 The following HANCESTRO release files are provided 
 
-* https://github.com/EBISPOT/ancestro/blob/main/hancestro.owl
-* https://github.com/EBISPOT/ancestro/blob/main/hancestro_inferred.owl - pre-inferred version of HANCESTRO
-* https://github.com/EBISPOT/ancestro/blob/main/hancestro_bfo.owl - version of HANCESTRO fitted into the BFO upper hierarchy for ease of integration with other ontologies
+* https://github.com/EBISPOT/hancestro/blob/main/hancestro.owl
+* https://github.com/EBISPOT/hancestro/blob/main/hancestro_inferred.owl - pre-inferred version of HANCESTRO
+* https://github.com/EBISPOT/hancestro/blob/main/hancestro_bfo.owl - version of HANCESTRO fitted into the BFO upper hierarchy for ease of integration with other ontologies
 
 Please see our [FAQ](/faq.md) for some more information.
 
@@ -53,3 +53,4 @@ Convenience grouping of geographic areas larger than countries but smaller than
 
 
 
+/hancestro

docs/odk-workflows/ManageDocumentation.md

@@ -38,9 +38,9 @@ The documentation is _not_ automatically updated from the Markdown, and needs to
    If everything was successful, you will see a message similar to this one:
 
    ```
-   INFO    -  Your documentation should shortly be available at: https://ebispot.github.io/ancestro/ 
+   INFO    -  Your documentation should shortly be available at: https://ebispot.github.io/hancestro/ 
    ```
-3. Just to double check, you can now navigate to your documentation pages (usually https://ebispot.github.io/ancestro/). 
+3. Just to double check, you can now navigate to your documentation pages (usually https://ebispot.github.io/hancestro/). 
    Just make sure you give GitHub 2-5 minutes to build the pages!
 
 

docs/odk-workflows/ReleaseWorkflow.md

@@ -44,7 +44,7 @@ Once your [CI checks](ContinuousIntegration.md) have passed, and your reviews ar
 
 ## Create a GitHub release
 
-1. Go to your releases page on GitHub by navigating to your repository, and then clicking on releases (usually on the right, for example: https://github.com/ebispot/ancestro/releases). Then click "Draft new release"
+1. Go to your releases page on GitHub by navigating to your repository, and then clicking on releases (usually on the right, for example: https://github.com/ebispot/hancestro/releases). Then click "Draft new release"
 1. As the tag version you **need to choose the date on which your ontologies were build.** You can find this, for example, by looking at the `hancestro.obo` file and check the `data-version:` property. The date needs to be prefixed with a `v`, so, for example `v2020-02-06`.
 1. You can write whatever you want in the release title, but we typically write the date again. The description underneath should contain a concise list of changes or term additions.
 1. Click "Publish release". Done.

mkdocs.yaml

@@ -17,12 +17,13 @@ markdown_extensions:
   - pymdownx.mark
   - pymdownx.tilde
 
-site_url: https://ebispot.github.io/ancestro/
-repo_url: https://github.com/ebispot/ancestro/
+site_url: https://ebispot.github.io/hancestro/
+repo_url: https://github.com/ebispot/hancestro/
 
 nav:
   - Getting started: index.md
   - Cite: cite.md
+  - Frequent asked questions: faq.md
   - How-to guides:
       - Standard ODK workflows:
           - Overview: odk-workflows/index.md
@@ -36,5 +37,5 @@ nav:
           - Managing your automated testing: odk-workflows/ManageAutomatedTest.md
           - Continuous Integration: odk-workflows/ContinuousIntegration.md
           - Your ODK Repository Overview: odk-workflows/RepositoryFileStructure.md 
-      - Contributing: contributing.md
+  - Contributing: contributing.md
 

src/metadata/hancestro.yml

@@ -4,16 +4,16 @@ idspace: HANCESTRO
 base_url: /obo/hancestro
 
 products:
-- hancestro.owl: https://raw.githubusercontent.com/EBISPOT/ancestro/main/hancestro_inferred.owl
+- hancestro.owl: https://raw.githubusercontent.com/EBISPOT/hancestro/main/hancestro_inferred.owl
 
 term_browser: ontobee
 example_terms:
 - HANCESTRO_0004
 
 entries:
 - exact: /hancestro.owl
-  replacement: https://raw.githubusercontent.com/EBISPOT/ancestro/main/hancestro.owl
+  replacement: https://raw.githubusercontent.com/EBISPOT/hancestro/main/hancestro.owl
 - exact: /hancestro_inferred.owl
-  replacement: https://raw.githubusercontent.com/EBISPOT/ancestro/main/hancestro_inferred.owl
+  replacement: https://raw.githubusercontent.com/EBISPOT/hancestro/main/hancestro_inferred.owl
 - exact: /hancestro_bfo.owl
-  replacement: https://raw.githubusercontent.com/EBISPOT/ancestro/main/hancestro_bfo.owl
+  replacement: https://raw.githubusercontent.com/EBISPOT/hancestro/main/hancestro_bfo.owl

src/ontology/README-editors.md

@@ -67,8 +67,8 @@ Finally type
 
 IMMEDIATELY AFTERWARDS (do *not* make further modifications) go here:
 
- * https://github.com/EBISPOT/ancestro/releases
- * https://github.com/EBISPOT/ancestro/releases/new
+ * https://github.com/EBISPOT/hancestro/releases
+ * https://github.com/EBISPOT/hancestro/releases/new
 
 The value of the "Tag version" field MUST be
 

src/ontology/hancestro-odk.yaml

@@ -2,7 +2,7 @@ id: hancestro
 title: "The Human Ancestry Ontology"
 github_org: ebispot
 git_main_branch: main
-repo: ancestro
+repo: hancestro
 report_fail_on: ERROR
 reasoner: hermit
 documentation: 

src/ontology/imports/bfo_import.owl

@@ -7,9 +7,9 @@ Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)
 
 
 Ontology(<http://purl.obolibrary.org/obo/hancestro/imports/bfo_import.owl>
-<http://purl.obolibrary.org/obo/hancestro/releases/2023-07-25/imports/bfo_import.owl>
+<http://purl.obolibrary.org/obo/hancestro/releases/2023-07-28/imports/bfo_import.owl>
 Annotation(<http://purl.org/dc/elements/1.1/source> <http://purl.obolibrary.org/obo/bfo/2019-08-26/bfo.owl>)
-Annotation(owl:versionInfo "2023-07-25")
+Annotation(owl:versionInfo "2023-07-28")
 
 Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000001>))
 Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000002>))

src/ontology/imports/geo_import.owl

@@ -7,8 +7,8 @@ Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)
 
 
 Ontology(<http://purl.obolibrary.org/obo/hancestro/imports/geo_import.owl>
-<http://purl.obolibrary.org/obo/hancestro/releases/2023-07-25/imports/geo_import.owl>
-Annotation(owl:versionInfo "2023-07-25")
+<http://purl.obolibrary.org/obo/hancestro/releases/2023-07-28/imports/geo_import.owl>
+Annotation(owl:versionInfo "2023-07-28")
 
 Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000001>))
 Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000002>))

src/ontology/imports/obi_import.owl

@@ -7,9 +7,9 @@ Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)
 
 
 Ontology(<http://purl.obolibrary.org/obo/hancestro/imports/obi_import.owl>
-<http://purl.obolibrary.org/obo/hancestro/releases/2023-07-25/imports/obi_import.owl>
-Annotation(<http://purl.org/dc/elements/1.1/source> <http://purl.obolibrary.org/obo/obi/2023-03-10/obi-base.owl>)
-Annotation(owl:versionInfo "2023-07-25")
+<http://purl.obolibrary.org/obo/hancestro/releases/2023-07-28/imports/obi_import.owl>
+Annotation(<http://purl.org/dc/elements/1.1/source> <http://purl.obolibrary.org/obo/obi/2023-07-25/obi-base.owl>)
+Annotation(owl:versionInfo "2023-07-28")
 
 Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000040>))
 Declaration(Class(<http://purl.obolibrary.org/obo/OBI_0000181>))

src/ontology/imports/ro_import.owl

@@ -7,9 +7,9 @@ Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)
 
 
 Ontology(<http://purl.obolibrary.org/obo/hancestro/imports/ro_import.owl>
-<http://purl.obolibrary.org/obo/hancestro/releases/2023-07-25/imports/ro_import.owl>
+<http://purl.obolibrary.org/obo/hancestro/releases/2023-07-28/imports/ro_import.owl>
 Annotation(<http://purl.org/dc/elements/1.1/source> <http://purl.obolibrary.org/obo/ro/releases/2023-06-28/ro-base.owl>)
-Annotation(owl:versionInfo "2023-07-25")
+Annotation(owl:versionInfo "2023-07-28")
 
 Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000002>))
 Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000003>))