http: => https: globally for links

hcnv · Sep 12, 2024 · e7acac7 · e7acac7
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diff --git a/README.md b/README.md
@@ -1,4 +1,4 @@
 ## Website of the Human Copy Number Variation Community
 
-The [website](http://hcnv.github.io) of the _Human Copy Number Variation Community_ (hCNV) is a resource originating in ELIXIR's h-CNV Community Implementation Study (2019-2021).
+The [website](https://hcnv.github.io) of the _Human Copy Number Variation Community_ (hCNV) is a resource originating in ELIXIR's h-CNV Community Implementation Study (2019-2021).
 
diff --git a/docs/contacts/Cezard-Timothee.md b/docs/contacts/Cezard-Timothee.md
@@ -14,4 +14,4 @@ name_tag: cezard_t
 
 * email: tcezard [at] ebi.ac.uk
 * web: [EBI](https://www.ebi.ac.uk/about/people/timothee-cezard)
-* ORCID iD: [0000-0002-5626-270X](http://europepmc.org/search?query=AUTHORID:%220000-0002-5626-270X%22&sortby=Date)
+* ORCID iD: [0000-0002-5626-270X](https://europepmc.org/search?query=AUTHORID:%220000-0002-5626-270X%22&sortby=Date)
diff --git a/docs/contacts/Grüning-Björn.md b/docs/contacts/Grüning-Björn.md
@@ -8,4 +8,4 @@ name_tag: gruening_b
 
 * University of Freiburg
 * ELIXIR Galaxy Community
-* [www](http://www.bioinf.uni-freiburg.de/team.html)
+* [www](https://www.bioinf.uni-freiburg.de/team.html)
diff --git a/docs/contacts/Kanitz-Alexander.md b/docs/contacts/Kanitz-Alexander.md
@@ -13,4 +13,4 @@ name_tag: kanitz_a
 #### Links
 
 * email: [[email protected]](mailto:[email protected])
-* web: [Biozentrum](http://www.biozentrum.unibas.ch/)
+* web: [Biozentrum](https://www.biozentrum.unibas.ch/)
diff --git a/docs/contacts/Paloots-Rahel.md b/docs/contacts/Paloots-Rahel.md
@@ -7,4 +7,4 @@ excerpt_link: 'https://info.baudisgroup.org/group/Rahel_Paloots/'
 
 * [Department of Molecular Life Sciences](https://info.baudisgroup.org/group/Rahel_Paloots), University of Zurich
 * Swiss Institute of Bioinformatics SIB
-* [Progenetix](http://progenetix.org) project
+* [Progenetix](https://progenetix.org) project
diff --git a/docs/contacts/Yang-Ziying.md b/docs/contacts/Yang-Ziying.md
@@ -6,4 +6,4 @@ excerpt_link: 'https://info.baudisgroup.org/group/Ziying_Yang/'
 ---
 
 * [Department of Molecular Life Sciences](https://info.baudisgroup.org/group/Ziying_Yang/), University of Zurich
-* [Progenetix](http://progenetix.org) project
+* [Progenetix](https://progenetix.org) project
diff --git a/docs/contacts/Zhao-Hangjia.md b/docs/contacts/Zhao-Hangjia.md
@@ -6,4 +6,4 @@ excerpt_link: 'https://info.baudisgroup.org/group/Hangjia_Zhao/'
 ---
 
 * [Department of Molecular Life Sciences](https://info.baudisgroup.org/group/Hangjia_Zhao/), University of Zurich
-* [Progenetix](http://progenetix.org) project
+* [Progenetix](https://progenetix.org) project
diff --git a/docs/contacts/people.tsv b/docs/contacts/people.tsv
@@ -16,10 +16,10 @@ European Bioinformatics Institute EBI	52.079936724614800	0.18652979910338700	Kir
 University of Bradford	53.7915944357949	-1.7660797296964700	Krzysztof Poterlowicz	https://www.bradford.ac.uk/staff/KPoterlowicz1	marker
 University of Bradford	53.7915944357949	-1.7660797296964700	Katarzyna Kamieniecka	https://elixiruknode.org/team/katarzyna-kamieniecka/	marker
 University of Bradford	53.7915944357949	-1.7660797296964700	Khaled Jumah	https://www.bradford.ac.uk/staff/kjumah/	marker
-University of Freiburg	48.014799717966200	7.83356072785665	Bjoern Gruening	http://www.bioinf.uni-freiburg.de/team.html	marker
+University of Freiburg	48.014799717966200	7.83356072785665	Bjoern Gruening	https://www.bioinf.uni-freiburg.de/team.html	marker
 ELIXIR	52.07799561917700	0.1868099991033470	Katharina Heil	https://elixir-europe.org/about-us/who-we-are/hub	marker
 ELIXIR	52.07799561917700	0.1868099991033470	Giselle Kerry	https://elixir-europe.org/about-us/who-we-are/hub	marker
-Biozentrum Basel	47.5643495531957	7.580929650422590	Alexander Kanitz	http://www.biozentrum.unibas.ch/	marker
+Biozentrum Basel	47.5643495531957	7.580929650422590	Alexander Kanitz	https://www.biozentrum.unibas.ch/	marker
 Erasmus MC	51.91101673038920	4.467823983754840	Andrew Stubbs	https://www.erasmusmc.nl/en/research/groups/pathology-stubbs	marker
 Maastricht University	50.84796245891005	5.687935349976222	Friederike Ehrhart	https://www.maastrichtuniversity.nl/f-ehrhart	marker
 University of Leicester	52.62150673759715	-1.1245697272888708	Tim Beck	https://le.ac.uk/people/tim-beck	marker
diff --git a/docs/img/elixir-white-48x36.svg b/docs/img/elixir-white-48x36.svg
diff --git a/docs/img/hCNV-Elixir-logo.svg b/docs/img/hCNV-Elixir-logo.svg
diff --git a/docs/img/hCNV-logo.svg b/docs/img/hCNV-logo.svg
diff --git a/docs/index.md b/docs/index.md
@@ -7,7 +7,7 @@ authors:
 
 # ELIXIR Human Copy Number Variation community
 
-<object style="float: right; width: 610px; margin-left: 15px; margin-bottom-10px; overflow: hidden" id="map" width="100%" height="500px" standby="loading data, please wait..." data="https://progenetix.org/services/geolocations?plotType=map&plotPars=map_w_px=600::map_h_px=480::marker_type=marker&inputfile=https://raw.githubusercontent.com/hcnv/hcnv.github.io/main/docs/contacts/people.tsv"></object>Among the different types of inherited and acquired genomic variants, regional genomic copy number variations (CNV) contribute - if measured by affected genomic sequences - contribute by far the largest amount of genomic changes, contributing both to many syndromic diseases as well as the vast majority of human cancers. The [website](http://hcnv.github.io) of the _Human Copy Number Variation Community_
+<object style="float: right; width: 610px; margin-left: 15px; margin-bottom-10px; overflow: hidden" id="map" width="100%" height="500px" standby="loading data, please wait..." data="https://progenetix.org/services/geolocations?plotType=map&plotPars=map_w_px=600::map_h_px=480::marker_type=marker&inputfile=https://raw.githubusercontent.com/hcnv/hcnv.github.io/main/docs/contacts/people.tsv"></object>Among the different types of inherited and acquired genomic variants, regional genomic copy number variations (CNV) contribute - if measured by affected genomic sequences - contribute by far the largest amount of genomic changes, contributing both to many syndromic diseases as well as the vast majority of human cancers. The [website](https://hcnv.github.io) of the _Human Copy Number Variation Community_
 (hCNV) is a resource originated in ELIXIR's h-CNV Community Implementation Study
 (2019-2021) with the aim to provide a resource hub and knowledge exchange space for scientists and practitioners working with - or being interested in - genomic copy number variations in health and diseases. However, the scope of the community extends beyond CNVs and includes definition of and work with other types of genomic variations with a focus on structural variants.
 

diff --git a/docs/news/2021-06-30-publication-Progenetix-2021.md b/docs/news/2021-06-30-publication-Progenetix-2021.md
@@ -20,15 +20,15 @@ hide:
 * PMCID: PMC8285936.
 * bioRxiv. doi: https://doi.org/10.1101/2021.02.15.428237
 
-![DATABASE logo](http://info.baudisgroup.org/img/logo-database-journal-300x150.png){: style="float: right; width: 150px; margin-top: -150px;"}This article provides an overview of recent changes and additions to the Progenetix database and the services provided through the resource.
+![DATABASE logo](https://info.baudisgroup.org/img/logo-database-journal-300x150.png){: style="float: right; width: 150px; margin-top: -150px;"}This article provides an overview of recent changes and additions to the Progenetix database and the services provided through the resource.
 
 <!--more-->
 
 #### Abstract
 
 In cancer, copy number aberrations (CNAs) represent a type of nearly ubiquitous and frequently extensive structural genome variations. To disentangle the molecular mechanisms underlying tumorigenesis as well as identify and characterize molecular subtypes, the comparative and meta-analysis of large genomic variant collections can be of immense importance. Over the last decades, cancer genomic profiling projects have resulted in a large amount of somatic genome variation profiles, however segregated in a multitude of individual studies and datasets. The Progenetix project, initiated in 2001, curates individual cancer CNA profiles and associated metadata from published oncogenomic studies and data repositories with the aim to empower integrative analyses spanning all different cancer biologies. During the last few years, the fields of genomics and cancer research have seen significant advancement in terms of molecular genetics technology, disease concepts, data standard harmonization as well as data availability, in an increasingly structured and systematic manner. For the Progenetix resource, continuous data integration, curation and maintenance have resulted in the most comprehensive representation of cancer genome CNA profiling data with 138 663 (including 115 357 tumor) copy number variation (CNV) profiles. In this article, we report a 4.5-fold increase in sample number since 2013, improvements in data quality, ontology representation with a CNV landscape summary over 51 distinctive National Cancer Institute Thesaurus cancer terms as well as updates in database schemas, and data access including new web front-end and programmatic data access.
 
-Database URL: <http://progenetix.org>
+Database URL: <https://progenetix.org>
 
 #### Notes
 
@@ -38,4 +38,4 @@ The first version of the article had been posted at biorXiv on 2021-02-15.
 
 * article at [OUP DATABASE](https://academic.oup.com/database/article/doi/10.1093/database/baab043/6323245)
 * article at [biorXiv](https://www.biorxiv.org/content/10.1101/2021.02.15.428237v)
-* article [PDF](http://info.baudisgroup.org/pdf/2021-06-30___Huang-et-al.__The-Progenetix-oncogenomic-resource-in-2021__DATABASE.pdf)
+* article [PDF](https://info.baudisgroup.org/pdf/2021-06-30___Huang-et-al.__The-Progenetix-oncogenomic-resource-in-2021__DATABASE.pdf)
diff --git a/docs/news/2021-11-19-cnvar-domain.md b/docs/news/2021-11-19-cnvar-domain.md
@@ -9,14 +9,14 @@ hide:
   # - toc
 ---
 
-The homepage of the hCNV community has now been mapped to the [**cnvar.org**](http://cnvar.org)
+The homepage of the hCNV community has now been mapped to the [**cnvar.org**](https://cnvar.org)
 domain.
 
 <!--more-->
 
 Since the site is still hosted as a [Github Pages](https://pages.github.com) project
-the old [hcnv.github.io](http://hcnv.github.io) still works.
+the old [hcnv.github.io](https://hcnv.github.io) still works.
 
 The domain is managed by [Michael Baudis](https://info.baudisgroup.org/group/Michael_Baudis/).
 Please let him now about e.g. ideas for subdomains/targets; for example we currently map
-the [progenetix.cnvar.org](http://progenetix.cnvar.org) to the Progenetix resource.
+the [progenetix.cnvar.org](https://progenetix.cnvar.org) to the Progenetix resource.
diff --git a/docs/news/2021-12-22-cnv-ontology-proposal-note.md b/docs/news/2021-12-22-cnv-ontology-proposal-note.md
@@ -25,7 +25,7 @@ live on January 21.
 Everybody is welcome to contribute to the editing of the proposal at the SO & VRS Github repositories!
 
 
-#### 2021-01-21: `copy number assessment` term tree now [live on EFO](http://www.ebi.ac.uk/efo/EFO_0030063)
+#### 2021-01-21: `copy number assessment` term tree now [live on EFO](https://www.ebi.ac.uk/efo/EFO_0030063)
 
 The `copy number assessment` term tree has been accepted into the Experimental Factor Ontology and can be used for referencing CNV types. 
 

diff --git a/docs/news/2023-12-14-Paris-Medecine.md b/docs/news/2023-12-14-Paris-Medecine.md
@@ -9,9 +9,9 @@ date: 2023-12-14
 pdf_file_name:
 links:
   - '[Seminar slides](/pdf/2023-12-14___Michael-Baudis__Beaconize-This__Seminar-Institut-Imagine-Paris.pdf)'
-  - "[Progenetix cancer genomics resource](http://progenetix.org)"
+  - "[Progenetix cancer genomics resource](https://progenetix.org)"
   - '[`bycon` software project](https://github.com/progenetix/bycon/)'
-  - "[Beacon documentation](http://docs.genomebeacons.org)"
+  - "[Beacon documentation](https://docs.genomebeacons.org)"
   - '[ELIXIR hCNV Community](https://cnvar.org)'
 ---