From 307d40483b0e21e2481236ef07bcfff396ae0ca1 Mon Sep 17 00:00:00 2001 From: Jorge Alvarez Jarreta Date: Wed, 3 Dec 2025 13:21:05 +0000 Subject: [PATCH] updates, bugfixes and typo corrections --- htdocs/das/das.xsl | 6 +++--- htdocs/info/about/contact/index.html | 16 ++++++++-------- htdocs/info/about/index.html | 6 +++--- htdocs/info/about/jobs.html | 4 ++-- htdocs/info/about/legal/disclaimer.html | 2 +- htdocs/info/about/legal/logo_policy.html | 2 +- htdocs/info/about/legal/privacy_old.html | 6 +++--- htdocs/info/about/outreach/geek4aweek.html | 2 +- htdocs/info/about/outreach/index.html | 10 +++++----- .../info/website/trackhubs/adding_trackhubs.html | 4 ++-- htdocs/info/website/upload/var.html | 10 +++++----- htdocs/new_species/tree.htm | 2 +- modules/EnsEMBL/Web/Document/HTML/Export.pm | 2 +- 13 files changed, 36 insertions(+), 36 deletions(-) diff --git a/htdocs/das/das.xsl b/htdocs/das/das.xsl index 08979aef56..27ce1718c7 100644 --- a/htdocs/das/das.xsl +++ b/htdocs/das/das.xsl @@ -47,11 +47,11 @@ h3.boxed { margin: 0 0 0.5em 0; padding: 0.5em; background-color: #8fa0c4 } diff --git a/htdocs/info/about/contact/index.html b/htdocs/info/about/contact/index.html index 369f37a53e..e25f4b59f7 100644 --- a/htdocs/info/about/contact/index.html +++ b/htdocs/info/about/contact/index.html @@ -31,23 +31,23 @@

Mailing Lists

We have two public mailing lists:

More information...

Social Media

-

Wordpress -Visit our blog for details of releases, +

Wordpress +Visit our blog for details of releases, workshops and other tidbits of information about the Ensembl project - comments welcome!

-

Twitter -Follow us on Twitter for the latest +

Twitter +Follow us on Twitter for the latest breaking Ensembl news and service status updates.

-

Facebook -Like us on Facebook for the latest +

Facebook +Like us on Facebook for the latest breaking Ensembl news and service status updates.

Collaborations

diff --git a/htdocs/info/about/index.html b/htdocs/info/about/index.html index 5e4e535c1c..6e4bcebe45 100644 --- a/htdocs/info/about/index.html +++ b/htdocs/info/about/index.html @@ -19,7 +19,7 @@

About the Ensembl Project

sequence would not be able to offer researchers timely access to the latest data. The goal of Ensembl was therefore to automatically annotate the genome, integrate this annotation with other available biological data and make all this publicly available via the web. Since the -website's launch in July 2000, many more genomes have been added to Ensembl and the range of available data has +website's launch in July 2000, many more genomes have been added to Ensembl and the range of available data has also expanded to include comparative genomics, variation and regulatory data.

In 2009, the Ensembl Genomes project was launched with specific web portals for plant, fungal, @@ -31,9 +31,9 @@

About the Ensembl Project

The Ensembl project is co-lead by Rob Finn and Andy Yates and receives input from an independent scientific advisory board. Our resources are created by a talented group numbering over 70 people, split into thematic teams developing our analysis methods, executing these analyses, developing our online resources and providing engagement with the wider scientific community.

-

Ensembl is based at the European Molecular Biology Laboratory's European Bioinformatics Institute, which is located on the Wellcome Genome Campus in Hinxton, south of the city of Cambridge, United Kingdom.

+

Ensembl is based at the European Molecular Biology Laboratory's European Bioinformatics Institute, which is located on the Wellcome Genome Campus in Hinxton, south of the city of Cambridge, United Kingdom.

-

You can read more about ongoing developments in Ensembl on our blog.

+

You can read more about ongoing developments in Ensembl on our blog.

If you would like to cite Ensembl, we recommend referring to our most recent NAR overview article.

The "Geek for a Week" scheme allows developers and researchers to work alongside Ensembl team members for a short intensive collaborative project.

Formal requests such as large scale collaborations, legal issues, etc., are best sent to Rob Finn and/or Andy Yates at EMBL-EBI.

diff --git a/htdocs/info/about/jobs.html b/htdocs/info/about/jobs.html index a8f9f018a7..3986972fc6 100644 --- a/htdocs/info/about/jobs.html +++ b/htdocs/info/about/jobs.html @@ -19,9 +19,9 @@

Jobs

diff --git a/htdocs/info/about/legal/disclaimer.html b/htdocs/info/about/legal/disclaimer.html index 2e13878fcd..62438f8559 100644 --- a/htdocs/info/about/legal/disclaimer.html +++ b/htdocs/info/about/legal/disclaimer.html @@ -24,7 +24,7 @@

Disclaimer

-The European Molecular Biology Laboratory's +The European Molecular Biology Laboratory's European Bioinformatics Institute (EMBL-EBI) provides this data and software in good faith, but make no warranty, express or implied, nor assume any legal liability or responsibility for any purpose for which they are used. diff --git a/htdocs/info/about/legal/logo_policy.html b/htdocs/info/about/legal/logo_policy.html index 937e814df5..4de35646f2 100644 --- a/htdocs/info/about/legal/logo_policy.html +++ b/htdocs/info/about/legal/logo_policy.html @@ -70,7 +70,7 @@

5. Use of the "Powered by Ensembl" Logo

Ensembl Developers are encouraged to use the Ensembl code for any purpose. Those developers wishing to acknowledge this contribution should use the Powered by Ensembl logo (see above), which incorporates the Ensembl logo. A citation of relevant Ensembl publications related to the tools would be appropriate.

-Developers using the empowered logo should contact the Ensembl helpdesk and their projects may be added to our list of tools and sites using Ensembl technology. The current project list and a link to download the Powered by Ensembl logo may be found at http://www.ensembl.org/info/about/ensembl_powered.html. +Developers using the empowered logo should contact the Ensembl helpdesk and their projects may be added to our list of tools and sites using Ensembl technology. The current project list and a link to download the Powered by Ensembl logo may be found at https://www.ensembl.org/info/about/ensembl_powered.html.

Before contacting Ensembl to be added to the list of Ensembl-derived projects the Powered by Ensembl logo should be visible on the relevant site. Inclusion of any project on the Ensembl maintained list of derived projects is not intended as an endorsement of the site or its content. diff --git a/htdocs/info/about/legal/privacy_old.html b/htdocs/info/about/legal/privacy_old.html index 3b3a1ff8b6..793cb5c09a 100644 --- a/htdocs/info/about/legal/privacy_old.html +++ b/htdocs/info/about/legal/privacy_old.html @@ -9,7 +9,7 @@

Ensembl Privacy Statement

Information provided to or gathered by ensembl.org is controlled by the Ensembl Project, -based at the European Bioinformatics Institute near Cambridge, UK.

+based at the European Bioinformatics Institute near Cambridge, UK.

Ensembl.org gathers information about users solely to improve the usability and usefulness of the site, and not for any commercial purposes. No use is made of users' contact information except when @@ -18,12 +18,12 @@

Ensembl Privacy Statement

collected in server log files and used for statistical analysis of traffic patterns.

Ensembl and its satellite sites (including archives) conform to the -EBI terms of use. .

+EBI terms of use. .

Use of Cookies

A full list of cookies used by EBI sites, including ones from Ensembl, may be found -on the EBI cookie control page, +on the EBI cookie control page, along with instructions on how to manage cookies in your web browser.

Additional information held in user accounts

diff --git a/htdocs/info/about/outreach/geek4aweek.html b/htdocs/info/about/outreach/geek4aweek.html index a44af4f91e..fcd6170f65 100644 --- a/htdocs/info/about/outreach/geek4aweek.html +++ b/htdocs/info/about/outreach/geek4aweek.html @@ -36,7 +36,7 @@

Geek for a Week

For users interested primarily in learning about Ensembl's tools, we offer a series of short course both at the EMBL-EBI and around the world. These courses include modules focused on the Ensembl genome browser, -the Ensembl APIs, and the Ensembl BioMart. Please see the Ensembl blog +the Ensembl APIs, and the Ensembl BioMart. Please see the Ensembl blog for the current list of courses.

For more information about Ensembl courses or the Geek for a Week experience, please contact the diff --git a/htdocs/info/about/outreach/index.html b/htdocs/info/about/outreach/index.html index dc124895d9..484f050cff 100644 --- a/htdocs/info/about/outreach/index.html +++ b/htdocs/info/about/outreach/index.html @@ -18,7 +18,7 @@

Outreach

-

e.g. http://www.ensembl.org/Trackhub?url=http://www.coolgenomics.ac.uk/hub.txt;species=Homo_sapiens;r=X:123456-123789

+

e.g. https://www.ensembl.org/Trackhub?url=http://www.coolgenomics.ac.uk/hub.txt;species=Homo_sapiens;r=X:123456-123789

Important note: You must use semicolons, not ampersands, between parameters, otherwise your track hub will not attach. This is because some track hubs use dynamic URLs containing question marks and ampersands, which need to be encoded separately from the other parameters passed to the Ensembl URL.

diff --git a/htdocs/info/website/upload/var.html b/htdocs/info/website/upload/var.html index d1f08a55dd..3814c5f5ba 100644 --- a/htdocs/info/website/upload/var.html +++ b/htdocs/info/website/upload/var.html @@ -84,7 +84,7 @@

Input format

to RefSeq transcripts in the Ensembl VEP script.
  • Variant identifiers - these should be e.g. dbSNP rsIDs, or any synonym for a variant present in the Ensembl Variation database. See here for a list + href="/info/genome/variation/species/sources_documentation.html">here for a list of identifier sources in Ensembl.
    • @@ -127,10 +127,10 @@

    Output format

  • HIGH_INF_POS - a flag indicating if the variant falls in a high information position of a transcription factor binding profile (TFBP)
  • MOTIF_SCORE_CHANGE - The difference in motif score of the reference and variant sequences for the TFBP
  • CANONICAL - a flag indicating if the transcript is denoted as the canonical transcript for this gene
    • -
  • CCDS - the CCDS identifer for this transcript, where applicable
    • +
  • CCDS - the CCDS identifier for this transcript, where applicable
  • INTRON - the intron number (out of total number)
  • EXON - the exon number (out of total number)
    • -
  • DOMAINS - the source and identifer of any overlapping protein domains
    • +
  • DOMAINS - the source and identifier of any overlapping protein domains
    • @@ -162,7 +162,7 @@

    Output format

    ## CANONICAL : Indicates if transcript is canonical for this gene ## CCDS : Indicates if transcript is a CCDS transcript ## HGNC : HGNC gene identifier -## ENSP : Ensembl protein identifer +## ENSP : Ensembl protein identifier ## HGVSc : HGVS coding sequence name ## HGVSp : HGVS protein sequence name ## SIFT : SIFT prediction @@ -170,7 +170,7 @@

    Output format

    ## Condel : Condel SIFT/PolyPhen consensus prediction ## EXON : Exon number ## INTRON : Intron number -## DOMAINS : The source and identifer of any overlapping protein domains +## DOMAINS : The source and identifier of any overlapping protein domains ## MOTIF_NAME : The source and identifier of a transcription factor binding profile (TFBP) aligned at this position ## MOTIF_POS : The relative position of the variation in the aligned TFBP ## HIGH_INF_POS : A flag indicating if the variant falls in a high information position of the TFBP diff --git a/htdocs/new_species/tree.htm b/htdocs/new_species/tree.htm index 6c7c99a2c0..9562fc5c6d 100644 --- a/htdocs/new_species/tree.htm +++ b/htdocs/new_species/tree.htm @@ -148,7 +148,7 @@
    - +
    diff --git a/modules/EnsEMBL/Web/Document/HTML/Export.pm b/modules/EnsEMBL/Web/Document/HTML/Export.pm index c0f209f326..72733660b7 100644 --- a/modules/EnsEMBL/Web/Document/HTML/Export.pm +++ b/modules/EnsEMBL/Web/Document/HTML/Export.pm @@ -42,7 +42,7 @@ sub render { push @services, qq(the REST API); } if ($sd->HAS_API_DOCS) { - push @services, qq(the MySQL server); + push @services, qq(the MySQL server); } my $ftp = $sd->ENSEMBL_FTP_URL; if ($ftp) {