50ce78a22e9684817d8e5519e372ef2c313d343e max Fri Sep 4 10:54:48 2026 -0700 Fix licensing page ambiguities and LICENSE tag spelling, refs #37781 The license/index.html page had several passages easy to misread: a claim that liftOver was the "only" data exception directly contradicted by the clinical-genetics exceptions listed two paragraphs later, a header/body tension in the graphics-reuse section, a garbled sentence about entity type, a missing "than", and two same-named "Software:" headings covering opposite licensing outcomes (free vs. commercial-restricted). Also fixes the SPDX tag referenced on that page: the LICENSE files in restricted directories used the misspelled "LicenceRef-proprietary" rather than the standard "LicenseRef-proprietary", so grepping the tree for the tag as documented turned up almost nothing. Adds a link to the (currently sandboxed) list of tracks we cannot distribute, next to the clinical-genetics exception examples. diff --git src/hg/htdocs/license/index.html src/hg/htdocs/license/index.html index a144630c3dd..fcda259756c 100755 --- src/hg/htdocs/license/index.html +++ src/hg/htdocs/license/index.html @@ -1,216 +1,219 @@ <!DOCTYPE html> <!--#set var="TITLE" value="Genome Browser Licensing" --> <!--#set var="ROOT" value=".." --> <!-- Relative paths to support mirror sites with non-standard GB docs install --> <!--#include virtual="$ROOT/inc/gbPageStart.html" --> <h1>Website: No license or permission is needed to use the website, API and public MySQL server for academic, commercial or any other use</h1> <p>This is a public website. There is no license or permission needed to use the website and any services (API, etc) on it. You can also load your own data onto our website and look at it there, and use track hubs or custom tracks to configure -how it is displayed, as a commercial, non-commercial or any other entity. However, +how it is displayed, regardless of whether you are a commercial, non-commercial or any other +type of entity. However, when you use the UCSC Genome Browser in your work, please cite one of our <a href="../goldenPath/pubs.html">publications</a>. </p> <br> <h1>Graphics: No permission is needed to reproduce a graphic produced by the Genome Browser</h1> -<p>Permission is granted for reuse of all graphics produced -by the UCSC Genome Browser website. There is no need to contact us to get permission. If your +<p>Blanket permission for reuse of all graphics produced +by the UCSC Genome Browser website is hereby granted to everyone. There is no need to contact us to get permission. If your publisher, notably Elsevier, insists on getting approval, please direct them to this webpage. However, when you use the UCSC Genome Browser in your work, please cite one of our <a href="../goldenPath/pubs.html">publications</a>.</p> <br> <h1>Data: No license is needed for the data files and database tables used by the Genome Browser</h1> <p> As far as the UCSC Genome Browser group is concerned, the raw table data and binary files used to create the graphics by the browser is freely available for both public and commercial use. This applies to data that is downloaded as files via http, https, ftp or rsync, and equally when data is accessed through -the public MySQL server or via the web API. The only exception are the liftOver chain files, -they can be linked, downloaded, used and redistributed, but only for non-commercial use +the public MySQL server or via the web API. One exception is the liftOver chain files, +which can be linked, downloaded, used and redistributed, but only for non-commercial use; see the <a href="http://hgdownload.gi.ucsc.edu/goldenpath/hg38/liftOver/">liftOver README</a>. +A further set of exceptions, for certain clinical genetics tracks, is described below. </p> <p>Sometimes, the source databases or authors place restrictions on data. In very rare cases, the genomes come with citation requirements. The README.txt file in the download directory of each assembly shows the original restrictions pertaining to the genome sequence itself by the original authors; most assemblies do not have any restrictions. </p> <p> Certain genome annotation data, mostly on the human genome and in the domain of clinical genetics, have specific restrictions. For some of these, we are not allowed to make the data available. Usually the data must be obtained from the source database directly in the -original format or licensed, rather from UCSC. Examples are HGMD, LOVD, OMIM, Decipher, -Genomenon, Genehancer and COSMIC. For viral genomes, any GISAID-sequences or any data -derived from GISAID sequences cannot be shared by us. Please see the respective +original format or licensed, rather than from UCSC. Examples are HGMD, LOVD, OMIM, Decipher, +Genomenon, GeneHancer and COSMIC. For viral genomes, any GISAID-sequences or any data +derived from GISAID sequences cannot be shared by us. See this <a href="/trackLists.html">list +of tracks that we cannot distribute</a> for the exact set. Please see the respective track documentation pages on these assemblies for more details, by selecting the assembly and clicking the track title in the genome browser. They usually list or link to the exact license conditions. Files for these tracks are not available from our download servers, please contact us for questions or if you need a pointer to the respective conversion scripts in our Github code repository.</p><br> -<h1 id="free">Software: Most command-line tools and directories are freely available for all uses</h1> +<h1 id="free">Command-line tools: Most command-line tools and directories are freely available for all uses</h1> <p> The majority of the Genome Browser source code is available under the MIT license, see <a href="https://github.com/ucscGenomeBrowser/kent/blob/master/LICENSE" target=_blank>the LICENSE file in our source code repository</a>. As such, the <a href="https://hgdownload.gi.ucsc.edu/downloads.html#utilities_downloads"> Unix command line utilities</a> needed to build tracks, track hub files, computational pipelines, and our hundreds of tools to filter, sort, rearrange, join, and process genome annotation files can be used and redistributed freely via package managers and installation tools, even for commercial use (except BLAT/LiftOver). Notable examples are bedToBigBed, wigToBigWig, overlapSelect, featureBits, pslMap, pslFilter and pslCDnaFilter. </p> <p> The exceptions are source code directories with special LICENSE files in them. These are <code>kent/src/blat</code>, <code>kent/src/isPcr</code>, <code>kent/src/jkOwnLib</code>, and the programs that produce the graphical images or user interface for the UCSC Genome Browser. This includes the following subdirectories under <code>kent/src/hg</code>: </p> <p><code>cgilib hgApi hgCollection hgFileSearch hgFileUi hgGateway hgGene hgGenome hgIntegrator hgPal hgPcr hgPhyloPlace hgPublicSessions hgSession hgSuggest hgTables hgTrackUi hgTracks hgVai hgc hubApi near visiGene liftOver</code> </p> <p> See the LICENSE file in the top level of our source code for a listing of licenses and directories that they apply to: <a href="https://github.com/ucscGenomeBrowser/kent/blob/master/LICENSE"> https://github.com/ucscGenomeBrowser/kent/blob/master/LICENSE</a>. Directories under non-commercial licenses have LICENSE files in them that start with the "LicenseRef-proprietary" SPDX tag. </p> <p>When you use the UCSC Genome Browser in your work, please cite one of our <a href="../goldenPath/pubs.html">publications</a>.</p> <br> -<h1>Software: Download and installation of the graphical Genome Browser software +<h1>Graphical browser software: Download and installation of the graphical Genome Browser software and access to the source code is free for non-commercial uses but not commercial usage</h1> <p>Non-commercial usage for the Genome Browser graphical interface (primarily the "hgTracks" program), including download and local installation, aka setting up a <a href="../goldenPath/help/mirror.html">"mirror"</a>, is free. When you use the UCSC Genome Browser in your work, please cite one of our <a href="../goldenPath/pubs.html">publications</a>. </p> <p> For commercial use, a license is required for download and local installation of certain Genome Browser webserver CGI binaries and source code. In the source code repository, the respective directories are marked by special LICENSE files in them. As specified above, this applies to <code>kent/src/blat</code>, <code>kent/src/isPcr</code>, <code>kent/src/jkOwnLib</code>, and the following subdirectories and programs under <code>kent/src/hg</code>. The majority of license protected files are the programs that produce the graphical images and the graphical user interface for the UCSC Genome Browser:</p> <br> <p><code>cgilib hgApi hgCollection hgFileSearch hgFileUi hgGateway hgGene hgGenome hgIntegrator hgPal hgPcr hgPhyloPlace hgPublicSessions hgSession hgSuggest hgTables hgTrackUi hgTracks hgVai hgc hubApi near visiGene liftOver</code> </p> <p> Also, BLAT and isPCR, if needed, are covered by a separate license (see below). This concerns the source code directories <code>kent/src/blat</code>, <code>kent/src/isPcr</code> and <code>kent/src/jkOwnLib</code>. </p> <p> To purchase a commercial license for Genome Browser source code, LiftOver, GBiB, or GBiC, please visit the <a href="https://genome-store.ucsc.edu">Genome Browser store</a>. </p> <p> We also have an <a href="../FAQ/FAQlicense.html">FAQ on licensing questions</a> which may help to clarify questions on how to license the code. We also have documentation on how to choose the best option for a local installation of a <a target=_blank href="../goldenPath/help/mirror.html">Genome Browser "mirror"</a>. </p> <p> If you would like to purchase the Genome Browser source code without going through our store, please follow these instructions: <ol> <li> Read and sign the <A HREF="gbLicense2020.pdf" target=_blank>licensing agreement</a>.</li> <li> Email a signed copy of the license agreement to the UCSC Office for IP Management (<A HREF="mailto:genome-browser-store-group@ucsc. edu">genome-browser-store-group@ucsc. edu</A>). <!-- above address is genome-browser-store-group at ucsc.edu --></li> <li> Follow the instructions in the license agreement for submitting the signed original copy and payment.</li> <li> After your license application has been processed, you will receive instructions for downloading the browser software and data.</li> </ol></p> <p> Genome Browser licensing questions should be directed to <A HREF="mailto:genome-browser-store-group@ucsc. edu">genome-browser-store-group@ucsc. edu</A>. <!-- above address is genome-browser-store-group at ucsc.edu --> For information about commercial licensing of the Blat and In-Silico PCR tools, see the <a href="http://www.kentinformatics.com" target=_blank>Kent Informatics</a> website or contact <a href="mailto:kent@soe.ucsc.edu">kent@soe.ucsc.edu</a>.</p> <!-- above address is kent at soe.ucsc.edu --> <p> See the LICENSE file in the top level of our source code for a listing of licenses and directories that they apply to: <a href="https://github.com/ucscGenomeBrowser/kent/blob/master/LICENSE"> https://github.com/ucscGenomeBrowser/kent/blob/master/LICENSE</a>.</p> <br> <h1>Fonts</h1> <p> <b>Atkinson Hyperlegible:</b> Designed by Braille Institute, Applied Design Works, Elliott Scott, Megan Eiswerth, Linus Boman, Theodore Petrosky <br> Copyright 2020 Braille Institute of America, Inc. This Font Software is licensed under the SIL Open Font License, Version 1.1 . This license is copied below, and is also available with a FAQ at: https://openfontlicense.org SIL OPEN FONT LICENSE Version 1.1 - 26 February 2007 </p><p> <b>Lexend:</b> Designed by Bonnie Shaver-Troup, Thomas Jockin, Santiago Orozco, Héctor Gómez, Superunion <br> Copyright 2018 The Lexend Project Authors (https://github.com/googlefonts/lexend), with Reserved Font Name “RevReading Lexend”. This Font Software is licensed under the SIL Open Font License, Version 1.1 . This license is copied below, and is also available with a FAQ at: https://openfontlicense.org SIL OPEN FONT LICENSE Version 1.1 - 26 February 2007 </p> <br> <h1>Acknowledgements</h1> <p> This software includes software made by open-source projects: <ul> <li> htslib, see <a href="https://doi.org/10.1093/gigascience/giab007" target=_blank> Bonfield et al, 2021</a>: Copyright (C) 2012-2020 Genome Research Ltd., see <code>kent/src/htslib</code></li> <li> optimalLeaf, see <a href="https://www.ncbi.nlm.nih.gov/pubmed/12801867" target=_blank> Bar-Joseph et al. 2003</a>: released into the public domain by Ziv Bar-Joseph, see <code>kent/src/optimalLeaf</code>.</li> <li> Portions of this software are copyright 2020 The FreeType Project (www.freetype.org). All rights reserved.</li> <li> This software uses the (URW)++ fonts, Copyright 1999 by (URW)++ Design & Development. The files are not in git but can be obtained via rsync or ftp from hgdownload.gi.ucsc.edu/htdocs.</li> <li>MySQL connectivity is provided via the MariaDB C client library provided under LGPL. <a href="https://mariadb.com/kb/en/the-mariadb-library/mariadb-connector-c/">https://mariadb.com/kb/en/the-mariadb-library/mariadb-connector-c/</a></li> <li>It includes software developed by the OpenSSL Project for use in the OpenSSL Toolkit (http://www.openssl.org/). This product includes cryptographic software written by Eric Young (eay@cryptsoft.com). This product includes software written by Tim Hudson (tjh@cryptsoft.com).</li> <li>We use Font Awesome by Dave Gandy - http://fontawesome.io</li> <li><a href="https://www.flaticon.com/free-icons/genome" title="genome icons">Genome icons created by Kalashnyk - Flaticon</a></li> </ul> </p> <!--#include virtual="$ROOT/inc/gbPageEnd.html" -->