Download Pathways

From WikiPathways

Revision as of 16:24, 5 August 2009 (view source) AlexanderPico (Talk | contribs) ← Previous diff		Current revision (14:50, 11 April 2024) (view source) Khanspers (Talk | contribs) (April data release)
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-	| __TOC__	+	| __NOTOC__
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-	Choose one of the file types below to download a set of pathways in that format. Choose between the following sets:	+	=== Versioned Releases ===
-	;Featured pathways: Only pathways that have been explicitly marked with the 'Featured pathway' curation tag. This includes pathways that have been carefully curated and typically excludes draft or test pathways not intended for distribution. ''(recommended)''	+	Each month we release an updated set of pathways in various data and image formats. These pathways have been reviewed and tagged as approved, and are considered ready for analysis and data overlays.
-	;All pathways: Includes non-featured pathways, but still excludes test or tutorial pathways (such as the [[Pathway:Homo sapiens:Sandbox|Sandbox pathway]]).	+
-	== GPML ==
-	Click on one of the links below to download all pathways in GPML format. You can view and edit GPML files in [http://pathvisio.org PathVisio]. From [http://pathvisio.org PathVisio] you can also export these files to the [www.genmapp.org GenMAPP] mapp format and [http://en.wikipedia.org/wiki/Portable_Document_Format PDF].
-	{|class="prettytable"	+	<font size=4>'''Current version: [http://data.wikipathways.org/20240410/ 20240410 (10 April 2024)]'''</font>
-	!All pathways	+
-	!Featured pathways	+
-	|- valign="top"	+
-	|<batchDownload filetype="gpml" excludetags="Curation:Tutorial"></batchDownload>	+
-	|<batchDownload filetype="gpml" tag="Curation:FeaturedPathway"></batchDownload>	+
-	|}	+
-	'''KEGG pathways''' for select species are available in GPML format at [http://www.pathvisio.org/Download#Step_3 PathVisio.org]. ''(KEGG content current as of April 7th, 2009)''
-	== Eu.Gene ==
-	Click on one of the links below to download all pathways in the [http://www.ducciocavalieri.org/bio.htm Eu.Gene] format (pwf). Eu.Gene is a tool for microarray analysis in context of biological pathways ([http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=retrieve&db=pubmed&list_uids=17599938&dopt=AbstractPlus read more]).
-	{|class="prettytable"	+	=== Vertebrates ===
-	!All pathways	+
-	!Featured pathways	+
-	|- valign="top"	+
-	|<batchDownload filetype="pwf" excludetags="Curation:Tutorial"></batchDownload>	+
-	|<batchDownload filetype="pwf" tag="Curation:FeaturedPathway"></batchDownload>	+
-	|}	+
-	== Plain text ==	+	* '''[http://data.wikipathways.org/20240410/gpml/wikipathways-20240410-gpml-Bos_taurus.zip Bos taurus]'''
-	Click on one of the links below to download all pathways in plain text format. This format contains a list of all datanodes, with the identifier in the first	+	* '''[http://data.wikipathways.org/20240410/gpml/wikipathways-20240410-gpml-Canis_familiaris.zip Canis familiaris]'''
-	column, and the database system in the second column.	+	* '''[http://data.wikipathways.org/20240410/gpml/wikipathways-20240410-gpml-Danio_rerio.zip Danio rerio]'''
		+	* '''[http://data.wikipathways.org/20240410/gpml/wikipathways-20240410-gpml-Equus_caballus.zip Equus caballus]'''
		+	* '''[http://data.wikipathways.org/20240410/gpml/wikipathways-20240410-gpml-Gallus_gallus.zip Gallus gallus]'''
		+	* '''[http://data.wikipathways.org/20240410/gpml/wikipathways-20240410-gpml-Homo_sapiens.zip Homo sapiens]'''
		+	* '''[http://data.wikipathways.org/20240410/gpml/wikipathways-20240410-gpml-Mus_musculus.zip Mus musculus]'''
		+	* '''[http://data.wikipathways.org/20240410/gpml/wikipathways-20240410-gpml-Pan_troglodytes.zip Pan troglodytes]'''
		+	* '''[http://data.wikipathways.org/20240410/gpml/wikipathways-20240410-gpml-Rattus_norvegicus.zip Rattus norvegicus]'''
		+	* '''[http://data.wikipathways.org/20240410/gpml/wikipathways-20240410-gpml-Sus_scrofa.zip Sus scrofa]'''
-	{|class="prettytable"	+	=== Invertebrates ===
-	!All pathways	+
-	!Featured pathways	+
-	|- valign="top"	+
-	|<batchDownload filetype="txt" excludetags="Curation:Tutorial"></batchDownload>	+
-	|<batchDownload filetype="txt" tag="Curation:FeaturedPathway"></batchDownload>	+
-	|}	+
-	== PDF ==	+	* '''[http://data.wikipathways.org/20240410/gpml/wikipathways-20240410-gpml-Anopheles_gambiae.zip Anopheles gambiae]'''
-	Click on one of the links below to download all pathways in Portable Document Format (PDF).	+	* '''[http://data.wikipathways.org/20240410/gpml/wikipathways-20240410-gpml-Caenorhabditis_elegans.zip Caenorhabditis elegans]'''
		+	* '''[http://data.wikipathways.org/20240410/gpml/wikipathways-20240410-gpml-Drosophila_melanogaster.zip Drosophila melanogaster]'''
-	{|class="prettytable"	+	=== Plants ===
-	!All pathways	+	* '''[http://data.wikipathways.org/20240410/gpml/wikipathways-20240410-gpml-Arabidopsis_thaliana.zip Arabidopsis thaliana]'''
-	!Featured pathways	+	* '''[http://data.wikipathways.org/20240410/gpml/wikipathways-20240410-gpml-Hordeum_vulgare.zip Hordeum vulgare]'''
-	|- valign="top"	+	* '''[http://data.wikipathways.org/20240410/gpml/wikipathways-20240410-gpml-Oryza_sativa.zip Oryza sativa]'''
-	|<batchDownload filetype="pdf" excludetags="Curation:Tutorial"></batchDownload>	+	* '''[http://data.wikipathways.org/20240410/gpml/wikipathways-20240410-gpml-Populus_trichocarpa.zip Populus trichocarpa]'''
-	|<batchDownload filetype="pdf" tag="Curation:FeaturedPathway"></batchDownload>	+	* '''[http://data.wikipathways.org/20240410/gpml/wikipathways-20240410-gpml-Solanum_lycopersicum.zip Solanum lycopersicum]'''
-	|}	+	* '''[http://data.wikipathways.org/20240410/gpml/wikipathways-20240410-gpml-Zea_mays.zip Zea mays]'''
		+	<!-- * '''[http://data.wikipathways.org/20240410/gpml/wikipathways-20240410-gpml-Beta_vulgaris.zip Beta vulgaris]''' -->
-	== SVG ==	+	=== Eukaryotic microorganisms ===
-	Click on one of the links below to download all pathways in [http://www.w3.org/Graphics/SVG/ SVG] format. The [http://www.w3.org/Graphics/SVG/ SVG] files can be used to create high quality images for publication purposes. You can edit and convert the SVG files using [http://www.inkscape.org Inkscape].	+
-	{|class="prettytable"	+	* '''[http://data.wikipathways.org/20240410/gpml/wikipathways-20240410-gpml-Gibberella_zeae.zip Gibberella zeae]'''
-	!All pathways	+	* '''[http://data.wikipathways.org/20240410/gpml/wikipathways-20240410-gpml-Saccharomyces_cerevisiae.zip Saccharomyces cerevisiae]'''
-	!Featured pathways	+	* '''[http://data.wikipathways.org/20240410/gpml/wikipathways-20240410-gpml-Plasmodium_falciparum.zip Plasmodium falciparum]'''
-	|- valign="top"	+
-	|<batchDownload filetype="svg" excludetags="Curation:Tutorial"></batchDownload>	+
-	|<batchDownload filetype="svg" tag="Curation:FeaturedPathway"></batchDownload>	+
-	|}	+
-	== PNG ==	+	=== Bacteria ===
-	Click on one of the links below to download all pathways in the Portable Network Graphics (png) format.	+
-	{|class="prettytable"	+	* '''[http://data.wikipathways.org/20240410/gpml/wikipathways-20240410-gpml-Bacillus_subtilis.zip Bacillus subtilis]'''
-	!All pathways	+	* '''[http://data.wikipathways.org/20240410/gpml/wikipathways-20240410-gpml-Escherichia_coli.zip E.coli]'''
-	!Featured pathways	+	* '''[http://data.wikipathways.org/20240410/gpml/wikipathways-20240410-gpml-Mycobacterium_tuberculosis.zip Mycobacterium tuberculosis]'''
-	|- valign="top"	+
-	|<batchDownload filetype="png" excludetags="Curation:Tutorial"></batchDownload>	+
-	|<batchDownload filetype="png" tag="Curation:FeaturedPathway"></batchDownload>	+
-	|}	+
-	== Flatfile ==
-	Click on one of the links below to download all pathways in either a tab-delimited or HTML table format. The output includes gene, protein and small molecule contents.
-	* '''All species''' ([{{SERVER}}{{SCRIPTPATH}}/wpi/pathway_content_flatfile.php?output=tab tab], [{{SERVER}}{{SCRIPTPATH}}/wpi/pathway_content_flatfile.php?output=html html])	+	== Programmatic Access ==
-	* Homo sapiens ([{{SERVER}}{{SCRIPTPATH}}/wpi/pathway_content_flatfile.php?species=Homo%20sapiens&output=tab tab], [{{SERVER}}{{SCRIPTPATH}}/wpi/pathway_content_flatfile.php?species=Homo%20sapiens&output=html html])	+	The archive of current and past collections of pathways in various formats at data.wikipathways.org is accessible programmatically as well. Depending on your preferences, there are many ways to identify and download the collection you need.
-	* Mus Musculus ([{{SERVER}}{{SCRIPTPATH}}/wpi/pathway_content_flatfile.php?species=Mus%20musculus tab], [{{SERVER}}{{SCRIPTPATH}}/wpi/pathway_content_flatfile.php?species=Mus%20musculus&output=html html])	+
-	* Rattus norvegicus ([{{SERVER}}{{SCRIPTPATH}}/wpi/pathway_content_flatfile.php?species=Rattus%20norvegicus&output=tab tab], [{{SERVER}}{{SCRIPTPATH}}/wpi/pathway_content_flatfile.php?species=Rattus%20norvegicus&output=html html])	+	''Note: Our files contain the date of creation in their names so that you can be sure which collection your are using and to avoid overwriting local copies of these files.''
-	* Drosophila melanogaster ([{{SERVER}}{{SCRIPTPATH}}/wpi/pathway_content_flatfile.php?species=Drosophila%20melanogaster&output=tab tab], [{{SERVER}}{{SCRIPTPATH}}/wpi/pathway_content_flatfile.php?species=Drosophila%20melanogaster&output=html html])	+
-	* Caenorhabditis elegans ([{{SERVER}}{{SCRIPTPATH}}/wpi/pathway_content_flatfile.php?species=Caenorhabditis%20elegans&output=tab tab], [{{SERVER}}{{SCRIPTPATH}}/wpi/pathway_content_flatfile.php?species=Caenorhabditis%20elegans&output=html html])	+	# '''[https://github.com/wikipathways/rwikipathways rWikiPathways]''' is an R package that provides an helper function called ''downloadPathwayArchive'' that will retrieve the latest file for you per species and format, e.g.,  <pre>downloadPathwayArchive(organism="Mus musculus”, format=‘gmt’)</pre>
-	* Saccharomyces cerevisiae ([{{SERVER}}{{SCRIPTPATH}}/wpi/pathway_content_flatfile.php?species=Saccharomyces%20cerevisiae&output=tab tab], [{{SERVER}}{{SCRIPTPATH}}/wpi/pathway_content_flatfile.php?species=Saccharomyces%20cerevisiae&output=html html])	+	# '''Filename pattern''' allows you to infer the filename of the latest collection given the current date. For example, since we always release our archive collections on the 10th of each month, you know that the latest filename is the nearest prior date matching that pattern, e.g., 20180910 would be the current file from Sep 10 to Oct 10, 2018. ''Caution: this might break if for some unforeseen reason we are unable to produce the archive on schedule.''
-	* Danio rerio ([{{SERVER}}{{SCRIPTPATH}}/wpi/pathway_content_flatfile.php?species=Danio%20rerio&output=tab tab], [{{SERVER}}{{SCRIPTPATH}}/wpi/pathway_content_flatfile.php?species=Danio%20rerio&output=html html])	+	# '''Bash scripting''' allows you to scrape the currently available filenames and guarantee that you are getting the latest file no matter what the name might be.  Here is an example of a one-liner to get a list of all the current GMT files: <pre>echo "cat //html/body/div/table/tbody/tr/td/a" |  xmllint --html --shell http://data.wikipathways.org/current/gmt/ | grep -o -E ">(.*gmt)<" | sed -E 's/(<|>)//g'</pre> And here is a version that would return the latest GMT for mouse: <pre>echo "cat //html/body/div/table/tbody/tr/td/a" |  xmllint --html --shell http://data.wikipathways.org/current/gmt/ | grep -o -E ">.*Mus_musculus.gmt<" | sed -E 's/(<|>)//g'</pre>
-	* Arabidopsis thaliana ([{{SERVER}}{{SCRIPTPATH}}/wpi/pathway_content_flatfile.php?species=Arabidopsis%20thaliana&output=tab tab], [{{SERVER}}{{SCRIPTPATH}}/wpi/pathway_content_flatfile.php?species=Arabidopsis%20thaliana&output=html html])	+
-	* Oryza japonica ([{{SERVER}}{{SCRIPTPATH}}/wpi/pathway_content_flatfile.php?species=Oryza%20japonica&output=tab tab], [{{SERVER}}{{SCRIPTPATH}}/wpi/pathway_content_flatfile.php?species=Oryza%20japonica&output=html html])	+
		+	== Other Collections ==
		+
		+	<font size=3>
		+	* [http://data.wikipathways.org Prior monthly releases]
		+	* [[Daily_Download|Daily curated releases]]
		+	* [http://www.wikipathways.org//wpi/batchDownload.php?species=Homo%20sapiens&fileType=gpml&tag=Curation:Reactome_Approved  Reactome Human Collection]
		+	* [http://data.wikipathways.org/current/gmt Gene lists per pathway (GMT)]
		+	* [http://data.wikipathways.org/current/svg Pathway image files (SVG)]
		+	* [http://data.wikipathways.org/current/rdf Linked data files (RDF)]
		+	* [http://data.wikipathways.org/current/index Database index files (index)]
		+	* [[Help:FileFormats|Other file formats]]
		+	</font>

---

Current revision

Versioned Releases

Each month we release an updated set of pathways in various data and image formats. These pathways have been reviewed and tagged as approved, and are considered ready for analysis and data overlays.

Current version: 20240410 (10 April 2024)

Vertebrates

• Bos taurus
• Canis familiaris
• Danio rerio
• Equus caballus
• Gallus gallus
• Homo sapiens
• Mus musculus
• Pan troglodytes
• Rattus norvegicus
• Sus scrofa

Invertebrates

• Anopheles gambiae
• Caenorhabditis elegans
• Drosophila melanogaster

Plants

• Arabidopsis thaliana
• Hordeum vulgare
• Oryza sativa
• Populus trichocarpa
• Solanum lycopersicum
• Zea mays

Eukaryotic microorganisms

• Gibberella zeae
• Saccharomyces cerevisiae
• Plasmodium falciparum

Bacteria

• Bacillus subtilis
• E.coli
• Mycobacterium tuberculosis

Programmatic Access

The archive of current and past collections of pathways in various formats at data.wikipathways.org is accessible programmatically as well. Depending on your preferences, there are many ways to identify and download the collection you need.

Note: Our files contain the date of creation in their names so that you can be sure which collection your are using and to avoid overwriting local copies of these files.

1. rWikiPathways is an R package that provides an helper function called downloadPathwayArchive that will retrieve the latest file for you per species and format, e.g.,

   downloadPathwayArchive(organism="Mus musculus”, format=‘gmt’)

2. Filename pattern allows you to infer the filename of the latest collection given the current date. For example, since we always release our archive collections on the 10th of each month, you know that the latest filename is the nearest prior date matching that pattern, e.g., 20180910 would be the current file from Sep 10 to Oct 10, 2018. Caution: this might break if for some unforeseen reason we are unable to produce the archive on schedule.
3. Bash scripting allows you to scrape the currently available filenames and guarantee that you are getting the latest file no matter what the name might be. Here is an example of a one-liner to get a list of all the current GMT files:

   echo "cat //html/body/div/table/tbody/tr/td/a" |  xmllint --html --shell http://data.wikipathways.org/current/gmt/ | grep -o -E ">(.*gmt)<" | sed -E 's/(<|>)//g'

   And here is a version that would return the latest GMT for mouse:

   echo "cat //html/body/div/table/tbody/tr/td/a" |  xmllint --html --shell http://data.wikipathways.org/current/gmt/ | grep -o -E ">.*Mus_musculus.gmt<" | sed -E 's/(<|>)//g'

Other Collections

• Prior monthly releases
• Daily curated releases
• Reactome Human Collection
• Gene lists per pathway (GMT)
• Pathway image files (SVG)
• Linked data files (RDF)
• Database index files (index)
• Other file formats