Download Pathways

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__NOEDITSECTION__ <!-- Turn off section editing -->
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{| align="right"
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Accession
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  | __NOTOC__
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  |}
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=== Versioned Releases ===
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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.
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<font size=4>'''Current version: [http://data.wikipathways.org/20210810/ 20210810 (10 August 2021)]'''</font>
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=== Vertebrates ===
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* '''[http://data.wikipathways.org/20210810/gpml/wikipathways-20210810-gpml-Bos_taurus.zip Bos taurus]'''
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* '''[http://data.wikipathways.org/20210810/gpml/wikipathways-20210810-gpml-Canis_familiaris.zip Canis familiaris]'''
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* '''[http://data.wikipathways.org/20210810/gpml/wikipathways-20210810-gpml-Danio_rerio.zip Danio rerio]'''
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* '''[http://data.wikipathways.org/20210810/gpml/wikipathways-20210810-gpml-Equus_caballus.zip Equus caballus]'''
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* '''[http://data.wikipathways.org/20210810/gpml/wikipathways-20210810-gpml-Gallus_gallus.zip Gallus gallus]'''
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* '''[http://data.wikipathways.org/20210810/gpml/wikipathways-20210810-gpml-Homo_sapiens.zip Homo sapiens]'''
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* '''[http://data.wikipathways.org/20210810/gpml/wikipathways-20210810-gpml-Mus_musculus.zip Mus musculus]'''
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* '''[http://data.wikipathways.org/20210810/gpml/wikipathways-20210810-gpml-Pan_troglodytes.zip Pan troglodytes]'''
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* '''[http://data.wikipathways.org/20210810/gpml/wikipathways-20210810-gpml-Rattus_norvegicus.zip Rattus norvegicus]'''
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* '''[http://data.wikipathways.org/20210810/gpml/wikipathways-20210810-gpml-Sus_scrofa.zip Sus scrofa]'''
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=== Invertebrates ===
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* '''[http://data.wikipathways.org/20210810/gpml/wikipathways-20210810-gpml-Anopheles_gambiae.zip Anopheles gambiae]'''
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* '''[http://data.wikipathways.org/20210810/gpml/wikipathways-20210810-gpml-Caenorhabditis_elegans.zip Caenorhabditis elegans]'''
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* '''[http://data.wikipathways.org/20210810/gpml/wikipathways-20210810-gpml-Drosophila_melanogaster.zip Drosophila melanogaster]'''
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=== Plants ===
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* '''[http://data.wikipathways.org/20210810/gpml/wikipathways-20210810-gpml-Arabidopsis_thaliana.zip Arabidopsis thaliana]'''
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* '''[http://data.wikipathways.org/20210810/gpml/wikipathways-20210810-gpml-Hordeum_vulgare.zip Hordeum vulgare]'''
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* '''[http://data.wikipathways.org/20210810/gpml/wikipathways-20210810-gpml-Oryza_sativa.zip Oryza sativa]'''
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* '''[http://data.wikipathways.org/20210810/gpml/wikipathways-20210810-gpml-Populus_trichocarpa.zip Populus trichocarpa]'''
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* '''[http://data.wikipathways.org/20210810/gpml/wikipathways-20210810-gpml-Solanum_lycopersicum.zip Solanum lycopersicum]'''
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* '''[http://data.wikipathways.org/20210810/gpml/wikipathways-20210810-gpml-Zea_mays.zip Zea mays]'''
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<!-- * '''[http://data.wikipathways.org/20210810/gpml/wikipathways-20210810-gpml-Beta_vulgaris.zip Beta vulgaris]''' -->
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=== Eukaryotic microorganisms ===
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* '''[http://data.wikipathways.org/20210810/gpml/wikipathways-20210810-gpml-Gibberella_zeae.zip Gibberella zeae]'''
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* '''[http://data.wikipathways.org/20210810/gpml/wikipathways-20210810-gpml-Saccharomyces_cerevisiae.zip Saccharomyces cerevisiae]'''
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* '''[http://data.wikipathways.org/20210810/gpml/wikipathways-20210810-gpml-Plasmodium_falciparum.zip Plasmodium falciparum]'''
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=== Bacteria ===
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* '''[http://data.wikipathways.org/20210810/gpml/wikipathways-20210810-gpml-Bacillus_subtilis.zip Bacillus subtilis]'''
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* '''[http://data.wikipathways.org/20210810/gpml/wikipathways-20210810-gpml-Escherichia_coli.zip E.coli]'''
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* '''[http://data.wikipathways.org/20210810/gpml/wikipathways-20210810-gpml-Mycobacterium_tuberculosis.zip Mycobacterium tuberculosis]'''
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== Programmatic Access ==
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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.
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''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.''
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# '''[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>
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# '''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.''
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# '''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>
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== Other Collections ==
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<font size=3>
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* [http://data.wikipathways.org Prior monthly releases]
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* [[Daily_Download|Daily curated releases]]
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* [http://www.wikipathways.org//wpi/batchDownload.php?species=Homo%20sapiens&fileType=gpml&tag=Curation:Reactome_Approved  Reactome Human Collection]
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* [http://data.wikipathways.org/current/gmt Gene lists per pathway (GMT)]
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* [http://data.wikipathways.org/current/svg Pathway image files (SVG)]
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* [http://data.wikipathways.org/current/rdf Linked data files (RDF)]
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* [http://data.wikipathways.org/current/index Database index files (index)]
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* [[Help:FileFormats|Other file formats]]
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</font>
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Revision as of 23:39, 10 August 2021

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Q8VHG0 P28704-2 P26231 Q00560 Q99NH2-3 Q99NH2-5 E9Q557 P26039 Q4PZA2-1 Q4PZA2-2 Q4PZA2-3 Q4PZA2-4 Q06335 Q06335-2 Q9DBE0 Q6ZWQ0-1 O08917 Q99NH2-2 P21619 Q99NH2 Q9R008 O09172 P34152-9 Q80W21 Q9QZ06 Q9Z329-2 Q8C015 P97813 Q62120 Q6PDN3-4 Q9EPK5 Q9EPK5-2 Q61017 P21619-2 Q9D7J9 P16125 P31809-4 P35710-1 P35710-2 P35710-3 P40645-1 P40645-2 Q64435 Q64471 Q9WVM8 P16546-2 P62746 Q9QX60 Q9QX60-2 Q8BW75 P30999-1 Q61982 Q9CRB3 P34152-2 P34152-4 P34152 P34152-3 P61793-1 P61793-2 P48999 Q8K3H0 Q02858 Q61739-1 Q61739-2 P31809-3 Q6PEE3 P84444 P86793 Q8R3P0 O88507 Q80XC3-1 Q80XC3-2 O55033 Q9JK42 P51163 Q8VC52 Q8BWG8-1 Q8BWG8-2 Q9Z0M6-2 P16056 P34152-7 P17563 P34152-5 P34152-6 Q8R3B1 P08228 Q8QZR5 Q7TMS5 Q9WUT3 P30999-2 P30999-3 Q61001 P24270 Q61161 Q8C996 P26618 P03888 P35576 Q8VBX6 Q8VBX6-2 Q8VBX6-4 Q9WV85 P63044 Q62165 Q00915 P47880 P18293 Q61503 P54320 Q00262 Q9WVK4 O54732 O08911 P70236 Q8BFP9 P16546 Q9CX99 Q62172 Q9WUB3 P24472 Q64520 Q8R1H0 Q8R5M8-6 Q8R5M8-7 Q9EQJ9-2 Q61292 P16054 Q64133 P33622 P05480 P34152-8 Q8CG03 P48776 P31324 P10833 Q80SZ7 P11152 P53657-1 Q61469 Q60692 Q9ERL9 Q9Z2D6 Q9Z2D6-2 Q9WVB4 O35683 O54865 Q9WTI7-4 Q02257 O70469 Q9JLY7 Q9WTI7-1 Q8BTF8-1 Q8BTF8-2 Q9WTI7-2 Q6PDN3-1 G5E8Q8 Q9QZ47-1 Q9QZ47-10 Q9QZ47-11 Q9QZ47-12 Q9QZ47-13 Q9QZ47-14 Q9QZ47-2 Q9QZ47-3 Q9QZ47-4 Q9QZ47-5 Q9QZ47-6 Q9QZ47-7 Q9QZ47-8 Q9QZ47-9 Q9QZS0 P05532-1 P05532-2 E9Q4S1 Q9EQJ9-1 Q62523 P09813 O55222 Q61288 P47738 Q9D379 Q9ESL4-2 P0C605-1 P0C605-2 O54967-1 O54967-2 O54967-3 Q5SWW4 P35969 P52843 Q9WTQ5-2 Q62190 Q62270 P57722-1 P57722-2 Q9WTQ5-1 P51830 Q9WVC3 P12367 Q61087 Q91WR5 P30115 P34928 P70345 P70345-2 Q62470-2 Q60751 P21278 Q9R069 Q62417 Q62417-3 Q62417-2 Q62417-4 Q62417-5 Q62417-6 Q62470 Q8R5M8 Q8R5M8-2 Q8R5M8-3 Q8R5M8-4 O08967 Q9QZR9 Q62470-3 Q05020 Q99JY8 Q6Q477 Q6Q477-2 P19137 Q64518 Q64518-2 Q80T19 Q64518-3 Q91ZP3-1 Q91ZP3-2 Q61371 P24549 Q61851-1 P16092 P16092-2 P16092-3 P16092-4 P16092-5 P16092-6 P21803-1 P21803-2 Q8R5M8-5 O08553 P50285 Q05895 Q9R1W5 Q61879 P21279 Q9QYY0 Q80TS3-6 P43142 Q80TS3 Q80TS3-2 Q80TS3-3 Q80TS3-5 Q62417-7 Q61092 Q6PIE5 E9Q816 P70658 P70658-2 P62071 Q6ZWQ0-3 P20444 O08989 P18762 P97447-1 O88393 Q62101 P15626 Q64669 Q64727 P33267 Q9WTI7-3 P48193-2 P61953 Q61012 Q02956 P27090 Q61789 Q9WUP0 P04202 O55234 Q04736 P49813 P48193 Q61789-2 P21107 P36423 Q8BZF8 Q9D6P8 P04370-2 Q9DCZ1 P09242 Q8BH64 O54931-2 O54931-1 O54931-5 O54931-4 P24815 P06837 Q9Z0X4 Q9CQ19 P10637-1 P49817 P09470 P09470-2 Q9QUG9 Q9QUG9-2 O35469 P26149 Q8K2I3 P12791 Q9JI60 Q9ES46 P49817-2 P51637 Q9D6F9 O35608 P04370-1 P10637-5 P20722 P10637-6 Q9QUG9-3 P39876 P10637-2 P10637-3 P10637-4 Q64264 Q6A152 Q8BHL4 P10649 Q80TS3-4 Q03350 O54942 O09164 Q06318 Q08857 Q80XA6 Q64462 D3YVF0 P12388 P35441 O54931-3 P97431 Q99PG4 Q9WV92-4 Q9WV92-6 Q9WV92-7 Q9WV92-8 Q8CIZ8 P04370-11 P04370-13 P04370-14 P04370-8 Q61146 P04370-6 O88783 P40936 P32037 P61148 P18872 P18872-2 P15306 Q8BHE5 A2ARA8-1 P00848 A2ARA8-2 Q8CIZ8-2 P43252 O55042 O55042-2 Q01102 P31428 P52800 P04370-10 P04370-4 P04370-5 P04370-7 P04370-9 P19091 Q8VCC1 P39655 O54890 Q61391 Q9QUM0 Q9Z126 O70443 P48302

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