About the state of KEGG-related packages
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enricoferrero ▴ 660
@enricoferrero-6037
Last seen 3.1 years ago
Switzerland
Dear list, I will soon be doing some pathway enrichment analysis and would like to make the most of what Bioconductor has to offer, but I am a bit confused about the current state of packages relying upon KEGG, such as clusterProfiler, KEGGgraph, keggorthology, KEGGprofile, PathNet and pathview, just to name a few. As you probably know, KEGG has moved to a subscription-based model for accessing his FTP site in 2011 [1]. The following is my understanding of how this has affected Bioconductor, but corrections and clarifications are welcome. The KEGG.db and KEGGSOAP packages are no longer updated and any package that relies on them is also outdated. On the other hand, since KEGG has continued to offer access through its REST API, the KEGGREST package is now the preferred way to pull up to date information out of KEGG. On top of this, some package maintainers may have used their own implementation to access KEGG, so there's no easy way to filter packages with updated or outdated information based on what they depend on. Provided this is broadly correct, my question is: how do I know which KEGG-related packages are reliable in terms of up-to-dateness and which not? Thank you. [1] http://www.kegg.jp/kegg/download/ Best, -- Enrico Ferrero PhD Student Steve Russell Lab - Department of Genetics FlyChip - Cambridge Systems Biology Centre University of Cambridge e.ferrero at gen.cam.ac.uk http://flypress.gen.cam.ac.uk/
KEGGSOAP KEGGgraph keggorthology clusterProfiler KEGGprofile PathNet KEGGSOAP KEGGgraph • 2.3k views
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Luo Weijun ★ 1.6k
@luo-weijun-1783
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Hi Enrico, Pathview downloads the latest KEGG pathway data in real time following REST-like URL mechanism. It was written for pathway analysis and data visualization/integration. Should fits your needs well. The package is available at: http://bioconductor.org/packages/release/bioc/html/pathview.html It was published recently at: http://bioinformatics.oxfordjournals.org/content/29/14/1830.full The package vignette describes workflows/exmaples on microarray data (gene data) and metabolomics data (compound data), although it works for arbitrary others data types mappable to pathways. I also described a Pathview+GAGE workflow on RNA-seq data pathway analysis at: https://stat.ethz.ch/pipermail/bioconductor/2013-July/054021.html HTH. Weijun On 29 July 2013 19:37, Marc Carlson <mcarlson at="" fhcrc.org=""> wrote: > Hi Enrico, > > In general, I think you should assume that almost all KEGG resources are out > of date since KEGG basically cut the world off with a pay wall some time > ago. > > The only exception I know of with any certainty is KEGGREST. And that is > only because KEGG has (at least for now) decided to allow continued access > to their REST API. > > > Marc > > > > > > On 07/28/2013 02:42 PM, Enrico Ferrero wrote: >> >> Dear list, >> >> I will soon be doing some pathway enrichment analysis and would like >> to make the most of what Bioconductor has to offer, but I am a bit >> confused about the current state of packages relying upon KEGG, such >> as clusterProfiler, KEGGgraph, keggorthology, KEGGprofile, PathNet and >> pathview, just to name a few. >> >> As you probably know, KEGG has moved to a subscription-based model for >> accessing his FTP site in 2011 [1]. >> >> The following is my understanding of how this has affected >> Bioconductor, but corrections and clarifications are welcome. >> The KEGG.db and KEGGSOAP packages are no longer updated and any >> package that relies on them is also outdated. On the other hand, since >> KEGG has continued to offer access through its REST API, the KEGGREST >> package is now the preferred way to pull up to date information out of >> KEGG. >> On top of this, some package maintainers may have used their own >> implementation to access KEGG, so there's no easy way to filter >> packages with updated or outdated information based on what they >> depend on. >> >> Provided this is broadly correct, my question is: how do I know which >> KEGG-related packages are reliable in terms of up-to-dateness and >> which not? >> >> Thank you. >> >> [1] http://www.kegg.jp/kegg/download/ >> >> Best, >> >
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Dear Calin and Weijun, Thanks for your suggestions, I will look at both packages. Best, On 30 July 2013 02:42, Luo Weijun <luo_weijun at="" yahoo.com=""> wrote: > Hi Enrico, > Pathview downloads the latest KEGG pathway data in real time following REST-like URL mechanism. It was written for pathway analysis and data visualization/integration. Should fits your needs well. > > The package is available at: http://bioconductor.org/packages/release/bioc/html/pathview.html > It was published recently at: http://bioinformatics.oxfordjournals.org/content/29/14/1830.full > The package vignette describes workflows/exmaples on microarray data (gene data) and metabolomics data (compound data), although it works for arbitrary others data types mappable to pathways. > I also described a Pathview+GAGE workflow on RNA-seq data pathway analysis at: https://stat.ethz.ch/pipermail/bioconductor/2013-July/054021.html > HTH. > Weijun > > > On 29 July 2013 19:37, Marc Carlson <mcarlson at="" fhcrc.org=""> wrote: >> Hi Enrico, >> >> In general, I think you should assume that almost all KEGG resources are out >> of date since KEGG basically cut the world off with a pay wall some time >> ago. >> >> The only exception I know of with any certainty is KEGGREST. And that is >> only because KEGG has (at least for now) decided to allow continued access >> to their REST API. >> >> >> Marc >> >> >> >> >> >> On 07/28/2013 02:42 PM, Enrico Ferrero wrote: >>> >>> Dear list, >>> >>> I will soon be doing some pathway enrichment analysis and would like >>> to make the most of what Bioconductor has to offer, but I am a bit >>> confused about the current state of packages relying upon KEGG, such >>> as clusterProfiler, KEGGgraph, keggorthology, KEGGprofile, PathNet and >>> pathview, just to name a few. >>> >>> As you probably know, KEGG has moved to a subscription-based model for >>> accessing his FTP site in 2011 [1]. >>> >>> The following is my understanding of how this has affected >>> Bioconductor, but corrections and clarifications are welcome. >>> The KEGG.db and KEGGSOAP packages are no longer updated and any >>> package that relies on them is also outdated. On the other hand, since >>> KEGG has continued to offer access through its REST API, the KEGGREST >>> package is now the preferred way to pull up to date information out of >>> KEGG. >>> On top of this, some package maintainers may have used their own >>> implementation to access KEGG, so there's no easy way to filter >>> packages with updated or outdated information based on what they >>> depend on. >>> >>> Provided this is broadly correct, my question is: how do I know which >>> KEGG-related packages are reliable in terms of up-to-dateness and >>> which not? >>> >>> Thank you. >>> >>> [1] http://www.kegg.jp/kegg/download/ >>> >>> Best, >>> >> -- Enrico Ferrero PhD Student Steve Russell Lab - Department of Genetics FlyChip - Cambridge Systems Biology Centre University of Cambridge e.ferrero at gen.cam.ac.uk http://flypress.gen.cam.ac.uk/
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Marc Carlson ★ 7.2k
@marc-carlson-2264
Last seen 8.4 years ago
United States
Hi Enrico, In general, I think you should assume that almost all KEGG resources are out of date since KEGG basically cut the world off with a pay wall some time ago. The only exception I know of with any certainty is KEGGREST. And that is only because KEGG has (at least for now) decided to allow continued access to their REST API. Marc On 07/28/2013 02:42 PM, Enrico Ferrero wrote: > Dear list, > > I will soon be doing some pathway enrichment analysis and would like > to make the most of what Bioconductor has to offer, but I am a bit > confused about the current state of packages relying upon KEGG, such > as clusterProfiler, KEGGgraph, keggorthology, KEGGprofile, PathNet and > pathview, just to name a few. > > As you probably know, KEGG has moved to a subscription-based model for > accessing his FTP site in 2011 [1]. > > The following is my understanding of how this has affected > Bioconductor, but corrections and clarifications are welcome. > The KEGG.db and KEGGSOAP packages are no longer updated and any > package that relies on them is also outdated. On the other hand, since > KEGG has continued to offer access through its REST API, the KEGGREST > package is now the preferred way to pull up to date information out of > KEGG. > On top of this, some package maintainers may have used their own > implementation to access KEGG, so there's no easy way to filter > packages with updated or outdated information based on what they > depend on. > > Provided this is broadly correct, my question is: how do I know which > KEGG-related packages are reliable in terms of up-to-dateness and > which not? > > Thank you. > > [1] http://www.kegg.jp/kegg/download/ > > Best, >
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Hi Marc, Thanks for your answer. So, apparently, the only two packages relying on KEGGREST are PAPi and ROntoTools, an unfortunately limited selection. May I ask, given the current situation, what is the most advisable way to perform pathway enrichment analysis using Bioconductor? Thank you. Best, On 29 July 2013 19:37, Marc Carlson <mcarlson at="" fhcrc.org=""> wrote: > Hi Enrico, > > In general, I think you should assume that almost all KEGG resources are out > of date since KEGG basically cut the world off with a pay wall some time > ago. > > The only exception I know of with any certainty is KEGGREST. And that is > only because KEGG has (at least for now) decided to allow continued access > to their REST API. > > > Marc > > > > > > On 07/28/2013 02:42 PM, Enrico Ferrero wrote: >> >> Dear list, >> >> I will soon be doing some pathway enrichment analysis and would like >> to make the most of what Bioconductor has to offer, but I am a bit >> confused about the current state of packages relying upon KEGG, such >> as clusterProfiler, KEGGgraph, keggorthology, KEGGprofile, PathNet and >> pathview, just to name a few. >> >> As you probably know, KEGG has moved to a subscription-based model for >> accessing his FTP site in 2011 [1]. >> >> The following is my understanding of how this has affected >> Bioconductor, but corrections and clarifications are welcome. >> The KEGG.db and KEGGSOAP packages are no longer updated and any >> package that relies on them is also outdated. On the other hand, since >> KEGG has continued to offer access through its REST API, the KEGGREST >> package is now the preferred way to pull up to date information out of >> KEGG. >> On top of this, some package maintainers may have used their own >> implementation to access KEGG, so there's no easy way to filter >> packages with updated or outdated information based on what they >> depend on. >> >> Provided this is broadly correct, my question is: how do I know which >> KEGG-related packages are reliable in terms of up-to-dateness and >> which not? >> >> Thank you. >> >> [1] http://www.kegg.jp/kegg/download/ >> >> Best, >> > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor -- Enrico Ferrero PhD Student Steve Russell Lab - Department of Genetics FlyChip - Cambridge Systems Biology Centre University of Cambridge e.ferrero at gen.cam.ac.uk http://flypress.gen.cam.ac.uk/
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Enrico, The ROntoTools package uses the KEGGREST to download and parse the KEGG data into graph objects. In addition it performs both an over- representation analysis and a more advanced impact analysis on the given set of pathways. If you want just to use the pathway data (as downloaded and parsed by this package), by using the function keggPathwayGraphs("hsa") or keggPathwayGraphs("hsa", updateCache = TRUE) to re-download the data you can obtain a list of graph objects representing the pathways in KEGG. Regards, Calin On Jul 29, 2013, at 4:31 PM, Enrico Ferrero <enricoferrero86 at="" gmail.com=""> wrote: > Hi Marc, > > Thanks for your answer. > So, apparently, the only two packages relying on KEGGREST are PAPi and > ROntoTools, an unfortunately limited selection. > May I ask, given the current situation, what is the most advisable way > to perform pathway enrichment analysis using Bioconductor? > > Thank you. > Best, > > > On 29 July 2013 19:37, Marc Carlson <mcarlson at="" fhcrc.org=""> wrote: >> Hi Enrico, >> >> In general, I think you should assume that almost all KEGG resources are out >> of date since KEGG basically cut the world off with a pay wall some time >> ago. >> >> The only exception I know of with any certainty is KEGGREST. And that is >> only because KEGG has (at least for now) decided to allow continued access >> to their REST API. >> >> >> Marc >> >> >> >> >> >> On 07/28/2013 02:42 PM, Enrico Ferrero wrote: >>> >>> Dear list, >>> >>> I will soon be doing some pathway enrichment analysis and would like >>> to make the most of what Bioconductor has to offer, but I am a bit >>> confused about the current state of packages relying upon KEGG, such >>> as clusterProfiler, KEGGgraph, keggorthology, KEGGprofile, PathNet and >>> pathview, just to name a few. >>> >>> As you probably know, KEGG has moved to a subscription-based model for >>> accessing his FTP site in 2011 [1]. >>> >>> The following is my understanding of how this has affected >>> Bioconductor, but corrections and clarifications are welcome. >>> The KEGG.db and KEGGSOAP packages are no longer updated and any >>> package that relies on them is also outdated. On the other hand, since >>> KEGG has continued to offer access through its REST API, the KEGGREST >>> package is now the preferred way to pull up to date information out of >>> KEGG. >>> On top of this, some package maintainers may have used their own >>> implementation to access KEGG, so there's no easy way to filter >>> packages with updated or outdated information based on what they >>> depend on. >>> >>> Provided this is broadly correct, my question is: how do I know which >>> KEGG-related packages are reliable in terms of up-to-dateness and >>> which not? >>> >>> Thank you. >>> >>> [1] http://www.kegg.jp/kegg/download/ >>> >>> Best, >>> >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > -- > Enrico Ferrero > PhD Student > Steve Russell Lab - Department of Genetics > FlyChip - Cambridge Systems Biology Centre > University of Cambridge > > e.ferrero at gen.cam.ac.uk > http://flypress.gen.cam.ac.uk/ > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Calin Voichita Ph.D. Candidate Intelligent Systems and Bioinformatics Laboratory (ISBL) Department of Computer Science - Wayne State University Phone: +1(313)577-5070 Fax: +1(313)577-6868 Detroit, MI 48202, USA http://vortex.cs.wayne.edu
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