Which Are All The Databases For Annotations Of Biological Pathways?

Question

[Giovanni M Dall'Olio]

I know some public databases that offer annotations on pathways: for example, KEGG/Pathways or the Reactome.

Do you know other resources apart from these two? Can you recommend any specific one?

Answer 1

[Pierre Lindenbaum]

In my delicious bookmarks:

• http://www.ncbi.nlm.nih.gov/biosystems
• http://www.biocarta.com/genes/index.asp
• http://biocyc.org/
• http://www.wikipathways.org/index.php/WikiPathways

Answer 2

[Andrew Su]

http://www.pathwaycommons.org and of course the commercial players Ingenuity and GeneGo...

[Mndoci]

For what it's worth the commercial DB's are pretty darn good and if you can spend the money, worth looking at

Answer 3

[Khader Shameer]

I have used KEGG, PID and Panther. You may also check PathGuide: Pathguide contains information about 318 biological pathway resources.

[Hanif Khalak]

PathGuide is amazingly useful, especially with its "free/$/unavailable" designation!

Answer 4

[Fred Fleche]

http://pid.nci.nih.gov/index.shtml

Personally I like KEGG Pathways because they provide an XML file related to each graphical representation of the pathway. It gives you the location in x,y coordinates of all the items that are in the pathway. So, with some Ajax and SVG you can easily draw interactive pathways and higlight proteins that match different kind of criteria (e.g. : In this pathway, what are the kinases, Proteases, mutated Proteins or Proteins tested by Western Blot in a given cell lines etc.).

Please find below a screen shot of such a generated SVG file.

It seems that Wikipathways also provide such XML files with each pathway.

[Giovanni M Dall'Olio]

Where do you get the XML files from? do you mean the KGMLs?

[Fred Fleche]

@giovanni : Yes the KGMLs files are XML files

[Fred Fleche]

@giovanni : Yes the KGMLs files are the XML files I was refering to.

[Chris Evelo]

WikiPathways pathways are im GPML (GenMAPP pathway markup languauge) which is XML based,