Question: How Do Pathway Databases Compare?
16
gravatar for Shigeta
9.9 years ago by
Shigeta460
Berkeley, CA
Shigeta460 wrote:

Is KEGG still the reigning champion? Any comparisions of MetaCyc? It looks fairly complete for Ecoli at least.

pathway database subjective • 14k views
ADD COMMENTlink modified 9.5 years ago by Diana840 • written 9.9 years ago by Shigeta460

I tried using SEED for a pipeline and got frustrated with inconsistencies in different database files: subsystems, subsystems2role, etc.

ADD REPLYlink written 9.9 years ago by Science_Robot1.1k

Thanks for the input - i am being lazy as there are so many DBs and so many references. Feel like I can start with these answers. Ideally some combination of accuracy and coverage is best. After 10 years working in bioinformatics, I find the 'subjective' tag applies in way more cases than I had expected.

ADD REPLYlink written 9.9 years ago by Shigeta460
26
gravatar for Giovanni M Dall'Olio
9.9 years ago by
London, UK
Giovanni M Dall'Olio27k wrote:

I have been doing some annotation work for Reactome. Compared with KEGG, Reactome stores a lot of information more:

  • the GeneOntology Ids for the Metabolic Process of each reaction, plus the GO for the localization of each component of a reaction
  • a text to describe what is happening in each reaction, plus a reference
  • the names of the author of each annotated pathway
  • the SBML and BioPax version of the pathway

The problem with KEGG is, in my opinion, that they do not put neither references nor description for the reactions. A certain pathway may be annotated in a way and if there is something unclear about a reaction, there is no way to find the references that have been used to justify it, and it is difficult to contact the original authors of the pathway. The entries in KEGG are 'authored by experts in the field' but it is impossible to know who these experts are, neither why they made certain choices.

Moreover, KEGG has a somewhat artificial distinction between metabolic and protein-protein interaction pathways; in Reactome, you can use the GO ids to distinguish the types of reactions, without splitting the reactome artificially.

Finally, there are other databases for pathways:

ADD COMMENTlink modified 5.6 years ago • written 9.9 years ago by Giovanni M Dall'Olio27k

thanks i'll take a look~

ADD REPLYlink written 9.9 years ago by Shigeta460

The UniProt pathways are maintained via http://www.grenoble.prabi.fr/obiwarehouse/unipathway

ADD REPLYlink written 8.7 years ago by Jerven650
10
gravatar for Neilfws
9.9 years ago by
Neilfws48k
Sydney, Australia
Neilfws48k wrote:

The creators of MetaCyc have compared it with other pathway databases:

I don't know about independent comparisons, but searching PubMed for "metabolic pathway databases" throws up about 80 review articles.

In general, it's difficult to compare different resources objectively. They often have slightly different aims, design philosophies and of course, data access tools and formats. Most people choose one based on "look and feel" and how well it suits their particular project needs.

ADD COMMENTlink written 9.9 years ago by Neilfws48k

i agree the emphasis on metabolic pathways is a little to confining, but good point

ADD REPLYlink written 9.9 years ago by Shigeta460
7
gravatar for User 4910
9.9 years ago by
User 491070
User 491070 wrote:

I am in total agreement with Giovanni, KEGG is definitely loosing their edge, for several reason,

  • Strict licensing policy of KEGG. Contrary to that Reactome is released under CC so it gives you a lot freedom especially if you are a commercial user.
  • People use KEGG due to their maps but it seems their approach lacks interoperability with other tools and formats. In terms of interoperability, Reactome is ahead of others, they have support for BioPAX, SBML and latest release includes SBGN.

As matter of fact none of pathways are as comprehensive as they claim, see following reports

Pathway analysis software: Annotation errors and solutions

Consistency, comprehensiveness, and compatibility of pathway databases.

ADD COMMENTlink modified 9.9 years ago by Giovanni M Dall'Olio27k • written 9.9 years ago by User 491070

interesting articles. I fixed a typo in the second link.

ADD REPLYlink written 9.9 years ago by Giovanni M Dall'Olio27k

i agree about kegg - very little of the data is open enough.

ADD REPLYlink written 9.9 years ago by Shigeta460
6
gravatar for Alastair Kerr
9.9 years ago by
Alastair Kerr5.2k
Manchester/UK/Cancer Biomarker Centre at CRUK-MI
Alastair Kerr5.2k wrote:

EcoCyc (and Metacyc) seems to have the philosophy of 'know as much about a pathway as possible' where as KEGG seems to have a 'know as many pathways as possible' approach. Typically I would always look in EcoCyc first as my gold standard before going to another database: but perhaps I am biased as I used to work for a group that curated EcoCyc.

I guess it just depends the question you are asking, the species and the area you are working on as well as your definition of 'pathway' (e.g. is a protein-protein interaction a part of a pathway?)

For example biogrid is excellent for some of the pathways that they focus on, especially if you want to know any possible connections and are willing to look at the evidence for each part of the pathway/interaction. e.g. they have put a lot of work into arabidopsis and are currently working on the ubiquitin 'pathway'.

Also as a previous post mentioned, reactome is worth looking at: a new version has just been released.

ADD COMMENTlink modified 9.9 years ago • written 9.9 years ago by Alastair Kerr5.2k
6
gravatar for Miranda
8.7 years ago by
Miranda330
Netherlands
Miranda330 wrote:

I compared five pathway databases that describe the human metabolic network and the differences are quite large. For example, only 510 of the 3858 genes they have combined could be found in all five databases. For further detail see: http://www.biomedcentral.com/1752-0509/5/165.

There is no easy answer to which one is "best", as this really depends also on the analyses you are using it for.

ADD COMMENTlink written 8.7 years ago by Miranda330
1

That's a nice paper. Thanks for posting the link.

ADD REPLYlink written 8.7 years ago by Alex Paciorkowski3.4k
3
gravatar for Khader Shameer
9.9 years ago by
Manhattan, NY
Khader Shameer18k wrote:

Pathway databases are curated by companies or different research groups and these resource have lot inconsistencies. I have noticed that the different databases have different number of genes in same pathway. Different databases use modified/specific pathway names etc. So a direct comparison of pathway database will be difficult.

I would recommend you to be motivated by what is your biological question, select appropriate data resources or take union or intersection of different resources. While selecting resources do consider the curation strategy and experimental method used to associate the genes with pathway.

Inaddition to the resources listed here: I would recommend you to take a look at WikiPathways and Pathway Commons, which provide a unified resource to access different pathway databases.

ADD COMMENTlink modified 9.9 years ago • written 9.9 years ago by Khader Shameer18k
2
gravatar for Larry_Parnell
9.9 years ago by
Larry_Parnell16k
Boston, MA USA
Larry_Parnell16k wrote:

Look to see what the top research groups in your field are using - check their publications or ask them directly by email/telephone/at conference. In this manner, you will be using the "accepted" database. If you still consider another pathway database superior, then use both and offer a comparison - doing such will add to the conversation about comparing the two.

ADD COMMENTlink written 9.9 years ago by Larry_Parnell16k
2
gravatar for Suk211
9.9 years ago by
Suk2111.0k
state college
Suk2111.0k wrote:

I have never used BRENDA , but have heard it's more comprehensive compared to other pathway databases.

ADD COMMENTlink written 9.9 years ago by Suk2111.0k
1
gravatar for Jdnavarro
9.9 years ago by
Jdnavarro410
Sevilla, Spain
Jdnavarro410 wrote:

If you are looking for cancer and immune pathways you might want to check http://netpath.org. They pathways they have are quite comprenhensive and can be downloaded in BioPax format.

ADD COMMENTlink written 9.9 years ago by Jdnavarro410
0
gravatar for Diana
8.5 years ago by
Diana840
Germany
Diana840 wrote:

I work for ProteinLounge that has a commercial database of biological pathways(http://www.proteinlounge.com/pathways/). The graphics make it easier to visualize than other databases like say KEGG. As others have said, each pathway database has their own look and feel. However, if someone wants a database that is more visually eye catching than the ProteinLounge pathway database is definitely one that a user should look into.

ADD COMMENTlink written 8.5 years ago by Diana840
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