A Comparison of the Pathway Tools Software with the Reactome Software
AA Comparison of the Pathway Tools Software with theReactome Software
Peter D. KarpBioinformatics Research GroupSRI International, Menlo Park, [email protected] 30, 2020
Abstract
This document compares SRI’s Pathway Tools (PTools) software with the Reactome software. Both soft-ware systems serve the pathway bioinformatics area, including representation and analysis of metabolicpathways and signaling pathways. The comparison covers pathway bioinformatics capabilities, but doesnot cover other major facets of Pathway Tools that are completely absent from the Reactome software:Pathway Tools genome-informatics capabilities, regulatory informatics capabilities, and table-based anal-ysis tools (SmartTables).Our overall findings are as follows. (1) PTools is significantly ahead of Reactome in its basic informa-tion pages. For example, PTools pathway layout algorithms have been developed to an advanced stateover several decades, whereas Reactome pathway layouts are illegible, omit important information, andare created manually and therefore cannot scale to thousands of genomes. (2) PTools is far ahead ofReactome in omics analysis. PTools includes all of the omics-analysis methods that Reactome provides,and includes multiple methods that Reactome lacks. (3) PTools contains a metabolic route search tool(searching for paths through the metabolic network), which Reactome lacks. (4) PTools is significantlyahead of Reactome in inference of metabolic pathways from genome information to create new metabolicdatabases. (5) PTools has an extensive complement of metabolic-modeling tools whereas Reactome hasnone. (6) PTools is more scalable than Reactome, handling 18,000 genomes versus 90 genomes for Re-actome. (7) PTools has a larger user base than Reactome. PTools powers 17 websites versus two forReactome. PTools has been licensed by 10,800 users (Reactome licensed user count is unknown).
This document compares SRI’s Pathway Tools software [3, 4] with the Reactome software [2]. Both soft-ware systems serve the pathway bioinformatics area, including representation and analysis of metabolicpathways and signaling pathways. The comparison covers pathway bioinformatics capabilities, but doesnot cover other major facets of Pathway Tools that are completely absent from the Reactome software:Pathway Tools genome-informatics capabilities, regulatory informatics capabilities, and table-based anal-ysis tools (SmartTables).Pathway Tools (PTools) powers the BioCyc.org website and 16 other pathway websites [5]. TheReactome software powers Reactome.org and plantreactome.gramene.org.This comparison is divided into three sections: 1 a r X i v : . [ q - b i o . M N ] S e p igure 1: Reactome pathway page for serine biosynthesis pathway. The legibility of this figure is quitesimilar when this PDF is viewed at 100% magnification to how the pathway diagram appears in theReactome web page. • Comparison of pathway pages, reaction pages, and metabolite pages • Comparison of pathway-informatics analysis tools • Comparison of metabolic modeling toolsPathway Tools has been shown to scale to 18,000 genomes (biocyc.org). Reactome has been shownto scale to 90 genomes (reactome.org).
The most basic and essential aspect of a pathway database and website is the ability to legibly depictmeaningful pathway diagrams. Reactome fails in this regard: pathway diagrams shown in Reactomepathway pages are not legible (i.e., metabolite names are not readable in these diagrams), even fora small pathway such as serine biosynthesis (see Figure 1 ( https://reactome.org/content/detail/R-CFA-977347 ). Larger pathways are even harder to make out. If the user clicks on the pathwaydiagram in the preceding Reactome page to display the same diagram within the “pathway browser”, thediagram can then be zoomed to a magnification where the metabolite names are legible. However, themetabolite names shown are abbreviations, many of which will not be meaningful to most users. (Mostlikely the abbreviations are being used in an effort to make the pathway diagrams smaller.)Further, Reactome pathway diagrams lack enzyme names, gene names, and EC numbers — all ofwhich are important facets of communicating the pathway. Magnifying this diagram eventually resultsin depiction of metabolite chemical structures, although at this point the diagram must be zoomed somuch that only one reaction from the pathway is visible, and the chemical structures are barely legible(see Figure 2).In contrast, the HumanCyc L-serine biosynthesis pathway produced by Pathway Tools ( https://biocyc.org/HUMAN/NEW-IMAGE?type=PATHWAY&object=SERSYN-PWY ) is easily legible both with andwithout chemical structures (see Figures 3 and 4), and the PTools diagram can be customized to depictany combination of gene names, enzyme names, EC numbers, and chemical structures.2igure 2: Reactome pathway browser, serine biosynthesis pathway, zoomed until chemical structures arevisible. The legibility of this figure is quite similar to that of the Reactome web page.Figure 3: BioCyc serine biosynthesis pathway page generated by Pathway Tools; the legibility of thisfigure is quite similar when this PDF is viewed at 100% magnification to how the pathway diagramappears in the BioCyc web page. 3igure 4: BioCyc serine biosynthesis pathway page, showing chemical structures.Comparisons between Reactome and HumanCyc signaling pathways are similar in terms of legibil-ity. The Reactome pathway for BMP Signaling is illegible ( https://reactome.org/content/detail/R-HSA-201451 ), whereas the HumanCyc pathway for BMP Signaling is easily legible ( https://humancyc.org/HUMAN/NEW-IMAGE?type=PATHWAY&object=PWY66-11 ).Reactome provides two full-metabolic-network diagrams. The “pathway browser” ( https://reactome.org/PathwayBrowser/ ) shows a set of cascading circular diagrams for different pathway categories. How-ever, the diagram essentially conveys no information other than the grouping of pathways in functionalcategories. In contrast, the PTools Cellular Overview diagram ( https://humancyc.org/overviewsWeb/celOv.shtml?orgid=HUMAN ) not only groups related pathways together, it also depicts the reactions andmetabolites within a pathway at high zoom levels; the diagram also supports painting of omics dataonto the pathway diagrams, with animations used to depict multiple time points. This PTools diagramcan also be searched by pathway, gene, enzyme, and metabolite names. The second Reactome networkdiagram, the “Voronoi diagram” [2], is simply a hierarchical listing of all Reactome pathways withoutthe pathway diagrams; it conveys essentially no information, is not searchable, and does not supportnavigation to individual pathway diagrams.Table 1 assesses the capabilities of information pages for pathways, reactions, and metabolites inPTools and Reactome, as well as interactive editors associated with pathways, reactions, and metabolites.An explanation of the rows within Table 1 is as follows. • Pathway Page : Is a metabolic-pathway information page with pathway diagram provided? • Depict Full Metabolite Names : Do pathway diagrams include meaningful metabolite names(as opposed to abbreviations such as “O-P-Ser” or “3POPA”)? • Depict Metabolite Structures : Can pathway diagrams show the chemical structures of metabo-lites? • Depict Enzyme Names : Do pathway diagrams include enzyme names? • Depict EC Numbers : Do pathway diagrams include EC numbers?4igure 5: Reactome BMP Signaling pathway. The legibility of this figure is quite similar when this PDFis viewed at 100% magnification to how the pathway diagram appears in the Reactome web page.
Tool PTools Reactome
Metabolic Pathway Page YES YES– Depict Full Metabolite Names YES no– Depict Metabolite Structures YES illegible– Depict Enzyme Names YES no– Depict EC numbers YES no– Depict Compartment Information YES YES– Depict Enzyme Regulation YES YES– Depict Genetic Regulation YES YES– Automatic Pathway Layout YES no– Paint Omics Data onto Pathway YES YESCustomizable Multi-Pathway Diagram YES no– Paint Omics Data onto Multi-Pathway YES noSignaling Pathway Page YES YESMetabolite Page YES noReaction Page YES no– Reaction Atom Mappings YES noInteractive Metabolic Pathway Editor YES YESInteractive Signaling Pathway Editor YES YESInteractive Reaction Editor YES YESInteractive Metabolite Editor YES noTable 1:
Pathway Page Comparison. • Depict Compartment Information : Do pathway diagrams depict cellular compartments andmembranes? • Depict Enzyme Regulation : Can pathway diagrams show regulation of enzymes by metabolites,to depict information such as feedback inhibition?5igure 6: BioCyc BMP Signaling pathway generated by Pathway Tools. The legibility of this figure isquite similar when this PDF is viewed at 100% magnification to how the pathway diagram appears inthe BioCyc web page. 6
Depict Genetic Regulation : Can pathway diagrams show genetic regulation of enzymes, suchas by transcription factors and attenuation? • Automatic Pathway Layout : Are pathway diagrams generated automatically by the software,thereby avoiding manual drawing, and enabling scalability to thousands of organisms? • Paint Omics Data onto Pathway : Can a user visualize omics data on pathway diagrams? • Customizable Multi-Pathway Diagram : Can users interactively create diagrams consisting ofmultiple interacting metabolic pathways? • Paint Omics Data onto Multi-Pathway : Can a user visualize omics data on multi-pathwaydiagrams? • Signaling Pathway Page : Is a signaling-pathway information page with pathway diagram pro-vided? • Metabolite Page : Does the site provide a metabolite page, showing relevant information such assynonyms, chemical structure, and reactions in which the metabolite occurs? • Reaction Page : Does the site provide a reaction page, showing relevant information such as ECnumbers, reaction equation, and enzymes catalyzing the reaction? • Reaction Atom Mappings : Can the reaction equation be shown with metabolite structures thatdepict the trajectories of atoms from reactants to products? • Interactive Metabolic Pathway Editor : Does the software provide an editor for interactivecreation and modification of metabolic pathways? • Interactive Signaling Pathway Editor : Does the software provide an editor for interactivecreation and modification of signaling pathways? • Interactive Reaction Editor : Does the software provide an editor for interactive creation andmodification of reactions? • Interactive Metabolite Editor : Does the software provide an editor for interactive creation andmodification of metabolites?
Table 2 assesses a number of analysis capabilities within the two software packages. • Full Metabolic Network Diagram : Can the entire metabolic reaction network of an organismbe depicted and explored by an interactive graphical interface? • Zoomable Metabolic Network : Does the metabolic network browser enable real-time semanticzooming of the network? • Paint Omics Data onto Network : Can a user visualize an omics dataset (e.g., gene expression,metabolomics) on the metabolic network diagram? • Animated Omics Data Painting : Can several omics measurements be visualized as an animationon the metabolic network diagram? 7 ool PTools Reactome
Full Metabolic Network Diagram YES YES– Zoomable Metabolic Network YES YES– Paint Omics Data onto Diagram YES no– Animated Omics Data Painting YES no– Metabolic Poster YES noMetabolic Reconstruction YES YESRoute Search Tool YES noGenome-Scale Reactome Comparison YES noGenome-Scale Pathway Comparison YES noTranscriptomics Enrichment Analysis YES YESMetabolomics Enrichment Analysis YES YESMetabolomics Pathway Covering Analysis YES YESTable 2:
Pathway Informatics Tools Comparison. • Metabolic Poster : Can the portal generate a printable wall-sized poster of the organism’smetabolic network? • Metabolic Reconstruction : Starting from a functionally annotated genome, can the softwareinfer the organism’s metabolic reaction network and pathways? Reactome apparently has an al-gorithm for this, but it has never been published. Further, because Reactome does not have areference pathway database that spans all domains of life as does the MetaCyc [1] database usedby PTools for metabolic reconstruction, Reactome cannot accurately predict pathways across alldomains of life as can PTools. • Route Search Tool : Given a starting and an ending metabolite, can the site compute an optimalseries of known reactions (routes) that converts the starting metabolite to the ending metabolite? • Transcriptomics Enrichment Analysis : Can the site compute statistical enrichment of path-ways from transcriptomics data? • Metabolomics Enrichment Analysis : Can the site compute statistical enrichment of pathwaysfrom metabolomics data? • Metabolomics Pathway Covering Analysis : Can the site compute a minimal set of metabolicpathways that cover a set of metabolites from a metabolomics experiment?
Table 3 assesses metabolic-modeling capabilities within the two software packages. • Execute Metabolic Model : Can a user execute a steady-state metabolic flux model using theflux-balance analysis approach? • Gene Knock-Out Analysis : Can a user run flux-balance analysis (FBA) on the metabolic net-work by systematically disabling (knocking-out) various genes, to investigate how knock-outs per-turb the network, and to predict gene essentiality? • Flux-Variability Analysis : Can a user run flux-variability analysis to compute the range of fluxeseach reaction can attain? 8 ool PTools Reactome
Execute Metabolic Model YES no– Gene Knock-Out Analysis YES no– Flux-Variability Analysis YES noModel Organism Communities YES noReaction Gap Filling YES noChokepoint Analysis YES noDead-End Metabolite Analysis YES noBlocked-Reaction Analysis YES noTable 3:
Metabolic Modeling Comparison. • Model Organism Communities : Does the software enable modeling of organism communitiesas well as single organisms? • Reaction Gap Filling : Does the software have a tool for automatically proposing reactions toadd to the model to fill gaps in the metabolic network? • Chokepoint Analysis : Can the site compute chokepoint reactions (possible drug targets) in thefull metabolic reaction network? A chokepoint reaction is a reaction that either uniquely consumesa specific reactant or uniquely produces a specific product in the metabolic network. • Dead-End Metabolite Analysis : Can the portal compute dead-end metabolites in the fullmetabolic reaction network? Dead-end metabolites are those that are either only consumed, oronly produced, by the reactions within a given cellular compartment, including transport reactions. • Blocked-Reaction Analysis : Can the portal compute blocked reactions in the full metabolicreaction network? Blocked reactions cannot carry flux because of dead-end metabolites upstreamor downstream of the reactions.
Our overall findings are as follows. • PTools is significantly ahead of Reactome in its basic information pages. For example, PToolspathway layout algorithms have been developed to an advanced state over several decades, whereasReactome pathway layouts are illegible, omit important information, and are created manually andtherefore cannot scale to thousands of genomes. • PTools includes a full metabolic network diagram that includes real-time semantic zooming and isfar ahead of the comparable tools in Reactome. • PTools is far ahead of Reactome in omics analysis. PTools includes all of the omics-analysis methodsthat Reactome provides, and includes multiple methods that Reactome lacks, such as an OmicsDashboard and depiction of omics data on a zoomable metabolic map diagram. • PTools contains a metabolic route search tool (searching for paths through the metabolic network),which Reactome lacks. • PTools is significantly ahead of Reactome in inference of metabolic pathways from genome infor-mation to create new metabolic databases. 9
PTools has an extensive complement of metabolic-modeling tools whereas Reactome has none. • PTools is more scalable than Reactome, handling 18,000 genomes versus 90 genomes for Reactome. • PTools has a larger user base than Reactome. PTools powers 17 websites versus two for Reactome.PTools has been licensed by 10,800 users (Reactome licensed user count is unknown).If the Reactome data were made available via PTools, the accessibility of those data would be greatlyenhanced through legible pathway diagrams. Further, users could apply a wider variety of analysis toolsand operations to those data, such as for omics data analysis, metabolic route searching, and metabolicmodeling.
References [1] R. Caspi, R. Billington, , I. M. Keseler, A. Kothari, M. Krummenacker, P. E. Midford, W. K. Ong,S. Paley, P. Subhraveti, and P. D. Karp. The MetaCyc database of metabolic pathways and enzymes— a 2019 update.
Nuc Acids Res , 2020. in press.[2] B. Jassal, L. Matthews, G. Viteri, C. Gong, P. Lorente, A. Fabregat, K. Sidiropoulos, J. Cook,M. Gillespie, R. Haw, F. Loney, B. May, M. Milacic, K. Rothfels, C. Sevilla, V. Shamovsky, S. Shorser,T. Varusai, J. Weiser, G. Wu, L. Stein, H. Hermjakob, and P. D’Eustachio. The Reactome pathwayknowledgebase.
Nuc Acids Res , 48(D1):D498–D503, 2020.[3] P. D. Karp, P.E. Midford, R. Billington, A. Kothari, , M. Krummenacker, W.K. Ong, P. Subhraveti,R. Caspi, I.M Keseler, and S. M. Paley. Pathway Tools version 23.0 update: Software for path-way/genome informatics and systems biology.
Brief Bioinform , 2019. in press.[4] P.D. Karp, P.E. Midford, S.M. Paley, M. Krummenacker, R. Billington, A. Kothari, W.K. Ong,P. Subhraveti, I.M. Keseler, and R. Caspi. Pathway Tools version 23.0: Integrated software forpathway/genome informatics and systems biology. arXiv , pages 1–111, 2019. http://arxiv.org/abs/1510.03964v3 .[5] Pathway Tools Based Databases and Websites. https://biocyc.org/otherpgdbs.shtmlhttps://biocyc.org/otherpgdbs.shtml