Training Example: HumanCyc – Review the Data, Give Your Score & Compare to the Real AI Evaluation

[IMG: HumanCyc]

[H3] Heme, Not Just the Red Pigment in Blood.

[H3] Heme, an iron-containing porphyrin, functions as a prosthetic
group in numerous proteins. These range from
components of the electron transport chain to many enzymes.
No wonder the biosynthesis of heme is highly conserved in evolution!

Learn More

[IMG: Scanning Electron Microscope Image of Blood Cells]
Scanning Electron Microscope Image of Blood Cells, put in the public domain by NCI/Donald BlissBruce Wetzel and Harry Schaefer.

[H3] Navigate Metabolic Map for Pathways

[H3] The Cellular Overview enables you to
browse through a zoomable metabolic map diagram that
displays pathways according to groups based on biological
function, or classes of metabolites
produced/consumed.

Learn More

[IMG: a portion of a Cellular Overview diagram,
showing several pathway classes]
Cellular overview image generated by Pathway Tools

[H3] Important Mammalian Pathways: The Urea Cycle

[H3]
The urea cycle is responsible for mediating excretion of nitrogenous
waste. It was the first metabolic pathway to be discovered, five years
before the discovery of the TCA cycle. The cycle occurs across both the
cytosol and the mitchondrion.
Learn More

[IMG: colorized electron micrograph of mitochondria in
a mammalian lung cell]
colorized selection from Mitochondria, mammalian lung - TEMput in the Public Domain by author, Louisa Howard.

[H3] RouteSearch: Search for Paths through the Metabolic Network

[H3] Search for lowest-cost paths through the metabolic network of the selected organism. Or, design lowest-cost pathways to novel compounds by adding reactions from MetaCyc.

Learn More

[IMG: a schematic showing 3 hypothetical
routes from one compound to another, one
that is very long, one that is short but
most of the atoms from the starting compound
do not end up in the target compound, and
the best route, which is intermediate in
length but conserves the atoms in the
starting compound.]

.

[H3] A Pathway Linked to Central Nervous System Disorders

[H3] The GABA shunt forms a closed loop in the CNS for conserving the supply
of the excitatory neurotransmitter GABA. One of the enzymes of this
pathway, 4-aminobutyrate aminotransferase is a target for the
anti-epileptic drug vigabatrin.

Learn More

[IMG: Brain MRI]
selection from Brain MRI Source: Dr. Leon Kaufman. UCSF.

[H3] Metabolomics Data Analysis

[H3] Multiple tools are available in this website for metabolomics data analysis.

Learn More

[IMG: Enrichment dialog displayed over SmartTable]
SmartTable display generated by Pathway Tools.

[H3] The Truth about the Thanksgiving Turkey...

[H3] Of the 20 amino acids, at least 9 are essential. Essential L-tryptophan is required for serotonin,
melatonin and niacin synthesis. Its requirement for NAD biosynthesis was
discovered when humans stricken with pellagra
recovered after the addition of tryptophan or niacin to their diets.
Learn More

[IMG: photo of a roast turkey]
Some rights reserved by QUOI Media.

[H3] Gene Expression Data Analysis

[H3] Multiple tools are available in this website for analysis of gene expression data.

Learn More

[IMG: a portion of a cellular overview diagram,
overlaid with a gene expression time series
dataset. Detail popups are shown for three
reactions in three different styles: a bar
chart, a heatmap, and a line graph.]
Cellular Overview Omics Viewer image generated by Pathway Tools.

[H1] HumanCyc: Encyclopedia of Human Genes and Metabolism

HumanCyc provides an encyclopedic reference on human metabolic pathways, the human genome, and human metabolites.

HumanCyc is part of the larger BioCyc collection of thousands of Pathway/Genome Databases for sequenced genomes. Click the "Change Current Database" button above to explore the available databases.
For more information on HumanCyc, see our article
"Computational prediction of human metabolic pathways from the complete human genome" in Genome Biology.
User Guide
Try Free

Request Free Classroom Use

[H2] What people are saying...

"BsubCyc is a tool of the utmost value."
[IMG: Penn State]
Paul BabitzkeProf. of Biochemistry& Molecular Biology

"My lab uses these resources on a daily basis."
[IMG: University of Wisconsin]
Patricia Kiley,Professor and Chair,Dep't. of Biomolecular Chemistry

"We rely on BioCyc's Gene Pages and Overview Diagrams almost daily."
[IMG: University of Minnesota]
Arkady KhodurskyAssoc. Prof. Biochemistry

"We use BioCyc and MetaCyc extensively to investigate the metabolic and regulatory processes of organisms we study."
[IMG: Pacific Northwest National Lab]
William Cannon, Team LeadComputational Biology

"BioCyc is the go-to resource of knowledge and tools for Ginkgo scientists."
[IMG: Ginkgo Bioworks]

"BioCyc is a tremendous resource for pathway analysis in metabolomics."
[IMG: University of Georgia]
Art Edison, Dept of Genetics

"We make extensive use of the BioCyc full metabolic network diagram for omics data analysis."
[IMG: Great Lakes Bioenergy]
Timothy J. Donohue, Director

"I have not found another database that has a better interface than BioCyc."
[IMG: University of Michigan]
Gary B. Huffnagle, ProfessorMicrobiology and Immunology
See more BioCyc testimonials

[H2] Learning Library

[H3] Tutorial Videos

Tutorial #1: Introduction to BioCyc

Quick Introduction to BioCyc (4:30)
Searching in BioCyc (17:00)
Genes (15:00)
Genome Browser (11:45)
Pathways (13:19)
Reactions (3:37)
Compounds (6:42)

Tutorial #2: Introduction to SmartTables
The following Tutorial will guide you through SmartTables, which enable you
to create, upload, share, and analyze sets of genes, metabolites, pathways, and sequence sites.
The Tutorial is broken up into parts, ranging from basic operations to more advanced uses such
as gene expression analysis and metabolomics.
SmartTables Overview (4:30)
SmartTables Basics (12:43)
SmartTables Transformations (8:08)
SmartTables Import and Export (9:00)
SmartTables Gene Expression Analysis (7:40)
Metabolomics Analysis with SmartTables (6:45)

Tutorial #3: Zoomable Metabolic Map, Comparative Tools, Regulatory Network
This tutorial introduces users to many of the advanced tools available on the BioCyc.org website for navigating cellular networks, analyzing large-scale datasets, and comparing organisms.
The Cellular Overview: Navigating metabolic networks (17:15)
Comparative Genomics (21:06)
Ortholog Viewing (10:02)
The Regulatory Overview -- exploring transcriptional regulatory networks (15:21)

Tutorial #4: Omics Data Analysis
This tutorial will show you how to use BioCyc's tools for omics data analysis, including the cellular omics viewer, the omics dashboard, and other tools.
Transcriptomics Analysis Tools [brief tour (2:40)
Metabolomics Analysis Tools (3:26) [click here for a detailed tutorial]
Omics Dashboard (16:35)
Omics Dashboard Part (24:29)

Tutorial #5: Pathway Collages
Pathway collages are multi-pathway diagrams that you can customize
by, for example, overlaying omics data, altering the relative
positions of pathways, and modifying connections among pathways.
Learn how to generate, customize and export
high-quality pathway-collage diagrams showing collections of user-specified pathways.
Pathway Collages (22:39)

Tutorial #6: Creating a Pathway/Genome Database
Learn the entire process of building a BioCyc-like Pathway/Genome Database (PGDB)
for an organism with a sequenced and annotated
genome. Build a PGDB for your own lab or for the whole scientific community.
Part 1A: Introduction to Database Building and Pathologic (14:04)
Part 1B: Building a Database: Detailed Pathologic Example (23:53)
Part 2A: General Editing Strategies (8:00)
Part 2B: Creating and Editing Reactions and Compounds (17:32)
Part 2C: Updating Proteins, Citations, GO Terms, and Enzymatic Reactions (26:10)
Part 2D: Making and Editing Pathways (9:42)

Tutorial #7: Using the Structured Advanced Query Page
An introduction to the Structured Advanced Query Page, which allows
complex queries and queries across one or more databases in the
BioCyc collection. You'll learn about:The basic steps of setting up an advanced query;
Four examples of increasingly complex queries, including how to query across multiple databases;
Where to learn more about the structure of BioCyc databases.
Structured Advanced Query Page Quick Introduction (6:27)
Structured Advanced Query Page Full Tutorial (42:15)

Not FoundThe server doesn't know how to respond to http://humancyc.org/%5BORGID%5D/select-gen-el/. Please make sure you have the correct URL.Host: biocyc18Report Errors or Provide Feedback
Page generated by Pathway Tools version 29.5 (software by SRI International) on Sat Jun 20, 2026, BIOCYC18.EcoCyc version 29.6.

[H1] BioCyc and Pathway Tools Publications
If you use BioCyc databases or the Pathway Tools software in
your research, we ask that you cite relevant publications from the
following list.
Like to learn more? View one or more BioCyc
Web seminars.
[H2] Publications on the Full BioCyc Database Collection
[BioCyc19]
Karp, P.D., et al.,
The BioCyc collection of microbial genomes and metabolic pathways
Briefings in Bioinformatics (2019).
[H2] Publications on the EcoCyc Database
[EcoCyc25]
Karp, P.D., Paley, S., Caspi, R., Kothari, A., Krummenacker, M., Midford, P., Moore, L.R., Subhraveti, P., Gama-Castro, S., Tierrafria, V., Paloma, L.,
Muñiz-Rascado, L., Bonavides-Martinez, C., Santos-Zavaleta, A., Mackie, A., Sun, G., Ahn-Horst, T.A., Choi, H., Covert, M.W., Collado-Vides, J.
and Paulsen, I.,
The EcoCyc database (2025)
EcoSal Plus doi:10.1128/ecosalplus.ESP-0019-2024 PMID:40304522
[EcoCyc24]
Moore, L.R.,Caspi, R., Boyd, D., Berkem, M., Mackie, A., Paley, S., Karp, P.D.
Revisiting the y-ome of Escherichia coli
Nucleic Acids Research doi::10.1093/nar/gkae857 (2024)
[EcoCyc21]
Keseler, I.M., Gama-Castro, S., Mackie, A., Billington, R., Billington, R., Caspi, R., Kothari, A., Krummenacker, M., Midford, P., Muñiz-Rascado, L., Ong, W., Paley, S., Santos-Zavaleta, A., Subhraveti, P., Tierrafria, V., Wolfe, A., Collado-Vides, J., Paulsen, I., and Karp, P.D.
The EcoCyc database in 2021
Front Microbiol 2021; 12: 711077.
See also: The EcoCyc
publications page.
[H2] Publications on the MetaCyc Database
[MetaCyc20]
R.Caspi, R.Billington, I.M. Keseler, A.Kothari, M.Krummenacker, P.E.Midford, W.K. Ong, S.Paley, P.Subhraveti, P.D. Karp
The MetaCyc database of metabolic pathways and enzymes - a 2019 update
Nucleic Acids Res48(D1):D445-D453.doi: 10.1093/nar/gkz862.(2020)
[MetaCyc13]
Caspi R., Dreher K., and Karp P.D.
The challenge of constructing, classifying, and representing metabolic pathways.
FEMS Microbiol Lett. doi: 10.1111/1574-6968.12194. (2013)
[MetaCyc11]
Karp P.D., and Caspi R.,
A survey of metabolic databases emphasizing the MetaCyc family
Archives of Toxicology 85:1015-33 (2011)
[H2] Publications on the HumanCyc Database
[HumanCyc04] P.Romero., J.Wagg., M.L.Green., D.Kaiser., M.Krummenacker., and P.D.KarpComputational
prediction of human metabolic pathways from the complete human
genome,Genome Biology 6:R2 R2.1-17 (2004)
[H2] Publications on the CyanoCyc Portal
[CyanoCyc04] Moore, L.R., Caspi, R., Campbell, D.A., Casey, J.R., Crevecoeur, S., Lea-Smith, D.J., Long, B., Omar, N.M., Paley, S.M., Schmelling, N.M., Torrado, A., Zehr, J.P., and P.D.KarpCyanoCyc cyanobacterial web portal,Front. Microbiol.,doi: 10.3389/fmicb.2024.1340413 (2024)
[H2] Publications on the Pathway Tools Software Behind BioCyc
Latest Comprehensive Description of Pathway Tools:
[PTools24]P. D. Karp, S.M. Paley, M. Krummenacker, A. Kothari, P.E. Midford, P. Subhraveti, A. Swart, L. Moore, and R. Caspi.
Pathway Tools version 28.0: Integrated software for Pathway/Genome informatics and Systems Biology, arXiv:1510.03964:1–107, 2024. doi: 10.48550/arXiv.1510.03964.
[PTools19Survey] Karp, P.D. and Midford, P.E. and Paley, S.M. and Krummenacker, M. and Billington, R. and
Kothari, A. and Ong, W.K. and Subhraveti, P. and Keseler, I.M. and Caspi, R.,
Pathway Tools version 23.0: Integrated Software for Pathway/Genome Informatics and Systems Biology,
arXiv (2020).
Overviews of Pathway Tools:
[PTools19] Karp P.D., Midford, P.E., Billington, R., Kothari A., Krummenacker M., Latendresse, M., Ong, W.K., Subhraveti P., Caspi R., Fulcher C.A., Keseler I.M., Paley S.M.
Pathway Tools version 23.0 update: software for pathway/genome informatics and systems biologyBriefings in
Bioinformatics doi: 10.1093/bib/bbz104. (2019)
[PTools15] Karp P.D., Latendresse M., Paley S.M., Krummenacker M., Ong Q., Billington R., Kothari A., Weaver D., Lee T., Subhraveti P., Spaulding A., Fulcher C.A., Keseler I.M., Caspi R.
Pathway
Tools version 19.0: Integrated Software for Pathway/Genome
Informatics and Systems BiologyBriefings in
Bioinformatics doi: 10.1093/bib/bbv079. (2015)
[PTools10] P.D.Karp., S.M.Paley., M. Krummenacker. et al
Pathway
Tools version 13.0: Integrated Software for Pathway/Genome
Informatics and Systems BiologyBriefings in
Bioinformatics 11:40-79 (2010)
Genome Browser:
[PTools24]
Herson, J. , Krummenacker, M. , Spaulding, A. , O’Maille, P. and Karp,P.D.The Genome Explorer genome browser,mSystems doi:10.1128/msystems.00267-24 (2024)
Comparative Genome Dashboard and Omics Dashboard:
[PTools24]
Paley Suzanne , Caspi Ron , O'Maille Paul , Karp Peter D., .The Comparative Genome DashboardFrontiers in Microbiology. doi:10.3389/fmicb.2024.1447632 (2024)
[PTools24]
Paley Suzanne , Karp Peter D., .The Omics Dashboard for Interactive Exploration of Metabolomics and Multi-Omics DataMetabolites. doi:10.3390/metabo14010065 (2024)
Transcriptomics Data Analysis:
[PTools17]
Austin Swart, Ron Caspi, Suzanne Paley and P.D. Karp.Visual analysis of multi-omics data.Frontiers in bioinformatics
doi: 10.3389/fbinf.2024.1395981 (2024).
[PTools17]
Suzanne Paley, Karen Parker, Aaron Spaulding, Jean-Francois Tomb, Paul O'Maille, and Peter Karp.The Omics Dashboard for interactive exploration of gene-expression data,Nucleic Acids Research 45:12113-24 doi:10.1093/nar/gkx910 (2017)
[PTools06] S.M. Paley and P.D. Karp.The
Pathway Tools Cellular Overview Diagram and Omics Viewer,Nucleic
Acids Research 34:3771-8 (2006)
Metabolomics Data Analysis:
[PTools15] P.D. Karp., Billington. R., Holland. T.A., Kothari. A., Krummenacker. M., Weaver. D., M. Latendresse., Paley. S. Computational Metabolomics Operations at BioCyc.org,DATABASE - Metabolites — Open Access Metabolism & Metabolomics Journal , doi: 10.3390/metabo5020291, (2015)
SmartTables(Groups):[PTools13]
Mike Travers., S.M Paley., J.Shrager., T.A Holland., and Peter KarpGroups:knowledge spreadsheets for symbolic biocomputingDatabase, doi:10.1093/database/bat061 (2013)
Flux Balance Analysis (FBA) and Multiple Gap-Filling:
[PTools22] M. Latendresse, W.K. Ong, P.D. KarpMetabolic Modeling with MetaFluxMethods Mol Biol doi: 10.1007/978-1-0716-1585-0_12 (2022)
[PTools20] W.K. Ong, P.E. Midford, P.D. KarpTaxonomic weighting improves the accuracy of a gap-filling algorithm for metabolic modelsBioinformatics36(6):1823-1830 doi: 10.1093/bioinformatics/btz813 (2020)
[PTool18]P.D. Karp, D. Weaver, M.LatendresseHow accurate is automated gap filling of metabolic modelsBMC Syst Biol12(1):73 doi: 10.1186/s12918-018-0593-7 (2018)
[PTools14] Mario Latendresse,
Efficiently Gap-Filling Reaction Networks,
BMC Bioinformatics, 15:225, doi:10.1186/1471-2105-15-225, (June 2014)
[PTools12]
Mario Latendresse, Markus Krummenacker, Miles Trupp, and Peter KarpConstruction and Completion of Flux-Balance Models from Pathway DatabasesBioinformatics, doi: 10.1093/bioinformatics/btr681, (2012)
Metabolic and Regulatory Network
Visualization:
[PTools21]
Suzanne Paley and Peter
D. KarpThe
BioCyc Metabolic Network Explorer,BMC Bioinformatics 22:208, (2021)
[PTools21]
S. Paley, R. Billington, J. Herson, M. Krummenacker and
P. D. KarpPathway
Tools Visualization of Organism-Scale Metabolic Networks,Metabolites 11:64, (2021)
[PTools11]
Suzanne M Paley, Mario Latendresse and Peter D. KarpRegulatory network operations in the Pathway Tools software,BMC Bioinformatics 13:243, (2012)
[PTools11]Mario Latendresse and Peter D. KarpWeb-based metabolic network visualization with a zooming user interface,BMC Bioinformatics 12:176, (2011)
Metabolic Route Search:
[PTools19] M. Krummenacker, M. Latendresse, P.D. Karp
Metabolic route computation in organism communities Microbiome7(1):89. doi: 10.1186/s40168-019-0706-6. (2019)
[PTools14] M. Latendresse, M.Krummenacker, P.D. Karp
Optimal metabolic route search based on atom mappings Bioinformatics30(14) doi: 10.1093/bioinformatics/btu150.(2014)Atom Mapping:[PTools12]
Mario Latendresse, Jeremiah P. Malerich, Mike Travers, and Peter D. KarpAccurate Atom-Mapping Computation for Biochemical ReactionsDATABASE - The Journal of Chemical Information and Modelling(ACS)doi:10.1021/ci3002217, (2012)
Biological Database Querying:[PTools10b]
Mario Latendresse and Peter D. KarpAn advanced web query interface for biological databasesDATABASE - The Journal of Biological Databases and Curation doi: 10.1093/database/baq006, (2010)
Pathway Tools APIs:[PTools05]
M. Krummenacker., S. Paley., L. Mueller., T. Yan., and P.D.
Karp.Querying
and Computing with BioCyc Databases,Bioinformatics
21:3454-5 (2005)
Pathway
Drawing Algorithms:
[PTools16] S.Paley, P.E.O'Maille, D.Weaver and P.D. Karp
Pathway collages: personalized multi-pathway diagrams BMC Bioinformatics17(1):529 doi: 10.1186/s12859-016-1382-1.(2016)
The
Pathway Tools Cellular Overview Diagram and Omics Viewer,Nucleic
Acids Research 34:3771-8 2006. [PTools94] P.D. Karp and S.M.
Paley
Automated drawing of metabolic pathways [PDF]
[PS]Proceedings
of the Third International Conference on Bioinformatics and Genome
Research, pp225-38 (1994)
Pathway Prediction/Metabolic Reconstruction:
[PTools14]N.W. Hanson, K.M. Konwar, A.K. Hawley, T. Altman, P.D. Karp, S.J. Hallam.Metabolic pathways for the whole community BMC Genomics15(1) :619. doi: 10.1186/1471-2164-15-619. (2014)
[PTools11] P.D. Karp., M. Latendresse., R. Caspi.The Pathway Tools pathway prediction algorithm.Standards in Genomic Sciences5(3): 424–429. doi: 10.4056/sigs.1794338 (2011)
[PTools10a] J.M Dale., L. Popescu., and P.D. KarpMachine
learning methods for metabolic pathway prediction.BMC
Bioinformatics 8:15 (2010)
[PTools02a] S.M.Paley and P.D.KarpEvaluation
of computational metabolic-pathway predictions for H.
pyloriBioinformatics 18:715-24 (2002)
Pathway Hole Filling
Algorithm:[PTools04] M.Green and P.D.KarpA
Bayesian method for identifying missing enzymes in predicted
metabolic pathway databases.BMC Bioinformatics
5:76 (2004)
Operon Predictor: [PTools04a]
P.Romero and P.D.KarpUsing
functional and organizational information to improve genome-wide
computational prediction of transcription units on pathway/genome
databases. Bioinformatics (2004)
Predictor of Transport
Reactions:[PTools08] T.J.Lee., I. Paulsen., and P.D.KarpAnnotation-based
inference of transporter function.Bioinformatics
24:i259-67 (2008)
[H2] Publications on the Pathway Tools Ontology
[PTools04b] P.D.Karp., S. Paley., C.J. Krieger., and Zhang P.An
Evidence Ontology for use in Pathway/Genome Databases.Pacific
Symposium on Biocomputing 9:190-201 (2004)
[PTools00] P.D.KarpAn
ontology for biological function based on molecular
interactions.Bioinformatics 16:269-85 (2000)
[PTools94a] P. Karp and S. PaleyRepresentations
of metabolic knowledge: Pathwaysin Proceedings of
the Second International Conference on Intelligent Systems for
Molecular Biology. (Altman, R. and Brutlag, D. and Karp, P. and
Lathrop, R. and Searls, D. eds.), (Menlo Park, CA), AAAI Press, (1994)
[PTools93] P. Karp and M. RileyRepresentations
of metabolic knowledgein Proceedings of the First
International Conference on Intelligent Systems for Molecular Biology.
(L. Hunter, D. Searls, and J. Shavlik, eds.), (Menlo Park, CA), pp.
207-215, AAAI Press, (1993)
[H2] Publications on the Ocelot Object-Oriented DBMS Underlying Pathway Tools
[Ocelot99] P.D.Karp, V.K.Chaudhri, and
S.M PaleyA
collaborative environment for authoring large knowledge basesJ
Intelligent Information Systems. 13:155-94 (1999)
[H2] Other Pathway Bioinformatics Publications
[Pathway05] M.L.Green and P.D.
KarpGenome
Annotation Errors in Pathway Databases Due to Semantic Ambiguity in
Partial EC Numbers.Nucleic Acids Research
33:4035-9 (2005)
[Pathway06] M.L Green and P.D.
KarpThe
outcomes of pathway database computations depend on pathway
ontology.Nucleic Acids Research 34:3687-97 (2006)

Not FoundThe server doesn't know how to respond to http://humancyc.org/%5BORGID%5D/class-tree/. Please make sure you have the correct URL.Host: biocyc18Report Errors or Provide Feedback
Page generated by Pathway Tools version 29.5 (software by SRI International) on Sat Jun 20, 2026, BIOCYC18.EcoCyc version 29.6.