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

Archaea
467
databases

Bacteria
19,488
databases

Eukaryota
41
databases

MetaCyc
Metabolic Encyclopedia

[H2] Is Flawed Data Compromising Your Research?

[H3] BioCyc curators correct several hundred annotation errors per genome
in our Tier 1-2 databases, ensuring your publications and proposals
stand on a solid foundation.

Learn More

[IMG: Portion of Genome Browser]
Genome Browser image

[H2] A Vast Set of Bioinformatics Tools

[H3] Browsers for genomes, metabolic networks, and regulatory networks. Transcriptomics and metabolomics data analysis, comparative analysis, and metabolic route search. Sequence search and alignment.

Learn More

[IMG: Collage of screenshots of portions of
4 different BioCyc Tools. Upper left: the Regulatory
Overview, with some connections
shown. Upper right: the Cellular Overview
with omics data overlaid. Lower left: the
Omics Dashboard. Lower right: the
Comparative Genome Browser.]

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[H2] BioCyc for Synthetic Biology

[H3] Curated Pathway/Genome Databases for key chassis organisms enable trustworthy engineering of cellular networks.

Learn More

[IMG: synbio]
&nbsp

[H2] Explore Metabolic Maps for Thousands of Organisms

[H3] The Cellular Overview enables you to browse through zoomable metabolic map diagrams that are customized to each BioCyc organism.

Learn More

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

[H2] RouteSearch: Search for Paths Through the Metabolic Network

[H3] Search for lowest-cost paths
through the metabolic network of the selected
organism.

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.]

[H2] Metabolic Reconstruction from Sequenced Genomes

[H3] Install SRI's Pathway Tools
software (free to academics) to predict metabolic
pathways for sequenced genomes, generate metabolic
models.

Learn More

[IMG: Two men looking at two screens, one
showing a genome browser display, the other a
regulatory overview display. Behind the
screens is a blue background with a portion
of a cellular overview diagram visible.]

[H2] 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.

[H2] Comparative Genome Analysis

[H3] Multiple comparative analysis tools are available in this website including aligning genomes at orthologous genes.

Learn More

[IMG: A fragment of a Comparative Genome
Browser display showing the region around
the trpA gene for 5 E. coli
strains. Orthologous genes are colored
the same color in each strain.]
Multi-organism Genome Browser image generated by Pathway Tools.

[H2] The BioCyc Database Collection

[H3] Tier 1 databases such as EcoCyc are the most highly curated. BioCyc databases are computationally derived from MetaCyc.

Learn More

Request Addition of New Genome to BioCyc

[IMG: Diagram of three tiers of Databases within BioCyc]
BioCyc Database Collection

[H2] The Omics Dashboard: A New View of Omics Data

[H3] Visualize omics data as a set of graphs hierarchically organized by functional category. Drill down for more detail in areas of interest.

Learn More

[IMG: A portion of an Omics Dashboard display,
showing panels for Biosynthesis and
Degradation, and a popup showing details
for L-alanine biosynthesis.]
Cellular Dashboard image generated by Pathway Tools.

[H2] 20,090 Pathway/Genome Databases to Search

BioCyc is a collection of 20,090 Pathway/Genome
Databases (PGDBs) covering humans, model eukaryotes, and thousands of microbes.
These databases are curated from 167,000 publications.
Short two minute video tutorials show what you can do with BioCyc.

BioCyc contains 60+ software tools for searching and analyzing its databases,
including a high-speed genome browser and metabolic network viewer.

The databases for E. coli K-12 and Faecalibacterium prausnitzii A2-165 are freely available. Access to the other BioCyc databases requires a paid subscription.

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BioCyc Intro

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)

[H1] Web Site User’s Guide for Pathway Tools-Based Web Sites
A note on browsers:
At present, our preferred browsers are Firefox and
Chrome (often faster)
Less recommended are Safari and Edge.
[H1] Contents
1  Overview
2  Selecting the Database to Search
3  Searching Pathway/Genome Databases
3.1  Quick Search
3.2  Search Menu: Object Searches
3.3  Tools Menu → Search → Cross Organism Search
3.4  Tools Menu → Search → BLAST search
3.5  Tools Menu → Search → Google This Site
3.6  Tools Menu → Search → Search Full-text Articles
4  Web Accounts
5  Genome Explorer Genome Browser and Circular Genome Viewer
5.1  New Genome Browser: Basic Mode
5.2  New Genome Browser: Comparative Mode
5.3  New Genome Browser: Tracks Mode
5.4  Circular Genome Viewer
6  Older Genome Browser
6.1  Older Genome Browser: Tracks Mode
6.2  Older Genome Browser: Comparative Mode
7  SmartTables
7.1  SmartTable Structure and Display
7.2  SmartTable Directory
7.3  Creating a SmartTable
7.4  Adding SmartTable Columns
7.5  Other SmartTable Manipulations
7.6  SmartTable Analysis Operations
7.7  Exporting and Sharing a SmartTable
7.8  Publishing a SmartTable
7.9  Browsing SmartTables and Users
8  Omics Data Analysis
9  Cellular Overview (Metabolic Map Diagram)
9.1  Summary of Commands and Controls
9.2  Searching and Highlighting
9.3  Cellular Omics Viewer — Overlay Experimental Data
10  Metabolic Models
10.1  How to Use the Web-MetaFlux Modeling Tool
10.2  Selecting a Model of Interest
10.3  Executing a Model
10.4  Inspecting and Modifying a Metabolic Model
11  Metabolic Route Search and Metabolic Network Explorer
11.1  Metabolic Route Search
11.2  Metabolic Network Explorer
12  Pathway Collages
13  Regulatory Overview (Regulatory Network Diagram)
14  Comparative Analysis
14.1  Show this Gene/Compound/Reaction/Pathway in Other Databases
14.2  Compare Individual Pathways and Reactions
14.3  Comparative Analysis Tables
14.4  Comparative Genome Dashboard
15  Sequence Search and Alignment
15.1  BLAST Search
15.2  PatMatch Sequence Search
15.3  Sequence Alignment Viewer
16  Translation Services
16.1  Metabolite Translation Service
16.2  Map Sequence Coordinates
17  How to Learn More
[H1] 1  Overview
This document describes how to use Web sites based on the Pathway
Tools software from SRI International. Since multiple Web sites such
as BioCyc, YeastCyc, AraCyc, and MouseCyc are all based on the same
underlying software, the same usage instructions apply to all. (Note
that differences in configuration and in software version may
introduce some variability among sites).
Please note that the desktop version of Pathway Tools that you can install
locally provides some additional operations compared to the Web
capabilities described here. Click
here for more details.
[H1] 2  Selecting the Database to Search
Most searches within this website search within a
single organism database. The database against
which searches will be conducted is indicated below the Quick Search
box just below the menu bar (see figure below).
In most cases, a database describes a single organism
– although a small number of multi-organism Pathway/Genome Databases exist (examples
include MetaCyc and PlantCyc). Operations that search multiple
databases are described in
Sections Object Searches,
Cross Organism Search,
and Google This Site.
[IMG: PToolsWebsiteHowto-images/quicksearch.png]
To change the default organism database for searches, click on the
“Change Current Database” button
above the Quick Search box. In
the “Select an organism database” window that pops up, you can search for the organism of
interest in several possible ways. You can type in any combination of
its genus name, species name, and strain name — for example, the
strain name is often a quick way to find an organism because it is
usually unique. You can also find organisms by
taxonomy, or by querying various organism properties.
If the Website supports user accounts, and you are logged in, you may
save one database as your preferred database by checking the box in
the bottom-left corner of the “Select an organism database” window. This database will be
your default selection when starting a new web session.
Once you have selected the desired database from one of the tabs
described below, click OK to exit the
organism-selection dialog. This will navigate to the page of summary
statistics for the selected database.
Note that if you follow a link to a page for a different organism
database, then the selected database for searching will change to
match the organism of the currently displayed page.
[H2] Organism Selector: By Name Tab
By default, the By Name tab will initially be selected in the
“Select an organism database” window. If a
small number of databases is available, a full scrollable list of
databases is present to select from. When a large
number of databases is available, you must start typing or select a
starting letter from the alphabetical index to the left
of the database list in order to see the list of matching databases.
If you start typing an organism name or select a starting letter,
the full list of databases (if available) will be replaced by a list
of databases matching the typed string or starting with the selected
letter — you can use the mouse or the up/down
arrows on your keyboard to select the desired database. An organism
name will match the string you type if any word in its name
(i.e., genus, species, or strain name) starts with the string you type.
In the list of matching databases, some database names may be
displayed with a colored background – these indicated databases that
have had some level of manual review and/or curation. Tier 1
databases, i.e. those that have received at least a year of
literature-based curation, will have an orange background. Tier 2
databases, i.e. those with a lower level of manual curation, will have
a blue background. All others are Tier 3 databases, which means
they have been computationally generated with little or no manual
review.
Lists of your
recently used databases and the site’s most popular databases on the
left side of the selection window provide
shortcuts for selecting those databases.
[H2] Organism Selector: By Taxonomy Tab
The By Taxonomy tab allows you to select an organism by browsing for
it. After the name of each class of organisms is listed the number of
organism databases in that class. The taxonomy tree does not include
all taxonomy classes, only those that contain at least one organism
database – if a particular taxon does not appear in the tree, it
means there is no database available for it or its children. Clicking
on a class name will show or hide its list of child taxa. Clicking on
an organism name will select that database and show its name at the
top.
You may search for any taxon by starting to type its name in the text
box. If you select one of the options from the resulting
auto-complete box, the taxonomy will automatically expand to show the
selected taxon (you must still click on the organism name in the
taxonomy to select that database, however).
[H2] Organism Selector: By Organism Properties Tab
The By Organism Properties tab allows you to query for all
organisms that have (or do not have) some property. The types of
properties that can be queried (known as the organism “metadata”)
include attributes of the organism and sample, such as when and where and from what host the
sample was collected, whether or not the organism is a pathogen, its
relationship to oxygen (e.g. aerobic or anaerobic), and
attributes of the database, such as how many pathways or genes or Gene
Ontology terms it has. Not all
organism databases contain data for each of these attributes. In the
list of properties from which to select, the number of databases that
have values for that property as well as a description of the property
is listed in the tooltip.
After selecting a property, you can constrain its value, or just
select all databases that have (or do not have) any value for that
property. To select from a list of all available values, click in the
text box. In the resulting list of possibilities, the number in
parentheses after each value is the total number of organisms that
match that value. If you start to type, the list of visible
options will be limited to those that match the string you have typed.
Multiple options may be selected by clicking in the text box again
after selecting a value – in that case, an organism will satisfy the
constraint if it matches any of the selected values (i.e. the values
are connected by an implicit OR). For properties whose values consist
of free text, you may also query by substring. The first few values
that match your substring are shown, but you are not obligated to
select any of them. For properties whose values are numeric, a
variety of numeric operators are available, as well as the option to
select from all available values. If you specify an = constraint,
an organism will satisfy the constraint if its value falls within a
small range on either side of the specified value – the size of this
range depends on the property, and is indicated below with the
description of each property. To specify a different range, use a
combination of < and > constraints.
Up to six different constraints may be specified (use the “Add
Constraint” button to add a new constraint, up to the limit). These
may be connected by either AND (an organism must satisfy both
constraints) or OR (an organism may satisfy either constraint). Since
there is no way to group constraints, if you are are building a query
that combines both ANDs and ORs, ordering becomes very important.
Queries are processed in a left-to-right order, so
X AND Y OR P AND Q is interpreted as
((X AND Y) OR P) AND Q. If the ordering of constraints do not allow for a desired
query, you may be better off splitting your query into multiple
queries and searching for the desired organism one part of the query
at a time.
The following properties are available for searching:
Environment: This property encompasses terms that
describe the environmental features and habitats where the sample
was taken. This can include biome-level terms, such as desert,
deciduous woodland, coral reef; geographic features such as harbor,
cliff, lake; and/or environmental material such as air, soil, water.
It can also include terms related to host environment (e.g. blood,
skin, oral cavity, gut). This slot combines the MIGS concepts
biome, feature, material, body_habitat, body_site and body_product.
Ideally, terms should be taken from the
EnvO or the
FMA
ontologies, but can also be free text. An organism may have
multiple different values for this property.
Geographic Location: The geographical origin of the
sample, defined by country or sea name, and/or specific region
name. This property can have multiple values, e.g. one might be a
country name, another a region name, and another text describing the
specific location.
Latitude: The latitude of the geographical origin of
the sample. Values are reported in decimal degrees, in the WGS84
system. Positive numbers are North, negative numbers are South. If
you specify an = constraint for this property, all organisms whose
latitude is within 10 degrees of the requested value will be
included in the result. If you wish a different size range, you
will need to specify it explicitly by combining < and > constraints.
Longitude: The longitude of the geographical origin of
the sample. Values are reported in decimal degrees, in the WGS84
system. Positive numbers are East, negative numbers are West. If
you specify an = constraint for this property, all organisms whose
longitude is within 10 degrees of the requested value will be
included in the result. If you wish a different size range, you
will need to specify it explicitly by combining < and >
constraints.
Depth/Altitude: The depth or altitude in meters at
which the sample was collected. Negative numbers are depths,
positive numbers are altitudes. If
you specify an = constraint for this property, all organisms whose
depth or altitude is within 20% of the requested value will be
included in the result. If you wish a different size range, you
will need to specify it explicitly by combining < and >
constraints.
Collection Date: The year the sample was collected.
Relationship to Oxygen: Whether the organism is an
aerobe or anaerobe, and what form.
Trophic Level: The position of the organism in a food
chain.
Temperature Range: A qualitative description of what
kind of temperature range the organism grows best in. A mesophile
grows best in moderate temperatures, typically between 20 and 45
degrees Celsius. A psychrophile prefers colder environments,
whereas a thermophile prefers warmer ones, and a hyperthermophile
thrives in extremely hot environments of 60 degrees Celsius and
higher.
Biotic Relationship: Whether the organism is
free-living or in a host, and if the latter, what type of
relationship is observed.
Pathogenicity: The general class of organisms to which
the organism is pathogenic.
Host: The host from which the sample was isolated.
Human Microbiome Body Site: For organisms that are part
of the Human Microbiome Project or otherwise have human hosts, the
general body site where the sample was collected, e.g. blood, oral,
gastrointestinal tract.
Health/Disease State: The health or disease state of
the specific host at the time of collection.
Ploidy: The ploidy level of the genome, e.g. haploid,
diploid, triploid, allopolyploid.
Genome Size: The size of the organism’s genome in base pairs.
# of Pathways: The number of pathways in the database.
# of Genes: The number of genes in the database.
# of Enzymes: The number of enzymes in the database.
# of GO Terms: The number of Gene Ontology terms that have
annotations to them in the database.
# of Gene Essentiality Datasets: The number of gene
essentiality datasets that have been incorporated into the database.
# of Genes with Essentiality Data: The number of genes in
the database that have essentiality information from at least one
gene essentiality dataset.
# of Transporters: The number of transporters in the database.
# of Transcriptional Regulatory Interactions: The number
of transcriptional regulatory interactions in the database.
# of Phenotype Microarray Datasets: The number of
phenotype microarray datasets that have been incorporated into the database.
# of Protein Features: The number of protein features in the database.
Once you have specified the desired constraints, use the “Find
Organisms” button to search for all matching organisms. In the
result

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