Pathway Tools Schema and Semantic Inference Layer Genes, Operons, and Replicons

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Pathway Tools Schema and Semantic Inference Layer Genes, Operons, and Replicons

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Title: Pathway Tools Schema and Semantic Inference Layer Genes, Operons, and Replicons

1
Pathway Tools Schema and Semantic Inference
LayerGenes, Operons, and Replicons
2
Representing a Genome
product
components
Product1
Gene1
Gene2
CHROM1
genome
Gene3
CHROM2
ORG
PLASMID1

Classes
ORG is of class Organisms
CHROM1 is of class Chromosomes
PLASMID1 is of class Plasmids
Gene1 is of class Genes
Product1 is of class Polypeptides or RNA

(defun genes-of-chrom (chrom)
(loop for x in (get-slot-values chrom
components)
when (instance-all-instance-of-p x
Genes)
collect x)
)

4
Polynucleotides
Review slots of COLI and of COLI-K12
5
Genetic-Elements

Sequence is stored in a separate file or database
table

6
Polymer-Segments
Review slots of Genes
7
Complexities of Gene / Gene-ProductRelationships

The Product of a gene can be an instance of
Polypeptides or RNAs
An instance of Polypeptides can have more than
one gene encoding it
Sequence position
Nucleotide positions of starting and ending
codons specified in Left-End-Position and
Right-End-Position (usually greater, except at
origin)
Transcription-Direction / -
Alternative splicing
Nucleotide positions of starting and ending
codons specified in Left-End-Position and
Right-End-Position
Intron positions specified in Splice-Form-Introns
of gene product
(200 300) (350 400)

8
Gene Reaction Schematic
9
Substring Search Example

Find all genes that contain a given substring
within their common name or synonym list.
(defun find-gene-by-substring (substring)
(let (result)
(loop for g in (get-class-all-instances
'Genes)
do
(loop for name in (get-slot-values
g 'names)
when (search substring
name test 'string-equal)
do (pushnew g result)
) )
result
) )

10
Proteins
11
Proteins and Protein Complexes

Polypeptide the monomer protein product of a
gene (may have multiple isoforms, as indicated at
gene level)
Protein complex proteins consisting of multiple
polypeptides or protein complexes
Example DNA pol III
DnaE is a polypeptide
pol III core is DnaE and two other polypeptides
pol III holoenzymes is several protein complexes
combined

12
Protein Complex Relationships
13
Slots of a protein (DnaE)

catalyzes
Is it a regulator/reactant/etc?
comment
component-of
dblinks
features (edited in feature editor)
Many other attributes possible

14
A complex at the frame level (pol III)

Most of the same attributes as polypeptide frame
component-of and components
note coefficients

15
Protein Complex Relationships
16
Relationships are Defined in Many Places

component-of comes from creating a complex
appears-in-left-side-of comes from defining a
reaction (as do modified forms)
regulates comes from an enzymatic reaction or TU
can only edit dna-footprint if protein has been
associated with a TU

17
Semantic Inference Layer

Reactions-of-protein (prot)
Returns a list of rxns this protein catalyzes
Transcription-units-of-proteins(prot)
Returns a list of TUs activated/inhibited by the
given protein
Transporter? (prot)
Is this protein a transporter?
Polypeptide-or-homomultimer?(prot)
Transcription-factor? (prot)
Obtain-protein-stats
Returns 5 values
Length of all-polypeptides, complexes,
transporters, enzymes, etc

18
Example

Find all enzymes that use pyridoxal phosphate as
a cofactor or prosthetic group
(loop for protein in (get-class-all-instances
Proteins)
for enzrxn (get-slot-value protein
enzymatic-reaction)
when (and enzrxn
(or (member-slot-value-p enzrxn cofactors
pyridoxal_phosphate)
(member-slot-value-p enzrxn
prosthetic-groups pyridoxal_phosphate))
collect protein)
(member-slot-value-p frame slot value) T if
Value is one of the values of Slot of Frame.

19
Sample

Find all proteins without
a comment anywhere

20
RNAs
21
RNAs

PGDBs only represent RNAs that are terminal gene
products
tRNAs
rRNAs
Regulatory RNAs
Miscellaneous small RNAs
Slots similar to proteins
tRNAs can have an anticodon

22
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23
The RNA Ontology
24
Compounds / Reactions / Pathways
25
Compounds / Reactions / Pathways

Think of a three tiered structure
Reactions built on top of compounds
Pathways built on top of reactions
Metabolic network defined by reactions alone
pathways are an additional optional structure
Some reactions not part of a pathway
Some reactions have no attached enzyme
Some enzymes have no attached gene

26
Compounds

Relatively few aspects of a compound defined
within the compound editor
MW, formula calculated from edited structure
Most aspects defined in other editors
Pathway reactions comes from reaction editing
followed by pathway editing
Activator, etc come from the protein editor

27
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28
(print-frame TRP) -- Instance TRP ---
Types Amino-Acid, Aromatic-Amino-Acids,
Non-polar-amino-acids APPEARS-IN-LEFT-SIDE-OF
RXN0-287, TRANS-RXN-76, TRYPTOPHAN-RXN,
TRYPTOPHAN--TRNA-LIGASE-RXN
APPEARS-IN-RIGHT-SIDE-OF RXN0-2382, RXN0-301,
TRANS-RXN-76, TRYPSYN-RXN CHEMICAL-FORMULA (C
11), (H 12), (N 2), (O 2) COMMON-NAME
"L-tryptophan" DBLINKS (LIGAND-CPD "C00078"
NIL kaipa 3311532640 NIL NIL), (CAS
"6912-86-3"), (CAS "73-22-3") NAMES
"L-tryptophan", "W", "tryptacin", "trofan",
"trp", "tryptophan", "2-amino-3-indolylp
ropanic acid" SMILES "c1(c(CC(N)C(O)O)c2(c(n
H1)cccc2))" SYNONYMS "W", "tryptacin",
"trofan", "trp", "tryptophan",
"2-amino-3-indolylpropanic acid" _________________
___________________________
29
Where is diphosphate in the ontology?
30
Semantic Inference Layer

Reactions-of-compound (cpd)
Pathways-of-compound (cpd)
Is-substrate-an-autocatalytic-enzyme-p (cpd)
Activated/inhibited-by? (cpds slots)
Returns a list of enzrxns for which a cpd in cpds
is a modulator (example slots activators-all,
activators-allosteric)
All-substrates (rxns)
All unique substrates specified in the given rxns
Has-structure-p (cpd)
Obtain-cpd-stats
Returns two values
Length of all-cpds, cpds with structures

31
Miscellaneous things.

History List
Back/Forward and History buttons
Default list is 50 items
Show frame
(print-frame frame)

32
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33
Queries with Multiple Answers

Navigator queries
Example Substring search for pyruvate
Selected list is placed on the Answer list
Use Next Answer button to view each one of them
Lisp queries
Example Find reactions involving pyruvate as a
substrate
(get-class-all-instances Compounds)
(loop for rxn in (get-class-all-instances
Reactions)
when (member pyruvate (get-slot-values rxn
substrates)
collect rxn)
(replace-answer-list )

34
Reactions
35
Reactions

Represents information about a reaction that is
independent of enzymes that catalyze the reaction
Connected to enzyme(s) via enzymatic reaction
frames
Classified with EC system when possible
Example 2.7.7.7 DNA-directed DNA
polymerization
Carried out by five enzymes in E. coli

36
Reaction Ontology
37
Where is 2.7.7.7 in the Ontology?
38
Slots of Reaction Frames

Balance-state
EC-number
Enzymatic-reaction
Generated in protein or reaction editor
In-pathway
Generated in pathway editor
Left and Right (reactants / products)
Can include modified forms of proteins, RNAs, etc
here
Not all reactants/products need to be frames

39
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40
Reaction relationships
41
Enzymatic Reactions (DnaE and 2.7.7.7)

A necessary bridge between enzymes and generic
versions of reactions
Carries information specific to an
enzyme/reaction combination
Cofactors and prosthetic groups
Alternative substrates
Links to regulatory interactions
Frame is generated when protein is associated
with reaction (via protein or reaction editor)

42
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43
Regulation of Enzyme Activity
44
Semantic Inference Layer

Genes-of-reaction (rxn)
Substrates-of-reaction (rxn)
Enzymes-of-reaction (rxn)
Lacking-ec-number (organism)
Returns list of rxns with no ec numbers in that
database
Get-reaction-direction-in-pathway (pwy rxn)
Reaction-type(rxn)
Indicates types of Rxn as Small molecule rxn,
transport rxn, protein-small-molecule rxn (one
substrate is protein and one is a small
molecule), protein rxn (all substrates are
proteins), etc.
All-rxns(type)
Specify the type of reaction (see above for type)
Obtain-rxn-stats
Returns six values
Length of all-rxns, transport, non-transport,
etc

45
Find all small-molecule reactions that have no
enzyme but are not spontaneous (orphan
reactions) (defun orphan-reactions (optional
(verbose? t)) (loop for r in (all-rxns
small-molecule) when (and (not
(slot-has-value-p r 'enzymatic-reaction))
(not (get-slot-value r
'spontaneous?))) collect r) )
46
Reaction Direction

Left/Right reflect direction of reaction as
written by Enzyme Commission
Reflects systematic direction for different
reaction classes
Left/Right do not necessarily correspond to
physiological direction of a reaction
Get-rxn-direction(rxn)
Returns L2R or R2L or BOTH or NIL
Integrates all available info about direction of
this reaction
Direction(s) it occurs in all pathways in the
PGDB
Direction(s) as specified in Enzymatic-Reactions

47
Pathways
48
Outline

Pathways
Representation of Pathways
Querying Pathways Programmatically
How Pathway Diagrams are Generated
Future Work Signalling Pathways
Cellular Overview Diagram
New Functionality
Under the Hood
How Overview Diagram is Generated
Using Overview Diagram for Global Queries

49
What is a Pathway?

An ordered set of interconnected, directed
biochemical reactions
Reactions form a coherent unit, e.g.
Regulated as a single unit
Evolutionarily conserved across organisms as a
single unit
When combined, perform a single cellular function
Historically grouped together as a unit
Includes metabolic pathways and signalling
pathways
Evidence for all reactions in a single organism
Pathways can be linear, cyclical, branched, or
some combination

50
Internal Representation of Pathways

REACTION-LIST unordered list of reactions that
comprise the pathway
PREDECESSORS list of reaction pairs that define
ordering relationships between reactions.
E.g. R1 R2 C
A B
R3 D
(R2 R1) Predecessor of R2 is R1
(R3 R1) Predecessor of R3 is R1
(R1) R1 has no predecessor (can be omitted)

51
What is missing from Pathway Representation?

Reaction directions
Some reactions are unidirectional, but many are
reversible how do we know in which direction to
draw the reaction?
Main vs. side substrates
A B
C
D E
F
Main compounds form the backbone of the pathway
substrates shared between connecting reactions
major inputs and outputs.
Side compounds omitted from pathway diagrams at
low detail levels
Individual reactions do not necessarily have main
and side compounds a particular substrate may
be either a main or a side depending on the
pathway context.

52
Computing Directionality and Mains/Sides

Our philosophy Enable curator to specify as
little as possible. Compute as much as possible.
This reduces redundancy and potential for
inconsistencies.
Example
Reactions R1 A B ? C D
R2 B ? E
Predecessors (R2 R1)
Only substrate overlap is B
B must be a main substrate
A must be a side substrate,
R1 must proceed from right to left
R2 must proceed from left to right
C D ? B ? E
A

53

But

Unfortunately, mains, sides and reaction
directions are sometimes ambiguous
At beginnings and ends of pathways
Use heuristics to determine main/side substrates
at beginnings, ends of pathways
Not always what the curator wants
Substrate overlap with both sides of a reaction,
e.g. A B ? C D
C B ? E
Solution Additional slot PRIMARIES, should only
be populated when necessary
PRIMARIES (R (A B) (C)) says that for reaction
R, A and B are both main reactants, and C is a
main product.

54
More Complications

ENZYME-USE a reaction may be catalyzed by
multiple enzymes, but not all the enzymes
necessarily participate in a given pathway
Not present in the same compartment with rest of
pathway enzymes
Down-regulated or not expressed under conditions
in which pathway is active
ENZYME-USE slot tells us which enzymes catalyze
reaction in pathway, if not all.
LAYOUT-ADVICE helps software draw pathway
correctly, e.g. in a cyclical pathway, tells
which substrate should be at the top.
HYPOTHETICAL-REACTIONS list of reactions in the
pathway that are considered hypothetical (i.e. no
direct experimental evidence)

55
Polymerization Pathways

? Xn Xn1 X10
POLYMERIZATION-LINKS specifies reactions that
should be connected by a polymerization link
(X R1 R1) --- REACTANT-NAME-SLOT
N-NAME
---
PRODUCT-NAME-SLOT N1-NAME
CLASS-INSTANCE-LINKS specifies when a link
should be drawn between a substrate class and
some instance of it (necessary only if instance
is not a member of some reaction, so no
predecessor relationship can be defined)
R1 --- PRODUCT-INSTANCES X10

56
Super-Pathways

Collection of pathways that connect to each other
via common substrates or reactions, or as part of
some larger logical unit
Can contain both sub-pathways and additional
connecting reactions
Can be nested arbitrarily
REACTION-LIST a pathway ID instead of a reaction
ID in this slot means include all reactions from
the specified pathway
PREDECESSORS a pathway ID instead of a tuple in
this slot means include all predecessor tuples
from the specified pathway

57
Pathway Links

Can be used as an alternative or in addition to
defining super-pathways
Link must be to or from some main substrate in
the pathway
Other end of link can be a pathway, a reaction,
or an arbitrary text string
Software automatically computes direction of
link, but curator can override it

58
Querying Pathways Programmatically

See http//bioinformatics.ai.sri.com/ptools/ptools
-resources.html
(all-pathways)
(base-pathways)
Returns list of all pathways that are not
super-pathways
(genes-of-pathway pwy)
(unique-genes-of-pathway pwy)
Returns list of all genes of a pathway that are
not also part of other pathways
(enzymes-of-pathway pwy)
(substrates-of-pathway pwy)
(variants-of-pathway pwy)
Returns all pathways in the same variant class as
a pathway
(get-predecessors rxn pwy), (get-successors rxn
pwy)
(get-rxn-direction-in-pathway pwy rxn)
(pathway-inputs pwy), (pathway-outputs pwy)
Returns all compounds consumed (produced) but not
produced (consumed) by pathway (ignores
stoichiometry)

59
Example Queries

Find all genes involved in metabolic pathways
(remove-duplicates
(loop for p in (all-pathways)
append (genes-of-pathway p)))
Find all compounds that are unique to a single
pathway
(loop for p in (base-pathways)
append
(loop for c in (substrates-of-pathway p)
when (null (remove p
(pathways-of-compound c)))
collect (list c p)))

60
Regulation
61
Regulation

Reorganization and expansion of regulation under
way in Pathway Tools
Initial application to EcoCyc
Class Regulation with subclasses that describe
different biochemical mechanisms of regulation
Slots
Regulator
Regulated-Entity
Mode
Mechanism

62
Regulation of Enzyme Activity

Class Regulation-of-Enzyme-Activity
Each instance of the class describes one
regulatory interaction
Slots
Regulator -- usually a small molecule
Regulated-Entity -- an Enzymatic-Reaction
Mechanism -- One of
Competitive, Uncompetitive, Noncompetitive,
Irreversible, Allosteric, Other
Mode -- One of , -
Physiologically-relevant? true/false

63
Transcription Initiation

Class Regulation-of-Transcription-Initiation
Transcription factor binds to DNA binding site to
regulate transcription initiation from a promoter
Slots
Regulator -- instance of Proteins or Complexes
(a transcription-factor)
Regulated-Entity -- instance of Promoters
Mode -- One of , -
Associated-binding-site a DNA-Binding-Site

64
Attenuation

Class Transcriptional-Attenuation
Several subclasses depending on type of
attenuation
Slots common to all
Regulator -- Depends on subtype of attenuation
Regulated-Entity -- instance of Terminators
Mode -- One of , -

65
Attenuation Subtypes

Ribosome-Mediated-Attenuation
E.g. trp operon ribosome pauses based on levels
of charged tRNA, determines formation of
terminator or antiterminator
RNA-Mediated-Attenuation
RNA (tRNA or sRNA) binds to transcript,
determines formation of terminator or
antiterminator
Protein-Mediated-Attenuation
Protein binds to transcript, determines formation
of terminator or antiterminator
Small-Molecule-Mediated-Attenuation
Small molecule binds to transcript, determines
formation of terminator or antiterminator
Rho-Blocking-Antitermination
RNA-Polymerase-Modification
Regulatory protein binds to site in transcription
unit and interacts with RNA polymerase to
determine termination

66
Transcriptional Regulation
trp
rxn001
apoTrpR
TrpRtrp
reg001
site001
pro001
trpL
trpLEDCBA
trpE
trpD
trpC
trpB
trpA
term001
reg002
charged-tRNAtrp
67
Data Exchange
68
Data Exchange