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August 2012
This work is licensed under the Creative Commons Attribution 3.0 Unported License. To view a copy of this license, visit http://creativecommons.org/licenses/by/3.0/ or send a letter to Creative Commons, 444 Castro Street, Suite 900, Mountain View, California, 94041, USA.
BEL Framework v2.0.0
BEL Framework Overview
• Current version 2.0.0 released June 29, 2012– Open source
• The BEL Framework includes:– BEL Compiler– KAM store– Tools– Web and Java APIs
• API = Application Programming Interface– Can be used by software to access information from KAMs
• KAM Navigator uses the Web API• Whistle uses the Java API
– Web Server
Knowledge User Workflow: BEL Framework and Applications
Multiple KAMs can be imported for use by the application
BEL Compiler
Encrypted portable KAM
BEL Framework BEL Framework API
KAM Store
Application
BEL Documents
3
Contents
• KAMs and the KAM store• BEL Compiler
– Running the BEL Compiler– Phase I - Compiler Expansions– Phase II - Equivalencing– Phase III – Compiler Augmentations
• BEL Framework Tools
4
Knowledge Assembly Model (KAM)
• A knowledge base in network form• Composed of Nodes (KamNode) and Edges
(KamEdge)• Each KamNode represents one or more BEL Terms
drawn from one or more BEL Documents• Each KamEdge represents one or more BEL
Statements from from one or more BEL Documents
5
KamNodes
• Nodes represent one or more BEL terms• KamNodes are coalesced wherever possible by the equivalencing engine
(Phase II)
6
KamEdges
• Represent assertions supported by one or more BEL Statements
• Querying a KamEdge will return:– Each BEL Statement supporting the assertion– Assertions are coalesced based solely on semantic triple
after equivalencing, independent of Annotations
• Querying a BEL Statement will return:– The BEL Document the statement was recorded in– The list of assertions for the statement
7
© 2012, Open BEL Community 8
KAM Store
• The database that stores KAMs• Default database is Derby
– Can configure to use MySQL or other databases
• Put KAMs into the KAM Store by:– Compiling a KAM (belc.cmd)– Importing a KAM (tools\KamManager.cmd --import)
• Access KAMs via:– APIs– Exporting a KAM (tools\KamManager.cmd –export)
Contents
• KAMs and the KAM store• BEL Compiler
– Running the BEL Compiler– Phase I - Compiler Expansions– Phase II - Equivalencing– Phase III – Compiler Augmentations
• BEL Framework Tools
9
KAMs Are Compiled from BEL Documents
• The BEL Compiler compiles one or more BEL Documents into a Knowledge Assembly Model (KAM)
• Multi-Phase compiler/assembler:1. Compiler – compiles each BEL Document into a proto-network2. Equivalencer – merges proto-networks by equivalencing
analogous nodes across namespaces3. Augmenter – increases KAM computability by injecting terms
and relationships from additional sources of prior knowledge (e.g. relationships connecting RNAs to their corresponding proteins)
4. Assembler – Generates final network and supporting evidence structures
• Users can change compiler parameters to control the knowledge assembly process
10
KAM Compilation Phases
Compiler Equivalencer Augmentor Final Assembler
CompiledKAM
BEL Documents
EquivalenceTables
Other Prior Knowledge
Namespace &Annotation
Tables
Network Resources
11
Contents
• KAMs and the KAM store• BEL Compiler
– Running the BEL Compiler– Phase I - Compiler Expansions– Phase II - Equivalencing– Phase III – Compiler Augmentations
• BEL Framework Tools
12
Running the BEL Compiler
• From BEL Framework folder: – belc.cmd (Windows) – belc.sh (Linux or OS X)
• Ensure that the server is not running• Required:
– BEL document(s)• Specify filename(s) with –f • OR specify path to folder of BEL documents with -p
– KAM name• Specify with -k
– KAM description• Specify with –d
13
>belc.cmd –f myDoc.bel –k myKAM –d "my KAM description"
Contents
• KAMs and the KAM store• BEL Compiler
– Running the BEL Compiler– Phase I - Compiler Expansions– Phase II - Equivalencing– Phase III – Compiler Augmentations
• BEL Framework Tools
14
Phase I Expansions
• List expansions • Inner terms• Protein modifications• Reactions• Nested statements• Reciprocal statements
15
List Expansion - hasMembers• Phase I expands hasMembers relationships to individual
hasMember relationships• All hasMembers relationship statements are removed
p(PFH:"AKT Family") hasMember p(HGNC:AKT1)p(PFH:"AKT Family") hasMember p(HGNC:AKT2)p(PFH:"AKT Family") hasMember p(HGNC:AKT3)
becomes
16
p(PFH:"AKT Family") hasMembers \ list(p(HGNC:AKT1),p(HGNC:AKT2),p(HGNC:AKT3))
List Expansion - hasComponents
• Phase I expands hasComponents relationships to individual hasComponent relationships
• All hasComponents relationship statements are removed
17
complex(NCH:"IkappaB Kinase Complex") hasComponent p(HGNC:CHUK)complex(NCH:"IkappaB Kinase Complex") hasComponent p(HGNC:IKBKB)complex(NCH:"IkappaB Kinase Complex") hasComponent p(HGNC:IKBKG)
becomes
complex(NCH:"IkappaB Kinase Complex") hasComponents \ list(p(HGNC:CHUK), p(HGNC:IKBKB), p(HGNC:IKBKG))
complexAbundance Expansion
• Phase I preprocesses complexAbundance() terms and injects individual hasComponent relationships
18
complex(p(HGNC:GTF2E1),p(HGNC:GTF2E2))complex(p(HGNC:GTF2E1),p(HGNC:GTF2E2))\ hasComponent p(HGNC:GTF2E1)complex(p(HGNC:GTF2E1),p(HGNC:GTF2E2))\ hasComponent p(HGNC:GTF2E2)
becomes
complex(p(HGNC:GTF2E1),p(HGNC:GTF2E2))
compositeAbundance Expansion
• Phase I preprocesses compositeAbundance() terms and injects individual includes relationships
composite(a(CHEBI:"deoxyribonucleic acid"), a(CHEBI:"NAD(+)"))composite(a(CHEBI:"deoxyribonucleic acid"), a(CHEBI:"NAD(+)")) includes \ a(CHEBI:"deoxyribonucleic acid"),composite(a(CHEBI:"deoxyribonucleic acid"), a(CHEBI:"NAD(+)")) includes \ a(CHEBI:"NAD(+)")
becomes
19
composite(a(CHEBI:"deoxyribonucleic acid"), a(CHEBI:"NAD(+)")) \ -> ribo(p(HGNC:PARP1))
Inner Terms Expansion
• Phase I expands inner terms to relate abundances to activity terms using actsIn relationships
becomes
phos(p(HGNC:DUSP1)) =| kin(p(HGNC:MAPK8))p(HGNC:DUSP1) actsIn phos(p(HGNC:DUSP1)) p(HGNC:MAPK8) actsIn kin(p(HGNC:MAPK8))
20
phos(p(HGNC:DUSP1)) =| kin(p(HGNC:MAPK8))
Protein Modification Expansion
• Phase I expands proteinModification() sub-terms to associate a modified protein abundance with the root protein abundance
p(HGNC:MAPK1, pmod(P, T)) => kin(p(HGNC:MAPK1))p(HGNC:MAPK1) hasModification p(HGNC:MAPK1, pmod(P,T)) p(HGNC:MAPK1) actsIn kin(p(HGNC:MAPK1))
becomes
21
p(HGNC:MAPK1, pmod(P,T)) => kin(p(HGNC:MAPK1))
Variant Expansion• Phase I expands fusion(), truncation(), and substitution()
sub-terms to associate a protein variant abundance with the parent (reference) protein abundance
p(HGNC:KRAS, sub(G,12,V))p(HGNC:KRAS) hasVariant p(HGNC:KRAS, sub(G,12,V))
becomes
22
p(HGNC:KRAS, sub(G,12,V))
Reaction Expansion
• Phase I expands reactants() and products() reaction sub-terms to associate the reactant and product lists with their abundances
reaction(reactants(a(CHEBI:superoxide)), \ products(a(CHEBI:"hydrogen peroxide"),a(CHEBI:oxygen))a(CHEBI:superoxide) reactantIn \ reaction(reactants(a(CHEBI:superoxide)), \ products(a(CHEBI:"hydrogen peroxide"),a(CHEBI:oxygen))reaction(reactants(a(CHEBI:superoxide)), \ products(a(CHEBI:"hydrogen peroxide"),a(CHEBI:oxygen)) \ hasProduct a(CHEBI:"hydrogen peroxide")reaction(reactants(a(CHEBI:superoxide)), \ products(a(CHEBI:"hydrogen peroxide"),a(CHEBI:oxygen)) \ hasProduct a(CHEBI:oxygen)
becomes
23
reaction(reactants(a(CHEBI:superoxide)), products(a(CHEBI:"hydrogen peroxide"),a(CHEBI:oxygen))
Nested Statement Expansion
• The compiler will automatically expand nested statements and create additional relationships from the subject of the statement to the object of the nested statement– can be turned off using the --no-statement-expansion
switch
24
Default Nested Statement Expansion
• Phase I expands nested statements to link the subject of the statement to the object of the nested statement
• The original statement is preserved as supporting evidence for the derived assertions
p(HGNC:CLSPN) -> p(HGNC:CHEK1, pmod(P))kin(p(HGNC:ATR)) => p(HGNC:CHEK1, pmod(P))
p(HGNC:ATR) actsIn kin(p(HGNC:ATR))p(HGNC:CHEK1) hasModification p(HGNC:CHEK1, pmod(P))
becomes
25
p(HGNC:CLSPN) -> (kin(p(HGNC:ATR)) => p(HGNC:CHEK1, pmod(P)))
Modified Nested Statement Expansion
• When the –no-statement-expansion switch is set, the compiler will instantiate the subject of the statement and expand the nested statement but not couple the two together.
• The original statement is removed
becomes
26
kin(p(HGNC:ATR)) => p(HGNC:CHEK1, pmod(P))p(HGNC:CLSPN)
p(HGNC:ATR) actsIn kin(p(HGNC:ATR))p(HGNC:CHEK1) hasModification p(HGNC:CHEK1, pmod(P))
p(HGNC:CLSPN) -> (kin(p(HGNC:ATR)) => p(HGNC:CHEK1, pmod(P)))
Reciprocal Statement Expansion
• All KAM edges are directed• Non-directed BEL relationships (positiveCorrelation,
negativeCorrelation, association) are expanded to be expressed in both directions:
27
r(HGNC:IL8) positiveCorrelation path(MESHD:"Lung Neoplasms")path(MESHD:"Lung Neoplasms") positiveCorrelation r(HGNC:IL8)
becomes
r(HGNC:IL8) positiveCorrelation path(MESHD:"Lung Neoplasms")
r(HGNC:IL8) positiveCorrelation path(MESHD:"Lung Neoplasms")path(MESHD:"Lung Neoplasms") positiveCorrelation r(HGNC:IL8)
Contents
• KAMs and the KAM store• BEL Compiler
– Running the BEL Compiler– Phase I - Compiler Expansions– Phase II - Equivalencing– Phase III – Compiler Augmentations
• BEL Framework Tools
28
Phase II Equivalences
• Nodes are equivalenced based on:– Namespace value UUID
• In .beleq resource file
– Equivalent unordered list • complexes, composites, rxns
29
The BEL Framework Manages Equivalences Between External IDs
• Equivalences between terms from different vocabularies are provided to the BEL compiler– AKT3 in the HGNC namespace and Entrez Gene ID 10000 refer to the
same gene– p(HGNC:AKT3) and p(EG:10000) coalesce to a single node in a KAM
• Selection of preferred namespaces “Dialect” slated for future
30
Contents
• KAMs and the KAM store• BEL Compiler
– Running the BEL Compiler– Phase I - Compiler Expansions– Phase II - Equivalencing– Phase III – Compiler Augmentations
• BEL Framework Tools
31
Phase III Augmentations
• Gene Scaffolding• Protein Families• Named Complexes• Orthology
32
Network Augmentation Order
Protein Family
Inclusion
Named ComplexInclusion
Protein Family
Expansion
NamedComplex
Expansion
GeneScaffolding
OptionalStages
Basic Stages
33
Orthology
Gene Scaffolding• Default behavior is to insert p(), r(), and g() nodes
and corresponding edges wherever a protein, rna, or gene abundance term is detected
• The compiler will only insert missing nodes and edges– Can be turned off with the --no-gene-scaffolding switch
becomes
p(HGNC:KRAS, sub(G, 12, V)) -> \ path(MESH:Neoplasms)p(HGNC:KRAS) hasVariant \ p(HGNC:KRAS, sub(G, 12, V))r(HGNC:KRAS) >> p(HGNC:KRAS)g(HGNC:KRAS) :> r(HGNC:KRAS)
34
p(HGNC:KRAS, sub(G, 12, V)) -> path(MESHD:Neoplasms)
Protein Family Expansion
• The compiler will automatically include protein family members when a protein family term is identified – Can be turned off using the --no-protein-families switch
• The compiler can also search for protein families to include when a protein family member is identified– Can be enabled using the --expand-protein-families switch
• The compiler will automatically connect protein family activity terms with the corresponding family member activity terms
35
Protein Family Example 1 (Default Behavior)
becomesp(HGNC:KRAS, sub(G,12,D)) -> kin(p(PFH:"MAPK JNK Family"))p(HGNC:KRAS) hasVariant p(HGNC:KRAS, sub(G,12,D)) p(PFH:"MAPK JNK Family") actsIn kin(p(PFH:"MAPK JNK Family"))
p(PFH:"MAPK JNK Family") hasMember p(HGNC:MAPK8)p(PFH:"MAPK JNK Family") hasMember p(HGNC:MAPK9)p(PFH:"MAPK JNK Family") hasMember p(HGNC:MAPK10)
Gene scaffolding will also be added to p(HGNC:KRAS) , p(HGNC:MAPK8), p(HGNC:MAPK9), and p(HGNC:MAPK10)
36
p(HGNC:KRAS, sub(G,12,D)) -> kin(p(PFH:"MAPK JNK Family"))
Protein Family Example 2 (Default Behavior)
becomes
kin(p(HGNC:AKT1)) -> p(HGNC:RELA)kin(p(PFH:"AKT Family")) =| bp(MESHPP:Apoptosis)p(HGNC:AKT1) actsIn kin(p(HGNC:AKT1)) p(PFH:"AKT Family") actsin kin(p(PFH:"AKT Family"))p(PFH:"AKT Family") hasMember p(HGNC:AKT1) p(PFH:"AKT Family") hasMember p(HGNC:AKT2) p(PFH:"AKT Family") hasMember p(HGNC:AKT3) kin(p(HGNC:AKT1)) isA kin(p(PFH:"AKT Family"))
Gene scaffolding would then be applied to p(HGNC:AKT1), p(HGNC:AKT2), p(HGNC:AKT3), and p(HGNC:RELA)
37
kin(p(HGNC:AKT1)) -> p(HGNC:RELA)kin(p(PFH:"AKT Family")) =| bp(MESHPP:Apoptosis)
Protein Family Example 3 (--expand-protein-families enabled)
becomes
kin(p(HGNC:AKT1)) -> p(HGNC:RELA)p(HGNC:AKT1) actsIn kin(p(HGNC:AKT1)) p(PFH:"AKT Family") hasMember p(HGNC:AKT1) p(PFH:"AKT Family") hasMember p(HGNC:AKT2) p(PFH:"AKT Family") hasMember p(HGNC:AKT3)
Gene scaffolding would then be applied to p(HGNC:AKT1), p(HGNC:AKT2), p(HGNC:AKT3), and p(HGNC:RELA)
38
kin(p(HGNC:AKT1)) -> p(HGNC:RELA)
Named Complex Expansion
• The compiler will automatically include named complex components when a named complex member is identified – can be turned off using the --no-named-complexes switch
• The compiler can also search for named complexes to include when a named complex member is identified– Can be enabled using the --expand-named-complexes
switch
39
Named Complex Expansion(Default Behavior)
becomes
kin(complex(NCH:"IkappaB Kinase Complex")) => \ p(HGNC:NFKBIA, pmod(P,S,32))complex(NCH:"IkappaB Kinase Complex") actsIn \ kin(complex(NCH:"IkappaB Kinase Complex")) p(HGNC:NFKBIA) hasModification p(HGNC:NFKBIA, pmod(P, S, 32)) complex(NCH:"IkappaB Kinase Complex") hasComponent p(HGNC:CHUK)complex(NCH:"IkappaB Kinase Complex") hasComponent p(HGNC:IKBKB)complex(NCH:"IkappaB Kinase Complex") hasComponent p(HGNC:IKBKG)
Gene scaffolding would then be applied to p(HGNC:CHUK) , p(HGNC:NFKBIA), p(HGNC:IKBKB), and p(HGNC:IKBKG)
40
kin(complex(NCH:"IkappaB Kinase Complex")) => \ p(HGNC:NFKBIA, pmod(P,S,32))
Contents
• KAMs and the KAM store• BEL Compiler
– Running the BEL Compiler– Phase I - Compiler Expansions– Phase II - Equivalencing– Phase III – Compiler Augmentations
• BEL Framework Tools
41
BEL Framework Tools
• Found in the “tools” folder of the BEL Framework• Two versions for each:
– .cmd (Windows) – .sh (Linux, OS X)
• KamManager– Use with –h to get full options list– list KAMs in KAM store, export KAM to XGMML, delete KAM
• BelCheck – check BEL document validity
• DocumentConverter – convert between BEL script and xbel formats
• CacheManager– Manage cached resources
42