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SRI International Bioinformatics 1 Computing with Pathway/Genome Databases.

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Presentation on theme: "SRI International Bioinformatics 1 Computing with Pathway/Genome Databases."— Presentation transcript:

1 SRI International Bioinformatics 1 Computing with Pathway/Genome Databases

2 SRI International Bioinformatics 2 Aprox presentation time: 1.5 hrs

3 SRI International Bioinformatics 3 Overview Summary of Pathway Tools data access mechanisms and formats Pathway Tools APIs Overview of Pathway Tools schema

4 SRI International Bioinformatics 4 Motivations to Understanding Schema When writing complex queries to PGDBs, those queries must refer to classes and slots within the schema l Queries using Lisp, Perl, Java APIs l Queries using Structured Advanced Query Form l Queries using BioVelo Find all monomers longer than 1,000 amino acids l (loop for g in (get-class-all-instances |Genes|) when (< 1000 (abs (- (get-slot-value g left-end-position) (get-slot-value g right-end-position) )) collect (get-slot-value g product) )

5 SRI International Bioinformatics 5 Pathway Tools Implementation Details Platforms: l Macintosh, PC/Linux, and PC/Windows platforms Same binary can run as desktop app or Web server Production-quality software l Version control l Two regular releases per year l Extensive quality assurance l Extensive documentation l Auto-patch l Automatic DB-upgrade 420,000 lines of Lisp code

6 SRI International Bioinformatics 6 More Information Pathway Tools Web Site, Tutorial Slides l l PTools APIs: l Web services: Guide to the Pathway Tools Schema l Curator's Guide l

7 SRI International Bioinformatics 7 References Ontology Papers section of l "An Evidence Ontology for use in Pathway/Genome Databases" l "An ontology for biological function based on molecular interactions" l "Representations of metabolic knowledge: Pathways" l "Representations of metabolic knowledge"

8 SRI International Bioinformatics 8 Data Exchange APIs: Lisp API, Java API, and Perl API l Read and modify access Web services Cyclone Export to files l BioPAX Export l Export PGDB genome to Genbank format l Export entire PGDB as column-delimited and attribute-value file formats l Export PGDB reactions as SBML -- l Import/Export of Pathways: between PGDBs l Import/Export of Selected Frames, for Spreadsheets l Import/Export of Compounds as Molfile, CML BioWarehouse : Loader for Flatfiles, SQL access l l BMC Bioinformatics 7:

9 SRI International Bioinformatics 9 Pathway Tools Ontology / Schema Ontology classes: 1621 l Datatype classes: Define objects from genomes to pathways l Classification systems for pathways, chemical compounds, enzymatic reactions (EC system) l Protein Feature ontology l Controlled vocabularies: u Cell Component Ontology u Evidence codes Comprehensive set of 279 attributes and relationships

10 SRI International Bioinformatics 10 High-Level Classes in the Pathway Tools Ontology Chemicals-- All molecules Polymer-Segments-- Regions of polymers Protein-Features-- Features on proteins Organisms Reactions-- Biochemical reactions Enzymatic-Reactions-- Link enzymes to reactions they catalyze Pathways-- Metabolic and signaling pathways Regulation-- Regulatory interactions CCO-- Cell Component Ontology Evidence -- Evidence ontology Gene-Ontology-Terms-- GO Growth-Observations-- Observations of growth of organism Notes-- Timestamped, person-stamped notes Organizations, People Publications

11 SRI International Bioinformatics 11 Navigating the Schema

12 SRI International Bioinformatics 12 Use GKB Editor to Inspect the Pathway Tools Ontology GKB Editor = Generic Knowledge Base Editor Type in Navigator window: (GKB) or [Right-Click] Edit->Ontology Editor View->Browse Class Hierarchy [Middle-Click] to expand hierarchy To view classes or instances, select them and: l Frame -> List Frame Contents l Frame -> Edit Frame

13 SRI International Bioinformatics 13 Use the SAQP to Inspect the Schema

14 SRI International Bioinformatics 14 Pathway Tools Schema Guide to the Pathway Tools Schema Schema overview diagram

15 SRI International Bioinformatics 15 Principal Classes Class names are capitalized, plural, separated by dashes Genetic-Elements, with subclasses: l Chromosomes l Plasmids Genes Transcription-Units RNAs l rRNAs, snRNAs, tRNAs, Charged-tRNAs Proteins, with subclasses: l Polypeptides l Protein-Complexes

16 SRI International Bioinformatics 16 Principal Classes Reactions, with subclasses: l Transport-Reactions Enzymatic-Reactions Pathways Compounds-And-Elements

17 SRI International Bioinformatics 17 Principal Classes Regulation

18 SRI International Bioinformatics 18 Slot Links Sdh-flavoSdh-Fe-SSdh-membrane-1Sdh-membrane-2 sdhA sdhB sdhCsdhD Succinate + FAD = fumarate + FADH 2 Enzymatic-reaction Succinate dehydrogenase TCA Cycle product component-of catalyzes reaction in-pathway

19 SRI International Bioinformatics 19 Programmatic Access to BioCyc Common LISP Native language of Pathway Tools Interactive & Mature Environment Full Access to the Data & Many Utility Functions Source code is available for academics PerlCyc API of Functions, Exposed to Perl Communication through UNIX Socket JavaCyc API of Functions, Exposed to Java Communication through UNIX Socket Cyclone

20 SRI International Bioinformatics 20 Cyclone Developed by Schachter and colleagues from Genoscope Cyclone is a Java-based system that: l Extracts data from a Pathway Tools PGDB l Converts it to an XML schema l Maps the data to Java objects and to a relational database l Changes made to the data on the Java side can be committed back to a Pathway Tools PGDB

21 SRI International Bioinformatics 21 Lisp API Accessible whenever you start Pathway Tools with the –lisp argument Lisp queries evaluate against the running Pathway Tools binary and execute very fast

22 SRI International Bioinformatics 22 Ocelot Object Database

23 SRI International Bioinformatics 23 Pathway Tools Implementation Details Platforms: l Macintosh, PC/Linux, and PC/Windows platforms Same binary can run as desktop app or Web server Production-quality software l Version control l Two regular releases per year l Extensive quality assurance l Extensive documentation l Auto-patch l Automatic DB-upgrade 600,000 lines of Lisp code

24 SRI International Bioinformatics 24 Pathway Tools Architecture Ocelot DBMS GFP API Pathway Genome Navigator Web Mode Desktop Mode Protein Editor Pathway Editor Reaction Editor Oracle or MySQL Disk File Lisp Perl Java

25 SRI International Bioinformatics 25 Ocelot Object Database Frame data model l Classes, instances, inheritance l Frames have slots that define their properties, attributes, relationships l A slot has one or more values u Datatypes include numbers, strings, etc. Slotunit frames define metadata about slots: l Domain, range, inverse l Collection type, number of values, value constraints

26 SRI International Bioinformatics 26 Storage System Architecture File KBs Read-only applications can be distributed without a relational DBMS l Load all objects and code into Lisp memory l Dump virtual memory to binary executable file

27 SRI International Bioinformatics 27 Ocelot Storage System Architecture Persistent storage via disk files, MySQL or Oracle DBMS l Concurrent development: MySQL or Oracle l Single-user development: disk files Relational DBMS storage l RDBMS is submerged within Ocelot, invisible to users l Frames transferred from RDBMS to Ocelot u On demand u By background prefetcher u Memory cache u Persistent disk cache to speed performance via Internet

28 SRI International Bioinformatics 28 Transaction Logging Relational DBMS stores l The latest version of each Ocelot frame l A log of all GFP operations applied to KB Transaction log enables: l Reconstruction of earlier versions of KB l View history of changes to an object l Update replicates of a KB l Detection of update conflicts during concurrency control l Undo of updates

29 SRI International Bioinformatics 29 Optimistic Concurrency Control Locking approach: edits to one object can require locking all connected objects No locking User performs updates in local workspace When user commits changes, storage system compares user changes against all other committed changes

30 SRI International Bioinformatics 30 Ocelot Knowledge Server Schema Evolution FRSs store and process class and instance information similarly Application can query schema information as easily as it can query instances Schema is stored within the DB Schema is self documenting Schema evolution facilitated by l Easy addition/removal of slots, or alteration of slot datatypes l Flexible data formats that do not require dumping/reloading of data

31 SRI International Bioinformatics 31 Generic Frame Protocol (GFP) A library of procedures for accessing Ocelot DBs GFP specification: l A small number of GFP functions are sufficient for most complex queries

32 SRI International Bioinformatics 32 Example of a Single GFP Call The General Pattern: gfp-function(frame slot value...) (gfp-function frame slot value …) LISP (get-slot-values 'TRYPSYN-RXN 'LEFT) ==> (INDOLE-3-GLYCEROL-P SER)

33 SRI International Bioinformatics 33 Frame References At the GFP level, every Ocelot frame can be referred to using either symbol frame name or frame object Most GFP functions return frame objects Importance of using fequal for comparisons

34 SRI International Bioinformatics 34 Generic Frame Protocol get-class-all-instances (Class) l Returns direct and indirect instances of Class coercible-to-frame-p (Thing) l Is Thing a frame? Returns True if Thing is the name of a frame, or a frame object; else False

35 SRI International Bioinformatics 35 Generic Frame Protocol Notation Frame.Slot means a specified slot of a specified frame. Note: Slot must be a symbol! get-slot-value(Frame Slot) l Returns first value of Frame.Slot get-slot-values(Frame Slot) l Returns all values of Frame.Slot as a list slot-has-value-p(Frame Slot) l Returns True if Frame.Slot has at least one value; else False member-slot-value-p(Frame Slot Value) l Returns True if Value is one of the values of Frame.Slot; else False Instance-all-instance-of-p(Instance Class) l Returns True if Instance is an all-instance of Class

36 SRI International Bioinformatics 36 Generic Frame Protocol print-frame(Frame) l Prints the contents of Frame

37 SRI International Bioinformatics 37 Generic Frame Protocol – Update Operations put-slot-value(Frame Slot Value) l Replace the current value(s) of Frame.Slot with Value put-slot-values(Frame Slot Value-List) l Replace the current value(s) of Frame.Slot with Value-List, which must be a list of values add-slot-value(Frame Slot Value) l Add Value to the current value(s) of Frame.Slot, if any remove-slot-value(Frame Slot Value) l Remove Value from the current value(s) of Frame.slot replace-slot-value(Frame Slot Old-Value New-Value) l In Frame.Slot, replace Old-Value with New-Value remove-local-slot-values(Frame Slot) l Remove all of the values of Frame.Slot

38 SRI International Bioinformatics 38 Generic Frame Protocol – Update Operations save-kb l Saves the current KB

39 SRI International Bioinformatics 39 Additional Pathway Tools Functions – Semantic Inference Layer Semantic inference layer defines built-in functions to compute commonly required relationships in a PGDB fns.html fns.html

40 SRI International Bioinformatics 40 PerlCyc and JavaCyc Work on Unix (Solaris or Linux) only Start up Pathway Tools with the –api arg Pathway Tools listens on a Unix socket – perl program communicates through this socket Supports both querying and editing PGDBs Must run perl or java program on the same machine that runs Pathway Tools l This is a security measure, as the API server has no built-in security Can only handle one connection at a time

41 SRI International Bioinformatics 41 Obtaining PerlCyc and JavaCyc Download from PerlCyc written and maintained by Lukas Mueller at Boyce Thompson Institute for Plant Research. JavaCyc written by Thomas Yan at Carnegie Institute, maintained by Lukas Mueller. Easy to extend…

42 SRI International Bioinformatics 42 Examples of PerlCyc, JavaCyc Functions GFP functions (require knowledge of Pathway Tools schema): l get_slot_values l get_class_all_instances l put_slot_values Pathway Tools functions (described at l genes_of_reaction l find_indexed_frame l pathways_of_gene l transport_p l getSlotValues l getClassAllInstances l putSlotValues l genesOfReaction l findIndexedFrame l pathwaysOfGene l transportP

43 SRI International Bioinformatics 43 Writing a PerlCyc or JavaCyc program Create a PerlCyc, JavaCyc object: perlcyc -> new (ORGID) new Javacyc (ORGID) Call PerlCyc, JavaCyc functions on this object: my $cyc = perlcyc -> new (ECOLI); = $cyc -> all_pathways (); Javacyc cyc = new Javacyc(ECOLI); ArrayList pathways = cyc.allPathways (); Functions return object IDs, not objects. l Must connect to server again to retrieve attributes of an object. foreach my $p { print $cyc -> get_slot_value ($p, COMMON-NAME);} for (int i=0; I < pathways.size(); i++) { String pwy = (String) pathways.get(i); System.out.println (cyc.getSlotValue (pwy, COMMON-NAME); }

44 SRI International Bioinformatics 44 Sample PerlCyc Query Number of proteins in E. coli use perlcyc; my $cyc = perlcyc -> new (ECOLI); = $cyc-> get_class_all_instances("|Proteins|"); my $protein_count = print "Protein count: $protein_count.\n";

45 SRI International Bioinformatics 45 Sample PerlCyc Query Print IDs of all proteins with molecular weight between 10 and 20 kD and pI between 4 and 5. use perlcyc; my $cyc = perlcyc -> new (ECOLI); foreach my $p ($cyc->get_class_all_instances("|Proteins|")) { my $mw = $cyc->get_slot_value($p, "molecular-weight-kd"); my $pI = $cyc->get_slot_value($p, "pi"); if ($mw = 10 && $pI = 4) { print "$p\n"; }

46 SRI International Bioinformatics 46 Sample PerlCyc Query List all the transcription factors in E. coli, and the list of genes that each regulates: use perlcyc; my $cyc = perlcyc -> new (ECOLI); foreach my $p ($cyc->get_class_all_instances("|Proteins|")) { if ($cyc->transcription_factor_p($p)) { my $name = $cyc->get_slot_value($p, "common-name"); my %genes = (); foreach my $tu ($cyc->regulon_of_protein($p)) { foreach my $g ($cyc->transcription_unit_genes($tu)) { $genes{$g} = $cyc->get_slot_value($g, "common-name"); } print "\n\n$name: "; print join " ", values %genes; }

47 SRI International Bioinformatics 47 Sample Editing Using PerlCyc Add a link from each gene to the corresponding object in MY-DB (assume ID is same in both cases) use perlcyc; my $cyc = perlcyc -> new (HPY); = $cyc->get_class_all_instances (|Genes|); foreach my $g { $cyc->add_slot_value ($g, DBLINKS, (MY-DB \$g\)); } $cyc->save_kb();

48 SRI International Bioinformatics 48 Sample JavaCyc Query: Enzymes for which ATP is a regulator import java.util.*; public class JavacycSample { public static void main(String[] args) { Javacyc cyc = new Javacyc("ECOLI"); ArrayList regframes = cyc.getClassAllInstances("|Regulation-of-Enzyme-Activity|"); for (int i = 0; i < regframes.size(); i++) { String reg = (String)regframes.get(i); boolean bool = cyc.memberSlotValueP(reg, Regulator", "ATP"); if (bool) { String enzrxn = cyc.getSlotValue (reg, Regulated-Entity); String enzyme = cyc.getSlotValue (enzrxn, Enzyme); System.out.println(enz); } } } }

49 SRI International Bioinformatics 49 Simple Lisp Query Example: Enzymes for which ATP is a regulator (defun atp-inhibits () (loop for x in (get-class-all-instances '|Regulation-of-Enzyme-Activity|) ;; Does the Regulator slot contain the compound ATP, and the mode ;; of regulation is negative (inhibition)? when (and (member-slot-value-p x Regulator 'ATP) (member-slot-value-p x Mode -) ) ;; Whenever the test is positive, we collect the value of the slot Enzyme ;; of the Regulated-Entity of the regulatory interaction frame. ;; The collected values are returned as a list, once the loop terminates. collect (get-slot-value (get-slot-value x Regulated-Entity) Enzyme) ) ) ;;; invoking the query: (select-organism :org-id 'ECOLI) (atp-inhibits) (get-slot-values 'TRYPSYN-RXN 'LEFT) ==> (INDOLE-3-GLYCEROL-P SER)

50 SRI International Bioinformatics 50 Simple Perl Query Example: Enzymes for which ATP is a regulator use perlcyc; my $cyc = perlcyc -> new("ECOLI"); = $cyc -> get_class_all_instances("|Regulation-of-Enzyme- Activity|"); ## We check every instance of the class foreach my $reg { ## We test for whether the INHIBITORS-ALL ## slot contains the compound frame ATP my $bool1 = $cyc -> member_slot_value_p($reg, Regulator", "Atp"); my $bool2 = $cyc -> member_slot_value_p($reg, Mode", -"); if ($bool1 && $bool2) { ## Whenever the test is positive, we collect the value of the slot ENZYME. ## The results are printed in the terminal. my $enzrxn = $cyc -> get_slot_value($reg, Regulated-Entity"); my $enz = $cyc -> get_slot_value($enzrxn, "Enzyme"); print STDOUT "$enz\n"; }

51 SRI International Bioinformatics 51 Getting started with Lisp pathway-tools –lisp (load file) (compile-file file.lisp) Emacs is a useful editor Pathway Tools source code is available: ask Overview of Lisp information resources: l Documented Pathway Tools Lisp functions: l

52 SRI International Bioinformatics 52 Viewing Results via the Answer List (loop for r in (get-class-all-instances '|Reactions|) when (< 3 (length (get-slot-values r 'left))) collect r) (setq answer *) (object-table answer) (replace-answer-list answer) (pt) Next Answer

53 SRI International Bioinformatics 53 Query Gotchas Study schema carefully :test #fequal Cascade of slot-values: check for NIL

54 SRI International Bioinformatics 54 Semantic Inference Layer relationships.lisp Library of functions that encapsulate common query building blocks and intricacies of navigating the schema enzymes-of-gene reactions-of-gene pathways-of-gene genes-of-pathway pathway-hole-p reactions-of-compound top-containers(protein) all-rxns(type) (:metab-smm :metab-all :metab-pathways :enzyme :transport etc.) l (all-rxns :metab-pathways)

55 SRI International Bioinformatics 55 Pathway Tools Schema and Semantic Inference Layer Genes, Operons, and Replicons

56 SRI International Bioinformatics 56 Representing a Genome Classes: l ORG is of class Organisms l CHROM1 is of class Chromosomes l PLASMID1 is of class Plasmids l Gene1 is of class Genes l Product1 is of class Polypeptides or RNA ORG CHROM1 CHROM2 PLASMID1 Gene1 Gene2 Gene3 genome components Product1 product

57 SRI International Bioinformatics 57 Polynucleotides Review slots of COLI and of COLI-K12

58 SRI International Bioinformatics 58 Genetic-Elements Sequence is stored in a separate file or database table

59 SRI International Bioinformatics 59 Polymer-Segments Review slots of Genes

60 SRI International Bioinformatics 60 Complexities of Gene / Gene-Product Relationships 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: l Nucleotide positions of starting and ending codons specified in Left-End- Position and Right-End-Position (usually greater, except at origin) l Transcription-Direction + / - Alternative splicing: l Nucleotide positions of starting and ending codons specified in Left-End- Position and Right-End-Position l Intron positions specified in Splice-Form-Introns of gene product u ( ) ( )

61 SRI International Bioinformatics 61 Gene Reaction Schematic

62 SRI International Bioinformatics 62 Exercises Find all genes on a given chromosome Find all ribosomal RNAs Find the DNA sequence of a given gene Find all proteins longer than 1,000 amino acids

63 SRI International Bioinformatics 63 Exercises Find all genes on a given chromosome (defun genes-of-chrom (chrom) (loop for x in (get-slot-values chrom components) when (instance-all-instance-of-p x |Genes|) collect x) ) Find all ribosomal RNAs l (get-class-all-instances |rRNAs|) Find the DNA sequence of a given gene l (get-gene-sequence gene)

64 SRI International Bioinformatics 64 Exercises Find all monomers longer than 1,000 nucleotides l (loop for g in (get-class-all-instances |Genes|) for p = (get-slot-value g product) when (and (< 1000 (abs (- (get-slot-value g left-end-position) (get-slot-value g right-end-position) ))) (instance-all-instance-of-p p |Polypeptides|) ) collect p )

65 SRI International Bioinformatics 65 Proteins

66 SRI International Bioinformatics 66 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 l DnaE is a polypeptide l pol III core is DnaE and two other polypeptides l pol III holoenzymes is several protein complexes combined

67 SRI International Bioinformatics 67 Protein Complex Relationships

68 SRI International Bioinformatics 68 Slots of a protein (DnaE) catalyzes Is it an activator/reactant/etc? comments component-of dblinks features (edited in feature editor) Many other features possible

69 SRI International Bioinformatics 69 A complex at the frame level (pol III) Same features as polypeptide frame, different use comment component-of and components l note coefficients

70 SRI International Bioinformatics 70 Protein Complex Relationships

71 SRI International Bioinformatics 71 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) inhibitor-of comes from an enzymatic reaction can only edit dna-footprint if protein has been associated with a TU

72 SRI International Bioinformatics 72 Semantic Inference Layer Reactions-of-protein (prot) l Returns a list of rxns this protein catalyzes Transcription-units-of-proteins(prot) l Returns a list of TUs activated/inhibited by the given protein Transporter? (prot) l Is this protein a transporter? Polypeptide-or-homomultimer?(prot) Transcription-factor? (prot) Obtain-protein-stats l Returns 5 values u Length of : all-polypeptides, complexes, transporters, enzymes, etc…

73 SRI International Bioinformatics 73 Example Find all enzymes that use pyridoxal phosphate as a cofactor or prosthetic group l (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.

74 SRI International Bioinformatics 74 Example Queries Find all homomultimers Find proteins whose pI > 10, and that reside on the negative strand of the first chromosome

75 SRI International Bioinformatics 75 Sample Find all proteins without a comment anywhere

76 SRI International Bioinformatics 76 Compounds / Reactions / Pathways

77 SRI International Bioinformatics 77 Compounds / Reactions / Pathways Think of a three tiered structure: l Reactions built on top of compounds l 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

78 SRI International Bioinformatics 78 Compounds

79 SRI International Bioinformatics 79

80 SRI International Bioinformatics 80 Compounds Relatively few aspects of a compound defined within the compound editor l MW, formula calculated from edited structure Most aspects defined in other editors l Pathway reactions comes from reaction editing followed by pathway editing l Activator, etc come from the enzymatic reaction editor

81 SRI International Bioinformatics 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| NIL NIL), (CAS " "), (CAS " ") NAMES: "L-tryptophan", "W", "tryptacin", "trofan", "trp", "tryptophan", "2-amino-3-indolylpropanic acid" SMILES: "c1(c(CC(N)C(=O)O)c2(c([nH]1)cccc2))" SYNONYMS: "W", "tryptacin", "trofan", "trp", "tryptophan", "2-amino-3-indolylpropanic acid" ____________________________________________

82 SRI International Bioinformatics 82 Where is diphosphate in the ontology?

83 SRI International Bioinformatics 83 Semantic Inference Layer Reactions-of-compound (cpd) Pathways-of-compound (cpd) Is-substrate-an-autocatalytic-enzyme-p (cpd) Activated/inhibited-by? (cpds slots) l Returns a list of enzrxns for which a cpd in cpds is a modulator (example slots: activators-all, activators-allosteric) All-substrates (rxns) l All unique substrates specified in the given rxns Has-structure-p (cpd) Obtain-cpd-stats l Returns two values: u Length of :all-cpds, cpds with structures

84 SRI International Bioinformatics 84 Miscellaneous things…. History List l Back/Forward and History buttons l Default list is 50 items Show frame (print-frame frame)

85 SRI International Bioinformatics 85

86 SRI International Bioinformatics 86 Queries with Multiple Answers Navigator queries: l Example: Substring search for pyruvate l Selected list is placed on the Answer list l Use Next Answer button to view each one of them Lisp queries: Example : Find reactions involving pyruvate as a substrate u (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 * )

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