;;  Load the VSPACE python space

;; to start in MeTTaLog use    ./MeTTa 8-FlybaseQuestions.metta --repl

!(extend-py! mettalog)

!(pragma! load debug)
!(pragma! exec debug)

!(pragma! eval debug)
!(pragma! case debug)
!(pragma! case nodebug)

; !(nodebug! (@ metta case))

!(fb-info!)

!(pwd!)
;; MeTTaLog only:
!(ensure-loaded! ../../data/whole_flybase_2)

!(fb-info!)

;;; Types Used in Predicates

; Type Declarations
(: GeneticIdentifierType TypeType)
(: GeneticSymbolType TypeType)
(: OrganismTaxonomyType TypeType)
(: MolecularBiologyType TypeType)
(: GeneticMappingType TypeType)
(: PublicationType TypeType)
(: BiologicalFunctionType TypeType)
(: TextType TypeType)
(: MetadataType TypeType)

; Genetic Identifier Types
(: GeneID GeneticIdentifierType)
(: AlleleID GeneticIdentifierType)
(: ParalogGeneID GeneticIdentifierType)
(: DmelGeneID GeneticIdentifierType)
(: StartingGeneID GeneticIdentifierType)
(: InteractingGeneID GeneticIdentifierType)
(: GroupMemberFBGene GeneticIdentifierType)
(: PrimaryFBid GeneticIdentifierType)
(: FBgn GeneticIdentifierType)
(: CloneID GeneticIdentifierType)
(: TranscriptID GeneticIdentifierType)
(: PolypeptideID GeneticIdentifierType)
(: FBtiID GeneticIdentifierType)  ; FlyBase Transposable Element Insertion ID
(: FBcl GeneticIdentifierType)    ; FlyBase cDNA clone ID

; Genetic Symbol Types
(: GeneSymbol GeneticSymbolType)
(: AlleleSymbol GeneticSymbolType)
(: ParalogGeneSymbol GeneticSymbolType)
(: DmelGeneSymbol GeneticSymbolType)
(: StartingGeneSymbol GeneticSymbolType)
(: InteractingGeneSymbol GeneticSymbolType)
(: GroupMemberFBGeneSymbol GeneticSymbolType)
(: CurrentSymbol GeneticSymbolType)

; Organism and Taxonomy Types
(: OrganismAbbreviation OrganismTaxonomyType)
(: Genus OrganismTaxonomyType)
(: Species OrganismTaxonomyType)
(: NCBITaxon OrganismTaxonomyType)

; Gene Expression and Molecular Biology Types
(: NucleotideAccession MolecularBiologyType)
(: CDNAaccession MolecularBiologyType)
(: ESTaccession MolecularBiologyType)
(: UniprotAccession MolecularBiologyType)
(: RepresentativeProtein MolecularBiologyType)
(: IdenticalProtein MolecularBiologyType)
(: RNAProcess MolecularBiologyType)

; Genetic Location and Mapping Types
(: MapID GeneticMappingType)
(: RecombinationLoc GeneticMappingType)
(: CytogeneticLoc GeneticMappingType)
(: SequenceLoc GeneticMappingType)
(: ArmScaffold GeneticMappingType)
(: Location GeneticMappingType)
(: GenomicLocation GeneticMappingType)
(: Range GeneticMappingType)
(: Orientation GeneticMappingType)

; Publications and References Types
(: PublicationID PublicationType)
(: ReferenceFBrf PublicationType)
(: PubMedID PublicationType)
(: DOI PublicationType)
(: PMCID PublicationType)

; Phenotypes, Diseases, and Biological Functions Types
(: Phenotype BiologicalFunctionType)
(: Disease BiologicalFunctionType)
(: GeneRegulation BiologicalFunctionType)
(: EnzymeFunction BiologicalFunctionType)
(: DOTerm BiologicalFunctionType)
(: SOTermName BiologicalFunctionType)
(: GOID BiologicalFunctionType)
(: ECNumber BiologicalFunctionType)
(: PhenotypeID BiologicalFunctionType)
(: DiseaseAnnotation BiologicalFunctionType)
(: InteractionType BiologicalFunctionType)

; Textual Data Types
(: GeneFullName TextType)
(: GeneSnapshotText TextType)
(: SummaryText TextType)
(: SnapshotText TextType)
(: MiniRef TextType)  ; Short reference or description
(: DatasetMetadataName TextType)
(: ItemName TextType)
(: EntityName TextType)
(: CloneName TextType)
(: R6ConversionNotes TextType)

; Miscellaneous and Metadata Types
(: DatasetMetadataID MetadataType)
(: ItemID MetadataType)
(: EntityID MetadataType)
(: FBGroupID MetadataType)
(: FBGroupSymbol MetadataType)
(: FBGroupName MetadataType)
(: ParentFBGroupID MetadataType)
(: TaxidInteractorA MetadataType)
(: TaxidInteractorB MetadataType)
(: CGNumber MetadataType)
(: PhysicalInteraction MetadataType)

% NondetReturn means these are are backtrackable predicates instead of functions
(: query-info (-> EnglishText  Atom Atom NondetReturn))

(: allele_genetic_interactions! (-> AlleleSymbol AlleleFBal Interaction ReferenceFBrf NondetReturn))
(: allele_phenotypic! (-> AlleleSymbol AlleleFBal Phenotype ReferenceFBrf NondetReturn))
(: automated_gene_summaries! (-> GeneID SummaryText NondetReturn))
(: best_gene_summary! (-> GeneID GeneSymbol SummarySource Summary NondetReturn))
(: cDNA_clone_data! (-> CloneID OrganismAbbreviation CloneName DatasetMetadataName (List CDNAaccession) (List ESTaccession) NondetReturn))
(: cyto-genetic-seq! (-> CytogeneticMapPosition GeneticMapPosition SequenceCoordinatesRelease6 R6ConversionNotes NondetReturn))
(: dataset_metadata! (-> DatasetMetadataID DatasetMetadataName ItemID ItemName NondetReturn))
(: disease_model_annotations! (-> GeneID GeneSymbol HGNC DOQualifier DO DOTerm AlleleUsedInModelFBal AlleleUsedInModelSymbol BasedOnOrthologyWithHGNCID BasedOnOrthologyWithSymbol EvidenceInteractingAlleles ReferenceFBrf NondetReturn))
(: Dmel_enzyme! (-> GeneGroupID GeneGroupName (List GeneGroupGOID) (List GeneGroupGOName) (List GeneGroupECNumber) (List GeneGroupECName) GeneID GeneSymbol GeneName (List GeneECNumber) (List GeneECName) NondetReturn))
(: dmel_gene_sequence_ontology_annotations! (-> GenePrimaryID GeneSymbol SOTermName SOTermID NondetReturn))
(: dmel_human_orthologs_disease! (-> DmelGeneID DmelGeneSymbol HumanGeneHGNC HumanGeneOMIM HumanGeneSymbol DIOPTScore OMIMPhenotypeIDs OMIMPhenotypeNames NondetReturn))
(: dmel_paralogs! (-> GeneID GeneSymbol ArmScaffold Location Strand ParalogGeneID ParalogGeneSymbol ParalogArmScaffold ParalogLocation ParalogStrand DIOPTScore NondetReturn))
(: dmel_unique_protein_isoforms! (-> GeneID GeneSymbol RepresentativeProtein (List IdenticalProtein) NondetReturn))
(: entity_publication! (-> EntityID EntityName FlyBasePublication PubMedID NondetReturn))
(: fb_synonym! (-> PrimaryFBid OrganismAbbreviation CurrentSymbol CurrentFullname (List FullnameSynonym) (List SymbolSynonym) NondetReturn))
(: fbal_to_fbgn! (-> AlleleID AlleleSymbol GeneID GeneSymbol NondetReturn))
(: fbgn_annotation_ID! (-> GeneSymbol OrganismAbbreviation GeneID (List SecondaryFBgn) AnnotationID (List SecondaryAnnotationID) NondetReturn))
(: fbgn_exons2affy1_overlaps! (-> GeneID (List AffyID1) NondetReturn))
(: fbgn_exons2affy2_overlaps! (-> GeneID (List AffyID2) NondetReturn))
(: fbgn_fbtr_fbpp! (-> GeneID TranscriptID PolypeptideID NondetReturn))
(: fbgn_fbtr_fbpp_expanded! (-> Organism GeneType GeneID GeneSymbol GeneFullname AnnotationID TranscriptType TranscriptID TranscriptSymbol PolypeptideID PolypeptideSymbol NondetReturn))
(: fbgn_gleanr! (-> OrganismAbbreviation GeneSymbol GeneID GLEANR NondetReturn))
(: fbgn_NAseq_Uniprot! (-> GeneSymbol OrganismAbbreviation GeneID NucleotideAccession NABasedProteinAccession UniprotAccession EntrezGene RefSeqTranscripts RefSeqProteins NondetReturn))
(: fbgn_uniprot! (-> GeneID GeneSymbol CGNumber UniprotAccession NondetReturn))
(: fbrf_pmid_pmcid_doi! (-> ReferenceFBrf PMID PMCID DOI PubType MiniRef PMIDAdded NondetReturn))
(: gene_functional_complementation! (-> DmelGeneSymbol DmelGeneID OrthologGeneSymbol OrthologGeneID ReferenceFBrf NondetReturn))
(: gene_genetic_interactions! (-> (List StartingGeneSymbol) (List StartingGeneID) (List InteractingGeneSymbol) (List InteractingGeneID) InteractionType PublicationFBrf NondetReturn))
(: gene_group! (-> FBGroupID FBGroupSymbol FBGroupName ParentFBGroupID ParentFBGroupSymbol GroupMemberFBGene GroupMemberFBGeneSymbol NondetReturn))
(: gene_groups_HGNC! (-> FBGroupID FBGroupSymbol FBGroupName HGNCFamily NondetReturn))
(: gene_map_table! (-> OrganismAbbreviation CurrentSymbol PrimaryFBid RecombinationLoc CytogeneticLoc SequenceLoc NondetReturn))
(: gene_rpkm_matrix! (-> GenePrimaryID GeneSymbol GeneFullName GeneType DataSampleName NondetReturn))
(: gene_rpkm_report! (-> ReleaseID GeneID GeneSymbol ParentLibraryFBlc ParentLibraryName RNASourceFBlc RNASourceName RPKMValue BinValue UniqueExonBaseCount TotalExonBaseCount CountUsed NondetReturn))
(: gene_snapshots! (-> GeneID GeneSymbol GeneName Datestamp GeneSnapshotText NondetReturn))
(: genomic_clone! (-> CloneID OrganismAbbreviation CloneName Accession NondetReturn))
(: genotype_phenotype_data! (-> (List GenotypeSymbols) (List GenotypeIDs) PhenotypeName PhenotypeID (List QualifierNames) (List QualifierIDs) Reference NondetReturn))
(: insertion_mapping! (-> InsertionSymbol FBtiID GenomicLocation Range Orientation EstimatedCytogeneticLocation ObservedCytogeneticLocation NondetReturn))
(: organism_list! (-> Genus Species Abbreviation CommonName NCBITaxon DrosophilidFlag NondetReturn))
(: pathway_group! (-> FBGroupID FBGroupSymbol FBGroupName ParentFBGroupID ParentFBGroupSymbol GroupMemberFBGene GroupMemberFBGeneSymbol NondetReturn))
(: physical_interactions_mitab! (-> (List IDInteractorA) (List IDInteractorB) (List AltIDInteractorA) (List AltIDInteractorB) (List AliasInteractorA) (List AliasInteractorB) (List InteractionDetectionMethod) (List Publication1stAuthor) (List Publication) TaxidInteractorA TaxidInteractorB (List InteractionType) (List SourceDatabase) (List InteractionIdentifier) (List ConfidenceValue) (List ExpansionMethod) (List BiologicalRoleInteractorA) (List BiologicalRoleInteractorB) (List ExperimentalRoleInteractorA) (List ExperimentalRoleInteractorB) (List TypeInteractorA) (List TypeInteractorB) (List XrefInteractorA) (List XrefInteractorB) (List InteractionXref) (List AnnotationInteractorA) (List AnnotationInteractorB) (List InteractionAnnotation) (List HostOrganism) InteractionParameters CreationDate UpdateDate (List ChecksumInteractorA) (List ChecksumInteractorB) InteractionChecksum Negative (List FeatureInteractorA) (List FeatureInteractorB) StoichiometryInteractorA StoichiometryInteractorB (List IdentificationMethodParticipantA) (List IdentificationMethodParticipantB) NondetReturn))
(: pmid_fbgn_uniprot! (-> ReferenceFBrf PMID GeneID UniProtDatabase UniProtID NondetReturn))
(: scRNA-Seq_gene_expression! (-> PubID PubMiniRef ClusteringAnalysisID ClusteringAnalysisName SourceTissueSex SourceTissueStage SourceTissueAnatomy ClusterID ClusterName ClusterCellTypeID ClusterCellTypeName GeneID GeneSymbol MeanExpression Spread NondetReturn))
(: synonym! (-> PrimaryFBid OrganismAbbreviation GeneSymbol CurrentFullname (List FullnameSynonym) (List SymbolSynonym) NondetReturn))

(arity allele_genetic_interactions 4)
(arity automated_gene_summaries 3)
(arity best_gene_summary 4)
(arity cDNA_clone_data 6)
(arity cyto-genetic-seq 4)
(arity disease_model_annotations 12)
(arity Dmel_enzyme_data 11)
(arity dmel_gene_sequence_ontology_annotations 4)
(arity dmel_human_orthologs_disease 8)
(arity dmel_paralogs 11)
(arity dmel_unique_protein_isoforms 4)
(arity entity_publication 4)
(arity fb_synonym 6)
(arity fbal_to_fbgn 4)
(arity fbgn_annotation_ID 6)
(arity fbgn_exons2affy1_overlaps 2)
(arity fbgn_exons2affy2_overlaps 2)
(arity fbgn_fbtr_fbpp 3)
(arity fbgn_fbtr_fbpp_expanded 11)
(arity fbgn_gleanr 4)
(arity fbgn_NAseq_Uniprot 9)
(arity fbgn_uniprot 4)
(arity fbrf_pmid_pmcid_doi 7)
(arity gene_functional_complementation 5)
(arity gene_genetic_interactions 6)
(arity gene_group_data 7)
(arity gene_map_table 6)
(arity gene_rpkm_matrix 170)
(arity gene_rpkm_report 12)
(arity gene_snapshots 5)
(arity genome-cyto-seq 3)
(arity genomic_clone_data 4)
(arity genotype_phenotype_data 7)
(arity gp_information 10)
(arity insertion_mapping 7)
(arity organism_list 6)
(arity pathway_group_data 7)
(arity physical_interactions_mitab 42)
(arity pmid_fbgn_uniprot 5)
(arity transposon_sequence_set 62)

(arity obo-allele-common-terms 2)
(arity obo-allele-expression-desc-text 2)
(arity obo-allele-image2 6)
(arity obo-allele-images 2)
(arity obo-allele-major-stages 2)
(arity obo-allele-major-tissues 2)
(arity obo-allele-name 2)
(arity obo-allele-pubs 2)
(arity obo-allele-rex-gene 2)
(arity obo-allele-stocks 2)
(arity obo-allele-transposons 2)
(arity obo-alt-id 2)
(arity obo-attached-to 3)
(arity obo-attached-to-part-of 3)
(arity obo-charge 2)
(arity obo-comment 2)
(arity obo-common-terms 1)
(arity obo-consider 2)
(arity obo-continuous-with 3)
(arity obo-created-by 2)
(arity obo-creation-date 2)
(arity obo-crossReferenceIds 1)
(arity obo-def 4)
(arity obo-derives-from 3)
(arity obo-develops-directly-from 3)
(arity obo-develops-from 3)
(arity obo-develops-into 3)
(arity obo-directory 2)
(arity obo-disjoint-from 3)
(arity obo-electrically-synapsed-to 3)
(arity obo-exon-locations 8)
(arity obo-exons-chromosome 1)
(arity obo-exons-endPosition 1)
(arity obo-exons-INSDC-accession 1)
(arity obo-exons-startPosition 1)
(arity obo-expression-desc-text 1)
(arity obo-fasciculates-with 3)
(arity obo-fbid 1)
(arity obo-format-version 2)
(arity obo-formula 2)
(arity obo-gene 6)
(arity obo-gene-geneId 1)
(arity obo-gene-locusTag 2)
(arity obo-gene-name 2)
(arity obo-gene-symbol 2)
(arity obo-gene-synonyms 2)
(arity obo-gene-url 2)
(arity obo-has-fasciculating-neuron-projection 3)
(arity obo-has-functional-parent 2)
(arity obo-has-origin 3)
(arity obo-has-parent-hydride 2)
(arity obo-has-part 3)
(arity obo-has-quality 3)
(arity obo-has-role 2)
(arity obo-has-sensory-dendrite-in 3)
(arity obo-has-soma-location 3)
(arity obo-has-synaptic-IO-in 3)
(arity obo-id-type 2)
(arity obo-imageDescription 1)
(arity obo-images 1)
(arity obo-immediately-preceded-by 3)
(arity obo-inchi 2)
(arity obo-inchikey 2)
(arity obo-innervated-by 3)
(arity obo-innervates 3)
(arity obo-insertions 1)
(arity obo-is-a 2)
(arity obo-is-conjugate-acid-of 2)
(arity obo-is-conjugate-base-of 2)
(arity obo-is-enantiomer-of 2)
(arity obo-is-obsolete 2)
(arity obo-is-substituent-group-from 2)
(arity obo-is-tautomer-of 2)
(arity obo-is-transitive 2)
(arity obo-major-tissues 1)
(arity obo-mass 2)
(arity obo-monoisotopicmass 2)
(arity obo-name 2)
(arity obo-namespace 2)
(arity obo-negatively-regulates 3)
(arity obo-overlaps 3)
(arity obo-part-of 3)
(arity obo-pathname 2)
(arity obo-positively-regulates 3)
(arity obo-primaryId 1)
(arity obo-pubFigure 1)
(arity obo-publicationId 1)
(arity obo-publications 1)
(arity obo-pubs 1)
(arity obo-receives-input-from 3)
(arity obo-receives-synaptic-input-from-neuron 3)
(arity obo-receives-synaptic-input-in-region 3)
(arity obo-receives-synaptic-input-throughout 3)
(arity obo-regulates 3)
(arity obo-relatedSequences 3)
(arity obo-relatedSequences-sequenceId 1)
(arity obo-remark 2)
(arity obo-replaced-by 2)
(arity obo-rex-gene 1)
(arity obo-sends-synaptic-output-throughout 3)
(arity obo-sends-synaptic-output-to-cell 3)
(arity obo-sends-synaptic-output-to-region 3)
(arity obo-sequence 1)
(arity obo-smiles 2)
(arity obo-soTermId 1)
(arity obo-stocks 1)
(arity obo-subset 2)
(arity obo-subsetdef 3)
(arity obo-substage-of 3)
(arity obo-symbol 1)
(arity obo-symbolSynonyms 1)
(arity obo-synapsed-via-type-Ib-bouton-to 3)
(arity obo-synapsed-via-type-II-bouton-to 3)
(arity obo-synapsed-via-type-III-bouton-to 3)
(arity obo-synapsed-via-type-Is-bouton-to 3)
(arity obo-synonym 5)
(arity obo-synonymtypedef 4)
(arity obo-transposon 6)
(arity obo-transposon-cross-references 2)
(arity obo-transposon-publications 2)
(arity obo-transposons 1)
(arity obo-transposon-synonyms 2)
(arity obo-url 1)




;;  do some queries

(: number-of (-> Countable Number))
(= (number-of $query $length)
    (length! (match &self $query t) $length))

;; inside flybase we only see 74 answers
!(match &flybase (gene_map_table $Org $Sym $G 3-59 $D $E) ($Sym $G $D $E))

;; should return no results in &self
!(match &self (gene_map_table $Org $Sym $G 3-59 $D $E) ($Sym $G $D $E))

;; our special hack to see into other spaces
!(number-of (gene_map_table! $Org $Sym $G 3-59 $D $E)) ;; 74

; !(repl!)

!(get-atoms &flybase (gene_map_table $Org $Sym $G 3-59 $D $E))



;;     flybase space answer should be 0
!(number-of (gene_map_table $Org $Sym $G 3-59 $D $E)) ;; 0

;; use the host system limiter of 5
!(number-of  (limit 5 (gene_map_table! $Org $Sym $G 3-59 $D $E)))  ;; 5

!(assertEqual (number-of (gene_map_table! $MapID $OrganismAbbreviation $ParalogGeneID 3-59 $CytogeneticLoc $SequenceLoc)) 74)

; (gene_map_table! $MapID $OrganismAbbreviation $ParalogGeneID $RecombinationLoc $CytogeneticLoc $SequenceLoc)


;; What recombination locations have 74 Paralog Genes?
;; !(,  (gene_map_table! $_ $_ $_ $RecombinationLoc $_ $_) (== 74 (number-of (gene_map_table! $_ $_ $ParalogGeneID $RecombinationLoc $_ $_))))



;; print no more than the first 5 answers2
(= (query-info2 $English $template $query)
 (,
   (println!  ($English  "=" $query))
   (println!  (limit 5 (match &flybase $query $template)))
   (println! ("time was = " (time! (number-of $query $count))))
   (println! ("total of query = " $count))))


;; print no more than the first 5 answers

(= (query-info $English $template $query)
   (println!  ($English  "=" $query))
   (max-time 30 (limit 5 (match &flybase $query $template ) ) ))

;; Query: Find the Gene Symbols and Summary Texts for Genes Involved in a Specific Disease
(query-info-not "Show the gene symbols and summary texts for genes that are associated with a particular disease model."
    (gene-symbols-and-summaries $Disease $GeneSymbol $SummaryText)
   (, (disease_model_annotations! $FBgn $GeneSymbol $_ $_ $Disease $_ $_ $_ $_ $_ $_ $_ )
      (automated_gene_summaries! $FBgn $SummaryText ) ) )


;; Query: Find the Gene Symbols and Summary Texts for Genes Involved in a Specific Disease
(query-info-not "Show the gene symbols and summary texts for genes that are associated with a particular disease model."
    (gene-symbols-and-summaries $Disease $GeneSymbol $SummaryText)
   (, (disease_model_annotations! $FBgn $GeneSymbol $_ $_ $Disease $_ $_ $_ $_ $_ $_ $_ )
      (automated_gene_summaries! $FBgn $SummaryText ) ) )


;; !(match &self (automated_gene_summaries! FBgn0020237 $S) (get-metatype $S))


;; !(repl!)



;; Query: Identify Alleles and Their Phenotypes for a Specific Gene
;;!(query-info "List all alleles and their associated phenotypes for a given gene symbol."
;;    (alleles-and-phenotypes $GeneSymbol $AlleleSymbol $Phenotype)
;;   (, (fbal_to_fbgn! $_ $AlleleSymbol $_ $GeneSymbol)
;;      (allele_phenotypic! $AlleleSymbol $_ $Phenotype $_))
;;)




;; Query: Retrieve Gene Interaction Information and Corresponding Publications
!(query-info "Find interactions between genes and the related publications."
    (gene-interactions-and-publications $GeneSymbol1 $GeneSymbol2 $InteractionType $Publication)
   (, (gene_genetic_interactions! $StartingGeneSymbols $_ $InteractingGeneSymbols $_ $InteractionType $PublicationFBrf)
      (fb-member! $GeneSymbol1 $StartingGeneSymbols)
      (fb-member! $GeneSymbol2 $InteractingGeneSymbols)
      (fbrf_pmid_pmcid_doi! $PublicationFBrf $Publication $_ $_ $_ $_ $_))
)

;; Query: Associate Gene Symbols with Their Orthologous Human Genes and Diseases
!(query-info "Link Drosophila genes to their human orthologs and associated diseases."
    (gene-orthologs-and-diseases $OrgGeneSymbol $HumanGeneSymbol $Disease)
   (, (dmel_human_orthologs_disease! $_ $OrgGeneSymbol $_ $_ $HumanGeneSymbol $_ $_ $DiseaseIDs)
      (fb-member! $DiseaseID $DiseaseIDs)
      (disease_model_annotations! $_ $_ $HumanGeneSymbol $_ $Disease $_ $_ $_ $_ $_ $_ $_))
)




;; Query: Count the Number of Known RNA Processing Related Genes and Select Those with Less Than 2 Instances
!(query-info "Find the number of known RNA processing related genes and select those with less than 2 instances."
    (genes-rna-process-<-two $GeneSymbol $RNAProcess $NumberOf)
    (, (gene_rpkm_matrix! $GeneSymbol $_ $_ $RNAProcess $_)
       (number-of (gene_rpkm_matrix! $GeneSymbol $_ $_ $RNAProcess $_) $NumberOf)
       (< $NumberOf 2))
)

;; Query: Identify Genes with More Than 4 Physical Interactions
!(query-info "Identify genes that have more than 4 physical interactions."
    (genes-physical-interactions-more-than-four $GeneSymbol $PhysicalInteraction $NumberOf)
    (, (physical_interactions_mitab! $GeneSymbol $_ $_ $PhysicalInteraction $_ $_ $_)
       (number-of (physical_interactions_mitab! $GeneSymbol $_ $_ $PhysicalInteraction $_ $_ $_) $NumberOf)
       (> $NumberOf 4))
)

!(repl!)





;; Query: Count Genes Associated with Specific Diseases and Select Those with More Than 3 Associations
!(query-info "Count genes associated with specific diseases and select those with more than 3 associations."
    (genes-disease-associations-more-than-three $GeneSymbol $Disease $NumberOf)
    (, (disease_model_annotations! $GeneSymbol $_ $_ $_ $_ $_ $_ $Disease $_ $_ $_)
       (number-of (disease_model_annotations! $GeneSymbol $_ $_ $_ $_ $_ $_ $Disease $_ $_ $_) $NumberOf)
       (> $NumberOf 3))
)

;; Query: Find the Number of Gene Synonyms and Select Those with Less Than 5 Synonyms
!(query-info "Find the number of synonyms for genes and select those with less than 5 synonyms."
    (genes-synonyms-<-five $GeneSymbol $Synonym $NumberOf)
    (, (fb_synonym! $GeneSymbol $_ $_ $Synonym $_)
       (number-of (fb_synonym! $GeneSymbol $_ $_ $Synonym $_) $NumberOf)
       (< $NumberOf 5))
)

;; Query: Count Genes Involved in Gene Regulation and Exclude Those with Less Than 2 Instances
!(query-info "Count genes involved in gene regulation and exclude those with less than 2 instances."
    (genes-regulation-naf-<-two $GeneSymbol $GeneRegulation $NumberOf)
    (, (gene_functional_complementation! $GeneSymbol $_ $_ $GeneRegulation $_ $_)
       (number-of (gene_functional_complementation! $GeneSymbol $_ $_ $GeneRegulation $_ $_) $NumberOf)
       (naf (< $NumberOf 2)))
)

;; Query: Identify Genes with Allelic Variants and Select Those with More Than 6 Variants
!(query-info "Identify genes with allelic variants and select those with more than 6 variants."
    (genes-allelic-variants-more-than-six $GeneSymbol $AlleleSymbol $NumberOf)
    (, (allele_genetic_interactions! $AlleleSymbol $_ $_ $_ $GeneSymbol)
       (number-of (allele_genetic_interactions! $AlleleSymbol $_ $_ $_ $GeneSymbol) $NumberOf)
       (> $NumberOf 6))
)



;; Query: Find All Known Paralogs of a Specific Gene and Their Expression Levels
!(query-info "Display all paralogs of a given gene and their mean expression levels."
    (gene-paralogs-and-expression $GeneSymbol $ParalogSymbol $MeanExpression)
   (, (dmel_paralogs! $_ $GeneSymbol $_ $ParalogSymbol $_)
      (scRNA-Seq_gene_expression! $ParalogSymbol $_ $MeanExpression $_))
 )

;; Query: Correlate Gene Expression with Specific Stages of Tissue Development
!(query-info "Find genes with their expression levels at various stages of tissue development."
    (gene-expression-by-stage $GeneSymbol $TissueStage $MeanExpression)
   (, (scRNA-Seq_gene_expression! $_ $_ $_ $_ $TissueStage $_ $MeanExpression $_)
      (dmel_gene_sequence_ontology_annotations! $GeneSymbol $_ $_))
)

;; Query: Associate Genetic Map Positions with Corresponding Enzyme Activities
!(query-info "Relate genetic map positions to the enzyme activities of associated genes."
    (map-position-and-enzyme-activity $MapPosition $GeneSymbol $EnzymeActivity)
   (, (cyto-genetic-seq! $_ $MapPosition $_ $_)
      (Dmel_enzyme! $GeneSymbol $_ $_ $_ $EnzymeActivity))
)

;; Query: Link Alleles with Their Genetic and Physical Interactions
!(query-info "Connect alleles to their genetic interactions and the physical interactions they are involved in."
    (allele-genetic-and-physical-interactions $AlleleSymbol $GeneticInteraction $PhysicalInteraction)
   (, (allele_genetic_interactions! $AlleleSymbol $_ $GeneticInteraction $_)
      (physical_interactions_mitab! $_ $_ $_ $_ $_ $PhysicalInteraction))
)

;; Query: Find cDNA Clones Related to Specific Diseases
!(query-info "Identify cDNA clones linked to genes associated with certain diseases."
    (cDNA-clones-and-diseases $CloneName $Disease)
   (, (cDNA_clone_data! $_ $_ $CloneName $_)
      (disease_model_annotations! $_ $_ $_ $_ $Disease $_)
)
)

;; Query: Determine Disease Models Based on Specific Gene Sequences
!(query-info "Ascertain disease models associated with particular gene sequences."
    (gene-sequences-and-disease-models $Sequence $DiseaseModel)
   (, (dmel_gene_sequence_ontology_annotations! $_ $_ $_ $Sequence)
      (disease_model_annotations! $_ $_ $_ $_ $DiseaseModel $_))
)

;; Query: Associate Gene Symbols with Known Allele Phenotypes and Interactions
!(query-info "Connect gene symbols with the phenotypes and interactions of their alleles."
    (gene-alleles-phenotypes-and-interactions $GeneSymbol $AllelePhenotype $Interaction)
   (, (fbal_to_fbgn! $_ $_ $_ $GeneSymbol)
      (allele_phenotypic! $_ $_ $AllelePhenotype $_)
      (allele_genetic_interactions! $_ $AllelePhenotype $Interaction $_))
)

;; Query: Link Gene Symbols with Their Enzyme Functions and Synonyms
!(query-info "Relate gene symbols to their enzyme functions and any known synonyms."
    (gene-enzyme-functions-and-synonyms $GeneSymbol $EnzymeFunction $Synonym)
   (, (Dmel_enzyme! $GeneSymbol $_ $_ $EnzymeFunction $_)
      (fb_synonym! $_ $_ $GeneSymbol $_ $Synonym)
)
)

;; Query: Associate Gene Expression with Specific Cell Types
!(query-info "Correlate gene expression levels with specific cell types."
    (gene-expression-and-cell-type $GeneSymbol $CellType $ExpressionLevel)
   (, (scRNA-Seq_gene_expression! $_ $_ $_ $_ $_ $_ $CellType $_ $ExpressionLevel)
      (dmel_gene_sequence_ontology_annotations! $GeneSymbol $_ $_))
)

;; Query: Identify Genes with Specific Protein Isoforms and Their Disease Associations
!(query-info "Find genes that have specific protein isoforms and their links to diseases."
    (genes-protein-isoforms-and-diseases $GeneSymbol $ProteinIsoform $Disease)
   (, (dmel_unique_protein_isoforms! $_ $GeneSymbol $_ $ProteinIsoform)
      (disease_model_annotations! $_ $_ $_ $_ $_ $_ $_ $_ $_ $Disease))
)

;; Query: Relate Genomic Clones to Their Expression in Different Tissues
!(query-info "Connect genomic clones to their expression profiles in various tissues."
    (clones-and-tissue-expression $CloneName $TissueType $ExpressionLevel)
   (, (genomic_clone! $_ $_ $CloneName $_)
      (gene_rpkm_report! $_ $_ $_ $_ $TissueType $_ $ExpressionLevel))
)

;; Query: Find Genes Involved in Specific Pathways and Their Genetic Interactions
!(query-info "Identify genes that are part of certain pathways and their genetic interactions."
    (genes-in-pathways-and-interactions $Pathway $GeneSymbol $Interaction)
   (, (pathway_group! $_ $_ $Pathway $_)
      (gene_genetic_interactions! $_ $GeneSymbol $_ $Interaction $_))
)




;; Query: Determine the Expression of Specific Genes in Different Tissues and Stages
!(query-info "Find the mean expression of specific genes across different tissues and developmental stages."
    (gene-expression-across-tissues-and-stages $GeneSymbol $Tissue $Stage $MeanExpression)
   (, (scRNA-Seq_gene_expression! $PubID $_ $_ $_ $Tissue $Stage $_ $ClusterID $_ $_ $_ $GeneID $GeneSymbol $MeanExpression $_)
      (fbgn_annotation_ID! $GeneSymbol $_ $GeneID $_ $_ $_ $_))
)

;; Query: Relate cDNA Clones to Their Corresponding Genes and Accessions
!(query-info "Link cDNA clones to their corresponding genes and accessions."
    (cdna-clone-gene-link $CloneName $GeneSymbol $CDNAaccession)
   (, (cDNA_clone_data! $_ $_ $CloneName $_ $CDNAaccession $_)
      (fbgn_annotation_ID! $GeneSymbol $_ $_ $_ $_ $_))
)

;; Query: Associate Alleles with Genetic Interactions and References
!(query-info "Find genetic interactions involving specific alleles and their references."
    (allele-genetic-interactions-and-references $AlleleSymbol $Interaction $Reference)
   (, (allele_genetic_interactions! $AlleleSymbol $_ $Interaction $_ $Reference)
      (fbrf_pmid_pmcid_doi! $Reference $_ $_ $_ $_ $_ $_))
)

;; Query: Explore Paralogous Genes and Their Genomic Locations
!(query-info "Identify paralogous genes and their genomic locations."
    (gene-paralogs-and-locations $GeneSymbol $ParalogGeneSymbol $Location)
   (, (dmel_paralogs! $GeneID $GeneSymbol $_ $Location $_ $_ $Paralog_FBgn $Paralog_GeneSymbol $_ $_ $_ $_)
      (fbgn_annotation_ID! $GeneSymbol $_ $GeneID $_ $_ $_))
)


;; Query: Trace Genes to Their Synonyms and Organism Abbreviations
!(query-info "Trace genes to their synonyms and organism abbreviations."
    (gene-synonyms-and-organisms $GeneSymbol $Synonym $OrganismAbbreviation)
   (, (fb_synonym! $_ $OrganismAbbreviation $GeneSymbol $_ $Synonym $_ $_)
      (gene_map_table! $OrganismAbbreviation $GeneSymbol $_ $_ $_ $_ $_))
)

;; Query: Link Gene Annotations with Corresponding Protein Accessions
!(query-info "Connect gene annotations with their respective protein accessions."
    (gene-annotations-and-protein-accessions $GeneSymbol $AnnotationID $ProteinAccession)
   (, (fbgn_annotation_ID! $GeneSymbol $_ $_ $AnnotationID $_ $_)
      (fbgn_NAseq_Uniprot! $GeneSymbol $_ $_ $_ $_ $ProteinAccession $_ $_ $_))
)

;; Query: Correlate Gene Expression with Specific RNA and Protein Data
!(query-info "Correlate gene expression levels with RNA and protein data."
    (gene-expression-rna-protein-correlation $GeneSymbol $ExpressionValue $RNAaccession $ProteinAccession)
   (, (gene_rpkm_matrix! $_ $GeneSymbol $_ $_ $ExpressionValue $_)
      (fbgn_NAseq_Uniprot! $GeneSymbol $_ $_ $RNAaccession $_ $ProteinAccession $_ $_ $_))
)

;; Query: Associate Genes with Disease Models and Relevant Alleles
!(query-info "Associate genes with disease models and the alleles used in these models."
    (genes-disease-models-and-alleles $GeneSymbol $Disease $AlleleSymbol)
   (, (disease_model_annotations! $GeneID $GeneSymbol $_ $_ $Disease $_ $_ $_ $AlleleSymbol $_ $_ $_ $_)
      (fbal_to_fbgn! $GeneID $AlleleSymbol $_ $GeneSymbol))
)


;; Query: Match Genes with Their Corresponding Publication References
!(query-info "Match genes with their corresponding publication references."
    (gene-publication-matches $GeneSymbol $Publication)
   (, (fbgn_annotation_ID! $GeneSymbol $_ $_ $_ $_ $_)
      (entity_publication! $_ $GeneSymbol $Publication $_))
)

;; Query: Find Alleles and Their Interactions with Genes
!(query-info "Find alleles and their interactions with specific genes."
    (alleles-and-gene-interactions $AlleleSymbol $GeneSymbol $Interaction)
   (, (allele_genetic_interactions! $AlleleSymbol $_ $Interaction $_ $_)
      (fbal_to_fbgn! $_ $AlleleSymbol $_ $GeneSymbol))
)

;; Query: Associate Genes with Pathways, Disease Models, and Human Orthologs
!(query-info "Link genes to their associated pathways, disease models, and human orthologs."
    (genes-pathways-diseases-orthologs $GeneSymbol $Pathway $Disease $HumanOrtholog)
   (, (gene_groups_HGNC! $GeneSymbol $_ $_ $Pathway)
      (disease_model_annotations! $GeneSymbol $_ $_ $_ $Disease)
      (dmel_human_orthologs_disease! $GeneSymbol $_ $_ $HumanOrtholog))
)

;; Query: Link Alleles to Phenotypes, Genetic Interactions, and Publications
!(query-info "Connect alleles to their phenotypes, genetic interactions, and related publications."
    (alleles-phenotypes-interactions-publications $AlleleSymbol $Phenotype $Interaction $Publication)
   (, (allele_phenotypic! $AlleleSymbol $_ $Phenotype)
      (allele_genetic_interactions! $AlleleSymbol $_ $Interaction)
      (fbrf_pmid_pmcid_doi! $Interaction $Publication $_ $_ $_))
)

;; Query: Correlate Gene Expressions with cDNA Clones and Protein Accessions
!(query-info "Correlate gene expressions with corresponding cDNA clones and protein accessions."
    (gene-expression-cdna-protein $GeneSymbol $ExpressionValue $CloneName $ProteinAccession)
   (, (gene_rpkm_matrix! $GeneSymbol $_ $_ $ExpressionValue)
      (cDNA_clone_data! $_ $_ $CloneName $_)
      (fbgn_NAseq_Uniprot! $GeneSymbol $_ $_ $ProteinAccession))
)

;; Query: Determine Gene Functions and Map them to Genetic and Physical Interactions
(query-info-not "Determine gene functions and map them to genetic and physical interactions."
    (gene-functions-genetic-physical-interactions $GeneSymbol $Function $GeneticInteraction $PhysicalInteraction)
   (, (automated_gene_summaries! $GeneSymbol $Function)
      (gene_genetic_interactions! $GeneSymbol $_ $_ $GeneticInteraction)
      (physical_interactions_mitab! $_ $_ $GeneSymbol $PhysicalInteraction))
)

;; Query: Explore Gene Synonyms, Genetic Map Positions, and Disease Associations
!(query-info "Explore gene synonyms, genetic map positions, and disease associations."
    (gene-synonyms-map-diseases $GeneSymbol $Synonym $MapPosition $Disease)
   (, (fb_synonym! $GeneSymbol $_ $_ $Synonym)
      (cyto-genetic-seq! $GeneSymbol $_ $_ $MapPosition)
      (disease_model_annotations! $GeneSymbol $_ $_ $_ $Disease))
)

;; Query: Associate Gene Expression with Cell Types and Developmental Stages
!(query-info "Associate gene expression with specific cell types and developmental stages."
    (gene-expression-cell-types-stages $GeneSymbol $ExpressionValue $CellType $Stage)
   (, (gene_rpkm_matrix! $GeneSymbol $_ $_ $ExpressionValue)
      (scRNA-Seq_gene_expression! $_ $_ $_ $_ $Stage $_ $CellType))
)

;; Query: Link Genomic Clones to Genes, Proteins, and Synonyms
!(query-info "Link genomic clones to their corresponding genes, proteins, and synonyms."
    (genomic-clone-gene-protein-synonym $CloneName $GeneSymbol $ProteinAccession $Synonym)
   (, (genomic_clone! $CloneName $_ $_ $_)
      (fbgn_NAseq_Uniprot! $GeneSymbol $_ $_ $ProteinAccession)
      (fb_synonym! $_ $_ $GeneSymbol $Synonym))
)

;; Query: Relate Gene Snapshots to Disease Models and Human Orthologs
!(query-info "Relate gene snapshots to disease models and their human orthologs."
    (gene-snapshots-diseases-orthologs $GeneSymbol $SnapshotText $Disease $HumanOrtholog)
   (, (gene_snapshots! $GeneSymbol $_ $_ $SnapshotText)
      (disease_model_annotations! $GeneSymbol $_ $_ $_ $Disease)
      (dmel_human_orthologs_disease! $GeneSymbol $_ $_ $HumanOrtholog))
)

;; Query: Connect Genes to Their Enzymatic Functions and Disease Models
!(query-info "Connect genes to their enzymatic functions and associated disease models."
    (genes-enzymes-diseases $GeneSymbol $EnzymeFunction $Disease)
   (, (Dmel_enzyme! $GeneSymbol $_ $_ $_ $EnzymeFunction)
      (disease_model_annotations! $GeneSymbol $_ $_ $_ $Disease))
)

;; Query: Associate Pathway Groups with Gene Functions and Physical Interactions
(query-info-not "Associate pathway groups with gene functions and physical interactions."
    (pathway-gene-function-physical-interaction $Pathway $GeneFunction $PhysicalInteraction)
   (, (pathway_group! $Pathway $_ $_ $_)
      (automated_gene_summaries! $_ $GeneFunction)
      (physical_interactions_mitab! $_ $_ $_ $PhysicalInteraction))
)


;; Query: Associate Disease Models with Gene Transcripts, Protein Isoforms, Gene Summaries, and Snapshots
!(query-info "Link disease model annotations with corresponding gene transcripts, unique protein isoforms, the best gene summaries, and gene snapshots."
   (gene-disease-models-transcripts-proteins-summaries-snapshots $GeneID $GeneSymbol $ProteinID $GeneSummaryID $GeneSnapshotID)
   (, (disease_model_annotations! $GeneID $_ $_ $_ $_ $_ $_ $_ $_ $_ $_ $_)
      (fbgn_fbtr_fbpp_expanded! $TranscriptType $TranscriptID $GeneID $GeneSymbol $GeneFullName $AnnotationID $_ $_ $_ $_ $_)
      (dmel_unique_protein_isoforms! $ProteinID $GeneSymbol $ProteinSymbol $_)
      (best_gene_summary! $GeneSummaryID $GeneSymbol $SummarySource $SummaryText)
      (gene_snapshots! $GeneSnapshotID $GeneSymbol $GeneName $Datestamp $SnapshotText))
)


;; Query: Link Paralogous Genes with Gene Mapping, Transcripts, Protein Isoforms, and Summaries
!(query-info "Connect paralogous genes to their gene mapping, transcripts, protein isoforms, and gene summaries."
   (paralogs-gene-mapping-transcripts-proteins-summaries $GeneID $GeneSymbol $ParalogGeneID $MapID $ProteinID)
   (, (dmel_paralogs! $GeneID $GeneSymbol $Arm $Location $Strand $ParalogGeneID $ParalogGeneSymbol $_ $_ $_ $_)
      (gene_map_table! $MapID $OrganismAbbreviation $GeneID $RecombinationLoc $CytogeneticLoc $SequenceLoc)
      (fbgn_fbtr_fbpp_expanded! $TranscriptType $TranscriptID $TranscriptSymbol $MapID $_ $_ $_ $_ $_ $_)
      (dmel_unique_protein_isoforms! $ProteinID $ProteinSymbol $TranscriptSymbol $_)
      (best_gene_summary! $GeneSummaryID $ProteinSymbol $SummarySource $SummaryText))
)


;; Query: Correlate Expanded Gene Transcripts with Protein Isoforms, Paralogs, Gene Mapping, and Synonyms
!(query-info "Associate expanded gene transcripts with corresponding protein isoforms, paralogs, gene mapping data, and synonyms."
   (transcripts-proteins-paralogs-mapping-synonyms $GeneID $TranscriptID $ProteinID $ParalogGeneID $MapID)
   (, (fbgn_fbtr_fbpp_expanded! $GeneID $TranscriptType $TranscriptID $GeneSymbol $GeneFullName $AnnotationID $_ $_ $_ $_ $_)
      (dmel_unique_protein_isoforms! $ProteinID $ProteinSymbol $TranscriptSymbol $_)
      (dmel_paralogs! $ParalogGeneID $ProteinSymbol $_ $_ $_ $_ $_ $_ $_ $_ $_)
      (gene_map_table! $MapID $OrganismAbbreviation $ParalogGeneID $RecombinationLoc $CytogeneticLoc $SequenceLoc)
      (synonym! $SynonymID $MapID $CurrentSymbol $CurrentFullName $_ $_))
)

(was (number-of
   (, (fbgn_fbtr_fbpp_expanded! $GeneID $TranscriptType $TranscriptID $GeneSymbol $GeneFullName $AnnotationID $_ $_ $_ $_ $_)
      (dmel_unique_protein_isoforms! $ProteinID $ProteinSymbol $TranscriptSymbol $_)
      (dmel_paralogs! $ParalogGeneID $ProteinSymbol $_ $_ $_ $_ $_ $_ $_ $_ $_)
      (gene_map_table! $MapID $OrganismAbbreviation $ParalogGeneID $RecombinationLoc $CytogeneticLoc $SequenceLoc)
      (synonym! $SynonymID $MapID $CurrentSymbol $CurrentFullName $_ $_))))


;; Query: Connect Gene Mapping with Expanded Transcripts, Protein Isoforms, Gene Summaries, and Basic Transcripts
!(query-info "Link gene mapping data with expanded transcripts, unique protein isoforms, gene summaries, and basic transcript information."
   (mapping-transcripts-proteins-summaries $MapID $GeneSymbol $TranscriptID $ProteinID $GeneSummaryID)
   (, (gene_map_table! $MapID $OrganismAbbreviation $GeneSymbol $RecombinationLoc $CytogeneticLoc $SequenceLoc)
      (fbgn_fbtr_fbpp_expanded! $TranscriptType $TranscriptID $TranscriptSymbol $OrganismAbbreviation $_ $_ $_ $_ $_ $_)
      (dmel_unique_protein_isoforms! $ProteinID $ProteinSymbol $TranscriptSymbol $_)
      (best_gene_summary! $GeneSummaryID $ProteinSymbol $SummarySource $SummaryText)
      (fbgn_fbtr_fbpp! $GeneSummaryID $_ $_))
)



;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;

;; Query: Associate Gene Expression with Developmental Stages and Publications
!(query-info "Link gene expression data to specific developmental stages and corresponding publications."
    (gene-expression-stages-publications $GeneID $ExpressionValue $Stage $Publication)
    (, (gene_rpkm_report! $GeneID $ExpressionValue $_ $_ $_ $Stage $_ $_ $_ $_ $_ $_ $_ $_)
       (fbrf_pmid_pmcid_doi! $_ $Publication $_ $_ $_ $_ $_ $_))
)

;; Query: Link Gene Functional Data with Enzymatic Activities and Disease Models
(query-info-not "Connect gene functional data with enzymatic activities and their relevance to disease models."
    (gene-function-enzyme-disease $GeneSymbol $Function $EnzymeActivity $Disease)
    (, (automated_gene_summaries! $GeneSymbol $Function)
       (Dmel_enzyme! $GeneSymbol $_ $_ $_ $_ $_ $_ $_ $_ $_ $_)
       (disease_model_annotations! $_ $GeneSymbol $_ $_ $_ $Disease $_ $_ $_ $_ $_ $_))
)

;; Query: Relate Genes to Their Allelic Variants and Phenotypic Effects
!(query-info "Relate genes to their allelic variants and the resulting phenotypic effects."
    (genes-alleles-phenotypes $GeneSymbol $AlleleSymbol $Phenotype)
    (, (fbal_to_fbgn! $_ $AlleleSymbol $_ $GeneSymbol)
       (allele_phenotypic! $AlleleSymbol $_ $Phenotype $_))
)

;; Query: Correlate Genes with their Physical Interactions and Pathway Involvements
!(query-info "Correlate genes with their physical interactions and pathway involvements."
    (genes-physical-interactions-pathways $GeneID $PhysicalInteraction $Pathway)
    (, (physical_interactions_mitab! $GeneID $_ $_ $PhysicalInteraction $_ $_ $_ $_ $_ $_ $_ $_ $_ $_ $_ $_ $_ $_ $_ $_ $_ $_ $_ $_ $_ $_ $_ $_ $_)
       (pathway_group! $Pathway $_ $_ $_ $_ $_ $GeneID $_ $_))
)

;; Query: Connect Genes with Disease Annotations and Relevant Publication Data
!(query-info "Connect genes with disease annotations and relevant publication data."
    (genes-disease-annotations-publications $GeneSymbol $DiseaseAnnotation $Publication)
    (, (disease_model_annotations! $_ $GeneSymbol $_ $_ $_ $DiseaseAnnotation $_ $_ $_ $_ $_ $_ $_ $_)
       (fbrf_pmid_pmcid_doi! $_ $Publication $_ $_ $_ $_ $_ $_))
)

;; Query: Associate Gene Sequences with Synonyms and Protein Isoforms
!(query-info "Associate gene sequences with their synonyms and protein isoforms."
    (gene-sequences-synonyms-proteins $GeneID $Synonym $ProteinIsoform)
    (, (dmel_gene_sequence_ontology_annotations! $GeneID $_ $_ $_)
       (fb_synonym! $_ $_ $GeneID $_ $Synonym $_)
       (dmel_unique_protein_isoforms! $_ $_ $GeneID $ProteinIsoform $_))
)

;; Query: Link Genotype Data with Phenotypes and Corresponding References
!(query-info "Link genotype data with phenotypes and their corresponding references."
    (genotype-phenotypes-references $GenotypeSymbols $Phenotype $Reference)
    (, (genotype_phenotype_data! $GenotypeSymbols $_ $Phenotype $_ $_ $_ $_ $Reference $_)
       (fbrf_pmid_pmcid_doi! $Reference $_ $_ $_ $_ $_ $_ $_))
)

;; Query: Correlate Gene Snapshots with Their Enzymatic Functions and Disease Models
!(query-info "Correlate gene snapshots with their enzymatic functions and disease models."
    (gene-snapshots-enzymes-diseases $GeneSymbol $SnapshotText $EnzymeFunction $Disease)
    (, (gene_snapshots! $GeneSymbol $_ $_ $SnapshotText $_)
       (Dmel_enzyme! $GeneSymbol $_ $_ $_ $_ $_ $_ $_ $_)
       (disease_model_annotations! $_ $GeneSymbol $_ $_ $_ $Disease $_ $_ $_ $_ $_ $_))
)

;; Query: Associate Genes with Their cDNA Clones and Disease Models
!(query-info "Associate genes with their cDNA clones and relevant disease models."
    (genes-cdna-disease-models $GeneSymbol $CloneName $Disease)
    (, (cDNA_clone_data! $_ $_ $CloneName $_ $_ $_)
       (gene_map_table! $_ $GeneSymbol $_ $_ $_ $_ $_)
       (disease_model_annotations! $_ $GeneSymbol $_ $_ $_ $Disease $_ $_ $_ $_ $_ $_))
)

;; Query: Connect Genes to Publications and Allelic Interactions
!(query-info "Connect genes to relevant publications and their allelic interactions."
    (genes-publications-allelic-interactions $GeneSymbol $Publication $AlleleInteraction)
    (, (entity_publication! $_ $GeneSymbol $Publication $_)
       (allele_genetic_interactions! $_ $_ $AlleleInteraction $_ $GeneSymbol))
)


;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;ORs ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;

;; Query: Identify Genes Either Involved in Physical Interactions or Associated with Specific Diseases
!(query-info "Find genes that are either involved in physical interactions or associated with specific diseases."
    (genes-physical-or-disease $GeneSymbol $PhysicalInteraction $Disease)
    (, (gene_map_table! $GeneSymbol $_ $_ $_ $_ $_)
       (or (physical_interactions_mitab! $GeneSymbol $_ $_ $PhysicalInteraction $_ $_ $_)
           (disease_model_annotations! $GeneSymbol $_ $_ $_ $_ $_ $_ $Disease $_ $_ $_)))
)

;; Query: Retrieve Gene Snapshots or Enzymatic Functions for Specific Genes
!(query-info "Get gene snapshots or enzymatic functions for specific genes."
    (gene-snapshots-or-enzymes $GeneSymbol $SnapshotText $EnzymeFunction)
    (, (gene_map_table! $GeneSymbol $_ $_ $_ $_ $_)
       (or (gene_snapshots! $GeneSymbol $_ $_ $SnapshotText $_)
           (Dmel_enzyme! $GeneSymbol $_ $_ $_ $EnzymeFunction $_ $_ $_)))
)

;; Query: Find Genes with Either cDNA Clones or Related to Specific Pathways
!(query-info "Identify genes that have cDNA clones or are related to specific pathways."
    (genes-cdna-or-pathways $GeneSymbol $CloneName $Pathway)
    (, (gene_map_table! $GeneSymbol $_ $_ $_ $_ $_)
       (or (cDNA_clone_data! $CloneName $_ $GeneSymbol $_ $_)
           (pathway_group! $GeneSymbol $_ $_ $_ $Pathway $_ $_)))
)

;; Query: Associate Genes with Synonyms or Protein Isoforms
!(query-info "Associate genes with either their synonyms or protein isoforms."
    (genes-synonyms-or-proteins $GeneSymbol $Synonym $ProteinIsoform)
    (, (gene_map_table! $GeneSymbol $_ $_ $_ $_ $_)
       (or (fb_synonym! $GeneSymbol $_ $_ $Synonym $_)
           (dmel_unique_protein_isoforms! $GeneSymbol $_ $_ $ProteinIsoform $_)))
)

;; Query: Link Alleles to Phenotypes or Genetic Interactions
!(query-info "Link alleles to their phenotypes or to their genetic interactions."
    (alleles-phenotypes-or-interactions $AlleleSymbol $Phenotype $Interaction)
    (, (fbal_to_fbgn! $AlleleSymbol $_ $_ $_)
       (or (allele_phenotypic! $AlleleSymbol $_ $Phenotype $_)
           (allele_genetic_interactions! $AlleleSymbol $_ $Interaction $_)))
)

;; Query: Find Genes Involved in RNA Processing or Gene Regulation
!(query-info "Find genes involved in RNA processing or gene regulation."
    (genes-rna-or-regulation $GeneSymbol $RNAProcess $GeneRegulation)
    (, (gene_map_table! $GeneSymbol $_ $_ $_ $_ $_)
       (or (gene_rpkm_matrix! $GeneSymbol $_ $_ $RNAProcess $_)
           (gene_functional_complementation! $GeneSymbol $_ $_ $GeneRegulation $_)))
)

;; Query: Retrieve Publications Related to Genes or Their Allelic Variants
!(query-info "Retrieve publications related to genes or their allelic variants."
    (publications-genes-or-alleles $GeneSymbol $Publication $AlleleSymbol)
    (, (gene_map_table! $GeneSymbol $_ $_ $_ $_ $_)
       (or (entity_publication! $Publication $_ $GeneSymbol $_)
           (allele_genetic_interactions! $AlleleSymbol $_ $_ $_ $GeneSymbol)))
)

;; Query: Correlate Genes with Their Expression in Tissues or During Specific Stages
!(query-info "Correlate genes with their expression in tissues or during specific developmental stages."
    (genes-expression-tissues-or-stages $GeneSymbol $Tissue $Stage)
    (, (gene_map_table! $GeneSymbol $_ $_ $_ $_ $_)
       (or (scRNA-Seq_gene_expression! $_ $_ $_ $_ $Tissue $Stage $_ $_)
           (gene_rpkm_report! $GeneSymbol $_ $_ $_ $_ $_ $_ $Stage $_)))
)


;; Query: Find Genes Involved in RNA Processing but Not in Gene Regulation
!(query-info "Identify genes involved in RNA processing but naf in gene regulation."
    (genes-rna-naf-regulation $GeneSymbol $RNAProcess)
    (, (gene_rpkm_matrix! $GeneSymbol $_ $_ $RNAProcess $_)
       (naf (gene_functional_complementation! $GeneSymbol $_ $_ $_ $_ $_)))
)

;; Query: Retrieve Publications Related to Specific Genes but Not Their Allelic Variants
!(query-info "Retrieve publications related to specific genes but naf their allelic variants."
    (publications-genes-naf-alleles $GeneSymbol $Publication)
    (, (entity_publication! $Publication $_ $GeneSymbol $_)
       (naf (allele_genetic_interactions! $_ $_ $_ $GeneSymbol)))
)

;; Query: Identify Genes with cDNA Clones but Not Involved in Specific Pathways
!(query-info "Identify genes that have cDNA clones but are naf involved in specific pathways."
    (genes-cdna-naf-pathways $GeneSymbol $CloneName)
    (, (cDNA_clone_data! $CloneName $_ $GeneSymbol $_ $_ $_)
       (naf (pathway_group! $GeneSymbol $_ $_ $_ $_ $_ $_)))
)

;; Query: Associate Genes with Synonyms but Exclude Certain Protein Isoforms
!(query-info "Associate genes with their synonyms but exclude certain protein isoforms."
    (genes-synonyms-naf-proteins $GeneSymbol $Synonym)
    (, (fb_synonym! $GeneSymbol $_ $_ $Synonym $_)
       (naf (dmel_unique_protein_isoforms! $GeneSymbol $_ $_ $_)))
)

;; Query: Link Alleles to Phenotypes but Exclude Specific Genetic Interactions
!(query-info "Link alleles to their phenotypes but exclude specific genetic interactions."
    (alleles-phenotypes-naf-interactions $AlleleSymbol $Phenotype)
    (, (allele_phenotypic! $AlleleSymbol $_ $Phenotype $_)
       (naf (allele_genetic_interactions! $AlleleSymbol $_ $_ $_)))
)

;; Query: Find Genes Involved in Physical Interactions but Not Associated with Diseases
!(query-info "Find genes involved in physical interactions but naf associated with specific diseases."
    (genes-physical-naf-disease $GeneSymbol $PhysicalInteraction)
    (, (physical_interactions_mitab! $GeneSymbol $_ $_ $PhysicalInteraction $_ $_ $_ $_ $_)
       (naf (disease_model_annotations! $GeneSymbol $_ $_ $_ $_ $_ $_ $_ $_ $_)))
)

;; Query: Retrieve Gene Snapshots but Exclude Those Related to Enzymatic Functions
!(query-info "Retrieve gene snapshots but exclude those related to enzymatic functions."
    (gene-snapshots-naf-enzymes $GeneSymbol $SnapshotText)
    (, (gene_snapshots! $GeneSymbol $_ $_ $SnapshotText $_)
       (naf (Dmel_enzyme! $GeneSymbol $_ $_ $_ $_ $_ $_ $_)))
)

;; Query: Correlate Genes with Expression in Tissues but Not During Specific Stages
!(query-info "Correlate genes with their expression in tissues but naf during specific developmental stages."
    (genes-expression-tissues-naf-stages $GeneSymbol $Tissue)
    (, (scRNA-Seq_gene_expression! $_ $_ $_ $_ $Tissue $_ $_ $_ $GeneSymbol $_ $_)
       (naf (gene_rpkm_report! $GeneSymbol $_ $_ $_ $_ $_ $_ $_ $_ $_ $_ $_)))
)


;; Query: Find Genes with Specific Transcripts or Protein Isoforms but Not Involved in Certain Pathways
!(query-info "Identify genes that have specific transcripts or protein isoforms but are naf involved in certain pathways."
    (genes-transcripts-proteins-naf-pathways $GeneSymbol $TranscriptID $ProteinIsoform $ExcludedPathway)
    (, (gene_map_table! $GeneSymbol $_ $_ $_ $_ $_)
       (, (or (fbgn_fbtr_fbpp! $GeneSymbol $TranscriptID $_ $_ $_)
                 (dmel_unique_protein_isoforms! $GeneSymbol $_ $ProteinIsoform $_))
            (naf (pathway_group! $GeneSymbol $_ $_ $_ $ExcludedPathway $_ $_))))
)

;; Query: Retrieve Gene Snapshots or Allelic Variants but Exclude Genes with Certain Phenotypes
!(query-info "Retrieve gene snapshots or allelic variants but exclude genes associated with certain phenotypes."
    (gene-snapshots-alleles-naf-phenotypes $GeneSymbol $SnapshotText $AlleleSymbol $ExcludedPhenotype)
    (, (gene_map_table! $GeneSymbol $_ $_ $_ $_ $_)
       (, (or (gene_snapshots! $GeneSymbol $_ $SnapshotText $_)
                 (allele_genetic_interactions! $AlleleSymbol $_ $_ $_ $GeneSymbol))
            (naf (allele_phenotypic! $AlleleSymbol $_ $ExcludedPhenotype $_))))
)

;; Query: Link Genes to Physical Interactions or Publications but Not to Specific Disease Models
!(query-info "Link genes to physical interactions or relevant publications but naf to specific disease models."
    (genes-interactions-publications-naf-disease $GeneSymbol $PhysicalInteraction $Publication $ExcludedDisease)
    (, (gene_map_table! $GeneSymbol $_ $_ $_ $_ $_)
       (, (or (physical_interactions_mitab! $GeneSymbol $_ $_ $PhysicalInteraction $_ $_)
                 (entity_publication! $Publication $_ $GeneSymbol $_))
            (naf (disease_model_annotations! $GeneSymbol $_ $_ $_ $_ $_ $_ $ExcludedDisease))))
)

;; Query: Associate Genes with cDNA Clones or Enzymatic Functions but Exclude Certain Synonyms
!(query-info "Associate genes with cDNA clones or enzymatic functions but exclude certain synonyms."
    (genes-cdna-enzymes-naf-synonyms $GeneSymbol $CloneName $EnzymeFunction $ExcludedSynonym)
    (, (gene_map_table! $GeneSymbol $_ $_ $_ $_ $_)
       (, (or (cDNA_clone_data! $CloneName $_ $GeneSymbol $_)
                 (Dmel_enzyme! $GeneSymbol $_ $_ $EnzymeFunction $_))
            (naf (fb_synonym! $GeneSymbol $_ $_ $ExcludedSynonym $_))))
)

;; Query: Find Genes Involved in RNA Processing or Gene Regulation but Not Linked to Specific Protein Accessions
!(query-info "Find genes involved in RNA processing or gene regulation but naf linked to specific protein accessions."
    (genes-rna-regulation-naf-proteins $GeneSymbol $RNAProcess $GeneRegulation $ExcludedProteinAccession)
    (, (gene_map_table! $GeneSymbol $_ $_ $_ $_ $_)
       (, (or (gene_rpkm_matrix! $GeneSymbol $_ $_ $RNAProcess $_)
                 (gene_functional_complementation! $GeneSymbol $_ $_ $GeneRegulation $_))
            (naf (fbgn_NAseq_Uniprot! $GeneSymbol $_ $_ $ExcludedProteinAccession $_ $_ $_)))))



;; Rust only:
!(mettalog::vspace-main)