We describe our proposed Conceptual Schema (CS) to work with Citrus genome information (CSCG). The presented CS is being used in a real-world industrial case to validate it and gather expert domain feedbackGarcía Simón, A.; Pastor López, O. (2020). CSCG: Conceptual Schema of the Citrus Genome. http://hdl.handle.net/10251/14423

García Simón, Alberto

Pastor López, Oscar

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1CSCG: Conceptual Schema of the Citrus GenomeTechnical ReportAlberto Garcı´a S., Oscar PastorRef # PROS-TR-2020-1Title CSCG: Conceptual Schema of the Citrus GenomeAuthor(s) Alberto Garcı´a S., Oscar PastorCorresponding author(s) algarsi3@pros.upv.es, opastor@pros.upv.esDocument version number 1Final version -Release date -Keywords CSCG, Conceptual Schema, Evlution, Citrus Genome2CONTENTSAppendix A: CSCG: Biological Perspective 3Appendix B: CSCG: Technological Perspective 4B-A Scaffold Module . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4B-B GO Module . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5B-C VCF Module . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6B-D ANN Module . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7Appendix C: CSCG: Final CS 8We describe our proposed Conceptual Schema (CS) to work with Citrus genome information (CSCG). The presented CS isbeing used in a real-world industrial case to validate it and gather expert domain feedback. The CSCG is divided into twodifferent perspectives, namely, the biological and the technological perspective.The biological perspective deal with pure biological concepts and its mission is to understand how life works and what areits internals. 17 classes have been defined in the biological perspective: Chromosome, Sequence part, variation, Species, Gene,Intron, Exon, Primary transcript, mRNA, 5’ UTR, CDS, 3’ UTR, Protein, Domain, Enzyme, Ortholog, Pathway. The biologicalperspective can be found in Annex A.The technological perspective tries to integrate the biological perspective with the real world. Technology has limitations,knowledge is very limited and real-world genomic information needs to be analysed and understood as a separate problem. Wedefine independent knowledge blocks that can be plugged into the biological perspective to enrich it. The first version of theCSHG defines four different blocks:• Scaffold Module: real-life sequencing is far from perfect. It is not possible to correctly obtain the genome sequence.Therefore, gaps are encountered.◦ The scaffold chromosome represents the chromosome whose sequence is stored in the linked scaffold.• Gene Otology (GO) Module: GO ontology tries to provide a standard way to define biological processes, molecularfunctions that are part of biological processes and cellular components where they are carried on. Then, links genes orgene products to the previously defined concepts.◦ GO consider genes and proteins functional elements, therefore, they are specialisation types of functional elements.• Variant Call Format (VCF) Module: VCF files are used to report identified variations when comparing a given sequence toa sequence of reference. Along with variations, there is plenty of additional information like quality attributes or genotypeinformation.◦ Variations of the VCF are linked to biological variations. This way, a variation can be identified in multiple VCFfiles and with different quality attributes.◦ Each sample of a VCF file will be a specie.• SnpEff Module: variations can be automatically annotated with the predicted effect that will cause.◦ Since annotations are included to VCF files, we link each annotation to a VCF variation. A variation can have zero ormultiple annotations and an annotation will belong to only one VCF variation. An VCF variation present in differentVCF files may have different annotations depending on the parameters of SnpEff when annotating the VCF file.◦ ANN value can be linked to primary transcripts and genes. The reason is that the SnpEff standard has two field tolink the annotation (effect caused by the variation) to a element. The element has to be either a gene or a primarytranscript. Gene cardinality is two at most because a VCF variation is linked to two genes when it is annotated asintergenic.The technological perspective can be found in Annex B. By joining the biological perspective with the defined knowledge blocksin the technological perspective, the final schema arises. It can be found in Annex C3APPENDIX ACSCG: BIOLOGICAL PERSPECTIVE4APPENDIX BCSCG: TECHNOLOGICAL PERSPECTIVEA. Scaffold ModuleID: 0 Description: Scaffold sequencing technology.Fig. 1. Scaffold-id : int-name : String-length : int-sequence : StringScaffold-id : int-name : StringScaffold_ChromosomeClass31 1..*pertains toPowered ByVisual Paradigm Community EditionTABLE I. SCAFFOLD KNOWLEDGE ELEMENTSKnowledge chainsKnowledge Block Output CSID Description Input Class CS Class- - - - -Knowledge equalitiesKnowledge Block Output CSID Description Input Class CS Class0.e.0 Scaffold Chromosome is ontologically equivalent tobiological chromosomeScaffold Chromosome Biological Oracle Chromosome5B. GO ModuleID: 1 Description: Gene Ontology knowledgebase.Fig. 2. Gene OntologyTABLE II. GENE ONTOLOGY KNOWLEDGE ELEMENTSKnowledge chainsKnowledge Block Output CSID Description Input Class CS Class- - - - -Knowledge equalitiesKnowledge Block Output CSID Description Input Class CS Class1.e.0 Go Gene is ontologically equivalent to biologicalgeneGO Gene Biological Oracle Gene1.e.1 Gene Product is ontologically equivalent to proteins Gene Product Biological Oracle Protein6C. VCF ModuleID: 2 Description: Variant Call Format file format.Fig. 3. VCF-chrom : String-pos : int-id : String-ref : alt-qual : intVCF Variation-id : String-description : StringFILTER key-pass : booleanFILTER value-id : String-number : String-type : String-description : StringINFO key-value : "INFO key type"INFO value-id : String-name : StringVCF file-id : String-number : String-type : String-description : StringFORMAT key-id : StringSAMPLE-value : "FORMAT key ype"FORMAT valueClass411..*1..* 1..*1..*1..*1..** 1..*1..*1..*1..*Powered ByVisual Paradigm Community EditionTABLE III. VCF KNOWLEDGE ELEMENTSKnowledge chainsKnowledge Block Output CSID Description Input Class CS Class2.c.0 VCF Variation is linked to biological variation VCF Variation [1..*] Biological Oracle Variation [1]2.c.1 Sample is linked to biological species Sample [*] Biological Oracle Species [1]Knowledge equalitiesKnowledge Block Output CSID Description Input Class CS Class2.e.0 VCF Variation is ontologically equivalent to ANNVCF VariationVCF Variation ANN KnowledgeBlockANN VCFVariation2.e.1 VCF file is ontologically equivalent to ANN VCFfileVCF file ANN KnowledgeBlockANN VCF file7D. ANN ModuleID: 3 Description: ANN field inside Variant Call Format file format.Fig. 4. ANN-id : String-name : StringANN VCF File-chrom : String-pos : int-id : String-ref : String-alt : String-qual : intANN VCF Variation-id : char-description : String-value : StringANN key-value : "ANN key value"ANN value-id : String-name : StringANN gene-id : String-name : StringANN transcriptClass51..*0..21 1..*0..11..*1..*1..*Powered ByVisual Paradigm Community EditionTABLE IV. ANN KNOWLEDGE ELEMENTSKnowledge chainsKnowledge Block Output CSID Description Input Class CS Class- - - - -Knowledge equalitiesKnowledge Block Output CSID Description Input Class CS Class3.e.0 ANN VCF Variation is ontologically equivalent toVCF VariationVCF Variation VCF KnowledgeBlockVCF Variation3.e.1 ANN VCF file is ontologically equivalent to VCFfileVCF file VCF KnowledgeBlockVCF file3.e.2 ANN gene is ontologically equivalent to biologicalgeneANN gene Biological Oracle gene3.2.3 ANN transcript is ontologically equivalent to biolog-ical Primary transcriptANN transcript Biological Oracle Primary transcript8APPENDIX CCSCG: FINAL CS-id : int-name : String-description : String- / sequence : StringProtein-id : int-name : String-description : StringDomainEnzyme-id : int-name : String-description : StringOrtholog-id : String[]-description : StringPathwayGene Intron Exon-id : int-name : String- / sequence : StringmRNA-id : int-name : String- / sequence : StringPrimary_transcript-id : int-name : String-description : String-sequence : StringChromosome-id : int-name : String-direction : char-start : int-end : int- / sequence : StringSequence_part-position : int-ref : String-alt : StringVariation-id : int-name : String-description : StringSpecies-id : int-name : String-description : String-start : int-end : int- / sequece : String5' UTR-id : int-name : String-description : String-start : int-end : int- / sequece : StringCDS-id : int-name : String-description : String-start : int-end : int- / sequece : String3' UTR-id : int-name : String-length : int-sequence : StringScaffold-code : String-description : StringEvidence-id : String-description : StringReference-qualifier : NOT | contributes | colocalizes-source : String-date : dateAnnotation-id : String-description : StringGOMolecular FunctionCellular Component Biological Process-id : int-name : String-description : StringFunctional Element-chrom : String-pos : int-id : String-ref : alt-qual : intVCF Variation-id : String-description : StringFILTER key-pass : booleanFILTER value-id : String-number : String-type : String-description : StringINFO key-value : "INFO key type"INFO value-id : String-name : StringVCF file-id : String-number : String-type : String-description : StringFORMAT key-id : StringSAMPLE-value : "FORMAT key ype"FORMAT value-id : char-description : String-value : StringANN key-value : "ANN key value"ANN valueClass611..**1..*1..*1..**0..21 1..*1 11..**11 *1*1..** *1*1..*1..***11..*11..*1..*11* ***1..*11..*1..***1*111..*intervenes1..* **0..1in_ortholog* 1..*1..*1..*1..* 1..*is ais a is a{ part of | regulates }pertains tohas_variationvariation_in_partrna_processingtranscriptiontranslationrelated_toPowered ByVisual Paradigm Community Edition

CSCG: Conceptual Schema of the Citrus Genome

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CSCG: Conceptual Schema of the Citrus Genome

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