RNAXL Schema-Semantic Computing and Bioinformatics-Handout, Exercises of Semantics of Programming Languages

Download RNAXL Schema-Semantic Computing and Bioinformatics-Handout and more Exercises Semantics of Programming Languages in PDF only on Docsity! 1 RNA XML SCHEMA Docsity.com 2 Contents 1. Domain Introduction ....................................................................................................................... 4 2. Itemized List .................................................................................................................................... 4 2.1 RNA sequences ....................................................................................................................... 4 2.2 RNA Mutations ........................................................................................................................ 4 2.3 RNA Structure ......................................................................................................................... 4 2.4 RNA Structure Annotation ...................................................................................................... 4 3. Types of RNA In accord to Function ................................................................................................ 4 3.1 TYPE 1: RNAs involved in protein synthesis ........................................................................... 4 3.1.1 Messenger RNA ...................................................................................................................... 4 3.1.2 Ribosomal RNA ....................................................................................................................... 4 3.1.3 Signal Recognition Particle RNA ............................................................................................. 4 3.1.4 Transfer RNA .......................................................................................................................... 5 3.1.5 Transfer-messenger RNA ....................................................................................................... 5 3.2 TYPE 2 : RNAs involved in post-transcriptional modification or DNA replication ................. 5 3.2.1 Small nuclear RNA .................................................................................................................. 5 3.2.2 Small nucleolar RNA ............................................................................................................... 5 3.2.3 Small Cajal body-specific RNA ................................................................................................ 5 3.2.4 SmY RNA ................................................................................................................................. 5 3.2.5 Guide RNA ........................................................................................................................... 5 3.2.6 Ribonuclease P ................................................................................................................ 6 3.2.7 Ribonuclease MRP .............................................................................................................. 6 3.2.8 Telomerase RNA ................................................................................................................. 6 3.3 TYPE : 3 RNAs Involved in Regulatory RNA ............................................................................ 6 3.3.1 Antisense RNA .................................................................................................................... 6 3.3.2 CRISPR RNA.......................................................................................................................... 6 3.3.3 Micro RNA .......................................................................................................................... 6 3.3.4 Piwi-interacting RNA .......................................................................................................... 6 3.3.5 Small Interfering RNA ......................................................................................................... 6 3.3.6 Trans-acting siRNA .............................................................................................................. 7 3.3.7 Repeat Associated siRNA .................................................................................................... 7 3.4 TYPE : 4 RNAs involved in Parasitic RNAs ................................................................................ 7 3.4.1 Retrotransposon ................................................................................................................. 7 Docsity.com 5  Distribution- All organisms 3.1.4 Transfer RNA  Abbreviation (tRNA)  Function – Translation  Distribution - All organisms 3.1.5 Transfer-messenger RNA Abbreviation (tmRNA) Function-Rescuing Stalled ribosomes Distribution – Bacteria 3.2 TYPE 2 : RNAs involved in post-transcriptional modification or DNA replication 3.2.1 Small nuclear RNA  Abbreviation (snRNA)  Function – mRNA splicing  Distribution- Eukaryotes and archaea 3.2.2 Small nucleolar RNA  Abbreviation (snoRNA)  Function – modification of ribosomal RNA  Distribution - Eukaryotes and archaea 3.2.3 Small Cajal body-specific RNA  Abbreviation (scaRNA)  Function – Type of snoRNA ; involved in modification of RNA 3.2.4 SmY RNA  Abbr – SmY  Function-m RNA transsplicing  Distribution – Nematodes 3.2.5 Guide RNA  Abbr – gRNA  Function- mRNA nucleotide modification Docsity.com 6 3.2.6 Ribonuclease P  Abbr – RNase P  Function – tRNA maturation  Distribution – All organisms 3.2.7 Ribonuclease MRP  Abbr – RNase MRP  Function – rRNA maturation, DNA replication  Distribution – Eukaryotes 3.2.8 Telomerase RNA  Abbr- NIL  Function- Telomere Synthesis  Distribution- Eukaryotes 3.3 TYPE : 3 RNAs Involved in Regulatory RNA 3.3.1 Antisense RNA  Abbr – aRNA  Function – Transcriptional attenuation / mRNA degradation and stabilization / Translation Block  Distribution – All organisms 3.3.2 CRISPR RNA  Abbr – crRNA  Function - Resistance to parasites, probably by targeting their DNA  Distribution – Bacteria and archaea 3.3.3 Micro RNA  Abbr – miRNA  Function – Gene Regulation  Distribution – Most eukaryotes 3.3.4 Piwi-interacting RNA  Abbr – piRNA  Function – Transposon defense  Distribution – All animals 3.3.5 Small Interfering RNA  Abbr – siRNA  Function – Gene Regulation  Distribution – Most eukaryotes Docsity.com 7 3.3.6 Trans-acting siRNA  Abbr- tasiRNA  Function – Gene Regulation  Distribution – Land Plants 3.3.7 Repeat Associated siRNA  Abbr – rasiRNA  Function – Type of piRNA, transposon defense  Distribution – Drosophila Melanogaster 3.4 TYPE : 4 RNAs involved in Parasitic RNAs 3.4.1 Retrotransposon  Function – Self-propagation  Distribution – Eukaryotes and some bacteria 3.4.2 Viral Genome  Function – Information Carrier  Distribution – Double Stranded RNA viruses, positive-sense RNA viruses, negative-sense RNA viruses, satellite viruses, reverse-transcribing viruses 3.4.3 Viroid  Function-Self-propagation  Distribution- Infected Plants 3.4.4 Satellite RNA  Function- Self-propagation  Distribution- Infected plants Docsity.com 10 <xs:attribute name="analysis-ids" type="xs:IDREFS"/> <xs:attribute name="database-ids" type="xs:IDREFS"/> </xs:complexType> </xs:element> <xs:element name="numbering-range"> <xs:complexType> <xs:sequence> <xs:element ref="start"/> <xs:choice> <xs:element ref="end"/> <xs:element ref="length"/> </xs:choice> </xs:sequence> <xs:attribute name="comment" type="xs:string"/> <xs:attribute name="reference-ids" type="xs:IDREFS"/> <xs:attribute name="analysis-ids" type="xs:IDREFS"/> <xs:attribute name="database-ids" type="xs:IDREFS"/> </xs:complexType> </xs:element> <xs:simpleType name="numberingElements"> <xs:list itemType="xs:positiveInteger"/> </xs:simpleType> <xs:element name="numbering-table"> <xs:complexType> <xs:simpleContent> <xs:extension base="numberingElements"> <xs:attribute name="length" type="xs:positiveInteger" use="required"/> <xs:attribute name="comment" type="xs:string"/> <xs:attribute name="reference-ids" type="xs:IDREFS"/> <xs:attribute name="analysis-ids" type="xs:IDREFS"/> <xs:attribute name="database-ids" type="xs:IDREFS"/> </xs:extension> </xs:simpleContent> </xs:complexType> </xs:element> <xs:simpleType name="seq-data-string"> <xs:restriction base="xs:string"> <xs:pattern value="[GAUCRYMKSWHBVDN]+"/> </xs:restriction> </xs:simpleType> <xs:element name="seq-data"> <xs:complexType> <xs:simpleContent> <xs:extension base="seq-data-string"> <xs:attribute name="comment" type="xs:string"/> <xs:attribute name="reference-ids" type="xs:IDREFS"/> <xs:attribute name="analysis-ids" type="xs:IDREFS"/> <xs:attribute name="database-ids" type="xs:IDREFS"/> </xs:extension> </xs:simpleContent> Docsity.com 11 </xs:complexType> </xs:element> <xs:element name="seq-annotation"> <xs:complexType> <xs:choice maxOccurs="unbounded" minOccurs="0"> <xs:element ref="modification"/> <xs:element ref="segment"/> </xs:choice> <xs:attribute name="comment" type="xs:string"/> <xs:attribute name="reference-ids" type="xs:IDREFS"/> <xs:attribute name="analysis-ids" type="xs:IDREFS"/> <xs:attribute name="database-ids" type="xs:IDREFS"/> </xs:complexType> </xs:element> <xs:element name="modification"> <xs:complexType> <xs:sequence> <xs:element ref="base-id"/> <xs:element ref="modified-type"/> </xs:sequence> <xs:attribute name="comment" type="xs:string"/> <xs:attribute name="reference-ids" type="xs:IDREFS"/> <xs:attribute name="analysis-ids" type="xs:IDREFS"/> <xs:attribute name="database-ids" type="xs:IDREFS"/> </xs:complexType> </xs:element> <xs:element name="modified-type" type="xs:string"/> <xs:element name="segment"> <xs:complexType> <xs:sequence> <xs:element minOccurs="0" ref="seg-name"/> <xs:element ref="base-id-5p"/> <xs:choice> <xs:element ref="base-id-3p"/> <xs:element ref="length"/> </xs:choice> </xs:sequence> <xs:attribute name="comment" type="xs:string"/> <xs:attribute name="reference-ids" type="xs:IDREFS"/> <xs:attribute name="analysis-ids" type="xs:IDREFS"/> <xs:attribute name="database-ids" type="xs:IDREFS"/> </xs:complexType> </xs:element> <xs:element name="seg-name" type="xs:string"/> <xs:element name="structure"> <xs:complexType> <xs:sequence maxOccurs="unbounded" minOccurs="0"> <xs:element ref="model"/> </xs:sequence> Docsity.com 12 <xs:attribute name="comment" type="xs:string"/> <xs:attribute name="reference-ids" type="xs:IDREFS"/> <xs:attribute name="analysis-ids" type="xs:IDREFS"/> <xs:attribute name="database-ids" type="xs:IDREFS"/> </xs:complexType> </xs:element> <xs:element name="model"> <xs:complexType> <xs:sequence> <xs:element minOccurs="0" ref="model-info"/> <xs:element maxOccurs="unbounded" minOccurs="0" ref="base"/> <xs:element minOccurs="0" ref="str-annotation"/> <xs:element minOccurs="0" ref="secondary-structure-display"/> </xs:sequence> <xs:attribute name="id" type="xs:ID"/> <xs:attribute name="comment" type="xs:string"/> <xs:attribute name="reference-ids" type="xs:IDREFS"/> <xs:attribute name="analysis-ids" type="xs:IDREFS"/> <xs:attribute name="database-ids" type="xs:IDREFS"/> </xs:complexType> </xs:element> <xs:element name="model-info"> <xs:complexType> <xs:sequence> <xs:element minOccurs="0" ref="method"/> <xs:element minOccurs="0" ref="resolution"/> <xs:element maxOccurs="unbounded" minOccurs="0" ref="free- energy"/> </xs:sequence> <xs:attribute name="comment" type="xs:string"/> <xs:attribute name="reference-ids" type="xs:IDREFS"/> <xs:attribute name="analysis-ids" type="xs:IDREFS"/> <xs:attribute name="database-ids" type="xs:IDREFS"/> </xs:complexType> </xs:element> <xs:element name="method"> <xs:complexType> <xs:simpleContent> <xs:extension base="xs:string"> <xs:attribute name="comment" type="xs:string"/> <xs:attribute name="reference-ids" type="xs:IDREFS"/> <xs:attribute name="analysis-ids" type="xs:IDREFS"/> <xs:attribute name="database-ids" type="xs:IDREFS"/> </xs:extension> </xs:simpleContent> </xs:complexType> </xs:element> <xs:element name="resolution"> <xs:complexType> <xs:simpleContent> <xs:extension base="xs:float"> Docsity.com 15 <xs:element ref="base-pair"/> <xs:element ref="base-triple"/> <xs:element ref="base-stack"/> <xs:element ref="helix"/> <xs:element ref="pseudoknot"/> <xs:element ref="single-strand"/> <xs:element ref="distance-constraint"/> <xs:element ref="surface-constraint"/> </xs:choice> <xs:attribute name="comment" type="xs:string"/> <xs:attribute name="reference-ids" type="xs:IDREFS"/> <xs:attribute name="analysis-ids" type="xs:IDREFS"/> <xs:attribute name="database-ids" type="xs:IDREFS"/> </xs:complexType> </xs:element> <xs:element name="base-conformation"> <xs:complexType> <xs:sequence> <xs:element ref="base-id"/> <xs:element minOccurs="0" ref="pucker"/> <xs:element minOccurs="0" ref="glycosyl"/> <xs:element minOccurs="0" ref="base-torsion-angles"/> </xs:sequence> <xs:attribute name="comment" type="xs:string"/> <xs:attribute name="reference-ids" type="xs:IDREFS"/> <xs:attribute name="analysis-ids" type="xs:IDREFS"/> <xs:attribute name="database-ids" type="xs:IDREFS"/> </xs:complexType> </xs:element> <xs:element name="pucker" type="xs:string"/> <xs:element name="glycosyl" type="xs:string"/> <xs:element name="base-torsion-angles"> <xs:complexType> <xs:sequence> <xs:element minOccurs="0" ref="alpha"/> <xs:element minOccurs="0" ref="beta"/> <xs:element minOccurs="0" ref="gamma"/> <xs:element minOccurs="0" ref="delta"/> <xs:element minOccurs="0" ref="epsilon"/> <xs:element minOccurs="0" ref="zeta"/> <xs:element minOccurs="0" ref="chi"/> <xs:element minOccurs="0" ref="nu0"/> <xs:element minOccurs="0" ref="nu1"/> <xs:element minOccurs="0" ref="nu2"/> <xs:element minOccurs="0" ref="nu3"/> <xs:element minOccurs="0" ref="nu4"/> </xs:sequence> <xs:attribute name="comment" type="xs:string"/> <xs:attribute name="reference-ids" type="xs:IDREFS"/> <xs:attribute name="analysis-ids" type="xs:IDREFS"/> <xs:attribute name="database-ids" type="xs:IDREFS"/> </xs:complexType> Docsity.com 16 </xs:element> <xs:element name="alpha" type="xs:float"/> <xs:element name="beta" type="xs:float"/> <xs:element name="gamma" type="xs:float"/> <xs:element name="delta" type="xs:float"/> <xs:element name="epsilon" type="xs:float"/> <xs:element name="zeta" type="xs:float"/> <xs:element name="chi" type="xs:float"/> <xs:element name="nu0" type="xs:float"/> <xs:element name="nu1" type="xs:float"/> <xs:element name="nu2" type="xs:float"/> <xs:element name="nu3" type="xs:float"/> <xs:element name="nu4" type="xs:float"/> <xs:element name="base-pair"> <xs:complexType> <xs:sequence> <xs:element ref="base-id-5p"/> <xs:element ref="base-id-3p"/> <xs:element minOccurs="0" ref="edge-5p"/> <xs:element minOccurs="0" ref="edge-3p"/> <xs:element minOccurs="0" ref="bond-orientation"/> <xs:element minOccurs="0" ref="strand-orientation"/> </xs:sequence> <xs:attribute name="comment" type="xs:string"/> <xs:attribute name="reference-ids" type="xs:IDREFS"/> <xs:attribute name="analysis-ids" type="xs:IDREFS"/> <xs:attribute name="database-ids" type="xs:IDREFS"/> </xs:complexType> </xs:element> <xs:element name="base-id-5p"> <xs:complexType> <xs:sequence> <xs:element ref="base-id"/> </xs:sequence> </xs:complexType> </xs:element> <xs:element name="base-id-3p"> <xs:complexType> <xs:sequence> <xs:element ref="base-id"/> </xs:sequence> Docsity.com 17 </xs:complexType> </xs:element> <xs:element name="edge-5p" type="xs:string"/> <xs:element name="edge-3p" type="xs:string"/> <xs:element name="bond-orientation" type="xs:string"/> <xs:element name="strand-orientation" type="xs:string"/> <xs:element name="base-triple"> <xs:complexType> <xs:sequence> <xs:choice> <xs:element ref="base-pair"/> <xs:element ref="base-pair-id"/> </xs:choice> <xs:choice> <xs:element ref="base-pair"/> <xs:element ref="base-pair-id"/> </xs:choice> <xs:choice> <xs:element ref="base-pair"/> <xs:element ref="base-pair-id"/> </xs:choice> </xs:sequence> <xs:attribute name="comment" type="xs:string"/> <xs:attribute name="reference-ids" type="xs:IDREFS"/> <xs:attribute name="analysis-ids" type="xs:IDREFS"/> <xs:attribute name="database-ids" type="xs:IDREFS"/> </xs:complexType> </xs:element> <xs:element name="base-stack"> <xs:complexType> <xs:sequence> <xs:element ref="base-id"/> <xs:element ref="base-id"/> </xs:sequence> <xs:attribute name="comment" type="xs:string"/> <xs:attribute name="reference-ids" type="xs:IDREFS"/> <xs:attribute name="analysis-ids" type="xs:IDREFS"/> <xs:attribute name="database-ids" type="xs:IDREFS"/> </xs:complexType> </xs:element> <xs:element name="helix"> <xs:complexType> <xs:sequence> <xs:element ref="base-id-5p"/> <xs:element ref="base-id-3p"/> <xs:element ref="length"/> </xs:sequence> <xs:attribute name="id" type="xs:ID"/> <xs:attribute name="comment" type="xs:string"/> Docsity.com 20 <xs:element ref="molecule-id"/> <xs:element ref="numbering-system"/> <xs:element ref="consensus-molecule"/> <xs:element ref="alignment"/> </xs:choice> </xs:sequence> <xs:attribute name="comment" type="xs:string"/> <xs:attribute name="reference-ids" type="xs:IDREFS"/> <xs:attribute name="analysis-ids" type="xs:IDREFS"/> <xs:attribute name="database-ids" type="xs:IDREFS"/> </xs:complexType> </xs:element> <xs:element name="consensus-molecule"> <xs:complexType> <xs:sequence> <xs:element ref="alignment-id"/> <xs:element ref="molecule"/> </xs:sequence> <xs:attribute name="comment" type="xs:string"/> <xs:attribute name="reference-ids" type="xs:IDREFS"/> <xs:attribute name="analysis-ids" type="xs:IDREFS"/> <xs:attribute name="database-ids" type="xs:IDREFS"/> </xs:complexType> </xs:element> <xs:element name="alignment"> <xs:complexType> <xs:sequence> <xs:element maxOccurs="unbounded" minOccurs="0" ref="ali- sequence"/> </xs:sequence> <xs:attribute name="id" type="xs:ID" use="required"/> <xs:attribute name="comment" type="xs:string"/> <xs:attribute name="reference-ids" type="xs:IDREFS"/> <xs:attribute name="analysis-ids" type="xs:IDREFS"/> <xs:attribute name="database-ids" type="xs:IDREFS"/> </xs:complexType> </xs:element> <xs:element name="ali-sequence"> <xs:complexType> <xs:sequence> <xs:element ref="molecule-id"/> <xs:element ref="seq-data"/> </xs:sequence> <xs:attribute name="comment" type="xs:string"/> <xs:attribute name="reference-ids" type="xs:IDREFS"/> <xs:attribute name="analysis-ids" type="xs:IDREFS"/> <xs:attribute name="database-ids" type="xs:IDREFS"/> </xs:complexType> </xs:element> <xs:element name="interactions"> <xs:complexType> <xs:sequence maxOccurs="unbounded" minOccurs="0"> Docsity.com 21 <xs:element ref="str-annotation"/> </xs:sequence> <xs:attribute name="comment" type="xs:string"/> <xs:attribute name="reference-ids" type="xs:IDREFS"/> <xs:attribute name="analysis-ids" type="xs:IDREFS"/> <xs:attribute name="database-ids" type="xs:IDREFS"/> </xs:complexType> </xs:element> <xs:element name="taxonomy"> <xs:complexType> <xs:sequence> <xs:element minOccurs="0" ref="domain"/> <xs:element minOccurs="0" ref="kingdom"/> <xs:element minOccurs="0" ref="phylum"/> <xs:element minOccurs="0" ref="class"/> <xs:element minOccurs="0" ref="order"/> <xs:element minOccurs="0" ref="family"/> <xs:element minOccurs="0" ref="genus"/> <xs:element minOccurs="0" ref="species"/> <xs:element minOccurs="0" ref="strain"/> </xs:sequence> <xs:attribute name="comment" type="xs:string"/> <xs:attribute name="reference-ids" type="xs:IDREFS"/> <xs:attribute name="analysis-ids" type="xs:IDREFS"/> <xs:attribute name="database-ids" type="xs:IDREFS"/> </xs:complexType> </xs:element> <xs:element name="domain" type="xs:string"/> <xs:element name="kingdom" type="xs:string"/> <xs:element name="phylum" type="xs:string"/> <xs:element name="class" type="xs:string"/> <xs:element name="order" type="xs:string"/> <xs:element name="family" type="xs:string"/> <xs:element name="genus" type="xs:string"/> <xs:element name="species" type="xs:string"/> <xs:element name="strain" type="xs:string"/> <xs:element name="reference"> <xs:complexType> <xs:choice maxOccurs="unbounded" minOccurs="0"> <xs:element ref="author"/> <xs:element ref="title"/> <xs:element ref="journal"/> <xs:element ref="date"/> <xs:element ref="pubmed-id"/> <xs:element ref="book-title"/> Docsity.com 22 <xs:element ref="editor"/> <xs:element ref="volume"/> <xs:element ref="issue"/> <xs:element ref="pages"/> <xs:element ref="path"/> </xs:choice> <xs:attribute name="id" type="xs:ID" use="required"/> <xs:attribute name="comment" type="xs:string"/> </xs:complexType> </xs:element> <xs:element name="author"> <xs:complexType> <xs:sequence> <xs:element ref="person"/> </xs:sequence> </xs:complexType> </xs:element> <xs:element name="title" type="xs:string"/> <xs:element name="journal" type="xs:string"/> <xs:element name="pubmed-id" type="xs:string"/> <xs:element name="book-title" type="xs:string"/> <xs:element name="editor" type="xs:string"/> <xs:element name="volume" type="xs:integer"/> <xs:element name="issue" type="xs:integer"/> <xs:element name="pages"> <xs:simpleType> <xs:restriction base="xs:string"> <xs:pattern value="[0-9]+,[0-9]+"/> </xs:restriction> </xs:simpleType> </xs:element> <xs:element name="database-entry"> <xs:complexType> <xs:sequence> <xs:element ref="database"/> <xs:element ref="entry"/> <xs:element minOccurs="0" ref="path"/> </xs:sequence> <xs:attribute name="id" type="xs:ID" use="required"/> <xs:attribute name="comment" type="xs:string"/> <xs:attribute name="reference-ids" type="xs:IDREFS"/> <xs:attribute name="analysis-ids" type="xs:IDREFS"/> <xs:attribute name="database-ids" type="xs:IDREFS"/> </xs:complexType> </xs:element> Docsity.com 25 <xs:complexType> <xs:attribute name="ref" type="xs:IDREF" use="required"/> </xs:complexType> </xs:element> <xs:element name="model-id"> <xs:complexType> <xs:attribute name="ref" type="xs:IDREF"/> </xs:complexType> </xs:element> <xs:element name="strand" type="xs:string"/> <xs:element name="base-pair-id"> <xs:complexType> <xs:attribute name="ref" type="xs:IDREF" use="required"/> </xs:complexType> </xs:element> <xs:element name="alignment-id"> <xs:complexType> <xs:attribute name="ref" type="xs:IDREF" use="required"/> </xs:complexType> </xs:element> </xs:schema> Docsity.com a &, Schema == rnaml "iS molecule ™S identity = name GE sequence ST} GQ) secuence fy number ing-system GE seq-data (FE seq-annotation strand length circular comment reference-ids analysis—ids database-ids Seee2eee "OS numbering-system |S number ing-range T number ingE lements xSt xs? Net xs xs xSt xe xe? atring string positiveInteger tboolean istring IDREFS IDREFS IDREFS 26 Docsity.com