XML Representation of Protein Data: DTD and XML Schema with Reference to Bioinformatics, Slides of Semantics of Programming Languages

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DTD REFERENCE AND XML S TO BIOINFORMATICSCHEMA WITH

EXAMPLE: PROTEIN

PROTEIN

 Proteins of one or more polypeptides typically folded into a are biochemical compounds consisting

globular or fibrous form, facilitating a biologicalfunction.

EXAMPLE OF DTD

……………… SUBUNIT: Heterodimer of an alpha and a beta

chain. SUBCELLULAR LOCATION: Type I membrane protein.

SIMILARITY: BELONGS TO THE CYTOKINE FAMILY OF RECEPTORS.

Receptor Glycoprotein Signal

</PROTEIN-SET>

   (^) ANY:EMPTY:#PCDATA: the element can contain any text or any child element(s).the element cannot contain any text or anythe element can contain regular text. child elements.   Child Elements: the element can contain a specific set of child elements.MIXED: the element can contain text data interspersed with child element

Critical Evaluation of the DTD

XML SCHEMA

Visual overview of the protein.xsd schema. (Diagram was created withXMLSpy Docsity.com

<xs:complexType> <xs:complexContent> <xs:restriction base="xs:anyType"> <xs:sequence> <xs:element name="accession" type="xs:string"/> <xs:element name="entry-name" type="xs:string"/> <xs:element name="protein-name" type="xs:string"/> <xs:element name="gene-name" type="xs:string" maxOccurs="unbounded"/> <xs:element ref="organism"/> <xs:element ref="cross-reference" minOccurs="0" maxOccurs="unbounded"/> <xs:element name="comment" type="xs:string" minOccurs="0" maxOccurs="unbounded"/> <xs:element name="keyword" type="xs:string" minOccurs="0" maxOccurs="unbounded"/> </xs:sequence> </xs:restriction> </xs:complexContent>

<gene-name>CSF2RB2</gene-name> <gene-name>AI2CA</gene-name> <gene-name>IL3RB2</gene-name> <gene-name>IL3R</gene-name>

P26954 <entry-name>IL3B-MOUSE</entry-name> <protein-name>Interleukin-3 receptor class II

beta chain [Precursor]