VIOLINML.dtd: Elements - Entities - Source | Index

<!-- ***************************************************************-->
<!--             VIOLIN Markup Language (VIOLINML)                  -->
<!--               Document Type Definition (DTD)                   -->
<!--              He Group, University of Michigan                  -->
<!--                                                                -->
<!-- Description: Data exchange format for VIOLIN data              -->
<!-- Authors: Yongqun He, Zuoshuang Xiang                           -->
<!-- Date: July 31, 2007                                            -->
<!-- Version: 1.0                                                   -->
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<!-- 'VIOLIN' defines the top level structure of VIOLIN information. -->
<!ELEMENT VIOLIN (pathogen, host*, vaccine*, gene*, reference*, curation*)>
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<!--                 Pathogen Information                           -->
<!-- ***************************************************************-->
<!-- 'pathogen' describes the pathogen information -->
<!ELEMENT pathogen (name, taxon_id, pathogenesis, disease_name, protective_immunity, host_range, introduction)>
<!-- 'pathogen_id' is a unique ID assigned to a pathogen. -->
<!ATTLIST pathogen
    pathogen_id ID #REQUIRED
>
<!-- 'disease_name' is the name(s) of a disease. -->
<!ELEMENT disease_name (#PCDATA)>
<!-- 'pathogenesis' describes how a pathogen causes a disease. -->
<!ELEMENT pathogenesis (#PCDATA)>
<!-- 'refs' describes the reference IDs assigned in the 'references' section and were used for any references that provide information for current section. -->
<!ATTLIST pathogenesis
    refs IDREFS #IMPLIED
>
<!-- 'protective_immunity' describes protective immunity required for a vaccine to protect against pathogenic infection. -->
<!ELEMENT protective_immunity (#PCDATA)>
<!-- 'refs' describes the reference IDs assigned in the 'references' section and were used for any references that provide information for current section. -->
<!ATTLIST protective_immunity
    refs IDREFS #IMPLIED
>
<!-- 'host_range' describes the infection range of a pathogen. -->
<!ELEMENT host_range (#PCDATA)>
<!-- 'refs' describes the reference IDs assigned in the 'references' section and were used for any references that provide information for current section. -->
<!ATTLIST host_range
    refs IDREFS #IMPLIED
>
<!-- 'introduction' includes introductory information. -->
<!ELEMENT introduction (#PCDATA)>
<!-- 'refs' describes the reference IDs assigned in the 'references' section and were used for any references that provide information for current section. -->
<!ATTLIST introduction
    refs IDREFS #IMPLIED
>
<!-- ***************************************************************-->
<!--                 Host Information                           -->
<!-- ***************************************************************-->
<!-- 'host' describes a host species. -->
<!ELEMENT host (common_name, scientific_name, taxon_id)>
<!-- 'host_id' is a unique ID assigned to a host in VIOLIN.  -->
<!ATTLIST host
    host_id ID #REQUIRED
>
<!-- 'common_name' describes the common name of a species, or variant. -->
<!ELEMENT common_name (#PCDATA)>
<!-- 'scientific_name' describes a scientific name of a species, or a variant. -->
<!ELEMENT scientific_name (#PCDATA)>
<!-- 'taxon_id' describes a NCBI taxonomy ID. -->
<!ELEMENT taxon_id (#PCDATA)>
<!-- ***************************************************************-->
<!--                 Vaccine Information                           -->
<!-- ***************************************************************-->
<!-- '' describes  -->
<!ELEMENT vaccine (name, brand_name, type, description, adjuvant, storage, virulence, preparation, antigen, gene_engineering*, host_response*)>
<!-- 'vaccine_id' is a unique ID assigned to a vaccine.  -->
<!ATTLIST vaccine
    vaccine_id ID #REQUIRED
>
<!-- 'name' is a name. -->
<!ELEMENT name (#PCDATA)>
<!-- 'brand_name' describes a commercial brand name of a vaccine. -->
<!ELEMENT brand_name (#PCDATA)>
<!-- 'type' describes a specific type. -->
<!ELEMENT type (#PCDATA)>
<!-- 'description' describes information about a specific topic. -->
<!ELEMENT description (#PCDATA)>
<!-- 'refs' describes the reference IDs assigned in the 'references' section and were used for any references that provide information for current section. -->
<!ATTLIST description
    refs IDREFS #IMPLIED
>
<!-- 'adjuvant' describes the adjuvant used for vaccine immunization. An adjuvant boosts immune response stimulated by a vaccine. -->
<!ELEMENT adjuvant (#PCDATA)>
<!-- 'refs' describes the reference IDs assigned in the 'references' section and were used for any references that provide information for current section. -->
<!ATTLIST adjuvant
    refs IDREFS #IMPLIED
>
<!-- 'storage' describes how a vaccine is stored. -->
<!ELEMENT storage (#PCDATA)>
<!-- 'refs' describes the reference IDs assigned in the 'references' section and were used for any references that provide information for current section. -->
<!ATTLIST storage
    refs IDREFS #IMPLIED
>
<!-- 'virulence' describes virulence of a vaccine. -->
<!ELEMENT virulence (#PCDATA)>
<!-- 'refs' describes the reference IDs assigned in the 'references' section and were used for any references that provide information for current section. -->
<!ATTLIST virulence
    refs IDREFS #IMPLIED
>
<!-- 'preparation' describes how a vaccine is prepared. -->
<!ELEMENT preparation (#PCDATA)>
<!-- 'refs' describes the reference IDs assigned in the 'references' section and were used for any references that provide information for current section. -->
<!ATTLIST preparation
    refs IDREFS #IMPLIED
>
<!-- 'antigen' describes an antigen that is able to stimulate immune response in a host. -->
<!ELEMENT antigen (#PCDATA)>
<!-- 'refs' describes the reference IDs assigned in the 'references' section and were used for any references that provide information for current section. -->
<!ATTLIST antigen
    refs IDREFS #IMPLIED
>
<!-- 'gene_engineering' describes the genetic engineering of a pathogen gene(s) for the purpose of vaccine development. -->
<!ELEMENT gene_engineering (type, description)>
<!-- 'gene_engineering_id' is a unique ID assigned to a section of gene engineering data stored in VIOLIN. 'gene_id' refers to an ID for a specific gene stored in VIOLIN.  -->
<!ATTLIST gene_engineering
    gene_engineering_id ID #REQUIRED
    gene_id IDREF #REQUIRED
>
<!-- 'host_response' describes  -->
<!ELEMENT host_response (immune_response, host_strain, vaccination_protocol, persistence, protection_efficacy, side_effects, challenge_protocol, host_gene_response*, description)>
<!-- 'host_response_id' is a unique ID assigned for a specific host response. 'host_id' refers to an ID for a specific host stored in VIOLIN. -->
<!ATTLIST host_response
    host_response_id ID #REQUIRED
    host_id IDREF #REQUIRED
>
<!-- 'immune_response' describes a host response to a vaccine. -->
<!ELEMENT immune_response (#PCDATA)>
<!-- 'refs' describes the reference IDs assigned in the 'references' section and were used for any references that provide information for current section. -->
<!ATTLIST immune_response
    refs IDREFS #IMPLIED
>
<!-- 'host_strain' is a strain of a host species, for example, BALB/c mice. -->
<!ELEMENT host_strain (#PCDATA)>
<!-- 'refs' describes the reference IDs assigned in the 'references' section and were used for any references that provide information for current section. -->
<!ATTLIST host_strain
    refs IDREFS #IMPLIED
>
<!-- 'vaccination_protocol' is the vaccination_protocol of a vaccine vaccination.  NOTE: This one will be DELETED. -->
<!ELEMENT vaccination_protocol (#PCDATA)>
<!-- 'refs' describes the reference IDs assigned in the 'references' section and were used for any references that provide information for current section. -->
<!ATTLIST vaccination_protocol
    refs IDREFS #IMPLIED
>
<!-- 'persistence' describes the persistence (how long it stays) of a vaccine in a host body. -->
<!ELEMENT persistence (#PCDATA)>
<!-- 'refs' describes the reference IDs assigned in the 'references' section and were used for any references that provide information for current section. -->
<!ATTLIST persistence
    refs IDREFS #IMPLIED
>
<!-- 'protection_efficacy' describes the protection_efficacy of a vaccine. -->
<!ELEMENT protection_efficacy (#PCDATA)>
<!-- 'refs' describes the reference IDs assigned in the 'references' section and were used for any references that provide information for current section. -->
<!ATTLIST protection_efficacy
    refs IDREFS #IMPLIED
>
<!-- 'side_effects' describes the side effects of a vaccine in a host. -->
<!ELEMENT side_effects (#PCDATA)>
<!-- 'refs' describes the reference IDs assigned in the 'references' section and were used for any references that provide information for current section. -->
<!ATTLIST side_effects
    refs IDREFS #IMPLIED
>
<!-- 'challenge_protocol' describes a protocol for a challenge experiment. -->
<!ELEMENT challenge_protocol (#PCDATA)>
<!-- 'refs' describes the reference IDs assigned in the 'references' section and were used for any references that provide information for current section. -->
<!ATTLIST challenge_protocol
    refs IDREFS #IMPLIED
>
<!-- 'host_gene_response' describes an gene expression profile of a host gene.  -->
<!ELEMENT host_gene_response (description)>
<!-- 'host_gene_response_id' is a unique ID for a section of host gene response; 'gene_id' is an reference to a gene that is stored in VIOLIN. -->
<!ATTLIST host_gene_response
    host_gene_response_id ID #REQUIRED
    gene_id IDREF #REQUIRED
>
<!-- ***************************************************************-->
<!--                 Gene Information                               -->
<!-- ***************************************************************-->
<!-- 'gene' describes information about a gene stored in the VIOLIN database. -->
<!ELEMENT gene (gene_name, ncbi_gene_id, xrefs, phi_annotation, dna_sequence, protein_sequence, strain, taxonomy_id, ncbi_protein_id, protein_refseq, protein_name, chromosome, segment, gene_locus_tag, gene_start, gene_end, gene_strand, gene_refseq, protein_note, protein_annotation, protein_pi, protein_weight, protein_length, phi_function, plasmid)>
<!-- 'gene_id' is a unique ID assigned to a gene.  -->
<!ATTLIST gene
    gene_id ID #REQUIRED
>
<!-- 'gene_name' is the short name of the name. -->
<!ELEMENT gene_name (#PCDATA)>
<!-- 'ncbi_gene_id' is the Gene ID of the NCBI Gene database. -->
<!ELEMENT ncbi_gene_id (#PCDATA)>
<!-- 'xrefs' describes cross reference ID from other databases. It has a format of "DB_name: DB_id; another_DB_name: another_DB_id" -->
<!ELEMENT xrefs (#PCDATA)>
<!-- 'phi_annotation' is the annotation of pathogen host interaction  -->
<!ELEMENT phi_annotation (#PCDATA)>
<!-- 'dna_sequence' is the sequence of a DNA fragment  -->
<!ELEMENT dna_sequence (#PCDATA)>
<!-- 'protein_sequence' is the sequence of a protein. -->
<!ELEMENT protein_sequence (#PCDATA)>
<!-- 'strain' is the name of a sequenced microorganism, for example, a bacterium, a virus, or a parasite. -->
<!ELEMENT strain (#PCDATA)>
<!-- 'taxonomy_id' is the NCBI taxonomy ID. -->
<!ELEMENT taxonomy_id (#PCDATA)>
<!-- 'ncbi_protein_id' is the NCBI protein ID. It should be a integer. -->
<!ELEMENT ncbi_protein_id (#PCDATA)>
<!-- 'protein_refseq' is the NCBI protein RefSeq No. -->
<!ELEMENT protein_refseq (#PCDATA)>
<!-- 'protein_name' is the name of the coded protein. -->
<!ELEMENT protein_name (#PCDATA)>
<!-- 'chromosome' is the chromosome on which the gene located. -->
<!ELEMENT chromosome (#PCDATA)>
<!-- 'segment' is the segement on which the gene located. -->
<!ELEMENT segment (#PCDATA)>
<!-- 'gene_locus_tag' is the NCBI gene locus tag. -->
<!ELEMENT gene_locus_tag (#PCDATA)>
<!-- 'gene_start' is the starting position of the gene. -->
<!ELEMENT gene_start (#PCDATA)>
<!-- 'gene_end' is the the ending position of the gene. -->
<!ELEMENT gene_end (#PCDATA)>
<!-- 'gene_strand' is the coding direction of the gene. -->
<!ELEMENT gene_strand (#PCDATA)>
<!-- 'gene_refseq' is the NCBI gene RefSeq No. -->
<!ELEMENT gene_refseq (#PCDATA)>
<!-- 'protein_note' is the note about the protein. -->
<!ELEMENT protein_note (#PCDATA)>
<!-- 'protein_annotation' is the annotation about the protein. -->
<!ELEMENT protein_annotation (#PCDATA)>
<!-- 'protein_pi' is the pI of the protein. -->
<!ELEMENT protein_pi (#PCDATA)>
<!-- 'protein_weight' is the weight of the protein. -->
<!ELEMENT protein_weight (#PCDATA)>
<!-- 'protein_length' is the length of the protein. -->
<!ELEMENT protein_length (#PCDATA)>
<!-- 'phi_function' is the function category in terms of pathogen host interaction. -->
<!ELEMENT phi_function (#PCDATA)>
<!-- 'plasmid' is the plasmid on wchich the gene located. -->
<!ELEMENT plasmid (#PCDATA)>
<!-- ***************************************************************-->
<!--                         Reference                              -->
<!-- ***************************************************************-->
<!-- 'references' describes the data sources used in the document. Data may be obtained from journals, books, websites, and theses -->
<!ELEMENT reference (name, type, authors, title, year, volume, issue, pages, journal_book_name, publisher, publisher_location, book_editors, isbn, university, university_location, degree, url, file_name)>
<!-- 'reference_id' is a unique ID assigned to a reference.  -->
<!ATTLIST reference
    reference_id ID #REQUIRED
>
<!-- 'authors' is the list of the authors of a reference.  -->
<!ELEMENT authors (#PCDATA)>
<!-- 'title' is the title of a reference. -->
<!ELEMENT title (#PCDATA)>
<!-- 'year' is the year when a reference is published. -->
<!ELEMENT year (#PCDATA)>
<!-- 'volume' describes a journal volume  -->
<!ELEMENT volume (#PCDATA)>
<!-- 'issue' describes a journal issue -->
<!ELEMENT issue (#PCDATA)>
<!-- 'pages' is the range of pages for an article.  -->
<!ELEMENT pages (#PCDATA)>
<!-- 'journal_book_name' is the name of a journal or a book.  -->
<!ELEMENT journal_book_name (#PCDATA)>
<!-- 'publisher' is the book publisher -->
<!ELEMENT publisher (#PCDATA)>
<!-- 'publisher_location' is the location of a book publisher. -->
<!ELEMENT publisher_location (#PCDATA)>
<!-- 'book_editors' means the editors of a book.  -->
<!ELEMENT book_editors (#PCDATA)>
<!-- 'isbn' menas International Standard Book Number. It is a unique commercial book identifier barcode.  -->
<!ELEMENT isbn (#PCDATA)>
<!-- 'degree' means a Ph.D. or M.S. or other academic degree.  -->
<!ELEMENT degree (#PCDATA)>
<!-- 'university' is the name of a university  -->
<!ELEMENT university (#PCDATA)>
<!-- 'university_location' is the location of a univerisity, it should include city name, state/province, and country name. -->
<!ELEMENT university_location (#PCDATA)>
<!-- 'url' stands for Uniform resource locator, it represents a web page address.  -->
<!ELEMENT url (#PCDATA)>
<!-- 'file_name' is the name of an updated file  -->
<!ELEMENT file_name (#PCDATA)>
<!-- ***************************************************************-->
<!--                     Curation Information                       -->
<!-- ***************************************************************-->
<!-- 'curation' describes curation information-->
<!ELEMENT curation (user_name, type, date)>
<!-- 'user_name' is the name of a curator.  -->
<!ELEMENT user_name (#PCDATA)>
<!-- 'date' is the curation submission data.  -->
<!ELEMENT date (#PCDATA)>
<!--        The End        -->