VIOLINML.dtd: Elements - Entities - Source | Index

VIOLINML.dtd

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'VIOLIN' defines the top level structure of VIOLIN information.

<VIOLIN>'s children Name Cardinality curation Any number gene Any number host Any number pathogen Only one reference Any number vaccine Any number

(pathogen, host*, vaccine*, gene*, reference*, curation*)

'pathogen' describes the pathogen information

<pathogen>'s children Name Cardinality disease_name Only one host_range Only one introduction Only one name Only one pathogenesis Only one protective_immunity Only one taxon_id Only one

<pathogen>'s attributes Name Values Default pathogen_id Match the ID rules.

(name, taxon_id, pathogenesis, disease_name, protective_immunity, host_range, introduction)

'pathogen_id' is a unique ID assigned to a pathogen.

Possible values: Match the ID rules. - Required

'disease_name' is the name(s) of a disease.

'pathogenesis' describes how a pathogen causes a disease.

<pathogenesis>'s attributes Name Values Default refs Match the IDREFS rules.

'refs' describes the reference IDs assigned in the 'references' section and were used for any references that provide information for current section.

Possible values: Match the IDREFS rules.

'protective_immunity' describes protective immunity required for a vaccine to protect against pathogenic infection.

<protective_immunity>'s attributes Name Values Default refs Match the IDREFS rules.

'refs' describes the reference IDs assigned in the 'references' section and were used for any references that provide information for current section.

Possible values: Match the IDREFS rules.

'host_range' describes the infection range of a pathogen.

<host_range>'s attributes Name Values Default refs Match the IDREFS rules.

'refs' describes the reference IDs assigned in the 'references' section and were used for any references that provide information for current section.

Possible values: Match the IDREFS rules.

'introduction' includes introductory information.

<introduction>'s attributes Name Values Default refs Match the IDREFS rules.

'refs' describes the reference IDs assigned in the 'references' section and were used for any references that provide information for current section.

Possible values: Match the IDREFS rules.

'host' describes a host species.

<host>'s children Name Cardinality common_name Only one scientific_name Only one taxon_id Only one

<host>'s attributes Name Values Default host_id Match the ID rules.

(common_name, scientific_name, taxon_id)

'host_id' is a unique ID assigned to a host in VIOLIN.

Possible values: Match the ID rules. - Required

'common_name' describes the common name of a species, or variant.

'scientific_name' describes a scientific name of a species, or a variant.

'taxon_id' describes a NCBI taxonomy ID.

'' describes

<vaccine>'s children Name Cardinality adjuvant Only one antigen Only one brand_name Only one description Only one gene_engineering Any number host_response Any number name Only one preparation Only one storage Only one type Only one virulence Only one

<vaccine>'s attributes Name Values Default vaccine_id Match the ID rules.

(name, brand_name, type, description, adjuvant, storage, virulence, preparation, antigen, gene_engineering*, host_response*)

'vaccine_id' is a unique ID assigned to a vaccine.

Possible values: Match the ID rules. - Required

'name' is a name.

'brand_name' describes a commercial brand name of a vaccine.

'type' describes a specific type.

'description' describes information about a specific topic.

<description>'s attributes Name Values Default refs Match the IDREFS rules.

'refs' describes the reference IDs assigned in the 'references' section and were used for any references that provide information for current section.

Possible values: Match the IDREFS rules.

'adjuvant' describes the adjuvant used for vaccine immunization. An adjuvant boosts immune response stimulated by a vaccine.

<adjuvant>'s attributes Name Values Default refs Match the IDREFS rules.

'refs' describes the reference IDs assigned in the 'references' section and were used for any references that provide information for current section.

Possible values: Match the IDREFS rules.

'storage' describes how a vaccine is stored.

<storage>'s attributes Name Values Default refs Match the IDREFS rules.

'refs' describes the reference IDs assigned in the 'references' section and were used for any references that provide information for current section.

Possible values: Match the IDREFS rules.

'virulence' describes virulence of a vaccine.

<virulence>'s attributes Name Values Default refs Match the IDREFS rules.

'refs' describes the reference IDs assigned in the 'references' section and were used for any references that provide information for current section.

Possible values: Match the IDREFS rules.

'preparation' describes how a vaccine is prepared.

<preparation>'s attributes Name Values Default refs Match the IDREFS rules.

'refs' describes the reference IDs assigned in the 'references' section and were used for any references that provide information for current section.

Possible values: Match the IDREFS rules.

'antigen' describes an antigen that is able to stimulate immune response in a host.

<antigen>'s attributes Name Values Default refs Match the IDREFS rules.

'refs' describes the reference IDs assigned in the 'references' section and were used for any references that provide information for current section.

Possible values: Match the IDREFS rules.

'gene_engineering' describes the genetic engineering of a pathogen gene(s) for the purpose of vaccine development.

<gene_engineering>'s children Name Cardinality description Only one type Only one

<gene_engineering>'s attributes Name Values Default gene_engineering_id Match the ID rules. gene_id Match the IDREF rules.

(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.

Possible values: Match the ID rules. - Required

'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.

Possible values: Match the IDREF rules. - Required

'host_response' describes

<host_response>'s children Name Cardinality challenge_protocol Only one description Only one host_gene_response Any number host_strain Only one immune_response Only one persistence Only one protection_efficacy Only one side_effects Only one vaccination_protocol Only one

<host_response>'s attributes Name Values Default host_id Match the IDREF rules. host_response_id Match the ID rules.

(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.

Possible values: Match the ID rules. - Required

'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.

Possible values: Match the IDREF rules. - Required

'immune_response' describes a host response to a vaccine.

<immune_response>'s attributes Name Values Default refs Match the IDREFS rules.

'refs' describes the reference IDs assigned in the 'references' section and were used for any references that provide information for current section.

Possible values: Match the IDREFS rules.

'host_strain' is a strain of a host species, for example, BALB/c mice.

<host_strain>'s attributes Name Values Default refs Match the IDREFS rules.

'refs' describes the reference IDs assigned in the 'references' section and were used for any references that provide information for current section.

Possible values: Match the IDREFS rules.

'vaccination_protocol' is the vaccination_protocol of a vaccine vaccination. NOTE: This one will be DELETED.

<vaccination_protocol>'s attributes Name Values Default refs Match the IDREFS rules.

'refs' describes the reference IDs assigned in the 'references' section and were used for any references that provide information for current section.

Possible values: Match the IDREFS rules.

'persistence' describes the persistence (how long it stays) of a vaccine in a host body.

<persistence>'s attributes Name Values Default refs Match the IDREFS rules.

'refs' describes the reference IDs assigned in the 'references' section and were used for any references that provide information for current section.

Possible values: Match the IDREFS rules.

'protection_efficacy' describes the protection_efficacy of a vaccine.

<protection_efficacy>'s attributes Name Values Default refs Match the IDREFS rules.

'refs' describes the reference IDs assigned in the 'references' section and were used for any references that provide information for current section.

Possible values: Match the IDREFS rules.

'side_effects' describes the side effects of a vaccine in a host.

<side_effects>'s attributes Name Values Default refs Match the IDREFS rules.

'refs' describes the reference IDs assigned in the 'references' section and were used for any references that provide information for current section.

Possible values: Match the IDREFS rules.

'challenge_protocol' describes a protocol for a challenge experiment.

<challenge_protocol>'s attributes Name Values Default refs Match the IDREFS rules.

'refs' describes the reference IDs assigned in the 'references' section and were used for any references that provide information for current section.

Possible values: Match the IDREFS rules.

'host_gene_response' describes an gene expression profile of a host gene.

<host_gene_response>'s children Name Cardinality description Only one

<host_gene_response>'s attributes Name Values Default gene_id Match the IDREF rules. host_gene_response_id Match the ID rules.

(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.

Possible values: Match the ID rules. - Required

'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.

Possible values: Match the IDREF rules. - Required

'gene' describes information about a gene stored in the VIOLIN database.

<gene>'s children Name Cardinality chromosome Only one dna_sequence Only one gene_end Only one gene_locus_tag Only one gene_name Only one gene_refseq Only one gene_start Only one gene_strand Only one ncbi_gene_id Only one ncbi_protein_id Only one phi_annotation Only one phi_function Only one plasmid Only one protein_annotation Only one protein_length Only one protein_name Only one protein_note Only one protein_pi Only one protein_refseq Only one protein_sequence Only one protein_weight Only one segment Only one strain Only one taxonomy_id Only one xrefs Only one

<gene>'s attributes Name Values Default gene_id Match the ID rules.

(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.

Possible values: Match the ID rules. - Required

'gene_name' is the short name of the name.

'ncbi_gene_id' is the Gene ID of the NCBI Gene database.

'xrefs' describes cross reference ID from other databases. It has a format of "DB_name: DB_id; another_DB_name: another_DB_id"

'phi_annotation' is the annotation of pathogen host interaction

'dna_sequence' is the sequence of a DNA fragment

'protein_sequence' is the sequence of a protein.

'strain' is the name of a sequenced microorganism, for example, a bacterium, a virus, or a parasite.

'taxonomy_id' is the NCBI taxonomy ID.

'ncbi_protein_id' is the NCBI protein ID. It should be a integer.

'protein_refseq' is the NCBI protein RefSeq No.

'protein_name' is the name of the coded protein.

'chromosome' is the chromosome on which the gene located.

'segment' is the segement on which the gene located.

'gene_locus_tag' is the NCBI gene locus tag.

'gene_start' is the starting position of the gene.

'gene_end' is the the ending position of the gene.

'gene_strand' is the coding direction of the gene.

'gene_refseq' is the NCBI gene RefSeq No.

'protein_note' is the note about the protein.

'protein_annotation' is the annotation about the protein.

'protein_pi' is the pI of the protein.

'protein_weight' is the weight of the protein.

'protein_length' is the length of the protein.

'phi_function' is the function category in terms of pathogen host interaction.

'plasmid' is the plasmid on wchich the gene located.

'references' describes the data sources used in the document. Data may be obtained from journals, books, websites, and theses

<reference>'s children Name Cardinality authors Only one book_editors Only one degree Only one file_name Only one isbn Only one issue Only one journal_book_name Only one name Only one pages Only one publisher Only one publisher_location Only one title Only one type Only one university Only one university_location Only one url Only one volume Only one year Only one

<reference>'s attributes Name Values Default reference_id Match the ID rules.

(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.

Possible values: Match the ID rules. - Required

'authors' is the list of the authors of a reference.

'title' is the title of a reference.

'year' is the year when a reference is published.

'volume' describes a journal volume

'issue' describes a journal issue

'pages' is the range of pages for an article.

'journal_book_name' is the name of a journal or a book.

'publisher' is the book publisher

'publisher_location' is the location of a book publisher.

'book_editors' means the editors of a book.

'isbn' menas International Standard Book Number. It is a unique commercial book identifier barcode.

'degree' means a Ph.D. or M.S. or other academic degree.

'university' is the name of a university

'university_location' is the location of a univerisity, it should include city name, state/province, and country name.

'url' stands for Uniform resource locator, it represents a web page address.

'file_name' is the name of an updated file

'curation' describes curation information

<curation>'s children Name Cardinality date Only one type Only one user_name Only one

(user_name, type, date)

'user_name' is the name of a curator.

'date' is the curation submission data.