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<?xml encoding="UTF-8"?>
<!-- Content model for content and presentation -->
<!-- and browser interface tags in bioml based -->
<!-- on the bioml.dtd draft. syntax = XML -->
<!-- date = March 24, 1999 -->
<!-- Author: Ronald Beavis -->
<!-- source: bioml@proteometrics.com -->
<!-- Official version: -->
<!-- http://www.proteometrics.com/BIOML/bioml.dtd -->
<!-- Additions: -->
<!-- 1 -->
<!-- January 6, 1999 -->
<!-- name, organism, and species elements added. -->
<!-- David J. States, Washington University -->
<!-- 2 -->
<!-- January 20, 1999 -->
<!-- group element added -->
<!-- Ronald Beavis -->
<!-- 3 -->
<!-- February 20, 1999 -->
<!-- 1) xml:space attribute added to some -->
<!-- elements, as suggested by Paul Gordon, IMB, -->
<!-- NRCC, Halifax (keep_space entity); -->
<!-- 2) local.xx.yy entities added for easy -->
<!-- extension of selected elements; -->
<!-- 3) id entity removed and id placed in global;-->
<!-- 4) element contents have been rationalized; -->
<!-- 5) group extended to contain ANY element; and-->
<!-- 6) query and alt_common_name elements removed-->
<!-- as redundant. -->
<!-- 4 -->
<!-- February 26, 1999 -->
<!-- 1) xml:space attribute added to some -->
<!-- additional elements -->
<!-- 2) an error in the "organism" content list -->
<!-- was corrected. -->
<!-- 5 -->
<!-- March 6, 1999 - responding to comments from -->
<!-- Paul Gordon. -->
<!-- 1) an error in the rvariant attribute list -->
<!-- was corrected -->
<!-- 2) the definition of the "comp" entity was -->
<!-- added. -->
<!-- 3) *'s were added to dna-related element -->
<!-- content descriptions to bring them into line -->
<!-- with the rna & protein elements. -->
<!-- 4) The content description of the form -->
<!-- element was expanded to include input and -->
<!-- text elements. -->
<!-- 6 -->
<!-- March 24, 1999 -->
<!-- Changes by Ronald Beavis -->
<!-- 1) "name" removed from the data model for -->
<!-- "peptide" and "domain"; -->
<!-- 2) "rend" replaced with "rstop" in the data -->
<!-- model for "rna" and "rdomain"; -->
<!-- 3) an asterisk was added to the data model -->
<!-- "taxon"; and -->
<!-- 4) character entity definitions changed to -->
<!-- use explicit hex code entities. -->
<!-- ************************************-->
<!-- general entity definitions -->
<!-- ************************************-->
<!ENTITY % local.aa_type.value "">
<!ENTITY % aa_type "type (A|B|C|D|E|F|G|H|I|K|L|M
|N|P|Q|R|S|T|V|W|X|Y|Z
%local.aa_type.value;)
#REQUIRED">
<!ENTITY % at "at CDATA #IMPLIED">
<!ENTITY % local.biopolymer.content "">
<!ENTITY % biopolymer "protein|peptide|subunit|dna|rna
%local.biopolymer.content;">
<!ENTITY % local.db_attributes.attrib "">
<!ENTITY % db_attributes "name CDATA #IMPLIED
entry CDATA #IMPLIED
%local.db_attributes.attrib;">
<!ENTITY % local.dna_type.value "">
<!ENTITY % dna_type "type (A|a|T|t|G|g|C|c
%local.dna_type.value;)
#REQUIRED">
<!ENTITY % local.dom_type.value "">
<!ENTITY % dom_type "type (mature|propeptide|signal
|alpha-helix|beta-strand
|turn|variable
%local.dom_type.value;)
#REQUIRED">
<!ENTITY % end "end CDATA #IMPLIED">
<!ENTITY % local.format.value "">
<!ENTITY % format "format (TEXT|BINARY|ZIP
|GZIP|JPEG|MSDCS|GIF
%local.format.value;)
#REQUIRED ">
<!ENTITY % local.global.attrib "">
<!ENTITY % global "state (hidden|open|close) #IMPLIED
label CDATA #IMPLIED
id CDATA #IMPLIED
%local.global.attrib;">
<!ENTITY % keep_space "xml:space (default|preserve)
'preserve'">
<!ENTITY % local.nr.content "">
<!ENTITY % nr "name|note|reference|db_entry|file
|group
%local.nr.content;">
<!ENTITY % occupied "occ CDATA #IMPLIED">
<!ENTITY % order "order CDATA #IMPLIED">
<!ENTITY % local.rna_type.value "">
<!ENTITY % rna_type "type (A|a|U|u|G|g|C|c
%local.rna_type.value;)
#REQUIRED">
<!ENTITY % start "start CDATA #IMPLIED">
<!ENTITY % local.text_format.value "">
<!ENTITY % text_format "format (PIR|GENBANK|SPROT|PDB|FASTA
%local.text_format.value;)
#REQUIRED">
<!ENTITY % to "to CDATA #IMPLIED">
<!ENTITY % type "type CDATA #IMPLIED">
<!ENTITY % url "url CDATA #IMPLIED
query CDATA #IMPLIED">
<!ENTITY % comp "comp CDATA #IMPLIED">
<!-- ************************************-->
<!-- character entity definitions -->
<!-- ************************************-->
<!ENTITY angstrom "Å">
<!ENTITY plusminus "±">
<!ENTITY emdash "—">
<!ENTITY endash "–">
<!ENTITY degree "°">
<!ENTITY registered "©">
<!ENTITY copyright "®">
<!ENTITY bullet "•">
<!ENTITY tab " ">
<!ENTITY newline "
">
<!ENTITY paragraph "&newline;&tab;">
<!ENTITY point "&newline;•">
<!-- **********************************-->
<!-- : bioml elements -->
<!-- **********************************-->
<!ELEMENT bioml ANY>
<!-- **********************************-->
<!-- : bioml protein elements -->
<!-- **********************************-->
<!ELEMENT protein (#PCDATA|subunit|peptide|%nr;)*>
<!ATTLIST protein %global;
%comp;>
<!ELEMENT subunit (#PCDATA|peptide|%nr;)*>
<!ATTLIST subunit %global;
%comp;>
<!ELEMENT peptide (#PCDATA|domain|aa|%nr;)*>
<!ATTLIST peptide %global;
%start;
%end;>
<!ELEMENT domain (#PCDATA|aa|%nr;)*>
<!ATTLIST domain %global;
%start;
%end;
%dom_type;>
<!ELEMENT homolog (#PCDATA|species|taxon|%nr;)*>
<!ATTLIST homolog %global;>
<!ELEMENT aa (#PCDATA|amod|alink|avariant|aconflict|%nr;)*>
<!ATTLIST aa %aa_type;
%global;
%at;
%to;>
<!ELEMENT amod (#PCDATA|%nr;)*>
<!ATTLIST amod %type;
%global;
%at;
%to;
%occupied;>
<!ELEMENT alink (#PCDATA|%nr;)*>
<!ATTLIST alink %type;
%global;
%at;
%to;
%occupied;>
<!ELEMENT avariant (#PCDATA|%nr;)*>
<!ATTLIST avariant %global;
%aa_type;
%at;
%occupied;>
<!ELEMENT aconflict (#PCDATA|%nr;)*>
<!ATTLIST aconflict %global;
%aa_type;
%at;>
<!-- ***************************************-->
<!-- : bioml general gene-related elements-->
<!-- *************************************** -->
<!ELEMENT chromosome (#PCDATA|sts_domain|dna|locus|gene|%nr;)*>
<!ATTLIST chromosome %global;
number CDATA #IMPLIED>
<!ELEMENT sts_domain (#PCDATA|dna|locus|gene|%nr;)*>
<!ATTLIST sts_domain %global;
%start;
%end;>
<!ELEMENT clone (#PCDATA|locus|gene|dna|%nr;)*>
<!ATTLIST clone %global;>
<!ELEMENT plasmid (#PCDATA|locus|gene|dna|%nr;)*>
<!ATTLIST plasmid %global;>
<!ELEMENT locus (#PCDATA|dna|gene|%nr;)*>
<!ATTLIST locus %global;
%start;
%end;>
<!-- ***************************************-->
<!-- : bioml dna gene-related elements -->
<!-- ***************************************-->
<!ELEMENT dna (#PCDATA|clone|promotor|ddomain|exon
|intron|da|dmod|dvariant|dstart|dstop|%nr;)*>
<!ATTLIST dna %global;
%start;
%end;>
<!ELEMENT promotor (#PCDATA|%nr;)*>
<!ATTLIST promotor %global;
%start;
%end;>
<!ELEMENT gene (#PCDATA|dna|%nr;)*>
<!ATTLIST gene %global;
%start;
%end;
%comp;>
<!ELEMENT exon (#PCDATA|%nr;)*>
<!ATTLIST exon %global;
%start;
%end;>
<!ELEMENT intron (#PCDATA|%nr;)*>
<!ATTLIST intron %global;
%start;
%end;>
<!ELEMENT ddomain (#PCDATA|da|dstart|dstop|%nr;)*>
<!ATTLIST ddomain %global;
%start;
%end;>
<!ELEMENT da (#PCDATA|dmod|dvariant|%nr;)*>
<!ATTLIST da %at;
%global;
%dna_type;>
<!ELEMENT dmod (#PCDATA|%nr;)*>
<!ATTLIST dmod %at;
%global;
%type;
%occupied;>
<!ELEMENT dvariant (#PCDATA|%nr;)*>
<!ATTLIST dvariant %global;
%at;
%type;
%occupied;>
<!ELEMENT dstart (#PCDATA|%nr;)*>
<!ATTLIST dstart %at;
%global;>
<!ELEMENT dstop (#PCDATA|%nr;)*>
<!ATTLIST dstop %at;
%global;>
<!-- **********************************-->
<!-- : bioml rna gene-related elements-->
<!-- **********************************-->
<!ELEMENT rna (#PCDATA|clone|ra|rstart|rstop
|rdomain|%nr;)*>
<!ATTLIST rna %global;
%start;
%end;>
<!ELEMENT ra (#PCDATA|rmod|rvariant|%nr;)*>
<!ATTLIST ra %at;
%global;
%rna_type;>
<!ELEMENT rdomain (#PCDATA|ra|rstart|rstop
|%nr;)*>
<!ATTLIST rdomain %global;
%start;
%end;>
<!ELEMENT rmod (#PCDATA|%nr;)*>
<!ATTLIST rmod %at;
%global;
%type;
%occupied;>
<!ELEMENT rvariant (#PCDATA|%nr;)*>
<!ATTLIST rvariant %global;
%at;
%type;
%occupied;>
<!ELEMENT rstart (#PCDATA|%nr;)*>
<!ATTLIST rstart %at;
%global;>
<!ELEMENT rstop (#PCDATA|%nr;)*>
<!ATTLIST rstop %at;
%global;>
<!-- ***************************************-->
<!-- : bioml general elements added by DJS 1/6/99 -->
<!-- *************************************** -->
<!ELEMENT name (#PCDATA|%nr;)*>
<!ATTLIST name %global;
%keep_space;>
<!ELEMENT note (#PCDATA|%nr;)*>
<!ATTLIST note %global;
%keep_space;>
<!ELEMENT organism (#PCDATA|species|common_name|taxon|tissue|cell
|chromosome|plasmid|organelle|particle
|%biopolymer;|%nr;)*>
<!ATTLIST organism %global;>
<!ELEMENT species (#PCDATA)>
<!ATTLIST species %global;
%keep_space;>
<!-- ***********************************-->
<!-- : bioml organism specific elements-->
<!-- ***********************************-->
<!ELEMENT common_name (#PCDATA)>
<!ATTLIST common_name %global;
%keep_space;>
<!ELEMENT taxon (#PCDATA|species|%nr;)*>
<!ATTLIST taxon %global;
%keep_space;>
<!ELEMENT tissue (#PCDATA|organelle|cell|particle|%biopolymer;|%nr;)*>
<!ATTLIST tissue %global;>
<!ELEMENT cell (#PCDATA|organelle|particle|%biopolymer;|%nr;)*>
<!ATTLIST cell %global;>
<!ELEMENT organelle (#PCDATA|particle|%biopolymer;|%nr;)*>
<!ATTLIST organelle %global;>
<!ELEMENT particle (#PCDATA|%biopolymer;|%nr;)*>
<!ATTLIST particle %global;>
<!-- ************************************-->
<!-- : bioml reference specific elements-->
<!-- ************************************-->
<!ELEMENT reference (#PCDATA|author|title|journal|book_title|editor
|volume|pages|%nr;)*>
<!ATTLIST reference %global;
%keep_space;>
<!ELEMENT author (#PCDATA)>
<!ATTLIST author %global;
%keep_space;>
<!ELEMENT title (#PCDATA)>
<!ATTLIST title %global;
%keep_space;>
<!ELEMENT journal (#PCDATA)>
<!ATTLIST journal %global;
%keep_space;>
<!ELEMENT book_title (#PCDATA)>
<!ATTLIST book_title %global;
%keep_space;>
<!ELEMENT editor (#PCDATA)>
<!ATTLIST editor %global;
%keep_space;>
<!ELEMENT volume (#PCDATA)>
<!ATTLIST volume %global;
%keep_space;>
<!ELEMENT pages (#PCDATA)>
<!ATTLIST pages %global;
%keep_space;>
<!-- ****************************************-->
<!-- : bioml remote data referencing elements-->
<!-- ****************************************-->
<!ELEMENT db_entry (#PCDATA)>
<!ATTLIST db_entry %global;
%db_attributes;
%text_format;
%url;>
<!ELEMENT file (#PCDATA)>
<!ATTLIST file %format;
%global;
%url;>
<!-- *****************************************-->
<!-- : bioml data special formatting elements -->
<!-- *****************************************-->
<!ELEMENT binary (#PCDATA)>
<!ATTLIST binary %format;
%global;>
<!ELEMENT data (#PCDATA)>
<!ATTLIST data %text_format;
%global;>
<!ELEMENT copyright (#PCDATA)>
<!ATTLIST copyright %global;>
<!-- *****************************************-->
<!-- : bioml form elements -->
<!-- *****************************************-->
<!ELEMENT form (#PCDATA|input|text)*>
<!ATTLIST form %global;
action CDATA #REQUIRED>
<!ELEMENT input (#PCDATA)>
<!ATTLIST input %global;
type (hidden|value) #IMPLIED
name CDATA #IMPLIED
value CDATA #IMPLIED
width CDATA #IMPLIED>
<!ELEMENT text (#PCDATA)>
<!ATTLIST text %global;>
<!-- *****************************************-->
<!-- : bioml generalized grouping element -->
<!-- *****************************************-->
<!ELEMENT group ANY>
<!ATTLIST group %global;>
<!-- **********************************-->
<!-- : end of bioml DTD -->
<!-- **********************************-->
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