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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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