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|
<!-- ============================================
::DATATOOL:: Generated from "ncbimime.asn"
::DATATOOL:: by application DATATOOL version 1.9.0
::DATATOOL:: on 04/10/2008 16:04:22
============================================ -->
<!-- ============================================ -->
<!-- This section is mapped from module "NCBI-Mime"
================================================= -->
<!--
$Revision: 6.12 $
****************************************************************
NCBI MIME type (chemical/ncbi-asn1-ascii and chemical/ncbi-asn1-binary)
by Jonathan Epstein, February 1996
****************************************************************
-->
<!-- Elements used by other modules:
Ncbi-mime-asn1 -->
<!-- Elements referenced from other modules:
Biostruc,
Biostruc-annot-set FROM MMDB,
Cdd FROM NCBI-Cdd,
Seq-entry FROM NCBI-Seqset,
Seq-annot FROM NCBI-Sequence,
Medline-entry FROM NCBI-Medline,
Cn3d-style-dictionary,
Cn3d-user-annotations FROM NCBI-Cn3d -->
<!-- ============================================ -->
<!ELEMENT Ncbi-mime-asn1 (
Ncbi-mime-asn1_entrez |
Ncbi-mime-asn1_alignstruc |
Ncbi-mime-asn1_alignseq |
Ncbi-mime-asn1_strucseq |
Ncbi-mime-asn1_strucseqs |
Ncbi-mime-asn1_general)>
<!-- just a structure -->
<!ELEMENT Ncbi-mime-asn1_entrez (Entrez-general)>
<!-- structures & sequences & alignments -->
<!ELEMENT Ncbi-mime-asn1_alignstruc (Biostruc-align)>
<!-- sequence alignment -->
<!ELEMENT Ncbi-mime-asn1_alignseq (Biostruc-align-seq)>
<!-- structure & sequences -->
<!ELEMENT Ncbi-mime-asn1_strucseq (Biostruc-seq)>
<!-- structure & sequences & alignments -->
<!ELEMENT Ncbi-mime-asn1_strucseqs (Biostruc-seqs)>
<!--
all-purpose "grab bag"
others may be added here in the future
-->
<!ELEMENT Ncbi-mime-asn1_general (Biostruc-seqs-aligns-cdd)>
<!-- generic bundle of sequence and alignment info -->
<!ELEMENT Bundle-seqs-aligns (
Bundle-seqs-aligns_sequences?,
Bundle-seqs-aligns_seqaligns?,
Bundle-seqs-aligns_strucaligns?,
Bundle-seqs-aligns_imports?,
Bundle-seqs-aligns_style-dictionary?,
Bundle-seqs-aligns_user-annotations?)>
<!-- sequences -->
<!ELEMENT Bundle-seqs-aligns_sequences (Seq-entry*)>
<!-- sequence alignments -->
<!ELEMENT Bundle-seqs-aligns_seqaligns (Seq-annot*)>
<!-- structure alignments -->
<!ELEMENT Bundle-seqs-aligns_strucaligns (Biostruc-annot-set)>
<!-- imports (updates in Cn3D) -->
<!ELEMENT Bundle-seqs-aligns_imports (Seq-annot*)>
<!-- Cn3D stuff -->
<!ELEMENT Bundle-seqs-aligns_style-dictionary (Cn3d-style-dictionary)>
<!ELEMENT Bundle-seqs-aligns_user-annotations (Cn3d-user-annotations)>
<!ELEMENT Biostruc-seqs-aligns-cdd (
Biostruc-seqs-aligns-cdd_seq-align-data,
Biostruc-seqs-aligns-cdd_structures?,
Biostruc-seqs-aligns-cdd_structure-type?)>
<!ELEMENT Biostruc-seqs-aligns-cdd_seq-align-data (
Biostruc-seqs-aligns-cdd_seq-align-data_bundle |
Biostruc-seqs-aligns-cdd_seq-align-data_cdd)>
<!-- either seqs + alignments -->
<!ELEMENT Biostruc-seqs-aligns-cdd_seq-align-data_bundle (Bundle-seqs-aligns)>
<!-- or CDD (which contains these) -->
<!ELEMENT Biostruc-seqs-aligns-cdd_seq-align-data_cdd (Cdd)>
<!-- structures -->
<!ELEMENT Biostruc-seqs-aligns-cdd_structures (Biostruc*)>
<!-- type of structures to load if -->
<!ELEMENT Biostruc-seqs-aligns-cdd_structure-type %ENUM;>
<!--
ncbi-backbone - not present; meanings and
ncbi-all-atom - values are same as MMDB's
pdb-model - Model-type
-->
<!ATTLIST Biostruc-seqs-aligns-cdd_structure-type value (
ncbi-backbone |
ncbi-all-atom |
pdb-model
) #REQUIRED >
<!ELEMENT Biostruc-align (
Biostruc-align_master,
Biostruc-align_slaves,
Biostruc-align_alignments,
Biostruc-align_sequences,
Biostruc-align_seqalign,
Biostruc-align_style-dictionary?,
Biostruc-align_user-annotations?)>
<!ELEMENT Biostruc-align_master (Biostruc)>
<!ELEMENT Biostruc-align_slaves (Biostruc*)>
<!-- structure alignments -->
<!ELEMENT Biostruc-align_alignments (Biostruc-annot-set)>
<!-- sequences -->
<!ELEMENT Biostruc-align_sequences (Seq-entry*)>
<!ELEMENT Biostruc-align_seqalign (Seq-annot*)>
<!ELEMENT Biostruc-align_style-dictionary (Cn3d-style-dictionary)>
<!ELEMENT Biostruc-align_user-annotations (Cn3d-user-annotations)>
<!-- display seq structure align only -->
<!ELEMENT Biostruc-align-seq (
Biostruc-align-seq_sequences,
Biostruc-align-seq_seqalign,
Biostruc-align-seq_style-dictionary?,
Biostruc-align-seq_user-annotations?)>
<!-- sequences -->
<!ELEMENT Biostruc-align-seq_sequences (Seq-entry*)>
<!ELEMENT Biostruc-align-seq_seqalign (Seq-annot*)>
<!ELEMENT Biostruc-align-seq_style-dictionary (Cn3d-style-dictionary)>
<!ELEMENT Biostruc-align-seq_user-annotations (Cn3d-user-annotations)>
<!-- display structure seq added by yanli -->
<!ELEMENT Biostruc-seq (
Biostruc-seq_structure,
Biostruc-seq_sequences,
Biostruc-seq_style-dictionary?,
Biostruc-seq_user-annotations?)>
<!ELEMENT Biostruc-seq_structure (Biostruc)>
<!ELEMENT Biostruc-seq_sequences (Seq-entry*)>
<!ELEMENT Biostruc-seq_style-dictionary (Cn3d-style-dictionary)>
<!ELEMENT Biostruc-seq_user-annotations (Cn3d-user-annotations)>
<!-- display blast alignment along with neighbor's structure added by yanli -->
<!ELEMENT Biostruc-seqs (
Biostruc-seqs_structure,
Biostruc-seqs_sequences,
Biostruc-seqs_seqalign,
Biostruc-seqs_style-dictionary?,
Biostruc-seqs_user-annotations?)>
<!ELEMENT Biostruc-seqs_structure (Biostruc)>
<!-- sequences -->
<!ELEMENT Biostruc-seqs_sequences (Seq-entry*)>
<!ELEMENT Biostruc-seqs_seqalign (Seq-annot*)>
<!ELEMENT Biostruc-seqs_style-dictionary (Cn3d-style-dictionary)>
<!ELEMENT Biostruc-seqs_user-annotations (Cn3d-user-annotations)>
<!ELEMENT Entrez-style %ENUM;>
<!ATTLIST Entrez-style value (
docsum |
genbank |
genpept |
fasta |
asn1 |
graphic |
alignment |
globalview |
report |
medlars |
embl |
pdb |
kinemage
) #REQUIRED >
<!ELEMENT Entrez-general (
Entrez-general_title?,
Entrez-general_data,
Entrez-general_style,
Entrez-general_location?)>
<!ELEMENT Entrez-general_title (#PCDATA)>
<!ELEMENT Entrez-general_data (
Entrez-general_data_ml |
Entrez-general_data_prot |
Entrez-general_data_nuc |
Entrez-general_data_genome |
Entrez-general_data_structure |
Entrez-general_data_strucAnnot)>
<!ELEMENT Entrez-general_data_ml (Medline-entry)>
<!ELEMENT Entrez-general_data_prot (Seq-entry)>
<!ELEMENT Entrez-general_data_nuc (Seq-entry)>
<!ELEMENT Entrez-general_data_genome (Seq-entry)>
<!ELEMENT Entrez-general_data_structure (Biostruc)>
<!ELEMENT Entrez-general_data_strucAnnot (Biostruc-annot-set)>
<!ELEMENT Entrez-general_style (Entrez-style)>
<!ELEMENT Entrez-general_location (#PCDATA)>
|
