cdd.asn
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上传日期：2007-06-13
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- --$Revision: 1000.3 $
- --**********************************************************************
- --
- -- Definitions for CDD's
- --
- -- NCBI Structure Group
- --
- -- National Center for Biotechnology Information
- -- National Institutes of Health
- -- Bethesda, MD 20894 USA
- --
- -- October 1999
- --
- -- asntool -m cdd.asn -w 100 -o cdd.h
- -- asntool -B objcdd -m cdd.asn -G -w 100 -I objseq.h objsset.h -K cdd.h
- -- -M asn.all
- --**********************************************************************
- NCBI-Cdd DEFINITIONS ::=
- -- NCBI Conserved Domain Definition
- BEGIN
- EXPORTS Cdd-id, Cdd-id-set, Cdd, Cdd-set, Cdd-tree, Cdd-tree-set, Cdd-pref-nodes, Cdd-Project;
- IMPORTS Date FROM NCBI-General
- Pub FROM NCBI-Pub
- Biostruc-annot-set FROM MMDB
- Bioseq FROM NCBI-Sequence
- Seq-annot FROM NCBI-Sequence
- Seq-entry FROM NCBI-Seqset
- Org-ref FROM NCBI-Organism
- Seq-id FROM NCBI-Seqloc
- Seq-interval FROM NCBI-Seqloc
- Seq-loc FROM NCBI-Seqloc
- Seq-feat FROM NCBI-Seqfeat
- Score-set FROM NCBI-Seqalign
- Cn3d-style-dictionary,
- Cn3d-user-annotations FROM NCBI-Cn3d
- Score-matrix-parameters FROM NCBI-ScoreMat;
-
- -- dealing with lists of preferred tax-nodes
- Cdd-org-ref ::= SEQUENCE {
- reference Org-ref,
- active BOOLEAN DEFAULT TRUE
- }
- Cdd-org-ref-set ::= SET OF Cdd-org-ref
- Cdd-pref-node-descr ::= CHOICE {
- create-date Date,
- description VisibleString
- }
- Cdd-pref-node-descr-set ::= SET OF Cdd-pref-node-descr
- Cdd-pref-nodes ::= SEQUENCE {
- preferred-nodes Cdd-org-ref-set,
- model-organisms Cdd-org-ref-set OPTIONAL,
- optional-nodes Cdd-org-ref-set OPTIONAL,
- description Cdd-pref-node-descr-set OPTIONAL
- }
- -- Cdd's should not exist without a unique accession, but alternative id's may
- -- be present as well. It is conceivable that a CD which is created as a merged
- -- product of two highly redundant CDs will retain the source ids in addition
- -- to its new unique id
- Global-id ::= SEQUENCE {
- accession VisibleString, -- SMART, Pfam, LOAD or CD accession
- release VisibleString OPTIONAL, -- to hold CD-Database release number
- -- if desired, currently not used
- version INTEGER OPTIONAL, -- version 0 is the seed, version
- -- numbers increase with update/curate
- -- cycles
- database VisibleString OPTIONAL -- this is NOT the source!, rather the
- } -- database the object resides in
- -- currently not in use
- Cdd-id ::= CHOICE {
- uid INTEGER, -- for synchronization with Entrez
- -- holds PSSM-Ids
- gid Global-id -- holds accession/version pairs
- }
- Cdd-id-set ::= SEQUENCE OF Cdd-id
- Cdd-repeat ::= SEQUENCE { -- record whether the CD contains
- -- repeated sequence/structure motifs
- count INTEGER, -- number of tandem repeats in the CD
- location Seq-loc OPTIONAL, -- location on the representative
- avglen INTEGER OPTIONAL -- average repeat length
- }
- Cdd-book-ref ::= SEQUENCE { -- record a link to Entrez Books
- bookname VisibleString, -- abbreviated book title
- textelement ENUMERATED { unassigned(0), -- type of element
- section(1), -- a section or paragraph
- figgrp(2), -- a figure or set of figures
- table(3), -- a table
- chapter(4), -- a whole chapter
- biblist(5), -- a lisf of references
- box(6), -- an inserted box
- glossary(7), -- glossary
- appendix(8), -- appendix
- other(255) },
- elementid INTEGER, -- address of the text-element
- subelementid INTEGER OPTIONAL -- exact address, used with section
- }
- -- The description of CDD's refers to the specific set of aligned sequences,
- -- the region that is being aligned and the information contained in the
- -- alignment. It may contain a lengthy comment
- -- describing the function of the domain as well as its origin and all
- -- other anecdotal information that can't be pressed into a rigid scheme.
- -- Crosslinks to reference papers available in PubMed are possible as well.
- -- There can be as many of these as you want in the CDD.
- Cdd-descr ::= CHOICE {
- othername VisibleString, -- alternative names for the CDD
- -- if domain has several common names
- category VisibleString, -- intracellular, extracellular, etc.
- -- to record spatial and/or temporal
- -- expression in free-text format
- comment VisibleString, -- this is where descriptions go
- reference Pub, -- a citation describing the domain
- create-date Date, -- Date of first creation/dump
- tax-source Org-ref, -- holds the highest common tax node
- source VisibleString, -- the database the seeds were created
- -- from, e.g. SMART, PFAM, etc..
- status INTEGER { unassigned(0),
- finished-ok(1), -- a public curated CD
- pending-release(2), -- needs work done, not yet released
- other-asis(3), -- imported as-is, immediate release
- matrix-only(4), -- CD holds a Psi-Blast PSSM only,
- -- does not contain alignment data
- update-running(5), -- has been flagged for
- -- update (in queue)
- auto-updated(6), -- update finished, no
- -- work necessary
- claimed(7), -- is earmarked for curation
- curated-complete(8),-- public curated member of a
- -- completed family
- other(255) }, -- for CD production?
- update-date Date, -- Date of last version change
- scrapbook SEQUENCE OF VisibleString, -- for storing curation notes
- -- those won't make it into public
- -- distributions
- source-id Cdd-id-set, -- for linking back to source db
- repeats Cdd-repeat, -- to record repeat counts
- old-root Cdd-id-set, -- to record short-term history
- curation-status INTEGER { unassigned(0), -- to record curation status
- prein (1), -- when CD is checked out from
- ofc (2), -- the tracking database, for
- iac (3), -- use within curation software
- ofv1 (4),
- iav1 (5),
- ofv2 (6),
- iav2 (7),
- postin (8),
- other (255) },
- readonly-status INTEGER { unassigned(0), -- to record read-only status
- readonly (1), -- when CD is checked out from
- readwrite (2), -- the tracking database, for
- other (255) }, -- use within curation software
- book-ref Cdd-book-ref
- }
- Cdd-descr-set ::= SET OF Cdd-descr
- -- the Cdd-tree stores the hierarchy of CDDs. These objects are stored separate
- -- from the CDs to allow for fast retrieval and use as an 'index' into CDs
- -- all the components in a CD-tree match components in the full-sized CD
- -- and should be synchronized
- Cdd-tree ::= SEQUENCE {
- name VisibleString, -- short name copied from CD
- id Cdd-id-set, -- IDs copied from CD
- description Cdd-descr-set OPTIONAL, -- description copied from CD
- parent Cdd-id OPTIONAL, -- CD is the result of a split/merge
- children Cdd-id-set OPTIONAL, -- this CD has been split
- siblings Cdd-id-set OPTIONAL, -- related CDs (have common hits)
- neighbors Cdd-id-set OPTIONAL -- co-occurring CDs (non-overlapping
- -- hits to same sequences)
- }
- Cdd-tree-set ::= SEQUENCE OF Cdd-tree
- -- Matrix definitions, these are supposed to store PSSMs and corresponding
- -- matrices of relative residue frequencies.
- -- the number of columns and rows is listed explicitly, values in columns
- -- are stored column by column, i.e. in groups of nrows values for each column
- Matrix ::= SEQUENCE {
- ncolumns INTEGER,
- nrows INTEGER,
- row-labels SEQUENCE OF VisibleString OPTIONAL,
- scale-factor INTEGER,
- columns SEQUENCE OF INTEGER
- }
- -- definition for matrix of pairwise "distances", stored as the upper
- -- triangle of a squared n x n matrix (excluding the diagonal), this is
- -- supposed to store pairwise percentages of identical residues, pairwise
- -- alignment scores or E-values from pairwise BLAST sequence comparisons
- Triangle ::= SEQUENCE {
- nelements INTEGER,
- scores Score-set OPTIONAL,
- div-ranks SEQUENCE OF INTEGER OPTIONAL
- }
- -- Update-align is supposed to contain alignments that still need some work
- -- done to fit into the CD-proper alignment. These originate from the
- -- CD update process (generated by Blast, for example) or may be created in
- -- an editing session to save its state
- Update-comment ::= CHOICE {
- comment VisibleString, -- free text to describe nature of
- -- Update-align
- addthis Seq-loc, -- suggestion for inclusion in the CD
- -- without corresponding alignment
- replaces Seq-loc, -- if one or several alignment rows are
- -- to be replaced by the Update-align
- reject-loc Seq-loc, -- if used with Reject-id, specify a
- -- location on a sequence which should
- -- not be used
- reference Pub -- if update alignment imported from
- -- citation and for whenever it seems
- -- necessary to cite
- }
- -- Both fields are optional, as the Update-align may be a Seq-annot without
- -- description, or a suggestion to add a sequence without the corresponding
- -- alignment
- Update-align ::= SEQUENCE {
- description SEQUENCE OF Update-comment OPTIONAL,
- seqannot Seq-annot OPTIONAL, -- contains the SeqAlign
- type INTEGER { unassigned(0),
- update(1),
- update-3d(2),
- demoted(51),
- demoted-3d(52),
- other(255)}
- }
- Reject-id ::= SEQUENCE {
- description SEQUENCE OF Update-comment OPTIONAL,
- ids SET OF Seq-id
- }
- Feature-evidence ::= CHOICE {
- comment VisibleString, -- so we can spell out what doesn't
- -- fit in any other category
- reference Pub, -- evidence via a literature reference
- bsannot Biostruc-annot-set, -- evidence via Biostruc-features, such
- -- as structure superpositions
- seqfeat Seq-feat, -- evidence is a Sequence feature found
- -- elsewhere
- book-ref Cdd-book-ref -- evidence is a book chapter or figure
- }
- Align-annot ::= SEQUENCE {
- location Seq-loc, -- points to a location in one of the
- -- aligned sequences, usually the
- -- master/representative
- description VisibleString OPTIONAL, -- to hold descriptions/names like
- -- "Heme binding site" or "catalytic
- -- triad" etc., something that should
- -- be used for labels in visualization
- evidence SEQUENCE OF Feature-evidence OPTIONAL -- evidence we can
- -- compute with
- }
- Align-annot-set ::= SEQUENCE OF Align-annot
- -- the Domain-parent records an evolutionary relationship which may not be
- -- as simple as a classical parent-child relationship in a typical hierarchy,
- -- i.e. where a CD is merely a specific subgroup ("child") of a more general
- -- diverse alignment model ("parent"). A CD alignment model may be the result
- -- of an ancient fusion event, combining two or more domains into a bigger unit
- -- which has subsequently undergone a divergent evolutionary process similar to
- -- what may have happened to a single "domain". A CD alignment model may
- -- also reflect the result of a deletion event, where a specific subgroup
- -- lacks part of a (set of) domain(s), but where the part present is found to
- -- be highly similar to a putative "parent", with some added evidence for
- -- an actual deletion, like from the distribution of truncated copies in phylogenetic
- -- lineages. Deletion events which affect different parts of a set of
- -- duplicated domain architectures may be indistinguishable from actual
- -- fission events, which means that we may want to represent the latter as
- -- deletions after duplication and do not need a special case for fissions.
- Domain-parent ::= SEQUENCE {
- parent-type INTEGER { classical (0), -- the classification of parent child relations
- fusion (1),
- deletion (2),
- permutation (3),
- other (255) },
- parentid Cdd-id, -- identify the section parent by accession
- seqannot Seq-annot OPTIONAL -- contains the sequence alignment linking
- -- CD alignment models, should align the
- -- masters/representatives of each CD
- }
- -- record sequence trees generated by a suitable algorithm.
- Sequence-tree ::= SEQUENCE {
- cdAccession VisibleString OPTIONAL,
- algorithm Algorithm-type,
- isAnnotated BOOLEAN DEFAULT FALSE,
- root SeqTree-node
- }
- SeqTree-node ::= SEQUENCE {
- isAnnotated BOOLEAN DEFAULT FALSE,
- name VisibleString OPTIONAL,
- distance REAL OPTIONAL,
- children CHOICE {
- children SEQUENCE OF SeqTree-node,
- footprint SEQUENCE {
- seqRange Seq-interval,
- rowId INTEGER OPTIONAL
- }
- },
- annotation Node-annotation OPTIONAL
- }
- Algorithm-type ::= SEQUENCE {
- scoring-Scheme INTEGER { unassigned (0),
- percent-id (1),
- kimura-corrected (2),
- aligned-score (3),
- aligned-score-ext (4),
- aligned-score-filled (5),
- blast-footprint (6),
- blast-full (7),
- other (255) },
- clustering-Method INTEGER { unassigned (0),
- single-linkage (1),
- neighbor-joining (2),
- fast-minimum-evolution (3),
- other (255) },
- score-Matrix INTEGER { unassigned (0),
- blosum45 (1),
- blosum62 (2),
- blosum80 (3),
- pam30 (4),
- pam70 (5),
- pam250 (6),
- other (255) } OPTIONAL,
- gapOpen INTEGER OPTIONAL,
- gapExtend INTEGER OPTIONAL,
- gapScaleFactor INTEGER OPTIONAL,
- nTerminalExt INTEGER OPTIONAL,
- cTerminalExt INTEGER OPTIONAL
- }
- Node-annotation ::= SEQUENCE {
- presentInChildCD VisibleString OPTIONAL,
- note VisibleString OPTIONAL
- }
- -- the Cdd is the basic ASN.1 object storing an annotated and curated set of
- -- alignments (formulated as a set of pairwise master-slave alignments).
- -- The alignment data are contained in Seq-annots, and a special type of
- -- object, the Update-align, contains additional alignment data from unfinished
- -- editing sessions and update processes. The Biostruc-annot-set holds
- -- structure superposition information for multiple structure-derived rows in
- -- the alignment.
- -- Version numbers in Global-ids are meant to be updated every time the Cdd is
- -- changed in a way that does not require Global-ids to be changed (sequences
- -- added in update cycle, annotation changed, alignment errors fixed)
- Cdd ::= SEQUENCE {
- name VisibleString, -- a short name (can be the accession..)
- id Cdd-id-set, -- this CD's Ids
- description Cdd-descr-set OPTIONAL, -- status, references, etc.
- seqannot SEQUENCE OF Seq-annot OPTIONAL, -- contains the CD alignment
- features Biostruc-annot-set OPTIONAL, -- contains structure
- -- alignment data
- -- or "core" definitions
- sequences Seq-entry OPTIONAL, -- store as bioseq-set inside seq-entry
- profile-range Seq-interval OPTIONAL, -- profile for this region only
- -- also stores the Seq-id of the master
- trunc-master Bioseq OPTIONAL, -- holds the truncated master, which
- -- may be something like a consensus,
- -- uses the same sequence coordinate
- -- frame as the profile-range
- posfreq Matrix OPTIONAL, -- relative residue frequencies
- scoremat Matrix OPTIONAL, -- Position dependent score matrix
- distance Triangle OPTIONAL, -- pairwise distances for all seqs.
- parent Cdd-id OPTIONAL, -- this CD is the result of a split
- children Cdd-id-set OPTIONAL, -- this CD has been split, not used
- siblings Cdd-id-set OPTIONAL, -- related CDs (common hits), not used
- neighbors Cdd-id-set OPTIONAL, -- co-occurring CDs, not used
- pending SEQUENCE OF Update-align OPTIONAL, -- contains alignments from
- -- update or "lower panel"
- rejects SEQUENCE OF Reject-id OPTIONAL, -- SeqIds of rejected CD-
- -- members, ignore in update
- master3d SET OF Seq-id OPTIONAL, -- record if CD has a 3D representative
- alignannot Align-annot-set OPTIONAL, -- alignment annotation
- style-dictionary Cn3d-style-dictionary OPTIONAL, -- record rendering styles
- user-annotations Cn3d-user-annotations OPTIONAL, -- user annotations in Cn3D
- ancestors SEQUENCE OF Domain-parent OPTIONAL, -- list of parents
- scoreparams Score-matrix-parameters OPTIONAL,
- seqtree Sequence-tree OPTIONAL
- }
- Cdd-set ::= SET OF Cdd
- -- Cdd projects store a set of CDs, typically related to each other
- -- relationships would be specified using the ancestors fields in the
- -- individual CD objects. For use with CD-Tree, a program to visualize
- -- curated CD hierarchies and evidence for hierarchical family structures.
- Cdd-Viewer-Rect ::= SEQUENCE {
- top INTEGER, -- top coordinate
- left INTEGER, -- left coordinate
- width INTEGER, -- width
- height INTEGER -- height
- }
- Cdd-Viewer ::= SEQUENCE {
- ctrl INTEGER { -- viewer type
- unassigned (0),
- cd-info (1),
- align-annot (2),
- seq-list (3),
- seq-tree (4),
- merge-preview (5),
- cross-hits (6),
- notes (7),
- tax-tree (8),
- dart (9),
- dart-selected-rows (10),
- other (255)
- },
- rect Cdd-Viewer-Rect OPTIONAL, -- viewer rectangle
- accessions SEQUENCE OF VisibleString -- list of accessions associated with a viewer
- }
- Cdd-Script ::= SEQUENCE {
- type INTEGER {
- unassigned (0),
- user-recorded (1),
- server-generated (2),
- other (255)
- } OPTIONAL,
- name VisibleString OPTIONAL, -- user assigned name/description
- commands VisibleString -- actual script commands
- }
- -- cd colors are as: 0000FF for red, 00FF00 for green, FF0000 for blue
- Cdd-Project ::= SEQUENCE {
- cds SEQUENCE OF Cdd , -- cds
- cdcolor SEQUENCE OF INTEGER, -- colors
- viewers SEQUENCE OF Cdd-Viewer, -- Sequence viewers
- log VisibleString, -- log
- scripts SEQUENCE OF Cdd-Script OPTIONAL -- command scripts
- }
- END
English
