cdd.asn

ncbi源码

--$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