131 lines
2.8 KiB
Groff
131 lines
2.8 KiB
Groff
HomoloGene DEFINITIONS ::=
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BEGIN
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IMPORTS Date FROM NCBI-General
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Seq-loc FROM NCBI-Seqloc
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Seq-align FROM NCBI-Seqalign;
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-- HomoloGeneEntry taxid is the tax id of the group node, which can
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-- be the same as the Gene tax id in case of singletons
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HG-EntrySet ::= SEQUENCE {
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entries SET OF HG-Entry -- homologene entry
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}
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HG-Entry ::= SEQUENCE {
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hg-id INTEGER,
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version INTEGER OPTIONAL,
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title VisibleString OPTIONAL,
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caption VisibleString OPTIONAL,
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taxid INTEGER OPTIONAL,
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genes SET OF HG-Gene OPTIONAL,
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cr-date Date OPTIONAL,
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up-date Date OPTIONAL,
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distances SET OF HG-Stats OPTIONAL,
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commentaries SET OF HG-CommentarySet OPTIONAL,
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warnings SET OF VisibleString OPTIONAL,
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node HG-Node OPTIONAL
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}
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HG-Gene ::= SEQUENCE {
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geneid INTEGER,
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otherid INTEGER OPTIONAL, -- internal use only!!!!!
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symbol VisibleString OPTIONAL,
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aliases SET OF VisibleString OPTIONAL,
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title VisibleString,
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taxid INTEGER, --taxid of gene node
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prot-gi INTEGER OPTIONAL,
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prot-acc VisibleString OPTIONAL,
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prot-len INTEGER OPTIONAL,
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nuc-gi INTEGER OPTIONAL,
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nuc-acc VisibleString OPTIONAL,
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gene-links SET OF HG-Link OPTIONAL,
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prot-links SET OF HG-Link OPTIONAL,
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domains SET OF HG-Domain OPTIONAL,
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chr VisibleString OPTIONAL,
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location Seq-loc OPTIONAL, -- location on the genome
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locus-tag VisibleString OPTIONAL
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}
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HG-Stats ::= SEQUENCE {
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gi1 INTEGER,
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gi2 INTEGER,
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nuc-change REAL,
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nuc-change-jc REAL,
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prot-change REAL,
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ka REAL,
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ks REAL,
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knr REAL,
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knc REAL,
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recip-best BOOLEAN OPTIONAL
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}
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HG-Commentary ::= SEQUENCE {
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link HG-Link,
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description VisibleString OPTIONAL, -- main description
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caption VisibleString OPTIONAL, -- extra text
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provider VisibleString OPTIONAL,
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other-links SET OF HG-Link OPTIONAL,
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other-commentaries SET OF HG-Commentary OPTIONAL,
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taxid INTEGER OPTIONAL,
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geneid INTEGER OPTIONAL
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}
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HG-CommentarySet ::= SEQUENCE {
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hg-id INTEGER OPTIONAL,
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title VisibleString,
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commentaries SET OF HG-Commentary
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}
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HG-CommentaryContainer ::= SET OF HG-CommentarySet
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HG-Link ::= SEQUENCE {
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hypertext VisibleString,
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url VisibleString OPTIONAL
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}
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HG-Domain ::= SEQUENCE {
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begin INTEGER,
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end INTEGER,
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pssm-id INTEGER OPTIONAL, -- entrez uid
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cdd-id VisibleString OPTIONAL,
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cdd-name VisibleString OPTIONAL
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}
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HG-Node ::= SEQUENCE {
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type ENUMERATED {
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family(0),
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ortholog(1),
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paralog(2),
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leaf(3)
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},
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id HG-Node-id,
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caption VisibleString OPTIONAL,
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current-node BOOLEAN DEFAULT FALSE,
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children SET OF HG-Node OPTIONAL,
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branch-len INTEGER OPTIONAL
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}
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HG-Node-id ::= SEQUENCE {
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id INTEGER OPTIONAL,
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id-type ENUMERATED {
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none(0),
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geneid(1),
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hid(2)
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}
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}
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HG-Alignment ::= SEQUENCE {
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hg-id INTEGER,
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alignment Seq-align
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}
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HG-AlignmentSet ::= SET OF HG-Alignment
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END
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