Changes between Version 15 and Version 16 of AnnotationExtensionSyntax


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Timestamp:
Jun 6, 2012, 2:48:46 PM (9 years ago)
Author:
gomidori
Comment:

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  • AnnotationExtensionSyntax

    v15 v16  
    1 This page describes the syntax used to make annotation extensions [[BR]]
    2 (to go back to the wiki: [https://sourceforge.net/apps/trac/pombase/wiki/])
     1This page describes the syntax used to make annotation extensions. Also see the [http://wiki.geneontology.org/index.php/Annotation_Extension GO Annotation Extension wiki page].
    32
    43== Compound terms: ==
    54
    6 These are separated by a comma ',' and relate back to the term in conjunction.
     5These are separated by a comma ',' and relate back to the term in conjunction (i.e. both apply simultaneously), e.g.
    76
    87{{{
    98
    10 
    11 e.g
    129gene x
    1310protein kinase activity
    1411has_substrate(gene y),during(GO:processZ)
    1512
     13}}}
     14
    1615should be interpreted as gene x phosphorylates protein Y during process Z
    17 }}}
    1816
    1917== Independent annotations: ==
     
    2321{{{
    2422
    25 e.g
    2623gene x
    2724protein kinase activity
    2825has_substrate(gene y),happens_during(GO:processZ)|has_substrate(gene a),happens_during(GO:processB)
    2926
     27}}}
     28
    3029should be interpreted as
    31 gene x phosphorylates protein Y during process Z
    32 gene x phosphorylates protein A during process B
     30 * gene x phosphorylates protein Y during process Z, and
     31 * gene x phosphorylates protein A during process B
    3332
    34 Note that you cannot use "pipes" in combinations of qualifiers  in Artemis becasue they cannot be disambiguated.
    35 For example,  you can have a single pipe in the residues field
     33Note that you cannot use "pipes" in combinations of qualifiers in Artemis becasue they cannot be disambiguated. For example,  you can have a single pipe in the residues field, e.g.
    3634
     35{{{
    3736/GO="aspect=F; term=calcium ion binding; GOid=GO:0005509;
    3837 residue=99|108; evidence=IDA; db_xref=PMID:12943532;  date=20040602"
     38}}}
    3939
    40 but, if we have to add 2 annotation extension each of which only applied to  one of the modifications
    41 (for example the residues were phosphorylated by different kinases), to
    42 disambiguate we would need to make 2 separate annotations
     40but, if we have to add 2 annotation extension, each of which only applied to one of the modifications (for example, the residues were phosphorylated by different kinases), to disambiguate we would need to make 2 separate annotations:
    4341
     42{{{
    4443/GO="aspect=F; term=calcium ion binding; GOid=GO:0005509;
    4544residue=99;  annotation_extension=phosphorylated_by(x); evidence=IDA; db_xref=PMID:12943532;
     
    4948 residue=99; evidence=IDA;  annotation_extension=phophorylated_by(z); db_xref=PMID:12943532;
    5049 date=20040602"
     50}}}
    5151
    52 If you used pipes in both places it would not be possible for a human, or computer to disambiguate
     52If you used pipes in both places it would not be possible for a human or computer to disambiguate.
    5353
    54 }}}
    5554
    5655== Nested terms: ==
    5756
    58 (Note we are trying to avoid nested terms as these are not handled, by Chado, or GO)
     57(Note: we are trying to avoid nested terms as these are not handled by Chado or GO)
    5958
    60 For extensions attached to an entity which is itself and extension
     59For extensions within extensions (i.e. an extension points to an entity which itself is a term+extension)
    6160
    6261{{{
    6362
    64 e.g
     63e.g.
    6564gene x
    6665meiotic telomere clustering
    6766dependent_on(GO:0005515^has_substrate(bqt3))
    6867
    69 should be interpreted as gene x is involved in process and is dependent on protein binding to substrate bqt3
    7068}}}
    7169
     70should be interpreted as "gene x is involved in the process 'meiotic telomere clustering' and its involvement is dependent on protein binding to substrate Bqt3"
    7271
     72----
     73[WikiStart Return to main page] or [CurationGuidelines Curation Guidelines]
    7374
    74