#12 TAIR relationships

open
nobody
5
2008-02-06
2008-02-06
Seung Yon Rhee
No

Here are relationship types used in TAIR. If you have any questions about specific terms, please consult Tanya Berardini at TAIR (tberardi@acoma.stanford.edu).

Thanks,
Sue

Discussion

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    We use our relationship types for several purposes:

    1. to describe relationships between gene products and controlled vocabulary terms (GO, PO) (involved_in, functions_as)
    2. to describe relationships between gene products and other gene products (has protein-DNA interaction with, acts downstream of)
    3. to describe relationships between CV terms and other CV terms (is_a, part_of, develops_from, regulates, negatively_regulates, positively_regulates)

    Do all of these types of relationships fall into what would be included in the Relationship Ontology?

     
  • Chris Mungall
    Chris Mungall
    2008-04-09

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    Pasting contents of file:

    involved in Used to describe relationship between gene product and biological process term. gene2term
    functions as Used to describe relationship between gene product and molecular function term. gene2term
    expressed in Used to describe relationship between gene product (mRNA) and cellular component or anatomy term. gene2term
    not involved in Used to describe relationship between gene product and biological process term. gene2term
    not functions as Used to describe relationship between gene product and molecular function term. gene2term
    not expressed in Used to describe relationship between gene product (mRNA) and cellular component or anatomy term. gene2term
    related to Used to describe relationship between gene product and molecular function term. gene2term
    not related to Used to describe relationship between gene product and molecular function term. gene2term
    required for Used to describe relationship between gene product and biological process term. gene2term
    not required for Used to describe relationship between gene product and biological process term. gene2term
    located in Used to describe gene product (protein) and cellular component term. gene2term
    not located in Used to describe gene product (protein) and cellular component term. gene2term
    is subunit of Used to describe relationship between gene product (protein) and cellular component term. gene2term
    constituent of Used to describe relationship between gene product (protein) and cellular component term. gene2term
    regulates Used to describe relationship between one gene product and biological process term. gene2term
    functions in Used to describe relationship between gene product and molecular function term. gene2term
    represses Used to describe relationship between gene product and biological process term. gene2term
    IS_A \N term2term
    PART_OF \N term2term
    DEVELOPS_FROM \N term2term
    is regulated by Used to describe relationship between gene product and biological process term. gene2gene
    suppresses gene Used to describe relationship between one gene product and another gene product. gene2gene
    enhances gene Used to describe relationship between one gene product and another gene product. gene2gene
    matches Used to describe substring text match between Reference text description and Keyword name. article2term
    partially enhances gene \N gene2gene
    partially suppresses gene \N gene2gene
    expressed during \N gene2term
    expressed only in \N gene2term
    expressed only during \N gene2term
    is downregulated by Used to describe relationship between one gene product and biological process term. gene2term
    has Used to describe relationship between gene product and molecular function term. gene2term
    has protein-protein physical interaction with Used to describe relationship between one gene product and another gene product. gene2gene
    binds to cis-element of Used to describe relationship between one gene product and another gene product. gene2gene
    none none gene2term
    acts upstream of Used to describe relationship between one gene product and another gene product. gene2gene
    acts downstream of Used to describe relationship between one gene product and another gene product. gene2gene
    member of Used to describe relationship of gene product (protein) to a term. gene2term
    has protein-DNA interaction with Used to describe relationship between one gene product and another gene product. gene2gene
    has protein modification of type Used to describe relationship between one gene product and a biological process term under the node 'protein modification.' gene2term
    protein is modified by Used to describe relationship between a gene product and another gene product. Not to be used for gene to term annotations. gene2gene
    does not have Used to describe relationship between a gene product and a molecular function term that ends in the word 'activity'. gene2term
    contributes to "Used to describe relationship between a gene product that is part of a complex and the molecular function activity of that complex, when the specific activity of that gene product is not known. Should be used in conjunction with the evidence code IC when" gene2term
    describes method Used to describe the relationship between a protocol and a method\
    protocol2term n 4/21/2004
    colocalizes with Used to describe relationship between a gene product and a cellular component term. Meant for transient associations. gene2term
    does not function in "Used to describe relationship between a gene product and a molecular function term ending in ""binding""." gene2term
    is upregulated by Used to describe relationship between two gene products. gene2gene
    is not regulated by Used to describe relationship between a gene product and a biological process term. gene2term
    is not a constituent of Used to describe relationship between a gene product and a cellular component term. gene2term
    not expressed during Used to describe relationship between a gene product and a developmental stage term. gene2term