Table 1 |
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List of relations and predicates. |
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Symbol |
Long name of predicate |
Remarks |
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MSeq(x) |
molecular sequence |
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SSeq(x) |
syntactic sequence |
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ASeq(x) |
abstract sequence |
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Jun(x) |
junction |
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PBS(x) |
primitive biological symbol |
x is a syntactic sequence (SSeq). |
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DMSeq(x) |
directed molecular sequence |
x is a molecular sequence (MSeq). |
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DSSeq(x) |
directed syntactic sequence |
x is a syntactic sequence (SSeq). |
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mPO(x, y) |
molecular part of |
x and y are molecular sequences (MSeq). |
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sPO(x, y) |
syntactic part of |
x and y are syntactic sequences (SSeq). |
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aPO(x, y) |
abstract part of |
x and y are abstract sequences (ASeq). |
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mPPO(x, y) |
molecular proper part of |
x and y are molecular sequences (MSeq). |
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sPPO(x, y) |
syntactic proper part of |
x and y are syntactic sequences (SSeq). |
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aPPO(x, y) |
abstract proper part of |
x and y are abstract sequences (ASeq). |
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moverlap(x, y) |
molecular overlap |
x and y are molecular sequences (MSeq). |
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soverlap(x, y) |
syntactic overlap |
x and y are syntactic sequences (SSeq). |
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aoverlap(x, y) |
abstract overlap |
x and y are abstract sequences (ASeq). |
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mdisjoint(x, y) |
molecular disjointness |
x and y are molecular sequences (MSeq). |
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sdisjoint(x, y) |
syntactic disjointness |
x and y are syntactic sequences (SSeq). |
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adisjoint(x, y) |
abstract disjointness |
x and y are abstract sequences (ASeq). |
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sto(x, y) |
syntactic token of |
x is a syntactic (SSeq), y an abstract sequence (ASeq). |
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mto(x, y) |
molecular token of |
x is a molecular (MSeq), y an abstract sequence (ASeq). |
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Rep(x, y) |
representation |
x is a syntactic (SSeq), y a molecular sequence (MSeq). |
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between(j, p1, p2, s) |
between |
j is a junction (Jun), p1 and p2 are primitive symbols (PBS) and s is a syntactic sequence (SSeq). j is a junction between p1 and p2 in the syntactic sequence s. |
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end(j, p, s) |
ends |
j is a junction (Jun), p a primitive symbol (PBS) and s is a syntactic sequence (SSeq). The junction j ends the syntactic sequence s and is adjacent to the primitive symbol p (which is the first or last symbol of s). |
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first(j, p, s) |
first |
j is a junction (Jun), p a primitive symbol (PBS) and s a syntactic sequence (SSeq). |
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last(j, p, s) |
last |
j is a junction (Jun), p a primitive symbol (PBS) and s a syntactic sequence (SSeq). |
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in(j, s) |
in |
j is a junction (Jun) and s a syntactic sequence (SSeq). |
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s1 ≡ s2 |
equivalence |
s1 and s2 are directed syntactic sequences (DSSeq). |
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conn(j1, j2) |
connection |
j1 and j2 are junctions (Jun). |
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The table shows the list of predicates used in the axiom system. Unary predicates represent categories, all other predicates represent relations. In this table, we included relations that are used in the implementation but are not further discussed. For example, the relations adisjoint and mdisjoint are included in the axiom system and are defined similar to sdisjoint (see formula 13). |
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Hoehndorf et al. BMC Bioinformatics 2009 10:377 doi:10.1186/1471-2105-10-377 |
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