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Navigation to Related Objects
Mario Latendresse
October 2010, Pathway Tools Workshop
Bioinformatics Research Group
SRI International
[email protected]
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Available on the Web
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Applies for compounds, genes, proteins,
reactions, pathways
Once such an object is found, a new menu
appears on the right on the top menu bar
The menu offers to search the object found:
1. In all databases
or
2. Another database
The “In all databases” is demanding (BioCyc
has over 1000 databases); more so for genes
and proteins
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Does this Object Exist in Other PGDBs?
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How is Similarity Computed?
 For
pathways, reactions, and compounds: based
on frame-ids (unique identifiers)
 For
proteins and genes: based on names,
synonyms, and orthologs
 The result page tells you, for each database, if found based
on name/synonyms or orthologs, or both
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Demo
on
the
“another database”
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Web
At BioCyc.org, select E. coli K12 as the
database to search
Search for the glycolysis pathway using the
Search->Pathways command
Once the glycolysis pathway is displayed,
Select the command Pathway->Show this
pathway in another database
Select the database to search (e.g., MetaCyc)
If it exists in the other database, the glycolysis
pathway is displayed for this database
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of
Demo on the Web of “in all databases”
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At BioCyc.org, select E. coli K12 as the
database to search
Search for compound N-methyltryptophan.
Once the compound is displayed, select the
command Compound->Show this compound in
all databases
About 28 databases (the number depends on
the current version of BioCyc.org) are found
containing that compound
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Result for “In all databases” for a
Compound
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For Genes and Proteins
 The
search for similar proteins and genes is
based on names (name and synonyms) and
orthologs
 The result page gives the reasons of the match
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Result “In all databases” for a Gene
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Implementation
The two commands are implemented using
BioVelo. A general purpose query language for
Pathway Tools
The query itself can be saved since it appears as a
URL in the browser
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Implementation (2)
 Searching
all databases for a pathway
[ ( Z1,r ): Z1<-dbs, r := Z1~GLYCOLYSIS ]
 Searching
all databases for a compound
[ (Z1,r,r^Chemical-formula): Z1 <- dbs, r:=Z1~PEPTIDE-TRYPTOPHAN ]
 Searching
all databases for a reaction
[ (Z1,r,r^EC-number): Z1 <- dbs, r := Z1~L-IDITOL-2-DEHYDROGENASE-RXN ]
 Searching
all databases for a gene
[ r : l1 := find-objects(META,ECOLI~EG11024),
l2 := find-orthologs(META,ECOLI~EG11024),
both := l1**l2 , ort := l2 -- both, sim := l1 -- both,
r <- … both … ort … sim …]
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Navigation to Related Objects
Questions?
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