Embed Size (px)
Citation preview
SRI International Bioinformatics1
Navigation to Related Objects
Bioinformatics Research Group
SRI International
Mario Latendresse
October 2010, Pathway Tools Workshop
SRI International Bioinformatics2
Available on the Web
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 or2. Another database
The “In all databases” is demanding (BioCyc has over 1000 databases); more so for genes and proteins
SRI International Bioinformatics3
Does this Object Exist in Other PGDBs?
SRI International Bioinformatics4
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
SRI International Bioinformatics5
Demo on the Web of “another database”
1. At BioCyc.org, select E. coli K12 as the database to search
2. Search for the glycolysis pathway using the Search->Pathways command
3. Once the glycolysis pathway is displayed, Select the command Pathway->Show this pathway in another database
4. Select the database to search (e.g., MetaCyc)
5. If it exists in the other database, the glycolysis pathway is displayed for this database
SRI International Bioinformatics6
Demo on the Web of “in all databases”
1. At BioCyc.org, select E. coli K12 as the database to search
2. Search for compound N-methyltryptophan.
3. Once the compound is displayed, select the command Compound->Show this compound in all databases
4. About 28 databases (the number depends on the current version of BioCyc.org) are found containing that compound
SRI International Bioinformatics7
Result for “In all databases” for a Compound
SRI International Bioinformatics8
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
SRI International Bioinformatics9
Result “In all databases” for a Gene
SRI International Bioinformatics10
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
SRI International Bioinformatics11
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 …]
SRI International Bioinformatics12
Navigation to Related Objects
Questions?
