1 / 12

Navigation to Related Objects

Navigation to Related Objects. Mario Latendresse. October 2010, Pathway Tools Workshop. Bioinformatics Research Group SRI International latendre@ai.sri.com. Available on the Web. Applies for compounds, genes, proteins, reactions, pathways

alanowens
Download Presentation

Navigation to Related Objects

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. Navigation to Related Objects Mario Latendresse October 2010, Pathway Tools Workshop Bioinformatics Research Group SRI International latendre@ai.sri.com

  2. 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 or 2. Another database • The “In all databases” is demanding (BioCyc has over 1000 databases); more so for genes and proteins

  3. Does this Object Exist in Other PGDBs?

  4. 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

  5. Demo on the Web of “another database” • 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

  6. Demo on the Web of “in all databases” • 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

  7. Result for “In all databases” for a Compound

  8. 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

  9. Result “In all databases” for a Gene

  10. 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

  11. 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 …]

  12. Navigation to Related Objects Questions?

More Related