1. SRI International Bioinformatics 1 Web Services

2. SRI International Bioinformatics 2 Kinds of Web Services Data retrieval Web Services l PTools-XML l BioPAX Visualization Web Services l Overview highlights l Generating pathway images l Adding omics data to overviews or pathways Resources: l http://biocyc.org/web-services.shtml l Help -> Website User Guide

3. SRI International Bioinformatics 3 Ptools-XML Closely follows Pathway Tools schema Element tags for frames l Gene, Protein, Pathway, Reaction, Compound, Regulation, Transcription-Unit, Publication, etc. l Contain orgid and frameid attributes l Capitalized names Element tags for slots l Values can be literals, embedded frame elements, or references to frame elements defined elsewhere in the document l Lower-case names Metadata tag describes query, PGDB, number of results.

4. SRI International Bioinformatics 4 Ptools-XML Queries Retrieve a single object by frame id l Specify PGDB, frame-id, detail-level (defaults to full detail) http://biocyc.org/getxml? [ORGID] : [FRAMEID] http://biocyc.org/getxml?id= [ORGID] : [FRAMEID] &detail= [none|low|full ] Examples: l http://biocyc.org/getxml?BSUB:GLYCOLYSIS u Retrieve the glycolysis pathway from Bacillus subtilis l http://biocyc.org/getxml?id=META:ASPARTATEKIN-RXN u Retrieve the aspartate kinase reaction from MetaCyc l http://biocyc.org/getxml?id=ECOLI:TRYPSYN- APROTEIN&detail=low u Retrieve the trpA gene product from EcoCyc at low detail level

5. SRI International Bioinformatics 5 Ptools-XML Queries – API functions A subset of API functions available by web services l E.g. pathways-of-gene, compounds-of-pathway, genes- regulated-by-gene, etc. l Full list available at http://biocyc.org/web-services.shtml l http://biocyc.org/apixml?fn=[API- FN]&id=[ORGID]:[FRAMEID]&detail=[none|low|full] Detail level: l None: Frame references (orgid and frameid) only l Low: Only selected slots and frame references included u This is the default for queries that potentially return multiple frames l Full: All supported slots, with embedded frames

6. SRI International Bioinformatics 6 Ptools-XML – Example API Queries http://biocyc.org/apixml?fn=genes-of- pathway&id=BSUB:GLYCOLYSIS l Retrieve the genes that participate in the glycolysis pathway in Bacillus subtilis. Results are provided at low detail level http://biocyc.org/apixml?fn=genes-regulated-by- gene&id=ECOLI:EG10164&detail=none l Retrieve the set of genes (IDs only) regulated by the crp gene in EcoCyc http://biocyc.org/apixml?fn=enzymes-of- reaction&id=META:TRYPSYN-RXN&detail=full l Get detailed information on all enzymes in MetaCyc that catalyze the tryptophan synthase reaction

7. SRI International Bioinformatics 7 Ptools-XML – BioVelo Queries A subset of BioVelo supported by web services l Only BioVelo queries that return a single list of frames l Queries must be properly escaped for HTML Resources for constructing BioVelo queries: l http://biocyc.org/bioveloLanguage.shtml l Search ->Advanced, Switch to Free Form Advanced Query Page http://biocyc.org?xmlquery?[QUERY] or http://biocyc.org?xmlquery?query=[QUERY]&deta il=[none|low|full]

8. SRI International Bioinformatics 8 Ptools-XML – BioVelo Examples http://biocyc.org/xmlquery?[x:x<-ecoli^^pathways] l Retrieve the complete set of pathways in EcoCyc http://biocyc.org/xmlquery?query=[x:x<- ecoli^^genes,x^name=trpA]&detail=full l Retrieve detailed information about the gene(s) in EcoCyc that have the name trpA http://biocyc.org/xmlquery?dbs l Retrieve the list of available PGDBs http://biocyc.org/xmlquery?[x:x<- meta^^proteins,aspartate instringci x^names] l Retrieve the set of proteins in MetaCyc that have the word aspartate in their common-name or synonyms

9. SRI International Bioinformatics 9 BioPAX BioPAX is an XML-based standard for exchange of pathway data – see http://biopax.org Two different BioPAX formats: level 2 and level 3 l If not specified, default is level 3 http://biocyc.org/[ORGID]/pathway- biopax?type=[2|3]&object=[PATHWAY] Examples: l http://biocyc.org/META/pathway-biopax?object=PWY-5025 u Retrieve the IAA biosynthesis pathway in MetaCyc in BioPAX level 3 format l http://biocyc.org/AFER243159/pathway- biopax?type=2&object=CYSTSYN-PWY u Retrieve the cysteine biosynthesis pathway in Acidithiobacillus ferrooxidans in BioPAX level 2 format

10. SRI International Bioinformatics 10 Visualization-Based Web Services – Cellular Overview Diagram Highlighting the Cellular Overview Diagram l http://biocyc.org/overviewsWeb/celOv.shtml?zoomlevel= &orgid= & = l Zoomlevel is integer, 0-6 l Op determines what gets highlighted (reactions, pathways, genes, compounds, proteins – all either name or substring) Omics data can be submitted using the GET method by supplying the URL for datafile Omics data can be submitted using the POST method to upload a datafile

11. SRI International Bioinformatics 11 Visualization-Based Web Services – Pathway Diagrams Single pathway display l Can customize detail level l Can overlay omics data – submit URL via GET method Table of pathways l With or without omics data overlaid l Specified pathways only l All pathways that have a data value that exceeds threshold

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