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Web Services

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

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Web Services

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  1. Web Services

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

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

  4. Ptools-XML Queries • Retrieve a single object by frame id • 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: • http://biocyc.org/getxml?BSUB:GLYCOLYSIS • Retrieve the glycolysis pathway from Bacillus subtilis • http://biocyc.org/getxml?id=META:ASPARTATEKIN-RXN • Retrieve the aspartatekinase reaction from MetaCyc • http://biocyc.org/getxml?id=ECOLI:TRYPSYN-APROTEIN&detail=low • Retrieve the trpA gene product from EcoCyc at low detail level

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

  6. Ptools-XML – Example API Queries • http://biocyc.org/apixml?fn=genes-of-pathway&id=BSUB:GLYCOLYSIS • 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 • 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 • Get detailed information on all enzymes in MetaCyc that catalyze the tryptophan synthase reaction

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

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

  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 • If not specified, default is level 3 • http://biocyc.org/[ORGID]/pathway-biopax?type=[2|3]&object=[PATHWAY] • Examples: • http://biocyc.org/META/pathway-biopax?object=PWY-5025 • Retrieve the IAA biosynthesis pathway in MetaCyc in BioPAX level 3 format • http://biocyc.org/AFER243159/pathway-biopax?type=2&object=CYSTSYN-PWY • Retrieve the cysteine biosynthesis pathway in Acidithiobacillusferrooxidans in BioPAX level 2 format

  10. Visualization-Based Web Services – Cellular Overview Diagram • Highlighting the Cellular Overview Diagram • http://biocyc.org/overviewsWeb/celOv.shtml?zoomlevel=<integer>&orgid=<orgid>&<op>=<value> • Zoomlevel is integer, 0-6 • 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. Visualization-Based Web Services – Pathway Diagrams • Single pathway display • Can customize detail level • Can overlay omics data – submit URL via GET method • Table of pathways • With or without omicsdata overlaid • Specified pathways only • All pathways that have a data value that exceeds threshold

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