1 / 12

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.

ninon
Download Presentation

Web Services

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. 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

More Related