web-services - Bioinformatics Research Group at SRI

Report
Web Services
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Kinds of Web Services
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
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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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.

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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



http://biocyc.org/getxml?id=META:ASPARTATEKIN-RXN


Retrieve the aspartate kinase reaction from MetaCyc
http://biocyc.org/getxml?id=ECOLI:TRYPSYNAPROTEIN&detail=low
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Retrieve the glycolysis pathway from Bacillus subtilis
Retrieve the trpA gene product from EcoCyc at low detail level
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Ptools-XML Queries – API functions
A
subset of API functions available by web
services
 E.g. pathways-of-gene, compounds-of-pathway, genesregulated-by-gene, etc.
 Full list available at http://biocyc.org/web-services.shtml
 http://biocyc.org/apixml?fn=[APIFN]&id=[ORGID]:[FRAMEID]&detail=[none|low|full]
 Detail level:
 None: Frame references (orgid and frameid) only
 Low: Only selected slots and frame references included
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This is the default for queries that potentially return multiple frames
Full: All supported slots, with embedded frames
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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-bygene&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-ofreaction&id=META:TRYPSYN-RXN&detail=full
 Get detailed information on all enzymes in MetaCyc that
catalyze the tryptophan synthase reaction
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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]&deta
il=[none|low|full]
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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” instringci x^names]
 Retrieve the set of proteins in MetaCyc that have the word
“aspartate” in their common-name or synonyms
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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]/pathwaybiopax?type=[2|3]&object=[PATHWAY]
 Examples:
 http://biocyc.org/META/pathway-biopax?object=PWY-5025



http://biocyc.org/AFER243159/pathwaybiopax?type=2&object=CYSTSYN-PWY
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Retrieve the IAA biosynthesis pathway in MetaCyc in BioPAX level 3
format
Retrieve the cysteine biosynthesis pathway in Acidithiobacillus
ferrooxidans in BioPAX level 2 format
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Visualization-Based Web Services –
Cellular Overview Diagram
 Highlighting
the Cellular Overview Diagram
 http://biocyc.org/overviewsWeb/celOv.shtml?zoomlevel=<inte
ger>&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
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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 omics data overlaid
 Specified pathways only
 All pathways that have a data value that exceeds threshold
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