Searches via Web Services

GiardiaDB provides programmatic access to its searches, via REST Web Services. The result of a web service request is a list of records (genes, ESTs, etc) in either XML or JSON format. REST services can be executed in a browser by typing a specific URL.

For example, this URL:
http://GiardiaDB.org/webservices/GeneQuestions/GenesByMolecularWeight.xml?
min_molecular_weight=10000&
max_molecular_weight=50000&
reference_strains_only=Yes&
organism=Giardia Assemblage A,Giardia Assemblage B&
o-fields=gene_type,organism

Corresponds to this request:
Find all (Giardia Assemblage A,Giardia Assemblage B) genes that have molecular weight between 10,000 and 50,000.
For each gene ID in the result, return its gene type and organism.
Provide the result in an XML document.


Downloading DNA sequences in a text file in FASTA format:

For specific genomic segments:

• To download one sequence, please use one of the following URL formats:
  http://GiardiaDB.org/cgi-bin/contigSrt?project_id=GiardiaDB&ids=GLCHR05&start=14&end=700
  http://GiardiaDB.org/cgi-bin/contigSrt?project_id=GiardiaDB&ids=GLCHR05:14..700
• For multiple sequences use the line feed character (%0A) as separator (comma or semicolon or carriage return do not work):
  http://GiardiaDB.org/cgi-bin/contigSrt?project_id=GiardiaDB&ids=GLCHR05:14..700%0AGLCHR05:800..900

For gene related regions:

• To download one sequence, please use one of the following URL format:
  http://GiardiaDB.org/cgi-bin/geneSrt?project_id=GiardiaDB&ids=GL50803_102438&type=genomic&upstreamAnchor=Start&upstreamSign=minus&upstreamOffset=10&downstreamAnchor=End&downstreamSign=plus&downstreamOffset=2000

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WADLs: how to generate web service URLs

Click on a search below to access its WADL (Web Application Description Language).

• A WADL is an XML document that describes in detail how to form a URL to call the search as a web service request. For more details go to How to read a WADL at the bottom of this page.
• Note: some browsers (e.g.: Safari) do not know how to render an XML file properly (you will see a page full of terms with no structure).
• To construct the URL in the example above, you would check the Molecular Weight WADL located below under Protein Attributes

• Search for Gene Attributes

  •   Text
    •        Text (product name, notes, etc.)
  •   Gene models
    •        Gene Type
    •        Exon Count
  •   Annotation, curation and identifiers
    •        Gene ID(s)
    •        User Comments
  •   Link outs
    •        ID
    •        transcript ID
  •   Genomic Location
    •        Genomic Location
    •        Proximity to Telomeres
  •   Taxonomy
    •        Organism
  •   Orthology and synteny
    •        Paralog Count
    •        Orthology Phylogenetic Profile
    •        Orthologs and Paralogs
  •   Transcriptomics
    •        EST Evidence
    •       Fold Change
      •            G. Assemblage A isolate WB Encystation in trophozoites Microarray (fold change)
      •            G. Assemblage A isolate WB Time-dependent transcriptional changes in axenic trophozoites RNASeq (fold change)
      •            G. Assemblage A isolate WB Trophozoite Transcriptome of Giardia assemblage A strain AS175 RNASeq (fold change)
      •            G. Assemblage A isolate WB Transcript Profiling of Host-parasite Interactions Microarray (fold change)
    •       Differential Expression
      •            G. Assemblage A isolate WB Trophozoite Transcriptome of Giardia assemblage A strain AS175 RNASeq (Differential Expression)
      •            G. Assemblage A isolate WB Time-dependent transcriptional changes in axenic trophozoites RNASeq (Differential Expression)
      •            G. Assemblage A isolate WB Assemblage A intestine foci transcriptome RNASeq (Differential Expression)
    •       Direct Comparison
      •            G. Assemblage A isolate WB Stress Response in Trophozoites - Temparature Redox Microarray (direct comparison)
      •            G. Assemblage A isolate WB Stress Response in Trophozoites - Incubation Time Microarray (direct comparison)
    •       Percentile
      •            G. Assemblage A isolate WB Trophozoite Transcriptome of Giardia assemblage A strain AS175 RNASeq (percentile)
      •            S. salmonicida ATCC50377 Transcriptome from pooled trophozoite exponential and stationary stages RNASeq (percentile)
      •            G. Assemblage A isolate WB Encystation in trophozoites Microarray (percentile)
      •            G. Assemblage A isolate WB Time-dependent transcriptional changes in axenic trophozoites RNASeq (percentile)
      •            G. Assemblage A isolate WB Stress Response in Trophozoites - Incubation Time Microarray (percentile)
      •            G. Assemblage E isolate P15 (P15) Trophozoite Transcriptome RNASeq (percentile)
      •            G. Assemblage A isolate WB Stress Response in Trophozoites - Temparature Redox Microarray (percentile)
      •            G. Assemblage B isolate GS (GS) Trophozoite Transcriptome RNASeq (percentile)
      •            G. Assemblage A isolate WB Assemblage A intestine foci transcriptome RNASeq (percentile)
      •            G. Assemblage A isolate WB (WB) Trophozoite Transcriptome RNASeq (percentile)
      •            G. Assemblage A isolate WB Transcript Profiling of Host-parasite Interactions Microarray (percentile)
      •            G. Assemblage A isolate WB Trophozoite transcriptome RNASeq (percentile)
    •       SenseAntisense
      •            G. Assemblage A isolate WB Trophozoite Transcriptome of Giardia assemblage A strain AS175 changes in sense and antisense transcripts
  •   Sequence analysis
    •        Protein Motif Pattern
    •        BLAST
  •   Structure analysis
    •        PDB 3D Structures
    •        Protein Secondary Structure
  •   Protein features and properties
    •        Molecular Weight
    •        InterPro Domain
    •        Isoelectric Point
  •   Protein targeting and localization
    •        Transmembrane Domain Count
    •        Cellular Localization Imaging
    •        Predicted Signal Peptide
  •   Function prediction
    •        GO Term
    •        EC Number
  •   Pathways and interactions
    •        Metabolic Pathway
    •        Substrates/Products
  •   Proteomics
    •        Mass Spec. Evidence
    •       Direct Comparison
      •            G. Assemblage A isolate WB Metranidazole-resistant Giardia proteomes and post-translational modifications Proteomics (direct comparison)
    •       Direct Confidence Comparison
      •            Metranidazone-resistant Giardia proteomes and post-translational modifications (direct comparison)
  •   Immunology
    •        Epitope Presence (IEDB)

• Search for Genomic Sequences

  •        Genomic Sequence ID(s)
  •        Organism
  •        BLAST

• Search for Genomic Segments (DNA Motif)

  •        Genomic Location
  •        DNA Motif Pattern

• Search for ESTs

  •        EST Accession(s)
  •        Gene ID
  •        BLAST
  •        Genomic Location
  •        Library
  •        Extent of Gene Overlap

• Search for ORFs

  •        Genomic Location
  •        Orf ID(s)
  •        Protein Motif Search
  •        BLAST

• Search for Metabolic Pathways

  •        Pathway Name/ID
  •        Identifier (pathway, gene, compound, etc.)
  •        Reaction
  •        Genes
  •        Compounds
  •        Transform to Pathways
  •        Transform to Pathways

• Search for Compounds

  •        Compound ID
  •        Text (synonym, InChI, etc.)
  •        Enzymes
  •        Metabolic Pathway
  •        Molecular Weight
  •        Molecular Formula
  •        Transform to Compounds
  •        Transform to Compounds

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How to read a WADL

• (1) What is the name and purpose of the search.
  Under <method name=....>
  In our example: <doc title="description">Find genes whose ..... Molecular weights are ......</doc>


• (2) What is the service URL.
  Under <resource path=....>.
  It includes an extension that indicates the format requested for the result (XML or JSON).
  In our example: http://GiardiaDB.org/webservices/GeneQuestions/GenesByMolecularWeight.xml


• (3) How to constrain your search.
  Under <param name=.....>.
  If a default value is provided under <doc title="default">.....</doc>, then providing the parameter is optional.
  In our example: min_molecular_weight=10000, max_molecular_weight=50000.


• (4) What to return for each ID in the result.
  Under <param name=.....> too.
  These are the same for all searches of a given record type (e.g., for all gene searches). Output-fields are single-valued attributes while output-tables are multi-valued (array).
  In our example: o-fields=gene_type,organism_full&o-tables=EcNumber