Searches via Web Services
TrichDB 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:
Corresponds to this request:
Find all (Trichomonas vaginalis) 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:
- For multiple sequences use the line feed character (%0A) as separator (comma or semicolon or carriage return do not work):
- To download one sequence, please use one of the following URL format:
WADLs: how to generate web service URLsClick 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
- Gene models
- Annotation, curation and identifiers
- Link outs
- Genomic Location
- Orthology and synteny
- Sequence analysis
- Structure analysis
- Protein features and properties
- Protein targeting and localization
- Function prediction
- Pathways and interactions
Search for Genomic Sequences
Search for Genomic Segments (DNA Motif)
Search for ESTs
Search for ORFs
Search for Metabolic Pathways
Search for Compounds
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://TrichDB.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