Resource URLs

The GO/wr URLs are given in the URI template notation (described by Gregorio et al, IETF draft, Nov 26, 2007). Briefly, the curly braces "{ }" define a variable embedded in the URI template. The variable must be replaced by the appropriate value to create a valid URI.

**URLs for GO/wr resources.**

Base: http://www.avatar.se/
URL	Query parameters	Representations	Description
/GO/wr/ /GO/wr/index	-	HTML, XML	Index of the ontology root terms.
/GO/wr/term/{goacc}	-	HTML, XML	The representation of the term given by {goacc}.
/GO/wr/terms;index?{query}	search={field} value={strvalue} exact={boolean}	HTML, XML	Index of terms found by searching the database using the given field and its value. See Query parameters.
/GO/wr/terms/{goaccs}	-	XML only	The representations of the terms given by {goaccs}. See More than one term.
/GO/wr/associations/{goacc}	-	HTML, XML
/GO/wr/gene_product/{dbxref}	-	HTML, XML
/GO/wr/gene_products;index?{query}	search={field} value={strvalue} exact={boolean}	HTML, XML
/GO/wr/gene_products	-	XML only

HTTP methods

The GO/wr resources are read-only. Therefore, the only important HTTP method is GET. The HEAD and OPTIONS methods have not yet been implemented.

URL-encoding values

The {goacc} and query parameter values may contain characters that are not allowed in URLs. For instance, a space character cannot be included as-is in a URL. Such characters must be URL-encoded. The space (blank) character is encoded as '+', while most special characters are converted to ASCII-based hexadecimal percent codes, e.g. '!' to '%21'. URL-encoding is also called Percent-encoding.

Specifying the representation

The representation of the retrieved data, i.e. the format, can be specified by appending a suffix, such as '.xml', to the URL. See Representations. Currently, the available formats are HTML and XML.

Specifying a term

The GO accession code (identifier) is the basic specification to use when retrieving a record in the GO database. The GO term accession code is a seven-digit number (with leading zeroes), optionally with the 'GO:' prefix.

It is also possible to use the URL-encoded form of the explicit term name. This is not recommended, since the term name is likely to be less stable between GO releases than the GO accession code. The term name may be updated as circumstances dictate, but as long as the meaning is the same, the accession code is fixed.

More than one term

It is possible to fetch more than one term representation in a single XML document (currently not possible in HTML). Use the 'terms/{goaccs}' URL, where {goaccs} is a semicolon-delimited string of GO accession codes. The order of the terms in the XML document is undefined.

This is a much more efficient way of retrieving several terms representations than issuing one request per term. We recommend using this feature whenever possible. The only caveat is that the URL cannot be longer than some badly defined maximum length. Keep it shorter than 4,000 characters in total.

Query parameters

Parameter

key=value Description

search=key Search progressively for terms that match the string value. See below.