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G-Links

G-Links is a rapid data "broker" service that collects and adds related information to a given gene (or gene set).

With the availability of numerous curated databases, researchers are nowadays able to efficiently utilize the multitude of biological data by integrating these resources by hyperlinks and cross references. A large proportion of bioinformatics research tasks, however, is comprised of labor-intensive tasks in fetching, parsing, and merging of these datasets and functional annotations from dispersed databases and web-based services. Therefore, data integration is one of the key challenges of bioinformatics. We here present G-Links, a gateway server for querying and retrieving gene annotation data. The system supports rapid querying with numerous gene IDs from multiple databases or nucleotide/amino acid sequences, by internally centralizing gene annotations based on UniProt entries. This system therefore first converts the query into UniProt ID by ID conversion or by sequence similarity search, and returns related annotations and cross references. Moreover, users are able to run external web-based tools based on the query gene. G-Links is implemented as a RESTful service, so users can easily access this tool from any web browser. This service and documentations are freely available at http://link.g-language.org/.

Base URL

Quick Start

Input sequence (Amino acid or Nucleotide) or Gene ID


Output Format :
E-value :
Identity :
Feeling lucky :

Documentations

Usage (Syntax)

This section describes the G-Links URI syntax conventions: for usage examples, scroll below. G-Link is provided by REST interface. Database cross-references information related as given gene ID or sequence (nucleotide or amino acid) can be accessed through HTTP GET/POST request using unique URI.

REST URI conventions

URL Syntax of G-Links. G-Links is implemented as a RESTful service that can be queried by altering the URL.

HTML output

HTML output example of BRCA1_HUMAN (UniProt ID of BRCA1 gene in humans). By default, access to G-Links with web browsers display the results in interactive HTML, with related image gallery implemented with CoverFlow (http://imageflow.finnrudolph.de/) on the top, followed by a large table of annotations and cross-references.

Qualifiers

Standard qualifiers
  • GENE
    • Sequence (nucleotide or amino acid)
    • Gene ID (Available ID list is here)
      • Note: NCBI Entrez Gene ID needs to be specified as "GeneID:¥d", since G-Links considers IDs in numbers-only as taxonomy ID.
    • NCBI tax ID (i.e. 9606)
    • RefSeq Genome ID (i.e. NC_000913)
Optional qualifiers

List of available databases (IDs)

Overview of supported databases and web services in G-Links:

Detailed list is as follows:

Usage Examples

Query URLs

Sample Scripts

    • Ruby script to get "DISEASE" and SNP (dbSNP & SNPedia) info about H.sapiens "cancer" genes which have "GOslim component" annotation related to "metabolic" in slimed TSV format.

Example of programatic access

One of the strength of G-Links is its programmatic access. For example, GO slim classification of all genes of E.coli for GO:Process ontology can be retrieved from the following URL:

This result is shown as a formatted HTML page when viewed in a browser, but when it is accessed from the command line or from programs, the result is automatically returned as TSV file. Using this, simple combination of UNIX commands can produce a classification summary of all genes in E.coli with GOslim:Process terms. Here is an example:

$ curl -v http://link.g-language.org/NC_000913/extract=GOslim_process  |grep \# |cut -f 2,3 |grep GO: |sort |uniq -c |sort -rn

License

Reference

glinks.1445423628.txt.gz · Last modified: 2015/10/21 10:33 by gaou