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Gene Ontology Consortium: going forward.

- Nucleic Acids Res. (2014)

Bottom Line: The GOC has a new and improved web site summarizing new developments and documentation, serving as a portal to GO data.Users can perform GO enrichment analysis, and search the GO for terms, annotations to gene products, and associated metadata across multiple species using the all-new AmiGO 2 browser.We encourage and welcome the input of the research community in all biological areas in our continued effort to improve the Gene Ontology.

View Article: PubMed Central - PubMed

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The new Gene Ontology browser AmiGO 2. (A) The entry portal page, where simple or complex queries can be performed, as well as term enrichment analysis. (B) Sample output from a ‘Quick Search’ on a GO term (recombinational repair). (C) Graphical Display and (D) Tree View of this GO term and its placement within the ontology.
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Figure 2: The new Gene Ontology browser AmiGO 2. (A) The entry portal page, where simple or complex queries can be performed, as well as term enrichment analysis. (B) Sample output from a ‘Quick Search’ on a GO term (recombinational repair). (C) Graphical Display and (D) Tree View of this GO term and its placement within the ontology.

Mentions: AmiGO 2 is the new official web-based open-source set of tools for querying, browsing, and visualizing the GO data (Figure 2). Publicly released in the spring of 2014, this new framework provides many architectural changes and improvements to help keep pace with the needs of the community. There are huge improvements in speed and in the variety of search modes, as well as the availability of additional data types, such as the display of annotation extensions and display of protein forms (splice variants and proteins with post translational modifications) (Figure 3). The AmiGO 2 set of tools also provides a JavaScript API for better access and integration with other tools, and both provides and consumes REST APIs to help better integrate resources, such as the PANTHER database (http://pantherdb.org, (24)) for enrichment analysis. There has also been a complete re-skinning of most of the tools with modern methods and styles to improve usability and access across diverse platforms. Under the hood, AmiGO 2 is broken into two distinct layers: (i) the various client software tools and (ii) the data backend. This client/server-oriented architecture allows for greater flexibility and more efficient addition of new functionality. The client software is now mostly written in JavaScript, allowing search-as-you-type interfaces and greater user interactivity, and some Perl for handling synchronous operations. For the backend, the data store for AmiGO 2 has moved away from a MySQL relational database backend and instead uses a specially generated schema for the Solr search platform (http://lucene.apache.org/solr/; dubbed GOlr) to allow for complex and efficient ontology and data queries.


Gene Ontology Consortium: going forward.

- Nucleic Acids Res. (2014)

The new Gene Ontology browser AmiGO 2. (A) The entry portal page, where simple or complex queries can be performed, as well as term enrichment analysis. (B) Sample output from a ‘Quick Search’ on a GO term (recombinational repair). (C) Graphical Display and (D) Tree View of this GO term and its placement within the ontology.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4383973&req=5

Figure 2: The new Gene Ontology browser AmiGO 2. (A) The entry portal page, where simple or complex queries can be performed, as well as term enrichment analysis. (B) Sample output from a ‘Quick Search’ on a GO term (recombinational repair). (C) Graphical Display and (D) Tree View of this GO term and its placement within the ontology.
Mentions: AmiGO 2 is the new official web-based open-source set of tools for querying, browsing, and visualizing the GO data (Figure 2). Publicly released in the spring of 2014, this new framework provides many architectural changes and improvements to help keep pace with the needs of the community. There are huge improvements in speed and in the variety of search modes, as well as the availability of additional data types, such as the display of annotation extensions and display of protein forms (splice variants and proteins with post translational modifications) (Figure 3). The AmiGO 2 set of tools also provides a JavaScript API for better access and integration with other tools, and both provides and consumes REST APIs to help better integrate resources, such as the PANTHER database (http://pantherdb.org, (24)) for enrichment analysis. There has also been a complete re-skinning of most of the tools with modern methods and styles to improve usability and access across diverse platforms. Under the hood, AmiGO 2 is broken into two distinct layers: (i) the various client software tools and (ii) the data backend. This client/server-oriented architecture allows for greater flexibility and more efficient addition of new functionality. The client software is now mostly written in JavaScript, allowing search-as-you-type interfaces and greater user interactivity, and some Perl for handling synchronous operations. For the backend, the data store for AmiGO 2 has moved away from a MySQL relational database backend and instead uses a specially generated schema for the Solr search platform (http://lucene.apache.org/solr/; dubbed GOlr) to allow for complex and efficient ontology and data queries.

Bottom Line: The GOC has a new and improved web site summarizing new developments and documentation, serving as a portal to GO data.Users can perform GO enrichment analysis, and search the GO for terms, annotations to gene products, and associated metadata across multiple species using the all-new AmiGO 2 browser.We encourage and welcome the input of the research community in all biological areas in our continued effort to improve the Gene Ontology.

View Article: PubMed Central - PubMed

Show MeSH