× You are using the Cyverse mirror of the Planteome Ontology Browser. The main site is at browser.planteome.org.

Explore Planteome data

• Home allows simple quick searches using autocomplete and the new SOlr backend.

• Interactively search and filter the Planteome data as you type. These pages allow you to use a powerful search syntax (including boolean operators).

  • Ontology terms: Ontology Term, Synonym, or Definition
  • Bioentities: Bioentities associated with ontology terms
  • Annotations: Associations between Planteome terms and bioentities
• 
Drill-down browser can be used to explore the ontologies and annotation from the top levels by opening direct descendant terms individually to create a custom view.
• Visualization creator for graphs. Freely make your own ontology graph, including label and color changes. Please see the documentation for more details.
• Base statistics can give a high-level view of what kind of data is available in AmiGO.
• PubMed ID search takes you to a page with summary information and all GO annotations using the inputted ID.
  Search
• Medial search returns match counts for the different search personalities and allows users to select which one they wish to continue with.
  Search

Instance information

• Schema details what fields are recognized by AmiGO 2 on the Solr server.
• Load details about which files are being used in this instance of AmiGO 2 and when they were loaded.
• OWLTools information for the bundled version with this instance of AmiGO.
• Xrefs lists the cross-references currently understood by AmiGO.

Pages for non-JavaScript users and spiders

• For users unable to use JavaScript and spiders, the root Planteome terms can be found here.

  • biological process
  • cellular component
  • molecular function
  • plant anatomical entity
  • plant structure development stage
  • plant trait
  • plant experimental condition
• Simple search is a limited non-JavaScript search client for primitive access to SOlr data.

AmiGO 2 Software in the Lab

• Bulk search the GO data for groups of identifiers.

  • Ontology terms: Ontology Term, Synonym, or Definition
  • Bioentities: Bioentities associated with ontology terms
  • Annotations: Associations between Planteome terms and bioentities
• Browse the Gene Ontology term data in an interactive hierarchical form. Either from the roots or from a specific term.
• Gannet is the Solr analog to GOOSE.
• REPL is an interactive JavaScript environment for working with BBOP JS against the GO data.
• Freeform creator for graphs, including label and color changes. Please see the documentation for more information.
• All models in the fold.
• All ontology terms in the fold.

AmiGO 2 Software in the Garage

• Experimental tree viewer test (Mitch's widget).
• Experimental graph browser using cytoscape.js.
• Phylotree/Graph test using new generic graph system (single static data set).
• Phylotree/Graph of PTHR10170 test using new generic graph system (hand-coded test of PTHR10170).
• Drill Down experimental tree browser using a jQuery plugin. Not too smart, but lightweight.
• Visual IC lets you enter terms and see them in the graph along with their information content in a static image.
• Scratch space for test pieces not part of something else--a rotating guest list.