Bioscape Web Resources

From irefindex
NoteNotePlease note that this documentation covers an unreleased product and is for internal use only.

The Bioscape Web resources provide the principal end-user interface to Bioscape as described in the "Using the Bioscape Web Application" document. Typically, a user will follow a specific workflow supported by a number of resources described in the application's "site map", found in the bsweb package (specifically in the __init__.py source file) in the bsweb distribution. The following table summarises the source code organisation:

Pages Logic package/module Database access package/module Templates
home (search), index (advanced search) bsweb.pages bsweb.pages.collections home_template.xhtml, index_template.xhtml
gene disambiguation, gene summary bsweb.genes bsweb.genes.collections gene_disambiguation_template.xhtml
gene_summary_template.xhtml
gene and evidence mention summaries bsweb.documents bsweb.documents.viewers text_mentions_template.xhtml
text_evidence_mentions_template.xhtml
document lists bsweb.documents bsweb.documents.collections text_index_generation_documents_template.xhtml
text_search_generation_documents_template.xhtml
text_results_generation_documents_template.xhtml
text_evidence_generation_documents_template.xhtml
annotated documents bsweb.documents bsweb.documents.viewers text_index_generation_document_template.xhtml
text_search_generation_document_template.xhtml
text_results_generation_document_template.xhtml
text_evidence_generation_document_template.xhtml
mention scoring summaries bsweb.documents bsweb.documents.collections text_scored_bioentity_template.xhtml
text_scored_bioentities_template.xhtml

To summarise, page functionality typically resides in the top-level of a package, database queries providing lists of results reside in collections modules, and the special database/text index combination supporting annotated documents resides in the viewers module in the bsweb.documents package.