MOD User Interfaces: outline of topics

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An outline of user interface aspects for
answering common genome questions in model organism/genome databases.

Searches, Outputs, Data Mining, Combining MOD with user and external genome data, Visualizations, Analyses, Human Compter Interactions

This is a tentative list of questions that presenters should address from their
organism/genome database project's perspective:

  • How to search for name of gene, view information (gene page)
    -- How do we handle the most common use of genome databases?
  • Search for genes that cause a phenotype or GO association (ie, by some attribute)
    -- How does a scientist best find genome information related to various biological concepts.
  • Generate a customized report on selected aspects of a gene
    -- How can a scientist distill those portions of interest from fuller gene and genomic information?
  • Generate bulk output based on a query
    -- How can a scientist answer a question involving hundreds or thousands of genes, perhaps with a table suited to spreadsheet use.
  • Combine the results at your MOD with information from other data sources
    -- Many scientists work with several genome websites to answer a research question. How do MODs facilitate this?

Here is a more general list of topics that these presentations might touch on:

* Search / Filter by
-- simple/general, "search by" genome classes
-- advanced (database fields, combining operators, structured queries, ...)
-- hierarchical/ontology searches (e.g. biological concepts search)
-- full text, bio-text/semantic searches
-- analysis searches ( but see below Analysis section)
-- query history use, cross-class linking/following,

* Output (common, basic, frequent types) :
-- single gene/data reports
-- user-customized reports and result tables
-- bulk data: sequence, database tables, structured data objects, specialty tables
-- content, format choices (fasta, gff, xml, genbank/embl, ...)

* Data mining and Bulk data (aspect of search/output)
-- methods for usable search/retrieval of 1000s of genes, features
-- UI problems: paging, efficient formats versus readable formats
-- to what extent can any searches/filters be combined with any outputs
-- SQL, WebServices, Web-REST, related programmed query support

* Combining MOD with user and external genome data
-- many scientists draw on several genome/bio databases to answer a research problem. How best can MODs facilitate this? includes methods for "external data" searches, standard accessions, standard/cross-database input and output
-- in searches, analyses, visualizations, reports
-- forms with input URLS to external data

* Human Interface (HCI/UI) issues
-- what you see/ask/search is what you get
.. search result highlighting
-- context-sensitive help and answers (highlighting..)
.. suggesting alternate searches
-- navigating the database: site maps, tutorials,
-- common, across-MOD methods (e.g. simple search box)

o Biology specifics:
-- MOD FAQs: projects often collect lists of genomic questions and best ways
to answer from a project interface. These can include some complex, but interesting genomics questions. If these FAQs are published at project websites, please bring to the Caucus's attention (e.g. links here).
-- some categories deserving "how to answer" FAQs:
Finding candidate genes for QTL
Comparative, Orthology, Species, ...
Alleles, SNP, reagents,
Literature, experimental groupings
Function, Expression
Pathways (cell, metabolic, ..)
Ontologies / semantic classifications
Database cross references, synonyms, ...
-- distinguish search and output for almost any biology criteria?

o Visualizations (a topic for later):
genome sequence, (comparative) genetic maps
pathway maps
expression graphs, various experiment result graphs
phylogenetic tree views
multiple alignments
other data reduction visualizations ?

o Analyses (a topic for later):
sequence (blast, blat, ...)
seq. pattern searches
gene, genome feature predictions?