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:
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
phylogenetic?
gene, genome feature predictions?