vanaukenk
commented
8 years ago I think this issue is central to users having a good, intuitive search experience at TPC. There is too much buried under the customized ontology list and having the different branches of ontologies like ChEBI spread out makes it harder for people to appreciate everything that is available for searching. Also, then when we need to add more ontologies or vocabularies, e.g. Drosophila gene names or zebrafish phenotypes, those new categories have a logical place to go.
Here's a suggested re-organization of the list similar to what I posted above but with more detail. Each of the headings farthest to the left would be the starting point for browsing. I think something along these lines would make it easier for users, especially non-curators, to browse and effectively use the TPC categories.
Alleles and Variations allele (C. elegans) Variation (C. elegans) Anatomy and Cells anatomical structure C. elegans Cell and Anatomy Ontology Basic Formal Ontology (BFO) material entity quality Chemicals and Molecules chemical entity (ChEBI) Molecules (uncategorized) role (ChEBI) subatomic particle (ChEBI) Disease human disease Gene Ontology (GO) biological_process cellular_component molecular_function Gene Ontology Curation Cellular Component (CC) Localization assay terms Localization cellular components Localization verbs Molecular Function Molecular Function Enzymatic Activity (MFEA) MFEA assay terms MFEA verbs Molecular Function Physical Interactions (MFINT) MFINT assay terms MFINT verbs Genes and Proteins Gene (C. elegans) Protein (C. elegans) Genetics genetic interaction (WormBase curation) genetic perturbation (WormBase curation) phenotypic perturbation (WormBase curation) Variant Life Stages Nematoda Life Stage Phenotype and Trait Ontology (PATO) quality Sequence Ontology (SO) sequence_attribute sequence_collection sequence_feature sequence_variant
goldturtle
We should think about how best to organize the category list so that users can more easily see what is available to them. One idea is a top-level list like this (alphabetized): Alleles and Variations Anatomy and Cell Types Basic Formal Ontology (BFO) CHEBI Gene Ontology (GO) Genes and Proteins Human Disease Life Stages Phenotype and Trait Ontology (PATO) Sequence Ontology (SO)
That would then open up to the more extensive list of category options.
Also, is it necessary for the user to see the parenthetical ID after the category name?