This is the requirements doc for the LIS gene search to be implemented on the LIS Jekyll web site.
Version: 1.2.0
A draft of this specification was completed in March 2023. Based on initial implementation of the spec and review of that implementation issue #128, additional changes were made to better handle pagination and back-navigation from the modal linkouts results window.
After another round of review in mid-July 2023, the intermediate output was changed from vertical layout of the results for each gene to a tabular layout per gene, based on this rationale from Alan (Aug 4, lis-developers discussion thread): "... the generic paginated search class the component is based on draws results using a table, but the gene search component overrides this to draw results as a list. While the list is aesthetically pleasing, it can only be configured by forking the repository and modifying the code, whereas the table can be configured at run-time, i.e. no forking necessary."
Initial public release of this web component at legumeinfo.org was on August 9. Code for this spec-1.1 release is documented here.
The history above predates a versioning system for these website-ui specs. In September 2023, semantic versioning was added, with 1.1.0 being used in this spec to reflect the first production release of this gene-search web component -- minor version 1 indicating that significant changes were made in June-July after review of the initial implementation in March.
September 19: update spec version to 1.1.1 -- the minor version increment reflecting that the Gene search field should be parameterizable in the web component, to allow fixing the genus to e.g. Arachis or Glycine, for use at a genus-specific site or context. Note: This was a new feature and should have bumped the version to 1.2.0.
November 17: similar to the September 19 update, the spec was updated to allow the species parameter to also be parameterizable. As such, the spec version was incremented to 1.2.0.
- genus (selector with "any" on top). In single-genus contexts (e.g. PeanutBase or SoyBase), allow this value to be pre-set.
- Species (selector populated if genus specified, otherwise only "any" - unless pre-set to some value, e.g. max)
- strain (selector populated if species specified, otherwise only "any")
- gene identifier (text input)
- gene description (text input)
- gene family identifier (text input)
- search button
Examples are shown below each text input element. (Selectors are self-explanatory.)
The output will be in a tabular layout, with the following content in each gene-anchored row:
- gene name (typically originating from Name attribute in LIS GFF) e.g.
Ae01g16390 - full LIS identifier (linked to Linkout Service) e.g.
aesev.CIAT22838.gnm1.ann1.Ae01g16390 - locations, e.g.
glyma.Wm82.gnm2.Gm13:44545582-44550666 (1) (chromosome) - gene description (typically originating from Note attribute in LIS GFF) e.g.
oxygen-evolving enhancer protein; IPR008797 (Photosystem II PsbQ, oxygen evolving ... - gene family identifier (linked to Linkout Service) e.g.
legfed_v1_0.L_KK1G2X - genus, e.g. Glycine
- species, e.g. max
- strain, e.g. Wm82
Note that this tabular layout differs from the initial specification of a vertical list layout per gene. See rationale under the specification version notes.
- the query will be a GraphQL query run by a web component, which in turn runs an InterMine path query against LegumeMine.
- the linkouts are not specified here -- those are the purview of the Linkout Service specification, which also specifies how they are implemented on web components like this.