Methods & Data Organization
This page summarizes the workflow, result semantics, and information architecture of PlantSME v1.0 so users can understand the data boundaries and the site structure.
Version: v1.0
Libraries: 6
Workflow
The current site uses one unified workflow for online identification and resource organization, producing standardized results from official reference libraries.
1Use pathway-oriented reference libraries to organize family and pathway-module metadata together with model files
2Run BLAST, HMM, and evidence integration on target protein FASTA files and produce standardized output directories
3Import structured results into PlantSME and expose them through species-, pathway-, module-, family-, and gene-centered browsing
4Append lightweight result analytics such as family overviews and physicochemical profiles on single-job result pages
Data Organization
category
Represents the real pathway name and acts as the top pathway-level entry on this site.
pathway
In the current deployment, represents a functional module or enzyme-step node inside a pathway rather than an enzyme family.
family
Represents the enzyme-family layer and anchors family detail pages as well as family-level job summaries.
Result Semantics
- The result page defaults to a pass-focused formal hit view to prioritize the most credible members.
- The all view may include lower-confidence candidate records beyond pass and is intended for supplementary inspection rather than formal interpretation.
- When a result page is focused on a single family, the system further exposes family composition and physicochemical summaries.
v1.0 Data Boundary
- v1.0 is a browsable, downloadable, and online-identification-ready public version that provides a stable entry point.
- Statistics shown on the homepage reflect the current public version, and future expansions will be added in later versions.
- The download center exposes the software package and official reference libraries for local reuse of the same identification workflow.
Official Libraries
The table below summarizes the currently active official libraries and their pathway scopes to clarify the public data boundary.
| Library | Pathway | Module | Version |
|---|---|---|---|
| Alkaloid Official Library alkaloid/portable_core |
Alkaloid pathway | Alkaloid portable pathway | v1.0 |
| Flavonoid Official Library flavonoid/portable_core |
Flavonoid pathway | Flavonoid portable pathway | v1.0 |
| Phenylpropanoid Official Library phenylpropanoid/portable_core |
Phenylpropanoid pathway | Phenylpropanoid portable pathway | v1.0 |
| Rosmarinic acid Official Library rosmarinic_acid/portable_core |
Rosmarinic acid pathway | Rosmarinic acid portable pathway | v1.0 |
| Steroid Official Library steroid/portable_core |
Steroid pathway | Steroid portable pathway | v1.0 |
| Terpenoid Official Library terpenoid/portable_core |
Terpenoid pathway | Terpenoid portable pathway | v1.0 |