{"id":3804,"date":"2026-07-01T13:57:04","date_gmt":"2026-07-01T21:57:04","guid":{"rendered":"https:\/\/bien.nceas.ucsb.edu\/bien\/?page_id=3804"},"modified":"2026-07-03T06:49:24","modified_gmt":"2026-07-03T14:49:24","slug":"methods-and-workflow","status":"publish","type":"page","link":"https:\/\/bien.nceas.ucsb.edu\/bien\/methods-and-workflow\/","title":{"rendered":"Methods and Workflow"},"content":{"rendered":"
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Methods & Workflow<\/p>\n

How BIEN turns raw observations into analysis-ready data<\/h2>\n

BIEN combines occurrence, plot, trait, and range information through a documented, modular workflow built for transparency and reproducibility. Every record passes through four coordinated services — TNRS, GNRS, GVS, and NSR — each adding quality-control flags so results can be filtered explicitly and reproduced.<\/p>\n<\/section>\n

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The big picture<\/p>\n

An integrated, modular workflow<\/h3>\n

BIEN ingests diverse biodiversity observations from three primary sources — specimens (herbaria, museums, and citizen-science platforms), vegetation-plot surveys, and field trait measurements — and consolidates them into one standardized, analysis-ready framework. Counts and labels are outputs of specific query and validation pathways; interpretations should include dataset version, query constraints, and QA context.<\/p>\n<\/section>\n

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Figure 1 · The BIEN modular workflow<\/span><\/div>\n

\"The

A modular workflow integrating diverse observation data.<\/strong> BIEN consolidates specimens, plot surveys, and trait measurements into a unified framework — standardizing data, reducing biases, and enabling reproducible workflows across cross-scale ecological and evolutionary analyses. Source: Enquist et al. (2026), Methods in Ecology and Evolution<\/em> 17(5), Fig. 1. CC BY-NC-ND 4.0.<\/span><\/figcaption><\/figure>\n
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The four core services<\/h3>\n

All records entering the workflow pass through four services, accessible via web apps, APIs, and R packages. Each augments records with flags you can use to filter and subset the data.<\/p>\n<\/section>\n

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\n \"TNRS<\/p>\n
TNRS<\/div>\n
Taxonomic Name Resolution Service<\/div>\n

Open service<\/a>
\n R vignette<\/a>\n <\/div>\n

\n \"GNRS<\/p>\n
GNRS<\/div>\n
Geographic Name Resolution Service<\/div>\n

Open service<\/a>
\n R vignette<\/a>\n <\/div>\n

\n \"GVS<\/p>\n
GVS<\/div>\n
Geocoordinate Validation Service<\/div>\n

Open service<\/a>
\n R vignette<\/a>\n <\/div>\n

\n \"NSR<\/p>\n
NSR<\/div>\n
Native Species Resolver<\/div>\n

Open service<\/a>
\n R vignette<\/a>\n <\/div>\n<\/p><\/div>\n

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Figure 2 · The four core services<\/span><\/div>\n

\"The

Four services augment every record.<\/strong> (1) TNRS resolves taxonomic inconsistencies; (2) GNRS standardizes geographic metadata; (3) GVS flags spatial errors and validates coordinates; (4) NSR determines native and cultivated status. They operate together or independently, via APIs and the BIEN R package. Source: Enquist et al. (2026), Methods in Ecology and Evolution<\/em> 17(5), Fig. 2. CC BY-NC-ND 4.0.<\/span><\/figcaption><\/figure>\n
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The validation sequence<\/h3>\n

The diagram below traces the four validation steps applied to every record as it becomes analysis-ready.<\/p>\n<\/section>\n

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Workflow at a glance<\/span><\/div>\n

\"BIEN

Standardization and validation in four steps:<\/strong> (1) taxonomic standardization with the TNRS, (2) geographic standardization with the GNRS, (3) geographic validation of coordinates and political divisions, and (4) status validation inferring native and cultivation status. Figure reproduced from Enquist et al. (2019), “The commonness of rarity,” Science Advances<\/em> 5(11):eaaz0414, doi.org\/10.1126\/sciadv.aaz0414<\/a> (open access, CC BY-NC).<\/span><\/figcaption><\/figure>\n
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Workflow sequence<\/h3>\n
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  1. Ingestion and source harmonization<\/li>\n
  2. Taxonomic reconciliation (TNRS)<\/li>\n
  3. Geographic name and coordinate validation (GNRS, GVS)<\/li>\n
  4. Native-status resolution and integration (NSR)<\/li>\n
  5. Versioned export for analysis-ready products<\/li>\n<\/ol>\n<\/section>\n
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    Related BIEN package links<\/h3>\n