READMEs

README.md

+# Taxonomy Tools
+
+This is the parent project to two tools:
+
+* Library to read the [GRIN-Global Taxonomy data](gringlobal-taxonomy) and
+* A [Taxonomy Validation tool](taxonomychecker-cli)
+

taxonomychecker-cli/README.md

+
+# Taxonomy Checker & Validation Tool
+
+**TC** tool will read a CSV file that includes the standard MCPD taxonomy columns
+and will check these against the [GRIN-Global Taxonomy][ggt] data.
+
+[ggt]: https://npgsweb.ars-grin.gov/gringlobal/taxon/taxonomyquery.aspx
+
+## Using TC
+
+1. Prepare a valid CSV file to validate.
+1. You will need Java 1.8 JRE.
+1. Download the `tc-${project.version}-all.jar` to a folder on your computer
+1. Download GRIN-Global Taxonomy data from [ggtd] and unpack the archive to this 
+		folder
+1. Run the tool
+
+[ggtd]: http://www.ars-grin.gov/~dbmuke/cgi-bin/gringlobal/1.9.6.2/taxonomy_data.cab
+
+## Source data
+
+The GRIN-Taxonomy CAB file is available from the [official website][ggtd].
+
+## Input file template
+
+The input file uses MCPD taxonomy column names and uses these as input for analysis. 
+All other columns in the input spreadsheet are ignored.
+
+|Accession Number| GENUS | SPECIES|SPAUTHOR|SUBTAXA|SUBTAUTHOR|
+| -------- | -------- | -------- | -------- | -------- | -------- |
+|TMe-419| Manihot|esculenta|Crantz|subsp. flabellifolia|(Pohl) Cif.|
+
+## Results
+
+The tool produces a new CSV with extra columns containing suggested values:
+
+|Accession Number| GENUS|GENUS_check|SPECIES|SPECIES_check|SPAUTHOR|SPAUTHOR_check|SUBTAXA|SUBTAXA_check|SUBTAUTHOR_check|
+| -------- | -------- | -------- | -------- | -------- | -------- |-------- |-------- |-------- |-------- |-------- |
+|TMe-419| Manihot|--------|esculenta|-------- |Crantz|-------- |subsp. flabellifolia|-------- |(Pohl) Cif.|-------- |
+
+The `_check` columns are inserted next to the originals. When the original value
+is valid there will be no suggestions in the corresponding `_check` column.
+
+## Configuration options
+
+TODO: The tool can be configured to resolve to the *current* taxonomy instead of only
+checking for spelling mistakes.
+
+## Filling gaps
+
+The values for `SPAUTHOR` and `SUBTAUTHOR` are commonly not provided by crop 
+gene banks. When *genus* and *species* provided are valid (i.e. no suggestions 
+for change) the tool will suggest the species authority name from GRIN Taxonomy
+database. Similarly, when all other data is valid, value for `SUBTAUTHOR` will
+be suggested.
+
+Even when these values exist in the source data, we only include suggestions as
+describe above.
+
+