This repository is a proof-of-concept for a versioned storage as per the Plazi Actionable Accessible Archive (PAAA) arhitecture.
The actual data is now here: https://git.ld.plazi.org/plazi/treatments-xml.git
The repository contains all treatments in the Plazi Root Format GG-XML that pass the TreatmentBank Gatekeeper rules for LOD data, all other formats offered by Plazi can be derived from this format. A GitHub Workflow exemplifies the transformation to another format. It uses xalan and rapper to transform the documents to RDF whenever they are changed or added.
Changed XML is uploaded to this repository (currently this is always from TreatmentBank). All XML Documents and their history is available in the data folder in this Git Repository.
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A webhook is sent to our server where https://github.com/plazi/gg2rdf transform all changed XML to RDF turtle.
to do so it uses this XSLT and the Raptor RDF Library.
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The same Github Action uploads the genrated RDF to the treatments-rdf repository
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That repository triggers a Webhook on our server, where PSPS takes in the data and stores it in an internal triplestore.
(Exposed SPARQL-Endpoint at https://treatment.ld.plazi.org/sparql )
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PSPS then uploads all this data to lindas, which reloads itself every 24h, from where Synospecies gets its data by default
| source | destination | check | type | message |
|---|---|---|---|---|
| SRS | LOD | (./category[./@name = 'taxonomicNames']/type[./@name = 'missingRank' and $detailId and (./@errors-blocker > 0 or ./@errors-critical > 0)]) | taxonomicNames/missingRank | Unresolved treatment taxon issues |
| SRS | LOD | (./category[./@name = 'taxonomicNames']/type[./@name = 'missingAuthority' and $detailId and (./@errors-blocker > 0 or ./@errors-critical > 0)]) | taxonomicNames/missingAuthority | Unresolved treatment taxon issues |
| SRS | LOD | (./category[./@name = 'taxonomicNames']/type[./@name = 'missingFamily' and $detailId and (./@errors-blocker > 0 or ./@errors-critical > 0)]) | taxonomicNames/missingFamily | Unresolved treatment taxon issues |
| SRS | LOD | (./category[./@name = 'taxonomicNames']/type[./@name = 'missingOrder' and $detailId and (./@errors-blocker > 0 or ./@errors-critical > 0)]) | taxonomicNames/missingOrder | Unresolved treatment taxon issues |
| SRS | LOD | (./category[./@name = 'taxonomicNames']/type[./@name = 'missingKingdom' and $detailId and (./@errors-blocker > 0 or ./@errors-critical > 0)]) | taxonomicNames/missingKingdom | Unresolved treatment taxon issues |
| SRS | LOD | (./category[./@name = 'taxonomicNames']/type[./@name = 'brokenFamily' and $detailId and (./@errors-blocker > 0 or ./@errors-critical > 0)]) | taxonomicNames/brokenFamily | Unresolved treatment taxon issues |
| SRS | LOD | (./category[./@name = 'taxonomicNames']/type[./@name = 'brokenOrder' and $detailId and (./@errors-blocker > 0 or ./@errors-critical > 0)]) | taxonomicNames/brokenOrder | Unresolved treatment taxon issues |
| SRS | LOD | (./category[./@name = 'treatments']/type[./@name = 'missingTaxon' and $detailId and ./@errors-blocker > 0]) | treatments/missingTaxon | Unresolved treatment boundary issues |
| SRS | LOD | (./category[./@name = 'treatments']/type[./@name = 'brokenBoundaries' and $detailId and (./@errors-blocker > 0 or ./@errors-critical > 0)]) | treatments/brokenBoundaries | Unresolved treatment boundary issues |
| SRS | LOD | (./category[./@name = 'treatments']/type[./@name = 'brokenStructure' and $detailId and (./@errors-blocker > 0 or ./@errors-critical > 0)]) | treatments/brokenStructure | Unresolved treatment structure issues |
| SRS | LOD | (./category[./@name = 'treatments']/type[./@name = 'missingStructure' and $detailId and (./@errors-blocker > 0 or ./@errors-critical > 0)]) | treatments/missingStructure | Unresolved treatment structure issues |
| SRS | LOD | (./category[./@name = 'treatments']/type[./@name = 'missingNomenclature' and $detailId and (./@errors-blocker > 0 or ./@errors-critical > 0)]) | treatments/missingNomenclature | Unresolved treatment structure issues |
| SRS | LOD | (./category[./@name = 'treatments']/type[./@name = 'spuriousTreatment' and $detailId and ./@errors-blocker > 0]) | treatments/spuriousTreatment | Treatment too small to be valid |
| SRS | LOD | (./category[./@name = 'treatments']/type[./@name = 'mingledTreatments' and $detailId and ./@errors-blocker > 0]) | treatments/mingledTreatments | Treatment might be aggregate of multiple treatments |
| SRS | LOD | (./category[./@name = 'treatments']/type[./@name = 'brokenReferenceGroup' and $detailId and (./@errors-blocker > 0 or ./@errors-critical > 0)]) | treatments/brokenReferenceGroup | Reference group cites suspicious taxon names |
| // | fallback for missing error protocol: uploaded 2020-06-01 or later | |||
| SRS | LOD | (./@checkinTime > 1590926399000) | document/missingQc | QC is required for LOD export of treatments extracted from IMF documents uploaded after 2020-05-31 |