eDNAqua-Plan

Apologies: the name of this repo. is wrong it should have been eDNAqua-Plan i.e. with just one A

eDNAqua-Plan code and data used for some of the deliverables of the overall eDNAAquaPlan. N.B. This code is rough and ready! It is generating tables and plots for the report.

This currently focuses on the needs of T2.2 in WP2. D2.2: Report containing an inventory of the ongoing and completed eDNA initiatives and repositories, identifying their geographical, ecological and taxonomic coverages.

Much data is being generated collated by the bioinformatics team of WP2, including: Yannis Kavakiotis and Dawid Krawczyk.

Biodiversity and marine guidance from Joana Pauperio and Stephane Pesant.

Review of aquatic environmental DNA Initiatives and Projects

We will contrast current eDNA data from projects/repositories with information on spatial distribution (geographical/ecological gradients), ecological diversity and ecosystem types.

flowchart TD

      eDNA_explore("Exploring eDNA Initiatives"):::ready-->bix("bioinfomatics_inventory_of_well_known_repos"):::ready
      bix-->bix_db:::ready
      bix-->ena("ENA/INSDC deep analysis"):::ready

      eDNA_explore-->survey("Questionnaire survey of initiatives"):::ready
      survey-->qu:::ready

      eDNA_explore-.->llm("LLM mining of papers"):::in_progress
      llm-.->llm_anal("LLM analysis script")

      subgraph analysis
      llm_anal-.->plots
      llm_anal-.->tables

      bix_db("mine_bioinformatics_eval.py")-->tables:::ready
      bix_db-->plots["plots"]:::ready

      ena-->plots
      ena-->tables

      qu(mine_questionnaire_eval.py)-->tables
      qu-->plots
      end

      tables-->gap_analysis:::in_progress
      plots-->gap_analysis

      gap_analysis<--Reviewing-->report:::in_progress

      classDef finished fill:#66ff99
      classDef in_progress fill:#f96
      classDef ready fill:#66ccff

Focus on ENA/INSDC environmental DNA

flowchart TD

      overall("run_ena_get_filter_analysis.py"):::startclass-->get('1- get_environmental_info.py'):::startclass
      Filter<-->tax("taxonomy.py")
      Filter<-->geog("geography.py")
      get-->Filter{Filter for aquatic}:::aquaticclass
      Filter-->analyse("2) analyse_environmental_info.py"):::decisionclass
      analyse<-->tax
      analyse<-->geog
      analyse-->tables["tables"]
      analyse-->plots["plots"]

      classDef startclass fill:#66ff99
      classDef decisionclass fill:#f96
      classDef aquaticclass fill:#66ccff

Woolly-at-EBI / eDNAAqua-Plan

readme

eDNAqua-Plan

Review of aquatic environmental DNA Initiatives and Projects

Focus on ENA/INSDC environmental DNA

Other Information