GenomicsStandardsConsortium
target_gene eNum suggestion
Current term details Please supply the current details of the term that you would like to update:
Term name - target gene
Term ID - MIXS:0000044
Structured comment name - target_gene
Definition - Targeted gene or locus name for marker gene studies
Expected value - `16S rRNA, 18S rRNA, nif, amoA, rpo`
Current our list of expected values is very restricted and infact misleading in certain cases (16S rRNA is not specific, the eukaryotic 16S rRNA is not homologous to the bacterial 16S rRNA, see comments in linked ticket below)
Suggested update(s) There is ongoing work by GBIF and the eDNA group that are suggesting a list of possible target gene terms that we can consider as the controlled vocab list of possible values for this term: https://github.com/gbif/metabarcoding-data-toolkit-ui/issues/93
Additional context
After discussions with GBIF and the FAIR eDNA (FAIRe) working group, the target_gene controlled vocabulary list in the FAIRe checklist is as follows:
- 12S rRNA (SSU mitochondria)
- 16S rRNA (LSU mitochondria)
- 16S rRNA (SSU prokaryote)
- 23S rRNA (LSU prokaryote)
- 18S rRNA (SSU eukaryote)
- 28S rRNA (LSU eukaryote)
- rbcL
- CytB
- COI
- COII
- COIII
- nifH
- ITS
- ND1
- ND2
- ND3
- ND4
- ND5
- ND6
- amoA
- rpoB
- rpoC1
- rpoC2
- matK
- trnH
- trnL
- psbK
- D-loop
- other:
